gebhart/patrepeval huggingface dataset:
Detection of simple mutations and polymorphisms in large genomic regions (2001)

We have developed a novel technology that makes it possible to detect simple nucleotide polymorphisms directly within a sample of total genomic DNA. It allows, in a single Southern blot experiment, the determination of sequence identity of genomic regions with a combined length of hundreds of kilobases. This technology does not require PCR amplification of the target DNA regions, but exploits preparative size-fractionation of restriction-digested genomic DNA and a newly discovered property of the mismatch-specific endonuclease CEL I to cleave heteroduplex DNA with a very high specificity and sensitivity. We have used this technique to detect various simple mutations directly in the genomic DNA of isogenic pairs of recombinant Pseudomonas aeruginosa, Escherichia coli and Salmonella isolates. Also, by using a cosmid DNA library and genomic fractions as hybridization probes, we have compared total genomic DNA of two clinical P.aeruginosa clones isolated from the same patient, but exhibiting divergent phenotypes. The mutation scan correctly detected a GA insertion in the quorum-sensing regulator gene rhlR and, in addition, identified a novel intragenomic polymorphism in rrn operons, indicating very high stability of the bacterial genomes under natural non-mutator conditions.
Leucine Zipper (2001)

Abstract The leucine zipper is a protein–protein interaction domain consisting of amphipathic α helices that dimerize in parallel, either as homodimers or heterodimers, to form a coiled‐coil.
QUANTUM YIELD OF SINGLET OXYGEN PRODUCTION BY XANTHENE DERIVATIVES (1983)

Abstract The singlet oxygen quantum yield (ϕ 1 o 2 ) of 11 purified fluorescein derivatives was determined by reaction with singlet oxygen acceptors in aqueous and ethanolic solutions; in both solvents ϕ 1 o 2 was enhanced with increasing halogenation. Tryptophan and 2,2,6,6‐tetramethylpiperidone were found to be unadapted for the determination of ϕ 1 o 2 , in our systems; however, the use of 9.10‐dipropionic anthracene acid andp‐nitrosodimethylaniline in conjunction with imidazole derivatives was suitable for 1 O 2 detection in water. Both methods lead to results in excellent agreement. As in ethanol. ϕ 1 o 2 , was equal to the triplet state quantum yield (ϕ T ), the comparison between the two solvents showed that ϕ T in water was greater than in ethanol. The comparison between our values obtained with polychromatic light with published data obtained with monochromatic light suggests that the triplet quantum yield of fluorescein derivatives is wavelength independent.
The Fundamental Design Issues of Jeliot 3 (2004)

Programming and algorithms are hard subjects to teach and learn. Especially novices seem to have problems to grasp the basic concepts of programming and algorithms. Software visualization has tried to provide help for teaching and learning these subjects. The Jeliot family is a group of program and algorithm visualization tools to help novices to form the new concepts of programming and algorithms. In this thesis, a new version of Jeliot, called Jeliot 3, and its design are introduced. The new version is meant especially for novice students who are learning programming in Java language. It visualizes the data and the control flow of the programs as well as the object-oriented concepts such as constructors and objects. In the design, we have used a modular approach that connects an interpreter and a visualization engine to each other. Our design allows the utilization of two existing systems, Jeliot 2000 as a visualization engine and DynamicJava as an interpreter, to create the basis for this new system. To connect these two systems, we have created a new intermediate language. This new language also allows a formation of different kinds of visualizations with relative ease making the system extensible. In the design of the visualization, we have used the results from studies conducted in the fields of educational psychology and software visualization, and come into the conclusion that the program visualization for novices should be as complete, continuous and consistent as possible. Jeliot 3 extends the visualization capabilities of previous members of the Jeliot family with object-oriented concepts.
A network of RNA and protein interactions in Fronto Temporal Dementia (2015)

