Miracle-dz/UniFAR-FTUs huggingface dataset:
Wiretap channels: Roles of rate splitting and channel prefixing

Csiszár and Körner's characterization of the rate-equivocation region of a general wiretap channel involves two auxiliary random variables: U, which represents rate splitting and V, which represents channel prefixing. For some channels, one or both of these auxiliary random variables are unnecessary, simplifying the expression and evaluation of the rate-equivocation region. In this paper, we provide new conditions under which channel prefixing or rate splitting does not improve the rate-equivocation region. In particular, we show that when the main channel is more capable than the eavesdropping channel, channel prefixing is unnecessary; the entire rate-equivocation region can be achieved by rate splitting alone. Conversely, we show under a mild assumption that if the main receiver is not more capable, then channel prefixing is strictly necessary. Moreover, we show that if the main channel is more capable but not less noisy, then rate splitting is strictly necessary. Next, we focus on the set of cyclic shift symmetric channels. We prove that for these channels, if in addition I(X; Y) − I(X;Z) is maximized at the uniform distribution, then rate splitting is unnecessary. Our results apply to BSC-BEC and BEC-BSC wiretap channels. We identify the conditions on the parameters of the BSC and BEC under which channel prefixing and/or rate splitting are unnecessary.
The Brightness of Colour

Background The perception of brightness depends on spatial context: the same stimulus can appear light or dark depending on what surrounds it. A less well-known but equally important contextual phenomenon is that the colour of a stimulus can also alter its brightness. Specifically, stimuli that are more saturated (i.e. purer in colour) appear brighter than stimuli that are less saturated at the same luminance. Similarly, stimuli that are red or blue appear brighter than equiluminant yellow and green stimuli. This non-linear relationship between stimulus intensity and brightness, called the Helmholtz-Kohlrausch (HK) effect, was first described in the nineteenth century but has never been explained. Here, we take advantage of the relative simplicity of this ‘illusion’ to explain it and contextual effects more generally, by using a simple Bayesian ideal observer model of the human visual ecology. We also use fMRI brain scans to identify the neural correlates of brightness without changing the spatial context of the stimulus, which has complicated the interpretation of related fMRI studies. Results Rather than modelling human vision directly, we use a Bayesian ideal observer to model human visual ecology. We show that the HK effect is a result of encoding the non-linear statistical relationship between retinal images and natural scenes that would have been experienced by the human visual system in the past. We further show that the complexity of this relationship is due to the response functions of the cone photoreceptors, which themselves are thought to represent an efficient solution to encoding the statistics of images. Finally, we show that the locus of the response to the relationship between images and scenes lies in the primary visual cortex (V1), if not earlier in the visual system, since the brightness of colours (as opposed to their luminance) accords with activity in V1 as measured with fMRI. Conclusions The data suggest that perceptions of brightness represent a robust visual response to the likely sources of stimuli, as determined, in this instance, by the known statistical relationship between scenes and their retinal responses. While the responses of the early visual system (receptors in this case) may represent specifically the statistics of images, post receptor responses are more likely represent the statistical relationship between images and scenes. A corollary of this suggestion is that the visual cortex is adapted to relate the retinal image to behaviour given the statistics of its past interactions with the sources of retinal images: the visual cortex is adapted to the signals it receives from the eyes, and not directly to the world beyond.
Behavioral Alterations in Response to Fear-Provoking Stimuli and Tranylcypromine Induced by Perinatal Exposure to Bisphenol A and Nonylphenol in Male Rats

The purpose of this study was to examine whether perinatal exposure to two major environmental endocrine-disrupting chemicals, bisphenol A (BPA; 0.1 mg/kg/day orally) and nonylphenol [NP; 0.1 mg/kg/day (low dose) and 10 mg/kg/day (high dose) orally] daily from gestational day 3 to postnatal day 20 (transplacental and lactational exposures) would lead to behavioral alterations in the male offspring of F344 rats. Neither BPA nor NP exposure affected behavioral characteristics in an open-field test (8 weeks of age), in a measurement of spontaneous motor activity (12 weeks of age), or in an elevated plus-maze test (14 weeks of age). A passive avoidance test (13 weeks of age) showed that both BPA- and NP-treated offspring tended to delay entry into a dark compartment. An active avoidance test at 15 weeks of age revealed that BPA-treated offspring showed significantly fewer avoidance responses and low-dose NP-treated offspring exhibited slightly fewer avoidance responses. Furthermore, BPA-treated offspring significantly increased the number of failures to avoid electrical unconditioned stimuli within 5-sec electrical shock presentation compared with the control offspring. In a monoamine-disruption test using 5 mg/kg (intraperitoneal) tranylcypromine (Tcy), a monoamine oxidase inhibitor, both BPA-treated and low-dose NP-treated offspring at 22–24 weeks of age failed to show a significant increment in locomotion in response to Tcy, whereas control and high-dose NP-treated offspring significantly increased locomotion behavior after Tcy injection. In addition, when only saline was injected during a monoamine-disruption test, low-dose NP-treated offspring showed frequent rearing compared with the control offspring. The present results indicate that perinatal low-dose BPA or NP exposure irreversibly influenced the reception of fear-provoking stimuli (e.g., electrical shock), as well as monoaminergic neural pathways.
COCO: A simple tool to enrich the representation of conformational variability in NMR structures

