gebhart/patrepeval huggingface dataset:
Value of PSA measured in middle age in predicting diagnosis of advanced prostate cancer in an unscreened population (2007)

5006 Background: The association between PSA-levels in blood and prostate cancer (PCa) is currently under intense debate as many benign conditions also affect blood levels. We recently reported that PSA-levels in blood predicted very strongly later PC-diagnosis at any stage in a large representative population-based cohort in Malmö, Sweden (MPM) where the rate of PSA-testing is very low. Now, we studied predictors of stages =T3 or metastatic (M+) PCa at the time of cancer diagnosis. Material: Among archived bloods from 22,439 men (aged =50 or 60) during 1974–86, 192/549 men diagnosed with PCa until Dec 31, 1999, were eligible cases with =T3 or M+ at time of diagnosis. Median delay from baseline to diagnosis was 17 years among cases aged =50 (n=161) and 10 years among men aged 60 (n=31). Conditional logistic regression between cases and controls nested within our study cohort determined association and interaction between analyte levels, time to diagnosis, and age. Results: There was strong evidence that plasma levels of all PSA-forms and kallikrein 2 (hK2) associate with case status (p&lt;0.01), and even a small elevation in total PSA (tPSA) markedly increased the risk of subsequent event. A tPSA of 2.1 - 3.0 ng/ml raised the odds of subsequent event 22-fold compared to a tPSA =0.5 ng/ml and men with tPSA =2 ng/ml had a predicted probability of advanced prostate cancer of 12% - three times the population mean. AUC for a model with tPSA alone, compared to tPSA+cPSA+%fPSA+hK2 were higher in men aged 60 (AUC increase of 0.054) compared to men aged =50 (AUC increase of 0.030). This is consistent with the results of interaction analysis showing that the association between hK2-level and cases status grows stronger as the interval between date of venipuncture and diagnosis decreases. Similarly, the effect of %fPSA on case status was dependent on age suggesting that the association between %fPSA and case status is stronger in older compared to younger men. Conclusion: Very strong associations exist between levels of all PSA-forms and hK2 measured at middle age and decade(s) before diagnosis of advanced stages of prostate cancer. There is an urgent need to validate these data in independent study cohorts as they could contribute important arguments in the revision of current PC- screening guidelines. No significant financial relationships to disclose.
Oscillations in Coupled Systems: Response to a Noise-Contaminated Signal (2007)

Recently, we have shown the emergence of oscillations in overdamped undriven nonlinear dynamic systems subject to carefully crafted coupling schemes and operating conditions. Here, we outline the existing theoretical results obtained on a system of N = 3 unidirectionally nonlinear elements; the oscillatory behavior is triggered when the coupling constant exceeds a threshold value (bifurcation point), and the oscillation frequency exhibits a characteristic scaling behavior with the “separation” of the coupling constant from its threshold value, as well as with an external target dc signal. We then introduce a different (asymmetric) coupling topology and demonstrate that it leads to an enhancement of the system response (quantified by a SNR) to an external target signal that is noise‐contaminated.
A genome-wide association study identifies two novel susceptibility loci and trans population polygenicity associated with bipolar disorder (2017)

Genome-wide association studies (GWASs) have identified several susceptibility loci for bipolar disorder (BD) and shown that the genetic architecture of BD can be explained by polygenicity, with numerous variants contributing to BD. In the present GWAS (Phase I/II), which included 2964 BD and 61 887 control subjects from the Japanese population, we detected a novel susceptibility locus at 11q12.2 (rs28456, P=6.4 × 10<sup>-9</sup>), a region known to contain regulatory genes for plasma lipid levels (FADS1/2/3). A subsequent meta-analysis of Phase I/II and the Psychiatric GWAS Consortium for BD (PGC-BD) identified another novel BD gene, NFIX (P<sub>best</sub>=5.8 × 10<sup>-10</sup>), and supported three regions previously implicated in BD susceptibility: MAD1L1 (P<sub>best</sub>=1.9 × 10<sup>-9</sup>), TRANK1 (P<sub>best</sub>=2.1 × 10<sup>-9</sup>) and ODZ4 (P<sub>best</sub>=3.3 × 10<sup>-9</sup>). Polygenicity of BD within Japanese and trans-European-Japanese populations was assessed with risk profile score analysis. We detected higher scores in BD cases both within (Phase I/II) and across populations (Phase I/II and PGC-BD). These were defined by (1) Phase II as discovery and Phase I as target, or vice versa (for 'within Japanese comparisons', P<sub>best</sub>~10<sup>-29</sup>, R<sup>2</sup>~2%), and (2) European PGC-BD as discovery and Japanese BD (Phase I/II) as target (for 'trans-European-Japanese comparison,' P<sub>best</sub>~10<sup>-13</sup>, R<sup>2</sup>~0.27%). This 'trans population' effect was supported by estimation of the genetic correlation using the effect size based on each population (liability estimates~0.7). These results indicate that (1) two novel and three previously implicated loci are significantly associated with BD and that (2) BD 'risk' effect are shared between Japanese and European populations.
Leukocyte trafficking: Can we bring the fight to the tumor? (2016)

