Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Imprinted Chromosomal Regions Are Historical Hot-Spots of Recombination

Human recombination rates vary along the chromosomes as well as between the two sexes. There is growing evidence that epigenetic factors may have an important influence on recombination rates, as well as on crossover position. Using both public database analysis and wet-bench approaches, we revisited the relationship between increased rates of meiotic recombination and genome imprinting. We constructed metric linkage disequilibrium (LD) maps for all human chromosomal regions known to contain one or more imprinted genes. We show that imprinted regions contain significantly more LD units (LDU) and have significantly more haplotype blocks of smaller sizes than flanking nonimprinted regions. There is also an excess of hot-spots of recombination at imprinted regions, and this is likely to do with the presence of imprinted genes, per se. These findings indicate that imprinted chromosomal regions are historical “hot-spots” of recombination. We also demonstrate, by direct segregation analysis at the 11p15.5 imprinted region, that there is remarkable agreement between sites of meiotic recombination and steps in LD maps. Although the increase in LDU/Megabase at imprinted regions is not associated with any significant enrichment for any particular sequence class, major sequence determinants of recombination rates seem to differ between imprinted and control regions. Interestingly, fine-mapping of recombination events within the most male meiosis–specific recombination hot-spot of Chromosome 11p15.5 indicates that many events may occur within or directly adjacent to regions that are differentially methylated in somatic cells. Taken together, these findings support the involvement of a combination of specific DNA sequences and epigenetic factors as major determinants of hot-spots of recombination at imprinted chromosomal regions.
Differential expression of NO-sensitive guanylyl cyclase subunits during the development of rat cerebellar granule cells: regulation via N-methyl-D-aspartate receptors

In primary cultures of rat cerebellar granule cells with a functional network of glutamatergic neurons, the expression pattern of the different subunits of nitric-oxide (NO)-sensitive guanylyl cyclase changes during cell differentiation. These cells express the α1,α 2 and β1 subunits of NO-sensitive guanylyl cyclase and synthesize cyclic guanosine monophosphate (cGMP) in response to exogenous or endogenous nitric oxide. In this study, we determined the protein content of the α1 and β1 subunits and quantified α1, α2 and β1 mRNA by reverse transcription coupled to a polymerase chain reaction (RT-PCR). Expression of the β1 subunit increased with the degree of cell differentiation, although most marked changes occurred at the α subunit level. In cells freshly isolated from rat pups on postnatal day 7 (P7) the most abundant α subunit was α1, whileα 2 appeared as the predominant subunit of this type in cultured cells. N-methyl-D-aspartate (NMDA) receptor stimulation in 7- or 14-day-cultured cells led to the upregulation of guanylyl cyclase subunit mRNAs; α2 mRNA levels undergoing most significant change. This enhanced subunit expression was accompanied by an increase in the amount of cGMP synthesized in response to NO. Thus, it seems thatα 2 subunits are increasingly expressed as granule cells mature. The presence of this subunit in the guanylyl cyclase heterodimer facilitates its localization at synaptic membranes, where the enzyme acts as a sensor for NO formed by the postsynaptic protein 95 (PSD-95)-associated neuronal NO synthase.
Respiratory disease associated with solid biomass fuel exposure in rural women and children: systematic review and meta-analysis