NMR structures are typically deposited in databases such as the PDB in the form of an ensemble of structures. Generally, each of the models in such an ensemble satisfies the experimental data and is equally valid. No unique solution can be calculated because the experimental NMR data is insufficient, in part because it reflects the conformational variability and dynamical behavior of the molecule in solution. Even for relatively rigid molecules, the limited number of structures that are typically deposited cannot completely encompass the structural diversity allowed by the observed NMR data, but they can be chosen to try and maximize its representation. We describe here the adaptation and application of techniques more commonly used to examine large ensembles from molecular dynamics simulations, to the analysis of NMR ensembles. The approach, which is based on principal component analysis, we call COCO (“Complementary Coordinates”). The COCO approach analyses the distribution of an NMR ensemble in conformational space, and generates a new ensemble that fills “gaps” in the distribution. The method is very rapid, and analysis of a 25‐member ensemble and generation of a new 25 member ensemble typically takes 1–2 min on a conventional workstation. Applied to the 545 structures in the RECOORD database, we find that COCO generates new ensembles that are as structurally diverse—both from each other and from the original ensemble—as are the structures within the original ensemble. The COCO approach does not explicitly take into account the NMR restraint data, yet in tests on selected structures from the RECOORD database, the COCO ensembles are frequently good matches to this data, and certainly are structures that can be rapidly refined against the restraints to yield high‐quality, novel solutions. COCO should therefore be a useful aid in NMR structure refinement and in other situations where a richer representation of conformational variability is desired—for example in docking studies. COCO is freely accessible via the website www.ccpb. ac.uk/COCO. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Other extensions incorporate the probabilistic distribution of the operators effects and a Abstraction Hierarchies for Engineering Design

Complex engineering design problems consist of numerous factors of varying criticalities. Considering fundamental features of design and inferior details alike will result in an extensive waste of time and effort. Design parameters should be introduced gradually as appropriate based on their significance relevant to the problem context. This motivates the representation of design parameters at multiple levels of an abstraction hierarchy. However, developing abstraction hierarchies is an area that is not well understood. Our research proposes a novel hierarchical abstraction methodology to plan effective engineering designs and processes. It provides a theoretically sound foundation to represent, abstract and stratify engineering design parameters and tasks according to causality and criticality. The methodology creates abstraction hierarchies in a recursive and bottom-up approach that guarantees no backtracking across any of the abstraction levels. The methodology consists of three main phases, representation, abstraction, and layering to multiple hierarchical levels. The effectiveness of the developed methodology is demonstrated by a design problem. Keywords—Hierarchies, Abstraction, Loop-free, Engineering Design
α3β1 integrin promotes keratinocyte cell survival through activation of a MEK/ERK signaling pathway

Inadequate or inappropriate adhesion of epithelial cells to extracellular matrix leads to a form of apoptosis known as anoikis. During various tissue remodelling events, such as wound healing or carcinoma invasion, changes in the physical properties, and/or composition of the extracellular matrix, can lead to anoikis of epithelial cells that lack appropriate receptor-matrix interactions. Laminin-5 is the major ligand for keratinocyte adhesion in the epidermis, and it also promotes keratinocyte survival in vivo and in vitro. Integrins α3β1 and α6β4 are the major receptors for laminin-5; however, specific roles for these integrins in keratinocyte survival have not been determined. In the current study, we exploited keratinocyte cell lines derived from wild-type or α3 integrin knockout mice to reveal a critical role for α3β1 in protecting keratinocytes from apoptosis upon serum withdrawal. We show that α3β1-mediated adhesion to laminin-5 extracellular matrix inhibits proteolytic activation of caspase-3 and TUNEL-staining, both hallmarks of apoptosis. We also show that α3β1-mediated adhesion activates focal adhesion kinase (FAK) and extracellular signal-regulated kinase (ERK), and that inhibition of either FAK or ERK signaling leads to apoptosis of keratinocytes attached to laminin-5. α6β4-mediated adhesion to laminin-5 only partially protects cells from apoptosis in the absence of α3β1, and α6β4 is not necessary for cell survival in the presence of α3β1. These results suggest that α3β1 is necessary and sufficient for maximal keratinocyte survival on laminin-5. We propose a model to address the potential importance of α3β1-mediated survival for migrating keratinocytes at the leading edge of a cutaneous wound.
Safety paradigm: genetic evaluation of therapeutic grade human embryonic stem cells

