Miracle-dz/UniFAR-FTUs huggingface dataset:
Biogeochemical cycling in the global ocean: 1. A new, analytical model with continuous vertical resolution and high‐latitude dynamics

A new, simple analytical model of ocean chemistry is presented which includes continuous vertical resolution, high-latitude dynamics, air-sea exchange and sea ice cover. In this high-latitude exchange/interior diffusion-advection (HILDA) model, ocean physics are represented by four parameters: k and w, an eddy diffusion coefficient and a deep upwelling velocity in the stratified interior; q, a rate of lateral exchange between the interior and a well-mixed, deep polar ocean; and u, an exchange velocity between surface and deep layers in the polar ocean. First, estimates are made of ice-free and ice-covered areas at high latitudes, surface temperatures, and air-sea exchange velocities from available data. Then values of the physical parameters are estimated from simultaneous, least mean square fits of model solutions for temperature (T) and “abiotic” carbon 14 (Δ14C) to interior profiles of T and Δ14C and surface layer Δ14C values all derived from available data. Best fit values for k, w, q, and u are 3.2×10−5 m2 s−1, 2.0×10−8 m s−1, 7.5×10−11 s−1 and 1.9×10−6 m s−1 respectively. These results are interpreted in terms of modes of ocean circulation and mixing and compared with results from other simplier and more complex models. In parts 2 and 3 of this series, these values for k, w, q and u are taken as inputs for studying phosphorus, oxygen, and carbon cycling in the global ocean with the HILDA model.
Precambrian Crustal Evolution in the Great Falls Tectonic Zone: Insights from Xenoliths from the Montana Alkali Province

Zircon U-Pb ages, Lu-Hf data, and whole-rock Sm-Nd data from xenoliths in the Eocene Grassrange diatremes of central Montana reveal the presence of Proterozoic-Archean crust at depth in the Great Falls tectonic zone. The data suggest that the Proterozoic granitoids are not part of the juvenile Little Belt magmatic arc but likely involved melting of Neoarchean crust after closure of the Little Belt ocean. Zircons in the Archean granites suggest their source(s) was part of the Medicine Hat block, not the northern Wyoming craton, and that the samples represent crustal material that was reworked during the Paleoproterozoic collision.
EERF (Eastern Environmental Radiation Facility) standard operating procedures for radon-222 measurement using charcoal canisters. Final report

The passive nature of activated charcoal allows both adsorption and desorption, and, in addition, the adsorbed radon undergoes radioactive decay during the exposure period. Therefore, the canister cannot uniformly integrate over the entire exposure period. However, the canisters can be calibrated to yield precise results for radon concentrations in structures during the deployment period of 48 hours used by the US Environmental Protection Agency (EPA).
Wnt signaling and its downstream target N-myc regulate basal progenitors in the developing neocortex

Basal progenitors (also called non-surface dividing or intermediate progenitors) have been proposed to regulate the number of neurons during neocortical development through expanding cells committed to a neuronal fate, although the signals that govern this population have remained largely unknown. Here, we show that N-myc mediates the functions of Wnt signaling in promoting neuronal fate commitment and proliferation of neural precursor cells in vitro. Wnt signaling and N-myc also contribute to the production of basal progenitors in vivo. Expression of a stabilized form of β-catenin, a component of the Wnt signaling pathway, or of N-myc increased the numbers of neocortical basal progenitors, whereas conditional deletion of the N-myc gene reduced these and, as a likely consequence, the number of neocortical neurons. These results reveal that Wnt signaling via N-myc is crucial for the control of neuron number in the developing neocortex.
Evaluation of a protocol for the quantification of black carbon in sediments

