Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryptic deletions are a common finding in “balanced” reciprocal and complex chromosome rearrangements: a study of 59 patients

Using array comparative genome hybridisation (CGH) 41 de novo reciprocal translocations and 18 de novo complex chromosome rearrangements (CCRs) were screened. All cases had been interpreted as “balanced” by conventional cytogenetics. In all, 27 cases of reciprocal translocations were detected in patients with an abnormal phenotype, and after array CGH analysis, 11 were found to be unbalanced. Thus 40% (11 of 27) of patients with a “chromosomal phenotype” and an apparently balanced translocation were in fact unbalanced, and 18% (5 of 27) of the reciprocal translocations were instead complex rearrangements with >3 breakpoints. Fourteen fetuses with de novo, apparently balanced translocations, all but two with normal ultrasound findings, were also analysed and all were found to be normal using array CGH. Thirteen CCRs were detected in patients with abnormal phenotypes, two in women who had experienced repeated spontaneous abortions and three in fetuses. Sixteen patients were found to have unbalanced mutations, with up to 4 deletions. These results suggest that genome-wide array CGH may be advisable in all carriers of “balanced” CCRs. The parental origin of the deletions was investigated in 5 reciprocal translocations and 11 CCRs; all were found to be paternal. Using customised platforms in seven cases of CCRs, the deletion breakpoints were narrowed down to regions of a few hundred base pairs in length. No susceptibility motifs were associated with the imbalances. These results show that the phenotypic abnormalities of apparently balanced de novo CCRs are mainly due to cryptic deletions and that spermatogenesis is more prone to generate multiple chaotic chromosome imbalances and reciprocal translocations than oogenesis.
Bipartite graph partitioning and data clustering

Many data types arising from data mining applications can be modeled as bipartite graphs, examples include terms and documents in a text corpus, customers and purchasing items in market basket analysis and reviewers and movies in a movie recommender system. In this paper, we propose a new data clustering method based on partitioning the underlying bipartite graph. The partition is constructed by minimizing a normalized sum of edge weights between unmatched pairs of vertices of the bipartite graph. We show that an approximate solution to the minimization problem can be obtained by computing a partial singular value decomposition (SVD) of the associated edge weight matrix of the bipartite graph. We point out the connection of our clustering algorithm to correspondence analysis used in multivariate analysis. We also briefly discuss the issue of assigning data objects to multiple clusters. In the experimental results, we apply our clustering algorithm to the problem of document clustering to illustrate its effectiveness and efficiency.
Mixed-Mode Stress Intensity Factors for Tubes under Pure Torsion Loading

Although it seems like a common load-geometry configuration, there is neither an analytical nor a numerical solution for Stress Intensity Factors (SIF) in cracked tubes under pure torsion. Standards such as API 579, BS 7910 or handbooks do not present such case. There is plenty of solutions based on FEM or weight functions calculations for an extensive load-geometry combinations, but not for tubes under pure torsion. This paper shows curves of KI, KII, and KIII for through-wall cracks obtained with ANSYS simulations for slim tubes, under pure torsion with a rounded horizontal slit, numerically calculated via J-integral. Additionally KI, KII, and KIII are calculated using relative displacement between two points along the crack lips using Linear Elastic Fracture Mechanics (LEFM) formulations for Crack Tip Opening Displacement (COD) and Crack Tip Sliding Displacement (CTSD). Results are compared with experimentally measured SIF using the Digital Image Correlation (DIC) technique for fatigued-growth cracks reported in literature.
Synthesis of minimal-error control software

Software implementations of controllers for physical systems are at the core of many embedded systems. The design of controllers uses the theory of dynamical systems to construct a mathematical control law that ensures that the controlled system has certain properties, such as asymptotic convergence to an equilibrium point, and optimizes some performance criteria such as LQR-LQG. However, owing to quantization errors arising from the use of fixed-point arithmetic, the implementation of this control law can only guarantee practical stability: under the actions of the implementation, the trajectories of the controlled system converge to a bounded set around the equilibrium point, and the size of the bounded set is proportional to the error in the implementation. The problem of verifying whether a controller implementation achieves practical stability for a given bounded set has been studied before. In this paper, we change the emphasis from verification to automatic synthesis. We give a technique to synthesize embedded control software that is Pareto optimal w.r. t. both performance criteria and practical stability regions. Our technique uses static analysis to estimate quantization-related errors for specific controller implementations, and performs stochastic local search over the space of possible controllers using particle swarm optimization. The effectiveness of our technique is illustrated using several standard control system examples: in most examples, we find controllers with close-to-optimal LQR-LQG performance but with implementation errors, hence regions of practical stability, several times as small.
A Machine Learning Framework for Register Placement Optimization in Digital Circuit Design

