Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial coherence measurement and partially coherent diffractive imaging

The complete characterization of spatial coherence is difficult because the mutual coherence function is a complex-valued function of four independent variables. This difficulty limits the ability of controlling and optimizing spatial coherence in a broad range of key applications. Here we propose a method for measuring the complete mutual coherence function, which does not require any prior knowledge and can be scaled to measure arbitrary coherence properties for any wavelength. Our method can also be used to retrieve objects illuminated by partially coherent beam with unknown coherence properties. This study is particularly useful for coherent diffractive imaging of nanoscale structures in the X-ray or electron regime. Our method is not limited by any assumption about the illumination and hence lays the foundation for a branch of new diffractive imaging algorithms.
risk factors for chronic obstructive pulmonary disease among never-smokers in Korea

Background: Chronic obstructive pulmonary disease (COPD) patients include those who have never smoked. However, risk factors other than smoking in never-smokers have not been elucidated sufficiently. This study investigated the risk factors for COPD among never-smokers in Korea using population-based data. Methods: The data were retrieved from the Korean National Health and Nutrition Survey IV conducted from 2007 to 2009. Among subjects aged 40 years or older who underwent appropriate pulmonary function tests, never-smokers not diagnosed with asthma and not showing a restrictive pattern on pulmonary function tests were enrolled. Risk factors of COPD in never-smokers were analyzed using logistic regression models. Results: Among 24,871 participants in the representative Korean cohort, 3,473 never-smokers were enrolled. COPD patients accounted for 7.6% of the never-smokers. In the logistic regression analysis, low education status (odds ratio [OR]: 2.0; 95% confidence interval [CI]: 1.2–3.2), occupational exposure (OR: 2.6; 95% CI: 1.3–5.3), a history of tuberculosis (OR: 4.5; 95% CI: 2.3–8.7), bronchiectasis (OR: 6.0; 95% CI: 1.4–25.4), male sex (OR: 4.2; 95% CI: 2.6–6.7), advanced age (60–69 years vs 40–49 years; OR: 3.8; 95% CI: 2.0–7.0), and being underweight (body mass index  18.5 vs 18.0–24.9 kg/m 2 ; OR: 3.1; 95% CI: 1.0–9.4) were associated with the development of COPD. Conclusion: Low education status, manual labor, a history of tuberculosis and bronchiectasis, as well as male sex, advanced age and being underweight were risk factors for COPD in Korean
Remote sensing analysis of physical complexity of North Pacific Rim rivers to assist wild salmon conservation

Salmon populations are highly variable in both space and time. Accurate forecasting of the productivity of salmon stocks makes effective management and conservation of the resource extremely challenging. Furthermore, widespread and consistent data on the productivity of species‐specific and total salmon stocks in a river are almost nonexistent. Ranking rivers based on physical complexity derived from remote sensing allows rivers to be objectively compared. Our approach considered rivers with great geomorphic complexity (e.g. having expansive, multichanneled floodplains and/or on‐channel lakes) as likely to have greater productivity of salmon than rivers flowing in constrained or canyon‐bound channels. Our objective was to develop a database of landscape metrics that could be used to rank the rivers in relation to potential salmon productivity. We then examined the rankings in relation to existing empirical (monitoring) data describing productivity of salmon stocks. To extract the metrics for each river basin we used a digital elevation model and multispectral satellite imagery. We developed procedures to extract channel networks, floodplains, on‐channel lakes and other catchment features; variables such as catchment area, channel elevation, main channel length, floodplain area, and density of hydrojunctions (nodes) were measured. We processed 1509 catchments in the North Pacific Rim including the Kamchatka Peninsula in Russia and western North America. Overall, catchments were most physically complex in western Kamchatka and western Alaska, and particularly on the Arctic North Slope of Alaska. We could not directly examine coherence between potential and measured productivity except for a few rivers, but the expected relationship generally held. The resulting database and systematic ranking are objective tools that can be used to address questions about landscape structure and biological productivity at regional to continental extents, and provide a way to begin to efficiently prioritize the allocation of funding and resources towards salmon management and conservation. Copyright © 2010 John Wiley & Sons, Ltd.
Tolerance to the antimicrobial peptide colistin in Pseudomonas aeruginosa biofilms is linked to metabolically active cells, and depends on the pmr and mexAB‐oprM genes

