Miracle-dz/UniFAR-FTUs huggingface dataset:
Allergic Bronchopulmonary Mycosis due to Exposure to Eurotium herbariorum after the Great East Japan Earthquake

Abstract Background Indoor mold levels typically increase after natural disasters, flooding, and water damage. Eurotium herbariorum is the sexual stage of Aspergillus glaucus. Case Presentation A 66-year-old, Japanese male, ex-smoker had been diagnosed with bronchial asthma when he was five years old; he achieved remission at the age of 13 years. He was displaced from his home during the Great East Japan Earthquake on March 11, 2011 and moved to temporary housing in Miyagi Prefecture in June 2011. He experienced the first episode of chest tightness, coughing, and wheezing in February 2012, when he again was diagnosed as having bronchial asthma. Mycofloral surveillance detected high counts of Eurotium in the air of his bedroom, kitchen, and living room, with a maximal fungal count of 163,200 colony-forming units per cubic meter (CFU/m3). Although Cladosporium and Penicillium typically predominate in the indoor air of residential dwellings, only low levels of these organisms were present in the patient’s home. Morphologic identification confirmed the isolates as E. herbariorum. The patient had positive reactions to E. herbariorum in skin prick testing and the presence of antigen-specific precipitating antibodies to E. herbariorum. Computed tomography of the chest in August 2013 revealed central bronchiectasis and bronchial wall thickening. The patient experienced late reactions after provocation testing with E. herbariorum. Conclusion This report presents the rare case of a patient who developed allergic bronchopulmonary mycosis (ABPM) due to exposure to E. herbariorum during temporary housing after the Great East Japan Earthquake. OshikataC, WatanabeM, SaitoA, IshidaM, KobayashiS, KonumaR, KamataY, TerajimaJ, ChoJ, YanaiM, TsurikisawaN. Allergic bronchopulmonary mycosis due to exposure to eurotium herbariorum after the Great East Japan Earthquake. Prehosp Disaster Med. 2017;32(6):688–690.
Experimental design trade-offs for gene regulatory network inference: An in silico study of the yeast Saccharomyces cerevisiae cell cycle

Time-series of high throughput gene sequencing data intended for gene regulatory network (GRN) inference are often short due to the high costs of sampling cell systems. Moreover, experimentalists lack a set of quantitative guidelines that prescribe the minimal number of samples required to infer a reliable GRN model. We study the temporal resolution of data vs. quality of GRN inference in order to ultimately overcome this deficit. The evolution of a Markovian jump process model for the Ras/cAMP/PKA pathway of proteins and metabolites in the Gx phase of the Saccharomyces cerevisiae cell cycle is sampled at a number of different rates. For each time-series we infer a linear regression model of the GRN using the LASSO method. The inferred network topology is evaluated in terms of the area under the precision-recall curve (AUPR). By plotting the AUPR against the number of samples, we show that the tradeoff has a, roughly speaking, sigmoid shape. An optimal number of samples corresponds to values on the ridge of the sigmoid.
Photoreceptor types, visual pigments, and topographic specializations in the retinas of hydrophiid sea snakes

