Miracle-dz/UniFAR-FTUs huggingface dataset:
Correction: Loss of Abdominal Muscle in Pitx2 Mutants Associated with Altered Axial Specification of Lateral Plate Mesoderm

Sequence specific transcription factors (SSTFs) combinatorially define cell types during development by forming recursively linked network kernels. Pitx2 expression begins during gastrulation, together with Hox genes, and becomes localized to the abdominal lateral plate mesoderm (LPM) before the onset of myogenesis in somites. The somatopleure of Pitx2 null embryos begins to grow abnormally outward before muscle regulatory factors (MRFs) or Pitx2 begin expression in the dermomyotome/myotome. Abdominal somites become deformed and stunted as they elongate into the mutant body wall, but maintain normal MRF expression domains. Subsequent loss of abdominal muscles is therefore not due to defects in specification, determination, or commitment of the myogenic lineage. Microarray analysis was used to identify SSTF families whose expression levels change in E10.5 interlimb body wall biopsies. All Hox9-11 paralogs had lower RNA levels in mutants, whereas genes expressed selectively in the hypaxial dermomyotome/myotome and sclerotome had higher RNA levels in mutants. In situ hybridization analyses indicate that Hox gene expression was reduced in parts of the LPM and intermediate mesoderm of mutants. Chromatin occupancy studies conducted on E10.5 interlimb body wall biopsies showed that Pitx2 protein occupied chromatin sites containing conserved bicoid core motifs in the vicinity of Hox 9-11 and MRF genes. Taken together, the data indicate that Pitx2 protein in LPM cells acts, presumably in combination with other SSTFs, to repress gene expression, that are normally expressed in physically adjoining cell types. Pitx2 thereby prevents cells in the interlimb LPM from adopting the stable network kernels that define sclerotomal, dermomyotomal, or myotomal mesenchymal cell types. This mechanism may be viewed either as lineage restriction or specification. Citation: Eng D, Ma H-Y, Xu J, Shih H-P, Gross MK, et al. (2012) Loss of Abdominal Muscle in Pitx2 Mutants Associated with Altered Axial Specification of Lateral Plate Mesoderm. PLoS ONE 7(7): e42228. doi:10.1371/journal.pone. 0042228 Editor: Michael Schubert, Ecole Normale Supérieure de Lyon, France Received October 11, 2011; Accepted July 5, 2012; Published July 31, 2012 Copyright: 2012 Eng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This research was supported by NIH-NIAMS grant AR054406 to CK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: michael.gross@oregonstate.edu (MKG); chrissa.kioussi@oregonstate.edu (CK)
Automated landmark extraction in digital images - performance evaluation

In this study, we present an automated system for feature recognition in digital images. Such a system is very important for morphometric analysis as it will replace the time consuming and labour intensive process of manual identification. The analysis system is constructed from four key stages: a feature based detection of the fly wing structure, recording the compact invariant shape descriptors using the pairwise geometric histogram (PGH) representation, global estimation of the pose using the probabilistic Hough transform and finally a correlation based refinement of individual features. The performance of the system, its reliability and robustness are evaluated in comparison to the expert manual performance.
Counting good truth assignments of random k-SAT formulae

We present a deterministic approximation algorithm to compute <i>logarithm</i> of the number of 'good' truth assignments for a random <i>k</i>-satisfiability (<i>k</i>-SAT) formula in polynomial time (by 'good' we mean that violates a small fraction of clauses). The relative error is bounded above by an arbitrarily small constant ε with high probability<sup>1</sup> as long as the clause density (ratio of clauses to variables) α < α<inf>u</inf>(<i>k</i>) = 2<i>k</i><sup>-1</sup>log<i>k</i>(1 + <i>o</i>(1)). The algorithm is based on computation of marginal distribution via belief propagation and use of an interpolation procedure. This scheme substitutes the traditional one based on approximation of marginal probabilities via MCMC, in conjunction with self-reduction, which is not easy to extend to the present problem. Our results are expected hold for a reasonable non-random setup with locally tree-like sparse <i>k</i>-SAT formulas. We derive 2<i>k</i><sup>-1</sup> log <i>k</i>(1+<i>o</i>(1)) as threshold for uniqueness of the Gibbs distribution on satisfying assignment of random infinite tree <i>k</i>-SAT formulae to establish our results, which is of interest in its own right.
Finance and Productivity Growth: Firm-Level Evidence

Using data on a broad set of European firms, we find a strong positive relationship between the use of external financing and future productivity (TFP) growth within firms. This relationship is robust to various measures of financing and productivity, and strengthens as financing costs increase. We provide evidence against a reverse-causality explanation by showing that this relationship arises from the component of TFP that is outside the information set of the firm. These findings indicate that financial development supports productivity growth within firms, and helps explain why economic activity remains persistently depressed following financial crisis.
Precision multi-epoch astrometry with VLT cameras FORS1/2 ⋆