Bacteria living as biofilm are frequently reported to exhibit inherent tolerance to antimicrobial compounds, and might therefore contribute to the persistence of infections. Antimicrobial peptides are attracting increasing interest as new potential antimicrobial therapeutics; however, little is known about potential mechanisms, which might contribute to resistance or tolerance development towards these compounds in biofilms. Here we provide evidence that a spatially distinct subpopulation of metabolically active cells in Pseudomonas aeruginosa biofilms is able to develop tolerance to the antimicrobial peptide colistin. On the contrary, biofilm cells exhibiting low metabolic activity were killed by colistin. We demonstrate that the subpopulation of metabolically active cells is able to adapt to colistin by inducing a specific adaptation mechanism mediated by the pmr operon, as well as an unspecific adaptation mechanism mediated by the mexAB‐oprM genes. Mutants defective in either pmr‐mediated lipopolysaccharide modification or in mexAB‐oprM‐mediated antimicrobial efflux were not able to develop a tolerant subpopulation in biofilms. In contrast to the observed pattern of colistin‐mediated killing in biofilms, conventional antimicrobial compounds such as ciprofloxacin and tetracycline were found to specifically kill the subpopulation of metabolically active biofilm cells, whereas the subpopulation exhibiting low metabolic activity survived the treatment. Consequently, targeting the two physiologically distinct subpopulations by combined antimicrobial treatment with either ciprofloxacin and colistin or tetracycline and colistin almost completely eradicated all biofilm cells.
Lagartos iguanios del Colhuehuapense (Mioceno Temprano) de Gaiman (provincia del Chubut, Argentina)

Resumen. Los sedimentos del Mioceno Temprano de la Formacion Sarmiento en Gaiman, provincia del Chubut (Argentina) han provisto una de las mas importantes colecciones de escamosos del Mioceno, incluyendo iguanios, teidos, boideos y colubridos. En este trabajo se describen restos fragmentarios de iguanios asignados a los actuales Pristidactylus y Liolaemus, constituyendo los registros mas antiguos para estos generos. Los cambios climaticos y ambientales ocurridos durante el Neogeno en las areas patagonicas habrian impactado diferencialmente sobre la fauna de escamosos, produciendo la retraccion en la distribucion de los teidos tupinambinos y las serpientes boideas y, contrariamente, la diversificacion de los iguanios a ambos lados de los Andes. Abstract. IGUANIAN LIZARDS FROM THE COLHUEHUAPIAN (EARLY MIOCENE) OF GAIMAN, (CHUBUT PROVINCE,ARGENTINA). The Early Miocene beds of the Sarmiento Formation at Gaiman, Chubut Province (Argentina) have provided one of the most relevant collection of Miocene squamates, including iguanians, teiids, boids, and colubrids. Fragmentary remains assigned to the extant iguanians Pristidactylus and Liolaemus are here described, representing the earliest records of these genera. Climatic and environmental changes occurred during the Neogene in Patagonian areas would have influenced differentially the squamate fauna, producing the retraction in the distribution of tupinambine teiids and boid snakes, and, in contrast, the diversification of iguanians on both sides of the Andes.
Hydrogen peroxide, organic peroxides, carbonyl compounds, and organic acids measured at Pabstthum during BERLIOZ