Sea snakes have evolved numerous anatomical, physiological, and behavioral adaptations to suit their wholly aquatic lifestyle. However, although sea snakes use vision for foraging and mate selection, little is known about their visual abilities. We used microspectrophotometry, light microscopy, and scanning electron microscopy to characterize the retinal photoreceptors of spine‐bellied (Lapemis curtus) and horned (Acalyptophis peronii) sea snakes. Both species have three types of visual pigment sensitive to short (SWS; wavelength of maximum absorbance, λmax 428–430 nm), medium (MWS; λmax 496 nm), and long wavelengths of light (LWS; λmax 555–559 nm) in each of three different subtypes of cone‐like single photoreceptor. They also possess a cone‐like double photoreceptor subtype, both the principal and accessory member of which contain the LWS visual pigment. Conventional rods were not observed, although the MWS photoreceptor may be a “transmuted” rod. We also used stereology to measure the total number and topographic distribution of neurons in the ganglion cell layer of L. curtus, the olive sea snake (Aipysurus laevis), and the olive‐headed sea snake (Disteira major). All species have a horizontal visual streak with specialized areas in the nasal and temporal retina. Both L. curtus and D. major also have a specialized area in the ventral retina, which may reflect differences in habitat usage and/or foraging behavior compared to A. laevis. Maximal spatial resolution was estimated at 1.1, 1.6, and 2.3 cycles deg−1 in D. major, L. curtus, and A. laevis, respectively; the superior value for A. laevis may reflect its specialized crevice‐foraging hunting technique. J. Comp. Neurol. 520:1246–1261, 2012. © 2011 Wiley Periodicals, Inc.
Environmental conditions during early life determine the consequences of inbreeding in Agrostemma githago (Caryophyllaceae)

In an inbred population, selection may reduce the frequency of deleterious recessive alleles through a process known as purging. Empirical studies suggest, however, that the efficacy of purging in natural populations is highly variable. This variation may be due, in part, to variation in the expression of inbreeding depression available for selection to act on. This experiment investigates the roles of life stage and early‐life environment in determining the expression of inbreeding depression in Agrostemma githago. Four population‐level crosses (‘self’, ‘within’, ‘near’ and ‘far’) were conducted on 20 maternal plants from a focal population. Siblings were planted into one of three early environmental treatments with varying stress levels. Within the focal population, evidence for purging of deleterious recessive alleles, as well as for variation in the expression of inbreeding depression across the life cycle was examined. In addition, the effect of early environment on the expression of inbreeding depression and the interaction with cross‐type was measured. We find that deleterious recessive alleles have not been effectively purged from our focal population, the expression of inbreeding depression decreases over the course of the life cycle, and a stressful early environment reduces the variance in inbreeding depression expressed later in life, but does not consistently influence the relative fitness of inbred versus outcrossed individuals.
UvA-DARE (Digital Academic Repository) Using term clouds to represent segment-level semantic content of podcasts

Spoken audio, like any time-continuous medium, is notoriously difﬁcult to browse or skim without support of an interface providing semantically annotated jump points to signal the user where to listen in. Creation of time-aligned metadata by human anno-tators is prohibitively expensive, motivating the investigation of representations of segment-level semantic content based on transcripts generated by automatic speech recognition (ASR). This paper examines the feasibility of using term clouds to provide users with a structured representation of the semantic content of podcast episodes. Podcast episodes are visualized as a series of sub-episode segments, each represented by a term cloud derived from a transcript generated by automatic speech recognition (ASR). Quality of segment-level term clouds is measured quantitatively and their util-ity is investigated using a small-scale user study based on human labeled segment boundaries. Since the segment-level clouds generated from ASR-transcripts prove useful, we examine an adaptation of text tiling techniques to speech in order to be able to generate segments as part of a completely automated indexing and structuring system for browsing of spoken audio. Results demonstrate that the segments generated are comparable with human selected segment boundaries.
Characterizing Group Behavior ∗

We study the demand function of a group of S members facing a global budget constraint. Any vector belonging to the budget set can be consumed within the group, with no restriction on the form of individual preferences, the nature of individual consumptions or the form of the decision process beyond efficiency. Moreover, only the group aggregate behavior, summarized by its demand function, is observable. We provide necessary and (locally) sufficient restrictions that fully characterize the group’s demand function, with and without distribution factors. We show that the private or public nature of consumption within the group is not testable from aggregate data on group behavior. Journal of Economic Literature Classification Numbers: D11, D13, C65.
Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies

Strategies for the identification of functional genetic variation underlying phenotypic traits of ecological and evolutionary importance have received considerable attention in the literature recently. This paper aims to bring together and compare the relative strengths and limitations of various potentially useful research strategies for dissecting functionally important genetic variation in a wide range of organisms. We briefly explore the relative strengths and limitations of traditional and emerging approaches and evaluate their potential use in free‐living populations. While it is likely that much of the progress in functional genetic analyses will rely on progress in traditional model species, it is clear that with prudent choices of methods and appropriate sampling designs, much headway can be also made in a diverse range of species. We suggest that combining research approaches targeting different functional and biological levels can potentially increase understanding the genetic basis of ecological and evolutionary processes both in model and non‐model organisms.
Auto-Correlation based Spectrum Sensing at Low SNR for Cognitive Radio

A challenging problem in Cognitive radio is that the secondary users in cognitive radios must be able to detect primary users under low signal-to-noise ratio (SNR) and dispersive channel. Spectrum sensing based on autocorrelation of the received signal samples being more prone to correlate under dispersive condition, has been investigated. Simplified theoretical expressions for probability of false alarm and probability of detection of the auto-correlation based algorithm are derived in the presence of multi-path fading channel. Spectrum of an unknown primary signal has been obtained through auto-regressive parametric signal modeling. By the proposed auto-correlation technique the detection probability near unity can be achieved at finite input samples and at a very low SNR for OFDM DVB-T signal and a wireless FM microphone signal in VHF band. It is found that dimension of auto-correlation matrix and signal sample duration is inversely proportional to achieve unity detection probability.
Emotions represented and induced by music : the role of individual differences

Vuoskoski, Jonna Katariina Emotions represented and induced by music: The role of individual differences Jyväskylä: University of Jyväskylä, 2012, 58 p. (Jyväskylä Studies in Humanities ISSN 1459-4331; 174) ISBN 978-951-39-4681-4 (nid) ISBN 978-951-39-4682-1 (PDF) Finnish summary Diss. The primary aim of this work was to investigate how listener attributes such as personality, empathy, and mood contribute to different emotional phenomena in the context of music. Predictions arising from personality and emotion theories were applied to music-related emotional phenomena, and tested using methods of experimental psychology. The emotional phenomena under investigation were perceived emotions, felt emotions, and preference for music expressing different emotions. A related aim was to systematically compare the applicability of different emotion models in the measurement of emotions expressed and induced by music. The work comprises five publications, each investigating a different aspect of the main aims. The findings suggest that personality, mood, and empathy contribute notably to individual differences in music-related emotional phenomena. Temporary mood was reliably associated with mood-congruent biases in ratings of perceived emotions, while personality traits correlated with preference ratings for music excerpts expressing different emotions. In the case of music-induced emotions, both mood and personality were associated with the intensity of emotional responses evoked by different types of excerpts, whereas trait empathy contributed to the susceptibility to music-induced sadness. Regarding the results of the emotion model comparisons, it is concluded that the dimensional model of affect may provide the most coherent and reliable ratings in studies where varied musical stimuli are used. Implications for future studies are raised concerning the significance of individual differences in musical contexts, as well as the selection of an appropriate emotion model for the study of emotions represented and induced by music.
Human Peripheral Blood Mononuclear Cell Function and Dendritic Cell Differentiation Are Affected by Bisphenol-A Exposure

