gebhart/patrepeval huggingface dataset:
Multiple genes at 17q23 undergo amplification and overexpression in breast cancer. (2000)

Studies by comparative genomic hybridization imply that amplification of the chromosomal region 17q22-q24 is common in breast cancer. Here, amplification and expression levels of six known genes located at 17q23 were examined in breast cancer cell lines. Four of them (RAD51C, S6K, PAT1, and TBX2) were found to be highly amplified and overexpressed. To investigate the involvement of these genes in vivo, fluorescence in situ hybridization analysis of a tissue microarray containing 372 primary breast cancers was used. S6K, PAT1, and TBX2 were coamplified in about 10% of tumors, whereas RADS1C amplification was seen in only 3% of tumors. Expression analysis in 12 primary tumors showed that RAD51C and S6K were consistently expressed in all cases in which they were amplified and also in some tumors without amplification. These data suggest that 17q23 amplification results in simultaneous up-regulation of several genes, whose increased biological activity may jointly contribute to the more aggressive clinical course observed in patients with 17q23-amplified tumors.
An open-labeled, randomized study comparing systemic interferon-α-2A and prednisolone enemas in the treatment of left-sided ulcerative colitis (2001)

OBJECTIVE: The aim of this study was to compare the treatment efficacies of subcutaneous interferon-α-2A (IFN-α-2A) injections versus prednisolone enemas in active left-sided ulcerative colitis in an open-labeled, randomized study. METHODS: Sixteen ulcerative colitis patients received IFN-α-2A subcutaneously (dosage: first wk, 9 MIU three times weekly [t.i.w.]; second wk, 6 MIU t.i.w.; wk 3–12, 3 MIU t.i.w.), and 16 received prednisolone enemas for 30 days (100 ml once daily, 0.25 mg of prednisolone/ml). The Powell-Tuck Index, Inflammatory Bowel Disease Questionnaire (IBDQ) score, and rectal histological activities were assessed before and after treatment. Thirteen patients in the IFN-α-2A group and all 16 in the prednisolone enema group completed the treatment. RESULTS: IFN-α-2A treatment showed significant improvements in the Powell-Tuck Index (p = 0.0002), IBDQ score (p = 0.002), and rectal histological activity scores (p = 0.02). In the enema group, significant improvements were found in the Powell-Tuck Index (p = 0.0009), whereas no significant improvements were detected in the IBDQ scores (p = 0.055) or rectal histological scores (p = 0.052). There were no differences between scores of the two groups either before or after treatment. Only moderate side effects from the IFN-α-2A treatment were seen during the first 2–4 wk of treatment. CONCLUSION: IFN-α-2A treatment resulted in significant depression of the disease activity as reflected by the Powell-Tuck Index, IBDQ score, and histological disease activity scoring. The preliminary trial thus suggests that IFN-α-2A may be effective in the treatment of active left-sided ulcerative colitis. Larger, randomized trials are, however, warranted to confirm this finding, owing to possible type II errors in group comparisons.
Automated tuning of large-scale multivariable model predictive controllers for spatially-distributed processes (2006)

This paper presents an automated tuning method of a large-scale multivariable model predictive controller for multiple array paper machine cross-directional (CD) processes. Paper machine CD processes are large-scale spatially-distributed dynamical systems. Due to these systems' (almost) spatially invariant nature, the closed-loop transfer functions are approximated by transfer matrices with rectangular circulant matrix blocks, whose input and output singular vectors are the Fourier components of dimension equivalent to either number of actuators or number of measurements. This approximation enables the model predictive controller for these systems to be tuned by a numerical search over optimization weights in order to shape the closed-loop transfer functions in the two-dimensional frequency domain for performance and robustness. A real industrial multiple array CD process is used for illustrating the effectiveness of this method
In vivo immobilization of enzymatically active polypeptides on the cell surface of Staphylococcus carnosus (1996)

