Miracle-dz/UniFAR-FTUs huggingface dataset:
Bivalent-Like Chromatin Markers Are Predictive for Transcription Start Site Distribution in Human

Deep sequencing of 5′ capped transcripts has revealed a variety of transcription initiation patterns, from narrow, focused promoters to wide, broad promoters. Attempts have already been made to model empirically classified patterns, but virtually no quantitative models for transcription initiation have been reported. Even though both genetic and epigenetic elements have been associated with such patterns, the organization of regulatory elements is largely unknown. Here, linear regression models were derived from a pool of regulatory elements, including genomic DNA features, nucleosome organization, and histone modifications, to predict the distribution of transcription start sites (TSS). Importantly, models including both active and repressive histone modification markers, e.g. H3K4me3 and H4K20me1, were consistently found to be much more predictive than models with only single-type histone modification markers, indicating the possibility of “bivalent-like” epigenetic control of transcription initiation. The nucleosome positions are proposed to be coded in the active component of such bivalent-like histone modification markers. Finally, we demonstrated that models trained on one cell type could successfully predict TSS distribution in other cell types, suggesting that these models may have a broader application range.
Cost-Benefit Analyses of Active Distribution Network Management, Part I: Annual Benefit Analysis

With more and more renewable energy generation (REG) connections, busbar voltage violation and line overloading problems may occur for some parts of a distribution network. However, building new circuits to accommodate REG may have high monetary and environmental costs. This paper considers distribution automation as a supplementary scheme to traditional primary asset investments and analyzes the operational benefits from introducing an autonomous regional active network management system (AuRA-NMS) to a practical distribution system with rich renewable sources. The benefits are quantified in terms of optimal power flow control and investment deferral, and the resulting quantification will inform distribution network operators of the trade-offs between investment in the automation system and in the primary assets, thus helping them to make cost-effective investment decisions. Time-series-based simulation for over an entire year is implemented to calculate the benefits of active power loss and curtailment reductions for AuRA-NMS over the current practice. Part I of this paper illustrates the current schemes for voltage control and constraint management, advanced voltage control and constraint management enabled by the distribution automation, and the annual benefit by introducing the AuRA-NMS to the system with different considerable new DG integrations. Part II analyzes the investment deferral benefit by deploying AuRA-NMS.
The costs of being cool: a dynamic model of nocturnal hypothermia by small food‐caching birds in winter

Many birds could expend substantially less energy at night by using hypothermia, but generally do not. This suggests that the potential savings are offset by costs; one of these costs is presumed to be the risk of predation at night. If this assumption is correct, a bird will face one of two tradeoffs: (1) it can avoid the cost of hypothermia by gaining fat to decrease the risk of starvation, but this increases energetic costs of fat maintenance and risk of diurnal predation, or (2) it can maintain lower fat reserves and use hypothermia at night, but this option increases the risk of nocturnal predation. We used a dynamic model to investigate these trade-offs and how the use of nocturnal hypothermia changes energy management tactics in food-caching birds. Our model predicted that: (i) optimal daily routines of fat reserves, feeding rate, food caching, and cache retrieval should be similar in hypothermic and non-hypothermic birds; (ii) low fat reserves, small cache size, low ambient temperature, and high variability in foraging success favor increased use of hypothermia; (iii) the effect of ambient temperature on the use of hypothermia is especially important at higher levels of variance in foraging success; (iv) hypothermic birds are predicted to have lower mass at dusk than non-hypothermic individuals while their morning mass should be more similar. Many of these predictions have been supported by empirical data. Also, survival rates are predicted to be higher for birds using hypothermia, especially in the most severe environmental conditions. This is the first attempt to evaluate the role of cache maintenance and variance in foraging success in the use of hypothermia. This is also the first discussion of the relationship between behavior hypothermia and diurnal patterns of energy management.
Functional spatial contextualisation of the effects of multiple stressors in marine bivalves

Abstract. Many recent studies have revealed that the majority of environmental stressors experienced by marine organisms (ocean acidification, global warming, hypoxia etc.) occur at the same time and place, and that their interaction may complexly affect a number of ecological processes. Here, we experimentally investigated the effects of pH and hypoxia on the functional and behavioural traits of the mussel Mytilus galloprovincialis, we then simulated the potential effects on growth and reproduction dynamics trough a Dynamic Energy Budget (DEB) model under a multiple stressor scenario. Our simulations showed that hypercapnia had a remarkable effect by reducing the maximal habitat size and reproductive output differentially as a function of the trophic conditions, where modelling was spatially contextualized. This study showed the major threat represented by the hypercapnia and hypoxia phenomena for the growth, reproduction and fitness of mussels under the current climate change context, and that a mechanistic approach based on DEB modelling can illustrate complex and site-specific effects of environmental change, producing that kind of information useful for management purposes, at larger temporal and spatial scales.
Non‐specific binding of the experimental anti‐cancer drug 5,6‐dimethylxanthenone‐4‐acetic acid (DMXAA) in liver microsomes from various species

