gebhart/patrepeval huggingface dataset:
Fabrication and performance of transmission engineered molybdenum-rich phase structures in the EUV regime (Conference Presentation) (2017)

For applications in the Extreme Ultraviolet (EUV) region, phase-shift structures play an important role in pushing the throughput and performance of optical systems. While EUV optical elements are typically designed and fabricated for use in reflection, there are important applications in transmission as well where phase shift structures can provide substantial throughput gains. Examples are EUV microscopy and interferometry using gratings or zone plates. In the EUV regime, few materials offer a better combination of phase shift and absorption properties than molybdenum (Mo), however, drawbacks for Mo include crystalline growth complicating the etch process, and ease of oxidation which leads to diminished performance with time. Here we develop a fabrication process for transmission optical elements made of an engineered molybdenum-rich film on free-standing silicon membranes and show the performance of these phase structures in the EUV regime. We chose the fabrication of simple binary gratings of 72nm half pitch (Fig. 1) in order to establish a baseline for performance. We further addressed the oxidation concerns for Mo by developing a process to passivate the surface using atomic layer deposition (ALD) to coat a thin and conformal layer of silicon nitride while incurring minimum throughput loss. The gratings were measured for efficiency in three stages of fabrication at Lawrence Berkeley Laboratory’s Advance Light Source (Beamline 6.3.2) in Berkeley California (Fig. 2). The first measurement was prior to ALD passivation, the second measurement was immediately after passivation, and the third measurement was performed after exposure of the gratings to UV ozone used as an accelerated oxidation test. The conformal coating of silicon nitride was effective in passivating the surface of Mo features. The measurement results show that we were able to achieve a grating efficiency of approximately 18% in the 1st and -1st orders (compared to 8% possible with a conventional absorber grating on Si membrane). The results also demonstrate the effectiveness of the ALD passivation process in mitigating oxidation effects with minimal effect on performance.
Mission Operation Concepts For Robotic Missions (2011)

The German Aerospace Center (DLR) is presently involved in the preparation of the robotic mission DEOS. The objective of DEOS is to demonstrate the capture of a tumbling non-supportive client satellite. This mission has been preceded by several robotic experiments in space, ROTEX on the Shuttle flight STS 55 in 1993, GETEX on ETS VII in 1999 and ROKVISS from 2005 to 2010 on the ISS. Experience regarding the approach navigation was gained by operating the close formation of TanDEM-X (&lt; 200m) and the technology demonstration PRISMA (&lt;1m).&#13;\n&#13;\nIn order to consolidate the experience gained during the past decades, a study of Mission Control Concepts for Robotic Operations (MICCRO) is currently being conducted by VCS and DLR. The study shall reveal the commonalities in the operations of past and current robotic space missions in order to find a representative mission control concept for robotic missions. The existing operational concepts, responsibilities and information flows during the different mission phases are taken into account. A particular emphasis is put on the possible interaction between different autonomous components (on-board and on-ground), their synchronization and the possible shift of autonomy borders during different mission phases. Additionally, communication constraints are investigated including the impact of telepresence on the communication architecture. Finally, we also investigate the consequence on roles and responsibilities, since telepresence introduces a new time scale in decision making.&#13;\n
Influence of glass-based dental ceramic type and thickness with identical shade on the light transmittance and the degree of conversion of resin cement (2018)

