Miracle-dz/UniFAR-FTUs huggingface dataset:
Entanglement of Identical Particles

Unlike for bipartite states consisting of distinguishable particles, in the case of identical parties the notion of entanglement is still under debate. In the following, we review two different approaches to the entanglement of systems consisting of two Bosons or Fermions; the first approach is based on the particle aspect typical of first quantization and identifies separable pure states as those that allow to assign two orthogonal single particle vector states to both parties. The second approach makes full use of the mode aspect of second quantization whereby separability can be formulated as absence of non-local correlation among two different sets of modes. While the first approach applies to pure states only, the second one is more general and characterizes generic entangled states. In the following, we shall show that the mode-based approach indeed contains the particle-based one.
Non-Markovian Quantum Probes

We review the most recent developments in the theory of open quantum systems focusing on situations in which the reservoir memory effects, due to long-lasting and non-negligible correlations between system and environment, play a crucial role. These systems are often referred to as non-Markovian systems. After a brief summary of different measures of non-Markovianity that have been introduced over the last few years we restrict our analysis to the investigation of information flow between system and environment. Within this framework we introduce an important application of non-Markovianity, namely its use as a quantum probe of complex quantum systems. To illustrate this point we consider quantum probes of ultracold gases, spin chains, and trapped ion crystals and show how properties of these systems can be extracted by means of non-Markovianity measures.
The Global versus Local Hamiltonian Description of Quantum Input-Output Theory

The aim of this paper is to derive the global Hamiltonian form for a quantum system and bath, or more generally a quantum network with multiple quantum input field connections, based on the local descriptions. We give a new simple argument which shows that the global Hamiltonian for a single Markov component arises as the singular perturbation of the free translation operator. We show that the Fermi analogue takes an equivalent form provided the parity of the coefficients is correctly specified. This allows us to immediately extend the theory of quantum feedback networks to Fermi systems.
Selective plane illumination microscopy techniques in developmental biology

Selective plane illumination microscopy (SPIM) and other fluorescence microscopy techniques in which a focused sheet of light serves to illuminate the sample have become increasingly popular in developmental studies. Fluorescence light-sheet microscopy bridges the gap in image quality between fluorescence stereomicroscopy and high-resolution imaging of fixed tissue sections. In addition, high depth penetration, low bleaching and high acquisition speeds make light-sheet microscopy ideally suited for extended time-lapse experiments in live embryos. This review compares the benefits and challenges of light-sheet microscopy with established fluorescence microscopy techniques such as confocal microscopy and discusses the different implementations and applications of this easily adaptable technology.
Primary cilia regulate Shh activity in the control of molar tooth number

Primary cilia mediate Hh signalling and mutations in their protein components affect Hh activity. We show that in mice mutant for a cilia intraflagellar transport (IFT) protein, IFT88/polaris, Shh activity is increased in the toothless diastema mesenchyme of the embryonic jaw primordia. This results in the formation of ectopic teeth in the diastema, mesial to the first molars. This phenotype is specific to loss of polaris activity in the mesenchyme since loss of Polaris in the epithelium has no detrimental affect on tooth development. To further confirm that upregulation of Shh activity is responsible for the ectopic tooth formation, we analysed mice mutant for Gas1, a Shh protein antagonist in diastema mesenchyme. Gas1 mutants also had ectopic diastema teeth and accompanying increased Shh activity. In this context, therefore, primary cilia exert a specific negative regulatory effect on Shh activity that functions to repress tooth formation and thus determine tooth number. Strikingly, the ectopic teeth adopt a size and shape characteristic of premolars, a tooth type that was lost in mice around 50-100 million years ago.
Non-canonical Wnt signaling regulates cell polarity in female reproductive tract development via van gogh-like 2

