gebhart/patrepeval huggingface dataset:
A programmable CMOS RF frequency synthesizer for multi-standard wireless applications (2004)

This paper deals with a new frequency synthesizer dedicated to multi-standard wireless applications. It converts a 50 MHz wave clock into two outputs in quadrature phase. It takes advantage of the DLL topology in terms of jitter and phase noise and has no external element. Simulations of the structure designed with a 130 nm SOI CMOS technology confirming the performance of the system are also presented.
Protein/CaCO3/Chitin Nanofiber Complex Prepared from Crab Shells by Simple Mechanical Treatment and Its Effect on Plant Growth (2016)

A protein/CaCO₃/chitin nanofiber complex was prepared from crab shells by a simple mechanical treatment with a high-pressure water-jet (HPWJ) system. The preparation process did not involve chemical treatments, such as removal of protein and calcium carbonate with sodium hydroxide and hydrochloric acid, respectively. Thus, it was economically and environmentally friendly. The nanofibers obtained had uniform width and dispersed homogeneously in water. Nanofibers were characterized in morphology, transparency, and viscosity. Results indicated that the shell was mostly disintegrated into nanofibers at above five cycles of the HPWJ system. The chemical structure of the nanofiber was maintained even after extensive mechanical treatments. Subsequently, the nanofiber complex was found to improve the growth of tomatoes in a hydroponics system, suggesting the mechanical treatments efficiently released minerals into the system. The homogeneous dispersion of the nanofiber complex enabled easier application as a fertilizer compared to the crab shell flakes.
SiC Substrate Doping Profiles Using Commercial Optical Scanners (2006)

Presented is the use of a commercial optical scanner for the mapping of doping density ( ) D N of SiC substrates and as a local probe for D N in different regions. This method provides a fast and cost effective method for determining D N homogeneity, examining local electrical characteristics, and recognizing defect sites including areas of different polytypes or polycrystallinity. Micro-Raman spectroscopy was used to calibrate the transmission intensity with D N . It is shown that features presented in the calculated D N maps strongly correlate to those observed in Lehighton resistivity maps.
“The Same Sort of Seed in Different Earths”: Tobacco Types and Their Regional Variation in Colonial Virginia (2006)

When tobacco planting spread out of the Jamestown area in the 620s in Virginia and production began the following decade in Maryland, planters soon realized that something strange was happening in their fields. Using the same seeds from the same sources and using identical cultivation and curing practices, they found that “the same sort of Seed in different Earths” produced tobaccos “much different, as to goodness.” By the middle of the seventeenth century, planters recognized two distinct types of tobacco: “sweet-scented” and “Oronoco.”2 Those tobaccos would dominate the agricultural systems of Virginia and Maryland throughout the Colonial Period and sweetscented tobacco dominated Virginia’s tobacco market until well into the eighteenth century. Until recently, historians of the Chesapeake had only touched upon the general differences between sweet-scented and Oronoco tobaccos and their regional variations.3 Lorena Walsh has recognized the implications of the difference and has become the first scholar of the Chesapeake to approach the subregional level based on tobacco production regions rather than often arbitrary and sometimes ill-applied physiographic divisions.4 This study examines why different tobacco subregions (particularly a sweet-scented one) existed in Virginia. Emphasis is placed on how a combination of natural and human parameters created different tobacco subregions. The differences between sweet-scented and Oronoco tobaccos – especially in terms of appearance, soil requirements, and production – will be analyzed from an agroecological perspective by using historical descriptions and data, as well as modern applications of plant physiology, geomorphology, and soil science.5 Because the real focus here is on Virginia’s unique sweet-scented tobacco, close attention is paid to the nature and location of sweetscented tobacco in Tidewater Virginia, the ultimate extent of the sweetscented tobacco subregion, and important environmental and economic
Lower Gastrointestinal Endoscopic Surveillance and Ablative Therapy for Post Operative Familial Adenomatous Polyposis Patients (2006)