Background Numerous studies with varying associations between domestic use of solid biomass fuels (wood, dung, crop residue, charcoal) and respiratory diseases have been reported. Objective To present the current data systematically associating use of biomass fuels with respiratory outcomes in rural women and children. Methods Systematic searches were conducted in 13 electronic databases. Data were abstracted from original articles that satisfied selection criteria for meta-analyses. Publication bias and heterogeneity of samples were tested. Studies with common diagnoses were analysed using random-effect models. Results A total of 2717 studies were identified. Fifty-one studies were selected for data extraction and 25 studies were suitable for meta-analysis. The overall pooled ORs indicate significant associations with acute respiratory infection in children (OR 3.53, 95% CI 1.94 to 6.43), chronic bronchitis in women (OR 2.52, 95% CI 1.88 to 3.38) and chronic obstructive pulmonary disease in women (OR 2.40, 95% CI 1.47 to 3.93). In contrast, no significant association with asthma in children or women was noted. Conclusion Biomass fuel exposure is associated with diverse respiratory diseases in rural populations. Concerted efforts in improving stove design and lowering exposure to smoke emission may reduce respiratory disease associated with biomass fuel exposure.
Cross-Cultural Comparison of Self-Construal and Well-Being between Japan and South Korea: The Role of Self-Focused and Other-Focused Relational Selves

Relational self, along with individual and collective selves, is a fundamental aspect that makes up self-concept. Proposing its two aspects: self-focused relational self (i.e., perceiving the self as the object of other people's referential awareness or intentionality) and other-focused relational self (i.e., perceiving the self as being attuned and empathetically connected to close others), the current study explored the way the four selves affect well-being in Japan and South Korea, the East Asian cultures that have been assumed to be homogeneously collectivistic in previous psychological literature. Japanese and Korean participants rated a set of well-being and self-related scales. There were visible sample differences within culture by collection method (classroom vs. online) in relative degrees of selves and related constructs, possibly associated with generational differences. Other-focused relational self was greater in the Korean classroom sample than the Japanese counterpart, whereas no difference was found between the online samples. On the other hand, it was consistent between cultures that the two types of relational self showed different associations with social anxiety and self-esteem as expected, and that they predicted well-being in different ways. We discuss implications for the generational differences and their interactions with culture and the importance of separating the two aspects of relational self in the study of self and culture.
Preasymptotic Stability and Homogeneous Approximations of Hybrid Dynamical Systems

Hybrid dynamical systems are systems that combine features of continuous-time dynamical systems and discrete-time dynamical systems, and can be modeled by a combination of differential equations or inclusions, difference equations or inclusions, and constraints. Preasymptotic stability is a concept that results from separating the conditions that asymptotic stability places on the behavior of solutions from issues related to existence of solutions. In this paper, techniques for approximating hybrid dynamical systems that generalize classical linearization techniques are proposed. The approximation techniques involve linearization, tangent cones, homogeneous approximations of functions and set-valued mappings, and tangent homogeneous cones, where homogeneity is considered with respect to general dilations. The main results deduce preasymptotic stability of an equilibrium point for a hybrid dynamical system from preasymptotic stability of the equilibrium point for an approximate system. Further results relate the degree of homogeneity of a hybrid system to the Zeno phenomenon that can appear in the solutions of the system.
Reading between Eye Saccades

Background Skilled adult readers, in contrast to beginners, show no or little increase in reading latencies as a function of the number of letters in words up to seven letters. The information extraction strategy underlying such efficiency in word identification is still largely unknown, and methods that allow tracking of the letter information extraction through time between eye saccades are needed to fully address this question. Methodology/Principal Findings The present study examined the use of letter information during reading, by means of the Bubbles technique. Ten participants each read 5,000 five-letter French words sampled in space-time within a 200 ms window. On the temporal dimension, our results show that two moments are especially important during the information extraction process. On the spatial dimension, we found a bias for the upper half of words. We also show for the first time that letter positions four, one, and three are particularly important for the identification of five-letter words. Conclusions/Significance Our findings are consistent with either a partially parallel reading strategy or an optimal serial reading strategy. We show using computer simulations that this serial reading strategy predicts an absence of a word-length effect for words from four- to seven letters in length. We believe that the Bubbles technique will play an important role in further examining the nature of reading between eye saccades.
Smart Middleware and Light Ends ( SMILE ) for Simplifying Data Integration

