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Abstract Objectives This study presents a framework for the calculation of supraspinatus (SSP) muscle pennation angles (PAs) from diffusion tensor imaging (DTI). Materials and methods Ten healthy individuals (five females and five males; age 32.0 ± 4.7 years) underwent three sessions of 3-T MRI, including a stimulated echo acquisition mode DTI sequence. The imaging plane of the DTI sequence was angled along the intramuscular part of the SSP tendon. A custom-built software was developed and implemented to compute DTI-based PAs of the anterior and posterior SSP in relation to the orientation of the tendon. Subsequently, three readers measured PAs from the post-processed images. Test-retest reliability, inter-reader agreement, and intra-reader agreement of PA measurements were evaluated with intraclass correlation coefficients (ICCs). Results The mean PA in the anterior SSP was 15.6 ± 2.1° and 10.7 ± 0.9° in the posterior SSP. MRI-derived PAs showed good to excellent test-retest reliability (ICC: 0.856–0.945), inter-reader agreement (ICC: 0.863–0.955), and intra-reader agreement (ICC: 0.804–0.955). Conclusion PAs derived from DTI demonstrated good to excellent test-retest reliability, inter-reader agreement, and intra-reader agreement. We successfully implemented a highly standardized technique for evaluating PAs of the SSP muscle. Critical relevance statement This proposed low-complex method might facilitate the increased use of the PA as a biomarker for pathological conditions of the rotator cuff. Key Points A low-complex method for measuring PAs of the SSP might help identify pathology early. The mean PA was 15.6 ± 2.1° and 10.7 ± 0.9° in the anterior and posterior SSP, respectively. ICCs were ≥ 0.856 for test-retest reliability, ≥ 0.863 for inter-reader agreement, and ≥ 0.804 for intra-reader agreement. Graphical Abstract

Abstract Background The diagnostic value of clinical rotator cuff (RC) tests is controversial, with only sparse evidence available about their anatomical specificity. We prospectively assessed regional RC muscle activation patterns by means of intravoxel incoherent motion (IVIM) diffusion-weighted magnetic resonance imaging (MRI) after the execution of common clinical RC tests. Methods Ten healthy subjects (five males, five females) underwent three sessions of diffusion-weighted 3-T shoulder MRI before and after testing the supraspinatus (SSP, Jobe test, session 1), subscapularis (SSC, lift-off test, session 2, at least 1 week later), and infraspinatus muscle (ISP, external rotation test, session 3, another week later). IVIM parameters (perfusion fraction, f; pseudo-diffusion coefficient. D*; and their product, fD*) were measured in regions of interest placed in images of the SSP, SSC, ISP, and deltoid muscle. The Wilcoxon signed-rank test was used for group comparisons; p-values were adjusted using the Bonferroni correction. Results After all tests, fD* was significantly increased in the respective target muscles (SSP, SSC, or ISP; p ≤ 0.001). After SSP testing, an additional significant increase of fD* was observed in the deltoid, the SSC, and the ISP muscle (p

Recent studies have begun to explore the potential of enhanced benthic weathering (EBW) in the Baltic Sea as a measure for climate change mitigation. To augment the understanding of EBW under seasonally changing conditions, this study aims to investigate weathering processes under anoxia to hypoxia in corrosive bottom waters, which reflect late summer conditions in the Baltic Sea. Dunite and calcite were added to sediment cores retrieved from Eckernförde Bay (Western Baltic Sea) with a constant flow-through of deoxygenated, CO2-enriched Baltic Sea bottom water. The addition of both materials increased benthic alkalinity release by 2.94 μmol cm−2 d−1 (calcite) and 1.12 μmol cm−2 d−1 (dunite), compared to the unamended control experiment. These excess fluxes are significantly higher than those obtained under winter conditions. The comparison with bottom water oxygen concentrations emphasizes that highest fluxes of alkalinity were associated with anoxic phases of the experiment. An increase in Ca and Si fluxes showed that the enhanced alkalinity fluxes could be attributed to calcite and dunite weathering. First order rate constants calculated based on these data were close to rates published in previous studies conducted under different conditions. This highlights the suitability of these proxies for mineral dissolution and justifies the use of these rate constants in modeling studies investigating EBW in the Baltic Sea and areas with similar chemical conditions. Generally stable pH profiles over the course of the experiment, together with the fact that the added minerals remained on the sediment surface, suggest that corrosive bottom waters were the main driving factor for the dissolution of the added minerals. These factors have important implications for the choice of mineral and timing for EBW as a possible marine carbon dioxide removal method in seasonally hypoxic to anoxic regions of the Baltic Sea.

