gebhart/patrepeval huggingface dataset:
Social capital, community driven development, and empowerment : a short note on concepts and operations (2003)

This paper explores the relationships among, social capital, community driven development (CDD), and empowerment. There are, some important mutually supportive links among social capital, CDD and empowerment, as it will be seen, these links are more accurately viewed as tendencies, rather than deterministic relations hips. Success in enhancing the level of any one of these concepts will have the tendency as well of improving the prospects for the other two concepts. There is, however, nothing determinate or automatic about any of these relationships. Social capital relates to communities' innate capacity for action, CDD helps provide them with complementary resources and opportunities for self development, and empowerment is concerned with improving both the internal capacity of groups and also the external environment in which they function. These are complementary agendas, but they are not related hierarchically in the sense that implementing any one is tantamount to implementing the others. They must be simultaneously and separately pursued.
Machine Learning for Dental Image Analysis (2016)

In order to study the application of artificial intelligence (AI) to dental imaging, we applied AI technology to classify a set of panoramic radiographs using (a) a convolutional neural network (CNN) which is a form of an artificial neural network (ANN), (b) representative image cognition algorithms that implement scale-invariant feature transform (SIFT), and (c) histogram of oriented gradients (HOG).
Heart rate variability and experimentally induced pain in healthy adults: A systematic review (2013)

HRV has several advantages compared to other measures of autonomic reactivity in studies investigating physiological response to nociceptive stimulation. Future studies should focus on comparisons between different methods of pain induction, interindividual variability in pain sensitivity by baseline autonomic activity, and the implications of both on the use of HRV within routine clinical evaluations.
Assessing the Molecular Structure of Alkanethiol Monolayers in Hybrid Bilayer Membranes with Vibrational Spectroscopies (1998)

Hybrid bilayer membranes (HBMs), consisting of a lipid monolayer covering a self-assembled alkanethiol monolayer on a metal surface, are useful models for studying the structure and function of cell membranes. Surface-enhanced Raman spectroscopy (SERS) and reflection absorption infrared spectroscopy (RAIRS) are used to study HBMs with various alkanethiol and lipid components. Together, these two techniques clearly indicate that the lipid forms a well-ordered, non-interdigitated layer on the alkanethiol with the head groups of the lipids oriented away from the metal surface. Both techniques reveal that the formation of an HBM produces small changes in the alkanethiols, which are similar to those caused by a reduction in temperature, indicative of an increase in order. The small magnitude of the perturbations in the alkanethiol monolayer upon addition of the lipid layer will simplify the further study of HBMs.
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition (2010)

We characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes in vitro DNA fragmentation and adaptor incorporation simultaneously. We apply this method to sequencing a human genome and find that coverage biases are comparable to those of conventional protocols. We also extend its capabilities by developing protocols for sub-nanogram library construction, exome capture from 50 ng of input DNA, PCR-free and colony PCR library construction, and 96-plex sample indexing.
Az R szoftver alkalmazása az Adatbányászat tárgy oktatásában (2015)

Az adatbányászat egy tipikus informatikához köthető terület. A gazdaságinformatikus hallgatók számára különösen nagy jelentőséggel bír a gazdasági kötődés miatt. Bemutatjuk az általános elvárásokat az adatbányászati szoftverekkel szemben és konkrétan az R program alkalmazhatóságát az Adatbányászat oktatásában.
Adeno-Associated Virus (AAV) Type 5 Rep Protein Cleaves a Unique Terminal Resolution Site Compared with Other AAV Serotypes (1999)

Adeno-associated virus (AAV) replication depends on two viral components for replication: the AAV nonstructural proteins (Rep) in trans, and inverted terminal repeat (ITR) sequences in cis. AAV type 5 (AAV5) is a distinct virus compared to the other cloned AAV serotypes. Whereas the Rep proteins and ITRs of other serotypes are interchangeable and can be used to produce recombinant viral particles of a different serotype, AAV5 Rep proteins cannot cross-complement in the packaging of a genome with an AAV2 ITR. In vitro replication assays indicated that the block occurs at the level of replication instead of at viral assembly. AAV2 and AAV5 Rep binding activities demonstrate similar affinities for either an AAV2 or AAV5 ITR; however, comparison of terminal resolution site (TRS) endonuclease activities showed a difference in specificity for the two DNA sequences. AAV2 Rep78 cleaved only a type 2 ITR DNA sequence, and AAV5 Rep78 cleaved only a type 5 probe efficiently. Mapping of the AAV5 ITR TRS identified a distinct cleavage site (AGTG TGGC) which is absent from the ITRs of other AAV serotypes. Comparison of the TRSs in the AAV2 ITR, the AAV5 ITR, and the AAV chromosome 19 integration locus identified some conserved nucleotides downstream of the cleavage site but little homology upstream.
Crystal Structure of GaN Grown on 3C-SiC Substrates by Metalorganic Vapor Phase Epitaxy (1997)

