Miracle-dz/UniFAR-FTUs huggingface dataset:
ALG: Automated Genotype Calling of Luminex Assays

Single nucleotide polymorphisms (SNPs) are the most commonly used polymorphic markers in genetics studies. Among the different platforms for SNP genotyping, Luminex is one of the less exploited mainly due to the lack of a robust (semi-automated and replicable) freely available genotype calling software. Here we describe a clustering algorithm that provides automated SNP calls for Luminex genotyping assays. We genotyped 3 SNPs in a cohort of 330 childhood leukemia patients, 200 parents of patient and 325 healthy individuals and used the Automated Luminex Genotyping (ALG) algorithm for SNP calling. ALG genotypes were called twice to test for reproducibility and were compared to sequencing data to test for accuracy. Globally, this analysis demonstrates the accuracy (99.6%) of the method, its reproducibility (99.8%) and the low level of no genotyping calls (3.4%). The high efficiency of the method proves that ALG is a suitable alternative to the current commercial software. ALG is semi-automated, and provides numerical measures of confidence for each SNP called, as well as an effective graphical plot. Moreover ALG can be used either through a graphical user interface, requiring no specific informatics knowledge, or through command line with access to the open source code. The ALG software has been implemented in R and is freely available for non-commercial use either at http://alg.sourceforge. net or by request to mathieu.bourgey@umontreal.ca
Aménagement des fins de carrière : entre reconfiguration des temps sociaux et transformations normatives

L’objectif de cet article est de comprendre les transformations des temporalites actuelles, a travers le prisme des fins de carriere. Il s’agira de montrer combien le developpement de dispositifs specifiques de reduction du temps de travail en Belgique transforment les vecus dans et hors travail des seniors, dans une recomposition des temps sociaux et des parcours de vie. Cet article repose sur l’analyse de 491 questionnaires recoltes dans deux secteurs d’activite contrastes et de 42 entretiens semi-directifs de beneficiaires de credit-temps. Ces donnees permettent de repenser les cadres temporels d’aujourd’hui a travers deux focales : la gestion des fins de parcours professionnel et l’articulation des temps sociaux a l’interieur d’une cohorte particuliere.
Volume upper bounds for 3D graph drawing

Many systems, particularly those which present relational information, include a graph drawing function. Such systems have motivated a great deal of research on algorithms for drawing graphs; a recent survey lists over 250 references. Almost all this work has been oriented toward two-dimensional drawings. This paper describes an investigation of mathematically fundamental aspects of three-dimensional graph drawing. In particular we give three results concerning the space required for three-dimensional drawings.We showhow to produce a grid drawing of an arbitrary n-vertex graph with all vertices located at integer grid point, in an n × 2n × 2n grid, such that no pair of edges cross. This grid size is optimal to within a constant. We also show how to convert an orthogonal two-dimensional drawing in a H × V integer grid to a three-dimensional drawing with ⌈√H⌉ × ⌈√H⌉ × V volume. Using this technique we show, for example, that three-dimensional drawings of binary trees can be computed with volume ⌈√n⌉ × ⌈√n⌉ × ⌈logn⌉. We give an algorithm for producing drawings of rooted trees in which the z coordinate of a node represents the depth of the node in the tree; our algorithm minimizes the footprint of the drawing, that is, the size of the projection in the xy plane.Finally, we list significant unsolved problems in algorithms for three-dimensional graph drawing.
Evaluation of X-Inactivation Status and Cytogenetic Stability of Human Dermal Fibroblasts after Long-Term Culture