Sediment fluxes to the seafloor govern the fate of elements and compounds in the ocean and serve as a prerequisite for research on elemental cycling, benthic processes and sediment management strategies. To quantify these fluxes over seafloor areas, it is necessary to scale up sediment mass accumulation rates (MAR) obtained from multiple sample stations. Conventional methods for spatial upscaling involve averaging of data or spatial interpolation. However, these approaches may not be sufficiently precise to account for spatial variations of MAR, leading to poorly constrained regional sediment budgets. Here, we utilize a machine learning approach to scale up porosity and 210Pb data from 145 and 65 stations, respectively, in the Skagerrak. The models predict the spatial distributions by considering several predictor variables that are assumed to control porosity and 210Pb rain rates. The spatial distribution of MAR is based on the predicted porosity and existing sedimentation rate data. Our findings reveal highest MAR and 210Pb rain rates to occur in two parallel belt structures that align with the general circulation pattern in the Skagerrak. While high 210Pb rain rates occur in intermediate water depths, the belt of high MAR is situated closer to the coastlines due to lower porosities at shallow water depths. Based on the spatial distributions, we calculate a total MAR of 34.7 Mt yr-1 and a 210Pb rain rate of 4.7 · 1014 dpm yr-1. By comparing atmospheric to total 210Pb rain rates, we further estimate that 24% of the 210Pb originates from the local atmospheric input, with the remaining 76% being transported laterally into the Skagerrak. The updated MAR in the Skagerrak is combined with literature data on other major sediment sources and sinks to present a tentative sediment budget for the North Sea, which reveals an imbalance with sediment outputs exceeding the inputs. Substantial uncertainties in the revised Skagerrak MAR and the literature data might close this imbalance. However, we further hypothesize that previous estimates of suspended sediment inputs into the North Sea might have been underestimated, considering recently revised and elevated estimates on coastal erosion rates in the surrounding region of the North Sea.

Abstract This prospective study aimed to present, compare, and evaluate the suitability of five different magnetic resonance imaging (MRI) protocols (3D double-echo steady-state (DESS), 3D fast spin echo short-tau inversion recovery (SPACE-STIR), 3D fast spin echo spectral attenuated inversion recovery (SPACE-SPAIR), volumetric interpolated breath-hold examination (T1-VIBE-Dixon), and ultrashort echo time (UTE)) and for orthopantomogram (OPG)-like MRI reconstructions using a novel mandibular coil. Three readers assessed MR-OPGs of 21 volunteers regarding technical image quality (4, excellent; 0, severely reduced), susceptibility to artifacts (3, absence; 0, massive), and visualization of anatomical structures in the oral cavity and surrounding skeletal structures (4, fine details visible; 0, no structures visible). Average image quality was good (3.29 ± 0.83) for all MRI protocols, with UTE providing the best image quality (3.52 ± 0.62) and no to minor artifacts (2.56 ± 0.6). Full diagnostic interpretability of the osseous structures is best in VIBE-Dixon and UTE MR-OPGs. DESS provided excellent visualization of the finest details of the nervous tissue (3.95 ± 0.22). Intra-reader and inter-reader agreement between the readers was good to excellent for all protocols (ICCs 0.812–0.957). MR-OPGs provide indication-specific accurate imaging of the oral cavity and could contribute to the early detection of pathologies, staging, and radiological follow-up of oral and maxillofacial diseases.

This study identifies the rapidness of marine mineral reactions, directly after an extreme rainfall event. The reactions have the potential to affect marine cation and CO2 cycling, impacting element turnover on human time scales

Enhanced mineral dissolution in the benthic environment is currently discussed as a potential technique for ocean alkalinity enhancement (OAE) to reduce atmospheric CO2 levels. This study explores how biogeochemical processes affect the dissolution of alkaline minerals in surface sediments during laboratory incubation experiments. These involved introducing dunite and calcite to organic-rich sediments from the Baltic Sea under controlled conditions in an oxic environment. The sediment cores were incubated with Baltic Sea bottom water. Findings reveal that the addition of calcite increased the benthic alkalinity release from 0.4 μmol cm−2 d−1 (control) to 1.4 μmol cm−2 d−1 (calcite) as well as other weathering products such as calcium. However, these enhanced fluxes returned to lower fluxes after approximately 4 weeks yet still higher than the un-amended controls. Microbial activity appeared to be the primary driver for lowering pore water pH and thus enhanced weathering. In several sediment cores, pH profiles taken at the start of the experiments indicated activity of sulfur oxidizing Beggiatoa spp, which was verified by RNA-profiling of 16S rRNA genes. The pH profiles transitioned to those commonly associated with the activity of cable bacteria as the experiments progressed. The metabolic activity of cable bacteria would explain the significantly lower pH values (~5.6) at sediment depths of 1–3 cm, which would favor substantial calcite dissolution. However, a high abundance of cable bacteria was not reflected in 16S rRNA sequence data. Total alkalinity (TA) fluxes in these cores increased by a factor of ~3, with excess TA/calcium ratios indicating that the enhanced flux originated from calcite dissolution. The dissolution of dunite or the potential formation of secondary minerals could not be identified due to the strong natural flux of silicic acid, likely due to biogenic silica dissolution. Furthermore, no accumulation of potentially harmful metals such as nickel was observed, as highlighted as a potential risk in other studies concerning OAE. Given the complexity of sediment chemistry and changes of the benthic conditions induced by the incubation, it remains challenging to distinguish between natural and enhanced mineral weathering. Further investigation, including the identification of suitable tracers for mineral dissolution, are necessary to assess the feasibility of benthic weathering as a practical approach for OAE and climate change mitigation.