Wnt signaling effectors direct the development and adult remodeling of the female reproductive tract (FRT); however, the role of non-canonical Wnt signaling has not been explored in this tissue. The non-canonical Wnt signaling protein van gogh-like 2 is mutated in loop-tail (Lp) mutant mice (Vangl2Lp), which display defects in multiple tissues. We find that Vangl2Lp mutant uterine epithelium displays altered cell polarity, concommitant with changes in cytoskeletal actin and scribble (scribbled, Scrb1) localization. The postnatal mutant phenotype is an exacerbation of that seen at birth, exhibiting more smooth muscle and reduced stromal mesenchyme. These data suggest that early changes in cell polarity have lasting consequences for FRT development. Furthermore, Vangl2 is required to restrict Scrb1 protein to the basolateral epithelial membrane in the neonatal uterus, and an accumulation of fibrillar-like structures observed by electron microscopy in Vangl2Lp mutant epithelium suggests that mislocalization of Scrb1 in mutants alters the composition of the apical face of the epithelium. Heterozygous and homozygous Vangl2Lp mutant postnatal tissues exhibit similar phenotypes and polarity defects and display a 50% reduction in Wnt7a levels, suggesting that the Vangl2Lp mutation acts dominantly in the FRT. These studies demonstrate that the establishment and maintenance of cell polarity through non-canonical Wnt signaling are required for FRT development.
Improving Supervised Learning by Sample Decomposition

This paper introduces a new ensemble technique, cluster-based concurrent decomposition (CBCD) that induces an ensemble of classifiers by decomposing the training set into mutually exclusive sub-samples of equal-size. The CBCD algorithm first clusters the instance space by using the K-means clustering algorithm. Afterwards it produces disjoint sub-samples using the clusters in such a way that each sub-sample is comprised of tuples from all clusters and hence represents the entire dataset. An induction algorithm is applied in turn to each subset, followed by a voting mechanism that combines the classifier's predictions. The CBCD algorithm has two tuning parameters: the number of clusters and the number of subsets to create. Using a suitable meta-learning it is possible to tune these parameters properly. In the experimental study we conducted, the CBCD algorithm, using an embedded C4.5 algorithm, outperformed the bagging algorithm of the same computational complexity.
Ga-Based Optimization of tapering Windows for Artifact Reduction in Fourier electron Magnetic Resonance Images

Optimization of tapering windows for artifact reduction in two-dimensional (2D) Fourier electron magnetic resonance (EMR) tomography using genetic algorithm (GA) is presented. EMR imaging (EMRI) is a fast emerging functional imaging modality for studying free radicals in biological systems. EMRI by single point imaging (SPI) modality is a Fourier imaging technique. The bioclearance of the imaging agent as well as the need to minimize the radio frequency power deposition on the live animals, dictate reduced k-space sampling. This leads to ringing (Gibbs) artifacts in both directions of the 2D image, because, unlike the conventional MRI, SPI is phase encoding in both directions. To dampen the high-frequency components, data tapering windows are multiplicatively applied to provide tolerable blurred resultant image with reduced Gibbs ringing. To find a compromise between blur and ringing artifact, in this paper a method of optimizing the window functions by using GA is proposed. Our experiments suggest GA-based Kaiser window shows better performance by visual as well as quantitative evaluation.
Longitudinal Analysis of Quantitative Virologic Measures in Human Immunodeficiency Virus-Infected Subjects with ⩾400 CD4 Lymphocytes: Implications for Applying Measurements to Individual Patients