The purpose of this study was to assess the influence of the types and thicknesses of glass ceramic plates on light transmittance and compare the degrees of conversion (DC) of resin cement under the ceramic materials. Three ceramic plates with thicknesses of 0.5, 1.0, 2.0, and 4.0 mm were fabricated from each of five commercial ceramic blocks in shade A2: high-translucency and low-translucency IPS Empress CAD (Emp_HT and Emp_LT); high-translucency and low-translucency IPS e.max CAD (Emx_HT and Emx_LT); and Vita Mark II (Vita). The translucency parameter was obtained using a colorimeter. The light transmittance rate was measured using a photodetector attached to an optical power meter. The DC of a resin cement (Variolink N) underneath the ceramic plates was examined by Fourier transform infrared spectroscopy. The translucency parameter, light transmittance rate, and DC showed significant differences by ceramic type and thickness (P < 0.05). The Emp_HT specimens showed the highest light transmission and DCs, and the Emx_LT showed the least light transmission and the lowest DCs. The high-translucency Empress showed significantly higher DCs than the low-translucency types (P < 0.05), but there was no significant difference in e.max (P > 0.05). Both type and thickness of the glass ceramics significantly influenced the light transmittance and DC of the light-cured resin cement beneath the ceramic of the same shade.
TH‐C‐330A‐08: Soft‐Tissue Detectability Limits in Cone‐Beam CT: 2AFC Tests of Human Observer Performance in Relation to Contrast, Spatial Resolution, and the 3D Noise‐Power Spectrum (2006)

Purpose: To quantify the contrast‐detail detectability limits of soft‐tissue structures in cone‐beam CT (CBCT) and to investigate the influence of the plane of visualization (axial/sagittal) and level of prior knowledge on observer performance. Method and Materials: Custom‐built cylindrical phantoms containing spherical lesions of varying size and contrast were imaged on a CBCT bench across a broad range of dose. Two‐alternative forced choice (2AFC) tests were conducted under controlled conditions using 7 observers (physicists and radiation therapists). For each 2AFC test, the proportion of correct responses, Pcorr, was analyzed as a function of lesion size (1.6 – 12.7mm) and contrast (20 – 165HU), dose (2.1 – 6.4mGy), plane of visualization (axial/sagittal), apodization filter (smooth Hanning to sharp Ram‐Lak), and degree of prior knowledge provided to the observer (ranging from Signal‐Known‐Exactly (SKE) to Signal‐Unknown (SUK)). Results: 2AFC analysis provided valuable quantitation of contrast‐detail detectability limits. For example, the lowest contrast lesion (20 HU) was detected at Pcorr&gt;70% for diameters down to ∼6mm at doses &gt;2mGy, but smaller 20 HU lesions (&lt;3.2mm) were barely detectable (Pcorr&lt;60%) at any dose. Detectability was significantly improved in axial versus sagittal planes, and the effect was amplified by sharper apodization filters in a manner consistent with 3D noise‐power spectrum asymmetry. Prior knowledge had a marked influence on detectability — e.g., a ∼6mm (20 HU) sphere was detected at Pcorr∼70–85% for SKE conditions, compared to Pcorr∼55–65% under SUK conditions across the same range of dose. Conclusion: Comprehensive human observer tests provide valuable quantitation of soft‐tissue detectability limits in CBCT and help to define low‐dose techniques for specific imaging tasks. Two factors in particular — plane of visualization and prior knowledge — hold significant practical implications: axial planes typically offer improved detectability, and performance is maintained at significantly lower dose under SKE conditions (e.g., lesion‐known image guidance) than in SUK conditions (lesion‐unknown diagnostic imaging).
Reproductive history and cigarette smoking as risk factors for thyroid cancer in women: a population-based case-control study. (1996)

A population-based case-control study was conducted in Northern Norway and Central Sweden to investigate hormonal and reproductive factors and cigarette smoking as determinants of papillary and follicular thyroid carcinoma in women. Information on 191 histologically confirmed cases and 341 age-matched controls was included. No clear association was found with regard to the number of live births, number of pregnancies, a history of incomplete pregnancies, or the use of oral contraceptives or hormonal replacement therapy. However, an early first childbirth (before 20 years of age, or less than 5 years after menarche) was associated with an increased risk of thyroid cancer. There was an increased risk of thyroid cancer among women with a history of artificial menopause compared to those with a spontaneous menopause [odds ratio (OR), 2.52; 95% confidence interval (CI), 0.96-6.62], which was more pronounced for the papillary carcinoma and after adjustment for age at menopause and use of replacement therapy. Cigarette smokers had a decreased risk of borderline statistical significance compared to nonsmokers (OR, 0.69; 95% CI, 0.47-1.01), particularly among premenopausal women (OR, 0.60; 95% CI, 0.38-0.96). This negative association persisted after adjustment for parity, hormonal treatments, and education. Women who started smoking before the age of 15 experienced a marked reduction in risk (OR, 0.38%; 95% CI, 0.18-0.80¿). Moreover, there was a suggestion of a dose-response effect with the amount of cigarettes smoked daily and with duration of the habit. Both the increased risk of artificial menopause and the negative association with smoking are compatible with a relation between levels of estrogens and thyroid cancer among women.
Vaccination of Mice with Neospora caninum: Response to Oral Challenge with Toxoplasma gondii Oocysts (1998)