Purpose: Preventative surgery for Familial Adenomatous Polyposis (FAP) aims to minimize colon cancer risk. Yet, post surgical time intervals for endoscopic surveillance are unknown. The aims of this study were 1) To determine the prevalence of adenomatous disease in FAP patients following various types of prophylactic colorectal surgery, 2) To determine the safety and effectiveness of lower GI endoscopic surveillance and ablative therapy. Methods: Retrospective analysis of clinical, demographic, endoscopic, surgical and histological records of 41 FAP patients (M/F: 18/23) enrolled in a lower GI surveillance and ablative therapy program from 1992 to 2006. Results: Endoscopic surveillance began at a median of 11 years (Range 0–33) following colectomy, with a presentation age for surveillance of 40 years (Range 13–65). Prior surgical history included: subtotal colectomy (n = 10), ileoanal J pouch anastomosis (n = 10), colectomy with ileorectal anastomosis (n = 6), Brooke ileostomy (n = 5), proctocolectomy with ileostomy (n = 4), Kock pouch ileostomy (n = 3) and colectomy with ileoanal pull through (n = 3). Patients had a median of 4 procedures of which 2 (Range 0–12) were therapeutic over 49 month follow-up (Range 0–155). Initial endoscopy identified polyps in all patients ranging in number from one to numerous. Polyp location included: residual rectum (16/16), J pouch (9/10), efferent ileal limb (2/10), stoma (8/9), ileo anal anastomosis (3/3), and nipple valve (2/3). Diminutive polyps 17/41 were not sampled. In the remaining 24 patients, histology of larger polyps (up to 40mm) confirmed adenomatous tissue with low and high grade dysplasia in 16/24 and 1/24 respectively. Two patients, 12 and 13 years post subtotal colectomy had evidence of rectal stump cancer. Ablative therapy complications included: YAG laser ulcer induced hemorrhage (n = 1) and rectal perforation post polypectomy (n = 1). One patient (1/41) with a Kock pouch histologically progressed from low to high grade dysplasia despite ablative therapy over 30 months surveillance. Conclusions: Following prophylactic colorectal surgery, all patients had residual polyp burden. Initial endoscopy detected advanced neoplasia in 7%, leading to surgical intervention. Despite ablative therapy, 3% of patients progressed histologically.
The usefulness of combined measurements of squamous cell carcinoma antigens 1 and 2 in diagnosing atopic dermatitis (2012)

Combined measurements of SCCA1 and SCCA2 are very useful in estimating the severity of allergic diseases, making it possible to distinguish allergic diseases from cancers.
Insights for curriculum design from design research (2013)

The paper considers how research in product/process design methodologies can be used to design engineering curricula. Following the Function-Behavior-Structure (FBS) framework for product design, we show how the curriculum design task can be separated into functionality of the curriculum, student behaviors and course structures. We then describe possible ways in which such a design could help us explore the possibilities of designing different types of curricula with the same functionality so that we could develop flexible, fault tolerant, scalable curricula that evolves with changing circumstances. These requirements are not generally included as curriculum design criteria and an approach that highlights the role of “robustness” would be useful.
Entropy-Constrained Linear Vector Predict ion for Motion-Compensated Video Coding (1998)

Theoretical and experimental results for motion-compensated linear prediction of video signals are presented. The rate distortion theory of motion-compensated prediction is extended to linear predictive models. For practical implementations, linear vector predictors are employed. The rate of the motion data is controlled by minimizing a Lagrangian cost function where rate is weighted against distortion using a Lagrange multiplier. An adaptive algorithm for optimally selecting the number of input signals to the linear vector predictor is given. I. Theoretical Analysis Following the framework for the rate distortion analysis of motion-compensated prediction in [1], we derive a closed form expression, where the power spectrum of the prediction error is related to the displacement pdfs of an arbitrary number of scalar input signals to the linear predictor. Previous work of Girod on the subject can be found in [2]. Let s[x; y] be a scalar two-dimensional signal sampled on an orthogonal gr...
Characterization of Six Murine Monoclonal Antibodies Specific for Toxin B of Clostridium difficile (1994)

