Miracle-dz/UniFAR-FTUs huggingface dataset:
The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Contiguous assemblies are fundamental to decipher the exact composition of extant genomes. In molluscs, this task is considerably challenging owing to their large size, heterozygosity, and widespread content of repetitive content. Consequently, the usage of long-read sequencing technologies is fundamental to achieve high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, has been produced recently. However, the current genome is highly fragmented since the assembly relied solely on short-read approaches. To overcome this caveat, here, a new improved reference genome assembly is produced using a combination of PacBio CLR long reads and Illumina paired-end short reads. This novel genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4Mbp. The ab initio gene prediction resulted in a total of 48,314 protein-coding genes. This new assembly represents a substantial improvement and is an essential resource for studying this species’ unique biological and evolutionary features that ultimately will help to promote its conservation.
Abundance and Distribution of Diamonds in Eclogite Revealed by Volume Visualization of CT X-Ray Scans

A diamond-bearing eclogite has been studied using industrial high-energy computed tomography and volume visualization techniques. Using this non-destructive technique, in which distinction between phases is based on density differences, seven diamonds (five completely enclosed in the rock) have been isolated and viewed in three dimensions. Six diamonds appear to be single crystals of well-formed to malformed octahedra. One is a spinel twin (macle). Partial to complete rimming by secondary barite provides sufficient density contrast with surrounding silicates to allow the diamonds to be easily recognized by their morphology. They appear to be confined to a 1 cm-wide layer. Diamonds range in size from 0.9 to 2.4 mm in maximum dimension and are estimated to constitute 0.19 wt % of the sample, equivalent to a "grade" of 9500 carats per metric ton. Several models for diamond genesis can be ruled out for this sample (e.g., pseudomorphs of graphite by diamond, precipitation as glomeroporphyritic aggregates from a magma), based on the details of diamond distribution.
Sedimentation during carbonate ramp-to-slope evolution in a tectonically active area: Bowland Basin (Dinantian), northern England

The Bowland Basin (northern England) contains a series of carbonates and terrigenous mudstones deposited during the Ivorian to early Brigantian. Two regional depositional environments are indicated by facies and facies associations. Wackestone/packstone and calcarenite facies indicate deposition in a carbonate ramp environment, while lime mudstone/wackestone, calcarenite and limestone breccia/conglomerate facies, often extensively slumped, represent a carbonate slope environment. Stratigraphic relations suggest that the depositional environment evolved from a ramp into a slope through the Dinantian. Two main sediment sources are indicated by the sequence; an extra-basinal terrigenous mud source and a supply of carbonate from the margins of the basin. Deposition from suspension and from sediment gravity flows, in situ production and remobilization of sediment during sedimentary sliding were important processes operating within the basin. Periods of enhanced tectonic activity in the late Chadian to early Arundian and late Asbian to early Brigantian are indicated by basin-wide horizons of sedimentary slide and mass flow deposits. Both intervals were marked by a decline in carbonate production resulting from inundation and uplift/emergence. The first of these intervals separates deposition on a seafloor with gentle topography (carbonate ramp) from a situation where major lateral thickness and facies variations were present and deposition took place in a carbonate slope environment. The second interval marks the end of major carbonate deposition within the Bowland Basin and the onset of regional terrigenous sedimentation.
Developments in forest hydrology

Studies of the effect of vegetation on hydrology have been made by workers from many different disciplines with various objectives in mind. Most have been concerned, either directly or indirectly, with assessing the effects of various types of vegetation chiefly forests on run-off and with the effects of forests and agricultural crops on evaporation. Within the field of forest hydrology emphases have varied considerably. Some workers have concentrated on assessments of interception quantities by certain canopy types, others have investigated the effect of
Spatial Patterns of Ecological Integrity in South Carolina Watersheds