Human primary fibroblasts are a popular type of somatic cells for the production of induced pluripotent stem (iPS) cells. Here we characterized biological properties of primary fibroblasts in terms of cell-growth rate, cytogenetic stability, and the number of inactive X chromosomes during long-term passaging. We produced eight lines of female human dermal fibroblasts (HDFs) and found normal karyotype and expected pattern of X chromosome inactivation (XCI) at low passages (Passage P1-5). However, four out of the eight HDF lines at high passage numbers (≥ P10) exhibited duplicated hallmarks of inactive X chromosome including two punctuate signals of histone H3 lysine 27 trimethylation (H3K27me3) and X inactive-specific transcript (XIST) RNA signals in approximately 8.5–18.5% of the cells. Our data suggest that the copy number of inactive X chromosomes in a subset of female HDF is increased by a two-fold. Consistently, DNA fluorescent in situ hybridization (FISH) identified 3-4 copies of X chromosomes in one nucleus in this subset of cells with two inactive Xs. We conclude that female HDF cultures exhibit a higher risk of genetic anomalies such as carrying an increased number of X chromosomes including both active and inactive X chromosomes at a high passage (≥ P10).
Comparison of two Dutch follow-up care models for spinal cord-injured patients and their impact on health problems, re-admissions and quality of care

Objective: To evaluate whether transmural care for people with spinal cord injury living in the community has more impact on health outcomes than traditional follow-up care within the Netherlands. Design: Quasi-experiment with 12 months of follow-up. Setting: Eight Dutch rehabilitation centres. Subjects: Thirty-one patients who received transmural care in two `experimental' rehabilitation centres were compared with a matched sample of 31 patients having received `usual follow-up care' in six other rehabilitation centres. Intervention: The core component of the transmural care consists of a transmural nurse, who `liaises' between former patients living in the community, primary care professionals and the rehabilitation team. The transmural care model provides activities to support patients and their family/partners and activities to promote continuity of care. Main measures: The prevalence of pressure sores and urinary tract infections; the number and duration of re-admissions to hospital and rehabilitation centre due to pressure sores, bladder and bowel problems; and the experienced quality of follow-up care. Results: The transmural care, as implemented, did not influence the health outcomes. The prevalence of pressure sores, urinary tract infections and the number of re-admissions (due to pressure sores, bladder and bowel problems) was respectively 13, 13 and 4 in the intervention group versus 14, 15 and 6 in the usual follow-up care group. Since the transmural care had been incompletely implemented and there were methodological and practical limitations, we formulated no final conclusions regarding its effectiveness. Conclusion: Implementing the transmural care model strictly according to protocol may improve its effectiveness.
Robust PCA Based on Incoherence With Geometrical Interpretation

Robust principal component analysis, which extracts low-dimensional data from high-dimensional data, can also be regarded as a source separation problem of the sparse error matrix and the low-rank matrix. Until recently, various methods have attempted to precisely predict the discrete rank function by assigning a weight to the nuclear norm. However, if the weights are not in ascending order, the algorithms will diverge and exhibit high computational complexity. Moreover, from the viewpoint of source separation, these methods overlook the fact that two components must be sufficiently different for accurate demixing. In this paper, we employ the incoherence term with convex shape, which considers that components must appear different from one another for boosting separability. Since it is intractable to directly exploit mutual incoherence defined in linear algebra, we guarantee the incoherence by indirectly making the sparse matrix lack the low-rank property by using the duality norm principle. This approach can also be associated with the null space. To analyze the results of the proposed algorithm geometrically, we measure the geodesic distance between the tangent spaces of the manifolds of two separate components. As this distance increases, the degree of dissimilarity of the two components is adequately assured; thus, separation succeeds. Furthermore, this paper is the first to provide insights into the relationship between source separation conditions and the derivatives of the nuclear norm and $L_{1}$ norm. Experiments are conducted on still image separation and background subtraction to confirm the superiority of the proposed methods both qualitatively and quantitatively.
"Avoidable" mortality and health services: a review of aggregate data studies.

