gebhart/patrepeval huggingface dataset:
Histologic transformation of follicular lymphoma to diffuse lymphoma represents tumor progression by a single malignant B cell. (1991)

To investigate the clonal relationship between follicular lymphoma (FL) and transformed diffuse lymphoma (tDL), we examined the expression of tumor idiotype, immunoglobulin (Ig) gene rearrangements and sequence of Ig variable genes in paired tissue specimens. All 16 cases analyzed expressed surface immunoglobulin (sIg) on both the FL and the tDL, though the immunophenotype of one case of FL could not be definitively determined. In 14 of 15 cases, the surface immunophenotype was preserved; the exception was likely secondary to a class switch from IgM to IgG. In 12 of 13 cases, antiidiotypic monoclonal antibodies prepared against the FL reacted with the paired tDL. Analysis of Ig gene rearrangements in four cases by Southern blot hybridization showed evidence of clonal relationships in all cases though concordance was not seen with all probes tested (C kappa, C lambda, JH, PFL1, and PFL2). In the one case that had a discordant L chain rearrangement, sequence analysis of the L chain demonstrated a common mature B cell origin for both the FL and tDL. To determine whether tDL arose from one or more FL cells, the sequences of the H chain variable genes were analyzed. Individual clones of the V region gene of the FL showed a random distribution of changes throughout the sequence. In contrast, individual clones of the V region gene from tDL shared numerous nonrandom sequence alterations, implying a common single cell origin. In conclusion, tDL is a mature B cell and arises by transformation of a single FL cell.
Highly Flexible and Transparent Multilayer MoS2 Transistors with Graphene Electrodes (2013)

A highly flexible and transparent transistor is developed based on an exfoliated MoS2 channel and CVD-grown graphene source/drain electrodes. Introducing the 2D nanomaterials provides a high mechanical flexibility, optical transmittance (∼74%), and current on/off ratio (>10(4)) with an average field effect mobility of ∼4.7 cm(2) V(-1) s(-1), all of which cannot be achieved by other transistors consisting of a MoS2 active channel/metal electrodes or graphene channel/graphene electrodes. In particular, a low Schottky barrier (∼22 meV) forms at the MoS2 /graphene interface, which is comparable to the MoS2 /metal interface. The high stability in electronic performance of the devices upon bending up to ±2.2 mm in compressive and tensile modes, and the ability to recover electrical properties after degradation upon annealing, reveal the efficacy of using 2D materials for creating highly flexible and transparent devices.
SIP dealing with location based information (2001)

This paper introduces an approach for providing Location Based Services (LBS) using Spatial Location (SLO) information within the Session Initiation Protocol (SIP). The aim of the paper is to set up the framework for providing LBS services in devices connected to wire and wireless IP networks. This method uses SIP as transport and the SLO as data format inserted in the SIP pay-load. It analyses the relationship among the network elements involved in the architecture, and its functionality for providing access to network services regardless of the user location. In conclusion, this proposal enables SIP to support location-related services such as messaging, location-based commerce, and any location-based computing. Furthermore, it describes the advantage of adding the user location information for network resources optimization in mobile environments and future networks.
Computationally efficient self-consistent born approximation treatments of phonon scattering for coupled-mode space non-equilibrium Green’s function (2011)

Efficient schemes for the non-equilibrium Green’s function simulation in the mode space formalism of electron-phonon scattering using the self-consistent Born approximation in nanoscale devices are presented, both using an “exact” and phenomenological Büttiker probe treatment of electron-phonon-scattering. In both cases we have generalized the expressions previously developed for the case of uncoupled mode space to coupled mode space. In the case of the phenomenological Büttiker probe treatment, we have also adapted the expressions used in the exact treatment in order to propose a new microscopic approach of phonon scattering using no analytical or average relaxation time approximations. This allows us to evaluate the accuracy and validity of the Büttiker probe assumption of the existence of a Fermi function in nanoscale devices. Our findings are that if the trends of the exact scattering are approximately reproduced by the Büttiker probe method, it seems to overestimate the on-current for a large range of devices with a channel length of a few tens of nanometers and a drain voltage higher than 100 mV.
Tracing an ancestral mutation: genealogical and haplotype analysis of the infantile onset spinocerebellar ataxia locus. (1996)

