Miracle-dz/UniFAR-FTUs huggingface dataset:
Batch Effect Confounding Leads to Strong Bias in Performance Estimates Obtained by Cross-Validation

Background With the large amount of biological data that is currently publicly available, many investigators combine multiple data sets to increase the sample size and potentially also the power of their analyses. However, technical differences (“batch effects”) as well as differences in sample composition between the data sets may significantly affect the ability to draw generalizable conclusions from such studies. Focus The current study focuses on the construction of classifiers, and the use of cross-validation to estimate their performance. In particular, we investigate the impact of batch effects and differences in sample composition between batches on the accuracy of the classification performance estimate obtained via cross-validation. The focus on estimation bias is a main difference compared to previous studies, which have mostly focused on the predictive performance and how it relates to the presence of batch effects. Data We work on simulated data sets. To have realistic intensity distributions, we use real gene expression data as the basis for our simulation. Random samples from this expression matrix are selected and assigned to group 1 (e.g., ‘control’) or group 2 (e.g., ‘treated’). We introduce batch effects and select some features to be differentially expressed between the two groups. We consider several scenarios for our study, most importantly different levels of confounding between groups and batch effects. Methods We focus on well-known classifiers: logistic regression, Support Vector Machines (SVM), k-nearest neighbors (kNN) and Random Forests (RF). Feature selection is performed with the Wilcoxon test or the lasso. Parameter tuning and feature selection, as well as the estimation of the prediction performance of each classifier, is performed within a nested cross-validation scheme. The estimated classification performance is then compared to what is obtained when applying the classifier to independent data.
Microstructure and materials characterisation of the novel Al–Cu–Y alloy

ABSTRACT The microstructure, hot cracking susceptibility, and mechanical properties of a novel Al–Cu–Y alloy were investigated. The Al–4.7Cu–1.6Y alloy demonstrated very good casting properties, hot cracking susceptibility that is similar to Al–Si–Mg alloys. Analysis of the solidification process showed that the primary Al solidification is followed by the eutectic reaction Liquid→τ1(Al8Cu4Y)+Al and the peritectic reactions Liquid+τ6(Al,Cu)11Y3)→Al+τ1(Al8Cu4Y) (612°C) and Liquid+η(AlCu)→τ1(Al8Cu4Y)+θ(Al2Cu) (595°C). The τ1(Al8Cu4Y) eutectic phase demonstrated high thermal stability during homogenisation treatment. The recrystallisation temperature was in the range 250–350°C after rolling with previous quenching at 540 and 590°C and without heat treatment. The recommended annealing mode for material in the as-rolled condition is 100°C for 1 h: YS = 273 MPa, UTS = 305 MPa and El. = 6.6%.
Learning to Prune Deep Neural Networks via Layer-wise Optimal Brain Surgeon

How to develop slim and accurate deep neural networks has become crucial for real- world applications, especially for those employed in embedded systems. Though previous work along this research line has shown some promising results, most existing methods either fail to significantly compress a well-trained deep network or require a heavy retraining process for the pruned deep network to re-boost its prediction performance. In this paper, we propose a new layer-wise pruning method for deep neural networks. In our proposed method, parameters of each individual layer are pruned independently based on second order derivatives of a layer-wise error function with respect to the corresponding parameters. We prove that the final prediction performance drop after pruning is bounded by a linear combination of the reconstructed errors caused at each layer. Therefore, there is a guarantee that one only needs to perform a light retraining process on the pruned network to resume its original prediction performance. We conduct extensive experiments on benchmark datasets to demonstrate the effectiveness of our pruning method compared with several state-of-the-art baseline methods.
Agnostic Estimation of Mean and Covariance

