gebhart/patrepeval huggingface dataset:
Numerical analysis of the linear and nonlinear vortex-sound interaction in a T-junction (2020)

T-junctions correspond to a classical academic configuration employed to unravel the vortex-sound interaction leading to self-sustained oscillations. It is composed of a closed deep cavity exposed to a low-Mach grazing flow, in which an unstable shear layer can develop. Many studies usually consider this hydrodynamic instability either as a “flapping shear layer", or as a “discrete vortex shedding", which then couples with the acoustic field. This paper follows the idea that these two descriptions are related to the linear and non-linear regimes of the shear layer response to acoustic waves, and thus intends to further analyze these regimes and their transition. To do so, a typical T-junction turbulent flow is computed by forced Large Eddy Simulation (LES) where acoustic waves are injected at several amplitudes. The flow response is extracted, and exhibits a linear regime as well as two distinct non-linear regimes where a partial saturation of the response occurs. The post-processing of the flow field in the three situations reveals that a flapping mechanism exists at low wave amplitudes, whereas a vortex shedding appears for highest acoustic levels. For moderate wave amplitudes, the behavior of the shear layer lies between these two classical views. This suggests that during self-sustained oscillations, a transition between these scenarios occurs, starting from a flapping motion followed by a vortex shedding.
The Celtic World (2012)

The Celtic World is a detailed and comprehensive study of the Celts from the first evidence of them in the archaeological and historical record to the early post-Roman period. The strength of this volume lies in its breadth - it looks at archaeology, language, literature, towns, warfare, rural life, art, religion and myth, trade and industry, political organisations, society and technology. The Celtic World draws together material from all over pagan Celtic Europe and includes contributions from British, European and American scholars. Much of the material is new research which is previously unpublished. The book addresses some important issues - Who were the ancient Celts? Can we speak of them as the first Europeans? In what form does the Celtic identity exist today and how does this relate to the ancient Celts? For anyone interested in the Celts, and for students and academics alike, The Celtic World will be a valuable resource and a fascinating read.
Neoadjuvante Therapie des Rektumkarzinoms: Response Evaluation mit Multislice-CT, 1, 5T-MRT, oder FDG-PET? (2004)

Ziele: Die Einschätzung des Ansprechens von Rektumkarzinomen auf neoadjuvante Therapie ist für die Therapieoptimierung und prognostische Aussagen entscheidend. Ziel der Studie war es, die FDG-PET als funktionelles Verfahren im Vergleich zur CT und MRT bei der Response-Evaluation zu bewerten. Methode: 23 konsekutive Patienten mit histopathologisch gesichertem, primärem Rektumkarzinom im Stadium T3/4 unterzogen sich einer präoperativen Radiochemotherapie mit kombinierter regionaler Hyperthermie. Vor Beginn und 2–4 Wochen nach Beendigung der Therapie wurde jeweils eine kontrastmittelgestützte (i.v. und intrarektal) 1,5T-MRT (n=7) in Phased-Array-Technik, eine kontrastmittelgestützte MS (4)-CT (n=21) und eine 18F-FDG-PET (n=23) durchgeführt. Die histopathologische Evaluation nach Tumorresektion diente als Goldstandard. T-Stadium und Tumorgröße im Verlauf stellten die Response-Parameter in CT und MRT. In der FDG-PET sollte eine Änderung des Glukose-Uptakes (SUV) nach neoadjuvanter Therapie das Ansprechen repräsentieren (EORTC-Kriterien). Ergebnis: Ein Therapieansprechen wurde in 13 Fällen festgestellt. Als Non-Responder wurden 10 Fälle eingestuft. Die mittlere SUV-Reduktion von Respondern (60±14%) und Non-Respondern (31±10%) unterschied sich signifikant (p=0,03; KI=95%). Mit einem Schwellenwert von 36% für die SUV-Reduktion gelang die Identifikation einer Response mittels FDG-PET mit einer Sensitivität von 100% (CT 45%/MRT 80%), einer Spezifität von 60% (CT 56%/MRT 50%), sowie positivem und negativem prädiktiven Wert von 76% (CT 56%/MRT 80%) und 100% (CT 45%/MRT 50%) (PET: p=0,002, KI=95%; MRT und CT: nicht signifikant). In CT und MRT zeigte sich eine Tendenz zum Overstaging nach neoadjuvanter Therapie. Schlussfolgerung: Diese ersten Ergebnisse zeigen, dass die FDG-PET den morphologisch orientierten Verfahren, auch unter Anwendung moderner Akquisitionstechniken, bei der Response-Beurteilung nach neoadjuvanter Therapie fortgeschrittener Rektumkarzinome überlegen ist.
Lightweight reranking for language model generations (2023)

