Results of ultra-low level 71ge counting for application in the Gallex-solar neutrino experiment at the Gran Sasso Underground Physics Laboratory

It has been experimentally verified that the Ultra-Low-Level Counting System for the Gallex solar neutrino experiment is capable of measuring the expected solar up silon-flux to plus or minus 12% during two years of operation

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly

Background: The lack of genomic resources can present challenges for studies of non-model organisms. Transcriptome sequencing offers an attractive method to gather information about genes and gene expression without the need for a reference genome. However, it is unclear what sequencing depth is adequate to assemble the transcriptome de novo for these purposes. Results: We assembled transcriptomes of animals from six different phyla (Annelids, Arthropods, Chordates, Cnidarians, Ctenophores, and Molluscs) at regular increments of reads using Velvet/Oases and Trinity to determine how read count affects the assembly. This included an assembly of mouse heart reads because we could compare those against the reference genome that is available. We found qualitative differences in the assemblies of whole-animals versus tissues. With increasing reads, whole-animal assemblies show rapid increase of transcripts and discovery of conserved genes, while single-tissue assemblies show a slower discovery of conserved genes though the assembled transcripts were often longer. A deeper examination of the mouse assemblies shows that with more reads, assembly errors become more frequent but such errors can be mitigated with more stringent assembly parameters. Conclusions: These assembly trends suggest that representative assemblies are generated with as few as 20 million reads for tissue samples and 30 million reads for whole-animals for RNA-level coverage. These depths provide a good balance between coverage and noise. Beyond 60 million reads, the discovery of new genes is low and sequencing errors of highly-expressed genes are likely to accumulate. Finally, siphonophores (polymorphic Cnidarians) are an exception and possibly require alternate assembly strategies

Testing the reconstruction of modelled particulate organic carbon from surface ecosystem components using PlankTOM12 and machine learning

Understanding the relationship between surface marine ecosystems and the export of carbon to depth by sinking organic particles is key to representing the effect of ecosystem dynamics and diversity, and their evolution under multiple stressors, on the carbon cycle and climate in models. Recent observational technologies have greatly increased the amount of data available, both for the abundance of diverse plankton groups and for the concentration and properties of particulate organic carbon in the ocean interior. Here we use synthetic model data to test the potential of using machine learning (ML) to reproduce concentrations of particulate organic carbon within the ocean interior based on surface ecosystem and environmental data. We test two machine learning methods that differ in their approaches to data-fitting, the random forest and XGBoost methods. The synthetic data are sampled from the PlankTOM12 global biogeochemical model using the time and coordinates of existing observations. We test 27 different combinations of possible drivers to reconstruct small (POCS) and large (POCL) particulate organic carbon concentrations. We show that ML can successfully be used to reproduce modelled particulate organic carbon over most of the ocean based on ecosystem and modelled environmental drivers. XGBoost showed better results compared to random forest thanks to its gradient boosting trees' architecture. The inclusion of plankton functional types (PFTs) in driver sets improved the accuracy of the model reconstruction by 58 % on average for POCS and by 22 % for POCL. Results were less robust over the equatorial Pacific and some parts of the high latitudes. For POCS reconstruction, the most important drivers were the depth level, temperature, microzooplankton and PO4, while for POCL it was the depth level, temperature, mixed-layer depth, microzooplankton, phaeocystis, PO4 and chlorophyll a averaged over the mixed-layer depth. These results suggest that it will be possible to identify linkages between surface environmental and ecosystem structure and particulate organic carbon distribution within the ocean interior using real observations and to use this knowledge to improve both our understanding of ecosystem dynamics and of their functional representation within models.</p

Dead zone or oasis in the open ocean? Zooplankton distribution and migration in low-oxygen modewater eddies

