gebhart/patrepeval huggingface dataset:
Comparison of Nuclear DNA Content in Primary and Metastatic Differentiated Thyroid Carcinoma (1988)

Nuclear DNA content of 20 cases of primary differentiated thyroid carcinoma, 27 corresponding cervical lymph node metastases, and 2 local recurrent tumors was determined by flow cytometry. Evidence of DNA aneuploidy was found in either the primary tumor or in the corresponding metastases in 10 (63%) of the 16 papillary carcinomas, in all 3 follicular carcinomas, and in the case of medullary carcinoma studied. In all but one case, the aneuploid stemlines found in the regional metastases were also found in the primary or in the recurrent tumor. In four cases diploid metastatic tissue was found to originate from a tumor with DNA aneuploidy, and in three other cases two stemlines of tumor cells with different DNA indices could be shown in the primary tumor, further indicating clonal heterogeneity in differentiated thyroid carcinomas. None of the 11 patients with either diploid or aneuploid primary tumor with a DNA index less than 1.2 evaluated for 4-12 years died from thyroid cancer, whereas 5 of the 7 patients with primary tumor DNA index greater than 1.2 died from thyroid cancer (P less than 0.01).
A Bayesian method to predict the optimal diffusion coefficient in random fixational eye movements (2009)

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Load Balancing for SIP Server Clusters (2009)

This paper introduces several novel load balancing algorithms for distributing session initiation protocol (SIP) requests to a cluster of SIP servers. Our load balancer improves both throughput and response time versus a single node, while exposing a single interface to external clients. We present the design, implementation and evaluation of our system using a cluster of Intel x86 machines running Linux. We compare our algorithms with several well-known approaches and present scalability results for up to 10 nodes. Our best algorithm, transaction least-work-left (TLWL), achieves its performance by integrating several features: knowledge of the SIP protocol; dynamic estimates of back-end server load; distinguishing transactions from calls; recognizing variability in call length; and exploiting differences in processing costs for different SIP transactions. By combining these features, our algorithm provides finer-grained load balancing than standard approaches, resulting in throughput improvements of up to 24 percent and response time improvements of up to two orders of magnitude. We present a detailed analysis of occupancy to show how our algorithms significantly reduce response time.
Fluorescence ImmunoPrecipitation (FLIP): a Novel Assay for High-Throughput IP (2016)

Altogether, our characterizations of this new methodology show that FLIP is an appealing and reliable tool for any application of high-throughput IP.
Fatigue characteristics of SrBi2Ta2O9 thin films prepared by metalorganic decomposition (1998)

Polycrystalline SrBi2Ta2O9 (SBT) ferroelectric thin films were synthesized on Pt/Ti/SiO2/Si substrates by metalorganic decomposition. Electric measurements demonstrate that fatigue increases with decreasing switching voltage and frequency, and the suppressed polarization caused at a lower switching voltage can be recovered by switching at a higher voltage. This suggests that the domain walls of SBT thin films are weakly pinned and easily depinned by a higher external field. The polarization of SBT thin films annealed in air shows more degradation than that annealed in oxygen, which indicates that the oxygen vacancy also plays an important role in fatigue behavior of SBT thin films.
Hybrid grating–prism stretcher–compressor system with cubic phase and wavelength tunability and decreased alignment sensitivity (1994)

A novel stretcher–compressor design for chirped-pulse amplification systems is presented. The stretcher, which incorporates high-groove-density gratings and an intragrating prism pair, is shown to be highly cubic-phase tunable. Using a hybrid stretcher with 2400-line/mm gratings and off-the-shelf prisms, we have demonstrated amplification of sub-100-fs pulses. In addition, this cubic-phase tunability combined with the broadband efficiency of high-groove-density (2000 lines/mm) gratings allows for the possibility of a system that is tunable in wavelength.
Sequencing a genome by walking with clone-end sequences (abstract) (2000)

One important approach to sequencing a large genome is (i) to sequence a collection of non-overlapping `seed' chosen from a genomic library of large-insert clones (such as bacterial artificial chromosome (BACs)) and then (ii) to take successive `walking' steps by selecting and sequencing minimally overlapping clones, using information such as clone-end sequences to identify the overlaps. We analyze the strategic issues involved in using this approach. We derive formulas showing how two key factors, the initial density of seed clones and the depth of the genomic library used for walking, affect the cost and time of a sequencing project—that is, the amount of redundant sequencing and the number of steps to cover the vast majority of the genome. We also discuss a variant strategy in which a second genomic library with clones having a somewhat smaller insert size is used to close gaps. This approach can dramatically decrease the amount of redundant sequencing, without affecting the rate at which the genome is covered.
Collective magnetic dynamics in artificial spin ice probed by ac susceptibility (2020)