SMILE is a stateful publish-subscribe system that allows subscribers to request continually updated derived views, specified as relational algebraic expressions over published data histories. The derived views can be specified using aggregations, joins, and other transforms. We achieve these for applications that do not require ACID properties but only require that the information they receive is never false and arrives eventually. We formalize this by introducing an “eventual correctness” guarantee and our implementation enforces it using a monotonic type system. We present preliminary performance results of our
Benchmarking Java against C/C++ for interactive scientific visualization

Interactive scientific visualization applications require both high performance graphics and numerical computation capabilities. C/C++ programs are able to take direct advantage of specialized graphics rendering hardware (referred to as a Graphics Processing Unit or GPU) for display and special SIMD instructions within the CPU for computation. The former using for example the OpenGL library and latter using compiler extensions. Software developed in Java offers portability, robustness and security. However, the graphics rendering performance, memory efficiency, and computational speed of Java for visualization of large scientific data sets has not been well characterized. Benchmarking experiments were done using the JLoop (Java) and Loop (C/C++) visualization software for animation of 2D datasets. Preliminary results for six different hardware platforms showed that compared to the C/C++ version, the Java implementation was four to five times slower for graphics image animation, used on average 2.5 to three times more memory, and was up to 3.6 times slower using a pure numerical benchmark that simulated image pixel operations. Such benchmarks should be used to improve the Java VM performance across platforms, similar to JIT-compiler design.
Bipartite network model for inferring hidden ties in crime data

Certain crimes are difficult to be committed by individuals but carefully organised by group of associates and affiliates loosely connected to each other with a single or small group of individuals coordinating the overall actions. A common starting point in understanding the structural organisation of criminal groups is to identify the criminals and their associates. Situations arise in many criminal datasets where there is no direct connection among the criminals. In this paper, we investigate ties and community structure in crime data in order to understand the operations of both traditional and cyber criminals, as well as to predict the existence of organised criminal networks. Our contributions are twofold: we propose a bipartite network model for inferring hidden ties between actors who initiated an illegal interaction and objects affected by the interaction, we then validate the method in two case studies on pharmaceutical crime and underground forum data using standard network algorithms for structural and community analysis. The vertex level metrics and community analysis results obtained indicate the significance of our work in understanding the operations and structure of organised criminal networks which were not immediately obvious in the data. Identifying these groups and mapping their relationship to one another is essential in making more effective disruption strategies in the future.
Quantitative analysis of volumetric TPLSM data

This paper describes initial algorithm development in support of research on a new all-optical histology technique based on two-photon laser scanning microscopy (TPLSM) and laser tissue ablation. This new imaging modality makes it possible to obtain quantitative information that can be used to measure physiological parameters of interest. We present our initial image processing approach and volumetric rendering results. Two examples of useful quantitative parameters are presented: measurement of blood vessel volume fraction and cell counting.
Imaging the elastic properties of tissue: the 20 year perspective

After 20 years of innovation in techniques that specifically image the biomechanical properties of tissue, the evolution of elastographic imaging can be viewed from its infancy, through a proliferation of approaches to the problem to incorporation on research and then clinical imaging platforms. Ultimately this activity has culminated in clinical trials and improved care for patients. This remarkable progression represents a leading example of translational research that begins with fundamentals of science and engineering and progresses to needed improvements in diagnostic and monitoring capabilities applied to major categories of disease, surgery and interventional procedures. This review summarizes the fundamental principles, the timeline of developments in major categories of elastographic imaging, and concludes with recent results from clinical trials and forward-looking issues.
Self-creating and organizing neural networks

