Ultra-high pressure liquid chromatography-mass spectrometry for plant metabolomics: a systematic comparison of high-resolution quadrupole-time-of-flight and single stage Orbitrap mass spectrometers.

The response of Arabidopsis to stress caused by mechanical wounding was chosen as a model to compare the performances of high resolution quadrupole-time-of-flight (Q-TOF) and single stage Orbitrap (Exactive Plus) mass spectrometers in untargeted metabolomics. Both instruments were coupled to ultra-high pressure liquid chromatography (UHPLC) systems set under identical conditions. The experiment was divided in two steps: the first analyses involved sixteen unwounded plants, half of which were spiked with pure standards that are not present in Arabidopsis. The second analyses compared the metabolomes of mechanically wounded plants to unwounded plants. Data from both systems were extracted using the same feature detection software and submitted to unsupervised and supervised multivariate analysis methods. Both mass spectrometers were compared in terms of number and identity of detected features, capacity to discriminate between samples, repeatability and sensitivity. Although analytical variability was lower for the UHPLC-Q-TOF, generally the results for the two detectors were quite similar, both of them proving to be highly efficient at detecting even subtle differences between plant groups. Overall, sensitivity was found to be comparable, although the Exactive Plus Orbitrap provided slightly lower detection limits for specific compounds. Finally, to evaluate the potential of the two mass spectrometers for the identification of unknown markers, mass and spectral accuracies were calculated on selected identified compounds. While both instruments showed excellent mass accuracy (<2.5ppm for all measured compounds), better spectral accuracy was recorded on the Q-TOF. Taken together, our results demonstrate that comparable performances can be obtained at acquisition frequencies compatible with UHPLC on Q-TOF and Exactive Plus MS, which may thus be equivalently used for plant metabolomics.

Isolation of genetic mutation leading to abnormal phenotype in human through ultra-high-throughput sequencing (UHTS)

The introduction of Next Generation Sequencing (NGS) facilitated the task of localizing DNA variation and identifying the genetic cause of yet unsolved Mendelian disorders. Using Whole Exome Capture method and NGS, we identified the causative genetic aberration responsible for a number of monogenic disorders previously undetermined. Due to the novelty of the NGS method we benchmarked different algorithms to assess their merits and defects. This allowed us to establish a pipeline that we successfully used to pinpoint genes responsible for a form of West's syndrome, a Complex Intellectual Disability syndrome associated with patellar dislocation and celiac disease, and correcting some erroneous molecular diagnosis of Alport's syndrome in a Saudi Arabian family.

Fast analysis of doping agents in urine by ultra-high-pressure liquid chromatography-quadrupole time-of-flight mass spectrometry. II: Confirmatory analysis.

For doping control, analyses of samples are generally achieved in two steps: a rapid screening and, in the case of a positive result, a confirmatory analysis. A two-step methodology based on ultra-high-pressure liquid chromatography coupled to a quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) was developed to screen and confirm 103 doping agents from various classes (e.g., beta-blockers, stimulants, diuretics, and narcotics). The screening method was presented in a previous article as part I (i.e., Fast analysis of doping agents in urine by ultra-high-pressure liquid chromatography-quadrupole time-of-flight mass spectrometry. Part I: screening analysis). For the confirmatory method, basic, neutral and acidic compounds were extracted by a dedicated solid-phase extraction (SPE) in a 96-well plate format and detected by MS in the tandem mode to obtain precursor and characteristic product ions. The mass accuracy and the elemental composition of precursor and product ions were used for compound identification. After validation including matrix effect determination, the method was considered reliable to confirm suspect results without ambiguity according to the positivity criteria established by the World Anti-Doping Agency (WADA). Moreover, an isocratic method was developed to separate ephedrine from its isomer pseudoephedrine and cathine from phenylpropanolamine in a single run, what allowed their direct quantification in urine.

Deep accidental hypothermia with core temperature below 24°c presenting with vital signs.

