julilili42/papers huggingface dataset:
Online SVR training by solving the primal optimization problem
2009-09-01

Online regression estimation becomes important in presence of drifts and rapid changes in the training data. In this article we propose a new online training algorithm for SVR, called PRIONA, which is based on the idea of computing approximate solutions to the primal optimization problem. We explore different unconstrained optimization methods for the solution of the primal SVR problem and investigate the impact of different buffering strategies. By using a line search PRIONA does not require a priori selection of a learning rate which facilitates its practical application. Further PRIONA is shown to perform better in terms of prediction accuracy on various benchmark data sets in comparison to the NORMA and SILK online SVR algorithms.
OP02.03: Dependency of fetal NT thickness on the position of the fetal head
2009-09-01

To assess the intra- and interobserver reproducibility in the measurement of the fetal nuchal translucency (NT) at 11 + 0 to 13 + 6 weeks of gestation and to investigate the effect of deviations from the true mid-sagittal view on these measurements. 60 consecutive 3D volumes were obtained with the fetal head in a midsagittal position. Two FMF-UK certified operators measured fetal NT in the true mid-sagittal view and repeated the measurement after lateral rotation of the head by 5° to 25° away from the vertical position of the occipitofrontal diameter axis. The operators were blinded to their measurements; the 60 3D blocks were analysed twice by each operator. Mean difference and 95% limits of agreement between paired measurements of fetal NT by the same and by two different sonographers were determined. In the mid-sagittal plane the median NT was 1.8. The median NT at 5° to 25° was significantly lower (−0.1, −0.3, −0.4, −0.5, −0.6 mm) than in the mid-sagittal plane. The 95% limits of agreement for NT in the mid-sagittal section were −0.1 to 0.3 mm and −0.1 to 0.5 mm for both operators. At 15° for delta NT, 95% of the cases were between −0.2 to 0.7 mm and −0.3 to 0.5 mm, respectively. Between operators it was −0.1 to 0.2 in the mid-sagittal section and −0.1 to 0.4 at a deviation of 15°. Fetal NT measurement depends on the position of the fetal head. The measurement is biggest in the mid-sagittal plane, which is clearly defined and smaller in lateral planes.
P11.12: Effect of deviation of free β-hCG and PAPP-A on the performance of screening for trisomy 21
2009-09-01

To examine the effect of deviations in the median MoM levels of free β-hCG and PAPP-A on the performance of screening for trisomy 21 by maternal age, fetal nuchal translucency thickness (NT) and maternal serum biochemistry. We simulated NT measurements and MoM values for PAPP-A and free β-hCG for 500,000 euploid and 500,000 trisomy 21 pregnancies at 12 weeks of gestation. Detection rates for trisomy 21 and false positive rates were calculated without adjustments of the MoM values and after increasing/decreasing the individual MoM values by 5% to 30%. The detection rate of trisomy 21 for a fixed false positive rate of 3% in screening by maternal age, fetal NT and serum free β-hCG and PAPP-A was 86%. At a risk cut off of 1 : 100, the detection rate was 84% for a false positive rate of 2.7%. For a fixed 3% false positive rate, an under- or overestimate of the MoM values reduced the detection rates for trisomy 21. At a fixed screen positive cut-off of 1 : 100, an underestimation of PAPP-A increased the detection and false positive rates to 87% and 3.3%. Similarly, an overestimation of free β-hCG led to an increase in the rates to 86% and 3.1%. An underestimation of PAPP-A in combination with an overestimation of free β-hCG increased the rates further to 88% and 4.0%. High performance of screening necessitates appropriate measurement of free β-hCG and PAPP-A and the possibility to adjust for local differences.
OP20.08: Holoprosencephaly, megacystis and exomphalos and the risk for chromosomal abnormalities
2009-09-01