The use of stem cells for regenerative medicine has captured the imagination of the public, with media attention contributing to rising expectations of clinical benefits. Human embryonic stem cells (hESCs) are the best model for capital investment in stem cell therapy and there is a clear need for their robust genetic characterization before scaling-up cell expansion for that purpose. We have to be certain that the genome of the starting material is stable and normal, but the limited resolution of conventional karyotyping is unable to give us such assurance. Advanced molecular cytogenetic technologies such as array comparative genomic hybridization for identifying chromosomal imbalances, and single nucleotide polymorphism analysis for identifying ethnic background and loss of heterozygosity should be introduced as obligatory diagnostic tests for each newly derived hESC line before it is deposited in national stem cell banks. If this new quality standard becomes a requirement, as we are proposing here, it would facilitate and accelerate the banking process, since end-users would be able to select the most appropriate line for their particular application, thus improving efficiency and streamlining the route to manufacturing therapeutics. The pharmaceutical industry, which may use hESC-derived cells for drug screening, should not ignore their genomic profile as this may risk misinterpretation of results and significant waste of resources.
Maximizing Scales Do Not Reliably Predict Maximizing Behavior in Decisions from Experience

In this paper, we explore the relationships between psychometric and behavioral measures of maximization in decisions from experience (DfE). In two experiments, we measured choice behavior in two experimental paradigms of DfE and self-reported maximizing tendencies using three prominent scales of maximization. In the repeated consequentialist choice paradigm, participants made repeated choices between two unlabeled options and received consequential feedback on each trial. In the sampling paradigm, participants freely sampled from two options and received feedback on their sampling before making a single consequential choice. Individuals exhibited different degrees of maximizing behavior in both paradigms and across different payoff distributions, but none of the maximizing scales predicted this behavior. These results indicate that maximization scales address constructs that are different from the maximization behavior observed in DfE, and that these measures will need to be improved to reflect behavioral aspects of choice and search from experience. Copyright © 2017 John Wiley & Sons, Ltd. key words maximizing; decisions from experience; individual differences; decision-making style
Is Leasing Greener than Selling?

Based on the proposition that leasing is environmentally superior to selling, some firms have adopted a leasing strategy and others promote their existing leasing programs as environmentally superior to “green” their image. The argument is that because a leasing firm retains ownership of the off-lease units, it has an incentive to remarket them or invest in designing a more durable product, resulting in a lower volume of new production and disposal. However, leasing might be environmentally inferior because of the direct control the firm has over the off-lease products, which may prompt the firm to remove them from the market to avoid cannibalizing the demand for new products. Motivated by these issues, we adopt a life-cycle environmental impact perspective and analytically investigate if leasing can be both more profitable and have a lower total environmental impact. We find that leasing can be environmentally worse despite remarketing all off-lease products and greener than selling despite the mid-life removal of off-lease products. Our analysis also provides insights for environmental groups and entities that use different approaches to improve the environmental performance of business practices. We show that imposing disposal fees or encouraging remanufacturing, under some conditions, can actually lead to higher environmental impact. We also identify when educating consumers to be more environmentally conscious can improve the relative environmental performance of leasing. This paper was accepted by J. Miguel Villas-Boas, marketing.
Whiteoak: introducing structural typing into java

This paper presents WHITEOAK: a JAVA extension that introduces structural type equivalence and subtyping into the language. We argue that structural subtyping addresses common software design problems, and promotes the development of loosely coupled modules without compromising type safety. We discuss language design issues, including subtyping in face of self-referencing structural types, compile-time operators for computing the new types from existing ones, and the semantics of constructors and non-abstract methods in structural types. We describe implementation techniques, including the compile-time and run-time challenges that we faced (in particular, preserving the identity of objects). Measurement indicate that the performance of our implementation of structural dispatching is comparable to that of the JVM's standard invocation mechanisms.
A genome wide scan for early onset primary hypertension in Scandinavians.