[1] Gas-phase H2O2, organic peroxides, carbonyl compounds, and carboxylic acids were measured from mid-July to early August 1998 during the Berlin ozone (BERLIOZ) campaign in Pabstthum, Germany. The rural site, located 50 km northwest from Berlin, was chosen to measure the pollutants downwind during a summer smog episode. The hydroperoxides showed pronounced diurnal variations with peak mixing ratios in the early afternoon. The maximum mixing ratios were 1.4 ppbv (H2O2), 0.64 ppbv (methylhydroperoxide), and 0.22 ppbv (hydroxymethyl-hydroperoxide). H2O2 was formed through photochemical activity, but originated also from vertical transport from air residing above the local inversion layer in the morning hours. Sometimes a second maximum was observed in the late afternoon-evening: This H2O2 might be formed from ozonolysis of biogenic alkenes. Ratios of H2O2/HNO3 were used as indicators for the determination of NOx-sensitive versus volatile organic compound (VOC)-sensitive regimes for photochemical production of ozone. Diurnal profiles were measured for alkanals (C2–C10), showing maximum mixing ratios decreased from C2 (0.6 ppbv) to C5 (0.1 ppbv) alkanals, which originate primarily from anthropogenic hydrocarbon degradation processes. However, higher C6, C9, and C10 alkanals show strong fluctuations (0.25, 0.17, and 0.13 ppbv, respectively), showing evidence of biogenic emissions. Both primary unsaturated carbonyl (methyl vinyl ketone, methacrolein) and secondary oxidation products of isoprene (hydroxyacetone and glycolaldehyde, up to 0.16 and 0.20 ppbv, respectively) showed excellent correlation. Diurnal profiles of glyoxal, methylglyoxal, biacetyl, benzaldehyde, and pinonaldehyde were also obtained. Formaldehyde was measured continuously by long-path DOAS and by an instrument based on the “Hantzsch” reaction; however, mixing ratios measured by DOAS (maximum 7.7 ppbv) were systematically larger by a factor of 1.3 on average, but by a factor of 1.7 during high photochemical activity. Homologous series of monocarboxylic acids were determined: Formic and acetic acid varied between 0.6 and 3.0 ppbv. The mixing ratio of the other dropped from 0.1 to 0.2 ppbv for C3 to typical 0.01 to 0.03 ppbv for C6, and from 0.01 to 0.002 ppbv for C7 to C9 monocarboxylic acids.
Development of a remotely controlled debris flow monitoring system in the Dolomites (Acquabona, Italy)

Direct measurements of the hydrological conditions for the occurrence of debris flows and of flow behaviour are of the outmost importance for developing effective flow prevention techniques. An automated and remotely controlled monitoring system was installed in Acquabona Creek in the Dolomites, Italian Eastern Alps, where debris flows occur every year. Its present configuration consists of three on‐site stations, located in the debris‐flow initiation area, in the lower channel and in the retention basin. The monitoring system is equipped with sensors for measuring rainfall, pore‐water pressure in the mobile channel bottom, ground vibrations, debris flow depth, total normal stress and fluid pore‐pressure at the base of the flow. Three video cameras take motion pictures of the events at the initiation zone, in the lower channel and in the deposition area. Data from the on‐site stations are radio‐transmitted to an off‐site station and stored in a host PC, from where they are telemetrically downloaded and used by the Padova University for the study of debris flows. The efficiency of the sensors and of the whole monitoring system has been verified by the analysis of data collected so far. Examples of these data are presented and briefly discussed. If implemented at the numerous debris‐flow sites in the Dolomitic Region, the technology used, derived from the development of this system, will provide civil defence and warn residents of impending debris flows. Copyright © 2003 John Wiley & Sons, Ltd.
Interpreting variability in global SST data using independent component analysis and principal component analysis

Component extraction techniques are used widely in the analysis and interpretation of high‐dimensional climate datasets such as global sea surface temperatures (SSTs). Principal component analysis (PCA), a frequently used component extraction technique, provides an orthogonal representation of the multivariate dataset and maximizes the variance explained by successive components. A disadvantage of PCA, however, is that the interpretability of the second and higher components may be limited. For this reason, a Varimax rotation is often applied to the PCA solution to enhance the interpretability of the components by maximizing a simple structure. An alternative rotational approach is known as independent component analysis (ICA), which finds a set of underlying ‘source signals’ which drive the multivariate ‘mixed’ dataset.
Attentional bias and attentional control in posttraumatic stress disorder