To examine whether in fetuses with holoprosencephaly, megacystis and exomphalos, the combined risk for trisomies 21, 18 and 13 based on maternal age, fetal nuchal translucency (NT), PAPP-A and free β-hCG can distinguish between euploid and aneuploid fetuses. Prospective screening for trisomy 21 by maternal age, fetal NT, free β-hCG and PAPP-A at 11 − 13 + 6 weeks of gestation in singleton pregnancies, including 56 376 normal cases, 395 with trisomy 21, 122 with trisomy 18 and 61 with trisomy 13. In addition to fetal NT, major fetal defects such as holoprosencephaly, megacystis and exomphalos were diagnosed at the time of screening. Risks for trisomy 21, 18 and 13 were calculated and the sum of all three risks was used to calculate detection and false positive rates by taking the proportions with risks above a given risk threshold. In the study population of 57,119 pregnancies, there were 44 (0.08%) cases with holoprosencephaly, 150 (0.3%) cases with exomphalos and 35 (0.06%) cases with megacystis. Of the fetuses with holoprosencephaly, 29 (65.9%) were chromosomally abnormal. Of those with exomphalos and megacystis the karypype was abnormal in 83 (55.3%) and 11 (31.4%), respectively. Applying a risk cut off of 1 : 100 would detect 96.7%, 96.4% and 100% of the aneuploid fetuses with holoprosencephaly, exomphalos and megacystis for respective false positive rates of 6.7%, 16.4% and 4.2%. In fetuses with holoprosencephaly, exomphalos and megacystis, the combined risk for trisomies can help to distinguish between euploid and aneuploid fetuses. However, in view of the following pregnancy, karyotyping is still recommended.
OC26.01: Fetal weight estimation in fetuses of 1500g or less
2009-09-01

To assess the accuracy of the commonly used weight estimation formulae in fetuses with a birth weight (FBW) of 1500g or less. A search of the perinatal database was performed to detect fetuses with a birth weight of 1500g or less and no structural abnormalities and a time interval of 7 days or less from the last ultrasound examination until delivery. For each case estimated fetal weight (EFW) was calculated according to 23 commonly used weight estimation formulae (Birmholz, Hadlock (6 formulae), Halaska, Hansmann, Higginbottom, Shinozouka, Masal, Merz, Rose &McCallum, Schild (2 formulae), Scott, Shepard, Siemer, Thurnau, Weiner (2 fomulae) and Warsof). To assess the accuracy of the formulae the differences between FBW and EFW (expressed as grams, as percentage of FBW and as absolute percentage (|FBW − EFW|/FBW) were calculated. To assess whether the accuracy changes with increasing FBW a linear regression analysis was performed. 193 pregnancies fulfilled the inclusion criteria with a mean FBW of 1001g. The mean differences between FBW and EFW were within 10% with the formulae from Hadlock I and III, Scott, Hadlock IV, Hadlock II and Masal (absolute percentage of FBW: 9.2%, 9.2%, 9.3%, 9.4%, 9.9% and 9.9%). Of those, EFW and FBW was within 10% of the FBW in more than 60% of the cases with the formulae from Hadlock I and III and with the Scott formula (64.2%, 61.1%, 60.6%). Linear regression showed that with the Hadlock I and III formulae the accuracy did not change with increasing fetal weight (r = 0.936 and p = 0.938, p < 0,0001, intercept and slope not significantly different from 0 and 1). With these weight estimation formulae, the 95% limits of agreement between FBW and EFW were − 19% to 19% (Hadlock I) and − 17.3% to 20.1% (Hadlock III) of the FBW. Of the 23 commonly available weight estimation formulae, the Hadlock I (BPD-HC-AC-FL) and III (BPD-AC-FL) formulae were most accurate in estimating fetal weight in fetuses with a birth weight of 1500g or less.
Target oriented selection of electrophysiological endpoints in preclinical and clinical trials
2009-09-01

Abstract Purpose The design of pre‐clinical and clinical studies, especially multi‐centre studies shall be discussed concerning the assessment of retinal function, retinal diseases and retinal circuitry as well as biochemistry and the selection of the proper electrophysiological “markers” for appropriate endpoints on the basis of knowledge on possible actions of particular compounds on visual function. Methods Quality has to be ensured by extended standard operating procedures and case report forms that implement also data that test the quality of procedures and calibrations. This includes harmonized quality standards, quality control, central reading and monitoring as well as data management. Results On the basis of standards and recommendations of International Society for Clinical Electrophysiology of Vision and EVI.CT.SE, extended protocols have been developed, targeted at rod and cone function, including sensitivity assessment of the retina by V‐log I‐functions, submicrovolt recording for clinical trials in patients with very small responses, ON and the OFF pathway differentiation. Additionally, ERG recovery after a strong bleach is recommended to target alterations in the visual cycle that involves photoreceptors as well as RPE cells. Conclusion First investigations with such refined standardized protocols have already been performed successfully showing a clear improvement of quality. Normative data are available for the various protocols.
Treatment of chronic hepatitis C with PegIFN-alfa2b and ribavirin within a large German multicentric observational study: response to therapy depends on patients' age
2009-09-01

