gebhart/patrepeval huggingface dataset:
Abstract #677: Design, synthesis and preclinical efficacy of a carboxylesterase 2-activated prodrug of doxazolidine: Pentyl PABC-Doxaz (2009)

AACR Annual Meeting-- Apr 18-22, 2009; Denver, CO

Doxazolidine (Doxaz) is the formaldehyde conjugate of doxorubicin (Dox) that induces cancer cell death in sensitive and MDR cells by cross-linking DNA. Doxaz is orders of magnitude more active than Dox but has a half-life of 3 min. under physiological conditions with respect to hydrolysis to Dox. A carboxylesterase 2-activted prodrug, pentyl PABC-Doxaz (PPD), was designed to be hydrolytically robust and to selectively deliver Doxaz to cancer cells that express the enzyme. Carboxylesterase 2 (CES2) is expressed in cytosol by liver, non-small cell lung, colon, pancreatic, renal, and thyroid cancer cells and is involved in the activation of the clinical prodrugs irinotecan and capecitabine. Cancer cell growth inhibition by PPD correlated with CES2 expression as indicated by gene array analysis. Hep G2 and N-Hep G2 hepatocarcinoma cells and H-1435 non small cell lung cancer cells were identified as highly responsive to PPD. NOD SCID mice were implanted s.c. with N-Hep G2 cells, and nude mice were implanted s.c. with H1435 cells. Tumor growth was monitored in i.v. dose escalation experiments versus no-drug and Dox controls. At termination, heart and liver sections were examined for evidence of cardio- and hepatotoxicity. Inhibition of tumor growth by PPD followed dose escalation and exceeded inhibition of tumor growth by doxorubicin near its maximum tolerated dose. In general PPD was well tolerated. Some weight loss with the maximum dose of PPD was observed at three weeks but mostly disappeared at five weeks. Heart sections of PPD-treated mice showed significantly less evidence of cardiotoxicity than heart sections of doxorubicin-treated mice. Liver sections showed more evidence of toxicity from PPD, consistent with hepatic expression of murine CES2. This study reports a strong rationale for further in vivo evaluation of PPD for treatment of tumors that express CES2.

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 677.
Development of a Disposable Bio-Microfluidic Package With Reagents Self-Contained Reservoirs and Micro-Valves for a DNA Lab-on-a-Chip (LOC) Application (2009)

A disposable self-contained microfluidic package has been developed and tested for on-chip DNA extraction from human blood for practical lab-on-a-chip platform. The microfluidic package has been customized to allow easy interface between the microscale sample injection to the Si-based microscale sample preparation chip. For precise sample dispensing and to minimize dead volume and/or sample lost conical-shaped reservoirs have been employed. Reservoirs filled with reagents are sealed by a highly elastic thin rubber membrane. Automated actuation system has been designed and implemented for programmable sample/reagent dispensing using thin rubber membrane-plunger mechanism. The packaged DNA chip has been tested using blood sample and the testing protocol has been optimized to meet the requirements for DNA extraction.
EWS-FLI1 Suppresses NOTCH-Activated p53 in Ewing's Sarcoma (2008)