Neospora caninum is a protozoan parasite that can cause severe disease in mammals. Two experiments were conducted to examine the effects of subcutaneous (s.c.) vaccination with Hank's balanced salt solution (HBSS), 1 x 10(5) N. caninum NC-1 strain tachyzoites or 1 x 10(5) Toxoplasma gondii TS-4 strain tachyzoites on challenge oral infections in mice with sporulated VEG strain T. gondii oocysts (1 X 10(3) oocysts exp. 1 and 5 x 10(3) oocysts exp. 2). An additional study, experiment 3, evaluated s.c. challenge with 2.5 X 10(3) tachyzoites of the highly virulent RH strain of T. gondii after vaccination with HBSS, NC-1 tachyzoites, or TS-4 tachyzoites. Mice vaccinated with NC-1 strain tachyzoites survived significantly (P < 0.05) longer than mice given HBSS in experiment 1, but not in experiments 2 and 3. Mice vaccinated with TS-4 strain tachyzoites survived significantly longer than HBSS-vaccinated mice in experiments 1, 2, and 3 and significantly longer than mice vaccinated with the NC-1 strain in experiments 2 and 3. Toxoplasma gondii tissue cyst numbers were significantly lower for mice vaccinated with TS-4 strain tachyzoites than mice vaccinated with HBSS or the NC-1 strain tachyzoites in experiment 1. No difference was observed in tissue cyst numbers in mice vaccinated with HBSS or NC-1 strain tachyzoites in experiment 1. No HBSS-vaccinated mice survived experiment 2, and the numbers of T. gondii tissue cysts were significantly lower for mice vaccinated with the TS-4 strain tachyzoites compared to NC-1 strain tachyzoites. No HBSS- or NC-1-vaccinated mice survived RH strain challenge in experiment 3. Results of these experiments indicate that infection with N. caninum provides some protection against fatal oral infection with T gondii oocysts of a moderately pathogenic strain but not tachyzoites of a highly pathogenic strain. The protection provided by N. caninum is much less than that provided by previous exposure to T. gondii, and the numbers of tissue cysts in the brains of mice are not significantly (P > 00.5) lowered.
Regulation of the oxidoreductase ERp57/Grp58 by the stress transcription co-activator LEDGF/p75 in prostate cancer cells (2007)

