Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative analysis of methylation of genomic loci in early-stage rectal cancer predicts distant recurrence.

PURPOSE There are no accurate prognostic biomarkers specific for rectal cancer. Epigenetic aberrations, in the form of DNA methylation, accumulate early during rectal tumor formation. In a preliminary study, we investigated absolute quantitative methylation changes associated with tumor progression of rectal tissue at multiple genomic methylated-in-tumor (MINT) loci sequences. We then explored in a different clinical patient group whether these epigenetic changes could be correlated with clinical outcome. PATIENTS AND METHODS Absolute quantitative assessment of methylated alleles was used to assay methylation changes at MINT 1, 2, 3, 12, 17, 25, and 31 in sets of normal, adenomatous, and malignant tissues from 46 patients with rectal cancer. Methylation levels of these biomarkers were then assessed in operative specimens of 251 patients who underwent total mesorectal excision (TME) without neoadjuvant radiotherapy in a multicenter clinical trial. RESULTS Methylation at MINT 2, 3, and 31 increased 11-fold (P = .005), 15-fold (P < .001), and two-fold (P = .02), respectively, during adenomatous transformation in normal rectal epithelium. Unsupervised grouping analyses of quantitative MINT methylation data of TME trial patients demonstrated two prognostic subclasses. In multivariate analysis of node-negative patients, this subclassification was the only predictor for distant recurrence (hazard ratio [HR], 4.17; 95% CI, 1.72 to 10.10; P = .002), cancer-specific survival (HR, 3.74; 95% CI, 1.4 to 9.43; P = .003), and overall survival (HR, 2.68; 95% CI, 1.41 to 5.11; P = .005). CONCLUSION Methylation levels of specific MINT loci can be used as prognostic variables in patients with American Joint Committee on Cancer stage I and II rectal cancer. Quantitative epigenetic classification of rectal cancer merits evaluation as a stratification factor for adjuvant treatment in early disease.
A novel gain control LNA for 2.4GHz application using 0.18/spl mu/m CMOS

This paper presents a novel gain control method for 2.4 GHz LNA applications. In this design, a digital mode gain control concept was implemented. This chip can accept an appropriate control bit that come from base band to achieve power saving. With digital mode gain control to achieve low noise and high 1dB compression point simultaneously without increasing any circuit and power consumption. Depend on receiving signal strength, there are four gain modes can be selecting automatically. The compact CMOS LNA is optimized for low-power-consuming ISM band applications and is fabricated using commercial 0.18mum CMOS process. With current re-use technology, the power consumption and linearity can be optimizing. The fully integrated 2.4GHz gain controllable LNA exhibits 15.2dB maximum gain, 4.1dB minimum gain, respectively. Also, the LNA has excellent noise performance at high gain mode; 1.55dB of noise figure is achieved in this work. The digital modes gain controllable LNA produces a 1-dB compression output power of -10 dBm. It consumes 2.5mA current from a supply voltage of 1.8V
Bis[2-((4,6-dimethylpyrimidin-2-yl){2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]ethyl}amino)ethyl] disulfide

Bis[2-(4,6-dimethylpyrimidin-2-ylsulfanyl)ethyl]amine under hydrothermal conditions has unexpectedly been transformed into the title compound, C32H44N10S4. In the title molecule, the zigzag 3,10-diaza-6,7-disulfanyldodecyl skeleton has two dimethylpyrimidinylsulfanyl groups at both ends, and the aza atoms each carry a dimethylpyrimidinyl unit. The N atoms in the skeleton show a planar coordination.
Disease classification and prediction via semi-supervised dimensionality reduction

We present a new semi-supervised algorithmfor dimensionality reduction which exploits information of unlabeled data in order to improve the accuracy of image-based disease classification based on medical images. We perform dimensionality reduction by adopting the formalismof constrainedmatrix decomposition of [1] to semi-supervised learning. In addition, we add a new regularization term to the objective function to better captur the affinity between labeled and unlabeled data. We apply our method to a data set consisting of medical scans of subjects classified as Normal Control (CN) and Alzheimer (AD). The unlabeled data are scans of subjects diagnosedwith Mild Cognitive Impairment (MCI), which are at high risk to develop AD in the future. We measure the accuracy of our algorithm in classifying scans as AD and NC. In addition, we use the classifier to predict which subjects with MCI will converge to AD and compare those results to the diagnosis given at later follow ups. The experiments highlight that unlabeled data greatly improves the accuracy of our classifier.
3D-Stereoscopic X Windows