Assessing and monitoring the ecological integrity of terrestrial and aquatic ecosystems is a vital component of effective water resource management, sustainable land use planning, and bio-diversity protection and management. Our objective was to quantify, evaluate and map measures of ecological condition and vulnerability for 32 sub-basins in South Carolina. Principal Component Analysis of 29 integrity measures identified six significant components that explained 78.5 percent of the variance in indicator values among watersheds. These components corresponded to indicators associated with urban development and human stressors, habitat extent and priority species occurrences, agricultural development and land protection, riparian land use and stream impairment, and agricultural conversion and abandonment. Composite measures of watershed integrity provided a simple means for prioritizing watersheds for potential management activities. The approach used in this study ultimately provides a flexible means for assessing broad-scale patterns of biotic integrity that can be tailored to highlight specific management needs or goals while facilitating the selection of a suite of complementary measures that effectively characterize system properties.
The Role of Benchmarking on Sustainability Performance in Food and Beverage Companies of Malaysia

There has been discrepancies in the literature findings related to association between benchmarking and sustainable performance. Hence, this research has considered conducting more investigations on the impacts of other variables which could be better explained the nature of this relationship. In the past studies, several theories have opined that the connections between resources, capabilities and strategies are the keys to organizational sustainability. Therefore, to examine the critical factors of benchmarking being one of the elements of total quality management (TQM) while desiring sustainable performance is the main purpose of this study. Best practice identification, best practice comparison, and implementation and improvement are the benchmarking steps considered in this study. Questionnaires were distributed to 250 Malaysian food and beverages companies while SPSSV23 shall be used as analysis technique. The study found that best practice identification, best practice comparison, and implementation and improvement have significant and positive impact on sustainable performance.
Contemporaneous deposition of phyllosilicates and sulfates: Using Australian acidic saline lake deposits to describe geochemical variability on Mars

Studies of the origin of the Martian sulfate and phyllosilicate deposits have led to the hypothesis that there was a marked, global‐scale change in the Mars environment from circum‐neutral pH aqueous alteration in the Noachian to an acidic evaporitic system in the late Noachian to Hesperian. However, terrestrial studies suggest that two different geochemical systems need not be invoked to explain such geochemical variation. Western Australian acidic playa lakes have large pH differences separated vertically and laterally by only a few tens of meters, demonstrating how highly variable chemistries can coexist over short distances in natural environments. We suggest diverse and variable Martian aqueous environments where the coetaneous formation of phyllosilicates and sulfates at the Australian sites are analogs for regions where phyllosilicates and sulfates coexist on Mars. In these systems, Fe and alkali earth phyllosilicates represent deep facies associated with upwelling neutral to alkaline groundwater, whereas aluminous phyllosilicates and sulfates represent near‐surface evaporitic facies formed from more acidic brines.
A Bayesian Demonstration of Reliability for Encapsulated Implanted Electronics

The long term performance of implanted medical devices is critically affected by their packaging materials. Traditional hermetic enclosures are a hindrance to miniaturisation which might be avoided by polymer encapsulation. However, much uncertainty remains regarding such an approach for chronic implants. It is difficult to extract meaning from lifetime experiments performed on arbitrary test structures and before many highly reliable devices have actually failed. In this study, we describe an accelerated aging experiment on devices that employ test structures fabricated on a silicone encapsulated 0.35 μm CMOS technology. Samples are aged at 47, 67 and 87 °C under a constant 5V DC bias. After over 300 days of aging, of the 36 samples under test, there have only been four failures. Three failures are attributed to the interconnect to the measurement system, with the remaining failure due to delamination of the silicone encapsulant over wirebonds. By employing a Bayesian reliability analysis of the near-zero failure data we demonstrate a 1st failure percentile for the CMOS components of greater than 92 days when aged at 87 °C, calculated at a 95% confidence level, which approximately corresponds to over 8 years at 37 °C.
New insights into Martian dust distribution and water‐ice cloud microphysics

