SWECO25: a cross-thematic raster database for ecological research in Switzerland.

Standard and easily accessible cross-thematic spatial databases are key resources in ecological research. In Switzerland, as in many other countries, available data are scattered across computer servers of research institutions and are rarely provided in standard formats (e.g., different extents or projections systems, inconsistent naming conventions). Consequently, their joint use can require heavy data management and geomatic operations. Here, we introduce SWECO25, a Swiss-wide raster database at 25-meter resolution gathering 5,265 layers. The 10 environmental categories included in SWECO25 are: geologic, topographic, bioclimatic, hydrologic, edaphic, land use and cover, population, transportation, vegetation, and remote sensing. SWECO25 layers were standardized to a common grid sharing the same resolution, extent, and geographic coordinate system. SWECO25 includes the standardized source data and newly calculated layers, such as those obtained by computing focal or distance statistics. SWECO25 layers were validated by a data integrity check, and we verified that the standardization procedure had a negligible effect on the output values. SWECO25 is available on Zenodo and is intended to be updated and extended regularly.

Catchment-based sampling of river eDNA integrates terrestrial and aquatic biodiversity of alpine landscapes.

Monitoring of terrestrial and aquatic species assemblages at large spatial scales based on environmental DNA (eDNA) has the potential to enable evidence-based environmental policymaking. The spatial coverage of eDNA-based studies varies substantially, and the ability of eDNA metabarcoding to capture regional biodiversity remains to be assessed; thus, questions about best practices in the sampling design of entire landscapes remain open. We tested the extent to which eDNA sampling can capture the diversity of a region with highly heterogeneous habitat patches across a wide elevation gradient for five days through multiple hydrological catchments of the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at five sites per catchment for a total volume of 1800 L. Using an eDNA metabarcoding approach focusing on vertebrates and plants, we detected 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 families across ten catchments. For mammals, fishes, amphibians and plants, the detected taxa covered some of the most common species in the region according to long-term records while including a few more rare taxa. We found marked turnover among samples from distinct elevational classes indicating that the biological signal in alpine rivers remains relatively localised and is not aggregated downstream. Accordingly, species compositions differed between catchments and correlated with catchment-level forest and grassland cover. Biomonitoring schemes based on capturing eDNA across rivers within biologically integrated catchments may pave the way toward a spatially comprehensive estimation of biodiversity.

Linking plant and vertebrate species to Nature's Contributions to People in the Swiss Alps.

Since the late 1990s, Nature's Contributions to People (NCPs; i.e. ecosystem services) were used as a putative leverage for fostering nature preservation. NCPs have largely been defined and mapped at the landscape level using land use and cover classifications. However, NCP mapping attempts based directly on individual species are still uncommon. Given that species shape ecosystems and ultimately deliver NCPs, mapping NCPs based on species distribution data should deliver highly meaningful results. This requires first establishing a census of the species-to-NCP relationships. However, datasets quantifying these relationships across several species and NCPs are rare. Here, we fill this gap by compiling literature and expert knowledge to establish the relationships of 1816 tracheophyte and 250 vertebrate species with 17 NCPs in the Swiss Alps. We illustrated the 31,098 identified species-NCP relationships for the two lineages and discuss why such a table is a key initial step in building spatial predictions of NCPs directly from species data, e.g. to ultimately complement spatial conservation planning.

Widefield OCT-Angiography and Fluorescein Angiography Assessments of Nonperfusion in Diabetic Retinopathy and Edema Treated with Anti-Vascular Endothelial Growth Factor.