The natural variability of quantitative virologicmeasures among human immunodeficiency virus (HIV) type 1-infected persons was prospectively studied in 29 untreated persons with >600 CD4 cells/ILL and in 15 persons receiving zidovudine monotherapy who had 400-550 CD4 cells/ILL at study entry. Cell- and plasma-associated infectious HIV-1, provirus, and virion RNA were deter­ mined monthly as were numbers of CD4 and CD8 cells. HIV-1 replication varied widely among subjects with similar CD4 cell counts. The within-individual variability was significantly less than the variability between subjects for all virologicmeasures. Plasma virion HIV-1 RNA levels had the least variability. A mathematical model was devised to assess whether a potential therapeutic intervention significantlyalters peripheral HIV-1 load. The model indicated that three measurements of plasma RNA would be outside the 95th percentile for the expected change in an individual due to natural variability. This approach can be used to accurately assess a therapeutic intervention among persons with low plasma HIV-1 titers. A number of studies have found that human immunodefi­ ciency virus (HIV) type 1 persistently replicates during the course of infection [1-5]. Both acute and chronic infections are associated with detectable levels of virus in the peripheral circulation [6-8]. Although lymphoid tissue is the primary tissue site of HIV -1 replication, cross-sectional studies have shown an inverse correlation between a high titer of HIV-1 in peripheral blood mononuclear cells (PBMC) and plasma and low CD4 cell counts [9-13]. While some studies have shown a correlation between increases in virus load and the progres­ sion of infection [14-18], few have quantitated HIV-l load among untreated clinically asymptomatic individuals over time, and little is known about the natural variation in these virus load measurements. We performed detailed analyses of the proviral, viral RNA, and infectious load in the peripheral blood of a group of HIV-l-infected subjects with >400 CD4 cells/ f.LL in order to develop a model by which one could measure in a single person the degree of change indicative of virologic progression or significant inhibition by a therapeutic inter­ vention.
An Intelligent Computer Assistance System for Artifact Restoration Based on Genetic Algorithms with Plane Image Features

Restoration work of archaeological artifacts broken into pieces is similar to putting together a jigsaw puzzle. The purpose of this study is to construct an intelligent computer assistance system to conveniently restore archaeological discoveries from some fragments. AReal-Coded Genetic Algorithm (RCGA) was applicable for solving the positioning problem of a three-dimensional (3D) restoration. The fitness function value for RCGA was calculated from image similarity between the target and correct patterns in plane images at multiple camera angles. Image features of a 3D object were obtained by the ORB (Oriented FAST and Rotated BRIEF), BRISK (Binary Robust Invariant Scalable Keypoints), and Accelerated KAZE (AKAZE) techniques; they were considered as a part of the fitness function value. Simulation study revealed that the RCGA approach was capable of automatically and efficiently adjusting the positions of 3D fragments, especially in the AKAZE technique. A user interface with the functions of design drawing was also created to assist in repair work. The interactive assistance interface for 3D restoration based on RCGA and followed by the hill-climbing algorithm would be applied to practical applications for digital archives of artifacts.
Ensemble Empirical Mode Decomposition: a Noise-Assisted Data Analysis Method

A new Ensemble Empirical Mode Decomposition (EEMD) is presented. This new approach consists of sifting an ensemble of white noise-added signal (data) and treats the mean as the final true result. Finite, not infinitesimal, amplitude white noise is necessary to force the ensemble to exhaust all possible solutions in the sifting process, thus making the different scale signals to collate in the proper intrinsic mode functions (IMF) dictated by the dyadic filter banks. As EEMD is a time–space analysis method, the added white noise is averaged out with sufficient number of trials; the only persistent part that survives the averaging process is the component of the signal (original data), which is then treated as the true and more physical meaningful answer. The effect of the added white noise is to provide a uniform reference frame in the time–frequency space; therefore, the added noise collates the portion of the signal of comparable scale in one IMF. With this ensemble mean, one can separate scales naturall.
Hindbrain patterning requires fine-tuning of early krox20 transcription by Sprouty 4

Vertebrate hindbrain segmentation is an evolutionarily conserved process that involves a complex interplay of transcription factors and signalling pathways. Fibroblast growth factor (FGF) signalling plays a major role, notably by controlling the expression of the transcription factor Krox20 (Egr2), which is required for the formation and specification of two segmental units: rhombomeres (r) 3 and 5. Here, we explore the molecular mechanisms downstream of FGF signalling and the function of Sprouty 4 (Spry4), a negative-feedback regulator of this pathway, in zebrafish. We show that precise modulation of FGF signalling by Spry4 is required to determine the appropriate onset of krox20 transcription in r3 and r5 and, ultimately, rhombomere size in the r3-r5 region. FGF signalling acts by modulating the activity of krox20 initiator enhancer elements B and C; in r5, we show that this regulation is mediated by direct binding of the transcription factor MafB to element B. By contrast, FGF signalling does not control the krox20 autoregulatory element A, which is responsible for amplification and maintenance of krox20 expression. Therefore, early krox20 transcription sets the blueprint for r3-r5 patterning. This work illustrates the necessity for fine-tuning in a common and fundamental patterning process, based on a bistable cell-fate choice involving the coupling of an extracellular gradient with a positive-feedback loop. In this mode of patterning, precision and robustness can be achieved by the introduction of a negative-feedback loop, which, in the hindbrain, is mediated by Spry4.
A Low-Cost Range-Free Localization Scheme for Three-Dimensional Underwater Sensor Networks

