gebhart/patrepeval huggingface dataset:
Abstract 3308: Urine epigenetic biomarkers for NSCLC diagnosis (2018)

Abstract Purpose: The National Lung Cancer Screening Trial showed mortality reduction on patients with NSCLC by the use of Low-dose CT screening. The study exhibits an unreasonably high false positive rate of 96.6%, which can to lead to significant morbidity and mortality from unnecessary tests. This study aim to determine if methylated promoter regions of a panel of genes that are correlated with Non-Small Cell Lung Cancer can be detected in urine from patients with lung cancer versus those without. Materials and Methods: We conducted a prospective case-control study recruiting subjects from the Lung Cancer Spore Trial. Urine and pre-operative CT scans were obtained from all patients. We processed the urine using the Methylation on Beads assay to isolate and bisulfite treat circulating DNA and then employed Quantitative Methylation Specific Real-Time PCR to detect promoter methylation status of the genes: CDO1, TAC1, HOXA7, HOXA9, SOX17 and ZFP42. Sensitivity, specificity, PPV and NPV values were calculated for each gene methylation status. Results: 34 patients were studied, including 23 patients with NSCLC and 11 patients with benign non-cancerous lesions. The sensitivity, specificity, PPV and NPV values for lung cancer detection in urine are shown in Table 1. Sensitivities ranged 43-96%, Specificities 64-91%, PPV 71-100% and NPV 40-67%. Promoter methylation of the gene panel CDO1, TAC1, HOXA7, HOXA9, SOX17 and ZPF42 has a 78% sensitivity, 91% specificity, 95% PPV and 67% NPV for lung cancer detection. Conclusion: Our study suggests that urine can provide a highly sensitive and specific non-invasive route for lung cancer detection. These results are very promising and could potentially reduce unnecessary morbidity and mortality in people undergoing screening for NSCLC by use of a non-invasive method that could be more accessible on primary care centers. However, further studies and validation with larger sample sizes and different populations are necessary before its application to clinical practice. Patients with positive gene methylation from urine samples and its accuracy for NSCLC detection.Cancer (n=23)Cancer (n=23)Control (n=11)Control (n=11)nSensitivitynSpecificityPPVNPVCDO114611919353TAC11565010010058SOX1716704648050HOXA711483737940HOXA910431919143ZPF4222969187167Panel of genes18781919567 Citation Format: Lane Lerner, Lily Zheng, Anastasia Kottorou, Chen Chen, Tomoaki Ito, Kristen Rodgers, Beverly Lee, Robert Winn, Enrico Benedetti, Tza- Huei Wang, Malcolm V. Brock, James G. Herman, Alicia Hulbert. Urine epigenetic biomarkers for NSCLC diagnosis [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 3308.
Comp-GAN (2019)

Facial expression is important in understanding our social interaction. Thus the ability to recognize facial expression enables the novel multimedia applications. With the advance of recent deep architectures, research on facial expression recognition has achieved great progress. However, these models are still suffering from the problems of lacking sufficient and diverse high quality training faces, vulnerability to the facial variations, and recognizing a limited number of basic types of emotions. To tackle these problems, this paper proposes a novel end-to-end Compositional Generative Adversarial Network (Comp-GAN) that is able to synthesize new face images with specified poses and desired facial expressions; and such synthesized images can be further utilized to help train a robust and generalized expression recognition model. Essentially, Comp-GAN can dynamically change the expression and pose of faces according to the input images while keeping the identity information. Specifically, the generator has two major components: one for generating images with desired expression and the other for changing the pose of faces. Furthermore, a face reconstruction learning process is applied to re-generate the input image and constrains the generator for preserving the key information such as facial identity. For the first time, various one/zero-shot facial expression recognition tasks have been created. We conduct extensive experiments to show that the images generated by Comp-GAN are helpful to improve the performance of one/zero-shot facial expression recognition.
Possible Autoregulatory Roles of Interleukin 1 for Normal Human Epithelial Cells, Monocytes and B Lymphocytes (1985)

