Miracle-dz/UniFAR-FTUs huggingface dataset:
Macular segmentation with optical coherence tomography.

PURPOSE To develop a software algorithm to perform automated segmentation of retinal layer structures on linear macular optical coherence tomography (StratusOCT; Carl Zeiss Meditec, Inc., Dublin, CA) scan images and to test its performance in discriminating normal from glaucomatous eyes in comparison with conventional circumpapillary nerve fiber layer (cpNFL) thickness measurement. METHODS Four layer structures within the retina were defined: the macular nerve fiber layer (mNFL), the inner retinal complex (IRC; retinal ganglion cell [RGC] layer + inner plexiform and nuclear layers), outer plexiform layer (OPL), and outer retinal complex (ORC; outer nuclear layer + photoreceptor layer). Normal and glaucomatous eyes underwent fast macular map and fast NFL OCT scans. Linear macular images were analyzed using the developed algorithm, and the results were compared with the cpNFL thickness measurement. RESULTS Forty-seven subjects (23 normal and 24 with glaucoma) were analyzed. mNFL, cpNFL, IRC, and the total retinal thicknesses were significantly greater in normal than in glaucomatous eyes (P < or = 0.0002; Wilcoxon), whereas OPL thickness did not show a significant difference (P = 0.46). ORC thickness was significantly greater in glaucomatous than normal eyes (P = 0.035). Areas under the receiver operator characteristic curve (AROCs) for discriminating normal from glaucomatous eyes were highest with mNFL + IRC (0.97) and lowest with OPL (0.56). AROCs for OPL and ORC were significantly smaller than those for mNFL, IRC, mNFL+IRC, and cpNFL (P < or = 0.01). AROCs for IRC, mNFL + IRC, and cpNFL were significantly larger than for retinal thickness (P < or = 0.049). Among the best-performing parameters (mNFL, IRC, mNFL + IRC, and cpNFL) there was no significant difference in AROCs (P > or = 0.15). CONCLUSIONS The newly developed macular segmentation algorithm described herein demonstrated its ability to quantify objectively the glaucomatous damage to RGCs and NFL and to discriminate between glaucomatous and normal eyes. Further algorithm refinement and improvements in resolution and image quality may yield a more powerful methodology for clinical glaucoma evaluation.
A logic of trust and reputation

The aim of this paper is to present a logical framework in which the concepts of trust and reputation can be formally characterized and their properties studied. We start from the definition of trust proposed by Castelfranchi & Falcone (C&F). We formalize this definition in a logic of time, action, beliefs and choices. Then, we provide a refinement of C&F’s definition by distinguishing two general types of trust: occurrent trust and dispositional trust. In the second part of the paper we present a definition of reputation that is structurally similar to the definition of trust but moves the basic concept of belief to a collective dimension of group belief.
A Survey of Aspect-Oriented Programming Languages

Aspect-Oriented Software Development (AOSD) is one of the newest approaches for managing complexity by further modularizing code for large software systems. Software code continues to grow in size as well as complexity [1]. Aspect-Oriented Programming (AOP) is meant to improve modularity, and reduce complexity by separation of concerns in code. AOP is designed to work with programming languages, not to replace them [1]. AOP allows developers to express design decisions via a separate piece of code, instead of interlacing the code concerned with the design decision throughout the application code [2].
Evaluation of antioxidant and anti-melanogenic activities of different extracts from aerial parts of Nepeta binaludensis Jamzad in murine melanoma B16F10 cells

