Miracle-dz/UniFAR-FTUs huggingface dataset:
The use of PARAFAC modeling to trace terrestrial dissolved organic matter and fingerprint water masses in coastal Canadian Arctic surface waters

[1] The optical properties of chromophoric dissolved organic matter (CDOM) were investigated in the Canadian Archipelago and coastal Beaufort Sea surface waters using fluorescence spectroscopy coupled with parallel factor analysis (PARAFAC). Environmental dynamics of individual components were evaluated and compared to salinity, in situ fluorescence, absorption at 312 nm (a312), dissolved organic carbon, and lignin phenol concentrations. A positive linear relationship between four fluorescent components and lignin phenols suggests a terrestrial origin, whereas two components were unrelated to a river source, suggesting an autochthonous source. Elevated concentrations of terrestrial components were observed in the Mackenzie River plume near the coast of Alaska and decreased as water was transported to the Canadian Archipelago. The two nonterrestrial components exhibited only background levels in concentrations along the transect, suggesting minimal productivity within plume and archipelago surface waters. The relative abundance of terrestrial components in relation to nonterrestrial components allowed us to distinguish water masses including Atlantic, Archipelago, and Mackenzie River plume, respectively. This study illustrates the usefulness of PARAFAC to fingerprint water masses based on the optical characteristics of CDOM and shows promise to improve our understanding of upper Arctic Ocean ventilation.
Roundup 2.0: enabling comparative genomics for over 1800 genomes

Summary: Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved using FASTA sequence search. All source code and orthologs are freely available. Availability: http://roundup.hms.harvard.edu Contact: dpwall@hms.harvard.edu; todd_deluca@hms.harvard.edu
LocusZoom: regional visualization of genome-wide association scan results

Summary: Genome-wide association studies (GWAS) have revealed hundreds of loci associated with common human genetic diseases and traits. We have developed a web-based plotting tool that provides fast visual display of GWAS results in a publication-ready format. LocusZoom visually displays regional information such as the strength and extent of the association signal relative to genomic position, local linkage disequilibrium (LD) and recombination patterns and the positions of genes in the region. Availability: LocusZoom can be accessed from a web interface at http://csg.sph. umich.edu/locuszoom. Users may generate a single plot using a web form, or many plots using batch mode. The software utilizes LD information from HapMap Phase II (CEU, YRI and JPT+CHB) or 1000 Genomes (CEU) and gene information from the UCSC browser, and will accept SNP identifiers in dbSNP or 1000 Genomes format. Single plots are generated in ∼20 s. Source code and associated databases are available for download and local installation, and full documentation is available online. Contact: cristen@umich.edu
Role of small ice crystals in radiative properties of cirrus: a case study

Aircraft observations of cirrus cloud were made near Coffeyville, Kansas, during November 1991 as part of the FIRE II project. Cloud ice particle spectra measurements were made using both a PMS 2DC probe and an ice particle replicator. Particles larger than 200 μm were column rosettes. The replicator shows the presence of large numbers of ice crystals smaller than 66 μm (two PMS size bins) that are not recorded by the PMS 2DC probe. Calculations based on the replicator data of the geometrical blocked area and absorption cross section of the cloud per unit volume show that small particles can contribute significantly to and sometimes dominate both the solar extinction and the infrared emission. Intercomparison is made of the ice particle size, area, and mass distributions determined by these different instruments. Power law relationships for area occluded by a crystal as a function of crystal maximum dimension were computed from the PMS 2DC data. The wavelength-dependent infrared absorption cross section per volume was computed using a simple model based on anomalous diffraction and area and mass dimensional relationships for the ice crystals.
MODELING THE HYDROLOGIC IMPACTS OF FOREST HARVESTING ON FLORIDA FLATWOODS 1

