Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of stress in amorphous silicon nitride and implications to c-Si surface passivation

In this work we study stress in amorphous silicon nitride (SiNx) deposited by semi-remote microwave plasma-enhanced chemical vapor deposition. The film stress, determined from the change in wafer curvature before and after SiNx deposition, is found to depend on SiNx stoichiometry irrespective of process conditions. We demonstrate that an increase in stress correlates to a shift of the Si-H stretching vibrational peak to a higher wavenumber and an increase of total bond density of N-related bonds (sum of Si-N and N-H bond densities). We also find that there is no dominant relationship between stress and the effective surface recombination velocity or the interface defect density, but for SiNx prepared by varying a single process condition such as gas ratio, there does exist correlation between electrical interface properties and stress. These results suggest that the Si-SiNx interfacial electrical properties are less dependent on stress than they are on other factors such as ion bombardment or hydrogen passivation that can be altered by varying process variables.
On proving left termination of constraint logic programs

The Constraint Logic Programming (CLP) Scheme merges logic programming with constraint solving over predefined domains. In this article, we study proof methods for universal left termination of constraint logic programs. We provide a sound and complete characterization of left termination for ideal CLP languages which generalizes acceptability of logic programs. The characterization is then refined to the notion of partial acceptability, which is well suited for automatic modular inference. We describe a theoretical framework for automation of the approach, which is implemented. For nonideal CLP languages and without any assumption on their incomplete constraint solvers, even the most basic sound termination criterion from logic programming does not lift. We focus on a specific system, namely CLP(R), by proposing some additional conditions that make (partial) acceptability sound.
A Web-enabled Configuration System for Interior Design

Web-enabling technologies represent the next generation of design environments to design and manufacture complex systems, such as them characterizing contract furniture. In the context of web applications to facilitate and support teamwork in collaborative product development, the paper presents a CAD-based infrastructure for the 3D visualization of co-designed solutions, the on-line customization of furniture items and the creation of a shared relational database of products, architectural scenes and knowledge-based rules guiding configuration. A double-level geometry is presented to manage 3D web representation and product structure. A use case is adopted to show main platform functionalities and possible advantages for the extensible contract furniture cluster.
Complete scanning of the CDK4 gene by denaturing gradient gel electrophoresis: A novel missense mutation but low overall frequency of mutations in sporadic metastatic malignant melanoma

The cyclin‐dependent kinase 4 (CDK4) is a key component in regulation of the mammalian cell cycle. The recent discovery of a common missense mutation (Arg24Cys) in both sporadic and familial forms of malignant melanoma strongly supports the candidacy of CDK4 as a proto‐oncogene. To study further the role of CDK4 in melanoma pathogenesis, we have established a method based on polymerase chain reaction (PCR) in combination with denaturing gradient gel electrophoresis (DGGE) to scan the CDK4 gene for point mutations. By analyzing the entire coding sequence of the CDK4 gene in 56 sporadic metastatic malignant melanomas, we identified a novel missense mutation, Asn41Ser. This mutation was also found in the germline of the patient who had no family history of melanoma. Analysis of a tumor‐derived cell line demonstrated equal expression of the mutant and wild‐type CDK4 alleles, together with lack of functional p16. Our findings suggest that an oncogenic mechanism of the CDK4‐Asn41Ser variant would be different from the CDK4‐Arg24Cys variant. Altogether, our data demonstrate that point mutation of CDK4 is a rare event in melanoma pathogenesis. Int. J. Cancer 72:780–783, 1997. © 1997 Wiley‐Liss, Inc.
Clinical Evluation of a Verifi cation Strategy for Personal FM Systems and Nonlinear Hearing Aids

The primary aim of this study was to characterize the problems that may arise when following the ASHA 2002 guideline for fi tting of FM systems to conduct electroacoustic verifi cation of the FM advantage provided by nonlinear hearing aids. Electroacoustic output of FM systems coupled to nonlinear digital hearing aids was determined using the ASHA recommended procedure. When the ASHA recommended +10 dB FM advantage was not obtained, gain of the FM receiver was adjusted and additional electroacoustic measurements were conducted to illustrate changes in output, distortion, and equivalent input noise that may occur when increases in FM receiver gain are provided.
Applying flow-sensitive CQUAL to verify MINIX authorization check placement