Total (added) drug concentrations other than unbound concentrations have been used to estimate the in‐vitro enzyme kinetic parameters for 5,6‐dimethylxanthenone‐4‐acetic acid (DMXAA), an experimental anti‐cancer drug. This study aimed to investigate the non‐specific binding of DMXAA to liver microsomes from various species and to microsomes from human lymphoblastoid cells expressing drug‐metabolising enzymes, and to examine the effect of the binding on the estimation of enzyme kinetic parameters for DMXAA in‐vitro. The separation of unbound DMXAA was conducted by ultrafiltration and DMXAA concentrations were determined by validated HPLC. The results indicated that DMXAA was bound to liver microsomes and lymphoblastoid cell microsomes to a small extent (free fraction in microsomes, fu(mic) mostly > 0.85). Correction for the unbound DMXAA concentration resulted in slightly lower apparent Michaelis‐Menten constant (Km) values, but with the maximal velocity of reaction (Vmax) unchanged, leading to slightly higher unbound Vmax/Km values. These results indicate that the non‐specific binding of DMXAA to microsomes is insignificant and has little impact on the enzyme kinetic estimation in‐vitro.
Aqueous Humor Natural Convection of the Human Eye induced by Electromagnetic Fields: In the Supine Position

This study presents the simulation of the specific absorption rate (SAR), fluid flow and heat transfer in an anatomical human eye exposed to EM fields in the supine position. In this study, the frequencies of 900 and 1800 MHz were chosen for our simulations. This work focuses on the aqueous humor natural convection of the lying human eye induced by electromagnetic (EM) fields. In this study, the effect of operating frequency on the SAR, fluid flow and heat transfer in the eye was systematically investigated. The SAR value and the temperature distribution in various tissues in the eye during exposure to EM fields were obtained by numerical simulation of EM wave propagation and a heat transfer model was then developed based on the natural convection and porous media theories. The findings demonstrate the potential of aqueous humor natural convection in enhancing heat transfer of the eye in the supine position. 
Prospex: Protocol Specification Extraction

Protocol reverse engineering is the process of extracting application-level specifications for network protocols. Such specifications are very useful in a number of security-related contexts, for example, to perform deep packet inspection and black-box fuzzing, or to quickly understand custom botnet command and control (C\&C) channels.Since manual reverse engineering is a time-consuming and tedious process, a number of systems have been proposed that aim to automate this task. These systems either analyze network traffic directly or monitor the execution of the application that receives the protocol messages. While previous systems show that precise message formats can be extracted automatically, they do not provide a protocol specification.The reason is that they do not reverse engineer the protocol state machine.In this paper, we focus on closing this gap by presenting a system that is capable of automatically inferring state machines. This greatly enhances the results of automatic protocol reverse engineering, while further reducing the need for human interaction. We extend previous work that focuses on behavior-based message format extraction,and introduce techniques for identifying and clustering different types of messages not only based on their structure, but also according to the impact of each message on server behavior.Moreover, we present an algorithm for extracting the state machine.We have applied our techniques to a number of real-world protocols, including the command and control protocol used by a malicious bot. Our results demonstrate that we are able to extract format specifications for different types of messages and meaningful protocol state machines. We use these protocol specifications to automatically generate input for a stateful fuzzer,allowing us to discover security vulnerabilities in real-world applications.
Characteristic behavior of a side branch in a dendritic crystal growth

This study investigates the characteristic behavior of disturbances on the interface of a needle crystal, Ivantsove parabola, based on an asymptotic analysis as well as a numerical study. Focusing on tip growth and width behavior, we examine anisotropy in surface energy, initial strength of the disturbances. It is found that a tip grows as ftip = exp(Ct) close to the tip region and ftip = exp(Ct) at far field and wave-length, λo, does not show large variation to different initial conditions so that the width of a disturbance behaves as ∆y ∼ yλo. This constant wave-length, λo, suggests that the possibility of the existence of an attractor in λo. An evolution of finger competition between two disturbances with different initial strengths is investigated to understand the selection mechanism.
Comparison of prognostic factors for survival and recurrence in malignant melanoma of the skin, clinical stage I

Potential prognostic factors for survival time, 5‐year survival rate, recurrence‐free time, and 5‐year recurrence‐free rate were explored for 262 patients with malignant melanoma of the skin, Stage I, using the log‐rank test, proportional hazards (Cox) regression, and linear logistic regression. Breslow's thickness was the most important variable in each analysis. A thinner Breslow's thickness was associated with a better prognosis. After adjusting for Breslow's thickness, sex was the next most important variable in each analysis. Women had a better prognosis than men. After adjusting for Breslow's thickness and sex, there were no additional significant prognostic factors for survival time; Clark's level was significant for 5‐year survival rate; the number of mitoses, evidence of regression, and presence of vascular invasion were significant for recurrence‐free time; and the presence of vascular invasion and number of mitoses were significant for 5‐year recurrence‐free rate. It is recommended that in future prospective studies of adjuvant therapy of Stage I melanoma, patients be stratified into treatment groups on the basis of Breslow's thickness and sex.
Sexual agency versus relational factors: a study of condom use antecedents among high-risk young African American women.