Frontotemporal dementia (FTD) is a neurodegenerative disorder characterized by degeneration of the fronto temporal lobes and abnormal protein inclusions. It exhibits a broad clinicopathological spectrum and has been linked to mutations in seven different genes. We will provide a picture, which connects the products of these genes, albeit diverse in nature and function, in a network. Despite the paucity of information available for some of these genes, we believe that RNA processing and post-transcriptional regulation of gene expression might constitute a common theme in the network. Recent studies have unraveled the role of mutations affecting the functions of RNA binding proteins and regulation of microRNAs. This review will combine all the recent findings on genes involved in the pathogenesis of FTD, highlighting the importance of a common network of interactions in order to study and decipher the heterogeneous clinical manifestations associated with FTD. This approach could be helpful for the research of potential therapeutic strategies.
Cardiovascular Mortality in Haemodialysis Patients Treated with Epoetin Beta – A Retrospective Study (2000)

The cardiovascular mortality risk decreased over time in this population of ESRD patients. The beneficial effects of long-term anaemia correction by epoetin-beta therapy was a likely cause of this favourable development.
Green and Efficient Synthesis of Some Pyrido[2,3-D]Pyrimidin-4(3h)-One Derivatives Via Iodine Catalyst in Aqueous Media and Evaluation the Synthesized Compounds as Anticancer (2013)

A series of new 2-propylpyrido[2,3-d]pyrimidin-4(3H)-one with different substituents at position 3 were syn-thesized by traditional method and Iodine catalyst method. The effect of the newly synthesized compounds was tested as anti-cancer in National Cancer Institute(NCI)in USA. Some of the synthesized compounds exploited potent antitumor activity, especially the compounds pyrido[2,3-d][1,3]oxazin (2), 3-amino derivative 3a, 3b and hydroxy derivative 3c dis-played the highest activity among the test compounds with IC50 > 5 mg/mL
γ-Protocadherins, Presenilin-mediated Release of C-terminal Fragment Promotes Locus Expression (2005)

gamma-Protocadherins (gamma-pcdhs) are type I membrane-spanning glycoproteins, widely expressed in the mammal and required for survival. These cell adhesion molecules are expressed from a complex locus comprising 22 functional variable exons arranged in tandem, each encoding extracellular, transmembrane and intracellular sequence, and three exons for an invariant C-terminal domain (gamma-ICD). However, the signaling mechanisms that lie downstream of gamma-pcdhs have not been elucidated. Here we report that gamma-pcdhs are subject to presenilin-dependent intramembrane cleavage (PS-IP), accompanied by shedding of the extracellular domain. The cleaved intracellular domain (gamma-ICD) translocates to the cell nucleus and was detected in subsets of cortical neurons. Notably, gene-targeted mice lacking functional gamma-ICD sequence showed severely reduced gamma-pcdh mRNA levels and neonatal lethality. Most importantly, inhibition of gamma-secretase decreased gamma-pcdh locus expression. Luciferase reporter assays demonstrated that gamma-pcdh promoter activity is increased by gamma-ICD. These results reveal an intracellular signaling mechanism for gamma-pcdhs and identify a novel vital target for the gamma-secretase complex.
Synthetic Prodiginine Obatoclax (GX15‐070) and Related Analogues: Anion Binding, Transmembrane Transport, and Cytotoxicity Properties (2011)

Synthetic prodiginine obatoclax shows promise as a potential anticancer drug. This compound promotes apoptosis of cancer cells, although the mechanism of action is unclear. To date, only the inhibition of BCL-2 proteins has been proposed as a mechanism of action. To gain insight into other possible modes of action, we have studied the anion-binding properties of obatoclax and related analogues in solution, in the solid state, and by means of density functional theory calculations. These compounds are well suited to interact with anions such as chloride and bicarbonate. The anion-transport properties of the compounds synthesized were assayed in model phospholipid liposomes by using a chloride-selective-electrode technique and (13)C NMR spectroscopy. The results demonstrated that these compounds are efficient anion exchangers that promote chloride, bicarbonate, and nitrate transport through lipid bilayers at very low concentrations. In vitro studies on small-cell lung carcinoma cell line GLC4 showed that active ionophores are able to discharge pH gradients in living cells and the cytotoxicity of these compounds correlates well with ionophoric activity.
Hofmeister Effects of Common Monovalent Salts on the Beetle Antifreeze Protein Activity (2009)

