Miracle-dz/UniFAR-FTUs huggingface dataset:
Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models

After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.
Modelling the chemical evolution of ω Centauri using three-dimensional hydrodynamical simulations

We present a hydrodynamical and chemical model for the globular cluster ω Centauri (ω Cen), under the assumption that it is the remnant of an ancient dwarf spheroidal galaxy (dSph), the bulk of which was disrupted and accreted by our Galaxy ∼10 Gyr ago. We highlight the very different roles played by Type II and Type Ia supernovae (SNeII and SNeIa, respectively) in the chemical enrichment of the inner regions of the putative parent dSph. While the SNeII pollute the interstellar medium rather uniformly, the SNIa ejecta may remain confined inside dense pockets of gas as long as successive SNII explosions spread them out. Stars forming in such pockets have lower α-to-iron ratios than the stars forming elsewhere. Owing to the inhomogeneous pollution by SNeIa, the metal distribution of the stars in the central region differs substantially from that of the main population of the dwarf galaxy, and resembles that observed in ω Cen. This inhomogeneous mixing is also responsible for a radial segregation of iron-rich stars with depleted [α/Fe] ratios, as observed in some dSphs. Assuming a star formation history of ∼1.5 Gyr, our model succeeds in reproducing both the iron and the calcium distributions observed in ω Cen and the main features observed in the empirical α/Fe versus Fe/H plane. Finally, our model reproduces the overall spread in the colour–magnitude diagram, but fails in reproducing the morphology of the anomalous subgiant branch and the double morphology of the main sequence. However, the inhomogeneous pollution reduces (but does not eliminate) the need for a significantly enhanced helium abundance to explain the anomalous position of the blue main sequence. Further models taking into account the dynamical interaction of the parent dwarf galaxy with the Milky Way and the effect of asymptotic giant branch pollution will be required.
WHY REGIONS OF THE WORLD ARE IMPORTANT: REGIONAL SPECIFICITIES AND REGION-WIDE DIFFUSION OF DEMOCRACY

In this paper we articulate two reasons why regions of the world are important in comparative politics: causal heterogeneity by region and intra-regional dissemination and diffusion. The first section of the paper argues that little work in comparative politics has shown that regions are sometimes important units of analysis. In sections two and three we illustrate causal heterogeneity, showing that the effects of per capita income on democracy have been different in Latin America than in other regions of the world. Sections four and five address intra-regional dissemination and diffusion of democratic and authoritarian regimes. For Latin America, intraregional dissemination has been stronger than cross-regional dissemination, and we briefly explore the reasons for this phenomenon. We emphasize the need to avoid simplistic generalizations about regions as homogeneous entities while at the same time giving them a prominent role in some research questions. At a broad methodological level, regional specificities suggest the need for caution about universalistic generalizations and indicate the need to consider causal heterogeneity, domain restrictions, and bounded generalizations. Valerie Bunce, Michael Coppedge, Frances Hagopian, Mala Htun, Wendy Hunter, Gerardo Munck, Susan Stokes, Kurt Weyland, and seminar participants at the Pompeu Fabra University gave us valuable criticisms on earlier drafts of this paper.
Simulations of mechanics and structure of nanomaterials --- from nanoscale to coarser scales

We discuss how simulations of mechanical properties of materials require descriptions at many different length scales --- from the nanoscale where an atomic description is appropriate, through a mesoscale where dislocation based descriptions may be useful, to macroscopic length scales. In some materials, such as nanocrystalline metals, the range of length scales is compressed and a polycrystalline material may be simulated at the atomic scale. The first part of the paper describes such simulations of nanocrystalline copper. We observe how the grain boundaries contribute actively to the deformation. At grain sizes below 10-15 nm deformation in the grain boundaries dominate over the traditional dislocation-based deformation mechanisms. This results in a reversal of the normal grain size dependence of the yield stress: we observe that the material becomes softer when the grain size is reduced. The second part of the paper gives an overview over simulation techniques appropriate for problems too large to be treated in atomic-scale simulations, and how they can be combined to describe the interplay between phenomena at different length scales through multiscale modelling.
LatticeRnn: Recurrent Neural Networks Over Lattices

