Miracle-dz/UniFAR-FTUs huggingface dataset:
Lessons from a decade of integrating cancer copy number alterations with gene expression profiles

Over the last decade, multiple functional genomic datasets studying chromosomal aberrations and their downstream effects on gene expression have accumulated for several cancer types. A vast majority of them are in the form of paired gene expression profiles and somatic copy number alterations (CNA) information on the same patients identified using microarray platforms. In response, many algorithms and software packages are available for integrating these paired data. Surprisingly, there has been no serious attempt to review the currently available methodologies or the novel insights brought using them. In this work, we discuss the quantitative relationships observed between CNA and gene expression in multiple cancer types and biological milestones achieved using the available methodologies. We discuss the conceptual evolution of both, the step-wise and the joint data integration methodologies over the last decade. We conclude by providing suggestions for building efficient data integration methodologies and asking further biological questions.
An open question on the existence of Gabor frames in general linear position

Uncertainty principles for functions defined on finite Abelian groups generally relate the cardinality of a function to the cardinality of its Fourier transform. We examine how the cardinality of a function is related to the cardinality of its short--time Fourier transform. We illustrate that for some cyclic groups of small order, both, the Fourier and the short--time Fourier case, show a remarkable resemblance. We pose the question whether this correspondence holds for all cyclic groups.
Response Patterns in a Test of Logical Inference

are based on the assumption that psychological test scores and test responses can be more fruitfully interpreted if account is taken of the relationships existing among them. The evidence previously reviewed (4) supports the contention that more penetrating quantitative descriptions can be obtained by studying the manner in which measured traits (viz., test scores) and attributes (viz., test responses) are associated in and by the individual. Because they consider the configurational as well as the additive aspects of psychometric data, patterned scoring, as advocated by Meehl (7) and Zubin (io), and configural analysis, as developed by McQuitty (6), constitute first steps toward meeting the criticisms of atomism and inflexibility frequently leveled at psychometric research by Gestalt and dynamic psychologists.
The use of live models in the teaching of gross anatomy

Live models were introduced into the first‐year gross anatomy course to provide medical students with an opportunity to apply to the living person what they learned from cadaver dissection. After each major segment of the cadaver dissection, clinical correlation sessions were presented for the students by clinicians, using live models for demonstration, examination and correlation. At the completion of the course, an evaluation questionnaire was given to students. Their response indicated that the new teaching technique made anatomy seem more relevant to clinical medicine than using cadavers alone. Live models were rated superior to using cadavers, especially in demonstrating superficial anatomical structures and landmarks.
Speech enhancement based on audible noise suppression

A novel speech enhancement technique is presented based on the definition of the psychoacoustically derived quantity of audible noise spectrum and its subsequent suppression using optimal nonlinear filtering of the short-time spectral amplitude (STSA) envelope. The filter operates with sparse spectral estimates obtained from the STSA, and, when these parameters are accurately known, significant intelligibility gains, up to 40%, result in the processed speech signal. These parameters can be also estimated from noisy data, resulting into smaller but significant intelligibility gains.
When's a Smile a Smile? Or how to Detect a Message by Digitizing the Signal

What's in a smile? Why do we respond so powerfully to this visual display? Or, phrased in information processing terms: What characteristics of the signal define the boundaries of the social message? We have used digital image analysis and subject ratings to answer this question for videotaped smiles. A simple measure of the information provided by facial movement—the entropy of the distribution of pixel intensities in the subtracted or difference images—traced the changing facial expression (the signal) through time. Raters categorized the individual videoprints in order to locate message boundaries. We found a remarkable coincidence between changes in signal entropy and message. In each smile, rapid increases in positive messages occurred within entropy crests. We conclude that quantitative measures of information transmission can be used to locate message boundaries and provide insight into how receivers parse the behavioral stream.
Studies on the Secondary Metabolites of a Pseudoalteromonas sp. Isolated from Sediments Collected at the Northeastern Coast of Brazil

