Miracle-dz/UniFAR-FTUs huggingface dataset:
Epithelium and Stroma Identification in Histopathological Images Using Unsupervised and Semi-Supervised Superpixel-Based Segmentation

We present superpixel-based segmentation frameworks for unsupervised and semi-supervised epithelium-stroma identification in histopathological images or oropharyngeal tissue micro arrays. A superpixel segmentation algorithm is initially used to split-up the image into binary regions (superpixels) and their colour features are extracted and fed into several base clustering algorithms with various parameter initializations. Two Consensus Clustering (CC) formulations are then used: the Evidence Accumulation Clustering (EAC) and the voting-based consensus function. These combine the base clustering outcomes to obtain a more robust detection of tissue compartments than the base clustering methods on their own. For the voting-based function, a technique is introduced to generate consistent labellings across the base clustering results. The obtained CC result is then utilized to build a self-training Semi-Supervised Classification (SSC) model. Unlike supervised segmentations, which rely on large number of labelled training images, our SSC approach performs a quality segmentation while relying on few labelled samples. Experiments conducted on forty-five hand-annotated images of oropharyngeal cancer tissue microarrays show that (a) the CC algorithm generates more accurate and stable results than individual clustering algorithms; (b) the clustering performance of the voting-based function outperforms the existing EAC; and (c) the proposed SSC algorithm outperforms the supervised methods, which is trained with only a few labelled instances.
The Architectural Transcription Factor High Mobility Group I(Y) Participates in Photoreceptor-Specific Gene Expression

The nonhistone chromosomal proteins high mobility group I(Y) [HMG I(Y)] have been shown to function as architectural transcription factors facilitating enhanceosome formation on a variety of mammalian promoters. Specifically, they have been shown to act as a “molecular glue” mediating protein–protein and protein–DNA contacts within the enhanceosome complex. HMG I(Y) proteins are expressed at high levels in embryonic and transformed cells and have been implicated in transcriptional regulation in these cells. Terminally differentiated cells, however, have been reported to express only minimal, if any, HMG I(Y). In contrast to these observations, we show here that adult mouse retinal photoreceptors, which are terminally differentiated cells, express high levels of these proteins. Using retinoblastoma cells as an approximate model, we further demonstrate in transiently transfected cells that inhibition of HMG I(Y) expression and mutation of HMG I(Y) binding sites significantly reduce rhodopsin promoter activity. DNase I footprint analysis indicates that HMG I protein interacts with a discrete site within the rhodopsin proximal promoter. This site overlaps with the binding site for Crx, a paired-like homeodomain transcription factor that is essential for photoreceptor functioning and that when mutated causes several forms of human photoreceptor degeneration. Both biochemical and functional experiments demonstrate that HMG I(Y) physically associate with Crx and that their interaction with DNA is required for high-level transcription of the rhodopsin gene. These data provide the first demonstration that HMG I(Y) can be important for gene activation in terminally differentiated cells.
Behavioural characterization of four endemic Stachys taxa

We performed a basic behavioral characterization of methanol extracts of four Balkan endemic Stachys taxa: S. anisochila (SA), S. beckeana (SB), S. plumosa (SP) and S. alpina subsp. dinarica (SAD). The behavioral activity of extracts dosed intraperitoneally in the range 100–400 mg/kg was examined in adult male Wistar rats, in the elevated plus maze, spontaneous locomotor activity, and grip strength tests, mainly predictive of anxiolytic, sedative and myorelaxant actions, respectively. All investigated Stachys extracts lacked anxiolytic or myorelaxant activities, while SB at 400 mg/kg exerted an anxiogenic‐like effect. The study with the selective antagonist β‐CCt showed that the sedative effect of SAD was only partially mediated by GABAA receptors containing the α1‐subunit. While discernible, the behavioral effects of SA and SP were not distinct. In all extracts, chlorogenic acid and verbascoside were identified. In SA, SB, and SAD the flavonoid fraction was constituted of isoscutellarein and hypolaetine glycosides, while in SP chrysoeriol and apigenin glycosides were present. The results reveal the psychotropic potential of four endemic Stachys taxa, of which SAD appeared most promising as a natural sedative. Copyright © 2010 John Wiley & Sons, Ltd.
Intrauterine and early-life malnutrition in rats disrupts the circadian rhythm programming of energy metabolites through adulthood