In modern digital circuit back-end design, designers heavily rely on electronic-design-automoation (EDA) tool to close timing. However, the heuristic algorithms used in the place and route tool usually does not result in optimal solution. Thus, significant design effort is used to tune parameters or provide user constraints or guidelines to improve the tool performance. In this paper, we targeted at those optimization space left behind by the EDA tools and propose a machine learning framework that helps to define what are the guidelines and constraints for registers placement, which can yield better performance and quality for back-end design. In other words, the framework is trying to learn what are the flaws of the existing EDA tools and tries to optimize it by providing additional information. We discuss what is the proper input feature vector to be extracted, and what is metric to be used for reference output. We also develop a scheme to generate perturbed training samples using existing design based on Gaussian randomization. By applying our methodology, we are able to improve the design runtime by up to 36% and timing quality by up to 23%.
Logic Circuits Operating in Subthreshold Voltages

In this paper different logic circuit families operating in the subthreshold region are analyzed. Their performance in terms of power and speed are of particular interest. The study complements existing work that has reported static CMOS circuit performance under different body biasing schemes in the subthreshold region. Further it offers assurances on noise margins with scaling going beyond the 100 nm technology node. Simulations have been performed at the 180 nm technology node using a 6 metal layer TSMC process. A tunable body biasing scheme that allows bulk CMOS circuits to operate efficiently at subthreshold as well as above threshold voltages is introduced. The scheme improves a five-stage NAND ring oscillator switching speed 6times better than the static CMOS configuration while dissipating 18% less power
Motif Discovery as a Multiple-Instance Problem

Motif discovery from bio sequences, a challenging task both experimentally and computationally, has been a topic of immense study in recent years. In this paper, we formulate the motif discovery problem as a multiple-instance problem and employ a multiple-instance learning method, the MILES method, to identify motif from biological sequences. Each sequence is mapped into a feature space defined by instances in training sequences with a novel instance-bag similarity measure. We employ I-norm SVM to select important features and construct classifiers simultaneously. These high-ranked features correspond to discovered motifs. We apply this method to discover transcriptional factor binding sites in promoters, a typical motif finding problem in biology, and show that the method is at least comparable to existing methods
Test procedure for stress damage of ferromagnetic materials based on metal magnetic memory effects

Abstract The metal magnetic memory effect is highly sensitive to stress. This experimental investigation of the magnetic memory signal characteristic of a ferromagnetic material at different stress-strain states has been performed using X80 steel specimens. The magnetic signals were measured in accordance with these procedures at twice the elastic deformation and once the elastic deformation to fracture under the tensile load. The results indicate that magnetic memory signals linearly decrease with increasing tensile load in the elastic state and the reverse in the plastic stage. The intensity clearly increases when damage occurs which can be taken as evidence for damage caused by stress. The test was performed on an actual pipeline with a crack created by a special device. The effect of metal magnetic memory for the evaluation of damage caused by stress has thus been verified by this engineering procedure.
Serologic abnormalities in multiple sclerosis

Acute phase reactants. In the search for an even more sensitive gauge of disease activity, we measured serum levels of the fourth component of the classical complement pathway (C4) in MS patients. Serum levels of C4 were determined by radial immunodiffusion in 90 MS patients manifesting a wide spectrum of disease activity and neurologic impairment. Twentythree patients had significantly elevated levels of C4 when compared to normal controls. At least 16 of these patients had experienced a recent exacerbation of MS or had rapidly progressing neurologic deficits. C3 proactivator, as well as the acute phase reactants C-reactive protein and orosomucoid, were found to be significantly increased in most of these patients, whereas another component of the classical complement pathway, C3, was rarely abnormal. These findings suggest that C4 acts as an acute phase reactant in some exacerbations of MS and that serial measurements may be of value in assessing disease activity in certain patients.
TGFβ1 Attenuates Expression of Prolactin and IGFBP-1 in Decidualized Endometrial Stromal Cells by Both SMAD-Dependent and SMAD-Independent Pathways