[1] In this paper we use a direct method which combines microphysics and photometric simulations of the Martian atmosphere. This approach allows us to reproduce vertical profiles of the light scattered by the haze at the limb of Mars. Subsequent results are compared to a multiple-color image provided by the Viking Orbiter camera. The “free parameters” of our study are related to vertical transport and dust size distribution. A sensitivity study has been conducted, encompassing a relevant range of parameters, in order to obtain the most satisfying multispectral modeled profile with respect to the one inferred from data. Except for an unlikely distribution of submicron particles (reff ∼ 0.2 μm), no consistent fit can be obtained. This implies that size distributions of dust suggested by previous studies are not in agreement with the present analysis. This apparent discrepancy can be resolved by adding a separate peak of submicron particles to the size distribution previously extracted from Viking Lander images. Only in that case can spectral and vertical structures of haze be successfully matched. While a bimodal distribution would change the current picture of Martian dust, such distribution is a common representation of soil-derived aerosol size function in Earth deserts. We also attempted to derive information from the cloud shown in the Viking limb image. Our estimates suggest that cloud particle effective radius is around 1.2–1.8 μm, while the cloud visible opacity is 0.02.
Nutrient losses from rain‐fed bench terraced cultivation systems in high rainfall areas of the mid‐hills of Nepal

Between the elevations of 1000 and 2000 m in the mid‐hills of Nepal, over 12 million people subsist on land‐holdings of less than 0·5 ha. These farmers have limited access to commercial inputs such as fertilisers and are reliant on organic manures for soil fertility maintenance. Participatory research was conducted with farmers on bari land (upper slope rain‐fed crop terraces) in the hill community of Landruk (bench terraces 0–5° slope, 3000–3500 mm annual rainfall, which aimed to develop soil and water management interventions that controlled erosion without resulting in high leaching, and so were effective in minimising total nutrient losses. Interventions tested were the control of water movement through diversion of run‐on and planting fodder grasses on terrace risers on bench terraces. The interventions were effective in reducing soil loss from the bari land in comparison with existing farmer practices, but no effect was observed on nutrient losses in solution form through runoff and leaching. Losses of NO3‐N in leachate ranged from 17·3 to 99·7 kg ha−1 yr−1, but only 0·7 to 5·6 kg ha−1 yr−1 in runoff. The overall nutrient balance suggests that the system is not sustainable. Fertility is heavily dependent on livestock inputs and if the current trends of declining livestock numbers due to labour constraints continue, further losses in productivity can be expected. However, farmers are interested in interventions that tie ecosystem services with productivity enhancement and farmers' priorities should be used as entry points for promoting interventions that are system compatible and harness niche opportunities. Copyright © 2007 John Wiley & Sons, Ltd.
Effects of melt fractional crystallization on Sr-Nd and Lu-Hf isotope systems: a case study of Triassic migmatite in the Sulu UHP terrane

The Weihai migmatite in the Sulu ultra-high-pressure (UHP) metamorphic terrane, eastern China, underwent partial melting in the Late Triassic during its exhumation. The primary partial melts experienced a decompressional fractional crystallization (DFC) process to produce plagioclase (Pl)-rich leucosome crystallized under eclogite to granulite facies conditions and K-feldspar (Kfs)-rich pegmatitic veins crystallized under amphibolite-facies conditions. In this study, our results demonstrate that the DFC process can cause decoupling between whole-rock Sr and Nd isotopes. The Pl-rich leucosome has εNd(t) values (–10.4 to −15.0) and initial (87Sr/86Sr) ratios (0.708173–0.712476) very similar to those of the melanosome, but the Kfs-rich pegmatitic veins have homogeneous εNd(t) values (−14.8 to −15.2) and significantly high initial (87Sr/86Sr) ratios (0.713882–0.716284). Our results also suggest that the DFC process can change zircon 176Yb/177Hf and 176Lu/177Hf isotopic ratios, with no effect on 176Hf/177Hf ratios or εHf (t) values. Zircon 176Yb/177Hf and 176Lu/177Hf ratios increase dramatically from the Pl-rich leucosome to the Kfs-rich pegmatitic veins, but zircon 176Hf/177Hf ratios (Pl-rich leucosomes = 0.282330 ± 0.000017; Kfs-rich pegmatitic veins = 0.282321 ± 0.000026) and εHf (t) values (Pl-rich leucosomes = −10.9 ± 0.6; Kfs-rich pegmatitic veins = −11.6 ± 0.8) remain almost unchanged. We propose that the isotopic decoupling between the Pl-rich leucosome and Kfs-rich pegmatitic vein might be caused by melt fractional crystallization occurring too rapidly to allow complete equilibrium between them.
Pebble shape (and size

