Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural network-based closure for modeling short-fiber suspensions

Fiber orientation tensors enjoy widespread application in short-fiber reinforced polymer composite simulations because they provide a compact form for describing complex fiber orientation states. The orientation of reinforcing fibers within a short-fiber composite directly affects the mechanical and thermal properties of the processed part, requiring that an accurate and efficient simulation method be available for use in product and process design. It is well understood that the equation of motion for each even-ordered orientation tensor is dependent on the next higher even-ordered orientation tensor, necessitating the use of a closure approximation. This article presents a new class of fitted orientation tensor closures where components of the fourth-order tensor are computed from corresponding second-order tensors using an artificial neural network (ANN). The ANN offers a unique advantage here because it is computationally efficient and is able to represent complex relationships between inputs and outputs where representative mathematical models do not exist. After a brief review of fiber orientation analysis, the new neural network closure (NNET) is defined along with a detailed description of the associated training procedure. The accuracy and computational efficiency of the NNET closure is then demonstrated with both simple and complex flow simulations.It is shown that simulations with the new NNET closure are as accurate as those using current orthotropic fitted closures at a computation cost that approaches the less accurate Hybrid closure. POLYM. COMPOS. , 31:1125–1141, 2010. © 2009 Society of Plastics Engineers
Effect of team diversity on software project performance

Purpose – This research seeks to investigate the relationship between knowledge diversity (KD) in software teams and project performance. Previous research has shown that member diversity affects team performance; most of that work, however, has focused on diversity in personal or social attributes, such as gender or social category. Current research targets at the knowledge level aim to facilitate the implementation of knowledge management in organizations.Design/methodology/approach – A research framework was developed based on conflict theory and empirically tested on software teams in Taiwan.Findings – It was found that KD increases task conflict, which in turn has significant positive effects on team performance and that value diversity (VD) increases relationship conflict, which in turn negatively affects team performance.Research limitations/implications – The findings indicate that task conflict can enhance team performance, while relationship conflict can reduce team performance. Therefore, it is.
Multi-level approximate logic synthesis under general error constraints

We address the problem of multi-level approximate logic synthesis. Our strategy assumes existence of an optimized exact Boolean network, which is critical in practice since arithmetic blocks are rarely synthesized from 2-level representation automatically. The goal is to produce minimum cost circuits whose logic function deviates in a controlled manner from the exact function with deviations quantified by the magnitude and frequency of errors. We rely on network simplifications allowed by external don't cares (EXDCs). We formulate the error-magnitude constrained problem by using Boolean relations to capture the allowed error behavior in a more general manner compared to incompletely specified functions. Our key contribution is in finding sets of external don't cares that maximally approach the Boolean relation. The algorithm starts with an EXDC set that is overly relaxed and iteratively, and in a greedy fashion, identifies a feasible EXDC set by solving a series of conventional EXDC-based network optimizations. The algorithm then ensures compliance to error frequency constraints by recovering the correct outputs on the sought number of error-producing inputs while aiming to minimize the network cost increase. We applied the algorithm to several well-known adder and multiplier designs of varying bit-width. Even for small error magnitudes, the algorithm produces networks with gate count reduced by 30-50%, when the error frequency constraint is loose. This is up to 20% fewer gates than a naive EXDC-based approach.
A method to visualize transdermal nickel permeation in mouse skin using a nickel allergy patch

Metal patch test is often used in clinical settings when metal-induced contact dermatitis is suspected. However, the transdermal permeation behavior of metal ions from the patch test remains unclear. Current patch tests using high concentrations of metal salt solutions have some side effects, e.g. acute skin reactions to high concentrations of metal salt. To resolve these, estimating metal ion transdermal permeation is wished. In this study, synchrotron radiation X-ray fluorescence (SR-XRF) and micro-focused particle-induced X-ray emission (micro-PIXE) were used to visualize the time-dependent Ni permeation in mouse skin. The cross-sectional diffusion of Ni was visualized in a time-dependent manner. Our results indicate that maximum Ni permeation occurs after 24 h of patch treatment, and the permeated Ni content was high in the epidermis and spread into the dermis beyond the basal layer. This method may be useful to determine the appropriate solution concentration and duration of administration for the patch test.
Reproductive Biology and Endocrinology Open Access Kit Ligand Promotes First Polar Body Extrusion of Mouse Preovulatory Oocytes