Objective(s): Nepeta binaludensis Jamzad (Lamiaceae) has been used in folk medicine of Iran to cure various diseases. The plant is an endemic species to the country that has recently been identified in Razavi Khorasan province. To evaluate the antioxidant and anti-melanogenesis of N. binaludensis, in this study the inhibitory activity of different extracts of N. binaludensis in murine melanoma B16F10 cells is investigated. Materials and Methods: The effects of petroleum ether, dichloromethane, ethyl acetate, and methanol extracts isolated from the plant on melanogenesis in B16 melanoma cells were investigated. To assess the inhibitory effects of this plant on melanogenesis, various assays were used including cytotoxicity, inhibition of mushroom tyrosinase and cellular tyrosinase, determination of melanin content, the effect of extracts on reactive oxygen species and western blot analysis of proteins involved in melanogenesis process. Results: The content of melanin and the activity of tyrosinase were significantly reduced with different extracts of N. binaludensis in cells. Reactive oxygen species was also significantly decreased following the treatment of cell with the mentioned extracts, while a resazurin assay showed no cytotoxicity. Furthermore, we have found that the plant decreased the amount of tyrosinase and microphthalmia-associated transcription factor proteins, which verify the role of suppression of microphthalmia-associated transcription factor protein in melanogenesis inhibition. Conclusion: Taken together the data indicate that N. binaludensis has inhibitory activity on melanin synthesis with no cytotoxic effects in B16 melanoma cells. Therefore, it merits future investigations to apply as whitening agent in hyperpigmentation.
PROTEIN SUBCELLULAR LOCALIZATION PREDICTION

ORGANIZATION. Section 1. We first provide the motivation for prediction of protein subcellular localization sites, as well as discuss changes being brought about by progress in proteomics. Section 2. After that, we describe the biology of protein subcellular location. In particular, we explain the principle of protein sorting signals. Section 3. Then we present several experimental techniques for determining protein subcellular localization sites. The techniques surveyed include traditional methods such as immunofluorescence microscopy, as well as large-scale methods such as green fluorescent protein. Section 4. Next we mention some of the general issues involved in predicting protein subcellular localization, such as what are the sites? how many sites per protein? how good are the predictions? and so on. We also discuss the distinction between features that reflect causal influences on localization versus features that merely reflect correlation with localization.
Adult Native Language Literacy: A Synthesis and Plan for Research and Action.

The report summarizes findings of research activities conducted over 2 years by the Center for Applied Linguistics (CAL) on the mother tongue and English-as-a-Second-Language (ESL) literacy. The first section provides a review of existing literature in native language literacy for adults, including a summary of surveys, review of studies on native language literacy, analysis of rationales that programs give for offering native language literacy, and a cescription of key articles written by practitioners. The second section presents findings of a 1992 CAL working group on native language literacy, whose participants included teachers and administrators from native language literacy programs in the United States and other researchers and experts in the field. Overviews of activities and promising practices at six sites offering instruction in Spanish, Haitian Creole, and Hmong native language literacy are included. The third section identifies key issues that need to be addressed to move the field forward, and makes recommendations for research and policy formation. One key issue is the funding of demonstration projects that can be linked to studies of the relationship between native language literacy and second language acquisition, student retention, and other learner goals. (MSE) (Adjunct ERIC Clearinghouse on Literacy Education) Reproductions supplied by EDRS are the best that can be made from the original document. **************************************7 ************ Adult Native Language Literacy A Synthesis and Plan for Research and Action Marilyn Gillespie Eugenie Ballering Center for Applied Linguistics Washington, D.C.
pcaL 1 : An Implementation in R of Three Methods for L 1-Norm Principal Component Analysis

pcaL1 is a package for the R environment for finding principal components using methods based on the L1 norm. The principal components derived using traditional principal component analysis (PCA) can be interpreted as an optimal solution to several optimization problems involving the L2 norm. Using the L1 norm in these problems provides an alternative that is more robust to outlier observations in moderate-sized datasets. Replacing the L2 norm with the L1 norm in the different optimization problems yields different principal components. The package pcaL1 implements three algorithms: PCA-L1, L1PCA, and L1-PCA∗. Results are presented for test datasets that indicate the conditions under which each method performs best and the computation time required by each implementation.
Butyrylated starch is less susceptible to enzymic hydrolysis and increases large-bowel butyrate more than high-amylose maize starch in the rat