BACKGROUND The influence that female partners exert regarding condom use is not well known. In the present study, the relative roles of personal sexual agency and relational factors in determining whether young African American women engaged in unprotected vaginal sex (UVS) were studied. METHODS A cross sectional study of 713 young, African American women (aged 15-21 years) was conducted. Data were collected using an audio-computer assisted self-interview. Three measures of sexual agency were assessed and three relational factors were assessed. To help assure validity in the outcome measure, condom use was assessed in five different ways. Multivariate analyses were used to determine whether variables independently predicted UVS. RESULTS Two of the six predictor variables achieved multivariate significance with all five measures of condom use: (1) fear of negotiating condom use with male partners, and (2) indicating that stopping to use condoms takes the fun out of sex. A relational factor (male-dominated power imbalances) achieved multivariate significance for four of the five measures of UVS. A sexual agency factor (whether young women greatly enjoyed sex) achieved multivariate significance for three of the five measures. CONCLUSION The results suggest that young African American women at high-risk of sexually transmissible infections (STI)/HIV acquisition may experience male-dominated power imbalances and also fear the process of negotiating condom use with their male partners. Although these factors were independently associated with UVS, two factors pertaining to sexual agency of these young women were also important predictors of UVS. Intervention efforts designed to avert STI/HIV acquisition among young African American women should therefore include programs to address both sexual agency and relational factors.
Improved Bounds for Subband-Adaptive Iterative Shrinkage/Thresholding Algorithms

This paper presents new methods for computing the step sizes of the subband-adaptive iterative shrinkage-thresholding algorithms proposed by Bayram & Selesnick and Vonesch & Unser. The method yields tighter wavelet-domain bounds of the system matrix, thus leading to improved convergence speeds. It is directly applicable to non-redundant wavelet bases, and we also adapt it for cases of redundant frames. It turns out that the simplest and most intuitive setting for the step sizes that ignores subband aliasing is often satisfactory in practice. We show that our methods can be used to advantage with reweighted least squares penalty functions as well as L1 penalties. We emphasize that the algorithms presented here are suitable for performing inverse filtering on very large datasets, including 3D data, since inversions are applied only to diagonal matrices and fast transforms are used to achieve all matrix-vector products.
Bullying in middle school: results from a 2008 survey

Abstract A survey conducted in 2008 among 346 American middle school students in several cities determined that 82.7% of respondents found bullying to be a problem of some degree, with 46.0% rating it a “medium”, “bad”, or “very bad” problem. It was found that 89% had witnessed an act of bullying and 49.1% said they had been the victim of a bully. Boys were significantly more likely than girls to say that a victim deserved to be bullied (11.1% vs. 1.3%, p=0.01), whereas girls were significantly more likely than boys to fail to intervene because they did not know what to do (30.3% for girls vs. 11.1%, p<0.01). There was no significant difference in this study between boys and girls in terms of being a bully: 43.6% admitted they had bullied another (46.2% boys, 41.1% girls, p=0.34); however, girls were significantly more likely than boys to bully by excluding others and gossiping about them than by hitting, teasing, or threatening. Cyberbullying, surveyed as a distinct entity, had affected 31.1% of respondents directly, with similar results from 2006 to 2007 surveys. Of those who found conventional bullying a “bad” or “very bad” problem at their schools, numbers fell from 17.3% in 2006–2007 vs. 11.3% in 2008.
Antennapedia homeobox peptide enhances growth and branching of embryonic chicken motoneurons in vitro

