gebhart/patrepeval huggingface dataset:
Identification of Site(s) of Insulin Nitration by Peroxynitrite and Characterization of Its Structural Change (2008)

Insulin nitration mediated by peroxynitrite (ONOO(-)) has been implicated in diabetes and diabetic cardiovascular complications. In this study, we identified the nitration sites of porcine insulin by infusion of ONOO(-) and quantified its secondary structural change. Insulin was cleaved with V8 protease to six peptides (four of them contained each tyrosine residue), then analyzed by HPLC-MS and further confirmed the nitration sites by HPLC-MS/MS. At low accumulated doses of peroxynitrite, the main products were two different mono-nitrated insulin species at Tyr-A19 and Tyr-B26 with Tyr-A19 being predominant as shown by peptide mapping. Also, the content of alpha-helix structure of insulin reduced to 22.9 % and random-coil structure increased to 30.2 % (compare with native insulin of 41.7 % and 13.7 %, respectively) as determined by FTIR spectra.
Azurocidin and a homologous serine protease from neutrophils. Differential antimicrobial and proteolytic properties. (1990)

Two 29-kD polypeptides, azurocidin and p29b, were purified to homogeneity from human neutrophils by acid extraction of azurophil granule membrane-associated material followed by gel filtration and reverse-phase chromatography. Azurocidin and p29b share NH2-terminal sequence homology with each other as well as with elastase, cathepsin G, and other serine proteases. p29b bound [3H]diisopropyl fluorophosphate and hydrolyzed elastin, casein, and hemoglobin. A peptide substrate for p29b could not be identified. Azurocidin neither bound [3H]diisopropyl fluorophosphate nor hydrolyzed any of the proteins, peptides, or esters tested. In microbicidal assays, purified azurocidin was comparable to p29b in activity against Escherichia coli, Streptococcus faecalis, and Candida albicans. The antimicrobial activity of azurocidin was enhanced under mildly acidic conditions, but was inhibited in a dose-dependent manner by NaCl, CaCl2, or serum. Immunoblot analysis with monospecific antibodies localized greater than 90% of the azurocidin and greater than 75% of the p29b to azurophil granule-rich fractions of PMN lysates. Immunoelectron microscopy confirmed the localization of azurocidin to the azurophil granules. Azurocidin associated with the azurophil granule membrane, but did not appear to be an integral membrane protein. Thus, azurocidin and p29b are members of a family of serine protease homologs stored in azurophil granules and may play a role in inflammatory and antimicrobial processes involving PMN.
Therapy of Murine Aspergillosis with Amphotericin B in Combination with Rifampin or 5-Fluorocytosine (1977)

Suboptimal doses of amphotericin B in combination with either rifampin or 5-fluorocytosine were better than single-drug therapy in the treatment of disseminated Aspergillus fumigatus infection in mice. Despite the increased effectiveness of combination therapy, none of the therapeutic regimens we used completely eradicated infections in the mice when evaluated by mycological culture, even in long-term survivors.
Analysis of Adaptive Digital Feedback Linearization Techniques (2009)

A new lookup-table linearization technique is developed based on the digital feedback and digital feedback/predistortion (DFBPD) concepts. The linearization characteristics are investigated through system simulation of a real power-amplifier model with 90-W peak envelope power. The DFB suppresses forward-path nonlinear distortion as a gain reduction due to the FB effect, and this technique enhances the system tolerance without any bandwidth limitation. As the PD network is added to the FB loop, the linearization performance and system tolerance are further improved because of more accurate PD signal extraction. In addition, the gain is purely determined by the FB path, so the gain fluctuation in the forward path, including amplifier aging and temperature effects, is suppressed. The analysis and simulation allow experimental evaluation of the linearization mechanism and performance of the DFBPD technique for an 802.16 e mobile Worldwide Interoperability for microwave access signal.
Faraday rotation in silicon waveguides (2017)

We investigate the possibility of using silicon waveguides as Faraday rotators for optical isolators. We employ multimode waveguides with a square cross-section. This approach offers the opportunity to introduce integrated nonreciprocal components into the silicon-on-insulator platform without complication of an additional magneto-optical material.
An Improved LR-aided K-Best Algorithm for MIMO Detection (2013)