With the aim of identifying hypertension susceptibility loci, we performed a genome wide scan in Scandinavian sib-pairs with early onset primary hypertension. To be classified as affected, a diagnosis of primary hypertension at age </=50 years was required. Two hundred and forty three patients with onset of primary hypertension at 40.0+/-7.7 (mean+/-SD) years from 91 families (91 sib-ships with a mean of 2.7 and a range of 2-6 affected members per sib-ship) were genotyped with 362 microsatellite markers with a density of approximately 10 cM. Loci obtaining nominal P</=0.016 (LOD score >/= 1.0) were fine mapped with additional markers. Multipoint non-parametric linkage analysis was performed using GENEHUNTER v 2.0. Using simulations, a nominal P</=0.0002 was determined to be a genome wide significant evidence of linkage. In the 10 cM genome wide scan, nominal P</=0.016 were found on chromosomes 1 at 81 cM (P=0.007), 2 at 115 cM (P=0.006), 3 at 108 cM (P=0.006), 14 at 45 cM (P=0.0002) and at 99 cM (P=0.001), 17 at 42 cM (P=0.015) and 19 at 89 cM (P=0.007). After fine mapping of these loci, one of the chromosome 14 loci just obtained the level of genome wide significance (P=0.0002 at 41 cM) and the chromosome 2 locus reached suggestive evidence of linkage (P=0.002 at 118 cM). Our data suggest a hypertension susceptibility locus on chromosome 14 around 41 cM. The locus on chromosome 2 is also promising as it has been implicated in hypertension and blood pressure regulation in earlier genome scans.
Target identification strategies in plant chemical biology

The current needs to understand gene function in plant biology increasingly require more dynamic and conditional approaches opposed to classic genetic strategies. Gene redundancy and lethality can substantially complicate research, which might be solved by applying a chemical genetics approach. Now understood as the study of small molecules and their effect on biological systems with subsequent target identification, chemical genetics is a fast developing field with a strong history in pharmaceutical research and drug discovery. In plant biology however, chemical genetics is still largely in the starting blocks, with most studies relying on forward genetics and phenotypic analysis for target identification, whereas studies including direct target identification are limited. Here, we provide an overview of recent advances in chemical genetics in plant biology with a focus on target identification. Furthermore, we discuss different strategies for direct target identification and the possibilities and challenges for plant biology.
Enhanced movement tracking with Kinect supported by high-precision sensors

The paper presents a proposal of sensor fusion combining data derived from a Kinect device and high-precision sensors. The main idea was to enhance the tracking of a human arm in order to obtain precise coordinates. The Kinect plays the role of a calibration device and sensors' data are used in kinematics equations for enhanced tracking of the arm. This way the resulting information has less uncertainty and can be directly transmitted to another system, e.g. robotics one. The system has been implemented using kinematics-based approach with transformation operators as well as quaternions. In terms of accuracy the main result is that the Kinect performs very similar with sensors.
Impairment of Vocal Expression of Negative Emotions in Patients with Alzheimer’s Disease

Vocal expression of emotions (EE) in retrieval of events from autobiographical memory was investigated in patients in early stages of Alzheimer’s disease (AD). Twenty-one AD patients and 19 controls were interviewed, and EE of the reported memories was rated by 8 independent evaluators. The AD group had lower EE of both recent and remote memory than controls, although EE in remote memories was better preserved in both groups. We observed positive correlations between EE and indicators of cognitive competence in AD patients. AD Patients are impaired in the ability to express emotions already at early stages of the disease, and EE seems to deteriorate along with the progression of cognitive impairment.
Carnitine-Dependent Transport of Acetyl Coenzyme A in Candida albicans Is Essential for Growth on Nonfermentable Carbon Sources and Contributes to Biofilm Formation

ABSTRACT In eukaryotes, acetyl coenzyme A (acetyl-CoA) produced during peroxisomal fatty acid β-oxidation needs to be transported to mitochondria for further metabolism. Two parallel pathways for acetyl-CoA transport have been identified in Saccharomyces cerevisiae; one is dependent on peroxisomal citrate synthase (Cit), while the other requires peroxisomal and mitochondrial carnitine acetyltransferase (Cat) activities. Here we show that the human fungal pathogen Candida albicans lacks peroxisomal Cit, relying exclusively on Cat activity for transport of acetyl units. Deletion of the CAT2 gene encoding the major Cat enzyme in C. albicans resulted in a strain that had lost both peroxisomal and mitochondrion-associated Cat activities, could not grow on fatty acids or C2 carbon sources (acetate or ethanol), accumulated intracellular acetyl-CoA, and showed greatly reduced fatty acid β-oxidation activity. The cat2 null mutant was, however, not attenuated in virulence in a mouse model of systemic candidiasis. These observations support our previous results showing that peroxisomal fatty acid β-oxidation activity is not essential for C. albicans virulence. Biofilm formation by the cat2 mutant on glucose was slightly reduced compared to that by the wild type, although both strains grew at the same rate on this carbon source. Our data show that C. albicans has diverged considerably from S. cerevisiae with respect to the mechanism of intracellular acetyl-CoA transport and imply that carnitine dependence may be an important trait of this human fungal pathogen.