Large Language Models (LLMs) can exhibit considerable variation in the quality of their sampled outputs. Reranking and selecting the best generation from the sampled set is a popular way of obtaining strong gains in generation quality. In this paper, we present a novel approach for reranking LLM generations. Unlike other techniques that might involve additional inferences or training a specialized reranker, our approach relies on easy to compute pairwise statistics between the generations that have minimal compute overhead. We show that our approach can be formalized as an extension of self-consistency and analyze its performance in that framework, theoretically as well as via simulations. We show strong improvements for selecting the best k generations for code generation tasks as well as robust improvements for the best generation for the tasks of autoformalization, summarization, and translation. While our approach only assumes black-box access to LLMs, we show that additional access to token probabilities can improve performance even further.
P4‐220: The Measurement of Hippocampal Atrophy Rates With MRI for A 3‐Year Study Appears to Be at Least 3 Times More Sensitive Than A 1‐Year Study Based on Back‐To‐Back Reproducibility (2016)

Hippocampal atrophy rate measurements from MRI scans are often used as a biomarker of Alzheimer's disease including in clinical trials. This study rigorously assessed how much the signal to noise of hippocampal atrophy rates is improved by comparing the measurements over intervals of 1 and 3 years. While rarely mentioned in the literature, as part of the first Alzheimer's Disease Neuroimaging Initiative (ADNI1), two 3D T1 weighted MPRAGEs were acquired back-to-back (BTB) during each subject visit - with the acquisition of the second MPRAGE usually starting within seconds of completion of the first - providing an excellent data set for reproducibility and noise measurements. To measure the noise of the atrophy rate, the reproducibilities of 5 fully automated methods - FSL/FIRST 5.0.4, FreeSurfer 5.3.0 cross sectional, FreeSurfer 5.3.0 longitudinal, Multiple-Atlas Propagation and Segmentation algorithm (MAPS) independently and MAPS combined with the boundary shift integral (MAPS-HBSI) - were calculated. A total of 264 patients in the ADNI1 study with BTB 1.5T MPRAGE MRIs at baseline, year 1 and year 3 were used. The BTB reproducibility hippocampus over 1 year and 3 years were compared with a simple statistical test based on the binomial sign test that handled outlying data points robustly. The noise in the atrophy rate, as measured by the reproducibility in units of percentage points, showed no statistical difference between 1 and 3 years in 4 of the 5 methods. FSL/FIRST was slightly noisier in both left and right hippocampi over 1 year than 3 years (p=0.002 & p=0.002). For example, the noise for the left hippocampus of FreeSurfer longitudinal was 2.0% over 1 year and 2.2% over 3 years while the corresponding median atrophy rates were 1.9% and 5.2%. The noise of measuring hippocampal atrophy rates over 3 years was no worse than over 1 year. Therefore, if the atrophy rate was stable over the 3 years, the 3 year study would be at least 3 times as sensitive as the 1 year study to changes in atrophy rate.
Introduction to Functional Foods and Nutraceuticals (2018)

Functional foods and nutraceuticals play a major role in combating and mitigating various lifestyle-related illnesses and disorders. These foods contain dietary ingredients that help maintain a healthy lifestyle and may even cure certain diseases. A food can be described as functional if it has a significant health effect that extends beyond basic traditional nutrition. Nutraceutical products are derived from foods that contain essential components which, like functional foods, have therapeutic effects. Their beneficial components may be isolated and purified from plant, animal, or marine sources. They are readily available and have good stability. This chapter focuses on the basic concepts of functional foods and nutraceuticals and examines some of their sources, including fruits, vegetables, cereals, and legumes. Functional foods and nutraceuticals have attracted worldwide attention and they constitute an expanding global market.
Synthesis and characterization of a new family of unsaturated triangular rhenium cluster anions of formula [Re3(µ-H)4(CO)9L]–(L = neutral two-electron donor ligand). X-Ray crystal and molecular structures of the tetraethylammonium salts of the anions with L = triphenylphosphine and pyridine (1986)