Formation of highly condensed black carbon (BC) from vegetation fires and wood fuel combustion presumably transfers otherwise rapidly cycling carbon from the atmosphere‐biosphere cycle into a much slower cycling geological form. Recently reported BC fractions of total organic carbon (TOC) in surficial marine sediments span a wide range (2‐90%), leaving it presently unclear whether this variation reflects natural processes or is largely due to method differences. In order to elucidate the importance of BC to carbon burial the specificity of applied methods needs to be constrained. Here the operating range and applicability of a commonly used chemothermal oxidation (CTO) method is evaluated using putative BC standards, potentially interfering substances, and natural matrix standards. Test results confirm the applicability of the method to marine sediments. Integrity tests with model substrates suggest applicability to low‐carbon soils but only with a lower specificity to seawater particulate matter. The BC content of marine sediment samples in a set of studies employing the CTO method proved to be consistent with associated geochemical information. The radiocarbon content of the BC isolate in an environmental matrix standard was shown to be similar to the radiocarbon signature of pyrogenic polycyclic aromatic hydrocarbons (PAHs), here serving as molecular markers of combustion (fraction modern fM of BC was 0.065 ± 0.014 and of PAHs 0.056 ± 0.020), while being clearly distinct from the radiocarbon content of the bulk TOC (fM = 0.61 ± 0.08). Urgent questions such as the global accumulation rate of black carbon in soils and sediments may prove approachable with the chemothermal oxidation technique of BC quantification.
A REPORT OF 20 CASES

A description is given of 20 patients with winging of the scapula. The majority had suffered spontaneous severe pain in the region of the shoulder followed about two weeks later by the deformity and associated loss of function. Only in three patients was there a clear history of trauma. Some patients may have strained the arm, but in the m*jority no single factor heralded the problem. Most of the patients were followed up for more than two years and it became clear that functional recovery could take up to this time to be complete. However, careful examination revealed that often a slight degree of winging remained. No specific treatment apart from gentle physiotherapy was prescribed and certainly no operative procedures. It is considered that a number of these cases were examples of neuralgic amyotrophy. Classical winging of the scapula is due to paralysis of the serratus anterior muscle which is supplied by the long thoracic nerve. This is a tidy anatomical unit, one motor nerve (arising from three cervical roots, CS, 6, 7), one muscle to supply and one main function for that muscle, namely to hold the scapula against the chest wall during movements of the shoulder joint. Paralysis of the muscle causes not only winging of the scapula but also results in lack of stabilisation and proper scapular rotation. This precludes normal movement of the shoulder and abduction is markedly limited. The patient may complain of an ugly prominence of the shoulder blade which tends to be uncomfortable when in contact with a hard surface, of weakness when lifting the arm and of considerable discomfort after repeated effort.
Maximum likelihood identification of neural point process systems

The invention relates to a drive for a straddle type berry harvester suitable in particular for harvesting raspberries. The harvester has a frame mounted on wheels movable over a row of berry plants and having opposed rotatable upright cylindrical tined shakers connected above by universals to output shafts of a drive and mounted above conveyors in laterally slidable bearings to avoid obstructions in their path. Spring-mounted interleaved deflector plates lie between and beneath the shakers inclined towards the conveyors to guide berries shaken off by the shakers and falling therebetween. The shakers are rotated by cooperation of the tines with the plants as the harvester moves thereover.
Low-pressure granulite facies metamorphism in the Larsemann Hills area, East Antarctica; petrology and tectonic implications for the evolution of the Prydz Bay area