Many surface proteins of Gram-positive bacteria are covalently anchored to the cell wall by a ubiquitous mechanism, involving a specific, C-terminal sorting signal. To achieve cell-wall immobilization of a normally secreted enzyme in vivo, we constructed a hybrid protein consisting of Staphylococcus hyicus lipase and the C-terminal region of Staphylococcus aureus fibronectin binding protein B (FnBPB). This region comprised the authentic cell-wall-spanning region and cell-wall sorting signal of FnBPB. Expression of the hybrid protein in Staphylococcus carnosus resulted in efficient cell-wall anchoring of enzymatically active lipase. The cell-wall-immobilized lipase (approximately 10,000 molecules per cell) retained more than 80% of the specific activity, compared to the C-terminally unmodified S. hyicus lipase secreted by S.carnosus cells. After releasing the hybrid protein from the cell wall by lysostaphin treatment. Its specific activity was indistinguishable from that of the unmodified lipase. Thus, the C-terminal region of FnBPB per se was fully compatible with folding of the lipase to an active conformation. To study the Influence of the distance between the cell-wall sorting signal and the C-terminus of the lipase on the activity of the immobilized lipase, the length of this spacer region was varied. Reduction of the spacer length gradually reduced the activity of the surface-immobilized lipase. On the other hand, elongation of this spacer did not stimulate the activity of the immobilized lipase, indicating that the spacer must exceed a critical length of approx. 90 amino acids to allow efficient folding of the enzyme, which probably can only be achieved outside the peptidoglycan web of the cell wall. When the lipase was replaced by another enzyme, the Escherichia coli beta-lactamase, the resulting hybrid was also efficiently anchored in an active conformation to the cell wall of S. carnosus. These results demonstrate that it is possible to immobilize normality soluble enzymes on the cell wall of S. carnosus-without radically altering their catalytic activity-by fusing them to a cell-wall-immobilization unit, consisting of a suitable cell-wall-spanning region and a standard cell-wall sorting signal.
Assessing Pain by Facial Expression: Facial Expression as Nexus (2009)

The experience of pain is often represented by changes in facial expression. Evidence of pain that is available from facial expression has been the subject of considerable scientific investigation. The present paper reviews the history of pain assessment via facial expression in the context of a model of pain expression as a nexus connecting internal experience with social influence. Evidence about the structure of facial expressions of pain across the lifespan is reviewed. Applications of facial assessment in the study of adult and pediatric pain are also reviewed, focusing on how such techniques facilitate the discovery and articulation of novel phenomena. Emerging applications of facial assessment in clinical settings are also described. Alternative techniques that have the potential to overcome barriers to the application of facial assessment arising out of its resource intensiveness are described and evaluated, including recent work on computer- based automatic assessment.
Use of spherical harmonic deconvolution methods to compensate for nonlinear gradient effects on MRI images (2004)

Spatial encoding in MR techniques is achieved by sampling the signal as a function of time in the presence of a magnetic field gradient. The gradients are assumed to generate a linear magnetic field gradient, and typical image reconstruction relies upon this approximation. However, high-speed gradients in the current generation of MRI scanners often sacrifice linearity for improvements in speed. Such nonlinearity results in distorted images. The problem is presented in terms of first principles, and a correction method based on a gradient field spherical harmonic expansion is proposed. In our case, the amount of distortion measured within a typical field of view (FOV) required for head imaging is sufficiently large that without the use of some distortion correction technique, the images would be of limited use for stereotaxy or longitudinal studies, where precise volumetric information is required.
Design of RNA enzymes distinguishing a single base mutation in RNA (1989)

RNA enzymes (ribozymes) which can cleave RNA by recognizing sequences of 9-15 bases are described. Substrates must contain UX (X = U, C or A). A ribozyme consisting of two oligoribonucleotides (19 mer and 15 mer) was shown to cleave a ribo 11 mer catalytically with Km and kcat values of 0.53 microM and 0.03 min-1, respectively. A non-cleavable substrate-ribozyme complex containing 2'-O-methylnucleoside was prepared and CD spectra were compared at different temperature. In order to obtain an efficient ribozyme, a one-strand RNA with a chain length of 37 was prepared. The ribozyme was shown to distinguish a single base mutation in mRNA's which were prepared by transcription of two synthetic DNA duplexes coding for positions 7-26 of c-Ha-ras protein. The mutant (Val-12) mRNA which had GUU was cleaved but the wild type mRNA which contained GGU was not changed, when treated by the ribozymes in the presence of Mg2+.
Development of Ternary and Quaternary Catalysts for the Electrooxidation of Glycerol (2012)