We have developed a self-creating and organizing unsupervised learning algorithm for artificial neural networks. In this study, we introduce SCONN and SCONN2 as two versions of self-creating and organizing neural network (SCONN) algorithms. SCONN creates an adaptive uniform vector quantizer (VQ), whereas SCONN2 creates an adaptive nonuniform VQ by neural-like architecture. SCONN's begin with only one output node, which has a sufficiently wide activation level, and the activation level decrease depending upon the time or the activation history. SCONN's decide automatically whether to adapt the weights of existing nodes or to create a new "son node. " They are compared with two famous algorithms-the Kohonen's self organizing feature map (SOFM) (1988) as a neural VQ and the Linde-Buzo-Gray (LBG) algorithm (1980) as a traditional VQ. The results show that SCONN's have significant benefits over other algorithms.
Brittle Deformation in an Ancient Accretionary Prism Setting: Lopez Structural Complex, San Juan Islands, NW Washington

Fault-bounded slices of allochthonous Paleozoic to Mesozoic bedrock of the San Juan Islands in northwest Washington provide a locality in which to study terrane translation and ductile and brittle deformation in an accretionary wedge setting, as well as the factors involved in preservation of blueschist-facies terranes. This study contributes to understanding of the tectonic evolution of the Lopez Structural Complex, a major Late Cretaceous terrane-bounding fault zone in the San Juan Thrust System. Structural study is combined with X-ray diffraction and fluid inclusion analysis to constrain the relative timing, kinematics, and P-T conditions of fabric formation and post-fabric brittle deformation in the Lopez Structural Complex. Deformation is characterized by multiple generations of ductile and brittle structures. After formation of a regional flattening fabric by two processes, pressure solution and localized bi-directional shearing, the area was crosscut by brittle structures including: 1) early strike-slip structures related to bi-directional northwest/southeast shear, 2) southwest-vergent thrusts, 3) extension veins and normal faults related to northwest/southeast extension, and 4) conjugate strike-slip structures also related to northwest/southeast extension. The presence of comparable structures in the eastern San Juan Islands (Lamb and Schermer, 2003) and adjacent to the Lopez Structural Complex indicates this sequence of brittle deformation is widespread in the San Juan nappes. X-ray diffraction and petrographic observations of vein material identify aragonite- and prehnite-bearing veins associated with thrust, normal, and strike-slip structures, although most of the latest strike-slip faults contain only prehnite and calcite. High pressure minerals constrain brittle deformation to have occurred at greater than ~ 20 km depth and at most ~ 200° C. Fluid inclusion analyses of aqueous and methane-bearing inclusions in vein quartz are in agreement with low temperature conditions after vein formation and tentatively suggest rapid exhumation to shallow depths under near isothermal conditions. Sustained high-pressure - low-temperature conditions and the preservation of widespread aragonite are possible only if structures formed in an accretionary prism during active subduction. Therefore, meter-scale brittle structures in rocks of the Lopez Structural Complex record a pattern of internal wedge deformation at depth or early during uplift of the San Juan nappes. The sequence observed is generally consistent with internal orogen-normal contraction and vertical thickening followed by vertical thinning and lateral along-strike extension. Possible mechanisms for brittle deformation include a change in the angle or magnitude of plate convergence vectors, a large underplating or accretion event, or the collision of the Cretaceous prism with the margin of Wrangellia.
Highly stretchable, transparent ionic touch panel

Soft and still responsive Transparent touch screens, from large-panel interactive information maps to advanced cell phones, have become a part of daily life. However, such devices all use hard materials. Kim et al. have developed a soft touch panel based on polyacrylamide hydrogels (cross-linked polymers swollen with water) that are highly transparent and contain trapped LiCl to enhance conductivity. The hydrogels are soft and can be stretched extensively while still maintaining touch sensitivity. Science, this issue p. 682 Stretchable touch panels are made from polyacrylamide hydrogels loaded with lithium chloride. Because human-computer interactions are increasingly important, touch panels may require stretchability and biocompatibility in order to allow integration with the human body. However, most touch panels have been developed based on stiff and brittle electrodes. We demonstrate an ionic touch panel based on a polyacrylamide hydrogel containing lithium chloride salts. The panel is soft and stretchable, so it can sustain a large deformation. The panel can freely transmit light information because the hydrogel is transparent, with 98% transmittance for visible light. A surface-capacitive touch system was adopted to sense a touched position. The panel can be operated under more than 1000% areal strain without sacrificing its functionalities. Epidermal touch panel use on skin was demonstrated by writing words, playing a piano, and playing games.
Role of the Bloodstream Impacting Force and the Local Pressure Elevation in the Rupture of Cerebral Aneurysms