Of all the hormones and growth factors that have been tested only interleukin 1 and 2 (IL 1 and 2) have been documented to be costimulants of thymocyte proliferation. Consequently the operational definition of IL 1 is that of a comitogenic factor for thymocytes that, in contrast with IL 2, does not support the growth of IL 2 dependent lymphocyte cell lines. Another difference between these two cytokines is that IL 2 is produced only by T lymphocytes and some large granular lymphocytes (LGL) (1), whereas IL 1 is produced by many types of cells including monocyte/ macrophages, LGL, keratinocytes, mesangial cells of the kidney, astrocytes, some EBV transformed B cell lines fibroblasts, melanoma cell lines, endothelial cells, and glioma cell lines (as reviewed in 2). Although some of the IL 1 activities derived from non-macrophage cell sources have been partially purified, their precise relationship to macrophage-derived IL 1 will be clarified only when their amino acid sequences become known.
Enabling Data Offload and Proximity Services Using Device to Device Communication over Licensed Cellular Spectrum with Infrastructure Control (2013)

The viability of device to device (D2D) communication on uplink resources [1] as also the benefits accruing from network control over such communication, on licensed spectrum [2], are quite well understood today. We investigate the merits of a particular system instantiation based on these two tenets. The challenge of scheduling communication between two devices using remote schedulers at one or more base stations is addressed with minimal changes to the current signaling mechanisms in a 3GPP LTE based framework. This system maintains as tight a control over device to device communication as is currently maintained over device to infrastructure communication. Furthermore the benefits of such a system range from optimized routing and resource allocation to metered charging for data exchanged on the D2D link to lawful intercept to dynamic local broadcast. We also provide a comparison of this system with the available option of D2D communications over unlicensed spectrum using Wi-Fi.
Cross-Sectional Analysis of CuInS2Thin Film Prepared from Electroplated Precursor (2003)

Thin CuInS2 films were prepared by sulfurization of Cu/In bi-layers. The precursor layer was firstly electroplated onto the treated surface of Mo-coated glass. The observation of the cross- section prepared by focused ion beam (FIB) etching revealed that the void-free film was initially formed on the top surface of the precursor and subsequently continued to grow until the advancing front of the film reached the Mo layer. Then followed the nucleation of voids near the bottom of the CuInS2 film. Prolonged sulfurization caused the voids to increase in size. Thin film solar cells were fabricated using the CuInS2 film as an optical absorber layer. It was found that the optimization of a sulfurization period is important in order to improve the cell efficiency.
Purification and characterization of cysteine protease from germinating cotyledons of horse gram (2009)

It appears that the newly synthesized protease is inactive, and activation takes place during germination. CPRHG has a broad substrate specificity and stability in pH, temperature, etc. therefore, this protease may turn out to be an efficient choice for the pharmaceutical, medicinal, food, and biotechnology industry.
Exchanging pairwise secrets efficiently (2013)

We consider the problem where a group of wireless nodes, connected to the same broadcast domain, want to create pairwise secrets, in the presence of an adversary Eve, who tries to listen in and steal these secrets. Existing solutions assume that Eve cannot perform certain computations (e.g., large-integer factorization) in useful time. We ask the question: can we solve this problem without assuming anything about Eve's computational capabilities? We propose a simple secret-agreement protocol, where the wireless nodes keep exchanging bits until they have agreed on pairwise secrets that Eve cannot reconstruct with very high probability. Our protocol relies on Eve's limited network presence (the fact that she cannot be located at an arbitrary number of points in the network at the same time), but assumes nothing about her computational capabilities. We formally show that, under standard theoretical assumptions, our protocol is information-theoretically secure (it leaks zero information to Eve about the secrets). Using a small wireless testbed of smart-phones, we provide experimental evidence that it is feasible for 5 nodes to create thousands of secret bits per second, with their secrecy being independent from the adversary's capabilities.
Pathogenic mechanisms of a non-agglutinable Vibrio cholerae strain: demonstration of invasive and enterotoxigenic properties (1977)

