Miracle-dz/UniFAR-FTUs huggingface dataset:
Extensive and systematic rewiring of histone post-translational modifications in cancer model systems

Abstract Histone post-translational modifications (PTMs) generate a complex combinatorial code that regulates gene expression and nuclear functions, and whose deregulation has been documented in different types of cancers. Therefore, the availability of relevant culture models that can be manipulated and that retain the epigenetic features of the tissue of origin is absolutely crucial for studying the epigenetic mechanisms underlying cancer and testing epigenetic drugs. In this study, we took advantage of quantitative mass spectrometry to comprehensively profile histone PTMs in patient tumor tissues, primary cultures and cell lines from three representative tumor models, breast cancer, glioblastoma and ovarian cancer, revealing an extensive and systematic rewiring of histone marks in cell culture conditions, which includes a decrease of H3K27me2/me3, H3K79me1/me2 and H3K9ac/K14ac, and an increase of H3K36me1/me2. While some changes occur in short-term primary cultures, most of them are instead time-dependent and appear only in long-term cultures. Remarkably, such changes mostly revert in cell line- and primary cell-derived in vivo xenograft models. Taken together, these results support the use of xenografts as the most representative models of in vivo epigenetic processes, suggesting caution when using cultured cells, in particular cell lines and long-term primary cultures, for epigenetic investigations.
Involvement of the caudate nucleus head and its networks in sporadic amyotrophic lateral sclerosis-frontotemporal dementia continuum

Abstract We investigated common structural and network changes across the sporadic amyotrophic lateral sclerosis (ALS)-frontotemporal dementia (FTD) continuum. Based on cluster analysis using the frontotemporal assessment battery, 51 patients with sporadic ALS were subdivided into three groups: 25 patients with ALS with cognitive deficiency (ALS-CD); seven patients who satisfied FTD criteria (ALS-FTD), and 19 patients with ALS with normal cognitive function (ALS-NC). Compared with the controls, gray matter images from patients with ALS-FTD showed atrophic changes in the following order of severity: caudate head, medial frontal gyrus, thalamus, amygdala, putamen, and cingulate gyrus (peak level, uncorrected p < 0.001). The caudate head was significant at the cluster level using FWE correction (p < 0.05). Diffusion tensor imaging with tract-based spatial statistics revealed white matter changes in the areas surrounding the caudate head, the internal capsule, and the anterior horn of the lateral ventricle in the ALS-CD and ALS-FTD. Probabilistic diffusion tractography showed a significant decrease in structural connectivity between the caudate head and the dorsomedial frontal cortex and the lateral orbitofrontal cortex, even in the ALS-NC. Our results indicated that the caudate head and its networks were the most vulnerable to lesion in sporadic ALS-FTD-spectrum patients associated with cognitive decline with FTD features.
Invasive predator tips the balance of symmetrical competition between native coral-reef fishes.

The importance of competition and predation in structuring ecological communities is typically examined separately such that interactions between these processes are seldom understood. By causing large reductions in native prey, invasive predators may modify native species interactions. I conducted a manipulative field experiment in The Bahamas to investigate the possibility that the invasive Pacific red lionfish (Pterois volitans) alters competition between planktivorous fairy and blackcap basslets (Gramma loreto and Gramma melacara, respectively). Competition between these coral-reef fishes is known to have symmetrical effects on the juveniles of both species, whereby the feeding positions under reef ledges and growth rates of these individuals are hindered. Following baseline censuses of local populations of competing basslets, I simultaneously manipulated the abundance of lionfish on entire reefs, and the abundance of basslets in local populations under isolated ledges within each reef, resulting in three treatments: unmanipulated control populations of both basslets, reduced abundance of fairy basslet, and reduced abundance of blackcap basslet. For eight weeks, I measured the change in biomass and feeding position of 2-5 cm size classes of each basslet species and calculated the growth rates of ~2 cm individuals using a standard mark-and-recapture method. Experimental populations were filmed at dusk using automated video cameras to quantify the behavior of lionfish overlapping with basslets. Video playback revealed lionfish hunted across all ledge positions, regardless of which basslet species were present, yet lionfish differentially reduced the biomass of only juvenile (2 cm) fairy basslet. Predation reduced the effects of interspecific competition on juvenile blackcap basslet as evidenced by corresponding shifts in feeding position toward coveted front edges of ledges and increases in growth rates that were comparable to the response of these fish in populations where competition was experimentally reduced. Thus, an invasive marine predator altered the outcome of interspecific competition via differential predation, which tipped the balance of competition between native prey species from symmetrical to asymmetrical effects on juveniles. This study reveals a newly demonstrated context in which predation can indirectly facilitate prey, further broadening our understanding of the interactive effects of predation and competition in the context of invasive species.
Online-learning and planning in high dimensions with finite element goal babbling