ABSTRACT The mathematical technique of R-mode factor analysis was applied to the long, intermediate and short axes of one synthetic random data set and three sets of natural pebbles to extract the three fundamental factors related to these parameters. One factor corresponds to size, which is best described by the mean of the axes. Two further factors correspond to shape: sphericity and disc-rodness. These factors are revealed whether synthetic data or natural pebble samples are analyzed. Extending the factor analysis to include shape indices revealed which indices are equivalent, which are most useful, and which should be discarded. Sphericity is best described with the Corey shape index, S/(IL), and disc-rodness is best described with the disc-rod index, (L - I)/(L - S). Accordingly, the most effective shape diagram is a triangular plot of these two shape indices; the three end-members of shape are spheres, discs and rods. Shape is best investigated using this shape diagram; a 2-D technique such as contouring point density on this diagram should be used to determine the mean and standard deviation of shape. "While others ask themselves 'What is there to do? ', I ask myself 'What is there that I can avoid doing? '" Masanobu Fukuoka, One Straw Revolution
Increased working memory load does not modulate the attentional blink

The human capacity to process and encode stimuli in working memory is limited, and one way to test this capacity is the attentional blink. In this paradigm, participants are usually able to correctly identify a �rst target but fail to correctly identify a second target presented shortly after. In the current experiment, we combined the attentional blink paradigm with a visual working memory manipulation to examine the modulation of the target identi�cation by reduced cognitive capacity. Bottleneck theories predict an increased attentional blink with limited resources. In contrast, the overinvestment hypothesis predicts an inverted-u shaped relationship between attentional resources and the attentional blink. In support of the former explanation, we found an increase in the attentional blink with increasing working memory load. However, we did not �nd an interaction between the target lag and the working memory load, which indicates that the working memory load did not modulate the attentional blink but affected the perceptual encoding of the second target.
Swell transformation across the continental shelf. Part I: Attenuation and directional broadening

Abstract Extensive wave measurements were collected on the North Carolina–Virginia continental shelf in the autumn of 1999. Comparisons of observations and spectral refraction computations reveal strong cross-shelf decay of energetic remotely generated swell with, for one particular event, a maximum reduction in wave energy of 93% near the Virginia coastline, where the shelf is widest. These dramatic energy losses were observed in light-wind conditions when dissipation in the surface boundary layer caused by wave breaking (whitecaps) was weak and wave propagation directions were onshore with little directional spreading. These observations suggest that strong dissipation of wave energy takes place in the bottom boundary layer. The inferred dissipation is weaker for smaller-amplitude swells. For the three swell events described here, observations are reproduced well by numerical model hindcasts using a parameterization of wave friction over a movable sandy bed. Directional spectra that are narrow off the s.
Size-fractionated Iron Concentrations and Fe(III) Hydroxide Solubilities in Various Coastal Waters

