Miracle-dz/UniFAR-FTUs huggingface dataset:
Coherent Hierarchical Culling: Hardware Occlusion Queries Made Useful

We present a simple but powerful algorithm for optimizing the usage of hardware occlusion queries in arbitrary complex scenes. Our method minimizes the number of issued queries and reduces the delays due to the latency of query results. We reuse the results of occlusion queries from the last frame in order to initiate and schedule the queries in the next frame. This is done by processing nodes of a spatial hierarchy in a front‐to‐back order and interleaving occlusion queries with rendering of certain previously visible nodes. The proposed scheduling of the queries makes use of spatial and temporal coherence of visibility. Despite its simplicity, the algorithm achieves good culling efficiency for scenes of various types. The implementation of the algorithm is straightforward and it can be easily integrated in existing real‐time rendering packages based on common hierarchical data structures.
Structuration Concepts as a Framework for Revealing a 'Socially Rich' Concept of the User

Current constructs of the user limits our understanding of service channel selection, improvisation, communication, and exchange within multi-channel social contexts. Based on a recent longitudinal case study of an electronic service use in a healthcare insurance context, the paper uses key concepts from structuration theory to examine how users interact with a technology in their ongoing practices, and enact structures which shape their emergent and situated use of the technology among alternative channels. The paper portrays the complex and multiple roles that external users fulfil while reflexively adopting, adapting and using an electronic service. In doing so, the paper responds to the call by Lamb and Kling (2003) to shift from the “thin” user concept to a “rich” concept of a social actor. The ways in which firms employ technology to interact with their customers have changed noticeably and will continue to evolve. To empower users, this study advocates that practitioners balance their internally-biased perspectives with perspectives that are attentive to the current social practices of their targeted user community.
Development of a Real-Time PCR Assay for Rapid Detection and Quantification of Alexandrium minutum (a Dinoflagellate)

ABSTRACT The marine dinoflagellate genus Alexandrium includes a number of species which produce neurotoxins responsible for paralytic shellfish poisoning (PSP), which in humans may cause muscular paralysis, neurological symptoms, and, in extreme cases, death. A. minutum is the most widespread toxic PSP species in the western Mediterranean basin. The monitoring of coastal waters for the presence of harmful algae also normally involves microscopic examinations of phytoplankton populations. These procedures are time consuming and require a great deal of taxonomic experience, thus limiting the number of specimens that can be analyzed. Because of the genetic diversity of different genera and species, molecular tools may also help to detect the presence of target microorganisms in marine field samples. In this study, we developed a real-time PCR-based assay for rapid detection of all toxic species of the Alexandrium genus in both fixative-preserved environmental samples and cultures. Moreover, we developed a real-time quantitative PCR assay for the quantification of A. minutum cells in seawater samples. Alexandrium genus-specific primers were designed on the 5.8S rDNA region. Primer specificity was confirmed by using BLAST and by amplification of a representative sample of the DNA of other dinoflagellates and diatoms. Using a standard curve constructed with a plasmid containing the ITS1-5.8S-ITS2 A. minutum sequence and cultured A. minutum cells, we determined the absolute number of 5.8S rDNA copies per cell. Consequently, after quantification of 5.8S rDNA copies in samples containing A. minutum cells, we were also able to estimate the number of cells. Several fixed A. minutum bloom sea samples from Arenys Harbor (Catalan Coast, Spain) were analyzed using this method, and quantification results were compared with standard microscopy counting methods. The two methods gave comparable results, confirming that real-time PCR could be a valid, fast alternative procedure for the detection and quantification of target phytoplankton species during coastal water monitoring.
A Systematic Review of the Effects of Hormone Therapy on Psychological Functioning and Quality of Life in Transgender Individuals

Abstract Objectives: To review evidence from prospective cohort studies of the relationship between hormone therapy and changes in psychological functioning and quality of life in transgender individuals accessing hormone therapy over time. Data Sources: MEDLINE, PsycINFO, and PubMed were searched for relevant studies from inception to November 2014. Reference lists of included studies were hand searched. Results: Three uncontrolled prospective cohort studies, enrolling 247 transgender adults (180 male-to-female [MTF], 67 female-to-male [FTM]) initiating hormone therapy for the treatment of gender identity disorder (prior diagnostic term for gender dysphoria), were identified. The studies measured exposure to hormone therapy and subsequent changes in mental health (e.g., depression, anxiety) and quality of life outcomes at follow-up. Two studies showed a significant improvement in psychological functioning at 3–6 months and 12 months compared with baseline after initiating hormone therapy. The third study showed improvements in quality of life outcomes 12 months after initiating hormone therapy for FTM and MTF participants; however, only MTF participants showed a statistically significant increase in general quality of life after initiating hormone therapy. Conclusions: Hormone therapy interventions to improve the mental health and quality of life in transgender people with gender dysphoria have not been evaluated in controlled trials. Low quality evidence suggests that hormone therapy may lead to improvements in psychological functioning. Prospective controlled trials are needed to investigate the effects of hormone therapy on the mental health of transgender people.
The Effects of Mindfulness-Based Cognitive Therapy on Affective Memory Recall Dynamics in Depression: A Mechanistic Model of Rumination