Infantile onset spinocerebellar ataxia (IOSCA) is a progressive neurological syndrome exhibiting an autosomal recessive pattern of inheritance. The characteristic features were described in Finland in the beginning of 1990s. Having shown that IOSCA does not segregate with any of the markers linked to other hereditary ataxias and thus represents a genetically distinct disease, we assigned the locus of this new hereditary ataxia to 10q23.3-q24.1. To approximate the age of the Finnish IOSCA mutation and to investigate the possible existence of more than one mutation underlying the disease, the ancestors of 13 IOSCA families were identified by use of church records dating back to the 1500s. The IOSCA pedigrees were frequently merged, providing support for these having one common ancestor. Analysis of the extended IOSCA haplotypes exposed ancient recombination events and revealed one core haplotype of four markers on a region of approximately 2 cM, which was unequivocally present in 92% of disease chromosomes. Both genealogical and haplotype data thus suggest that a single IOSCA ancestral mutation was introduced into the Finnish population most probably approximately 30-40 generations ago before the time when the general east-west migration took place within Finland.
Interpreting Networks in Systems Biology (2013)

Implementation of network systems biology principles offers unparalleled opportunity to synthesize and integrate inherently complex high-throughput data for meaningful interpretation. Nonstochastic network templates constructed from extant knowledge facilitate large data set prioritization and prognostication, identifying context-dependent candidates for follow-up functional validation and interpretation. In conjunction, enrichment and representation assessment refines comprehension of network-associated molecular functions and biological processes. Together, exploiting intrinsic network properties provides a value-added decision-support instrument for data deconvolution in systems biomedicine.
Polarized cytokinesis in vacuolate cells of Arabidopsis (2002)

The view of plant-cell cytokinesis commonly depicted in textbooks is of a symmetrical process, with the phragmoplast initiating in the center of the cell and growing outward to the parental cell membrane. In contrast to this picture, we observe that cell-plate development in Arabidopsis shoot cells is highly polarized along the plane of division. Three-dimensional live-cell imaging reveals that the mitotic spindle and phragmoplast are laterally displaced, and that the growing cell plate anchors on one side of the cell at an early stage of cytokinesis. Growth of phragmoplast across the cell creates a new partition in its wake, giving the visual effect of a curtain being pulled across the cell. Throughout this process, the advancing front of the phragmoplast is in intimate contact with the parental wall, suggesting that short-range interactions between the phragmoplast and plasma membrane may play important roles in guiding the cell plate throughout much of its development. Polarized cytokinesis was observed in a wide variety of vacuolate shoot cells and in some small root cells, implying that it is not solely a function of cell size. This mode of cytokinesis may provide a mechanically robust mechanism for cell-plate formation in large cells and suggests a simple explanation for the occurrence of cell wall stubs observed upon drug treatment or in cytokinetic mutants.
Pharmacology of a Novel, Orally Active PDE4 Inhibitor (2009)

Our results report the development of a promising, novel PDE4 inhibitor, NIS-62949, with a wider therapeutic window as compared to second-generation PDE4 inhibitors such as roflumilast.
MO-E-T-618-01: An Integrated CT-Based Monte Carlo Dose-Evaluation System for Brachytherapy and Its Application to Permanent Prostate Implant Postprocedure Dosimetric Analysis (2005)

