gebhart/patrepeval huggingface dataset:
2‐Hydroxyglutarate concentration in serum from patients with gliomas does not correlate with IDH1/2 mutation status or tumor size (2011)

IDH1/2 mutations occur at high frequency in diffusely infiltrating gliomas of the WHO grades II and III and were identified as a strong prognostic marker in all WHO grades of gliomas. Mutated IDH1 or IDH2 protein leads to the generation of excessive amounts of the metabolite 2-hydroxyglutarate (2HG) in tumor cells. Here, we evaluated whether 2HG levels in preoperative serum samples from patients with gliomas correlate with the IDH1/2 mutation status and whether there is an association between 2HG levels and glioma size. In contrast to the strong accumulation of 2HG in the serum of patients with IDH1/2 mutated acute myeloid leukaemia, no accumulation was observed in this series of IDH1/2 mutated gliomas. Furthermore, we found no association between glioma size measured by magnetic resonance imaging and 2HG levels. We conclude that 2HG levels in preoperative sera from patients with diffusely infiltrating gliomas of the WHO grades II and III cannot be used as a marker to differentiate between tumors with versus without IDH1/2 mutation. Furthermore, the observation that there is no correlation between 2HG levels and tumor volume may indicate that 2HG cannot be utilized as marker to monitor tumor growth in gliomas.
An Analysis/Synthesis Tool for Transient Signals (1998)

: A flexible analysis/synthesis tool for transient signals, which is the frequency domain dual to sinusoidal modeling, is presented. This parametric model for transients allows the extension of current sinusoidal and sines+noise models for audio to sines+transients+noise. The model not only permits the realistic analysis/synthesis of signals with sharp attacks, it also permits a wide range of transformations on the analyzed signal. INTRODUCTION Sinusoidal modeling has enjoyed a rich history in both speech and audio [1, 2, 3]. Providing a low order parametric model for a signal that allows meaningful transformations is one motivation for sinusoidal models. Because transient signals are not well suited by sinusoidal or sinusoidal+noise models [2, 3], a flexible, low order model for transient signals was introduced in [4] and refined in [5]. The transient model is the frequency domain dual to sinusoidal modeling. It therefore compliments current models and allows a robust sines+transient...
SHE-NVFF: Spin Hall Effect-Based Nonvolatile Flip-Flop for Power Gating Architecture (2014)

A novel nonvolatile flip-flop (NVFF) using a magnetic tunnel junction (MTJ) is presented for power gating architecture. The proposed NVFF exploits spin Hall effect (SHE) for fast and low-power data backup into MTJs before the power is gated off. Owing to the high spin injection efficiency of SHE, the estimated write current for backup operation is lower than 40 μA. Due to the low write current requirement, we do not introduce a dedicated write driver circuit. Instead, we utilize the cross-coupled inverters in the slave latch to perform the backup operation, resulting in low area overhead. The simulation results show 10× improvement in backup energy when compared with previous works on spin transfer torque-based NVFFs.
Heterogeneous Response Dynamics in Retinal Ganglion Cells: The Interplay of Predictive Coding and Adaptation (2010)

To make efficient use of their limited signaling capacity, sensory systems often use predictive coding. Predictive coding works by exploiting the statistical regularities of the environment--specifically, by filtering the sensory input to remove its predictable elements, thus enabling the neural signal to focus on what cannot be guessed. To do this, the neural filters must remove the environmental correlations. If predictive coding is to work well in multiple environments, sensory systems must adapt their filtering properties to fit each environment's statistics. Using the visual system as a model, we determine whether this happens. We compare retinal ganglion cell dynamics in two very different environments: white noise and natural. Because natural environments have more power than that of white noise at low temporal frequencies, predictive coding is expected to produce a suppression of low frequencies and an enhancement of high frequencies, compared with the behavior in a white-noise environment. We find that this holds, but only in part. First, predictive coding behavior is not uniform: most on cells manifest it, whereas off cells, on average, do not. Overlaid on this nonuniformity between cell classes is further nonuniformity within both cell classes. These findings indicate that functional considerations beyond predictive coding play an important role in shaping the dynamics of sensory adaptation. Moreover, the differences in behavior between on and off cell classes add to the growing evidence that these classes are not merely homogeneous mirror images of each other and suggest that their roles in visual processing are more complex than expected from the classic view.
Detection of Chlamydia pneumoniae antigenin PBMNCs of healthy blood donors (2001)