Dissolved silicate (H4SiO4) is essential for the formation of the opaline skeletal structures of diatoms and other siliceous plankton. A fraction of particulate biogenic silica (bSi) formed in surface waters sinks to the seabed, where it either dissolves and returns to the water column or is permanently buried. Global silica budgets are still poorly constrained since data on benthic bSi cycling are lacking, especially on continental margins. This study describes benthic bSi cycling in the Skagerrak, a sedimentary depocenter for particles from the North Sea. Biogenic silica burial fluxes, benthic H4SiO4 fluxes to the water column and bSi burial efficiencies are reported for nine stations by evaluating data from in-situ benthic landers and sediment cores with a diagenetic reaction-transport model. The model simulates bSi contents and H4SiO4 concentrations at all sites using a novel power law to describe bSi dissolution kinetics with a small number of adjustable parameters. Our results show that, on average, 1100 mmol m-2 yr-1 of bSi rains down to the Skagerrak basin seafloor, of which 50% is released back to overlying waters, with the remainder being buried. Biogenic silica cycling in the Skagerrak is generally consistent with previously reported global trends, showing higher Si fluxes and burial efficiencies than deep-sea sites and similar values compared to other continental margins. A significant finding of this work is a molar bSi-to-organic carbon burial ratio of 0.22 in Skagerrak sediments, which is distinctively lower compared to other continental margins. We suggest that the continuous dissolution of bSi in suspended sediments transported over long distances from the North Sea leads to the apparent decoupling between bSi and organic carbon in Skagerrak sediments.

Abstract Fossil benthic foraminifera are used to trace past methane release linked to climate change. However, it is still debated whether isotopic signatures of living foraminifera from methane-charged sediments reflect incorporation of methane-derived carbon. A deeper understanding of isotopic signatures of living benthic foraminifera from methane-rich environments will help to improve reconstructions of methane release in the past and better predict the impact of future climate warming on methane seepage. Here, we present isotopic signatures (δ13C and δ18O) of foraminiferal calcite together with biogeochemical data from Arctic seep environments from c. 1200 m water depth, Vestnesa Ridge, 79° N, Fram Strait. Lowest δ13C values were recorded in shells of Melonis barleeanus, − 5.2‰ in live specimens and − 6.5‰ in empty shells, from sediments dominated by aerobic (MOx) and anaerobic oxidation of methane (AOM), respectively. Our data indicate that foraminifera actively incorporate methane-derived carbon when living in sediments with moderate seepage activity, while in sediments with high seepage activity the poisonous sulfidic environment leads to death of the foraminifera and an overgrowth of their empty shells by methane-derived authigenic carbonates. We propose that the incorporation of methane-derived carbon in living foraminifera occurs via feeding on methanotrophic bacteria and/or incorporation of ambient dissolved inorganic carbon.

Benthic nitrogen cycling in the Mauritanian upwelling region (NW Africa) was studied in June 2014 from the shelf to the upper slope where minimum bottom water O2 concentrations of 25 µM were recorded. Benthic incubation chambers were deployed at 9 stations to measure fluxes of O2, dissolved inorganic carbon (DIC) and nutrients (NO3-, NO2-, NH4+, PO43-, H4SiO4) along with the N and O isotopic composition of nitrate (δ15N-NO3- and δ18O-NO3-) and ammonium (δ15N-NH4+). O2 and DIC fluxes were similar to those measured during a previous campaign in 2011 whereas NH4+ and PO43- fluxes on the shelf were 2 – 3 times higher and possibly linked to a long-term decline in bottom water O2 concentrations. The mean isotopic fractionation of NO3- uptake on the margin, inferred from the loss of NO3- inside the chambers, was 1.5 ± 0.4 ‰ for 15/14N (15ϵapp) and 2.0 ± 0.5 ‰ for 18/16O (18ϵapp). The mean 18ϵapp:15ϵapp ratio on the shelf (< 100 m) was 2.1 ± 0.3, and higher than the value of 1 expected for microbial NO3-reduction. The 15ϵapp are similar to previously reported isotope effects for NO3- respiration in marine sediments but lower than determined in 2011 at a same site on the shelf. The sediments were also a source of 15N-enriched NH4+ (9.0 ± 0.7 ‰). A numerical model tuned to the benthic flux data and that specifically accounts for the efflux of 15N-enriched NH4+ from the seafloor, predicted a net benthic isotope effect of N loss (15ϵsed) of 3.6 ‰; far above the more widely considered value of ~0‰. This result is further evidence that the assumption of a universally low or negligible benthic N isotope effect is not applicable to oxygen-deficient settings. The model further suggests that 18ϵapp:15ϵapp trajectories > 1 in the benthic chambers are most likely due to aerobic ammonium oxidation and nitrite oxidation in surface sediments rather than anammox, in agreement with published observations in the water column of oxygen deficient regions.