Control of leukocyte trafficking plays a critical role in the establishment of effective immune responses. It is now well established that the number or ratio of effector to suppressor immune cells within the tumor microenvironment can significantly impact tumor growth and clinical outcomes. Recently approved immunotherapies by the FDA, and those in development, aim to stimulate effector immune cell function. For example, many checkpoint inhibitors seek to stimulate an immune response to tumors by reversing T-cell exhaustion. However, activation of the immune response outside the tumor microenvironment can lead to sometimes fatal immune-mediated adverse events -- the result of "on-target, off-tumor" effects. Thus, control of localization of these activated effector cells remains a critical component of optimizing tumor response while minimizing immune-mediated adverse events. Chemokines and chemoattractants, along with their receptors on immune cells, govern leukocyte trafficking; thus, understanding their expression pattern in the context of the tumor microenvironment and developing approaches to favorably alter those should lead to improved efficacy of current immunotherapeutics. This review highlights the background of cancer immunotherapy, leukocyte trafficking, and some novel approaches being utilized to optimize recruitment of effector immune cells into the tumor microenvironment. Future combinatorial immunotherapy should incorporate therapeutics aimed at 1) favorably altering the tumor microenvironment, 2) activating effector immune cells, and 3) optimizing effector cell trafficking into tumors.
X‐ray Stain Localization with Near‐Field Ptychographic Computed Tomography (2022)

Although X-ray contrast agents offer specific characteristics in terms of targeting and attenuation, their accumulation in the tissue on a cellular level is usually not known and difficult to access, as it requires high resolution and sensitivity. Here, quantitative near-field ptychographic X-ray computed tomography is demonstrated to assess the location of X-ray stains at a resolution sufficient to identify intracellular structures by means of a basis material decomposition. On the example of two different X-ray stains, the nonspecific iodine potassium iodide, and eosin Y, which mostly interacts with proteins and peptides in the cell cytoplasm, the distribution of the stains within the cells in murine kidney samples is assessed and compared to unstained samples with similar structural features. Quantitative nanoscopic stain concentrations are in good agreement with dual-energy micro computed tomography measurements, the state-of-the-art modality for material-selective imaging. The presented approach can be applied to a variety of X-ray stains advancing the development of X-ray contrast agents.
Grafting of Maleic Anhydride onto Isotactic Polypropylene in the Presence of Supercritical Carbon Dioxide as a Solvent and Swelling Fluid (2004)

Grafting of maleic anhydride (MA) onto isotactic polypropylene (iPP) was carried out by thermal decomposition of dicumylperoxide (DCP) using supercritical carbon dioxide (scCO2) as a solvent and swelling fluid. Provided that the initial concentration of anhydride dissolved in scCO2 is higher than 1% w/w, the grafting occurs without significant molecular weight modification of the polymer, and with a proper selection of the operative conditions, a grafting level higher than 0.5% w/w with respect to the polymer mass was obtained. The amount of grafted MA was determined by FT-IR spectroscopy and polymer degradation was monitored by dynamic mechanical tests in the melt state. The effect of MA and DCP concentration, of the scCO2 density, and of the reaction time on the grafting yield and on the melt flow behavior was studied. Maleic anhydride homopolymerization during the grafting is suggested by FTIR spectra. The home-synthesized maleated iPP was used as effective compatibilizing agent in the preparation of iPP/Nylon-6 blends.
A04 The role of splicing factor SRSF6 in incomplete splicing of the HTT transcript (2018)