Abstract Pasquier, Mathieu, Noemi Zurron, Barbara Weith, Pierre Turini, Fabrice Dami, Pierre-Nicolas Carron, and Peter Paal. Deep accidental hypothermia with core temperature below 24°C presenting with vital signs. High Alt Med Biol. 15:58-63, 2014.-Background: According to the Swiss hypothermia clinical staging, patients with stage III are unconscious with preserved vital signs, with core temperature usually between 24° and 28°C. With stage IV, vital signs are absent with core temperature <24°C. Aims: To describe a patient presenting with HT stage III with vital signs but a core temperature of <24°C, and to search for similar patients in the medical literature. Materials and methods: MEDLINE was used to search for cases of deep accidental hypothermia (<24°C) and preserved vital signs. Results: We found 22 cases in addition to our case (n=23). Median age was 44 years (IQR 36; range 4-83) and median core temperature 22°C (IQR 1.7; 17-23.8). Vital signs were often minimal. Seven patients developed ventricular fibrillation (VF). Twenty patients survived with excellent neurological outcome. Conclusions: Vital signs can be present in hypothermic patients with core temperature <24°C. In deeply hypothermic patients, a careful check and prolonged check of vital functions should be made, as vital signs may be minimal. The clinical Swiss staging remains valuable in the prehospital evaluation of hypothermic patients; its correlation with core temperature should be better defined.

Detailed assessment of the deep-seated gravitational deformation at Stampa above Flåm, Norway

The unstable rock slope above the village of Flåm shows signs of active and postglacial gravitational deformation over an area of 11 km2. We performed detailed structural field mapping, annual differential Global Navigation Satellite System (GNSS) surveys, and generated a detailed topographic model based on airborne and terrestrial laser scanning. Kinematic analyses of the structural data indicates that deformation is complex and varies over the slope. Both sliding and toppling are locally feasible. Using differential GNSS, 18 points were measured annually over a period of up to 6 years. Two of these points show an average yearly movement of around 10 mm/year. They are located at the frontal cliff on almost completely detached blocks. Large fractures indicate deep-seated gravitational deformation of volumes up to 80 million m3, but the movement rates in these areas are below 2 mm/year. Based upon these combined observations, we interpret that small collapses of blocks along the frontal cliff will be more frequent. Larger collapses of free-standing blocks along the cliff with volumes >100,000 m3, thus large enough to reach the fjord, cannot be ruled out. A large collapse involving more than 10 million m3, however, is of very low likelihood at present.

In vivo study comparing an X-shaped polymethylmethacrylate and a cylindrical collagen implant for deep sclerectomy.

Background:  Study in vivo characteristics of a polymethylmethacrylate (PMMA) implant compared to the standard cylindrical collagen implant for deep sclerectomy (DS). Design:  Six-month comparative study. Samples:  Twenty eyes of ten rabbits. Methods:  Eyes were randomized to have DS with PMMA implant in one eye and collagen implant in the opposite eye. The growth of the new subconjunctival drainage vessels was assessed by combined fluorescein and indocyanin green anterior segment angiography; intrascleral and subconjunctival blebs were imaged by ultrasound biomicroscopy (UBM). At six months, outflow facility (C) was measured by anterior chamber perfusion and portions of one side of the DS were compared to portions on the 180° opposite side and native sclera on histology. Results:  The mean IOP preoperatively and at one, four, twelve, and twenty-four weeks was comparable in both groups (P > 0.1). UBM showed a statistically insignificant quicker regression of the subconjunctival bleb as well as a durable intrascleral lake in the PMMA group (P > 0.05). New drainage vessels were initially observed one month after surgery; they were more numerous in the PMMA group on angiographic and histological findings at 6 months (P < 0.05). The mean C increased significantly after surgery compared to preoperative values (P < 0.05) and no difference was observed between the implants (0.24 ± 0.06 µl/min/mmHg [PMMA] and 0.23 ± 0.07 µl/min/mmHg [collagen implant]) (P = 0.39). Conclusions:  Deep sclerectomy performed with PMMA or collagen implants showed similar IOP lowering effects, outflow facility increase, and degree of inflammatory reaction.