Maternal malnutrition plays a crucial role in functional development, resulting in behavioral, cognitive, and metabolic abnormalities and disturbances. “Cafeteria diet” has been linked to obesity, metabolic syndrome, diabetes, and other metabolic disruptions in the mammalian lifespan. However, there are very few reports about the effect of intrauterine and early postnatal malnutrition on the circadian rhythm programming of energy metabolites. In mammals, circadian rhythm central control is fundamental for correct interaction with the environment and physiological regulation. Exposure to malnutrition during development imprints metabolic programming throughout life on the central nervous system and peripheral systems. Lifespan studies exploring the effect of high fat/low protein diet administered during critical periods of development are scarce. The present study explored the effect of intrauterine and perinatal malnutrition induced by a high fat/low protein diet (Cafeteria Diet) on circadian and peripheral oscillators controlling glucose, insulin, and triglycerides in rats at 40 and 90 days of age. We evaluated plasma glucose and triglyceride levels in 6 Zeitgeber times, in addition to an intraperitoneal glucose tolerance test (IpTGT) and homeostasis model assessment of insulin resistance (HOMA-IR) at two time-points over 24h. Our results show that offspring of malnourished dams fed cafeteria diet present alterations in circadian rhythmicity of glucose and triglycerides associated with a change in glucose tolerance and insulin sensibility differentially regulated at the development stage and time of day. Intrauterine and early malnutrition due to a cafeteria diet produces maladaptive responses and programs energetic metabolism at several developmental stages during the lifespan.
How Related Are the Prices of Organic and Conventional Corn and Soybean

ABSTRACT Cointegration was tested between organic and conventional corn and soybean markets in several locations throughout the U.S. using a unique dataset. Organic prices were found to behave like pure jump processes rather than diffusions. A simple specification for pure jump processes is introduced and used with Monte Carlo methods to compute appropriate critical values for unit‐root and cointegration tests. The findings indicate that no long‐run relationship exists between organic and conventional prices, implying that price determination for organic corn and soybean is independent from that of the conventional crops. This suggests that organic corn and soybean prices are driven by demand and supply forces idiosyncratic to the organic market. For each crop, cointegrating spatial relationships are found between prices at the main organic markets. However, such relationships are generally weaker than the ones for the corresponding conventional prices, implying that organic markets are more affected by idiosyncratic shocks than conventional markets. [JEL Classification: Q130 – Agricultural Markets and Marketing; Cooperatives; Agribusiness Q180 – Agricultural Policy; Food Policy].
Designing Workflows based on product structures

Workflow management promises a new solution to an age-old problem: controlling, monitoring, optimizing and supporting business processes. What is new about workflow management is the explicit representation of the business process logic which allows for computerized support. Business processes supported by a workflow management system are case-driven in the sense that tasks are executed for specific cases. A case corresponds to a service to the environment. Approving a loan, processing an insurance claim and handling a traffic violation are examples of case-driven processes. A case corresponds to a product that needs to be produced. Although the product is not a physical object, it has an internal structure, i.e., it is an informational object assembled from components. Therefore, the well-known bill-of-materials can be used to describe the product that is manufactured using a workflow management system. This paper describes a technique to automatically generate a workflow process based on a bill-of-materials. It allows workflow designers to think in terms of the end-product instead of the internal process and constitutes a basis for the automatic configuration of a workflow management system on the basis of a bill-of-materials.
SoK: A Comprehensive Analysis of Game-Based Ballot Privacy Definitions

We critically survey game-based security definitions for the privacy of voting schemes. In addition to known limitations, we unveil several previously unnoticed shortcomings. Surprisingly, the conclusion of our study is that none of the existing definitions is satisfactory: they either provide only weak guarantees, or can be applied only to a limited class of schemes, or both. Based on our findings, we propose a new game-based definition of privacy which we call BPRIV. We also identify a new property which we call strong consistency, needed to express that tallying does not leak sensitive information. We validate our security notions by showing that BPRIV, strong consistency (and an additional simple property called strong correctness) for a voting scheme imply its security in a simulation-based sense. This result also yields a proof technique for proving entropy-based notions of privacy which offer the strongest security guarantees but are hard to prove directly: first prove your scheme BPRIV, strongly consistent (and correct), then study the entropy-based privacy of the result function of the election, which is a much easier task.
Adsorption of N, He and Ne on CGe nanoribbons for sensing and optoelectronic applications