ABSTRACT: The great temporal and spatial variability of pine flat‐woods hydrology suggests traditional short‐term field methods may not be effective in evaluating the hydrologic effects of forest management. The FLATWOODS model was developed, calibrated and validated specifically for the cypress wetland‐pine upland landscape. The model was applied to two typical flatwoods sites in north central Florida. Three harvesting treatments (Wetland Harvesting, Wetland + Upland Harvesting, and Control) under three typical climatic conditions (dry, wet, and normal precipitation years) were simulated to study the potential first‐year effects of common forest harvesting activities on flatwoods. Long‐term (15 years) simulation was conducted to evaluate the hydrologic impacts at different stages of stand rotation. This simulation study concludes that forest harvesting has substantial effects on hydrology during dry periods and clear cutting of both wetlands and uplands has greater influence on the water regimes than partial harvesting. Compared to hilly regions, forest harvesting in the Florida coastal plains has less impact on water yield.
The Palaeolithic Societies of Europe

List of figures List of tables Acknowledgements Preface 1. Pulling aside the Palaeolithic curtain 2. The individual, society and networks 3. A Palaeolithic framework: locales, rhythms and regions 4. The first European societies 500,000-300,000 years ago 5. Neanderthal societies 300,000 to 60,000 years ago 6. The rhythms of social life 60,000-21,000 years ago: the transition from the Middle to Upper Palaeolithic in Europe 7. The extension of social life 60,000-21,000 years ago: regions and locales, networks and landscapes 8. The Palaeolithic societies of Europe Notes Bibliography Site index General index.
VISCOUS PROPERTIES OF GRANULAR MATERIALS HAVING DIFFERENT PARTICLE SHAPES IN DIRECT SHEAR

The viscous properties of air-dried relatively poorly-graded granular materials having different particle shapes were evaluated by performing a series of direct shear (DS) tests. The applied loading histories include repeated step changes in the shear displacement rate (s) or repeated sustained loading stages during otherwise monotonic loading (ML) at a constant s under constant vertical stress. Test results of an angular gravelly soil (i.e., Chiba gravel-a) obtained from the present study and those of a wide variety of poorly-graded granular materials (i.e., glass beads and natural sands including Toyoura, Hostun, Silica No. 6a, Ticino, Silver Leighton Buzzard, Ottawa, Albany and Monterey sands) previously obtained by the authors are analysed. The viscous properties of granular materials can be adequately described by three basic parameters: i.e., the rate-sensitivity coefficient, the residual rate-sensitivity coefficient (or their ratio, i.e., the viscosity-type parameter) and the decay parameter. These parameters, as well as the viscosity type (i.e., Isotach, Combined, TESRA and P&N), are strongly affected by particle shape as quantified in terms of the degree of particle angularity while being rather independent of particle size. The creep deformation that takes place by sustained loading increases with an increase in the shear stress level, and it also increases with changes in the viscosity type associated with an increase in mainly the particle angularity and partly the coefficient of uniformity. The various viscous property types and transitions among them can be described by a single general equation incorporating these parameters. A non-linear three component model incorporating this general equation can simulate very well all of the various viscous responses observed in the DS tests referred to in the paper.
Transverse Ranges and neotectonics of southern California

The Transverse Ranges and the east-trending folds and reverse faults that elevate them began forming in mid-Pleistocene time by regional north-south crustal shortening. The adjacent Mojave Desert and Basin and Range provinces continue to respond to this regional strain by east-west crustal extension. Before ∼5 Ma the regional structure was characterized by conjugate northwest-trending right-slip faults (San Andreas set) and northeast-trending left-slip faults (Garlock set). Thereafter, the San Andreas set of faults became simple shears separating the North American and Pacific plates. With the mid-Pleistocene inception of the Transverse Ranges, the San Andreas fault deviated from its N40°-45°W trend in short N75°W-trending segments on the north and south sides of these mountains in response to the new, and local, strain system of upward crustal extension.
Deformation of western Turkey from a combination of permanent and campaign GPS data: Limits to block‐like behavior

