gebhart/patrepeval huggingface dataset:
Co-transfer of vancomycin and other resistance genes from Enterococcus faecalis NCTC 12201 to Staphylococcus aureus (1992)

Conjugative transfer, in the apparent absence of plasmid DNA, of high-level vancomycin resistance from Enterococcus faecalis NCTC 12201 to Staphylococcus aureus B111 has been demonstrated in vivo and in vitro. Selection of transconjugants on media containing erythromycin or chloramphenicol may result in the transfer of resistance to erythromycin, chloramphenicol, gentamicin, streptomycin and vancomycin though these are capable of separate transfer. Vancomycin resistance has not been transmitted from staphylococcus to staphylococcus though transfer of erythromycin and of chloramphenicol resistance has been achieved.
Novel Vesicular Aggregates of Crown-Appended Cholesterol Derivatives Which Act as Gelators of Organic Solvents and as Templates for Silica Transcription (2000)

New diazacrown-appended cholesterol gelators 1 and 2 were synthesized, and their gelation ability was evaluated in organic solvents. Very surprisingly, 1 + acetic acid gel results in spherical vesicles with two distinct sizes 200 and 2500 nm in diameter. In particular, the smaller vesicles are linked linearly, which is considered to serve as a driving-force for gelation. In contrast, 2 has a multilayered tubular structure. To characterize their aggregation modes in the gel phase, the organogels were observed by CD spectroscopy. The CD spectrum of 1 + acetic acid gel exhibits a negative sign for the first Cotton effect, indicating that the dipole moments in the gelator aggregate orient into an anticlockwise direction. On the other hand, 2 exhibits a positive sign for the first Cotton effect, indicating that they orient into a clockwise direction. The results indicate that the aggregate of 2 is stabilized by intermolecular cholesterol−cholesterol and azobenzene−azobenzene interactions, whereas the CD sign from the aggregate of 1 is indicative of an intramolecular azobenzene−azobenzene interaction. The spherical vesicle structures of organogel 1 were successfully transcribed into silica structures by the sol−gel polymerization of tetraethoxysilane (TEOS) in the gel phase. The TEM observation established that the wall of the spherical silica obtained in the acidic conditions consists of the multilayered vesicle structure. On the other hand, addition of Pd(NO3)2 changed the silica structure into fluffy globules with ∼6000 nm in diameter. The EPMA observation established that Pd(II) ions are densely deposited on the surface of this globular silica. Hence, this process is useful as a new method to create metal catalytic sites on the silica support. These results indicate that the spherical multilayered structure of the organogel can be precisely transcribed into the silica structure. We thus believe that the sol−gel polymerization using molecular assembly templates strongly built in the organogel phase is a new strategy to create superstructured silica materials.
Rapid Suppression of Cytokine Transcription in Human CD4+CD25− T Cells by CD4+Foxp3+ Regulatory T Cells: Independence of IL-2 Consumption, TGF-β, and Various Inhibitors of TCR Signaling (2007)

CD4+CD25(high) forkhead box P3+ regulatory T cells (Treg) are critical mediators of peripheral self-tolerance and immune homeostasis. Treg suppress proliferation and cytokine production of conventional T cells (Tcon). The exact mechanism of suppression, however, is still unknown. To gain a better understanding of Treg function, we investigated the kinetics of cytokine suppression in Tcon reisolated from cocultures with preactivated human Treg. Treg inhibited induction of Th1 cytokine mRNA as early as 1 h after stimulation, whereas induction/suppression of Th2 cytokines was delayed to 10-15 h. We show that immediate cytokine mRNA suppression in Tcon was neither dependent on TGF-beta/IL-10 or IL-2 consumption, nor on induction of the transcriptional-repressor forkhead box P3 or other anergy-related genes (e.g., gene related to anergy, transducer of ErbB-2, forkhead homolog-4, repressor of GATA, inducible cAMP early repressor). In contrast, lymphocyte activation gene 3, suppressor of cytokine signaling 1, and suppressor of cytokine signaling 3 mRNA were strongly up-regulated in Tcon in the presence of Treg. However, protein analysis did not confirm a role for these proteins in early suppression. Thus, the identification of a fast inhibitory mechanism in Tcon induced by Treg constitutes an important step for future efforts to unravel the entire elusive suppressive mechanism.
Development of a quantitative PCR assay for monitoring HCV viraemia levels in patients with chronic hepatitis C (1997)