Objectives: converging research suggests that mindfulness training exerts its therapeutic effects on depression by reducing rumination. Theoretically, rumination is a multifaceted construct that aggregates multiple neurocognitive aspects of depression, including poor executive control, negative and overgeneral memory bias, and persistence or stickiness of negative mind states. Current measures of rumination, most-often self-reports, do not capture these different aspects of ruminative tendencies, and therefore are limited in providing detailed information about the mechanisms of mindfulness. Methods: we developed new insight into the potential mechanisms of rumination, based on three model-based metrics of free recall dynamics. These three measures reflect the patterns of memory retrieval of valenced information: the probability of first recall (Pstart) which represents initial affective bias, the probability of staying with the same valence category rather than switching, which indicates strength of positive or negative association networks (Pstay), and probability of stopping (Pstop) or ending recall within a given valence, which indicates persistence or stickiness of a mind state. We investigated the effects of Mindfulness-Based Cognitive Therapy (MBCT; N = 29) vs. wait-list control (N = 23) on these recall dynamics in a randomized controlled trial in individuals with recurrent depression. Participants completed a standard laboratory stressor, the Trier Social Stress Test, to induce negative mood and activate ruminative tendencies. Following that, participants completed a free recall task consisting of three word lists. This assessment was conducted both before and after treatment or wait-list. Results: while MBCT participant’s Pstart remained relatively stable, controls showed multiple indications of depression-related deterioration toward more negative and less positive bias. Following the intervention, MBCT participants decreased in their tendency to sustain trains of negative words and increased their tendency to sustain trains of positive words. Conversely, controls showed the opposite tendency: controls stayed in trains of negative words for longer, and stayed in trains of positive words for less time relative to pre-intervention scores. MBCT participants tended to stop recall less often with negative words, which indicates less persistence or stickiness of negatively valenced mental context. Conclusion: MBCT participants showed a decrease in patterns that may perpetuate rumination on all three types of recall dynamics (Pstart, Pstay, and Pstop), compared to controls. MBCT may weaken the strength of self-perpetuating negative associations networks that are responsible for the persistent and “sticky” negative mind states observed in depression, and increase the positive associations that are lacking in depression. This study also offers a novel, objective method of measuring several indices of ruminative tendencies indicative of the underlying mechanisms of rumination.
Threat(s) and conformity deconstructed: Perceived threat of infectious disease and its implications for conformist attitudes and behavior

Threat has been linked to conformity, but little is known about the specific effects of different kinds of threat. We test the hypothesis that perceived threat of infectious disease exerts a unique influence on conformist attitudes and behavior. Correlational and experimental results support the hypothesis. Individual differences in Perceived Vulnerability to Disease predict conformist attitudes; these effects persist when controlling for individual differences in the Belief in a Dangerous World. Experimentally manipulated salience of disease threat produced stronger conformist attitudes and behavior, compared with control conditions (including a condition in which disease-irrelevant threats were salient). Additional results suggest that these effects may be especially pronounced in specific domains of normative behavior that are especially pertinent to pathogen transmission. These results have implications for understanding the antecedents of conformity, the psychology of threat, and the social consequences of infectious disease. Copyright © 2011 John Wiley & Sons, Ltd.
Inhibitor-2 induced M-phase arrest in Xenopus cycling egg extracts is dependent on MAPK activation

The evolutionarily-conserved protein phosphatase 1 (PP1) plays a central role in dephosphorylation of phosphoproteins during the M phase of the cell cycle. We demonstrate here that the PP1 inhibitor inhibitor-2 protein (Inh-2) induces an M-phase arrest in Xenopus cycling egg extracts. Interestingly, the characteristics of this M-phase arrest are similar to those of mitogen-activated protein kinase (p42MAPK)-induced M-phase arrest. This prompted us to investigate whether Inh-2-induced M-phase arrest was dependent on activation of the p42MAPK pathway. We demonstrate here that MAPK activity is required for Inh-2-induced M-phase arrest, as inhibition of MAPK by PD98059 allowed cycling extracts to exit M phase, despite the presence of Inh-2. We next investigated whether Inh-2 phosphorylation by the MAPK pathway was required to induce an M-phase arrest. We discovered that while p90Rsk (a MAPK protein required for M-phase arrest) is able to phosphorylate Inh-2, this phosphorylation is not required for Inh-2 function. Overall, our results suggest a novel mechanism linking p42MAPK and PP1 pathways during M phase of the cell cycle.
R/qtl: QTL Mapping in Experimental Crosses