STUDY OBJECTIVE--The aim of the study was to review published work reporting mortality from conditions amenable to medical intervention and compare the methods used and the results obtained. SOURCE MATERIAL--Two types of analysis were examined: (1) analyses of time trends, relating decline in mortality from amenable conditions to improvements in medical care (3 papers); (2) analyses of geographical variation, either between or within countries, in which mortality was related to the availability of health care resources and to other factors (8 papers). RESULTS--Time-trend studies have in general shown that mortality from amenable causes has declined faster over the past decades than most other causes of death. Studies of geographical variation have shown that mortality from amenable causes is consistently associated with socioeconomic factors, and that the association with the provision of health care resources is rather weak and inconsistent. CONCLUSIONS--(1) The low levels of mortality from amenable causes which presently prevail in industrialised countries are likely to reflect, at least in part, the increased effectiveness of health services; (2) geographical variation in mortality from amenable causes has not yet been shown to reflect differences in effectiveness of health services; and (3) if geographical variation in avoidable mortality does reflect such differences, they must arise from circumstances other than the level of supply, for example from more specific aspects of health care delivery, and are probably closely related to socioeconomic circumstances. In depth studies at the individual level are now more likely to produce information about factors limiting the effectiveness of health services than further studies of aggregate data.
Optimum Diversity-Multiplexing Tradeoff in the Multiple Relays Network

In this paper, a multiple-relay network in considered, in which $K$ single-antenna relays assist a single-antenna transmitter to communicate with a single-antenna receiver in a half-duplex mode. A new Amplify and Forward (AF) scheme is proposed for this network and is shown to achieve the optimum diversity-multiplexing trade-off curve.
Question asking as a tool for novice computer skill acquisition

Two experiments examined the utility of a menu-based question-construction help system as part of basic instruction for UNIX. The first experiment indicated that novice or naive users have great difficulty formulating their own questions; a menu-based interface that helps structure questions increased question asking and improved performance during training. A second experiment demonstrated that initial learning benefits more from “procedural” than from “causal” questions. A retention test showed that “correct response” feedback, when coupled with an appropriate problem-solving learning environment, can produce performance comparable to that in the question asking conditions; such feedback, however, did not provide equivalent understanding of the system. These results are discussed in the context of user models of the system and the potential role of constraint in designing question-asking systems.
Implementing A Neural Cache LSTM

6 We re-implement the Grave et al. Neural Cache on our own LSTM 7 model, reproducing the perplexity results and performing additional 8 hyper parameter tuning. We additionally test the perplexity of different 9 authors’ text on other authors’ trained LSTMs with the Neural Cache 10 implementation. 11 12
Serum CA19-9 as a Predictor of Malignancy in Primary Ovarian Mucinous Tumors: A Matched Case-Control Study

Background This study was designed to investigate the clinical characteristics correlated with serum CA19-9 elevation in primary mucinous ovarian tumors and to evaluate the role of serum CA19-9 in predicting borderline or malignant tumors. Material/Methods We retrospectively identified 27 women with pathologically-confirmed primary ovarian mucinous neoplasms (16 borderline and 11 malignant), who had been preoperatively checked for serum CA19-9 and CA125 levels. The control group was established by 1:2 matching for age among all women with pathologically-confirmed benign mucinous tumors over the same time period. The associations of the serum CA19-9 elevation and clinical characteristics, including tumor pathology, were evaluated. Results Serum CA19-9 was more frequently elevated in borderline or malignant than benign tumors (57.9% vs. 16.7%, P=0.001), although the mean value of serum CA19-9 was not significantly different among histological subtypes. CA19-9 elevation was correlated with large tumor size (largest diameter ≥15 cm; p=0.028), serum CA125 elevation (p=0.006), and tumor pathology (borderline or malignant tumors; p=0.001). Other clinical characteristics, including parity, menopause, bilateral tumor involvement, and torsion were not correlated with CA19-9 elevation. Multivariate analysis revealed that tumor pathology was the only independent factor for CA19-9 elevation in primary ovarian mucinous tumors (odds ratio 3.842, 95% CI 1.277–11.558, p=0.017). Interestingly, subgroup analysis in women with normal serum CA 125 level revealed that CA19-9 was significantly correlated with borderline and malignant tumors but not with benign tumors (odds ratio 6.3, 95% CI 1.438–19.648, p=0.014). Conclusions Serum CA19-9 can be a useful complementary marker in differentiating benign from borderline or malignant mucinous tumors in the ovaries, particularly when serum CA125 level is not elevated.
Inflammation in Peritoneal Dialysis

