Miracle-dz/UniFAR-FTUs huggingface dataset:
Multifunctional oxidosqualene cyclases and cytochrome P450 involved in the biosynthesis of apple fruit triterpenic acids

Summary Apple (Malus × domestica) accumulates bioactive ursane‐, oleanane‐, and lupane‐type triterpenes in its fruit cuticle, but their biosynthetic pathway is still poorly understood. We used a homology‐based approach to identify and functionally characterize two new oxidosqualene cyclases (MdOSC4 and MdOSC5) and one cytochrome P450 (CYP716A175). The gene expression patterns of these enzymes and of previously described oxidosqualene cyclases were further studied in 20 apple cultivars with contrasting triterpene profiles. MdOSC4 encodes a multifunctional oxidosqualene cyclase producing an oleanane‐type triterpene, putatively identified as germanicol, as well as β‐amyrin and lupeol, in the proportion 82 : 14 : 4. MdOSC5 cyclizes 2,3‐oxidosqualene into lupeol and β‐amyrin at a ratio of 95 : 5. CYP716A175 catalyses the C‐28 oxidation of α‐amyrin, β‐amyrin, lupeol and germanicol, producing ursolic acid, oleanolic acid, betulinic acid, and putatively morolic acid. The gene expression of MdOSC1 was linked to the concentrations of ursolic and oleanolic acid, whereas the expression of MdOSC5 was correlated with the concentrations of betulinic acid and its caffeate derivatives. Two new multifuntional triterpene synthases as well as a multifunctional triterpene C‐28 oxidase were identified in Malus × domestica. This study also suggests that MdOSC1 and MdOSC5 are key genes in apple fruit triterpene biosynthesis.
Human Disturbance Influences Reproductive Success and Growth Rate in California Sea Lions (Zalophus californianus)

The environment is currently undergoing changes at both global (e.g., climate change) and local (e.g., tourism, pollution, habitat modification) scales that have the capacity to affect the viability of animal and plant populations. Many of these changes, such as human disturbance, have an anthropogenic origin and therefore may be mitigated by management action. To do so requires an understanding of the impact of human activities and changing environmental conditions on population dynamics. We investigated the influence of human activity on important life history parameters (reproductive rate, and body condition, and growth rate of neonate pups) for California sea lions (Zalophus californianus) in the Gulf of California, Mexico. Increased human presence was associated with lower reproductive rates, which translated into reduced long-term population growth rates and suggested that human activities are a disturbance that could lead to population declines. We also observed higher body growth rates in pups with increased exposure to humans. Increased growth rates in pups may reflect a density dependent response to declining reproductive rates (e.g., decreased competition for resources). Our results highlight the potentially complex changes in life history parameters that may result from human disturbance, and their implication for population dynamics. We recommend careful monitoring of human activities in the Gulf of California and emphasize the importance of management strategies that explicitly consider the potential impact of human activities such as ecotourism on vertebrate populations.
The Elastic Analysis of Compressible Piles and Pile Groups

Synopsis The response of rigid and compressible single piles embedded in a homogeneous isotropic linear elastic medium has been obtained by a rigorous analysis based on Mindlin's solutions for a point load in the interior of an ideal elastic medium. The analytical method is described and is extended to analyse axially loaded rigid and compressible pile groups with floating caps spaced in an arbitrary manner. The results are presented as a series of graphs showing the effect of variation of the ratios of pile length to a diameter, the ratio of the modulus of elasticity of the pile to the shear modulus of the medium Ep/G and the effect of base enlargement on the load displacement characteristics of single axially loaded piles. Graphs are also presented showing the effect of length to diameter ratio, pile spacing and Ep/G ratio on the response of a range of typical pile groups. The results are compared with published data from more approximate solutions and laboratory and full-scale pile loading tests. The l.
Auditory Profiles of Classical, Jazz, and Rock Musicians: Genre-Specific Sensitivity to Musical Sound Features

