gebhart/patrepeval huggingface dataset:
Abstract P3-12-03: Utilizing the genomically adjusted dose (GAD) to personalize radiotherapy in adjuvant breast cancer management (2016)

Abstract Background: We have previously validated a multi-gene model of tumor radiosensitivity (RSI) with validation in multiple independent cohorts including breast, rectal, esophageal, head and neck, glioblastoma, and prostate malignancies. Utilizing the linear quadratic model and RSI, we derived an expression for the genomically adjusted dose (GAD) to model radiation dose effect for individual patients. Methods: As RSI models the surviving fraction of cells at 2 Gy (SF2), we are able to derive a patient specific alpha. These terms were used in the linear quadratic model to calculate a GAD to model radiation effect and its association with local control. A higher GAD implies a higher predicted radiation therapy effect. Clinical and array-based gene expression were obtained from 75 ER negative patients from the Netherlands Cancer Institute (NKI) and the Institut Curie treated with breast conservation therapy. Results: Median follow-up for all patients was 10 years with a median age of 42 years (range: 23-50 years). Adjuvant radiation dose to the whole breast was 50 Gy (range: 45-55 Gy). When assessing local recurrence on multivariate analysis, we found GAD to be a significant predictor of local recurrence when dichotomized at the median (GAD-low vs GAD-high Hazard Ratio (HR) 4.5; 95% CI 1.7-13.5; p=0.0031). GAD was also significant per unit change (HR 0.91; 95% CI 0.83-0.99; p=0.021). We then modeled GAD for an escalated dose up to 60 Gy and found an additional 48% of GAD-low patients could achieve a GAD-high with dose escalation. Conclusions: We found GAD to be significantly correlated with local control following breast conservation therapy. Modeling dose escalation with GAD, we identified a select population of patients whom we hypothesize may benefit from genomically guided increased dose in the adjuvant setting. This population may represent a cohort for future clinical trial enrollment. Citation Format: Ahmed KA, Venkat PS, Scott JG, Diaz RJ, Fulp WJ, Torres-Roca JF. Utilizing the genomically adjusted dose (GAD) to personalize radiotherapy in adjuvant breast cancer management. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-12-03.
Facile Peptide Thioester Synthesis via Solution‐Phase Tosylamide Preparation. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Tape transport mechanism. [air sample collecting by porous tape for remote working level meter] (1979)

A device is provided for transporting, in a stepwise manner, tape between a feed reel and takeup reel. An indexer moves across the normal path of the tape displacing it while the tape on the takeup reel side of the indexer is braked. After displacement, the takeup reel takes up the displaced tape while the tape on the feed reel side of the indexer is braked, providing stepwise tape transport in precise intervals determined by the amount of displacement caused by the indexer.
Cyclic Prefix Based Enhanced Data Recovery in OFDM (2010)

In this correspondence, we show how the cyclic prefix (CP) can be used to enhance the performance of an orthogonal-frequency-division multiplexing (OFDM) receiver. Specifically, we show how an OFDM symbol transmitted over a block fading channel can be blindly detected using the output symbol and associated CP. The algorithm boils down to a nonlinear relationship involving the input and output data only that can be used to search for the maximum-likelihood (ML) estimate of the input. This relationship becomes much simpler for constant modulus (CM) data. We also propose iterative methods to reduce the computational complexity involved in the ML search of the input for CM data.
Automatic target segmentation in color dental images (2007)

Automatic target segmentation is critical to computerized dental imaging systems, which are designed to reduce human effort and error. We have developed an automatic algorithm that is capable of outlining an intra-oral reference bar and the tooth of interest. In particular, the algorithm first locates the reference bar using unique color and shape cues. The located reference bar provides an estimate for the tooth of interest in terms of both its scale and location. Next, the estimate is used to initialize a trained active shape model (ASM) consisting of the bar and the tooth. Finally, a search process is performed to find a match between the ASM and the local image structures. Experimental results have shown that our fully automatic algorithm provides accurate segmentation of both the reference bar and the tooth of interest, and it is insensitive to lighting, tooth color, and tooth-shape variations.
The mineralization inducing peptide derived from dentin sialophosphoprotein for bone regeneration (2012)