We present the first use of flow-sensitive CQUAL to verify the placement of operating system authorization checks. Our analysis of MINIX 3 system servers and discovery of a non-exploitable Time-Of-Check/Time-Of-Use bug demonstrate the effectiveness of flow sensitive CQUAL and its advantage over earlier flow-insensitive versions. We also identify and suggest alternatives to current CQUAL usability features that encourage analysts to make omissions that cause the otherwise sound tool to produce false-negative results.
The TS-tree: efficient time series search and retrieval

Continuous growth in sensor data and other temporal data increases the importance of retrieval and similarity search in time series data. Efficient time series query processing is crucial for interactive applications. Existing multidimensional indexes like the R-tree provide efficient querying for only relatively few dimensions. Time series are typically long which corresponds to extremely high dimensional data in multidimensional indexes. Due to massive overlap of index descriptors, multidimensional indexes degenerate for high dimensions and access the entire data by random I/O. Consequently, the efficiency benefits of indexing are lost. In this paper, we propose the TS-tree (time series tree), an index structure for efficient time series retrieval and similarity search. Exploiting inherent properties of time series quantization and dimensionality reduction, the TS-tree indexes high-dimensional data in an overlap-free manner. During query processing, powerful pruning via quantized separator and meta data information greatly reduces the number of pages which have to be accessed, resulting in substantial speed-up. In thorough experiments on synthetic and real world time series data we demonstrate that our TS-tree outperforms existing approaches like the R*-tree or the quantized A-tree.
Reliability of the Modified Ashworth Scale in the assessment of plantarflexor muscle spasticity in patients with traumatic brain injury

Although the Modified Ashworth Scale (MAS) is commonly used to assess the severity of muscle spasticity for ankle plantarflexors, its reliability has only been established for elbow muscles. Interrater reliability, intrarater reliability and temporal (between-days) reliability were examined in this study. Also, interrater reliability for use of the scale with plantarflexors was compared with reported results from the measurement of elbow flexors. Thirty adult volunteers with traumatic brain injuries participated. There were 20 men and 10 women; the mean age was 28.3 years (SD = 10.8). Two physical therapists used the MAS to score the subjects independently. Measurements were repeated to yield multiple scores for intrarater reliability assessment. Twenty-one of the subjects returned individually on separate days to be measured again, so that temporal reliability could be assessed. Spearman's correlation coefficients were 0.73 for interrater reliability 0.74 and 0.55 for intrarater reliability, and 0.82 for temporal reliability. Overall, reliability of the MAS for assessing plantarflexor spasticity in patients with traumatic brain injury was found to be minimally adequate to support its continued use. However, interrater reliability was less than that which has been reported for elbow flexors, and intrarater reliability findings were mixed.
Catalytic Growth of Zinc Oxide Nanowires by Vapor Transport