Aims: The current treatment of choice for hepatitis C is a combination of pegylated interferon-alfa (PegIFN-alfa) plus ribavirin. No age dependency of SVR has been described recently from the WIN-R cohort comparing patients older than 65 (SVR=46%) with those younger than 65 years (SVR=46%). A subgroup of patients between 18 to 25 years experienced higher SVR-rates of 57%. We evaluated the correlation of age and SVR within age decades 20 to 30 (group I), 30 to 40 (group II), 40 to 50 (group III), 50 to 60 (group IV) and 60 to 70 (group V) years, respectively.
OP02.02: Effect of deviation of nuchal translucency measurements on the performance of screening for trisomy 21
2009-09-01

To examine the effect of deviations in the median nuchal translucency (NT) thickness and the spread in measurements on the performance of screening for trisomy 21 by maternal age and fetal NT and by maternal age, fetal NT and maternal serum biochemistry. We simulated the NT and MoM values for PAPP-A and free β-hCG for 500,000 euploid and 500,000 trisomy 21 pregnancies at 12 weeks of gestation. Detection rates for trisomy 21 and false positive rates were calculated without adjustments in NT and by adding or subtracting values ranging from 0.1 to 1.0 mm to each observed measurement. In addition, the effects of variation in the scatter of NT measurements were examined by applying a multiplicative factor ranging from 0.5 to 2 to the standard deviation (SD). The detection rate of trisomy 21 for a fixed false positive rate of 3% in screening by maternal age, fetal NT and serum free β -hCG and PAPP-A was 86%. At a risk cut off of 1 : 100, the detection rate was 84% for a false positive rate of 2.7%. An under- or overestimate in the measured NT reduced the detection rate of trisomy 21 for a fixed false positive rate (e.g. overestimation by 0.5 mm: DR 83%; underestimation by 0.5 mm DR 84%). At a fixed screen positive cut-off, an underestimate in fetal NT reduced predominantly the detection rate while an overestimate in NT increased predominantly the false positive rate (e.g. risk cut off 1 : 100: overestimation by 0.5 mm: DR 78% and FPR 1.6%; underestimation of 0.5 mm: DR 91% and FPR 7.0%). A widening in the scatter of measurements had only a small impact on the detection rate but it caused a major increase in the false positive rate (e.g. widening by 50%: DR 85% and FPR 4.3%). High performance of screening necessitates appropriate measurement of fetal NT.
Molecular Analyses of theBORISGene in Children with Silver-Russell Syndrome
2009-09-01

Silver-Russell syndrome (SRS) is a heterogeneous disorder associated with intrauterine and postnatal growth retardation, skeletal asymmetry and facial dysmorphisms. In 7-10% of patients maternal uniparental disomy for chromosome 7 can be observed, nearly 50% of patients carry an epimutation resulting in hypomethylation of the imprinting center region 1 (ICR1) in 11p15. This leaves 40% of patients with unknown genetic aetiology. Based on the observation that the CTCFhomologue BORISis involved in imprinted gene expression and that it binds to methylated alleles we assumed that loss-of-function mutations in BORISmight have similar functional consequences as an ICR1 hypomethylation. On the other hand, there is evidence that BORISmutations may disturb the methylation process and therefore cause hypomethylation in the ICR1. In our study we searched for BORISgene mutations in a mixed cohort of SRS patients with and without 11p15 hypomethylation to determine whether this gene is involved in SRS aetiology. Mutation analyses revealed eight genomic variants but pathogenic mutations were not observed. Thus we conclude that alterations of the BORISgene are probably not associated with SRS.
Analyses of Resected Human Brain Metastases of Breast Cancer Reveal the Association between Up-Regulation of Hexokinase 2 and Poor Prognosis
2009-09-02