When compared with individuals without explicit training in music, adult musicians have facilitated neural functions in several modalities. They also display structural changes in various brain areas, these changes corresponding to the intensity and duration of their musical training. Previous studies have focused on investigating musicians with training in Western classical music. However, musicians involved in different musical genres may display highly differentiated auditory profiles according to the demands set by their genre, i.e., varying importance of different musical sound features. This hypothesis was tested in a novel melody paradigm including deviants in tuning, timbre, rhythm, melody transpositions, and melody contour. Using this paradigm while the participants were watching a silent video and instructed to ignore the sounds, we compared classical, jazz, and rock musicians' and non-musicians' accuracy of neural encoding of the melody. In all groups of participants, all deviants elicited an MMN response, which is a cortical index of deviance discrimination. The strength of the MMN and the subsequent attentional P3a responses reflected the importance of various sound features in each music genre: these automatic brain responses were selectively enhanced to deviants in tuning (classical musicians), timing (classical and jazz musicians), transposition (jazz musicians), and melody contour (jazz and rock musicians). Taken together, these results indicate that musicians with different training history have highly specialized cortical reactivity to sounds which violate the neural template for melody content.
Clay clast aggregates in gouges: New textural evidence for seismic faulting

[1] Spherical aggregates named clay-clast aggregates (CCAs) have been reported from recent investigations on retrieved clay-bearing fault gouges from shallow depth seismogenic faults and rotary shear experiments conducted on clay-bearing gouge at seismic slip rates. The formation of CCAs appears to be related to the shearing of a smectite-rich granular material that expands and becomes fluidized. We have conducted additional high-velocity rotary shear experiments and low-velocity double-shear experiments. We demonstrate that a critical temperature depending on dynamic pressure-temperature conditions is needed for the formation of CCAs. This temperature corresponds to the phase transition of pore water from liquid to vapor or to critical, which induced gouge pore fluid expansion and therefore a thermal pressurization of the fault. A detailed examination by energy dispersive X-ray spectrometry (EDX-SEM) element mapping, SEM, and transmission electron microscopy (TEM) shows strong similar characteristics of experimental and natural CCAs with a concentric well-organized fabric of the cortex and reveals that their development may result from the combination of electrostatic and capillary forces in a critical reactive medium during the dynamic slip weakening. Accordingly, the occurrence of CCAs in natural clay-rich fault gouges constitutes new unequivocal textural evidence for shallow depth thermal pressurization and consequently for past seismic faulting.
The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt

Saccharomyces cerevisiae strain W303 is a widely used model organism. However, little is known about its genetic origins, as it was created in the 1970s from crossing yeast strains of uncertain genealogy. To obtain insights into its ancestry and physiology, we sequenced the genome of its variant W303-K6001, a yeast model of ageing research. The combination of two next-generation sequencing (NGS) technologies (Illumina and Roche/454 sequencing) yielded an 11.8 Mb genome assembly at an N50 contig length of 262 kb. Although sequencing was substantially more precise and sensitive than whole-genome tiling arrays, both NGS platforms produced a number of false positives. At a 378× average coverage, only 74 per cent of called differences to the S288c reference genome were confirmed by both techniques. The consensus W303-K6001 genome differs in 8133 positions from S288c, predicting altered amino acid sequence in 799 proteins, including factors of ageing and stress resistance. The W303-K6001 (85.4%) genome is virtually identical (less than equal to 0.5 variations per kb) to S288c, and thus originates in the same ancestor. Non-S288c regions distribute unequally over the genome, with chromosome XVI the most (99.6%) and chromosome XI the least (54.5%) S288c-like. Several of these clusters are shared with Σ1278B, another widely used S288c-related model, indicating that these strains share a second ancestor. Thus, the W303-K6001 genome pictures details of complex genetic relationships between the model strains that date back to the early days of experimental yeast genetics. Moreover, this study underlines the necessity of combining multiple NGS and genome-assembling techniques for achieving accurate variant calling in genomic studies.
Quantifying change in patterned semi-arid vegetation by Fourier analysis of digitized aerial photographs