PURPOSE: To assess change in retinal nonperfusion (NP) after anti-vascular endothelial growth factor (VEGF) therapy for diabetic macular edema (DME) using 2 different imaging modalities: swept-source widefield (SS-WF) OCT angiography (OCTA) and ultra-widefield (UWF) fluorescein angiography (FA). DESIGN: Observational case series. PARTICIPANTS: Ten eyes of 9 patients with severe nonproliferative diabetic retinopathy (NPDR) or proliferative DR (PDR) initiating 3 monthly anti-VEGF intravitreal injections for DME. METHODS: All eyes were imaged with UWF color fundus photographs (CFPs), UWF FA, and SS-WF OCTA at baseline (M0) and 1 month after the third anti-VEGF injection (M3). All images were aligned and divided into 16 boxes for analysis of NP areas by 2 blinded retina specialists. MAIN OUTCOME MEASURES: The number of discrepancies between SS-WF OCTA and UWF FA regarding the detection of NP areas and small vessels passing through NP areas; assessment of DR severity on UWF CFP; and change in each NP area between M0 and M3: number of boxes/eye with presence of at least 1 NP area, number of arterioles or venules that disappeared or reappeared, and number of NP areas in which capillaries disappeared or reappeared. RESULTS: The diabetic retinopathy (DR) severity score improved by at least 1 stage in 8 of 10 eyes, with a significant decrease in the mean number of microaneurysms and retinal hemorrhages on UWF CFP at M3 versus M0 (n = 40±28 vs. 121±57; P = 0.0020) and regression of fundus neovascularization when present. All NP areas detected on FA were seen on SS-WF OCTA, but additional NP areas were detected on SS-WF OCTA at M0 in 29% (46/160) of boxes. No reperfusion of arterioles or venules was observed at M3 on FA or SS-WF OCTA. Retinal capillaries were only visible on OCTA, and no reperfusion in NP areas was observed even when a reduction in dark areas was visible on FA. CONCLUSIONS: No reperfusion of vessels or capillary network was detected in NP areas using 2 imaging techniques, UWF FA and SS-WF OCTA, in eyes with DR after 3 anti-VEGF injections. The detection rate of NP areas was higher with SS-WF OCTA than with UWF FA.

Variability of shoulder girdle proprioception in 44 healthy volunteers.

BACKGROUND: Improved knowledge of normal shoulder girdle proprioception should benefit the treatment and rehabilitation of shoulder disorders. Whereas many of the available methods for assessing joint position sense (JPS) are costly and complex, Balke et al. have described a simple test. The primary objective of this study was to use this test to identify factors that influence shoulder-girdle JPS evaluation in healthy individuals. The secondary objective was to determine reference values based on the values obtained and on the factors associated with their variability. HYPOTHESIS: Age and dominant limb influence the results of shoulder girdle JPS evaluation, creating a need for reference values that take these factors in account. PATIENTS AND METHODS: A single-centre prospective study of healthy volunteers was performed between September 2012 and January 2013. In each volunteer, shoulder repositioning accuracy was assessed bilaterally as described by Balke et al. A line was drawn on the floor parallel to and 1 metre away from a wall. A target on the wall showed marks corresponding to three angles of arm elevation: 55°, 90°, and 125°. The volunteer was asked to raise the arm to the three positions, in abduction and in flexion, while memorising the joint positions, then to replicate the same positions with the eyes closed. The absolute differences between the replicated positions and the reference positions, designated angle deviations, were measured in degrees. Age, sex, and dominant upper limb were recorded. RESULTS: The 88 shoulders of 44 healthy volunteers were studied. No significant difference was found between males and females (p>0.05). The only significant difference between sides was better replication by the dominant arm of flexion at 55° (p=0.03). By univariate analysis, age was the only factor significantly associated with repositioning errors (p=0.003); neither dominant limb nor sex were significant (p=0.29 and p=0.59, respectively). In flexion, the angle deviation increased significantly with movement amplitude. The measurements were used to create a chart of expected angle deviations in healthy individuals according to age and to plane and amplitude of movement. DISCUSSION: The test described by Balke et al. is simple and feasible in everyday practice. Age, dominance, and plane of movement should be considered when evaluating abnormal shoulders. Further studies in larger numbers of individuals are needed to better define normal angle deviations related to these factors. LEVEL OF EVIDENCE: IV.

Functional treatment of metacarpal diaphyseal fractures by buddy taping: A prospective single-center study.

Metacarpal diaphyseal fractures are classically treated using a non-removable glove for 4 to 6 weeks. Here, we report the results of treatment by immediate active protected mobilization (buddy taping for four weeks) of minimally displaced M2 to M5 fractures. Fifty-four fractures (15 transverse or short oblique and 39 spiral or long oblique) in 51 patients were included during a one-year period; the average age of patients was 31 years. Clinical and radiographic assessments were carried out at day 15 and then months 1, 2 and 6 post-fracture. Thirty-one cases were reviewed at day 15, 27 at 1 month, and 22 at 2 months. The initial volar tilt was 26° on average for the short oblique or transverse fractures, and 11.5° for the long oblique or spiral fractures. Six fractures (11%) experienced 16.6° of secondary displacement on average. The fracture was healed in 37% of cases at 1 month, and in 100% of cases at 2 months in the patients who were reviewed clinically. Reduction in the QuickDASH and VAS for pain was evidence of fast functional recovery. The range of motion was comparable to that of the contralateral side in 90% cases after 2 months. Grip and pinch strength was 33% less than the contralateral side at 2 months. Although secondary displacement occurs in some cases, the functional results of this simple and practical treatment method are good after 2 months, as there is little pain, stiffness, strength loss and no cases of nonunion.

