gebhart/patrepeval huggingface dataset:
Molecular genetics of the chloramphenicol‐resistance transposon Tn<i>4451</i> from <i>Clostridium perfringens:</i> the TnpX site‐specific recombinase excises a circular transposon molecule (1995)

The chloramphenicol-resistance transposon Tn4451 undergoes precise conjugative deletion from its parent plasmid plP401 in Clostridium perfringens and precise spontaneous excision from multicopy plasmids in Escherichia coli. The complete nucleotide sequence of the 6338 bp transposon was determined and it was found to encode six genes. Genetic analysis demonstrated that the largest Tn4451-encoded gene, tnpX, was required for the spontaneous excision of the transposon in both E. coli and C. perfringens, since a Tn4451 derivative that lacked a functional tnpX gene was completely stable in both organisms. Because the ability of this derivative to excise was restored by providing the tnpX gene on a compatible plasmid, it was concluded that this gene encoded a trans-acting site-specific recombinase. Allelic exchange was used to introduce the tnpX delta 1 allele onto plP401 and it was shown that TnpX was also required for the conjugative excision of Tn4451 in C. perfringens. It was also shown by hybridization and polymerase chain reaction (PCR) studies that TnpX-mediated transposon excision resulted in the formation of a circular form of the transposon. The TnpX recombinase was unique because it potentially contained the motifs of two independent site-specific recombinase families, namely the resolvase/invertase and integrase families. Sequence analysis indicated that the resolvase/invertase domain of TnpX was likely to be involved in the excision process by catalysing the formation of a 2 bp staggered nick on either side of the GA dinucleotide located at the ends of the transposon and at the junction of the circular form. The other Tn4451-encoded genes include tnpZ, which appears to encode a second potential site-specific recombinase. This protein has similarity to plasmid-encoded Mob/Pre proteins, which are involved in plasmid mobilization and multimer formation. Located upstream of the tnpZ gene was a region with similarity to the site of interaction of these mobilization proteins.
DNA Immunization with Minigenes: Low Frequency of Memory Cytotoxic T Lymphocytes and Inefficient Antiviral Protection Are Rectified by Ubiquitination (1998)

Our previous studies have shown that isolated cytotoxic T lymphocyte (CTL), B-cell, and T-helper epitopes, for which we coined the term minigenes, can be effective vaccines; when expressed from recombinant vaccinia viruses, these short immunogenic sequences confer protection against a variety of viruses and bacteria. In addition, we have previously demonstrated the utility of DNA immunization using plasmids encoding full-length viral proteins. Here we combine the two approaches and evaluate the effectiveness of minigenes in DNA immunization. We find that DNA immunization with isolated minigenes primes virus-specific memory CTL responses which, 4 days following virus challenge, appear similar in magnitude to those induced by vaccines known to be protective. Surprisingly, this vigorous CTL response fails to confer protection against a normally lethal virus challenge, although the CTL appear fully functional because, along with their high lytic activity, they are similar in affinity and cytokine secretion to CTL induced by virus infection. However this DNA immunization with isolated minigenes results in a low CTL precursor frequency; only 1 in approximately 40,000 T cells is epitope specific. In contrast, a plasmid encoding the same minigene sequences covalently attached to the cellular protein ubiquitin induces protective immunity and a sixfold-higher frequency of CTL precursors. Thus, we show that the most commonly employed criterion to evaluate CTL responses-the presence of lytic activity following secondary stimulation-does not invariably correlate with protection; instead, the better correlate of protection is the CTL precursor frequency. Recent observations indicate that certain effector functions are active in memory CTL and do not require prolonged stimulation. We suggest that these early effector functions of CTL, immediately following infection, are critical in controlling virus dissemination and in determining the outcome of the infection. Finally, we show that improved performance of the ubiquitinated minigenes most probably requires polyubiquitination of the fusion protein, suggesting that the enhancement results from more effective delivery of the minigene to the proteasome.
A meta-analysis of male breast cancer in Africa (2012)