Six murine hybridoma cell lines producing monoclonal antibodies (MAbs) specific for Toxin B of Clostridium difficile have been generated from toxin-immunized female RBF/DnJ mice. All six antibodies were reactive in Western blots with a > 200-kD protein in the supernatants of the toxigenic strain 10463 and were unreactive with similarly prepared material from the nontoxigenic strain 2037. Polyclonal antisera from rabbits immunized with Toxin B reacted on Western blots primarily with Toxin B, a 40-kD and a 55-kD band with a minor set of triplet bands at approximately 100 kD. None of the MAbs reacted in a direct EIA with purified Toxin A from C. difficile but two MAbs reacted weakly with a trypsin-sensitive band (> 200 kD) in Western blots of C. sordellii. Polyclonal antisera developed against Toxin B reacted strongly with supernatants from C. sordellii, C. bifermentans, and the nontoxigenic strain 2037. Toxin B-specific antisera was unreactive with supernatants from C. perfringens or purified Toxin A from C. difficile in direct EIA. Toxin B-specific MAbs linked to an affinity column were able to deplete bacterial supernatant of cytotoxigenic activity.
Human recombinant interleukin 4 induces normal B cells to produce soluble CD23/IgE‐binding factor analogous to that spontaneously released by lymphoblastoid B cell lines (1988)

Surface-labeled Epstein-Barr virus (EBV)-transformed lymphoblastoid RPMI 8866 cells release in their supernatant a radiolabeled 25-kDa polypeptide which reacts with the Fc epsilon RL/CD23-specific monoclonal antibody (mAb) 25 and which binds to IgE but not IgG (IgE BF/sCD23). IgE BF/sCD23 had an isoelectric point of 4.5-5.0. The reactivity of mAb 25 with IgE BF/sCD23 allowed us to set up a radioimmunoassay for detection of IgE BF/sCD23 in cell culture supernatants. Supernatants from Fc epsilon RL/CD23+ cell lines were found to contain IgE BF/sCD23. Addition of human recombinant interleukin 4 (IL 4) to normal human B cells cultures induced the production of IgE BF/sCD23. Activation of B cells with anti-IgM antibody coupled to beads enhanced the IL 4-induced production of IgE BF/sCD23 when compared to nonactivated B cells. This correlates with the finding that anti-IgM antibody-activated B cells cultured with IL 4 express more Fc epsilon RL/CD23 than B cells cultured with IL 4 alone. The biochemical characteristics of radiolabeled IgE BF/sCD23 immunoprecipitated by mAb 25 from the supernatants of normal B cells cultured with IL 4 were identical to those of the IgE BF/sCD23 isolated from EBV-transformed cell line supernatants. Addition of interferon-gamma to B cells cultured with IL 4 strongly decreased the level of IgE BF/sCD23 in culture supernatants correlating with the observed decrease of Fc epsilon RL/CD23 on B cell surface. These data demonstrate that normal human B cells cultured in the presence of IL 4 produce an IgE-binding factor (sCD23) biochemically and antigenically equivalent to that spontaneously produced by EBV-transformed lymphoblastoid cell lines.
A Common Polymorphism in the Caspase Recruitment Domain of RIG-I Modifies the Innate Immune Response of Human Dendritic Cells (2010)

Infection of human dendritic cells (DCs) by negative-strand RNA viruses, such as Newcastle disease virus, leads to the induction of the IFNbeta gene, IFNB1, through the activation of the RNA helicase RIG-I, which is encoded by DDX58. Expression levels of IFNB1 and DDX58 in infected DCs showed positive correlations at the population and the single-cell levels. DDX58 has a common and potentially functional single nucleotide polymorphism, rs10813831 (A/G), encoding an Arg7Cys amino acid change in the RIG-I protein caspase recruitment domain (CARD). Quantitative RT-PCR analysis on Newcastle disease virus-infected primary DCs from 130 individuals revealed a significant association of the Arg7Cys single nucleotide polymorphism with increased IFNB1 and DDX58 transcription. Allelic imbalance analysis ruled out allele-specific DDX58 message levels and suggested that the observed association between Arg7Cys and IFNB1 and DDX58 transcription originated from a functional change in RIG-I due to the amino acid substitution in the CARD. DDX58 transfection experiments in 293T cells confirmed a biological functional difference between RIG-I 7Cys and the more common RIG-I 7Arg. Taken together, these data indicate that the innate immune response to viral infection of human cells is modified by a functional polymorphism in the RIG-I CARD.
Phantom analysis for characterization and comparison of PET detector sampling and reconstruction settings (2015)

PET scanners are designed to function over a wide dynamic range of imaging conditions. Clinical constraints, such as injected activity and imaging time, often limit the realization of optimal system capability. The `working range' of image quality for a given imaging situation is dictated by a trade-off of signal to noise. By adjusting scan time and reconstruction parameters, an acceptable trade-off is fixed into a protocol. This study develops the use of quantitative measures using hot and cold rods inserts in head and body-sized phantoms to quantitatively and visually assess two different PET scanner geometries and multiple reconstruction methods in order to further understand optimal scanner design and use in different imaging conditions.
Abstract 3448: Targeting the dopamine receptor 2 in BRAF mutant colorectal cancer (2018)