SUMMARY R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines. It is implemented as an add-on package for the freely-available statistical software, R, and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two-QTL genome scans by multiple methods, with the possible inclusion of covariates. AVAILABILITY The package is freely available at http://www.biostat. jhsph.edu/~kbroman/qtl.
Segmenting Neuronal Growth Cones Using Deep Convolutional Neural Networks

Connections form between neurons during neural development guided by growth cones, highly dynamic structures at the tips of growing axons. Understanding the biological mechanisms underlying this guidance requires understanding the dynamic morphology of growth cones, and this requires the segmentation of growth cone outlines from potentially very long timelapse movies. Previous approaches to this problem have been based either on time-consuming human input, or on algorithms customised for specific datasets. Here we evaluate the effectiveness of deep convolutional neural networks (CNNs) for growth cone segmentation. First, we apply a deep CNN to a standard benchmark cell nuclei segmentation problem, and show that it achieves performance comparable to standard image processing techniques after training with only one image. Second, we show that the deep CNN can achieve good segmentation of a large set of phase-contrast timelapse movies of growth cones after training with only a few frames. Thus, deep CNNs provide a general method for growth cone image segmentation that is broadly applicable and require very little training.
RVX-297, a BET Bromodomain Inhibitor, Has Therapeutic Effects in Preclinical Models of Acute Inflammation and Autoimmune Disease

Bromodomain (BD) and extra-terminal domain containing proteins (BET) are chromatin adapters that bind acetylated histone marks via two tandem BDs, BD1 and BD2, to regulate gene transcription. BET proteins are involved in transcriptional reprogramming in response to inflammatory stimuli. BET BD inhibitors (BETis) that are nonselective for BD1 or BD2 have recognized anti-inflammatory properties in vitro and counter pathology in models of inflammation or autoimmune disease. Although both BD1 and BD2 bind acetylated histone residues, they may independently regulate the expression of BET-sensitive genes. Here we characterized the ability of RVX-297, a novel orally active BETi with selectivity for BD2, to modulate inflammatory processes in vitro, in vivo, and ex vivo. RVX-297 suppressed inflammatory gene expression in multiple immune cell types in culture. Mechanistically, RVX-297 displaced BET proteins from the promoters of sensitive genes and disrupted recruitment of active RNA polymerase II, a property shared with pan-BETis that nonselectively bind BET BDs. In the lipopolysaccharide model of inflammation, RVX-297 reduced proinflammatory mediators assessed in splenic gene expression and serum proteins. RVX-297 also countered pathology in three rodent models of polyarthritis: rat and mouse collagen-induced arthritis, and mouse collagen antibody–induced arthritis. Further, RVX-297 prevented murine experimental autoimmune encephalomyelitis (a model of human multiple sclerosis) disease development when administered prophylactically and reduced hallmarks of pathology when administered therapeutically. We show for the first time that a BD2-selective BETi maintains anti-inflammatory properties and is effective in preclinical models of acute inflammation and autoimmunity.
Stacks of cyclic covers of projective spaces

We define stacks of uniform cyclic covers of Brauer–Severi schemes, proving that they can be realized as quotient stacks of open subsets of representations, and compute the Picard group for the open substacks parametrizing smooth uniform cyclic covers. Moreover, we give an analogous description for stacks parametrizing triple cyclic covers of Brauer–Severi schemes of rank 1 that are not necessarily uniform, and give a presentation of the Picard group of the substacks corresponding to smooth triple cyclic covers.
Simulations of exercise and brain effects of acute exposure to carbon monoxide in normal and vascular-diseased persons

At some level, carboxyhemoglobin (COHb) due to inhalation of carbon monoxide (CO) reduces maximum exercise duration in both normal and ischemic heart patients. At high COHb levels in normal subjects, brain function is also affected and behavioral performance is impaired.These are findings from published experiments that are, due to ethical or practical considerations, incomplete in that higher or lower ranges of COHb, and exercise have not been well studied. To fill in this knowledge base, a whole-body human physiological model was used to make estimates of physiological functioning by the simulation of parametric exposures to CO and various exercise levels. Ischemic heart disease was simulated by introducing a stenosis in the left heart arterial supply. Brain blood flow was also limited by such a stenosis. To lend credibility to such estimation, the model was tested by simulating experiments from the published literature. Simulations permitted several new conclusions. Increases in COHb produced the largest decreases in exercise duration when exercise was least strenuous and when COHb was smallest. For ischemic heart disease subjects, the greatest change in exercise duration produced by COHb increase was when ischemia and COHb was smallest. Brain aerobic metabolism was unaffected until COHb exceeded 25%, unless the maximum brain blood supply was limited by a stenosis greater than 50% of normal. For higher levels of stenosis, aerobic brain metabolism was reduced for any increase in COHb level, implying that behavior would be impaired with no “threshold” for COHb.
Monotonicity Implies Strategy-Proofness For Correspondences