<h3>Background</h3> Huntington’s disease (HD) is caused by an expanded CAG repeat in exon 1 of the HTT gene. In models of HD, an expanded CAG repeat in HTT causes premature termination of HTT RNA during transcription; this occurs by a process called incomplete splicing. Incompletely spliced HTT (HTTexon1) includes exon 1 of the coding region of HTT, as well as a 5’ region of intron 1, which is non-coding. HTTexon1 encodes a truncated exon 1 HTT protein, which is implicated in HD pathogenesis. Although the precise RNA processing mechanism of Httexon1 is unknown, splicing factor SRSF6 has been shown to co-precipitate with transcripts containing Htt intron 1 in HD mice. <h3>Aim</h3> To elucidate the role of splicing factor SRSF6 in incomplete splicing of Htt in HD mice. <h3>Methods</h3> Heterozygous Srsf6 knock-out (KO) mice (Srsf6±) were generated by CRISPR/Cas9. Characterisation of Srsf6± mice was undertaken by quantitative RT-PCR and western blotting. Viability of homozygous Srsf6 KO (Srsf6-/-) mice was examined by inbreeding of Srsf6± mice. To assess the modulation of incomplete splicing by decreasing SRSF6, Srsf6± mice were bred to HD knock in mice (zQ175) and tissues were analysed. Levels of Httexon1 were measured by Quantigene, a gene expression assay. <h3>Results</h3> Srsf6-/- homozygotes were embryonic lethal, limiting us to the use of Srsf6± mice only. In Srsf6± heterozygotes, Srsf6 mRNA was decreased by 50% in brain and peripheral regions, and SRSF6 protein was decreased by 70% in brain compared to wild type mice. However, heterozygosity for Srsf6 knock out did not modulate the level on incomplete splicing in zQ175 mice. <h3>Conclusion</h3> Ablation of a single Srsf6 allele did not reduce levels of incomplete splicing in HD mice and therefore, further Srsf6 knock down may be required. Accordingly, mouse embryonic fibroblasts (MEFs) have been generated and will be used to measure Httexon1 levels after further Srsf6 knockdown by RNA interference. This work is supported by the CHDI foundation.
Optimum filtering for optically preamplified direct detection: the influence of photon-count statistics (2005)

The quantum limited bit error rate for optical communications systems is calculated in case of intensity modulation and optically preamplified direct-detection. The impact of optical and electrical filtering onto the effective photon-count statistics is accounted for, in correspondence to different combinations of optical and electrical filters. The optimum values of the optical and electrical bandwidths, which minimize the receiver sensitivity, are calculated and compared with the values obtained by means of the commonly used Gaussian approximation.
Code Optimization and Power Management (2006)

This chapter contains sections titled: Code Optimization C Optimization Techniques Using Assembly Code for Efficient Programming Power Consumption and Management in the Blackfin Processor Sample Rate Conversion with Blackfin Simulator Sample Rate Conversion with BF533/BF537 EZ-KIT Sample Rate Conversion with LabVIEW Embedded Module for Blackfin Processors More Exercise Problems
Qualification of PET cameras and imaging sites for 11C-methionine PET on brain tumor in Japan (2014)

2060 Objectives Although methionine PET (metPET) is useful for brain tumor diagnosis, small lesions detectability, SUV, and L/N ratio depend on the camera model and the scanning conditions. Japanese Society of Nuclear Medicine issued the standard protocol for metPET, and defined the procedures for imaging sites qualification (J-PEQi). Methods Auditors visit a PET center to examine the maintenance and calibration of the camera and peripherals as well as the scan environment. The camera performance is evaluated with a newly designed phantom, which is a 20 cm diameter cylinder containing 6 hot spheres having 5, 7.5, 10, 16, 27, and 38 mm diameters. These are filled with 3 times the activity as the background (2.65 kBq/mL 18F). These values correspond to typical activity of tumor and normal tissues and expected cutoff level for detecting tumors. J-PEQi requests visual recognizability of 7.5 mm sphere, the relative contrast of 13% for 7.5 mm sphere, and the recovery coefficient of 0.45 for 10 mm sphere. The SUV in the background should be 1.00±5% with uniform distribution. Results The procedure was applied to 7 centers (5 camera models and 3 vendors) participating in a clinical research on a new drug for cerebral radiation necrosis. 2 of them fulfilled the criteria, and the others did not. After modifying scanning parameters and tuning the cameras, some of them achieved the criteria. Conclusions J-PEQi is beneficial for universal and reliable metPET by assuring high quality PET data and is useful for multicenter clinical trials. Research Support J-PEQi is supported by Health Labour Science Research Grant, Ministry of Health, Labour and Welfare, Japan, from 2011 to 2014.
Formal verification of an ATM switch fabric using multiway decision graphs (2002)