The distribution of iron in two size fractions (<0·025 and <0·45μm) was studied in various coastal waters from northern Japan and in oceanic water, and it was found that estuarine waters and surface waters in Funka Bay (Hokkaido) had the highest colloidal iron concentrations (0·025–0·45-μm fraction, 7–19 nM), with a large portion (85–93%) in the <0·45μm fraction. The high colloidal iron concentrations in estuarine and bay surface waters were probably due to the rapid formation or contribution of colloidal iron through riverine and atmospheric inputs, respectively. Dissolved organic substances, such as humic substances and other organic Fe(III) chelators, possibly contributed to the formation and stabilization of the colloidal iron fraction in seawater. In addition, ultraviolet (UV)-irradiation treatment of coastal and estuarine waters reduced the iron concentrations in all size fractions (<0·025μm, 0·025–0·45μm, <0·45 μm) and the Fe(III) hydroxide solubilities, resulting from the decomposition of natural organic iron chelators. These results suggest that natural organic Fe(III) chelators control the colloidal and dissolved iron concentrations in seawater.
Do self-management interventions in COPD patients work and which patients benefit most? an individual patient data meta-analysis

Background: Self-management interventions are considered effective in patients with COPD, but trials have shown inconsistent results and it is unknown which patients benefit most. This study aimed to summarize the evidence on effectiveness of self-management interventions and identify subgroups of COPD patients who benefit most. Methods: Randomized trials of self-management interventions between 1985 and 2013 were identified through a systematic literature search. Individual patient data of selected studies were requested from principal investigators and analyzed in an individual patient data meta-analysis using generalized mixed effects models. Results: Fourteen trials representing 3,282 patients were included. Self-management interventions improved health-related quality of life at 12 months (standardized mean difference 0.08, 95% confidence interval [CI] 0.00–0.16) and time to first respiratory-related hospitalization (hazard ratio 0.79, 95% CI 0.66–0.94) and all-cause hospitalization (hazard ratio 0.80, 95% CI 0.69–0.90), but had no effect on mortality. Prespecified subgroup analyses showed that interventions were more effective in males (6-month COPD-related hospitalization: interaction P = 0.006), patients with severe lung function (6-month all-cause hospitalization: interaction P = 0.016), moderate self-efficacy (12-month COPD-related hospitalization: interaction P = 0.036), and high body mass index (6-month COPD-related hospitalization: interaction P = 0.028 and 6-month mortality: interaction P = 0.026). In none of these subgroups, a consistent effect was shown on all relevant outcomes. Conclusion: Self-management interventions exert positive effects in patients with COPD on respiratory-related and all-cause hospitalizations and modest effects on 12-month health-related quality of life, supporting the implementation of self-management strategies in clinical practice. Benefits seem similar across the subgroups studied and limiting self-management interventions to specific patient subgroups cannot be recommended.
EFFECTS OF DEFORESTATION ON THE PROPERTIES OF SOIL OF SAL FORESTS IN BANGLADESH

This study examined the effect of deforestation on the soil properties (physico-chemical and bacterial) of the Sal ( Shorea robusta Roxb. Ex Gaertn.) forests in Bangladesh. Physico-chemical properties and the bacterial colony counts of soil were studied by comparing a natural Sal forest site with deforested and planted with Menjium site , deforested and planted with Mahogoni site, as well as deforested but not planted but covered with profuse growth of Axonopus compressus grass species site. Moisture content was significantly lower in the deforested and planted with Menjium site and deforested and planted with Mahogoni site than the natural forest site and the deforested but not planted site. Total organic carbon, total nitrogen and available nitrogen contents were significantly lower in the natural forest site. Significantly higher number of bacterial colony and higher organic carbon and moisture contents were found in the deforested but not planted site indicating that both organic carbon and moisture content were important for microbial growth. The present study clearly showed that deforestation significantly altered the soil physico-chemical and bacterial communities of the Sal forests. It was also revealed that plantation with different exotic plants were found to be different in influencing soil properties. Key words: Bacterial colony; Deforestation effects; Sal forest; Soil physico-chemical properties DOI: http://dx.doi. org/10.3329/dujbs.v19i1. 8945 DUJBS 2010; 19(1): 63-72