Purpose: To develop a novel integrated CT-based Monte Carlo (MC) dose-evaluation system and use it to investigate the effect of tissue heterogeneities and interseed attenuation on brachytherapy dose distributions. Method and Materials: A MC photon-transport (MCPT) brachytherapy dose-calculation engine, PTRAN_CT, which uses x-ray CT to estimate tissue cross-sections, is developed based on PTRAN_CCG version 7.44. PTRAN_CT uses fast ray tracing that combines patient anatomy modeling via 3D voxel arrays with modeling of sources and applicators via a general combinatorial geometry code. A generalized phase-space source is used for further increasing efficiency. PTRAN_CT uses cross-section data derived from a single-energy CT image. PTRAN_CT was incorporated into an integrated system for performing postimplant dosimetric analysis of permanent prostate implants. A clinical implant consisting of 78 Model-6711 I-125 seeds was investigated to quantify interseed and tissue heterogeneity effects. Three scenarios were simulated a) comprehensive MC simulation including tissue heterogeneities and complete seed geometry b) complete seed geometry in homogeneous water and c) homogeneous water using 2D TG-43 source superposition. Results: Compared to case b), tissue heterogeneities (case a)) reduce doses by 5.8% on average in the target volume, after excluding artifacts from CT data. Interseed effects (case b) vs c)), reduce doses by 3% on average. The seed streaking artifact in CT data can affect MC result as large as 6%. The efficiency of PTRAN_CT relative to the predecessor code PTRAN_CCG is increased by factors of two and five, respectively, with and without enabling the phase-space option. In case b), PTRAN_CT yields the same dose distribution as benchmarked PTRAN_744. Conclusion: A novel post-implant dose evaluation system, based upon an accelerated CT-based Monte Carlo brachytherapy dose-calculation engine, has been developed and its accuracy and efficiency demonstrated. Preliminary results suggest that tissue heterogeneity effects can be incorporated into the clinical planning process.
Optical Wave Propagation through von Kármán Vortex Streets (2013)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text J. Minet, C. G. Nunalee, M. A. Vorontsov, and S. Basu, "Optical Wave Propagation through von Kármán Vortex Streets," in Imaging and Applied Optics, OSA Technical Digest (online) (Optica Publishing Group, 2013), paper PW3F.3. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Cutaneous Sporotrichosis Treated with Photodynamic Therapy: An in Vitro and in Vivo Study (2013)

PDT with intralesional 1% methylene blue (MB) in combination with intermittent low doses of itraconazole obtained complete microbiological and clinical response.
High speed silicon modulators (2009)

Recent silicon modulator research using ring modulators, electroabsorption modulators, and Mach-Zehnder modulators are reviewed and compared for specific applications.
What is the IEEE AP-S Education Committee Doing for You? [Education Column] (2007)

'would like to say thank you to the many contributors, reviewers, and other -great folks who have written to me about the Education Column, shared their teaching wisdoms and woes with me, and otherwise made this one of the particularly fun aspects of being a professor. However, now I am ready to share a little of this fuan, and I am passing the torch to Dr. David Kelley, a superb teac-her at Bucknell University in Pennsylvania. I will continue to be active in this committee as Past Chair (one of the best ways of getting a new volunteer is to agree to continue to help themn!). I would encourage anyone who is reading this column who is passionate about education and would like to be more involved to please volunteer to be on the Education Committee. We need people from both academics and industry to be sure that we serve everyone. We need people to help administer scholarships, manage the Web site, solicit articles, contribute ideas, and work with the Expert Now program. This committee is truly international, as you can see from the roster below.
JANUS (2012)

This paper addresses the problem of reducing unnecessary conflicts in optimistic synchronization. Optimistic synchronization must ensure that any two concurrently executing transactions that commit are properly synchronized. Conflict detection is an approximate check for this condition. For efficiency, the traditional approach to conflict detection conservatively checks that the memory locations mutually accessed by two concurrent transactions are accessed only for reading. We present JANUS, a parallelization system that performs conflict detection by considering sequences of operations and their composite effect on the system's state. This is done efficiently, such that the runtime overhead due to conflict detection is on a par with that of write-conflict-based detection. In certain common scenarios, this mode of refinement dramatically improves the precision of conflict detection, thereby reducing the number of false conflicts. Our empirical evaluation of JANUS shows that this precision gain reduces the abort rate by an order of magnitude (22x on average), and achieves a speedup of up to 2.5x, on a suite of real-world benchmarks where no parallelism is exploited by the standard approach.
Beiträge zur Chemie des Bors, 185 Reaktionen von Metallcarben‐Komplexen mit (tert‐Butylimino)‐ (2,2,6,6‐tetramethylpiperidino)boran (1987)

