Miracle-dz/UniFAR-FTUs huggingface dataset:
Letter to the Editor Correcting for a Potential Bias in the Pedigree Disequilibrium Test

To the Editor: Recently, we proposed the pedigree disequilibrium test (PDT) as a test for allelic association and linkage (linkage disequilibrium) in general pedigrees (Martin et al. 2000). We have discovered that, in certain cases in extended pedigrees, the PDT can be biased under the null hypothesis. In this letter we describe the nature of the bias and illustrate a model in which the bias arises. We offer two alternative modifications to the PDT statistic, both of which result in valid tests of linkage disequilibrium over all genetic models and family structures. In constructing the PDT statistic, we considered two types of families within a pedigree. Informative nuclear families are those in which there is at least one affected individual, with both parents genotyped at the marker and at least one parent heterozygous. Informative discordant sibships have at least one affected and one unaffected sibling with different marker genotypes. For a marker locus with two alleles, M 1 and M 2 , we defined the random variables X Tj , for the jth triad (affected individual and both parents) in the pedigree, and X Sj , for the jth discordant sib pair (DSP) in the pedigree: X Tj p (no. of M 1 transmitted) Ϫ (no. of M 1 not transmitted) and X Sj p (no. of M 1 in affected sib) Ϫ (no. of M 1 in unaffected sib), respectively. In our previous study (Mar-tin et al. 2000), we defined a measure of association (D) for a pedigree containing n T triads from informative nuclear families and n S DSPs from informative discordant sibships: n n T S 1 D p X ϩ X. (1) ͸ ͸ [ ] Tj Sj n ϩ n jp1 jp1 T S Let D i be the measure of association in the ith pedigree in a sample of N independent pedigrees. The PDT statistic is given by. The critical as-N N 2 ͱ T p S D / S D jp1 i j p1 i sumption is that the T is asymptotically normal, with mean 0 and variance 1, under the null hypothesis of no linkage disequilibrium. The difficulty that can be encountered is that, for some cases under the null hypothesis, the expected value of T may actually be different from 0, a situation that results in an inflated type I error. This is best illustrated by an example. Consider a fully …
Where Broken Windows Should Be Fixed

Objectives: Introduce a systematic method to identify areas with similar levels of disorder (from serene, to “tipping,” to crime-ridden) which is crucial for a valid empirical test of Broken Windows Theory (BWT). Methods: Systematic social observation data are used of almost 2,000 locations in the city of Amsterdam, the Netherlands. Spatially constrained hierarchical agglomerative clustering is used to aggregate individual observation locations to form homogeneous areas. Davies–Bouldin index and intraclass correlation coefficient are used to objectively identify the optimum number of clusters. Results: The newly identified areas differ from administrative neighborhoods as well as hot spots of disorder. The regionalization method provides a tentative solution to both the “zonation” and “aggregation” problems of the modifiable areal unit problem liable to affect empirical studies of BWT. Conclusions: Hot spot analysis fails to identify areas with moderate levels of disorder, which impedes testing the basic precept of BWT. Our results may partly explain why the evidence on the effectiveness of order maintenance policing remains inconclusive. We suggest that randomized controlled trials of order maintenance policing should be performed on these new areas rather than in hot spots of disorder.
Diffracting Diffraction: Cutting Together-Apart

Diffraction owes as much to a thick legacy of feminist theorizing about difference as it does to physics. As such, I want to begin by re-turning – not by returning as in reflecting on or going back to a past that was, but re-turning as in turning it over and over again – iteratively intra-acting, re-diffracting, diffracting anew, in the making of new temporalities (spacetimematterings), new diffraction patterns. We might imagine re-turning as a multiplicity of processes, such as the kinds earthworms revel in while helping to make compost or otherwise being busy at work and at play: turning the soil over and over – ingesting and excreting it, tunnelling through it, burrowing, all means of aerating the soil, allowing oxygen in, opening it up and breathing new life into it. It might seem a bit odd to enlist an organic metaphor to talk about diffraction, an optical phenomenon that might seem lifeless. But diffraction is not only a lively affair, but one that troubles dichotomies, including some of the most sedimented and stabilized/stabilizing binaries, such as organic/ inorganic and animate/inanimate. Indeed, the quantum understanding of diffraction troubles the very notion of dicho-tomy – cutting into two – as a singular act of absolute differentiation, fracturing this from that, now from then.
Book Reviews: Cynthia Hardy: Strategies for Rentrenchment and Turnaround: The Politics of Survival