Surface sediments of the coastal mud belt in the Benguela Upwelling System (BUS) off Namibia host extensive communities of chemotrophic large sulfur bacteria (LSB) of the family Beggiatoaceae such as Thiomargarita spp. and Candidatus Maribeggiatoa spp. In order to understand the role of these bacteria in N and P cycling, biogeochemical data from three sites in the mud belt were simulated with a biogeochemical model including LSB catabolic pathways. Organic carbon remineralization was dominated by the reduction of sulfate to hydrogen sulfide (5.0–7.7 mmol C m−2 d−1). At the two stations where LSB were observed, produced hydrogen sulfide was almost completely oxidized by LSB using nitrate as the electron acceptor. Modeled rates of nitrate reduction to N2 by LSB were over two times higher than nitrate reduction to ammonium. This points toward a potential negative feedback by LSB on primary production. Furthermore, loss of fixed N strongly enriched the benthic fluxes in P relative to N. Although the model included intracellular polyphosphate accumulation by LSB and subsequent breakdown to phosphate, a clear link between polyphosphate dynamics and hydroxyapatite precipitation and burial could not be clearly substantiated. This is partly due to simplifying assumptions in the model and analytical uncertainties in distinguishing between authigenic hydroxyapatite and allochthonous hydroxyapatite (e.g., fish bones), both of which are major components of particulate P in the BUS. Our modeling suggests a significant control of LSB on benthic N and P fluxes to the water column. Given the extensive coverage of LSB on the shelf (>30,000 km2), more accurate forecasts of nutrient cycling and primary production in the BUS necessitate a closer inspection of benthic P sources and sinks in the mud belt and a clearer understanding of the controls on the end product of nitrate reduction by LSB.

Fatigue-related subchondral bone injuries of the third metacarpal/metatarsal (McIII/MtIII) bones are common causes of wastage, and they are welfare concerns in racehorses. A better understanding of bone health and strength would improve animal welfare and be of benefit for the racing industry. The porosity index (PI) is an indirect measure of osseous pore size and number in bones, and it is therefore an interesting indicator of bone strength. MRI of compact bone using traditional methods, even with short echo times, fail to generate enough signal to assess bone architecture as water protons are tightly bound. Ultra-short echo time (UTE) sequences aim to increase the amount of signal detected in equine McIII/MtIII condyles. Cadaver specimens were imaged using a novel dual-echo UTE MRI technique, and PI was calculated and validated against quantitative CT-derived bone mineral density (BMD) measures. BMD and PI are inversely correlated in equine distal Mc/MtIII bone, with a weak mean r value of −0.29. There is a statistically significant difference in r values between the forelimbs and hindlimbs. Further work is needed to assess how correlation patterns behave in different areas of bone and to evaluate PI in horses with and without clinically relevant stress injuries.

Abstract In organisms with dormant stages, life‐history responses to past pollution can be studied retrospectively. Here, we study such responses in a rotifer (Brachionus calyciflorus) from the once heavily copper‐polluted Lake Orta (Italy). We extracted resting eggs from sediments, established clonal lineages from hatchlings, and exposed newborns of these lineages to one of three copper concentrations that each mimicked a specific period in the lake's pollution history. For each rotifer, we daily collected life‐table data. We then estimated treatment‐specific vital rates and used a stage‐structured population model to project population growth rate λ. We also estimated elasticities of λ to vital rates and contributions of vital rates to observed Δλ between copper treatments. As expected, λ decreased with increasing copper concentration. This decrease resulted mostly from a decline in juvenile survival rate (SJ) and partly from a decline in the survival rate of asexually reproducing females (SA). Maturation rate, and with one exception fecundity, also declined but did not contribute consistently to Δλ. λ was most elastic to SJ and SA, indicating that survival rates were under stronger selection than maturation rate and fecundity. Together, our results indicate that variation in juvenile survival is a key component in the rotifers’ copper response. The consistent decrease in SJ with increasing copper stress and the sensitivity of λ to that decrease also suggest that juvenile survival is a useful indicator of population performance under environmental pollution.