Continuing search for anticancer compounds from the marine environment, we have studied microorganisms that inhabit intertidal sediments of the northeastern Brazilian coast. Of the 32 strains isolated, 13 were selected for biological evaluation of their crude extracts. The acetate extract obtained from a Gram‐negative bacterium was strongly active against cancer cell lines with IC50 values that ranged from 0.04 (HL60 leukemia cells) to 0.26 μg/ml (MDA MB‐435 melanoma cells). The bacterium was identified as a Pseudoalteromonas sp. based on 16S rRNA gene sequencing. A bioassay‐guided fractionation of the active extract led to the isolation of prodigiosin, a well‐known tripyrrole red pigment with immunosuppressive and anticancer activities. Further experiments with ErbB‐2 overexpressing cell lines, including HB4a‐C3.6 (moderate overexpression), HB4a‐C5.2 (high overexpression), and the parental HB4a cell line, were performed. Prodigiosin was moderately active toward HB4a cells with an IC50 of 4.6 μg/ml, while it was 115 and 18 times more active toward HB4a‐C3.6 cells (IC50 of 0.04 μg/ml) and HB4a‐C5.2 (IC50 of 0.26 μg/ml) cells, respectively. These data suggest that, in spite of its previously described apoptosis‐inducing properties, prodigiosin can selectively recognize cells overexpressing ErbB‐2, which could be highly appealing in human breast cancer therapy.
Bioinspired polymer microstructures for directional transport of oily liquids

Nature has always served as an inspiration for scientists, helping them to solve a large diversity of technical problems. In our case, we are interested in the directional transport of oily liquids and as a model for this application we used the flat bug Dysodius lunatus. In this report, we present arrays of drops looking like polymer microstructures produced by the two-photon polymerization technique that mimic the micro-ornamentation from the bug's cuticle. A good directionality of oil transport was achieved, directly controlled by the direction of the pointed microstructures at the surface. If the tips of the drop-like microstructures are pointing towards the left side, the liquid front moves to the right and vice versa. Similar effects could be expected for the transport of oily lubricants. These results could, therefore, be interesting for applications in friction and wear reduction.
Does Online News Reading and Sharing Shape Perceptions of the Internet as a Place for Public Deliberations?

With the rapid development of interactive communication technology, the Internet is a major source of news and also plays an important role in connecting individual members of society. However, Internet users may have different perspectives on whether the Internet positively functions as a medium for public deliberation. Based on the assumption that being exposed to information on public affairs is a crucial step for one's civic engagement, this study explores how individuals’ motives related to news consumption, elaborative online news reading, and online news sharing influence their perceptions of online deliberation using structural equation modeling method (N = 998). The study finds significant relationships between news consumption motives and elaborative news reading and sharing behaviors, but only elaborative reading behavior had a significant effect on one's perceptions of online deliberation. The implications of these findings are discussed.
Status Epilepticus in Children: Etiology, Clinical Features, and Outcome

Between August 1984 and September 1986, data were gathered prospectively on 114 episodes of convulsive status epilepticus, defined as seizure duration longer than 30 minutes, affecting 97 children. Status epilepticus was symptomatic in 72% (chronic 59%, acute 13%) and idiopathic or febrile in 28%. We identified precipitating factors in 63% of episodes. The most common factors were inadequate blood levels of anticonvulsants (32 of 60 episodes in children with prior seizures) and febrile illnesses, excluding meningitis or encephalitis (38 of 114 episodes). There was an elevated peripheral white blood cell count in 60%, acidosis with a pH of <7.0 in 12.5%, and cerebrospinal fluid pleocytosis not due to meningitis or encephalitis in 8 of 64 episodes. Eight children died, three with severe pre-existing brain damage, two with meningitis, and two with a poorly defined encephalopathy. Eighteen children developed a new neurologic deficit. Outcome was associated with the etiology and duration of status epilepticus, with age at the time of status a minor factor. A permanent deficit occurred in only five children with idiopathic or febrile status epilepticus. (J Child Neurol 1988;3:167-173).
Individual differences and strategy selection in reasoning