To characterize male breast cancer in Africa in recent decades, we systematically reviewed literature and conducted a meta-analysis of available data on male breast cancer in Africa. A paper was included if both male and female breast cancer were available. If two publications covered the same geographic area, only the publication with a longer study period was included. Random effects models and mixed effect meta-regressions were used to analyze data of 1201 male and 36,172 female breast cancer patients from 27 African countries. We showed that the male-to-female breast cancer ratio was 0.042 overall and it has decreased in recent years. Additionally, male breast cancer patients in Africa had the disease at age 54.6 on average, 7 years older than female patients. In conclusion, male breast cancers in Africa are characterized as late onset and male-to-female breast cancer ratio in Africa is higher than populations in developed countries.
Multiresolution color patch extraction (2006)

Certain applications require the extraction of patches of color from an image, their size and location. These applications may be: color harmonization algorithms, non-photorealistic rendering, etc. These applications use not too big a palette of colors, and in both cases large areas of homogeneous color are favored along with high detail preserved in the smaller areas with a lot of color activity. The main problem this paper will tackle is to identify the underlying color in an image region, which will be referred to as its underlying color patch, and also try to protect as much as possible the high color activity detail areas. No perfect scene object segmentation is intended in this process, since different objects may be quantized to the same color, the result may be a merged color patch.
The different biological effects of telomestatin and TMPyP4 can be attributed to their selectivity for interaction with intramolecular or intermolecular G-quadruplex structures. (2003)

Demonstration of the existence of G-quadruplex structures in telomeres of Stylonychia macronuclei and in the promoter of c-myc in human cells has validated these secondary DNA structures as potential targets for drug design. The next important issue is the selectivity of G-quadruplex-interactive agents for the different types of G-quadruplex structures. In this study, we have taken an important step in associating specific biological effects of these drugs with selective interaction with either intermolecular or intramolecular G-quadruplex structures formed in telomeres. Telomestatin is a natural product isolated from Streptomyces anulatus 3533-SV4 and has been shown to be a very potent telomerase inhibitor through its G-quadruplex interaction. We have demonstrated that telomestatin interacts preferentially with intramolecular versus intermolecular G-quadruplex structures and also has a 70-fold selectivity for intramolecular G-quadruplex structures over duplex DNA. Telomestatin is able to stabilize G-quadruplex structures that are formed from duplex human telomeric DNA as well as from single-stranded DNA. Importantly, telomestatin stabilizes these G-quadruplex structures in the absence of monovalent cations, which is a unique characteristic among G-quadruplex-interactive compounds. At noncytotoxic concentrations, telomestatin suppresses the proliferation of telomerase-positive cells within several weeks. In contrast, TMPyP4, a compound that preferentially facilitates the formation of intermolecular G-quadruplex structures, suppresses the proliferation of alternative lengthening of telomeres (ALT)-positive cells as well as telomerase-positive cells. We have also demonstrated that TMPyP4 induces anaphase bridges in sea urchin embryos, whereas telomestatin did not have this effect, leading us to conclude that the selectivity of telomestatin for intramolecular G-quadruplex structures and TMPyP4 for intermolecular G-quadruplex structures is important in mediating different biological effects: stabilization of intramolecular G-quadruplex structures produces telomerase inhibition and accelerated telomere shortening, whereas facilitation of the formation of intermolecular G-quadruplex structures induces the formation of anaphase bridges.
Targeting DCIR on human plasmacytoid dendritic cells results in antigen presentation and inhibits IFN-α production (2008)

C-type lectin receptors (CLRs) fulfill multiple functions within the immune system by recognition of carbohydrate moieties on foreign or (altered) self-structures. CLRs on myeloid dendritic cells (DCs) have been well characterized as pattern-recognition receptors (PRRs) combining ligand internalization with complex signaling events. Much less is known about CLR expression and function in human plasmacytoid DCs (pDCs), the major type I interferon (IFN) producers. In this study, we demonstrate that, next to the CLR BDCA-2, human pDCs express DC immunoreceptor (DCIR), a CLR with putative immune-inhibitory function, but not dectin-1, mannose receptor, or DC-specific ICAM-3-grabbing nonintegrin. DCIR surface levels are reduced on pDC maturation after TLR9 triggering. Interestingly, DCIR triggering inhibits TLR9-induced IFN-alpha production while leaving up-regulation of costimulatory molecule expression unaffected. Furthermore, DCIR is readily internalized into pDCs after receptor triggering. We show that DCIR internalization is clathrin-dependent because it can be inhibited by hypertonic shock and dominant-negative dynamin. Importantly, antigens targeted to pDCs via DCIR are presented to T cells. These findings indicate that targeting DCIR on pDCs not only results in efficient antigen presentation but also affects TLR9-induced IFN-alpha production. Collectively, the data show that targeting of DCIR can modulate human pDC function and may be applied in disease prevention and treatment.
CXCL10+ T cells and NK cells assist in the recruitment and activation of CXCR3+ and CXCL11+ leukocytes during Mycobacteria-enhanced colitis (2008)