We present a new model called L ATTICE R NN , which generalizes recurrent neural networks (RNNs) to process weighted lattices as input, instead of sequences. A L ATTICE R NN can encode the complete structure of a lattice into a dense representation, which makes it suitable to a variety of problems, including rescoring, classifying, parsing, or translating lattices using deep neural networks (DNNs). In this paper, we use L ATTICE R NN s for a classiﬁcation task: each lattice represents the output from an automatic speech recognition (ASR) component of a spoken language understanding (SLU) system, and we classify the intent of the spoken utterance based on the lattice embedding computed by a L ATTICE R NN . We show that making decisions based on the full ASR output lattice, as opposed to 1-best or n -best hypotheses, makes SLU systems more robust to ASR errors. Our experiments yield improvements of 13% over a base-line RNN system trained on transcriptions and 10% over an n - best list rescoring system for intent classiﬁcation.
Implicit complexity in recursive analysis

Recursive analysis is a model of analog computation which is based on type 2 Turing machines. Various classes of functions computable in recursive analysis have recently been characterized in a machine independent and algebraical context. In particular nice connections between the class of computable functions (and some of its sub and sup-classes) over the reals and algebraically defined (sub- and sup-) classes of R-recursive functions a la Moore have been obtained. We provide in this paper a framework that allows to dive into complexity for functions over the reals. It indeed relates classical computability and complexity classes with the corresponding classes in recursive analysis. This framework opens the field of implicit complexity of functions over the reals. While our setting provides a new reading of some of the existing characterizations, it also provides new results: inspired by Bellantoni and Cook's characterization of polynomial time computable functions, we provide the first algebraic characterization of polynomial time computable functions over the reals.
Identification and characterization of calcium and manganese transporting ATPase (PMR1) gene of Pichia pastoris

A gene homologous to Saccharomyces cerevisiae PMR1 has been cloned in the methylotrophic yeast Pichia pastoris. The entire P. pastoris PMR1 gene (PpPMR1) codes a protein of 924 amino acids. Sequence analysis of the PpPMR1 cDNA and the genomic DNA revealed that there is no intron in the coding region. The putative gene product contains all of the conserved regions observed in P‐type ATPases and exhibits 66.2%, 60.3% and 50.6% identity to Pichia angusta (Hansenula polymorpha), Saccharomyces cerevisiae PMR1 and human ATP2C1 gene products, respectively. A pmr1 null mutant strain of P. pastoris exhibited growth defects in media with the addition of EGTA, but with supplementation of Ca2+ to a calcium‐deficient media reversed the growth defects of the mutant strain. Manganese reversed the growth defects of the mutant strain; however, the cell growth was not as profound as the Ca2+‐supplemented media. The results demonstrated that the P. pastoris gene encodes the functional homologue of the S. cerevisiae PMR1 gene product, a P‐type Ca2+/Mn2+‐ATPase. The DNA sequence of the P. pastoris PMR1 gene has been submitted to GenBank under Accession No. DQ239958. Copyright © 2006 John Wiley & Sons, Ltd.
Case Studies of the Structure, Dynamics, and Outcomes of Interdisciplinary Team Organization in Oregon Middle Schools

An abstract of the dissertation of Gail Lyon for the Doctor of Education in Educational Leadership: Administration and Supervision presented December 8, 1993. Title: Case Studies of the Structure, Dynamics, and outcomes of Interdisciplinary Team organization in Oregon Middle Schools Middle school literature advocates interdisciplinary team organization as a structure that enhances student learning and teacher satisfaction. In an interdisciplinary team, teachers responsible for different content areas collaboratively plan the instructional program for a shared group of students. Yet, fewer than fifty percent of the nation's middle schools use an interdisciplinary team structure, and research indicates that teams are fragile and temporary. Few studies were found 'that described interdisciplinary team organization at the team or individual teacher level. The purpose of this case study is to describe the structure, dynamics, and outcomes of interdisciplinary teams of teachers in middle schools. The collection, analysis, and evaluation of data focused on four areas: (a) team structure -. --_ _---_. _ -. _--2 including goals, roles, and leadership; (b) team dynamics ("tearnness"), including collaboration, cohesion, and communication; (C) teacher affective outcomes of satisfaction, efficacy, and stress; and (d) teacher behavioral outcomes of curriculum and instruction and co~nseling and discipline. The researcher collected data from five sources of evidence including documents, structured interviews, key informant interviews, direct observation, and questionnaires. Two middle schools that were implementing interdisciplinary team organization for the first year were selected for the study. Their differences in demographics, teaming structure, and district/school history allowed for a basis of comparison and contrast. The data were organized and presented in four case studies of interdisciplinary teams and two cross-case analyses, providing a descriptive account of the experiences of teachers involved in an interdisciplinary team structure. The results of the study indicated that: 1. Structural variables affected team planning. 2. The level of teacher collaboration on teams was a developmental process. 3. Teachers derived professional benefits and personal satisfaction from teaming and experienced a reduction of
Walking Up the Down Escalator: Public Investment and Fiscal Stability