[1] We present a new geodetic velocity field covering western Turkey, south of the North Anatolian fault. Our velocity field is derived from a combination of continuously recording GPS stations operating since 2003, survey-type GPS measurements carried out in the period 1997–2005, and velocities from Reilinger et al. (2006). The velocity field indicates that western Turkey currently undergoes extension whose rate increases from the Anatolia plateau to the Aegean coast. The overall extension in westernmost Turkey is about 20 mm/yr, making it one of the fastest areas of continental extension in the world. We test whether the observed deformation is better represented by the rotation of crustal blocks or by more distributed deformation. While no deformation is detected in the central Anatolian plateau, we observe a deformation field west of the plateau that cannot be explained by block models, unless the blocks are so small as to be essentially indistinguishable from a continuum. Although concentration of strain rates (up to 140 nstrain/yr) are found across the major grabens, strain rates above 50 nstrain/yr are found throughout western Turkey. The distributions of topography and crustal thickness in western Turkey agree with the distributions expected if the crust there had a constant thickness at 5 Ma, equal to that of the present central Anatolian plateau, and had subsequently been thinned at the present-day distribution of strain rates. Our results, therefore, suggest that extensional strain affects the whole continental lithosphere of western Turkey, rather than being restricted to a small number of block boundaries.
The California Current system in the Southern California Bight and the Santa Barbara Channel

Recent observations in the Santa Barbara Channel and over the California Cooperative Oceanic Fisheries Investigations (CalCOFI) southern California grid are used to examine seasonal circulation patterns in and near the Southern California Bight, defined as the region east of the Santa Rosa Ridge and including the Santa Barbara Channel. Poleward flow relative to 500 m is found throughout the bight, in all seasons except for spring and all subregions except the western part of the Santa Barbara Channel. In spring there is equatorward flow throughout the bight at all depths to 500 m, though it tends to be surface or midcolumn intensified. Equatorward flow offshore of the bight, present in all seasons, narrows and accelerates into a jet-like feature and simultaneously moves close to the Santa Rosa Ridge in summer. Current meter data from the eastern entrance to the Santa Barbara Channel are consistent with the seasonal results from the CalCOFI data and further show an upward propagation of phase at annual period, with a phase speed of 1 to 2 m d−1. Comparison with the CalCOFI ship winds suggests that poleward flow in the bight may be the result of positive wind stress curl, through a Sverdrup balance, though the observed transport is only about 75% of that expected from the curl amplitude. Equatorward flow in the bight may be the result of coastal upwelling, though the transport is larger than expected from the relatively weak winds in the bight, and the offshore extent of the equatorward flow is about 10 Rossby radii, farther than might be expected for linearized coastal upwelling. Equatorward flow outside the bight cannot be explained as a Sverdrup flow because the wind stress curl is positive throughout most of the region. Upward propagation of phase and downward propagation of energy may be indicative of forcing by remote wind equatorward of the bight. Given the complexity of possible forcing mechanisms for circulation in and near the bight, a model that includes effects of remote wind forcing, Ekman pumping, and topography is needed to explain the observations in a satisfactory way.
Treatments in depression

Major depression is believed to be a multifactorial disorder involving predisposing temperament and personality traits, exposure to traumatic and stressful life events, and biological susceptibility. Depression, both unipolar and bipolar, is a “phasic” disease. Stressful life events are known to trigger depressive episodes, while their influence seems to decrease over the course of the illness. This suggests that depression is associated with progressive stress response abnormalities, possibly linked to impairments of structural plasticity and cellular resilience. It therefore appears crucial to adequately treat depression in the early stages of the illness, in order to prevent morphological and functional abnormalities. While evidence suggests that a severely depressed patient needs antidepressant drug therapy and that a non-severely depressed patient may benefit from other approaches (ie, “nonbiological”), little research has been done on the effectiveness of different treatments for depression. The assertion that the clinical efficacy of antidepressants is comparable between the classes and within the classes of those medications may be true from a statistical viewpoint, but is of limited value in practice. The antidepressant drugs may produce differences in therapeutic response and tolerability. Among the possible predictors of outcome in depression treatment, those derived from clinical assessment, neuroendocrine investigations, polysomnographic sleep parameters, genetic variables, and brain imaging techniques have been extensively studied. This article also reviews therapeutic strategies used when initial treatment fails, and describes briefly new concepts in antidepressant therapies such as the regulation of disturbances in circadian rhythms. The treatment of depressive illness does not stop with treatment of acute episodes, and has to be envisaged as a continuous therapeutic intervention, of which we are still not able to determine the optimal duration of treatment and the moment that it should be ceased.
On the Global Distribution of Hydrothermal Vent Fields

