gebhart/patrepeval huggingface dataset:
Abstract 1391: Gene expression profiling for cancer classification in circulating tumor cells (2016)

Abstract Background: Enumeration and molecular characterization of circulating tumor cells (CTCs) offer a non-invasive method for tumor analysis, particularly in cases where the biopsy is difficult to obtain or has been exhausted by conventional diagnostic methods. The 92-gene assay (CancerTYPE ID®, bioTheranostics, Inc.) is a clinically-validated cancer classifier based on the collective expression of 87 informative genes, many of which are involved in lineage commitment and signal transduction. The objective of this study was to determine the feasibility of a blood-based application using differential gene expression. Methods: Technical feasibility studies for cancer cell enrichment and RNA viability were conducted by purifying cancer cell lines that were spiked into donor blood using a microfluidic chip (Celsee PREP™100 system, Celsee Diagnostics) followed by immunodepletion of leukocytes. Quantitative RT-PCR and immunoflourescence were performed on cells harvested at different steps of the purification workflow. Quantitative RT-PCR on individual genes specific to each lineage compartment was used to estimate cell types and cell numbers that were co-purified by the workflow. Gene expression was evaluated by the 92-gene assay. Results: An integrated workflow was established that allows for the molecular characterization of cancer cells purified from blood. Cell enrichment on the microfluidic chip followed by purification using immunodepletion resulted in efficient recovery (&amp;gt; 80% of input cells) and viable RNA from cancer cells spiked into whole blood. A key result of this study was the demonstration that the level of cancer-specific gene expression in purified samples was similar to the level of expression from an equivalent number of unspiked cancer cells suggests that significant cell loss does not occur during the purification workflow. A comparison of gene expression profiles from purified and mixed cell populations allowed for the identification of subsets of genes that are differentially expressed in cancer cells compared with leukocytes. Conclusion: A functional workflow with viable RNA and efficient recovery of cancer cells that are within the technical specifications of the 92-gene assay was established. Findings from this feasibility study are fundamental to the potential for CTC-based cancer classification. Citation Format: Harris S. Soifer, Ranelle C. Salunga, Tristan G. Harris, Jose Ramirez, Priyadarshini Gogoi, Yixin Wang, Saedeh Sepehri, Kalyan Handique, Catherine A. Schnabel. Gene expression profiling for cancer classification in circulating tumor cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1391.
Low-Temperature Kinetics of Localized Excitons in Quantum-Well Structures (1998)

We present a kinetic theory of low-temperature localized-exciton energy relaxation in the multiple hopping regime under steady-state and pulsed optical excitation. The theory permits to relate the lineshape and the temporal redshift of photoluminescence spectra to the exciton kinetic parameters and band-tail density of states. A series of (Zn,Cd)Se/Zn(S,Se) quantum wells of different thickness and content has been studied using cw and time-resolved photoluminescence techniques. A 20 Å Zn0.8Cd0.2Se/ZnSe quantum well is selected for the detailed comparison between experiment and theory and for the evaluation of localized-exciton parameters.
Biometrology of physical properties of skin in thyroid dysfunction (2008)

This multipronged exploratory study shows that direct or indirect effects of TSH may influence the stratum corneum hydration. This correlation seemed very sensitive, as no other specific biophysical parameter was significantly correlated with the thyroid hormonal concentrations in the serum. However, our findings do not exclude the possibility of some other skin changes supervening in case of more severe thyroid dysfunction. The mechanism by which TSH alters the stratum corneum hydration is yet unknown.
Investigation of the Feasibility of RTL Concept for Fusion Energy (2001)

No abstract prepared.
Chemical Analysis of Activation Process of LSM Thin Film Electrode (2017)

In this study, the activation process of strontium-doped lanthanum manganite (LSM) was investigated. LSM thin films on yttria-stabilized zirconia (YSZ) half cells were fabricated with an LSCF counterelectrode and the effects of cathodic current density and overpotential on the polarization behavior of the LSM thin film electrode were investigated. The surface morphology as well as surface chemistry and bonding environment of LSM before and after polarization were investigated using scanning electron microscope (SEM) and X-ray photoelectron spectroscopy (XPS), respectively. The formation of SrO was found on the LSM surface after polarization. The cross-section microstructures of LSM were examined using transmission electron microscope (TEM) and TEM-based energy dispersive X-ray spectroscopy (EDS). The presence of Mn-rich phases were observed before and after polarization. The pre- and post-activation electrode performances were investigated, which help reveal the nature of the activation mechanism in combination with the microstructural and chemical analysis.
Supplementary Figures 1-5 from The Telomerase Inhibitor Imetelstat Depletes Cancer Stem Cells in Breast and Pancreatic Cancer Cell Lines (2023)