This work consisted in the preparation of platinum-based catalysts supported on carbon (Vulcan XC-72) and investigation of their physicochemical and electrochemical properties. Catalysts of the C/Pt-Ni-Sn-Me (Me = Ru or Ir) type were prepared by the Pechini method at temperature of 350°C. Four different compositions were homemade: C/Pt(60)Sn(10)Ni(30), C/Pt(60)Sn(10)Ni(20)Ru(10), C/Pt(60)Sn(10)Ni(10)Ru(20), and C/Pt(60)Sn(10)Ni(10)Ir(20). These catalysts were electrochemically and physically characterized by cyclic voltammetry (CV), chronoamperometry (CA) in the presence of glycerol 1.0 mol dm(-3), X-ray diffraction (XRD), and high-resolution transmission electron microscopy (HRTEM). XRD results showed the main peaks of face-centered cubic Pt. The particle sizes obtained from XRD and HRTEM experiments were close to values ranging from 3 to 8.5 nm. The CV results indicate behavior typical of Pt-based catalysts in acid medium. The CV and CA data reveal that quaternary catalysts present the highest current density for the electrooxidation of glycerol.
Fetal Hemoglobin and F-Cell Responses to Long-Term Hydroxyurea Treatment in Young Sickle Cell Patients (1998)

We have studied the cellular and molecular responses to long-term hydroxyurea (HU) treatment in 29 severely affected young patients with sickle cell disease (mean age, 10.9 +/- 4.1 years). Patients received HU at 20 mg/kg/d on 4 consecutive days per week initially, with a monthly escalated dose avoiding marrow-toxicity (mean steady-state dose, 34.2 +/- 4.6 mg/kg/d) for 12 to 36 months (mean duration, 22 months). The studied parameters were hemoglobin F (HbF), F reticulocytes (F retics), F cells, the amount of HbF per F cell (F/F cell), polymer tendency at 40% and 70% oxygen saturation, and hemolysis. Initial HbF (Fi) was dispersed (from 0.85% to 13.9%). HbF increased in all patients but 1. HbF at maximal response (Fmax) reached a sustained level varying from a 1.5-fold to a 16-fold Fi after a variable delay (6 to 24 months). Fmax was not related to HU dosage, but triangle upF (Fmax - Fi) was strongly correlated to triangle upMCV (MCVmax - MCVi). HbF increase resulted from the increase of both F cells and F/F cell. In this rather short series, Fi and Fmax were not significantly associated with age, gender, or beta-globin haplotype. Neither Fmax nor triangle upF was related to bone marrow reserve, as measured by baseline reticulocyte or neutrophil counts. However, Fmax was highly dependent on Fi. When patients are individualized into three groups according to Fmax (group 1, Fmax >20% [12 patients]; group 2, 10% < Fmax < 20% [11 patients]; group 3, Fmax <10% [5 patients]), Fi is significantly different between groups, being the highest in group 1. In addition, the best responders (group 1) were significantly different from patients in the two other groups with higher levels of total hemoglobin, decreased bilirubin, and decreased polymer tendency.
Functional implications of microRNAs in acute myeloid leukemia by integrating microRNA and messenger RNA expression profiling (2011)

Our results indicate that by integrating the transcriptome and microRNome in AML cells, it is possible to identify previously unidentified putative functional miRNA-mRNA interactions in AML.
Packet transport of VBR interframe DCT compressed digital video on a CSMA/CD LAN (2003)

The feasibility of providing teleconference/picturephone video services over 10-Mb/s IEEE 802.3 CSMA/CD (carrier sense multiple access with collision detection) local area networks is examined. The system considered is based on variable-bit-rate (VBR) video codecs which produce an interframe discrete cosine transform/differential pulse code modulation (DCT/DPCM) codec output format compatible with the evolving CCITT H.261 standard for px64 kb/s motion video. Transport-level protocol functions (such as delay compensation, flow control, and error control) required to support real-time video at an acceptable quality level are identified and discussed. A simulation model used for assessing the performance of the LAN with several video and data users is described. The model provides quantitative measures of network performance (such as packet loss or delay vs. throughput). Preliminary performance evaluation results demonstrate that, with appropriate transport-level delay compensation, potentially acceptable video and data quality levels can be provided on a well-loaded ( approximately 55%) CSMA/CD LAN. With appropriate transport buffering, acceptably low video packet loss rates can be achieved, although the corresponding subjective quality has yet to be established.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cross-Reactive Immunity Among Flaviviruses (2020)

