gebhart/patrepeval huggingface dataset:
Membrane topology of the cyanobacterial bicarbonate transporter, BicA, a member of the SulP (SLC26A) family (2009)

We have completed the first comprehensive transmembrane topology determination for a member of the ubiquitous and important SulP/SLC26 family of coupled anion transporters found in eukaryotes and prokaryotes. The prokaryotic member that we have mapped, namely BicA from Synechococcus PCC7002, is an important Na(+)-dependent bicarbonate transporter that is likely to play a major role in global primary productivity via the CO(2) concentrating mechanism in cyanobacteria. We experimentally determined the topology based on phoA-lacZ topology mapping combined with reference to a range of predictive models based on hydropathy analysis and positive charge distribution. The 12-TMH structure for BicA is characterized by tight turns between several pairs of TMH and it features a prominent cytoplasmically-located STAS domain that is characteristic of the SulP family. A key difference from previous predicted models is that we identify a cytoplasmic loop between helices 8 and 9 where previous models suggested a TMH. This region includes a highly conserved motif that defines the SulP family. The identification of this region as cytoplasmic, rather than transmembrane, has implications for the function and perhaps regulation of SulP family members. This finding is used to reinterpret mutagenesis data relating to highly conserved residues in this region from both plant and human SulP transporters.
A probabilistic approach for SNP discovery in high-throughput human resequencing data (2009)

New high-throughput sequencing technologies are generating large amounts of sequence data, allowing the development of targeted large-scale resequencing studies. For these studies, accurate identification of polymorphic sites is crucial. Heterozygous sites are particularly difficult to identify, especially in regions of low coverage. We present a new strategy for identifying heterozygous sites in a single individual by using a machine learning approach that generates a heterozygosity score for each chromosomal position. Our approach also facilitates the identification of regions with unequal representation of two alleles and other poorly sequenced regions. The availability of confidence scores allows for a principled combination of sequencing results from multiple samples. We evaluate our method on a gold standard data genotype set from HapMap. We are able to classify sites in this data set as heterozygous or homozygous with 98.5% accuracy. In de novo data our probabilistic heterozygote detection ("ProbHD") is able to identify 93% of heterozygous sites at a <5% false call rate (FCR) as estimated based on independent genotyping results. In direct comparison of ProbHD with high-coverage 1000 Genomes sequencing available for a subset of our data, we observe >99.9% overall agreement for genotype calls and close to 90% agreement for heterozygote calls. Overall, our data indicate that high-throughput resequencing of human genomic regions requires careful attention to systematic biases in sample preparation as well as sequence contexts, and that their impact can be alleviated by machine learning-based sequence analyses allowing more accurate extraction of true DNA variants.
Nested loops (1985)

This unit also deals with FOR-NEXT loops, but for those cases where one loop is placed or nested inside another.
Oxygen Reduction Characteristics of Heat‐Treated Catalysts Based on Cobalt‐Porphyrin Ion Complexes (1998)

Oxygen reduction characteristics of graphite electrodes modified with aggregated cobalt‐porphyrins heat‐treated at various temperatures and then impregnated in Nafion polymer were investigated systematically The aggregated cobalt‐porphyrin compound was adsorbed on graphite powder and then heat‐treated at various temperatures ranging from 200 through 1200 °C. The catalysts were evaluated for electroreduction performances of oxygen on modified electrodes in sulfuric acid solutions. The electrocatalytic performances of catalysts as measured in rotating ring‐disk electrodes showed that the most effective catalytic activity for oxygen reduction was attained for the aggregated cobalt‐porphyrin compounds on graphite powder heat‐treated at temperatures between 600 and 800 °C. The surface concentration of Co and N as measured by X‐ray photoelectron spectroscopy increased as the heat‐treatment temperature was increased up to 800 °C. The electrochemical performance of pyrolyzed cobalt‐porphyrin catalysts changed in parallel with the surface concentration of Co and N. In the temperature range 600–800 °C, it appeared that the increased catalytic activity originated from the well‐dispersed , moiety or from fragments of the original molecules still retaining the cobalt bound to nitrogen atoms. In the higher temperature region, bonds were no longer detected, and the presence of cobalt in the metallic states (β‐Co) in the catalysts was confirmed by X‐ray diffraction analysis. From the results of the stability tests, the pyrolyzed cobalt porphyrin electrode systems were found to be more stable than the nonheat‐treated catalysts.
Induction of Antigen-Specific CTL Responses Using Antigens Conjugated to Short Peptide Vectors (2003)