We report on the study of the thermal dynamics of square artificial spin ice, probed by means of temperature- and frequency-dependent ac susceptibility. Pronounced influence of the interisland coupling strength was found on the frequency response of the samples. Through the subsequent analysis of the frequency- and coupling-dependent freezing temperatures, we discuss the phenomenological parameters obtained in the framework of the Vogel-Fulcher-Tammann law in terms of the samples' microscopic features. The high sensitivity and robust signal to noise ratio of ac susceptibility validate the latter as a promising and simple experimental technique for resolving the dynamics and temperature driven dynamics crossovers for the case of artificial spin ice.
Assessment of trabecular bone structure using fuzzy distance transform based on Min-Max operations (2015)

Trabecular bone consists of a network of tiny strands and plates. Micro-structural features of trabecular bone include thickness, relative volume, spacing and connectivity. The accurate evaluation of these features is of significant interest in the assessment of the mechanical and transport properties of bone. Extracting these features from μCT and μMRI images is difficult and measurements vary substantially according to image processing technique used. In this paper, we propose a fuzzy distance transform (FDT) method to measure trabecular bone thickness based on Min-Max operations and using an additive weighting term. Due to the employed fuzzy Min-Max operations along with the additive weighing term, the FDT method is performed in integer number space to consequently produce a computationally fast, robust and efficient use of memory method with taking into account the gray level of pixels. This method has been used to measure the trabecular thickness of bone samples with different bone volume fractions (BVF). Additionally, its performance was studied considering parameters such as image resolution, object rotation, noise and running time. The algorithm has proven to be very robust, precise and faster.
Demand Responsive Transportation (2017)

The term &quot;demand responsive transportation&quot; (DRT) refers to modes of transport that adjust the supply of services to the demand at any one time, including variations in schedule and/or variations in trip route. DRT is an important, but often overlooked, component of public transportation that provides unique opportunities and challenges for accessibility. The success of transportation network companies (TNCs), like Uber and Lyft and other vehicle sharing services, is rapidly changing the DRT scene, creating both opportunities and challenges for accessible transportation. Some sources use DRT as a synonym for special transport services (STSs), or paratransit, as it is called in North America; some exclude STS from their definition, focusing on services available to a wider rider base; some include taxis; some exclude taxis. Mobile phones and crowdsourcing are disruptive technologies that are changing the nature of DRT. These two technologies have enabled the rapid development of vehicle sharing services.
Femtosecond two-dimensional Fourier transform electronic spectroscopy (2007)

Two-dimensional spectra are obtained by Fourier transformation of four-wave mixing signal fields with respect to time delays between femtosecond pulses. We discuss peak shapes, experimental distortions, and dispersion relations. Two-dimensional electronic spectra revealing solvent and electronic motion are used as illustrations.
Optical-Based Analysis of Soft Tissue Structures (2016)

