Miracle-dz/UniFAR-FTUs huggingface dataset:
NEUROSPORA AND THE DEAD‐END HYPOTHESIS: GENOMIC CONSEQUENCES OF SELFING IN THE MODEL GENUS

It is becoming increasingly evident that adoption of different reproductive strategies, such as sexual selfing and asexuality, greatly impacts genome evolution. In this study, we test theoretical predictions on genomic maladaptation of selfing lineages using empirical data from the model fungus Neurospora. We sequenced the genomes of four species representing distinct transitions to selfing within the history of the genus, as well as the transcriptome of one of these, and compared with available data from three outcrossing species. Our results provide evidence for a relaxation of purifying selection in protein‐coding genes and for a reduced efficiency of transposable element silencing by Repeat Induced Point mutation. A reduction in adaptive evolution was also identified in the form of reduced codon usage bias in highly expressed genes of selfing Neurospora, but this result may be confounded by mutational bias. Potentially counteracting these negative effects, the nucleotide substitution rate and the spread of transposons is reduced in selfing species. We suggest that differences in substitution rate relate to the absence, in selfing Neurospora, of the asexual pathway producing conidia. Our results support the dead‐end theory and show that Neurospora genomes bear signatures of both sexual and asexual reproductive mode.
Reestablishment of ion homeostasis during chill-coma recovery in the cricket Gryllus pennsylvanicus

The time required to recover from cold-induced paralysis (chill-coma) is a common measure of insect cold tolerance used to test central questions in thermal biology and predict the effects of climate change on insect populations. The onset of chill-coma in the fall field cricket (Gryllus pennsylvanicus, Orthoptera: Gryllidae) is accompanied by a progressive drift of Na+ and water from the hemolymph to the gut, but the physiological mechanisms underlying recovery from chill-coma are not understood for any insect. Using a combination of gravimetric methods and atomic absorption spectroscopy, we demonstrate that recovery from chill-coma involves a reestablishment of hemolymph ion content and volume driven by removal of Na+ and water from the gut. Recovery is associated with a transient elevation of metabolic rate, the time span of which increases with increasing cold exposure duration and closely matches the duration of complete osmotic recovery. Thus, complete recovery from chill-coma is metabolically costly and encompasses a longer period than is required for the recovery of muscle potentials and movement. These findings provide evidence that physiological mechanisms of hemolymph ion content and volume regulation, such as ion-motive ATPase activity, are instrumental in chill-coma recovery and may underlie natural variation in insect cold tolerance.
Use of Heuristics to Facilitate Scientific Discovery Learning in a Simulation Learning Environment in a Physics Domain

This article describes a study into the role of heuristic support in facilitating discovery learning through simulation‐based learning. The study compares the use of two such learning environments in the physics domain of collisions. In one learning environment (implicit heuristics) heuristics are only used to provide the learner with guidance derived from heuristics, without presenting the heuristics themselves; in the other (explicit heuristics) the heuristics themselves are also made explicit to the learner. The two learning environments are tested with 46 students from two schools. The results show that learners in both conditions gain domain knowledge from pre‐test to post‐test. Regression analyses show that pre‐test results can predict post‐test results in the implicit heuristics condition but not in the explicit heuristic condition. Process analyses suggest that presenting the heuristics explicitly facilitate more self‐regulation in students.
Efficient sparse matrix multiple-vector multiplication using a bitmapped format

The problem of obtaining high computational throughput from sparse matrix multiple-vector multiplication routines is considered. Current sparse matrix formats and algorithms have high bandwidth requirements and poor reuse of cache and register loaded entries, which restrict their performance. We propose the mapped blocked row format: a bitmapped sparse matrix format that stores entries as blocks without a fill overhead, thereby offering blocking without additional storage and bandwidth overheads. An efficient algorithm decodes bitmaps using de Bruijn sequences and minimizes the number of conditionals evaluated. Performance is compared with that of popular formats, including vendor implementations of sparse BLAS. Our sparse matrix multiple-vector multiplication algorithm achieves high throughput on all platforms and is implemented using platform neutral optimizations.
Distribution of Nitrergic Neurons in the Dorsal Root Ganglia of the Bottlenose Dolphin (Tursiops truncatus)