Linear peptides (SynB vectors) with specific sequence motifs have been identified that are capable of enhancing the transport of a wide range of molecules into cells. These peptide vectors have been used to deliver exogenous peptides and protein Ags across the cell membrane and into the cytoplasm of cells. Specifically, in vitro analysis indicated that these SynB peptides enhanced the uptake of two 9-mer peptide Ags, NP(147-155) and Mtb(250-258) (T cell epitopes of influenza nucleoprotein and Mycobacterium tuberculosis, respectively) and the M. tuberculosis Ag Mtb8.4 protein, into K562 cells when covalently linked to the respective Ags. Furthermore, selected SynB vectors, when conjugated to these same Ags and used as immunogens, resulted in considerably enhanced Ag-specific CTL responses. Several SynB vectors were tested and resulted in varying levels of cellular uptake. The efficiency of uptake correlated with the ability of the SynB construct to deliver each epitope in vivo and induce specific CTL responses in mice. These data suggest that peptide vectors, such as SynB that transport target Ags across the cell membrane in a highly efficient manner, have significant potential for vaccine delivery.
Differential Inhibition of Human Immunodeficiency Virus Type 1 Fusion, gp120 Binding, and CC-Chemokine Activity by Monoclonal Antibodies to CCR5 (1999)

The CC-chemokine receptor CCR5 mediates fusion and entry of the most commonly transmitted human immunodeficiency virus type 1 (HIV-1) strains. We have isolated six new anti-CCR5 murine monoclonal antibodies (MAbs), designated PA8, PA9, PA10, PA11, PA12, and PA14. A panel of CCR5 alanine point mutants was used to map the epitopes of these MAbs and the previously described MAb 2D7 to specific amino acid residues in the N terminus and/or second extracellular loop regions of CCR5. This structural information was correlated with the MAbs' abilities to inhibit (i) HIV-1 entry, (ii) HIV-1 envelope glycoprotein-mediated membrane fusion, (iii) gp120 binding to CCR5, and (iv) CC-chemokine activity. Surprisingly, there was no correlation between the ability of a MAb to inhibit HIV-1 fusion-entry and its ability to inhibit either the binding of a gp120-soluble CD4 complex to CCR5 or CC-chemokine activity. MAbs PA9 to PA12, whose epitopes include residues in the CCR5 N terminus, strongly inhibited gp120 binding but only moderately inhibited HIV-1 fusion and entry and had no effect on RANTES-induced calcium mobilization. MAbs PA14 and 2D7, the most potent inhibitors of HIV-1 entry and fusion, were less effective at inhibiting gp120 binding and were variably potent at inhibiting RANTES-induced signaling. With respect to inhibiting HIV-1 entry and fusion, PA12 but not PA14 was potently synergistic when used in combination with 2D7, RANTES, and CD4-immunoglobulin G2, which inhibits HIV-1 attachment. The data support a model wherein HIV-1 entry occurs in three stages: receptor (CD4) binding, coreceptor (CCR5) binding, and coreceptor-mediated membrane fusion. The antibodies described will be useful for further dissecting these events.
<title>Fiber-grating-based WDM transmitters for OC-48 applications</title> (1997)

WDM semiconductor sources with precise and stable wavelength registration are needed to fulfill the requirements of future high-speed, all-optical fiber networks. The source should meet the tight requirements on wavelength accuracy and stability over lifetime, high-speed operation, and low cost of future WSM systems. New fiber-grating based devices offer an attractive solution for such sources at a potentially lower cost than conventional DFBs.
Postmortem analysis of adrenal–medulla–to–caudate autograft in a patient with parkinson's disease (1989)

A 53-year-old physician who had a 10-year history of progressive idiopathic parkinsonism survived for 4 months after an autologous adrenal-medulla-to-right-caudate autograft but he received little clinical benefit. A small number of chromaffin cells in the graft site survived; they expressed neurofilament proteins and chromogranin A, but scant tyrosine hydroxylase. The striatum on both sides showed almost complete loss of [3H]mazindol binding to dopamine-uptake sites; the density of dopamine receptors was decreased adjacent to the transplant but increased rostral to the transplant. These results demonstrate that autografted chromaffin cells can survive for 4 months after transplantation and that related changes in dopamine receptors can be quantified.
Dual-Function Vaccine for Pseudomonas aeruginosa : Characterization of Chimeric Exotoxin A-Pilin Protein (2001)

