Miracle-dz/UniFAR-FTUs huggingface dataset:
Returning incidental findings from genetic research to children: views of parents of children affected by rare diseases

Purpose To explore parental perceptions and experiences regarding the return of genomic incidental research findings in children with rare diseases. Methods Parents of children affected by various rare diseases were invited to participate in focus groups or individual telephone interviews in Montreal and Ottawa. Fifteen participants were interviewed and transcriptions were analysed using thematic analysis. Results Four emergent themes underscored parental enthusiasm for receiving incidental findings concerning their child's health: (1) right to information; (2) perceived benefits and risks; (3) communication practicalities: who, when, and how; and (4) service needs to promote the communication of incidental findings. Parents believed they should be made aware of all results pertaining to their child's health status, and that they are responsible for transmitting this information to their child, irrespective of disease severity. Despite potential negative consequences, respondents generally perceived a favourable risk-benefit ratio in receiving all incidental findings. Conclusions Understanding how parents assess the risks and benefits of returning incidental findings is essential to genomic research applications in paediatric medicine. The authors believe the study findings will contribute to establishing future best practices, although further research is needed to evaluate the impact of parental decisions on themselves and their child.
Uncertainty in the global oceanic CO2 uptake induced by wind forcing: Quantification and spatial analysis

Abstract. The calculation of the air–water CO2 exchange (FCO2) in the ocean not only depends on the gradient in CO2 partial pressure at the air–water interface but also on the parameterization of the gas exchange transfer velocity (k) and the choice of wind product. Here, we present regional and global-scale quantifications of the uncertainty in FCO2 induced by several widely used k formulations and four wind speed data products (CCMP, ERA, NCEP1 and NCEP2). The analysis is performed at a 1° × 1° resolution using the sea surface pCO2 climatology generated by Landschutzer et al. (2015a) for the 1991–2011 period, while the regional assessment relies on the segmentation proposed by the Regional Carbon Cycle Assessment and Processes (RECCAP) project. First, we use k formulations derived from the global 14C inventory relying on a quadratic relationship between k and wind speed (k = c ⋅ U102; Sweeney et al., 2007; Takahashi et al., 2009; Wanninkhof, 2014), where c is a calibration coefficient and U10 is the wind speed measured 10 m above the surface. Our results show that the range of global FCO2, calculated with these k relationships, diverge by 12 % when using CCMP, ERA or NCEP1. Due to differences in the regional wind patterns, regional discrepancies in FCO2 are more pronounced than global. These global and regional differences significantly increase when using NCEP2 or other k formulations which include earlier relationships (i.e., Wanninkhof, 1992; Wanninkhof et al., 2009) as well as numerous local and regional parameterizations derived experimentally. To minimize uncertainties associated with the choice of wind product, it is possible to recalculate the coefficient c globally (hereafter called c∗) for a given wind product and its spatio-temporal resolution, in order to match the last evaluation of the global k value. We thus performed these recalculations for each wind product at the resolution and time period of our study but the resulting global FCO2 estimates still diverge by 10 %. These results also reveal that the Equatorial Pacific, the North Atlantic and the Southern Ocean are the regions in which the choice of wind product will most strongly affect the estimation of the FCO2, even when using c∗.
Gene Expression Profiling of Multiple Histone Deacetylase ( HDAC ) Inhibitors : Defining a Common Gene Set Produced by HDAC Inhibition in T 24 and MDA Carcinoma Cell Lines