Supplementary Figures 1-5 from The Telomerase Inhibitor Imetelstat Depletes Cancer Stem Cells in Breast and Pancreatic Cancer Cell Lines
Heterogeneities in Fullerene Nanoparticle Aggregates Affecting Reactivity, Bioactivity, and Transport (2010)

Properties of nanomaterial suspensions are typically summarized by average values for the purposes of characterizing these materials and interpreting experimental results. We show in this work that the heterogeneity in aqueous suspensions of fullerene C(60) aggregates (nC(60)) must be taken into account for the purposes of predicting nanomaterial transport, exposure, and biological activity. The production of reactive oxygen species (ROS), microbial inactivation, and the mobility of the aggregates of the nC(60) in a silicate porous medium all increased as suspensions were fractionated to enrich with smaller aggregates by progressive membrane filtration. These size-dependent differences are attributed to an increasing degree of hydroxylation of nC(60) aggregates with decreasing size. As the quantity and influence of these more reactive fractions may increase with time, experiments evaluating fullerene transport and toxicity end points must take into account the evolution and heterogeneity of fullerene suspensions.
Design and optimization of 32-core rod/trench assisted square-lattice structured single-mode multi-core fiber (2017)

We propose and design a kind of heterogeneous rod-assisted and trench-assisted multi-core fiber (Hetero-RA-TA-MCF) with 32 cores arranged in square-lattice structure (SLS), and then we introduce the design method for Hetero-RA-TA-MCF. Simulation results show that the Hetero-RA-TA-32-Core-Fiber achieves average effective area (A<sub>eff</sub>) of about 74 μm<sup>2</sup>, low crosstalk (XT) of about -31 dB/100km, threshold value of bending radius (R<sub>pk</sub>) of 7.0 cm, relative core multiplicity factor (RCMF) of 8.74, and cable cutoff wavelength (λ<sub>cc</sub>) of less than 1.53 μm.
3D Neglect Test: Functional Assessment of Exploration and Orientation Skills in Left Visuo-Spatial Neglect Patients within the Framework of Virtual Reality (2004)

keywords: Biomechatronics &amp; Rehabilitation Technology, Neglect, Virtual Reality, BIT
Contextual vector quantization modeling of hand-printed Chinese character recognition (2002)

A hand-printed Chinese character recognizer based on contextual vector quantization (CVQ) has been built. The idea of CVQ is to quantize each pixel to a codeword by considering not just the pixel itself but its neighbors and their codeword identities as well. 100 samples of each character are collected from 100 writers, among them, 92 are used for training and 8 for testing. The characters are scanned by a 300 dpi scanner, which are then noise removed, thinned, segmented and size normalized. Stroke counts and segment strengths are adopted as observation features. For a vocabulary of 470 simplified Chinese characters, a recognition rate of 97% is achieved.
Limitations of reduced-field irradiated volume and technique in conventional radiation therapy of prostate cancer:Implications for conformal 3-D treatment (2000)

In order to define technical limitations of conventional external beam irradiation for clinically localized prostate cancer, we evaluated the impact of several reduced-field treatment factors, such as reduced-field (RF) irradiated volume, RF technique, photon energy of treatment, and dose on survival endpoints and local control in a retrospective series. Several survival endpoints, such as disease-specific survival, freedom from relapse survival, biochemical no-evidence of disease (bNED) survival, and local control were associated with several treatment variables using univariate and multivariate analyses in 329 patients. Reduced-field technique appeared to predict survival outcome, with patients treated by bilateral 120 degrees arcs faring less well than those treated by full 360 degrees rotational fields. The irradiated volume of the reduced-field was also significantly associated with survival outcome, with patients treated with smaller volumes faring less well. Local failure rates also appeared increased, although not statistically, in patients treated with smaller RF sizes. In an attempt to explain these detected deficiencies, dose-volume histograms for prostate coverage were created for a small sample of patients. The deficiencies related to small reduced-field volume appeared to be largely attributable to poor dosimetric coverage of the prostate. These results underscore the limitations of conventional external beam treatment for prostate carcinoma when conventional techniques are employed, particularly if small reduced fields are used, and further supports the development of improved treatment techniques, such as conformal irradiation, as alternatives.
TOWARDS PATHOGEN DETECTION VIA OPTICAL INTERROGATION OF MAGNETIC MICRODISCS (2016)

We present progress in the development of a micro/nanobased scheme for portable, rapid, low-cost detection of foodborne bacterial pathogens, such as Escherichia coli, Listeria monocytogenes, or Salmonella. The system uses magnetic microdiscs that are functionalized for selective binding to target pathogens. The presence of a target pathogen is evaluated by optically monitoring the rotation of the microdiscs when subjected to a rotating magnetic field. This article summarizes the following advancements: (1) wafer-level microfabrication of 600 million gold-coated microdiscs per substrate; (2) functionalization of the microdiscs with DNA aptamers and subsequent binding to E. coli O157:H7; and (3) magnetic manipulation of the bound bacteria.
Development Of The Textbook, Conservation Principles In Bioengineering (2020)