Pseudomonas aeruginosa is the major infectious agent of concern for cystic fibrosis patients. Strategies to prevent colonization by this bacterium and/or neutralize its virulence factors are clearly needed. Here we characterize a dual-function vaccine designed to generate antibodies to reduce bacterial adherence and to neutralize the cytotoxic activity of exotoxin A. To construct the vaccine, key sequences from type IV pilin were inserted into a vector encoding a nontoxic (active-site deletion) version of exotoxin A. The chimeric protein, termed PE64Delta553pil, was expressed in Escherichia coli, refolded to a near-native conformation, and then characterized by various biochemical and immunological assays. PE64Delta553pil bound specifically to asialo-GM1, and, when injected into rabbits, produced antibodies that reduced bacterial adherence and neutralized the cell-killing activity of exotoxin A. Results support further evaluation of this chimeric protein as a vaccine to prevent Pseudomonas colonization in susceptible individuals.
Heme Oxygenase Overexpression Attenuates Glucose-Mediated Oxidative Stress in Quiescent Cell Phase: Linking Heme to Hyperglycemia Complications (2005)

Heme oxygenase (HO-1) is a stress protein, which has been suggested to participate in defense mechanisms against glucose induced oxidative injury. The purpose of this study was to examine the role of human HO-1 in attenuating glucose-mediated oxidative stress. We investigated the effect of high ambient glucose (15, 33 and 66 mM) on HO-1 gene expression in endothelial cells grown in a serum deprived media compared to the effect of glucose on exponentially grown cells (10% FBS). High glucose at 15 and 33 mM caused significant inhibition of HO-1 protein and activity in G0/G1 and in cells exponentially grown. Glucose concentration at 66 mM caused a significant increase in HO-1. Addition of heme (10 microM) increased HO-1 protein and bilirubin formation in G0/G1, in a time dependent manner peaking at 16 h. Glucose attenuated heme mediated increase in HO-1 proteins. RT-PCR demonstrated that glucose decreased the levels of HO-1 mRNA in both G0/G1 or cells grown in 10% FBS. The rate of HO-1 induction in response to heme was several fold higher in serum-starved cells compared to cells cultured in 10% FBS. Cells exposed to high glucose for up to 24 h had a significant increase in cellular heme and potentiated heme-mediated increase in generation of superoxide anion and 8-epi-isoprostane PGF(2alpha). HO-1 gene transduction prevented glucose-mediated elevation of 8-epi-isoprostane PGF(2alpha). These results imply that expression of HO-1 in G0/G1 cells may be a key player in decreasing cellular heme, associated with increased generation of bilirubin, and in attenuating glucose mediated oxidative stress.
Purification and characterization of a novel bacterial non-heme chloroperoxidase from Pseudomonas pyrrocinia. (1988)

The first bacterial chloroperoxidase that is capable of catalyzing the chlorination of indole to 7-chloroindole was detected in Pseudomonas pyrrocinia ATCC 15958, a bacterium that produces the antifungal antibiotic pyrrolnitrin (Wiesner, W., van Pée, K.H., and Lingens, F. (1986) FEBS Lett. 209, 321-324). Here we describe the purification and characterization of this bacterial non-heme chloroperoxidase. The enzyme was purified by DEAE-cellulose chromatography at different pH values, molecular sieve chromatography, and Bio-Gel HTP hydroxylapatite. After the last purification step, chloroperoxidase was homogeneous by polyacrylamide gel electrophoresis and ultracentrifugation. Based on gel filtration and ultracentrifugation results, the molecular weight of the enzyme was 64,000 +/- 3,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a single band with the mobility of a 32,000 molecular weight species. Therefore, in solution at neutral pH, this chloroperoxidase is a dimer. The enzyme did not exhibit any absorbance in the visible region of the spectrum. The isoelectric point was 4.1. Chloroperoxidase was specific for I-, Br-, and Cl- and was not inhibited by azide, but was inhibited by cyanide and F-. This procaryotic chloroperoxidase catalyzed the bromination of monochlorodimedone but not its chlorination and has no peroxidase or catalase activity. The pH optimum of the enzyme was between 4.0 and 4.5, and the enzyme was stable between pH 3.5 and 8.5 and showed no loss of activity when incubated at 60 degrees C for 2 h. Chloroperoxidase also chlorinated 4-(2-amino-3-chlorophenyl) pyrrole to yield aminopyrrolnitrin, the immediate precursor of pyrrolnitrin. This suggests very strongly that chloroperoxidase is involved in the biosynthesis of the antibiotic pyrrolnitrin.
Three Dimensional Human Neuro-Spheroid Model of Alzheimer’s Disease Based on Differentiated Induced Pluripotent Stem Cells (2016)