Recently, lattice reduction (LR) technique has caught great attention for multi-input multi-output (MIMO) receiver because of its low complexity and high performance. However, when the number of antennas is large, LR-aided linear detectors and successive interference cancellation (SIC) detectors still exhibit considerable performance gap to the optimal maximum likelihood detector (MLD). To enhance the performance of the LR-aided detectors, the LR-aided K-best algorithm was developed at the cost of the extra complexity on the order $\mathcal{O}(N_t^2 K + N_t K^2)$, where $N_t$ is the number of transmit antennas and $K$ is the number of candidates. In this paper, we develop an LR-aided K-best algorithm with lower complexity by exploiting a priority queue. With the aid of the priority queue, our analysis shows that the complexity of the LR-aided K-best algorithm can be further reduced to $\mathcal{O}(N_t^2 K + N_t K {\rm log}_2(K))$. The low complexity of the proposed LR-aided K-best algorithm allows us to perform the algorithm for large MIMO systems (e.g., 50x50 MIMO systems) with large candidate sizes. Simulations show that as the number of antennas increases, the error performance approaches that of AWGN channel.
Efficacy and Safety of Once- versus Twice-Daily Carbamazepine Extended-Release Capsules for the Treatment of Manic Symptoms in Patients with Bipolar I Disorder. (2008)

These results suggest QHS dosing may be a safe and effective alternative to BID dosing of CBZ-ERC for treating manic episodes for many adults with bipolar I disorder, although additional studies are needed to confirm this finding.
Oxidation of hydrogen sulfide by Thiobacillus denitrificans: Desulfurization of natural gas (1987)

Abstract It has been demonstrated that Thiobacillus denitrificans may be readily cultivated anaerobically in batch reactors on H 2 S (g) under sulfide‐limiting conditions. Under these conditions sulfide concentrations in the culture medium were less than 1 μ M , resulting in very low concentrations of H 2 S in the reactor outlet gas. The stoichiometry of the reaction was determined, and stable reactor operation was demonstrated at reactor loadings as high as 4–5 mmol H 2 S oxidized/h g biomass. Maximum loading was estimated at 5.4–7.6 mmol H 2 S/h g biomass under the conditions employed in this study. Indicators of reactor upset were determined and recovery from upset conditions demonstrated. Barotolerance of T. denitrificans to 12.5 MPa as well as a relative insensitivity to pressurization–depressurization cycles were also demonstrated. T. denitrificans was observed to be very sensitive to CH 3 SH but relatively tolerant of CS 2 , COS, and CH 3 SCH 3 .
Selective Erasure of a Fear Memory (2009)

Memories are thought to be encoded by sparsely distributed groups of neurons. However, identifying the precise neurons supporting a given memory (the memory trace) has been a long-standing challenge. We have shown previously that lateral amygdala (LA) neurons with increased cyclic adenosine monophosphate response element-binding protein (CREB) are preferentially activated by fear memory expression, which suggests that they are selectively recruited into the memory trace. We used an inducible diphtheria-toxin strategy to specifically ablate these neurons. Selectively deleting neurons overexpressing CREB (but not a similar portion of random LA neurons) after learning blocked expression of that fear memory. The resulting memory loss was robust and persistent, which suggests that the memory was permanently erased. These results establish a causal link between a specific neuronal subpopulation and memory expression, thereby identifying critical neurons within the memory trace.
Hydroxybenzamide/Pyrrole Pair Distinguishes T·A from A·T Base Pairs in the Minor Groove of DNA (2000)

A new aromatic pair, 2-hydroxy-6-methoxybenzamide/1-methylpyrrole at the terminal position of hairpin polyamides has been designed for distinguishing T·A from A·T base pairs and both from G·C/C·G in the minor groove of DNA. Four eight-ring hairpin polyamides with benzamide (Bz), 2-hydroxybenzamide (Hb-1), 2-hydroxy-6-methylbenzamide (Hb-2), and 2-hydroxy-6-methoxybenzamide (Hb-3) at the N-terminal position were synthesized. The equilibrium association constants (Ka) were determined at four DNA sites which differ at a single common position, 5‘-TNTACA-3‘ (N = T, A, G, C). Quantitative DNase I footprint titration experiments reveal that (Hb-3)PyPyPy-(R)H2Nγ-ImPyPyPy-β-Dp (4) bound the sequences 5‘-TTTACA-3‘ and 5‘-TATACA-3‘ with high affinity; Ka = 2.6 × 1010 M-1 and Ka = 8.4 × 109 M-1, respectively, a 3-fold specificity for T vs A was found. Importantly, the sequences 5‘-TGTACA-3‘ and 5‘-TCTACA-3‘ are bound with 50 and 200 times lower affinity, revealing an overall specificity of Hb-3/Py of T > A ≫ G > C. These results expand the repertoire of sequences targetable by hairpin polyamides.
Static gas-liquid interfacial direct current discharge plasmas using ionic liquid cathode (2009)

