Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient identification of identical-by-descent status in pedigrees with many untyped individuals

Motivation: Inference of identical-by-descent (IBD) probabilities is the key in family-based linkage analysis. Using high-density single nucleotide polymorphism (SNP) markers, one can almost always infer haplotype configurations of each member in a family given all individuals being typed. Consequently, the IBD status can be obtained directly from haplotype configurations. However, in reality, many family members are not typed due to practical reasons. The problem of IBD/haplotype inference is much harder when treating untyped individuals as missing. Results: We present a novel hidden Markov model (HMM) approach to infer the IBD status in a pedigree with many untyped members using high-density SNP markers. We introduce the concept of inheritance-generating function, defined for any pair of alleles in a descent graph based on a pedigree structure. We derive a recursive formula for efficient calculation of the inheritance-generating function. By aggregating all possible inheritance patterns via an explicit representation of the number and lengths of all possible paths between two alleles, the inheritance-generating function provides a convenient way to theoretically derive the transition probabilities of the HMM. We further extend the basic HMM to incorporate population linkage disequilibrium (LD). Pedigree-wise IBD sharing can be constructed based on pair-wise IBD relationships. Compared with traditional approaches for linkage analysis, our new model can efficiently infer IBD status without enumerating all possible genotypes and transmission patterns of untyped members in a family. Our approach can be reliably applied on large pedigrees with many untyped members, and the inferred IBD status can be used for non-parametric genome-wide linkage analysis. Availability: The algorithm is implemented in Matlab and is freely available upon request. Contact: jingli@cwru.edu Supplementary information: Supplementary data are available on Bioinformatics online.
Questionnaire of General Labor Well-Being: Structure and Psychometric Properties

The general work well-being questionnaire (qBLG) was developed with the aim of providing a measurement tool particularly sensitive to the psychosocial dimension of work well-being of care workers, and to the bipolar nature of the well-being experience. 1252 professionals of health care (medical and nursing) and of higher education employed in hospitals and universities from Brazil, Chile, Colombia and Spain, respectively, answered a series of closed items from a questionnaire organized according with a theoretical model of general work well-being. Factor analysis found two independent factors in the qBLG, the first one including three scales of psychosocial well-being and the second three scales of collateral effects. All scales showed high internal consistency. The qBLG faithfully reproduces the structure of the proposed theoretical model, and combines the required psychometric properties for the evaluation of work well-being of health care and of higher education professionals.
A Posteriori Error Estimates and Adaptive Mesh Refinement for the Coupling of the Finite Volume Method and the Boundary Element Method

We consider the coupling of the finite volume method and the boundary element method of Erath [SIAM J. Numer. Anal. , 50 (2012), pp. 574--594] in two and three dimensions. This method can be used, for example, to approximate a solution of the transport of a concentration in a fluid, where no boundary conditions are available. We derive residual-based a posteriori estimates (also for an upwind version). These upper and lower bounds measure the error in an energy (semi)norm between the exact solution and the numerical solution. The upper bound is robust in the sense that it does not depend on the variation of the model data. The lower bound, however, depends additionally on the local Peclet number. The local contributions of the a posteriori estimates are used to steer an adaptive mesh-refining algorithm. This strategy turns out to be very suitable for the numerical treatment of transmission problems, which have singularities or boundary/internal layers. Several numerical examples illustrate the effectivenes.
Phenotypic study after cultivated limbal epithelial transplantation for limbal stem cell deficiency.

OBJECTIVE To report phenotypic analysis of epithelia before and following cultivated limbal epithelial transplantation (CLET) for eyes with limbal stem cell deficiency. METHODS Six patients with limbal stem cell deficiency (3 with alkali burns, 2 with Stevens-Johnson syndrome, and 1 with pseudo-ocular cicatricial pemphigoid) were subjected to CLET and subsequent keratoplasty. Immunohistochemical analysis for cytokeratin 3, cytokeratin 13, MUC5AC (Mucin 5 subtype AC), and alpha smooth muscle actin was performed in specimens obtained at CLET and keratoplasty. Clinical outcome was assessed according to epithelial phenotype, visual acuity, neovascularization, and graft clarity. RESULTS Secondary keratoplasty was performed following CLET during a mean interval of 6.8 months. Postoperative visual acuity improved by more than 2 lines over a mean +/- SD observation period of 25.1 +/- 13.2 months following keratoplasty, with reduction of neovascularization. Phenotypic study revealed that epithelia were positive for cytokeratin 13 and MUC5AC, but negative for cytokeratin 3, with alpha smooth muscle actin-positive cells in the stroma in all patients before CLET. After CLET, 4 eyes showed positive immunostaining to cytokeratin 3 but negative immunostaining to cytokeratin 13 and MUC5AC, with no alpha smooth muscle actin-positive cells. CONCLUSION Cultivated limbal epithelial transplantation is a useful approach in the treatment of limbal stem cell deficiency, restoring a feasible microenvironment in the ocular surface and securing a corneal epithelial phenotype.
La gestion paradoxale des compétences de service