The magmatic budget hypothesis proposes that variability in magma supply is the primary control on the large-scale hydrothermal distribution pattern along oceanic spreading ridges. The concept is simple but several factors make testing the hypothesis complex: scant hydrothermal flux measurements, temporal lags between magmatic and hydrothermal processes, the role of permeability, nonmagmatic heat sources, and the uncertainties of vent-field exploration. Here we examine this hypothesis by summarizing our current state of knowledge of the global distribution of active vent fields, which presently number ∼280, roughly a quarter of our predicted population of ∼1000. Approximately 20% of the global ridge system has now been surveyed at least cursorily for active sites, but only half that length has been studied in sufficient detail for statistical treatment. Using 11 ridge sections totaling 6140 km we find a robust linear correlation between either site frequency or hydrothermal plume incidence and the magmatic budget estimated from crustal thickness. These trends cover spreading rates of 10-150 mm/yr and strongly support the magma budget hypothesis. A secondary control, permeability, may become increasingly important as spreading rates decrease and deep faults mine supplemental heat from direct cooling of the upper mantle, cooling gabbroic intrusions, and serpentinization of underlying ultramafics. Preliminary observations and theory suggest that hydrothermal activity on hotspot-affected ridges is relatively deficient, although paucity of data precludes generalizing this result. While the fullness of our conclusions depends upon further detailed study of vent field frequency, especially on slow-spreading ridges, they are consistent with global distributions of deep-ocean 3 He, an unequivocally magmatic tracer.
Long-term persistence of subduction earthquake segment boundaries: Evidence from Mejillones Peninsula, northern Chile

[1] The Mejillones Peninsula in northern Chile has been recognized as the surface expression of a segment boundary for large subduction zone earthquakes. The sharp contact between the rupture planes of two instrumentally recorded earthquakes, the Mw = 8.0 Antofagasta (1995) and the Mw = 7.7 Tocopilla (2007) events, is located beneath the central part of Mejillones Peninsula. We present new chronostratigraphic and structural data that allow reconstructing the evolution of the Peninsula at the surface and correlation of the latter with seismic cycle deformation on the plate interface. Uplift commenced after 3.4 Myr, as recorded in the western highland. The central graben area on the Peninsula started uplifting above sea level as an anticlinal hinge zone prior to 400 kyr ago, most probably 790 kyr ago. The resulting E-W trending hinge exactly overlies the limit between the rupture planes of the Antofagasta and Tocopilla earthquakes. By correlating the uplift data with the slip distribution of the above earthquakes, we demonstrate that deformation and uplift is focused during the postseismic and interseismic periods of the megathrust seismic cycle with coseismic deformation opposed to the long-term motion. Additionally, the slip deficit beneath the Peninsula accumulating between events is probably largely recovered by creep. Hence we suggest that Mejillones Peninsula owes its existence to the lateral variation of the propensity for unstable slip at the interface. Since the latter is a material property, the long-term spatial stability of the Peninsula as a barrier to rupture propagation since at least the middle Pleistocene is a necessary consequence.
Mixed-layer kaolinite-smectite minerals in a red-black soil sequence from basalt in Sardinia (Italy)