In this paper we present our results on formally verifying the implementation of an asynchronous transfer mode (ATM) network switching fabric using a new class of decision graphs, called Multiway Decision Graphs (MDG). The design we consider is in use for real applications in the Cambridge Fairisle network. We produced the description of the hardware implementation at different levels of abstraction. We then performed the verification of an abstract description model against the description of the gate-level implementation. Using this abstract model, we accomplished the verification of specific properties that reflect the behavior of the Fairisle ATM switch fabric.
Designing Machine Learning Pipeline Toolkit for AutoML Surrogate Modeling Optimization (2023)

The pipeline optimization problem in machine learning requires simultaneous optimization of pipeline structures and parameter adaptation of their elements.Having an elegant way to express these structures can help lessen the complexity in the management and analysis of their performances together with the different choices of optimization strategies.With these issues in mind, we created the AutoMLPipeline (AMLP) toolkit which facilitates the creation and evaluation of complex machine learning pipeline structures using simple expressions.We use AMLP to find optimal pipeline signatures, datamine them, and use these datamined features to speed-up learning and prediction.We formulated a two-stage pipeline optimization with surrogate modeling in AMLP which outperforms other AutoML approaches with a 4-hour time budget in less than 5 minutes of AMLP computation time.
DESIGNING THE AVERAGE PATELLA - AN ANATOMICAL PATELLA RESURFACING? (2016)

Introduction The trochlea of a typical patellofemoral replacement or anterior flange of a total knee replacement usually extends past the natural trochlea and continues onto the femoral anterior cortex. One reason for this is that it allows a simple patella button to be permanently engaged in the trochlea groove in an attempt to ensure stability. On the natural patella, the apex helps to guide it into the trochlea groove as the knee moves from full extension into flexion. The aim is to study whether a generalised patella can be created that is close in form to a healthy patella. Method MRI scans were taken of 30 patellae. Characteristics of these patellae (height, width, thickness, apex angle) were measured. The apex angle was found to be similar between patellae (mean=126 degrees, sd = 8.8), as were the ratios between height and width (mean width/height = 1.05, sd = 0.07) and between thickness and width (mean width/thickness = 1.8, sd = 0.19). These patellae were then segmented to create a surface including cartilage, resulting in 30 STL (stereolithography) files in which the surfaces are represented by triangle meshes. To design the average patella the individual patellae were aligned to a standard frame of reference by placing a set of landmarks on the proximal/distal, medial/lateral and anterior/posterior extents of each (fig.1). The vertical axis was defined as passing parallel to the proximal/distal points and the horizontal as passing parallel to the medial/lateral points when looking along the computed vertical axis. The origin centre of the frame of reference was chosen to be mid-way between these points. The mean width was then computed and each patella scaled linearly around the origin to give them all equal width. All the aligned patellae were then averaged together to provide a composite cartilaginous patella. The averaging process was achieved by taking one patella as a seed. The patella chosen for seed was that whose parameters were closest to the average width, height and thickness. An approximately normal vector was passed a point ‘P’ on the seeds, and the points at which these intersected the other models were then determined. The closest intersection point to ‘P’ on each model was chosen and these averaged together. ‘P’ is then replaced in the model with this average point. The averaging process then continues with all the remaining points on the seed model in the same manner to build the average models. Results and Discussion The mean patella was compared with individual patellae. This comparison was performed by taking each point on the mean patella and finding the closest point on individual patellae - a colour coded map of differences was obtained (fig.2) along with a mean of the absolute difference for each patella. The absolute mean difference ranged from 0.56mm to 1.33mm, averaging at 0.85mm. This shows a reasonable fit between the average patella and each individual example, raising the possibility of using the average shape in future research to develop anatomical patellofemoral replacements and for planning patella resurfacing.
ChemInform Abstract: Supported Au Nanoparticles as Efficient Catalysts for Aerobic Homocoupling of Phenylboronic Acid. (2012)