A non-agglutinable Vibrio cholerae strain isolated from the blood of a child with kwashiorkor and fever was shown to have the potential to invade as well as to produce a toxin resembling cholera toxin.
Fpga Implementation Of An Efficient Proportionate Affine Projection Algorithm For Echo Cancellation (2011)

Publication in the conference proceedings of EUSIPCO, Barcelona, Spain, 2011
On the use of multivariate regression for performance characterisation of JavaSpaces (2004)

This paper discusses research results on the performance characterisation of JavaSpaces. Whereas Design of Experiments provides a technique to obtain response surface models of second order with as few experiments as possible, the construction of higher order models makes more precise predictions possible. Analysis of Variance is iteratively used in combination with Linear Regression to obtain information about the performance characteristics of JavaSpaces, resulting in an accurate response surface model as a function of the input factors.
Assessment of suboptimal control for drag reduction in turbulent channel flow (2002)

A systematic analysis is made of suboptimal control for drag reduction. The influence of the amplitude of actuation (A) and the timescale of actuation (Δt + a ) are evaluated. Two wall-sensing variables are employed, (∂w/∂y| w and ∂p/∂z| w ), with two actuations (ϕ2 and ϕ3). To test the suboptimal control, direct numerical simulations of turbulent channel flow at Re τ = 100 are performed in a spectral domain. It is found that the effect of A and Δt + a on the drag reduction rate (D r ) is significant. The near-wall behaviours of the flow structure are analysed to characterize the drag reduction. An optimal timescale is obtained at Δt + a ≃ 1 and Δt + a should be less than Δt + a ∼ 100. The size effect of the sensor/actuator is examined. This article was chosen from selected Proceedings of the Second International Symposium on Turbulence and Shear Flow Phenomena (KTH-Stockholm, 27-29 June 2001) ed E Lindborg, A Johansson, J Eaton, J Humphrey, N Kasagi, M Leschziner and M Sommerfeld.
Position Statement on Crop Adaptation to Climate Change (2011)

ABSTRACT The Crop Science Society of America's (CSSA) position statement—Crop Adaptation to Climate Change—was researched and assembled by a working group of scientists from academia and industry. The statement (i) reviews the impacts of variable weather conditions arising from climate change on cropping systems, (ii) reports the progress to date in adapting crops and management practices to new conditions, and (iii) offers focus areas for increasing the speed at which global agricultural systems can adapt to climate change.
Thermo-Electro-Mechanical Behavior of Ferroelectric Materials Part I: A Computational Micromechanical Model Versus Experimental Results (2003)

A micro-electro-mechanical model of the behavior of piezoelectric ceramics including thermal effects is presented and compared to experimental data. Results include analytical and numerical investigations of the behavior of piezoelectric ceramics. The model is based on physical mechanisms and includes elastic, dielectric, and piezoelectric anisotropy. Moreover, the model is based on an internal energy approach so that work-energy relations may be directly applied. Results from the model give insight into material behavior.
High-Speed and Transparent Nanocrystalline ZnO Thin Film Transistors (2017)

Thin film transistors (TFTs) made from amorphous or organic semiconductors are commonly used in the control circuits of large-area display electronics such as flat-panel TV screens. Thin films of spontaneously ordered and closely packed nanocolumns of zinc oxide (ZnO) were used to fabricate high-speed and transparent TFTs. Ordered nanocrystalline (nc)-ZnO thin films composed of closely packed nanocolumns offer a unique solution to improving TFT performance to levels comparable to single crystal semiconductors while maintaining their thin film properties. TFTs are mostly used in circuits that do not require high-speed operation because of electron mobility limitations. However, with the demonstrated high electron mobility and the anticipated high electron velocity, ZnO-based TFTs have a greater potential for high-speed circuit applications than amorphous TFTs. The high-speed potential of nc-ZnO TFTs was examined in a series of designs fabricated on high-resistivity silicon substrates. Pulsed laser deposition-grown ZnO thin films were used to fabricate high-speed and transparent thin film transistors.
5G-TRANSFORMER meets Network Service Federation: design, implementation and evaluation (2020)

