Miracle-dz/UniFAR-FTUs huggingface dataset:
The shape of things to come in the study of the origin of species?

Perhaps Darwin would agree that speciation is no longer the mystery of mysteries that it used to be. It is now generally accepted that evolution by natural selection can contribute to ecological adaptation, resulting in the evolution of reproductive barriers and, hence, to the evolution of new species (Schluter & Conte ; Meyer ; Nosil ). From genes that encode silencing proteins that cause infertility in hybrid mice (Mihola et al. ), to segregation distorters linked to speciation in fruit flies (Phadnis & Orr ), or pollinator‐mediated selection on flower colour alleles driving reinforcement in Texan wildflowers (Hopkins & Rausher ), characterization of the genes that drive speciation is providing clues to the origin of species (Nosil & Schluter ). It is becoming apparent that, while recent work continues to overturn historical ideas about sympatric speciation (e.g. Barluenga et al. ), ecological circumstances strongly influence patterns of genomic divergence, and ultimately the establishment of reproductive isolation when gene flow is present (Elmer & Meyer ). Less clear, however, are the genetic mechanisms that cause speciation, particularly when ongoing gene flow is occurring. Now, in this issue, Franchini et al. ( ) employ a classic genetic mapping approach augmented with new genomic tools to elucidate the genomic architecture of ecologically divergent body shapes in a pair of sympatric crater lake cichlid fishes. From over 450 segregating SNPs in an F2 cross, 72 SNPs were linked to 11 QTL associated with external morphology measured by means of traditional and geometric morphometrics. Annotation of two highly supported QTL further pointed to genes that might contribute to ecological divergence in body shape in Midas cichlids, overall supporting the hypothesis that genomic regions of large phenotypic effect may be contributing to early‐stage divergence in Midas cichlids.
Bears and Numbers: Investigating How Short Sellers Exploit and Affect Earnings-Based Pricing Anomalies

We document that short sellers exploit both post-earnings-announcement drift and the accrual anomaly. In addition, using a unique dataset of shares available for borrowing as of the earnings announcement date, we find that short selling plays an important role in the pricing of accruals: the downside effect of high accruals disappears when at least 6.8% of a firm's shares are available for borrowing by short sellers. Furthermore, we demonstrate that this effect is distinct from that of institutional holdings, which can affect pricing of accruals in ways unrelated to short selling.
Intentionalism About Moods

According to intentionalism, phenomenal properties are identical to, supervenient on, or determined by representational properties. Intentionalism faces a special challenge when it comes to accounting for the phenomenal character of moods. First, it seems that no intentionalist treatment of moods can capture their apparently undirected phenomenology. Second, it seems that even if we can come up with a viable intentionalist account of moods, we would not be able to motivate it in some of the same kinds of ways that intentionalism about other kinds of states can be motivated. In this article, I respond to both challenges: First, I propose a novel intentionalist treatment of moods on which they represent unbound affective properties. Then, I argue that this view is indirectly supported by the same kinds of considerations that directly support intentionalism about other mental states.
Image Sensors Meet LEDs

A new class of visible light communication (VLC) systems, namely image sensor (IS) based VLC systems, has emerged. An IS consists of a two-dimensional (2D) array of photodetectors (PDs), and then VLC systems with an IS receiver are capable of exploiting the spatial dimensions invoked for transmitting information. This paper aims for providing a brief survey of topics related to the IS-based VLC, and then provides a matrix representation of how to map a series of one dimensional (1D) symbols onto a set of 2D symbols for efficiently exploit the associate grade of freedom offered by 2D VLC systems. As an example, the matrix representation is applied to the symbol mapping of layered space-time coding (L-STC), which is presented to enlarge the coverage of IS-based VLC that is limited by pixel resolution of ISs. key words: image sensor, LED, visible light communication (VLC), optical wireless communication (OWC), two-dimensional communication, spacetime coding (STC)
Comorbid psychopathology rates in children diagnosed with autism spectrum disorders according to the DSM-IV-TR and the proposed DSM-5