Background: Shortly after stimulation by the preovulatory surge of luteinizing hormone (LH), oocytes arrested at the late prophase I resume meiosis characterized by germinal vesicle breakdown (GVBD), chromosome condensation, and extrusion of the first polar body in preparation for fertilization and early embryonic development. However, oocytes express few or no LH receptors and are insensitive to direct LH stimulation. Thus, factors released by granulosa or theca cells expect to convey the LH stimuli to oocytes. To identify candidate ligand-receptor pairs potentially involved in the process of oocyte maturation, we performed DNA microarray analyses of ovarian transcripts in mice and identified Kit ligand (Kitl) as an ovarian factor stimulated by the LH/hCG surge. The purpose of this study is to investigate the roles of KITL in the nuclear and cytoplasmic maturation of preovulatory mouse oocytes.
EFFECT OF THE FEMALE SIZE ON EGG QUALITY AND FECUNDITY OF THE WILD ATLANTIC SALMON IN THE SUB-ARCTIC RIVER TENO

Reproduction of the northern Atlantic salmon population was studied to find out the effect of female size on quantity and quality of eggs. Total and relative fecundity of females were used for quantity measures. Size, energy and water contents of eggs and changes in them as well as mortality of eggs during the incubation were used as quality measures. The size of wild female Atlantic salmon had a positive effect on their total number of eggs and on the energy content of eggs. However, the effect of the female size on the egg size was weak and there was no correlation between the female size and relative fecundity. Overall, the benefit of body size was not only quantitative but also qualitative in reproduction success of the River Teno salmon.
Hippocampal Fast Glutamatergic Transmission Is Transiently Regulated by Corticosterone Pulsatility

In recent years it has become clear that corticosteroid hormones (such as corticosterone) are released in ultradian pulses as a natural consequence of pituitary-adrenal interactions. All organs, including the brain, are thus exposed to pulsatile changes in corticosteroid hormone level, important to ensure full genomic responsiveness to stress-induced surges. However, corticosterone also changes neuronal excitability through rapid non-genomic pathways, particularly in the hippocampus. Potentially, background excitability of hippocampal neurons could thus be changed by pulsatile exposure to corticosteroids. It is currently unknown, though, how neuronal activity alters during a sequence of corticosterone pulses. To test this, hippocampal cells were exposed in vitro to four consecutive corticosterone pulses with a 60 min inter-pulse interval. During the pulses we examined four features of hippocampal signal transfer by the main excitatory transmitter glutamate—i.e., postsynaptic responses to spontaneous release of presynaptic vesicles, postsynaptic GluA2-AMPA receptor dynamics, basal (evoked) field responses, and synaptic plasticity, using a set of high resolution imaging and electrophysiological approaches. We show that the first pulse of corticosterone causes a transient increase in miniature EPSC frequency, AMPA receptor trafficking and synaptic plasticity, while basal evoked field responses are unaffected. This pattern is not maintained during subsequent applications: responses become more variable, attenuate or even reverse over time, albeit with different kinetics for the various experimental endpoints. This may indicate that the beneficial effect of ultradian pulses on transcriptional regulation in the hippocampus is not consistently accompanied by short-term perturbations in background excitability. In general, this could be interpreted as a means to keep hippocampal neurons responsive to incoming signals related to environmental challenges.
Clinical characteristics and the usefulness of the QuantiFERON-TB Gold In-Tube test in hematologic patients with hepatic or splenic lesions

Background/Aims Hepatic or splenic lesions in hematologic patients are not defined well because they are not easy to evaluate due to limitations of invasive procedures. Management typically depends on the clinical diagnosis with few microbiological data. Methods We reviewed the medical records of consecutive hematologic patients with hepatic or splenic lesions in the infectious diseases unit from April 2009 to December 2010 at the Catholic Hematopoietic Stem Cell Transplantation Center in Korea. Results Twenty-six patients were identified. Their mean age was 46.0 ± 14.7 years, and 16 (61.5%) were male. Underlying diseases were acute myelogenous leukemia (n = 15, 57.7%) and myelodysplastic syndrome (n = 6, 23.1%). Among the nine nontuberculous infectious lesions, two bacterial, six fungal, and one combined infection were identified. The numbers of confirmed, probable, and possible tuberculosis (TB) cases were one, three, and four, respectively. Two patients had concurrent pulmonary TB. QuantiFERON-TB Gold In-Tube (QFT-GIT, Cellestis Ltd.) was positive in seven cases, among which six were diagnosed with TB. The sensitivity and specificity of QFT-GIT were 75% and 81.3%. Nine (34.6%) were defined as noninfectious causes. Conclusions Causes of hepatic or splenic lesion in hematologic patients were diverse including TB, non-TB organisms, and noninfectious origins. TB should be considered for patients not responding to antibacterial or antifungal drugs, even in the absence of direct microbiological evidence. QFT-GIT may be useful for a differential diagnosis of hepatosplenic lesions in hematologic patients.
Trust as a commodity

