Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome

What genomic landmarks render most genes silent while leaving others expressed on the inactive X chromosome in mammalian females? To date, signals determining expression status of genes on the inactive X remain enigmatic despite the availability of complete genomic sequences. Long interspersed repeats (L1s), particularly abundant on the X, are hypothesized to spread the inactivation signal and are enriched in the vicinity of inactive genes. However, both L1s and inactive genes are also more prevalent in ancient evolutionary strata. Did L1s accumulate there because of their role in inactivation or simply because they spent more time on the rarely recombining X? Here we utilize an experimentally derived inactivation profile of the entire human X chromosome to uncover sequences important for its inactivation, and to predict expression status of individual genes. Focusing on Xp22, where both inactive and active genes reside within evolutionarily young strata, we compare neighborhoods of genes with different inactivation states to identify enriched oligomers. Occurrences of such oligomers are then used as features to train a linear discriminant analysis classifier. Remarkably, expression status is correctly predicted for 84% and 91% of active and inactive genes, respectively, on the entire X, suggesting that oligomers enriched in Xp22 capture most of the genomic signal determining inactivation. To our surprise, the majority of oligomers associated with inactivated genes fall within L1 elements, even though L1 frequency in Xp22 is low. Moreover, these oligomers are enriched in parts of L1 sequences that are usually underrepresented in the genome. Thus, our results strongly support the role of L1s in X inactivation, yet indicate that a chromatin microenvironment composed of multiple genomic sequence elements determines expression status of X chromosome genes.
EARQ : Energy Aware Routing Protocol for Real-Time and Reliable Communication in Wireless Industrial Sensor Networks

the majority techniques for wireless sensor networks can be applied to the wireless industrial sensor networks. Though, for industrial applications of wireless industrial sensor networks, new requirements for example real-time, reliable delivery need to be considered. In this paper, we propose EAQR, which is a novel routing protocol for wireless industrial sensor networks. It provides real-time and reliable delivery of a packet, while considering energy awareness. In EAQR, a node estimates the cost of energy, delay and reliability of a path to the sink node; it’s based on only information from neighboring nodes. Next, it calculates the probability of selecting a path and using for the estimates. When packet forwarding is required, in that time it randomly selects the next node. A lower energy cost of path is likely to be selected, why because the probability is inversely proportional to the energy cost to the sink node. To accomplish real-time delivery, it only paths that may deliver to a packet in time are selected. To achieve dependability, it may send a redundant packet via an alternate path, but if it is only source of a packet. Experimental results show that EAQR is suitable for industrial applications, due to its capability for efficient energy, real-time and reliable communications.
Protein quality of feeding-stuffs

1. Twenty-two samples of high-protein feeding-stuffs, sixteen of them fish meals, were used in a collaborative study of the precision and the limits of discrimination of the Streptococcus zymogenes assay procedure, as applied to the estimation of available methionine, tryptophan and isoleucine contents. 2. All the participating laboratories ranked the test samples in much the same sequence with respect to content for all three amino acids. There were apparently systematic differences between laboratories which impaired the precision of some of the estimates, and these were greatly reduced by including a common reference sample in the tests as an auxiliary standard. 3. Values for available methionine content for eleven test samples were highly correlated (r 0.86) and quantitatively similar to those obtained for chick growth assays, but those for available tryptophan content were markedly lower and were probably in error.
Popper : Making Reproducible Systems Performance Evaluation Practical true

—Independent validation of experimental results in the field of parallel and distributed systems research is a challenging task, mainly due to changes and differences in software and hardware in computational environments. Recreating an environment that resembles the original systems research is difficult and time-consuming. In this paper we introduce the Popper Convention, a set of principles for producing scientific publications. Concretely, we make the case for treating an article as an open source software (OSS) project, applying software engineering best-practices to manage its associated artifacts and maintain the reproducibility of its findings. Leveraging existing cloud-computing infrastructure and modern OSS development tools to produce academic articles that are easy to validate. We present our prototype file system, GassyFS, as a use case for illustrating the usefulness of this approach. We show how, by following Popper, re-executing experiments on multiple platforms is more practical, allowing reviewers and students to quickly get to the point of getting results without relying on the author's intervention.
Optimal information for approximating periodic analytic functions