Localization is one of the fundamental tasks for underwater sensors networks (USNs). It is required for data tagging, target detection, route protocols, and so on. In this paper, we propose an efficient low-cost range-free localization scheme for 3D underwater sensor networks (3D-LRLS) without any additional hardware infrastructure. In our scheme, each anchor node has variable transmission power levels. At first, the power levels of each anchor are decided by the Delaunay triangulation for the network space. Then, ordinary sensors listen to the beacons sent from the anchor nodes. Based on the beacon messages, each node calculates its location individually by a low computational complexity method. The extensive simulation results demonstrate that 3D-LRLS is efficient in terms of both localization ratio and localization accuracy.
The decycling number of

A set of vertices of a graph whose removal leaves an acyclic graph is called a decycling set of the graph. The minimum size of a decycling set of a graph G is referred to as the decycling number of G, denoted by ∇(G). In this paper, we study the decycling number of the Cartesian product of two paths, ∇(Pm□Pn), and obtain several new results. Mainly, we prove that $\lceil \frac{(m-1)(n-1)+1}{3}\rceil \leq \nabla(P_{m} \square P_{n})\leq \lceil \frac{(m-1)(n-1)+1}{3} \rceil+1$. Moreover, we obtain the exact value of ∇(Pm□Pn) for some classes (modulo 6) of pairs (m, n).
Snail2 controls mesodermal BMP/Wnt induction of neural crest

The neural crest is an induced tissue that is unique to vertebrates. In the clawed frog Xenopus laevis, neural crest induction depends on signals secreted from the prospective dorsolateral mesodermal zone during gastrulation. The transcription factors Snail2 (Slug), Snail1 and Twist1 are expressed in this region. It is known that Snail2 and Twist1 are required for both mesoderm formation and neural crest induction. Using targeted blastomere injection, morpholino-based loss of function and explant studies, we show that: (1) Snail1 is also required for mesoderm and neural crest formation; (2) loss of snail1, snail2 or twist1 function in the C2/C3 lineage of 32-cell embryos blocks mesoderm formation, but neural crest is lost only in the case of snail2 loss of function; (3) snail2 mutant loss of neural crest involves mesoderm-derived secreted factors and can be rescued synergistically by bmp4 and wnt8 RNAs; and (4) loss of snail2 activity leads to changes in the RNA levels of a number of BMP and Wnt agonists and antagonists. Taken together, these results identify Snail2 as a key regulator of the signals involved in mesodermal induction of neural crest.
Dictation of Japanese Speech Based on Kana and Kanji Character String

In this paper, character-based Japanese dictation method is proposed. This method is based on the kana and kanji string language model proposed by Ito et al. First, sentences in the training corpus are split into character-based units (CBUs). Then strings of CBUs (CBUSes) are chosen from the CBU corpus based on a statistical criterion. We examined three criteria for the CBUS selection. They are the frequency-based selection, the mutual-information based selection and their combination. From the experimental results, it was found that the combined method gave the best result (7.19% and 8.75% CBU error rates for the 20k and the 60k word vocabulary conditions, respectively) which was better than the ordinary word-based method (7.61% and 9.15% CBU error rates for the 20k and the 60k word vocabulary conditions, respectively). In addition, we carried out a recognition experiment for the Corpus of Spontaneous Japanese to confirm that the proposed method is effective for not only the read speech but also for spontaneous speech. As a result, we obtained the best result (29.82%) using the frequency-based method, which is better than the word-based recognition result (32.80%).
Exploring the Granularity Level of Social Tags