2914 Prostate cancer (PCa) is the second leading cause of male cancer death in the United States, and is considered a health disparity disease because of its disproportionate incidence and mortality in African American males. A major challenge in PCa treatment is the resistance of advance tumors to therapy due in part to inhibition of apoptotic pathways by survival proteins. The stress response protein Lens Epithelium Derived Growth Factor/p75 (LEDGF/p75) is upregulated by oxidative stress and promotes cell survival by transcriptionally activating stress and anti-oxidant genes. Our group has previously shown that LEDGF/p75 is overexpressed in PCa cell lines and tumors and may act as a pro-survival protein in PCa. Furthermore, we have shown that RWPE-2 PCa cells stably overexpressing LEDGF/p75 significantly increased resistance to cell death induced by docetaxel. To better understand the mechanism by which LEDGF/p75 confers resistance to docetaxel-induced cell death we performed a protein expression profile in PCa cells overexpressing this protein using the Kinetworks Stress/Heat Shock Protein Screen. We observed a marked increase in the expression of ERp57 (endoplasmic reticulum protein 57) in cells stably overexpressing LEDGF/p75. ERp57, also known as glucose regulated protein 58 (Grp58), belongs to the family of thiol oxidoreductase proteins, which have been implicated in protection against cell death through their reactive oxygen species (ROS) scavenging properties. We hypothesized that ERp57 is a target gene of LEDGF/p75 whose upregulation might enhance prostate tumor resistance to docetaxel-induced cell death in PCa. Using luciferase reporter assays we observed transcriptional activation of the ERp57 promoter by LEDGF/p75, which provided evidence that ERp57 might be a target gene of LEDGF/p75. Both proteins were found to be highly expressed in prostate tumor tissues. However, we found little correlation in the protein expression levels of LEDGF/p75 and ERp57 in a panel of PCa cell lines and prostate tumor tissues. This was confirmed by the observation that siRNA-mediated LEDGF/p75 knock-down in PC3 cells did not decrease ERP57 expression. We conclude that while LEDGF/p75 contributes to the upregulation of ERp57, other transcription factors may also regulate ERp57 expression in PCa cells.
Data from Cancer Risk and Subsequent Survival after Hospitalization for Intermittent Claudication (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Intermittent claudication, muscle ischemia due to reduced arterial circulation, may be associated with an increased risk of cancer risk and death due to neoplasm-induced hypercoagulability and angiogenesis, or to shared risk factors, but the relation is not well understood.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; We conducted a population-based cohort study using the Danish National Registry of Patients to identify patients with intermittent claudication from 1980 to 2011 and no history of cancer. We followed these patients for incident cancers using the Danish Cancer Registry and compared cancer incidence among patients with intermittent claudication to that expected in the general population. We also compared the survival of patients with cancer with and without claudication, matched for sex, cancer site, stage, age at diagnosis, and diagnosis year.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; A total of 53,762 patients with intermittent claudication were identified. We observed 6,270 incident cancers over a total 269,430 years of follow-up (mean, 5.0), compared with 4,306 cancer cases expected [standardized incidence ratio = 1.46; 95% confidence interval (CI), 1.42–1.49]. Cancer risk also increased after the exclusion of patients with a prior diagnosis of cerebrovascular disease, myocardial infarction, or diabetes, particularly for tobacco-related cancers. The elevated cancer risk persisted over 10 years of follow-up. For patients with cancer, diagnosis of intermittent claudication within 3 months preceding the cancer diagnosis did not influence survival, but before 3 months, was associated with modestly worse survival (mortality rate ratio = 1.19; 95% CI, 1.14–1.25).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Intermittent claudication is associated with an increased risk of cancer and poorer subsequent survival.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Impact:&lt;/b&gt; Clinical attention following intermittent claudication diagnosis may reveal incident cancers. &lt;i&gt;Cancer Epidemiol Biomarkers Prev; 24(4); 744–8. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Low-level haskell code: measurements and optimization techniques (2012)

Haskell is a lazy functional language with a strong static type system and excellent support for parallel programming. The language features of Haskell make it easier to write correct and maintainable programs, but execution speed often suffers from the high levels of abstraction. While much past research focuses on high-level optimizations that take advantage of the functional properties of Haskell, relatively little attention has been paid to the optimization opportunities in the low-level imperative code generated during translation to machine code. One problem with current low-level optimizations is that their effectiveness is limited by the obscured control flow caused by Haskell’s high-level abstractions. My thesis is that trace-based optimization techniques can be used to improve the effectiveness of low-level optimizations for Haskell programs. I claim three unique contributions in this work. 
The first contribution is to expose some properties of low-level Haskell codes by looking at the mix of operations performed by the selected benchmark codes and comparing them to the low-level codes coming from traditional programming languages. The low-level measurements reveal that the control flow is obscured by indirect jumps caused by the implementation of lazy evaluation, higher-order functions, and the separately managed stacks used by Haskell programs. 
My second contribution is a study on the effectiveness of a dynamic binary trace-based optimizer running on Haskell programs. My results show that while viable program traces frequently occur in Haskell programs the overhead associated with maintaining the traces in a dynamic optimization system outweigh the benefits we get from running the traces. To reduce the runtime overheads, I explore a way to find traces in a separate profiling step. 
My final contribution is to build and evaluate a static trace-based optimizer for Haskell programs. The static optimizer uses profiling data to find traces in a Haskell program and then restructures the code around the traces to increase the scope available to the low-level optimizer. My results show that we can successfully build traces in Haskell programs, and the optimized code yields a speedup over existing low-level optimizers of up to 86% with an average speedup of 5% across 32 benchmarks.
Cesarean Section before the Onset of Labor and Subsequent Motor Function in Infants with Meningomyelocele Diagnosed Antenatally (1991)