Thermobarometric studies on various granulite facies areas along the Prydz Bay coast, East Antarctica (73°-79°E, 68°-70°S), show that, at around 1100 Ma, during a late Proterozoic orogeny, the rocks of the Larsemann Hills suffered a lower pressure metamorphic peak than the surrounding areas. Along the Prydz Bay coast, the rocks affected by this event include parts of the Vestfold Hills block plus all of the Rauer Group, the Larsemann Hills and the Munro Kerr Mountains. The dykes in the south-west corner of the Vestfold Hills were recrystallized during this event with little deformation at temperatures not quite as high as in the areas further south-west (650°C, 6.5 kbar) (Collerson et al., 1983), the Rauer Group was metamorphosed at 800°C and 7.5 kbar (Harley, 1987a), the Larsemann Hills at 750°C and 4.5 kbar, and the Munro Kerr Mountains probably at around 850°C and 5 kbar. Retrograde equilibration in the different areas occurred during decompression to about 10 km depth in all areas, followed by isobaric cooling at this depth. This paper shows that the peak metamorphism in the Larsemann Hills occurred at a pressure which is too low to have been the consequence of thermal relaxation of overthickened crust with normal mantle heat flow. Although other areas in Prydz Bay were metamorphosed at sufficiently high pressures so that their decompression paths are not inconsistent with a continental collision model, the inferred pre-metamorphic peak histories and the requirement of consistency with the Larsemann Hills, make it unlikely that collision followed by erosion-driven decompression is an appropriate model. We suggest that the thermal regime of the crust in the Larsemann Hills region was controlled by a perturbation in the asthenosphere, with magma invasion of the crust. We suggest that the 500 Ma event, represented in Prydz Bay by granitic outcrops at Landing Bluff and by several K/Ar ages from the Larsemann Hills area, was responsible for the final excavation of the terrane.
Consolidation Test at Constant Rate of Strain for Radial Drainage

A consolidometer for radial drainage under constant rate of strain (CRS) loading was developed. Theoretical solutions for determining the consolidation parameters, such as the coefficient of consolidation, compression index, recompression index, and preconsolidation pressure, from the test results were also proposed. Comparative experiments with CRS loading and incremental loading (IL) were carried out in radial drainage and also in vertical drainage. The results obtained from the developed CRS loading test agreed well with those of the conventional incremental loading test for radial drainage. They also showed that the CRS test enables the whole consolidation test to be completed in 2–6 h for commonly encountered fine grained soils.
BE-ACTIV: a staff-assisted behavioral intervention for depression in nursing homes.

PURPOSE This article (a) describes a 10-week, behavioral, activities-based intervention for depression that can be implemented in nursing homes collaboratively with nursing home activities staff and (b) presents data related to its development, feasibility, and preliminary outcomes. DESIGN AND METHODS We developed BE-ACTIV, which stands for Behavioral Activities Intervention, in two pilot study phases: a treatment development phase and a feasibility-outcome phase with a small, randomized trial. We first piloted the intervention with five depressed residents in a single nursing home in collaboration with the social services and activities staff. The second phase randomized 20 residents from six nursing homes to receive either the intervention or treatment as usual. RESULTS The intervention was well received by residents, family, and staff members. Experience with the intervention and input from staff members resulted in modifications to streamline the intervention and improve implementation. Results suggest that BE-ACTIV reduced institutional barriers to participation in pleasant activities, increased resident control over activity participation, increased overall activity participation, and improved depressive symptoms. Despite low power, statistical and graphical comparisons suggest superiority of the intervention over treatment as usual. IMPLICATIONS Because depression among nursing home residents is prevalent, heterogeneous, and often treatment resistant, there is a need for effective, low-cost interventions that are ecologically acceptable and efficient. BE-ACTIV is a promising intervention; it is brief, addresses institutional barriers, involves facility staff in treatment, and is acceptable to residents. As such, BE-ACTIV merits further evaluation to establish efficacy and effectiveness.
Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals

UNLABELLED Phylogenetic footprinting is an efficient approach for revealing potential transcription factor binding sites in promoter sequences. The idea is based on an assumption that functional sites in promoters should evolve much slower then other regions that do not bear any conservative function. Therefore, potential transcription factor (TF) binding sites that are found in the evolutionally conservative regions of promoters have more chances to be considered as "real" sites. The most difficult step of the phylogenetic footprinting is alignment of promoter sequences between different organisms (fe. human and mouse). The conventional alignment methods often can not align promoters due to the high level of sequence variability. We have developed a new alignment method that takes into account similarity in distribution of potential binding sites (motif-based alignment). This method has been used effectively for promoter alignment and for revealing new potential binding sites for various transcription factors. We made a systematic phylogenetic footprinting of human/mouse conserved non-coding sequences (CNS). 60 thousand potential binding sites were revealed in human and mouse genomes. We have developed a database of the predicted potential TF binding sites. AVAILABILITY http://compel.bionet. nsc.ru/FunSite/footprint/; www.gene-regulation.com/.
Holocene pine tree‐line evolution in the Swedish Scandes: Recent tree‐line rise and climate change in a long‐term perspective