Although individuals may use different strategies in order to solve reasoning problems, few attempts have been made to understand the processes that lead to strategy choice. One exception to this is work with the sentence-picture verification task in which it has been found that high spatial ability individuals tend to use a strategy that involves spatial representations while low spatial ability individuals tend to use a strategy that involves verbal representations. The first study reported here attempted to see whether these findings would generalize to another simple reasoning task with a particularly inefficient spatial strategy. This was found not to be the case; low spatial ability individuals used the spatial strategy while high spatial ability individuals avoided using it. Three explanations were suggested for this based upon (a) spatial ability, (b) intelligence or (c) knowledge. Results of two further studies favoured the spatial ability explanation; individuals do not have explicit prior knowledge of the most effective strategy for this task, and the level of spatial ability determines the degree to which they are able to develop and evaluate the more effective non-spatial strategies.
Aphasia in closed head injury and stroke

Abstract The question of whether closed head injured (CHI) aphasic patients present communication impairments similar to post-stroke (CVA) aphasic patients was addressed by comparing two equated groups at 3–6 months post-onset. When age and time since onset were controlled, aphasic CHI and CVA patients were more similar than different in linguistic task performance and overall functional communication effectiveness.
Individual and corporate dispute resolution: Using procedural fairness as a decision heuristic.

The research reported in this paper was supported by the National Science Foundation (grants 84-11142 and 85-18597), the American Bar Foundation, and the Institute for Civil Justice of the RAND Corporation. The authors are grateful to Barbara Meierhoefer, Pat Lombard, and the Federal Judicial Center for supplying the Study 2 data, to Ruth Kanfer and Chris Earley for permission to reanalyze data from their study with the first author, and to Tom Tyler, Robert Sutton, Gina Ke, Bob Bies, and Karen Cook for their comments on earlier versions of this manuscript. Two studies examined how litigants' evaluations of the outcome and process of lawsuits affected their judgments about the fairness of procedures and their acceptance of awards from court-ordered arbitration. The studies tested predictions concerning the operation of a "fairness heuristic"-that procedural justice judgments mediate the effects of process impressions and outcome evaluations on the decision to accept or reject the directives of an authority. Participants in the studies were corporate and individual litigants in federal tort and contract actions that were subject to court-ordered arbitration. In both studies the decision to accept the arbitrator's award or reject it and go to trial was strongly correlated with judgments of procedural justice, and much or all of the effect of outcome evaluations and process impressions on award acceptance was mediated by procedural justice judgments, which had a stronger effect than either subjective or objective measures of the arbitration award. Separate analyses of corporate and individual decision makers in the second study suggested that both groups relied heavily on procedural justice judgments in deciding whether or not to accept the arbitration award. The findings provide evidence of widespread use of a fairness heuristic and support the extension of justice-judgment research to corporate decision making. '
DroPNet: a web portal for integrated analysis of Drosophila protein–protein interaction networks

DroPNet (Drosophila Protein Network) is a Drosophila-dedicated web portal for generating and analyzing protein–protein interaction (PPI) networks. This platform integrates users’ experimental data provided as one or two lists of genes with PPI data from Drosophila and other species. These experimental data can, for example, come from RNAi screens, for which this approach is known to be valuable. DroPNet, therefore, provides an essential basis for further biological analysis by linking functional and physical interactions and reinforcing the relevance of each. DroPNet focuses on the search of PPIs between genes of the entry list, and includes the possibility of searching for intermediate genes for which the corresponding protein indirectly links two entry data. It also offers multiple functions for editing the networks obtained, providing users with interactive possibilities to progressively improve and refine the results. This approach gives a global view of the studied process and makes it possible to highlight specific interactions that have so far been understudied. DroPNet is freely available at http://dropnet.isima. fr.
PERSONALITY AND SOCIAL PSYCHOLOGY BULLETIN Granqvist / ATTACHMENT AND RELIGIOSITY IN ADOLESCENCE Attachment and Religiosity in Adolescence: Cross-Sectional and Longitudinal Evaluations