We consider the problem of estimating the mean and covariance of a distribution from i.i. d. samples in the presence of a fraction of malicious noise. This is in contrast to much recent work where the noise itself is assumed to be from a distribution of known type. The agnostic problem includes many interesting special cases, e.g., learning the parameters of a single Gaussian (or finding the best-fit Gaussian) when a fraction of data is adversarially corrupted, agnostically learning mixtures, agnostic ICA, etc. We present polynomial-time algorithms to estimate the mean and covariance with error guarantees in terms of information-theoretic lower bounds. As a corollary, we also obtain an agnostic algorithm for Singular Value Decomposition.
The luminosity, colour and morphology dependence of galaxy filaments in the Sloan Digital Sky Survey Data Release Four

We have tested for luminosity, colour and morphology dependence of the degree of filamentarity in seven nearly two-dimensional strips from the Sloan Digital Sky Survey Data Release Four . (SDSS DR4). The analysis was carried out at various levels of coarse graining allowing us to address different length-scales. We find that the brighter galaxies have a less filamentary distribution than the fainter ones at all levels of coarse graining. The distribution of red galaxies and ellipticals shows a higher degree of filamentarity compared to blue galaxies and spirals, respectively, at low levels of coarse graining. The behaviour is reversed at higher levels of coarse graining. We propose a picture where the ellipticals are densely distributed in the vicinity of the nodes where the filaments intersect while the spirals are sparsely distributed along the entire extent of the filaments. Our findings indicate that the regions with an excess of ellipticals are larger than galaxy clusters, protruding into the filaments. We have also compared the predictions of a semi-analytic model of galaxy formation (the Millennium Run galaxy catalogue) against our results for the SDSS. We find the two to be in agreement for the M* galaxies and for the red galaxies, while the model fails to correctly predict the filamentarity of the brighter galaxies and the blue galaxies.
Fuzzy Closure Operators

Closure operators (and closure systems) play a significant role in both pure and applied mathematics. In the framework of fuzzy set theory, several particular examples of closure operators and systems have been considered (e.g. so-called fuzzy subalgebras, fuzzy congruences, fuzzy topology etc.). Recently, fuzzy closure operators and fuzzy closure systems themselves (i.e. operators which map fuzzy sets to fuzzy sets and the corresponding systems of closed fuzzy sets) have been studied by Gerla et al., see e.g. [3, 4, 6, 7]. As a matter of fact, a fuzzy set A is usually defined as a mapping from a universe set X into the real interval [0, 1] in the above mentioned works. Therefore, the structure of truth values of the “logic behind” is fixed to [0, 1] equipped usually with minimum as the operation corresponding to logical conjunction. As it appeared recently in the investigations of fuzzy logic in narrow sense [9, 10] (i.e. fuzzy logic as a many-valued logical calculus), there are several logical calculi formalizing the intuitive idea of “fuzzy reasoning” which are complete with respect to the semantics over special structures of truth values. Among these structures, the most general one is that of a residuated lattice (it is worth noticing that residuated lattices (introduced originally in [12] as an abstraction in the study of ideal systems of rings) have been proposed as a suitable structure of truth values by Goguen in [8]). From this point of view, the need for a general notion of a “fuzzy closure” concept becomes apparent. The aim of this paper is to outline a general theory of fuzzy closure operators and fuzzy closure systems. In the next section we introduce the necessary concepts. In Section 3, fuzzy closure operators and systems are
Distributed Log-Based Reconciliation

Computer Supported Cooperative Work (CSCW) defines software tools and technology to support groups of people working together on a project, often at different sites [5]. In this work, we present four distributed algorithms for log-based reconciliation, an important NP-hard problem occurring in CSCW. Our methods remove the classical drawbacks of centralized systems like single point of failure, performance bottleneck and loss of autonomy. The problem is formalized using the Distributed Constraint Satisfaction paradigm (DisCSP). In the worst case, the message passing complexity of our methods range from O(p2) to O(2p) in a system of p nodes. Experimental results confirm our theoretical analysis and allow us to establish quality and efficiency trade-off for each method.
Dynamic Adjustments of Attentional Control in Healthy Aging

