Three-dimensional portable document format: a simple way to present 3-dimensional data in an electronic publication

Three-dimensional (3D) models of teeth and soft and hard tissues are tessellated surfaces used for diagnosis, treatment planning, appliance fabrication, outcome evaluation, and research. In scientific publications or communications with colleagues, these 3D data are often reduced to 2-dimensional pictures or need special software for visualization. The portable document format (PDF) offers a simple way to interactively display 3D surface data without additional software other than a recent version of Adobe Reader (Adobe, San Jose, Calif). The purposes of this article were to give an example of how 3D data and their analyses can be interactively displayed in 3 dimensions in electronic publications, and to show how they can be exported from any software for diagnostic reports and communications among colleagues.

Reduced incidence of insect-bite hypersensitivity in Icelandic horses is associated with a down-regulation of interleukin-4 by interleukin-10 and transforming growth factor-beta1

Insect bite hypersensitivity (IBH) is an allergic dermatitis of horses caused by IgE-mediated reactions to bites of insects of the genus Culicoides. IBH does not occur in Iceland due to the absence of Culicoides. However, Icelandic horses exported to mainland Europe as adults (1st generation) have a >/=50% incidence of developing IBH. In contrast, their progeny (2nd generation) has a <10% incidence of IBH. Here we show that peripheral blood mononuclear cells (PBMC) from Icelandic horses born in mainland Europe and belonging either to the IBH or healthy subgroup produce less interleukin (IL)-4 after polyclonal or allergen-specific stimulation when compared with counterparts from horses born in Iceland. We examined a role of IL-10 and transforming growth factor (TGF)-beta1 in down-regulation of IL-4 in healthy 2nd generation Icelandic horses. Supernatants of PBMC from 2nd generation healthy horses down-regulated the proportion of IL-4-producing cells and IL-4 production in stimulated cultures of PBMC from 1st generation IBH. This inhibition was mimicked by a combination of IL-10 and TGF-beta1 but not by the single cytokines. Cultures of stimulated PBMC of healthy 2nd generation horses produced a low level of IL-4, but IL-4 production was increased by anti-equine IL-10 and anti-human TGF-beta1. This shows for the first time that in horses, IL-10 and TGF-beta1 combined regulate IL-4 production in vitro. It is suggested that in this naturally occurring IgE-mediated allergy, IL-10 and TGF-beta1 have a role in the down-regulation of IL-4-induced allergen-specific Th2 cells, thereby reducing the incidence of IBH.

Differential optical densities of intraretinal spaces

PURPOSE: To test the hypothesis that hyporeflective spaces in the neuroretina found on optical coherence tomography (OCT) examination have different optical reflectivities according to whether they are associated with exudation or degeneration. METHODS: Retrospective analysis of eyes with idiopathic perifoveal telangiectasia (IPT), diabetic macular edema (DME), idiopathic central serous chorioretinopathy (CSC), retinitis pigmentosa (RP), or cone dystrophy (CD) and eyes of healthy control subjects. OCT scans were performed. Raw scan data were exported and used to calculate light reflectivity profiles. Reflectivity data were acquired by projecting three rectangular boxes, each 50 pixels long and 5 pixels wide, into the intraretinal cystoid spaces, centrally onto unaffected peripheral RPE, and onto the prefoveolar vitreous. Light reflectivity in the retinal pigment epithelium (RPE), vitreous, and intraretinal spaces for the different retinal conditions and control subjects were compared. RESULTS: Reflectivities of the vitreous and the RPE were similar among the groups. Hyporeflective spaces in eyes with exudation (DME, RP, and CSC) had higher reflectivity compared with the mean reflectivity of the vitreous, whereas the cystoid spaces in the maculae of the eyes without exudation (CD and IPT) had a lower reflectivity than did the normal vitreous. CONCLUSIONS: Analysis of the light reflectivity profiles may be a tool to determine whether the density of hyporeflective spaces in the macula is greater or less than that of the vitreous, and may be a way to differentiate degenerative from exudative macular disease.