Abstract Brain metastases of breast cancer seem to be increasingin incidence as systemic therapy improves. Metastatic disease in the brain is associated with high morbidity and mortality. We present the first gene expression analysis of laser-captured epithelial cells from resected human brain metastases of breast cancer compared with unlinked primary breast tumors. The tumors were matched for histology, tumor-node-metastasis stage, and hormone receptor status. Most differentially expressed genes were down-regulated in the brain metastases, which included, surprisingly, many genes associated with metastasis. Quantitative real-time PCR analysis confirmed statistically significant differences or strong trends in the expression of six genes: BMP1, PEDF, LAMγ3, SIAH, STHMN3, and TSPD2. Hexokinase 2 (HK2) was also of interest because of its increased expression in brain metastases. HK2 is important in glucose metabolism and apoptosis. In agreement with our microarray results, HK2 levels (both mRNA and protein) were elevated in a brain metastatic derivative (231-BR) of the human breast carcinoma cell line MDA-MB-231 relative to the parental cell line (231-P) in vitro. Knockdown of HK2 expression in 231-BR cells using short hairpin RNA reduced cell proliferation when cultures were maintained in glucose-limiting conditions. Finally, HK2 expression was analyzed in a cohort of 123 resected brain metastases of breast cancer. High HK2 expression was significantly associated with poor patient survival after craniotomy (P = 0.028). The data suggest that HK2 overexpression is associated with metastasis to the brain in breast cancer and it may be a therapeutic target. (Mol Cancer Res 2009;7(9):1438–45)
Ventricular tachycardia during hyperthermic intraperitoneal chemotherapy
2009-09-02

Summary Cytoreductive surgery with hyperthermic intraperitoneal chemotherapy (HIPEC) is used for selected gastrointestinal carcinomas. We report a case of ventricular tachycardia during HIPEC with cisplatin that persisted as long as the chemotherapy solution remained in the intra‐abdominal cavity. We hypothesise that high plasma levels of cisplatin with concomitant low magnesium levels caused the arrhythmia.
Biblical Theology
2009-09-02

Abstract This article gives an overview of the basic problems in biblical theology from the point of view of how they have developed since the beginnings of biblical theological work in the seventeenth century and how they appear today. This sketch of the problems will therefore concern itself less with a discussion of details than with major trends and contexts. After a definition of the term ‘biblical theology’ and a brief outline of the history of interpretation, there follows a sketch of those problems that are at present most intensively discussed. The main emphasis will be on the Old Testament and its significance for a theology of the whole Bible.
Very high energy γ-ray observations of the binary PSR B1259–63/SS2883 around the 2007 Periastron
2009-09-03

Aims. This article presents very-high-energy (VHE; E &gt; 100 GeV) data from the-ray binary PSRB1259-63 as taken during the years 2005, 2006 and before as well as shortly after the 2007 periastron passage. These data extend the knowledge of the lightcurve of this object to all phases of the 3.4 year binary orbit. The lightcurve constrains physical mechanisms present in this TeV source. Methods. Observations of VHE-rays with the HESS telescope array using the Imaging Atmospheric Cherenkov Technique were performed. The HESS instrument features an angular resolution of &lt;0.1° and an energy resolution of &lt;20%. Gamma-ray events in an energy range of 0.5-70 TeV were recorded. From these data, energy spectra and lightcurve with a monthly time sampling were extracted. Results. VHE-ray emission from PSRB1259-63 was detected with an overall significance of 9.5 standard deviations using 55 h of exposure, obtained from April to August 2007. The monthly flux of-rays during the observation period was measured, yielding VHE lightcurve data for the early pre-periastron phase of the system for the first time. No spectral variability was found on timescales of months. The spectrum is described by a power law with a photon index of G = 2.8 ± 0.2stat ± 0.2sys and flux normalisation F0 = (1.1 ± 0.1stat ± 0.2sys) × 10-12 TeV-1 cm-2 s-1. PSRB1259-63 was also monitored in 2005 and 2006, far from periastron passage, comprising 8.9 h and 7.5 h of exposure, respectively. No significant excess of-rays is seen in those observations. Conclusions.PSRB1259-63 has been re-confirmed as a variable TeV-ray emitter. The firm detection of VHE photons emitted at a true anomaly ? ≈-0.35 of the pulsar orbit, i.e. already 50 days prior to the periastron passage, disfavors the stellar disc target scenario as a primary emission mechanism, based on current knowledge about the companion star's disc inclination, extension, and density profile. © 2009 ESO.
2‐Acylaminopyridin‐4‐ylimidazoles as p38 MAP Kinase Inhibitors: Design, Synthesis, and Biological and Metabolic Evaluations
2009-09-03

