Miracle-dz/UniFAR-FTUs huggingface dataset:
Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs

The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years. Author summary From specific examples, it has been assumed by comparative biologists that the same gene in different species has the same function, whereas duplication of a gene inside one species to create several copies allows them to acquire different functions. Yet this model was little tested until recently, and then has proven harder than expected to confirm. One of the problems is defining “function” in a way which can be easily studied. We introduce a new way of considering function: how specific is the activity (“expression”) of a gene? Genes which are specific to certain tissues have functions related to these tissues, whereas genes which are broadly active over many or all tissues have more general functions for the organism. We find that this “tissue-specificity” evolves very slowly in the absence of duplication, while immediately after duplication the new gene copy differs. This shows that indeed duplication leads to a strong increase in the evolution of new functions.
Effects of Varying Processing Conditions on Carbon Foam Properties

Purified coal-tar was chosen as the raw material for foaming precursor. Distillation methods that refining light constituent was applied as preliminary treatment of pitch. Carbon foam was prepared by the self-foaming of the resultant pitch. The effects of distilling temperature as well as time on the micro structure, bulk density, porosity, compressive strength, and thermal conductivity of carbon foam were investigated in this paper. The compressive strength of produced carbon foam can reach 6.287 MPa and thermal conductivity can lower than 0.048 W·m -1 ·K -1 .
Endogenous viral genes: association with reduced egg production rate and egg size in White Leghorns.

Endogenous viral (ev) genes are DNA sequences residing permanently in the genome of most chickens that have a high degree of homology to avian leukosis viruses (ALV). Association of ev genes with production trait differences was studied in White Leghorns free of exogenous ALV. The Cornell Strain K and S chickens used in Experiment 1 had multiple ev genes. In each of four lines of chickens in Experiment 2, there was a 1:1 segregation of full-sibs free of ev genes and those carrying one ev gene: ev-12 that produces the complete endogenous virus, ev-3 or ev-6 that express certain viral antigens, or ev-1, a silent gene. In Experiment 1, the presence of genes ev-10 or ev-19, known to produce the complete virus, was associated with a 9% reduction in the annual egg production rate (P less than .05) in Strain S. Similarly, the presence of the virus-producing ev-12 in Experiment 2 was associated with an 8% reduction of annual egg production rate (P less than .05), a 2.2-g reduction in egg weight (P less than .01), and a . 003 reduction in egg specific gravity (P less than .01). No significant effects of ev genes on age at first egg, Haugh unit score, percentage of eggs with blood spots, and body weight of hens were observed. It was concluded that ev genes producing complete endogenous virus are associated with production trait differences similar to those associated with subclinical infections with exogenous ALV.
Developing mindfulness with children and young people: a review of the evidence and policy context

Purpose – This paper aims to explore the growing field of the teaching of mindfulness to young people, looking at its social and policy context, its applications, and other areas of work that it might support and within which it might fit. It focuses particularly on the state of the current evidence for such teaching and the conclusions that can be drawn from it.Design/methodology/approach – The paper is a literature review, drawing mainly on the 20 or so significant and good quality studies (i.e. those with significant numbers of participants, published in peer‐reviewed journals) that make up the evidence base for mindfulness and the young, along with some comments on the policy context into which mindfulness can and might fit.Findings – Work on mindfulness with young people is popular with both staff and students, has a developing presence and can be effective in promoting a very wide range of outcomes. When well taught and when practised regularly, it has been shown to be capable of improving mental he.
The Runner-Up Effect

Exploiting regression discontinuity designs in Brazilian, Indian, and Canadian first-past-the-post elections, we document that second-place candidates are substantially more likely than close third-place candidates to run in, and win, subsequent elections. Since both candidates lost the election and had similar electoral performance, this is the effect of being labeled the runner-up. Selection into candidacy is unlikely to explain the effect on winning subsequent elections, and we find no effect of finishing in third place versus fourth place. We develop a simple model of strategic coordination by voters that rationalizes the results and provides further predictions that are supported by the data.
Nonlinear control of various underactuated systems: Theoretical design and industrial applications

Compared with fully actuated systems, underactuated systems present such advantages as simpler structure, broader applications, and so on. Yet, the control of this kind of system proves to be a very challenging problem since the number of control inputs is less than that of the degrees of freedom, which thus attracts much attention from the control community during the past two decades. This paper mainly introduces the recent results on the modeling, trajectory planning, and nonlinear control of various underactuated systems, firstly for overhead cranes, later on extended to other systems such as offshore boom cranes, quadrotor transportation systems, and so on. In the latter part of the review, it is reported that some of the recently designed control strategies have been successfully applied to a 32 tons industrial overhead crane to achieve fully-automatic operation.
On neutrino Oscillations and Predicting the 125 GEV Two Photon Emission State from p-p Collisions Based on the 5D Homogeneous Space-Time Projection Model

