gebhart/patrepeval huggingface dataset:
Superconformal Bottom-Up Nickel Deposition in High Aspect Ratio Through Silicon Vias (2016)

This work demonstrates void-free nickel filling of 56 μm tall, annular Through Silicon Vias (TSVs) using a mechanism that couples suppression breakdown and surface topography to achieve controlled superconformal, void-free deposition. The chemistry, a Watts electrolyte containing a dilute suppressing additive, and processes are fully detailed. The impact of deposition potential and additive concentration on the filling of the patterned features is presented. Voltammetric measurements on planar substrates, including the impact of rotation rate and suppressor concentration on the rate of metal deposition and potential of suppression breakdown, are used to quantify the interplay between metal deposition and suppressor adsorption. The derived kinetics are then used to quantitatively predict the observed bottom-up filling in the TSVs using the S-shaped negative differential resistance (S-NDR) mechanism for superconformal deposition; the predictions capture the experimental observations. This work extends understanding and application of the additive-derived S-NDR mechanism developed with non-ferrous metals.
CCL17 transgenic mice show an enhanced Th2‐type response to both allergic and non‐allergic stimuli (2006)

CC chemokine ligand (CCL)17 is implicated in the pathogenesis of atopic dermatitis (AD). To study the effect of CCL17 produced by keratinocytes (KC) during inflammation, we created transgenic (Tg) mice in which CCL17 is overexpressed in KC. Th2-type contact hypersensitivity (CHS) was enhanced and Th1-type CHS was suppressed in these mice. Increased numbers of CC chemokine receptor (CCR)4(+) cells and mast cells infiltrated in Tg mice. Levels of IL-4 mRNA were higher and those of IFN-gamma mRNA were lower in both acute and chronic CHS. Higher levels of serum IgE were observed after CHS. Numbers of CCR4(+) cells among PBMC were increased in Tg mice challenged acutely on the trunk. Chronic irritation with croton oil induced dermatitis and an elevation of serum IgE levels. Tg mice showed enhanced ear swelling after tape stripping. CCL17 was thought to modify the inflammation caused by sensitizing reagents as well as irritant reagents by attracting CCR4(+) cells into the lesional skin and creating a Th2-dominant condition. AD-like conditions such as increased number of mast cells and elevated levels of serum IgE were observed. Thus, CCL17 may participate in the pathogenesis of skin diseases such as AD by regulating both allergic and irritant inflammation.
Super-resolution photothermal patterning in conductive polymers and nanowire patterning (2021)

The largest need in organic electronic devices is a universal method to produce micro- to nano-scale features for devices from semiconducting polymers cheaply, and at scale. We recently developed a solution method to optically pattern conjugated polymers with resolution that exceeds the linear Abbe diffraction limit. We examine the relationship between optical write intensity, write speed, and write wavelength on the resulting pattern fidelity. Finite element modeling reveals that nearly all patterning occurs as a result of local heating and superlinear resolution is a result of a highly non-linear dissolution rate for the polymer as a function of temperature. This result is general to any conjugated polymer. We used this new technique to fabricate P3HT/F4TCNQ nanowires We also demonstrate that a P3HT nanowires can be doped and de-doped from solution without changing the dimension of the wire.
Abstract LB-412: TargetRich™ cancer gene panels: targeted next generation sequencing in cancer samples (2012)