In standard attentional control tasks, interference effects are reduced following incongruent trials compared to congruent trials, a phenomenon known as the congruency sequence effect (CSE). Typical explanations of this effect suggest the CSE is due to changes in levels of control across adjacent trials. This interpretation has been questioned by the finding that older adults, individuals with impaired attentional control systems, have been shown to produce larger CSEs in the Stroop task compared with younger adult controls. In 2 experiments, we investigate the generality of this finding by examining how the CSE changes in healthy aging in 3 standard attentional control tasks—Stroop, Simon, and flanker—while controlling for additional confounds that have plagued some of the past literature. In both experiments, older adult participants exhibited a larger CSE in the Stroop task, replicating recent research, but smaller CSEs in both the Simon and flanker paradigms. These results are interpreted as reflecting a pathway priming mechanism in the Stroop task but a control adjustment process in Simon and flanker. Hence, there appears to be different mechanisms underlying the CSE which are engaged based on the type of attentional selection that is required by the task. More generally, these results question the use of the CSE in the Stroop task as a measure of dynamic adjustments in attentional control and highlight the importance of consideration of task-specific control systems underlying the CSE.
Induced subgraphs of prescribed size

A subgraph of a graph G is called trivial if it is either a clique or an independent set. Let q(G) denote the maximum number of vertices in a trivial subgraph of G. Motivated by an open problem of Erdős and McKay we show that every graph G on n vertices for which q(G)≤ C log n contains an induced subgraph with exactly y edges, for every y between 0 and nδ (C). Our methods enable us also to show that under much weaker assumption, i.e., q(G) ≤ n/14, G still must contain an induced subgraph with exactly y edges, for every y between 0 and $e^{\Omega} (\sqrt { \log\, n})$. © 2003 Wiley Periodicals, Inc. J Graph Theory 43: 239–251, 2003
Revision of the Late Jurassic teleosaurid genus Machimosaurus (Crocodylomorpha, Thalattosuchia)

Machimosaurus was a large-bodied genus of teleosaurid crocodylomorph, considered to have been durophagous/chelonivorous, and which frequented coastal marine/estuarine ecosystems during the Late Jurassic. Here, we revise the genus based on previously described specimens and revise the species within this genus. We conclude that there were three European Machimosaurus species and another taxon in Ethiopia. This conclusion is based on numerous lines of evidence: craniomandibular, dental and postcranial morphologies; differences in estimated total body length; geological age; geographical distribution; and hypothetical lifestyle. We re-diagnose the type species Machimosaurus hugii and limit referred specimens to only those from Upper Kimmeridgian–Lower Tithonian of Switzerland, Portugal and Spain. We also re-diagnose Machimosaurus mosae, demonstrate that it is an available name and restrict the species to the uppermost Kimmeridgian–lowermost Tithonian of northeastern France. We re-diagnose and validate the species Machimosaurus nowackianus from Harrar, Ethiopia. Finally, we establish a new species, Machimosaurus buffetauti, for the Lower Kimmeridgian specimens of France and Germany (and possibly England and Poland). We hypothesize that Machimosaurus may have been analogous to the Pliocene–Holocene genus Crocodylus in having one large-bodied taxon suited to traversing marine barriers and additional, geographically limited taxa across its range.
Neural Mechanisms of Visual Attention : How Top-Down Feedback Highlights Relevant Locations

Brain processing depends on the interactions between neuronal groups. Those interactions are governed by the pattern of anatomical connections and by yet unknown mechanisms that modulate the effective strength of a given connection. We found that the mutual influence among neuronal groups depends on the phase relation between rhythmic activities within the groups. Phase relations supporting interactions between the groups preceded those interactions by a few milliseconds, consistent with a mechanistic role. These effects were specific in time, frequency, and space, and we therefore propose that the pattern of synchronization flexibly determines the pattern of neuronal interactions.
Chemoprevention of Head and Neck Cancer by Simultaneous Blocking of Epidermal Growth Factor Receptor and Cyclooxygenase-2 Signaling Pathways: Preclinical and Clinical Studies