Dorsal root ganglia (DRGs) contain the cell bodies of primary afferent neurons that transmit sensory information from the periphery into the spinal cord. Distinct populations of DRG neurons have been characterized by a variety of different immunohistochemical markers. A subpopulation of ganglionic neurons containing neuronal nitric oxide synthase (nNOS), an enzyme known to generate nitric oxide, has been detected in a number of mammalian species. Despite previous studies, no information is known on the presence and exact distribution of nNOS‐immunoreactive neurons in the DRGs of the bottlenose dolphin. In this investigation, immunoperoxidase for nNOS was used to determine the distribution and the perikaryal size of nitrergic neurons in the DRGs of this species. Double immunofluorescence protocol was used to determine the percentage of nNOS‐immunoreactive (IR) neurons over the total primary afferent neurons. In addition, double immunostaining was used to verify whether there was colocalization of nNOS with substance P (SP). In all DRGs, a subpopulation of small‐ and medium‐sized neurons (about 9%) exhibited nNOS immunoreactivity. Data analysis revealed that the majority of nNOS‐IR neurons (81.3%) expressed SP. The density of nNOS‐immunoreactive and nNOS/SP‐double immunopositive cells was relatively constant throughout the ganglia. However, as observed in others mammals, the number of nitrergic neurons decreased in the caudalmost DRGs. Our results, in conjunction with previous observations, suggest that nNOS‐IR neurons may be involved in the afferent transmission of visceral and nociceptive information as well as in the regulation of the vascular tone. Anat Rec,, 2011. © 2011 Wiley‐Liss, Inc.
Co-targeting c-Met and COX-2 Leads to Enhanced Inhibition of Lung Tumorigenesis in a Murine Model with Heightened Airway HGF

Background: The hepatocyte growth factor (HGF)/c-Met pathway is often dysregulated in non–small-cell lung cancer (NSCLC). HGF activation of c-Met induces cyclooxygenase-2 (COX-2), resulting in downstream stimulation by prostaglandin E2 of additional pathways. Targeting both c-Met and COX-2 might lead to enhanced antitumor effects by blocking signaling upstream and downstream of c-Met. Methods: Effects of crizotinib or celecoxib alone or in combination were tested in NSCLC cells in vitro and in mice transgenic for airway expression of human HGF. Results: Proliferation and invasion of NSCLC cells treated with a combination of crizotinib and celecoxib were significantly lower compared with single treatments. Transgenic mice showed enhanced COX-2 expression localized to preneoplastic areas following exposure to the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, which was not present without carcinogen exposure. This shows that COX-2 activity is present during lung tumor development in a high HGF environment. After 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone treatment, a significant decrease in the number of lung tumors per animal was observed after 13-week treatments of crizotinib, celecoxib, or the combination compared with placebo (p < 0.001). With combination treatment, the number of tumors was also significantly lower than single agent treatment (p < 0.001). In the resulting lung tumors, P-c-Met, COX-2, prostaglandin E2, and P-MAPK were significantly downmodulated by combination treatment compared with single treatment. Expression of the epithelial-mesenchymal transition markers E-cadherin and snail was also modulated by combination treatment. Conclusions: In the presence of high HGF, dual inhibition of c-Met and COX-2 may enhance antitumor effects. This combination may have clinical potential in NSCLCs with high HGF/c-Met expression or epithelial-mesenchymal transition phenotype.
Un point de vue différent sur la place de la religion à l'école : étude exploratoire sur les perceptions religieuses et spirituelles d'adolescent-es de la fin secondaire du centre de Montréal

The following is an exploratory study aimed at bringing back the focus of this debate on those who are primarily concerned with the issue of if, and how, religion should be taught in school: the students. Using an anonymous questionnaire, where ample space for personal comments was given, the author tried to discover what participants, mostly from age 15 to 17, thought of the religions they were exposed to both at home and at school. The author also wanted to know if those youths found in religion, an adequate expression of their spirituality and if exposure to different religions made them more tolerant to difference. This thesis complements, by its emphasis on the participants' experience, the corpus of literature available on the topic of religion in schools in the province of Quebec, which mostly focuses on the legal or ideological aspects of this issue. Findings suggest that participants are much more concerned about issues such as the meaning of life, peace, social justice, and having harmonious relationships with others than what the media and popular belief portray. It also seems that they are curious about the ways in which different people believe and live their spirituality in their daily existence.
Efficient Distributed Semi-Supervised Learning using Stochastic Regularization over Affinity Graphs

We describe a computationally efficient, stochastic graph-regularization technique that can be utilized for the semi-supervised training of deep neural networks in a parallel or distributed setting. We utilize a technique, first described in [13] for the construction of mini-batches for stochastic gradient descent (SGD) based on synthesized partitions of an affinity graph that are consistent with the graph structure, but also preserve enough stochasticity for convergence of SGD to good local minima. We show how our technique allows a graph-based semi-supervised loss function to be decomposed into a sum over objectives, facilitating data parallelism for scalable training of machine learning models. Empirical results indicate that our method significantly improves classification accuracy compared to the fully-supervised case when the fraction of labeled data is low, and in the parallel case, achieves significant speed-up in terms of wall-clock time to convergence. We show the results for both sequential and distributed-memory semi-supervised DNN training on a speech corpus.
Using Self-Determination Theory in Correctional Education Program Development.