Abstract Crucial to the adoption of next-generation sequencing within clinical cancer research is the ability to deeply sequence hundreds to thousands of targeted genomic regions across a large number of patient samples. Several targeting (PCR) and capture (hybridization) methods have been developed for next-generation sequencing, however these methods have limited utility with cancer patient specimens due to drawbacks such as large input DNA quantity requirements, wasted off-target sequencing, high cost of reagents, low sample throughput, specialized equipment, and inflexible content design. We developed TargetRich cancer gene panels employing Nested PatchPCR, which enables the targeted sequencing of hundreds of genomic regions in large numbers of patient samples to fully and efficiently utilize next-generation sequencers. Nested PatchPCR required only 250 ng genomic DNA, and was compatible with the fragmented DNA obtained from formalin fixed paraffin embedded samples (FFPE). No special equipment was needed, only a standard PCR machine. Patient samples were processed in parallel in a single 96-well plate. For each patient sample, we simultaneously amplified hundreds of exons from genes that are frequently mutated in cancer. We utilized standard library construction and barcoding methods to sequence targeted genes from 96 patient samples on a single Illumina GAIIx flowcell. The TargetRich cancer gene panels were highly specific; 95% of sequencing reads aligned to the targeted regions. The high percentage of on-target sequence data and focused content, allowed us to achieve high coverage across the loci (average of 400X read depth) for the sensitive detection of cancer mutations. We have created two cancer panels: CR (157 regions covering exons from 10 genes) and CS (760 regions covering exons from 62 genes) for use on the Illumina MiSeq, GAIIx &amp; HiSeq platforms. Additionally, a CR panel for the Ion Torrent PGM has been developed with platform-specific primers added during the Nested PatchPCR reaction, allowing direct sequencing of products without time-consuming library construction. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-412. doi:1538-7445.AM2012-LB-412
Characterization of Genetically Engineered Mengoviruses in Mice (2000)

We have shown that genetically engineered mengoviruses containing artificially shortened 5' noncoding poly(C) tracts (e.g., C0 or C13UC10) are dramatically attenuated in adult Swiss/ICR mice when compared to wild-type virus or to a genetically engineered virus containing a wild-type length poly(C) tract (C44UC10). To explore further the relationship between poly(C) tracts and virulence, we have conducted more extensive characterizations of several engineered viruses in the murine model. Both short and long poly(C) tract viruses were highly virulent in newborn mice, underscoring the importance of age in poly(C)-mediated attenuation. Virus vMC24, with a tract sequence of C13UC10, was as attenuated in 4-week-old BALB/c, C.C3-H2k/LiMcdJ, and DBA/2 mice as in Swiss/ICR mice. But it was more pathogenic for C57BL/6 mice, and highly virulent for C3H/Hej and C3H/Hen mice, demonstrating the importance of murine genotype. As expected from its virulence in all mouse strains, vMwt, with a poly(C) of C44UC10, induced higher levels of viremia than vMC24. The vMwt also induced higher levels of circulating interferon and had reduced pathogenicity in chemically immunosuppressed Swiss/ICR mice. Similar immunosuppression did not increase the virulence of vMC24. Collectively, the data suggest that endogenous immune components and the immune competence of the host play significant roles in determining the susceptibility of mice to mengovirus infection.
On locality of Generalized Reed-Muller codes over the broadcast erasure channel (2016)

One to Many communications are expected to be among the killer applications for the currently discussed 5G standard. The usage of coding mechanisms is impacting broadcasting standard quality, as coding is involved at several levels of the stack, and more specifically at the application layer where Rateless, LDPC, Reed Solomon codes and network coding schemes have been extensively studied, optimized and standardized in the past. Beyond reusing, extending or adapting existing application layer packet coding mechanisms based on previous schemes and designed for the foregoing LTE or other broadcasting standards; our purpose is to investigate the use of Generalized Reed Muller codes and the value of their locality property in their progressive decoding for Broadcast/Multicast communication schemes with real time video delivery. Our results are meant to bring insight into the use of locally decodable codes in Broadcasting.
Combined proteomic and transcriptomic approaches reveal externalized keratin 8 as a potential therapeutic target involved in invasiveness of head and neck cancers (2020)

Keratin 8 (K8) expressed at the surface of cancer cells, referred as externalized K8 (eK8), has been observed in a variety of carcinoma cell lines. K8 has been previously reported to be expressed in poorly differentiated head and neck squamous cell carcinoma (HNSCC); however, its role during the invasive phase of upper aerodigestive tract tumorigenesis is unknown. Cohorts of HNSCC tumors for protein and mRNA expression and panel of cell lines were used for investigation. K8 was found to be externalized in a majority of HNSCC cell lines. Among the two main K8 protein isoforms only the 54 kDa was found to be present at the plasma membrane of HNSCC cells. The plasminogen-induced invasion of HNSCC cells was inhibited by the anti-eK8 D-A10 antagonist monoclonal antibody. Overexpression of K8 mRNA and protein were both correlated with tumor aggressive features and poor outcome. The effect of eK8 neutralization on invasion, its presence exclusively in cancer cells and the association of K8 expression with aggressive features and poor clinical outcome in HNSCC unravel eK8 as key player in invasion and a promising therapeutic target in HNSCC.
Bioluminescence DNA Hybridization Assay for <i>Plasmodium </i><i>f</i><i>alciparum</i> Based on the Photoprotein Aequorin (2007)