Tags are widely used in Web 2.0 applications, such as blogs and online bookmarks. Many characteristics of tags have been studied in previous works, but the granularity level of tags still remains untouched. Granularity level describes how focused a tag is, the lower the level, the more concrete concept the tag covers. The paper has three main contributions: 1) We propose a method to discover the concept level of tags automatically. 2) We apply the method to a real-world tag data set, and study the distribution of levels. 3) We perform tag recommendation concerning their concept levels. Experiments are conducted on a large-scale real world Chinese blog data set. We find that most tags are in more concrete levels, and the users tend to choose tags within the same concept level for a document. When predicting tags for a new document, tags in higher concept levels provide little help, yet may hurt the performance.
Retinoic acid-dependent and -independent gene-regulatory pathways of Pitx3 in meso-diencephalic dopaminergic neurons

Development of meso-diencephalic dopamine (mdDA) neurons requires the combined actions of the orphan nuclear receptor Nurr1 and the paired-like homeobox transcription factor Pitx3. Whereas all mdDA neurons require Nurr1 for expression of Th and survival, dependence on Pitx3 is displayed only by the mdDA subpopulation that will form the substantia nigra (SNc). Previously, we have demonstrated that Pitx3–/– embryos lack the expression of the retinoic acid (RA)-generating enzyme Ahd2, which is normally selectively expressed in the Pitx3-dependent DA neurons of the SNc. Restoring RA signaling in Pitx3–/– embryos revealed a selective dependence of SNc neurons on the presence of RA for differentiation into Th-positive neurons and maintenance throughout embryonic development. Whereas these data are suggestive of an important developmental role for RA in neurons of the SNc, it remained unclear whether other Nurr1 and Pitx3 target genes depend on RA signaling in a manner similar to Th. In the search for genes that were affected in Pitx3-deficient mdDA neurons and restored upon embryonic RA treatment, we provide evidence that Delta-like 1, D2R (Drd2) and Th are regulated by Pitx3 and RA signaling, which influences the mdDA terminal differentiated phenotype. Furthermore, we show that regulation of Ahd2-mediated RA signaling represents only one aspect of the Pitx3 downstream cascade, as Vmat2, Dat, Ahd2 (Aldh1a1), En1, En2 and Cck were unaffected by RA treatment and are (subset) specifically modulated by Pitx3. In conclusion, our data reveal several RA-dependent and -independent aspects of the Pitx3-regulated gene cascade, suggesting that Pitx3 acts on multiple levels in the molecular subset-specification of mdDA neurons.
Growth Hormone and Testosterone: Effects on Whole Body Metabolism and Skeletal Muscle in Adolescence

The characteristic changes in human puberty – increased muscle bulk, increased linear growth, and the mineralization of the skeleton – are due, in part, to the combined effects of growth hormone (GH), insulin-like growth factor I (IGF-I), sex hormones and insulin. GH and testosterone, but not oestrogen, are highly protein-anabolic in vivo, and the combined administration of GH and testosterone has synergistic effects on these measures, both in children and adults. GH has no significant effect on enhancing skeletal muscle strength in humans; however, testosterone is highly ergogenic and is largely responsible for the differences in muscle bulk apparent in late puberty between the genders. The results of recent detailed metabolic studies suggest that boys have higher rates of protein synthesis and IGF-I generation than girls, given comparable doses of GH. In patients with a constitutional delay in growth and maturation, relative deficiencies in testosterone and lower IGF-I concentrations are associated with greater rates of total energy expenditure, suggesting that this relatively hormone-insufficient state is associated with a hypermetabolic state. Whether added nutritional supplements, alone or in combination with GH, could improve the growth pattern and final height of these children deserves further study. In conclusion, the metabolic effects of GH and testosterone are complex and they synergize in puberty. These hormones could be of use as protein-anabolic agents in selected catabolic conditions.