Acetylation of histones in chromatin is one mechanism involved in the regulation of gene transcription and is tightly controlled by the balance of acetyltransferase and deacetylase (HDAC) activities. In cancer, some genes are repressed by the inappropriate recruitment of HDACs, e.g., tumor suppressor genes. To understand the genomic effects of HDAC inhibition on gene transcription we studied the gene expression profiles of T24 bladder and MDA breast carcinoma cells treated with three HDAC inhibitors, suberoylanilide hydroxamic acid, trichostatin A, and MS-27-275. The gene expression profiles of the HDAC inhibitors were generally similar to one another and differed substantially from those produced by structurally related inactive analogues; consequently, the changes in gene expression are mechanism-based. Hierarchical clustering of expression profiles demonstrated a greater similarity between the two hydroxamate-containing inhibitors (suberoylanilide hydroxamic acid and trichostatin A) than with MS-27275. This difference was also supported by cell phenotypic experiments. As many genes were downregulated as up-regulated by HDAC inhibitor treatment. Comparison of the data sets defined a common (“core”) set of 13 genes regulated by all of the HDAC inhibitors in three cell lines, 8 up-regulated and 5 down-regulated. Ten of 13 genes were confirmed in dose response studies in T24 cells by quantitativePCR. The core regulated genes are involved predominantly in cell cycle/apoptosis and DNA synthesis in response to HDAC inhibitors. These data will aide in understanding the complex set of events in cells in response to chromatin remodeling induced by HDAC inhibition, which may be responsible for antitumor effects.
Static Bug Detection Through Analysis of Inconsistent Clones

Existing software systems contain a significant amount of duplicated code. Such redundancy can negatively impact program correctness, since inconsistent updates to duplicated code fragments are prone to introduce subtle bugs. This paper outlines our work-in-progress to statically detect inconsistencies in duplicated code fragments in order to find clone-related bugs. We illustrate the problem of clone related bugs with the example of such a bug in Eclipse, outline our algorithm for detecting inconsistencies in clones and report initial experiences from an industrial case study conducted with the Munich Re Group.
Metformin normalizes endothelial function by suppressing vasoconstrictor prostanoids in mesenteric arteries from OLETF rats, a model of type 2 diabetes.

We previously reported that in mesenteric arteries from aged Otsuka Long-Evans Tokushima fatty (OLETF) rats (a type 2 diabetes model) endothelium-derived hyperpolarizing factor (EDHF)-type relaxation is impaired while endothelium-derived contracting factor (EDCF)-mediated contraction is enhanced (Matsumoto T, Kakami M, Noguchi E, Kobayashi T, Kamata K. Am J Physiol Heart Circ Physiol 293: H1480-H1490, 2007). Here we investigated whether acute and/or chronic treatment with metformin might improve this imbalance between the effects of the above endothelium-derived factors in mesenteric arteries isolated from OLETF rats. In acute studies on OLETF mesenteric arteries, ACh-induced relaxation was impaired and the relaxation became weaker at high ACh concentrations. Both metformin and 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranoside [AICAR, an AMP-activated protein kinase (AMPK) activator that is also activated by metformin] 1) diminished the tendency for the relaxation to reverse at high ACh concentrations and 2) suppressed both ACh-induced EDCF-mediated contraction and ACh-stimulated production of prostanoids (thromboxane A2 and PGE2). In studies on OLETF arteries from chronically treated animals, metformin treatment (300 mg.kg(-1). day(-1) for 4 wk) 1) improved ACh-induced nitric oxide- or EDHF-mediated relaxation and cyclooxygenase (COX)-mediated contraction, 2) reduced EDCF-mediated contraction, 3) suppressed production of prostanoids, and 4) reduced superoxide generation. Metformin did not alter the protein expressions of endothelial nitric oxide synthase (eNOS), phospho-eNOS (Ser1177), or COX-1, but it increased COX-2 protein. These results suggest that metformin improves endothelial functions in OLETF mesenteric arteries by suppressing vasoconstrictor prostanoids and by reducing oxidative stress. Our data suggest that within the timescale studied here, metformin improves endothelial function through this direct mechanism, rather than by improving metabolic abnormalities.
Efficient evaluation of right-, left-, and multi-linear rules