Panchromatic aerial photographs from 1955 and 1985 (scale: 1:50 000) were used to quantify changes in semi-arid patterned vegetation caused by a succession of dry years in the early 1980s. The study site is located in the northwest part of Burkina Faso (West Africa), and features a plain with a savanna physiognomy and gentle slopes covered by tiger bush. Digitized data (pixel size of 3.15 m) covered a belt transect of 9 km by 1.5 km that has been divided into 315 m 2 square quadrats. Four reference quadrats were digitized with a pixel of 0.83 m, for comparison with high-resolution outlooks from 1994. Pattern quantification relied on spectral analysis by Fourier transform, that yielded dominant wavelengths (radial spectrum) and main orientations (angular spectrum). The vegetation in the plain displayed important changes that were related to the collapse of the herbaceous cover (and associated scattered trees), and its partial post-drought recovery. Such changes were quantified as a relative decline of small spatial wavelengths (<40 m), followed by a bounce-back of wavelengths in the range 25-50 m. An underlying pattern of fragmented bands of woodland was also revealed with a dominant orientation and a characteristic wavelength ranging from 80 m up to more than 105 m. On the gentle slopes, dense wooded bands that constituted tiger bush (with a wavelength in the range 60-80 m) displayed only minor changes through time. Spectral analysis by Fourier transform proved to be a suitable way to monitoring patterned semi-arid vegetation for which periodicity and orientation are important characteristics. Consistent diachronic comparisons are possible even with historical photographs of varying scale and quality.
Soil temperature in Canada during the twentieth century: Complex responses to atmospheric climate change

[1] Most climate records and climate change scenarios projected by general circulation models are for atmospheric conditions. However, permafrost distribution as well as ecological and biogeochemical processes at high latitudes is mainly controlled by soil thermal conditions, which may be affected by atmospheric climate change. In this paper, the changes in soil temperature during the twentieth century in Canada were simulated at 0.5° latitude/longitude spatial resolution using a process-based model. The results show that the mean annual soil temperature differed from the mean annual air temperature by −2° to 7°C, with a national average of 2.5°C. Soil temperature generally responded to the forcing of air temperature but in complex ways. The changes in annual mean soil temperature during the twentieth century differed from that of air temperature by −3° to 3°C from place to place, and the difference was more significant in winter and spring. On average, for the whole of Canada the annual mean soil temperature at 20 cm depth increased by 0.6°C, while the annual mean air temperature increased by 1.0°C. Three mechanisms were investigated to explain this differentiation: air temperature change, which altered the thickness and duration of snow cover, thereby altering the response of soil temperature; seasonal differences in changes of air temperature; and changes in precipitation. The first two mechanisms generally buffer the response of soil temperature to changes in air temperature, while the effect of precipitation is significant and varies with time and space. This complex response of soil temperature to changes in air temperature and precipitation would have significant implications for the impacts of climate change.
Stable carbon isotopic evidence for climate change across the late Pleistocene to early Holocene from Lesotho, southern Africa

Although significant environmental and climatic changes are likely to have occurred across the Pleistocene/Holocene transition in southern Africa, records are sparse, with information regarding temperature change especially rare. We thus know little about the conditions facing Later Stone Age human populations at this time, particularly those in the highland interior where temperature shifts would have had strong impacts on floral and faunal distributions. In Lesotho, a well‐defined altitudinal distribution of C3 and C4 photosynthetic plant taxa, and their remains in soil organic matter, provides a means of estimating past temperature shifts. We applied this principle to stratified sediments from two archaeological sequences in the Lesotho lowlands (c. 1600 m a.s.l.) to produce a palaeotemperature record focusing on the period 14 000–9500 cal a BP. The results show an overall trend from exclusively C3 vegetation at the Last Glacial Maximum towards greater contributions of C4 taxa, and thus warmer conditions, during the Holocene. However, large temperature fluctuations are evident within this trend, with rapid changes of up to 4 °C visible between 11 200 and 9500 cal a BP. The continued presence of hunter‐gatherers during this time suggests that the region must have remained attractive to human populations despite significant climatic instability and cool episodes. Copyright © 2013 John Wiley & Sons, Ltd.
Semen quality and reproductive hormones in Faroese men: a cross-sectional population-based study of 481 men