A significant percentage of healthy donors carry C. pneumoniae, which may be a risk factor for some chronic diseases.
Oncology Pocket Guide to Chemotherapy (1994)

Intended primarily for oncology nurses, this pocket guide to chemotherapy should also be of interest to oncologists, pharmacists, medical and nursing students.
Overexpression, Amplification, and Androgen Regulation of TPD52 in Prostate Cancer (2004)

Gains in the long arm of chromosome 8 (8q) are believed to be associated with poor outcome and the development of hormone-refractory prostate cancer. Based on a meta-analysis of gene expression microarray data from multiple prostate cancer studies (D. R. Rhodes et al., Cancer Res 2002;62:4427-33), a candidate oncogene, Tumor Protein D52 (TPD52), was identified in the 8q21 amplicon. TPD52 is a coiled-coil motif-bearing protein, potentially involved in vesicle trafficking. Both mRNA and protein levels of TPD52 were highly elevated in prostate cancer tissues. Array comparative genomic hybridization and amplification analysis using single nucleotide polymorphism arrays demonstrated increased DNA copy number in the region encompassing TPD52. Fluorescence in situ hybridization on tissue microarrays confirmed TPD52 amplification in prostate cancer epithelia. Furthermore, our studies suggest that TPD52 protein levels may be regulated by androgens, consistent with the presence of androgen response elements in the upstream promoter of TPD52. In summary, these findings suggest that dysregulation of TPD52 by genomic amplification and androgen induction may play a role in prostate cancer progression.
Continuous Flow Hydroformylation of Alkenes in Supercritical Fluid−Ionic Liquid Biphasic Systems (2003)

A process for the hydroformylation of relatively low volatility alkenes (demonstrated for 1-dodecene) in a continuous flow system is described. The catalyst is dissolved in an ionic liquid while the substrate and gaseous reagents are transported into the reactor dissolved in supercritical CO(2), which simultaneously acts as a transport vector for aldehyde products. Decompression of the fluid mixture downstream yields products which are free of both reaction solvent and catalyst. The use of rhodium complexes of triaryl phosphites leads to ligand degradation through reaction of the ionic liquid with water and subsequent attack of the released HF on the phosphite. Sodium salts of sulfonated phosphines are insufficiently soluble in the ionic liquids to obtain acceptable rates, but replacing the sodium by a cation similar to that derived from the ionic liquid, allows good solubility and activity to be obtained. The nature of the ionic liquid is very important in achieving high rates, with 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amides giving the best activity if the alkyl chain is at least C(8). Catalyst turnover frequencies as high as 500 h(-1) have been observed, with the better rates at higher substrate flow rates. Rhodium leaching into the product stream can be as low as 0.012 ppm, except at low partial pressures of CO/H(2), when it is significantly higher. Oxygen impurities in the CO(2) feed can lead to oxidation of the phosphine giving higher rates, lower selectivities to the linear aldehyde, increased alkene isomerization and greater leaching of rhodium. However, it is found that under certain process conditions, the supercritical fluid-ionic liquid (SCF-IL) system can be operated continuously for several weeks without any visible sign of catalyst degradation. Comparisons with commercial hydroformylation processes are provided.
Phosphoinositide signaling disorders in human diseases (2003)

Phosphoinositides (PIs) play an essential role in diverse cellular functions. Their intracellular level is strictly regulated by specific PI kinases, phosphatases and phospholipases. Recent discoveries indicate that dysfunctions in the control of their level often lead to pathologies. This review will focus on some human diseases whose etiologies involve PI-metabolizing enzymes. The role of PTEN (phosphatase and tensin homolog deleted on chromosome ten) in cancer, the impact of the Src homology 2-containing inositol-5-phosphatase phosphatases in acute myeloid leukemia or diabetes, the involvement of myotubularin family members in genetic diseases and the implication of OCRL1 in Lowe syndrome will be emphasized. We will also review how some bacterial pathogens have evolved strategies to specifically manipulate the host cell PI metabolism to efficiently infect them.
Domain–domain communication in a miniature archaebacterial tRNA synthetase (1999)