All known technologies for displaying 3D-stereoscopic images are more or less incompatible with the X Window System. Applications that seek to be portable must support the 3D-display paradigms of multiple hardware implementations of 3D-stereoscopy. We have succeeded in modifying the functionality of X to construct generic tools for displaying 3D-stereoscopic imagery. Our approach allows for experimentation with visualization tools and techniques for interacting with these synthetic worlds. Our methodology inherits the extensibility and portability of X. We have demonstrated its applicability in two display hardware paradigms that are specifically discussed.
Power Hardware-in-the-Loop Testing of an Air Coil Superconducting Fault Current Limiter Demonstrator

This paper discusses power hardware-in-the-loop (PHIL) tests performed at the Center for Advanced Power Systems (CAPS) with a 60-kVA, 400-V, z= 6$% air coil (AC) superconducting fault current limiter (AC-SFCL) demonstrator. The demonstrator was designed, built, and successfully tested for fault current limitation at Karlsruhe Institute of Technology (KIT) . Initial PHIL testing at CAPS focused on a single-phase setup to verify the results obtained at KIT. Subsequent PHIL testing in a three-phase system was accomplished by interfacing the physical AC-SFCL to the simulated system in phase A and simulating the effect of AC-SFCL devices in the other two phases. This was done by estimating the resistance and inductance of the AC-SFCL through instantaneous voltage and current measurements and inserting this impedance in phases B and C for cases in which these phases were part of the short-circuit path. For these PHIL experiments, the modified damping impedance (DIM) interface algorithm was employed. It was possible to reproduce earlier reference measurements using the modified DIM PHIL interface algorithm. The PHIL system was then used to create a three-phase power system consisting of a generator, a load, and a short-circuit path. Symmetrical and unsymmetrical short circuits have been performed with and without ground connection. The PHIL system maintained stability throughout the experiments, and the results show suitable current limitation for all performed types of short circuits.
Computationally Efficient Kalman Filtering for a Class of Nonlinear Systems

This paper deals with recursive state estimation for the class of discrete time nonlinear systems whose nonlinearity consists of one or more static nonlinear one-variable functions. This class contains several important subclasses. The special structure is exploited to permit accurate computations without an increase in computational cost. The proposed method is compared with standard Extended Kalman Filter, Unscented Kalman Filter and Gauss-Hermite Kalman Filter in three illustrative examples. The results show that it yields good results with small computational cost.
The role of basal ganglia and cerebellum in motor learning. A computational model

Our research activity investigates the computational processes underlying the execution of complex sequences of movements and aims at understanding how different levels of the nervous system interact and contribute to the gradual improvement of motor performance during learning. Many research areas, from neuroscience to engineering, investigate, from different perspectives and for diverse purposes, the processes that allow humans to efficiently perform skilled movements. From a biological point of view, the execution of voluntary movements requires the interaction between nervous and musculoskeletal systems, involving several areas, from the higher cortical centers to motor circuits in the spinal cord. Understanding these interactions could provide important insights for many research fields, from machine learning to medicine, from the design of robotic limbs to the development of new treatments for movement disorders, such as Parkinson’s disease. This goal could be achieved by finding an answer to the following questions: • How does the central nervous system control and coordinate natural voluntary movements? • Which brain areas are involved in learning a new motor skill? What are the changes that happen in these neural structures? What are the aspects of the movement memorized? • Which is the process that allows people to perform a skilled task, such as playing an instrument, being apparently unaware of the movements they are performing? • What happen when a neurodegenerative disease affects the brain areas involved in executing
Three of the Four Nucleocapsid Proteins of Marburg Virus, NP, VP35, and L, Are Sufficient To Mediate Replication and Transcription of Marburg Virus-Specific Monocistronic Minigenomes