nanoparticles in dimethylsulfoxide onto the PLL film for about 20 min, after which it was rinsed in dimethylsulfoxide and then dichloromethane. From the molecular weight, the average length of the PLL is about 30 nm. Therefore, each polymer can accommodate about seven or eight nanoparticles. [20] L. Clarke, M. N. Wybourne, M. Yan, S. X. Cai, J. F. W. Keana, Appl. Phys. Lett. 1997, 71, 617. [21] A. A. Middleton, N. S. Wingreen, Phys. Rev. Lett. 1993, 71, 3198. [22] G. Y. Hu, R. F. O'Connell, Phys. Rev. B 1994, 49, 16 773. [23] A. J. Rimberg, T. R. Ho, J. Clarke, Phys. Rev. Lett. 1995, 74, 4714. [24] L. Clarke, M. N. Wybourne, M. Yan, S. X. Cai, L. O. Brown, J. Hutchison, J. F. W. Keana, J. Vac. Sci. Technol. B 1997, 15, 2925. [25] The capacitance matrix was calculated for different chain lengths using the software package FastCap MIT (1992). We used the nanoparticle dimensions given in the text and a ligand shell dielectric constant of 3. For nanoclusters away from the end of the chains we obtain Cdd » 0.04 aF and Cg » 0.17 aF. As expected, the value of Cg is slightly larger than the value calculated for an isolated metal sphere of radius a coated with a dielectric shell, Cg» (4pee0a)/(1 + (a/d)(e±1)) = 0.14 aF, where d is the total radius of the core plus ligand shell. [26] Simulations were carried out using both MOSES (Monte-Carlo SingleElectronics Simulator, R. H. Chen) and SIMON (Simulation of Nano Structures, C. Wasshuber). [27] S. Chen, R. S. Ingram, M. J. Hostetler, J. J. Pietron, R. W. Murray, T. G. Schaaff, J. T. Khoury, M. M. Alvarez, R. L. Whetton, Science 1998, 280, 2098. [28] L. Y. Gorelik, A. Isacsson, M. V. Voinova, B. Kasemo, R. I. Shekhter, M. Jonson, Phys. Rev. Lett. 1998, 80, 4526. [29] O. D. Häberlen, S. C. Chung, M. Stener, N. Rösch, J. Chem. Phys. 1997, 106, 5189. [30] Y. Awakuni, J. H. Calderwood, J. Phys. D: Appl. Phys. 1972, 5, 1038. [31] G. Markovich, C. P. Collier, J. R. Heath, Phys. Rev. Lett. 1998, 80, 3807. [32] C. P. Collier, R. J. Saykally, J. J. Shiang, S. E. Hendrichs, J. R. Heath, Science 1997, 277, 1978. [33] N. Mott, Metal Insulator Transitions, Taylor and Francis, London 1990.
ASSESSMENT OF AGE AND GENDER ON PACED AUDITORY SERIAL ADDITION TEST AND PACED VISUAL SERIAL ADDITION TEST IN NORMAL SUBJECTS

Paced Auditory Serial Addition Test (PASAT) has been used as a common research tool for different neurological disorders like Multiple Sclerosis. Recently, technology let researchers to introduce a new version of the visual test, the paced visual serial addition test (PVSAT). In this paper, the computerized versions of these two tests are introduced. The software calculates the number of true responses and the reaction time of subjects. We hypothesize that paying attention to the reaction time is valuable and should be concerned. For this purpose, sixty eight female normal subjects and fifty eight male normal subjects are enrolled in the study. We investigate the similarity between the PASAT3 and PVSAT3 in number of true responses and the new proposed criterion, the average reaction time of each subject. The similarity between two tests were rejected (p-value = 0.000) which means that these two tests differ. The effect of gender in the tests were not approved since the p-values of difference between PASAT3 and PVSAT3 in both gender is the same (p-value = 0.000) which means that male and female subjects performed the tests at no different level of performance. The new criterion shows a negative correlation with the age which offers aged normal subjects may have the same number of true responses as the young subjects but they have latent responses. This will give proof for the importance of reaction time.
Factor Analysis and Nuisance Attribute Projection Revisited

In the paper Factor Analysis (FA) and Nuisance Attribute Projection (NAP) are reviewed, analyzed and compared. Since nowadays FA become a part of most state-of-the-art recognition systems (used e.g. in the concept of i-vectors or PLDA models) it is of relevance to examine different insights into the problem. NAP was chosen as a counterpart to FA as an advanced PCA like method often utilized in speaker recognition systems along with FA. It is demonstrated how can be both FA and NAP expressed as solutions of Least Squares (LS), the consequences of the LS formulation are discussed, and it is shown in what extent do solutions of NAP and FA overlap.
Lectin microarray analysis of pluripotent and multipotent stem cells

Stem cells have a capability to self‐renew and differentiate into multiple types of cells; specific markers are available to identify particular stem cells for developmental biology research. In this study, we aimed to define the status of somatic stem cells and the pluripotency of human embryonic stem (hES) and induced pluripotent stem (iPS) cells using a novel molecular methodology, lectin microarray analysis. Our lectin microarray analysis successfully categorized murine somatic stem cells into the appropriate groups of differentiation potency. We then classified hES and iPS cells by the same approach. Undifferentiated hES cells were clearly distinguished from differentiated hES cells after embryoid formation. The pair‐wise comparison means based on ‘false discovery rate’ revealed that three lectins ‐Euonymus europaeus lectin (EEL), Maackia amurensis lectin (MAL) and Phaseolus vulgaris leucoagglutinin [PHA(L)]‐ generated maximal values to define undifferentiated and differentiated hES cells. Furthermore, to define a pluripotent stem cell state, we generated a discriminant for the undifferentiated state with pluripotency. The discriminant function based on lectin reactivities was highly accurate for judgment of stem cell pluripotency. These results suggest that glycomic analysis of stem cells leads to a novel comprehensive approach for quality control in cell‐based therapy and regenerative medicine.
Integrating full spectrum of sequence features into predicting functional microRNA-mRNA interactions