The unsaturated triangular cluster anion [Re3(µ-H)4(CO)10]– can undergo selective substitution of one of the axial carbonyl ligands of the Re(CO)4 vertex by neutral two-electron donor ligands L, giving unsaturated [Re3(µ-H)4(CO)9L]– derivatives. The anions with L = NCMe, PPh3, and pyridine (py) have been synthesized either by thermal activation or, more effectively, by carbonyl elimination using Me3NO·2H2O. X-Ray single-crystal analyses of the PPh3 and py derivatives, as [NEt4]+ salts, have been performed. Both species crystallize in the monoclinic system, space group P21/n, with a= 11.448(2), b= 25.311(6), c= 13.596(3)Å, β= 94.00(2)°, and Z= 4 for the PPh3 derivative, and a= 11.087(1), b= 15.951(2), c= 17.598(4)Å, β= 104.84(2)°, and Z= 4 for the py derivative. The geometries of the two anions are similar to that of the parent anion, with the PPh3 or the py ligand co-ordinated in an axial position with respect to the Re3 triangle, which presents a short Re–Re bond (close to 2.80 Å) doubly bridged by hydrides. The McCN derivative is the most reactive member of this new family, containing two active centres: the labile nitrile and the unsaturated moiety. Its reaction with methanol, leading to the anion [Re3(µ-H)3(CO)9(µ3-OMe)]–, exemplifies the possibility of new reaction paths involving both the active sites of this molecule.
Control of an electrowetting-based beam deflector (2010)

We experimentally demonstrate the feasibility of a small, low-power beam deflector based on electrowetting. The beam deflector deflects light by refraction at the flat interface (meniscus) between two immiscible and density-matched liquids, namely, a nonpolar oil mixture and an aqueous salt solution. The liquids are contained in a square pyramidal frustum with electrode-covered faces. The electrodes can be separately driven by voltage sources in order to control the contact angle between the meniscus and the frustum faces. By controlling the voltage on all four electrodes, a flat meniscus is obtained that can be tilted independently in two perpendicular directions. We present a capacitance-based feedback driving scheme and demonstrate that it can be used for accurate control of the meniscus shape and tilt. Independent, continuous, and accurate beam steering through an angle of ±6° was achieved on two deflection axes.
327: Updated Recurrence-Free Survival (RFS) Prediction Model Following Radical Prostatectomy (RRP) (2007)

You have accessJournal of UrologyPodium 11, Sunday, May 20, 2007 10:00 am - 12:00 pm1 Apr 2007327: Updated Recurrence-Free Survival (RFS) Prediction Model Following Radical Prostatectomy (RRP) Misop Han, Patrick C. Walsh, William J. Catalona, Marianna Zahurak, Steven Piantadosi, Kimberly A. Roehl, and Alan W. Partin Misop HanMisop Han More articles by this author , Patrick C. WalshPatrick C. Walsh More articles by this author , William J. CatalonaWilliam J. Catalona More articles by this author , Marianna ZahurakMarianna Zahurak More articles by this author , Steven PiantadosiSteven Piantadosi More articles by this author , Kimberly A. RoehlKimberly A. Roehl More articles by this author , and Alan W. PartinAlan W. Partin More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)30592-5AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "327: Updated Recurrence-Free Survival (RFS) Prediction Model Following Radical Prostatectomy (RRP)." The Journal of Urology, 177(4S), pp. 110–111 © 2016 by American Urological AssociationFiguresReferencesRelatedDetailsCited byEastham J, Scardino P and Kattan M (2008) Predicting an Optimal Outcome After Radical Prostatectomy: The Trifecta NomogramJournal of Urology, VOL. 179, NO. 6, (2207-2211), Online publication date: 1-Jun-2008. Volume 177Issue 4SApril 2007Page: 110-111 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Misop Han More articles by this author Patrick C. Walsh More articles by this author William J. Catalona More articles by this author Marianna Zahurak More articles by this author Steven Piantadosi More articles by this author Kimberly A. Roehl More articles by this author Alan W. Partin More articles by this author Expand All Advertisement PDF downloadLoading ...
Protein Kinase C Modulation of Insulin Receptor Substrate-1 Tyrosine Phosphorylation Requires Serine 612 (1997)