The need to improve the efficacy of anti-viral agents directed against the hepatitis C virus (HCV) has prompted the development of quantitative tests to monitor viraemia levels in relation to therapy. In this respect, we have produced a non-competitive, quantitative PCR assay (Amplicor HCV Monitor) which is based on the single, combined, reverse transcription and amplification of the 5' non-coding region of HCV RNA as well as of an internal standard which serves to assess the overall efficiency of the system. The dynamic range of the assay and its precision allows for an accurate quantification between 1000 and 1,000,000 copies of the viral genome per ml. The results of the first clinical evaluation of the test indicated that determination of viraemia may have predictive value when assessed prior to treatment, as patients with less than 50,000 HCV RNA copies per ml tend to show a long-term response to interferon-alpha (IFN-alpha) treatment. Moreover, a decrease of more than 1.5-2 logarithms occurring at 1 month post-initiation of therapy predicts response in a more timely and accurate fashion than ALT measurement. This may help in a better selection of patients to treat, therapy approaches and schedules and in the optimization of the cost-benefit balance.
B Cell Regulation of CD4+CD25+ T Regulatory Cells and IL-10 Via B7 is Essential for Recovery From Experimental Autoimmune Encephalomyelitis (2007)

CD4(+)CD25(+) T regulatory (Treg) cells expressing the Foxp3 transcription factor have been shown to be present in the CNS during the autoimmune disease experimental autoimmune encephalomyelitis (EAE) and can inhibit EAE clinical disease by an IL-10-dependent mechanism. In addition, IL-10 expression in the CNS late in the EAE disease course has been attributed to recovery. However, it is not known how Treg cells and IL-10 expressions are regulated during EAE. We have previously shown a requirement for B cells in recovery from EAE and here investigated whether this was due to a deficiency in Treg cells and IL-10 in the CNS. We found that B cell deficiency resulted in a delay in the emergence of Foxp3-expressing Treg cells and IL-10 in the CNS during EAE, but not in the periphery. Reconstitution with wild-type B cells resulted in disease recovery and normalized IL-10 and Foxp3 expression. However, reconstitution with B7-deficient B cells did not. Furthermore, we show that IL-10 and Foxp3 expression is enhanced in CNS nonencephalitogenic T cells. These data suggest a novel mechanism whereby B cells regulate CD4(+)CD25(+) Treg cells via B7 and subsequently enter the CNS and suppress autoimmune inflammation, mediating recovery.
Ribozyme cleaves rex/tax mRNA and inhibits bovine leukemia virus expression. (1993)

Bovine leukemia virus (BLV) encodes at least two regulatory proteins, Rex and Tax. Tax, the transactivating protein, stimulates the long terminal repeat to promote viral transcription and may be involved in tumorigenesis. Rex is involved in the transition from early expression of regulatory proteins to later expression of viral structural proteins. We have targeted ribozymes against the mRNA encoding Rex and Tax. The ribozymes consist of the hammer-head catalytic motif flanked by antisense sequences that hybridize with the complementary rex/tax mRNA. To evaluate cleavage in a cell-free system, we transcribed portions of rex/tax mRNA and incubated them with synthetic RNA ribozymes. A ribozyme was identified that cleaves > 80% of the target RNA. Synthetic DNA encoding this ribozyme was cloned into the expression vector pRc/RSV and transfected into BLV-infected bat lung cells. Intracellular cleavage of rex/tax mRNA was confirmed by reverse transcriptase PCR. In cells expressing the ribozyme, viral expression was markedly inhibited. Expression of the BLV core protein p24 was inhibited by 61%, and reverse transcriptase activity in supernatant was inhibited by 92%. Ribozyme inhibition of BLV expression suggests that cattle expressing these sequences may be able to control BLV replication.
A Novel Approach for Online Sensor Testing Based on an Encoded Test Stimulus (2007)