Previously the 5D homogeneous space-time metric was introduced with explicitly given projection operators in matrix form which map the 5D space-time manifold into a Lorentzian space-time. Based on this projection model, vector field and spinor solutions are found to be expressible in terms of SU(2)xL and SU(3)xL, where L is the 4D Lorentz space-time group. The spinor solutions give the SU(2) leptonic states arising from space-time projection, whereas the SU(3) representation arises from conformal projection and gives the quarks, and due to gauge requirement leads to mesons and baryons. This process of mapping the 5D space-time manifold into the 4D space-time is at the basis of an analysis of the recent CERN experimental results, the presence of neutrino oscillations and the observed 125 GeV resonance in the p-p collisions, respectively. In fact, it is found that the spinor solution contains an oscillating phase, and the 125 GeV resonance is shown to be predictable, thereby 1) eliminating the need to introduce a Higgs vacuum, and 2) can be shown possibly to be an indicator for a missing heavy baryon octet.
OlO A PARALLEL GRAPH COLORING HEURISTIC *

The problem of computing good graph colorings arises in many diverse applications, such as in the estimation of sparse Jacobians and in the development of efficient, parallel iterative methods for solving sparse linear systems. This paper presents an asynchronous graph coloring heuristic well suited to distributed memory parallel computers. Experimental results obtained on an Intel iPSC/860 are presented, which demonstrate that, for graphs arising from finite element applications, the heuristic exhibits scalable performance and generates colorings usually within three or four colors of the best-known linear time sequential heuristics. For bounded degree graphs, it is shown that the expected running time of the heuristic under the P-RAM computation model is bounded by EO(log(n)/log log(n)). This bound is an improvement over the previously known best upper bound for the expected running time of a random heuristic for the graph coloring problem. Key words, distributed memory computers, graph coloring heuristics, parallel algorithms, random algorithms, sparse matrices AMS(MOS) subject classifications. 65F10, 65F50, 65Y05, 68Q22,68R10
Homomorphic encryption and secure comparison

We propose a protocol for secure comparison of integers based on homomorphic encryption. We also propose a homomorphic encryption scheme that can be used in our protocol, makes it more efficient than previous solutions, and can also be used as the basis of efficient and general secure Multiparty Computation (MPC). We show how our comparison protocol can be used to improve security of online auctions, and demonstrate that it is efficient enough to be used in practice. For comparison of 16 bits numbers with security based on 1024 bits RSA (executed by two parties), our implementation takes 0.28 sec including all computation and communication. Using precomputation, one can save a factor of roughly 10.
The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti

Sinorhizobium meliloti is a soil bacterium that invades the root nodules it induces on Medicago sativa, whereupon it undergoes an alteration of its cell cycle and differentiates into nitrogen‐fixing, elongated and polyploid bacteroid with higher membrane permeability. In Caulobacter crescentus, a related alphaproteobacterium, the principal cell cycle regulator, CtrA, is inhibited by the phosphorylated response regulator DivK. The phosphorylation of DivK depends on the histidine kinase DivJ, while PleC is the principal phosphatase for DivK. Despite the importance of the DivJ in C. crescentus, the mechanistic role of this kinase has never been elucidated in other Alphaproteobacteria. We show here that the histidine kinases DivJ together with CbrA and PleC participate in a complex phosphorylation system of the essential response regulator DivK in S. meliloti. In particular, DivJ and CbrA are involved in DivK phosphorylation and in turn CtrA inactivation, thereby controlling correct cell cycle progression and the integrity of the cell envelope. In contrast, the essential PleC presumably acts as a phosphatase of DivK. Interestingly, we found that a DivJ mutant is able to elicit nodules and enter plant cells, but fails to establish an effective symbiosis suggesting that proper envelope and/or low CtrA levels are required for symbiosis.
Effect of Ibuprofen on Skeletal Muscle of Dysferlin-Null Mice