Due to the unique properties of ionic liquids such as their extremely low vapor pressure and high heat capacity, we have succeeded in creating the static and stable gas (plasmas)-liquid (ionic liquids) interfacial field using a direct current discharge under a low gas pressure condition. It is clarified that the ionic liquid works as a nonmetal liquid electrode, and furthermore, a secondary electron emission coefficient of the ionic liquid is larger than that of conventional metal electrodes. The plasma potential structure of the gas-liquid interfacial region, and resultant interactions between the plasma and the ionic liquid are revealed by changing a polarity of the electrode in the ionic liquid. By utilizing the ionic liquid as a cathode electrode, the positive ions in the plasma region are found to be irradiated to the ionic liquid. This ion irradiation causes physical and chemical reactions at the gas-liquid interfacial region without the vaporization of the ionic liquid.
Large spin pumping from epitaxial Y3Fe5O12thin films to Pt and W layers (2013)

Epitaxial Y${}_{3}$Fe${}_{5}$O${}_{12}$ thin films deposited by off-axis sputtering exhibit excellent crystalline quality enabling observation of large spin pumping signals in Pt/Y${}_{3}$Fe${}_{5}$O${}_{12}$ and W/Y${}_{3}$Fe${}_{5}$O${}_{12}$ bilayers driven by cavity ferromagnetic resonance. The inverse spin Hall voltages reach 2.10 and \ensuremath{-}5.26 mV in 5-mm-long Pt/Y${}_{3}$Fe${}_{5}$O${}_{12}$ and W/Y${}_{3}$Fe${}_{5}$O${}_{12}$ bilayers, respectively, excited by a radio-frequency magnetic field of 0.3 Oe. From the ferromagnetic resonance linewidth broadening, we obtain high interfacial spin mixing conductances of 4.56\ifmmode\times\else\texttimes\fi{}10${}^{14}$ and 2.30\ifmmode\times\else\texttimes\fi{}10${}^{14}$ ${\ensuremath{\Omega}}^{\ensuremath{-}1}$ m${}^{\ensuremath{-}2}$ for Pt/Y${}_{3}$Fe${}_{5}$O${}_{12}$ and W/Y${}_{3}$Fe${}_{5}$O${}_{12}$ bilayers, respectively.
Engineered Immunoglobulin Molecules as Vehicles for T Cell Epitopes (1993)

The variable regions (V) of immunoglobulins (Ig) bear antigenic determinants that can stimulate both humoral and cellular immune responses subsequent to hetero, allo or iso-immunization. The expression of these determinants by Igs usually correlates with the presence of specific amino acid residues within the CDR loops of the V regions. Since the CDR loops varies in length, we reasoned that they would represent permissive sites to insert foreign peptides and create antigenized Igs expressing selected determinants. Taking advantage of these properties and the fact that Igs are self and long-lived molecules, we expressed a CTL and a helper epitope of influenza virus nucleoprotein and hemagglutinin respectively, within the heavy chain CDR3 loop of an anti-arsonate antibody. We found that foreign peptides comprised of 11 to 15 amino acid residues can be expressed within the V region of the heavy chain without alteration of pairing with the light chain. More striking, the cellular processing machinery is able to generate the peptides from the Ig context which were then recognized by specific T cells. Furthermore, the engineered Igs are able to induce T cell responses specific for the inserted peptide and for influenza virus. The use of engineered Ig molecules as vehicles for T and B cell peptides might represent a valuable strategy to generate safe, long lived reagents able to stimulate strong specific immune responses. This would then overcome the short half life of synthetic peptides based vaccines and the side effects seen in case of recombinant viral proteins or inactivated viruses based vaccines.
An Energy Efficient Layered Decoding Architecture for LDPC Decoder (2009)