Cet article s’interesse aux competences de service mobilisees par les agents au contact de la clientele et qui sont la plupart du temps tacites. A ce titre, s’interroger sur la reconnaissance de ces competences et sur leur developpement constitue un enjeu de gestion pour les organisations. C’est d’autant plus important que de nombreux metiers de service allient faible qualification et fortes competences situees.
Vitamin B6 concentrations in patients with chronic liver disease and hepatocellular carcinoma.

Etude de 17 malades atteints de cirrhose dont 10 avec hepatome, 5 atteints d'hepatome sans cirrhose et 9 sujets sains. Les quantites totales de pridoxal plasmatique sont normales chez la plupart des malades. Une carence en pyridoxal-5-phosphate peut etre observee elle ne serait pas due a un apport insuffisant ni a un defaut d'absorption, mais plutot a un exces de degradation
Learning and Transferring Deep Joint Spectral–Spatial Features for Hyperspectral Classification

Feature extraction is of significance for hyperspectral image (HSI) classification. Compared with conventional hand-crafted feature extraction, deep learning can automatically learn features with discriminative information. However, two issues exist in applying deep learning to HSIs. One issue is how to jointly extract spectral features and spatial features, and the other one is how to train the deep model when training samples are scarce. In this paper, a deep convolutional neural network with two-branch architecture is proposed to extract the joint spectral–spatial features from HSIs. The two branches of the proposed network are devoted to features from the spectral domain as well as the spatial domain. The learned spectral features and spatial features are then concatenated and fed to fully connected layers to extract the joint spectral–spatial features for classification. When the training samples are limited, we investigate the transfer learning to improve the performance. Low and mid-layers of the network are pretrained and transferred from other data sources; only top layers are trained with limited training samples extracted from the target scene. Experiments on Airborne Visible/Infrared Imaging Spectrometer and Reflective Optics System Imaging Spectrometer data demonstrate that the learned deep joint spectral–spatial features are discriminative, and competitive classification results can be achieved when compared with state-of-the-art methods. The experiments also reveal that the transferred features boost the classification performance.
Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy

Antimicrobial drug development is increasingly lagging behind the evolution of antibiotic resistance, and as a result, there is a pressing need for new antibacterial therapies that can be readily designed and implemented. In this work, we engineered bacteriophage to overexpress proteins and attack gene networks that are not directly targeted by antibiotics. We show that suppressing the SOS network in Escherichia coli with engineered bacteriophage enhances killing by quinolones by several orders of magnitude in vitro and significantly increases survival of infected mice in vivo. In addition, we demonstrate that engineered bacteriophage can enhance the killing of antibiotic-resistant bacteria, persister cells, and biofilm cells, reduce the number of antibiotic-resistant bacteria that arise from an antibiotic-treated population, and act as a strong adjuvant for other bactericidal antibiotics (e.g., aminoglycosides and β-lactams). Furthermore, we show that engineering bacteriophage to target non-SOS gene networks and to overexpress multiple factors also can produce effective antibiotic adjuvants. This work establishes a synthetic biology platform for the rapid translation and integration of identified targets into effective antibiotic adjuvants.
Academic Self- Efficacy Scale: Validity Reliability Study

The goal of this study is to develop an assessment instrument in order to evaluate the beliefs of students about their academic sufficiency. Confirmatory fac- tor analysis was conducted in order to evaluate the validity of four factor structure that was formed as a result of exploratory factor analysis. At the end of confirmatory factor analysis that was firstly conducted, academic self sufficiency scale’s compli- ance values were analyzed. Compliance indexes that were obtained by confirmatory factor analysis are: X 2 = 513.04 (sd=148, p<.001), (/sd) =3.47, GFI=. 90, RMSEA=. 073, RMR=. 04. In addition to the confirmatory factor analysis, in order to evaluate the reliability levels of scores that were obtained through academic self- sufficiency scale, Cronbach alpha internal consistency coefficients that were calcu- lated on the basis of item analysis were examined. Coefficients were found for com- plete scale 91.
Processor assignment in heterogeneous parallel architectures

It has been already demonstrated that cost-effective multiprocessor designs may be obtained by combining in the same architecture processors of different speeds (heterogeneous architecture) so that the serial and critical portions of the application may benefit from a fast single processor. The paper presents a systematic way to build static heuristic scheduling algorithms for such environments. Several algorithms are proposed and their performances are compared through simulation. One of the proposed algorithms is shown to achieve substantial performance gains as the degree of heterogeneity of the architecture increases. <<ETX>>
Pioneering Plus a Broad Product Line Strategy: Higher Profits or Deeper Losses?

