Miracle-dz/UniFAR-FTUs huggingface dataset:
RECOGNIZE AND CLASSIFY FISH OOCYTES IN HISTOLOGICAL IMAGES

The study of biology and population dynamics of fish species requires the estimation of fecundity in individual fish in many fisheries laboratories. The traditional procedure used by fisheries research is to count manually the oocytes on a subsample of known weight of the ovary, and to measure a few oocytes under a binocular microscope. This process can be done on a computer using an interactive tool to count and measure oocytes. In both cases, the task is very time consuming, which implies that fecundity studies are rarely conducted routinely. We attempt to design a computer vision system which is able to recognize and classify the oocytes in a histological image. The boundary of oocytes is detected using an algorithm based on edge information. Afterwards, oocytes are classified in cells with and without nucleus. A statistical evaluation of both stages reveals correct detection and classification of 65% when a 80% of overlap is demanded.
Enhanced bone regeneration using an insulin-loaded nano-hydroxyapatite/collagen/PLGA composite scaffold

Insulin is widely considered as a classical hormone and drug in maintaining energy and glucose homeostasis. Recently, insulin has been increasingly recognized as an indispensable factor for osteogenesis and bone turnover, but its applications in bone regeneration have been restricted because of the short periods of activity and uncontrolled release. In this study, we incorporated insulin-loaded poly lactic-co-glycolic-acid (PLGA) nanospheres into nano-hydroxyapatite/collagen (nHAC) scaffolds and investigated the bioactivity of the composite scaffolds in vitro and in vivo. Bioactive insulin was successfully released from the nanospheres within the scaffold, and the release kinetics of insulin could be efficiently controlled by uniform-sized nanospheres. The physical characterizations of the composite scaffolds demonstrated that incorporation of nanospheres in nHAC scaffolds using this method did not significantly change the porosity, pore diameters, and compressive strengths of nHAC. In vitro, the insulin-loaded nHAC/PLGA composite scaffolds possessed favorable biological function for bone marrow mesenchymal stem cells adhesion and proliferation, as well as the differentiation into osteoblasts. In vivo, the optimized bone regenerative capability of this composite scaffold was confirmed in rabbit mandible critical size defects. These results demonstrated successful development of a functional insulin–PLGA–nHAC composite scaffold that enhances the bone regeneration capability of nHAC.
Hypothesis-driven approach to predict transcriptional units from gene expression data

MOTIVATION A major issue in computational biology is the reconstruction of functional relationships among genes, for example the definition of regulatory or biochemical pathways. One step towards this aim is the elucidation of transcriptional units, which are characterized by co-responding changes in mRNA expression levels. These units of genes will allow the generation of hypotheses about respective functional interrelationships. Thus, the focus of analysis currently moves from well-established functional assignment through comparison of protein and DNA sequences towards analysis of transcriptional co-response. Tools that allow deducing common control of gene expression have the potential to complement and extend routine BLAST comparisons, because gene function may be inferred from common transcriptional control. RESULTS We present a co-clustering strategy of genome sequence information and gene expression data, which was applied to identify transcriptional units within diverse compendia of expression profiles. The phenomenon of prokaryotic operons was selected as an ideal test case to generate well-founded hypotheses about transcriptional units. The existence of overlapping and ambiguous operon definitions allowed the investigation of constitutive and conditional expression of transcriptional units in independent gene expression experiments of Escherichia coli. Our approach allowed identification of operons with high accuracy. Furthermore, both constitutive mRNA co-response as well as conditional differences became apparent. Thus, we were able to generate insight into the possible biological relevance of gene co-response. We conclude that the suggested strategy will be amenable in general to the identification of transcriptional units beyond the chosen example of E.coli operons. AVAILABILITY The analyses of E.coli transcript data presented here are available upon request or at http://csbdb.mpimp-golm.mpg. de/
Hypothalamus, sexual arousal and psychosexual identity in human males: a functional magnetic resonance imaging study