This article focuses on the Holocene tree line (Pinus sylvestris) and climate change in the Swedish Scandes. A composite of three previously independently published data sets of megafossil tree remains (trunks, stumps and roots) from sites above today's tree line is analysed. Calibration of ages, adjustment for glacio‐isostatic land uplift and a larger sample provide new and more conclusive insights. The tree‐line altitude peaked about 11 200 cal. yr BP, 425 m higher than the position about a century ago, when it was at its Holocene low. At the millennial‐centennial scale, tree‐line retraction has been a smooth process, following a linear trend, which largely conforms to the Milankovitch model of orbital forcing of summer temperature evolution. Shorter excursions from this trend cannot be ruled out, as these are beyond the resolution of the analytical approach. During the earliest Holocene, summers may have been about 2.58C warmer than by the late‐19th century. Projection of the 20th‐century maximum tree‐line rise by 150–190 m upon the entire Holocene tree‐line chronology indicates that present‐day tree lines may be higher than ever during the past 5000 or even 7000 years. Indirectly, this might reflect an anomalous modern climatic regime for which there is supporting evidence from retreating mountain glaciers and recent evolution of the alpine plant cover and its zonation patterns. With this background, the evolution of the tree‐line ecotone in the case of continued warming is considered. Pine is likely to regain the dominant position held in the early Holocene. Its tree line may shift at least 400 m above its present position. Small outlier stands of mountain birch will establish in sheltered, moderately snow‐rich habitats high above the new pine tree line, but an overall alpine character of the landscape will prevail above the tree line of pine. Exotic tree species, mainly belonging to the genus Pinus may profit from a new climatic regime and establish in the tree‐line ecotone.
Tertiary foreland sedimentation in the Southern Subalpine Chains, SE France: a geodynamic appraisal

Tertiary foreland sedimentation in SE France occurred along the western sidewall of the Alpine orogen during collision of the Apulian indentor with the European passive margin. A detailed reappraisal of the stratigraphy and structure of the Southern Subalpine Chains (SSC) in SE France shows that Tertiary depocentres of differing character developed progressively toward the foreland during ongoing SW‐directed shortening. The geodynamic controls on each of four stages of basin development are evaluated using a flexural isostatic modelling package of thrust sheet emplacement and foreland basin formation. (1) The initial stage (mid to late Eocene) can be explained as a flexural basin that migrated toward the NW, closing off to the SW against the uplifting Maures–Esterel block. This broad, shallow basin can be reproduced in forward modelling by loading a lower lithospheric plate with an effective elastic thickness of 20 km. (2) The end of detectable flexural subsidence in the early Oligocene coincides with the emplacement of the internally derived Embrunais–Ubaye (E‐U) nappes, which caused 11 km of SW‐directed shortening in the underlying SSC. The lack of Oligocene flexural subsidence dictates that the E‐U units were emplaced as gravitational nappes. Within the SSC, Oligocene sedimentation was restricted to small thrust‐sheet‐top basins recording mainly continental conditions and ongoing folding. Further west, Oligocene to Aquitanian NNW–SSE extension generated the Manosque half‐graben as part of the European graben system that affected an area from the Gulf of Lion to the Rhine graben. (3) Following the Burdigalian breakup of the Gulf of Lion rift, a marine transgression migrated northward along the European graben system. Subsequent thermal subsidence allowed 1 km of marine sediments to be deposited across the Valensole and Manosque blocks, west of the active SSC thrust belt. (4) Mio‐Pliocene conglomeratic deposits (2 km thick) were trapped within the Valensole basin by the uplifting Vaucluse block to the west and the advancing Alpine thrust sheets to the east. Late Pliocene thrusting of the SSC across the Valensole basin (approx. 10.5 km) can be linked along a Triassic detachment to the hinterland uplift of the Argentera basement massif.
Collaborative processing to extract myocardium from a sequence of two-dimensional echocardiograms