Activation of the endogenous protein kinase Cs in human kidney fibroblast (293) cells was found in the present study to inhibit the subsequent ability of insulin to stimulate the tyrosine phosphorylation of an expressed insulin receptor substrate-1. This inhibition was also observed in an in vitro phosphorylation reaction if the insulin receptor and its substrate were both isolated from cells in which the protein kinase C had been activated. To test whether serine phosphorylation of the insulin receptor substrate-1 was contributing to this process, serine 612 of this molecule was changed to an alanine. The insulin-stimulated tyrosine phosphorylation and the associated phosphatidylinositol 3-kinase activity of the expressed mutant were found to be comparable to those of the expressed wild-type substrate. However, unlike the wild-type protein, activation of protein kinase C did not inhibit the insulin-stimulated tyrosine phosphorylation of the S612A mutant nor its subsequent association with phosphatidylinositol 3-kinase. Tryptic peptide mapping of in vivo labeled IRS-1 and the S612A mutant revealed that PMA stimulates the phosphorylation of a peptide from wild-type IRS-1 that is absent from the tryptic peptide maps of the S612A mutant. Moreover, a synthetic peptide containing this phosphoserine and its nearby tyrosine was found to be phosphorylated by the insulin receptor to a much lower extent than the same peptide without the phosphoserine. Activation of protein kinase C was found to stimulate by 10-fold the ability of a cytosolic kinase to phosphorylate this synthetic peptide as well as the intact insulin receptor substrate-1. Finally, cytosolic extracts from the livers of ob/ob mice showed an 8-fold increase in a kinase activity capable of phosphorylating this synthetic peptide, compared to extracts of livers from lean litter mates. These results indicate that activation of protein kinase C stimulates a kinase which can phosphorylate insulin receptor substrate-1 at serine 612, resulting in an inhibition of insulin signaling in the cell, posing a potential mechanism for insulin resistance in some models of obesity.
Novel PKCα-mediated phosphorylation site(s) on cofilin and their potential role in terminating histamine release (2012)

Using specific inhibitors, kinase-negative mutants, and small interfering RNA against protein kinase Cα (PKCα) or PKCβI, we find that PKCβI positively regulates degranulation in rat basophilic leukemia-2H3 cells, whereas PKCα negatively regulates degranulation. Mass spectrometric and mutagenic analyses reveal that PKCα phosphorylates cofilin at Ser-23 and/or Ser-24 during degranulation. Overexpression of a nonphosphorylatable form (S23,24A), but not that of a mutant-mimicking phosphorylated form (S23,24E), increases degranulation. Furthermore, the S23,24A mutant binds to F-actin and retains its depolymerizing and/or cleavage activity; conversely, the S23,24E mutant is unable to sever actin filaments, resulting in F-actin polymerization. In addition, the S23,24E mutant preferentially binds to the 14-3-3ζ protein. Fluorescence-activated cell sorting analysis with fluorescein isothiocyanate-phalloidin and simultaneous observation of degranulation, PKC translocation, and actin polymerization reveals that during degranulation, actin polymerization is dependent on PKCα activity. These results indicate that a novel PKCα-mediated phosphorylation event regulates cofilin by inhibiting its ability to depolymerize F-actin and bind to 14-3-3ζ, thereby promoting F-actin polymerization, which is necessary for cessation of degranulation.
A Bio–inspired Quadruped Robot Exploiting Flexible Shoulder for Stable and Efficient Walking (2020)

While most modern-day quadruped robots crouch their limbs during the stance phase to stabilize the trunk, mammals exploit the inverted-pendulum motions of their limbs and realize both efficient and stable walking. Although the flexibility of the shoulder region of mammals is expected to contribute to reconciling the discrepancy between the forelimbs and hindlimbs for natural walking, the complex body structure makes it difficult to understand the functionality of animal morphology. In this study, we developed a simple robot model that mimics the flexibility of shoulder region in the sagittal plane, and we conducted a two-dimensional simulation. The results suggest that the flexibility of the shoulder contributes to absorbing the different motions between the forelimbs and hindlimbs.
Heterogeneous PSMA expression on circulating tumor cells - a potential basis for stratification and monitoring of PSMA-directed therapies in prostate cancer (2016)