DESARROLLO DE UNA BASE DE DATOS Y UNA APLICACIÓN WEB DE ACCESO A LA MISMA PARA UN GRUPO DE INVESTIGACIÓN MARINA DE ORGANISMOS DE PROFUNDIDAD (DEEP-SEA)

Este proyecto se fraguó previamente a la elección de un trabajo final de carrera. Para poder entenderlo debo mencionar que trabajo como titulado superior de investigación y laboratorio en el Instituto de Ciencias del Mar (ICM)del Consejo Superior de Investigaciones Científicas (CSIC), dentro de un grupo de investigación en oceanografía biológica, concretamente en recursos marinos renovables. En base a mi experiencia con este tipo de entorno de investigación, observe que existían una serie de mejoras de carácter técnico que se podrían introducir, y que ha la larga iban a facilitar mucho más el trabajo científico del grupo.Este grupo durante muchos años se ha dedicado a la obtención de datos de dos especies marinas de interés comercial del mar Mediterráneo que tienen su hábitat en aguas profundas: la gamba rosada (Aristeus antennatus) y la cigala (Nephrops norvegicus). Por ende, de manera colateral, datos de las especies que interaccionan con ellas, y que por este hecho se ven influenciadas al ser pescadas las anteriores. En estos años ha ido en aumento la evidencia de que ecosistemas más someros de nuestros mares tienen una relación mucho mayor de lo que se suponía con los ecosistemas profundos de los mismos. Además estos ecosistemas profundos influyen en los someros, también más de lo que cabía esperar, actuando de refugio de larvas y especies que tienen capacidad de sobrevivir en rangos batimétricos amplios. Si desean tener una visión más profunda al respecto pueden ver algunas de las últimas referencias bibliográficas a las que hago referencia en este párrafo acerca de este hecho, así como del incremento de la importancia de los grupos de investigación en el mundo dedicados a este tipo de investigación. En algunas de estas publicaciones han participado miembros del grupo al cual va dirigido el trabajo que aquí expongo.A medida que crecía el número de miembros del grupo, la importancia del mismo, la mejora tecnológica empleada en los muestreos, las colaboraciones internacionales con otras instituciones y la cantidad de proyectos en el grupo de investigación, crecía a su vez proporcionalmente, la cantidad de datos y la disparidad en formatos y sistemas de almacenaje (Hojas MS Excel o bases de datos MS Access, archivos de texto, etc.). Se ha hecho necesaria entonces la creación de una herramienta que los gestione de una forma común, y una base de datos para el almacenaje de los mismos de una forma coherente y robusta. Así mismo el hecho de tener los datos en una fuente común, posibilitará su distribución a otras bases de datos mundiales sobre la materia con las cuales se colabora, dependientes de organismos tan en la cresta a de la ola, como el Census of marine life (COML), el Alfred Wegener Institute (AWI) y el Center for Marine Environmental Sciences (MARUM)de Alemania. Estos a su vez carecen de datos de las zonas geográficas pertenecientes al mar Mediterráneo foco de la investigación del grupo.

Added Value of Deep Sequencing Relative to Population Sequencing in Heavily Pre-Treated HIV-1-Infected Subjects.

OBJECTIVE: To explore the potential of deep HIV-1 sequencing for adding clinically relevant information relative to viral population sequencing in heavily pre-treated HIV-1-infected subjects. METHODS: In a proof-of-concept study, deep sequencing was compared to population sequencing in HIV-1-infected individuals with previous triple-class virological failure who also developed virologic failure to deep salvage therapy including, at least, darunavir, tipranavir, etravirine or raltegravir. Viral susceptibility was inferred before salvage therapy initiation and at virological failure using deep and population sequencing genotypes interpreted with the HIVdb, Rega and ANRS algorithms. The threshold level for mutant detection with deep sequencing was 1%. RESULTS: 7 subjects with previous exposure to a median of 15 antiretrovirals during a median of 13 years were included. Deep salvage therapy included darunavir, tipranavir, etravirine or raltegravir in 4, 2, 2 and 5 subjects, respectively. Self-reported treatment adherence was adequate in 4 and partial in 2; one individual underwent treatment interruption during follow-up. Deep sequencing detected all mutations found by population sequencing and identified additional resistance mutations in all but one individual, predominantly after virological failure to deep salvage therapy. Additional genotypic information led to consistent decreases in predicted susceptibility to etravirine, efavirenz, nucleoside reverse transcriptase inhibitors and indinavir in 2, 1, 2 and 1 subject, respectively. Deep sequencing data did not consistently modify the susceptibility predictions achieved with population sequencing for darunavir, tipranavir or raltegravir. CONCLUSIONS: In this subset of heavily pre-treated individuals, deep sequencing improved the assessment of genotypic resistance to etravirine, but did not consistently provide additional information on darunavir, tipranavir or raltegravir susceptibility. These data may inform the design of future studies addressing the clinical value of minority drug-resistant variants in treatment-experienced subjects.