The three-dimensional structure of tRNA is organized into two domains-the acceptor-TPsiC minihelix with the amino acid attachment site and a second, anticodon-containing, stem-loop domain. Aminoacyl-tRNA synthetases have a structural organization that roughly recapitulates the two-domain organization of tRNAs-an older primary domain that contains the catalytic center and interacts with the minihelix and a secondary, more recent, domain that makes contacts with the anticodon-containing arm. The latter contacts typically are essential for enhancement of the catalytic constant k(cat) through domain-domain communication. Methanococcus jannaschii tyrosyl-tRNA synthetase is a miniature synthetase with a tiny secondary domain suggestive of an early synthetase evolving from a one-domain to a two-domain structure. Here we demonstrate functional interactions with the anticodon-containing arm of tRNA that involve the miniaturized secondary domain. These interactions appear not to include direct contacts with the anticodon triplet but nonetheless lead to domain-domain communication. Thus, interdomain communication may have been established early in the evolution from one-domain to two-domain structures.
The N-best algorithms: an efficient and exact procedure for finding the N most likely sentence hypotheses (2002)

A search algorithm that provides a simple, clean, and efficient interface between the speech and natural language components of a spoken language system is introduced. The N-best algorithm is a time-synchronous Viterbi-style beam search procedure that is guaranteed to find the N most likely whole sentence alternatives that are within a given beam of the most likely sentence. The computation is linear with the length of the utterance, and faster than linear in N. When used together with a first-order statistical grammar, the correct sentence is usually within the first few sentence choices. The output of the algorithm, which is an ordered set of sentence hypotheses with acoustic and language model scores can easily be processed by natural language knowledge sources without the huge expansion of the search space that would be needed to include all possible knowledge sources in a top-down search. In experiments using a first-order statistical language model, the average rank of the correct answer was 1.8 and was within the first 24 choices 99% of the time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
First evidence for differences in fire blight resistance among transgenic pear clones expressing attacin E gene (1998)

*INRA Unité d'Amélioration des Espèces Fruitières et Ornementales Angers (FRA) Diffusion du document : INRA Unité d'Amélioration des Espèces Fruitières et Ornementales Angers (FRA)
Biostimulation of bone marrow cells with a diode soft laser (2000)

In recent years, the use of low-intensity red light in regeneration of soft tissue has been increasingly pursued. As far as hard tissue is concerned, the biostimulating effect of laser has already been demonstrated successfully in more rapid healing of tibial bone fractures in mice at a dosage of 2.4 J. However, the effect of light of a low dose laser directly on osteoblasts has not been investigated yet. The aim of this study was to determine the effect of continuous wave diode laser irradiation on osteoblasts derived mesenchymal cells. Three groups of 10 cultures each were irradiated 3 times (days 3, 5, 7) with a pulsed diode soft laser with a wavelength of 690 nm for 60 s. Another 3 groups of 10 cultures each were used as control groups. A newly developed method employing the fluorescent antibiotic tetracycline was used to compare bone growth on these culture substrates after a period of 8, 12 and 16 days, respectively. It was found that all lased cultures demonstrated significantly more fluorescent bone deposits than the non-lased cultures. The difference was significant, as tested by the Tukey Test (P < 0.0001) in the cultures examined after 16 days. Hence it is concluded that irradiation with a pulsed diode soft laser has a biostimulating effect on osteoblasts in vitro, which might be used in osseointegration of dental implants.
T cell activation by anti‐CD3 antibodies: function of Fc receptors on B cell blasts, but not resting B cells, and CD18 on the responding T cells (1987)

