Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison of models used to predict MLH1, MSH2 and MSH6 mutation carriers.

BACKGROUND MMRpro, prediction of mutations in MLH1 and MLH2 (PREMM(1,2)) and MMRpredict are models which were developed to predict the probability that an individual carries a Lynch syndrome-causing mutation. Each model utilizes data from personal and family histories of cancer. To date, no studies have compared these models in a cancer genetics clinic. The purpose of this study was to determine each model's ability to predict the probability of carrying a Lynch syndrome-causing mutation in individuals with a family history of colorectal cancer and to determine their clinical applicability. METHODS We obtained family pedigrees from 81 individuals who presented for Lynch syndrome testing due to a personal and/or family history of cancer. Data from each pedigree were entered into the models and analyzed using SPSS. RESULTS We found that MMRpredict, PREMM(1,2) and MMRpro showed similar performances with areas under the receiver-operating characteristic curve of 0.731, 0.765 and 0.732, respectively. MMRpro showed the least dispersion of mutation probability estimates with a P value of 0.205, compared with 0.034 for PREMM(1,2) and 0.001 for MMRpredict. CONCLUSION We found all three carried out well in a cancer genetics setting, with PREMM(1,2) giving slightly better estimates. There were some significant discrepancies between the models in cases where the proband had endometrial cancer.
Choosing among Confusably Distributed Stimuli with Specified Likelihood Ratios

A study of choice behavior for overlapping normally distributed stimuli, with specified distribution locations, separations, dispersions, and likelihood ratios was carried out. A distributed stimulus consisted of a set of dots sampled from a bivariate normal distribution and placed on separate cards. Cards with dots from two or three distributions were mixed together and shown one by one to S, who had to choose from which distribution each dot derived, and give a confidence rating. Two theoretical choice models succeeded in bracketing the results: (a) statistical decision theory and (b) a probability micromatching (Mμ) model. Mμ states that choices are made probabilistically and in the proportion defined by the likelihood ratio. Confidence was not always monotonic with likelihood. The perceived distance between distribution centers was about twice the true distance.
Irregular Dynamics in Up and Down Cortical States

Complex coherent dynamics is present in a wide variety of neural systems. A typical example is the voltage transitions between up and down states observed in cortical areas in the brain. In this work, we study this phenomenon via a biologically motivated stochastic model of up and down transitions. The model is constituted by a simple bistable rate dynamics, where the synaptic current is modulated by short-term synaptic processes which introduce stochasticity and temporal correlations. A complete analysis of our model, both with mean-field approaches and numerical simulations, shows the appearance of complex transitions between high (up) and low (down) neural activity states, driven by the synaptic noise, with permanence times in the up state distributed according to a power-law. We show that the experimentally observed large fluctuation in up and down permanence times can be explained as the result of sufficiently noisy dynamical synapses with sufficiently large recovery times. Static synapses cannot account for this behavior, nor can dynamical synapses in the absence of noise.
Developing Tonal Perception through Unsupervised Learning

The perception of tonal structure in music seems to be rooted both in low-level perceptual mechanisms and in enculturation, the latter accounting for cross-cultural differences in perceived tonal structure. Unsupervised machine learning methods are a powerful tool for studying how musical concepts may emerge from exposure to music. In this paper, we investigate to what degree tonal structure can be learned from musical data by unsupervised training of a Restricted Boltzmann Machine, a generative stochastic neural network. We show that even based on a limited set of musical data, the model learns several aspects of tonal structure. Firstly, the model learns an organization of musical material from different keys that conveys the topology of the circle of fifths (CoF). Although such a topology can be learned using principal component analysis (PCA) when using pitch-only representations, we found that using a pitch-duration representation impedes the extraction of the CoF topology much more for PCA than for the RBM. Furthermore, we replicate probe-tone experiments by Krumhansl and Shepard, measuring the organization of tones within a key in human perception. We find that the responses of the RBM share qualitative characteristics with those of both trained and untrained listeners.
Identification and annotation of multiple periodic pulse trains using dominant frequency and graph search: Applications in atrial fibrillation rotor detection

Biological signals, such as intracardiac electrograms during atrial fibrillation (AF), can contain multiple periodic components or peaks. We propose a method for identifying individual periodic peak trains in signals containing multiple such periodic sequences. We use dominant frequency-based periodicity detection along with a graph search algorithm to identify the most dominant periodic activation set or peaks of interest. We then remove these peaks and iterate until all periodic sequences are identified. The proposed method is tested on simulated AF intra-cardiac electrograms with periodic activation trains of three distinct frequencies corrupted by noise and complex aperiodic signal features. The method is shown to have high accuracy (up to 100% sensitivity and 100% specificity) in detecting the three individual periodic peak trains. The method has application in biomedical signal analysis, such as detecting the periodic activations of a rotor, amidst other periodic activations during AF.
Rapid PCR Detection of Helicobacter pylori-Associated Virulence and Resistance Genes Directly from Gastric Biopsy Material

