Miracle-dz/UniFAR-FTUs huggingface dataset:
Topology-based sparsification of graph annotations

Abstract Motivation Since the amount of published biological sequencing data is growing exponentially, efficient methods for storing and indexing this data are more needed than ever to truly benefit from this invaluable resource for biomedical research. Labeled de Bruijn graphs are a frequently-used approach for representing large sets of sequencing data. While significant progress has been made to succinctly represent the graph itself, efficient methods for storing labels on such graphs are still rapidly evolving. Results In this article, we present RowDiff, a new technique for compacting graph labels by leveraging expected similarities in annotations of vertices adjacent in the graph. RowDiff can be constructed in linear time relative to the number of vertices and labels in the graph, and in space proportional to the graph size. In addition, construction can be efficiently parallelized and distributed, making the technique applicable to graphs with trillions of nodes. RowDiff can be viewed as an intermediary sparsification step of the original annotation matrix and can thus naturally be combined with existing generic schemes for compressed binary matrices. Experiments on 10 000 RNA-seq datasets show that RowDiff combined with multi-BRWT results in a 30% reduction in annotation footprint over Mantis-MST, the previously known most compact annotation representation. Experiments on the sparser Fungi subset of the RefSeq collection show that applying RowDiff sparsification reduces the size of individual annotation columns stored as compressed bit vectors by an average factor of 42. When combining RowDiff with a multi-BRWT representation, the resulting annotation is 26 times smaller than Mantis-MST. Availability and implementation RowDiff is implemented in C++ within the MetaGraph framework. The source code and the data used in the experiments are publicly available at https://github.com/ratschlab/row_diff.
Melt processing of polyamide 12 and cellulose nanocrystals nanocomposites

The fabrication of nanocomposites of polyamide 12 (PA12) and cellulose nanocrystals (CNCs) isolated from cotton and tunicates is reported. Through a comparative study that involved solution-cast (SC) and melt-processed materials, it was shown that PA12/CNC nanocomposites can be prepared in a process that appears to be readily scalable to an industrial level. The results demonstrate that CNCs isolated from the biomass by phosphoric acid hydrolysis display both a sufficiently high thermal stability to permit melt processing with PA12, and a high compatibility with this polymer to allow the formation of nanocomposites in which the CNCs are well dispersed. Thus, PA12/CNC nanocomposites prepared by melt-mixing the two components in a co-rotating roller blade mixer and subsequent compression molding display mechanical properties that are comparable to those of SC reference materials. Young's modulus and maximum stress could be doubled in comparison to the neat PA12 by introduction of 10% (CNCs from tunicates) or 15% w/w (CNCs from cotton) CNCs. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42752.
Prevalence of Abortion, Calf Mortality and Proportion of Cattle Population in Commercial Dairy Farms of Bangladesh

| Abortion and calf mortality are representing significant economic loss in commercial dairy farms all over the world. The present study aimed to investigate the abortion rate, calf mortality and proportion of different types of cattle in commercial dairy farms of Bangladesh. A preset questionnaire was developed to collect information through active surveillance. This study was conducted in seven divisions a total of 73 registered dairy farms having 3260 cattle were considered as the source of population for epidemiological survey during 2014. The collected data revealed that the sex ratio was (752) 23.06% males and (2508) 76.94% female. Among of the total female cattle (2508), the milking cow, pregnant and heifers and female calf were 47.89%, 37.24%, 17.58% and 21.45% respectively. The results showed that a total of 98 abortion cases were observed in 1201 milch cows. The prevalence of abortion was 8.16%. The number of death calves was 126 among 1026 born calf. The calf mortality rate was revealed 12.28%. Finally the result found that total calf crop loss appears to be (8.16%+12.28%) 20.44%, which is very alarming in the growth of dairy industry. However, the study concluded that abortion and calf mortality are widely prevalent and distributed among commercial dairy farms in Bangladesh. Further studies need to be carried out by using this demographic data to prove the causes and implementation of preventive measures among the dairy farms to prevent abortion and calf mortality in Bangladesh.
Effects of Processing on the Quality of Preserved Quartered Artichokes Hearts