Purpose: We investigated the efficacy and underlying molecular mechanism of a novel chemopreventive strategy combining EGF receptor (EGFR) tyrosine kinase inhibitor (TKI) with cyclooxygenase-2 inhibitor (COX-2I). Experimental Design: We examined the inhibition of tumor cell growth by combined EGFR-TKI (erlotinib) and COX-2I (celecoxib) treatment using head and neck cancer cell lines and a preventive xenograft model. We studied the antiangiogenic activity of these agents and examined the affected signaling pathways by immunoblotting analysis in tumor cell lysates and immunohistochemistry (IHC) and enzyme immunoassay (EIA) analyses on the mouse xenograft tissues and blood, respectively. Biomarkers in these signaling pathways were studied by IHC, EIA, and an antibody array analysis in samples collected from participants in a phase I chemoprevention trial of erlotinib and celecoxib. Results: The combined treatment inhibited head and neck cancer cell growth significantly more potently than either single agent alone in cell line and xenograft models, and resulted in greater inhibition of cell-cycle progression at G1 phase than either single drug. The combined treatment modulated the EGFR and mTOR signaling pathways. A phase I chemoprevention trial of combined erlotinib and celecoxib revealed an overall pathologic response rate of 71% at time of data analysis. Analysis of tissue samples from participants consistently showed downregulation of EGFR, pERK, and pS6 levels after treatment, which correlated with clinical response. Conclusion: Treatment with erlotinib combined with celecoxib offers an effective chemopreventive approach through inhibition of EGFR and mTOR pathways, which may serve as potential biomarkers to monitor the intervention of this combination in the clinic. Clin Cancer Res; 19(5); 1244–56. ©2013 AACR.
Crystallographic preferred orientation (CPO) of gypsum measured by electron backscatter diffraction (EBSD)

An investigation by electron backscatter diffraction on gypsum shows that this technique can be used to study the microstructures and crystallographic preferred orientation of gypsum. Presented here are the methods, verification tests and data obtained from a naturally deformed sample of gypsum‐rich rock. The electron backscatter diffraction data show the sample has a strong crystallographic preferred orientation.
Community Detection in Sparse Random Networks

We consider the problem of detecting a tight community in a sparse random network. This is formalized as testing for the existence of a dense random subgraph in a random graph. Under the null hypothesis, the graph is a realization of an Erd\"os-R\'enyi graph on $N$ vertices and with connection probability $p_0$; under the alternative, there is an unknown subgraph on $n$ vertices where the connection probability is p1 > p0. In Arias-Castro and Verzelen (2012), we focused on the asymptotically dense regime where p0 is large enough that np0>(n/N)^{o(1)}. We consider here the asymptotically sparse regime where p0 is small enough that np0 0. As before, we derive information theoretic lower bounds, and also establish the performance of various tests. Compared to our previous work, the arguments for the lower bounds are based on the same technology, but are substantially more technical in the details; also, the methods we study are different: besides a variant of the scan statistic, we study other statistics such as the size of the largest connected component, the number of triangles, the eigengap of the adjacency matrix, etc. Our detection bounds are sharp, except in the Poisson regime where we were not able to fully characterize the constant arising in the bound.
The Effect of Oral Intake of Low-Temperature-Processed Whey Protein Concentrate on Colitis and Gene Expression Profiles in Mice