Let S β := {z ∈ C: |Im z| < β} be a strip in the complex plane. For fixed integer r ≥ 0 let H∞ ,β T denote the class of 2π-periodic functions f, which are analytic in S β and satisfy |f (r) (z)| ≤ 1 in S β . Denote by H∞ ,β r,R the subset of functions from H T ∞ ,β that are real-valued on the real axis. Given a function f ∈ H∞,β, we try to recover f(ζ) at a fixed point ζ ∈ R by an algorithm A on the basis of the information If = (a 0 (f), α 1 (f),. , α n-1 (f), b 1 (f),. , b n-1 (f)), where a j (f), b j (f) are the Fourier coefficients of f. We find the intrinsic error of recovery E(H∞ ,β r , I) = inf sup |f(ζ) - A(If)|. A: C 2n-1 →C f∈H∞ ,β r Furthermore the (2n-1)-dimensional optimal information error, optimal sampling error and n-widths of H r,R ∞,β in C, the space of continuous functions on [0,2π], are determined. The optimal sampling error turns out to be strictly greater than the optimal information error. Finally the same problems are investigated for the class Hp,β, consisting of all 2π-periodic functions, which are analytic in S β with p-integrable boundary values. In the case p = 2 sampling fails to yield optimal information as well in odd as in even dimensions.
Stop Complaining! The Social Costs of Making Attributions to Discrimination

Recent research indicates that stigmatized people may avoid claims of discrimination because such attributions are costly in terms of perceived control over outcomes and social self-esteem. The authors hypothesized that minimization of discrimination also occurs in part because negative social costs accompany attributions to discrimination. In Experiment 1, an African American who attributed a failing test grade to discrimination was perceived as a complainer and was less favorably evaluated in general than was an African American who attributed his failure to the quality of his test answers. This overall devaluation occurred regardless of the objective likelihood that discrimination occurred. Experiment 2 replicated these findings and revealed that this devaluation generally occurred only when the target made discrimination attributions, not when he made other external attributions. The social costs of making attributions to discrimination may prevent stigmatized people from confronting the discrimination they face in their daily lives.
Efficient Power Allocation under Global Power Cap and Application-Level Power Budget

In data center, applications which are typically multi-server, high-parallel, long-running like web-related applications are really common. They always compute over large-scale dataset and consume plenty of energy. Up until now, most researches focuses on trading a loss of performance for energy saving. However, managing the power is more important compared with reducing it. In this paper, we add energy consumption to the list of managed resources and help managers to control power profile of applications in data center. Tenants put forward the power budget and corresponding response time target of their own applications before they rent servers. We designed strategies to make every application in data center running under a global power cap and their own power budget. We first propose a Global Feedback Power Allocation Policy to periodically allocate the global power cap among the applications. We also devise a Local Efficient Power Policy to determine application-level power cap and allocate it among servers running the application. Extra budget during each period can be used in the rest of the tenancy to increase the application-level power cap to minimize the response time. We use Shell, WWW, DNS and Mail workloads to evaluate our policy.
IL-17 and the Th17 lineage in systemic lupus erythematosus

Purpose of reviewSystemic lupus erythematosus etiology includes both genetic and environmental factors. Evidence suggests that many genetic loci in humans and mouse models contribute to the occurrence and clinical presentation of lupus. This large array of different genes affects many aspects of immune cell function, including the activation and functional differentiation of B cells, T cells, dendritic cells and other immune cells. In particular, the T-cell components that contribute to systemic lupus erythematosus pathogenesis are incompletely defined. Recent findingsA major paradigm shift in understanding how CD4+ T cells contribute to autoimmunity recently occurred with the discovery of a new T-cell population that produces the cytokine IL-17 (IL-17A), termed ‘Th17’. Although Th17 cells contribute to autoimmune disease in rheumatoid arthritis and Crohn's disease, their role in systemic lupus erythematosus is far less clear. SummaryIn this review, we focus on an emerging role for the cytokine IL-17 and the cells that produce it in contributing to lupus in particular based on recent findings in animal models.
Exploitation of Quasi-Orthogonal Space Time Block Codes in Virtual Antenna Arrays: Part II Monte Carlo-Based throughput Evaluation

A full rate and full diversity closed-loop quasi-orthogonal space time block coding scheme due to Toker, Lambotharan and Chambers is proposed for application in virtual antenna arrays. The performance gain is achieved through closed-loop operation involving feedback of phase rotation angle(s) calculated from channel state information (CSI) to the transmitter array. Throughput performance of the proposed scheme, with and without power optimisation, is investigated through Monte Carlo simulation with QPSK constellation signals. The results confirm the improvement in throughput performance over orthogonal space time block codes.
V-fold cross-validation improved: V-fold penalization