[2 + 2] Cycloaddition of the aminoiminoborane 1 with Cp 2 ‐TiCH 2 yields a blue 1‐aza‐2‐bora‐4‐titanacyclobutane derivative 2 . In contrast, Fischer carbenes (CO) 5 M = C(OMe)Me (MCr, W) react in a complex way to produce 1 · M(CO) 5 ( 4 ), tmpB(NHCMe 3 )OMe ( 5 ), and the borylated acetylene derivative 6 .
An All-Words Sense Tagging Method for Resource-Deficient Languages (2016)

All-words sense tagging is the task of determining the correct senses of all content words in a given text. Many methods utilizing various language resources, such as a machine readable dictionary (MRD), sense tagged corpus, and WordNet, have been proposed for tagging senses to all words rather than a small number of sample words. However, sense tagging methods that require vast resources cannot be used for resource-deficient languages. The conventional sense tagging method for resource-deficient languages, which utilizes only an MRD, suffers from low recall and low precision because it determines senses only when a gloss word in the dictionary exactly matches a context word. In this study, we propose an all-words sense tagging method that is effective for resource-deficient languages in particular. It requires an MRD, which is the essential resource for all-words sense tagging, and a raw corpus, which is easily acquired and freely available. The proposed sense tagging method attempts to find semantically related context words based on the co-occurrence information extracted from the raw corpus and utilizes these words for tagging the senses of the target word. The experimental results of an evaluation of the proposed sense tagging algorithm on a Korean test corpus consisting of approximately 15 million words show that it can tag senses to all contents words automatically with high precision. Furthermore, we also show that a semantic concordancer can be developed based on the automatic sense tagged corpus.
End users creating effective software (2004)

Is it possible to bring the benefits of rigorous software engineering methodologies to end users? End users create software when they use spreadsheet systems, web authoring tools and graphical languages, when they write educational simulations, spreadsheets, and dynamic e-business web applications. Unfortunately, however, errors are pervasive in end-user software, and the resulting impact is sometimes enormous. A growing number of researchers and developers are working on ways to make the software created by end-users more reliable. This special interest group meeting will help start to form a community of researchers who are addressing this topic.
Electrospun mat of tyrosine-derived polycarbonate fibers for potential use as tissue scaffolding material (2006)

Desaminotyrosyl-tyrosine ethyl ester (DTE) and desaminotyrosyl-tyrosine (DT) were used as monomers in the synthesis of two tyrosine-derived polycarbonates: the slow degrading homopolymer poly(DTE carbonate) and the fast degrading co-polymer poly(DTE-co-20%DT carbonate). Ultrafine fibers of these polymers were successfully fabricated using an electrospinning process. The effects of some solution and process parameters (i.e., polymer concentration, electrostatic field strength and solvent system) on morphological appearance and diameters of the obtained fibers were investigated by scanning electron microscopy (SEM). Smooth fibers were obtained at high enough solution concentrations (i.e., 15 and 20% (w/v)). The average fiber diameter was found to increase with increasing polymer concentration and applied electrostatic field strength. The electrospinnability of poly(DTE-co-20%DT carbonate) in dichloromethane was enhanced when methanol was used as the co-solvent. In all of the conditions investigated, the average diameter of the obtained smooth fibers ranged between 1.9 and 5.8 microm. A qualitative assessment of an as-spun mat of poly(DTE carbonate) fibers as a tissue scaffolding material showed that three different cultured cell lines appeared to adhere and propagate well within the scaffold. For poly(DTE carbonate) exceptionally high cell densities could be achieved after 10 days of cell culture.
Designed protein logic to target cells with precise combinations of surface antigens (2020)