Although p53 is the most frequently mutated gene in cancer, half of human tumors retain wild-type p53, whereby it is unknown whether normal p53 function is compromised by other cancer-associated alterations. One example is Ewing's sarcoma family tumors (ESFT), where 90% express wild-type p53. ESFT are characterized by EWS-FLI1 oncogene fusions. Studying 6 ESFT cell lines, silencing of EWS-FLI1 in a wild-type p53 context resulted in increased p53 and p21(WAF1/CIP1) levels, causing cell cycle arrest. Using a candidate gene approach, HEY1 was linked to p53 induction. HEY1 was rarely expressed in 59 primary tumors, but consistently induced upon EWS-FLI1 knockdown in ESFT cell lines. The NOTCH signaling pathway targets HEY1, and we show NOTCH2 and NOTCH3 to be expressed in ESFT primary tumors and cell lines. Upon EWS-FLI1 silencing, NOTCH3 processing accompanied by nuclear translocation of the activated intracellular domain was observed in all but one p53-mutant cell line. In cell lines with the highest HEY1 induction, NOTCH3 activation was the consequence of JAG1 transcriptional induction. JAG1 modulation by specific siRNA, NOTCH-processing inhibition by either GSI or ectopic NUMB1, and siRNA-mediated HEY1 knockdown all inhibited p53 and p21(WAF1/CIP1) induction. Conversely, forced expression of JAG1, activated NOTCH3, or HEY1 induced p53 and p21(WAF1/CIP1). These results indicate that suppression of EWS-FLI1 reactivates NOTCH signaling in ESFT cells, resulting in p53-dependent cell cycle arrest. Our data link EWS-FLI1 to the NOTCH and p53 pathways and provide a plausible basis both for NOTCH tumor suppressor effects and oncogenesis of cancers that retain wild-type p53.
Accuracy of multiple sequence alignments as assessed by reference to structural alignments (1995)

In the last 20 years, many multiple-sequence alignment programs based on various principles have been developed. Continuous e orts have been devoted to solve two major problems: (1) how to evaluate the 'goodness' of an alignment, and (2) how to get the alignment with the optimal score. These problems are tightly interrelated, and other criteria are needed to objectively assess reliability of a certain alignment method. Recently, the number of protein three-dimensional (3D) structures determined by X-ray crystallography and high-resolution NMR methods is rapidly increasing. Comparison of the 3D structures makes it possible to align distantly related protein sequences based on their structural equivalence. A few collections of such structure-based alignments are now available [4]. Hence we can assess the quality of sequence alignments obtained by a given method by referring to the structural counterparts. McClure et al. [3] recently reported that the! most popular 'progressive' metho
An 8Kx8 dynamic RAM with self-refresh (1982)

The device uses a standard NMOS one-transistor cell and is fabricated with a double polysilicon HMOS technology using polysilicon word lines and folded metal bit lines. Self-refresh is implemented with an on-chip timer, arbiter, and refresh counter. A high-speed arbiter resolves conflicts between refresh cycles and memory accesses. A `ready' output is provided to the processor. A multiplexed bus is provided in the array to carry column addresses and also I/O data paths. Another multiplexed bus is used for data lines between the input buffers, write buffers, secondary sense amplifiers, and output buffers. Redundant rows and columns are used for increased manufacturing yield. Polysilicon fuses are electrically programmed to select redundant elements.
Conditional models for contextual human motion recognition (2005)

We present algorithms for recognizing human motion in monocular video sequences, based on discriminative conditional random field (CRF) and maximum entropy Markov models (MEMM). Existing approaches to this problem typically use generative (joint) structures like the hidden Markov model (HMM). Therefore they have to make simplifying, often unrealistic assumptions on the conditional independence of observations given the motion class labels and cannot accommodate overlapping features or long term contextual dependencies in the observation sequence. In contrast, conditional models like the CRFs seamlessly represent contextual dependencies, support efficient, exact inference using dynamic programming, and their parameters can be trained using convex optimization. We introduce conditional graphical models as complementary tools for human motion recognition and present an extensive set of experiments that show how these typically outperform HMMs in classifying not only diverse human activities like walking, jumping. running, picking or dancing, but also for discriminating among subtle motion styles like normal walk and wander walk
High Temperature Microelectromechanical Systems Using Piezoelectric Aluminum Nitride (2014)