ABSTRACT We have developed a PCR-based method to detect macrolide resistance and the virulence gene cagA in Helicobacter pylori within 24 h, thereby improving the lengthy process of culture-based approaches. Total DNA was prepared directly from stomach biopsy specimens. The procedure proved to be rapid and reliable and could be utilized for diagnostic purposes.
Compliant Control of Multicontact and Center-of-Mass Behaviors in Humanoid Robots

This paper presents a new methodology for the analysis and control of internal forces and center-of-mass (CoM) behavior, which are produced during multicontact interactions between humanoid robots and the environment. The approach leverages the virtual-linkage model that provides a physical representation of the internal and CoM resultant forces with respect to reaction forces on the supporting surfaces. A grasp/contact matrix describing the complex interactions between contact forces and CoM behavior is developed. Based on this model, a new torque-based approach for the control of internal forces is suggested and illustrated on the Asimo humanoid robot. The new controller is integrated into the framework for whole-body-prioritized multitasking, thus enabling the unified control of CoM maneuvers, operational tasks, and internal-force behavior. The grasp/contact matrix is also proposed to analyze and plan internal force and CoM control policies that comply with frictional properties of the links in contact.
Rotational fission of trans-Neptunian objects: the case of Haumea

This research was partially supported by Spanish grants AYA2008-06202-C03-01, AYA-06202-C03-02, AYA2008-06202-C03-03, P07-FQM-02998 and European FEDER funds. RD acknowledges financial support from the MICINN (contract Ramon y Cajal). DCR acknowledges support from the National Aeronautics and Space Administration under grant No. NNX08AM39G issued through the Office of Space Science.
SLOW INFORMATION DIFFUSION AND THE INERTIAL BEHAVIOR OF DURABLE CONSUMPTION

This paper studies the aggregate dynamics of durable and nondurable consumption under slow information diffusion (SID) due to noisy observations and learning within the permanent income hypothesis framework. We show that SID can significantly improve the model's predictions on the joint behavior of income, durable consumption, and nondurable consumption at the aggregate level. Specifically, we find that SID can significantly improve the model's predictions for: (i) smoothness in durable and nondurable consumption, (ii) autocorrelation of durable consumption, and (iii) contemporaneous correlation between durable and nondurable consumption.
Minimum node degree in inhomogeneous random key graphs with unreliable links

We consider wireless sensor networks under a heterogeneous random key predistribution scheme and an on-off channel model. The heterogeneous key predistribution scheme has recently been introduced by Yağan - as an extension to the Eschenauer and Gligor scheme - for the cases when the network consists of sensor nodes with varying level of resources and/or connectivity requirements, e.g., regular nodes vs. cluster heads. The network is modeled by the intersection of the inhomogeneous random key graph (induced by the heterogeneous scheme) with an Erdös-Rényi graph (induced by the on/off channel model). We present conditions (in the form of zero-one laws) on how to scale the parameters of the intersection model so that with high probability all of its nodes are connected to at least k other nodes; i.e., the minimum node degree of the graph is no less than k. We also present numerical results to support our results in the finite-node regime. The numerical results suggest that the conditions that ensure k-connectivity coincide with those ensuring the minimum node degree being no less than k.
On the Cutting Performance of Coated HSS Taps When Machining of Austenitic Steel

Abstract The paper deals with a quality of the PVD coated HSS taps when cutting the stainless austenitic chromiumnickel non-stabilized steel DIN 1.4301 (X5CrNi 18-10). The main attention is focused on the analysis of loading (cutting moment, specific energy) of the HSS taps by means of pieso-electrical dynamometer Kistler 9272 and the relation between the quality of duplex and triplex PVD coatings and their effects on the quality of machined thread surfaces and tool life of the taps. The results showed a safe and stabilized cutting with acceptable quality of threads for HSSE with the TiN+TiCN+DLC coating.
Random forest explorations for URL classification