Trust is central to all transactions and yet economists rarely discuss the notion. It is treated rather as background environment, present whenever called upon, a sort of ever-ready lubricant that permits voluntary participation in production and exchange. In the standard model of a market economy it is taken for granted that consumers meet their budget constraints: they are not allowed to spend more than their wealth. Moreover, they always deliver the goods and services they said they would. But the model is silent on the rectitude of such agents. We are not told if they are persons of honour, conditioned by their upbringing always to meet the obligations they have chosen to undertake, or if there is a background agency which enforces contracts, credibly threatening to mete out punishment if obligations are not fulfilled a punishment sufficiently stiff to deter consumers from ever failing to fulfil them. The same assumptions are made for producers. To be sure, the standard model can be extended to allow for bankruptcy in the face of an uncertain future. One must suppose that there is a special additional loss to becoming bankrupt a loss of honour when honour matters, social and economic ostracism, a term in a debtors’ prison, and so forth. Otherwise, a person may take silly risks or, to make a more subtle point, take insufficient care in managing his affairs, but claim that he ran into genuine bad luck, that it was Mother Nature’s fault and not his own lack of ability or zeal.
Multimodularity, Convexity, and Optimization Properties

In this paper we investigate the properties of multimodular functions. In doing so we give elementary proofs for properties already established by Hajek and we generalize some of his results. In particular, we extend the relation between convexity and multimodularity to some convex subsets of z m . We also obtain general optimization results for average costs related to a sequence of multimodular functions rather than to a single function. Under this general context, we show that the expected average cost problem is optimized by using regular sequences. We finally illustrate the usefulness of this theory in admission control into a D/D/1 queue with fixed batch arrivals, with no state information. We show that the regular policy minimizes the average queue length for the case of an infinite queue, but not for the case of a finite queue. When further adding a constraint on the losses, it is shown that a regular policy is also optimal for the finite queue case.
Bacteriophage-induced Inhibition of Host Functions

Degradation of bacterial deoxyribonucleic acid (DNA) after infection with T4 bacteriophage was studied in an endonuclease I-deficient host. The kinetics of degradation were similar to those seen in other hosts with a normal level of this enzyme. Irradiation of extracellular phage with ultraviolet (UV) destroyed the capacity of the infecting virus to induce extensive breakdown of host DNA, which was, however, converted to high-molecular-weight material. Addition of chloramphenicol to T4-infected cells provided data which can be interpreted to indicate the involvement of at least two endodeoxyribonucleases and one exodeoxyribonuclease having a high degree of specificity. A model is proposed showing the sequential action of two endodeoxyribonucleases followed by an exodeoxyribonuclease in the degradation of host DNA. The appearance of these hydrolytic enzymes requires protein synthesis. Infections leading to partial degradation only (UV-irradiated phages, gene 46 mutants) effectively inhibited the synthesis of bacterial messenger ribonucleic acid and of β-galactosidase.
The genetics of speciation: genes of small effect underlie sexual isolation in the Hawaiian cricket Laupala

Sexual behaviours often evolve rapidly and are critical for sexual isolation. We suggest that coordinated sexual signals and preferences generate stabilizing selection, favouring the accumulation of many small‐effect mutations in sexual communication traits. Rapid radiation of a sexual behaviour used in signalling, song pulse rate, has been observed in the Hawaiian cricket genus Laupala. Using marker‐assisted introgression, we isolated five known quantitative trait loci (QTL) influencing species‐level differences in pulse rate from one species, L. paranigra, into a closely related species, L. kohalensis. All five QTL were found to have a significant effect on song and appear to be largely additive in backcross introgression lines. Furthermore, all effect sizes were small in magnitude. Our data provide support for the hypothesis that stabilizing selection on sexual signals in Laupala creates genetic conditions favourable to incremental divergence during speciation, through the evolution of alleles of minor rather than major phenotypic effects.
LINEAR COMPLEMENTARITY AND ORIENTED MATROIDS

A combinatorial abstraction of the linear complementarity theory in the setting of oriented matroids was first considered by M.J. Todd. In this paper, we take a fresh look at this abstraction, and attempt to give a simple treatment of the combinatorial theory of linear complementarity. We obtain new theorems, proofs and algorithms in oriented matroids whose specializations to the linear case are also new. For this, the notion of sufficiency of square matrices, introduced by Cottle, Pang and Venkateswaran, is extended to oriented rnatroids. Then, we prove a sort of duality theorem for oriented matroids, which roughly states: exactly one of the primal and the dual system has a complementary solution if the associated oriented matroid satisfies "weak" sufficiency. We give two different proofs for this theorem, an elementary inductive proof and an algorithmic proof using the criss-cross method which solves one of the primal or dual problem by using surprisingly simple pivot rules (without any perturbation of the original problem).
In situ Studies and Simulations of Mould Filling with a Model System for PIM