Low-density parity-check (LDPC) decoder requires large amount of memory access which leads to high energy consumption. To reduce the energy consumption of the LDPC decoder, memory-bypassing scheme has been proposed for the layered decoding architecture which reduces the amount of access to the memory storing the soft posterior reliability values. In this work, we present a scheme that achieves the optimal reduction of memory access for the memory bypassing scheme. The amount of achievable memory bypassing depends on the decoding order of the layers. We formulate the problem of finding the optimal decoding order and propose algorithm to obtain the optimal solution. We also present the corresponding architecture which combines some of memory components and results in reduction of memory area. The proposed decoder was implemented in TSMC 0.18 μm CMOS process. Experimental results show that for a LDPC decoder targeting IEEE 802.11 n specification, the amount of memory access values can be reduced by 12.9-19.3% compared with the state-of-the-art design. At the same time, 95.6%-100% hardware utilization rate is achieved.
Inflatable mouse (2008)

Inflatable Mouse is a volume-adjustable user interface. It can be inflated up to the volume of a familiar mouse, but be deflated and stored flat in a PC card slot of a laptop computer when not in use. Inflatable Mouse functions just like a typical mouse; moreover, it provides new interaction techniques by sensing the air pressure in the balloon of the mouse. It also addresses some issues associated with pressure-sensing interactions such as the lack of bi-directional input and the lack of effective feedback. Moreover, it can be used as both a control tool and a display tool. In this paper, the design of an Inflatable Mouse prototype is described and potential application scenarios such as zooming in/out and fast scrolling using pressure control are explained. We also discuss the potential use of Inflatable Mouse as an emotional communication tool.
Mammalian target of rapamycin is a direct target for protein kinase B: identification of a convergence point for opposing effects of insulin and amino-acid deficiency on protein translation (1999)

Growth factor induced activation of phosphoinositide 3-kinase and protein kinase B (PKB) leads to increased activity of the mammalian target of rapamycin (mTOR). This subsequently leads to increased phosphorylation of eIF4E binding protein-1 (4EBP1) and activation of p70 ribosomal S6 protein kinase (p70(S6K)), both of which are important steps in the stimulation of protein translation. The stimulation of translation is attenuated in cells deprived of amino acids and this is associated with the attenuation of 4EBP1 phosphorylation and p70(S6K) activation. It has been suggested that PKB regulates mTOR function by phosphorylation although direct phosphorylation of mTOR by PKB has not been demonstrated previously. In the present work, we have found that PKB directly phosphorylates mTOR and, using phosphospecific antibodies, we have shown this phosphorylation occurs at Ser(2448). Insulin also induces phosphorylation on Ser(2448) and this effect is blocked by wortmannin but not rapamycin, consistent with the effect being mediated by PKB. Amino-acid starvation rapidly attenuated the reactivity of the Ser(2448) phosphospecific antibody with mTOR and this could not be restored by either insulin stimulation of cells or incubation with PKB in vitro. Our findings demonstrate that mTOR is a direct target for PKB and support the conclusion that regulation of phosphorylation of Ser(2448) is a point of convergence for the counteracting regulatory effects of growth factors and amino acid levels.
Pixel level optical-transfer-function design based on the surface-wave-interferometry aperture (2010)

The design of optical transfer function (OTF) is of significant importance for optical information processing in various imaging and vision systems. Typically, OTF design relies on sophisticated bulk optical arrangement in the light path of the optical systems. In this letter, we demonstrate a surface-wave-interferometry aperture (SWIA) that can be directly incorporated onto optical sensors to accomplish OTF design on the pixel level. The whole aperture design is based on the bull's eye structure. It composes of a central hole (diameter of 300 nm) and periodic groove (period of 560 nm) on a 340 nm thick gold layer. We show, with both simulation and experiment, that different types of optical transfer functions (notch, highpass and lowpass filter) can be achieved by manipulating the interference between the direct transmission of the central hole and the surface wave (SW) component induced from the periodic groove. Pixel level OTF design provides a low-cost, ultra robust, highly compact method for numerous applications such as optofluidic microscopy, wavefront detection, darkfield imaging, and computational photography.
Non-parametric similarity measures for unsupervised texture segmentation and image retrieval (2002)

In this paper we propose and examine non-parametric statistical tests to define similarity and homogeneity measures for textures. The statistical tests are applied to the coefficients of images filtered by a multi-scale Gabor filter bank. We demonstrate that these similarity measures are useful for both, texture based image retrieval and for unsupervised texture segmentation, and hence offer a unified approach to these closely related tasks. We present results on Brodatz-like micro-textures and a collection of real-word images.
A robust open-source algorithm to detect onset and duration of QRS complexes (2003)