Fibrous structures are an integral and dynamic feature of soft biological tissues that are directly related to the tissues' condition and function. A greater understanding of mechanical tissue behavior can be gained through quantitative analyses of structure alone, as well as its integration into computational models of soft tissue function. Histology and other nonoptical techniques have traditionally dominated the field of tissue imaging, but they are limited by their invasiveness, inability to provide resolution on the micrometer scale, and dynamic information. Recent advances in optical modalities can provide higher resolution, less invasive imaging capabilities, and more quantitative measurements. Here we describe contemporary optical imaging techniques with respect to their suitability in the imaging of tissue structure, with a focus on characterization and implementation into subsequent modeling efforts. We outline the applications and limitations of each modality and discuss the overall shortcomings and future directions for optical imaging of soft tissue structure.
Data from Loss of NAPRT1 Expression by Tumor-Specific Promoter Methylation Provides a Novel Predictive Biomarker for NAMPT Inhibitors (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; We sought to identify predictive biomarkers for a novel nicotinamide phosphoribosyltransferase (NAMPT) inhibitor.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We use a NAMPT inhibitor, GNE-617, to evaluate nicotinic acid rescue status in a panel of more than 400 cancer cell lines. Using correlative analysis and RNA interference (RNAi), we identify a specific biomarker for nicotinic acid rescue status. We next determine the mechanism of regulation of expression of the biomarker. Finally, we develop immunohistochemical (IHC) and DNA methylation assays and evaluate cancer tissue for prevalence of the biomarker across indications.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Nicotinate phosphoribosyltransferase (NAPRT1) is necessary for nicotinic acid rescue and its expression is the major determinant of rescue status. We demonstrate that &lt;i&gt;NAPRT1&lt;/i&gt; promoter methylation accounts for NAPRT1 deficiency in cancer cells, and &lt;i&gt;NAPRT1&lt;/i&gt; methylation is predictive of rescue status in cancer cell lines. Bisulfite next-generation sequencing mapping of the &lt;i&gt;NAPRT1&lt;/i&gt; promoter identified tumor-specific sites of &lt;i&gt;NAPRT1&lt;/i&gt; DNA methylation and enabled the development of a quantitative methylation-specific PCR (QMSP) assay suitable for use on archival formalin-fixed paraffin-embedded tumor tissue.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Tumor-specific promoter hypermethylation of &lt;i&gt;NAPRT1&lt;/i&gt; inactivates one of two NAD salvage pathways, resulting in synthetic lethality with the coadministration of a NAMPT inhibitor. NAPRT1 expression is lost due to promoter hypermethylation in most cancer types evaluated at frequencies ranging from 5% to 65%. NAPRT1-specific immunohistochemical or DNA methylation assays can be used on archival formalin paraffin-embedded cancer tissue to identify patients likely to benefit from coadministration of a Nampt inhibitor and nicotinic acid. &lt;i&gt;Clin Cancer Res; 19(24); 6912–23. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Phase-contrast cine MR angiography in chronic liver disease. (1993)

Thirty-one patients with portal venous hypertension underwent phase-contrast cine magnetic resonance (MR) angiography to validate the technique for assessment of main portal vein patency and blood flow direction. Correlative findings from Doppler ultrasonography, conventional angiography, and surgery were acquired in 30, 17, and 16 patients, respectively. Findings from MR angiography correlated well with those of the other methods for determining portal vein patency and flow direction. The main portal vein was patent in 29 patients and was thrombosed in two patients at MR angiography. With the use of a 40-mm slab projection acquisition that required 5 minutes, the splenic and superior mesenteric veins, as well as extensive varices (when present), were seen in the majority of cases. Phase-contrast cine MR angiography is an accurate method of rapidly assessing morphologic characteristics, patency, and flow direction of the portal venous system and thus is a useful method for evaluating the condition of patients with chronic liver disease.
Sonochemical Synthesis under a Magnetic Field: Fabrication of Nickel and Cobalt Particles and Variation of Their Physical Properties (2008)

We report on the variation of the physical properties of nickel and cobalt nanoparticles prepared by using ultrasound irradiation as energy source. First, we describe a sonochemical method for preparing aggregated particles. Second, we interpret the results on the basis of Einstein's theory (1905), which deals with a mathematical expression for the diffusivity of particles into solvents. This theory explains the stability of organosols of nickel and cobalt nanoparticles in polyethylene glycol. Finally, the effect of applying an external magnetic field during sonochemical formation of both aggregated particles and their stable colloids is investigated.
Prediction of Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions (2022)

The properties of soft electronic materials depend on the coupling of electronic and conformational degrees of freedom over a wide range of spatiotemporal scales. Description of such properties requires multiscale approaches capable of, at the same time, accessing electronic properties and sampling the conformational space of soft materials. This could in principle be realized by connecting the coarse-grained (CG) methodologies required for adequate conformational sampling to conformationally-averaged electronic property distributions via backmapping to atomistic-resolution level models and repeated quantum-chemical calculations. Computational demands of such approaches, however, have hindered their application in high-throughput computer-aided soft materials discovery. Here, we present a method that, combining machine learning and CG techniques, can replace traditional backmapping-based approaches without sacrificing accuracy. We illustrate the method for an emerging class of soft electronic materials, namely non-conjugated, radical-containing polymers, promising materials for all-organic energy storage. Supervised machine learning models are trained to learn the dependence of electronic properties on polymer conformation at CG resolutions. We then parametrize CG models that retain electronic structure information, simulate CG condensed phases, and predict the electronic properties of such phases solely from the CG degrees of freedom. We validate our method by comparing it against a full backmapping-based approach, and find good agreement between both methods. This work demonstrates the potential of the proposed method to accelerate multiscale workflows, and provides a framework for the development of CG models that retain electronic structure information.
Observation of Composite Materials Using Coupled Mechanical Testing and Computed Tomography (2008)

