Miracle-dz/UniFAR-FTUs huggingface dataset:
The Peano Software—Parallel, Automaton-based, Dynamically Adaptive Grid Traversals

We discuss the design decisions, design alternatives, and rationale behind the third generation of Peano, a framework for dynamically adaptive Cartesian meshes derived from spacetrees. Peano ties the mesh traversal to the mesh storage and supports only one element-wise traversal order resulting from space-filling curves. The user is not free to choose a traversal order herself. The traversal can exploit regular grid subregions and shared memory as well as distributed memory systems with almost no modifications to a serial application code. We formalize the software design by means of two interacting automata—one automaton for the multiscale grid traversal and one for the application-specific algorithmic steps. This yields a callback-based programming paradigm. We further sketch the supported application types and the two data storage schemes realized before we detail high-performance computing aspects and lessons learned. Special emphasis is put on observations regarding the used programming idioms and algorithmic concepts. This transforms our report from a “one way to implement things” code description into a generic discussion and summary of some alternatives, rationale, and design decisions to be made for any tree-based adaptive mesh refinement software.
A Tale of Tailless

Drosophila Tailless(Tll) and its vertebrate homologue Tlx are conserved orphan nuclear receptors specifically expressed in the eye and the forebrain. Tll and Tlx act primarily as transcriptional repressors through their interactions with transcriptional corepressors, Atrophin family proteins, and histone-tail/chromatin-modifying factors such as lysine-specific histone demethylase 1 and histone deacetylases. The functional importance of Tll and Tlx is made apparent by the recent discovery that they are expressed in neural stem cells (NSCs) and are required for self-renewal of these cells in both Drosophila and the mouse. This review provides a snapshot of current knowledge about Tll and Tlx and their transcriptional network, which maintains NSCs in developing and adult animals.
Local 3-approximation algorithms for weighted dominating set and vertex cover in quasi unit-disk graphs

We present a simple 3-approximation algorithm for minimum-weight dominating set and minimum-weight vertex cover in unit-disk graphs and quasi unit-disk graphs in which each node knows its coordinates. The algorithm is local: the output of a node depends solely on the input within its constantradius neighbourhood. The local horizon of the algorithm is small, both in the worst case and on average.
Liposomes Containing Lipid A Serve as an Adjuvant for Induction of Antibody and Cytotoxic T-Cell Responses against RTS,S Malaria Antigen

ABSTRACT Encapsulation of soluble protein antigens in liposomes was previously shown to result in processing of antigen via the major histocompatibility complex class I pathway, as evidenced by costaining of the trans-Golgi region of murine bone marrow-derived macrophages (BMs) by fluorophore-labeled liposomal antigen and by a trans-Golgi-specific fluorescent lipid. Evidence is presented here that free or liposome-encapsulated RTS,S, a particulate malaria antigen consisting of hepatitis B particles coexpressed with epitopes from the Plasmodium falciparumcircumsporozoite protein, also was localized in thetrans-Golgi after incubation with BMs, suggesting processing by the class I pathway. An in vivo cytotoxic T-lymphocyte (CTL) response was detected, however, only after immunization with RTS,S encapsulated in liposomes containing lipid A and not after immunization with free RTS,S or with RTS,S encapsulated in liposomes lacking lipid A. Therefore, intracellular delivery of antigen containing CTL epitopes to the Golgi of BMs does not necessarily result in a CTL response in vivo unless an additional adjuvant, such as liposomes containing lipid A, is utilized. Encapsulation of RTS,S in liposomes containing monophosphoryl lipid A (MPL) resulted in a dose-dependent enhancement of the NANP-specific immunoglobulin G (IgG) antibody response compared to that of free RTS,S. The IgG1 and IgG2a subclasses predominated after immunization with RTS,S encapsulated in liposomes containing MPL. These results demonstrate that encapsulation of a lipid-containing particulate antigen, such as RTS,S, in liposomes containing lipid A can enhance both humoral and cellular immune responses.
Crystal Plasticity and Evolution of Polycrystalline Microstructure