Extensive evidence exists for an association between attentional bias (AB; attentional vigilance or avoidance) and anxiety. Recent studies in healthy participants suggest that attentional control (AC) may facilitate inhibition of automatic attentional processes associated with anxiety. To investigate relationships among AC, trauma ‐ related AB, symptom severity and trait anxiety in patients with Posttraumatic Stress Disorder (PTSD), participants (N=91) completed self ‐ report measures of AC, posttraumatic stress symptoms (PTSS) and trait anxiety. AB was measured with a pictorial version of the Dot ‐ probe Test. AC moderated the relationship between PTSS and AB (threat avoidance). Patients high in PTSS and low in AC showed attentional avoidance. No significant association between PTSS and AB in patients with medium or high levels of AC was found. A similar pattern of results was observed for the relationship between trait anxiety, AC and AB. These results suggest that a low ability to control attention is a risk factor for AB in PTSD. This first clinical study corroborates the accumulating evidence from analogue studies that individual differences in top ‐ down attentional control are of considerable importance in the expression of AB in anxious psychopathology. attentional control and attentional avoidance of threat in healthy students using an emotional cueing task. However, only ACS was independently associated with avoidance (controlling for anxiety). This finding was recently replicated with an Emotional Stroop Task (EST). In a large student sample (n = 80), attentional control was found to predict threat interference as measured with the EST (Putman, Arias ‐ Garcia, Pantazi, & Van Schie, 2012b). Furthermore, results of a recent analogue study by Bardeen and Orcutt (2011) demonstrated a moderating effect of attentional control on the relationship between posttraumatic symptoms (PTSS) and attentional bias, in line with the results from the original Derryberry and Reed study. These findings suggest an important but hitherto much overlooked role for AC in attentional processes and affect regulation. However, since the participants in these studies were all unselected students, the extent to which these results generalize to patients with anxious psychopathology has yet to be determined. of a computer keyboard; color blindness. Information was collected regarding the participant’s age, living circumstances, ethnic background and trauma history. The data reported in this paper were collected at the pre ‐ treatment phase of a clinical trial for a novel treatment (Schoorl, Putman & Van Der Does, 2013). DPT data were collected for 99 patients.
HDAC and MAPK/ERK Inhibitors Cooperate to Reduce Viability and Stemness Phenotype in Medulloblastoma Running title: HDAC and MAPK/ERK in medulloblastoma

1 Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPEHCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil, 2 Children’s Cancer Institute, Porto Alegre, RS, Brazil, 3 Bioinformatics Core, Experimental Research Center, Clinical Hospital (CPE-HCPA), Porto Alegre, RS, Brazil, 4 The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada, 5 Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada, 6 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada, 7 Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada, 8 Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada, 9 Department of
Application of a lidar fluorosensor system to the continuous and remote monitoring of the Southern Ocean and Antarctic Ross Sea: Results collected during the XIII and XV Italian oceanographic campaigns

A mobile fluorosensor laboratory, including as main constituent a lidar fluorosensor apparatus for remote measurements at water surface and ancillary instruments dedicated to local analyses, was developed for extensive biooptical monitoring of the sea waters. Continuous remote and local measurements of Chl-a (Chlorophyll a) and CDOM (Chromophoric Dissolved Organic Matter) were performed during the XIII (1997/1998) and XV (1999/2000) marine campaigns in the South-western Ross Sea and along the Southern Ocean transects to New Zealand as part of the Italian Research Programme for Antarctica. Chla and CDOM fluorescence maps of the investigated areas revealed the bio-optical peculiarity of coastal zones and seasonal changes encountered.
III. Yeast sequencing reports. Sequence of the CDC10 region at chromosome III of Saccharomyces cerevisiae

A 4·74 kb DNA fragment from the right arm of chromosome III of Saccharomyces cerevisiae, adjacent to the centromere region was sequenced. Four open reading frames with an ATG initiation codon and larger than 200 bp were found in this fragment. The largest open reading frame of 966 bp was identified as the CDC10 gene.
XIV. Yeast sequencing reports. Sequence of MKT1, needed for propagation of M2 satellite dsRNA of the L‐A virus of Saccharomyces cerevisiae