ABSTRACT This paper describes the first reconstituted replication system established for a member of the Filoviridae, Marburg virus (MBGV). MBGV minigenomes containing the leader and trailer regions of the MBGV genome and the chloramphenicol acetyltransferase (CAT) gene were constructed. In MBGV-infected cells, these minigenomes were replicated and encapsidated and could be passaged. Unlike most other members of the orderMononegavirales, filoviruses possess four proteins presumed to be components of the nucleocapsid (NP, VP35, VP30, and L). To determine the protein requirements for replication and transcription, a reverse genetic system was established for MBGV based on the vaccinia virus T7 expression system. Northern blot analysis of viral RNA revealed that three nucleocapsid proteins (NP, VP35, and L) were essential and sufficient for transcription as well as replication and encapsidation. These data indicate that VP35, rather than VP30, is the functional homologue of rhabdo- and paramyxovirus P proteins. The reconstituted replication system was profoundly affected by the NP-to-VP35 expression ratio. To investigate whether CAT gene expression was achieved entirely by mRNA or in part by full-length plus-strand minigenomes, a copy-back minireplicon containing the CAT gene but lacking MBGV-specific transcriptional start sites was employed in the artificial replication system. This construct was replicated without accompanying CAT activity. It was concluded that the CAT activity reflected MBGV-specific transcription and not replication.
A Nanostructured Microfluidic Immunoassay Platform for Highly Sensitive Infectious Pathogen Detection

Rapid and simultaneous detection of multiple potential pathogens by portable devices can facilitate early diagnosis of infectious diseases, and allow for rapid and effective implementation of disease prevention and treatment measures. The development of a ZnO nanorod integrated microdevice as a multiplex immunofluorescence platform for highly sensitive and selective detection of avian influenza virus (AIV) is described. The 3D morphology and unique optical property of the ZnO nanorods boost the detection limit of the H5N2 AIV to as low as 3.6 × 103 EID50 mL−1 (EID50: 50% embryo infectious dose), which is ≈22 times more sensitive than conventional enzyme‐linked immunosorbent assay. The entire virus capture and detection process could be completed within 1.5 h with excellent selectivity. Moreover, this microfluidic biosensor is capable of detecting multiple viruses simultaneously by spatial encoding of capture antibodies. One prominent feature of the device is that the captured H5N2 AIV can be released by simply dissolving ZnO nanorods under slightly acidic environment for subsequent off‐chip analyses. As a whole, this platform provides a powerful tool for rapid detection of multiple pathogens, which may extent to the other fields for low‐cost and convenient biomarker detection.
Confinement of High-Strength Concrete Columns

The paper presents results from 4 high strength concrete specimens, 3 nonprismatic and 1 prismatic, tested under constant axial load and cyclic lateral loads simulating earthquake forces, and comparison is made with similar specimens of normal strength concrete. Concrete strength varied between 4500 and 8500 psi. Relevant provisions of the ACI Building Code are evaluated in light of the test data. Increase in the lateral steel contents resulted in an almost proportional increase in ductility and energy-absorption capacity of confined high strength concrete, just as in the case of normal strength concrete. The required amount of confining steel appears to be proportional to the strength of concrete for a certain column performance if the axial load is measured in terms of Po rather than as a fraction of f'c Ag. Comments are made on the useable compressive strain.
An improved reliability cuk based solar inverter with sliding mode control

Many photovoltaic inverter designs make use of a buck based switched mode power supply (SMPS) to produce a rectified sinusoidal waveform. This waveform is then unfolded by a low frequency switching structure to produce a fully sinusoidal waveform. The Cuk SMPS could offer advantages over the buck in such applications. Unfortunately the Cuk converter is considered to be difficult to control using classical methods. Correct closed loop design is essential for stable operation of Cuk converters. Due to these stability issues, Cuk converter based designs often require stiff low bandwidth control loops. In order to achieve this stable closed loop performance, traditional designs invariably need large, unreliable electrolytic capacitors. In this paper, an inverter with a sliding mode control approach is presented which enables the designer to make use of the Cuk converters advantages, while ameliorating control difficulties. This control method allows the selection of passive components based predominantly on ripple and reliability specifications while requiring only one state reference signal. This allows much smaller, more reliable non-electrolytic capacitors to be used. A prototype inverter has been constructed and results obtained which demonstrate the design flexibility of the Cuk topology when coupled with sliding mode control.
Monoclonal Antibody to the Receptor for Murine Coronavirus MHV-A59 Inhibits Viral Replication In Vivo