Antifreeze proteins (AFPs) noncolligatively depress the freezing point of a solution and produce a difference between the melting and freezing points termed thermal hysteresis (TH). While the mechanism of the enhancement effect is not well understood, various low-molecular-mass solutes including neutral salts have been identified to enhance the TH activities of AFPs. Here, the effect of monovalent salts on salting out an AFP from the beetle Dendroides canadensis (DAFP-1) on the ice was treated using a simple classical theory, and the relationship between the TH activity and the salt concentration was developed. The TH activities of DAFP-1 in the presence of the series of monovalent salts were assessed by differential scanning calorimetry (DSC), and the salting-out constants of DAFP-1 by these salts were determined. This study demonstrates an indirect way to determine the salting-out constants of AFPs by these salts. The results suggest that the Hofmeister effect is a potential mechanism for the TH enhancement effects of some common monovalent salts.
Using natural language processing for analyzing Arabic poetry rhythm (2017)

One from the most difficult tasks for Natural Language Processing (NLP) is to analyze poetry, which uses a different genre of language than that considered by computer-based techniques. Therefore, computational analysis is an interesting task when we use NLP in poetry, but it is also challenging. There are a number of researchers that entered this field from NLP and they got promising results using mathematical analysis for poetry, including rhythm analysis. In this paper we focused on providing solution for automating the rhythm detection of the Arabic poems and finding the number of rhythm for each verse in poem and the total percentage for each rhythm in all verses of poem, additional to other characteristics for the Arabic poem like percentage of mobile letter in Arabic “harf mutaharrik”, and The quiescent letter, in Arabic “harf sakin”, In spite of the number of studies in the computational analysis of poetry, we think it needs more, not only to make a better understanding of domain but also in developing applications, considering different literary tastes and the psychological effects, to give a recommendation to the readers and in plagiarism detection[1].
Ethanol Production from Alkaline Peroxide Pretreated Enzymatically Saccharified Wheat Straw (2006)

Wheat straw used in this study contained 44.24 ± 0.28% cellulose and 25.23 ± 0.11% hemicellulose. Alkaline H2O2 pretreatment and enzymatic saccharification were evaluated for conversion of wheat straw cellulose and hemicellulose to fermentable sugars. The maximum yield of monomeric sugars from wheat straw (8.6%, w/v) by alkaline peroxide pretreatment (2.15% H2O2, v/v; pH 11.5; 35 °C; 24 h) and enzymatic saccharification (45 °C, pH 5.0, 120 h) by three commercial enzyme preparations (cellulase, β-glucosidase, and xylanase) using 0.16 mL of each enzyme preparation per g of straw was 672 ± 4 mg/g (96.7% yield). During the pretreatment, no measurable quantities of furfural and hydroxymethyl furfural were produced. The concentration of ethanol (per L) from alkaline peroxide pretreated enzyme saccharified wheat straw (66.0 g) hydrolyzate by recombinant Escherichia coli strain FBR5 at pH 6.5 and 37 °C in 48 h was 18.9 ± 0.9 g with a yield of 0.46 g per g of available sugars (0.29 g/g straw). The ethanol concentration (per L) was 15.1 ± 0.1 g with a yield of 0.23 g/g of straw in the case of simultaneous saccharification and fermentation by the E. coli strain at pH 6.0 and 37 °C in 48 h.
Five ADNFLE Mutations Reduce the Ca<sup>2+</sup> Dependence of the Mammalian α4β2 Acetylcholine Response (2003)