MKT1 is required for maintenance of K2 above 30°C in strains with the L‐A‐HN variant of the L‐A double‐stranded RNA virus of Saccharomyces cerevisiae. We report that MKT1 encodes a 92 979 Da protein with serine‐rich regions and the retroviral protease signature, DTG, but with no substantial homology to proteins presently in the databases. This sequence is available from GenBank under Accession Number U09129.
Spatial Distribution Pattern of the Populations of Camellia japonica in Busan

The spatial distribution of geographical distances at five natural populations of Camellia japonica in Busan, Korea was studied. The four plots (Mollundae, Gadeok-do, Du-do, and Jwiseum) of C. japonica were uniformly distributed in the forest community and only one plot (Amnam-dong) was aggregately distributed in the forest community. Morisita index is related to the patchiness index showed that the plot 20 m × 50 m had an overly steep slope when the area was larger than 20 m × 20 m, which indicated that the degree of aggregation increased significantly with increasing quadrat sizes, while the patchiness indices did not change from the plot 5 m × 10 m to 10 m × 10 m. The spatial structure was quantified by Moran"s I, a coefficient of spatial autocorrelation. Ten of the significant values (76.9%) were positive, indicating similarity among individuals in the first 4 distance classes (80 m), i.e., pairs of individuals with dissimilarity characteristics can separate by more than 100 m.
Relaxed selection during a recent human expansion

Humans have colonized the planet through a series of range expansions, which deeply impacted genetic diversity in newly settled areas and potentially increased the frequency of deleterious mutations on expanding wave fronts. To test this prediction, we studied the genomic diversity of French Canadians who colonized Quebec in the 17th century. We used historical information and records from ∼4000 ascending genealogies to select individuals whose ancestors lived mostly on the colonizing wave front and individuals whose ancestors remained in the core of the settlement. Comparison of exomic diversity reveals that i) both new and low frequency variants are significantly more deleterious in front than in core individuals, ii) equally deleterious mutations are at higher frequencies in front individuals, and iii) front individuals are two times more likely to be homozygous for rare very deleterious mutations present in Europeans. These differences have emerged in the past 6-9 generations and cannot be explained by differential inbreeding, but are consistent with relaxed selection on the wave front. Modeling the evolution of rare variants allowed us to estimate their associated selection coefficients as well as front and core effective sizes. Even though range expansions had a limited impact on the overall fitness of French Canadians, they could explain the higher prevalence of recessive genetic diseases in recently settled regions. Since we show that modern human populations are experiencing differential strength of purifying selection, similar processes might have happened throughout human history, contributing to a higher mutation load in populations that have undergone spatial expansions.
Diagenetic compaction experiments on simulated anhydrite fault gouge under static conditions

Faults that crosscut subsurface CO2 storage systems offer potential leakage pathways, especially if fault reactivation and dilation occur. After reactivation, however, newly formed fault gouge is expected to gradually compact and seal as a function of time. To estimate the time scale on which this occurs, the processes that control compaction must be understood. We performed uniaxial compaction experiments on simulated anhydrite fault gouge to investigate the deformation mechanisms that operate under postslip conditions in faulted anhydrite caprocks. This involved constant stress (5–12 MPa) and stress stepping experiments (5/7.5/10 MPa) performed at 80°C, under dry and wet conditions, on fault gouge samples prepared from crushed natural anhydrite sieved into different grain size fractions in the range 20–500 µm. Dry samples showed little to no compaction creep, whereas wet samples (i.e., flooded with presaturated CaSO4 solution) showed rapid compaction. Our mechanical data and microstructural observations on wet samples suggest that for fine grain sizes (<50 µm) and low stresses, gouge compaction is controlled by diffusion‐controlled pressure solution. With increasing grain size and stress, fluid‐assisted subcritical microcracking becomes dominant. Pressurizing solution‐flooded samples with CO2 (15 MPa) led to no significant effect on compaction rates in fine‐grained material, but it decreased compaction rates in coarse samples. Since fine grain sizes are expected in reactivated faults, we infer that pressure solution will dominate in anhydrite (cap)rocks, with extrapolation of our lab data to reservoir conditions suggesting sealing time scales of a few decades.