The eastern tropical North Atlantic (ETNA) features a mesopelagic oxygen minimum zone (OMZ) at approximately 300–600 m depth. Here, oxygen concentrations rarely fall below 40 µmol O2 kg−1, but are expected to decline under future projections of global warming. The recent discovery of mesoscale eddies that harbour a shallow suboxic (< 5 µmol O2 kg−1) OMZ just below the mixed layer could serve to identify zooplankton groups that may be negatively or positively affected by ongoing ocean deoxygenation. In spring 2014, a detailed survey of a suboxic anticyclonic modewater eddy (ACME) was carried out near the Cape Verde Ocean Observatory (CVOO), combining acoustic and optical profiling methods with stratified multinet hauls and hydrography. The multinet data revealed that the eddy was characterized by an approximately 1.5-fold increase in total area-integrated zooplankton abundance. At nighttime, when a large proportion of acoustic scatterers is ascending into the upper 150 m, a drastic reduction in mean volume backscattering (Sv) at 75 kHz (shipboard acoustic Doppler current profiler, ADCP) within the shallow OMZ of the eddy was evident compared to the nighttime distribution outside the eddy. Acoustic scatterers avoided the depth range between approximately 85 to 120 m, where oxygen concentrations were lower than approximately 20 µmol O2 kg−1, indicating habitat compression to the oxygenated surface layer. This observation is confirmed by time series observations of a moored ADCP (upward looking, 300 kHz) during an ACME transit at the CVOO mooring in 2010. Nevertheless, part of the diurnal vertical migration (DVM) from the surface layer to the mesopelagic continued through the shallow OMZ. Based upon vertically stratified multinet hauls, Underwater Vision Profiler (UVP5) and ADCP data, four strategies followed by zooplankton in response to in response to the eddy OMZ have been identified: (i) shallow OMZ avoidance and compression at the surface (e.g. most calanoid copepods, euphausiids); (ii) migration to the shallow OMZ core during daytime, but paying O2 debt at the surface at nighttime (e.g. siphonophores, Oncaea spp., eucalanoid copepods); (iii) residing in the shallow OMZ day and night (e.g. ostracods, polychaetes); and (iv) DVM through the shallow OMZ from deeper oxygenated depths to the surface and back. For strategy (i), (ii) and (iv), compression of the habitable volume in the surface may increase prey–predator encounter rates, rendering zooplankton and micronekton more vulnerable to predation and potentially making the eddy surface a foraging hotspot for higher trophic levels. With respect to long-term effects of ocean deoxygenation, we expect avoidance of the mesopelagic OMZ to set in if oxygen levels decline below approximately 20 µmol O2 kg−1. This may result in a positive feedback on the OMZ oxygen consumption rates, since zooplankton and micronekton respiration within the OMZ as well as active flux of dissolved and particulate organic matter into the OMZ will decline

Changing nutrient stoichiometry affects phytoplankton production, DOP accumulation and dinitrogen fixation – a mesocosm experiment in the eastern tropical North Atlantic

Ocean deoxygenation due to climate change may alter redox-sensitive nutrient cycles in the marine environment. The productive eastern tropical North Atlantic (ETNA) upwelling region may be particularly affected when the relatively moderate oxygen minimum zone (OMZ) deoxygenates further and microbially driven nitrogen (N) loss processes are promoted. Consequently, water masses with a low nitrogen to phosphorus (N : P) ratio could reach the euphotic layer, possibly influencing primary production in those waters. Previous mesocosm studies in the oligotrophic Atlantic Ocean identified nitrate availability as a control of primary production, while a possible co-limitation of nitrate and phosphate could not be ruled out. To better understand the impact of changing N : P ratios on primary production and N2 fixation in the ETNA surface ocean, we conducted land-based mesocosm experiments with natural plankton communities and applied a broad range of N : P ratios (2.67–48). Silicic acid was supplied at 15 µmol L−1 in all mesocosms. We monitored nutrient drawdown, biomass accumulation and nitrogen fixation in response to variable nutrient stoichiometry. Our results confirmed nitrate to be the key factor determining primary production. We found that excess phosphate was channeled through particulate organic matter (POP) into the dissolved organic matter (DOP) pool. In mesocosms with low inorganic phosphate availability, DOP was utilized while N2 fixation increased, suggesting a link between those two processes. Interestingly this observation was most pronounced in mesocosms where nitrate was still available, indicating that bioavailable N does not necessarily suppress N2 fixation. We observed a shift from a mixed cyanobacteria–proteobacteria dominated active diazotrophic community towards a diatom-diazotrophic association of the Richelia-Rhizosolenia symbiosis. We hypothesize that a potential change in nutrient stoichiometry in the ETNA might lead to a general shift within the diazotrophic community, potentially influencing primary productivity and carbon export

Complete results for five years of GNO solar neutrino observations

We report the complete GNO solar neutrino results for the measuring periods GNO III, GNO II, and GNO I. The result for GNO III (last 15 solar runs) is [54.3 + 9.9 - 9.3 (stat.)+- 2.3 (syst.)] SNU (1 sigma) or [54.3 + 10.2 - 9.6 (incl. syst.)] SNU (1 sigma) with errors combined. The GNO experiment is now terminated after altogether 58 solar exposure runs that were performed between May 20, 1998 and April 9, 2003. The combined result for GNO (I+II+III) is [62.9 + 5.5 - 5.3 (stat.) +- 2.5 (syst.)] SNU (1 sigma) or [62.9 + 6.0 - 5.9] SNU (1 sigma) with errors combined in quadrature. Overall, gallium based solar observations at LNGS (first in GALLEX, later in GNO) lasted from May 14, 1991 through April 9, 2003. The joint result from 123 runs in GNO and GALLEX is [69.3 +- 5.5 (incl. syst.)] SNU (1 sigma). The distribution of the individual run results is consistent with the hypothesis of a neutrino flux that is constant in time. Implications from the data in particle- and astrophysics are reiterated.Comment: 22 pages incl. 9 Figures and 8 Tables. to appear in: Physics Letters B (accepted April 13, 2005) PACS: 26.65.+t ; 14.60.P