Goal babbling (GB) has proved to be a powerful tool in online learning of inverse kinematic models of high-dimensional redundant robots that are acting in low dimensional sensor-spaces. To only look for inverse models is however not sufficient. An inverse model will only tell the robot what posture it should have in order to reach a goal, but not how to reach that posture. As many environments restrict what motions are possible this becomes a limitation. This paper introduces a new method, Finite Element Goal Babbling (FEGB), that presents a natural extension to GB. By partitioning the sensor-space into a disjoint set of finite elements where every element is seen as an independent GB problem, a planning module can be added by observing transitions between the different elements. The method is evaluated on a high dimensional planar arm, acting in an environment that restricts its movements. The goal is to learn to control the position of the end-effector so that it can reach any position in the environment. The results show that FEGB is able to learn such control rapidly while naturally dealing with stationary obstacles and workspace limits that would prohibit the applicability of GB.
Learning to Play Best Response in duopoly Games

We consider a quantity-setting duopoly market where firms lack perfect knowledge of the market demand function. They use estimated and therefore misspecified demand functions instead and determine their optimal strategies from the corresponding subjective payoff functions. The central issue of this paper is the question under which conditions a firm can learn the true demand function as well as the response behavior of its competitor from repeated estimations of historical market data. As soon as estimation errors are negligible, a firm is able to play best response in the usual game theoretic sense.
Gravity drives the evolution of infrared dark hubs: JVLA observations of SDC13

Context. Converging networks of interstellar filaments, that is hubs, have been recently linked to the formation of stellar clusters and massive stars. Understanding the relationship between the evolution of these systems and the formation of cores and stars inside them is at the heart of current star formation research. Aims. The goal is to study the kinematic and density structure of the SDC13 prototypical hub at high angular resolution to determine what drives its evolution and fragmentation. Methods. We have mapped SDC13, a ~1000 M⊙ infrared dark hub, in NH3(1,1) and NH3(2,2) emission lines, with both the Jansky Very Large Array and Green Bank Telescope. The high angular resolution achieved in the combined dataset allowed us to probe scales down to 0.07 pc. After fitting the ammonia lines, we computed the integrated intensities, centroid velocities and line widths, along with gas temperatures and H2 column densities. Results. The mass-per-unit-lengths of all four hub filaments are thermally super-critical, consistent with the presence of tens of gravitationally bound cores identified along them. These cores exhibit a regular separation of ~0.37 ± 0.16 pc suggesting gravitational instabilities running along these super-critical filaments are responsible for their fragmentation. The observed local increase of the dense gas velocity dispersion towards starless cores is believed to be a consequence of such fragmentation process. Using energy conservation arguments, we estimate that the gravitational to kinetic energy conversion efficiency in the SDC13 cores is ~35%. We see velocity gradient peaks towards ~63% of cores as expected during the early stages of filament fragmentation. Another clear observational signature is the presence of the most massive cores at the filaments’ junction, where the velocity dispersion is largest. We interpret this as the result of the hub morphology generating the largest acceleration gradients near the hub centre. Conclusions. We propose a scenario for the evolution of the SDC13 hub in which filaments first form as post-shock structures in a supersonic turbulent flow. As a result of the turbulent energy dissipation in the shock, the dense gas within the filaments is initially mostly sub-sonic. Then gravity takes over and starts shaping the evolution of the hub, both fragmenting filaments and pulling the gas towards the centre of the gravitational well. By doing so, gravitational energy is converted into kinetic energy in both local (cores) and global (hub centre) potential well minima. Furthermore, the generation of larger gravitational acceleration gradients at the filament junctions promotes the formation of more massive cores.
Photoprotection through ultrafast charge recombination in photochemical reaction centres under oxidizing conditions

Engineering natural photosynthesis to address predicted shortfalls in food and energy supply requires a detailed understanding of its molecular basis and the intrinsic photoprotective mechanisms that operate under fluctuating environmental conditions. Long-lived triplet or singlet excited electronic states have the potential to cause photodamage, particularly in the presence of oxygen, and so a variety of mechanisms exist to prevent formation of such states or safely dissipate their energy. Here, we report a dramatic difference in spectral evolution in fully reduced and partially oxidized Rhodobacter sphaeroides reaction centres (RCs) following excitation of the monomeric bacteriochlorophyll (BChl) cofactors at 805 nm. Three types of preparation were studied, including RCs purified as protein/lipid nanodiscs using the copolymer styrene maleic acid. In fully reduced RCs such excitation produces membrane-spanning charge separation. In preparations of partially oxidized RCs the spectroscopic signature of this charge separation is replaced by that of an energy dissipation process, including in the majority sub-population of reduced RCs. This process, which appears to take place on both cofactor branches, involves formation of a BChl+/bacteriopheophytin− radical pair that dissipates energy via recombination to a vibrationally hot ground state. The possible physiological role of this dissipative process under mildly oxidizing conditions is considered. This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Effects of Beta-Alanine Supplementation on Brain Homocarnosine/Carnosine Signal and Cognitive Function: An Exploratory Study