In a recent functional magnetic resonance imaging study, a complex neural circuit was shown to be involved in human males during sexual arousal [A. Ferretti et al. (2005) Neuroimage, 26, 1086]. At group level, there was a specific correlation between penile erection and activations in anterior cingulate, insula, amygdala, hypothalamus and secondary somatosensory regions. However, it is well known that there are remarkable inter‐individual differences in the psychological view and attitude to sex of human males. Therefore, a crucial issue is the relationship among cerebral responses, sexual arousal and psychosexual identity at individual level. To address this issue, 18 healthy male subjects were recruited. Their deep sexual identity (DSI) was assessed following the construct revalidation by M. Olivetti Belardinelli [(1994) Sci. Contrib. Gen. Psychol. , 11, 131] of the Franck drawing completion test, a projective test providing, according to this revalidation, quantitative scores on ‘accordance/non‐accordance’ between self‐reported and psychological sexual identity. Cerebral activity was evaluated by means of functional magnetic resonance imaging during hard‐core erotic movies and sport movies. Results showed a statistically significant positive correlation between the blood oxygen level‐dependent signal in bilateral hypothalamus and the Franck drawing completion test score during erotic movies. The higher the blood oxygen level‐dependent activation in bilateral hypothalamus, the higher the male DSI profile. These results suggest that, in male subjects, inter‐individual differences in the DSI are strongly correlated with blood flow to the bilateral hypothalamus, a dimorphic brain region deeply implicated in instinctual drives including reproduction.
Collaborative Visualization in Medicine

One of the biggest areas of scientific visualization ( ViSC) application is Medicine: with the evolution of image acquisition techniques the capacity and fidelity of image diagnosis were extended. Due to the large number of medical exams that output images, several visualization systems have been developed dealing with specific problems in this area in the last few years. The growing of World Wide Web-based applications and the modern trend of cooperative work in scientific research gave rise to a new class of systems, the so-called collaborative visualization systems. This survey presents an overview of ViSC in Medicine emphasizing the different approaches for collaborative visualization, and discussing difficulties still found for its real utilization.
General Solution of Stability Problem for Plane Linear Switched Systems and Differential Inclusions

Characterization and control of stability of switched dynamical systems and differential inclusions have attracted significant attention in the recent past. The most of the current results for this problem are obtained by application of the Lyapunov function method which provides sufficient but frequently over conservative stability conditions. For planar systems, practically verifiable necessary and sufficient conditions are found only for switched systems with two subsystems. This paper provides explicit necessary and sufficient conditions for asymptotic stability of switched systems and differential inclusions with arbitrary number of subsystems; these conditions turned out to be identical for the both classes of systems. A precise upper bound for the number of switching points in a periodic solution, corresponding to the break of stability, is found. It is shown that, for a switched system, the break of stability may also occur on a solution with infinitely fast switching (chattering) between some two subsystems.
Cognitive Multi-Radio Mesh Networks on ISM bands: A cross-layer architecture

A wireless mesh network (WMN) has been popularly researched as a wireless backbone for Internet access with off-the-shelf and inexpensive equipments. Nowadays, several applications like contents sharing, multicast video streaming, vehicular networks encourage to build mesh networks in urban areas. However, the deployment of WMNs in unlicensed bands of dense urban areas imposes many challenges. While previous research has mostly focused on optimal channel allocation under inter or intra-flow interferences within mesh nodes, the practical deployment of WMNs also requires to consider the interference caused by external entities such as residential access points that do not belong to the WMN. To address this issue, we propose Urban-X which is a first attempt towards a new architecture for Multi-Radio Cognitive Mesh Networks. Based on a cross-layer scheme, we develop novel routing and forwarding schemes reflecting the residential traffic state of external users. Through an extensive simulation analysis using the ns-2 simulator, we demonstrate the feasibility of our routing scheme and we show its robustness to the variations of channel environment and external traffics.
Enhanced dielectric properties of PVDF-HFP/BaTiO3-nanowire composites induced by interfacial polarization and wire-shape