5G networks require flexibility, automation and programmability to satisfy the requirements of verticals industries. 5G-TRANSFORMER project proposes an SDN/NFV based network platform to enable this vision. Among its features, this platform allows the end-to-end deployment of parts of a network service (NS) in multiple administrative domains, which is known as network service federation (NSF). This feature increases network flexibility, opening the door to new business models. This paper complements our previous work by providing a detailed description of the 5G-TRANSFORMER NSF workflow, its interface and a profiling of the operations involved in the deployment of an NS between multiple administrative domains in a real experimental setup. Experimental results reveal i) that a federated NS can be deployed in the order of few minutes (less than 5 minutes), in line with the 5G target of reducing service setup to minutes, and ii) the impact of the NSF procedure in the deployment time is reduced when compared with the deployment of the same NS in a single administrative domain.
Inflammation in Viral Vector-Mediated Ocular Gene Therapy: A Review and Report From a Workshop Hosted by the Foundation Fighting Blindness, 9/2020 (2021)

Subclinical or clinical inflammation often arises during ocular gene therapy with viral vectors. Understanding the biological bases and impacts on efficacy are important for clinical management and the improvement of future therapies.
Effect of Different Derivatization Protocols on the Calculation of Trophic Position Using Amino Acids Compound-Specific Stable Isotopes (2020)

Amino acids compound-specific nitrogen stable isotope analysis (AA-CSIA) is an emerging tool in ecology for understanding trophic system dynamics. While it has been successfully used for several independent studies across a range of environments and study locations, researchers have encountered calculation issues for determining trophic position values. Most studies introduce modifications to the constants of trophic position equation calculations, but then fail to account for the equation variations when comparing across separate research studies. The broad acceptance of this approach is anchored in an underlying presumption that no addition of the exogenous nitrogen atom occurs in the different methods; and therefore, such variations should not affect the outcome. In this paper, we evaluate the use of the EZfaast amino acid derivatization kit (chloroformate) and compare it to the isotopic results of two other derivatization methods. We highlight new considerations for working with AA-CSIA that might account for some of the variations in the results and lead researchers to modify constants in the equation. This study concludes that developing unique constants per derivatization method is required to have more accurate cross-study comparisons of trophic positions.
MicroRNA Expression and Regulation of Hematopoiesis in CD34+ Cells: A Bioinformatic Circuit Diagram of the Hematopoietic Differentiation Control. (2006)

Abstract MicroRNAs (miRs) are a recently realized class of epigenetic elements which block translation of mRNA to protein. MicroRNAs have been shown to control cellular metabolism, apoptosis, differentiation and development in numerous organisms including drosophila, rat, mouse, and humans. Recently, miRs have been implicated in the control of hematopoiesis. Importantly, both aberrant expression and deletion of miRs are have been associated with the development of various cancers. In a previous study, we determined the gene expression profiles of HSC-enriched, HPC-enriched, and total CD34+ cells from human PBSC, BM, and CB. One rather surprising finding from this study was that virtually all of “hematopoietic important” genes were expressed at virtually identical levels within all populations examined. One of our hypotheses to explain this phenomena was that miRs may control differentiation by controlling protein expression from these “hematopoietic” RNAs. To examine the possible role of miRs in normal hematopoiesis and their relation to the HSPC transcriptome, we used mir-miroarrays to determine the miR expression profile of primary normal human mobilized blood and bone marrow CD34+ hematopoietic stem-progenitor cells (HSPCs). We have combined this miR data with (1) our extensive mRNA expression data obtained previously for CD34+ HSPCs, CD34+/CD38−/Lin- stem cell-enriched, CD34+/CD38+/Lin+ progenitor-enriched populations, and total CD34+ HSPC (Georgantas, Cancer Research 64:4434) and (2) miR target predictions from various published algorithms. Combining these datasets into one integrated database allowed us to bioinformaticly examine the global interaction of HSPC mRNAs and miRs during hematopoiesis. The 3′UTR sequences from many of these “hematopoietic” mRNA were cloned behind a luciferase reporter. K562 cells were transfected with these luc-3′UTR constructs, confirmating that expression of many important hematopoietic proteins are controlled by miRs. Based on our bioinformatic and protein expression studies, we present a global in silico model by which microRNAs control and direct hematopoietic differentiation. Actual in vitro and in vivo studies addressing the action of specific miRs in hematopoietic differentiation are presented in separate abstracts.
The use of urethral stents for the treatment of urethral strictures. (1993)