We report on the efforts at Sandia National Laboratories to develop high temperature capable microelectromechanical systems (MEMS). MEMS transducers are pervasive in today's culture, with examples found in cell phones, automobiles, gaming consoles, and televisions. There is currently a need for MEMS transducers that can operate in more harsh environments, such as automobile engines, gas turbines, nuclear and coal power plants, and petroleum and geothermal well drilling. Our development focuses on the coupling of silicon carbide (SiC) and aluminum nitride (AlN) thin films on SiC wafers to form a MEMS material set capable of temperatures beyond 1000°C. SiC is recognized as a promising material for high temperature capable MEMS transducers and electronics because it has the highest mechanical strength of semiconductors with the exception of diamond and its upper temperature limit exceeds 2500°C, where it sublimates rather than melts. Most transduction schemes in SiC are focused on measuring changes in capacitance or resistance, which require biasing or modulation schemes that can withstand elevated temperatures. Instead, we are coupling temperature hardened, micro-scale SiC mechanical components with piezoelectric AlN thin films. AlN is a non-ferroelectric piezoelectric material, enabling piezoelectric transduction at temperatures exceeding 1000°C. AlN is a favorable MEMS material due to its high thermal, electrical, and mechanical strength. It is also closely matched to SiC for coefficient of thermal expansion.
Linkage Query Writer (2009)

We present Linkage Query Writer (LinQuer), a system for generating SQL queries for semantic link discovery over relational data. The LinQuer framework consists of (a) LinQL, a language for specification of linkage requirements; (b) a web interface and an API for translating LinQL queries to standard SQL queries; (c) an interface that assists users in writing LinQL queries. We discuss the challenges involved in the design and implementation of a declarative and easy to use framework for discovering links between different data items in a single data source or across different data sources. We demonstrate different steps of the linkage requirements specification and discovery process in several real world scenarios and show how the LinQuer system can be used to create high-quality linked data sources.
Library Guides: Materials Science & Engineering Research Guide: What you need to know (2015)

Introductory guide to library research and resources for faculty, staff, and students in materials science and engineering.
CMP-free and CMP-less approaches for multilevel Cu/low-k BEOL integration (2002)

A CMP-free process by electropolishing (EP) the planar contact plating (CP) Cu film and TaN dry etching which eliminate the stress induced peeling during CMP was demonstrated. Nanometer smoothness and a highly <111> texture of Cu can be achieved by optimizing the EP process. A 4-level Cu/low-k interconnect with CMP-less process was demonstrated with excellent yield. This process improves the throughput on ECP and CMP by two and has less dishing.
Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array (2017)

Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.
In vitro recombination of bacteriophage T7 DNA detected by a direct physical assay (1983)

We developed a simple, direct, physical assay to detect genetic recombination of bacteriophage T7 DNA in vitro. In this assay two mature T7 DNA molecules, each having a unique restriction enzyme site, are incubated in the presence of a cell-free extract from T7-infected Escherichia coli cells. After extraction of the DNA, restriction enzyme digestion, and agarose gel electrophoresis, genetic recombination is detected by the appearance of a novel recombinant DNA band. Recombination frequencies as high as 13% have been observed. We used this assay to determine the genetic requirements for in vitro recombination. In agreement with results obtained previously with a biological assay, T7 recombination in vitro appears to proceed via two distinct pathways.
[Significance of tooth anomalies in personal identification]. (2005)

Described in the paper are the study results of the stomatological status of 385 cadavers, in whom the frequency rate of anomalies of separate teeth and of their varieties were evaluated as applicable to the personality identification tasks.
CO2 absorbing cost-effective ionic liquid for synthesis of commercially important alpha cyanoacrylic acids: A safe process for activation of cyanoacetic acid (2009)

Cost-effective and carbon dioxide absorbing ionic liquid, tri-(2-hydroxyethyl) ammonium acetate, was shown to perform multiple roles in Knoevenagel condensation. It acted as an environmentally benign solvent, as an activating catalyst for the less reactive cyanoacetic acid and also as a risk reduction medium for the unevenly generated large amount of CO2 gas for large scale reactions. The reaction was scaled up for multi-gram synthesis of commercially important alpha cyanoacrylic acids.
Tobacco specific nitrosamines: Carcinogenicity, metabolism, and possible role in human cancer (1983)