Different methods of processing preserved quartered artichoke hearts were studied. All methods involved blanching of the product and removal of bracts; however, the order of these 2 unitary operations was changed. The main objective was to compare the effects of the different manufacturing methods on the physico-chemical and sensory characteristics of the artichoke hearts. The traditional method (1st blanching of the fresh artichokes and then removal of bracts) provided quartered artichoke hearts with the best chemical and sensorial properties during storage at room temperature (20 °C ± 2 °C): slight acid taste, high artichoke flavor, white-yellowish color, and no presence of brown spots.
Single-and two-phase diversion cross-flows between triangle tight lattice rod bundle subchannels - Data on flow resistance and interfacial friction coefficients for the cross-flow

Single- and two-phase diversion cross-flows arising from the pressure difference between tight lattice subchannels are our concern in this study. In order to obtain a correlation of the diversion cross-flow, we conducted adiabatic experiments using a vertical multiple-channel with two subchannels simplifying the triangle tight lattice rod bundle for air-water flows at room temperature and atmospheric pressure. In the experiments, data were obtained on the axial variations in the pressure difference between the subchannels, the ratio of flow rate in one subchannel to the whole channel, the void fraction in each subchannel for slug-churn and annular flows in two-phase flow case. These data were analyzed by use of a lateral momentum equation based on a two-fluid model to determine both the cross-flow resistance coefficient between liquid phase and channel wall and the gas-liquid interfacial friction coefficient. The resulting coefficients have been correlated in a way similar to that developed for square lattice subchannel case by Kano et al. (2002); the cross-flow resistance coefficient data can be well correlated with a ratio of the lateral velocity due to the cross-flow to the axial one irrespective of single- and two-phase flows; the interfacial friction coefficient data were well correlated with a Reynolds number, which is based on the relative velocity between gas and liquid cross-flows as the characteristic velocity.Copyright © 2006 by ASME
12-Week of New Core Strength Exercise Enhanced Balance in Female Adolescents

Adolescence is a dynamically evolving theoretical construct informed through physiologic, psychosocial, temporal and cultural lenses. This critical developmental period is conventionally understood as the years between the onset of puberty and the establishment of social independence. The characteristic skeletal growth spurt generally occurs in females between the ages of 10-12 and 12-14 in males; terminating in adult stature between the ages of 17-19 in females and by the age of 20 in males. Developmental growth includes significant increases in height, weight, and internal organ size as well as changes in skeletal and muscular systems. Since bones are growing faster than muscles, young adolescents may experience coordination and balance issues. Actual growing pains result when muscles and tendons do not adequately protect bones. From the literature search, no well-designed and controlled studies have previously examined the effect of core strength exercise on the balance of female adolescents. Move over, the 360° TitaniUM Core Strength Exercise® is the new invented core strength exercise. Therefore, the main aim of this study was to examine a 12-week of intervention with the 360° TitaniUM Core Strength Exercise® on the balance of female adolescents between pre and post intervention. 20 females age 14 to 16 years old were recruited for this study.Results revealed that 12 weeks 360° TitaniUM Core Strength Exercise® enhanced significant improvements of balance in female adolescents between pretest and post-test [t (19) –5.753, p < . 001]. From the current results, we can assume that the 360° TitaniUM Core Strength Exercise® is appropriate and essential training method to improve the balance in female adolescents.
A statistical model of thermodynamic mixing properties of Ca-Mg-Fe2+ garnets