GaN films were grown on 3C-SiC substrates by metalorganic vapor phase epitaxy (MOVPE) using 1,1-dimethylhydrazine (DMHy) as the N source. The crystal structure was strongly affected by both the growth temperature and the V/III ratio. At 600° C, only hexagonal GaN films with their c -axis perpendicular to the substrate surface were grown. At 800° C, relatively high V/III ratios resulted in the growth of hexagonal GaN with their c -axis oriented in the [111] direction while cubic GaN films were obtained at lower V/III ratios. The origin of [111]-oriented hexagonal GaN is also discussed.
Induction of CD8+ Regulatory T Cells Protects Macaques against SIV Challenge (2012)

Efforts to develop a vaccine against HIV have so far met with limited success. Given that CD4(+) T cell activation drives the initial burst of viral replication, we explored in macaques whether an oral vaccine comprised of Lactobacillus plantarum, a commensal bacterium that favors immune tolerance, and inactivated simian immunodeficiency virus mac239 (SIVmac239) would induce CD4(+) T cell unresponsiveness/tolerance toward SIV antigens and thereby prevent the establishment of SIV infection. The tolerogenic vaccine induced MHC-Ib/E-restricted CD8(+) regulatory T cells (Tregs) that suppressed SIV-harboring CD4(+) T cell activation and ex vivo SIV replication in 15 of 16 animals without inducing SIV-specific antibodies or cytotoxic T lymphocytes. Of 16 macaques that were intrarectally challenged with SIVmac239 or heterologous strain SIVB670, 15 were sterilely protected. In four macaques that were rechallenged intravenously, plasma SIV levels peaked slightly and then dropped to undetectable levels, although the animals subsequently harbored intracellular SIV DNA. Infusion of CD8 antibodies confirmed the role of CD8(+) Tregs in preventing/suppressing SIV in vivo. These findings suggest a new avenue of research toward developing an HIV-1 vaccine.
Autoantibodies against the amino-terminal cadherin-like binding domain of pemphigus vulgaris antigen are pathogenic. (1992)

Complementary DNA cloning of the 130-kD pemphigus vulgaris (PV) autoantigen (PVA) has indicated that it is a member of the cadherin family of Ca(2+)-dependent cell adhesion molecules. By homology with typical cadherins, PVA has five extracellular domains (EC1 through EC5). To localize immunogenic domains and to determine whether antibodies against them might be pathogenic, we produced beta-galactosidase fusion proteins with cDNA encoding different portions of the extracellular domains of PVA (EC1-2, EC3-5, and each individual domain). Immunoblot analysis of these fusion proteins with 23 PV patients' sera demonstrated that major immunogenic regions of PVA are located on the EC1, EC2, and EC4 domains. IgG was affinity-purified from PV sera on fusion proteins representing the amino (EC1-2) and carboxy (EC3-5) terminus of the extracellular PVA, and injected into neonatal mice. PV IgG affinity-purified on the EC1-2 fusion protein caused suprabasilar acantholysis, the typical histological finding of PV, but IgG affinity-purified on the EC3-5 fusion protein or beta-galactosidase alone did not. These results indicate that at least one pathogenic epitope, which is sufficient to cause suprabasilar acantholysis in neonatal mice, is located on the amino-terminal region of PVA, an area thought to be important in cadherin homophilic adhesion.
Phenolic Compounds from Hypericum perforatum (2002)