The continuum slip theory of crystals provides a canonical framework of finite plasticity with physically well-defined roots in the dislocation mechanics of metals. Reliable algorithmic settings of crystal plasticity are not only needed for structural analyses of single crystals but also provide a cornerstone for multiscale computations of evolving anisotropic microstructures in metallic polycrystals. This article summarizes a current status of computational crystal plasticity and its application to the texture analysis of polycrystals. It outlines a basic constitutive structure of crystal plasticity, alternative deformation-driven stress update algorithms and a computational scheme for the nonlinear homogenization of polycrystalline aggregates. Particular emphasis is put on a canonical incremental variational formulation for Schmid-type crystal plasticity with potential hardening where an incremental stress potential is obtained from a local minimization problem with respect to the internal variables. The existence of this stress potential allows the formulation of IBVPs for elastic–plastic crystals as a sequence of incremental minimization problems. Furthermore, the nonlinear homogenization of polycrystalline microstructures may be recast into a principle of minimum averaged incremental energy. Within this variational setting of homogenization, a quasi-hyperelastic incremental macro-stress potential is obtained from a global minimization problem with respect to the fine-scale displacement fluctuation field. The performance of the formulations is demonstrated for benchmarks of single crystal plasticity and texture developments in polycrystals. Keywords: finite plasticity; crystals; polycrystals; microstructures; homogenization; multiscale analyses
Primordial black holes from cosmic necklaces

Cosmic necklaces are hybrid topological defects consisting of monopoles and strings. We argue that primordial black holes(PBHs) may have formed from loops of the necklaces, if there exist stable winding states, such as coils and cycloops. Unlike the standard scenario of PBH formation from string loops, in which the kinetic energy plays important role when strings collapse into black holes, the PBH formation may occur in our scenario after necklaces have dissipated their kinetic energy. Then, the significant difference appears in the production ratio. In the standard scenario, the production ratio $f$ becomes a tiny fraction $f\sim 10^{-20}$, however it becomes $f \sim 1$ in our case. On the other hand, the typical mass of the PBHs is much smaller than the standard scenario, if they are produced in the same epoch. As the two mechanisms may work at the same time, the necklaces may have more than one channel of the gravitational collapse. Although the result obtained in this paper depends on the evolution of the dimensionless parameter $r$, the existence of the winding state could be a serious problem in some cases. Since the existence of the winding state in brane models is due to the existence of a non-tivial circle in the compactified space, the PBH formation can be used to probe the structure of the compactified space. Black holes produced by this mechanism may have peculiar properties.
Laser Transformation Hardening

Abstract Surface hardening by inducing phase transformations through the heating effect of a laser beam was one of the first laser based fabrication methods to be commercialised, in the early 1970s. However, its industrial acceptance has been limited, in comparison with other laser based processes such as cutting, welding, and marking. The reasons lie in a lack of knowledge concerning the process, and the large number of more familiar surface hardening processes that are commercially available. Within the last five years important developments have taken place in the technology of laser sources, optics, and software, which now enable the process to be viewed more favourably against competing processes. More suitable laser sources, such as multikilowatt Nd:YAG and diode lasers, and beam delivery optics have been developed. Sophisticated system control software now enables mathematical process models to be integrated into production systems. Computer aided design (CAD) software enables products to be redesigned, and life cycle performance and process comparisons can be evaluated rapidly. Thus automated laser hardening systems are now becoming available, suitable for treating components of widely varying size and shape. The requirements of codes for hardening can be met in a wide range of steels and cast irons. This review summarises the state of the art in the process, industrial practice, properties of hardened materials, and the software now available, and describes the areas in which work is needed to extend the industrial application of the process.
Integrated β-catenin, BMP, PTEN, and Notch signalling patterns the nephron