Context. Aims. We investigate the astrometric performance of the FORS1 and FORS2 cameras of the VLT at long time scales with emphasis on systematic errors which normally prevent attainning a precision better than 1 mas. Methods. The study is based on multi-epoch time series of observations of a single sky region imaged with a time spacing of 2‐6 years at FORS1 and 1‐5 months at FORS2. Images were processed with a technique that reduces atmospheric image motion, geometric distortions, and takes into account relative displacement of reference stars in time. Results. We performed a detailed analysis of a random error of positions that was shown to be dominated by the uncertainty of the star photocenter determination. The component of the random error corresponding to image motion was found to be caused primarily by optical aberrations and variations of atmospheric PSF size but not by the effect of atmospheric image motion. Comparison of observed and model annual/monthly epoch average positions yielded estimates of systematic errors for which temporal properties and distribution in the CCD plane are given. At frame center, the systematic component is about 25� as. Systematic errors are shown to be caused mainly by a combined effect of the image asymmetry and seeing variations which therefore should be strongly limited to avoid generating random and systematic errors. For a series of 30 images, we demonstrated presicion of about 50� as stable on daily, monthly, and annual time scales. Small systematic errors and a Gaussian distribution of positional residuals at any tim e scale indicate that the astrometric accuracy of the VLT is comparable to the precision. Relative proper motion and trigonometric parallaxes of stars in the center of the test field were derived with a precision of 20� as yr −1 and 40� as for 17‐19 mag stars. Therefore, distances at 1 kpc could be determinable at a 4% precision if suitably distant reference objects are in the field. Conclusions. We prove that the VLT with FORS1/2 cameras are not subject to significant systematic errors at time scales from a few hours to a few years providing that observations are obtained in narrow seeing limits. The astrometric performance of the VLT imaging cameras meets requirements necessary for many astrophysical applications, in particular, exoplanet studies and determination of relative trigonometric distances by ensuring a high accuracy of observations, at least 50� as attained for image series of 0.5 hour.
Neural Networks For Negation Scope Detection

Automatic negation scope detection is a task that has been tackled using different classiﬁers and heuristics. Most systems are however 1) highly-engineered, 2) English-speciﬁc, and 3) only tested on the same genre they were trained on. We start by addressing 1) and 2) using a neural network architecture. Results obtained on data from the *SEM2012 shared task on negation scope detection show that even a simple feed-forward neural network us-ing word-embedding features alone, performs on par with earlier classiﬁers, with a bi-directional LSTM outperforming all of them. We then address 3) by means of a specially-designed synthetic test set; in doing so, we explore the problem of detecting the negation scope more in depth and show that performance suffers from genre effects and differs with the type of negation considered.
Slepian-Wolf Coding for General Sources and Its Duality with Channel Coding

We study the problem of Slepian-Wolf coding for general sources (not necessarily stationary) with finite alphabet. A linear codebook-level duality between Slepian-Wolf coding for general sources and channel coding for a class of cyclic-symmetric channels is established under optimal decoding, through which the general formula for the Slepian-Wolf limit can be reinterpreted using Verdu and Han's channel capacity formula.
Reduced Occipital Alpha Power Indexes Enhanced Excitability Rather than Improved Visual Perception

Several studies have demonstrated that prestimulus occipital alpha-band activity substantially influences subjective perception and discrimination of near-threshold or masked visual stimuli. Here, we studied the role of prestimulus power fluctuations in two visual phenomena called double-flash illusion (DFI) and fusion effect (FE), both consisting of suprathreshold stimuli. In both phenomena, human subjects' perception varies on a trial-by-trial basis between perceiving one or two visual stimuli, despite constant stimulation. In the FE, two stimuli correspond to veridical perception. In the DFI, two stimuli correspond to an illusory perception. This provides for a critical test of whether reduced alpha power indeed promotes veridical perception in general. We find that in both, DFI and FE, reduced prestimulus occipital alpha predicts the perception of two stimuli, regardless of whether this is veridical (FE) or illusory (DFI). Our results suggest that reduced alpha-band power does not always predict improved visual processing, but rather enhanced excitability. In addition, for the DFI, enhanced prestimulus occipital gamma-band power predicted the perception of two visual stimuli. These findings provide new insights into the role of prestimulus rhythmic activity for visual processing.
Mixing catadioptric and perspective cameras