The study offers the first investigation of cross-sectional and longitudinal associations between attachment and religiosity with adolescent participants. Adolescence is a life period linked to attachment transitions and religious changes. The research was conducted to help resolve inconsistent results from previous crosssectional versus longitudinal studies and studies on attachment to parents versus peer attachment. Time 1 questionnaire data was collected from 196 Swedish adolescents (M age = 16 years); 143 participants completed the 15-month follow-up. Results from the cross-sectional analyses generally supported the socialized correspondence and emotional compensation hypotheses, particularly in relation to attachment to mother. Results from the longitudinal analyses were more mixed. The discussion integrates the hypotheses with Kirkpatrick’s previous proposal, argues for a main focus on attachment to parents rather than peer attachment, and offers suggestions for future attachment and religion studies.
Azathioprine and 6-mercaptopurine for maintenance of remission in ulcerative colitis.

BACKGROUND Maintenance of remission is a major issue in inflammatory bowel disease. In ulcerative colitis, the evidence for the effectiveness of azathioprine and 6-mercaptopurine for the maintenance of remission is still controversial. OBJECTIVES To assess the effectiveness and safety of azathioprine and 6-mercaptopurine for maintaining remission of ulcerative colitis. SEARCH STRATEGY The MEDLINE database was used to search literature from 1966 to 2006. A manual search was also performed using references from these articles as well as review articles, proceedings from major gastrointestinal meetings and data available from the Cochrane Collaboration database. Authors of maintenance trials were asked about unpublished studies. SELECTION CRITERIA Randomized controlled trials of at least 12 months duration that compared azathioprine or 6-mercaptopurine with placebo or standard maintenance therapy (mesalamine) were included. DATA COLLECTION AND ANALYSIS Data were extracted by two raters using standard forms. Disagreements were solved by informal consent, including a third rater. Jadad scores were applied to assess study quality. Analyses were performed separately by type of control (placebo, or active comparator). Pooled odds ratios were calculated based on the fixed effects model unless heterogeneity was shown. MAIN RESULTS Six studies were identified including 286 patients with ulcerative colitis. The study quality was mostly poor. Azathioprine was shown to be superior for the maintenance of remission as compared to placebo based on four trials (failure to maintain remission: OR 0.41; 95% CI 0.24 to 0.70). Two trials that compared 6-mercaptopurine to mesalazine, or azathioprine to sulfasalazine showed significant heterogeneity. Both studies using active comparators were open label. Adverse effects occurred in 11 of 127 patients receiving azathioprine, including acute pancreatitis (3 cases) and significant bone marrow suppression (5 cases). AUTHORS' CONCLUSIONS Azathioprine may be an effective maintenance therapy for patients who have failed or cannot tolerate mesalazine or sulfasalazine and for patients who require repeated courses of steroids. More research is needed to evaluate superiority over standard maintenance therapy, especially in the light of a potential for adverse events from azathioprine.
From Individual Learning to Project Team Learning and Innovation: A Structured Approach.