Abstract At present the most widely used models of thermodynamic mixing properties of garnet are those that are optimized to fit the experimental phase-equilibrium data along various binary garnet joins using the method of mathematical programming. We conducted a thorough weighted regression analysis of the available volumetric, calorimetric, and phase- equilibrium data. This resulted in a much improved set of a-X relationships with the following Margules parameters (in joules, kelvins, bars). WGFeMg = -24166 + 22.09T - 0.034P, WGMgFe = 22265 - 12.40T + 0.050P, WGFeCa= 17526 - 14.51T + 0.135P, WGCaFe= -18113 + 15.51T + 0.040P, WGMgCa= 14306 - 2.49T + 0.140P, WGCaMg= 65182 - 20.82T+ 0.068P (all pfu containing 12 O atoms). The robust regression analyses allowed us to obtain the uncertainties associated with each of the parameters, quantities not available by mathematical programming analysis of phase-equilibrium data. Uncertainty estimates are essential for rigorous quantification of errors associated with mineralogic thermobarometers. From the probabilistic model developed here, we present detailed formulations for ascertaining errors of activity coefficients of the end-member components in any garnet solid solution. This provides an opportunity to evaluate the uncertainties in mineralogic thermobarometers involving garnets of compositions dissimilar to those used in the experiments on which the garnet mixing models are based. The results of this study elicit several significant points. The analysis strongly suggests that there is an excess entropy of mixing along the Fe-Mg join because Fe-Mg mixing in garnet is substantially nonideal. The excess entropy of mixing along the Ca-Mg and Ca-Fe joins is asymmetric and therefore assumption of a large symmetric entropy parameter or no entropy along these joins is an oversimplification. Large uncertainty in the mixing properties exists for Ca-rich garnets. There should be a Ca-Mg-Fe ternary interaction parameter (7110 J/mol).
Pseudogap Isotope Effect as a Probe of Bipolaron Mechanism in High Temperature Superconductors

A theory of a pseudogap phase of high-temperature superconductors where current carriers are translation invariant bipolarons is developed. A temperature T* of a transition from a pseudogap phase to a normal one is calculated. For the temperature of a transition to the pseudogap phase, the isotope coefficient is found. It is shown that the results obtained, in particular, the possibility of negative values of the isotope coefficient, are consistent with the experiment. New experiments on the influence of the magnetic field on the isotope coefficient are proposed.
Intuitively Assessing ML Model Reliability through Example-Based Explanations and Editing Model Inputs

Interpretability methods aim to help users build trust in and understand the capabilities of machine learning models. However, existing approaches often rely on abstract, complex visualizations that poorly map to the task at hand or require non-trivial ML expertise to interpret. Here, we present two interface modules that facilitate intuitively assessing model reliability. To help users better characterize and reason about a model’s uncertainty, we visualize raw and aggregate information about a given input’s nearest neighbors. Using an interactive editor, users can manipulate this input in semantically-meaningful ways, determine the effect on the output, and compare against their prior expectations. We evaluate our approach using an electrocardiogram beat classification case study. Compared to a baseline feature importance interface, we find that 14 physicians are better able to align the model’s uncertainty with domain-relevant factors and build intuition about its capabilities and limitations.
Visualization of Deep Reinforcement Autonomous Aerial Mobility Learning Simulations

This demo abstract presents the visualization of deep reinforcement learning (DRL)-based autonomous aerial mobility simulations. In order to implement the software, Unity-RL is used and additional buildings are introduced for urban environment. On top of the implementation, DRL algorithms are used and we confirm it works well in terms of trajectory and 3D visualization.
Quantum Chaos is Quantum

It is well known that a quantum circuit on N qubits composed of Clifford gates with the addition of k non Clifford gates can be simulated on a classical computer by an algorithm scaling as poly(N)exp⁡(k)\cite{bravyi2016improved}. We show that, for a quantum circuit to simulate quantum chaotic behavior, it is both necessary and sufficient that k=Θ(N). This result implies the impossibility of simulating quantum chaos on a classical computer.
Testing the turbulent origin of the stellar initial mass function