We analyze relations that exist between multiple views of a static scene, where the views can be taken by any mixture of para-catadioptric, perspective or affine cameras. Concretely, we introduce the notion of fundamental matrix, trifocal and quadrifocal tensors for the different possible combinations of these camera types. We also introduce the notion of plane homography for mixed image pairs. Generally speaking, these novel multi-view relations may form the basis for the typical geometric computations like motion estimation, 3D reconstruction or (self-) calibration. A few novel algorithms illustrating some of these aspects, are described, especially concerning what we call calibration transfer, using fundamental matrices, and self-calibration from plane homographies.
Evolving complex fuzzy classifier rules using a linear tree genetic representation

The paper proposes a linear representation of tree structures in order to evolve complex fuzzy rule sets for solving classification problems. In particular, linguistic rules are evolved, where the condition part of a rule can have an arbitrary structure of conjunctions and disjunctions. We describe an efficient rule representation scheme, which uses a genetic algorithm. The method is tested with a number of benchmark data sets and some results are reported.
Toxicogenomics analysis of mouse lung responses following exposure to titanium dioxide nanomaterials reveal their disease potential at high doses

Titanium dioxide nanoparticles (TiO2NPs) induce lung inflammation in experimental animals. In this study, we conducted a comprehensive toxicogenomic analysis of lung responses in mice exposed to six individual TiO2NPs exhibiting different sizes (8, 20 and 300nm), crystalline structure (anatase, rutile or anatase/rutile) and surface modifications (hydrophobic or hydrophilic) to investigate whether the mechanisms leading to TiO2NP-induced lung inflammation are property specific. A detailed histopathological analysis was conducted to investigate the long-term disease implications of acute exposure to TiO2NPs. C57BL/6 mice were exposed to 18, 54, 162 or 486 µg of TiO2NPs/mouse via single intratracheal instillation. Controls were exposed to dispersion medium only. Bronchoalveolar lavage fluid (BALF) and lung tissue were sampled on 1, 28 and 90 days post-exposure. Although all TiO2NPs induced lung inflammation as measured by the neutrophil influx in BALF, rutile-type TiO2NPs induced higher inflammation with the hydrophilic rutile TiO2NP showing the maximum increase. Accordingly, the rutile TiO2NPs induced higher number of differentially expressed genes. Histopathological analysis of lung sections on Day 90 post-exposure showed increased collagen staining and fibrosis-like changes following exposure to the rutile TiO2NPs at the highest dose tested. Among the anatase, the smallest TiO2NP of 8nm showed the maximum response. The anatase TiO2NP of 300nm was the least responsive of all. The results suggest that the severity of lung inflammation is property specific; however, the underlying mechanisms (genes and pathways perturbed) leading to inflammation were the same for all particle types. While the particle size clearly influenced the overall acute lung responses, a combination of small size, crystalline structure and hydrophilic surface contributed to the long-term pathological effects observed at the highest dose (486 µg/mouse). Although the dose at which the pathological changes were observed is considered physiologically high, the study highlights the disease potential of certain TiO2NPs of specific properties.
Miniband formation in a quantum dot crystal

We analyze the carrier energy band structure in a three-dimensional regimented array of semiconductor quantum dots using an envelope function approximation. The coupling among quantum dots leads to a splitting of the quantized carrier energy levels of single dots and formation of three-dimensional minibands. By changing the size of quantum dots, interdot distances, barrier height, and regimentation, one can control the electronic band structure of this artificial quantum dot crystal. Results of simulations carried out for simple cubic and tetragonal quantum dot crystal show that the carrier density of states, effective mass tensor and other properties are different from those of bulk and quantum well superlattices. It has also been established that the properties of artificial crystal are more sensitive to the dot regimentation rather then to the dot shape. The proposed engineering of three-dimensional mini bands in quantum dot crystals allows one to fine-tune electronic and optical properties of such nan.
Deaths from Symptomatically Identifiable Furious Rabies in India: A Nationally Representative Mortality Survey

Background It is estimated that India has more deaths from rabies than any other country. However, existing estimates are indirect and rely on non-representative studies. Methods and Principal Findings We examined rabies deaths in the ongoing Million Death Study (MDS), a representative survey of over 122,000 deaths in India that uses enhanced types of verbal autopsy. We estimated the age-specific mortality rates of symptomatically identifiable furious rabies and its geographic and demographic distributions. A total of 140 deaths in our sample were caused by rabies, suggesting that in 2005 there were 12,700 (99% CI 10,000 to 15,500) symptomatically identifiable furious rabies deaths in India. Most rabies deaths were in males (62%), in rural areas (91%), and in children below the age of 15 years (50%). The overall rabies mortality rate was 1.1 deaths per 100,000 population (99%CI 0.9 to 1.4). One third of the national rabies deaths were found in Uttar Pradesh (4,300) and nearly three quarters (8,900) were in 7 central and south-eastern states: Chhattisgarh, Uttar Pradesh, Odisha, Andhra Pradesh, Bihar, Assam, and Madhya Pradesh. Conclusions and Significance Rabies remains an avoidable cause of death in India. As verbal autopsy is not likely to identify atypical or paralytic forms of rabies, our figure of 12,700 deaths due to classic and clinically identifiable furious rabies underestimates the total number of deaths due to this virus. The concentrated geographic distribution of rabies in India suggests that a significant reduction in the number of deaths or potentially even elimination of rabies deaths is possible.
The Arabidopsis onset of leaf death5 Mutation of Quinolinate Synthase Affects Nicotinamide Adenine Dinucleotide Biosynthesis and Causes Early Ageing[W]