Abstract Targeting cytokines has become an important focus in the treatment of many inflammatory disorders. p38 MAP kinase (MAPK) is the key enzyme in regulating the biosynthesis and release of pro‐inflammatory cytokines such as IL‐1β and TNFα. Inhibition of p38 MAPK results in decreased expression of these cytokines. Tri‐ and tetrasubstituted pyridinylimidazoles are potent inhibitors of p38 MAPK. Substitution on the pyridinyl moiety allows the design of inhibitors that show increased selectivity and activity by targeting the enzyme's hydrophobic region II. The objective of this study was to synthesize novel 1,2,4,5‐tetrasubstituted imidazole derivates and to characterize them not only for their ability to inhibit p38 MAPK and modulate cytokine release in human whole blood, but also to evaluate their metabolic stability. Biological data and metabolic studies demonstrate that the introduction of a 2‐acylamino function at C2 of the pyridine results in highly efficient and metabolically stable inhibitors relative to C2‐alkylamino derivatives. A series of novel candidates was investigated for metabolic stability in human liver microsomes and in human whole blood. Additionally, metabolic S‐oxidation was investigated, and possible metabolites were synthesized.
Unexpected Conformational Properties of 1‐Trifluormethyl‐1‐Silacyclohexane, C5H10SiHCF3: Gas Electron Diffraction, Low Temperature NMR, and Quantum Chemical Calculations
2009-09-03

In their Full Paper published in 2007, Arnason and Oberhammer et al. studied the conformational behaviour of 1-trifluormethyl-1-silacyclohexane, in both the gas and the solvent phase. During the analysis of the low-temperature dynamic NMR spectroscopy measurements, the authors erroneously assumed that the resonance signal of the substituent in the axial position was, as is usual, at a lower chemical shift than for the equatorial conformer. B3LYP/6-311+G(d,p) GIAO calculations, however, reproduced the chemical shift difference exactly, but predicted the axial conformer at a higher chemical shift, contrary to the reported data. Consequently, the NMR-determined A value in Table 4 should be −0.4 kcal mol–1, rather than +0.4 kcal mol–1, and the solvent phase calculations need to be re-interpreted. The correct ratio of the equatorial NMR signal of 17 % instead of 83 % in Figure 6 shows that the solvent effects are negligible, and the shift in the fractional abundances as a function of temperature is best described by the gas phase entropic effects. The IPCM calculated solvent effects are, therefore, artefacts. This conclusion is further supported by recent Raman experiments on the title compound, which confirm the unexpected ab initio assignment of the NMR chemical shifts (unpublished results).
Superadiabatic transitions in quantum molecular dynamics
2009-09-04

We study the dynamics of a molecule’s nuclear wave function near an avoided crossing of two electronic energy levels for one nuclear degree of freedom. We derive the general form of the Schrödinger equation in the n th superadiabatic representation for all . Using these results, we obtain closed formulas for the time development of the component of the wave function in an initially unoccupied energy subspace when a wave packet travels through the transition region. In the optimal superadiabatic representation, which we define, this component builds up monotonically. Finally, we give an explicit formula for the transition wave function away from the avoided crossing, which is in excellent agreement with high-precision numerical calculations.
Enhancement of Tumour-Specific Immune Responses In Vivo by ‘MHC Loading-Enhancer’ (MLE)
2009-09-04

MLE can specifically increase the potency of a vaccine by facilitating the efficient transfer of the antigen onto the MHC molecule. They may therefore open a new way to improve vaccination efficacy and tumour-immunotherapy.
Resources for speech research: present and future infrastructure needs
2009-09-06

This paper introduces the EU-FP7 project CLARIN, a joint effort of over 150 institutions in Europe, aimed at the creation of a sustainable language resources and technology infrastructure for the humanities and social sciences research community.The paper briefly introduces the vision behind the project and how it relates to speech research with a focus on the contributions that CLARIN can and will make to research in spoken language processing.
Thousands of voices for HMM-based speech synthesis
2009-09-06

Our recent experiments with HMM-based speech synthesis systems have demonstrated that speaker-adaptive HMM-based speech synthesis (which uses an 'average voice model' plus model adaptation) is robust to non-ideal speech data that are recorded under various conditions and with varying microphones, that are not perfectly clean, and/or that lack of phonetic balance.This enables us consider building high-quality voices on 'non-TTS' corpora such as ASR corpora.Since ASR corpora generally include a large number of speakers, this leads to the possibility of producing an enormous number of voices automatically.In this paper we show thousands of voices for HMM-based speech synthesis that we have made from several popular ASR corpora such as the Wall Street Journal databases (WSJ0/WSJ1/WSJCAM0), Resource Management, Globalphone and Speecon.We report some perceptual evaluation results and outline the outstanding issues.