Phishing is a major concern on the Internet today and many users are falling victim because of criminal's deceitful tactics. Blacklisting is still the most common defence users have against such phishing websites, but is failing to cope with the increasing number. In recent years, researchers have devised modern ways of detecting such websites using machine learning. One such method is to create machine learnt models of URL features to classify whether URLs are phishing. However, there are varying opinions on what the best approach is for features and algorithms. In this paper, the objective is to evaluate the performance of the Random Forest algorithm using a lexical only dataset. The performance is benchmarked against other machine learning algorithms and additionally against those reported in the literature. Initial results from experiments indicate that the Random Forest algorithm performs the best yielding an 86.9% accuracy.
Thyroid bud morphogenesis requires CDC42- and SHROOM3-dependent apical constriction

ABSTRACT Early development of the gut endoderm and its subsequent remodeling for the formation of organ buds are accompanied by changes to epithelial cell shape and polarity. Members of the Rho-related family of small GTPases and their interacting proteins play multiple roles in regulating epithelial morphogenesis. In this study we examined the role of Cdc42 in foregut development and organ bud formation. Ablation of Cdc42 in post-gastrulation mouse embryos resulted in a loss of apical-basal cell polarity and columnar epithelial morphology in the ventral pharyngeal endoderm, in conjunction with a loss of apical localization of the known CDC42 effector protein PARD6B. Cell viability but not proliferation in the foregut endoderm was impaired. Outgrowth of the liver, lung and thyroid buds was severely curtailed in Cdc42-deficient embryos. In particular, the thyroid bud epithelium did not display the apical constriction that normally occurs concurrently with the outgrowth of the bud into the underlying mesenchyme. SHROOM3, a protein that interacts with Rho GTPases and promotes apical constriction, was strongly expressed in the thyroid bud and its sub-cellular localization was disrupted in Cdc42-deficient embryos. In Shroom3 gene trap mutant embryos, the thyroid bud epithelium showed no apical constriction, while the bud continued to grow and protruded into the foregut lumen. Our findings indicate that Cdc42 is required for epithelial polarity and organization in the endoderm and for apical constriction in the thyroid bud. It is possible that the function of CDC42 is partly mediated by SHROOM3. Summary: Conditional Cdc42 knockout revealed requirements for Cdc42 in endoderm polarity, and in thyroid apical constriction and morphogenesis. Shroom3 mutant embryos also displayed thyroid bud abnormalities, suggesting a possible functional interaction.
Uplink Downlink Rate Balancing and Throughput Scaling in FDD Massive MIMO Systems

In this work we extend the concept of uplink-downlink rate balancing to frequency division duplex (FDD) massive MIMO systems. In uplink-downlink balancing, we use part of the uplink capacity for CSI feedback in order to increase the downlink capacity. We consider a base station with large number antennas serving many single antenna users. We first show that any unused capacity in the uplink can be traded off for higher throughput in the downlink in a system that uses either dirty paper (DP) coding or zero-forcing (ZF) precoding. We then also study the scaling of the system throughput with the number of antennas in cases of Beamforming (BF) Precoding, ZF Precoding, and DP coding. We show that the downlink throughput is proportional to the logarithm of the number of antennas. While, this logarithmic scaling is lower than the linear scaling of the rate in the uplink, it can still bring significant throughput gains. For example, we demonstrate through analysis and simulation that increasing the number of antennas from 4 to 128 will increase the throughput by more than a factor of 5. We also show that a logarithmic scaling of downlink throughput as a function of the number of receive antennas can be achieved even when the number of transmit antennas only increases logarithmically with the number of receive antennas.
Flexible Concept Matching for Medical Information Retrieval

Extensive research efforts have been spent on concept based medical information retrieval, relying on rich domain resources and tools. In most cases, the identified medical concepts in a query are either matched strictly against a document (i.e. Concepts should be identical), or they are transformed into a bag of words. While the first approach has had limited success due to problems in concept identification, there is a serious loss in precision with the second approach. In this paper, we propose a flexible matching approach by considering a concept expression as a phrase, which can be matched strictly, or in some variant forms by allowing some flexibility in position and order. Such flexibility is naturally indicated by the great variations to express concepts in this area. In addition, we also incorporate synonym expressions in the matching process. Our experiments on several public test collections show that the flexible concept matching approach outperforms the traditional bag-of-words approach and the strict concept matching approach.
Energy-efficient link-layer jamming attacks against wireless sensor network MAC protocols