Objectives To determine semen quality and reproductive hormone levels in young Faroese men. Design Descriptive cross-sectional study of Faroese men compared with Danish men. Setting Faroese one-centre study. Participants 481 men born from 1981 to 1987 and investigated from 2007 to 2010. Outcome measures Sperm concentration, semen volume, total sperm count, sperm motility, sperm morphology and reproductive hormone levels. Results Sperm concentrations for the Faroese men were lower than for the Danish men (crude median 40 vs 48 mill/ml, p<0.0005). Semen volume was higher, and thus the total sperm counts did not differ (159 vs 151 mill, p=0.2). Motility and morphology did not differ between the Faroese and Danes. The inhibin B/follicle-stimulating hormone ratios for the Faroese men were lower than for the Danes (64 vs 76, p=0.001). Similarly, lower total testosterone/luteinising hormone (LH) ratio (4.6 vs 6.0, p<0.0005) and lower calculated free-testosterone/LH ratio (94 vs 134, p<0.0005) were detected for the Faroese men. Conclusions Semen quality among the Faroese men is at the same low level as reported for Danish men, and the reproductive hormone levels furthermore indicated a lower Leydig cell capacity for testosterone production. The influence of environmental exposure and genetic factors on semen quality has to be studied further.
Pore‐pressure diffusion: A possible triggering mechanism for the earthquake swarms 2000 in Vogtland/NW‐Bohemia, central Europe

Vogtland/NW‐Bohemia (VB) at the German/Czech border region is characterized by recurring intraplate earthquake swarms, Quaternary volcanism, intersecting fault systems, and an established connection between ascending magmatic fluids and seismicity. As the triggering mechanism of seismicity in VB is still unknown, this study aims to contribute by investigating the possible role of fluids in VB, based on poromechanics. We assume that ascending fluids, of magmatic origin, trigger earthquakes by the mechanism of pore‐pressure diffusion (i.e., relaxation). Two physical fields, the hydraulic diffusivity and the criticality (i.e., critical pore‐pressure value leading to failure), both heterogeneously distributed in rocks, mainly control this triggering process. The results of the analysis of the year 2000 earthquake swarm data support this concept. It is further strengthened by a numerical model, with correlated diffusivity and criticality fields, which successfully simulates the general spatio‐temporal seismicity pattern of the earthquake swarms 2000.
Mesozoic and Cenozoic Chronostratigraphy and Cycles of Sea-Level Change

Sequence-stratigraphic concepts are used to identify genetically related strata and their bounding regional unconformities, or their correlative conformities, in seismic, well-log, and outcrop data. Documentation and age dating of these features in marine outcrops in different parts of the world have led to a new generation of Mesozoic and Cenozoic sea-level cycle charts with greater event resolution than that obtainable from seismic data alone. The cycles of sea-level change, interpreted from the rock record, are tied to an integrated chronostratigraphy that combines state-of-the-art geochronologic, magnetostratigraphic and biostratigraphic data. In this article we discuss the reasoning behind integrated chronostratigraphy and list the sources of data used to establish this framework. Once this framework has been constructed, the depositional sequences from sections around the world, interpreted as having been formed in response to sea-level fluctuations, can be tied into the chronostratigraphy. Four cycle charts summarizing the chronostratigraphy, coastal-onlap patterns, and sea-level curves for the Cenozoic, Cretaceous, Jurassic, and Triassic are presented. A large-scale composite-cycle chart for the Mesozoic and Cenozoic is also included (in pocket). The relative magnitudes of sea-level falls, interpreted from sequence boundaries, are classified as major, medium, and minor, as are the condensed sections associated with the intervals of sediment starvation on the shelf and slope during the phase of maximum shelf flooding during each cycle. Generally, only the sequence boundaries produced by major and some medium-scale sea-level falls can be recognized at the level of seismic stratigraphic resolution; detailed well-log and/or outcrop studies are usually necessary to resolve the minor sequences.
Andesites and Dacites from Daisen Volcano, Japan: Partial-to-Total Remelting of an Andesite Magma Body