Background Decidualization (differentiation) of the endometrial stromal cells during the secretory phase of the menstrual cycle is essential for successful implantation. Transforming Growth Factor β1 (TGFβ1) canonically propagates its actions via SMAD signalling. A role for TGFβ1 in decidualization remains to be established and published data concerning effects of TGFβ1 on markers of endometrial decidualization are inconsistent. Methodology/Principal Findings Non-pregnant endometrial stromal cells (ESC) and first trimester decidual stromal cells (DSC) were cultured in the presence or absence of a decidualizing stimulus. Incubation of ESCs with TGFβ1 (10 ng/ml) down-regulated the expression of transcripts encoding the decidual marker proteins prolactin (PRL), insulin-like growth factor binding protein-1 (IGFBP-1) and tissue factor (TF). TGFβ1 also inhibited secretion of PRL and IGFBP-1 proteins by ESCs and surprisingly this response preceded down-regulation of their mRNAs. In contrast, DSCs were more refractory to the actions of TGFβ1, characterized by blunted and delayed down-regulation of PRL, IGFBP-1, and TF transcripts, which was not associated with a significant reduction in secretion of PRL or IGFBP-1 proteins. Addition of an antibody directed against TGFβ1 increased expression of IGFBP-1 mRNA in decidualised cells. Knockdown of SMAD 4 using siRNAs abrogated the effect of TGFβ1 on expression of PRL in ESCs but did not fully restore expression of IGFBP-1 mRNA and protein. Conclusions/Significance TGFβ1 inhibits the expression and secretion of decidual marker proteins. The impact of TGFβ1 on PRL is SMAD-dependent but the impact on IGFBP1 is via an alternative mechanism. In early pregnancy, resistance of DSC to the impact of TGFβ1 may be important to ensure tissue homeostasis.
Improving Responsiveness of Hard Real-Time Embedded Systems

Abstract--- Hard real-time systems are found in many critical embedded applications, for example aeroplane flight control, industrial production line control, and so on. The safe scheduling of tasks in these hard real-time systems is crucial to their correct operation, but the hard constraints of this type of scheduling reduce the responsiveness of the systems. In this paper we show the application of runtime analysis in informing the design of hard real-time embedded systems by allowing scheduled tasks to be dynamically re-ordered to improve the average responsiveness, while still meeting the hard constraints imposed by the system. The technique is semi-automated, and uses the reduce computer algebra system to precalculate a symbolic form of the runtime of scheduled tasks. The symbolic form is used to modify the source code of the scheduler.
Automatic summarization of Polish news articles by sentence selection

This paper describes the automatic summarization system developed for the Polish language. The system implements sentence-based extractive summarization technique, which consists in determining most important sentences in document due to their computed salience. A structure of the system is presented, as well as the evaluation method and achieved results. The presented attempt is intended to serve as the baseline for future solutions, as it is the first summarization project evaluated against the Polish Summaries Corpus, the standardized corpus of summaries for the Polish language.
Editorial: Perception–Cognition Interface and Cross-Modal Experiences: Insights into Unified Consciousness

The present Research Topic explores closely related aspects of mental functioning, namely an interplay between perception and cognition, interactions among various sensory modalities, and finally, more or less unified conscious experiences arising in the context of these relations. Contributions emphasize a high flexibility observed in perception and may be seen as potential challenges to the traditional modular architecture of perceptual systems. Although the articles describe different phenomena, they follow one common theme—to investigate broadly understood unified experience—by studying either perception–cognition integration or the integration between sensory modalities. These integrative processes may well apply to subpersonal unconscious representations. However, the aim here is to approach phenomenal experience and thus a straightforward way of thinking about it is in terms of conscious perception. One of the seemingly principled divisions in the human mind is between sense perception and high-level cognition. Traditionally, perception and cognition have been viewed as distinct, encapsulated domains operating independently of each other although the mentioned division between perceiving and reasoning may seem conceptually clear and unambiguous, these mental domains become closely intertwined when our beliefs, expectations, or desires affect what we see, hear, or taste, leading to complex phenomenal states of a hybrid nature. No matter whether we assume that there is no dichotomy between perception and cognition (Clark, 2013; Lupyan, 2015) or instead assume that there is a principled difference and a joint in nature between perception and cognition (Block, submitted; cf. Firestone and Scholl, 2015), cognitive-sensory interactions can and need to be accommodated within any of these accounts. Perception has typically been studied in a single sense, mostly in the visual or auditory modality (Haynes et al.
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping

MOTIVATION Calculating the edit-distance (i.e. minimum number of insertions, deletions and substitutions) between short DNA sequences is the primary task performed by seed-and-extend based mappers, which compare billions of sequences. In practice, only sequence pairs with a small edit-distance provide useful scientific data. However, the majority of sequence pairs analyzed by seed-and-extend based mappers differ by significantly more errors than what is typically allowed. Such error-abundant sequence pairs needlessly waste resources and severely hinder the performance of read mappers. Therefore, it is crucial to develop a fast and accurate filter that can rapidly and efficiently detect error-abundant string pairs and remove them from consideration before more computationally expensive methods are used. RESULTS We present a simple and efficient algorithm, Shifted Hamming Distance (SHD), which accelerates the alignment verification procedure in read mapping, by quickly filtering out error-abundant sequence pairs using bit-parallel and SIMD-parallel operations. SHD only filters string pairs that contain more errors than a user-defined threshold, making it fully comprehensive. It also maintains high accuracy with moderate error threshold (up to 5% of the string length) while achieving a 3-fold speedup over the best previous algorithm (Gene Myers's bit-vector algorithm). SHD is compatible with all mappers that perform sequence alignment for verification.
An Automated Method for Annual Cropland Mapping along the Season for Various Globally-Distributed Agrosystems Using High Spatial and Temporal Resolution Time Series