Background. Meningomyelocele can now be detected before birth. Few data are available on its natural history, however, and optimal management at the time of delivery is controversial, although it has been suggested that labor and vaginal delivery may cause pressure on exposed nerve roots, resulting in additional loss of neural function. Methods. To assess the effect of labor and the type of delivery on the level of motor function in fetuses with uncomplicated meningomyelocele, we identified 200 cases of this disorder, accounting for 95 percent of the cases that occurred in the state of Washington during our 10-year study period. We compared the outcomes of 47 infants delivered by cesarean section before labor began, 35 delivered by cesarean section after a period of labor, and 78 who were delivered vaginally (another 40 were ineligible for the study). In cases of meningomyelocele detected prenatally, cesarean section was performed before the onset of labor if isolated meningomyelocele without severe hydrocephalus was present. The infants delivered in this manner were compared with those who were delivered either vaginally or by cesarean section after labor began. Results. At two years of age, the infants who had been exposed to labor were 2.2 times more likely to have severe paralysis than those delivered by cesarean section without labor (95 percent confidence interval, 1.7 to 2.8). Infants delivered by cesarean section before the beginning of labor had a mean (+/- SD) level of paralysis 3.3 +/- 3.0 segments below the anatomical level of the spinal lesion at two years of age, as compared with 1.1 +/- 2.3 for infants delivered vaginally and 0.9 +/- 4.1 for infants delivered by cesarean section after the beginning of labor (P less than 0.001 for both comparisons). Exposure to labor did not affect the frequency of neonatal complications or later intellectual performance. Conclusions. For the fetus with uncomplicated meningomyelocele, delivery by cesarean section before the onset of labor may result in better subsequent motor function than vaginal delivery or delivery by cesarean section after a period of labor.
Lentiviral Gene Transfer of RPE65 cDNA in Two Knock–Out Mouse Models of Leber Congenital Amaurosis (2005)

667. Lentiviral Gene Transfer of RPE65 cDNA in Knock-Out Mouse Models of Leber Congenital Amaurosis Corinne Kostic, Alexis-Pierre Bemelmans, Muriel Jaquet, Dana Hornfeld, William W. Hauswirth, Janis Lem, Zhongyan Wang, Daniel F. Schorderet, Francis L. Munier, Andreas Wenzel, Yvan Arsenijevic. Oculogenetic Unit, Jules Gonin Eye Hospital, Lausanne, Switzerland; Dept. of Ophthalmology and Powell Gene Therapy Center, University of Florida, Gainsville, FL; Dept. of Ophthalmology and Program in Genetics, Tufts University School of Medicine, Boston, MA; Institut de Recherche en Ophtalmology, Sion, Switzerland; Dept. of Ophthalmology, University of Zurich, Zurich, Switzerland.
EIT-MESHER – Segmented FEM Mesh Generation and Refinement (2020)

EIT-MESHER (<a href="https://github.com/EIT-team/Mesher" target="_blank">https://github.com/EIT-team/Mesher</a>) is C++ software, based on the CGAL library, which generates high quality Finite Element Model tetrahedral meshes from binary masks of 3D volume segmentations. Originally developed for biomedical applications in Electrical Impedance Tomography (EIT) to address the need for custom, non-linear refinement in certain areas (e.g. around electrodes), EIT-MESHER can also be used in other fields where custom FEM refinement is required, such as Diffuse Optical Tomography (DOT). <strong>Funding statement:</strong> This work was supported by an ARCHER eCSE grant (eCSE13-11). James Avery was supported by the NIHR Imperial BRC.