Research into nanomaterials yields numerous exceptional applications in contemporary science and technology. The subject of this investigation is a one-dimensional nanostructure, six atoms wide, featuring hydrogen-functionalized edges. The theoretical foundation of this study relies on Density Functional Theory (DFT) and is executed through the utilization of the Vienna Ab initio Simulation Package (VASP). The outcomes demonstrate the stability of adsorption configurations, along with the preservation of a hexagonal honeycomb lattice. The pristine configuration, characterized by a wide bandgap, is well-suited for optoelectronic applications, whereas adsorption configurations find their application in gas sensing. Nitrogen (N) adsorption transforms the semiconducting system into a semimetallic one, with the spin-up state showing semiconductor characteristics and the spin-down state exhibiting metallic attributes. The intricate multi-orbital hybridization is explored through the analysis of partial states. While the pristine system remains non-magnetic, N adsorption introduces a magnetic moment of 0.588 μB. The examination of charge density differences indicates a significant charge transfer from N to the CGe substrate surface. Optical properties are systematically investigated, encompassing the dielectric function, absorption coefficient and electron–hole density. Notably, the real part of the dielectric function exhibits negative values, a result that holds promise for future communication applications.
Test-Retest Reliability of a Battery of Sensory, Motor and Physiological Measures of Aging

We report test-retest reliabilities for a battery of tests (vision, hearing, vibration sense, proprioception, forced expiratory volume, blood pressure, grip strength, and sway) shown previously to predict functional age. Fifty women aged 60 to 86 were retested on the battery after 3 months. All tests except proprioception and blood pressure had reliabilities between . 70 and . 94. We conclude that the battery provides reliable measures of sensory, motor, and physiological variables which may be used as markers of biological aging in psychological research.
A Phytoplankton Bloom Model with Seasonal Nutrient Input

A model for nutrient-phytoplankton dynamics is constructed and analyzed. A theoretical analysis shows that changes in the nutrient input can significantly change the qualitative behavior of the phytoplankton dynamics. In particular, the behavior can change from asymptotically stable to periodic. Numerical solutions of the model are carried out for seasonal nutrient inputs of a range of different frequencies and amplitudes. The numerical solutions confirm the non-oscillatory and oscillatory behaviors predicted from the theoretical analysis. The numerical simulations show that a periodic nutrient input can cause phytoplankton blooms and that changes in the frequency of the input can produce blooms with a wide range of different dynamical behaviors. In addition, it is shown that in some regions of parameter space, the oscillatory behavior recurs annually and agrees with observational data. Key-Words: Bloom dynamics, Frequencies, Nutrient-phytoplankton interaction, Oscillatory behavior, Periodically forced damped system, Seasonal nutrient input.
The Aurora and Medusa Projects

This document summarizes the research conducted in two inte rrelat d projects. The Aurora project being implemented at Brown and Brandeis under the direction of U ğur Çetintemel, Mitch Cherniack, Michael Stonebraker and Stan Zdonik strives to build a single-site h igh performance stream processing engine. It has an innovative collection of operators, workflow orien tation, and strives to maximize quality of service for connecting applications. A further goal of Auro ra is to extend this engine to a distributed environment in which multiple machines closely co-operate in achieving high quality of service. In contrast, the Medusa project being investigated at M.I. T . under the direction of Hari Balakrishnan and Michael Stonebraker is providing networking infras t ucture for Aurora operations. In addition, Medusa is stressing distributed environments where the var ious machines belong to different organizations. In this case, there can be no common goal, and much loos er c upling is needed. Medusa is working on an innovative agoric infrastructure in which various participants can co-operate in distributed streaming operations. Finally, some have questioned whether specialized stream p rocessing software is necessary. They speculate that conventional data base systems can adequate ly deal with the needs of stream-oriented applications. In order to answer this question one way or the other, both groups are working on a streamoriented benchmark, called the Linear Road benchmark, which we intend to run on both specialized and conventional system infrastructure.
Beyond Logarithmic Bounds in Online Learning

We prove logarithmic regret bounds that depend on the loss L T of the competitor rather than on the number T of time steps. In the general online convex optimization setting, our bounds hold for any smooth and exp-concave loss (such as the square loss or the logistic loss). This bridges the gap between theO(lnT) regret exhibited by expconcave losses and the O( p L T ) regret exhibited by smooth losses. We also show that these bounds are tight for specific losses, thus they cannot be improved in general. For online regression with square loss, our analysis can be used to derive a sparse randomized variant of the online Newton step, whose expected number of updates scales with the algorithm’s loss. For online classification, we prove the first logarithmic mistake bounds that do not rely on prior knowledge of a bound on the competitor’s norm.
Measuring music-induced emotion