This paper presents a technique that enables online testing of sensors through the superposition of the test stimulus onto the measurand. Perturbations due to the surrounding environment can very often introduce fluctuations in the test output that is a major concern for this type of sensor testing. This paper proposes a novel approach to tackle this problem by encoding the test stimulus using a pseudo-random sequence. The trade-off between the level of rejection of a perturbation and the overall test time is studied. In the case of the MEMS accelerometer considered in this paper, it is demonstrated that the rejection is more than 20 dB for a test time of 2.55s. Furthermore, excessively strong perturbations can be monitored so that the test status is updated only if the accuracy of the test signal permits so. It is shown that the proposed solution is compatible with the technique that consists of injecting the stimulus through the sensor bias for the case study MEMS accelerometer.
Movie genre classification with Convolutional Neural Networks (2016)

Automatic pattern recognition from videos is a high-complexity task, and well-established Machine Learning algorithms have difficulties in handling it in an efficient and effective fashion. Convolutional Neural Networks are the state-of-the-art method for supervised image classification, borrowing concepts from image processing in order to ensure some degree of scale and position invariance. They are capable of detecting primary features, which are then combined by subsequent layers of the CNN architecture, resulting in the detection of higher-order complex and relevant novel features. Considering that a video is a set of ordered images in time, we propose in this paper to explore CNNs in the context of movie trailers genre classification. Our contributions are twofold. First, we have developed a novel movie trailers dataset with more than 3500 trailers whose genres are known, and we make it publicly available for the interested reader. Second, we detail a novel classification method that encapsulates a CNN architecture to perform movie trailer genre classification, namely CNN-MoTion, and we compare it with state-of-the-art feature extraction techniques for movie classification such as Gist, CENTRIST, w-CENTRIST, and low-level feature extraction. Results show that our novel method significantly outperforms the current state-of-the-art approaches.
Databases of homologous gene families for comparative genomics (2009)

Three databases were developed using this procedure: HOVERGEN, HOGENOM and HOMOLENS. These databases share the same architecture but differ in their content. HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl. Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface. The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes. The three databases, as well as the software required to build and query them, can be used or downloaded from the PBIL (Pôle Bioinformatique Lyonnais) site at http://pbil.univ-lyon1.fr/.
Tau pathology in the olfactory bulb correlates with Braak stage, Lewy body pathology and apolipoprotein ɛ4 (2003)

Olfactory dysfunction increases with disease severity in Alzheimer's disease (AD), is early and independent of disease severity in Parkinson's disease (PD), but is absent in progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD). Previous histopathologic studies of olfactory bulbs in AD have shown neurofibrillary tangles (NFTs) and senile plaques while Lewy bodies (LBs) have been described in PD. Little is known about olfactory bulb pathology in PSP and CBD. Tau and alpha-synuclein pathology was assessed with immunohistochemistry in olfactory bulbs of AD (N=15), Lewy body disease (LBD; N=10), LBD with concurrent AD (AD/LBD; N=19), PSP (N=27), CBD (N=3) and cases with no significant neurodegenerative pathology (NSP; N=15). The Braak NFT stage, counts of senile plaques and NFT in cortical and hippocampal sections, and counts of LBs in amygdala and cortical sections were recorded for each case. Apolipoprotein E (APOE) genotypes were determined on DNA prepared from frozen brain tissue. All AD and AD/LBD cases and nine of 10 LBD cases had tau pathology in the anterior olfactory nucleus (AON), but it was uncommon in PSP (9/27), CBD (0/3) and NSP (5/15). Multiple linear regression analysis demonstrated that tau pathology in the AON correlated with Braak stage (P<0.001), cortical LB counts (P<0.001), as well as APOE epsilon4. Tau pathology is common in the olfactory bulb of AD and LBD but is minimal or absent in PSP and CBD. It correlates with APOE epsilon4, severity of tau pathology in the brain and surprisingly with cortical and amygdala LBs, suggesting a possible synergistic effect between tau and synuclein in the AON in cases with both pathologic processes.
Demonstration of in vivo metabolic effects of 3,5-di-iodothyronine (1996)