Precise cell targeting is challenging because most mammalian cell types lack a single surface marker that distinguishes them from other cells. A solution would be to target cells using specific combinations of proteins present on their surfaces. In this study, we design colocalization-dependent protein switches (Co-LOCKR) that perform AND, OR, and NOT Boolean logic operations. These switches activate through a conformational change only when all conditions are met, generating rapid, transcription-independent responses at single-cell resolution within complex cell populations. We implement AND gates to redirect T cell specificity against tumor cells expressing two surface antigens while avoiding off-target recognition of single-antigen cells, and three-input switches that add NOT or OR logic to avoid or include cells expressing a third antigen. Thus, de novo designed proteins can perform computations on the surface of cells, integrating multiple distinct binding interactions into a single output.
Polyelectrolyte effects in model photoresist developer solutions: roles of base concentration and added salts (2003)

We demonstrate that poly(4-hydroxystyrene) and (5, 15, and 20) % <i>tert</i>-butoxycarboxy protected copolymers are polyelectrolytes when dissolved in aqueous base solutions. The polyelectrolyte effect is quantified through the observation of a correlation peak, measured with small-angle neutron scattering. Polyelectrolyte effects are weakened with added salts and excess base. These studies emphasize that salt additives screen the electrostatic interactions, while pH leads to the ionization of the chain. Solvent quality is quantified and the chain configurations are measured in the limit of high ionic strength. It is speculated that the developer-resist interactions will play an important role in development-induced roughness, hence these equilibrium solution measurements can serve a predictive function for future photoresists dissolution models incorporating solvent quality as a parameter.
Cylindrical photonic crystals (2005)

In this thesis, we explore the properties of cylindrical photonic crystal waveguides in which light is confined laterally by the band gap of a cylindrically-layered photonic crystal. We show in particular that axially-uniform photonic band gap waveguides can exhibit novel behavior not encountered in their traditional index-guiding counterparts. Although the effects discussed in each chapter range from hollow-core transmission to zero and negative group velocity propagation and to high-Q cavity confinement, they are all a result of the photonic band gap guiding mechanism. The reflective cladding of the photonic crystal waveguide is unique in that it allows one to confine light in a low index of refraction region, and to work with guided modes whose dispersion relations lie above the light line of air, in a region where the longitudinal wave vector of the guided mode can approach zero. Chapter 2 discusses hollow-core photonic band gap fibers that can transmit light with minimal losses by confining almost all of the electromagnetic energy to a hollow core and preventing it from entering the lossy dielectric cladding. These fibers have
Particles for Local Delivery of Proteins Using Intra‐Articular Route (2016)

Designing a vehicle for local delivery of proteins using intra-articular route is an attractive option to minimize the adverse effects associated with systemic exposure and to maximize the efficacy. Slowly dissolving silylated microparticles are designed with specific size and shape that are capable of extending the retention time of a model protein (bovine serum albumin) in the murine knee joint. No cytotoxicity is observed for the reconstituted formulation when tested against synovial fibroblasts and RAW 264.7 macrophages.
A 1.5GHz third generation itanium® 2 processor (2003)

This 130nm Itanium® 2 processor implements the Explicitly Parallel Instruction Computing (EPIC) architecture and features an on-die 6MB, 24-way set associative L3 cache. The 374mm2 die contains 410M transistors and is implemented in a dual-Vt process with 6 layers copper interconnect and FSG dielectric. The processor runs at 1.5GHz at 1.3V and dissipates a maximum of 130W. This paper reviews circuit design and package details, power delivery, RAS, DFT and DFM features, as well as an overview of the design and verification methodology. The fuse-based clock de-skew circuit achieves 24ps skew across the entire die, while the scan-based skew control further reduces it to 7ps. The 128-bit front-side bus supports up to 4 processors on a single bus with a bandwidth of up to 6.4GB/s.