Supersonic turbulence in the interstellar medium (ISM) is closely linked to the formation of stars, and hencemany theories connect the stellar initial mass function (IMF) with the turbulent properties of molecular clouds. Here we test three turbulence-based IMFmodels (by Padoan & Nordlund 2002, Hennebelle & Chabrier 2008, and Hopkins 2012), which predict the relation between the high-mass slope (Γ) of the IMF, dN/d logM ∝ MΓ and the exponent n of the velocity power spectrum of turbulence, Ev (k) ∝ k−n, where n ≈ 2 corresponds to typical ISM turbulence. Using hydrodynamic simulations, we drive turbulence with an unusual index of n ≈ 1, measure Γ, and compare the results with n ≈ 2. We find that reducing n from 2 to 1 primarily changes the high-mass region of the IMF (beyond the median mass), where we measure high-mass slopes within the 95 per cent confidence interval of −1.5 < Γ < −1 for n ≈ 1 and −3.7 < Γ < −2.4 for n ≈ 2, respectively. Thus, we find that n = 1 results in a significantly flatter high-mass slope of the IMF, with more massive stars formed than for n ≈ 2. We compare these simulations with the predictions of the three IMF theories. We find that while the Padoan &Nordlund theory matches our simulations with fair accuracy, the other theories either fail to reproduce the main qualitative outcome of the simulations or require some modifications. We conclude that turbulence plays a key role in shaping the IMF, with a shallower turbulence power spectrum producing a shallower high-mass IMF, and hence more massive stars.
Validation and parameter optimization of a hybrid embedded/homogenized solid tumor perfusion model

The goal of this paper is to investigate the validity of a hybrid embedded/homogenized in‐silico approach for modeling perfusion through solid tumors. The rationale behind this novel idea is that only the larger blood vessels have to be explicitly resolved while the smaller scales of the vasculature are homogenized. As opposed to typical discrete or fully resolved 1D–3D models, the required data can be obtained with in‐vivo imaging techniques since the morphology of the smaller vessels is not necessary. By contrast, the larger vessels, whose topology and structure is attainable noninvasively, are resolved and embedded as one‐dimensional inclusions into the three‐dimensional tissue domain which is modeled as a porous medium. A sound mortar‐type formulation is employed to couple the two representations of the vasculature. We validate the hybrid model and optimize its parameters by comparing its results to a corresponding fully resolved model based on several well‐defined metrics. These tests are performed on a complex data set of three different tumor types with heterogeneous vascular architectures. The correspondence of the hybrid model in terms of mean representative elementary volume blood and interstitial fluid pressures is excellent with relative errors of less than 4%. Larger, but less important and explicable errors are present in terms of blood flow in the smaller, homogenized vessels. We finally discuss and demonstrate how the hybrid model can be further improved to apply it for studies on tumor perfusion and the efficacy of drug delivery.
Investigation of the Crystallinity of Freeze/Thaw Poly(vinyl alcohol) Hydrogels by Different Techniques

The crystallinity of freeze/thaw poly(vinyl alcohol) (PVA) hydrogels, either fresh or aged or obtained by dipping dried freeze/thaw gel samples in water immediately after their preparation, was investigated by using different techniques. Free induction decays obtained from 1H NMR experiments provide the most accurate measurement of the degree of crystallinity of these systems. Values thus obtained are in a good agreement with data obtained by X-ray diffraction for all the samples under study. The degrees of crystallinity, determined by using differential scanning calorimetry (DSC), instead, are lower than those obtained by the other two methods, for all the gel samples, but the aged gels. This result is due to the occurrence of the gel−sol transition during the heating scan which is characterized by the endothermic melting of the crystallites and the exothermic solubilization and solvation of PVA chains in water. In as-prepared and rehydrated gels, the endothermic and exothermic effects overlap, which lea.
Nearly Optimal Regret for Learning Adversarial MDPs with Linear Function Approximation

We study the reinforcement learning for ﬁnite-horizon episodic Markov decision processes with adversarial reward and full information feedback, where the unknown transition probability function is a linear function of a given feature mapping. We propose an optimistic policy optimization algorithm with Bernstein bonus and show that it can achieve (cid:101) O ( dH √ T ) regret, where H is the length of the episode, T is the number of interaction with the MDP and d is the dimension of the feature mapping. Furthermore, we also prove a matching lower bound of (cid:101) Ω( dH √ T ) up to logarithmic factors. To the best of our knowledge, this is the ﬁrst computationally eﬃcient, nearly minimax optimal algorithm for adversarial Markov decision processes with linear function approximation.
Neuroevolution in Deep Learning: The Role of Neutrality