Previous research suggests firms can build a market share advantage by preempting later entrants with a broad product line and expanding rapidly into related markets. Whether such a strategy leads to a pioneering profit advantage relative to followers also depends on its cost effects. In this paper, we examine when the market share advantage of a pioneering firm with a broad product line strategy translates into a profit advantage by examining the cost effects of this strategy. Using the profit impact of marketing strategies data and an estimation method that controls for various unobserved factors, we find significant differences between different industry settings. From these contrasting findings, we generate an emerging theoretical framework that we subject to empirical testing. We conjecture, and empirically verify, that creating a broad product line with a versioning strategy---creating variety from a standard product in anticipating customer demand---does not increase the pioneering cost disadvantage, and thus results in a pioneering profit advantage. On the other hand, with a tailoring strategy---creating variety by customizing a product to actual customer demand---a broad product line substantially increases the pioneering cost disadvantage, thereby making a preemption strategy counterproductive.
THE ALTITUDE DEPENDENCE OF THE OH ( X ’ II ) VIBRATIONAL DISTRIBUTION IN THE NIGHTGLOW : SOME MODEL EXPECTATIONS

A number of different OH Meinel band excitation models are used to investigate the extent to which quenching and vibrational deactivation processes could cause the nightglow OH vibrational distributions to vary with altitude. The various models. which are based upon those described by McDade and Llewellyn (198X, Phc,t. Spcrw Sc,i. 36. X97). are used to calculate the steady state OH vibrational distributions throughout the X0&100 km region. The results of the calculation show that. irrespective of the basic model assumptions. the OH vibrational distributions should not be strongly altitude dependent and that the emission proiiles ofthe Meinel bands from the 1~’ levels I through 9 should not differ in ;iltitude by more than one or two kilometers. The results of some recent laboratory studies pertaining to the Meinel band excitation mechanism arc also discussed and it is shown that stepwise collisional vibrational deactivation is unlikely to play a major role in controlling the observed nightglow OH vibrational distribution.
Intelligent, Fault Tolerant Control for Autonomous Systems

We present a methodology for intelligent control of an autonomous and resource constrained embedded system. Geared towards mastering permanent and transient faults by dynamic reconfiguration, our approach uses rules for describing device functionality, valid environmental interactions, and goals the system has to reach. Besides rules, we use functions that characterize a goal's target activity profile. The target activity profile controls the frequency our system uses to reach the corresponding goal. In the paper we discuss a first implementation of the given methodology, and introduce useful extensions. In order to underline the feasibility and effectiveness of the presented control system, we present a case study that has been carried out on a prototype system.
The credit crunch – the right time for credit unions to strike?

The origins of the cooperative movement can be traced to the Rochdale Society of Equitable Pioneers in 1844, from which similar institutions emerged in Central Europe, the North American continent and the rest of the world. Modern credit unions evolved from these small cooperative societies and have developed into mainstream providers of financial services in many jurisdictions. However, credit unions in the UK have not made a similar impact. There are several factors that have limited their growth – an inadequate legislative framework, an ineffective credit union regulatory system, inappropriate development models, an over-reliance on state subsidies and a disunited movement. The aim of this paper is to re-examine these factors in light of the level of political support provided by the government since 1997.
Sphere decoding inspired approximation method to compute the entropy of large Gaussian mixture distributions

The computation of mutual informations of large scale systems with finite input alphabet and Gaussian noise has often prohibitive complexities. In this paper, we propose a novel approach exploiting the sphere decoding concept to bound and approximate such mutual information term with reduced complexity and good accuracy. Using Monte-Carlo simulations, the method is numerically demonstrated for the computation of the mutual information of a frequency- and time-selective channel with QAM modulation.
Relation Between Laminin-5 γ2 Chain and Cell Surface Metalloproteinase MT1-MMP in Clear Cell Carcinoma of the Ovary