Flaviviruses consist of significant human pathogens responsible for hundreds of millions of infections each year. Their antigenic relationships generate immune responses that are cross-reactive to multiple flaviviruses and their widespread and overlapping geographical distributions, coupled with increases in vaccination coverage, increase the likelihood of exposure to multiple flaviviruses. Depending on the antigenic properties of the viruses to which a person is exposed, flavivirus cross-reactivity can be beneficial or could promote immune pathologies. In this review we describe our knowledge of the functional immune outcomes that arise from varied flaviviral immune statuses. The cross-reactive antibody and T cell immune responses that are protective versus pathological are also addressed.
Abundance‐Based Similarity Indices and Their Estimation When There Are Unseen Species in Samples (2006)

A wide variety of similarity indices for comparing two assemblages based on species incidence (i.e., presence/absence) data have been proposed in the literature. These indices are generally based on three simple incidence counts: the number of species shared by two assemblages and the number of species unique to each of them. We provide a new probabilistic derivation for any incidence-based index that is symmetric (i.e., the index is not affected by the identity ordering of the two assemblages) and homogeneous (i.e., the index is unchanged if all counts are multiplied by a constant). The probabilistic approach is further extended to formulate abundance-based indices. Thus any symmetric and homogeneous incidence index can be easily modified to an abundance-type version. Applying the Laplace approximation formulas, we propose estimators that adjust for the effect of unseen shared species on our abundance-based indices. Simulation results show that the adjusted estimators significantly reduce the biases of the corresponding unadjusted ones when a substantial fraction of species is missing from samples. Data on successional vegetation in six tropical forests are used for illustration. Advantages and disadvantages of some commonly applied indices are briefly discussed.
A bayesian approach to video expansions on parametric over-complete 2-d dictionaries (2005)

In this work, we explore a framework for the sparse representation of video sequences by means of spatio-temporal functions able to exploit the 2D nature of images and the temporal smoothness associated to object trajectories. Decomposition over redundant dictionaries formed by 2D functions capable to exploit image geometry, has shown to be well adapted for efficient sparse image approximations. Video representation by means of temporally evolving sets of such 2D functions seems thus a natural extension toward video approximation techniques. In the present paper we study the deformation of a geometry oriented image expansion based on matching pursuits (MP) (P. Vandergheynst and P. Frossard, May 2001), to obtain a parametric representation of frames transformation through time. We consider a modified MP approach based on a Bayesian decision criteria to deform geometrical primitives in a predictive fashion from frame to frame. Indeed, since motion stability is not guaranteed using a pure MP, a Bayesian framework is introduced to regularize motion among expansion terms of frames representations.
Investigation of the early killing of Staphylococcus aureus by daptomycin by using an in vitro pharmacodynamic model (1992)

The purpose of this study was to develop a pharmacodynamic model to describe the dependency of the rate of Staphylococcus aureus killing upon the concentration of daptomycin. A range of free (unbound) daptomycin concentrations ranging from 0.12 to 27 times the MIC were simulated in the peripheral compartment of a two-compartment pharmacokinetic model. Log-linear regression of free daptomycin concentrations versus growth or kill rate constants showed a significant correlation (r = -0.90; P less than 0.001). A Lineweaver-Burk plot of the reciprocal transformation of these data yielded a poor fit (r = -0.38; P greater than 0.05). When a Lineweaver-Burk-type regression analysis was performed on the reciprocal of the change in the rate constant rather than the rate constant itself, the result demonstrated good correlation (r = 0.90; P less than 0.0001). The observations were also well described by a sigmoidal maximum plateau pharmacologic effect model, in which the pharmacologic effect of daptomycin is a reduction in the bacterial exponential growth rate constant from the baseline in the absence of antibiotic to a lower (positive) growth or (negative) death rate constant observed in the presence of antibiotic. These data confirm that daptomycin exhibits concentration-dependent killing over a wide range of free daptomycin concentrations relative to the MIC and suggest that this is a saturable process similar to the Michaelis-Menten pharmacokinetic elimination of certain drugs.
ELAV protein HuA (HuR) can redistribute between nucleus and cytoplasm and is upregulated during serum stimulation and T cell activation (1998)