A variety of methods have been applied to the architectural configuration and learning or training of artificial deep neural networks (DNN). These methods play a crucial role in the success or failure of the DNN for most problems and applications. Evolutionary Algorithms (EAs) are gaining momentum as a computationally feasible method for the automated optimisation of DNNs. Neuroevolution is a term which describes these processes of automated configuration and training of DNNs using EAs. However, the automatic design and/or training of these modern neural networks through evolutionary algorithms is computanalli expensive. Kimura's neutral theory of molecular evolution states that the majority of evolutionary changes at molecular level are the result of random fixation of selectively neutral mutations. A mutation from one gene to another is neutral if it does not affect the phenotype. This work discusses how neutrality, given certain conditions, can help to speed up the training/design of deep neural networks.
Maximum Coverage in the Data Stream Model: Parameterized and Generalized

We present algorithms for the Max-Cover and Max-Unique-Cover problems in the data stream model. The input to both problems are $m$ subsets of a universe of size $n$ and a value $k\in [m]$. In Max-Cover, the problem is to find a collection of at most $k$ sets such that the number of elements covered by at least one set is maximized. In Max-Unique-Cover, the problem is to find a collection of at most $k$ sets such that the number of elements covered by exactly one set is maximized. Our goal is to design single-pass algorithms that use space that is sublinear in the input size. Our main algorithmic results are: If the sets have size at most $d$, there exist single-pass algorithms using $\tilde{O}(d^{d+1} k^d)$ space that solve both problems exactly. This is optimal up to polylogarithmic factors for constant $d$. If each element appears in at most $r$ sets, we present single pass algorithms using $\tilde{O}(k^2 r/\epsilon^3)$ space that return a $1+\epsilon$ approximation in the case of Max-Cover. We also present a single-pass algorithm using slightly more memory, i.e., $\tilde{O}(k^3 r/\epsilon^{4})$ space, that $1+\epsilon$ approximates Max-Unique-Cover. In contrast to the above results, when $d$ and $r$ are arbitrary, any constant pass $1+\epsilon$ approximation algorithm for either problem requires $\Omega(\epsilon^{-2}m)$ space but a single pass $O(\epsilon^{-2}mk)$ space algorithm exists. In fact any constant-pass algorithm with an approximation better than $e/(e-1)$ and $e^{1-1/k}$ for Max-Cover and Max-Unique-Cover respectively requires $\Omega(m/k^2)$ space when $d$ and $r$ are unrestricted. En route, we also obtain an algorithm for a parameterized version of the streaming Set-Cover problem.
Nonisothermal and isothermal oxidative degradation behavior of thermotropic liquid crystal polyesters containing kinked bisphenol AF and bisphenol A units

The polyester P–bisphenol AF 2.5 (BPAF 2.5) and P-bisphenol A 2.5 (BPA 2.5) with low melting temperature and high glass transition temperature can be obtained by introducing 2.5 mol% BPAF/BPA and terephthalic acid (TA) units respectively into the molecular chain of poly(oxybenzoate-co-oxynaphthoate) (P-HBA70). In this study, the nonisothermal and isothermal oxidative degradation behavior of polyester P-BPA2.5 and P-BPAF2.5 were investigated comparatively with parent polyester P-HBA70 by thermogravimetric analysis, Fourier transform infrared spectroscopy, and scanning electron microscopy measurements. The introduction of BPAF/BPA units into the molecular chain of P-HBA70 strongly influenced the degradation behavior of polyesters. Four multiple heating rate methods including Kissinger, Kim–Park, Flynn–Wall–Ozawa, and Friedman methods were applied to evaluate the dynamic thermal stability successfully. The following order of the activation energy values: P-BPAF2.5 > P-HBA70 > P-BPA2.5 can be found for the three samples. However, from the results obtained by the standard isoconversional method, the P-BPA2.5 showed a better thermal stability as compared to P-BPAF2.5 under isothermal atmosphere.