We show that Maskin monotone social choice correspondences on sufficiently rich domains satisfy a generalized strategy-proofness property, thus generalizing Muller and Satterthwaite''s (1977) theorem to correspondences. From the point of view of Nash implementation theory, the result yields a partial characterization of the restrictions entailed by Nash implementability. Alternatively, the result can be viewed as a possibility theorem on the dominant-strategy-implementability of monotone SCCs via set-valued mechanisms for agents who are completely ignorant about the finally selected outcome. It is shown by examples that stronger strategy-proofness properties fail easily.
Lipopolysaccharides from periodontal pathogens prime neutrophils for enhanced respiratory burst: differential effect of a synthetic lipid a precursor IVA (LA-14-PP).

When neutrophils are incubated with bacterial lipopolysaccharide (LPS), they become primed for enhanced release of superoxide anion (O2-) in response to stimulation by FMLP. We investigated the human neutrophil-priming activity of LPS from the periodontal pathogens, Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi) and Actinobacillus actinomycetemcomitans (Aa) in comparison with that of LPS from Escherichia coli (E. coli). The optimum conditions for LPS to prime neutrophils were assessed for every LPS and found to be as follows: Neutrophils were incubated with LPS in the presence of 10% heat-inactivated plasma and 1 mM EDTA at 37 degrees C for 30 min and then stimulated with 1 microM FMLP at 37 degrees C for 7 min. Under these conditions, half-maximum priming was observed at 6.2 ng/ml Pg-LPS, 45 ng/ml Pi-LPS, 1.5 ng/ml Aa-LPS and 1.5 ng/ml E. coli-LPS. The priming activity of each LPS was neutralized by polymyxin B. Anti-CD14 monoclonal antibody inhibited priming by all LPS. The priming by Aa-LPS and E. coli-LPS was inhibited by LA-14-PP, a synthetic lipid A precursor IVA, but that by Pg-LPS and Pi-LPS was not. Priming by tumor necrosis factor alpha was not affected by polymyxin B, anti-CD14 antibody or LA-14-PP. Gelation of Limulus amebocyte lysate occurred at 10 pg/ml Pg-LPS, 30 pg/ml Pi-LPS, 3 pg/ml Aa-LPS and 3 pg/ml E. coli-LPS. Thus LPS from different periodontal pathogens primed neutrophils with different efficacy. (ABSTRACT TRUNCATED AT 250 WORDS)
An Ultraconserved Element (UCE) controls homeostatic splicing of ARGLU1 mRNA

Abstract Arginine and Glutamate-Rich protein 1 (ARGLU1) is a protein whose function is poorly understood, but may act in both transcription and pre-mRNA splicing. We demonstrate that the ARGLU1 gene expresses at least three distinct RNA splice isoforms – a fully spliced isoform coding for the protein, an isoform containing a retained intron that is detained in the nucleus, and an isoform containing an alternative exon that targets the transcript for nonsense mediated decay. Furthermore, ARGLU1 contains a long, highly evolutionarily conserved sequence known as an Ultraconserved Element (UCE) that is within the retained intron and overlaps the alternative exon. Manipulation of the UCE, in a reporter minigene or via random mutations in the genomic context using CRISPR/Cas9, changed the splicing pattern. Further, overexpression of the ARGLU1 protein shifted the splicing of endogenous ARGLU1 mRNA, resulting in an increase in the retained intron isoform and nonsense mediated decay susceptible isoform and a decrease in the fully spliced isoform. Taken together with data showing that functional protein knockout shifts splicing toward the fully spliced isoform, our data are consistent with a model in which unproductive splicing complexes assembled at the alternative exon lead to inefficient splicing and intron retention.
Optimisation strategies in ultrasonic vibration assisted electrical discharge machining: a review

In this paper, an attempt has been made to review the literature on strategies formulated and tested in ultrasonic vibration assisted electrical discharge machining (USEDM). The strategies for optimisation of EDM performance include flushing, dimensional accuracy, cavitation, surface morphology, polluted gases and chemical effects etc have been highlighted. The major performance controllable parameters in EDM process have also been discussed in this study. The main emphasis is given on classification of USEDM process on the basis of mode of ultrasonic vibration (UV) action imparted to EDM system, which includes a tool, work piece and the dielectric medium. The ultimate purpose of this study is to generalise the variable relationships of various proposed strategies, which may be applied in industries to improve the performance of USEDM. At the end of this study, some limitations of implementing ultrasonic vibration in EDM have been discussed.