This paper presents a novel algorithm to detect onset and duration of QRS complexes. After low-pass filtering, the ECG signal is converted to a curve length signal by a transform in which a nonlinear scaling factor is introduced to enhance the QRS complex and to suppress unwanted noise. Adaptive thresholds are applied to the length signal to determine the onset and duration of the QRS complex. The algorithm was evaluated with the complete set of single channel ECGs (signal O) from the MIT-BlH Arrhythmia Database, and achieved a gross QRS sensitivity of 99.65% and a gross QRS positive predictive accuracy of 99.77%. The QRS onset determination is very stable and is insensitive to QRS morphology change. The noise tolerance of the algorithm was evaluated using the MIT-BIH Noise Stress Test Database. The C source code for the single-channel algorithm has been contributed to PhysioToolkit and is freely available from PhysioNet (www.physionet.org).
Dose-volume histogram representation of patient dose distribution in three-dimensional internal dosimetry (1994)

To understand tumor response and normal organ toxicity following internal emitter therapy a succinct yet adequate representation of the spatial dose distribution within the target is necessary. Using 3D-ID, a software package that implements a patient-specific, three-dimensional approach to dosimetry, we obtain the mean and a dose-volume histogram of the spatial dose distribution to a target volume. Registered CT/MR and SPECT/PET images (generated using Pelizzari/Chen registration software) are used to define the radioactivity distribution relative to patient anatomy. Target contours are drawn on side-by-side enlarged SPECT/PET and CT/MR image slices that are selected from a scrollable image display. Contours drawn in one modality simultaneously appear in the other. The user may switch between modalities by positioning the cursor in the appropriate window. This provides for the simultaneous use of both imaging modalities to define tumor (e.g. using SPECT) and normal organ (using CT/MR) contours. The dose to all voxels within the target volume is obtained by convolving the activity distribution with a point kernel table of absorbed dose versus distance. Patient-specific S-factors may be calculated by defining source organ contours and assigning unit activity to all voxels within each source. The {open_quotes}dose{close_quotes} to a given target is thus the patient-specificmore » S-factor In the first patient examined using 3D-ID, approximately 16% of the tumor volume received a dose that was 25% less than the mean dose. The liver to spleen S-factor for this patient differed from the standard man value by approximately 48%; when the value was adjusted for the patient`s (enlarged) spleen volume the difference was approximately 21%. Dose histograms and patient-specific organ and tumor S-factors generated using 3D-ID may provide useful information in understanding tumor response and organ toxicity in radioimmunotherapy.« less
Genomic cloning and characterization of a ricin gene fromRicinus Communis (1985)

A genomic clone that specifies a single polypeptide precursor for ricin, a toxic lectin of Ricinus communis (castor bean), was isolated, sequenced and Sl mapped. The gene encodes a 64 kDa precursor which contains, in the following order: a 24 or 35 amino acid signal peptide, the A chain, a 12 amino acid linker peptide, and the B chain. The 5'-end of the ricin mRNA maps approximately 35 bases upstream from the first methionine codon. Two putative TATA boxes and a possible CAAT box lie in the 5'-flanking region. Two possible polyadenylation signals were found in the 3' flanking region. No introns were found, which is typical of other lectin genes that have been sequenced. Southern blot analysis suggests that the castor bean genome contains approximately six ricin-like genes.
Localization of CD4+T cell epitope hotspots to exposed strands of HIV envelope glycoprotein suggests structural influences on antigen processing (2001)

The spectrum of immunogenic epitopes presented by the H2-IA(b) MHC class II molecule to CD4(+) T cells has been defined for two different (clade B and clade D) HIV envelope (gp140) glycoproteins. Hybridoma T cell lines were generated from mice immunized by a sequential prime and boost regime with DNA, recombinant vaccinia viruses, and protein. The epitopes recognized by reactive T cell hybridomas then were characterized with overlapping peptides synthesized to span the entire gp140 sequence. Evidence of clonality also was assessed with antibodies to T cell receptor Valpha and Vbeta chains. A total of 80 unique clonotypes were characterized from six individual mice. Immunogenic peptides were identified within only four regions of the HIV envelope. These epitope hotspots comprised relatively short sequences ( approximately 20-80 aa in length) that were generally bordered by regions of heavy glycosylation. Analysis in the context of the gp120 crystal structure showed a pattern of uniform distribution to exposed, nonhelical strands of the protein. A likely explanation is that the physical location of the peptide within the native protein leads to differential antigen processing and consequent epitope selection.