Dentin sialophosphoprotein (DSPP) has been shown to play a primary role in the formation and growth of hydroxyapatite crystals in an extracellular matrix of hard tissue such as bone and teeth. We hypothesized that the mineralization ability of DSPP might depend on a specific domain within it. Three peptides, which have hydroxyapatite (HA) binding affinity, denoted as mineralization inducing peptide (MIP1, MIP2, and MIP3) were identified from DSPP. The both of MIP2 and MIP3 had HA nucleation activity demonstrated by XRD. Among three MIPs, MIP3 significantly supported the human bone marrow stromal cell differentiation into osteoblastic cells. An immunoblot with antibodies specific for the phosphorylated forms of ERK was conducted with cells treated by MIP3. MIP3 transduced intracellular signals via the ERK pathways and was able to induce osteoblastic differentiation, as seen by high expression of ALP, type 1 collagen, OC, OPN, and Runx2 in accordance with applied MIP3 concentration. The Asp, Glu, and Ser residues in MIP3 play important roles for the affinity of calcium in HA bone mineral. Further animal experiment with MIP3 in combination with hydroxyapatite mineral induced marked new bone formation for 4 weeks at rabbit calvarial defect model. The new bone area was much higher in test group, implying that the peptide modified group had excellent biocompatibility when compared with the unmodified group. Taken together, the MIP from DSPP has potential to enhance mineralization followed by to enhance osteoblastic differentiation and bone regeneration.
Samarium-Promoted Coupling of 1,10-Phenanthroline with Carbonyl Compounds for Synthesis of New Ligands (2004)

1,10-Phenanthroline reacts with aldehydes and ketones in the presence of samarium diiodide to produce 2-(1-hydroxyalkyl)-1,10-phenanthrolines. The hydroxyalkyl substituent can be functionalized in numerous ways or removed to permit further ligand variation. The carbonyl coupling reaction can also be repeated to provide 2,9-disubstituted phenanthrolines. Taken together, these operations provide ready access to a large number of phenanthroline derivatives to serve as ligand libraries for catalyst exploration.
Vehicle-to-Business Communication: The Example of Claims Assistance in Motor Insurance (2010)

Due to consequent policy making and research funding in Europe, the US, and Japan, Intelligent Transportation Systems (ITS) are gaining momentum and provide mature concepts for vehicular communications enabling vehicles to communicate among themselves (Vehicle-to-Vehicle, V2V) and their immediate vicinity
A mammalian 2-5A system functions as an antiviral pathway in transgenic plants. (1996)

Resistance to virus infections in higher vertebrates is mediated in part through catalysis of RNA decay by the, interferon-regulated 2-5A system. A functional 2-5A system requires two enzymes, a 2-5A synthetase that produces 5'-phosphorylated, 2',5'-linked oligoadenylates (2-5A) in response to double-stranded RNA, and the 2-5A-dependent RNase L. We have coexpressed these human enzymes in transgenic tobacco plants by using a single plasmid containing the cDNAs for both human RNase L and a low molecular weight form of human 2-5A synthetase under control of different, constitutive promoters. Expression of the human cDNAs in the transgenic plants was demonstrated from Northern blots, by specific enzyme assays, and by immunodetection (for RNase L). Infection of leaves, detached or in planta, of the coexpressing transgenic plants by tobacco mosaic virus, alfalfa [correction of alfafa] mosaic virus, or tobacco etch virus resulted in necrotic lesions. In contrast, leaves expressing 2-5A synthetase or RNase L alone and leaves containing the plasmid vector alone produced typical systemic infections. While alfalfa mosaic virus produced lesions only in the inoculated leaves regardless of the concentration of virus in the inoculum, high, but not low, levels of tobacco etch virus inoculum resulted in escape of virus to uninoculated leaves. Nevertheless, there was a substantial reduction of tobacco etch virus yield as measured by ELISA assay in the coexpressing transgenic plants. These results indicate that expression of a mammalian 2-5A system in plants provides resistance to virus infections.
Scaling reliability and modeling of ferroelectric capacitors (2010)

We report on reliability properties of MOCVD PZT ferroelectric capacitors as a function of film thickness. Data is presented for fatigue, thermal depolarization, and imprint. It is important to be able to model these parameters as they can significantly affect the switching polarization, which in turn affects the signal margin of an FRAM circuit. A ferroelectric SPICE model is presented that can be used to accurately simulate hysteresis and switching polarization behavior. This model agrees with experimental data and can be used to simulate FRAM circuit behavior through "end of life".
Sensing optical cavity mismatch with a mode-converter and quadrant photodiode (2019)

We present a new technique for sensing optical cavity mode mismatch and alignment by using a cylindrical lens mode converting telescope, radio-frequency quadrant photodiodes, and a heterodyne detection scheme. The telescope allows the conversion of the Laguerre-Gauss bullseye mode (${\mathrm{LG}}_{01}$) into the 45\ifmmode^\circ\else\textdegree\fi{} rotated Hermite-Gauss (``pringle'') mode (${\mathrm{HG}}_{11}$), which can be easily measured with quadrant photodiodes. We show that we can convert to the HG basis optically, measure mode mismatched and alignment signals using widely produced radio-frequency quadrant photodiodes, and obtain a feedback error signal with heterodyne detection.
Silica-Polyamine Composite Materials for Heavy Metal Ion Removal, Recovery, and Recycling. II. Metal Ion Separations from Mine Wastewater and Soft Metal Ion Extraction Efficiency<sup>*</sup> (1999)