Abstract The processing conditions and the mould design are important parts of the powder injection moulding (PIM) process. In the present work, the mould filling phase of the process has been studied in situ with a special mould equipped with a sight glass using a high speed camera. Effects of features such as the mould temperature, the melt temperature, the surface roughness of the mould cavity, the gate dimensions, the mould design and the flow rate on the filling behaviour were demonstrated. In particular it was noted that a rougher mould surface to some extent facilitated the filling of the mould. The mould temperature, the nominal melt temperature and the flow rate affected the position of weld lines via the cooling of the feedstock and the corresponding change of the melt viscosity. The experimentally determined weld-line positions were compared with predictions from numerical simulations performed with the commercial software Moldex3D. The agreement between the experiment and the prediction was in most cases quite fair or good. The in situ observation of the mould filling also provided the possibility to study how the gate dimensions and the flow rate influenced the jetting behaviour.
Multilump Symmetric and Nonsymmetric Gravity-Capillary Solitary Waves in Deep Water

Multilump gravity-capillary solitary waves propagating in a fluid of infinite depth are computed numerically. The study is based on a weakly nonlinear and dispersive partial differential equation (PDE) with weak variations in the spanwise direction, a model derived by Akers and Milewski [Stud. Appl. Math., 122 (2009), pp. 249--274]. For a two-dimensional fluid, this model agrees qualitatively well with the full Euler equations for the bifurcation curves, wave profiles, and dynamics of solitary waves. Fully localized solitary waves are then computed for three-dimensional fluids. New symmetric lump solutions are computed by using a continuation method to follow the branch of elevation waves. It is then found that the branch of elevation waves has multiple turning points from which new solutions, consisting of multiple lumps separated by smaller oscillations, bifurcate. Nonsymmetric solitary waves, which also feature a multilump structure, are computed and found to appear via spontaneous symmetry-breaking bi.
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data

MOTIVATION ChIP-seq data are enriched in binding sites for the protein immunoprecipitated. Some sequences may also contain binding sites for a coregulator. Biologists are interested in knowing which coregulatory factor motifs may be present in the sequences bound by the protein ChIP'ed. RESULTS We present a finite mixture framework with an expectation-maximization algorithm that considers two motifs jointly and simultaneously determines which sequences contain both motifs, either one or neither of them. Tested on 10 simulated ChIP-seq datasets, our method performed better than repeated application of MEME in predicting sequences containing both motifs. When applied to a mouse liver Foxa2 ChIP-seq dataset involving ~ 12 000 400-bp sequences, coMOTIF identified co-occurrence of Foxa2 with Hnf4a, Cebpa, E-box, Ap1/Maf or Sp1 motifs in ~6-33% of these sequences. These motifs are either known as liver-specific transcription factors or have an important role in liver function. AVAILABILITY Freely available at http://www.niehs.nih.gov/research/resources/software/comotif/. CONTACT li3@niehs.nih.gov SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Anaplasma marginale (Rickettsiales: Anaplasmataceae): recent advances in defining host–pathogen adaptations of a tick-borne rickettsia

The tick-borne intracellular pathogen Anaplasma marginale (Rickettsiales: Anaplasmataceae) develops persistent infections in cattle and tick hosts. While erythrocytes appear to be the only site of infection in cattle, A. marginale undergoes a complex developmental cycle in ticks and transmission occurs via salivary glands during feeding. Many geographic isolates occur that vary in genotype, antigenic composition, morphology and infectivity for ticks. In this chapter we review recent research on the host–vector–pathogen interactions of A. marginale. Major surface proteins (MSPs) play a crucial role in the interaction of A. marginale with host cells. The MSP1a protein, which is an adhesin for bovine erythrocytes and tick cells, is differentially regulated and affects infection and transmission of A. marginale by Dermacentor spp. ticks. MSP2 undergoes antigenic variation and selection in cattle and ticks, and contributes to the maintenance of persistent infections. Phylogenetic studies of A. marginale geographic isolates using msp4 and msp1α provide information about the biogeography and evolution of A. marginale: msp1α genotypes evolve under positive selection pressure. Isolates of A. marginale are maintained by independent transmission events and a mechanism of infection exclusion in cattle and ticks allows for only the infection of one isolate per animal. Prospects for development of control strategies by use of pathogen and tick-derived antigens are discussed. The A. marginale/vector/host studies described herein could serve as a model for research on other tick-borne rickettsiae.
On Inconsistency−Aware Knowledge and Action Bases: Semantics and Verification

Description Logic Knowledge and Action Bases (KABs) have been recently introduced as a mechanism that provides a semantically rich representation of the information on the domain of interest in terms of a DL KB and a set of actions to change such information over time, possibly introducing new objects. In this setting, decidability of verification of sophisticated temporal properties over KABs, expressed in a variant of first-order μcalculus, has been shown. However, the established framework treats inconsistency in a simplistic way, by rejecting inconsistent states produced through action execution. We address this problem by showing how inconsistency handling based on the notion of repairs can be integrated into KABs, resorting to inconsistency-tolerant semantics. In this setting, we establish decidability and complexity of verification.