Polymer based composites with high dielectric constant were successfully fabricated using BaTiO3 nanowires with high aspect ratio as inorganic filler and PVDF-HFP as polymer matrix. PVDF-HFP/BaTiO3 nanoparticles composites were also prepared as a contrast. The BaTiO3 nanowires were synthesized via one-step hydrothermal method. The BaTiO3 nanowires and its two types of composites were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy and transmission electron microscopy. For the composites, breakdown strength measurements, tensile tests and broadband dielectric spectroscopy analyses were also carried out. The results show that the two types of fillers are homogeneously dispersed in the matrix. The dielectric constant of composites filled by BaTiO3 nanowires is larger than that filled by BaTiO3 nanoparticles at the same content. Stronger interfacial polarization was found in PVDF-HFP/BaTiO3 nanowire composites. Two theoretical models were employed to predict the dielectric constants of composites, and the experimental data were consistent with the estimated trend. The enhanced dielectric properties of PVDF-HFP/BaTiO3 nanowire composites are attributed to the superior interfacial polarization and high aspect ratio of BaTiO3 nanowires.
Uniform definition of comparable and searchable information on the web

Basically information means selection within a domain (value or definition set) of possibilities. For objectifiable, comparable and precise information the domain should be the same for all. Therefore the global (online) definition of the domain is proposed here. It is advantageous to define an ordered domain, because this allows using numbers for addressing the elements and because nature is ordered in many respects. The original data can be ordered in multiple independent ways. We can define a domain with multiple independent numeric dimensions to reflect this. Because we want to search information in the domain, for quantification of similarity we define a distance function or metric. Therefore we propose "Domain Spaces" (DSs) which are online defined nestable metric spaces. Their elements are called "Domain Vectors" (DVs) and have the simple form: URL (of common DS definition) plus sequence of numbers At this the sequence must be given so that the mapping of numbers to the DS dimensions is clear. By help of appropriate software DVs can be represented e.g. as words and numbers. Compared to words, however, DVs have (as original information) important objectifiable advantages (clear definition, objectivity, information content, range, resolution, efficiency, searchability). Using DSs users can define which information they make searchable and how it is searchable. DSs can be also used to make quantitative (numeric) data as uniform DVs interoperable, comparable and searchable. The approach is demonstrated in an online database with search engine (this http URL). The search procedure is called "Numeric Search". It consists of two systematic steps: 1. Selection of the appropriate DS e.g. by conventional word based search within the DS definitions. 2. Range and/or similarity search of DVs in the selected DS.
Centralized Cooperative Spectrum Sensing for Ad-Hoc Disaster Relief Network Clusters

Disaster relief networks have to be highly adaptable and resilient. Cognitive radio enhanced ad-hoc architecture have been put forward as a candidate to enable such networks. Spectrum sensing is the cornerstone of the cognitive radio paradigm, and it has been the target of intensive research. The main common conclusion was that the achievable spectrum sensing accuracy can be greatly enhanced through the use of cooperative sensing schemes. When considering applying Cognitive Radio to ad-hoc disaster relief networks, spectrum sensing cooperative schemes are paramount. A centralized cluster-based orchestration cooperative sensing scheme is proposed, where the cluster head controls and adapts the distribution of the cluster sensing's nodes according to the monitored spectrum state. The proposed scheme performance is evaluated through a framework, which allows gauging the accuracy of wideband multi-channel spectrum sensing cooperative schemes, showing that the proposed scheme performance reaches the theoretical maximum achievable accuracy while outperforming the round robin scheme.
Land Use Regression Modeling To Estimate Historic (1962−1991) Concentrations of Black Smoke and Sulfur Dioxide for Great Britain