Abstract Background: BRAFV600E mutations occur in ~10% of colorectal cancer (CRC), are associated with poor survival and have limited responses to BRAF/MEK inhibition with or without EGFR inhibition. There is an unmet need to understand the biology of poor prognostic BRAFMT CRC. Using gene expression data from BRAFMT CRC patient samples, we recently identified that dopamine receptor degradation and unfolded protein response are dominant pathways deregulated in the BRAFMT subgroup with the poorest outcome. The aim of this study was to investigate the role of the dopamine receptor 2 (DRD2) pathway as novel target in BRAFMT CRC cells. Methods: Small molecule DRD2 antagonists ONC-201 and ONC-206 (Oncoceutics Inc) and a panel of isogenic paired and non-isogenic BRAFMT and BRAFWT cells were used. MTT, Flow Cytometry, Western blotting and caspase- 8, 3/7 activity assays were used to measure cell survival/death. DR5 cell localization was performed using flow cytometry. A compound library including small molecules approved by the FDA was used. Results: BRAFMT CRC cells were highly sensitive to the DRD2 antagonists ONC-201 and ONC-206 with IC50 values between 1.9-4.5μM and 0.16 and 0.24μM respectively. Treatment with ONC-201 and ONC-206 resulted in marked increases in expression levels of the endoplasmic reticulum stress proteins ATF4, CHOP and the active (spliced) form of XBP1 (sXBP1) (indicators of activation of the PERK and IRE1α UPR branches), and this was associated with apoptosis induction as indicated by PARP cleavage, caspase-9 cleavage and increased caspase-3/7 activity in the BRAFMT VACO432 cell line but not in the WT VT1 clone. Importantly, no significant effect on proliferation or apoptosis was obtained in the normal colon CCD-18 fibroblast cell line following treatment with ONC-201 or ONC-206. Using a small molecule compound library, we found that the taxanes paclitaxel and docetaxel resulted in strong synergy and apoptosis when combined with ONC-201 or ONC-206, in particular in BRAFMT CRC cells. Mechanistically, we found that the apoptosis induced by combined ONC-201/paclitaxel treatment was dependent on caspase-8 activation and on up-regulation of the death receptor 5 (DR5). Conclusions: Taken together, we have identified a role for DRD2 signalling in the survival of BRAFMT CRC cells. Our data support the development of DRD2 antagonists, in particular in combination with taxanes, for the treatment of BRAFMT CRC tumours. Citation Format: Arman Javadi, Nicholas Forsythe, Alaa Refaat, Jessica-Ann Weir, Hajrah Khawaja, David Waugh, Rohinton Tarapore, Joshua E. Allen, Patrick Johnston, Sandra Van Schaeybroeck. Targeting the dopamine receptor 2 in BRAF mutant colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3448.
Maximum flow algorithms for maximum observability during FPGA debug (2013)

Due to the ever-increasing density and complexity of integrated circuits, FPGA prototyping has become a necessary part of the design process. To enhance observability into these devices, designers commonly insert trace-buffers to record and expose the values on a small subset of internal signals during live operation to help root-cause errors. For dense designs, routing congestion will restrict the number of signals that can be connected to these trace-buffers. In this work, we apply optimal network flow graph algorithms, a well studied technique, to the problem of transporting circuit signals to embedded trace-buffers for observation. Specifically, we apply a minimum cost maximum flow algorithm to gain maximum signal observability with minimum total wirelength. We showcase our techniques on both theoretical FPGA architectures using VPR, and with a Xilinx Virtex6 device, finding that for the latter, over 99.6% of all spare RAM inputs can be reclaimed for tracing across four large benchmarks.
BGP Control Plane Extensions for Segment Routing based Service Chaining (2018)

The BGP Control Plane for the SR service-chaining solution is
consistent with the BGP Control Plane for the topological Segment
Routing Traffic Engineering (SR-TE) solution. o BGP Link-State(BGP-LS)
address-family/sub-address-family[RFC7752] is used to discover service
and topological characteristics from the network. o SR-TE policies[I-D
.ietf-idr-segment-routing-te-policy] instantiate source-routed
policies that may mix service and topological segments.
DriveSense: Contextual handling of large-scale route map data for the automobile (2013)