This paper presents the results of a study on the response of living benthic foraminifera to progressing environmental successions in a cold-seep ecosystem. Sediment samples were collected from Vestnesa Ridge (79°N, Fram Strait) at ~1200 m water depth. The distribution of live (Rose Bengal-stained) foraminifera were analyzed in the upper sediment layers in relation to pore water biogeochemical data together with the distribution of sulfur-bacterial mats and Siboglinidae tubeworms. At methane cold seeps, the process of environmental succession is strongly connected to the duration and strength of methane seepage and the intensity of methane-related biological processes, e.g, aerobic and anaerobic oxidation of methane (MOx and AOM, respectively). The results show that the distribution patterns of benthic foraminifera change according to the progressing environmental succession. The benthic foraminifera seemed to thrive in sediments with a moderate activity of seepage, dominated by MOx, i.e, at an early stage of seepage or when seepage decreases at a late stage of the succession. Species composition of the foraminiferal fauna under these conditions was similar to the control sites (outside of pockmarks with no seepage); the dominant species being Melonis barleeanus and Cassidulina neoteretis. In sediments with strong seepage and high AOM activity, the hostile environmental conditions due to the presence of toxic sulfide caused a reduction in the foraminiferal population, and samples were almost barren of foraminifera. In environments of moderate methane seepage, the presence of chemosynthetic Siboglinidae tube worms potentially support communities of the epibenthic species Cibicidoides wuellerstorfi. Despite the very different environmental conditions, the foraminiferal assemblages were very similar (or nearly absent). Therefore, the foraminiferal faunas cannot be used as exclusive indicators of past strength of methane seepage in palaeoceanographic interpretations.

Small-angle X-ray scattering (SAXS) combines the high tissue penetration of X-rays with specificity to periodic nanostructures. The authors use SAXS tensor tomography (SAXS-TT) on intact mouse and human brain tissue samples, to quantify myelin levels and determine myelin integrity, myelinated axon orientation, and fibre tracts non-destructively.

Abstract The detection and assessment of cerebral lesions and traumatic brain injuries are of particular interest in forensic investigations in order to differentiate between natural and traumatic deaths and to reconstruct the course of events in case of traumatic deaths. For this purpose, computed tomography (CT) and magnetic resonance imaging (MRI) are applied to supplement autopsy (traumatic death) or to supplant autopsy (natural deaths). This approach is termed “virtual autopsy.” The value of this approach increases as more microlesions and traumatic brain injuries are detected and assessed. Focusing on these findings, this article describes the examination of two decedents using CT, 3-T, and 7-T MRI. The main question asked was whether there is a benefit in using 7-T over 3-T MRI. To answer this question, the 3-T and 7-T images were graded regarding the detectability and the assessability of coup/contrecoup injuries and microlesions using 3-point Likert scales. While CT missed these findings, they were detectable on 3-T and 7-T MRI. However, the 3-T images appeared blurry in direct comparison with the 7-T images; thus, the detectability and assessability of small findings were hampered on 3-T MRI. The potential benefit of 7-T over 3-T MRI is discussed.

Abstract To investigate abdominal volume determined by a new body scanner algorithm as anthropometric marker for Metabolic Syndrome (MetS) and its parameters compared to manually measured waist circumference (WC), we performed body scans in 411 participants (38% men, 20-81 years). WC and triglyceride, HDL-cholesterol, and fasting glucose concentrations, and blood pressure were assessed as MetS parameters. We used Spearman correlations and linear regression to investigate associations and goodness-of-fit (R², BIC) of abdominal volume and WC with MetS parameters, and logistic regression to analyse the discriminative power of WC and abdominal volume to assess likelihoods of MetS components and MetS. Correlations with triglyceride, HDL-cholesterol, and glucose concentration were slightly stronger for abdominal volume (r; 0.32, −0.32, and 0.34, respectively) than for WC (0.28, −0.28, and 0.29, respectively). Explained variances in MetS parameters were slightly higher and goodness-of-fit slightly better for abdominal volume than for WC, but differences were small. Exemplarily, glucose levels were 0.28 mmol/L higher (R² = 0.25; BIC = 945.5) per 1-SD higher WC, and 0.35 mmol/L higher (R² = 0.28; BIC = 929.1) per 1-SD higher abdominal volume. The discriminative power to estimate MetS components was similar for WC and abdominal volume. Our data show that abdominal volume allows metabolic characterization comparable to established WC.