A bioluminescence DNA hybridization assay for the detection of Plasmodium falciparum, the most deadly species of malaria, using the photoprotein aequorin as a bioluminescent label has been developed. The current gold standard for the detection of malaria is light microscopy, which can detect down to approximately 50 parasites/microL of blood, but has low-throughput, high costs, and requires high skill, which limit the applicability of the method, especially in the developing regions where malaria detection is mostly needed. The utilization of aequorin as a bioluminescence label offers the advantages of high signal-to-noise ratio and reliable detection down to attomole levels, allowing for the development of highly sensitive and miniaturized high-throughput bioluminescence assays. Herein, we developed a DNA hybridization assay for the detection of P. falciparum based on the competition between the target DNA and the signal generating DNA streptavidin-aequorin for hybridization with the probe DNA. This bioluminescence hybridization assay demonstrated a detection limit of 3 pg/microL and was employed for the detection of target DNA in standard and spiked human serum samples. The DNA hybridization assay was developed in a microplate format without the need for sample PCR amplification, showing the potential suitability of this method in the parallel analysis of samples by low-trained personnel, such as that typically encountered in developing regions.
First-in-Humans PET/MRI of In Vivo GD2 Expression in Osteosarcoma (2022)

Osteosarcoma is a malignant bone tumor with very limited therapeutic options ([ 1 ][1]). However, targeting the frequently overexpressed disialoganglioside GD2 was successful in preclinical studies with bispecific GD2 antibodies ([ 2 ][2]), and a clinical trial is ongoing using the clinically
Celecoxib Decreases Gcf Prostaglandin E2 Levels in Chronic Periodontitis Patients (2020)

Prostaglandin E2 (PGE2) is a key mediator associated with periodontal bone loss. We recently demonstrated (Yen, et al, J Periodontology 79:104, 2008) that adjunctive use of Celecoxib (a COX-2 selective inhibitor) in conjunction with Scaling and Root Planning (SRP) resulted in significant reduction in Pocket Depth (PD) and gain in Clinical Attachment (CAL) in Chronic Periodontitis (CP) patients.
Improved Therapeutic Responses in a Xenograft Model of Human B Lymphoma (Namalwa) for Liposomal Vincristine<b><i>versus</i></b>Liposomal Doxorubicin Targeted via Anti-CD19 IgG2a or Fab′ Fragments (2004)

Treatment of a B lymphoma model with single injections of anti-CD19-targeted liposomal formulations of VCR resulted in high levels of response and long-term survivors. Responses to anti-CD19-targeted liposomal DXR were more modest, although the longer circulation times of SIL[Fab'] versus SIL[alphaCD19] led to superior therapeutics for DXR-loaded immunoliposomes.
Immunologic cross-reactivity between structural proteins of human T-cell lymphotropic virus type I and the blood stage of Plasmodium falciparum (1994)

