Deep learning via semi-supervised embedding

We show how nonlinear embedding algorithms popular for use with shallow semi-supervised learning techniques such as kernel methods can be applied to deep multilayer architectures, either as a regularizer at the output layer, or on each layer of the architecture. This provides a simple alternative to existing approaches to deep learning whilst yielding competitive error rates compared to those methods, and existing shallow semi-supervised techniques.

Swiss EMBnet node web server.

EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a 'node', a group responsible for the maintenance of local services for their users (e.g. education, training, software, database distribution, technical support, helpdesk). Among these services a web portal with links and access to locally developed and maintained software is essential and different for each node. Our web portal targets biomedical scientists in Switzerland and elsewhere, offering them access to a collection of important sequence analysis tools mirrored from other sites or developed locally. We describe here the Swiss EMBnet node web site (http://www.ch.embnet.org), which presents a number of original services not available anywhere else.

Recent human-induced trophic change in the large and deep perialpine Lake Lucerne (Switzerland) compared to historical geochemical variations

This study investigates the sedimentological and geochemical changes that occurred during the last 2200 years in the meromictic Lake Lucerne (Switzerland), one of the largest freshwater lakes of Central Europe. The stable isotope composition (delta C-13 and delta O-18 values) of bulk carbonates is compared to changes in grain-size distribution (clay and silt fraction), natural trace element input (titanium and thorium concentrations), and organic material abundance (C-org, nitrogen and phosphorus) and composition (C/N ratios and hydrogen and oxygen indexes). A drop in carbonate accumulation and in the delta O-18 values of sediments between ca. AD 500 and 700 followed a large and consistent rise in chemical weathering, marked by increases in the silicate-clay fraction and in crustal element concentrations. During the following millennium, there was a long-term decreasing trend in the lithogenic trace element input and in the phosphorus loading, suggesting decreasing terrigeneous input from runoff water. The major sedimentological change over the studied period occurred after ca. AD 1800 with a significant increase in the erosion-driven silt-fraction and in the sedimentation rate. During the last century, human-induced increase in nutrient input to the lake highly enhanced the accumulation of organic matter in sediment. Changes in nutrients and oxygen conditions in the hypolimnion of Lake Lucerne during the eutrophication period (i.e., the last 40 years) highly modified the geochemical fluxes compared to the relatively stable oligotrophic conditions that prevailed during the previous 2000 years. Before the 19th century, climate driven meromixis had a limited impact on the organic matter flux to the sediments, but the accumulation of carbonate considerably decreased during periods of lower mechanical erosion rates and high chemical weathering rates. (C) 2012 Elsevier B.V. All rights reserved.

Phenotip - a web-based instrument to help diagnosing fetal syndromes antenatally.

Prenatal ultrasound can often reliably distinguish fetal anatomic anomalies, particularly in the hands of an experienced ultrasonographer. Given the large number of existing syndromes and the significant overlap in prenatal findings, antenatal differentiation for syndrome diagnosis is difficult. We constructed a hierarchic tree of 1140 sonographic markers and submarkers, organized per organ system. Subsequently, a database of prenatally diagnosable syndromes was built. An internet-based search engine was then designed to search the syndrome database based on a single or multiple sonographic markers. Future developments will include a database with magnetic resonance imaging findings as well as further refinements in the search engine to allow prioritization based on incidence of syndromes and markers.