We present an algorithm for the efficient evaluation of a useful subset of recursive queries. Like the magic sets transformation, the algorithm consists of a rewriting phase followed by semi-naive bottom-up evaluation of the resulting rules. We prove that on a wide range of recursions, this algorithm achieves a factor of &Ogr;(n) speedup over magic sets. Intuitively, the transformations in this algorithm achieve their performance by reducing the arity of the recursive predicates in the transformed rules.
THUNDERSTORM INDUCED GRAVITY WAVES AS A POTENTIAL HAZARD TO COMMERCIAL AIRCRAFT

tables, and brief excerpts from this work in scientific and educational works is hereby granted provided that the source is acknowledged. Any use of material in this work that is determined to be “fair use” under Section 107 of the U.S. Copyright Act or that satisfies the conditions specified in Section 108 of the U.S. Copyright Act (17 USC §108, as revised by P.L. 94-553) does not require the AMS’s permission. Republication, systematic reproduction, posting in electronic form on servers, or other uses of this material, except as exempted by the above statement, requires written permission or a license from the AMS. Additional details are provided in the AMS CopyrightPolicy, available on the AMS Web site located at (http://www.ametsoc.org/AMS) or from the AMS at 617-227-2425 or copyright@ametsoc.org.
eference values for lead , cadmium and mercury in the blood of adults from the etropolitan area of Sao Paulo , Brazil

Human biomonitoring is an important tool for the evaluation of environmental exposure to contaminants. The data that are obtained from these studies might be compared to appropriate reference values (RVs) in a specific population. The RVs were derived from the rounded values of the upper limit of the 95th confidence interval of the 95th percentile for lead (Pb), cadmium (Cd) and mercury (Hg) in blood from adults in the metropolitan area of Sao Paulo (MASP), Brazil to investigate the association between blood metals and sociodemographic and lifestyle factors. Blood samples from 653 nonsmoking blood donors without occupational exposure to the studied metals were collected in 2006. Our evaluations distinguished a younger group (18–39 years) and an older group (40–65 years). RVs in the younger group were 60 g Pb/L and 4 g Hg/L for men and 47 g Pb/L and 4 g Hg/L for women. RVs in the older group were 80 g Pb/L and 5 g Hg/L for men and 63 g Pb/L and 6 g Hg/L for women. The RV for Cd was nvironmental quality nvironmental health 0.6 g/L for adults aged 18–65 years. Pb and Cd levels demonstrated a significant association with sex and age. Male blood contained 50% more Pb, and the older group exhibited 23% more Pb. Fish consumption and amalgam fillings were primarily related to Hg levels. RVs for lead were similar to the Czech Republic and Germany but higher than the US population. The RV for Cd in Brazil was well below the RVs of these countries. The RVs for Hg in Brazil were similar to the US but higher than Germany and the Czech Republic.
In Search of Mechanisms. Conducting a Critical Realist Data Analysis

Critical realism has emerged as an alternative to positivist and interpretive research during the past decade. Yet, the number of empirical studies based on this perspective has so far been limited. This indicates a need for a more explicit method for critical realist data analysis. To address this, we extend former research on critical realist methodology by presenting a framework for identifying and understanding causal structures in critical realist studies, termed mechanisms. The framework consists of steps involved in identifying structural components of a mechanism, how these components interact to produce to an outcome, and contextual influences on this outcome. We illustrate the application of the framework through an example of the identification of IS innovation mechanisms in a case study in the airline industry. Overall, we argue that the mechanism approach can improve empirical studies in the IS field, by providing ontological depth, creative thinking and more precise explanations.
Does oxidative stress modulate limb muscle atrophy in severe COPD patients?

Oxidative stress may differentially regulate protein loss within peripheral muscles of severe chronic obstructive pulmonary disease (COPD) patients exhibiting different body composition. Oxidation levels of proteins, myosin heavy chain (MyHC) and myonuclei, superoxide anion, antioxidants, actin, creatine kinase, carbonic anhydrase-3, ubiquitin–proteasome system, redox-signalling pathways, inflammation and muscle structure, and damage were quantified in limb muscles of severe COPD patients with and without muscle wasting, and in sedentary controls. Compared with controls, in the quadriceps of muscle-wasted COPD patients, levels of protein carbonylation, oxidation of MyHC and myonuclei, superoxide anion production, superoxide dismutase, total protein ubiquinitation, E214k, atrogin-1, FoxO1 and p65 were higher, while content of MyHC, creatine kinase, carbonic anhydrase-3, myogenin, and fast-twitch fibre size were decreased. Importantly, in nonwasted COPD patients, where MyHC was more oxidised than in controls, its content was preserved. Muscle inflammation and glutathione levels did not differ between patients and controls. In all patients, muscle structure abnormalities were increased, while muscle force and exercise capacity were reduced. In severe COPD, while muscle oxidative stress increases regardless of their body composition, protein ubiquitination and loss of MyHC were enhanced only in patients exhibiting muscle atrophy. Oxidative stress does not seem to directly modulate muscle protein loss in these patients.
Improving contextual advertising by adopting collaborative filtering