We study the efficiency of V-fold cross-validation (VFCV) for model selection from the non-asymptotic viewpoint, and suggest an improvement on it, which we call ``V-fold penalization''. Considering a particular (though simple) regression problem, we prove that VFCV with a bounded V is suboptimal for model selection, because it ``overpenalizes'' all the more that V is large. Hence, asymptotic optimality requires V to go to infinity. However, when the signal-to-noise ratio is low, it appears that overpenalizing is necessary, so that the optimal V is not always the larger one, despite of the variability issue. This is confirmed by some simulated data. In order to improve on the prediction performance of VFCV, we define a new model selection procedure, called ``V-fold penalization'' (penVF). It is a V-fold subsampling version of Efron's bootstrap penalties, so that it has the same computational cost as VFCV, while being more flexible. In a heteroscedastic regression framework, assuming the models to have a particular structure, we prove that penVF satisfies a non-asymptotic oracle inequality with a leading constant that tends to 1 when the sample size goes to infinity. In particular, this implies adaptivity to the smoothness of the regression function, even with a highly heteroscedastic noise. Moreover, it is easy to overpenalize with penVF, independently from the V parameter. A simulation study shows that this results in a significant improvement on VFCV in non-asymptotic situations.
Antiplatelet Drugs

INTRODUCTION In the evolutionary sense, clotting is good for you. A complex system has developed, involving the coagulation cascade, platelets and fibrinolysis, all interacting and controlled by local and systemic factors. This benefits the organism by making sure that minor, and sometimes not so minor, injuries do not result in uncontrolled haemorrhage. Humans have come a long way since this mechanism developed. With increased affluence has come a change in diet and lifestyle, and modern medicine has ensured that we live longer. With these changes, there has been an increase in atherosclerosis and the accompanying diseases: cardiac, cerebrovascular and peripheral vascular. Platelet aggregation and embolisation is central to these and may result in myocardial infarction, TIA or CVA. Antiplatelet agents act to decrease this aggregation. Platelets have multiple receptors and enzyme systems which may be manipulated by drugs, which are being produced to inhibit the process at a number of sites of action including thromboxane synthesis, the ADP receptor and by acting directly on the GP IIb/IIIa receptor. This receptor is central to aggregation allowing cross linking of fibrinogen, thus binding platelets together into aggregates. Drug actions at the multiple sites are complementary, and patients may be treated with several medications.
Hsc70-induced Changes in Clathrin-Auxilin Cage Structure Suggest a Role for Clathrin Light Chains in Cage Disassembly

The molecular chaperone, Hsc70, together with its co‐factor, auxilin, facilitates the ATP‐dependent removal of clathrin during clathrin‐mediated endocytosis in cells. We have used cryo‐electron microscopy to determine the 3D structure of a complex of clathrin, auxilin401‐910 and Hsc70 at pH 6 in the presence of ATP, frozen within 20 seconds of adding Hsc70 in order to visualize events that follow the binding of Hsc70 to clathrin and auxilin before clathrin disassembly. In this map, we observe density beneath the vertex of the cage that we attribute to bound Hsc70. This density emerges asymmetrically from the clathrin vertex, suggesting preferential binding by Hsc70 for one of the three possible sites at the vertex. Statistical comparison with a map of whole auxilin and clathrin previously published by us reveals the location of statistically significant differences which implicate involvement of clathrin light chains in structural rearrangements which occur after Hsc70 is recruited. Clathrin disassembly assays using light scattering suggest that loss of clathrin light chains reduces the efficiency with which auxilin facilitates this reaction. These data support a regulatory role for clathrin light chains in clathrin disassembly in addition to their established role in regulating clathrin assembly.
TransCom model simulations of methane: Comparison of vertical profiles with aircraft measurements

To assess horizontal and vertical transports of methane (CH4) concentrations at different heights within the troposphere, we analyzed simulations by 12 chemistry transport models (CTMs) that participated in the TransCom‐CH4 intercomparison experiment. Model results are compared with aircraft measurements at 13 sites in Amazon/Brazil, Mongolia, Pacific Ocean, Siberia/Russia, and United States during the period of 2001–2007. The simulations generally show good agreement with observations for seasonal cycles and vertical gradients. The correlation coefficients of the daily averaged model and observed CH4 time series for the analyzed years are generally larger than 0.5, and the observed seasonal cycle amplitudes are simulated well at most sites, considering the between‐model variances. However, larger deviations show up below 2 km for the model‐observation differences in vertical profiles at some locations, e.g., at Santarem, Brazil, and in the upper troposphere, e.g., at Surgut, Russia. Vertical gradients and concentrations are underestimated at Southern Great Planes, United States, and Santarem and overestimated at Surgut. Systematic overestimation and underestimation of vertical gradients are mainly attributed to inaccurate emission and only partly to the transport uncertainties. However, large differences in model simulations are found over the regions/seasons of strong convection, which is poorly represented in the models. Overall, the zonal and latitudinal variations in CH4 are controlled by surface emissions below 2.5 km and transport patterns in the middle and upper troposphere. We show that the models with larger vertical gradients, coupled with slower horizontal transport, exhibit greater CH4 interhemispheric gradients in the lower troposphere. These findings have significant implications for the future development of more accurate CTMs with the possibility of reducing biases in estimated surface fluxes by inverse modeling.
A bioinspired 2-DOF throwing robot