as though they may be useful in helping companies to unfreeze and become creative about their strategic perspectives though they are more to do with attacking mind-sets than changing organizational arrangements. Others are somewhat mechanistic devices to ascribe risks and probabilities to elements of various scenarios. The second part of the book is less interesting. Its summaries of the standard U.S. literature on strategic management will be familiar to most O. S. readers and, although it is nice to see that the importance of culture change in strategic management is emphasised, this is now becoming commonplace. What is of more interest is the evidence that a number of modern management gurus are echoing some of the earliest management writers. For example, we are told that F. W. Taylor would have been the first to indict Taylorism and we are reminded that he called for a ’mental
Vibration Sensation in Humans

The proposition that the performer of music can use vibrotactile sensations to supplement auditory cues as feedback signals in order to enhance tonal control of the instrument is examined. As a basis for evaluating this proposition, we present some fundamental characteristics of human vibrotactile sensation, including measurements at the threshold of detectability, at suprathreshold levels, and of subject variables that could affect sensation. It is reasonable to assume that the sensory capacities of skin could enable tactile feedback cues to be used by singers and some instrumentalists in controlling the tone of their instruments.
Dynamic Video Face Transformation Using Multilinear and Autoregressive Models

In this paper we present a prototype system for altering perceived attributes of faces in video sequences, such as the apparent age, sex or emotional state. The system uses multilinear models to decompose the parameters coding for each frame into separate pose and identity parameters. The multilinear model is learnt automatically from the training video data. Statistical models of group identity are then used to alter the identity parameters from one group to another (e
Development of the Korean Version of the Consortium to Establish a Registry for Alzheimer's Disease Assessment Packet (CERAD-K)Clinical and Neuropsychological Assessment Batteries

A Korean version of the Consortium to Establish a Registry for Alzheimer’s Disease Assessment Packet (CERAD-K) was created. The English-American version of CERAD clinical and neuropsychological assessment batteries was translated into Korean, and the psychometrical properties of the cognitive tests in the CERAD-K were established. In the translation, including back-translation, the basic structures of all measures in the original CERAD batteries were maintained. The CERAD-K was administered in a standardized manner to 106 dementia patients (aged 70.4 � 8.1 years), including 78 Alzheimer’s disease (AD) patients, and 186 controls (aged 68.4 � 4.6 years) who were recruited from 3 university hospitals and 2 elderly welfare centers. The cognitive tests in the CERAD-K successfully differentiated controls from the dementia patients and from the AD patients. They also showed substantial interrater reliability and 1-month test-retest reliability. The CERAD-K is an equally reliable and valid equivalent for the English version of the CERAD clinical and neuropsychological assessment batteries. HE Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) developed the standardized clinical
Real or Unreal ?-An Evaluation Setting for Emotional Characters U sing Unreal

This paper sketches a setup to perform user experience tests on game characters which act emotionally based on their personality and situation. The test setting is primarily designed to benchmark Nemesys, a system designed to elicit emotions based on an artificial neural network that is able to learn six basic emotional states. Nemesys is based on models drawn from the state of the art in modeling emotions in the field of psychology and also includes the Five-Factor Model of Personality to represent different personalities. The test and application scenario employs the commercial 3D game engine from Unreal Tournament 2003, a stereoscopic projecting of the scene and biofeedback measurements of the affective state of the player.
Fixation of buried and surface-mounted magnets in high-speed permanent-magnet synchronous machines