Fiscal adjustment becomes like walking up the down escalator when growth-promoting spending is cut so much as to lower growth and thus the present value of future tax revenues to a degree that more than offsets the improvement in the cash deficit. Although short-term cash flows matter, a preponderant focus on them encourages governments to invest too little. Cash flow targets also encourage governments to shift investment spending off budget, by seeking private investment in public projects-irrespective of its real fiscal or economic benefits. To evade the action of cash flow targets, some have suggested excluding from their scope certain investments (such as those undertaken by public enterprises deemed commercial or financed by multilaterals). These stopgap remedies might sometimes help protect investment, but they do not provide a satisfactory solution to the underlying problem. Governments can more effectively reduce the biases created by the focus on short-term cash flows by developing indicators of the long-term fiscal effects of their decisions, including accounting and economic measures of net worth, and where appropriate including such measures in fiscal targets or even fiscal rules, replacing the exclusive focus on liquidity and debt.
Analytical Procedures for 2001: A Data Envelopment Analysis Approach

Ratio analysis and account balance comparisons are commonly used analytical tools to verify the performance of a client in an audit engagement. While ratios are easy to compute, which in part explains their wide appeal, their interpretation is problematic, especially when two or more ratios provide conflicting signals. Indeed, ratio analysis is often criticized on the grounds of subjectivity, i.e., the auditor must pick and choose ratios in order to assess the overall performance of a client. In this paper we argue that Data Envelopment Analysis (DEA) can augment the traditional ratio analysis. DEA can provide a consistent and reliable measure of managerial or operational efficiency of the client. We test the null hypothesis that there will be no relationship between DEA and traditional accounting ratios as measures of performance of a client. Our results reject the null hypothesis indicating that DEA can complement accounting ratios in analysis of the overall performance of the client.
Pathways to work: qualitative research on the Condition Management Programme

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cytokine production to favor a Th 1 response-dependent mechanism and by shifting + CD 25 + by a regulatory CD 4 Anti-CD 3 prevents factor VIII inhibitor development in hemophilia A mice

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Contact-Force Distribution Optimization and Control for Quadruped Robots Using Both Gradient and Adaptive Neural Networks

This paper investigates optimal feet forces' distribution and control of quadruped robots under external disturbance forces. First, we formulate a constrained dynamics of quadruped robots and derive a reduced-order dynamical model of motion/force. Consider an external wrench on quadruped robots; the distribution of required forces and moments on the supporting legs of a quadruped robot is handled as a tip-point force distribution and used to equilibrate the external wrench. Then, a gradient neural network is adopted to deal with the optimized objective function formulated as to minimize this quadratic objective function subjected to linear equality and inequality constraints. For the obtained optimized tip-point force and the motion of legs, we propose the hybrid motion/force control based on an adaptive neural network to compensate for the perturbations in the environment and approximate feedforward force and impedance of the leg joints. The proposed control can confront the uncertainties including approximation error and external perturbation. The verification of the proposed control is conducted using a simulation.
The Mediating Role of Resilience in the Relationship between Big Five Personality and Anxiety among Chinese Medical Students: A Cross-Sectional Study