During a re-investigation of phenolic compounds from the dried crude drug material of St. John's wort (Hypericum perforatum L.) 22 phenolic compounds were detected by HPLC; 14 of them were quantified using the same system. Twelve phenolic compounds were isolated from the plant material and their structures identified mainly by spectroscopic methods, among them quercetin-3-O-(2"-O-acetyl)-beta-D-galactoside as a new natural product. Cryptochlorogenic acid, protocatechuic acid, 3-O-[Z]-p-coumaroylquinic acid, isoorientin, cyanidin-3-O-alpha-L-rhamnoside, and astilbin were obtained for the first time from this source; the earlier suspected neochlorogenic acid, 3-O-[E]-p-coumaroylquinic acid, mangiferin, miquelianin and guaijaverin were confirmed.
Introduction (2005)

'… there probably exists no social unit in which convergent and divergent currents among its members are not inseparably interwoven.'G Simmel Der Streit (1908: trs 1955: 15)
The relation of protein synthesis to chondroitin sulphate biosynthesis in cultured bovine cartilage (1984)

The effect of cycloheximide on chondroitin sulphate biosynthesis was studied in bovine articular cartilage maintained in culture. Addition of 0.4 mM-cycloheximide to the culture medium was followed, over the next 4h, by a first-order decrease in the rate of incorporation of [35S]sulphate into glycosaminoglycan (half-life, t 1/2 = 32 min), which is consistent with the depletion of a pool of proteoglycan core protein. Addition of 1.0 mM-benzyl beta-D-xyloside increased the rate of incorporation of [35S]sulphate and [3H]acetate into glycosaminoglycan, but this elevated rate was also diminished by cycloheximide. It was concluded that cycloheximide exerted two effects on the tissue; not only did it inhibit the synthesis of the core protein, but it also lowered the tissue's capacity for chondroitin sulphate chain synthesis. Similar results were obtained with chick chondrocytes grown in high-density cultures. Although the exact mechanism of this secondary effect of cycloheximide is not known, it was shown that there was no detectable change in cellular ATP concentration or in the amount of three glycosyltransferases (galactosyltransferase-I, N-acetylgalactosaminyltransferase and glucuronosyltransferase-II) involved in chondroitin sulphate chain synthesis. The sizes of the glycosaminoglycan chains formed in the presence of cycloheximide were larger than those formed in control cultures, whereas those synthesized in the presence of benzyl beta-D-xyloside were consistently smaller, irrespective of the presence of cycloheximide. These results suggest that beta-D-xylosides must be used with caution to study chondroitin sulphate biosynthesis as an event entirely independent of proteoglycan core-protein synthesis, and they also indicate a possible involvement of the core protein in the activation of the enzymes of chondroitin sulphate synthesis.
Thermo-induced long-period fibre gratings (1997)

A new technique for long-period fibre grating fabrication using thermally activated diffusion of a core dopant to the cladding region has been proposed. Gratings written in a nitrogen-doped fibre with the help of a CO laser or an electric are have exhibited an excellent resistance to a thermal decay.
Relationship of the Respiration Waveform to a Chest Worn Inertial Sensor (2020)

Demand of portable health monitoring has been growing due to increasing cardiovascular and respiratory diseases. While both cardiovascular monitoring and respiratory monitoring have been developed independently, there lacks a simple integrated solution to monitor both simultaneously. Seismocardiography (SCG), a method of recording cardiac vibrations with an accelerometer can also be used to extract respiratory information via low frequency chest oscillations. This study used an inertial measurement unit which pairs a 3-axis accelerometer and a 3-axis gyroscope to monitor respiration while maintaining optimum placement protocol for recording SCG. Additionally, the connection between inertial measurement and both respiratory rate and volume were explored based on their correlation with a Spirometer. Respiratory volume was shown to have moderate correlation with chest motion with an average best-case correlation coefficient of 0.679 across acceleration and gyration. The techniques described will assist the design of future SCG algorithms by understanding the sources behind their modulation from respiration. This paper shows that a simplified processing technique can be added to SCG algorithms for respiration monitoring.
Synthesis of Orthogonally Protected 2,6-Diazaspiro[3.5]nonane and 2,6-Diazaspiro[3.4]octane Analogues as Versatile Building Blocks in Medicinal Chemistry (2015)

A novel and efficient synthesis of orthogonally protected spirocyclic amines is described for the first time.
On the Origin of the Extracellular Action Potential Waveform: A Modeling Study (2006)

