Miracle-dz/UniFAR-FTUs huggingface dataset:
Atonal and EGFR signalling orchestrate rok- and Drak-dependent adherens junction remodelling during ommatidia morphogenesis

Morphogenesis of epithelial tissues relies on the interplay between cell division, differentiation and regulated changes in cell shape, intercalation and sorting. These processes are often studied individually in relatively simple epithelia that lack the complexity found during organogenesis when these processes might all coexist simultaneously. To address this issue, we are making use of the developing fly retinal neuroepithelium. Retinal morphogenesis relies on a coordinated sequence of interdependent morphogenetic events that includes apical cell constriction, localized alignment of groups of cells and ommatidia morphogenesis coupled to neurogenesis. Here, we use live imaging to document the sequence of adherens junction (AJ) remodelling events required to generate the fly ommatidium. In this context, we demonstrate that the kinases Rok and Drak function redundantly during Myosin II-dependent cell constriction, subsequent multicellular alignment and AJ remodelling. In addition, we show that early multicellular patterning characterized by cell alignment is promoted by the conserved transcription factor Atonal (Ato). Further ommatidium patterning requires the epidermal growth factor receptor (EGFR) signalling pathway, which transcriptionally governs rok- and Drak-dependent AJ remodelling while also promoting neurogenesis. In conclusion, our work reveals an important role for Drak in regulating AJ remodelling during retinal morphogenesis. It also sheds new light on the interplay between Ato, EGFR-dependent transcription and AJ remodelling in a system in which neurogenesis is coupled with cell shape changes and regulated steps of cell intercalation.
Antibody response to Pseudomonas aeruginosa in cystic fibrosis patients: A marker of therapeutic success?—A 30‐year Cohort study of survival in Danish CF patients after onset of chronic P. aeruginosa lung infection

We studied the effects of increasingly intensive treatment regimens on anti‐pseudomonal antibody response and survival in five successive cohorts of a total of 157 Danish cystic fibrosis patients after they had acquired chronic P. aeruginosa lung infection. The time periods were 1971–1975 (N = 21), 1976–1980 (N = 64), 1981–1986 (N = 27), 1987–1993 (N = 26), and 1994–2000 (N = 19). During this 30‐year period, we introduced elective 2‐week courses of chemotherapy every third month in all chronically infected patients, early aggressive treatment with inhalation of colistin and oral ciprofloxacin for 3 months whenever P. aeruginosa was cultured in sputum from noncolonized patients, and inhalation of recombinant human dornase alfa. There was a significant correlation between the calendar year when chronic P. aeruginosa infection was acquired and the subsequent increase in the level of precipitins (P < 0.00001). The median number of precipitins increased by 5 per year in the oldest calendar year cohort, and 1 per year in the youngest. The median age of onset of chronic P. aeruginosa increased from 9.3 years from 1981–1986 to 13.8 years from 1987–2000. Survival after acquisition of chronic P. aeruginosa lung infection improved with time (P = 0.008). Our study shows that CF patients who are treated intensively have lower antibody responses and longer survival after acquisition of chronic P. aeruginosa lung infection. Pediatr Pulmonol. 2004; 37:427–432. © 2004 Wiely‐Liss, Inc.
Feedback Processes : A Theoretical Perspective