Background: Widespread white matter abnormalities are a frequent finding in chronic schizophrenia patients. More inconsistent results have been provided by the sparser literature on at-risk states for psychosis, i.e., emerging subclinical symptoms. However, considering risk as a homogenous construct, an approach of earlier studies, may impede our understanding of neuro-progression into psychosis. Methods: An analysis was conducted of 3-Tesla MRI diffusion and symptom data from 112 individuals (mean age, 21.97 ± 4.19) within two at-risk paradigm subtypes, only basic symptoms (n = 43) and ultra-high risk (n = 37), and controls (n = 32). Between-group comparisons (involving three study groups and further split based on the subsequent transition to schizophrenia) of four diffusion-tensor-imaging-derived scalars were performed using voxelwise tract-based spatial statistics, followed by correlational analyses with Structured Interview for Prodromal Syndromes responses. Results: Relative to controls, fractional anisotropy was lower in the splenium of the corpus callosum of ultra-high-risk individuals, but only before stringent multiple-testing correction, and negatively correlated with General Symptom severity among at-risk individuals. At-risk participants who transitioned to schizophrenia within 3 years, compared to those that did not transition, had more severe WM differences in fractional anisotropy and radial diffusivity (particularly in the corpus callosum, anterior corona radiata, and motor/sensory tracts), which were even more extensive compared to healthy controls. Conclusions: These findings align with the subclinical symptom presentation and more extensive disruptions in converters, suggestive of severity-related demyelination or axonal pathology. Fine-grained but detectable differences among ultra-high-risk subjects (i.e., with brief limited intermittent and/or attenuated psychotic symptoms) point to the splenium as a discrete site of emerging psychopathology, while basic symptoms alone were not associated with altered fractional anisotropy.

The snow leopard (Panthera uncia) is one of the world's most elusive felids. In Bhutan, which is one of the 12 countries where the species still persists, reliable information on its distribution and habitat suitability is lacking, thus impeding effective conservation planning for the species. To fill this knowledge gap, we created a country-wide species distribution model using “presence-only” data from 420 snow leopard occurrences (345 from a sign survey and 77 from a camera-trapping survey) and 12 environmental covariates consisting of biophysical and anthropogenic factors. We analyzed the data in an ensemble model framework which combines the outputs from several species distribution models. To assess the adequacy of Bhutan's network of protected areas and their potential contribution toward the conservation of the species, we overlaid the output of the ensemble model on the spatial layers of protected areas and biological corridors. The ensemble model identified 7,206 km2 of Bhutan as suitable for the snow leopard: 3,647 km2 as highly suitable, 2,681 km2 as moderately suitable, and 878 km2 as marginally suitable. Forty percent of the total suitable habitat consisted of protected areas and a further 8% of biological corridors. These suitable habitats were characterized by a mean livestock density of 1.3 individuals per hectare, and a mean slope of 25°; they closely match the distribution of the snow leopard's main wild prey, the bharal (Pseudois nayaur). Our study shows that Bhutan's northern protected areas are a centre for snow leopard conservation both at the national and regional scale.

From 2008 to 2019, a comprehensive research project, ‘SFB 754, Climate – Biogeochemistry Interactions in the Tropical Ocean,’ was funded by the German Research Foundation to investigate the climate-biogeochemistry interactions in the tropical ocean with a particular emphasis on the processes determining the oxygen distribution. During three 4-year long funding phases, a consortium of more than 150 scientists conducted or participated in 34 major research cruises and collected a wealth of physical, biological, chemical, and meteorological data. A common data policy agreed upon at the initiation of the project provided the basis for the open publication of all data. Here we provide an inventory of this unique data set and briefly summarize the various data acquisition and processing methods used.

We present schemes for simulating Brownian bridges on complete and connected Lie groups and homogeneous spaces. We use this to construct an estimation scheme for recovering an unknown left- or right-invariant Riemannian metric on the Lie group from samples. We subsequently show how pushing forward the distributions generated by Brownian motions on the group results in distributions on homogeneous spaces that exhibit a non-trivial covariance structure. The pushforward measure gives rise to new non-parametric families of distributions on commonly occurring spaces such as spheres and symmetric positive tensors. We extend the estimation scheme to fit these distributions to homogeneous space-valued data. We demonstrate both the simulation schemes and estimation procedures on Lie groups and homogenous spaces, including SPD(3)=GL+(3)/SO(3) and S2=SO(3)/SO(2).

Ever-increasing human pressures on cave biodiversity have amplified the need for systematic, repeatable, and intensive surveys of cave-dwelling arthropods to formulate evidence-based management decisions. We examined 110 papers (from 1967 to 2018) to: (i) understand how cave-dwelling invertebrates have been sampled; (ii) provide a summary of techniques most commonly applied and appropriateness of these techniques, and; (iii) make recommendations for sampling design improvement. Of the studies reviewed, over half (56) were biological inventories, 43 ecologically focused, seven were techniques papers, and four were conservation studies. Nearly one-half (48) of the papers applied systematic techniques. Few papers (24) provided enough information to repeat the study; of these, only 11 studies included cave maps. Most studies (56) used two or more techniques for sampling cave-dwelling invertebrates. Ten studies conducted ≥10 site visits per cave. The use of quantitative techniques was applied in 43 of the studies assessed. More than one-third (42) included some level of discussion on management. Future studies should employ a systematic study design, describe their methods in sufficient detail as to be repeatable, and apply multiple techniques and site visits. This level of effort and detail is required to obtain the most complete inventories, facilitate monitoring of sensitive cave arthropod populations, and make informed decisions regarding the management of cave habitats. We also identified naming inconsistencies of sampling techniques and provide recommendations towards standardization.