Ibuprofen, a nonsteroidal anti-inflammatory drug, and nitric oxide (NO) donors have been reported to reduce the severity of muscular dystrophies in mice associated with the absence of dystrophin or α-sarcoglycan, but their effects on mice that are dystrophic due to the absence of dysferlin have not been examined. We have tested ibuprofen, as well as isosorbide dinitrate (ISDN), a NO donor, to learn whether used alone or together they protect dysferlin-null muscle in A/J mice from large strain injury (LSI) induced by a series of high strain lengthening contractions. Mice were maintained on chow containing ibuprofen and ISDN for 4 weeks. They were then subjected to LSI and maintained on the drugs for 3 additional days. We measured loss of torque immediately following injury and at day 3 postinjury, fiber necrosis, and macrophage infiltration at day 3 postinjury, and serum levels of the drugs at the time of euthanasia. Loss of torque immediately after injury was not altered by the drugs. However, the torque on day 3 postinjury significantly decreased as a function of ibuprofen concentration in the serum (range, 0.67–8.2 µg/ml), independent of ISDN. The effects of ISDN on torque loss at day 3 postinjury were not significant. In long-term studies of dysferlinopathic BlAJ mice, lower doses of ibuprofen had no effects on muscle morphology, but reduced treadmill running by 40%. Our results indicate that ibuprofen can have deleterious effects on dysferlin-null muscle and suggest that its use at pharmacological doses should be avoided by individuals with dysferlinopathies.
Symbol choice and memory of visual models

Most business process modeling languages are visual languages. Yet, very little attention has been devoted to the choice of symbols used. This article contributes to the visual languages literature by providing an enriched understanding about how symbol choice affects the ease of memorizing and recalling visual diagrams. Specifically, the experiment reported here was designed to compare the effect of three different symbol sets of visual languages from the business process modeling domain on diagram recall. Quantitative analysis based on data collected from 37 business school students, revealed that symbol choice significantly influences memory of visual aspects of the diagrams as layout. However, the study did not find a significant effect of symbol choice on recognition accuracy of the semantic content of the diagrams. Overall, the findings underscore the relevance of symbol choice for visual language design.
Communication-Avoiding Optimization Methods for Distributed Massive-Scale Sparse Inverse Covariance Estimation

Author(s): Koanantakool, P; Ali, A; Azad, A; Buluc, A; Morozov, D; Oliker, L; Yelick, K; Oh, SY | Abstract: Copyright 2018 by the author(s). Across a variety of scientific disciplines, sparse inverse covariance estimation is a popular tool for capturing the underlying dependency relationships in multivariate data. Unfortunately, most estimators are not scalable enough to handle the sizes of modern high-dimensional data sets (often on the order of terabytes), and assume Gaussian samples. To address these deficiencies, we introduce HP-CONCORD, a highly scalable optimization method for estimating a sparse inverse covariance matrix based on a regularized pseudolikelihood framework, without assuming Gaussianity. Our parallel proximal gradient method uses a novel communication-avoiding linear algebra algorithm and runs across a multi-node cluster with up to 1k nodes (24k cores), achieving parallel scalability on problems with up to ≈819 billion parameters (1.28 million dimensions); even on a single node, HP-CONCORD demonstrates scalability, outperforming a state-of-the-art method. We also use HP-CONCORD to estimate the underlying dependency structure of the brain from fMRI data, and use the result to identify functional regions automatically. The results show good agreement with a clustering from the neuroscience literature.
Loop flattening & spherical sampling: Highly efficient model reduction techniques for SRAM yield analysis

The impact of process variation in deep-submicron technologies is especially pronounced for SRAM architectures which must meet demands for higher density and higher performance at increased levels of integration. Due to the complex structure of SRAM, estimating the effect of process variation accurately has become very challenging. In this paper, we address this challenge in the context of estimating SRAM timing variation. Specifically, we introduce a method called loop flattening that demonstrates how the evaluation of the timing statistics in the complex, highly structured circuit can be reduced to that of a single chain of component circuits. To then very quickly evaluate the timing delay of a single chain, we employ a statistical method based on importance sampling augmented with targeted, high-dimensional, spherical sampling. Overall, our methodology provides an accurate estimation with 650X or greater speed-up over the nominal Monte Carlo approach.
Predictors of Loss to Follow-up Among HIV-infected Patients in a Rural South-Eastern Nigeria Hospital: A 5-year Retrospective Cohort Study