The Nylon Scintillator Containment Vessels for the Borexino Solar Neutrino Experiment

Borexino is a solar neutrino experiment designed to observe the 0.86 MeV Be-7 neutrinos emitted in the pp cycle of the sun. Neutrinos will be detected by their elastic scattering on electrons in 100 tons of liquid scintillator. The neutrino event rate in the scintillator is expected to be low (~0.35 events per day per ton), and the signals will be at energies below 1.5 MeV, where background from natural radioactivity is prominent. Scintillation light produced by the recoil electrons is observed by an array of 2240 photomultiplier tubes. Because of the intrinsic radioactive contaminants in these PMTs, the liquid scintillator is shielded from them by a thick barrier of buffer fluid. A spherical vessel made of thin nylon film contains the scintillator, separating it from the surrounding buffer. The buffer region itself is divided into two concentric shells by a second nylon vessel in order to prevent inward diffusion of radon atoms. The radioactive background requirements for Borexino are challenging to meet, especially for the scintillator and these nylon vessels. Besides meeting requirements for low radioactivity, the nylon vessels must also satisfy requirements for mechanical, optical, and chemical properties. The present paper describes the research and development, construction, and installation of the nylon vessels for the Borexino experiment

Female bone physiology resilience in 750-300 BP ‘Polynesian Outlier’ community

Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in n = 69 individuals from 750 – 300 BP Taumako in Solomon Islands, a remote ‘Polynesian Outlier’ island in Melanesia. We tested whether bone remodelling indicators differed between age-at-death groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-to-osteon (~10%) did not differ between the sexes. Compared to males, the femora of Taumako females experienced higher frequencies of remodelling events, which mirrors bone health paradigms through the life-course today. However, contrary to modern populations, female femoral bone tissue did not decline with age. This matches findings in other archaeological samples, and is testament to ancient female bone physiology resilience also in the Pacific region.Introduction - The importance of bone remodelling through human life-course - Bone remodelling in archaeological humans Results - Trends in bone remodelling at Taumako Discussion - Sex-specific trends in cortical bone remodelling - Bone remodelling with age at Taumako Limitations and remarks on temporal and spatial data Conslusions Materials and Method

Female bone physiology resilience in a past Polynesian Outlier community

Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in 69 individuals from ca. 440–150 BP Taumako in Solomon Islands, a remote ‘Polynesian Outlier’ island in Melanesia. We tested whether bone remodelling indicators differed between age groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-osteon (~ 8%) did not differ between the sexes. Our results indicate that, compared to males, localised femoral bone tissue of the Taumako females did not drastically decline with age, contrary to what is often observed in modern populations. However, our results match findings in other archaeological samples—a testament to past female bone physiology resilience, also now observed in the Pacific region.Introduction - Bone remodelling through human life‑course. - Bone remodelling in archaeological humans. Results - Femoral vascular porosity and bone remodelling indicators at Taumako. Discussion - Sex and cortical bone histology at Taumako. - The effect of age on bone histology at Taumako. Remarks on temporal and spatial bone histology data Limitations Conclusions Materials and method

GNO Solar Neutrino Observations: Results for GNOI

We report the first GNO solar neutrino results for the measuring period GNOI, solar exposure time May 20, 1998 till January 12, 2000. In the present analysis, counting results for solar runs SR1 - SR19 were used till April 4, 2000. With counting completed for all but the last 3 runs (SR17 - SR19), the GNO I result is [65.8 +10.2 -9.6 (stat.) +3.4 -3.6 (syst.)]SNU (1sigma) or [65.8 + 10.7 -10.2 (incl. syst.)]SNU (1sigma) with errors combined. This may be compared to the result for Gallex(I-IV), which is [77.5 +7.6 -7.8 (incl. syst.)] SNU (1sigma). A combined result from both GNOI and Gallex(I-IV) together is [74.1 + 6.7 -6.8 (incl. syst.)] SNU (1sigma).Comment: submitted to Physics Letters B, June 2000. PACS: 26.65. +t ; 14.60 Pq. Corresponding author: [email protected] ; [email protected]