Abstract Because many strains of mouse hepatitis virus (MHV) infect laboratory mice, no effective vaccine has yet been developed. An alternative approach to control MHV disease is the use of a host cell receptor-targeted ligand. Toaddress the potential usefulness of this approach, a monoclonal antibody directed against the host cell receptor for the coronavirus MHV-A59 was administered to infant mice that were then challenged oronasally with 104 intracerebral infant mouse median lethal doses of MHV-A59. Antibody treatment of virus-challenged mice resulted in lower proportions of mice with MHV-A59 in target organs and markedly reduced viral titers in these organs compared with mock-treated infected mice. Some antibody-treated infected mice survived for 7 days after viral challenge, whereas no mock-treated, infected mice survived beyond day 3 after viral inoculation. These results support a receptor-targeted approach to intervention in coronavirus disease.
Chk2-dependent HuR phosphorylation regulates occludin mRNA translation and epithelial barrier function

Occludin is a transmembrane tight junction (TJ) protein that plays an important role in TJ assembly and regulation of the epithelial barrier function, but the mechanisms underlying its post-transcriptional regulation are unknown. The RNA-binding protein HuR modulates the stability and translation of many target mRNAs. Here, we investigated the role of HuR in the regulation of occludin expression and therefore in the intestinal epithelial barrier function. HuR bound the 3′-untranslated region of the occludin mRNA and enhanced occludin translation. HuR association with the occludin mRNA depended on Chk2-dependent HuR phosphorylation. Reduced HuR phosphorylation by Chk2 silencing or by reduction of Chk2 through polyamine depletion decreased HuR-binding to the occludin mRNA and repressed occludin translation, whereas Chk2 overexpression enhanced (HuR/occludin mRNA) association and stimulated occludin expression. In mice exposed to septic stress induced by cecal ligation and puncture, Chk2 levels in the intestinal mucosa decreased, associated with an inhibition of occludin expression and gut barrier dysfunction. These results indicate that HuR regulates occludin mRNA translation through Chk2-dependent HuR phosphorylation and that this influence is crucial for maintenance of the epithelial barrier integrity in the intestinal tract.
Scalable Task-Oriented Parallelism for Structure Based Incomplete LU Factorization

ILU(k) is a commonly used preconditioner for iterative linear solvers for sparse, non-symmetric systems. It is often preferred for the sake of its stability. We present TPILU(k), the first efficiently parallelized ILU(k) preconditioner that maintains this important stability property. Even better, TPILU(k) preconditioning produces an answer that is bit-compatible with the sequential ILU(k) preconditioning. In terms of performance, the TPILU(k) preconditioning is shown to run faster whenever more cores are made available to it --- while continuing to be as stable as sequential ILU(k). This is in contrast to some competing methods that may become unstable if the degree of thread parallelism is raised too far. Where Block Jacobi ILU(k) fails in an application, it can be replaced by TPILU(k) in order to maintain good performance, while also achieving full stability. As a further optimization, TPILU(k) offers an optional level-based incomplete inverse method as a fast approximation for the original ILU(k) preconditioned matrix. Although this enhancement is not bit-compatible with classical ILU(k), it is bit-compatible with the output from the single-threaded version of the same algorithm. In experiments on a 16-core computer, the enhanced TPILU(k)-based iterative linear solver performed up to 9 times faster. As we approach an era of many-core computing, the ability to efficiently take advantage of many cores will become ever more important. TPILU(k) also demonstrates good performance on cluster or Grid. For example, the new algorithm achieves 50 times speedup with 80 nodes for general sparse matrices of dimension 160,000 that are diagonally dominant.
Negative Self-Disclosure on the Web: The Role of Guilt Relief