ELAV proteins are implicated in regulating the stability and translation of cytokine and growth regulatory mRNAs such as GM-CSF, IL-2, c-myc, c-fos and GLUT1 by binding to their AU-rich 3'UTRs. The tissue-specific ELAV protein HuB (aka. Hel-N1) is predominantly cytoplasmic and has been shown to stabilize GLUT1 and c-myc mRNAs and to increase their translation following ectopic expression in 3T3-L1 cells. We report that the most widely expressed mouse ELAV protein, mHuA, is predominately nuclear in cultured NIH-3T3 cells, but is localized in the cytoplasm during early G1 of the cell cycle. Therefore, much like the primarily cytoplasmic HuB, HuA becomes temporally localized in the cytoplasm where it can potentially regulate the stability or translation of bound mRNAs. Moreover, we report that stimulation of mouse spleen cells using either mitogenic or sub-mitogenic levels of anti-CD3/CD28 resulted in a dramatic increase in the level of HuA. Upregulation of HuA corresponds to previously documented increases in cytokine expression which are due to increased mRNA stability following T cell activation. Consistent with these findings, HuA was down regulated in quiescent cells and upregulated in 3T3 cells following serum stimulation. The increase of murine HuA during the cell cycle closely resembles that of cyclin B1 which peaks in G2/M. Together with our earlier studies, these data indicate that mammalian ELAV proteins function during cell growth and differentiation due in part to their effects on posttranscriptional stability and translation of multiple growth regulatory mRNAs. This supports the hypothesis that ELAV proteins can function as transacting factors which affect a default pathway of mRNA degradation involved in the expression of growth regulatory proteins.
A Yoctoliter-Scale DNA Reactor for Small-Molecule Evolution (2009)

The center of DNA three-way junctions, constituting a yoctoliter (10(-24) L) volume, is applied as an efficient reactor to create DNA-encoded libraries of chemical products. Amino acids and short peptides are linked to oligonucleotides via cleavable and noncleavable linkers. The oligonucleotide sequences contain two universal assembling domains at the center and a distal codon sequence specific for the attached building block. Stepwise self-assembly and chemical reactions of these conjugates in a combinatorial fashion create a library of pentapeptides in DNA three-way junctions in a single reaction vessel. We demonstrate the formation of an evenly distributed library of 100 peptides. Each library member contains a short synthetic peptide attached to a unique genetic code creating the necessary "genotype-phenotype" linkage essential to the process of in vitro molecular evolution. Selective enrichment of the [Leu]-enkephalin peptide from an original frequency of 1 in 10 million in a model library to a final frequency of 1.7% in only two rounds of affinity selection is described and demonstrates successful molecular evolution for a non-natural system.
Thrombospondin 1 acts as a strong promoter of transforming growth factor β effects via two distinct mechanisms in hepatic stellate cells (2005)

Background and aims: Thrombospondin 1 (TSP-1) is an important activator of latent transforming growth factor β (TGF-β) but little is known of the expression patterns and functions of TSP-1 in liver cells. We therefore analysed if and how TSP-1 acts on TGF-β during fibrogenesis. Methods and results: Using reverse transcription-polymerase chain reaction, we demonstrated that hepatocytes from normal liver expressed no TSP-1 mRNA whereas Kupffer cells and sinusoidal endothelial cells did. TSP-1 mRNA and protein were detected in quiescent and activated cultured hepatic stellate cells (HSC) and TSP-1 expression was highly inducible by platelet derived growth factor BB (PDGF-BB) and, to a lesser extent, by tumour necrosis factor α in activated HSC. Furthermore, addition of PDGF-BB directly led to enhanced TGF-β mRNA expression and a TSP-1 dependent increase in TGF-β/Smad signalling. Using either a peptide specifically blocking the interaction of TSP-1 with latent TGF-β or antibodies against TSP-1 not only abrogated activation of latent TGF-β but also reduced the effects of the active dimer itself. Conclusions: Our data suggest that TSP-1 expression is important for TGF-β effects and that it is regulated by the profibrogenic mediator PDGF-BB in HSC. Furthermore, the presence of TSP-1 seems to be a prerequisite for effective signal transduction by active TGF-β not only in rat HSC but also in other cell types such as human dermal fibroblasts.