Objectives Two independent studies were conducted to examine the effects of 28 d of beta-alanine supplementation at 6.4 g d-1 on brain homocarnosine/carnosine signal in omnivores and vegetarians (Study 1) and on cognitive function before and after exercise in trained cyclists (Study 2). Methods In Study 1, seven healthy vegetarians (3 women and 4 men) and seven age- and sex-matched omnivores undertook a brain 1H-MRS exam at baseline and after beta-alanine supplementation. In study 2, nineteen trained male cyclists completed four 20-Km cycling time trials (two pre supplementation and two post supplementation), with a battery of cognitive function tests (Stroop test, Sternberg paradigm, Rapid Visual Information Processing task) being performed before and after exercise on each occasion. Results In Study 1, there were no within-group effects of beta-alanine supplementation on brain homocarnosine/carnosine signal in either vegetarians (p = 0.99) or omnivores (p = 0.27); nor was there any effect when data from both groups were pooled (p = 0.19). Similarly, there was no group by time interaction for brain homocarnosine/carnosine signal (p = 0.27). In study 2, exercise improved cognitive function across all tests (P<0.05), although there was no effect (P>0.05) of beta-alanine supplementation on response times or accuracy for the Stroop test, Sternberg paradigm or RVIP task at rest or after exercise. Conclusion 28 d of beta-alanine supplementation at 6.4g d-1 appeared not to influence brain homocarnosine/carnosine signal in either omnivores or vegetarians; nor did it influence cognitive function before or after exercise in trained cyclists.
A case for considering individual variation in diel activity patterns

Animal behaviors are often described on the population level. Bears in Scandinavia, for example, are generally assumed to be active in the morning and afternoon. Using GPS-radio collar data from 98 brown bears, we show that bears, in fact, differ in their activity tactic. We illustrate 4 distinct tactics from strictly day active to strictly night active and bears that were measured over multiple years often used the same activity tactic.
Joint State Estimation and Sparse Topology Error Detection for Nonlinear Power Systems

This paper proposes a new technique for robust state estimation in the presence of a small number of topological errors for power systems modeled by AC power flow equations. The developed method leverages the availability of a large volume of SCADA measurements and minimizes the `1 norm of nonconvex residuals augmented by a nonlinear, but convex, regularizer. We first study the properties of the solution obtained by the designed estimator and argue that, under mild conditions, this solution identifies a small subgraph of the network that can be used to find topological errors in the modeling of the state estimation problem. Then, we propose a method that can efficiently detect the topological errors by searching over this small subgraph. Furthermore, we develop a theoretical upper bound on the state estimation error to guarantee the accuracy of the underlying state estimation technique. The efficacy of the developed framework is demonstrated through numerical simulations on IEEE test systems.
The Comparative Health-Risk Behaviors between Boys and Girls of Freshmen at University of Tehran, Iran

Background and purpose: Priority health-risk behaviors, often are establish ed during childhood and adolescence, extend into adulthood, a nd are interrelated and preventable. This study was conducted to determine and compare the prevalence of risky behaviors on both sexes of freshman students enrolled in Tehran University, Iran. Materials and Methods: This study was a descriptive-analytical type of cro ss-sectional survey which has used stratified sampling to select 432 st udents during 2011-2012. A questionnaire including, 14 demographic questions and 38 questions about risky behaviors such as unintentional intentional injuries, smoking habits, alcohol and d rug use, sexual behaviors, nutritional habits, and physical activities was used as the instrument of t he study. Attending student’s club and passing medical examination, each student completed the self- reported questionnaire . Results: The mean age of participants was 23/2 ± 5/1, the ma jority of them were single (90.5%), 80.6% were unemployed, and 60.2% were from other cities. The prevalence of smoking cigarette (P 0.05). Conclusion: Some health risk behaviors in boys were more than girls, and there is a possibility of increasing these high-risk behaviors in the univ ersity environment. Thus, keeping students under surveillance and adopting preventive actions play a crucial role, and comprehensive training plans to promote health behavior should be designed and implemented. [Rahmati-Najarkolaei F, *Kamalikhah T, Goldoust-Marandy F, Jafari M. The Comparative Health-Risk Behaviors between Boys and Girls of Freshmen at University of Tehran, Iran . IJHS 2014; 2(3): 15-23] http://jhs.mazums. ac.ir
Linking farmers to community stores to increase consumption of local produce: a case study of the Navajo Nation