The immune geography of IgA induction and function

The production of immunoglobulin A (IgA) in mammals exceeds all other isotypes, and it is mostly exported across mucous membranes. The discovery of IgA and the realization that it dominates humoral mucosal immunity, in contrast to the IgG dominance of the systemic immune system, was early evidence for the distinct nature of mucosal immunology. It is now clear that IgA can function in high-affinity modes for neutralization of toxins and pathogenic microbes, and as a low-affinity system to contain the dense commensal microbiota within the intestinal lumen. The basic map of induction of IgA B cells in the Peyer's patches, which then circulate through the lymph and bloodstream to seed the mucosa with precursors of plasma cells that produce dimeric IgA for export through the intestinal epithelium, has been known for more than 30 years. In this review, we discuss the mechanisms underlying selective IgA induction of mucosal B cells for IgA production and the immune geography of their homing characteristics. We also review the functionality of secretory IgA directed against both commensal organisms and pathogens.

River loads and modern denudation of the Alps — A review

This paper presents the first comprehensive analysis of sediment and dissolved load across an entire mountain range. We investigate patterns and rates of modern denudation of the European Alps based on a compilation of data about river loads and reservoir sedimentation from 202 drainage basins that are between ca. 1 to 10,000 km2 large. The study basins cover about 50% of the total area of the Alps. Modern glaciated basins have the highest sediment yields of up to 7000 t km− 2 a− 1, which are on average 5 to 10 times higher than in non-glaciated basins. Likewise sediment yield and glacial cover are positively correlated. Instead, relief is a relatively weak predictor of sediment yield. The strong glacial impact in the correlations is due to glacier recession since the 19th century as well as due to glacial conditioning during repeated Quaternary glaciations which have produced the strong transient state of the Alpine landscape. We suggest that this is the major cause for ca. 3 fold enhanced denudation of the western compared to the eastern Alps. Chemical denudation rates are highest in the external Alps dominated by carbonate sedimentary rocks, where they make up about one third of total denudation. The high rates cannot be explained without anhydrite dissolution. We estimated that only 45% of the sediments mobilized in headwaters are exported out off the Alps, most sediments being trapped in artificial reservoirs. The total amount of sediment annually trapped within the Alps equates to 43 Mt. When corrected for sediment storage, we obtain an area-weighted mean total denudation rate for the Alps of about 0.32 mm a− 1. The pre-dam rate might be as high as 0.42 mm a− 1. In total, ca. 35 plus 23 Mt of mass are exported each year out of the Alps as solids and solutes, respectively. These rates are not enough to out pace modern rock uplift. Nevertheless, pattern of sediment yield across the Alps coincides roughly with the intensity of glacial conditioning and modern rock uplift, supporting the hypothesis of an erosion-driven uplift of the Alps.

Amplified inception of European Little Ice Age by sea ice-ocean-atmosphere feedbacks

The inception of the Little Ice Age (~1400–1700 AD) is believed to have been driven by an interplay of external forcing and climate system internal variability. While the hemispheric signal seems to have been dominated by solar irradiance and volcanic eruptions, the understanding of mechanisms shaping the climate on a continental scale is less robust. In an ensemble of transient model simulations and a new type of sensitivity experiments with artificial sea ice growth, the authors identify a sea ice–ocean–atmosphere feedback mechanism that amplifies the Little Ice Age cooling in the North Atlantic–European region and produces the temperature pattern suggested by paleoclimatic reconstructions. Initiated by increasing negative forcing, the Arctic sea ice substantially expands at the beginning of the Little Ice Age. The excess of sea ice is exported to the subpolar North Atlantic, where it melts, thereby weakening convection of the ocean. Consequently, northward ocean heat transport is reduced, reinforcing the expansion of the sea ice and the cooling of the Northern Hemisphere. In the Nordic Seas, sea surface height anomalies cause the oceanic recirculation to strengthen at the expense of the warm Barents Sea inflow, thereby further reinforcing sea ice growth. The absent ocean–atmosphere heat flux in the Barents Sea results in an amplified cooling over Northern Europe. The positive nature of this feedback mechanism enables sea ice to remain in an expanded state for decades up to a century, favoring sustained cold periods over Europe such as the Little Ice Age. Support for the feedback mechanism comes from recent proxy reconstructions around the Nordic Seas.