The textbook, Conservation Principles in Bioengineering, which covers the conservation laws with applications in biological and medical systems, has been written. Its publication by Prentice Hall is expected in 2005. The conservation
Formation and Transport of Nanotube-Integrated Vesicles in a Lipid Bilayer Network (2003)

We present a micromanipulation method to create, load, and transport vesicles (with diameters of ∼500 nm to 5 μm) between two surface-adhered giant vesicles conjugated by a suspended nanotube. The walls of the lipid bilayer (two-dimensional liquid crystal) of the nanotube-integrated mobile vesicles are continuous with the nanotube walls and, thus, are 2-fold open-ended. Nanotube-integrated vesicles are created by the injection of excess membrane material into a surface-adhered vesicle. The transport of vesicles along the nanotubes is controlled using a difference in membrane tension that is caused by shape deformation of the surface-adhered vesicles using micromanipulator-controlled carbon fibers. When reaching a surface-adhered vesicle, a mobile vesicle can empty its contents into it on demand. This way, reactants or other chemical or physical cargo can be delivered into a neighboring vesicle to, for example, titrate a chemical substance or provide reactants to initiate a chemical reaction. This system is capable of controlled transport and handling of minute volumes (10-12−10-18 L), via manipulation of the energy state of the device material itself, and creates new possibilities for performing chemistry in aqueous phases at the nanoscale and microscale, as well as in the construction of nanofluidic devices.
Evaluation of the percentage of sperm motility at 24 h and sperm survival ratio for prediction of in vitro fertilization (2009)

The present study was carried out to investigate the predictive value of the percentage of sperm motility after 24-h incubation and sperm survival ratio from semen and inseminated sperm suspension using grading of motility by WHO criteria with respect to the fertilization of oocytes in vitro. A total of 789 oocytes from 85 cases were inseminated and the mean fertilization rate obtained was 72.5%. There was no significant correlation between all of the sperm motility results with fertilization rate in vitro. All sperm motility results were not significantly different between the non-fertilizing group and the fertilizing group and also between the group of fertilization rate < or = 25th percentile (fertilization rate < or = 62.5%) and the group of fertilization rate > 62.5%. However, the initial percentage of rapid progressive sperm motility and progressive motility in semen and inseminated sperm suspension at 24 h gave significant differences between the group of fertilization < or = 50th percentile (fertilization rate < or = 80%) and the group of fertilization rate > 80%. Overall accuracy using these parameters for prediction of fertilization rate > 80% was only about 60%. In conclusion, the percentage of sperm motility at 24 h and sperm survival ratio in both semen and inseminated sperm suspension have no practical value in predicting fertilization rate in vitro. Moreover, detailed motility grading cannot improve the predictivity of these sperm motility parameters.
Fabrication of micro- and nanometre-scale polymer structures in liquid crystal devices for next generation photonics applications (2016)

Direct Laser Writing (DLW) by two-photon photopolymerization (TPP) enables the fabrication of micron-scale polymeric structures in soft matter systems. The technique has implications in a broad range of optics and photonics; in particular fast-switching liquid crystal (LC) modes for the development of next generation display technologies. In this paper, we report two different methodologies using our TPP-based fabrication technique. Two explicit examples are provided of voltage-dependent LC director profiles that are inherently unstable, but which appear to be promising candidates for fast-switching photonics applications. In the first instance, ~1 &mu;m-thick periodic walls of polymer network are written into a planar aligned (parallel rubbed) nematic pi-cell device containing a nematic LC-monomer mixture. The structures are fabricated when the device is electrically driven into a fast-switching nematic LC state and aberrations induced by the device substrates are corrected for by virtue of the adaptive optics elements included within the DLW setup. Optical polarizing microscopy images taken post-fabrication reveal that polymer walls oriented perpendicular to the rubbing direction promote the stability of the so-called optically compensated bend mode upon removal of the externally applied field. In the second case, polymer walls are written in a nematic LC-optically adhesive glue mixture. A polymer- LCs-polymer-slices or ‘POLICRYPS’ template is formed by immersing the device in acetone post-fabrication to remove any remaining non-crosslinked material. Injecting the resultant series of polymer microchannels (~1 &mu;m-thick) with a short-pitch, chiral nematic LC mixture leads to the spontaneous alignment of a fast-switching chiral nematic mode, where the helical axis lies parallel to the glass substrates. Optimal contrast between the bright and dark states of the uniform lying helix alignment is achieved when the structures are spaced at the order of the device thickness, which was also found to be the case for the achiral system. The high resolution DLW technique limits structures to the focal spot size of the beam, ~1 &mu;m in diameter, such that the transmittance is expected to be significantly enhanced relative to other stabilization techniques. Moreover, both devices remain stable under electrical and thermal cycling.
Physical road marker property estimation using monoscopic vision (2010)