The objective of the present study was to test in vivo the metabolic effects of 3,5-di-iodothyronine (3,5-T2) in unanesthetized and unrestrained male Sprague-Dawley rats. Amino acid and lipid metabolisms were investigated by breath tests using as tracers the 13C-carboxyl-labeled molecules of leucine, alpha-ketoisocaproic acid (KIC) and octanoic acid, in four different groups of rats: hypothyroid animals (receiving propylthiouracil (PTU) and iopanoic acid), hypothyroid animals treated with either a daily i.p. injection of 3,5-T2 (25 micrograms/100 g body weight), or tri-iodothyronine (T3) (1 microgram/100 g body weight), and control euthyroid animals receiving equivalent volumes of the vehicle solutions. Energy expenditure was measured by continuous monitoring of O2 consumption and CO2 production in these different groups. Daily energy expenditure was decreased by 30% in PTU-treated rats. The chronic treatments with 3,5-T2 and T3 restored daily energy expenditure to the control level. 13CO2 recovered in breath following the i.v. injection of octanoic acid-[1-13C] was decreased in hypothyroid animals compared with control animals (P < 0.05) and restored to control values by T3 and 3,5-T2 treatments. The 13CO2 recovered in breath after i.v. injection of leucine-[1-13C] was increased in PTU-treated compared with control animals (P < 0.05). Chronic treatment with either 3,5-T2 or T3 restored 13CO2 to control values. Excretion of 13CO2 recovered in breath following the i.v. injection of KIC-[1-13C] was increased in PTU-treated compared with control animals. Chronic treatments with either 3,5-T2 or T3 did not restore KIC decarboxylation. These results suggest that 3,5-T2 exerts metabolic effects on energy expenditure, on both lipid beta-oxidation and leucine metabolism in hypothyroid rats. We conclude that 3,5-T2 is a metabolically active iodothyronine.
Bdellastasin, a serine protease inhibitor of the antistasin family from the medical leech (Hirudo medicinalis) (1998)

We have reported earlier the isolation and amino acid composition of bdellin A from medical leech, and characterised it as an inhibitor of trypsin, plasmin and acrosin [Fritz, H., Gebhardt, M., Meister, R. & Fink, E. (1971) in Proceedings of the international research conference on proteinase inhibitors (Fritz, H. & Tschesche, H., eds) pp. 271-280, Walter de Gruyter, Berlin]. In the present study, one of several chromatographic forms of this inhibitor was isolated from a semi-pure preparation. Elucidation of its amino acid sequence revealed that bdellin A is a member of the antistasin family. Therefore, it was renamed bdellastasin to avoid confusion with bdellin B, which is another trypsin-plasmin inhibitor from the medical leech, but of the Kazal type. Furthermore, a synthetic gene of bdellastasin was constructed, and the protein expressed in Saccharomyces cerevisiae with yields of 29 mg/l. The recombinant bdellastasin was purified by hydrophobic interaction and anion-exchange chromatography. Comparison by mass spectroscopy, far-ultraviolet circular dichroism studies, sequence determination, and inhibition characteristics demonstrated the identity of recombinant and native bdellastasin. The Ki values of bdellastasin for inhibition of bovine trypsin and human plasmin are in the nanomolar range; no inhibition was detected for factor Xa, thrombin, tissue kallikrein, plasma kallikrein and chymotrypsin. Circular dichroism analyses indicated that bdellastasin is devoid of secondary-structural elements.
RET Is Dispensable for Maintenance of Midbrain Dopaminergic Neurons in Adult Mice (2006)

Glial cell-line derived neurotrophic factor (GDNF)-mediated RET tyrosine kinase signaling is implicated in the survival of several PNS and CNS neuronal populations that are important in the pathogenesis of several disorders including Parkinson's disease and drug addiction. However, it has been difficult to study these processes and the physiological importance of this pathway in adult mice because of the neonatal lethality of Gdnf and Ret null mice. We report successful creation of RET conditional reporter mice to investigate postnatal physiologic roles of RET and monitor the fate of RET-expressing cell types. To delete RET specifically in dopaminergic neurons and determine the physiologic requirement of RET in the maintenance of substantia nigra compacta (SNC) and ventral tegmental area (VTA), we bred the RET conditional mice with mice that specifically express Cre from the dopamine transporter (Dat) locus. A detailed morphometric and biochemical analysis including dopaminergic neuron number and size in SNC and VTA, and fiber density in the striatum and nucleus accumbens, and dopamine levels indicate that RET is not required for providing global trophic support to midbrain dopaminergic neurons in adult mice. Furthermore, RET deficiency in these neurons does not cause major sensorimotor abnormalities. Hence our results support the idea that RET signaling is not critical for the normal physiology of the SNC and VTA in adult mice.
Efficient Monophosphorus Ligands for Palladium-Catalyzed Miyaura Borylation (2011)