Contextual advertising can be viewed as an information filtering task aimed at selecting suitable ads to be suggested to the final “user”, that is, the Web page in hand. Starting from this insight, in this article we propose a novel system, which adopts a collaborative filtering approach to perform contextual advertising. In particular, given a Web page, the system relies on collaborative filtering to classify the page content and to suggest suitable ads accordingly. Useful information is extracted from “inlinks”, that is, similar pages that link to the Web page in hand. In so doing, collaborative filtering is used in a content-based setting, giving rise to a hybrid contextual advertising system. After being implemented, the system has been experimented with about 15000 Web pages extracted from the Open Directory Project. Comparative experiments with a content-based system have been performed. The corresponding results highlight that the proposed system performs better. A suitable case study is also provided to enable the reader to better understand how the system works and its effectiveness.
Outcome studies of schizoaffective disorders.

Outcome studies of schizoaffective disorder have taught us much about the long-term consequences of the syndrome, and they have provided some indication of the potential usefulness of maintaining "schizoaffective disorder" as a diagnostic category separate from schizophrenia and major affective disorder. In a review of outcome studies that compared schizoaffective patients to schizophrenic or affective patients, we found consistent results despite wide variations in diagnostic criteria, length of followup, and demographic characteristics. Global measures of outcome show that schizophrenic patients are more impaired than schizoaffective patients, who in turn are more impaired than affective patients. However, studies of specific outcome domains such as symptomatology, social functioning, and occupational functioning indicate that schizoaffective disorder is heterogeneous and that subtyping by polarity (e.g., schizoaffective-manic vs. schizoaffective-depressed) accounts for some of this variance. The consistency of these findings in the face of methodological variability suggests that it would be premature to classify schizoaffective patients with schizophrenia or affective disorder, but also that strict diagnostic criteria for schizoaffective disorder are at best preliminary and need to be thoroughly validated.
Selective induction of anti‐fibrillarin autoantibodies by silver nitrate in mice

Female SJL (H‐2s) mice developed serum IgG anti‐nucleolar antibodies (ANoA) after 5 weeks treatment with 0·05% or 0·01% silver nitrate (AgNO3) in drinking water. Five more weeks of treatment increased the ANoA titre to 3410 ± 853 and 640±175 (reciprocal mean ± s.e.m.), respectively. Controls receiving ordinary tap water and mice given 0·002% AgNO3, showed no antinucleolar antibodies. The high‐titre ANoA targeted a 34‐kD nucleolar protein identified as fibrillarin, the major autoantigen in murine mercury‐induced autoimmunity and in a fraction of patients with systemic scleroderma. Serum autoantibodies to chromatin or histones, kidney, spleen, stomach, thyroid, or skin antigens (except the nucleolus) were not found in any of the mice. There was no consistent significant increase of serum IgG1 igG2a, IgG2b, or IgG3 concentrations after AgNO3 treatment compared with controls. Mice treated with 0·05% AgNO3 for 10 weeks showed a slight decrease in serum IgG1, IgG2b and lgG3 concentrations. These mice also showed a small but statistically significant increase in renal, mesangial IgM deposits, which was not accompanied by any increase in C3c deposits, whereas mice given lower doses of silver nitrate showed no significant increase in mesangial immunoglobulin immune deposits. Systemic vessel wall immune deposits were not found in any of the mice. In mice given 0·05% silver nitrate, the kidney showed the highest concentration of silver (12·2±0·09 μg Ag/g wet weight; mean ± s.e.m.). followed by the spleen (8·7±1·3), and the liver (3·9±0·4). Treatment with 0·01% silver nitrate caused a different distribution of silver, with the highest concentration in the spleen (2·1±0·16 μg Ag/g), followed by the kidney (0·63±0·037), and the liver (< 0·29 μg Ag/g; mean). Silver seems to be a more specific inducer of antinucleolar/anti‐fibrillarin autoantibodies than mercury and gold, lacks the general immune stimulating potential of mercury, and has only a weak tendency to induce renal immune deposits. These observations suggest that the autoimmune sequelae induced in mice by metals is dependent, not only upon the genetic haplotype of the murine strain, but also on the metal under investigation.
Bioavailability and export of dissolved organic matter from a tropical river during base‐ and stormflow conditions