The testing of candidate drugs to slow progression of Alzheimer's disease (AD) requires clinical trials that are lengthy and expensive. Efforts to model the biochemical milieu of the AD brain may be greatly facilitated by combining two cutting edge technologies to generate three-dimensional (3D) human neuro-spheroid from induced pluripotent stem cells (iPSC) derived from AD subjects. We created iPSC from blood cells of five AD patients and differentiated them into 3D human neuronal culture. We characterized neuronal markers of our 3D neurons by immunocytochemical staining to validate the differentiation status. To block the generation of pathologic amyloid β peptides (Aβ), the 3D-differentiated AD neurons were treated with inhibitors targeting β-secretase (BACE1) and γ-secretases. As predicted, both BACE1 and γ-secretase inhibitors dramatically decreased Aβ generation in iPSC-derived neural cells derived from all five AD patients, under standard two-dimensional (2D) differentiation conditions. However, BACE1 and γ-secretase inhibitors showed less potency in decreasing Aβ levels in neural cells differentiated under 3D culture conditions. Interestingly, in a single subject AD1, we found that BACE1 inhibitor treatment was not able to significantly reduce Aβ42 levels. To investigate underlying molecular mechanisms, we performed proteomic analysis of 3D AD human neuronal cultures including AD1. Proteomic analysis revealed specific reduction of several proteins that might contribute to a poor inhibition of BACE1 in subject AD1. To our knowledge, this is the first iPSC-differentiated 3D neuro-spheroid model derived from AD patients' blood. Our results demonstrate that our 3D human neuro-spheroid model can be a physiologically relevant and valid model for testing efficacy of AD drug.
All-optical extended depth of field imaging system (2003)

We describe a novel approach whereby a phase mask consisting of several spatially multiplexed Fresnel lenses (FL) positioned in the pupil of an imaging system increases the depth of field (DOF) significantly. Each FL acts essentially as a corrective lens with a slightly different focal length. Keeping the detector plane in a fixed location, each individual FL provides perfect imaging for different object planes, with a certain DOF tolerance around it. Allowing the individual DOFs to overlap slightly, the resulting composite DOF of the imaging system is highly extended. Nevertheless, the increased DOF is coupled with a reduction in image contrast and resolution. System analysis and simulation results are presented.
Combined multilevel turbo-code with 8PSK modulation (2002)

Different concepts of iterative decoding algorithms for serial or parallel concatenated coding (called turbo-code) as well as for the special case of the generalized concatenated coding schemes have been introduced. These algorithms being very efficient, are based on soft output decoding, where, the soft decisions are used as feed-forward information for the next steps of iterations. In order to achieve the high performance expected by turbo-codes and to assume a great flexibility for the system, we combine a multilevel turbo-code with 8PSK modulation. This allow us to examine in detail the performance of this combination compared with different coding and decoding approaches: turbo-code with Gray mapping and iterative multistage decoding using convolutional codes or a combination of turbo codes, convolutional and single parity check codes. In all of our studies we consider a super-concatenated coding scheme, where the outer code is based on Reed-Solomon code. The results showed that the coding gain at a BER of 10/sup -4/ (since we employ a powerful outer RS decoder) for the iterative convolutional coding and for the combination of convolutional/turbo coding is quite the same compared to turbo coding with Gray mapping, which is 0.5 dB. However, compared to uncoded QPSK, the coding gain is 4 dB (at a BER of 10/sup -4/), which is quite significant.
A Light-Actuated Nanovalve Derived from a Channel Protein (2005)