Abstract Objective: To investigate differences in comorbid psychopathology rates between individuals who meet criteria of Autism Spectrum Disorders (ASDs) according to DSM-5 or the DSM-IV-TR. Methods: Comorbid psychopathology was measured using the Autism Spectrum Disorders- Comorbid for Children. 424 individuals between the ages of 2 and 18 years of age; including children who met criteria for an ASD according to the DSM-5, the DSM-IV-TR only, and a control group that did not meet either set of criteria. Results: Of the ASD participants, 36% would no longer meet criteria according to proposed DSM-5. Comorbidity rates for the ASD groups were significantly different from the control group; however, ASD groups were not significantly different in terms of total comorbid psychopathology. Conclusion: The results elucidate the need for further research regarding services and treatments for those individuals that will no longer meet criteria for an ASD but still have significant rates of comorbid psychopathology.
Quantitative susceptibility mapping of small objects using volume constraints

Microbleeds have been implicated to play a role in many neurovascular and neurodegenerative diseases. The diameter of each microbleed has been used previously as a possible quantitative measure for grading microbleeds. We propose that magnetic susceptibility provides a new quantitative measure of extravasated blood. Recently, a Fourier‐based method has been used that allows susceptibility quantification from phase images for any arbitrarily shaped structures. However, when very small objects, such as microbleeds, are considered, the accuracy of this susceptibility mapping method still remains to be evaluated. In this article, air bubbles and glass beads are taken as microbleed surrogates to evaluate the quantitative accuracy of the susceptibility mapping method. We show that when an object occupies only a few voxels, an estimate of the true volume of the object is necessary for accurate susceptibility quantification. Remnant errors in the quantified susceptibilities and their sources are evaluated. We show that quantifying magnetic moment, rather than the susceptibility of these small structures, may be a better and more robust alternative. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Email as a Speed-Facilitating Device: A Contribution to the Reduced-Cues Perspective on Communication

Reduced-cues theories of communication assume that the sensorial stimulation of face-to-face interaction is essential for an optimal communicative experience. From a motivational perspective, Wicklund and Vandekerckhove (2000) took this theory further by hypothesizing that people involved in rapid communication in a setting poor in sensorial stimulation would tend to have (a) brief and (b) egocentric exchanges. Two experiments were developed in order to test these points. In Experiment 1, participants had to simulate Communication with a long-lost friend either via a computer-typed letter (slow and without sensorial output media) or an email (fast and without sensorial output media), Results showed that email participants wrote shorter messages and were less likely to bring up friends hip-related memories than letter participants. The second quasi-experimental study succeeded in extending the external validity of Experiment 1's findings. Research limits as well as scope for future research are discussed in the conclusions.
Extended quests for value-added products and services in mobile commerce

The introduction and the development of m-commerce will be a major challenge, as the cost of 3G licenses in several EU countries appears already in the initial stages to be out of proportion. And it seems clear that without real substance in m-commerce products and services the investments in the new mobile technology may still fail. Yet, not much is known about what actually will be the m-commerce products and services. Here we will propose to build them around value-added product and service modules, some of which are going to be completely new as we can take advantage of the new mobile technology. We will argue that value-added products and services can (should) be built around smart/intelligent technologies, which would be part of the products and/or services themselves or form support systems for (i) the users, (ii) the producers and (iii) the management of m-commerce products and services. Some of the needed technologies are already available, and we can readily implement them for the coming prototypes of the new 3G-based systems. Index: mobile commerce, value-added products & services, intelligent information technologies 1. M-COMMERCE Although m-commerce is an emerging field in its early stages there are a number of ideas of what is going to constitute the key success factors for the actors in the global m-commerce arena (the material for these factors have been collected from [Durlacher Research, BroadVision, Vignette, Nokia and TechNews]). The key success factors include: 1. Customer ownership. Subscriber data may be key to the m-commerce market, which is shown by the recent boom in operator takeovers in the mobile industry. The user’s personal data and preferences are the key if we want to find ways to add value to the user’s experience. Nevertheless, questions can be raised if customer ownership is any better than a quickly shifting mirage as customers may change product and service providers very easily and without giving any notice. 2. Personalization. This is a key feature, which can be achieved by creating services that customise the end-user experience for the individual subscriber. It can be further enhanced if we add intelligent personalization platforms, which will optimise the interaction path for individual subscribers. 3. Localization. Location sensitive information is a key to m-commerce as it provides an easy access to relevant data sources at the locations where they are needed. The key target group will be travelling subscribers, which have diversified needs of high-quality information. 4. Ubiquity. This means that service is available at any time, anywhere. There are time-critical applications, which offer the ability to receive information and perform transactions from any location.
Protein extraction from plant tissues for 2DE and its application in proteomic analysis

Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE‐based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).
Virtual impedance adjustment in unconstrained motion for an exoskeletal robot assisting the lower limb