Although extracellular unit recording is typically used for the detection of spike occurrences, it also has the theoretical ability to report about what are typically considered intracellular features of the action potential. We address this theoretical ability by developing a model system that captures features of experimentally recorded simultaneous intracellular and extracellular recordings of CA1 pyramidal neurons. We use the line source approximation method of Holt and Koch to model the extracellular action potential (EAP) voltage resulting from the spiking activity of individual neurons. We compare the simultaneous intracellular and extracellular recordings of CA1 pyramidal neurons recorded in vivo with model predictions for the same cells reconstructed and simulated with compartmental models. The model accurately reproduces both the waveform and the amplitude of the EAPs, although it was difficult to achieve simultaneous good matches on both the intracellular and extracellular waveforms. This suggests that accounting for the EAP waveform provides a considerable constraint on the overall model. The developed model explains how and why the waveform varies with electrode position relative to the recorded cell. Interestingly, each cell's dendritic morphology had very little impact on the EAP waveform. The model also demonstrates that the varied composition of ionic currents in different cells is reflected in the features of the EAP.
Phase I trial of Marimastat, a novel matrix metalloproteinase inhibitor, administered orally to patients with advanced lung cancer. (1998)

Marimastat was well absorbed from the gastrointestinal tract, with high levels of the study drug detected in plasma within hours after drug administration. Plasma concentrations of Marimastat achieved at dose levels 2 and 3 (50 mg and 100 mg orally twice daily) were substantially higher than those required for MMP inhibition in vitro. The dose-limiting toxicity (DLT) was severe inflammatory polyarthritis, which seemed to be a cumulative toxicity.
4-Trifluoromethylimidazoles and 5-(4-pyridyl)-1,2,4-triazoles, new classes of xanthine oxidase inhibitors (1975)

The syntheses of a number of 2-substituted 4-trifluoromethylimidazoles and 3-substituted 5-(4-pyridyl)-1,2,4-triazoles are described. The trifluoromethylimidazoles were prepared from 3,3-dibromo-1,1,1-trifluoroacetone after hydrolysis with aqueous sodium acetate solution and condensation with an aldehyde in the presence of ammonia. Basic hydrolysis of the trifluoromethyl group was found to provide a facile method for the synthesis of imidazole-4-carboxylic acids. In the imidazole series a 2-aryl substituent and a free imino group were required for xanthine oxidase inhibitory activity. The triazoles were obtained through the reaction of an aroylhydrazine and an imino ether followed by thermal ring closure of the intermediate acylamidrazone. As in the imidazole series, a free imino group is an absolute requirement for in vitro activity. Additional structure-activity relationships of these compounds are presented.
Convenient synthesis and application of versatile nucleic acid lipid membrane anchors in the assembly and fusion of liposomes (2015)

Hydrophobic moieties like lipid membrane anchors are highly demanded modifications for nucleic acid oligomers. Membrane-anchor modified oligonucleotides are applicable in biomedicine leading to new delivery strategies as well as in biophysical investigations towards the assembly and fusion of liposomes or the construction of DNA origami structures. We present herein the synthesis and applications of versatile lipid membrane anchor building blocks suitable for solid-supported oligonucleotide synthesis. These are readily synthesized in bulk in five to seven steps from commercially available precursors and can be incorporated at any position within an oligonucleotide without significantly altering the duplex stability and structure as was proven by thermal denaturation experiments and circular dichroism. Furthermore, their applicability could be demonstrated by the assembly and fusion of liposomes mediated by lipid-modified oligonucleotides.
Downregulation of NUF2 inhibits tumor growth and induces apoptosis by regulating lncRNA AF339813. (2015)