The present study shows that CD and UC patients mount significant Mycobacteria-specific IgG1 > IgG2 and CXCR3 ligand responses. Several cellular mechanisms that drive spontaneous colitis also mediate Mycobacteria-enhanced colitis in IL-10-/- mice. Similar to IL-10-/- mice under conventional housing, we show that Mycobacteria-challenge IL-10-/- mice housed under otherwise pathogen-free conditions develop colitis that is driven by CXCR3- and CXCR3 ligand-expressing leukocytes, which underscores another important hallmark and molecular mechanism of colitis. Together, the data show that Mycobacteria-dependent host responses, namely CXCL10+ T cells and NK cells, assist in the recruitment and activation of CXCR3+ and CXCL11+ leukocytes to enhance colitis of susceptible hosts.
Noninvasive detection of lung cancer using exhaled breath (2013)

Early detection of lung cancer is a key factor for increasing the survival rates of lung cancer patients. The analysis of exhaled breath is promising as a noninvasive diagnostic tool for diagnosis of lung cancer. We demonstrate the quantitative analysis of carbonyl volatile organic compounds (VOCs) and identification of lung cancer VOC markers in exhaled breath using unique silicon microreactor technology. The microreactor consists of thousands of micropillars coated with an ammonium aminooxy salt for capture of carbonyl VOCs in exhaled breath by means of oximation reactions. Captured aminooxy-VOC adducts are analyzed by nanoelectrospray Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry (MS). The concentrations of 2-butanone, 2-hydroxyacetaldehyde, 3-hydroxy-2-butanone, and 4-hydroxyhexenal (4-HHE) in the exhaled breath of lung cancer patients (n = 97) were significantly higher than in the exhaled breath of healthy smoker and nonsmoker controls (n = 88) and patients with benign pulmonary nodules (n = 32). The concentration of 2-butanone in exhaled breath of patients (n = 51) with stages II though IV non-small cell lung cancer (NSCLC) was significantly higher than in exhaled breath of patients with stage I (n = 34). The carbonyl VOC profile in exhaled breath determined using this new silicon microreactor technology provides for the noninvasive detection of lung cancer.
Biological conversion of aripiprazole lauroxil − An N-acyloxymethyl aripiprazole prodrug (2014)

N-acyloxyalkylation of NH-acidic compounds can be a prodrug approach for e.g. tertiary or some N-heterocyclic amines and secondary amides and have the potential to modify the properties of the parent drug for specific uses, for example its physicochemical, pharmacokinetic or biopharmaceutical properties. Aripiprazole lauroxil was prepared as a model compound for such prodrugs and its bioconversion was investigated both in vitro and in vivo. Theoretically, N-acyloxyalkyl derivates of NH-acid compounds undergo a two-step bioconversion into the parent NH-acidic drug through an N-hydroxyalkyl intermediate. However, to our knowledge no published studies have investigated the formation of an intermediate in vivo. In the present study, it was demonstrated that the assumed N-hydroxymethyl intermediate was readily observed both in vitro and in vivo. In vivo, the observed plasma concentration of the intermediate was at the same level as the drug (aripiprazole). When prodrug intermediates are formed, it is important to make a proper pharmacological, pharmacokinetic and toxicological evaluation of the intermediates to ensure patient safety; however, several challenges were identified when testing an N-acyloxyalkyl prodrug. These included the development of a suitable bioanalytical method, the accurate prediction of prodrug bioconversion and thereby the related pharmacokinetics in humans and the toxicological potential of the intermediate.
Specific Covalent Immobilization of Proteins through Dityrosine Cross-Links (2006)