Concentrations, bioavailability, and export of dissolved organic matter (DOM), particulate organic matter (POM), and nutrients from the Wailuku River, Hawai'i, U.S.A. , were examined under base‐ and stormflow conditions. During storms, DOM and POM concentrations increased approximately by factors of 2 and 11, respectively, whereas NO3− concentrations decreased by a third. The organic carbon (OC) pool was dominated by dissolved OC (DOC) during baseflow conditions, whereas DOC and particulate OC contributed equally during storms. The nitrogen (N) pool was dominated by NO3− during baseflow conditions and by particulate organic N (PON) during storms. Dissolved organic N (DON) comprised a similar percentage of the N pool under base‐ and stormflow conditions. DOC and DON bioavailability both decreased by half during storms in the Wailuku River. Differences in DOM concentrations and bioavailability between base‐ and stormflow conditions suggest that DOM flowpaths to the river changed from deep to shallow, and that DOM sources switched from autochthonous to allochthonous. Although DOM bioavailability decreased during storms, calculations suggest that storms contributed >90% to the annual OC and N yields and >80% to the bioavailable DOM yield from the Wailuku River to coastal waters. Overall, our results suggest that storms are important for delivering bioavailable DOM to coastal waters, where they may stimulate primary and secondary production.
Quantifying seismic anisotropy induced by small-scale chemical heterogeneities

2-D isotropic models that exhibit a power spectrum of heterogeneities as what is expected for the Earth’s mantle, that is, varying as 1 / k , with k the wavenumber of these heterogeneities. The 1-D toy models correspond to simple layered media. In the 2-D case, our models depict marble-cake patterns in which an anomaly in shear wave velocity has been advected within convective cells. The long-wavelength equivalents of these models are computed using upscaling relations that link properties of a rapidly varying elastic medium to properties of the effective, that is, apparent, medium as seen by long-period waves. The resulting homogenized media exhibit extrinsic anisotropy and represent what would be observed in tomography. In the 1-D case, we analytically show that the level of anisotropy increases with the square of the amplitude of heterogeneities. This relation is numerically veriﬁed for both 1-D and 2-D media. In addition, we predict that 10 per cent of chemical heterogeneities in 2-D marble-cake models can induce more than 3.9 per cent of extrinsic radial S -wave anisotropy. We thus predict that a non-negligible part of the observed anisotropy in tomographic models may be the result of unmapped small-scale heterogeneities in the mantle, mainly in the form of ﬁne layering, and that caution should be taken when interpreting observed anisotropy in terms of LPO and mantle deformation. This effect may be particularly strong in the lithosphere where chemical heterogeneities are assumed to be the strongest.
Automatic Extraction of Time Expressions Accross Domains in French Narratives

The prevalence of temporal references across all types of natural language utterances makes temporal analysis a key issue in Natural Language Processing. This work adresses three research questions: 1/is temporal expression recognition specific to a particular domain? 2/if so, can we characterize domain specificity? and 3/how can subdomain specificity be integrated in a single tool for unified temporal expression extraction? Herein, we assess temporal expression recognition from documents written in French covering three domains. We present a new corpus of clinical narratives annotated for temporal expressions , and also use existing corpora in the newswire and historical domains. We show that temporal expressions can be extracted with high performance across domains (best F-measure 0.96 obtained with a CRF model on clinical narratives). We argue that domain adaptation for the extraction of temporal expressions can be done with limited efforts and should cover pre-processing as well as temporal specific tasks.