Five nicotinic acetylcholine receptor (nAChR) mutations are currently linked to autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE). The similarity of their clinical symptoms suggests that a common functional anomaly of the mutations underlies ADNFLE seizures. To identify this anomaly, we constructed rat orthologues (S252F, +L264, S256L, V262L, V262M) of the human ADNFLE mutations, expressed them in Xenopus oocytes with the appropriate wild-type (WT) subunit (alpha4 or beta2), and studied the Ca2+ dependence of their ACh responses. All the mutations significantly reduced 2 mM Ca2+-induced increases in the 30 microM ACh response (P < 0.05). Consistent with a dominant mode of inheritance, this reduction persisted in oocytes injected with a 1:1 mixture of mutant and WT cRNA. BAPTA injections showed that the reduction was not due to a decrease in the secondary activation of Ca2+-activated Cl- currents. The S256L mutation also abolished 2 mM Ba2+ potentiation of the ACh response. The S256L, V262L and V262M mutations had complex effects on the ACh concentration-response relationship but all three mutations shifted the concentration-response relationship to the left at [ACh] >= 30 microM. Co-expression of the V262M mutation with a mutation (E180Q) that abolished Ca2+ potentiation resulted in 2 mM Ca2+ block, rather than potentiation, of the 30 microM ACh response, suggesting that the ADNFLE mutations reduce Ca2+ potentiation by enhancing Ca2+ block of the alpha4beta2 nAChR. Ca2+ modulation may prevent presynaptic alpha4beta2 nAChRs from overstimulating glutamate release at central excitatory synapses during bouts of synchronous, repetitive activity. Reducing the Ca2+ dependence of the ACh response could trigger seizures by increasing alpha4beta2-mediated glutamate release during such bouts.
Epitaxy of GaAs thin film with low defect density and smooth surface on Si substrate (2014)

Device-quality GaAs thin films have been grown on miscut Ge-on-Si substrates by metal-organic chemical vapor deposition. A method of two-step epitaxy of GaAs is performed to achieve a high-quality top-layer. The initial thin buffer layer at 360 °C is critical for the suppression of anti-phase boundaries and threading dislocations. The etch pit density of GaAs epilayers by KOH etching could reach 2.25 × 105 cm−2 and high-quality GaAs top epilayers are observed by transmission electron microscopy. The band-to-band photoluminescence property of GaAs epilayers on different substrates is also investigated and negative band shifts of several to tens of meVs are found because of tensile strains in the GaAs epilayers. To achieve a smooth surface, a polishing process is performed, followed by a second epitaxy of GaAs. The root-mean-square roughness of the GaAs surface could be less than 1 nm, which is comparable with that of homo-epitaxial GaAs. These low-defect and smooth GaAs epilayers on Si are desirable for GaAs-based devices on silicon substrates.
Photocatalysts Based on Organic Semiconductors with Tunable Energy Levels for Solar Fuel Applications (2020)

Abstract The photocatalytic synthesis of solar fuels such as hydrogen and methane from water and carbon dioxide is a promising strategy to store abundant solar energy in order to overcome its intermittency. Although this approach has been studied for decades using inorganic semiconductor photocatalysts, organic semiconductors have only recently gained notable attention. The tunable energy levels of organic semiconductors can enable the design of photocatalysts with optimized solar light utilization. However, the solar conversion efficiency of organic semiconductor photocatalysts has so far been limited by their low quantum efficiencies. To address this issue, various photocatalyst design strategies including semiconductor energy level optimization, surface modification, and the fabrication of heterojunctions have been applied, resulting in substantial increases in photocatalytic efficiency. This progress report systematically describes the strategies employed to increase the efficiency of organic semiconductor photocatalysts for the generation of solar fuels from water and carbon dioxide. Particular attention is given to describing strategies to enhance quantum efficiency, and insights are provided on the mechanisms underlying their success to aid the rational design of future organic photocatalysts. Perspectives on the future challenges and promising research directions for the design of efficient organic photocatalysts for the generation of solar fuels are also provided.
Integrating indoor mobility, object manipulation, and intuitive interaction for domestic service tasks (2009)

Domestic service tasks require three main skills from autonomous robots: robust navigation, mobile manipulation, and intuitive communication with the users. Most robot platforms, however, support only one or two of the above skills. In this paper we present Dynamaid, a new robot platform for research on domestic service applications. For robust navigation, Dynamaid has a base with four individually steerable differential wheel pairs, which allow omnidirectional motion. For mobile manipulation, Dynamaid is additionally equipped with two anthropomorphic arms that include a gripper, and with a trunk that can be lifted as well as twisted. For intuitive multimodal communication, the robot has a microphone, stereo cameras, and a movable head. Its humanoid upper body supports natural interaction. It can perceive persons in its environment, recognize and synthesize speech. We developed software for the tests of the RoboCup@Home competitions, which serve as benchmarks for domestic service robots. With Dynamaid and our communication robot Robotinho, our team Nimbro@Home took part in the RoboCup German Open 2009 and RoboCup 2009 competitions in which we came in second and third, respectively. We also won the innovation award for innovative robot design, empathic behaviors, and robot-robot cooperation.
Colocalization Analysis in Fluorescence Micrographs: Verification of a More Accurate Calculation of Pearson's Correlation Coefficient (2010)