In this paper, we suggest people use anonymous online forums as platforms for self-disclosing actions they feel guilty about—such as transgressions and unethical behaviors—with the goal of achieving guilt relief through others’ reactions. We support this proposition by analyzing field data extracted from Yahoo Answers, an online question-and-answer website. Our analysis shows the level of guilt relief an answer is expected to offer the “asker” (the self-disclosing person) is positively associated with the asker’s likelihood of selecting that answer as the “best” response to the self-disclosure. Furthermore, following receipt of a guilt-relieving answer, an asker becomes less likely to engage in prosocial behavior, which is another type of guilt-relieving action.
Copyright 2009 by Human Factors and Ergonomics Society, Inc. All rights reserved. 10.1518/107118109X12524442637507

Memory for goals theory (Altmann & Trafton, 2002) describes how people suspend and resume an interrupted task by encoding, or rehearsing, the current problem state at the point of interruption and recalling this state after the interruption. In this work we investigated the timing of the encoding process, attempting to determine the most likely strategies for when to perform encoding of interrupted problem state. We examined several candidate encoding strategies and developed computational cognitive models to represent each strategy, embedding the models into a larger model of behavior in a interruption-tracking task. Comparison of the model simulations with recent empirical data suggests that encoding of problem state occurs for a short time at the start of the interruption period and is performed concurrently with the interrupting task.
RELIABLE BIOMETRIC AUTHENTICATION WITH PRIVACY PROTECTION

We propose a new scheme for reliable authentication of physical objects. The scheme allows not only the combination of noisy data with cryptographic functions but has the additional property that the stored reference information is non-revealing. By breaking into the database and retrieving the stored data, the attacker will not be able to obtain any realistic approximation of the original physical object. This technique has applications in secure storage of biometric templates in databases and in authentication of PUFs (Physical Uncloneable Functions).
HIC1 Modulates Prostate Cancer Progression by Epigenetic Modification

Purpose: Prostate cancer is the second leading cause of cancer deaths among men in Western counties, which has also occurred in Chinese male with markedly increasing incidence in recent years. Although the mechanism underlying its progression still remains unclear, epigenetic modifications are important ethological parameters. The purpose of this study is to determine the methylation status and function of hypermethylatioted in cancer 1 (HIC1) in prostate cancer progression. Experimental Design: The methylation status of HIC1 promoter was assayed in cell lines, tissues, and plasma of patients with prostate cancer by using methylation-specific PCR and bisulfate sequencing PCR. The ability of HIC1 to regulate proliferation, migration, and invasion was assessed by MTT, scratch-healing assay, and reconstituted extracellular matrices in porous culture chambers. Tumorigenesis, metastases, and bone destruction were analyzed in mice bearing prostate cancer cells restoring HIC1 by using Xenogen IVIS with radiographic system and small-animal positron emission tomography computed tomographic images. Microarrays were searched for genes that had correlated expression with HIC1 mRNA. Reporter gene assays were used to determine whether HIC1 affected the expression of CXCR7, and chromatin immunoprecipitation was used to determine whether HIC1 bound to CXCR7 promoters. All P values were determined using 2-sided tests. Results: The methylation status of 11 CpG sites within HIC1 promoter was abundantly methylated in cell lines, tissues, and plasma of patients with prostate cancer compared with those of respective normal controls. Restoring HIC1 expression in prostate cancer cells markedly inhibited proliferation, migration, and invasion and induced the apoptosis in these cells. Moreover, mice bearing prostate cancer–restoring HIC1 cells had a marked effect on reducing tumor growth, multiple tissue metastases, and bone destruction. Notably, we also identified that the chemokine receptor CXCR7 is a direct downstream target gene of HIC1. Finally, we showed that CXCR7 promoter in prostate cancer cells is negatively regulated by HIC1, which may be responsible for prostate cancer progression. Conclusions: Our data show for the first time that hypermethylation of HIC1 promoter results in loss of its repressive function, responsible for prostate cancer progression and invasion. These findings suggest that therapies targeting epigenetic events regulating HIC1 expression may provide a more effective strategy for prostate cancer treatment. Clin Cancer Res; 19(6); 1400–10. ©2012 AACR.