The objective of this paper is to establish the criteria for adjusting the virtual impedance of an exoskeletal robot for the lower limb in order to minimize the operator's physical stress in unconstrained motion. The exoskeletal robot HAL (Hybrid Assistive Limb)-3 which we developed for assisting the motor function of the lower limb was used for experiments in this research. To accomplish the objective (i) the physical parameters around the joint of HAL-3 were identified and (ii) the relationships between the virtual impedance values and the physical stress of operators were examined through experiments for swinging motions of the lower leg. The physical stress was evaluated with myoelectricity, the musculoskeletal moment of the operator and the operator's feelings during the experimental motion. As a result, we found that the physical stress tended to decline with the decrease of virtual inertia and virtual Coulomb friction, and to increase slightly with the decrease of virtual gravitational moment. The decrease of virtual viscous friction made the physical stress increase gradually after it declined to a trough during the positive virtual viscous friction. Based on the results, we could establish the criteria for adjusting the virtual impedance for minimizing the operator's physical stress in unconstrained motion.
Investment appraisal for sustainable ports

The sustainable development of a port is of vital economic and financial importance. Flexible designs and innovative solutions help to advance sustainability goals by addressing future uncertainty and risk. Lack of a suitable decision-making procedure or improper utilization of the standard analytical and evaluation techniques should not be allowed to stand in the way of flexibility. This paper illustrates how investment appraisal procedure in the port sector (or other infrastructure sectors) can be adapted, so that flexibility and sustainability considerations are integrated in the standard procedures, through a case study of Port of Rotterdam.
Lymphoid Enhancer Binding Factor 1 Regulates Transcription through Gene Looping1

Efficient transcription depends upon efficient physical and functional interactions between transcriptosome complexes and DNA. We have previously shown that IL-1β-induced lymphoid enhancer binding factor 1 (Lef1) regulates the transcription of its target genes COX2 and MMP13 in mouse chondrocytes by binding to the Lef1 binding sites located in the 3′ region. In this study, we investigated how the 3′ region-bound Lef1 regulates expression of target genes. IL-1β stimulation induced gene looping in COX2 and MMP13 genomic loci, which is mediated by the physical interaction of Lef1 with its binding partners, including β-catenin, AP-1, and NF-κB. As shown by chromosome conformation capture (3C) assay, the 5′ and 3′ genomic regions of these genes were juxtaposed in an IL-1β-stimulation dependent manner. Lef1 played a pivotal role in this gene looping; Lef1 knockdown decreased the incidence of gene looping, while Lef1 overexpression induced it. Physical interactions between the 3′ region-bound Lef1 and promoter-bound transcription factors AP-1 or NF-κB in COX2 and MMP13, respectively, were increased upon stimulation, leading to synergistic up-regulation of gene expression. Knockdown of RelA or c-Jun decreased the formation of gene loop and down-regulated cyclooxygenase 2 (COX2) or matrix metalloproteinase 13 (MMP13) transcription levels. However, overexpression of RelA or c-Jun along with Lef1 increased the looping and their expression levels. Our results indicate a novel function of Lef1, as a mediator of gene looping between 5′ and 3′ regions. Gene looping may serve to delineate the transcription unit in the inducible gene transcription of mammalian cells.
CALILLARY PRESSURE CURVE MEASUREMENT USING A SINGLE-MODERATE-SPEED CENTRIFUGE AND QUANTITATIVE MAGNETIC RESONANCE IMAGING

For traditional centrifugal capillary pressure curve measurements, a short core plug is often employed. The capillary pressure is assumed to be zero at the outflow boundary of the core. The traditional experiments are time consuming. Measurement of the full capillary pressure curve often requires 7 to10 different centrifuge speeds, thus requiring one day to several days for measurement. Different approximate solutions may be employed to deduce the capillary pressure curve from experimental data of average saturation and the corresponding rotational speed. In the current work, we propose a new method to measure the capillary pressure curve using a single-moderate-speed centrifuge experiment and one dimensional centric scan SPRITE (Single-Point Ramped Imaging with T1 Enhancement) magnetic resonance imaging (MRI) technique for long rock samples. As a pure phase encoding quantitative MRI technique, centric scan SPRITE offers unique advantages in the measurement of spatially resolved fluid saturation in rocks. The proposed method is rapid and accurate. Because the new method uses a long core to directly measure a large range of saturation distributions along the length of the core, at a single moderate centrifuge speed, this process will be much faster than a traditional measurement. There is no requirement for an approximate solution; the capillary pressure curve is directly determined by the measured saturation profile. Long cores can be employed, which leads to a smaller radial effect than short core plugs. Since a moderate centrifuge speed is employed, the effect of gravity will be very small and the outlet boundary condition of the core plug can be satisfied. A comparison of capillary pressure curves obtained by a single-speed centrifuge and SPRITE MRI with mercury intrusion methods yields remarkably consistent results.
Activation of neuroendocrine L-type channels (alpha1D subunits) in retinal pigment epithelial cells and brain neurons by pp60(c-src).