A typical wireless sensor node has little protection against radio jamming. The situation becomes worse if energy-efficient jamming can be achieved by exploiting knowledge of the data link layer. Encrypting the packets may help to prevent the jammer from taking actions based on the content of the packets, but the temporal arrangement of the packets induced by the nature of the protocol might unravel patterns that the jammer can take advantage of, even when the packets are encrypted. By looking at the packet interarrival times in three representative MAC protocols, S-MAC, LMAC, and B-MAC, we derive several jamming attacks that allow the jammer to jam S-MAC, LMAC, and B-MAC energy efficiently. The jamming attacks are based on realistic assumptions. The algorithms are described in detail and simulated. The effectiveness and efficiency of the attacks are examined. In addition, we validate our simulation model by comparing its results with measurements obtained from actual implementation on our sensor node prototypes. We show that it takes little effort to implement such effective jammers, making them a realistic threat. Careful analysis of other protocols belonging to the respective categories of S-MAC, LMAC, and B-MAC reveals that those protocols are, to some extent, also susceptible to our attacks. The result of this investigation provides new insights into the security considerations of MAC protocols.
Segmentation using Codebook Index Statistics for Vector Quantized Images

In this paper, the segmentation using codebook index statistics (SUCIS) method is proposed for vector-quantized images. Three different codebooks are constructed according to the statistical characteristics (mean, variance, and gradient) of the codewords. Then they are employed to generate three different index images, which can be used to analyze the image contents including the homogeneous, edge, and texture blocks. An adaptive thresholding method is proposed to assign all image blocks in the compressed image to several disjoint regions with different characteristics. In order to make the segmentation result more accurate, two post-processing methods: the region merging and boundary smoothing schemes, are proposed. Finally, the pixel-wise segmentation result can be obtained by partitioning the image blocks at the single-pixel level. Experimental results demonstrate the effectiveness of the proposed SUCIS method on image segmentation, especially for the applications on object extraction.
Query-Answer Causality in Databases: Abductive Diagnosis and View Updates

Causality has been recently introduced in databases, to model, characterize and possibly compute causes for query results (answers). Connections between query causality and consistency-based diagnosis and database repairs (wrt. integrity constrain violations) have been established in the literature. In this work we establish connections between query causality and abductive diagnosis and the view-update problem. The unveiled relationships allow us to obtain new complexity results for query causality -the main focus of our work- and also for the two other areas.
Orbits in the Bar of NGC 4314

We find the main families of simple periodic orbits in and around the bar of NGC 4314 and examine their stability. In many ways, our results agree with those found for model barred galaxies, yet our realistic potential allows us to go further in a comparison with the galaxy morphology. In particular, we underline the importance of the families of periodic orbits that are asymmetric with respect to the bar minor axis. The x1 family provides the building blocks for the bar. In the inner parts we find orbits that are roughly perpendicular to the bar, although their shape and orientation vary along the corresponding families. As in previous studies, we find a symmetric unstable 3:1 family, but we also find an asymmetric and stable 3:1 family. We also find asymmetric diamond-like orbits near corotation. We pay special attention to the orbital behavior at the ultraharmonic resonance region, and we investigate all possibilities offered by our study in explaining the boxy structure at the end of the bar.
Asymptotic isoperimetry on groups and uniform embeddings into Banach spaces

We characterize the possible asymptotic behaviors of the compression associated to a uniform embedding into some Lp-space, with 1 < p < ∞, for a large class of groups including connected Lie groups with exponential growth and word-hyperbolic finitely generated groups. In particular, the Hilbert compression rate of these groups is equal to 1. This also provides new and optimal estimates for the compression of a uniform embedding of the infinite 3-regular tree into some Lp-space. The main part of the paper is devoted to the explicit construction of affine isometric actions of amenable connected Lie groups on Lp-spaces whose compressions are asymptotically optimal. These constructions are based on an asymptotic lower bound of the Lp-isoperimetric profile inside balls. We compute the asymptotic of this profile for all amenable connected Lie groups and for all 1 ≤ p < ∞, providing new geometric invariants of these groups. We also relate the Hilbert compression rate with other asymptotic quantities such as volume growth and probability of return of random walks.
The Determinants of Care Home Closure

This study investigates the causes of full closure of care homes in the English care home/nursing home market. We develop theoretical arguments about two causes for closure that are triggered by errors or external shocks: poor economic sustainability and regulatory action. Homes aiming to operate with lower quality in the market are argued for a number of reasons to be more susceptible to errors/shocks in setting quality, especially negative errors, leading to an empirical hypothesis that observed quality should negatively affect closure chance. In addition, given quality, homes facing relatively high levels of local competition should also have an increased chance of closure. We use a panel of care homes from 2008 and 2010 to examine factors affecting their closure status in subsequent years. We allow for the potential endogeneity of home quality and use multiple imputation to replace missing data. Results suggest that homes with comparatively higher quality and/or lower levels of competition have less chance of closure than other homes. We discuss that the results provide some support for the policy of regulators providing quality information to potential purchasers in the market. © 2015 The Authors. Health Economics published by John Wiley & Sons Ltd.