MOTIVATION MicroRNAs (miRNAs) play important roles in general biological processes and diseases pathogenesis. Identifying miRNA target genes is an essential step to fully understand the regulatory effects of miRNAs. Many computational methods based on the sequence complementary rules and the miRNA and mRNA expression profiles have been developed for this purpose. It is noted that there have been many sequence features of miRNA targets available, including the context features of the target sites, the thermodynamic stability and the accessibility energy for miRNA-mRNA interaction. However, most of current computational methods that combine sequence and expression information do not effectively integrate full spectrum of these features; instead, they perceive putative miRNA-mRNA interactions from sequence-based prediction as equally meaningful. Therefore, these sequence features have not been fully utilized for improving miRNA target prediction. RESULTS We propose a novel regularized regression approach that is based on the adaptive Lasso procedure for detecting functional miRNA-mRNA interactions. Our method fully takes into account the gene sequence features and the miRNA and mRNA expression profiles. Given a set of sequence features for each putative miRNA-mRNA interaction and their expression values, our model quantifies the down-regulation effect of each miRNA on its targets while simultaneously estimating the contribution of each sequence feature to predicting functional miRNA-mRNA interactions. By applying our model to the expression datasets from two cancer studies, we have demonstrated our prediction results have achieved better sensitivity and specificity and are more biologically meaningful compared with those based on other methods. AVAILABILITY AND IMPLEMENTATION The source code is available at: http://nba.uth.tmc.edu/homepage/liu/miRNALasso. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT Yin.Liu@uth.tmc.edu.
Transgenic Mice Developing Osteosarcomas Simian Virus 40 Large T Antigen Epitopes in T Antigen Sequential Loss of Cytotoxic T Lymphocyte Responses to

ABSTRACT The role of CTL tolerance in tumor immunity to SV40 large T antigen(T ag)-induced tumors was studied using T ag transgenic mice of the line501 (H2 b ). 501 mice express SV40 T ag under the influence of thea-amylase promoter, which leads to the development of osteogenic osteo-sarcomas late in life and eventual death between 12 and 17 months of age.We determined the ability of 501 mice to respond to the four H2 b -restricted T ag CTL epitopes, which include epitope I (T ag 206–215),epitope II/III (T ag 223–231), the immunorecessive epitope V (T ag489–497), restricted by H2-D b , and epitope IV (T ag 404–411), restrictedby H2-K b . We demonstrate that 501 mice are partially tolerant to theH2 b -restricted T ag epitopes. Immunization of 4-month-old 501 mice withT ag-transformed syngeneic cell lines or a recombinant vaccinia virusexpressing full-length T ag elicited CTL responses against the H2-K b -restricted T ag epitope IV only. In contrast, immunization of 4-month-old501 mice with recombinant vaccinia viruses expressing individual T agepitopes as minigenes elicited CTLs against epitopes I, IV, and V, but notagainst epitope II/III. Complete tolerance to epitopes I, IV, and V devel-oped in 501 mice, but the age when tolerance was detected varied for eachepitope. Tolerance to epitope I occurred by 6 months of age and wasaccelerated in the absence of CD4
Nuclear Factor-κB Regulates βAPP and β- and γ-Secretases Differently at Physiological and Supraphysiological Aβ Concentrations*