Ten years follow-up after deep sclerectomy with collagen implant

RAPPORT DE SYNTHESE : BUT : Le but de ce sujet de recherche est d'évaluer le taux de succès et les complications à long terme de la sclérectomie profonde non pénétrante avec implant de collagène (SPIC) chez les patients atteints de glaucome à angle ouvert. METODES ET PATIENTS : Il s'agit d'une étude clinique, prospective, monocentrique, non-randomisée, effectuée sur 105 patients atteints d'un glaucome à angle ouvert médicalement non-contrôlé. Ces patients ont tous bénéficiés d'une SPIC, effectuée selon le geste chirurgicale standard (technique décrite dans l'article). Dans le cadre de cette étude, nous avons effectué un bilan ophtalmologique complet avant l'acte chirurgical puis un suivi postopératoire à 1 et 7 jours ; 1,2,3,6,9,12 mois et ensuite tous les 6 mois durant les dix années suivantes. RESULTATS : Le suivit moyen de cette étude s'étend sur 101.5 ± 43.1, [3-144] mois (moyenne ± écart type, [étendue]). La pression intraoculaire (PIO) préopératoire était élevée à 26.8 ± 7.7, (14-52] mmHg, et l'acuité visuelle corrigée à 0.71 ± 0.33, [0.02-1.5]. Au terme des dix années après le traitement chirurgical, le nombre de patients suivit était de 52 avec une pression intraoculaire abaissée à 12.2 ± 4.7, [6-20] mmHg et une acuité visuelle corrigée de 0.63 ± 0.34, [0.01-1.2]. Le nombre de médicaments par patient a diminué de 2.3 ± 0.7, [ 1-4] à 1.3 ± 1.1, [0-3]. Dix ans après la SPIC, une pression intraoculaire <_ 21 mmHg sans médicaments (succès complet) était obtenue chez 47.7 % des patients et 89 % avec ou sans traitement médicamenteux (succès relatif). Les gestes postopératoires additionnels par gonioponcture ont été effectués sur 61 yeux (59.8%) et les injections sous-conjonctival de 5-fluorouracil ont été pratiquées sur 25 yeux dont 5 incluant un needling. CONCLUSIONS : Le suivit à long terme sur une période de dix ans, démontre que la sclérectomie profonde avec implant de collagène (SPIC) est efficace dans le contrôle de la pression intraoculaire et présente peu de complications postopératoires.

Reconditioning of the trabeculo-descemet's membrane with the 532-nm Nd : YAG (SLT) laser after deep sclerectomy.

The purpose of this study was to evaluate the intraocular pressure (IOP)-lowering effect of modified goniopuncture with the 532-nm Nd : YAG selective laser trabeculoplasty (SLT) laser on eyes after deep sclerectomy with collagen implant (DSCI). This was an interventional cased series. The effects of modified goniopuncture on eyes with insufficient IOP-lowering after DSCI were observed. Goniopuncture was performed using a Q-switched, frequency-doubled 532-nm Nd : YAG laser (SLT-goniopuncture, SLT-G). Outcome measures were amount of IOP-lowering and rapidity of decrease after laser intervention. In all, 10 eyes of 10 patients with a mean age of 71.0±7.7 (SD) years were treated with SLT-G. The mean time of SLT-G after DSCI procedure was 7.1±10.9 months. SLT-G decreased IOP from an average of 16.1±3.4 mm Hg to 14.2±2.8 mm Hg (after 15 min), 13.6±3.9 mm Hg (at 1 day), 12.5±4.1 mm Hg (at 1 month), and 12.6±2.5 (at 6 months) (P<0.0125). There were no complications related to the intervention. Patients in this series achieved an average 22.5% of IOP reduction after SLT-G. The use of the SLT laser appears to be an effective and safe alternative to the traditional Nd : YAG laser for goniopuncture in eyes after DSCI, with potential advantages related to non-perforation of trabeculo-descemet's membrane (TDM).

Reconstruction of the recent history of a large deep prealpine lake (Lake Bourget, France) using subfossil chironomids, diatoms, and organic matter analysis: towards the definition of a lake-specific reference state

This paper presents the recent history of a large prealpine lake (Lake Bourget) using chironomids, diatoms and organic matter analysis, and deals with the ability of paleolimnological approach to define an ecological reference state for the lake in the sense of the European Framework Directive. The study at low resolution of subfossil chironomids in a 4-m-long core shows the remarkable stability over the last 2.5 kyrs of the profundal community dominated by a Micropsectra-association until the beginning of the twentieth century, when oxyphilous taxa disappeared. Focusing on this key recent period, a high resolution and multiproxy study of two short cores reveals a progressive evolution of the lake's ecological state. Until AD 1880, Lake Bourget showed low organic matter content in the deep sediments (TOC less than 1%) and a well-oxygenated hypolimnion that allowed the development of a profundal oxyphilous chironomid fauna (Micropsectra-association). Diatom communities were characteristic of oligotrophic conditions. Around AD 1880, a slight increase in the TOC was the first sign of changes in lake conditions. This was followed by a first limited decline in oligotrophic diatom taxa and the disappearance of two oxyphilous chironomid taxa at the beginning of the twentieth century. The 1940s were a major turning point in recent lake history. Diatom assemblages and accumulation of well preserved planktonic organic matter in the sediment provide evidence of strong eutrophication. The absence of profundal chironomid communities reveals permanent hypolimnetic anoxia. From AD 1995 to 2006, the diatom assemblages suggest a reduction in nutrients, and a return to mesotrophic conditions, a result of improved wastewater management. However, no change in hypolimnion benthic conditions has been shown by either the organic matter or the subfossil chironomid profundal community. Our results emphasize the relevance of the paleolimnological approach for the assessment of reference conditions for modern lakes. Before AD 1900, the profundal Micropsectra-association and the Cyclotella dominated diatom community can be considered as the Lake Bourget reference community, which reflects the reference ecological state of the lake.