Abstract Objective To understand the barriers to farmer participation in Farm-to-Table (F2T) programmes and to identify possible solutions to these obstacles. Design Cross-sectional analysis of farmer perspectives on F2T programmes. Setting Three service units on the Navajo Nation (Chinle, Tuba City and Fort Defiance). Subjects Forty-four Navajo farmers. Results Most participants reported that farming on the Navajo Nation is getting harder (61 %) but that it is very important to maintain Navajo farming traditions (98 %). A modest number of farmers (43 %) expressed interest in participating in an F2T programme. All farmers reported that childhood obesity was a very serious or serious problem in the Navajo Nation. The farmers expressed support for an F2T programme if key barriers to farming, including water access and pest control, could be addressed. Key barriers to participation identified included lack of fruits and vegetables to sell, sale price of crops and lack of certification of produce by the US Food and Drug Administration. Conclusions Navajo farmers are aware of the burden of childhood obesity on the Navajo Nation and feel that an F2T programme could be beneficial. To successfully implement a Farm-to-Table programme, the barriers to participation identified will need to be addressed.
Relationship of Office and Ambulatory Blood Pressure With Left Ventricular Global Longitudinal Strain.

BACKGROUND Left ventricular (LV) global longitudinal strain (GLS) is an early indicator of subclinical cardiac dysfunction, even when LV ejection fraction (LVEF) is normal, and is an independent predictor of cardiovascular events. Ambulatory blood pressure (BP) is a better predictor of cardiovascular events, including heart failure, than office BP. We investigated the association of office and ambulatory BP measurements with subclinical LV systolic dysfunction in a community-based cohort with normal LVEF. METHODS Two-dimensional speckle-tracking echocardiography and 24-hour ambulatory BP monitoring were performed in 577 participants (mean age 70±9 years; 60% women) with LVEF ≥50% from the Cardiovascular Abnormalities and Brain Lesions (CABL) study. Univariable and multivariable linear regression analyses were used to assess the associations of BP measures with GLS. RESULTS Higher ambulatory and office BP values were consistently associated with impaired GLS. After adjustment for pertinent covariates (age, sex, race/ethnicity, body mass index, diabetes mellitus, coronary artery disease, LV mass index, and antihypertensive medication), office diastolic BP and ambulatory systolic and diastolic BPs (24-hour, daytime and nighttime) were independently associated with GLS (P = 0.003 for office DBP, P ≤ 0.001 for all ambulatory BPs). When ambulatory and office BP values were included in the same model, all ambulatory BP measures remained significantly associated with GLS (all P < 0.01), whereas office BP values were not. CONCLUSIONS Ambulatory BP values are significantly associated with impaired GLS and the association is stronger than for office BP. Ambulatory BP monitoring might have a role in the risk stratification of hypertensive patients for early LV dysfunction.
A Fiber Optic Interferometric Sensor Platform for Determining Gas Diffusivity in Zeolite Films

Fiber optic interferometer (FOI) sensors have been fabricated by directly growing pure-silica MFI-type zeolite (i.e., silicalite) films on straight-cut endfaces of single-mode communication optical fibers. The FOI sensor has been demonstrated for determining molecular diffusivity in the zeolite by monitoring the temporal response of light interference from the zeolite film during the dynamic process of gas adsorption. The optical thickness of the zeolite film depends on the amount of gas adsorption that causes the light interference to shift upon loading molecules into the zeolitic channels. Thus, the time-dependence of the optical signal reflected from the coated zeolite film can represent the adsorption uptake curve, which allows computation of the diffusivity using models derived from the Fick’s Law equations. In this study, the diffusivity of isobutane in silicalite has been determined by the new FOI sensing method, and the results are in good agreement with literature values obtained by various conventional macroscopic techniques. The FOI sensor platform, because of its robustness and small size, could be useful for studying molecular diffusion in zeolitic materials under conditions that are inaccessible to the existing techniques.
The R Package MAMS for Designing Multi-Arm Multi-Stage Clinical Trials

In the early stages of drug development there is often uncertainty about the most promising among a set of different treatments, different doses of the same treatment, or combinations of treatments. Multi-arm multi-stage (MAMS) clinical studies provide an efficient solution to determine which intervention is most promising. In this paper we discuss the R package MAMS that allows designing such studies within the group-sequential framework. The package implements MAMS studies with normal, binary, ordinal, or timeto-event endpoints in which either the single best treatment or all promising treatments are continued at the interim analyses. Additionally unexpected design modifications can be accounted for via the use of the conditional error approach. We provide illustrative examples of the use of the package based on real trial designs.