(1983). Tobacco specific nitrosamines: Carcinogenicity, metabolism, and possible role in human cancer. Journal of Environmental Science and Health. Part C: Environmental Carcinogenesis Reviews: Vol. 1, No. 1, pp. 1-54.
Fetal age assessment based on 2nd trimester ultrasound in Africa and the effect of ethnicity (2008)

Significant ethnic differences between mothers were not reflected in fetal biometry at second trimester. The results support the recommendation that ultrasound in practical health care can be used to assess gestational age in various populations with little risk of error due to ethnic variation.
Vision-based Vehicle Detection and Inter-Vehicle Distance Estimation (2012)

In this paper, we propose a vision-based robust vehicle detection and inter-vehicle distance estimation algorithm for driving assistance system. It uses the directional edge features, as well as the Haar-like features of car rear-shadows for detection of front vehicles. The use of additional vehicle edge features greatly reduces the false-positive errors. And, after analyzing two inter-vehicle distance estimation methods: the vehicle position-based and the vehicle width-based algorithm, a novel improved inter-vehicle distance estimation algorithm that uses the advantage of both methods is proposed. Various experimental results show the effectiveness of the proposed method.
Establishment of pancreatic cancerogenesis model in immunocompetent mice and the changes of immune cell populations (2016)

Objective
To establish the pancreatic cancerogenesis model in mice and to observe the changes of the immune cell populations in peripheral blood and pancreatic lesions.


Methods
The in situ embedding of canerogen dimethylbenzanthracene (DMBA) was adopted to establish the pancreatic cancerogenesis process from chronic pancreatitis (CP) , pancreatic intraepithelial neoplasma (PanIN) to pancreatic cancer. Totally 60 C57BL/6J mice were used, and 8 weeks after embedding, the mice were killed. 20 mice were randomized selected, and 7 immune cell populations in the peripheral blood and pancreatic lesions were detected by flow cytometery (FCM) .


Results
During the observational peroid of 8 weeks, 14 (23.3%) mice died. Among the 46 survivors, 20 mice were randomized selected for FCM analysis. All of the 46 pancreatic lesions were pathologically analyzed. 12 cases were CP (26.1%) , 11 cases were lower grade PanIN (PanIN-1,2, LG-PanIN) (23.9%) , 9 cases were high grade PanIN (PanIN-3, HG-PanIN) (19.6%) and 14 cases were PC. Among the 20 randomized selected mice, 4 cases were CP, 7 cases were LG-PanIN, 4 cases were HG-PanIN and 5 cases were PC. The myeloid derived suppressor cells (MDSC) of HG-PanIN and CP were significantly more than that of LG-PanIN and CP. In the pancreatic lesions, the granulocytes, MDSC and M2 polarized TAM of HG-PanIN and PC were significantly more than that of LG-PanIN and CP. On the contrary, the T lymphocytes and M1 polarized TAM were significantly decreased.


Conclusions
In situ embedding of DMBA is a feasible and practical method to establish the spontaneous pancreatic cancerogenesis model in the immunocompetent mice. Pancreatic cancerogenesis can induce systemic and even stronger local immunosuppression, and the MDSC and M2 polarized TAM may play the vital roles.


Key words: 
Pancreatic Cancer; Cancerogenesis; Immunosuppression; Myeloid-derived suppressor cells; Tumor associated macrophages
Scanning Electron Microscopy: Systems and Applications 1973: Proceedings of a Conference held at the University of Newcastle Upon Tyne, 3–5 July 1973 (1974)

In its early days scanning electron microscopy was generally regarded by transmission electron microscopists and materials scientists as a possibly useful extension of qualitative optical microscopy. Recent technological advances, such as the introduction of field emitting cathodes and the subsequent imaging of single atoms by Crewe and his coworkers, have changed all this.
Diagnostic accuracy of anti-cyclic citrullinated Peptide antibodies in rheumatoid arthritis (2019)