Silica-polyamine composites have been synthesized which have metal ion capacities as high as 0.84 mmol/g for copper ions removed from aqueous solutions. In previous reports it has been demonstrated that these materials survive more than 3000 cycles of metal ion extraction, elution, and regeneration with almost no loss of capacity (less than 10%). This paper describes two modified silica-polyamine composite materials and reveals the results of tests designed to determine the effectiveness of these materials for extracting and separating metal ions from actual mining wastewater samples. Using these materials, the concentration of copper, aluminum, and zinc in Berkeley Pit mine wastewater is reduced to below allowable discharge limits. The recovered copper and zinc solutions were greater than 90% pure, and metal ion concentration factors of over 20 for copper were realized. Further, the ability of one of these materials to decrease low levels of the soft metals cadmium, mercury, and lead from National Sanitation Foundation recommended challenge levels to below Environmental Protection Agency allowable limits is also reported.
Robust Majorana magic gates via measurements (2019)

High-fidelity $\ensuremath{\pi}/8$ phase gates are an essential ingredient for the majority of universal quantum computation proposals. Here, the authors present a new way of implementing a $\ensuremath{\pi}/8$ gate in Majorana-based qubits that eliminates the leading noise sources, expected to limit other approaches. The scheme employs a combination of measurements and quantum evolution to optimize the fidelity of the final state when a favorable set of measurement outcomes has been achieved and, at the same time, guarantees a high-success probability for obtaining such measurement outcomes.
A novel two‐step method for the formation of tissue‐engineered cartilage by mature bovine chondrocytes: The alginate‐recovered‐chondrocyte (ARC) method (2002)

Most attempts to tissue-engineer cartilage have involved seeding of cultured cells into a biological or synthetic scaffold. We have developed a novel two-step culture approach that makes possible the in vitro formation of cartilaginous-like tissue by mature adult bovine chondrocytes without the aid of a synthetic matrix. The first step consists of culturing chondrocytes under conditions that maintain their rounded shape and their molecular phenotype as assessed by type II collagen and aggrecan production. This step was accomplished by culturing the isolated chondrocytes in alginate beads until the cells have reestablished a proteoglycan-rich cell-associated matrix (CM). The second step consists of culturing the cells with their CM, after recovery from the beads, on a tissue culture insert with a porous membrane. In this study, young adult bovine articular chondrocytes were cultured in alginate beads in the presence of 10% or 20% fetal bovine serum (FBS). After 7 days of culture, the alginate beads were dissolved by incubating the beads for 20 min in sodium citrate buffer, a calcium chelator. Following a brief centrifugation, the cells with their CM were recovered, resuspended in medium containing 10% or 20% FBS and seeded onto a tissue culture insert. After 1 week of culture on the insert, the individual cells with their CM progressively became incorporated into a mass of cartilaginous tissue. Culture with 20% FBS resulted in the best formation of tissues. These tissues, easily recovered from the insert, were then subjected to biochemical and histological analyses. The biochemical results showed that the chondrocytes remain phenotypically stable in the tissues. The de novo tissue has a relatively high ratio of PG/collagen. Histological examination of the tissue revealed it contained a cartilage-like matrix strongly stained with toluidine blue. This scaffold-free system appears ideal to study, in vitro, the development of transplantable cartilaginous tissue.
Discovery of allelic variants ofHOXA1 andHOXB1: Genetic susceptibility to autism spectrum disorders (2000)

The results support a role for HOXA1 in susceptibility to autism, and add to the existing body of evidence implicating early brain stem injury in the etiology of ASDs.
The Mad Hatter´s Cocktail Party: A Social Mobile Audio Space Supporting Multiple Simultaneous Conversations (2003)

This paper presents a mobile audio space intended for use by gelled social groups. In face-to-face interactions in such social groups, conversational floors change frequently, e.g., two participants split off to form a new conversational floor, a participant moves from one conversational floor to another, etc. To date, audio spaces have provided little support for such dynamic regroupings of participants, either requiring that the participants explicitly specify with whom they wish to talk or simply presenting all participants as though they are in a single floor. By contrast, the audio space described here monitors participant behavior to identify conversational floors as they emerge. The system dynamically modifies the audio delivered to each participant to enhance the salience of the participants with whom they are currently conversing. We report a user study of the system, focusing on conversation analytic results.
Sleep Switch Dual Threshold Voltage Domino Logic (2006)

This chapter contains sections titled: Existing Sleep Mode Circuit Techniques Dual Threshold Voltage Domino Logic Employing Sleep Switches Simulation Results Noise Immunity Compensation Summary
Optimized contrast reduction for crosstalk cancellation in 3D displays (2011)

