gebhart/patrepeval huggingface dataset:
Thermally assisted ion beam etching of polytetrafluoroethylene-a new technique for high aspect ratio etching of MEMS (2002)

In micromechanics, the etching of high aspect ratio structures in polymers is a prime technology. Normally, oxygen-based reactive ion etching or the LIGA technique are used to achieve this goal. This paper reintroduces a different idea to create deep trenches at high etch speed: the ion beam etching of Teflon. Because of its extraordinary properties the etch selectivity with respect to most other materials is over 1000. A model is proposed to explain the high etch rate and selectivity. Generally, the etching ions are highly energetic and material from different sources is sputtered on top of the sample. The high selectivity, high anisotropy, and sputtering of material are thought to be responsible for the forming of micrograss during etching a sample. Ways are given to decrease or increase this grass. The high potential of this technique will be discussed and applications will be shown. Especially, the use of etched Teflon for direct moulding is believed to become the main use of this technique.
DNA methylation profile to predict clinical outcome of anti-EGFR treatment in metastatic colorectal cancer. (2015)

e14574 Background: For metastatic colorectal cancer (mCRC) treatment, anti-epidermal growth factor receptor (EGFR) treatment is one of the major options. However, there are few reliable biomarkers to predict the clinical response to anti-EGFR treatment. We investigated the genome-wide DNA methylation status in metastatic colorectal cancer to identify associations between the methylation status and clinical response to anti-EGFR antibody. Methods: We retrospectively corrected the medical records of 45 patients who received anti-EGFR treatment for mCRC as 1st cohort, and of 52 patients as 2nd cohort. All cases were verified that they had no mutations at KRAS codon 12 or 13. We investigated the associations between the genome-wide DNA methylation status in the primary tumors and clinical response to anti-EGFR treatment, and evaluated the predictive power and value of the methylation status in mCRC statistically. Results: Unsupervised clustering analysis classified cases contained in each cohorts were classified into highly-methylated colorectal cancer (HMCC) and low-methylated colorectal cancer (LMCC) subgroups. In the 1st cohort, all examined clinical outcomes were significantly better in the LMCC subgroup than in the HMCC subgroup (response rate: 35.7% vs. 6.3%; P = 0.03, disease control rate: 75% vs. 31.3%; P = 0.005, hazard ratios for progression-free survival: 0.27; 95% CI, 0.13–0.57; P < 0.001 and overall survival: 0.19; 95% CI, 0.06–0.54; P < 0.001). These results were reproduced in the 2nd cohort. The genome-wide DNA methylation status was a strong predictive factor of progression-free survival and overall survival, and it was independent of RAS mutation status in both univariate and multivariate Cox regression analyses. Conclusions: The genome-wide DNA methylation status is a powerful epigenetic predictor of the anti-EGFR treatment in patients with KRAS wild-type metastatic colorectal cancer (UMIN000005490).
Ab initio studies of crystal field effects. VII. Structure of 2,3‐diketopiperazine using a 13‐molecule cluster, a calculation involving 1092 basis functions (1993)

Abstract The structure of 2,3‐diketopiperazine in a crystal phase ( P 2 1 / c ), modeled by a 13‐molecule cluster surrounded by point charges, was completely optimized using standard gradient procedures. The (ab initio) MIA approach was used to perform the SCF step, which using a 4‐21 G basis set, involves calculations using 1092 basis functions. Results are in very good agreement with experimental (X‐ray) data, in contrast to a previous study in which a model was used consisting of only point charges. © 1993 John Wiley &amp; Sons, Inc.
Development of a Fast-Response $CO_2$ Analyzer using NDIR Technique and Its Application to SI Engine (2007)