Dityrosine cross-links are widely observed in nature in structural proteins such as elastin and silk. Natural oxidative cross-linking between tyrosine residues is catalyzed by a diverse group of metalloenzymes. Dityrosine formation is also catalyzed in vitro by metal-peptide complexes such as Gly-Gly-His-Ni(II). On the basis of these observations, a system was developed to specifically and covalently surface immobilize proteins through dityrosine cross-links. Methacrylate monomers of the catalytic peptide Gly-Gly-His-Tyr-OH (GGHY) and the Ni(II)-chelating group nitrilotriacetic acid (NTA) were copolymerized with acrylamide into microbeads. Green fluorescent protein (GFP), as a model protein, was genetically tagged with a tyrosine-modified His6 peptide on its carboxy terminus. GFP-YGH6, specifically associated with the NTA-Ni(II) groups, was covalently coupled to the bead surface through dityrosine bond formation catalyzed by the colocalized GGHY-Ni(II) complex. After extensive washing with EDTA to disrupt metal coordination bonds, we observed that up to 75% of the initially bound GFP-YGH6 remained covalently bound to the bead while retaining its structure and activity. Dityrosine cross-linking was confirmed by quenching the reaction with free tyrosine. The method may find particular utility in the construction and optimization of protein microarrays.
Comparison of BN and AlN Substitution on the Structure and Electronic and Chemical Properties of C<sub>60</sub>Fullerene (2003)

A comparative study on BN and AlN substitution patterns in C60 fullerene and the chemical and electronic properties of these substitutionally doped heterofullerenes has been carried out using semiempirical (MNDO and PM3) and density functional (B3LYP) theories. Several basis sets, namely, 3-21G, 3-21G*, and 6-31G*, are used. Specific systems considered here are C60-2x(BN/AlN)x where x varies from 1 to 3. Both similarities and dissimilarities have been noticed in the substitution patterns between BN− and AlN−fullerenes. Some of the rules already established in BN substitution patterns are followed by its AlN counterpart. For example, like BN, AlN units prefer to stay together. However, the prominent “hexagon filling rule” of BN−fullerenes is disobeyed by AlN. Its larger atomic size and the weak nature of the Al−N and Al−C π-interaction may be the reason for such discrepancies. AlN substitution causes much more distortion of total electron density of C60 than its BN counterpart, making the fullerene easier to oxidize and reduce. The HOMO−LUMO gap (band gap) strongly depends on the number of substituent units, and the changes are minimal for the BN system in comparison to its compeer. Finally, the possibility of dimer formation of BN− and AlN−fullerenes has been studied.
Hydroxyapatite ceramics as a particulate embolic material: report of the physical properties of the hydroxyapatite particles and the animal study. (2003)

Hydroxyapatite microparticles are excellent biocompatible embolic materials with good visibility during injection control, capable of producing effective occlusion of the distal arteriocapillary bed.
Ultra-Fast Measurements of VTH Instability in SiC MOSFETs due to Positive and Negative Constant Bias Stress (2006)

One of the most important issues that limits the performance and reliability of SiC power MOSFETs is the threshold voltage instability under normal operation conditions. This phenomenon has been recently studied using dc sweep measurements. In this work, we studied the threshold voltage instability using fast I-V measurements. The results show that under positive bias, V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TH</sub> shifts to more positive values, while it shifts to more negative values under negative bias. Fast I-V measurements reveal the full extent of the V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TH</sub> instability, underestimated by the dc measurements. Furthermore, fast measurements allow the separation of negative and positive bias stress effects. A physical model involving fast transient charge trapping and de-trapping at and near the SiC/SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> interface is proposed
Acute electrophysiological effects of flecainide acetate on cardiac conduction and refractoriness in man. (1982)