To determine the serologic cross-reactivity between human T-cell lymphotropic virus type I (HTLV-I) and parasite antigens, we measured antibody responses against HTLV-I, Plasmodium falciparum, Plasmodium vivax, and Brugia malayi in serum specimens obtained from regions where malaria (n = 482) and filariasis (n = 101) are endemic. Analysis of immune reactivity to HTLV-I antigens showed that specimens from regions where malaria is endemic had significantly higher rates of enzyme immunoassay (EIA) reactivity (76 of 482 [15.8%] than those from regions where filariasis is endemic (0 of 101 [0%]). Western blot (immunoblot) analysis of the HTLV-I EIA-reactive specimens demonstrated predominant Gag reactivity (HTLV-Iind). Only two specimens each from Indonesia and Brazil and four specimens from Papua New Guinea had Env reactivity by radioimmunoprecipitation analysis. Furthermore, a positive correlation between HTLV-EIA and titers of antibody to the blood stage of P. falciparum (rs = 0.24, P < 0.005) was discerned; no correlation was observed between antibodies to the blood stage or the circumsporozoite protein of P. vivax and the circumsporozoite protein of P. falciparum. In addition, P. falciparum-infected erythrocyte lysate specifically abrogated binding of Gag-specific antibodies in HTLV-Iind specimens from regions where malaria is endemic without affecting binding in HTLV-I-seropositive specimens, suggesting that the immunologic cross-reactivity between HTLV Gag proteins and malaria parasites is restricted to the blood-stage antigens of plasmodia in specimens from regions where malaria is endemic. However, HTLV-seroindeterminate specimens from the United States did not demonstrate serologic cross-reactivity, suggesting that antigenic mimicry of HTLV proteins extends to other nonplasmodial antigens as well.
Interfacing reality (panel) (1997)

Article Interfacing reality (panel): exploring emerging trends between humans and machines Share on Authors: Eric Paulos University of California, Berkeley University of California, BerkeleyView Profile , John Canny University of California, Berkeley University of California, BerkeleyView Profile , Eduardo Kac School of the Art Institute of Chicago School of the Art Institute of ChicagoView Profile , Ken Goldberg University of California, Berkeley University of California, BerkeleyView Profile , Mark Pauline Survival Research Laboratories Survival Research LaboratoriesView Profile , Stelarc Performance Artist Performance ArtistView Profile Authors Info & Claims SIGGRAPH '97: Proceedings of the 24th annual conference on Computer graphics and interactive techniquesAugust 1997 Pages 448–451https://doi.org/10.1145/258734.258904Online:03 August 1997Publication History 0citation384DownloadsMetricsTotal Citations0Total Downloads384Last 12 Months0Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Two-Stage Shrinkage Behavior of Multielement-Molecular-Ion-Implantation-Induced Dislocation Loops Revealed by Real-Time TEM Observation (2023)

Complementary metal-oxide-semiconductor image sensors (CISs) have important functions in sensing devices in automotive, infrastructural, industrial, and medical applications. One of the most serious technical issues for complementary metal-oxide-semiconductor image sensors (CISs) is dark current originating from pixels. The representative origins of dark current are metal and oxygen impurities, and silicon dioxide (SiO$_{2})/$silicon (Si) interface state defects. Therefore, it is indispensable for high-performance CISs to develop technologies for removal of metal and oxygen impurities from pixels, and reduction of SiO$_{2}/$Si interface state defect density. Recently, we have developed hydrocarbon-molecular-ion $(C_{3} H_{5}$ ion)-implanted epitaxial silicon (Si) wafer as a functional wafer for CISs [1]. In $C_{3} H_{5} -$ion-implanted epitaxial Si wafer, C-interstitial Si precipitates act as gettering sinks [1]. $C_{3} H_{5} -$ion-implanted epitaxial Si wafer can reduce dark current in typical CISs with four-transistor-type pinned photodiode [1] owing to two attractive features of C-interstitial Si precipitates; one is the gettering of metal and oxygen (O) impurities [2], [3], and the another is the trapping of hydrogen (H) [4] and the reduction in SiO$_{2}/$Si interface state defect density by re-release of once-trapped hydrogen [5].
Perkin 1 Abstracts: Solid Phase Organic Synthesis (2001)

F. Anizon, J. Delaney, A. Gunn, H. Mamdani, C. McCusker, F. McKerlie and T. Wildman, J. Chem. Soc., Perkin Trans. 1, 2001, 23-ix DOI: 10.1039/B109854N
The Science and Technology of Cyber Operations (2009)