Land-use regression modeling was used to develop maps of annual average black smoke (BS) and sulfur dioxide (SO2) concentrations in 1962, 1971, 1981, and 1991 for Great Britain on a 1 km grid for use in epidemiological studies. Models were developed in a GIS using data on land cover, the road network, and population, summarized within circular buffers around air pollution monitoring sites, together with altitude and coordinates of monitoring sites to consider global trend surfaces. Models were developed against the log-normal (LN) concentration, yielding R2 values of 0.68 (n = 534), 0.68 (n = 767), 0.41 (n = 771), and 0.39 (n = 155) for BS and 0.61 (n = 482), 0.65 (n = 733), 0.38 (n = 756), and 0.24 (n = 153) for SO2 in 1962, 1971, 1981, and 1991, respectively. Model evaluation was undertaken using concentrations at an independent set of monitoring sites. For BS, values of R2 were 0.56 (n = 133), 0.41 (n = 191), 0.38 (n = 193), and 0.34 (n = 37), and for SO2 values of R2 were 0.71 (n = 121), 0.57 (n = 183), 0.26 (n = 189), and 0.31 (n = 38) for 1962, 1971, 1981, and 1991, respectively. Models slightly underpredicted (fractional bias: 0∼−0.1) monitored concentrations of both pollutants for all years. This is the first study to produce historic concentration maps at a national level going back to the 1960s.
Dietary fat and insulin action in humans

A high intake of fat may increase the risk of obesity. Obesity, especially abdominal obesity, is an important determinant of the risk of developing insulin resistance and non-insulin-dependent diabetes mellitus. It is suggested that a high proportion of fat in the diet is associated with impaired insulin sensitivity and an increased risk of developing diabetes, independent of obesity and body fat localization, and that this risk may be influenced by the type of fatty acids in the diet. Cross-sectional studies show significant relationships between the serum lipid fatty acid composition, which at least partly mirrors the quality of the fatty acids in the diet, and insulin sensitivity. Insulin resistance, and disorders characterized by insulin resistance, are associated with a specific fatty acid pattern of the serum lipids with increased proportions of palmitic (16 : 0) and palmitoleic acids (16 : 1 n-7) and reduced levels of linoleic acid (18 : 2 n-6). The metabolism of linoleic acid seems to be disturbed with increased proportions of dihomo-gamma linolenic acid (20 : 3 n-6) and a reduced activity of the Δ5 desaturase, while the activities of the Δ9 and Δ6 desaturases appear to be increased. The skeletal muscle is the main determinant of insulin sensitivity. Several studies have shown that the fatty acid composition of the phosholipids of the skeletal muscle cell membranes is closely related to insulin sensitivity. An increased saturation of the membrane fatty acids and a reduced activity of Δ5 desaturase have been associated with insulin resistance. There are several possible mechanisms which could explain this relationship. The fatty acid composition of the lipids in serum and muscle is influenced by diet, but also by the degree of physical activity, genetic disposition, and possibly fetal undernutrition. However, controlled dietary intervention studies in humans investigating the effects of different types of fatty acids on insulin sensitivity have so far been negative.
Multi-perspective evaluation of self-healing systems using simple probabilistic models

In this paper we construct an evaluation framework for a self-healing system, VM-Rejuv -- a virtual machine based rejuvenation scheme for web-application servers -- using simple, yet powerful, probabilistic models that capture the behavior of its self-healing mechanisms from multiple perspectives (designer, operator, and end-user). We combine these analytical models with runtime fault-injection to study the operation of VM-Rejuv, and use the results from the fault-injection experiments and model-analysis to reason about the efficacy of VM-Rejuv, its limitations and strategies for mitigating these limitations in system-deployments. Whereas we use VM-Rejuv as the subject of our evaluation in this paper, our main contribution is the demonstration of a practical evaluation approach that can be generalized to other self-healing systems.
Formation of nanoliter droplets in a confined microfluidic T-shaped junction: Formation time and droplet volume

Nanoliter droplet formation in a confined T-shaped junction is analyzed in detail in virtue of an experimental visualization system with a high speed camera. The movement of the back interface of the tip of disperse phase penetrated into the continuous phase plays an important role in determining droplet formation time and droplet volume. A simple model of droplet formation time based on the analysis of droplet formation process is developed. Influences of continuous phase viscosity and interfacial tension on droplet formation time and droplet volume are concluded in terms of capillary number together with the mean velocity of continuous phase. It is found that both the capillary number and the flow rate ratio of disperse phase to continuous phase have strong impacts on determining droplet volume. Two empirical equations are derived from the model for predicting droplet formation time and droplet volume, respectively.
Notice of RetractionA non-parametric estimator used the Support Vector Machine for expected shortfall