The electrophysiological effects of flecainide acetate (2 mg/kg as an intravenous infusion over five minutes) were assessed in 47 patients undergoing electrophysiological study. Seven patients had normal electrophysiology, 16 had a direct accessory atrioventricular pathway, 12 had dual atrioventricular nodal (AH) pathways, five had paroxysmal ventricular tachycardia, six had conduction system disease, and one patient had a left atrial tachycardia. No significant change occurred in sinus cycle length. The PA interval, AH interval, and HV interval were all significantly prolonged. The QRS complex duration increased significantly. The QT interval showed slight prolongation due entirely to the increase in QRS duration. Refractoriness of the atrial and ventricular myocardium was slightly prolonged, but was significant only at ventricular level. No significant change occurred in refractoriness of the normal atrioventricular node. Pronounced prolongation of retrograde "fast" AH pathway refractoriness was observed in those patients with dual AH pathways. Anterograde and retrograde accessory pathway refractoriness were both greatly increased. These electrophysiological properties strongly suggest that flecainide will be useful in the management of a wide variety of cardiac arrhythmias. It should be administered, however, with caution to patients with pre-existing conduction system disease. Because repolarization is not delayed flecainide is unlikely to induce ventricular arrhythmias related to prolongation of the QT interval.
Synthesis and Application of Some New Thienopyrimidine Derivatives as Antimicrobial Agents (1996)

Abstract The paper describes the synthesis of new ring system 5-phenylthieno[2,3-d]pyrimidine-4(3H)one (2). Chlorination of (2) with PCl5, POCl3 gave the corresponding 4-chloro derivative (4). Several derivatives of the latter compound have been synthesised and tested for antimicrobial activity.
Experimental system for real-time motion estimation (2004)

Motion can be a useful sensory dimension for autonomous navigation if it is available in real time. In this paper we present our approach to real time motion processing giving an outline of the algorithm and hardware architecture we have developed. We then describe in more detail how this architecture is being implemented using FPGA technology.
A Case of Staphylococcus aureus Enterocolitis: A Rare Entity. (2010)

Staphylococcus aureus is a common organism found in nosocomial and postoperative infections. Enter-ocolitis caused by this organism can be severe and sometimes fatal.1 In the 1950s and 1960s, S. aureus was implicated as a major pathogen in postoperative and antibiotic-associated enterocolitis.2-5 Although it continued to be a problem in Japan,1,6-8 its incidence in the United States has diminished.3 The clinical significance of S. aureus isolated from stool is unknown, as it is often seen unrelated to the clinical picture. We report a case of a patient with hemorrhagic enterocolitis who was initially suspected of having inflammatory bowel disease, but, based upon the diagnostic evaluation, was found to have S. aureus enterocolitis.
Therapeutic Aspects of Spondyloarthropathies - A Review (1998)

In the pathogenesis of spondyloarthropathies, infection and gut inflammation are the most important external triggering factors. Early antimicrobial therapy to treat urethritis caused by Chlamydia trachomatis is effective in preventing a recurrent reactive arthritis. When the arthritis appear, a short term conventional antimicrobial therapy is unable to modify its course. In acute chlamydia arthritis, patients benefit from a prolonged (3-month) treatment with tetracycline, while such a treatment has not proved to be effective in enteroarthritis or in chronic forms of reactive arthritis. The role of sulfasalazine in the treatment of patients with spondyloarthropathies is controversial. It might modify the disease course during acute and chronic reactive arthritis, and is working for patients with ankylosing spondylitis, especially patients with peripheral arthritis. Data showing an effect of sulfasalazine in the prevention of chronic spondyloarthropathy or in modification of the long-term prognosis of ankylosing spondylitis are, however, lacking.
Temporal radio channel variations with stationary terminal (2005)

In wireless communications, stationary terminal scenarios are becoming increasingly important as bitrates goes up. Consequently, the need to improve the knowledge about the channel behavior and to develop realistic channel models for these scenarios is also increasing. The present work comprises both measurements and modeling of the radio channel when the terminal is stationary. The measurements were performed at 5 GHz in indoor scenarios using a vector network analyzer. The measured channel was essentially static most of the time. Only about 1% of the time did it show substantial channel variations. An important finding is that the dominant cause for temporal channel variations in the measurements was the movement of persons in the vicinity of either antenna. This is also supported by a simple model, based on a single moving scatterer, which shows good agreement with measurements.