The prostate specific membrane antigen (PSMA) is the only clinically validated marker for therapeutic decisions in prostate cancer (PC). Characterization of circulating tumor cells (CTCs) obtained from the peripheral blood of PC patients might provide an alternative to tissue biopsies called "liquid biopsy". The aim of this study was to develop a reliable assay for the determination of PSMA on CTCs. PSMA expression was analyzed on tissue samples (cohort one, n = 75) and CTCs from metastatic PC patients (cohort two, n = 29). Specific signals for the expression of PSMA could be seen for different prostate cancer cell line cells (PC3, LaPC4, 22Rv1, and LNCaP) by Western blot, immunohistochemistry (IHC), immunocytochemistry (ICC), and FACS. PSMA expression was found to be significantly increased in patients with higher Gleason grade (p = 0.0011) and metastases in lymph nodes (p = 0.0000085) or bone (p = 0.0020) (cohort one). In cohort two, CTCs were detectable in 20 out of 29 samples (69 %, range from 1 - 1000 cells). Twelve out of 20 CTC-positive patients showed PSMA-positive CTCs (67 %, score 1+ to 3+). We found intra-patient heterogeneity regarding the PSMA status between CTCs and the corresponding primary tumors. The results of our study could help to address the question whether treatment decisions based on CTC PSMA profiling will lead to a measurable benefit in clinical outcome for prostate cancer patients in the near future.
SP1.1.7PBX4 functions as a novel oncogene and promotes angiogenesis in colorectal cancer: A comprehensive analysis of the PBX gene family (2021)

Abstract Aims Pre-B-cell Leukaemia (PBX) genes are important in organ development during embryogenesis. To date, four members of the PBX family (PBX1, PBX2, PBX3, PBX4) have been identified to be involved in human cancers, but little is known about their role in colorectal cancer (CRC). The aim of this study was to determine their differential expression, prognostic role and function in CRC. Methods Molecular and overall survival (OS) data from 614 patients with CRC were obtained from the National Cancer Institute, Tissue Cancer Genome Atlas (TCGA) database. To investigate the differential PBX gene mRNA expression, we performed a comparative cancer to normal computational analysis in edgeR. To determine PBXs prognostic value, we conducted Kaplan-Meier survival analysis and COX regression, selecting 10-year OS as primary outcome. Lastly, to explore the effect of PBX4 in CRC cell growth and angiogenesis, we performed gene expression modulation experiments using a PBX4-overexpressing plasmid-vector. Cell proliferation and VEGFA angiogenic factor expression were defined as primary and secondary in vitro outcomes respectively. Results Among PBXs only PBX4 was significantly upregulated showing a 4-fold increase in CRC vs normal colon (p &amp;lt; 0.0001). Survival analysis showed that only high PBX4 mRNA expression was associated with increased risk for worse OS in patients with CRC (HR:1.3 95%CI:1-1.6, p = 0.02). Functionally, overexpression of PBX4 significantly increased CRC cell proliferation in vitro (p &amp;lt; 0.001) and markedly upregulated the expression of VEGFA (p &amp;lt; 0.0001). Conclusions Comprehensive analysis of the PBX gene family identifies that PBX4 may function as a novel oncogene and may promote angiogenesis through VEGFA in CRC.
Figure S2 from A Potent Blood–Brain Barrier-Permeable Mutant IDH1 Inhibitor Suppresses the Growth of Glioblastoma with IDH1 Mutation in a Patient-Derived Orthotopic Xenograft Model (2023)

&lt;p&gt;DS-1001b demonstrates anti-neoplastic activity in IDH1 mutant glioblastoma xenografts.&lt;/p&gt;
Molecular description of a 3D in vitro model for the study of epithelial ovarian cancer (EOC) (2007)

Epithelial ovarian cancer (EOC) cell lines are useful tools for the molecular and biological characterization of ovarian cancer. The use of an in vitro multidimensional (3-D) culture model recapitulates some of the growth conditions encountered by tumor cells in vivo. Here we describe a molecular comparison of spheroid based 3D EOC models versus monolayer cultures and xenografts using cell lines from malignant ovarian tumors (TOV-21G and TOV-112D) and ascites (OV-90) previously established and characterized in our laboratory. Gene expression analyses of the three models were performed using the Affymetrix HG-U133A high density DNA array. Cluster analysis identified a set of genes that stratified expression profiles from the EOC cell lines grown as spheroids and xenografts from that of monolayer cultures. The gene expression analysis results were validated by Q-PCR analyses on an independent set of RNAs. Differential expression observed for the S100A6 gene between the monolayer, spheroid cultures and xenografts was confirmed at the protein level by immunohistochemistry. The analysis was extended to various ovarian tumor tissues using an EOC tissue array. This result represents an example of a gene that, if studied in vitro, is more representative of the in vivo disease in a 3D model rather than the monolayer culture. Identification of genes in spheroid models that mimic the in vivo tumor gene expression patterns may allow a better understanding of the community effect observed in human disease that is determined by direct or indirect interactions of cells with their environment or other surrounding cells.