I review the evidence for the importance of feedback from massive stars at small and large scales. The feedback mechanisms include accretion luminosity, ionizing radiation, collimated outflows, and stellar winds. The good news is that feedback doesn’t entirely prevent the formation of massive stars, while the bad news is that we don’t know what does limit their masses. Feedback from massive stars also influences their surroundings. I argue that this does not produce a triggering efficiency above unity, nor does it prevent lots of prompt star formation in GMCs, though it may preserve massive remnants of the clouds for many dynamical times. 1. Small Scale Feedback and the Upper Mass Limit Massive stars influence their surroundings through a wide variety of feedback mechanisms. Their ionizing radiation (e.g., Vacca, Garmany, & Shull 1996) and line-driven winds (Castor, Abbott, & Klein 1975) have been known for many years, while only more recently have collimated jets and wide-angle outflows been observed from young, massive stars (e.g., Beuther & Shepherd 2005). The initial mass function for stars above a solar mass or so follows a power law with slope -2.35 (Salpeter 1955) up to an upper cutoff mass of mup ∼ 100 M⊙ (Figer 2005). The two most favored ideas currently for what determines the slope of the IMF are turbulent fragmentation of the parent cloud (Padoan et al. 2007) or competitive accretion (Bonnell & Bate 2006). What determines the value of the cutoff mass mup remains unknown. Limitation of accretion by increasingly strong feedback in increasingly massive stars remains a viable candidate mechanism (Zinnecker & Yorke 2007). In fact, the limitation of accretion by radiative feedback had long been a severe problem in theories of massive star formation, because in models of spherically symmetric accretion, radiation pressure on standard interstellar dust prevents accretion on to stars with mass M > 30 M⊙ (Wolfire & Cassinelli 1987). However, recent models have called this conclusion into question because of better treatment of dust properties, non-spherical accretion, and the high accretion rates expected in high pressure cores (e.g., McKee & Tan 2003) such as those that have been identified by the Midcourse Space Experiment and Spitzer Space Telescope (Shirley et al. 2003). also Insitut für Theoretische Astrophysik, Zentrum für Astronomie der Universität Heidelberg, and Max-Planck-Insitut für Astronomie
List of Numerical Productivity Measures

1 List of Numerical Productivity Measures "* Refereed papers submitted but not yet published: 2 "* Refereed papers published: 7 "* Unrefereed reports and articles: 2 "* Books or parts thereof submitted but not yet published: 0 . "* Books or parts thereof published: 0 2 . ' 992 "* Patents filed but not yet granted: 0 "* Patents granted (include software copyrights): 0 "* Invited presentations: 12 "* Contributed presentations: 0 "* Honors received : 1 (Drew McDermott was Conference Chair of the First International Conference on Al Planning Systems) "* Prizes or awards received (Nobel, Japan, Turing, etc.): also include descriptions of the specific prizes. 0
Angiotensin II 1 receptor-mediated contraction of pulmonary artery and its modulation by prolylcarboxypeptidase.

To determine the subtype of angiotensin II (ANG II) receptor involved in the contraction of pulmonary artery and to elucidate its possible modulation by endogenous peptidases, we studied canine isolated pulmonary arterial rings under isometric conditions in vitro. Addition of ANG II caused a concentration-dependent contraction, an effect that was not altered by the ANG II 2 receptor antagonist EXP655 but was depressed by the ANG II 1 receptor antagonist DuP 753 so that the ANG II response curves were displaced to higher concentration by 1.5-2.0 log U (P < 0.001). Pretreatment of tissues with the prolylcarboxypeptidase (PCP) inhibitor p-methylphenyl sulfonyl-fluoride potentiated the ANG II-induced contraction, with the concentration required to produce a half-maximal effect of ANG II being decreased from 4.1 +/- 0.9 x 10(-9) to 3.8 +/- 0.5 x 10(-10) M (P < 0.001), whereas other peptidase inhibitors such as p-chloromercuriphenyl sulfonic acid, amastatin, and phosphoramidon had no effect. The p-methylphenyl sulfonylfluoride-induced potentiation was abolished by the removal of endothelium, but it was still observed in the presence of NG-nitro-L-arginine methyl ester in the endothelium-intact tissues. The PCP activity in the tissues was reduced by the removal of endothelium from 645 +/- 88 to 91 +/- 29 nmol.mg protein-1.h-1 (P < 0.001), and cultured endothelium had the activity of 404 +/- 39 nmol.mg protein-1.h-1. These results suggest that ANG II contracts pulmonary artery via ANG II 1 receptor and that PCP localized to the endothelium may have a modulatory role in the ANG II-induced pulmonary vasoconstriction.
A new mechanism for albuminuria-induced podocyte injury.