Subtractive crosstalk cancelation is an effective way to reduce the appearance of ghosting in 3D displays. However, effective cancelation requires the black level of the input images to be raised above zero, which reduces the image contrast and visual quality. Previous methods for selecting the raised black level do not consider the image content; they are either based on the worst case or they do not guarantee complete crosstalk cancelation. Previous methods also scale the red, green and blue channels independently, which results in images with washed out colors. This paper provides two contributions; first we derive the minimum amount that the black level has to be raised when using linear scaling in RGB space to ensure crosstalk can be fully cancelled out for a particular image. Second we propose that instead of scaling the images in RGB space, to scale the luma channel in YCbCr color space while keeping the chroma values constant to better preserve color. We also derive the minimum amount that the luma range has to be compressed to ensure that crosstalk can be fully canceled out. Experimental results show that our methods produce images with better color and contrast compared to scaling the RGB channels based on the worst case, while still guaranteeing crosstalk can be fully canceled out.
Nonlinear Optical Ellipsometric Studies of Chiral Systems (2005)

Nonlinear optical ellipsometry (NOE) was developed to interpret polarization information of the second harmonic generated (SHG) light at thin surface films. The experimentally simple instrument design allows for a mathematically straightforward evaluation of the data and yields greater information content than comparable intensity based techniques. The polarization- dependence of the SHG light yields the fully complex valued set of χ(2) nonlinear susceptibility tensor elements. The χ(2) tensor elements can then be related back to the structure of molecules at the silica/aqueous solution interface.
A Nipple-Areola Stencil for Three-Dimensional Tattooing: Nipple by Number (2019)

Medical tattooing is a critical reconstructive component in women following mastectomy. Recently, novel three-dimensional tattooing techniques mimicking depth by using light and shadow principles have allowed for aesthetically superior results. However, results are variable between providers, and professionals skilled in tattooing are often inaccessible to patients. To assess the need and obtain more background information regarding current practices, the authors recorded survey results from 753 plastic and reconstructive surgery offices. Results showed that 23 percent of facilities that offer reconstruction do not perform or refer for nipple-areola complex tattooing, leaving the patients to seek the service on their own. In this article, the authors present the nipple-by-number device, a three-dimensionally-printed stencil to ensure an accurate, consistent, and personalized aesthetic result during three-dimensional nipple-areola complex tattooing. The nipple-by-number device permits the plastic surgeon or supervised treating specialist to inexpensively, efficiently, and expeditiously perform the three-dimensional nipple-areola complex tattooing in their office. Furthermore, the device gives the patients the option of having their premorbid nipple-areola complex anatomy restored through preoperative photographs or choosing a different nipple-areola complex from a catalogue of designs. The device can be applied on any reconstructed breast mound whether or not a nipple projection procedure has been performed.
Group coordination support in networked multimedia systems (1999)

Advances in computer hardware and networking technology have incited the deployment of large-scale group-oriented applications for delivery or interactive development of multimedia content in the Internet. There is a growing number of protocols and techniques for group communication and membership services in the IP-multicast framework, however, group coordination support for telecollaborative tasks such as videoconferencing or distributed interactive simulation has received little attention. In this dissertation, we address network control and coordination functions to orchestrate synchronous multimedia groupwork, establishing a sharing discipline on multimedia resources and guaranteeing consistency of distributed activities with ordered multicasting. 
We introduce a formal framework for group coordination and a turn-taking abstraction useful for evaluating coordination protocols. Elemental design choices for group coordination architectures and the concept of aggregated processing of coordination information are discussed. 
A floor control methodology is presented to implement concurrency control for interactive, rather than transactive cooperation among users. Floors are dynamically generated, ephemeral permissions for using discrete or continuous media such as GUI objects, audio and video channels, or remote instruments. Floor control regulates user interaction and bandwidth consumption by throttling sources in sending information flows according to receiver interest. A novel taxonomy of floor control protocols and a comparative throughput analysis show that large-scale group coordination is most effectively supported by hierarchical host organization. Two new protocols are presented to provide floor control in fully-connected networks and in multicast trees, where the addition of group-relative address information permits more sophisticated coordination among end-nodes. 
Finally, we discuss the problem of out-of-sequence delivery in multicasting. A new taxonomy for ordered multicasting protocols and a comparison of message complexities elicit the benefits of aggregated, ordered multicasting. We present a novel multicast ordering protocol for more efficient total-order delivery of messages from multiple sources to multiple, potentially overlapping receiver groups in multicast trees. Previous solutions require the computation of a separate propagation graph to structure ordering relations and incur high cost, if sources change frequently. Our proposed mechanism is more flexible and efficient, because it relays ordering information in accordance with the hierarchical organization of end-hosts maintained by an underlying tree-based reliable multicast protocol.