Toward the realization of nanoscale device control, we report a molecular valve embedded in a membrane that can be opened by illumination with long-wavelength ultraviolet (366 nanometers) light and then resealed by visible irradiation. The valve consists of a channel protein, the mechanosensitive channel of large conductance (MscL) from Escherichia coli, modified by attachment of synthetic compounds that undergo light-induced charge separation to reversibly open and close a 3-nanometer pore. The system is compatible with a classical encapsulation system, the liposome, and external photochemical control over transport through the channel is achieved.
Sleep stages and EEG power spectrum in relation to acoustical stimulus arousal threshold in the rat. (1993)

This study was designed to functionally validate earlier described criteria for visual sleep scoring with respect to acoustical stimulus threshold for arousal. A further objective was to explore the relation between electroencephalographic (EEG) power spectrum and acoustical stimulus threshold for arousal. After habituation to an acoustical stimulus (a 1,000-Hz sine tone, increasing 1.5 dB per second for 45 seconds), values for latency to arousal after acoustical stimulus onset were analyzed. Arousal was determined based on EEG and electromyographic (EMG) criteria. There was a significant effect of sleep stage, with slow wave sleep 2 (SWS-2) having higher arousal threshold than slow wave sleep 1 (SWS-1), rapid eye movement (REM) sleep and transition type sleep. This indicates that the subdivision of nonrapid eye movement (NREM) sleep in the rat into SWS-1 and SWS-2 had functional validity in this paradigm. Time of day also had a significant effect, with lower arousal threshold in the last 2 hours (ninth and tenth hour of the light period) of the 8-hour registration period. Furthermore, there was a significant effect of EEG delta power density. Epochs with high delta power had increased arousal threshold relative to epochs with low arousal threshold. The results were consistent with the notion that delta activity is an indicator of depth within NREM sleep.
Lattice-ladder structured adaptive decorrelation filtering for co-channel speech separation (2002)

A lattice-ladder adaptive decorrelation filtering (ADF) algorithm is proposed with the aim of developing a more efficient co-channel speech separation system. It is shown that based on the joint forward and backward linear predictions, a lattice-ladder structure can be derived for ADF. Experimental results show that the proposed algorithm is effective in reducing cross-interference between co-channel speech sources and has better tracking ability on the variations in the acoustic environment compared to the original direct-form ADF algorithm.
External quantum efficiency of single porous silicon nanoparticles (1999)

We use a combination of single nanoparticle luminescence and scanning force microscopy to determine the quantum efficiency (QE) of single porous Si nanoparticles and to determine the ratio of luminescent nanoparticles deposited on a silica surface to the total nanoparticles. An estimate of the QE of bulk porous Si based on these data compares favorably to the QE measured experimentally. From this we conclude that the 1% QE of bulk porous Si measured experimentally results primarily from a statistical distribution of high QE quantum-confined Si chromophores.
HEAVY METALS REMOVAL FROM AQUEOUS SOLUTIONS USING TiO2, MgO, AND Al2O3NANOPARTICLES (2012)

Abstract This study investigated the removal of Cd2+, Cu2+, Ni2+, and Pb2+ from aqueous solutions using nanoparticle sorbents (TiO2, MgO, and Al2O3) with a range of experimental approaches. The maximum uptake values (sum of four metals) with multiple component solutions were 594.9, 114.6, and 49.4 mg g−1, for MgO, Al2O3, and TiO2, respectively. The sorption equilibrium isotherms were described using the Freundlich and Langmuir models. The best interpretation for experiment data was given by the Freundlich model for Cd2+, Cu2+, and Ni2+ in single- and multiple-component solutions. A first-order kinetic model adequately described the experimental data using MgO, Al2O3, and TiO2. SEM-EDX both before and after metal sorption and soil solution saturation indices (SI) in MgO nanoparticles indicated that the main sorption mechanism for heavy metals was attributable to adsorption and precipitation, whereas heavy metal sorption by TiO2 and Al2O3 adsorbents was due to adsorption. These nanoparticles may potentially be used as efficient sorbents for heavy metal removal from aqueous solutions. MgO nanoparticles were the most promising sorbents because of their high metal uptake. Keywords: Aqueous solutionsHeavy metalsNanoparticlesRemoval Notes a Data calculated from the XRD pattern according to the Scherrer equation. b Data from TEM analysis. *mg g−1 min−1. **(mg g−1)−1. a mg g−1.