Abstract A highly active and easily recyclable catalyst is prepared for the title synthesis.
Highly active and enhanced photocatalytic silicon nanowire arrays (2011)

Nanoporous and nonporous three-dimensional silicon nanowire arrays (SiNWAs) prepared with metal-assisted chemical etching method were investigated as photocatalysts in dye photodegradation systematically. In comparison with nonporous SiNWAs, nanoporous SiNWAs have higher surface area, larger pore volume, stronger light absorption and better photocatalytic activity. After the HF-treatment, the photocatalytic activity of all kinds of SiNWAs increased significantly and the nanoporous SiNWAs showed excellent stability. The photocatalytic activity of different types of SiNWAs with hydrogen surface termination can be recovered by HF treatment. This study also reveal that the hydrogen terminated surfaces on silicon nanowires (SiNWs) enhance the performance of SiNWAs by increasing their photocatalytic activity.
Self-Sensing Active Magnetic Dampers for Vibration Control (2009)

The aim of this paper is to investigate the potential of a self-sensing strategy in the case of an electromagnetic damper for the vibration control of flexible structures and rotors. The study has been performed in the case of a single degree of freedom mechanical oscillator actuated by a couple of electromagnets. The self-sensing system is based on a Luenberger observer. Two sets of parameters have been used: nominal ones (based on simplifications on the actuator model) and identified ones. In the latter case, the parameters of the electromechanical model used in the observer are identified starting from the open-loop system response. The observed states are used to close a state-feedback loop with the objective of increasing the damping of the system. The results show that the damping performance are good in both cases, although much better in the second one. Furthermore, the good correlation between the closed-loop model response and the experimental results validates the modeling, the identification procedure, the control design, and its implementation. The paper concludes on a sensitivity analysis, in which the influence of the model parameters on the closed-loop response is shown.
Targeting the vascular endothelial growth factor pathway in renal cell carcinoma: A tissue array based analysis (2005)

4536 Background: The Vascular Endothelial Growth Factor (VEGF) family includes distinct signaling pathways for angiogenesis and lymphangiogenesis. Understanding the expression of these markers may enhance selection of target specific therapies based on an individual’s unique tumor biology, and optimize the benefit of these agents in renal cell carcinoma (RCC). Methods: A tissue microarray was constructed from paraffin-embedded clear cell (n=340) and papillary (n=42) RCC specimens from patients treated with nephrectomy for localized or advanced disease. Immunohistochemistry was performed with antibodies directed against VEGF-A, VEGF-C, VEGF-D, VEGFR-1, VEGFR-2 and VEGFR-3. The percentage of tumor cells expressing each marker was scored in 3 locations and averaged. Expression of the receptors within tumor associated endothelium was also scored and averaged. The Kruskal-Wallis test was used to compare the expression of each marker between the two tumor histologies. Results: When examining the angiogenesis pathway, papillary RCC demonstrated a higher mean expression of VEGF-A and VEGFR-2 than clear cell RCC, while no difference was seen in the expression of VEGFR-1. Within the lymphangiogenesis pathway, clear cell RCC demonstrated a higher mean expression of VEGF-D, while papillary RCC demonstrated higher mean expression of VEGFR-3 and no difference was seen in the mean expression of VEGF-C. Within tumor associated endothelium, clear cell RCC demonstrated higher mean staining for VEGFR-1, VEGFR-2 and VEGFR-3. Conclusions: This data suggests that patients with papillary RCC should be considered for therapies targeting the VEGF-A pathway. Patients with clear cell RCC may be more likely to benefit from receptor kinase inhibitors targeting VEGFR-3. Knowledge of the expression of the VEGF family, regardless of histology, may guide future patient selection for anti-angiogenesis therapies. No significant financial relationships to disclose.