In this paper algorithms are presented to extract lane markers and their properties from monoscopic camera images. A filter approach that takes into account the visual appearance of the markers is presented. Another contribution constitutes the measurement of physical marker width and length from perspectively distorted images using only the calibrated camera images. Also distances between markers can be estimated. All algorithms are independent from a specific lane model.
Uppmärksamhetsstilar inom golf (1998)

Denna undersokning ar en enkatundersokning med randomisering av urvalsgruppen pa respektive golfklubb. Undersokningen amnar undersoka koncentrationen hos golfspelare for att sedan inrikta resultate ...
Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA (2016)

Patients with diffuse large B cell lymphoma (DLBCL) exhibit marked diversity in tumor behavior and outcomes, yet the identification of poor-risk groups remains challenging. In addition, the biology underlying these differences is incompletely understood. We hypothesized that characterization of mutational heterogeneity and genomic evolution using circulating tumor DNA (ctDNA) profiling could reveal molecular determinants of adverse outcomes. To address this hypothesis, we applied cancer personalized profiling by deep sequencing (CAPP-Seq) analysis to tumor biopsies and cell-free DNA samples from 92 lymphoma patients and 24 healthy subjects. At diagnosis, the amount of ctDNA was found to strongly correlate with clinical indices and was independently predictive of patient outcomes. We demonstrate that ctDNA genotyping can classify transcriptionally defined tumor subtypes, including DLBCL cell of origin, directly from plasma. By simultaneously tracking multiple somatic mutations in ctDNA, our approach outperformed immunoglobulin sequencing and radiographic imaging for the detection of minimal residual disease and facilitated noninvasive identification of emergent resistance mutations to targeted therapies. In addition, we identified distinct patterns of clonal evolution distinguishing indolent follicular lymphomas from those that transformed into DLBCL, allowing for potential noninvasive prediction of histological transformation. Collectively, our results demonstrate that ctDNA analysis reveals biological factors that underlie lymphoma clinical outcomes and could facilitate individualized therapy.
A Prospective Outcome Evaluation of Arthroscopic Bankart Repairs (2006)

Bankart repairs performed arthroscopically using properly implanted suture anchors and nonabsorbable sutures and in which associated pathoanatomy is addressed demonstrate low recurrence rates (10%) similar to historical open controls.
Balloon aortic valvuloplasty in a 1,600‐gram infant (2000)

We present a 1,600 g infant who underwent successful balloon aortic valvuloplasty from the right carotid artery approach. A simple technique to facilitate access to the left ventricle and expedite the procedure is described. Issues unique to performing balloon aortic valvuloplasty on such a small child are discussed.
Volumetric Quasi-conformal Mappings - Quasi-conformal Mappings for Volume Deformation with Applications to Geometric Modeling (2015)

Due to intrinsic differences between surfaces and higher dimensional objects, some important results regarding surfaces can not be extended to volumetric domains. Most significantly, there exist no conformal volumetric maps apart from Mobius transformations. Although it is sometime stated explicitly, it is often overlooked that existing methods of volume parameterization produce only quasi-conformal maps, which may be âfar from conformalityâ. We therefore introduce methods for assessing the extent of the local and global volumetric deformation by means of the amount of conformal distortion produced. To this end we first illustrate basic three-dimensional quasi-conformal deformations that are produced by parameterization techniques, and highlight theoretical issues associated with spatial quasi-conformal mappings, and the relation that exists between the geometry of the domain and conformal distortion.
One-shot Federated Learning without Server-side Training (2022)

Federated Learning (FL) has recently made significant progress as a new machine learning paradigm for privacy protection. Due to the high communication cost of traditional FL, one-shot federated learning is gaining popularity as a way to reduce communication cost between clients and the server. Most of the existing one-shot FL methods are based on Knowledge Distillation; however, {distillation based approach requires an extra training phase and depends on publicly available data sets or generated pseudo samples.} In this work, we consider a novel and challenging cross-silo setting: performing a single round of parameter aggregation on the local models without server-side training. In this setting, we propose an effective algorithm for Model Aggregation via Exploring Common Harmonized Optima (MA-Echo), which iteratively updates the parameters of all local models to bring them close to a common low-loss area on the loss surface, without harming performance on their own data sets at the same time. Compared to the existing methods, MA-Echo can work well even in extremely non-identical data distribution settings where the support categories of each local model have no overlapped labels with those of the others. We conduct extensive experiments on two popular image classification data sets to compare the proposed method with existing methods and demonstrate the effectiveness of MA-Echo, which clearly outperforms the state-of-the-arts. The source code can be accessed in \url{https://github.com/FudanVI/MAEcho}.