As funding has become available through the Second Chance Act of2007, many correctional facilities have developed new educational programs in an effort to ease the transition from prison to community. Many new programs are developed based on the belief that incarcerated individuals are a special and unique population of student. The present research takes the approach that incarcerated individuals in correctional education classes are students first, and have many of the same needs and challenges as students in any classroom. Public educators have recently used self-determination theory (Deci 9 Ryan, 2000) to discuss specific elements of courses that students say motivate them to actively engage in the learning process. Courses that foster feelings of competence and individual autonomy in learning are given higher ratings on course evaluations. The current study incorporates these two elements of self-determination theory in the development of a new educational program in a prison setting. Pre and post-test measures were used to assess mastery of the material presented during the course, and course evaluations that allowed individuals input into future course development were given at the end. Implications of results on development of future reentry programs are discussed. Development Recently, the Federal Bureau of Prisons has redesigned the reentry programming used in their facilities. The main intention of the programs offered pre-release is to help ease the transition back into society, as well as decrease the likelihood of recidivism. The educational programming created for use in federal correctional institutions has been specifically designed to increase competency in nine skills areas. These areas not only include courses in general
Testing the cognitive effort hypothesis of cognitive impairment in major depression

Background: It is widely accepted that depression is associated with deficits in a range of cognitive domains. However, there is no consensus regarding the neuropsychological profile in depression. Aim: The aim of the present report is to test the cognitive effort hypothesis as a possible framework for understanding the observed cognitive impairment in major depressive disorder (MDD), using the Delis Kaplan Executive Function system (D-KEFS). Method: Twenty-four patients with recurrent MDD, in the acute phase of illness, were compared with a healthy control group. We expected that the patient group would show impairment on tests that measure higher-level effortful cognitive processing, whereas basic cognitive skills would be equal to the control group. Results: There were no differences between the two groups on measures of basic cognitive skills, except for Colour Naming. Furthermore, MDD patients performed significantly worse than the control group on three out of seven of the cognitively effortful measures; namely Inhibition, Inhibition/Switching and Category Fluency. Conclusions: We could not find consistent support for the cognitive effort hypothesis in the present study. However, the results indicate that depressed patients have a specific impairment within the Executive Function domain affecting Inhibition, Inhibition/Switching and Category Fluency.
Sound symbolism: The frequency code underlies the sound-symbolic use of voice pitch

Sound symbolism is the term for a hypothesized systematic relationship between sound and meaning (Hinton, Nichols, & Ohala 1994). The idea that there might be a non-arbitrary relationship between the physical aspect of a speech signal and its meaning is quite an old idea, dating back at least to the time of Plato who, in his work Cratylus, had Socrates debating with two pupils the issue of whether the names for things are arbitrary or whether instead they are a natural reflection of the things named. There has been considerable speculation and anecdotal evidence on this point from then up to the present time (de Brosses 1765; Jespersen 1933). I believe that phonetic studies -combined with principles emerging from ethology, the science of comparative behavior -can provide a novel basis for further informed speculation on this issue. Moreover, the principles applied to this topic can also elucidate several other controversial topics including the cause of universal patterns in intonation, the origin of certain facial expressions involving the mouth, the reason for sexual dimorphism of the vocal anatomy in humans (and other species), and whether the human vocal anatomy shows any adaptation special to speech.
Focus Improvement of Highly Squinted Data Based on Azimuth Nonlinear Scaling

Since synthetic aperture technology was employed in radar signal processing, the information capability of radar has greatly been enhanced. A lot of imaging algorithms have also been developed. However, the high-resolution imaging for highly squinted synthetic aperture radar data is still a difficult issue due to large range migration and strong range dependence on the secondary range compression term that is relatively large and cubic with high focusing sensibilities for high resolution. To accommodate for this problem, the "squint-minimization" operation and azimuth nonlinear chirp scaling (CS) (ANCS) operation are studied in this paper. On the basis of these operations, we propose new imaging algorithms and analyze the characteristic of highly squinted data and the difficulty in focusing these data as well as discussing the principle of ANCS. We also introduce a new CS algorithm, and numerical examples show that the proposed algorithm is able to achieve 0.1 m of resolution under a squint angle as large as 70°s.
"Fair Play": A Videogame Designed to Address Implicit Race Bias Through Active Perspective Taking.