Risk management is one of the top priorities in the financial industry today. The research of quantifying risk is one of risk management's centers. Quantifying the risk of financial time series amounts to measuring their expected shortfall. Asymmetric Power Distribution(APD) is a new family of densities for expected shortfall. The main feature of the APD is that it combines the flexible tail decay property with the asymmetry, which makes it particularly suited for modeling the behavior of financial returns. In this paper, a non-parametric estimator, as a improvement to the traditional estimators, used the Support Vector Machine(SVM)for expected shortfall based on APD is proposed. The simulated studies show that this method can depict the distribution characters of Asymmetric Power Distribution with good results.
Identification and Characterization of the Flavin:NADH Reductase (PrnF) Involved in a Novel Two-Component Arylamine Oxygenase

ABSTRACT Two-component oxygenases catalyze a wide variety of important oxidation reactions. Recently we characterized a novel arylamine N-oxygenase (PrnD), a new member of the two-component oxygenase family (J. Lee et al., J. Biol. Chem. 280:36719-36728, 2005). Although arylamine N-oxygenases are widespread in nature, aminopyrrolnitrin N-oxygenase (PrnD) represents the only biochemically and mechanistically characterized arylamine N-oxygenase to date. Here we report the use of bioinformatic and biochemical tools to identify and characterize the reductase component (PrnF) involved in the PrnD-catalyzed unusual arylamine oxidation. The prnF gene was identified via sequence analysis of the whole genome of Pseudomonas fluorescens Pf-5 and subsequently cloned and overexpressed in Escherichia coli. The purified PrnF protein catalyzes reduction of flavin adenine dinucleotide (FAD) by NADH with a k cat of 65 s−1 (K m = 3.2 μM for FAD and 43.1 μM for NADH) and supplies reduced FAD to the PrnD oxygenase component. Unlike other known reductases in two-component oxygenase systems, PrnF strictly requires NADH as an electron donor to reduce FAD and requires unusual protein-protein interaction with the PrnD component for the efficient transfer of reduced FAD. This PrnF enzyme represents the first cloned and characterized flavin reductase component in a novel two-component arylamine oxygenase system.
Acknowledgment Time Delay Approach to Optimize TCP Performance in Hybrid Networked Systems

Transmission Control Protocol (TCP) is connection oriented transport protocol used on IP in wireless medium and it insists lossless data transmission in proper order. When TCP is used as a transmission protocol where physical layer is wireless medium, results high packet reordering due to bursty traffic and drastic variation in quality of service with respect to time. By sharing the same path for data and acknowledgement increases the traffic and collision, resulting in reduced throughput. In order to improve QoS this paper proposes a solution “Improved Delay the Duplicate Acknowledgement” (IDDA). This reduces traffic and spurious retransmissions, thereby improving TCP performance.
Multi-Modal Learning and Assessment in Second Life with quizHUD

In this paper, the early development and preliminary evaluation is presented of a new approach for delivering educational material, administering assessment, and gathering survey data, within the Second Life virtual world. The 'quizHUD' is part of the SLOODLE project, and is designed to encourage an exploratory attitude to learning, while administering assessment using a mixture of multiple choice and environment interaction questions.
Barge-in effects in Bayesian dialogue act recognition and simulation

Dialogue act recognition and simulation are traditionally considered separate processes. Here, we argue that both can be fruitfully treated as interleaved processes within the same probabilistic model, leading to a synchronous improvement of performance in both. To demonstrate this, we train multiple Bayes Nets that predict the timing and content of the next user utterance. A specific focus is on providing support for barge-ins. We describe experiments using the Let's Go data that show an improvement in classification accuracy (+5%) in Bayesian dialogue act recognition involving barge-ins using partial context compared to using full context. Our results also indicate that simulated dialogues with user barge-in are more realistic than simulations without barge-in events.