Safety of Lipofilling in Patients with Breast Cancer.

Lipotransfer represents a technical revolution in plastic surgery and is increasingly used worldwide. Although known for several decades, lipofilling has only recently found widespread use in patients with breast cancer to improve the results of breast reconstructions and to correct deformities after conservative treatment. The plastic surgery literature underlines the technique's versatility and the quality of the results, showing lipofilling as an effective cosmetic procedure and proposing it as a safe, neutral biological material that is able to restore the body contour. Several studies underline the power of transferred fat to regenerate blood supply in skin disorders following radiotherapy.

Long livestock farming history and human landscape shaping revealed by lake sediment DNA.

The reconstruction of human-driven, Earth-shaping dynamics is important for understanding past human/environment interactions and for helping human societies that currently face global changes. However, it is often challenging to distinguish the effects of the climate from human activities on environmental changes. Here we evaluate an approach based on DNA metabarcoding used on lake sediments to provide the first high-resolution reconstruction of plant cover and livestock farming history since the Neolithic Period. By comparing these data with a previous reconstruction of erosive event frequency, we show that the most intense erosion period was caused by deforestation and overgrazing by sheep and cowherds during the Late Iron Age and Roman Period. Tracking plants and domestic mammals using lake sediment DNA (lake sedDNA) is a new, promising method for tracing past human practices, and it provides a new outlook of the effects of anthropogenic factors on landscape-scale changes.

Experiments in searching small proteins in unannotated large eukaryotic genomes.

There is growing interest to use mass spectrometry data to search genome sequences directly. Previous work by other authors demonstrated that this approach is able to correct and complement available genome annotations. We discuss the practical difficulty of searching large eukaryotic genomes with peptide ion trap tandem mass spectra of small proteins (<40 kDa). The challenging problem of automatically identifying peptides that span across exon/intron boundaries is explored for the first time by using experimental data. In a human genome search, we find that roughly 30% of the peptides are missed, due to various reasons, compared to a Swiss-Prot search. We show that this percentage is significantly reduced with improved parent mass accuracy. We finally provide several examples of predicted gene structures that could be improved by proteomics data, in particular by peptides spanning across exon/intron boundaries.

In vitro and in silico processes to identify differentially expressed proteins.

We present an integrated proteomics platform designed for performing differential analyses. Since reproducible results are essential for comparative studies, we explain how we improved reproducibility at every step of our laboratory processes, e.g. by taking advantage of the powerful laboratory information management system we developed. The differential capacity of our platform is validated by detecting known markers in a real sample and by a spiking experiment. We introduce an innovative two-dimensional (2-D) plot for displaying identification results combined with chromatographic data. This 2-D plot is very convenient for detecting differential proteins. We also adapt standard multivariate statistical techniques to show that peptide identification scores can be used for reliable and sensitive differential studies. The interest of the protein separation approach we generally apply is justified by numerous statistics, complemented by a comparison with a simple shotgun analysis performed on a small volume sample. By introducing an automatic integration step after mass spectrometry data identification, we are able to search numerous databases systematically, including the human genome and expressed sequence tags. Finally, we explain how rigorous data processing can be combined with the work of human experts to set high quality standards, and hence obtain reliable (false positive < 0.35%) and nonredundant protein identifications.

High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics.

In a previous paper we introduced a novel model-based approach (OLAV) to the problem of identifying peptides via tandem mass spectrometry, for which early implementations showed promising performance. We recently further improved this performance to a remarkable level (1-2% false positive rate at 95% true positive rate) and characterized key properties of OLAV like robustness and training set size. We present these results in a synthetic and coherent way along with detailed performance comparisons, a new scoring component making use of peptide amino acidic composition, and new developments like automatic parameter learning. Finally, we discuss the impact of OLAV on the automation of proteomics projects.