Inflammatory bowel disease (IBD) is an autoimmune disease of unknown etiology and can lead to inflammation and cancer. Whey proteins contain many bioactive peptides with potential health benefits against IBD. We investigated the effect of low-temperature-processed whey protein concentrate (LWPC) on the suppression of IBD by using a dextran sodium sulfate (DSS)-induced colitis model in BALB/c mice. Oral intake of LWPC resulted in improved recovery of body weight in mice. Histological analysis showed that the epithelium cells of LWPC-treated mice were healthier and that lymphocyte infiltration was reduced. The increase in mucin due to the LWPC also reflected reduced inflammation in the colon. Transcriptome analysis of the colon by DNA microarrays revealed marked downregulation of genes related to immune responses in LWPC-fed mice. In particular, the expression of interferon gamma receptor 2 (Ifngr2) and guanylate-binding proteins (GBPs) was increased by DSS treatment and decreased in LWPC-fed mice. These findings suggest that LWPCs suppress DSS-induced inflammation in the colon by suppressing the signaling of these cytokines. Our findings suggest that LWPCs would be an effective food resource for suppressing IBD symptoms.
Properties and consequences of Thorn-independence

Abstract We develop a new notion of independence (ϸ-independence, read “thorn”-independence) that arises from a family of ranks suggested by Scanlon (ϸ-ranks). We prove that in a large class of theories (including simple theories and o-minimal theories) this notion has many of the properties needed for an adequate geometric structure. We prove that ϸ-independence agrees with the usual independence notions in stable, supersimple and o-minimal theories. Furthermore, we give some evidence that the equivalence between forking and ϸ-forking in simple theories might be closely related to one of the main open conjectures in simplicity theory, the stable forking conjecture. In particular, we prove that in any simple theory where the stable forking conjecture holds, ϸ-independence and forking independence agree.
Image Gallery: Palmoplantar hyperkeratosis in dermatomyositis with anti‐PM/Scl antibodies

DEAR EDITOR, The anti-PM/Scl antibody is associated with polymyositis/systemic scleroderma overlap syndromes. We found three patients with dermatomyositis with that antibody and summarized their clinical findings in a previous report. All three patients had palmoplantar hyperkeratosis (a–c) and interstitial lung disease, and two of the three patients had malignancies. The hyperkeratosis on the soles of one case (d) was aggravated (e) due to the use of ‘massage sandals’ (f). Palmoplantar hyperkeratosis is significantly more prevalent in antiPM/Scl antibody-positive dermatomyositis (three of three cases) than in anti-PM/Scl antibody-negative dermatomyositis (one of 123 cases, P < 0 001). We suggest that hyperkeratotic cutaneous symptoms might be distinguishing dermatological features of anti-PM/Scl antibody-positive dermatomyositis. T . TAK I Y . MURO Y. OGAWA M. AK I YAMA Department of Dermatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550 Japan Correspondence: Yoshinao Muro. E-mail: ymuro@med.nagoya-u.ac. jp
Joint User Pairing and Resource Allocation for LTE Uplink Transmission

In this paper, we investigate joint user pairing and resource allocation under the practical constraints in single-carrier frequency-division multiple access (SC-FDMA) LTE uplink systems. We first introduce a joint optimal algorithm based on branch-and-bound search as a benchmark. To reduce complexity, we divide the joint optimization problem into two subproblems: user pairing and resource allocation. For both these subproblems, we develop several low-complexity algorithms by exploiting the properties of the application of the optimization problem itself. It is shown by the simulation results that the proposed algorithms have better throughput and fairness than the conventional algorithms in and in for LTE uplink no matter whether power control is perfect or not.
Mechanisms of Natural Tolerance in the Intestine: Implications for Inflammatory Bowel Disease

Tolerance, the regulated inability to respond to a specific immunologic stimulant, is a physiological event important to normal immune function. Just as loss of tolerance to self-proteins results in autoimmune diseases, we assert that loss of tolerance to commensal flora in the intestinal lumen leads to inflammatory bowel disease (IBD). Mechanisms through which the mucosal immune system establishes and remains hyporesponsive toward the presence of food proteins and commensal flora, which we define as natural tolerance, are discussed. In addition to the contributions by commensal flora, the innate host defense and the adaptive immune systems promote natural tolerance to sustain normal mucosal homeostasis. Understanding the molecular and cellular events that mediate natural tolerance will lead to more advanced insights into IBD pathogenesis and improved therapeutic options.