Three types of urethral stents can be used in the treatment of recurrent strictures: Urolume/Wallstent is a self-expanding mesh which is incorporated into the urethral epithelium; the ASI Titanium stent is a short rigid mesh of Titanium wire which is also incorporated into the urethra; Nitinol is a flexible spring in one or two parts connected by a steel wire. It remains endoluminal. The Urolume/Wallstent has been used since 1987. It is indicated in iatrogenic strictures. No statistical results are presented. The ASI stent should be reserved for strictures of the prostatic and posterior urethra. The Niticol UroCoil system can be used at all levels of the urethra; two models are available: simple or twin. The author has inserted 65 stents in 56 patients. The stent was removed after one year in 41 patients. The use of these stents has considerably decreased the number of repeated dilatations and urethrotomies.
A Computation Control Motion Estimation Method for Complexity-Scalable Video Coding (2010)

In this paper, a new computation-control motion estimation (CCME) method is proposed which can perform motion estimation (ME) adaptively under different computation or power budgets while keeping high coding performance. We first propose a new class-based method to measure the macroblock (MB) importance where MBs are classified into different classes and their importance is measured by combining their class information as well as their initial matching cost information. Based on the new MB importance measure, a complete CCME framework is then proposed to allocate computation for ME. The proposed method performs ME in a one-pass flow. Experimental results demonstrate that the proposed method can allocate computation more accurately than previous methods and, thus, has better performance under the same computation budget.
The Photochemistry of Sulfur Analogues of Dialkyldiazomalonates (2000)

Laser flash photolysis studies (LFP) of O,S-diethylmonothiodiazomalonate (1) and S,S-diethyldithiodiazomalonate (2) in 1,1,2-trichlorotrifluoroethane (Freon-113) were consistent with the trapping of an intermediate with λmax = 425 nm, attributed, in the LFP of 1, to that of ylide 10, formed from the reaction of singlet O,S-carboethoxythioethoxycarbene (9) with pyridine. The deduced lifetime of both singlet O,S-dicarboethoxycarbene (9) and S,S-dicarbothioethoxycarbene (13) are essentially the same in Freon-113, but compared to dicarbomethoxycarbene 14, the lifetimes of 9 and 13 were found to be about six times shorter. The LFP studies, in addition to calculations at the B3LYP/6−31 G* level of theory, provide an explanation for the effect of sulfur perturbation that shortens the carbene lifetimes, as well as an explanation for the exclusive migration of the SEt group to ultimately form 5 upon light (300 nm) induced nitrogen extrusion and Wolff rearrangement of 1 in EtOH.
Stabilization of organic field-effect transistors in hexamethylenetetrathiafulvalene derivatives substituted by bulky alkyl groups (2009)

Hexamethylenetetrathiafulvalene (HMTTF) derivatives substituted by tert-butyl, n-pentyl, and 1,1-dimethylpropyl groups are prepared, and the transistor properties are investigated. The compounds substituted by bulky tertiary groups exhibit high mobilities up to 0.98 cm2/Vs in the thin-film transistors and 2.3 cm2/Vs in the single-crystal transistors. At the same time these compounds realize low threshold voltages close to zero and large on–off ratios. The high mobility and the low threshold voltage are maintained more than one month in air. The single-crystal X-ray structure analyses reveal uniform stacking structures. These observations demonstrate that the low threshold voltage and the stable device performance are not solely determined by the energy levels, but are remarkably improved by the closely packed structures derived from the bulky alkyl groups.