Computing sample means on Riemannian manifolds is typically computationally costly, as exemplified by computation of the Fréchet mean, which often requires finding minimizing geodesics to each data point for each step of an iterative optimization scheme. When closed-form expressions for geodesics are not available, this leads to a nested optimization problem that is costly to solve. The implied computational cost impacts applications in both geometric statistics and in geometric deep learning. The weighted diffusion mean offers an alternative to the weighted Fréchet mean. We show how the diffusion mean and the weighted diffusion mean can be estimated with a stochastic simulation scheme that does not require nested optimization. We achieve this by conditioning a Brownian motion in a product manifold to hit the diagonal at a predetermined time. We develop the theoretical foundation for the sampling-based mean estimation, we develop two simulation schemes, and we demonstrate the applicability of the method with examples of sampled means on two manifolds.

We survey the role of reduction by symmetry in the large deformation diffeomorphic metric mapping framework for registration of a variety of data types (landmarks, curves, surfaces, images and higher-order derivative data). Particle relabelling symmetry allows the equations of motion to be reduced to the Lie algebra allowing the equations to be written purely in terms of the Eulerian velocity field. As a second use of symmetry, the infinite dimensional problem of finding correspondences between objects can be reduced for a range of concrete data types, resulting in compact representations of shape and spatial structure. Using reduction by symmetry, we describe these models in a common theoretical framework that draws on links between the registration problem and geometric mechanics. We outline these constructions and further cases where reduction by symmetry promises new approaches to the registration of complex data types.

Diffusion magnetic resonance imaging (dMRI) is a compelling tool for investigating the structure and geometry of brain tissue based on indirect measurement of the diffusion anisotropy of water. Recent developments in global top-down tractogram optimizations enable the estimation of streamline weights, which characterize the connection between gray matter areas. In this work, the intra-axonal cross-sectional area coverage of the gray-to-white matter interface was examined by intersecting tractography streamlines with cortical regions of interest. The area coverage is the ratio of streamline weights divided by the surface area at the gray-to-white matter interface and assesses the estimated percentage which is covered by intra-axonal space. A high correlation (r = 0.935) between streamline weights and the cortical surface area was found across all regions of interest in all subjects. The variance across different cortical regions exhibits similarities to myelin maps. Additionally, we examined the effect of different diffusion gradient subsets at a lower, clinically feasible spatial resolution. Subsampling of the initial high-resolution diffusion dataset did not alter the tendency of the area coverage at the gray-to-white matter interface across cortical areas and subjects. However, single-shell acquisition schemes with lower b-values lead to a steady increase in area coverage in comparison to the full acquisition scheme at high resolution.

Despite its potential to provide new nitrogen (N) to the environment, knowledge on benthic dinitrogen (N2) fixation remains relatively sparse, and its contribution to the marine N budget is regarded as minor. Benthic N2 fixation is often observed in organic-rich sediments coupled to heterotrophic metabolisms, such as sulfate reduction. In the present study, benthic N2 fixation together with sulfate reduction and other heterotrophic metabolisms were investigated at six station between 47 and 1,108 m water depth along the 18°N transect traversing the highly productive upwelling region known as Mauritanian oxygen minimum zone (OMZ). Bottom water oxygen concentrations ranged between 30 and 138 μM. Benthic N2 fixation determined by the acetylene reduction assay was detected at all stations with highest rates (0.15 mmol m−2 d−1) on the shelf (47 and 90 m water depth) and lowest rates (0.08 mmol m−2 d−1) below 412 m water depth. The biogeochemical data suggest that part of the N2 fixation could be linked to sulfate- and iron-reducing bacteria. Molecular analysis of the key functional marker gene for N2 fixation, nifH, confirmed the presence of sulfate- and iron-reducing diazotrophs. High N2 fixation further coincided with bioirrigation activity caused by burrowing macrofauna, both of which showed high rates at the shelf sites and low rates in deeper waters. However, statistical analyses proved that none of these processes and environmental variables were significantly correlated with benthic diazotrophy, which lead to the conclusion that either the key parameter controlling benthic N2 fixation in Mauritanian sediments remains unidentified or that a more complex interaction of control mechanisms exists. N2 fixation rates in Mauritanian sediments were 2.7 times lower than those from the anoxic Peruvian OMZ.