Background and Purpose— Inertial force of the bloodstream results in the local elevation of intravascular pressure secondary to flow impact. Previous studies suggest that this “impacting force” and the local pressure elevation at the aneurysm may have a large contribution to the development of cerebral aneurysms. The goal of the present study is to evaluate how the bloodstream impacting force and the local pressure elevation at the aneurysm influences the rupture of cerebral aneurysms. Methods— A total of 29 aneurysms were created in 26 patient-specific vessel models, and computer simulations were used to calculate pressure distributions around the vessel branching points and the aneurysms. Results— Direct impact of the parent artery bloodstream resulted in local elevation in pressure at branch points, and bends in arteries (231.2±198.1 Pa; 100 Pa=0.75 mm Hg). The bloodstream entered into the aneurysm with a decreased velocity after it impacted on the branching points or bends. Thus, the flow impact at the aneurysm occurred usually weakly. At the top or the rupture point of the aneurysm, the flow velocity was always delayed. The local pressure elevation at the aneurysm was 119.3±91.2 Pa. Conclusions— The pressure elevation at the area of flow impact and at the aneurysm constituted only 1% to 2% of the peak intravascular pressure. The results suggest that the bloodstream impacting force and the local pressure elevation at the aneurysm may have less contribution to the rupture of cerebral aneurysms than was expected previously.
Inflammation, Endoplasmic Reticulum Stress, Autophagy, and the Monocyte Chemoattractant Protein-1/CCR2 Pathway

Numerous inflammatory cytokines have been implicated in the pathogenesis of cardiovascular diseases. Monocyte chemoattractant protein (MCP)-1/CCL2 is expressed by mainly inflammatory cells and stromal cells such as endothelial cells, and its expression is upregulated after proinflammatory stimuli and tissue injury. MCP-1 can function as a traditional chemotactic cytokine and also regulates gene transcription. The recently discovered novel zinc-finger protein, called MCPIP (MCP-1-induced protein), initiates a series of signaling events that causes oxidative and endoplasmic reticulum (ER) stress, leading to autophagy that can result in cell death or differentiation, depending on the cellular context. After a brief review of the basic processes involved in inflammation, ER stress, and autophagy, the recently elucidated role of MCP-1 and MCPIP in inflammatory diseases is reviewed. MCPIP was found to be able to control inflammatory response by inhibition of nuclear factor-&kgr;B activation through its deubiquitinase activity or by degradation of mRNA encoding a set of inflammatory cytokines through its RNase activity. The potential inclusion of such a novel deubiquitinase in the emerging anti-inflammatory strategies for the treatment of inflammation-related diseases such as cardiovascular diseases and type 2 diabetes is briefly discussed.
Establishing a Common Modeling Framework using UML to Effectively Support Faster-Than-Real-Time Simulation

Faster-than-real-time simulation (FRTS) is used when attempting to reach conclusions for the near future. FRTS experimentation phase deals with the complexity and hard real-time requirements imposed by the concurrent execution of the real world system and corresponding simulation model. It is important for the FRTS experiment designer to study timing constraints, thus to set limitations in the execution time of specific activities. As simulation activities and control data flows may be the same in diverse FRTS implementations, a common basis for FRTS system development is introduced based on the Real Time Unified Modeling Language (RT-UML). The proposed approach enables the detailed specification of critical time and synchronization requirements for FRTS components and an overall performance evaluation. The detailed specification for FRTS systems leads to standardized implementations of such systems that meet strict time requirements.