Background: Patient attrition has been a challenge in managing HIV programs in resource-limited settings. Aim: This study reviews the predictors of loss to follow-up (LTFU) in our hospital and suggests the best practices for dealing with the issue. Subjects and Methods: A 5-year retrospective cohort study of 1256 HIV-infected patients. Baseline CD4 counts, age, gender, year of enrolment, and antiretroviral therapy combination regimen were considered in this study. Kaplan–Meier models were used to estimate the univariate time-to-LTFU and Cox proportional hazards models to identify the multivariate predictors of LTFU. Results: Twenty-four percent (23.9% [301/1256]) of patients were lost to follow-up. Baseline CD4 count, year of enrolment, and drug combination were significant predictors of LTFU. Patients enrolled earlier (2008/2009) were twice as likely to be LTFU compared with those enrolled later (2010–2013). Gender and age did not significantly predict LTFU nor confound other predictors. Conclusion: The program showed higher LTFU rates than most studies in Nigeria and Africa, maybe due to difficulties with the access to the hospital and possible treatment fatigue. This study recommends the provision of transportation subsidies and proactive patient follow-up with “peer-tracking” to reduce LTFU among HIV infected patients, especially in resource-limited settings.
Study on the stress-strain relationship of FRP-confined concrete rectangular columns

Based on a large number of test data, the performance of fiber reinforced polymer/plastic(FRP)-confined concrete rectangular columns had been analyzed. It was pointed that the stress-strain responses of FRP-confined concrete rectangular columns will have strain-hardening components or strain-softening components. The stress and strain of transition point of FRP-confined concrete rectangular columns were mainly related to the ratio of FRP confinement modulus to the modulus of concrete, and equations are suggested to predict them. The ultimate stress and strain of FRP-confined concrete rectangular columns were mainly related to the confinement of FRP, the type of FRP, comer radius of cross section, concrete strength and other parameters. They can be predicted by reducing the corresponding ultimate strength and strain of equivalent concrete circular columns confined with equivalent FRP, and the equations for the reducing factors are proposed. Three simple stress-strain models for FRP-eonfined concrete rectangular columns are suggested and they match favorably with experimental results from past studies by other researchers each under specified conditions.
Distributed Dimensionality Reduction Fusion Estimation with Communication Delays in Cyber-Physical Systems

This paper studies the distributed dimensionality reduction fusion estimation problem with communication delays for a class of cyber-physical systems (CPSs). The raw measurements are preprocessed in each sink node to obtain the local optimal estimate (LOE) of a CPS, and the compressed LOE under dimensionality reduction encounters with communication delays during the transmission. Under this case, a mathematical model with compensation strategy is proposed to characterize the dimensionality reduction and communication delays. This model also has the property to reduce the information loss caused by the dimensionality reduction and delays. Based on this model, a recursive distributed Kalman fusion estimator (DKFE) is derived by optimal weighted fusion criterion in the linear minimum variance sense. A stability condition for the DKFE, which can be easily verified by the exiting software, is derived. In addition, this condition can guarantee that estimation error covariance matrix of the DKFE converges to the unique steady-state matrix for any initial values, and thus the steady-state DKFE (SDKFE) is given. Notice that the computational complexity of the SDKFE is much lower than that of the DKFE. Moreover, a probability selection criterion for determining the dimensionality reduction strategy is also presented to guarantee the stability of the DKFE. Two illustrative examples are given to show the advantage and effectiveness of the proposed methods.
The Value of Traditional Ecological Knowledge for the Environmental Health Sciences and Biomedical Research

Background: Traditional Ecological Knowledge (TEK) is a term, relatively new to Western science, that encompasses a subset of traditional knowledge maintained by Indigenous nations about the relationships between people and the natural environment. The term was first shared by tribal elders in the 1980s to help raise awareness of the importance of TEK. TEK has become a construct that Western scientists have increasingly considered for conducting culturally relevant research with Tribal nations. Objectives: The authors aim to position TEK in relation to other emerging schools of thought, that is, concepts such as the exposome, social determinants of health (SDoH), and citizen science, and to explore TEK’s relevance to environmental health research. This article provides examples of successful application of TEK principles in federally funded research when implemented with respect for the underlying cultural context and in partnership with Indigenous communities. Discussion: Rather than treating TEK as an adjunct or element to be quantified or incorporated into Western scientific studies, TEK can instead ground our understanding of the environmental, social, and biomedical determinants of health and improve our understanding of health and disease. This article provides historical and recent examples of how TEK has informed Western scientific research. Conclusions: This article provides recommendations for researchers and federal funders to ensure respect for the contributions of TEK to research and to ensure equity and self-determination for Tribal nations who participate in research. https://doi.org/10.1289/EHP858