High-speed applications involve technical and economical advantages because, as direct drives, they avoid the gear as an additional mechanical drive component. Permanent-magnet synchronous machines (PMSMs) are attracting growing attention for high-speed drives. Surface-mounted PMSMs request a glass- or carbon-fiber bandage to fasten the magnets to the rotor surface at high speed. At rotors with "buried" magnets, the rotor iron itself fixes the magnets. This paper presents simple calculation strategies and discusses their limits for the mechanical design of high-speed machines with either surface-mounted or buried magnets. The results of the calculations are compared with finite-element calculations
Learn to Detect Phishing Scams Using Learning and Ensemble ?Methods

Phishing attack is a kind of identity theft which tries to steal confidential data like on-line bank account information. In a phishing attack scenario, attacker deceives users by a fake email which is called scam. In this paper we employ three different learning methods to detect phishing scams. Then, we use ensemble methods on their results to improve our scam detection mechanism. Experimental results show that the proposed method can detect 94.4% of scam emails correctly, while only 0.08% of legitimate emails are classified as scams.
Genomic imbalances in AIDS-related lymphomas: relation with tumoral Epstein–Barr virus status

Background:The pathologic heterogeneity of AIDS related lymphomas (ARL) reflects several pathogenic mechanisms: chronic antigenic stimulation, Epstein–Barr virus (EBV) infection, and genomic abnormalities. Genetic abnormalities, known to play a major role in lymphomas of non-immunocompromised patients, are not well characterized in ARL. Objective:Characterization of the DNA copy number change (CNC) in ARL and comparison of our findings with tumoral EBV and immune status. Design and methods:We have studied by comparative genomic hybridization (CGH), 28 ARL well characterized for histopathologic, clonality and EBV findings. Results:DNA-CNC were detected in 50% of cases. Gains of chromosomal material were much more frequent than losses and involved chromosomes 9p, 11q, 12q, 17q, and 19q recurrently. DNA-CNC tended to be more frequent in EBV-positive lymphomas with latency type II/III than in EBV-positive latency I or EBV-negative lymphomas. Most chromosomal regions affected in HIV-related lymphoma were similar to those already reported in HIV-negative lymphomas. Conclusion:This CGH study allowed the identification of non-random chromosomal alterations in ARL. The results suggested an inverse relationship between EBV infection (latency II/III), associated with deep acquired immune suppression, and the number of chromosomal alterations which may be explained by a direct role of viral proteins in lymphomagenesis by activation of signalling pathways without needing several genomic alterations.
Uncertain Terms: Message Features of Online Cancer News

About 113 million Americans have reported seeking health information online; however, little is known about the quality (or qualities) of the information being retrieved. Users have reported seeking information about health issues in an attempt to reduce negatively appraised uncertainties (Brashers, 2007), but less is known about the ability of the retrieved information to increase or produce unwanted uncertainty. A content analysis of online cancer news was conducted and suggests that 65% of Internet-based cancer news contains message features previously linked to the production of uncertainty (e.g., ambiguous or complex information). Though future research is required regarding uncertainty-related content and its effects, this project provides a foundation for such future endeavors.
A Classroom Activity to Demonstrate Self-Other Agreement in Personality Judgments

This article describes a classroom activity to demonstrate (dis)agreement in personality judgments, using an exercise derived from Watson’s research on the accuracy of rating strangers’ personalities. On the first day of class, undergraduate students in psychology courses rated their own personality and the personality of a classmate, using items from the International Personality Item Pool (IPIP). Across five samples, self-other correlations were strong for extraversion but varied for the other four traits. Comparisons with control groups on relevant test items provided preliminary evidence that the exercise promotes learning of relevant material. This exercise can be used in introductory or personality psychology courses to facilitate discussion of various topics including interpersonal judgment and accuracy and methodological and statistical issues.
Endothelial Protection by Pentaerithrityl Trinitrate: Bilirubin and Carbon Monoxide as Possible Mediators