A large body of evidence describes the relationship between albuminuria and progressive renal damage. [1][1]–[3][2] Podocyte injury contributes to progressive albuminuria in diabetic and nondiabetic glomerular diseases, with antiproteinuric regimens providing a renoprotective effect. [4][3]–[6][4
Children's Social and Cognitive Development and Child-Care Quality: Testing for Differential Associations Related to Poverty, Gender, or Ethnicity

Secondary data analysis of data from 3 large child-care studies was conducted to address questions about whether factors such as poverty, minority ethnic background, gender, or parental authoritarian beliefs moderate the association between child-care quality and child cognitive and social outcomes. Data (N = 1,307) were combined to accrue a sufficient number of children who attended high-quality child-care centers who were from impoverished families or minority ethnic backgrounds to reliably compare their developmental outcomes with those of children in poorer quality care. Children's behavior, language skills, and preacademic skills were analyzed as a function of child-care quality (low-, medium-, and high-quality groups based on the Early Childhood Environment Rating Scale total scores), background risk factors, and parental attitudes to test hypotheses about risk and protective factors. Results provide further support for the hypothesis that quality of child care is related to children's development for all children and quite limited support that child-care quality may matter more for children experiencing social risk factors. Language development was the only outcome in which child-care quality interacted with a risk variable, ethnicity, suggesting that quality of care is differentially more important for language development for children of color than for White-non-Hispanic children.
More on Hamiltonicity of Claw-and Net-Free Graphs

An st-path is a path with the end-vertices s and t. An s-path is a path with an end-vertex s. The results of this paper include necessary and sufficient conditions for a {claw, net}-free graph G with s, t ∈ V (G) and e ∈ E(G) to have (1) Hamiltonian s-path, (2) a Hamiltonian st–path, (3) a Hamiltonian sand st-paths containing e when G has connectivity one, and (4) a Hamiltonian cycle containing e when G is 2–connected. These results imply that a connected {claw, net}-free graph has a Hamiltonian path and a 2–connected {claw, net}-free graph has a Hamiltonian cycle [3]. Our proofs of (1)−(4) are shorter than the proofs of their corollaries in [3], and provide polynomial-time algorithms for solving the corresponding Hamiltonicity problems.
Vectorization of thick digital lines using Farey sequence and geometric refinement

A novel algorithm for vectorization of line-shaped objects present in a gray-scale image is proposed. The algorithm derives the straight edges of maximal length from the object boundary using the notion of Farey sequence, and subsequently vectorizes them by an efficient technique of geometric refinement. The method would be computationally attractive when vectorization of a large database of grayscale images is in question. Experimental results on several datasets including road maps demonstrate the usefulness, efficiency, and elegance of the proposed algorithm.
Improving Ray Tracing Precision by Object Space Intersection Computation

Instead of computing intersections along a ray, an algorithm is proposed that determines a point of intersection in object space. The method is based on the classical refinement of a hierarchy of axis-aligned bounding boxes that is computed on the fly. Typical rendering artifacts are avoided by taking into consideration the precision of floating point arithmetic. In addition the method lends itself to a simple solution of the self-intersection problem. Considering the obtained precision the algorithm is efficient, simple to use, and to implement
Predictors and indicators of work status after traumatic brain injury: A meta-analysis

Abstract Heterogeneity of studies reporting data about predictive and indicative variables of return to work after traumatic brain injury led to a lack of clarity and reliability. A meta-analysis was performed to integrate and organise the results of studies reporting data about the relation between variables that are conceptually meaningful in rehabilitation and a dichotomous criteria of work status: employed or unemployed. The large quantity of variables were grouped chronologically according pre-, peri and post-traumatic phases. The results indicate that the highest and most reliable correlations were between unemployment and executive dysfunctions, emotional disturbances, deficits in activities of daily living, and less vocational rehabilitation services. Other variables, such as anosmia and post-coma activity level, show high correlations but are still to be corroborated.
Children's Social Interaction with Older, Younger, and Same-Age Peers