Background: NF-κB regulates BACE1 but there is little data suggesting βAPP and γ-secretase involvement. Results: NF-κB differentially regulates Aβ production at physiological and supraphysiological Aβ concentrations by modulating transactivation of βAPP and γ-secretase promoters, thereby controlling γ-secretase activity. Conclusion: Under physiological conditions, NF-κB regulates Aβ homeostasis while it contributes in increasing Aβ production in the pathological context. Significance: NF-κB may be seen as a potential therapeutic target. Anatomical lesions in Alzheimer disease-affected brains mainly consist of senile plaques, inflammation stigmata, and oxidative stress. The nuclear factor-κB (NF-κB) is a stress-activated transcription factor that is activated around senile plaques. We have assessed whether NF-κB could be differentially regulated at physiological or supraphysiological levels of amyloid β (Aβ) peptides. Under these experimental conditions, we delineated the putative NF-κB-dependent modulation of all cellular participants in Aβ production, namely its precursor βAPP (β-amyloid precursor protein) and the β- and γ-secretases, the two enzymatic machines involved in Aβ genesis. Under physiological conditions, NF-κB lowers the transcriptional activity of the promoters of βAPP, β-secretase (β-site APP-cleaving enzyme 1, BACE1), and of the four protein components (Aph-1, Pen-2, nicastrin, presenilin-1, or presenilin-2) of the γ-secretase in HEK293 cells. This was accompanied by a reduction of both protein levels and enzymatic activities, thereby ultimately yielding lower amounts of Aβ and AICD (APP intracellular domain). In stably transfected Swedish βAPP-expressing HEK293 cells triggering supraphysiological concentrations of Aβ peptides, NF-κB activates the transcription of βAPP, BACE1, and some of the γ-secretase members and increases protein expression and enzymatic activities, resulting in enhanced Aβ production. Our pharmacological approach using distinct NF-κB kinase modulators indicates that both NF-κB canonical and alternative pathways are involved in the control of Aβ production. Overall, our data demonstrate that under physiological conditions, NF-κB triggers a repressive effect on Aβ production that contributes to maintaining its homeostasis, while NF-κB participates in a degenerative cycle where Aβ would feed its own production under pathological conditions.
Recursive Identification of Piecewise Affine Hybrid Systems

In this paper we propose a procedure for recursive identification of discrete time piecewise affine (PWA) hybrid systems. The PWA identification problem involves the estimation of both the parameters of affine submodels and the partition of the PWA map from data. In this paper the submodel parameters estimation problem is solved via recursive k-plane clustering algorithm and the problem of region estimation is performed by incremental proximal support vector machine. Also, the effect of mode switching on the estimated parameters convergence is investigated
Vibrotactile sensitivity of slowly adapting type I sensory fibres associated with touch domes in cat hairy skin.

1. Recordings were made from single slowly adapting type I (SAI) afferent fibres associated with touch domes in the cat hairy skin. Controlled vibratory stimuli were used first, to characterize the precision with which these SAI afferents reflect the temporal aspects of vibrotactile stimuli, and second, to determine whether earlier disparate reports of SAI responsiveness to vibration may be attributable to highly specific stimulus requirements. 2. Eighteen SAI fibres from femoral cutaneous nerve branches were examined; each was associated with one to three touch domes. SAI responses to both steps and sinusoidal vibration (1‐1.5 s in duration) were affected profoundly by both probe size and position. Punctate stimulus probes (250 microns) produced much higher response levels and steeper stimulus‐response relations than those elicited with large (2 mm) probes, probably on account of focal distortion created within the dome by the smaller probes. SAI sensitivity to vibration was also affected markedly by the amplitude of any pre‐indentation on which the vibration was superimposed; sensitivity was much lower when the pre‐indentation exceeded 100 microns, in particular with larger stimulus probes. 3. Measures of both vibration sensitivity and the precision of impulse patterning demonstrated that, if appropriate stimulus parameters are chosen, the SAI fibres can respond to 1 s trains of vibration (amplitude < or = 100 microns) in a tightly phase‐locked, 1:1 manner for frequencies up to 500 Hz. At frequencies from approximately 100‐500 Hz the SAI fibres displayed broad 1:1 plateaus, where their response rate remained constant over a range of amplitudes, and phased‐locking was tightest. Responses remained phase‐locked up to 1000 Hz, but could not follow the vibration with a 1:1 pattern above 500 Hz. 4. The results demonstrate that with appropriate stimulus parameters, touch dome‐associated SAI fibres are capable of signalling vibrotactile information over a similar bandwidth of frequencies as do Pacinian sensory fibres. The variability in past reports of SAI vibration sensitivity may relate principally to differences in stimulus conditions. However, in view of the SAI capacity for responding to vibration with temporally precise, patterned activity, it appears that their reported failure to contribute to vibrotactile sensibility must be attributed to limitations imposed in the central processing of SAI signals.