Mouse anti-human CD3 (T3) antibodies can induce T cell proliferation in the presence of Fc receptor (FcR)-bearing accessory cells. Depending on whether the particular antibody can interact with the FcR, it can be mitogenic or otherwise. Previously, some of us (Smith, K. G. C. et al., Eur. J. Immunol. 1986. 16:478) examined human T cell responses to the murine anti-CD3 antibody switch variants UCHT1 (IgG1) and UCHT1B (IgG2b). Using a novel xenogeneic system with mouse macrophages (M phi) and an anti-FcR antibody, 2.4G2, we obtained direct evidence for accessory function of FcR in these responses. However, mouse B cells which also possess FcR were not accessory cells. Here we show that resting B cells do not inhibit anti-CD3 responses in the presence of other accessory cells, and they do not synergize with them. They appear to be inert in these responses but this is not simply because of their radiosensitivity. In contrast, B cell blasts proved to be potent stimulators of responses with UCHT1, UCHT1B and OKT3 (IgG2a). All three responses were inhibited by 2.4G2, whereas we have shown previously that the OKT3 response with M phi was not, in keeping with the known specificities of B cell and M phi FcR. These findings are discussed in relation to the molecular cloning of FcR, and we consider the possibility that distinct FcR could be expressed on resting and activated B cells. A report that anti-CD18 (LFA-1) antibodies blocked the UCHT1 response with human monocytes raised the possibility that this molecule might also be involved in accessory function. However, we show that this inhibition is in fact at the level of the T cell, since anti-human, but not anti-mouse CD18 antibodies, inhibited proliferative responses and clustering with both human and mouse accessory cells. Our results demonstrate that the principal contribution of accessory cells to anti-CD3 responses may be the provision of an FcR, and that CD18 is most probably required at the level of the T cell.
Pelvic floor damage and childbirth: a neurophysiological study (1990)

Ninety six nulliparous women were investigated to establish whether childbirth causes damage to the striated muscles and nerve supply of the pelvic floor. The techniques used were concentric needle electromyography (EMG), pudendal nerve conduction tests and assessment of pelvic floor contraction using a perineometer. There was EMG evidence of re-innervation in the pelvic floor muscles after vaginal delivery in 80% of those studied. Women who had a long active second stage of labour and heavier babies showed the most EMG evidence of nerve damage. Forceps delivery and perineal tears did not affect the degree of nerve damage seen. We conclude that vaginal delivery causes partial denervation of the pelvic floor (with consequent re-innervation) in most women having their first baby. In a few this is severe and is associated with urinary and faecal incontinence. For some it is likely to be the first step along a path leading to prolapse and/or stress incontinence.
[Effects of Rap2b gene on foci formation and wound-healing of NIH3T3 cells]. (2010)

The extrinsic expression of Rap2b could transform NIH3T3 cell using foci formation assay and wound-healing assay. Rap2b gene might play an oncogenic role in tumorigenesis.
A comparative evaluation of Golgi protein-73, fucosylated hemopexin, α-fetoprotein, and PIVKA-II in the serum of patients with chronic hepatitis, cirrhosis, and hepatocellular carcinoma (2011)

PIVKA-II showed superior sensitivity and specificity for HCC compared with the other three markers. GP73 may be useful for detecting cirrhosis as a risk factor for HCC. Fuc-HPX showed inferior sensitivity and specificity compared to the other markers.
Chronic Inhibition of Mammalian Target of Rapamycin Signaling Downregulates Insulin Receptor Substrates 1 and 2 and AKT Activation (2006)

Overactivation of the mammalian target of rapamycin (mTOR) branch downstream of the phosphatidylinositol 3-kinase-AKT pathway critically modulates insulin and growth factor signaling by insulin receptor substrates (IRS). On the basis of in vitro studies, the mTOR inhibitor rapamycin has been reported to lead to enhanced activation of AKT by relieving this feedback inhibition on IRS function. In view of the critical role of AKT in insulin signaling and tumorigenesis, the in vivo expression and activation of this kinase and of IRS-1 and IRS-2 were explored in PBMC of 30 patients who were treated long term with rapamycin. A marked decrease of basal and insulin-stimulated AKT phosphorylation, which correlated with the increase of patients' insulin resistance, and a significant increase of IRS total protein expression, together with a lower (IRS-2) or absent (IRS-1) increase of insulin-induced tyrosine phosphorylation, were found. Therefore, contrary to the expectations, long-term exposure to rapamycin caused the impairment of IRS signaling and AKT activation, and this would help to explain the antiproliferative effect and the possible deterioration of glucose metabolism that are observed in rapamycin-treated patients. These findings may form a novel basis for improved understanding of the role of mTOR inhibition in human diseases, such as diabetes and cancer.
Human antibody libraries: A race to engineer and explore a larger diversity (2007)