Individual Video Training iVT and Annotating Academic Videos AAV: two complementing technologies

Individual Video Training iVT and Annotating Academic Videos AAV: two complementing technologies 1. Recording communication skills training sessions and reviewing them by oneself, with peers, and with tutors has become standard in medical education. Increasing numbers of students paired with restrictions of financial and human resources create a big obstacle to this important teaching method. 2. Everybody who wants to increase efficiency and effectiveness of communication training can get new ideas from our technical solution. 3. Our goal was to increase the effectiveness of communication skills training by supporting self, peer and tutor assessment over the Internet. Two technologies of SWITCH, the national foundation to support IT solutions for Swiss universities, came handy for our project. The first is the authentication and authorization infrastructure providing all Swiss students with a nationwide single login. The second is SWITCHcast which allows automated recording, upload and publication of videos in the Internet. Students start the recording system by entering their single login. This automatically links the video with their password. Within a few hours, they find their video password protected on the Internet. They now can give access to peers and tutors. Additionally, an annotation interface was developed. This software has free text as well as checklist annotations capabilities. Tutors as well as students can create checklists. Tutor’s checklists are not editable by students. Annotations are linked to tracks. Tracks can be private or public. Public means visible to all who have access to the video. Annotation data can be exported for statistical evaluation. 4. The system was well received by students and tutors. Big numbers of videos were processed simultaneously without any problems. 5. iVT http://www.switch.ch/aaa/projects/detail/UNIBE.7 AAV http://www.switch.ch/aaa/projects/detail/ETHZ.9

Characterization of Phosphorylation- and RNA-Dependent UPF1 Interactors by Quantitative Proteomics

Human up-frameshift 1 (UPF1) is an ATP-dependent RNA helicase and phosphoprotein implicated in several biological processes but is best known for its key function in nonsense-mediated mRNA decay (NMD). Here we employed a combination of stable isotope labeling of amino acids in cell culture experiments to determine by quantitative proteomics UPF1 interactors. We used this approach to distinguish between RNA-mediated and protein-mediated UPF1 interactors and to determine proteins that preferentially bind the hypo- or the hyper-phosphorylated form of UPF1. Confirming and expanding previous studies, we identified the eukaryotic initiation factor 3 (eIF3) as a prominent protein-mediated interactor of UPF1. However, unlike previously reported, eIF3 binds to UPF1 independently of UPF1’s phosphorylation state. Furthermore, our data revealed many nucleus-associated RNA-binding proteins that preferentially associate with hyper-phosphorylated UPF1 in an RNase-sensitive manner, suggesting that UPF1 gets recruited to mRNA and becomes phosphorylated before being exported to the cytoplasm as part of the mRNP.

Selective uptake, distribution, and redistribution of Cd-109, Co-57, Zn-65, Ni-63, and Cs-134 via xylem and phloem in the heavy metal hyperaccumulator Solanum nigrum L

The focus of this article was to explore the translocation of Cd-109, Co-57, Zn-65, Ni-63, and Cs-134 via xylem and phloem in the newly found hyperaccumulator Solanum nigrum L. Two experiments with the uptake via the roots and transport of Cd-109, Co-57, and Zn-65 labeled by roots, and the redistribution of Cd-109, Zn-65, Co-57, Ni-63, and Cs-134 using flap label in S. nigrum in a hydroponic culture with a standard nutrient solution were conducted. The results showed that Cd-109 added for 24 h to the nutrient medium of young plants was rapidly taken up, transferred to the shoot, and accumulated in the cotyledons and the oldest leaves but was not efficiently redistributed within the shoot afterward leading to a rather low content in the fruits. In contrast, Co-57 was more slowly taken up and released to the shoot, but afterward, this element was redistributed from older leaves to younger leaves and maturing fruits. Zn-65 was rapidly taken up and transferred to the shoot (mainly to the youngest leaves and not to the cotyledons). Afterward, this radionuclide was redistributed within the shoot to the youngest organs and finally accumulated in the maturing fruits. After flap labeling, all five heavy metals tested (Cd-109, Co-57, Zn-65, Ni-63, Cs-134) were exported from the labeled leaf and redistributed within the plant. The accumulation in the fruits was most pronounced for Ni-63 and Zn-65, while a relatively high percentage of Co-57 was finally found in the roots. Cs-134 was roughly in the middle of them. The transport of Cd-109 differed from that previously reported for wheat or lupin and might be important for the potential of S. nigrum to hyperaccumulate cadmium.

Bilateral exchange rates and jobs

We study the labor market effects of realignment in fixed bilateral exchange rates, such as China's peg to the US dollar. We employ the open economy model by de Melo and Robinson to identify the core parameters of the real, trade side of the economy driving the unemployment effects of bilateral exchange rate realignment. A small open economy version of the model is explored analytically and a large multicountry version numerically. Analytics in the small open economy model show that unemployment effects of adjusting of a bilateral peg hinge on the fraction exported to and imported from the trading partner. A larger fraction exported to and a smaller fraction imported from the trading partner make it more likely that revaluation of a trading partner's currency has beneficial effects. Numerics in the large economy model show that Chinese revaluation can generate both positive and negative unemployment effects depending upon underlying parameter values. Adverse unemployment effects can go along with an improving trade balance.