Backgrounds The psychological distress of medical students is a major concern of public health worldwide. However, few studies have been conducted to evaluate anxiety symptoms of medical students in China. The purpose of this study was to investigate the anxiety symptoms among Chinese medical students, to examine the relationships between big five personality traits and anxiety symptoms among medical students, and to explore the mediating role of resilience in these relationships. Methods This multicenter cross-sectional study was conducted in June 2014. Self-reported questionnaires consisting of the Zung Self-Rating Anxiety Scale (SAS), Big Five Inventory (BFI), Wagnild and Young Resilience Scale (RS-14) and demographic section were distributed to the subjects. A stratified random cluster sampling method was used to select 2925 medical students (effective response rate: 83.57%) at four medical colleges and universities in Liaoning province, China. Asymptotic and resampling strategies were used to explore the mediating role of resilience. Results The prevalence of anxiety symptoms was 47.3% (SAS index score≥50) among Chinese medical students. After adjusting for the demographic factors, the traits of agreeableness, conscientiousness and openness were all negatively associated with anxiety whereas neuroticism was positively associated with it. Resilience functioned as a mediator in the relationships between agreeableness/conscientiousness/openness and anxiety symptoms. Conclusions Among Chinese medical students, the prevalence of anxiety symptoms was high and resilience mediated the relationships between big five personality traits and anxiety symptoms. Identifying at-risk individuals and undertaking appropriate intervention strategies that focus on both personality traits and resilience might be more effective to prevent and reduce anxiety symptoms.
Chapter 3 – HUMAN FACTORS ISSUES OF TACTILE DISPLAYS FOR MILITARY ENVIRONMENTS

The overall goal of this chapter is to give the reader insights into the human factors issues related to the use of tactile displays. Torso-mounted displays, which are particularly suited for direction and orientation cues, are emphasized. First, perceptual issues relevant to tactile stimulation are discussed. These include issues regarding spatial acuity and absolute localization of tactile cues on the torso, such as internal reference points, anchor points, and spatial accuracy. In addition, tactile illusions, burst durations, and temporal effects are discussed in relation to tactile torso display design. A second section focuses on issues related to coding principles; that is, how best to develop tactile patterns to be intuitively understood within a specific operational context. Cognitive issues are then addressed, such as how tactile stimulation can either alleviate or exacerbate attention tunneling, and the extent to which multiple tactile patterns can be used effectively. Cognitive processes related to tactile cueing are described, followed by issues related to multisensory integration and multifunction displays. Finally, issues related to user acceptance are discussed.
VSOP monitoring of the compact BL Lac object AO 0235 +164

In 1999, the highly compact and variable BL Lac object AO 0235+164 was identified as the highest brightness temperature active galactic nucleus observed with the VLBI Space Observatory Programme (VSOP), with T_B > 5.8 x 10^{13} K. The sub-milliarcsecond radio structure of this source has been studied with dual-frequency (1.6 and 5 GHz), polarization-sensitive VSOP observations during 2001 and 2002. Here we present the results of this monitoring campaign. At the time of these observations, the source was weakly polarized and characterized by a radio core that is clearly resolved on space-ground baselines.
Glucose Homeostasis and Weight Loss in Morbidly Obese Patients Undergoing Banded Sleeve Gastrectomy: A Prospective Clinical Study

OBJECTIVE To assess glucose homeostasis and weight loss in morbidly obese patients undergoing Silastic® ring sleeve gas-trectomy. METHODS This was a prospective clinical study. Thirty-three female patients with a mean body mass index (BMI) of 42.33 ± 1.50 kg/m2 (range: 40–45 kg/m2), a mean age of 36.7 ± 9.4 years and a mean waist circumference of 118.7 ± 5.98 cm were included in this study. Type 2 diabetes mellitus was observed in 11 patients (33.3%), and glucose intolerance was observed in 4 patients (12.1%). Mean plasma fasting glucose levels were 109.77 ± 44.19 mg/dl (75–320) in the preoperative period. All Silastic® ring sleeve gastrectomy procedures were performed by the same surgical team using the same anesthetic technique. The patients were monitored for at least 12 months after surgery. RESULTS The mean weight of the patients decreased from 107.69 ± 6.57 kg to 70.52 ± 9.36 kg (p < 0.001), the mean BMI decreased to 27.4 ± 2.42 kg/m2 (p < 0.001), and the mean waist circumference decreased to 89.87 cm ± 6.66 (p < 0.001) in the postoperative period. Excess BMI loss was 86.5 ± 14.2%. Fasting glucose levels were reduced to 80.94 ± 6.3 mg/dl (p < 0.001). Remission of diabetes and glucose intolerance was observed in all patients. CONCLUSION Silastic® ring sleeve gastrectomy was effective in promoting weight loss, waist circumference reduction and control of glucose homeostasis in morbidly obese patients.