In combination with the Bedford Pd precursor, the new biaryl monophosphorus ligand 5 was efficient for palladium-catalyzed Miyaura borylation of sterically hindered aryl bromides at low catalyst loadings.
Information retrieval on the web (2000)

In this paper we review studies of the growth of the Internet and technologies that are useful for information search and retrieval on the Web. We present data on the Internet from several different sources, e.g., current as well as projected number of users, hosts, and Web sites. Although numerical figures vary, overall trends cited by the sources are consistent and point to exponential growth in the past and in the coming decade. Hence it is not surprising that about 85% of Internet users surveyed claim using search engines and search services to find specific information. The same surveys show, however, that users are not satisfied with the performance of the current generation of search engines; the slow retrieval speed, communication delays, and poor quality of retrieved results (e.g., noise and broken links) are commonly cited problems. We discuss the development of new techniques targeted to resolve some of the problems associated with Web-based information retrieval and speculate on future trends.
Papaverine hydrochloride release from ethyl cellulose-walled microcapsules (1988)

The mechanism of papaverine hydrochloride release from ethyl cellulose-walled microcapsules in both simulated gastric and intestinal fluid is discussed. The microcapsules were prepared by coacervation using different core: wall ratios. The rupture of the thin-walled microcapsules after release in simulated gastric fluid was shown and attributed to the internal osmotic pressure, supporting a mechanism for drug dissolution. The internal osmotic pressure produced only a few small holes in the thin-walled microcapsules after release in simulated intestinal fluid. No rupture of the thick-walled microcapsules after release in either medium was shown. Therefore these release data fitted diffusion-type kinetics. It is suggested that the internal osmotic pressure developed after penetration of the medium is affected by the ratio between the core dissolution rate and the drug diffusion rate through the wall.
Optical Fluorescence and Its Application to an Intravascular Blood Gas Monitoring System (1986)

Optical fluorescence has an extensive history of application in the laboratory to the measurement of ionic concentrations and the partial pressures of oxygen and carbon dioxide. The use of optical fluorescence based sensors to fulfill a recognized need for continuous invasive monitoring of arterial blood gases offers a number of inherent advantages. However, the requirements placed upon a blood gas probe and supporting instrumentation appropriate for use in the clinical environment result in significant design challenges in selection of suitable fluorescent dyes, maintenance of mechanical integrity while obtaining required miniaturization of sensors, and in the transmission, acquisition, and processing of low level light signals. An optical fluorescence based intravascular blood gas monitoring system has been developed which is particularly suited for the critical care and surgical settings and which has a sensor probe that can be introduced into the patient via a radial artery catheter. This system has shown an excellent agreement of measured with true values of pH, pCO2, and P02 in both in vitro and animal studies. Linear regression analysis of typical in vitro data, where true levels were established via tonometry and standardization to a high accuracy laboratory pH measuring instrument, shows slope/intercept values very close to 1.0/0.0 and correlation coefficients of greater than 0.99 for all three parameters.
Exact Sampling Results for Some Classes of Parametric Nonbandlimited 2-D Signals (2004)

We present sampling results for certain classes of two-dimensional (2-D) signals that are not bandlimited but have a parametric representation with a finite number of degrees of freedom. While there are many such parametric signals, it is often difficult to propose practical sampling schemes; therefore, we will concentrate on those classes for which we are able to give exact sampling algorithms and reconstruction formulas. We analyze in detail a set of 2-D Diracs and extend the results to more complex objects such as lines and polygons. Unlike most multidimensional sampling schemes, the methods we propose perfectly reconstruct such signals from a finite number of samples in the noiseless case. Some of the techniques we use are already encountered in the context of harmonic retrieval and error correction coding. In particular, singular value decomposition (SVD)-based methods and the annihilating filter approach are both explored as inherent parts of the developed algorithms. Potentials and limitations of the algorithms in the noisy case are also pointed out. Applications of our results can be found in astronomical signal processing, image processing, and in some classes of identification problems.
Efficacy of Low-Dose Estradiol Vaginal Tablets in the Treatment of Atrophic Vaginitis (2008)

I.