Clay minerals from soils of a red-black soil complex developed from basaltic parent material in Sardinia are formed along a short toposequence (200 m). At the foot of the sequence, a clay-rich, black Vertisol forms, whereas at the summit, the soil is a dark reddish-brown Inceptisol. X-ray diffraction, infrared spectroscopy (FTIR), cation exchange capacity (CEC) and permanent and variable charges analyses were used, and the data show that clay minerals varied according to soil horizon and topographic position of the soil. Clay minerals in the Inceptisol are dominated by kaolinite and mixed-layer kaolinitesmectite (K-S, K:S >0.5), whereas the Vertisol contains smectites and K-S with K:S proportions <0.5. In the Vertisol, the proportion of kaolinitic layers in the K-S increases from the C horizon (K:S ∼0.35–0.40) to the Ap horizon (K:S ∼0.40–0.45). This soil clay-mineral distribution, in relation to topography, is similar to that reported for other (kaolinitic) red-black (smectitic) soil associations in subtropical and tropical areas. The sequence forms by downward drainage on summits and slopes, and buildup of ions in ‘lows’ produces smectites. Fourier transform infrared spectra indicate that two types of smectite are formed in the C horizon of the Vertisol; one is more ferric (Fe-beidellite, nontronite), the other more aluminous. Mineralogical evolution in the soil profile (from C to Ap horizon) shows a decreasing proportion of ferric smectite layers (compared to the more aluminous smectite layers). This would indicate that ferric smectite layers are preferentially transformed (or dissolved) to give kaolinite layers, with Fe precipitating as oxides and/or oxy-hydroxides or retained partly in kaolinite layers. Because the surface properties of clay minerals are related to mineralogy, the CEC (33–41 cmol kg−1) in the brown Inceptisol is ∼50% pH-dependent charge while in the Vertisol up to ∼75% of the CEC (48–61 cmol kg−1) comes from accessible permanent charges.
Dipalmitoylphosphatidic acid inhibits tumor growth in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a subtype of breast cancer with a poor prognosis, accounting for approximately 12-24% of breast cancer cases. Accumulating evidence has indicated that there is no effective targeted therapy available for TNBC. Dipalmitoylphosphatidic acid (DPPA) is a bioactive phospholipid. However, the function of DPPA in the growth of TNBC has not yet been studied. In this study, we employed TNBC cells and a subcutaneous tumor model to elucidate the possible effect of DPPA on tumor growth in TNBC. We showed that DPPA significantly inhibited tumor growth in the mouse subcutaneous tumor model and suppressed cell proliferation and angiogenesis in TNBC tumor tissues. This inhibition was mediated partly by suppressing the expression of cyclin B1 (CCNB1), which directly promoted the accumulation of cells in the G2 phase and arrested cell cycle progression in human TNBC. In addition, the inhibition of tumor growth by DPPA may also be mediated by the suppression of tumor angiogenesis in TNBC. This work provides initial evidence that DPPA might be vital as an anti-tumor drug to treat TNBC.
Understanding the climatic signal in the water stable isotope records from the NEEM shallow firn/ice cores in northwest Greenland

[1] Samples of precipitation and atmospheric water vapor were collected together with shallow firn/ice cores as part of the new deep drilling project in northwest Greenland: the NEEM project. These samples were analyzed for their isotope composition to understand the processes affecting the climatic signal archived in the water stable isotope records from the NEEM deep ice core. The dominant moisture source for the snow deposited at the NEEM-site may be originating as far south as 35°N from the western part of the Atlantic Ocean. The surface atmospheric water vapor appears in isotopic equilibrium with the snow surface indicating a large water exchange between the atmosphere and snowpack. The interannual variability of NEEM shallow firn/ice cores stable isotope data covering the last ∼40 years shows an unexpectedly weak NAO signal. Regional to global atmospheric models simulate a dominant summer precipitation in the NEEM area, suggesting that the intermittency of modern winter precipitation is responsible for the lack of a strong NAO imprint. The interannual variability of NEEM isotope data however shows a strong correlation with interannual variations of Baffin Bay sea ice cover, a relationship consistent with air mass trajectories. NEEM deep ice core isotopic records may therefore provide detailed information on past Baffin Bay sea ice extent. NEEM stable water isotope content increasing trend points to a local warming trend of ∼3.0°C over the last 40 years.