Voluminous andesite and dacite lavas of Daisen volcano, SW Japan, contain features suggesting the reverse of normal fractionation (anti-fractionation), in the sense that magma genesis progressed from dacite to andesite, accompanied by rises in temperature. A positive correlation exists between phenocryst content (0---40 vol. %) and wt % SiO2 (61---67%). Phenocryst-rich dacites contain hornblende and plagioclase that are generally unaltered, clear, and euhedral. However, phenocryst-poor rocks contain sieve-textured plagioclase, resorbed plagioclase, and opacite in which hornblendes are pseudomorphed. Some Daisen rocks contain two coexisting pyroxenes. Many orthopyroxene phenocrysts from two-pyroxene lavas have high-Ca overgrowth rims (up to 50 mm), a feature consistent with crystallization from a higher-temperature magma than the core. Rim compositions are similar from phenocryst to phenocryst in individual samples. Temperatures of 800---900 C are obtained from the cores, whereas temperatures of 1000---1100 C are indicated for the rims. Lavas ranging from aphyric andesite ( 61 wt % SiO2) to phenocryst-rich dacite ( 67 wt % SiO2) have similar Sr/Sr (0 7045---0 7052) and Nd/Nd (0 5127--0 5128). Isotopic variability within Daisen volcano is likely to be mantle-derived, reflecting isotopic variability within the magma source region associated with a single mantle diapir. The Daisen andesites and dacites have the same trace element signatures as the associated basalts and were probably derived from primary magmas at the same general depth ( 60 km). Our interpretation is that mantle-derived hydrous magnesian andesite, generated in the same mantle diapir as coexisting basalt magma, may be parental to the hydrous calc-alkaline magmas in Daisen volcano. We suggest a two-stage process, involving mid-crustal solidification of bodies of this calcalkaline magma followed by varying degrees of partial melting from body to body, to produce the magmatic trends and phenocryst zoning patterns observed. The heat required for this melting, according to our model, was supplied by the intermittent rise of subjacent basaltic magma.
The Epidemiology of Childhood Celiac Disease: A Social Epidemiological Perspective on Perinatal Factors

Celiac disease is a chronic gastrointestinal disease affecting approximately 1% of the population. It is precipitated in genetically predisposed individuals by ingestion of food containing gluten or similar proteins that are present in wheat, rye and barley. The disease might present with symtoms such as malnutrition, diarrhea or abdominal bloating, but a large proportion of those afflicted by the disease are asymptomatic. We set out to study risk factors for celiac disease in children using a social epidemiological approach; besides the individual risk factors we also consider the importance of societal structures in conditioning disease risk. We investigated all children born in Sweden between 1987 and 1993 by linking several nationwide registers. We apply epidemiological methods such as multilevel analyses and sibling designs in order to approach causality. We observed that children exposed to adverse perinatal circumstances such as being born small for gestational age, born in families with lower socioeconomic position or having a congenital anomaly had a higher risk of CD. These associations were stronger in boys. We also observed that maternal CD seems not to be the cause of the previously reported increased risk of CD in girls. Furthermore, we observed that maternal length of stay in Sweden seems to affect the risk of CD in second-generation immigrant children. Future studies are needed to investigate risk factors for celiac disease in children; focusing especially on the mechanisms behind the observed associations.