Ovarian clear cell carcinoma (CCC) characteristically shows stromal accumulation of the basement membrane material laminin-5 (LN-5). LN-5 works not only as a substrate for cell anchorage but also as a stimulator for cell migration. Our previous study showed that CCC cell increased migration over excessive LN-5 in vitro. However, it remains unclear why LN-5 rather promotes cell migration than cell anchorage. A recent study has shown that the processing of the LN-5 γ2 chain by membrane type 1-matrix metalloproteinase (MT1-MMP) was responsible for increasing cell migration activity but reducing cell anchoring activity of LN-5. In the present study, 3 CCC cell lines were examined for LN-5 γ2 chain levels by Western blotting. Processed γ2 chain (105 kDa) was detected in the extracellular matrix of all 3 CCC cell lines in vitro. Immunocytochemically they expressed MT1-MMP on the cell surface. In surgical specimens, 22 of 30 (73%) CCCs showed membranous expression of MT1-MMP, and stromal accumulation of the LN-5 γ2 chain, especially in the area of papillary architecture. These results indicate that proteolytic processing of the LN-5 γ2 chain by MT1-MMP is involved in cell migration and subsequent architectural organization in ovarian CCC.
Employability and Finnish University Graduates

In this article the authors concentrate on the change in the concept of employability during the Bologna process. They show that employability has gradually moved from a peripheral to a core presence in the most recent Bologna process documents. Using a Finnish university merger (University of Eastern Finland) as an example, the authors demonstrate that implementation of the Bologna process has reached the most remote eastern border of the European Union. The Bologna process is shaping the Finnish universities, and employability discussion is embedded in university reforms. The authors argue that the reason why employability has been raised as one of the core concepts of the Bologna process is labour market needs. Moreover, students want university education to help their transition to the world of work. On the other hand, employers want graduates who are well prepared for the world of work. In this way, the raison d'être for universities is to fulfil the needs of national economies and the labour market.
Chapter 5. Paper 1: Fast Rule-based Classification Using P-trees 5.1. Abstract 5.2. Introduction

Lazy classification does not require construction of a classifier. Decisions can, therefore, be based on the properties of the particular unknown sample rather than the set of all possible samples. We introduce a rule-based classifier that uses neighborhood membership rather than static intervalization to break up continuous domains. A distance function that makes neighborhood evaluation efficient for the P-tree data structure is chosen. We discuss information gain and statistical significance in a unified framework and observe that the commonly used formulation of information gain can be seen as an approximation to the exact entropy. A new algorithm for constructing and combining multiple classifiers is introduced and its improved performance demonstrated, especially for data sets with many attributes. Many data mining tasks involve predicting a discrete class label, such as whether a patient is sick, whether an e-mail message is spam, etc. Eager classification techniques construct a classifier from the training data before considering unknown samples. Eager algorithms include decision tree induction, which fundamentally views data as categorical and discretizes continuous data as part of the classifier construction [1]. Lazy classification predicts the class label attribute of an unknown sample based on the entire training data. Lazy versions of decision tree induction improve classification accuracy by using the information gain criterion based on the actual values of the unknown sample [2]. This
QoS-Resource Graph Model for Web Service Composition in Service Oriented Computing

SOC (service oriented computing) becomes a hot topic of research because it accelerates rapid application development by service reuse. Delivering end-to-end QoS (quality of service) in SOC environment is a critical and significant challenge. QoS is modeled for a single service based on this view: quality is seen as conformance. Then, QRGM (QoS-resource graph model) is adopted for service composition. An illustrative example is used to account for how to model end-to-end QoS in service composition using QRGM. At last, QRGM is compare with other current common service composition models. Conclusion is made that QRGM provides better support for QoS than other service composition models.
Pathway-based visualization of cross-platform microarray datasets

MOTIVATION Traditionally, microarrays were almost exclusively used for the genome-wide analysis of differential gene expression. But nowadays, their scope of application has been extended to various genomic features, such as microRNAs (miRNAs), proteins and DNA methylation (DNAm). Most available methods for the visualization of these datasets are focused on individual platforms and are not capable of integratively visualizing multiple microarray datasets from cross-platform studies. Above all, there is a demand for methods that can visualize genomic features that are not directly linked to protein-coding genes, such as regulatory RNAs (e.g. miRNAs) and epigenetic alterations (e.g. DNAm), in a pathway-centred manner. RESULTS We present a novel pathway-based visualization method that is especially suitable for the visualization of high-throughput datasets from multiple different microarray platforms that were used for the analysis of diverse genomic features in the same set of biological samples. The proposed methodology includes concepts for linking DNAm and miRNA expression datasets to canonical signalling and metabolic pathways. We further point out strategies for displaying data from multiple proteins and protein modifications corresponding to the same gene. Ultimately, we show how data from four distinct platform types (messenger RNA, miRNA, protein and DNAm arrays) can be integratively visualized in the context of canonical pathways. AVAILABILITY The described method is implemented as part of the InCroMAP application that is freely available at www.cogsys. cs.uni-tuebingen.de/software/InCroMAP. CONTACT clemens.wrzodek@uni-tuebingen.de or andreas.zell@uni-tuebingen.de.