Characteristics of children's social interaction with younger, older, and same-age peers are explored in this review in an attempt to discover those behaviours that are more likely than others to occur in different relative-age partnerships. It is hypothesized that symmetric behaviour functions (e.g., friendship) are most commonly seen in the interaction of children of similar ages, whilst asymmetric functions (e.g., leadership) are most frequent in interactions between individuals of different ages. It is, indeed, apparent that friendships most commonly occur between individuals of similar ages. Aggression occurs primarily with age-mates, but is also frequently directed toward younger peers. Some types of prosocial behaviour (e.g., nurturance, prosocial dominance, helping) are more frequently displayed with younger peers than with age-mates, while behaviours associated with fairness and morality may be more prevalent in the interaction of age-mates. Instruction and leadership behaviours are most frequently displayed by older children interacting with younger peers. The interactions of children who differ in developmental status thus differ from those between age-mates, and may have different implications for child socialization.
Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform

Unprecedented production of short reads from the new high-throughput sequencers has posed challenges to align short reads to reference genomes with high sensitivity and high speed. Many CPU-based short read aligners have been developed to address this challenge. Among them, one popular approach is the seed-and-extend heuristic. For this heuristic, the first and foremost step is to generate seeds between the input reads and the reference genome, where hash tables are the most frequently used data structure. However, hash tables are memory-consuming, making it not well-suited to memory-stringent many-core architectures, like GPUs, even though they usually have a nearly constant query time complexity. The Burrows-Wheeler transform (BWT) provides a memory-efficient alternative, which has the drawback of having query time complexity as a function of query length. In this paper, we investigate GPU-based fixed-length seed generation for computational genomics based on the BWT and Ferragina Manzini (FM)-index, where k-mers from the reads are searched against a reference genome (indexed using BWT) to find k-mer matches (i.e. seeds). In addition to exact matches, mismatches are allowed at any position within a seed, different from spaced seeds that only allow mismatches at predefined positions. By evaluating the relative performance of our GPU version to an equivalent CPU version, we intend to provide some useful guidance for the development of GPU-based seed generators for aligners based on the seed-and-extend paradigm.
In Vitro and in Vivo Activities of T-705 and Oseltamivir against Influenza Virus

T-705 (6-fluoro-3-hydroxy-2-pyrazinecarboxamide) has a potent and selective inhibitory activity against influenza virus. We studied the effects of an infectious dose on the anti-influenza virus activities of T-705 and oseltamivir, a commercially available neuraminidase inhibitor, both in vitro and in vivo. Plaque formation of influenza A/PR/8/34 virus was completely inhibited by 10 μg/ml of T-705 after 72 h incubation, whereas visible plaque formation was detected in the plate treated with GS 4071, the active form of oseltamivir (10 μg/ml). The antiviral activity of T-705 was not influenced by an increase in multiplicity of infection (MOI) from 0.0001 to 1, but that of GS 4071 was influenced in a yield reduction assay. No increase in viral yield was seen in either culture supernatant or cells after removal of T-705 (10 μg/ml) but, in contrast, productive infection recurred in culture supernatant and in cells after removal of GS 4071. In mice infected with a high challenge dose of influenza A/PR/8/34 virus, orally administered T-705 (200 and 400 mg/kg/day) completely prevented the death of mice and the survival rates of mice were significantly higher than those in mice treated with oseltamivir (P<0.01). When the treatment was delayed at 1, 13 and 25 h post infection, oral administration of 200 mg/kg of T-705 significantly prevented the death of mice (P<0.01), and the survival rates of mice treated with T-705 were comparable to those of mice treated with oseltamivir. These results suggest that T-705 has the potential to be a potent inhibitor of human influenza virus infections.
Self-Concept, Self-Regulation, and Psychological Vulnerability