During peritoneal dialysis, peritoneal cells are repeatedly exposed to a non-physiological hypertonic environment with high glucose content and low pH. Current sterile dialysis solutions cause inflammation in the submesothelial compact zone that leads to fibrosis, neoangiogenesis, progressive increases in solute transfer and even ultrafiltration failure. The peritoneal dysfunction will further be amplified with the development of an epithelial-to-mesenchymal transition of mesothelial cells and the dissipation of the osmotic driving force through increased area and solute transport that accompanied neoangiogenesis of the submesothelial microvasculature. The alteration in the peritoneal membrane will further be aggravated by peritonitis, advanced glycation end-products and glucose degradation products. Finally, there are emerging new data supporting a pro-inflammatory role of peritoneal adipocytes.
CNT-based RFID passive gas sensor

In this paper Single-Wall Carbon Nanotube (CNT) are examined for the design of a passive and maintenance-free wireless RFID sensor. CNT buckypaper is characterized from a dielectric and a sensititvity point of view, using an indirect way, by using antenna measurement and simulations in a controlled medium. A CNT-based prototype RFID tag is then described as the featured maintenance free sensor and experimentally verified for its applicability and sensitivity towards NH3
Tissue Engineering the Vascular Tree.

A major hurdle in the field of tissue engineering and regenerative medicine remains the design and construction of larger (> 1 cm3) in vitro tissues for biological studies and transplantation. While there has been success in creating three-dimensional (3D) capillary networks, relatively large arteries (diameter >3-5 mm), and more recently small arteries (diameter 500 μm-1 mm), there has been no success in the creation of a living dynamic blood vessel network comprising of arterioles (diameter 40-300 μm), capillaries, and venules. Such a network would provide the foundation to supply nutrients and oxygen to all surrounding cells for larger tissues and organs that require a hierarchical vascular supply. In this study, we describe the different technologies and methods that have been employed in an effort to create individual vessels and networks of vessels to support engineered tissues for in vivo and in vitro applications. A special focus is placed on the generation of blood vessels with average dimensions that span from microns (capillaries) to a millimeter (large arterioles). We also identify major challenges while exploring new opportunities to create model systems of the entire vascular tree, including arterioles and venules.
Non-Hematopoietic Cells in Lymph Nodes Drive Memory CD8 T Cell Inflation during Murine Cytomegalovirus Infection

During human and murine cytomegalovirus (MCMV) infection an exceptionally large virus-specific CD8 T cell pool is maintained in the periphery lifelong. This anomalous response is only seen for specific subsets of MCMV-specific CD8 T cells which are referred to as 'inflationary T cells'. How memory CD8 T cell inflation is induced and maintained is unclear, though their activated phenotype strongly suggests an involvement of persistent antigen encounter during MCMV latency. To dissect the cellular and molecular requirements for memory CD8 T cell inflation, we have generated a transgenic mouse expressing an MHC class I-restricted T cell receptor specific for an immunodominant inflationary epitope of MCMV. Through a series of adoptive transfer experiments we found that memory inflation was completely dependent on antigen presentation by non-hematopoietic cells, which are also the predominant site of MCMV latency. In particular, non-hematopoietic cells selectively induced robust proliferation of inflationary CD8 T cells in lymph nodes, where a majority of the inflationary CD8 T cells exhibit a central-memory phenotype, but not in peripheral tissues, where terminally differentiated inflationary T cells accumulate. These results indicate that continuous restimulation of central memory CD8 T cells in the lymph nodes by infected non-hematopoietic cells ensures the maintenance of a functional effector CD8 T pool in the periphery, providing protection against viral reactivation events.
Improved lower bounds on the randomized complexity of graph properties