Automakers are increasingly providing connectivity enhancements for vehicles to download navigational data, as well as to upload sensor information to the cloud. Generally, while more data may be better, for the driver on-the-go, information needs to be displayed in a manner that can be comprehended rather quickly. One of the major problems with visualizing route maps is that the amount of information visualized is always the same regardless of the fact that an individual may be more familiar with the region or whether an individual is driving at varying speeds. Research has shown that complex visualizations with visual clutter can cause cognitive overload that adversely affects the performance of a user. Additionally, the attention and interaction abilities of a driver are significantly compromised in a vehicular environment. We propose DriveSense, a context-sensitive visualization system that automatically varies the GPS updates and the corresponding visualization being displayed to the user based on the speed of the vehicle as well as the familiarity of the region that the user is driving in. Based on a user evaluation, we found that subjects preferred using the automatic visualizations of route maps generated by DriveSense than the visual representations shown by a standard GPS. We also computed visual clutter for our visualizations at varying speeds and found that the clutter was significantly less for the routes displayed by DriveSense for faster speeds as compared to slower speeds.
A low‐leakage and reduced current collapse AlGaN/GaN heterojunction field effect transistor with AlOx gate insulator formed by metal‐organic chemical vapor deposition (2008)

Abstract We report on metal‐insulator‐semiconductor (MIS) heterostructure field‐effect transistor (HFET) with AlO x gate insulator formed by metal‐organic chemical vapor deposition (MOCVD) method designed for achieving low gate leak and less current collapse. The AlO x insulator was formed successively onto the MOCVD‐grown AlGaN/GaN using trimethylaluminum (TMA) and n‐butyl ether as precursors. Flowing gas during the AlO x /AlGaN interface formation was mainly consisted of ammonia and nitrogen with the aim of preventing N vacancy creation and oxide formation on the AlGaN that could lead to the current collapse. The fabricated devices were evaluated under direct current mode. The gate leak current of the MIS‐HFET was three orders of magnitude lower than that of conventional (no insulator) HFET. The change in transition drain current examined as indicator of magnitude of the current collapse was found to be smaller in the MIS‐HFET than in the HFET. Advantages of the novel wafer preparation method and the MIS‐HFET were demonstrated. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Nanogymnastics: Visualization of Intercluster Reactions by High-Resolution Trapped Ion Mobility Mass Spectrometry (2019)

Although single-crystal X-ray diffraction is a proven technique to determine the structure of monolayer-protected coinage metal clusters in solid state, it is not readily applicable to the characterization of such cluster structures in solution. The complexity of the characterization problem increases further when intercluster reactions are studied, in which two reactive cluster ions interact to form final products using a sequence of structural changes involving exchange of metal atoms and ligands. Here, we present the first time-resolved structural study of such processes which occur when solutions of [TOA]+[Au25(PET)18]− and [PPh4]44+[Ag44(FTP)30]4– react upon mixing (PET: phenylethanethiolate; FTP: 4-fluorothiophenolate; and TOA: tetraoctylammonium ion). This is achieved using high-resolution trapped ion mobility mass spectrometry (TIMS). Specifically, we have used electrospray transfer to the TIMS apparatus followed by ion mobility measurements to probe the time-dependent structure of mass-selected AuxAg44–x(FTP)304– (x = 0–12) exchange products, with limited FTP for PET exchanges, formed in the reaction medium. Over the roughly 40 min reaction time before equilibration, with a product distribution centered around Au12Ag32(FTP)304–, we observe intermediate species, AuxAg44–x(FTP)304–, whose collision cross sections (CCSs) at a given x increase first relative to that of the Ag44(FTP)304– parent and decrease subsequently. We attribute this to an energy-driven migration of the incorporated Au atoms from the ligated “staples” at the cluster surface to its icosahedral core. Upon collisional heating of AuxAg44–x(FTP)304–, analogous back-migration of the heavier Au atoms from the core to the staples was observed in tandem mass spectrometry. To support our experimental observations, several isomeric structures (with all ligands) were calculated using density functional theory, and their CCS values were modeled using trajectory method calculations.