A fast response () analyzer for real-time measurement of carbon dioxide concentration during transient states of internal combustion engines has been developed. This analyzer uses non-dispersive infrared absorption (NDIR) technique for measuring concentration and Kalman filter for removing noise components from output signals. The analyzer has good linearity, repeatability and drift with a response time of 11 ms; it is sufficiently fast to detect concentration during transient states of internal combustion engines. The analyzer was used to measure transient concentration of exhaust gas of the SI engine with a standard gas analyzer, and the signal of the analyzer was compared to that of the standard gas analyzer. The two concentrations were well matched during the steady state, and the analyzer could measure the variations of concentration during the transient state.
ChemInform Abstract: A Fundamental Structural Study of Inclusion Chemistry: The Mutual Effects of Host and Guest in the Transition‐Metal Complexes of Superstructured Cyclidene Macrobicycles. (1989)

Abstract Detailed structural analysis is reported on the cavities of lacunar cyclidene complexes of the type (I) and (II) having polymethylidene chains as bridging groups.
Avrainvilloside, a 6-Deoxy-6-aminoglucoglycerolipid from the Green Alga Avrainvillea nigricans (2005)

Fractionation of the organic extract obtained from the Dominican green alga Avrainvillea nigricans led to the isolation of avrainvilloside (2), a new glycoglycerolipid bearing the extremely rare 6-deoxy-6-aminoglucose moiety. The structure of avrainvilloside has been established on the basis of spectroscopic data and methanolysis/GC-MS analysis.
Novel method for measuring beam parameter product and M-square (2015)

The majority of methods available for measuring the M-square or the beam parameter product of a laser employ a time averaging technique based upon the ISO 11146-1 beam metric standard. In the ISO standard five points must be measured within the first Rayleigh range to establish the beam waist and another five points measured beyond the second Rayleigh range to obtain the asymptote from the corresponding hyperbolic fit of the minimum ten data points measured. Other real time, i.e., instantaneous M-square methods exist but do not fully comply with the ISO 11146-1 standard to the exact letter of the document. One measurement technique is able to view three Rayleigh lengths in real time but due to gain and area limitations of the sensor, the third Rayleigh range is hard to measure to the full extent of the ISO standard or only can be under limited conditions. It is therefore desirable to have a technique that complies with the ISO standard and provide real time M-square or beam parameter product values. We present a technique that simultaneously measures outside the second Rayleigh range while at the same time measure the first Rayleigh range where the gain of the two regions are optimized and there is sufficient area available on the sensor to comply with the ISO standard.
Data from Transcriptional Repression by FoxM1 Suppresses Tumor Differentiation and Promotes Metastasis of Breast Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;The transcription factor Forkhead box M1 (FoxM1) is overexpressed in breast cancers and correlates with poor prognosis. Mechanistically, FoxM1 associates with CBP to activate transcription and with Rb to repress transcription. Although the activating function of FoxM1 in breast cancer has been well documented, the significance of its repressive activity is poorly understood. Using CRISPR–Cas9 engineering, we generated a mouse model that expresses FoxM1-harboring point mutations that block binding to Rb while retaining its ability to bind CBP. Unlike FoxM1-null mice, mice harboring Rb-binding mutant FoxM1 did not exhibit significant developmental defects. The mutant mouse line developed PyMT-driven mammary tumors that were deficient in lung metastasis, which was tumor cell-intrinsic. Single-cell RNA-seq of the tumors revealed a deficiency in prometastatic tumor cells and an expansion of differentiated alveolar type tumor cells, and further investigation identified that loss of the FoxM1/Rb interaction caused enhancement of the mammary alveolar differentiation program. The FoxM1 mutant tumors also showed increased Pten expression, and FoxM1/Rb was found to activate Akt signaling by repressing Pten. In human breast cancers, expression of FoxM1 negatively correlated with Pten mRNA. Furthermore, the lack of tumor-infiltrating cells in FoxM1 mutant tumors appeared related to decreases in pro-metastatic tumor cells that express factors required for infiltration. These observations demonstrate that the FoxM1/Rb-regulated transcriptome is critical for the plasticity of breast cancer cells that drive metastasis, identifying a prometastatic role of Rb when bound to FoxM1.&lt;/p&gt;Significance:&lt;p&gt;This work provides new insights into how the interaction between FoxM1 and Rb facilitates the evolution of metastatic breast cancer cells by altering the transcriptome.&lt;/p&gt;&lt;/div&gt;
Association of Flame-Retardant Clothing with Mycosis Fungoides: A Retrospective Analysis (2022)