This study develops chitosan/gelatin nanofiber membranes with sustained release capacity to prevent infection by delivering cinnamon extract (CE) in the implanted site. The effects of the incorporation of CE content (2-6%) on the properties of the nanofibers were evaluated. Morphological studies using SEM indicated that loading the extract did not affect the average diameter of nanofiber mats, which remained around 140-170 nm. TGA and FTIR spectroscopy results confirmed successful CE loading. Furthermore, the results showed that incorporating extract into the nanofibers enhanced their degradation behavior, antibacterial activity, and biocompatibility. Cultured cells attached to and proliferate on the nanofiber membrane with high cell viability capacity until the CE content reached 4%. The extract release profile consisted of a burst release in the first 6 h, followed by a controlled release in the next 138 h. Therefore, CE loaded chitosan/gelatin nanofiber is an excellent construct for biomedical applications.
Characterization of AQX‐1125, a small‐molecule SHIP1 activator (2012)

Consistent with the role of SHIP1 in cell activation and chemotaxis, the SHIP1 activator AQX-1125 inhibits Akt phosphorylation, inflammatory mediator production and leukocyte chemotaxis in vitro. The in vitro effects and the pharmacokinetic properties of the compound make it a suitable candidate for in vivo testing in various models of inflammation.
Estimation of Ethanol Yield in Corn Mash Fermentations Using Mass of Ash as a Marker (2005)

An equation to estimate the ethanol yield by mass of ash in fermentation was generated. The equation was based on the assumption that mass of ash does not change during the course of fermentation. Ethanol yield estimated by the mass of ash equation was validated by contrasting it to ethanol yield obtained by the distillation method. Results showed no difference (P = 0.925) in yields estimated by the aforementioned methods. Furthermore, this innovative method was tested in three fuel ethanol plants located in the American Midwest. The results from each of these plants showed that the ethanol yield estimated by mass of ash is valid, consistent and can be used to compare individual fermentations and/or treatments.
Characterization and modeling of the AuCuSn thin solder joint under thermal cycling (2014)

Thin Au <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> Sn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> solder joints have been identified to provide improved electrical and thermal device performance compared to thicker solder joints [1]. Both the material high thermal conductivity and the reduced joint thickness improve the thermal dissipation through the solder joint, making the thin Au <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> Sn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> solder layer very attractive for high power devices. In this paper, we establish a material model for the Au <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> Sn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> material in order to study solder thermal fatigue using finite element analysis.
The facts about Mechanical grease filters : Kitchen ventilation (2003)

Many kitchen hood manufacturers claim the efficiency of their grease filters is 90% or higher, and they reference several standards 1,2 to support the performance measurements. Unfortunately, none of these standards represents filter performance under cooking conditions. Grease emissions from cooking processes consist of particulate and vapor. Mechanical grease extractors are effective only at capturing particulate and are not able to extract vapor.
Effects of Lateral Eye Displacement on Comfort While Reading from a Video Display Terminal (2018)

Some small field-of-view (FOV) head worn displays (HWD), like Epson's Moverio BT-300, are mounted directly in the user's line of sight. In contrast, Google Glass is mounted “out of the way” and above the line of sight. Other displays like the Vuzix M100 or Optinvent ORA-1 allow the user to adjust the display position, and some users have expressed a desire for the display to be laterally displaced toward the ear, out of the main line of sight. How far toward the ear can a small FOV display be mounted and still be used comfortably? Using a 30-minute reading task and an emulated display with the FOV of a typical smart phone (9.2°x 16.3°), we study a user's perceived comfort level while reading at four horizontally displaced positions. We ask participants to rate their comfort every five minutes using a 5-point Likert scale knob (5 being most comfortable), for a total of seven measurements. Scores are summed over the seven measurements to form a summed comfort score. We find that 0° (Md = 34.0; p«0.001), 10° (Md = 33.5; p«c0.001), and 20° (Md = 33.5; p«c0.001) are more comfortable than 30° (Md = 29.5) and that 0° (p&lt;0.01) and 10° (p&lt;0.01) are more comfortable than 20°. Reading performance and workload measures were numerically similar across all conditions. Given the main results of the experiment, post-hoc analysis on other measurements such as preference and asthenopia, and participant comments, we suggest that small FOV displays should be mounted at lateral displacement angles of 20° and less for sustained use.