Leaf senescence in Arabidopsis thaliana is a strict, genetically controlled nutrient recovery program, which typically progresses in an age-dependent manner. Leaves of the Arabidopsis onset of leaf death5 (old5) mutant exhibit early developmental senescence. Here, we show that OLD5 encodes quinolinate synthase (QS), a key enzyme in the de novo synthesis of NAD. The Arabidopsis QS was previously shown to carry a Cys desulfurase domain that stimulates reconstitution of the oxygen-sensitive Fe-S cluster that is required for QS activity. The old5 lesion in this enzyme does not affect QS activity but it decreases its Cys desulfurase activity and thereby the long-term catalytic competence of the enzyme. The old5 mutation causes increased NAD steady state levels that coincide with increased activity of enzymes in the NAD salvage pathway. NAD plays a key role in cellular redox reactions, including those of the tricarboxylic acid cycle. Broad-range metabolite profiling of the old5 mutant revealed that it contains higher levels of tricarboxylic acid cycle intermediates and nitrogen-containing amino acids. The mutant displays a higher respiration rate concomitant with increased expression of oxidative stress markers. We postulate that the alteration in the oxidative state is integrated into the plant developmental program, causing early ageing of the mutant.
Take care! Responding to institutional complexity in Dutch childcare

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Impact of Employee Motivation on Customer Satisfaction: Study of Airline Industry in Pakistan

Employees are the most important factor in the success and failure of any organization. The airline industry is a service industry that sells seats to its passengers therefore employees motivation towards their job plays a very important role in serving the customer’s needs. This study focuses on the impact of employee motivation and its components e.g. work environment, pay and benefits, management systems and organizational vision on customer satisfaction in the airline industry of Pakistan. Correlation and regression analysis is used for this analysis. Results show that employee motivation as well as its four components e.g. work environment, pay and benefits, management systems and organizational vision have a significant positive influence on customer’s satisfaction. Those employees who have direct interaction with customer satisfaction highly influence the customer satisfaction level. It is evident from results that pay and benefits plays key role in motivating employees towards their organizational goal of higher customer satisfaction.
A Journey Through Homelessness: a Photovoice Project With Youth Experiencing Homelessness in Minnesota

The purpose of this project was to conduct a photovoice project with youth experiencing homelessness who frequent a drop-in center in the Midwest. Youth experiencing homelessness are a marginalized population whose numbers continue to grow. Photovoice is a method by which marginalized populations have an opportunity to express their lived experiences through photographs and what those photographs mean to them. Four youth from the drop-in center in the Midwest participated in the photovoice project. The youths were given cameras and instructions to take photographs of three broad areas: what homelessness means to them, their dreams for their futures and how has drop-in center helped them on their journey through homelessness. Their photographs and narratives are explained in this paper. The photographs were categorized into three themes: Caring Connections, Where Will I Sleep, and Dreams for the Future. Margaret Newman’s Health as Expanding Consciousness Theory and the concepts of health, nursing, human, and environment provided a framework and guided this project. A conceptual model was developed to represent the journey of the youths’ lives. Increased authentic connections using photovoice may change policy decisions, help communities deliver equitable services, and empower the participants of the photovoice project. Increased use of photovoice for community needs assessments, evaluation of programs, and a way to inform communities about issues should be considered.
Intermediate Performance Analysis of Growth Codes

Growth codes are a subclass of Rateless codes that have found interesting applications in data dissemination problems. Compared to other Rateless and conventional channel codes, Growth codes show improved intermediate performance which is particularly useful in applications where performance increases with the number of decoded data units. In this paper, we provide a generic analytical framework for studying the asymptotic performance of Growth codes in different settings. Our analysis based on Wormald method applies to any class of Rateless codes that does not include a precoding step. We evaluate the decoding probability model for short codeblocks and validate our findings by experiments. We then exploit the decoding probability model in an illustrative application of Growth codes to error resilient video transmission. The video transmission problem is cast as a joint source and channel rate allocation problem that is shown to be convex with respect to the channel rate. This application permits to highlight the main advantage of Growth codes that is improved performance (hence distortion in video) in the intermediate loss region.