Large-bowel fermentation of resistant starch produces SCFA that are believed to be important in maintaining visceral function. High-amylose maize starch (HAMS) and acylated starches are sources of resistant starch and are an effective means of increasing colonic SCFA. Cooking increases digestibility of starches but its effects on the capacity of these starches to raise large-bowel SCFA are unknown. We have examined the effects of cooking of HAMS and butyrylated HAMS (HAMSB) on amylolysis in vitro and their capacity to raise caeco-colonic SCFA in rats. The starches were boiled in excess water and microwaved, followed by drying at 100°C. Cooking increased in vitro glucose release for both starches but significantly less from HAMSB. Rat growth rates were unaffected when fed cooked resistant starch. Digesta pH was increased in the caecum and proximal colon of rats fed cooked HAMS. Distal colonic pH was highest in rats fed cooked HAMSB. Factorial analyses (2×2) of caecal SCFA pools showed significant differences between HAMS and HAMSB, and that cooking significantly lowered caecal butyrate pools. Portal venous butyrate concentrations were higher in both HAMSB groups than those fed HAMS. The data suggest that HAMSB is less susceptible to in vitro amylolysis than HAMS following cooking and delivers more butyrate to rat caecum than HAMS. This attribute may be useful in food applications for specific delivery of SCFA to the colon. Preparation of carbohydrates to simulate human food in animal experiments may be important to assess nutritional and physiological effects accurately.
Translation and validation of the Turkish version of the Psychosocial Impact of Dental Aesthetics Questionnaire

Objective The aim of this study was to translate the Psychosocial Impact of Dental Aesthetics Questionnaire (PIDAQ) into Turkish, validate the questionnaire, and provide a cross-cultural adaptation. Methods The translation process included the following steps, which were performed by a translation committee: (1) translation into Turkish, (2) back translation into English, (3) pretesting, and (4) cross-cultural adaptation. The Turkish version of the PIDAQ was produced subsequent to the translation process. Validity and reliability were measured using the Perception of Occlusion Scale and the aesthetic component of the Index of Orthodontic Treatment Need. The questionnaire was administered to 260 individuals (age range, 18–30 years; mean age, 20.50 ± 1.9 years). Structural validity was assessed via factor analysis, and internal consistency was measured using Cronbach's alpha coefficient. Results Factor analysis revealed a four-factor structure, with factor loadings for included items ranging from 0.380 to 0.868. Few questions were shuffled among domains various factor loadings. Cronbach's alphas for the Turkish version of the PIDAQ ranged from 0.534 to 0.904. Mean scores for the PIDAQ subscale and total scores differed significantly according to Index of Orthodontic Treatment Need and Perception of Occlusion Scale scores. Conclusions This study provided a Turkish version of the PIDAQ, which could be a useful tool in the evaluation of the psychosocial impact of malocclusion in young Turkish adults.
Moduli of \'etale subalgebras in an Azumaya algebra

Let $A$ be a sheaf of Azumaya algebras over a Noetherian base $S$. In this paper we describe using generalized Severi-Brauer varieties, a quasi-projective moduli space parametrizing sheaves of \`etale subalgebras of $A$. In the case that $S$ is the spectrum of a field, we study the geometry of this moduli space, and show that in certain cases it is a rational variety.
From Data to Decisions: Distributionally Robust Optimization is Optimal

We study stochastic programs where the decision maker cannot observe the distribution of the exogenous uncertainties but has access to a finite set of independent samples from this distribution. In this setting, the goal is to find a procedure that transforms the data to an estimate of the expected cost function under the unknown data-generating distribution, that is, a predictor, and an optimizer of the estimated cost function that serves as a near-optimal candidate decision, that is, a prescriptor. As functions of the data, predictors and prescriptors constitute statistical estimators. We propose a meta-optimization problem to find the least conservative predictors and prescriptors subject to constraints on their out-of-sample disappointment. The out-of-sample disappointment quantifies the probability that the actual expected cost of the candidate decision under the unknown true distribution exceeds its predicted cost. Leveraging tools from large deviations theory, we prove that this meta-optimization problem admits a unique solution: The best predictor-prescriptor-pair is obtained by solving a distributionally robust optimization problem over all distributions within a given relative entropy distance from the empirical distribution of the data. This paper was accepted by Chung Piaw Teo, optimization.
Pre-Movement Activity Activity During the Delay Period and Effect on Prior Information in Motor and Premotor Cortex:

[PDF] [Full Text] [Abstract] , August , 2010; 104 (2): 799-810. J Neurophysiol Stephen I. Ryu and Krishna V. Shenoy Matthew T. Kaufman, Mark M. Churchland, Gopal Santhanam, Byron M. Yu, Afsheen Afshar, Roles of Monkey Premotor Neuron Classes in Movement Preparation and Execution [PDF] [Full Text] [Abstract] , October 13, 2010; 30 (41): 13873-13882. J. Neurosci. Steven M. Chase, Andrew B. Schwartz and Robert E. Kass Latent Inputs Improve Estimates of Neural Encoding in Motor Cortex [PDF] [Full Text] [Abstract] , November , 2010; 104 (5): 2451-2461. J Neurophysiol Degenhart, Anto I. Bagic and Douglas J. Weber Wei Wang, Gustavo P. Sudre, Yang Xu, Robert E. Kass, Jennifer L. Collinger, Alan D. Decoding and Cortical Source Localization for Intended Movement Direction With MEG [PDF] [Full Text] [Abstract] , January 19, 2011; . Proc. R. Soc. B Kelsey L. Clark, Katherine M. Armstrong and Tirin Moore Probing neural circuitry and function with electrical microstimulation [PDF] [Full Text] [Abstract] , April 22, 2011; 278 (1709): 1121-1130. Proc. R. Soc. B Kelsey L. Clark, Katherine M. Armstrong and Tirin Moore Probing neural circuitry and function with electrical microstimulation
Research on Structure Ontology Characteristic of Blogosphere

Structure ontology characteristic of blogosphere is one of the hot topics in social computing. It has an important research value for blog dissemination, blog community discovery, blog mining etc. From the empirical research on a number of blogospheres in the real world, we find that the blogosphere is characterized by local centralized large-scale complex social network, whose characteristic is closely related to blog channel, and composed of multiple discrete small social networks. The previous methods by using structure reductionism or functional reductionism cannot fully explain the evolution and development of the blogosphere. Based on the structure ontological viewpoint, This paper presents the blogosphere is composed of belief space, group space and content space. The content space is a information network, the group space is a network of relationships, the belief space is a cultural network, among of which, each one has endogenous rules of evolution, and also interacts with each other, under the common actions of the downward causal relationship and the upward causal relationship, it shows a wealth of structural features.
The effects of open door policies for community colleges and achieving accountability

DISSERTATION PROJECT: The Effects of Open Door Policies for Community Colleges and Achieving Accountability STUDENT: Sara Shierling DEGREE: Doctor of Education COLLEGE: Teachers College DATE: May 2015 PAGES: 157 The history behind the evolution of the American postsecondary education has imitated the European system with the exception of the community college. The community college strives to meet the needs of all students with an enrollment open door policy. This study examined relationships between student demographics and the achievement of core performance indicators by Ohio community colleges. The core performance indicators measure technical skill attainment; credential, certificate, or degree achievement; student retention or transfer; student placement; and nontraditional participation and completion. Using archived data from 20072013 required by the Carl D. Perkins Career and Technical Education Act of 2006, a linear mixed model analysis was performed discovering significant relationships between the core performance indicators and other demographic factors such as, gender, race, students who meet the definition of students with disabilities, students who are economically disadvantaged, students who are displaced homemakers, students with limited English proficiency, and those students pursuing nontraditional careers for their gender. The linear mixed model was used due to the fixed effects of the student demographics, and the Ohio community colleges as random factors. The cohort years comprised the repeated measure. The results of the LMM indicated
Detail-preserving fully-Eulerian interface tracking framework