Several recombinant antibody libraries associated with different screening technologies have been generated since the first steps of antibody engineering 15 years ago, in order to isolate human monoclonal antibodies. In this race to isolate antibody with virtually any specificity, innovative strategies have been developed to clone natural antibody repertoires or to increase library diversity beyond the scope of the immune system. After the in vitro transfer of the natural diversity, the second generation of partly or completely man-designed libraries was based on the available structural data of the antibody binding. Efficient selection strategies have proven critical in exploiting the potential of a library's diversity. The development and improvement of screening methods such as phage display, yeast display, ribosome display and robotic platforms have provided innovative tools to efficiently screen and sort out the desired binding specificities of billions of antibodies. Efforts to improve diversity exploration have been mainly focused on screening conditions of display techniques and the new emerging techniques. Here we review some of these prominent approaches in the field of human recombinant antibody libraries.
The Synthesis of Novel 6,5- and 6,6-Membered Fused Heterocyclic Compounds Derived from Thymine (2000)

Novel pyrimido[1,2-a]pyrimidinones 14, 15 and 16 and imidazo[1,2-a] pyrimidinones 19 and 20, designed as conformationally constrained analogues of 1-(3-amino-2-hydroxypropyl)thymine and 1-(2-amino-3-hydroxypropyl)thymine, respective ly, were synthesized by the ring-opening/ ring-closure rearrangement of the corresponding byciclic oxygen-containing amino compounds 12 and 17.
A Second Photochromic Bacteriophytochrome from Synechocystis sp. PCC 6803:  Spectral Analysis and Down-Regulation by Light (2000)

It now appears that photosynthetic prokaryotes and lower eukaryotes possess higher plant phytochrome-like proteins. In this work, a second phytochrome-like gene was isolated, in addition to the recently identified Cph1 phytochrome, from the Synechocystis sp. PCC 6803, and its gene product was characterized photochemically. The open reading frame sll0821 (designated cph2 in this work) has structural characteristics similar to those of the plant phytochromes and the Synechocystis Cph1 with high amino acid sequence homology in the N-terminal chromophore binding domain. The predicted Cph2 protein consists of 1276 amino acids with a calculated molecular mass of 145 kDa. Interestingly, the Cph2 protein has two putative chromophore binding domains, one around Cys-129 and the other around Cys-1022. The Cph2 was overexpressed in E. coli as an Intein/CBD (chitin binding domain) fusion and in vitro reconstituted with phycocyanobilin (PCB) or phytochromobilin (PPhiB). Both the Cph2-PCB and Cph2-PPhiB adducts showed the typical photochromic reversibility with the difference spectral maxima at 643/690 and 655/701 nm, respectively. The Cys-129 was confirmed to be the chromophore binding residue by in vitro mutagenesis and Zn(2+) fluorescence. The microenvironment of the chromophore in Cph2 seems to be similar to that in plant phytochromes. The cph2 gene expression was dark-induced and down-regulated to a basal level by light, like the cph1 gene. These observations suggest that Synechocystis species have multiple photosensory proteins, probably with distinct roles, as in higher plants.
Synthetic Lethal Targeting of PTEN-Deficient Cancer Cells Using Selective Disruption of Polynucleotide Kinase/Phosphatase (2013)

A recent screen of 6,961 siRNAs to discover possible synthetic lethal partners of the DNA repair protein polynucleotide kinase/phosphatase (PNKP) led to the identification of the potent tumor suppressor phosphatase and tensin homolog deleted on chromosome 10 (PTEN). Here, we have confirmed the PNKP/PTEN synthetic lethal partnership in a variety of different cell lines including the PC3 prostate cancer cell line, which is naturally deficient in PTEN. We provide evidence that codepletion of PTEN and PNKP induces apoptosis. In HCT116 colon cancer cells, the loss of PTEN is accompanied by an increased background level of DNA double-strand breaks, which accumulate in the presence of an inhibitor of PNKP DNA 3'-phosphatase activity. Complementation of PC3 cells with several well-characterized mutated PTEN cDNAs indicated that the critical function of PTEN required to prevent toxicity induced by an inhibitor of PNKP is most likely associated with its cytoplasmic lipid phosphatase activity. Finally, we show that modest inhibition of PNKP in a PTEN knockout background enhances cellular radiosensitivity, suggesting that such a "synthetic sickness" approach involving the combination of PNKP inhibition with radiotherapy may be applicable to PTEN-deficient tumors.