Environmental pollutants, including endocrine disruptor chemicals (EDCs), interfere on human health, leading to hormonal, immune and metabolic perturbations. Bisphenol-A (BPA), a main component of polycarbonate plastics, has been receiving increased attention due to its worldwide distribution with a large exposure. In humans, BPA, for its estrogenic activity, may have a role in autoimmunity, inflammatory and allergic diseases. To this aim, we assessed the effect of low BPA doses on functionality of human peripheral blood mononuclear cells (PBMCs), and on in vitro differentiation of dendritic cells from monocytes (mDCs). Fresh peripheral blood samples were obtained from 12 healthy adult volunteers. PBMCs were left unstimulated or were activated with the mitogen phytohemagglutinin (PHA) or the anti-CD3 and anti-CD28 antibodies and incubated in presence or absence of BPA at 0.1 and 1nM concentrations. The immune-modulatory effect of BPA was assessed by evaluating the cell proliferation and the levels of interferon-γ (IFN-γ), interleukin-4 (IL-4), interleukin-10 (IL-10) and interleukin-13 (IL-13) secreted by PBMCs. mDCs were differentiated with IL-4 and GC-CSF with or without BPA and the expression of differentiation/maturation markers (CD11c, CD1a, CD86, HLA-DR) was evaluated by flow cytometry; furthermore, a panel of 27 different cytokines, growth factors and chemokines were assayed in the mDC culture supernatants. PBMCs proliferation significantly increased upon BPA exposure compared to BPA untreated cells. In addition, a significant decrease in IL-10 secretion was observed in PBMCs incubated with BPA, either in unstimulated or mitogen-stimulated cells, and at both 0.1 and 1nM BPA concentrations. Similarly, IL-13 was reduced, mainly in cells activated by antiCD3/CD28. By contrast, no significant changes in IFN-γ and IL-4 production were found in any condition assayed. Finally, BPA at 1nM increased the density of dendritic cells expressing CD1a and concomitantly decreased the expression of HLA-DR and CD86 activation markers. In conclusion, in humans the exposure to BPA causes on PBMCs a significant modulation of proliferative capacity and cytokine production, and on mDCs alteration in differentiation and phenotype. These immune cell alterations suggest that low dose chronic exposure to BPA could be involved in immune deregulation and possibly in the increased susceptibility to develop inflammatory and autoimmune diseases.
Partial calcaneal ostectomy for retrocalcaneal bursitis

Heel pain in runners is very common. Retrocalcaneal bursitis may be disabling to the competitive runner. When conservative treatment fails, surgery (partial cal caneal ostectomy) may be indicated. Ten patients un derwent partial calcaneal ostectomies at our clinic and returned to their desired level of activity within 6 months. When the surgeon adheres to the surgical principles outlined in this article, the results are uni formly good.
Neuropsychological Profile of Specific Executive Dysfunctions in Patients with Deficit and Non-deficit Schizophrenia

Objectives: Although it has been shown that there are more profound deficits present in deficit schizophrenia (DS) patients than in non-deficit schizophrenia (NDS) patients, there still remain some matters requiring further investigation. In this context, we formulated three research aims: (1) to compare executive functions between the investigated groups, (2) to determine the relationship between particular aspects of executive functions within the groups, and (3) to draw up a neuropsychological profile for executive functions. Methods: The study involved 148 schizophrenia patients divided into two groups on the basis of the Schedule for the Deficit Syndrome: DS (n = 70) and NDS (n = 78). Patients were matched for sex, age, years of education, and overall cognitive functioning. For assessing executive functions we used the Wisconsin Card Sorting Test (WCST), the Trail Making Test (TMT), the Phonemic Verbal Fluency Test (VFT P), the Stroop Color and Word Test (SCWT), and the Go/No Go task (GNG). Results: Deficit schizophrenia patients scored lower on the WCST and TMT (relative flexibility) than did the NDS patients. There were no inter-group differences in the VFT P, SCWT (relative inhibition), or GNG. There were significant correlations between WCST and TMT scores in both groups. The general neuropsychological profiles were similar in both groups. Conclusion: Deficit schizophrenia patients exhibited slightly greater interference with concept formation and non-verbal cognitive flexibility. Therefore, such problems may be specific to this particular type of schizophrenia. These results may be useful for the development of neuropsychological diagnostic methods for patients with schizophrenia.
Projected Destination Image Online: Website Content Analysis of Pictures and Text