The different segments of the nephron and glomerulus in the kidney balance the processes of water homeostasis, solute recovery, blood filtration, and metabolite excretion. When segment function is disrupted, a range of pathological features are presented. Little is known about nephron patterning during embryogenesis. In this study, we demonstrate that the early nephron is patterned by a gradient in β-catenin activity along the axis of the nephron tubule. By modifying β-catenin activity, we force cells within nephrons to differentiate according to the imposed β-catenin activity level, thereby causing spatial shifts in nephron segments. The β-catenin signalling gradient interacts with the BMP pathway which, through PTEN/PI3K/AKT signalling, antagonises β-catenin activity and promotes segment identities associated with low β-catenin activity. β-catenin activity and PI3K signalling also integrate with Notch signalling to control segmentation: modulating β-catenin activity or PI3K rescues segment identities normally lost by inhibition of Notch. Our data therefore identifies a molecular network for nephron patterning. DOI: http://dx.doi. org/10.7554/eLife.04000. 001
Notice of RetractionFinite element model updating based on complex modal analysis for unsymmetrical damping system

Finite element model updating with incomplete complex modal data and structural parameters coupled with mass, stiffness and damping matrixes simultaneously for unsymmetrical damping system using optimization method is presented. By the use of finite element software-NASTRAN and mathematical tool-MATLAB model updating based on complex eigenvalue sensitivity analysis is successfully accomplished in this piece of work. The updating for simulation example about flexible rotor system, taking many cases into experiment and modeling errors account, is performed using bearing stiffness, bearing damping and diametrical moment of inertia parameters simultaneously. The results proved the effectiveness of the method of updating using complex modal data for unsymmetrical damping system. The proposed method could be used and extended to engineering easily.
Performance of students with and without reading difficulties on decoding tasks.

PURPOSE To characterize the performance of students with and without reading difficulties in reading decoding tasks to investigate parameters that can facilitate reading assessment. METHODS Forty-eight school children, from 7 to 10 years old, who attended 2nd to 4th of Elementary Schoolgrades were studied. Based on their teacher's information, the children were divided into two groups: without reading difficulty (WRDG) and with reading difficulty (RDG). Thirty-six linguistic items were selected (words and pseudowords) and presented whole or segmented (letters and syllables) to assess the children's reading. The data were compared and statistically analyzed by Mann-Whitney and Friedman Tests. The hits, as well as sensitivity and specificity, were calculated. RESULTS WRDG had a better performance than RDG in all the tasks except whole pseudowords recognition. WRDG performed similarly in all the tasks. The RDG had more difficulty in reading pseudowords, particularly when presented syllable-by-syllable and letter-by-letter. Thirty-two point five proved to be a sensitive turning point: most of the children who decoded and read at least 32 items had been considered adequate by their teachers whereas most of those who did not had been classified by their teachers as having academic difficulty. CONCLUSION The WRDG performance in decoding reading was homogeneous and better than that of the RDG. The RDG performed worse on reading segmented items, particulary on pseudowords.
Reliability of Sentinel Lymph Node Biopsy after Neoadjuvant Chemotherapy in Breast Cancer Patients

Purpose Sentinel lymph node biopsy (SLNB) is an accurate and effective means of axillary nodal staging in early breast cancer. However its indication after neoadjuvant chemotherapy (NAC) is under constant debate. The present study evaluates the reliability of SLNB in assessing axillary nodal status after NAC. Methods Data from 281 patients who had received NAC and subsequent SLNB were reviewed. The identification and false negative rates of SLNB were determined and the clinicopathologic factors associated with false negative results were investigated using univariate analysis. Results The identification rate of SLNB after NAC was 93.6% and the false negative rate was 10.4%. Hormone receptor status, especially progesterone receptor positivity, was significantly associated with false negative results. The accuracy of intraoperative frozen section examination of sentinel lymph nodes was 91.2%. Conclusion The identification rate of SLNB and the accuracy of intraoperative frozen section examination after NAC are comparable to the results without NAC in patients with early breast cancer. However considering the high false negative rates, general application of SLNB after NAC should be avoided. Patients with progesterone-positive tumors and non-triple-negative breast cancers may be a select group of patients in whom SLNB can be employed safely after NAC, but further studies are necessary.
High-power mid-infrared interband cascade lasers