Spinal motoneuron development is regulated by a variety of intrinsic and extrinsic factors. Among these, a possible role for homeoproteins is suggested by their expression in the motoneuron at relatively late stages. To investigate their possible involvement in motoneuron growth, we adapted a novel technique recently developed in this laboratory, based on the ability of the 60 amino acid-long homeobox of Antennapedia (pAntp) to translocate through the neuronal membrane and to accumulate in the nucleus (Joliot, A. H., C. Pernelle, H. Deagostini-Bazin, and A. Prochiantz. 1991. Proc. Natl. Acad. Sci. USA. 88:1864-1868; Joliot, A. H., A. Triller, M. Volovitch, C. Pernelle, and A. Prochiantz. 1991. New Biol. 3:1121-1134). Motoneurons from E5 chicken spinal cord were incubated with pAntp, purified by panning on SC1 antibody and plated on polyornithine/laminin substrata without further addition of pAntp. After 24 h, neurite outgrowth was already extensive in controls. In cultures of motoneurons that had been preincubated with 10(-7) M pAntp, neurite length was doubled; a similar effect was obtained using postnatal muscle extracts. Morphological analysis using a neurofilament marker specific for axons indicated that the homeobox peptide enhances primarily axonal elongation and branching. To test the hypothesis that the biological activity of pAntp involves its specific attachment to cognate homeobox binding sites present in the genome, we generated a mutant of pAntp called pAntp40P2, that was still able to translocate through the motoneuron membrane and to reach the nucleus, but had lost the specific DNA-binding properties of the wild-type peptide. Preincubation of pAntp40P2 with purified motoneurons failed to increase neurite outgrowth. This finding raises the possibility that motoneuron growth is controlled by homeobox proteins.
Accommodating Species Climate-Forced Dispersal and Uncertainties in Spatial Conservation Planning

Abstract Spatial conservation prioritization should seek to anticipate climate change impacts on biodiversity and to mitigate these impacts through the development of dynamic conservation plans. Here, we defined spatial priorities for the conservation of amphibians inhabiting the Atlantic Forest Biodiversity Hotspot that overcome the likely impacts of climate change on the distribution of this imperiled fauna. First, we built ecological niche models (ENMs) for 431 amphibian species both for current time and for the mid-point of a 30-year period spanning 2071–2099 (i.e. 2080). For modeling species' niches, we combined six modeling methods and three different climate models. We also quantified and mapped model uncertainties. Our consensus models forecasted range shifts that culminate with high species richness in central and eastern Atlantic Forest, both for current time and for 2080. Most species had a significant range contraction (up to 72%) and 12% of species were projected to be regionally extinct. Most species would need to disperse because suitable climatic sites will change. Therefore, we identified a network of priority sites for conservation that minimizes the distance a given species would need to disperse because of changes in future habitat suitability (i.e. climate-forced dispersal) as well as uncertainties associated to ENMs. This network also maximized complementary species representation across currently established protected areas. Priority sites already include possible dispersal corridors linking current and future suitable habitats for amphibians. Although we used the a top-ranked Biodiversity Hotspot and amphibians as a case study for illustrating our approach, our study may help developing more effective conservation strategies under climate change, especially when applied at different spatial scales, geographic regions, and taxonomic groups.
Lower bounds for sparse recovery

We consider the following <i>k</i>-sparse recovery problem: design an <i>m</i> x <i>n</i> matrix <i>A</i>, such that for any signal <i>x</i>, given <i>Ax</i> we can efficiently recover x satisfying ||<i>x</i> -- x||<sub>i</sub> ≤ <i>C</i> min<sub><i>k</i></sub>-sparse <i>x</i>' ||<i>x</i> - <i>x</i>'||<sub>1</sub>. It is known that there exist matrices A with this property that have only <i>O</i>(<i>k</i> log(<i>n/k</i>)) rows. In this paper we show that this bound is tight. Our bound holds even for the more general <i>randomized</i> version of the problem, where <i>A</i> is a random variable, and the recovery algorithm is required to work for any fixed x with constant probability (over <i>A</i>).
A collocation-Galerkin finite element model of cardiac action potential propagation

A new computational method was developed for modeling the effects of the geometric complexity, nonuniform muscle fiber orientation, and material inhomogeneity of the ventricular wall on cardiac impulse propagation. The method was used to solve a modification to the FitzHugh-Nagumo system of equations. The geometry, local muscle fiber orientation, and material parameters of the domain were defined using linear Lagrange or cubic Hermite finite element interpolation. Spatial variations of time-dependent excitation and recovery variables were approximated using cubic Hermite finite element interpolation, and the governing finite element equations were assembled using the collocation method. To overcome the deficiencies of conventional collocation methods on irregular domains, Galerkin equations for the no-flux boundary conditions were used instead of collocation equations for the boundary degrees-of-freedom. The resulting system was evolved using an adaptive Runge-Kutta method. Converged two-dimensional simulations of normal propagation showed that this method requires less CPU time than a traditional finite difference discretization. The model also reproduced several other physiologic phenomena known to be important in arrhythmogenesis including: Wenckebach periodicity, slowed propagation and unidirectional block due to wavefront curvature, reentry around a fixed obstacle, and spiral wave reentry. In a new result, the authors observed wavespeed variations and block due to nonuniform muscle fiber orientation. The findings suggest that the finite element method is suitable for studying normal and pathological cardiac activation and has significant advantages over existing techniques. <<ETX>>