One of the most routine uses of fluorescence microscopy is colocalization, i.e., the demonstration of a relationship between pairs of biological molecules. Frequently this is presented simplistically by the use of overlays of red and green images, with areas of yellow indicating colocalization of the molecules. Colocalization data are rarely quantified and can be misleading. Our results from both synthetic and biological datasets demonstrate that the generation of Pearson's correlation coefficient between pairs of images can overestimate positive correlation and fail to demonstrate negative correlation. We have demonstrated that the calculation of a thresholded Pearson's correlation coefficient using only intensity values over a determined threshold in both channels produces numerical values that more accurately describe both synthetic datasets and biological examples. Its use will bring clarity and accuracy to colocalization studies using fluorescent microscopy.
TETRAHYDRO-1,3,2-OXAZONES AND SUBSTITUTED GAMMA-AMINO PROPANOLS (1923)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTETRAHYDRO-1,3,2-OXAZONES AND SUBSTITUTED GAMMA-AMINO PROPANOLSJ. S. Pierce and Roger AdamsCite this: J. Am. Chem. Soc. 1923, 45, 3, 790–795Publication Date (Print):March 1, 1923Publication History Published online1 May 2002Published inissue 1 March 1923https://pubs.acs.org/doi/10.1021/ja01656a035https://doi.org/10.1021/ja01656a035research-articleACS PublicationsRequest reuse permissionsArticle Views105Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Analysis of paraprotein transport into the saliva by using anti-idiotype antibodies. (1987)

To determine the extent of clonal involvement of the secretory immune system and the origin of salivary immunoglobulins (Ig) in monoclonal gammopathy patients, saliva and serum samples were collected from five affected individuals (two IgA myelomas, one IgG myeloma, one IgG benign monoclonal gammopathy, and one IgM lymphoma) and were assayed for the presence of monoclonal Ig. Purified polyclonal or monoclonal anti-idiotype (Id) antibodies were prepared against each of the isolated serum paraproteins. In all five individuals, the patient saliva samples inhibited the binding of 125I-labeled homologous Ig to the corresponding anti-Id antibodies, but normal saliva did not. The concentration of Id in patients' saliva varied from 1 to 400 micrograms/ml; i.e., 0.004 to 1.0% of the corresponding serum values. Saliva of a lymphoma patient whose IgM kappa protein exhibited rheumatoid factor (RF) activity also contained RF. The salivary Id-bearing molecules were found to have the same Ig isotype as the serum paraproteins. The myeloma IgA represented a minor component (0.4 and 3.9%) of the total salivary IgA. The salivary IgA myeloma proteins were associated at least in part with secretory component, but the salivary IgG paraproteins were not. In an IgA myeloma patient, a minority (17%) of the IgA+ plasma cells found in the lacrymal gland biopsy specimen were Id+, whereas the great majority (98%) of bone marrow IgA plasma cells were Id+. The results suggest active transport rather than passive transudation of myeloma IgA into the patients' saliva, and the integrity of the secretory immune system was not compromised by the neoplastic process.
Doppler positioning with a movable receiver antenna and a single pseudolite for indoor localization (2011)

Pseudolites are one of the most promising technologies for indoor localization because they can directly use off-the-shelf GPS/GNSS receivers with minor change of their firmware. However, pseudolites have some fundamental issues such as near-far, multipath, and synchronization problems. Many of these issues derive from using more than one transmitter and trilateration. In this paper, we propose a novel indoor positioning method using a movable receiver antenna and a single pseudolite. In this method, the position is determined by using the Doppler shift produced by a moving antenna. We conducted an experiment by testing different conditions of the moving antenna. The results show that our method has the potential to achieve the positioning with decimeter level accuracy.