OBJECTIVE Having diverse faculty in academic health centers will help diversify the healthcare workforce and reduce health disparities. Implicit race bias is one factor that contributes to the underrepresentation of Black faculty. We designed the videogame "Fair Play" in which players assume the role of a Black graduate student named Jamal Davis. As Jamal, players experience subtle race bias while completing "quests" to obtain a science degree. We hypothesized that participants randomly assigned to play the game would have greater empathy for Jamal and lower implicit race bias than participants randomized to read narrative text describing Jamal's experience. MATERIALS AND METHODS University of Wisconsin-Madison graduate students were recruited via e-mail and randomly assigned to play "Fair Play" or read narrative text through an online link. Upon completion, participants took an Implicit Association Test to measure implicit bias and answered survey questions assessing empathy toward Jamal and awareness of bias. RESULTS As hypothesized, gameplayers showed the least implicit bias but only when they also showed high empathy for Jamal (P=0.013). Gameplayers did not show greater empathy than text readers, and women in the text condition reported the greatest empathy for Jamal (P=0.008). However, high empathy only predicted lower levels of implicit bias among those who actively took Jamal's perspective through gameplay (P=0.014). CONCLUSIONS A videogame in which players experience subtle race bias as a Black graduate student has the potential to reduce implicit bias, possibly because of a game's ability to foster empathy through active perspective taking.
Medical dosimetry using optically stimulated luminescence dots and microStar readers

Landauer has developed a portable dosimetry system based on its Optically Stimulated Luminescence (OSL) technology. It is called the microStar, and its core technology is the same as that in its personnel monitors used throughout the world (more commonly known by their trade names, Luxel, and InLight). OSL using aluminium oxide doped with carbon (Al2O3:C) has been used extensively for personal radiation dosimetry for many years. It has the advantages of low detection threshold and re-analysis. Recently, single dots of OSL material and a portable reader have been developed with a view to medical applications. A number of organisations asked to make trials of this system. The acceptance of this system has grown worldwide with recent trials at various hospitals in France, the USA and the UK. Most recently, the IAEA has undertaken a Coordinated Research Program (CRP) to identify dosimetry systems for use in developing countries. The trials, some of which have already been reported in the scientific literature, have included studies of the energy and dose response, the stability of the readout and the overall accuracy of the measurements as compared to other systems used in patient dosimetry. It is evident that the OSL system is capable of achieving the high degree of accuracy required for medical applications (reproducibility (< 2%)) and has a number of advantages over current methodologies such as a wide dynamic range (0.01 mGy to 15 Gy) and negligible energy, angle, dose rate, and temperature dependence. In addition, one unique feature relative to TLD’s is the ability to re-read the dose many times (with potential application for archiving the dosemeter with patient records) as only a fraction of the stored charged is consumed in each analysis. This paper will review the results of these trials highlighting similarities and differences. Where differences were found, possible explanations will be presented. The overall properties of the system will be summarised drawing out the advantages and disadvantages over current systems (TLD, MOSFET and Diode dosimetry). In the light of the experience with these trials, new developments of the system will be presented.
Bullous Mastocytosis in an Infant Associated with the Use of a Nonprescription Cough Suppressant

Abstract: Bullous mastocytosis is an unusual expression of mastocytosis typically seen in young children, and many causes of the acute mast cell degranulatlon with bulla formation have been identified. We report a 6‐month‐old boy with urticaria pigmentosa and an extensive bullous eruption associated with the ingest ion of a non prescription cough suppressant containing dextrotmethorphan. The pathogenesis of mastocytosis and the care of patients with this disease are discussed.
Fundamental Mechanisms of Growth Failure in Inflammatory Bowel Disease

Growth failure is common in children with inflammatory bowel disease (IBD) and has been attributed chiefly to undernutrition. Liquid enteral feeding can reverse the calorie deficit and increase growth velocity. The inflammatory process per se may also directly inhibit linear growth. After institution of enteral nutrition, significant changes in serum growth factors and inflammatory indices have been observed before any changes in nutritional parameters [Bannerjee et al., Gastroenterology 2000;118:A526]. In rats with trinitrobenzenesulphonic acid (TNBS)-induced colitis, about 60% of the final growth impairment can be attributed to undernutrition, inflammation accounting for the remaining growth deficit. Young patients with Crohn’s disease and growth failure have normal stimulated and spontaneous growth hormone (GH) secretion and reduced plasma concentrations of insulin-like growth factor-1 (IGF-I), suggesting a degree of GH resistance. Rats with TNBS colitis also have normal plasma GH and reduced IGF-I concentrations, mediated by a combination of undernutrition and active inflammation. Immunoneutralization of interleukin-6 (IL-6) increases hepatic IGF-I mRNA expression, plasma concentrations of IGF-I and linear growth. In contrast, administration of anti-tumour necrosis factor-α antibodies (TNF-ab) had no effect on IGF-I in this model. TNFab did, however, increase linear growth, suggesting inhibitory effects of TNF-α on the growth axis by mechanisms other than reduction in IGF-I. Preliminary data suggests that TNF-α inhibits maturation of growth plate chondrocytes. We have identified IL-6 receptors on growth plate chondrocytes but to date have not identified the effect, if any, of IL-6 directly at the growth plate.