Pentaerithrityl tetranitrate (PETN) is a long-acting donor of nitric oxide (NO) and has recently been characterized as an antianginal agent that, in contrast with other nitric acid esters, does not induce oxidative stress and is therefore free of tolerance. Moreover, animal experiments have revealed that PETN actively reduces oxygen radical formation in vivoand specifically prevents atherogenesis and endothelial dysfunction. Because heme oxygenase-1 (HO-1) has been described as an antiatherogenic and cytoprotective gene in the endothelium, our aim was to investigate the effect of the active PETN metabolite pentaerithrityl trinitrate (PETriN) on HO-1 expression and catalytic activity in endothelial cells. Endothelial cells derived from human umbilical vein were incubated with PETriN (0.01–1 mM) for 8 hr. PETriN increased HO-1 mRNA and protein levels in a concentration-dependent fashion up to 3-fold over basal levels. Elevation of HO-1 protein was accompanied by a marked increase in catalytic activity of the enzyme as reflected by enhanced formation of both carbon monoxide and the endogenous antioxidant, bilirubin. Pretreatment of endothelial cells with PETriN or bilirubin at low micromolar concentrations protected endothelial cells from hydrogen peroxide-mediated toxicity. HO-1 induction and endothelial protection by PETriN were not mimicked by isosorbide dinitrate, another long-acting nitrate. The present study demonstrates that the active PETN metabolite, PETriN, stimulates mRNA and protein expression as well as enzymatic activity of the antioxidant defense protein, HO-1, in endothelial cells. Increased HO-1 expression and ensuing formation of bilirubin and carbon monoxide may contribute to and explain the specific antioxidant and antiatherogenic actions of PETN.
A Software Managed Stack Cache for Real-Time Systems

In a real-time system, the use of a scratchpad memory can mitigate the difficulties related to analyzing data caches, whose behavior is inherently hard to predict. We propose to use a scratchpad memory for stack allocated data. While statically allocating stack frames for individual functions to scratchpad memory regions aids predictability, it is limited to non-recursive programs and static allocation has to take different calling contexts into account. Using a stack cache that dynamically spills data to and fills data from external memory avoids these problems, while its simple design allows for efficiently deriving worst-case bounds through static analysis. In this paper we present the design and implementation of software managed caching of stack allocated data in a scratchpad memory. We demonstrate a compiler-aided implementation of a stack cache using the LLVM compiler framework and report on its efficiency. Our evaluation encompasses stack management overhead and impact on worst-case execution time analysis. The state-of-the-art worst-case execution time analysis tool aiT is able to correctly classify all stack cache accesses as accesses to the scratchpad memory.
LiViNG sTaNDarDs aND ma TeriaL cONDiTiONs OF yOuNG NeW ZeaLaND FamiLies

The purpose of this paper is to provide a descriptive profile of the personal characteristics and socio-economic circumstances of a cohort of young parents (N = 155) who had full-time care of at least one dependent child at 25 years of age. In addition, we investigated the extent to which these families were faced with material hardship and adverse living conditions, and examined the life-course pathways and concurrent risk factors that place young families at elevated risk of material hardship. Employing longitudinal data from the Christchurch Health and Development Study, the results showed that around one in five of these young families were experiencing moderate to severe material hardship. Higher levels of material hardship were predicted by a range of antecedent and concurrent life-course experiences, including family socio-economic status in childhood, mental health problems in adolescence, family structure, and employment- and income-related factors in young adulthood. These findings are discussed in light of current social and economic policy for income maintenance, employment facilitation and welfare reduction.
Column-Parallel Correlated Multiple Sampling Circuits for CMOS Image Sensors and Their Noise Reduction Effects