An element frequently missing from organisations is that of team learning. While recognised as critical, attempts to capture and apply team learning often result in only partial success. This paper (based on work carried out within a major UK automotive manufacturer) explains a methodology for capturing team learning that brings together the contribution of individuals into a team context while maintaining a focus throughout the process on the need for innovative change.
A simulation study of a new family of test statistics for the Behrens-Fisher problem

Purpose – To provide a new family of test statistics to solve the Behrens‐Fisher problem and to compare it with the classic test statistics through a different simulation studies.Design/methodology/approach – A general procedure for testing composite hypothesis to k samples of different size problems on the basis of the Renyi's divergence is used to develop a new parametric family of test statistics that contains as a particular case the classical likelihood ratio test. The scope of the paper is to find out if some member of the new family of test statistics it is preferable to the classical ones.Findings – Some members of the new parametric family of test statistics behave remarkably well in comparison to the classic ones, as the different computational studies reveal.Originality/value – This paper offers a new way to solve the Behrens‐Fisher problem that it is preferable in some cases to the known procedures.
Myosin XIK of Arabidopsis thaliana Accumulates at the Root Hair Tip and Is Required for Fast Root Hair Growth

Myosin motor proteins are thought to carry out important functions in the establishment and maintenance of cell polarity by moving cellular components such as organelles, vesicles, or protein complexes along the actin cytoskeleton. In Arabidopsis thaliana, disruption of the myosin XIK gene leads to reduced elongation of the highly polar root hairs, suggesting that the encoded motor protein is involved in this cell growth. Detailed live-cell observations in this study revealed that xik root hairs elongated more slowly and stopped growth sooner than those in wild type. Overall cellular organization including the actin cytoskeleton appeared normal, but actin filament dynamics were reduced in the mutant. Accumulation of RabA4b-containing vesicles, on the other hand, was not significantly different from wild type. A functional YFP-XIK fusion protein that could complement the mutant phenotype accumulated at the tip of growing root hairs in an actin-dependent manner. The distribution of YFP-XIK at the tip, however, did not match that of the ER or several tip-enriched markers including CFP-RabA4b. We conclude that the myosin XIK is required for normal actin dynamics and plays a role in the subapical region of growing root hairs to facilitate optimal growth.
Consequences of the existence of Auslander-Reiten triangles with applications to perfect complexes for self-injective algebras

In a k-linear triangulated category (where k is a field) we show that the existence of Auslander-Reiten triangles implies that objects are determined, up to shift, by knowing dimensions of homomorphisms between them. In most cases the objects themselves are distinguished by this information, a conclusion which was also reached under slightly different hypotheses in a theorem of Jensen, Su and Zimmermann. The approach is to consider bilinear forms on Grothendieck groups which are analogous to the Green ring of a finite group. We specialize to the category of perfect complexes for a self-injective algebra, for which the Auslander-Reiten quiver has a known shape. We characterize the position in the quiver of many kinds of perfect complexes, including those of lengths 1, 2 and 3, rigid complexes and truncated projective resolutions. We describe completely the quiver components which contain projective modules. We obtain relationships between the homology of complexes at different places in the quiver, deducing that every self-injective algebra of radical length at least 3 has indecomposable perfect complexes with arbitrarily large homology in any given degree. We find also that homology stabilizes away from the rim of the quiver. We show that when the algebra is symmetric, one of the forms considered earlier is Hermitian, and this allows us to compute its values knowing them only on objects on the rim of the quiver.
Synthesis Methods, Microscopy Characterization and Device Integration of Nanoscale Metal Oxide Semiconductors for Gas Sensing

A comparison is made between SnO2, ZnO, and TiO2 single-crystal nanowires and SnO2 polycrystalline nanofibers for gas sensing. Both nanostructures possess a one-dimensional morphology. Different synthesis methods are used to produce these materials: thermal evaporation-condensation (TEC), controlled oxidation, and electrospinning. Advantages and limitations of each technique are listed. Practical issues associated with harvesting, purification, and integration of these materials into sensing devices are detailed. For comparison to the nascent form, these sensing materials are surface coated with Pd and Pt nanoparticles. Gas sensing tests, with respect to H2, are conducted at ambient and elevated temperatures. Comparative normalized responses and time constants for the catalyst and noncatalyst systems provide a basis for identification of the superior metal-oxide nanostructure and catalyst combination. With temperature-dependent data, Arrhenius analyses are made to determine activation energies for the catalyst-assisted systems.