Our simulations project that the optimum number of cascading stages for an interband cascade laser operating cw at ambient temperature falls between 8 and 15, depending on the internal loss. In the present study, we fabricated and characterized ICLs with 5-15 stages and emitting at 3.2-3.5 μm. The growth of these type-II antimonide/arsenide structures with “W” active regions was on a Riber Compact 21T MBE system. Most of the devices were etched into 140-μm-wide ridges, with 100-μm-wide metal contact strips deposited in the middle, and operated epitaxial-side-up. Initial devices displayed lasing thresholds as low as 12 A/cm at 78 K, series resistances as low as 0.21 mΩ·cm, and voltage efficiencies as high as 96%. Cavitylength studies on a series of ICLs with 5, 10, and 15 stages determined that the internal efficiencies at 78 K were ≈ 80% in all cases, while the internal losses were 16, 27, and 37 cm, respectively. Our simulations of optimized devices project losses no higher than those of singlestage “W” diodes (≈ 7 cm). Some of the ICLs reached pulsed operating temperatures as high as 300 K. A 5-stage device with a cavity length of Lcav = 1.0 mm and HR/AR-coated facets displayed a maximum cw output power of 780 mW and wallplug efficiency of 21% at T = 78 K. A sister device with a 3-mm-long cavity produced >1.1 W of cw output power at 78 K. Higher powers and efficiencies are expected once the internal loss has been minimized, and once epitaxial-side down heatsinking or gold electro-plating is employed.
Continuous neurogenesis in the adult forebrain is required for innate olfactory responses

Although the functional significance of adult neurogenesis in hippocampal-dependent learning and memory has been well documented, the role of such neurogenesis in olfactory activity is rather obscure. To understand the significance of adult neurogenesis in olfactory functions, we genetically ablated newly born neurons by using tamoxifen-treated Nestin-CreERT2;neuron-specific enolase-diphtheria toxin fragment A (NSE-DTA) mice. In these mice, tamoxifen-inducible Cre recombinase allows the NSE (Eno2) gene to drive DTA expression in differentiating neurons, leading to the efficient ablation of newly born neurons in the forebrain. These mutant mice were capable of discriminating odors as competently as control mice. Strikingly, although control and mutant mice frequently showed freezing behaviors to a fox scent, a predator odor, mutant mice approached this odor when they were conditioned to associate the odor with a reward, whereas control mice did not approach the odor. Furthermore, although mutant males and females showed normal social recognition behaviors to other mice of a different sex, mutant males displayed deficits in male–male aggression and male sexual behaviors toward females, whereas mutant females displayed deficits in fertility and nurturing, indicating that sex-specific activities, which are known to depend on olfaction, are impaired. These results suggest that continuous neurogenesis is required for predator avoidance and sex-specific responses that are olfaction dependent and innately programmed.
Natural histories of chronic obstructive pulmonary disease.

Concepts relating to the natural history of chronic obstructive pulmonary disease (COPD) arise most importantly from the classic study of Fletcher and colleagues (The Natural History of Chronic Bronchitis and Emphysema, Oxford University Press, New York, 1976). This study, which evaluated working English men over 8 years, was used to construct a proposed life-long natural history. Although this is a classic study that has greatly advanced understanding of COPD, it has a number of limitations. Its duration is relatively short compared with the duration of COPD, so it is more cross-sectional than longitudinal. It was unable to distinguish among varied "natural histories. " It assessed primarily the FEV(1), and the natural history of other features of COPD is largely undescribed. With advances in understanding the clinical features of COPD and with the development of evaluating new tools to assess patients with COPD, longitudinal studies evaluating COPD in novel ways and for longer durations are needed.
Compiling polymorphism using intensional type analysis