A characteristic feature of the Daphnia (Crustacea: Cladocera) life cycle are the so-called ephippia, which are fertilised eggs that need to undergo diapause. When they are shed by the female, they sink to the lake bottom, where they may become embedded in the sediment and may remain viable for decades. Extracting and hatching ephippia in the laboratory and subjecting resurrected lineages to conditions representative of historic lake environments allows retrospective investigation of life-history responses to environmental change. Here we reanalyse data from such a resurrection experiment (Piscia et al., 2015: Bull. Environ. Contam. Toxicol. 94:46–51). Contemporary and past lineages of Daphnia galeata Sars 1863 were obtained from Lake Orta (Italy), a deep, subalpine lake with a well-documented history of industrial copper pollution. Experimental Daphnia were subjected to three copper treatments representative of two levels of historic as well as to current (i.e., unpolluted) lake conditions, and life-table data were collected. With these data at hand, we first estimated vital rates (survival, maturation, and reproduction) and used these rates to project the asymptotic population growth rates (λ) for each population-by-treatment combination. Next, we performed life-table response experiments (LTRE) to estimate the contributions of the vital rates to observed differences in λ. Finally, we used elasticity analysis to explore the functional relationship between λ and each of the vital rates. We found that survival rates were only compromised at elevated copper levels. Moreover, past, resurrected Daphnia had a higher λ at low copper concentrations compared to unpolluted conditions, but a lower λ when exposed to high copper levels. Contemporary Daphnia, on the other hand, only reproduced successfully in unpolluted water. Under these conditions, however, they had a higher population growth rate than the past Daphnia, suggesting a cost of copper tolerance in the latter. This cost was mainly due to a lower probability of reproduction and reduced fecundity, whereas survival remained largely unaffected. Finally, we found higher elasticity values of λ to survival than to reproductive rates. This suggests that any change in the environment that will affect survival rather than reproductive parameters will have a much larger impact on Lake Orta’s current Daphnia population.

Lake Orta experienced for a few decades a unique history of chronic pollution, with extreme changes in pH and copper concentration. Currently, the lake has recovered to its almost pristine oligotrophic conditions, but its sediments still preserve the record of all the changes that happened since the establishment of the first polluting factories in the 1920s, through to the liming activities in 1989-1990, and to the recovery phase that is still going on. Here we review the current knowledge for Lake Orta regarding rotifers, a diverse component of the zooplankton of the lake, through studies on living organisms and on their resting stages accumulated in the sediments. We also report a brief review of what is known in general on the effects of changes in pH and copper concentration on rotifers at the population, species and community level, providing expectations for such effects on the rotifers of Lake Orta. Then, we conclude our review with a perspective on the potential use of rotifers hatched from the resting stages in the sediment of Lake Orta with the description of experiments that can be performed in the future in the framework of resurrection ecology, in order to understand the mechanisms of past and future changes in the environment.

Microfluidics, or lab-on-a-chip (LOC) is a promising technology that allows the development of miniaturized chemical sensors. In contrast to the surging interest in biomedical sciences, the utilization of LOC sensors in aquatic sciences is still in infancy but a wider use of such sensors could mitigate the undersampling problem of ocean biogeochemical processes. Here we describe the first underwater test of a novel LOC sensor to obtain in situ calibrated time-series (up to 40 h) of nitrate+nitrite (ΣNOx) and nitrite on the seafloor of the Mauritanian oxygen minimum zone, offshore Western Africa. Initial tests showed that the sensor successfully reproduced water column (160 m) nutrient profiles. Lander deployments at 50, 100 and 170 m depth indicated that the biogeochemical variability was high over the Mauritanian shelf: The 50 m site had the lowest ΣNOx concentration, with 15.2 to 23.4 μM (median=18.3 μM); while at the 100 site ΣNOx varied between 21.0 and 30.1 μM over 40 hours (median = 25.1 μM). The 170 m site had the highest median ΣNOx level (25.8 μM) with less variability (22.8 to 27.7 μM). At the 50 m site, nitrite concentration decreased fivefold from 1 to 0.2 μM in just 30 hours accompanied by decreasing oxygen and increasing nitrate concentrations. Taken together with the time series of oxygen, temperature, pressure and current velocities, we propose that the episodic intrusion of deeper waters via cross-shelf transport leads to intrusion of nitrate-rich, but oxygen-poor waters to shallower locations, with consequences for benthic nitrogen cycling. This first validation of an LOC sensor at elevated water depths revealed that when deployed for longer periods and as a part of a sensor network, LOC technology has the potential to contribute to the understanding of the benthic biogeochemical dynamics.

We present evolution equations for a family of paths that results from anisotropically weighting curve energies in non-linear statistics of manifold valued data. This situation arises when performing inference on data that have non-trivial covariance and are anisotropic distributed. The family can be interpreted as most probable paths for a driving semi-martingale that through stochastic development is mapped to the manifold. We discuss how the paths are projections of geodesics for a sub-Riemannian metric on the frame bundle of the manifold, and how the curvature of the underlying connection appears in the sub-Riemannian Hamilton–Jacobi equations. Evolution equations for both metric and cometric formulations of the sub-Riemannian metric are derived. We furthermore show how rank-deficient metrics can be mixed with an underlying Riemannian metric, and we relate the paths to geodesics and polynomials in Riemannian geometry. Examples from the family of paths are visualized on embedded surfaces, and we explore computational representations on finite dimensional landmark manifolds with geometry induced from right-invariant metrics on diffeomorphism groups.