This paper introduces a fully-Eulerian interface tracking framework that preserves the fine details of liquids. Unlike existing Eulerian methods, the proposed framework shows good mass conservation even though it does not employ conventional Lagrangian elements. In addition, it handles complex merging and splitting of interfaces robustly due to the implicit representation. To model the interface more accurately, a high order polynomial reconstruction of the signed distance function is utilized based on a number of sub-grid quadrature points. By combining this accurate polynomial representation with a high-order re-initialization method, the proposed framework preserves the detailed structures of the interface. Moreover, the method is simple to implement, unconditionally stable, and is suitable for parallel computing environments.
Viral Ancestors of Antiviral Systems

All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the ‘Big Bang’ theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.
Exhaled breath profiling in diagnosing wheezy preschool children

Although wheeze is common in preschool children, the underlying pathophysiology has not yet been disentangled. Volatile organic compounds (VOCs) in exhaled breath may serve as noninvasive markers of early wheeze. We aimed to assess the feasibility of VOC collection in preschool children, and to study whether a VOC profile can differentiate between children with and without recurrent wheeze. We included children (mean (range) age 3.3 (1.9–4.5) yrs) with (n=202) and without (n=50) recurrent wheeze. Exhaled VOCs were analysed by gas chromatography–time-of-flight mass spectrometry. VOC profiles were generated by ANOVA simultaneous component analysis (ASCA) and sparse logistic regression (SLR). Exhaled breath collection was possible in 98% of the children. In total, 913 different VOCs were detected. The signal-to-noise ratio improved after correction for age, sex and season using ASCA pre-processing. An SLR model with 28 VOCs correctly classified 83% of the children (84% sensitivity, 80% specificity). After six-fold cross-validation, 73% were correctly classified (79% sensitivity, 50% specificity). Assessment of VOCs in exhaled breath is feasible in young children. VOC profiles are able to distinguish children with and without recurrent wheeze with a reasonable accuracy. This proof of principle paves the way for additional research on VOCs in preschool wheezing.
Syndecan-4 and integrins: combinatorial signaling in cell adhesion.

It is now becoming clear that additional transmembrane components can modify integrin-mediated adhesion. Syndecan-4 is a transmembrane heparan sulfate proteoglycan whose external glycosaminoglycan chains can bind extracellular matrix ligands and whose core protein cytoplasmic domain can signal during adhesion. Two papers in this issue of JCS demonstrate, through transfection studies, that syndecan-4 plays roles in the formation of focal adhesions and stress fibers. Overexpression of syndecan-4 increases focal adhesion formation, whereas a partially truncated core protein that lacks the binding site for protein kinase C(&agr;) and phosphatidylinositol 4, 5-bisphosphate acts as a dominant negative inhibitor of focal adhesion formation. Focal adhesion induction does not require interaction between heparan sulfate glycosaminoglycan and ligand but can occur when non-glycanated core protein is overexpressed; this suggests that oligomerization of syndecan-4 plays a major role in signaling from the extracellular matrix in adhesion.
Mining sequential patterns from multidimensional sequence data

The problem addressed in This work is to discover the frequently occurred sequential patterns from databases. Although much work has been devoted to this subject, to the best of our knowledge, no previous research was able to find sequential patterns from d-dimensional sequence data, where d>2. Without such a capability, many practical data would be impossible to mine. For example, an online stock-trading site may have a customer database, where each customer may visit a Web site in a series of days; each day takes a series of sessions and each session visits a series of Web pages. Then, the data for each customer forms a 3-dimensional list, where the first dimension is days, the second is sessions, and the third is visited pages. To mine sequential patterns from this kind of sequence data, two efficient algorithms have been developed in This work.