This special issue is an outgrowth of a two-day workshop which was organized and chaired by Carolyn Morf and Walter Mischel and supported by the National Institute of Mental Health (NIMH) in June of 2000. Because self-regulatory processes are intimately linked to a wide range of mental health issues, NIMH has a long history of supporting research on the many components of adaptive and maladaptive self-regulation. However, the various components have not been broadly integrated or synthesized. Thus, the workshop extended an invitation to a set of distinguished researchers who study self and self-regulation from a variety of different perspectives to seek an increasingly integrative ``cumulative science’’ conceptual framework for understanding how various aspects (cognition, emotion, interpersonal, social) of the self-system interact in self-regulation to in ̄uence psychological health and vulnerability. Research on the self and self-regulation has recently been thriving, if not exploding, illuminating many of the basic underlying mechanisms and processes that enable and drive self-regulation. As a result, numerous mini-theories have emerged regarding the various processes involved. Although these perspectives often overlap conceptually, relatively little attention has been directed at understanding how they interrelate. Thus, integration at the level of basic processes was one goal motivating the special conference. A second goal was to address the implications of self-regulation for mental health. Basic work on effective self-regulationÐparticularly on the dif®culties and failures of self-regulationÐhas the potential to inform mental health issues and policies. At this juncture, however, the speci®c relationships between regulatory processes and mental health outcomes have not been fully explored. The conference aimed to explore in depth the implications of these processes for the development and maintenance of psychological vulnerability and resilience. Rigorous scienti®c research typically demands a focus on highly speci®c processes and sub-processes, leading researchers to attend more to subtle ®ne-grained differences among research programs than to broader underlying similarities and Self and Identity, 1: 103– 104, 2002 Copyright # 2002 Psychology Press 1529-8868 /2002 $12.00 + . 00
User-level fairness delivered: Network resource allocation for adaptive video streaming

HTTP adaptive streaming (HAS) technology is becoming a popular vehicle for online video delivery. HAS applications often compete for network resources without any coordination between each other in a shared network. This leads to quality of experience (QoE) fluctuations and unfairness between end users. This paper introduces a user-level fairness model (UF) which exploits video quality, switching impact and cost efficiency as the fairness metrics to achieve user-level fairness in resource allocation. Experimental results demonstrate how this model is a foundation to orchestrate the resource consumption of HAS streams.
Neural and Behavioral Correlates of Aberrant Salience in Individuals at Risk for Psychosis

The “aberrant salience” model proposes that psychotic symptoms first emerge when chaotic brain dopamine transmission leads to the attribution of significance to stimuli that would normally be considered irrelevant. This is thought to occur during the prodromal phase of psychotic disorders, but this prediction has not been tested previously. In the present study, we tested this model in 18 healthy volunteers and 18 unmedicated individuals at ultra-high risk of psychosis. Subjects performed the Salience Attribution Test, which provides behavioral measures of adaptive and aberrant motivational salience, during functional magnetic resonance imaging to assess neural responses to relevant and irrelevant stimulus features. On a separate occasion, the same subjects were also studied with [18F]fluorodopa positron emission tomography to measure dopamine synthesis capacity. Individuals at ultra-high risk of psychosis were more likely to attribute motivational salience to irrelevant stimulus features (t(26.7) = 2.8, P = . 008), and this bias was related to the severity of their delusion-like symptoms (r = .62, P = .008). Ventral striatal responses to irrelevant stimulus features were also correlated with delusion-like symptoms in the ultra-high risk group (r = .59, P = .017). Striatal dopamine synthesis capacity correlated negatively with hippocampal responses to irrelevant stimulus features in ultra-high risk individuals, but this relationship was positive in controls. These data are consistent with the hypothesis that aberrant salience processing underlies psychotic symptoms and involves functional alterations in the striatum, hippocampus, and the subcortical dopamine system.