Recent studies have shown that NUF2 (Ndc80 kinetochore complex component) play important roles in multiple human cancers. In our previous report, NUF2 expression was stronger in tumor tissues than in normal pancreatic tissues. However, whether and how NUF2 play a role in pancreatic cancer progression remains largely unknown. The aim of our study is to investigate the expression and functional role of NUF2 in human PC. NUF2 expression was measured in 10 pairs of PC cancerous and noncancerous tissue samples by quantitative real-time PCR. The effects of NUF2 on PC cells were studied by RNA interference. Apoptosis and cell cycle were analyzed by flow cytometry. Cells viability was evaluated using MTT. CDK4/CDK6 activity was measured by Western blot assay. LncRNAs regulated by NUF2 were gained from bioinformatics analysis. The role of LncRNA AF339813, regulated by NUF2, was finally characterized in PC cells by siRNA. Our results showed that NUF2 mRNA and protein were significantly overexpressed in Human PC tissues and several PC cell lines. Through bioinformatics analysis and knockdown NUF2 in PC cells, we found LncRNA AF339813 was positively regulated by NUF2. We further demonstrated that knockdown of AF339813 by siRNA in PC cells significantly reduced cell proliferation and promoted apoptosis. Thus, we conclude that NUF2 is consistently overexpressed in human PC and NUF2 is closely linked with human PC progression through the meditator LncRNA AF339813. Our studies may contribute to understand the molecular mechanism of PC pathogenesis and clinical therapy.
Influenza viruses and the NF-κB signaling pathway – towards a novel concept of antiviral therapy (2008)

Influenza A virus remains a major public health concern, both in its annual toll in death and debilitation and its potential to cause devastating pandemics. Like any other virus, influenza A viruses are strongly dependent on cellular factors for replication. One of the hallmark signaling factors activated by viral pathogens is the transcription factor NF-kappaB. Activation of NF-kappaB leads to the up-regulation of a variety of antiviral genes. Thus, the factor is commonly regarded as a major regulator of the innate immune defense to infection. However, several recent studies indicate that influenza viruses have acquired the capability to reprogram this antiviral activity and to exploit the factor for efficient replication. These data provide novel insights into the pathophysiological function of NF-kappaB in the special environment of a virus-infected cell. Furthermore, the unexpected viral dependency on a cellular signaling factor may pave the path for novel antiviral approaches targeting essential cellular components rather than viral factors.
Glycopeptide and Oligosaccharide Libraries (2000)

Despite the burgeoning interest in the various biological functions and consequent therapeutic potential of the vast number of oligosaccharides found in nature on glycoproteins and cell surfaces, the development of combinatorial carbohydrate chemistry has not progressed as rapidly as expected. The reason for this imbalance is rooted in the difficulty of oligosaccharide assembly and analysis that renders synthesis a rather cumbersome endeavor. Parallel approaches that generate series of analogous compounds rather than real libraries have therefore typically been used. Since generally low affinity is obtained for interactions between carbohydrate receptors and modified oligosaccharides designed as mimetics of natural carbohydrate ligands, glycopeptides have been explored as alternative mimics. Glycopeptides have been proven in many cases to be superior ligands with higher affinity for a receptor than the natural carbohydrate ligand. High-affinity glycopeptide ligands have been found for several types of receptors including the E-, P-, and L-selectins, toxins, glycohydrolases, bacterial adhesins, and the mannose-6-phosphate receptor. Furthermore, the assembly of glycopeptides is considerably more facile than that of oligosaccharides and the process can be adapted to combinatorial synthesis with either glycosylated amino acid building blocks or by direct glycosylation of peptide templates. The application of the split and combine approach using ladder synthesis has allowed the generation of very large numbers of compounds which could be analyzed and screened for binding of receptors on solid phase. This powerful technique can be used generally for the identification and analysis of the complex interaction between the carbohydrates and their receptors.
Hypermutagenic PCR Involving All Four Transitions and a Sizeable Proportion of Transversions (1996)

Very complex mutant libraries of the dihydrofolate reductase (DHFR) gene encoded by the Escherichia coli plasmid R67 were created using hypermutagenic PCR with biased deoxynucleotide triphosphate (dNTP) concentrations. Exploiting the particular stability of the G:T mismatch, the DHFR gene could be enriched in A+T by employing biased deoxypyrimidine triphosphate concentrations, i.e. [dTTP] > [dCTP]. A sizeable fraction of hypermutants were functional. A combination of [dTTP] > [dCTP] and [dGTP] > [dATP] biases generated mutations at unexpectedly low frequencies. This could be overcome by the addition of Mn2+ cations. Overall mutation frequencies of 10% per amplification (range 4-18% per clone) could be attained. All four transitions and a smaller number of transversions were produced throughout the gene. PCR mutagenesis could be so extensive as to inactivate all amplified versions of the gene.