The aim of this study is to characterize the subtype of tyrosine kinase-regulated L-type Ca(2+) channels in retinal pigment epithelial (RPE) cells. Ca(2+) channel alpha1D-subunits were enriched by immunoprecipitation from membrane proteins isolated from rat RPE cells. Western blot analysis of the precipitates revealed coprecipitation of pp60(c-src). In addition, in precipitates obtained with antibodies against pp60(c-src), alpha1D-subunits were identified. The same was observed in immunoprecipitations from rat brain neurons. Tyrosine phosphorylation of alpha1D-subunits was confirmed using anti-phosphotyrosine antibodies. Ba(2+) currents through L-type channels in cultured rat RPE cells were increased by intracellular application of active pp60(c-src) (30 U/ml) (heat-inactivated pp60(c-src) had no effect). Thus, L-type channels of the neuroendocrine subtype can be expressed in epithelial cells and are activated by tyrosine kinase of the src subtype. This kind of regulation is also suggested for brain-derived neurons.
Mixed reality training application for an oil refinery: user requirements

Introducing mixed reality (MR) into safety-critical environment like oil refinery is difficult, since the environment and organization lays demanding restrictions for the application. In order to develop usable and safe MR application, we need to study the context of use and derive user requirements from it. This paper describes the user requirements for an MR based oil refinery training tool. The application is aimed to train employees of a specific process unit in the refinery. Training is currently done mainly in a classroom and on-site only when the process is closed down. On-site training is necessary, but expensive and rarely possible. The use of mixed reality offers a way to train employees on-site while the process is running. Users can virtually see "inside" the columns and can modify virtually the process.
Lipid Biosynthesis and Protein Concentration Respond Uniquely to Phosphate Supply during Leaf Development in Highly Phosphorus-Efficient Hakea prostrata1[W][OPEN]

The Australian Proteaceae Hakea prostrata transcriptionally regulates only a small number of genes to generate polar leaf lipid profiles associated with delayed greening and efficient phosphorus use. Hakea prostrata (Proteaceae) is adapted to severely phosphorus-impoverished soils and extensively replaces phospholipids during leaf development. We investigated how polar lipid profiles change during leaf development and in response to external phosphate supply. Leaf size was unaffected by a moderate increase in phosphate supply. However, leaf protein concentration increased by more than 2-fold in young and mature leaves, indicating that phosphate stimulates protein synthesis. Orthologs of known lipid-remodeling genes in Arabidopsis (Arabidopsis thaliana) were identified in the H. prostrata transcriptome. Their transcript profiles in young and mature leaves were analyzed in response to phosphate supply alongside changes in polar lipid fractions. In young leaves of phosphate-limited plants, phosphatidylcholine/phosphatidylethanolamine and associated transcript levels were higher, while phosphatidylglycerol and sulfolipid levels were lower than in mature leaves, consistent with low photosynthetic rates and delayed chloroplast development. Phosphate reduced galactolipid and increased phospholipid concentrations in mature leaves, with concomitant changes in the expression of only four H. prostrata genes, GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE1, N-METHYLTRANSFERASE2, NONSPECIFIC PHOSPHOLIPASE C4, and MONOGALACTOSYLDIACYLGLYCEROL3. Remarkably, phosphatidylglycerol levels decreased with increasing phosphate supply and were associated with lower photosynthetic rates. Levels of polar lipids with highly unsaturated 32:x (x = number of double bonds in hydrocarbon chain) and 34:x acyl chains increased. We conclude that a regulatory network with a small number of central hubs underpins extensive phospholipid replacement during leaf development in H. prostrata. This hard-wired regulatory framework allows increased photosynthetic phosphorus use efficiency and growth in a low-phosphate environment. This may have rendered H. prostrata lipid metabolism unable to adjust to higher internal phosphate concentrations.