Ultrasound-assisted versus conventional catheter-directed thrombolysis for acute iliofemoral deep vein thrombosis.

BACKGROUND: For patients with acute iliofemoral deep vein thrombosis, it remains unclear whether the addition of intravascular high-frequency, low-power ultrasound energy facilitates the resolution of thrombosis during catheter-directed thrombolysis. METHODS AND RESULTS: In a controlled clinical trial, 48 patients (mean age 50 ± 21 years, 52% women) with acute iliofemoral deep vein thrombosis were randomized to receive ultrasound-assisted catheter-directed thrombolysis (N = 24) or conventional catheter-directed thrombolysis (N = 24). Thrombolysis regimen (20 mg r-tPA over 15 hours) was identical in all patients. The primary efficacy end point was the percentage of thrombus load reduction from baseline to 15 hours according to the length-adjusted thrombus score, obtained from standardized venograms and evaluated by a core laboratory blinded to group assignment. The percentage of thrombus load reduction was 55% ± 27% in the ultrasound-assisted catheter-directed thrombolysis group and 54% ± 27% in the conventional catheter-directed thrombolysis group (P = 0.91). Adjunctive angioplasty and stenting was performed in 19 (80%) patients and in 20 (83%) patients, respectively (P > 0.99). Treatment-related complications occurred in 3 (12%) and 2 (8%) patients, respectively (P > 0.99). At 3-month follow-up, primary venous patency was 100% in the ultrasound-assisted catheter-directed thrombolysis group and 96% in the conventional catheter-directed thrombolysis group (P = 0.33), and there was no difference in the severity of the post-thrombotic syndrome (mean Villalta score: 3.0 ± 3.9 [range 0-15] versus 1.9 ± 1.9 [range 0-7]; P=0.21), respectively. CONCLUSIONS: In this randomized controlled clinical trial of patients with acute iliofemoral deep vein thrombosis treated with a fixed-dose catheter thrombolysis regimen, the addition of intravascular ultrasound did not facilitate thrombus resolution. CLINICAL TRIAL REGISTRATION URL: http://www.clinicaltrials.gov. Unique identifier: NCT01482273.

Surgical outcomes of deep sclerectomy versus Baerveldt aqueous shunt implantation following initial failed deep sclerectomy

Purpose: To examine the efficacy and safety of repeat deep sclerectomy (DS) versus Baerveldt shunt (BS) implantation as second line surgery following failed primary DS. Methods: Fifty one patients were prospectively recruited to undergo BS implantation following failed DS and 51 patients underwent repeat DS, for which data was collected retrospectively. All eyes had at least one failed DS. Surgical success was defined as IOP≤21mmHg and 20% reduction in IOP from baseline. Success rates, number of glaucoma medications (GMs), IOP, and complication rates were compared between the two groups at year 1, post-operatively. Results: Mean age, sex and the proportion of glaucoma subtypes were similar between groups. Preoperatively IOP was significantly lower in DS group vs BS group (18.8mmHg vs 23.8mmHg, p<0.01, two sample t-test). Postoperatively IOP was significantly higher in DS group than BS group (14.6mmHg vs 12.0mmHg, p<0.01, two-sample t-test). In the DS group, 47% of eyes did not achieve 20% reduction in IOP from baseline, as a result the success rates were significantly lower in eyes with DS (51%) than in eyes with BS (88%) (p=0.02, log-rank test). Preoperatively the number of GMs used in DS and BS groups were similar (2.2 vs 2.7 p=0.02, two sample t-test). Postoperatively there remained no significant difference in GMs between groups (0.9 vs 1.1, p= 0.58, two sample t-test). Complication rates were similar between the two groups (12% vs 10%). Conclusions: Baerveldt tube implantation was more effective in lowering IOP than repeat deep sclerectomy in eyes with failed primary DS, at year one. Complications were minor and infrequent in both groups

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.