We prove a lower bound of Ω(n4/3 log 1/3n) on the randomized decision tree complexity of any nontrivial monotone n‐vertex graph property, and of any nontrivial monotone bipartite graph property with bipartitions of size n. This improves the previous best bound of Ω(n4/3) due to Hajnal (Combinatorica 11 (1991) 131–143). Our proof works by improving a graph packing lemma used in earlier work, and this improvement in turn stems from a novel probabilistic analysis. Graph packing being a well‐studied subject in its own right, our improved packing lemma and the probabilistic technique used to prove it may be of independent interest. © 2007 Wiley Periodicals, Inc. Random Struct. Alg. , 2007
Sharing the pie: the Lutheran is neither opportunistic nor generous

This paper studies how individual religiosity affects people's behaviour. In particular here I study the behaviour of the second players in a standard trust game. They have the possibility of sharing some resources between themselves and their game mates. It results that more religious people tend to choose an even allocation of these resources, whilst the less religious participants are either opportunistic or generous.
Study on a Distribution Network Design under Supply Chain

This paper addresses the distribution network design problem under a supply chain system that involves selecting the optimum numbers, locations and capacities of plants and warehouses to open so that all customer demand is satisfied at minimum total costs of the distribution network. We develop a mixed integer programming allowing for multiple levels of capacities available to the warehouses and plants. The paper also provide an efficient heuristic solution procedure for this supply chain system problem, and presents a computational study to investigate the value of coordinating production and distribution planning.
Osteopontin and protein kinase C regulate PDLIM2 activation and STAT1 ubiquitination in LPS-treated murine macrophages.

Hongtao Guo, Zhiyong Mi, Dawn E. Bowles, Syamal D. Bhattacharya, and Paul C. Kuo This article has been retracted by the publisher. The same data were reused to represent different experimental conditions. Specifically, lanes 2– 4 and 6 – 8 of the actin immunoblot in Fig. 3A were duplicated. Additionally, the nuclear P-STAT1 immunoblot from Fig. 3A was reused as P-STAT1 in Fig. 3B. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 292, NO. 3, p. 1142, January 20, 2017 © 2017 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A.
NEW ELECTROPHYSIOLOGICAL CORRELATES ASSOCIATED WITH INTENTIONAL HEART FOCUS

This work utilizes the measurement of heart rate variability (HRV) as a vehicle to show that continued practice of certain specific techniques involving an intentional shift of focus to the area of the heart, and invoking specific feeling states such as "love" and "appreciation," automatically manifests in increased autonomic nervous system balance. In particular, (1) enhanced balance between the parasympathetic and sympathetic nervous system, (2) a shift of the high frequency and low frequency portions of the HRV power spectra to around 0.1 Hz range, (3) entrainment and frequency locking of multiple body oscillators (HRV, pulse transit time and respiration), (4) a shift in frequency of all the body's entrained systems, around O.IHz frequency, associated with a change in focus of the subject to a different heart feeling state, and (5) the intentional generation of a newly defined internal coherence state (near zero HRV), have all been achieved. These are electrophysiological correlates of certain mental and emotional states occupied by the individual. Three individual subjects plus a group study of twenty subjects are reported on and discussed. From these results, one sees that individuals can intentionally affect their autonomic nervous system balance, and thus, their HRV.
A New Evolution Mechanism Model for B2B E-Commerce Network

To study the structure and evolution mechanism of B2B e-commerce network, the authors propose a network with several layers description of B2B e-commerce market. The empirical analysis from Alibaba.com shows that degree distribution of the network structure follows power-law. Based on modified BA Barabasi-Albert model, a new model is proposed, adding layers, fitness parameters, and more reasonable growth mechanism. The model reveals that, the structure of the network is stable, and the average path length and clustering coefficient are small. The authors also find that the impact of parameters is not decisive, and the emergence of scale-free nature depends on the mechanism itself.