For low-noise complementary metal-oxide-semiconductor (CMOS) image sensors, the reduction of pixel source follower noises is becoming very important. Column-parallel high-gain readout circuits are useful for low-noise CMOS image sensors. This paper presents column-parallel high-gain signal readout circuits, correlated multiple sampling (CMS) circuits and their noise reduction effects. In the CMS, the gain of the noise cancelling is controlled by the number of samplings. It has a similar effect to that of an amplified CDS for the thermal noise but is a little more effective for 1/f and RTS noises. Two types of the CMS with simple integration and folding integration are proposed. In the folding integration, the output signal swing is suppressed by a negative feedback using a comparator and one-bit D-to-A converter. The CMS circuit using the folding integration technique allows to realize a very low-noise level while maintaining a wide dynamic range. The noise reduction effects of their circuits have been investigated with a noise analysis and an implementation of a 1Mpixel pinned photodiode CMOS image sensor. Using 16 samplings, dynamic range of 59.4 dB and noise level of 1.9 e− for the simple integration CMS and 75 dB and 2.2 e− for the folding integration CMS, respectively, are obtained.
Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype

Marine dinitrogen (N2) fixation studies have focused nearly exclusively on cyanobacterial diazotrophs; however γ-proteobacteria are an abundant component of the marine community and have been largely overlooked until recently. Here we present a phylogenetic analysis of all nifH γ-proteobacterial sequences available in public databases and qPCR data of a γ-proteobacterial phylotype, Gamma A (UMB), obtained during several research cruises. Our analysis revealed a complex diversity of diazotrophic γ-proteobacteria. One phylotype in particular, Gamma A, was described in several traditional and quantitative PCR studies. Though several γ-proteobacterial nifH sequences have been described as laboratory contaminants, Gamma A is part of a large cluster of sequences isolated from marine environments and distantly related to the clade of contaminants. Using a TaqMan probe and primer set, Gamma A nifH DNA abundance and expression were analyzed in nearly 1000 samples collected during 15 cruises to the Atlantic and Pacific Oceans. The data showed that Gamma A is an active, cosmopolitan diazotroph found throughout oxygenated, oligotrophic waters reaching maximum abundances of 8 x 104 nifH DNA copies l-1 and 5 x 105 nifH transcript copies l-1. Gamma A nifH transcript abundances were on average 3 fold higher than nifH DNA abundances. The widespread distribution and activity of Gamma A indicate that it has potential to be a globally important N2 fixing organism.
` p-Norm Multiple Kernel Learning

Learning linear combinations of multiple kernels is an appealing strategy when the right choice of features is unknown. Previous approaches to multiple kernel learning (MKL) promote sparse kernel combinations to support interpretability and scalability. Unfortunately, this `1-norm MKL is rarely observed to outperform trivial baselines in practical applications. To allow for robust kernel mixtures that generalize well, we extend MKL to arbitrary norms. We devise new insights on the connection between several existing MKL formulations and develop two efficient interleaved optimization strategies for arbitrary norms, that is `p-norms with p ≥ 1. This interleaved optimization is much faster than the commonly used wrapper approaches, as demonstrated on several data sets. A theoretical analysis and an experiment on controlled artificial data shed light on the appropriateness of sparse, non-sparse and `∞-norm MKL in various scenarios. Importantly, empirical applications of `p-norm MKL to three real-world problems from computational biology show that non-sparse MKL achieves accuracies that surpass the state-of-the-art. Data sets, source code to reproduce the experiments, implementations of the algorithms, and further information are available at http://doc.ml. tu-berlin.de/nonsparse_mkl/.
Structured collaborative filtering

In a general collaborative filtering (CF) setting, a user profile contains a set of previously rated items and is used to represent the user's interest. Unfortunately, most CF approaches ignore the underlying structure of user profiles. In this paper, we argue that a certain class of interest is best represented jointly by several items, drawing an analogy to "phrases" in text retrieval, which are not equivalent to the separate meaning of their words. At an alternative stance, we also consider the situation where, analogously to word synonyms, two items might be substitutable when representing a class of interest. We propose an approach integrating these two notions as opposing poles on a continuum spectrum. Upon this, we model the underlying structure in user profiles, drawing an analogy with text retrieval. The approach gives rise to a novel structured Vector Space Model for CF. We show that item-based CF approaches are a special case of the proposed method.