This study analyzes how destination identity is projected through the use of photographic imagery and narratives in an online environment in the context of marketing a fast growing tourist destination such as Dubai. Twenty Dubai-based websites, covering various sectors of the industry, were content analyzed in terms of the photographic material and textual representations presented. Results confirm that there are, as expected, considerable discrepancies in the way the private and public players project Dubai’s identity. Private sector organizations, in particular hospitality and transport, are product oriented and projected images relate primarily to the specific facilities and tourist activities on offer. In contrast, the destination marketing organization focuses on the projection of cultural identity and heritage.
Augmented Lagrangian Methods and Proximal Point Methods for Convex Optimization

We present a review of the classical proximal point method for nding zeroes of maximal monotone operators, and its application to augmented Lagrangian methods, including a rather complete convergence analysis. Next we discuss the generalized proximal point methods, either with Bregman distances or -divergences, which in turn give raise to a family of generalized augmented Lagrangians, as smooth in the primal variables as the data functions are. We give a sketch of the convergence analysis for the case of the proximal point method with Bregman distances for variational inequality problems. The di culty with these generalized augmented Lagrangians lies in establishing optimality of the cluster points of the primal sequence, which is rather immediate in the classical case. In connection with this issue we present two results. First we prove optimality of such cluster points under a strict complementarity assumption (basically that no tight constraint is redundant at any solution). In the absence of this assumption, we establish an ergodic convergence result, namely optimality of the cluster points of a sequence of weighted averages of the primal sequence given by the method, improving over weaker ergodic results previously known. Finally we discuss similar ergodic results for the augmented Lagrangian method with -divergences and give the explicit formulae of generalized augmented Lagrangian methods for di erent choices of the Bregman distances and the -divergences.
Predicting Long Term Student Retention using Expanded PFA and Clustering

The regularity lemma is a fundamental result from the extremal graph theory. It is to claim the existence of a regular partition, from which we can construct the reduced graph, hence preserve the consistent behavior inside the same partition, and also decrease the order of input graph significantly. It is a very important tool in theoretical proofs, but due to the requirement of very large graph, it has no practical applications so far. In this paper we discuss the possible modifications to make the regularity lemma applicable in practical setting. This leads to a brand new clustering algorithm: Spectral regularity algorithm. We apply it to an Educational Data mining task: predicting student test result from features derived from tutors, we also compare the result with using standard spectral clustering algorithm. The experimental results are
A Doppler Robust Design of Transmit Sequence and Receive Filter in the Presence of Signal-Dependent Interference

In this paper, we study the joint design of Doppler robust transmit sequence and receive filter to improve the performance of an active sensing system dealing with signal-dependent interference. The signal-to-noise-plus-interference (SINR) of the filter output is considered as the performance measure of the system. The design problem is cast as a max-min optimization problem to robustify the system SINR with respect to the unknown Doppler shifts of the targets. To tackle the design problem, which belongs to a class of NP-hard problems, we devise a novel method (which we call DESIDE) to obtain optimized pairs of transmit sequence and receive filter sharing the desired robustness property. The proposed method is based on a cyclic maximization of SINR expressions with relaxed rank-one constraints, and is followed by a novel synthesis stage. We devise synthesis algorithms to obtain high quality pairs of transmit sequence and receive filter that well approximate the behavior of the optimal SINR (of the relaxed problem) with respect to target Doppler shift. Several numerical examples are provided to analyze the performance obtained by DESIDE.
Space-time editing of elastic motion through material optimization and reduction

We present a novel method for elastic animation editing with space-time constraints. In a sharp departure from previous approaches, we not only optimize control forces added to a linearized dynamic model, but also optimize material properties to better match user constraints and provide plausible and consistent motion. Our approach achieves efficiency and scalability by performing all computations in a reduced rotation-strain (RS) space constructed with both cubature and geometric reduction, leading to two orders of magnitude improvement over the original RS method. We demonstrate the utility and versatility of our method in various applications, including motion editing, pose interpolation, and estimation of material parameters from existing animation sequences.