NMD3 regulates both mRNA and rRNA nuclear export in African trypanosomes via an XPOI-linked pathway

Trypanosomes mostly regulate gene expression through post-transcriptional mechanisms, particularly mRNA stability. However, much mRNA degradation is cytoplasmic such that mRNA nuclear export must represent an important level of regulation. Ribosomal RNAs must also be exported from the nucleus and the trypanosome orthologue of NMD3 has been confirmed to be involved in rRNA processing and export, matching its function in other organisms. Surprisingly, we found that TbNMD3 depletion also generates mRNA accumulation of procyclin-associated genes (PAGs), these being co-transcribed by RNA polymerase I with the procyclin surface antigen genes expressed on trypanosome insect forms. By whole transcriptome RNA-seq analysis of TbNMD3-depleted cells we confirm the regulation of the PAG transcripts by TbNMD3 and using reporter constructs reveal that PAG1 regulation is mediated by its 5'UTR. Dissection of the mechanism of regulation demonstrates that it is not dependent upon translational inhibition mediated by TbNMD3 depletion nor enhanced transcription. However, depletion of the nuclear export factors XPO1 or MEX67 recapitulates the effects of TbNMD3 depletion on PAG mRNAs and mRNAs accumulated in the nucleus of TbNMD3-depleted cells. These results invoke a novel RNA regulatory mechanism involving the NMD3-dependent nuclear export of mRNA cargos, suggesting a shared platform for mRNA and rRNA export.

The mitochondrial ADP/ATP carrier (SLC25 family): pathological implications of its dysfunction.

In aerobic eukaryotic cells, the high energy metabolite ATP is generated mainly within the mitochondria following the process of oxidative phosphorylation. The mitochondrial ATP is exported to the cytoplasm using a specialized transport protein, the ADP/ATP carrier, to provide energy to the cell. Any deficiency or dysfunction of this membrane protein leads to serious consequences on cell metabolism and can cause various diseases such as muscular dystrophy. Described as a decisive player in the programmed cell death, it was recently shown to play a role in cancer. The objective of this review is to summarize the current knowledge of the involvement of the ADP/ATP carrier, encoded by the SLC25A4, SLC25A5, SLC25A6 and SLC25A31 genes, in human diseases and of the efforts made at designing different model systems to study this carrier and the associated pathologies through biochemical, genetic, and structural approaches.

MorphoGraphX: A platform for quantifying morphogenesis in 4D

Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX (www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software’s modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.DOI: http://dx.doi.org/10.7554/eLife.05864.001Author keywordsResearch organism

Redistribution of Nickel, Cobalt, Manganese, Zinc, and Cadmium via the Phloem in Young and Maturing Wheat

The phloem mobility of heavy metals is relevant to the redistribution of micronutrients and pollutants and, ultimately, to the quality of harvested plant parts. The relative mobility in wheat may vary considerably between different cations. In the study reported here, radio-labeled nickel (Ni), cobalt (Co), manganese (Mn), zinc (Zn) and cadmium (Cd) were introduced into either intact young winter wheat (Triticum aestivum L. cv. Arina) via a leaf flap, or detached maturing shoots via the cut stem. Elements fed into the lamina of the second leaf of 21-day-old plants were translocated to the younger (expanding) leaves and to the roots but not or only in trace amounts to the first (already fully expanded) leaf. The 63Ni and 65Zn were exported more rapidly compared with the other heavy metals. Most of 54Mn was retained in the originally labeled leaf. The peduncle of some maturing shoots was steam-girdled below the ear to distinguish between xylem and phloem transport. This phloem interruption reduced the content of 63Ni in the ear to about 25%. Intermediate effects were observed for 65Zn, 57Co, and 109Cd. Total 54Mn accumulation in the ear was hardly affected by steam-girdling, indicating a transport of this element within the xylem to the ear. These results suggest that the relative phloem mobility of Ni and Zn in young wheat plants and in maturing wheat shoots is higher than the mobility of Co and Cd, whereas the mobility of Mn is very low.