Most previous studies investigating music-induced emotions have applied emotion models developed in other fields to the domain of music. The aim of this study was to compare the applicability of music-specific and general emotion models – namely the Geneva Emotional Music Scale (GEMS), and the discrete and dimensional emotion models – in the assessment of music-induced emotions. A related aim was to explore the role of individual difference variables (such as personality and mood) in music-induced emotions, and to discover whether some emotion models reflect these individual differences more strongly than others. One hundred and forty-eight participants listened to 16 film music excerpts and rated the emotional responses evoked by the music excerpts. Intraclass correlations and Cronbach alphas revealed that the overall consistency of ratings was the highest in the case of the dimensional model. The dimensional model also outperformed the other two models in the discrimination of music excerpts, and principal component analysis revealed that 89.9% of the variance in the mean ratings of all the scales (in all three models) was accounted for by two principal components that could be labelled as valence and arousal. Personality-related differences were the most pronounced in the case of the discrete emotion model. Personality, mood, and the emotion model used were also associated with the intensity of experienced emotions. Implications for future music and emotion studies are raised concerning the selection of an appropriate emotion model when measuring music-induced emotions.
Ellipsoid-tree construction for solid objects

As ellipsoids have been employed in the collision handling of many applications in physical simulation and robotics systems, we present a novel algorithm for generating a bounding volume hierarchy (BVH) from a given model with ellipsoids as primitives. Our algorithm approximates the given model by a hierarchical set of optimized bounding ellipsoids. The ellipsoid-tree is constructed by a top-down splitting. Starting from the root of hierarchy, the volume occupied by a given model is divided into k sub-volumes where each is approximated by a volume bounding ellipsoid. Recursively, each sub-volume is then subdivided into ellipsoids for the next level in the hierarchy. The k ellipsoids at each hierarchy level for a sub-volume bounding is generated by a bottom-up algorithm - simply, the sub-volume is initially approximated by m spheres (m » k), which will be iteratively merged into k volume bounding ellipsoids and globally optimized to minimize the approximation error. Benefited from the anisotropic shape of primitives, the ellipsoid-tree constructed in our approach gives tighter volume bound and higher shape fidelity than another widely used BVH, sphere-tree.
Optimal acoustic and language model weights for minimizing word verification errors

Generalized word posterior probability (GWPP), a confidence measure for verifying recognized words, needs to equalize and weight acoustic and language model likelihood contributions to minimize verification errors. In this study, we investigate the word verification error surface and use it to optimize these weights and the corresponding verification threshold in a development set. We test three different search algorithms for finding the optimal parameters, including: a full grid search, a gradient-based steepest descent search, and a downhill simplex search. The three search methods yield very similar solutions. Proper acoustic and language model weights, especially the ratio between them, changes with the relative importance (reliability) between the two knowledge sources. For a narrow beam width, the role of the acoustic model is less critical than language model in GWPP-based word verification, which is due to the noisy acoustic information maintained in a narrow beam. Using a large vocabulary continuous Japanese speech database (Basic Travel Expression Corpus), the largest relative improvement obtained is 33.2% for confidence error rate and 38.7% for a modified word accuracy.
Grid Scan: A Simple and Effective Approach for Coverage Issue in Wireless Sensor Networks

This paper describes a basic coverage issue, and proposes a scheme named Grid Scan which is applied to calculate the basic coverage rate with arbitrary sensing radius of each node. Based on Grid Scan, a re-deployment approach is suggested to meet any k-covered rate in some region according to application requirements. The objective of our re-deployment scheme is to get equivalent coverage rate using less number of sensor nodes or to achieve higher coverage rate with the same number of sensor nodes. The results of simulation experiments support that Grid Scan based re-deployment is more effective to cover monitored area than random spread.
Jingtong Granule: A Chinese Patent Medicine for Cervical Radiculopathy

Objective. This paper systematically assessed the efficacy and safety of Jingtong granule (JG) for cervical radiculopathy (CR). Methods. Randomized controlled trials comparing JG with no intervention, placebo, or conventional therapies were retrieved. The trials testing JG combined with conventional therapies versus conventional therapies were also enrolled. Study selection, methodological assessment, data extraction, and analysis were conducted in accordance with the Cochrane standards. The strength of evidence was evaluated according to GRADE approach. Results. Three trials with 400 participants were included. Methodological quality was evaluated as generally low. One study found that JG showed significant difference on decreasing pain scores compared with placebo. Meta-analysis indicated that JG plus conventional analgesic exhibited a significant immediate effect on the pain scores (WMD = 1.63; 95% CI: 1.29 to 1.98; P < 0.00001). Additionally, JG combined with analgesic presented beneficial immediate effect on neck disability index. However, the treatment effects of JG demonstrated in the trials were not large, and the safety of JG was unproven. Finally the evidence level was evaluated to be low. Conclusions. Our results indicated that JG showed some potential benefits for CR. Nevertheless, treatment effects are uncertain due to both the methodological concerns and the very modest reported improvements.