Abstract : The Air Force Research Laboratory provides the science and technology (S&T) vision, leadership, and products that enable the United States Air Force (USAF) to accomplish its mission to fly, fight, and win in air, space, and The dependence on cyberspace of US weapon systems, critical infrastructure, financial institutions, and our way of life creates an imperative to operate freely in this domain. The USAF vision of global vigilance, global reach, and global power depends vitally on the ability to dominate cyberspace through integrated defensive and offensive operations across blue, red, and gray cyber systems, as well as across the global cyberspace commons. This article describes an S&T perspective on cyber operations within the focus necessary to operate in a contested cyber domain and to assure critical military missions in land, sea, air, and space against threats in cyberspace.
Fosmidomycin, a Novel Chemotherapeutic Agent for Malaria (2003)

In previous studies, fosmidomycin has been shown to possess activity against Plasmodium falciparum in vitro and in the mouse model. It has a novel mode of action through inhibition of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, an enzyme of the nonmevalonate pathway of isoprenoid biosynthesis, which is absent in humans. In this open-label, uncontrolled trial, the efficacy and safety of fosmidomycin, in an oral dose of 1,200 mg every 8 h for 7 days, were evaluated in the treatment of acute uncomplicated Plasmodium falciparum malaria in 20 adult subjects in Gabon and Thailand. Clinical assessments were performed and thick blood smears were evaluated every 8 h until parasite clearance and resolution of symptoms were achieved; assessments continued at weekly intervals thereafter for the duration of the 28-day followup period. All subjects were clinically and parasitologically cured on day 7 (primary end point). Parasite and fever clearance were rapid, with means of 44 and 41 h, respectively. On day 28, seven out of nine subjects (78%) were cured in Gabon and two out of nine subjects (22%) were cured in Thailand. The drug was well tolerated, although mild gastrointestinal side effects were recorded for five subjects. Analysis of hematological and biochemical parameters showed no clinically significant changes throughout the study. Fosmidomycin is an effective and safe antimalarial drug, although its use as a single agent is restricted by the occurrence of recrudescent infections. However, its role in combination therapy should be explored.
Using a Steered-Response Power-Phase Transform to Optimize Speech Pickup in Reverberant Environments (2008)

Noise, interference, and echo present problems in the use of hands-free communication systems in cars. In this study a microphone system integrating various array signal processing technologies is developed to overcome these problems. The microphone array acts like a spatial filter so that both signal-to-noise ratio and directivity can be improved. In the system the method of steered-response power-phase transform, which is robust to reverberant environments, is employed to estimate the direction of arrival (DOA) of the incoming sound signal. Once the DOA is found, the main beam of the microphone array is steered electronically in that direction to receive the signals. In order to attain a sharp spatial resolution, a superdirective design is employed in beamforming. A low-pass filter is used in postprocessing the array output to enhance human speech. In addition the system copes with acoustic echo by using an adaptive filter based on the least-mean-squares method. All algorithms have been integrated and implemented on the platform of a digital signal processor. Experimental results demonstrate that the proposed system is effective in car hands-free applications.
The Application of High-Order Harmonics to Extreme Ultraviolet Polarimetry (2006)

We report on the construction of an extreme-ultraviolet polarimeter based on laser-generated high-order harmonics.
How Does Proliferative Homeostasis Change With Age? What Causes It and How Does It Contribute to Aging? (2009)

The notion that there might be a cellular basis for aging stems from research that began several decades ago and was proposed to explain the loss of proliferative homeostasis, which is a hallmark of complex animals. Recent years have seen growing support for the idea that two cell fates-apoptosis and cellular senescence, both now well-established tumor suppressor mechanisms-may be important drivers of aging phenotypes and age-related disease. However, there remain many unanswered questions, some quite basic, about how these processes change with age and how they might contribute to aging. It is now clear that failures in apoptosis or senescence can result in hyperproliferative diseases such as cancer. Less is known about whether and how increased apoptosis or senescence can cause tissue degeneration and aging. In addition, there is now a growing recognition that cellular senescence can have cell-nonautonomous effects within tissues. New molecular tools and model organisms, some already on the horizon, will need to be developed to better understand the roles of apoptosis and cellular senescence in age-associated changes in proliferative homeostasis.