Echocardiography is an important clinical method for identification and assessment of the entire spectrum of cardiac diseases. Visual assessment of the echocardiograms is tedious and subjective, but on the other hand, owing to the poor quality of the data, the automatic techniques are unreliable. One can minimize these drawbacks through collaborative processing. The authors describe a collaborative method to extract the myocardium from a sequence of two-dimensional echocardiograms. Initially, a morphologically adaptive thresholding scheme generates a rough estimate of the myocardium, and then a collaborative scheme refines the estimate. The threshold is computed at each pixel as a function of the local morphology and a default threshold. The points that have echodensities greater than the threshold form a rough estimate of the myocardium. This is collaboratively refined in accordance with the corrections specified by the operator, through mouse gestures. The gestures are mapped on to an image processing scheme that decides the precise boundaries of the intended regions that are to be added to or deleted from the estimated myocardium.
Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA cluster biogenesis in mosquitoes

Background The PIWI-interacting RNA (piRNA) pathway in culicine mosquitoes differs substantially from other model organisms in terms of an expanded PIWI gene family and ubiquitously expressed piRNAs in somatic tissues. Results Here, through comprehensive analyses of endogenous piRNAs in Aedes aegypti, we defined core piRNA clusters as small RNA source loci that showed ubiquitous expression in both somatic and germline tissues. These core piRNA clusters produced piRNAs from a single genomic strand and were enriched for non-retroviral endogenous viral elements (nrEVEs) in antisense orientation. Biogenesis of cluster-derived piRNAs depended on key factors, the mRNA exporter Nxf1, three Tudor proteins, Veneno, Tejas, and Yb, as well as the evolutionarily conserved cochaperone Shutdown. Combined transcriptional and chromatin state analyses showed that these core piRNA clusters do not have independent promoters, but instead depended on readthrough transcription from upstream genes for piRNA biogenesis. This biogenesis mechanism was evolutionarily conserved in other vector mosquito species, Aedes albopictus, Culex quinquefasciatus, and Anopheles gambiae. Interestingly, the upstream genes of many core piRNA clusters of the two Aedes mosquitoes were orthologous, but the downstream piRNA clusters differed both in size and sequence, especially evident by distinct nrEVE insertions from different virus families. We propose a model in which a conserved set of genes determine the loci for piRNA biogenesis, while the downstream piRNA clusters function as traps for nrEVEs, allowing adaptation to environmental challenges such as virus infection. Conclusions Our systematic analyses of piRNA cluster expression and chromatin state lay a solid foundation for future studies of piRNA and genome evolution in these important vector species.
Formation of miniature sorted patterns by shallow ground freezing: A field experiment

At an experimental site near sea level in Scotland, a miniature sorted net with cell diameters of 56–172 mm and stony borders 4–9 cm deep developed in frost-susceptible regolith over two winters. Pattern formation was evident after only 8 freeze-thaw cycles, during which the minimum surface temperature was −5.3°C and freezing extended to a maximum depth of 16–17 cm. The primary process of pattern development was repeated differential growth of near-surface needle ice, causing upcoming of a cover of coarse debris. During subsequent thaw, bending and melting of ice needles resulted in net migration of upheaved clasts towards dome margins, causing progressive concentration of clasts in stony borders surrounding finer cells. This differentiation of near-surface soil texture appears self-sustaining, promoting preferential growth of ice lenses and thus preferential heave in fine cells. The experiment suggests that miniature frost-sorted patterns are not necessarily diagnostic of present or former periglacial environments, but may develop on unvegetated soil of suitable composition in a wide range of mid- or even low-latitude environments where shallow ground freezing is accompanied by the growth of needle ice. © 1996 John Wiley & Sons, Ltd.