Cropland mapping relies heavily on field data for algorithm calibration, making it, in many cases, applicable only at the field campaign scale. While the recently launched Sentinel-2 satellite will be able to deliver time series over large regions, it will not really be compatible with the current mapping approach or the available in situ data. This research introduces a generic methodology for mapping annual cropland along the season at high spatial resolution with the use of globally available baseline land cover and no need for field data. The methodology is based on cropland-specific temporal features, which are able to cope with the diversity of agricultural systems, prior information from which mislabeled pixels have been removed and a cost-effective classifier. Thanks to the JECAM network, eight sites across the world were selected for global cropland mapping benchmarking. Accurate cropland maps were produced at the end of the season, showing an overall accuracy of more than 85%. Early cropland maps were also obtained at three-month intervals after the beginning of the growing season, and these showed reasonable accuracy at the three-month stage (>70% overall accuracy) and progressive improvement along the season. The trimming-based method was found to be key for using spatially coarse baseline land cover information and, thus, avoiding costly field campaigns for prior information retrieval. The accuracy and timeliness of the proposed approach shows that it has substantial potential for operational agriculture monitoring programs.
Cell surface receptors for herpes simplex virus are heparan sulfate proteoglycans

The role of cell surface heparan sulfate in herpes simplex virus (HSV) infection was investigated using CHO cell mutants defective in various aspects of glycosaminoglycan synthesis. Binding of radiolabeled virus to the cells and infection were assessed in mutant and wild-type cells. Virus bound efficiently to wild-type cells and initiated an abortive infection in which immediate-early or alpha viral genes were expressed, despite limited production of late viral proteins and progeny virus. Binding of virus to heparan sulfate-deficient mutant cells was severely impaired and mutant cells were resistant to HSV infection. Intermediate levels of binding and infection were observed for a CHO cell mutant that produced undersulfated heparan sulfate. These results show that heparan sulfate moieties of cell surface proteoglycans serve as receptors for HSV.
Organization of the retina of the mudpuppy, Necturus maculosus. II. Intracellular recording.

the optic nerve, it has been possible to specify many of the functions performed bv the vertebrate retina. These include brightness detection (16, 18, 27), centersurround contrast detection (1, 8, 20, 23), and motion detection (3, 4, 26-28). It has not been possible, however, to determine how the retina organizes the visual message recorded at the optic nerve, primarily because intracellular recording from single cells distal to the ganglion cells has been difficult. Detailed structural studies of the vertebrate retina, such as the one in the preceding paper (14), provide a framework within which the functional organization of the retina can be described. The anatomical studies show a limited number of clearly defined synaptic structures at which interaction between specific neurons can take place. In this paper we shall describe the intracellularly recorded response characteristics of each type of neuron in a vertebrate retina, and then relate the response of each neuron to the responses of those neurons to which it is synaptically coupled. By following the responses through the synaptic pathways, we can begin to describe how information from the visual field is abstracted and encoded in the retina. Intracellular recording throughout most retinas has been difficult because even the finest available micropipettes fail to penetrate the small retinal neurons consistently without damage. Bortoff (5-7) showed that this difficulty could be overcome by recording in an animal with larger retinal neurons: the mudpuppy, Nectwus maculosus. As described in the preceding paper (14),
Pharmaceuticals and Worker Productivity Loss: A Critical Review of the Literature

Many chronic illnesses that affect the working population can cause losses in productivity. The extent to which these productivity losses can be reduced by pharmacological treatment is of particular interest to employers, who bear the productivity costs and subsidize the cost of employees’ health care. In the past several years, the effects of pharmaceuticals on productivity losses have been tested in numerous studies, including randomized, double-blind, placebo-controlled trials. In this article, we summarize and critically review these studies and, where appropriate, provide quantitative overviews. The evidence is very good for about a dozen drug classes that pharmaceuticals reduce productivity losses caused by respiratory illnesses (ie, asthma, allergic disorders, bronchitis, upper respiratory infections, and influenza) diabetes, depression, dysmenorrhea, and migraine. We also discuss the calculation of productivity costs, reductions in which may partially or completely offset the costs of treatment. This information should be helpful to occupational physicians who are increasingly providing recommendations on employer benefit plan designs and pharmaceutical benefits.