FRC appears to be associated with development of MF through chronic antigen stimulation. Use of FRC is an occupational hazard for fire fighters. Any patient whose MF coincides with use of FRC should avoid further exposure through avoidance or switching to clothing made from inherently flame-resistant fibers.
OC13.05: Aortic coarctation: a comprehensive biomechanical analysis of shape, size and function of the fetal heart (2018)

We examined the four-chamber view (4CV) and right (RV) and left (LV) ventricles using 181 measurements to evaluate the shape, size, and function of the right (RV) and left (LV) ventricles of the heart in fetuses with coarctation of the aorta (CoA). This was a retrospective case series comparing the 4CV of CoA fetuses and controls. The 4CV end-diastolic area, length, width, and sphericity index were measured to determine configuration of the 4CV. Speckle tracking analysis was used to compute the RV and LV end-diastolic area, length, 24-segment sphericity index, 24-segment transverse width, and the following functional parameters: (1) fractional area change; (2) global, lateral, and septal strain; (3) basal-apical, lateral and septal annular displacement and fractional shortening; and (4) 24-segment transverse width fractional shortening. The z-score values of CoA versus 200 controls were compared using nonparametric testing. 51 CoA fetuses were compared to 200 controls. The 4CV CoA heart was significantly increased in width, decreased in length and more globular in shape. Abnormal CoA sphericity indices reflected a flatter LV and a more spherical shaped RV. The LV area, length, width, and RV length were decreased in size. The transverse width of the RV was increased in size. RV and LV global, longitudinal, and circumferential function were depressed in fetuses with CoA. This novel and comprehensive assessment demonstrates previously unappreciated differences in the shape, size and function of the heart in fetuses with CoA. These differences may assist examiners in differentiating fetuses with and without CoA.
Graphs whose vertices of degree at least 2 lie in a triangle (2022)

A pendant vertex is one of degree one and an isolated vertex has degree zero. A neighborhood star-free (NSF for short) graph is one in which every vertex is contained in a triangle except pendant vertices and isolated vertices. This class has been considered before for several contexts. In the present paper, we study the complexity of the dominating induced matching (DIM) problem and the perfect edge domination (PED) problem for NSF graphs. We prove the corresponding decision problems are NP-Complete for several of its subclasses. As an added value of this study, we have shown three connected variants of planar positive 1in3SAT are also NP-Complete. Since these variants are more basic in complexity theory context than many graph problems, these results can be useful to prove that other problems are NP-Complete.
Effects of delayed-release dimethyl fumarate on MRI measures in the Phase 3 DEFINE study (2014)

In the Phase 3 DEFINE study, delayed-release dimethyl fumarate (DMF) 240 mg twice (BID) and three times daily (TID) significantly reduced the mean number of new or enlarging T2-hyperintense lesions and gadolinium-enhancing (Gd+) lesion activity at 2 years in patients (MRI cohort; n = 540) with relapsing-remitting MS. The analyses described here expand on these results by considering additional MRI measures (number of T1-hypointense lesions; volume of T2-hyperintense, Gd+, and T1-hypointense lesions; brain atrophy), delineating the time course of the effects, and examining the generality of the effects across a diverse patient population. Reductions in lesion counts with delayed-release DMF BID and TID, respectively, vs. placebo were apparent by the first MRI assessment at 6 months [T2-hyperintense: 80 and 69 % reduction (both P < 0.0001); Gd+, 94 and 81 % reduction (both P < 0.0001); T1-hypointense: 58 % (P < 0.0001) and 48 % (P = 0.0005) reduction] and maintained at 1 and 2 years. Reductions in lesion volume were statistically significant beginning at 6 months for T2-hyperintense [P = 0.0002 (BID) and P = 0.0035 (TID)] and Gd+ lesions [P = 0.0059 (BID) and P = 0.0176 (TID)] and beginning at 1 year [P = 0.0126 (BID)] to 2 years [P = 0.0063 (TID)] for T1-hypointense lesions. Relative reductions in brain atrophy from baseline to 2 years (21 % reduction; P = 0.0449) and 6 months to 2 years (30 % reduction; P = 0.0214) were statistically significant for delayed-release DMF BID. The effect of delayed-release DMF on mean number of new or enlarging T2-hyperintense lesions and Gd+ lesion activity was consistent across pre-specified patient subpopulations. Collectively, these results suggest that delayed-release DMF favorably affects multiple aspects of MS pathophysiology.
Intravenous clusterin administration reduces myocardial infarct size in rats (2010)