A bio-inspired throwing robot with two degrees of freedom (DOF) was developed for a science center. It has a rotary axis to turn the robot like a human his body and a second rotary axis to throw objects like a human with his arm. With this kinematic, the robot is capable to throw objects into predefined positions within a given 3D-space. The goal of this robot is to demonstrate visitors in the science center robotic throwing with a simple kinematic. In experiments the visitors can learn how the angle of throwing and the speed of throwing determines the trajectories of thrown objects. Student-classes who want to spend more time for the robot can also calculate such trajectories. Therefore, the required mathematical models for this robot are also presented in this paper.
Harvesting Creative Templates for Generating Stylistically Varied Restaurant Reviews

Many of the creative and figurative elements that make language exciting are lost in translation in current natural language generation engines. In this paper, we explore a method to harvest templates from positive and negative reviews in the restaurant domain, with the goal of vastly expanding the types of stylistic variation available to the natural language generator. We learn hyperbolic adjective patterns that are representative of the strongly-valenced expressive language commonly used in either positive or negative reviews. We then identify and delexicalize entities, and use heuristics to extract generation templates from review sentences. We evaluate the learned templates against more traditional review templates, using subjective measures of convincingness, interestingness, and naturalness. Our results show that the learned templates score highly on these measures. Finally, we analyze the linguistic categories that characterize the learned positive and negative templates. We plan to use the learned templates to improve the conversational style of dialogue systems in the restaurant domain.
Using activity theory as a lens to analyse interaction in a university–school initial teacher education and training partnership

Abstract The development of beginning teachers' practice during a school placement is a multiplicity of mediated interactions between university- and school-based systems. Both systems have the common aim of training effective teachers. However, day-to-day internal institution matters can cause tension between the learning goals set out for the beginning teacher by the university and the schools' drive to ensure maximum student performance in ‘high stake’ national tests. This article reports on an intervention intended to equip beginning teachers with the capacity to learn, through purposive activity, in an authentic classroom environment. The context of the learning was to address the conceptual difficulties that secondary school pupils (aged 11-16) have in understanding scientific concepts within the constraints of a ‘curriculum delivery’ lead culture. The results show that beginning teachers are able to extract principles, which might assist them in new contexts in the future. The interactions which took place during the intervention within a school University Initial Teacher Education and Training partnership were analysed using activity systems.
Measuring Infants' Home Environment: The IT-HOME for Infants Between Birth and 12 Months in Four National Data Sets

Objective. This article examines new conceptually derived subscales for the Infant-Toddler Home Observation for Measurement of the Environment (IT-HOME) Inventory. Design. Data from 4 diverse national longitudinal data sets were used to assess several newly created subscales: the Infant Health and Development Program (N = 872), the National Institute of Child Health and Human Development Study of Early Child Care (N = 1,279), the National Longitudinal Survey of Youth (N = 2,374), and the Project on Human Development in Chicago Neighborhoods (N = 258). Validity and reliability of the newly created subscales were assessed. Results. In total, 7 new subscales emerged. Analyses demonstrate overall consistency in validity and reliability of these subscales. Conclusions. Although both observational and self-report items were included in analyses, observational items were in the majority. Researchers are encouraged to include observational items in future implementations of the IT-HOME. If designers of large-scale surveys find the cost of training observers to administer the IT-HOME prohibitive, they should consider selecting subscales rather than the entire Inventory.
Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review

Chorea-acanthocytosis (ChAc) is a rare autosomal recessive inherited syndrome characterized by hyperkinetic movements, seizures, cognitive impairment, neuropsychiatric symptoms, elevated serum biochemical indicators and acanthocytes detection in peripheral blood smear. Vacuolar protein sorting 13A (VPS13A) gene mutations have been proven to be genetically responsible for the pathogenesis of ChAc. Herein, based on the typical clinical symptoms and neuroimaging features, we present two suspected ChAc cases which are further genetically confirmed by four novel VPS13A gene mutations. Nevertheless, the sharp contrast between the population base and published ChAc reports implies that ChAc is considerably underdiagnosed in China. Therefore, we conclude several suggestive features and propose a diagnostic path of ChAc from a clinical, genetic and neuroimaging perspective, aiming to facilitate the diagnosis and management of ChAc in China.