Objective: To determine the diagnostic accuracy of anti-cyclic citrullinated peptide antibodies (Anti-CCP) in the diagnosis of rheumatoid arthritis (RA) in patients of joint pain keeping rheumatoid factor (RF) analysis, clinical and radiological features as the gold standard. Methods: A cross sectional study was performed at the Department of Chemical Pathology/Biochemical Laboratory Services, Liaquat National Hospital and Medical College, Karachi from January 2018 to June 2018. Over a period of six months, 363 samples of patients in the age group of 20–60 years having joint pain and suspected of suffering from rheumatoid arthritis were included after fulfilling inclusion and exclusion criteria. Patient demographics, age, sex, Anti-CCP results and RF levels were recorded. Results: There were 87 males and 283 females in the study. Sensitivity, specificity, Positive Predictive Value (PPV), Negative Predictive Value (NPV) and diagnostic accuracy were 69.2%, 98.5%, 97.8%, 77% and 84.2% respectively. Likelihood Ratio (LR)+ and LR- were 47 and 0.31 respectively. As per Receiver Operator Characteristic (ROC) curve analysis, the Area Under the Curve (AUC) is 0.839. The two-tailed test showed p<0.0001. The diagnostic accuracy of Anti-CCP antibodies in the diagnosis of Rheumatoid Arthritis in patients of joint pain was found to be 89.4%. The cutoff of anti-CCP was calculated by the Youden’s J. formula and was found to be 14 U/ml. Conclusion: Anti-CCP has a high sensitivity and specificity so it can be used for the diagnosis of rheumatoid arthritis in RF positive patients, which are common in Pakistan due to the high prevalence of Hepatitis C.
Is democratic nomination good for women's candidacy? Examining the case of Taiwan (2019)

In order to understand why women tend to be under-nominated even though they are more likely to be elected compared to men in Taiwan, this study focuses on the nomination systems of two major political parties. The country provides a critical case of inter-party and intra-party comparison for women’s nomination, as the two major parties diverge in their practice of candidate selection. Further, the electoral reforms from the SNTV (Single Non-Transferable Vote) system to the SMD (Single-Member District) system have led parties to alter their strategies in selecting women candidates. With the nomination dataset compiled over the past 20 years, this study finds that more centralized nomination is more conducive to women’s candidacy, even under different electoral systems. Under the old SNTV system, the more centralized KMT (Kuomintang) nominated more women candidates than did the decentralized DPP (Democratic Progressive Party). Under the new SMD system, women’s representation as a whole actually increased in Taiwan, which runs contrary to the general expectation, compared to the multimember-district system and so the SMD tends to inhibit women’s representation. The growing centralization in the major parties after the electoral rule changed to the new system, has enhanced women’s candidacies, but the higher male incumbent advantage is a hurdle still to be overcome in the long term. This study argues that although electoral rules have altered the parameters of party competition, party nomination are critical factors for explaining changing women’s representation.
Phase-shifting optical maskless lithography enabling ASICs at the 65- and 45-nm nodes (2004)

An architecture for SLM-based mask writing and optical maskless lithography has been described in previous articles. This work reports on phase-shifting capabilities of different SLM's in light of rasterization and image stability. The tilting mirror SLM proven in the Micronic Sigma7300 mask writer has in other papers been presented as comparable to an attenuated phase-shift reticle. This article will feature the novel tilting phase-step mirror SLM. which has phase shifting capabilities enabling it to emulate hard phase-shift reticles. For a straight-forward rasterization architecture where individual pixels are determined by local pattern data it is required that the complex amplitude created by a mirror is confined to the real axis. This is the case for both the normal tilting mirror and the tilting phase-step mirror. For other micro-mirror designs this might not be true and in the case of the piston-mirror SLM this requirement leads to the demand that two or several mirrors work collectively, loosing degrees of freedom and resolution. The tilting phase-step mirror SLM provides a new rule-set for lithography: no penalty for phase shifting or aggressive OPC, seamless pattern decompositions, choice of optimal tones for each pattern, etc. This gives performance and flexibility not possible before.