Our results thus show that clusterin has a protective effect on cardiomyocytes after acute myocardial infarction in vivo, independent of its receptor megalin. This indicates that clusterin, or a clusterin derivate, is a potential therapeutic agent in the treatment of MI.
Synthesis, photoluminescence and thermal properties of nanostructured organosilicon luminophore based on 2,2’-bithienyl and 4,7-diphenyl-2,1,3-benzothiadiazole (2020)

Annotation In this work, novel nanostructured organosilicon luminophore (NOL) containing four 2, 2’-bithienyl donor units connected via silicon atoms to 4, 7-diphenyl-2, 1, 3-benzothiadiazole acceptor unit was synthesized. Photophysical measurements of the NOL revealed the effect of solvents polarity on its photoluminescence quantum yield (PLQY). In THF solution the efficiency of photoluminescence was only 4%, whereas in toluene solution PLQY increased up to 76% without any changing the spectral characteristics. Under the normal conditions, the NOL synthesized is a viscous fluid, which contributes to its good solubility in various solvents. The NOL is thermostable up to 415 °C in argon atmosphere.
Multiwavelength Optical Intrinsic Signal Imaging of Cortical Spreading Depression (2002)

Cortical spreading depression (CSD) is an important disease model for migraine and cerebral ischemia. In this study, we exploit the high temporal and spatial resolution of optical imaging to characterize perfusion-dependent and -independent changes in response to CSD and to investigate the etiology of reflectance changes during CSD. In this experiment, we characterized the optical response to CSD at wavelengths that emphasize perfusion-related changes (610 and 550 nm), and we compared these results with 850 nm and blood volume data. Blood volume changes during CSD were recorded using an intravascular fluorescent dye, Texas Red dextran. We observed triphasic optical signals at 850 and 550 nm characterized by spreading waves of increased, decreased, then increased reflectance (Fig. 1) which expanded at a rate of approximately 3-5 mm/min. The signal at 610 nm had a similar initial phase, but the phase 2 response was slightly more complex, with a parenchymal decrease in reflectance but a vascular increase in reflectance. Reflectance values decreased in phase three. Blood volume signals were delayed relative to the optical intrinsic signals and corresponded temporally to phases 2 and 3. This is the first study to characterize optical imaging of intrinsic signal responses to CSD, in vivo, at multiple wavelengths. The data presented here suggest that changes in light scattering precede perfusion responses, the blood volume increase (phase 2) is accompanied by a reduction in deoxyhemoglobin, and the blood volume decrease (phase 3) is accompanied by an increase in deoxyhemoglobin. Previous studies have suggested the oligemia of spreading depression was a result of decreased metabolic demand. This study suggests that during the oligemic period there is a greater reduction in oxygen delivery than in demand.
Alzheimer disease β-amyloid activity mimics cholesterol oxidase (2005)

The abnormal accumulation of amyloid beta-peptide (Abeta) in the form of senile (or amyloid) plaques is one of the main characteristics of Alzheimer disease (AD). Both cholesterol and Cu2+ have been implicated in AD pathogenesis and plaque formation. Abeta binds Cu2+ with very high affinity, forming a redox-active complex that catalyzes H2O2 production from O2 and cholesterol. Here we show that Abeta:Cu2+ complexes oxidize cholesterol selectively at the C-3 hydroxyl group, catalytically producing 4-cholesten-3-one and therefore mimicking the activity of cholesterol oxidase, which is implicated in cardiovascular disease. Abeta toxicity in neuronal cultures correlated with this activity, which was inhibited by Cu2+ chelators including clioquinol. Cell death induced by staurosporine or H2O2 did not elevate 4-cholesten-3-one levels. Brain tissue from AD subjects had 98% more 4-cholesten-3-one than tissue from age-matched control subjects. We observed a similar increase in the brains of Tg2576 transgenic mice compared with nontransgenic littermates; the increase was inhibited by in vivo treatment with clioquinol, which suggests that brain Abeta accumulation elevates 4-cholesten-3-one levels in AD. Cu2+-mediated oxidation of cholesterol may be a pathogenic mechanism common to atherosclerosis and AD.
Front Matter: Volume 6505 (2007)