Traditional techniques for implementing polymorphism use a universal representation for objects of unknown type. Often, this forces a compiler to use universal representations even if the types of objects are known. We examine an alternative approach for compiling polymorphism where types are passed as arguments to polymorphic routines in order to determine the representation of an object. This approach allows monomorphic code to use natural, efficient representations, supports separate compilation of polymorphic definitions and, unlike coercion-based implementations of polymorphism, natural representations can be used for mutable objects such as refs and arrays. We are particularly interested in the typing properties of an intermediate language that allows run-time type analysis to be coded within the language. This allows us to compile many representation transformations and many language features without adding new primitive operations to the language. In this paper, we provide a core target language where type-analysis operators can be coded within the language and the types of such operators can be accurately tracked. The target language is powerful enough to code a variety of useful features, yet type checking remains decidable. We show how to translate an ML-like language into the target language so that primitive operators can analyze types to produce efficient representations. We demonstrate the power of the “user-level” operators by coding flattened tuples, marshalling, type classes, and a form of type dynamic within the language.
Damage Evolution in Composites with a Homogenization-based Continuum Damage Mechanics Model

This paper develops a 3D homogenization-based continuum damage mechanics (HCDM) model for fiber reinforced composites undergoing micromechanical damage. Micromechanical damage in the representative volume element (RVE) is explicitly incorporated in the form of fiber—matrix interfacial debonding. The model uses the evolving principal damage coordinate system as its reference in order to represent the anisotropic coefficients. This is necessary for retaining accuracy with nonproportional loading. The material constitutive law involves a fourth order orthotropic tensor with stiffness characterized as macroscopic internal variable. Damage in 3D composites is accounted for through functional forms of the fourth order damage tensor in terms of macroscopic strain components. The HCDM model parameters are calibrated by using homogenized micromechanical (HMM) solutions for the RVE for a few strain histories. The proposed model is validated by comparing the CDM results with HMM response of single and multiple fiber RVEs subjected to arbitrary loading history. Finally the HCDM model is incorporated in a macroscopic finite element code to conduct damage analysis in a structure. The effect of different microstructures on the macroscopic damage progression is examined through this study.
Natural Variation in Partial Resistance to Pseudomonas syringae Is Controlled by Two Major QTLs in Arabidopsis thaliana

Background Low-level, partial resistance is pre-eminent in natural populations, however, the mechanisms underlying this form of resistance are still poorly understood. Methodology/Principal Findings In the present study, we used the model pathosystem Pseudomonas syringae pv. tomato DC3000 (Pst) - Arabidopsis thaliana to study the genetic basis of this form of resistance. Phenotypic analysis of a set of Arabidopsis accessions, based on evaluation of in planta pathogen growth revealed extensive quantitative variation for partial resistance to Pst. It allowed choosing a recombinant inbred line (RIL) population derived from a cross between the accessions Bayreuth and Shahdara for quantitative genetic analysis. Experiments performed under two different environmental conditions led to the detection of two major and two minor quantitative trait loci (QTLs) governing partial resistance to Pst and called PRP-Ps1 to PRP-Ps4. The two major QTLs, PRP-Ps1 and PRP-Ps2, were confirmed in near isogenic lines (NILs), following the heterogeneous inbred families (HIFs) strategy. Analysis of marker gene expression using these HIFs indicated a negative correlation between the induced amount of transcripts of SA-dependent genes PR1, ICS and PR5, and the in planta bacterial growth in the HIF segregating at PRP-Ps2 locus, suggesting an implication of PRP-Ps2 in the activation of SA dependent responses. Conclusions/Significance These results show that variation in partial resistance to Pst in Arabidopsis is governed by relatively few loci, and the validation of two major loci opens the way for their fine mapping and their cloning, which will improve our understanding of the molecular mechanisms underlying partial resistance.