This PDF file contains the front matter associated with SPIE Proceedings Volume 6505, including the Title Page, Copyright information, Table of Contents, Introduction (if any), and the Conference Committee listing.
A Mass-Balance-Consistent Process Inventory Model for Ion-Exchange Resin Catalyzed Biodiesel Production (2022)

Calculation of life-cycle greenhouse gas (LC-GHG) emission is necessary to verify the rationale behind any biofuel production project, as a countermeasure for climate change. Here, a process inventory model was constructed based on pilot-scale experiments on biodiesel production using an ion-exchange resin catalyzed (IERC) process. The IERC process prevents soap formation, which also leads to the elimination of water-soluble contaminants entering the product biodiesel i.e., removes the two major problems in recently developed diesel engines with sophisticated injection mechanisms introduced for pollution reduction. Our mass-balance-consistent model reflects the influence of the FFA content in oil on the process inventory; therefore, it is capable of highlighting the characteristics of the technology. Simulated LC-GHG emissions per MJ of biodiesel fuel over varied (0–50 wt%) FFA content of feedstock oil shows that the product has lower LC-GHG emission than that of the fossil resource-based diesel fuel, and that it becomes even lower with a higher FFA content in the feedstock oil. Waste heat utilization would allow for the reduction of LC-GHG emissions to less than half of the fossil-based diesel, while large amounts of LC-GHGs are emitted through the conventional process to achieve fuel quality equivalent to that achieved by the IERC process.
Early relapse after high‐dose melphalan autologous stem cell transplant predicts inferior survival and is associated with high disease burden and genetically high‐risk disease in multiple myeloma (2020)

Predicting patient outcome in multiple myeloma remains challenging despite the availability of standard prognostic biomarkers. We investigated outcome for patients relapsing early from intensive therapy on NCRI Myeloma XI. Relapse within 12 months of autologous stem cell transplant was associated with markedly worse median progression-free survival 2 (PFS2) of 18 months and overall survival (OS) of 26 months, compared to median PFS2 of 85 months and OS of 91 months for later relapsing patients despite equal access to and use of subsequent therapies, highlighting the urgent need for improved outcome prediction and early intervention strategies for myeloma patients.
An operator interface for an autonomous mobile robot using whistle sound and a source direction detection system (2002)

We have developed a human interface system for the autonomous mobile robot, which uses whistle sound. It can detect whistle sound and its source direction in a noisy environment. The system consists of two electronic circuits. The first one discriminates and detects the whistle sound. The second measures the direction of the whistle sound source using differences in sound wave phases of three microphones. It detects whistle sound in an environment where several people are talking, and measures the source direction with an accuracy of about /spl plusmn/5 degrees at an open space outdoors or in a room, and /spl plusmn/10 degrees in a narrow corridor. A simple sequence of whistle sounds is designed and used to give commands to the robot. This system is installed on our experimental autonomous robot YAMABICO. With this system, YAMABICO can follow instructions given by the operator, for example, it can come toward the operator when the whistle is blown.
Designers wanted (2009)

We present design concepts and related mockups that support the user experience for projects hosted on CodePlex, an open source project hosting website. Rationale for the design concepts is grounded in the open source literature and a thirteen-week study with the CodePlex team. We propose that fostering ways to build trust, providing opportunities for merit, supporting crossover of work activities, and supporting user experience (UX) best practices in CodePlex will help dismantle the social and technological barriers for UX and encourage UX designer participation. We address UX designer motivation as a challenge for participation and conclude that the mockups presented are a first step in furthering the user experience in open source software development.