Application of compositional data analysis to geochemical data of marine sediments

In an earlier investigation (Burger et al., 2000) five sediment cores near the RodriguesTriple Junction in the Indian Ocean were studied applying classical statistical methods(fuzzy c-means clustering, linear mixing model, principal component analysis) for theextraction of endmembers and evaluating the spatial and temporal variation ofgeochemical signals. Three main factors of sedimentation were expected by the marinegeologists: a volcano-genetic, a hydro-hydrothermal and an ultra-basic factor. Thedisplay of fuzzy membership values and/or factor scores versus depth providedconsistent results for two factors only; the ultra-basic component could not beidentified. The reason for this may be that only traditional statistical methods wereapplied, i.e. the untransformed components were used and the cosine-theta coefficient assimilarity measure.During the last decade considerable progress in compositional data analysis was madeand many case studies were published using new tools for exploratory analysis of thesedata. Therefore it makes sense to check if the application of suitable data transformations,reduction of the D-part simplex to two or three factors and visualinterpretation of the factor scores would lead to a revision of earlier results and toanswers to open questions . In this paper we follow the lines of a paper of R. Tolosana-Delgado et al. (2005) starting with a problem-oriented interpretation of the biplotscattergram, extracting compositional factors, ilr-transformation of the components andvisualization of the factor scores in a spatial context: The compositional factors will beplotted versus depth (time) of the core samples in order to facilitate the identification ofthe expected sources of the sedimentary process.Kew words: compositional data analysis, biplot, deep sea sediments

Deep-brain stimulation for Parkinson's disease

Comment on N Engl J Med. 2010 Jun 3;362(22):2077-91 author reply 988.

Prévalence des troubles de l'humeur dans la maladie de Parkinson traitée par stimulation cérébrale profonde [Prevalence of mood disorders in Parkinson's disease patients treated with subthalamic nucleus deep brain stimulation].

Subthalamic nucleus deep brain stimulation (STN-DBS) is a recognized treatment for advanced and severe forms of Parkinson's Disease. The procedure improves motor signs and often allows a reduction of the medication. The impact of the procedure on cognitive and neuropsychiatric signs of the disease is more debated and there is an international consensus for the need of a multidisciplinary evaluation of patients undergoing such programs, including a neuropsychiatric assessment. We present a review of the literature as well as the experience at our centre focused on the short and long term outcome on mood following STN-DBS.

Laser-ultraviolet-A induced ultra weak photon emission in human skin cells: A biophotonic comparison between keratinocytes and fibroblasts.

Photons participate in many atomic and molecular interactions and processes. Recent biophysical research has discovered an ultraweak radiation in biological tissues. It is now recognized that plants, animal and human cells emit this very weak biophotonic emission which can be readily measured with a sensitive photomultiplier system. UVA laser induced biophotonic emission of cultured cells was used in this report with the intention to detect biophysical changes between young and adult fibroblasts as well as between fibroblasts and keratinocytes. With suspension densities ranging from 1-8 x 106 cells/ml, it was evident that an increase of the UVA-laser-light induced photon emission intensity could be observed in young as well as adult fibroblastic cells. By the use of this method to determine ultraweak light emission, photons in cell suspensions in low volumes (100 microl) could be detected, in contrast to previous procedures using quantities up to 10 ml. Moreover, the analysis has been further refined by turning off the photomultiplier system electronically during irradiation leading to the first measurements of induced light emission in the cells after less than 10 micros instead of more than 100 milliseconds. These significant changes lead to an improvement factor up to 106 in comparison to classical detection procedures. In addition, different skin cells as fibroblasts and keratinocytes stemming from the same donor were measured using this new highly sensitive method in order to find new biophysical insight of light pathways. This is important in view to develop new strategies in biophotonics especially for use in alternative therapies.

Ultra-fast recovery from right neglect after 'awake surgery' for slow-growing tumor invading the left parietal area

It is now possible to perform resections of slow-growing tumors in awake patients. Using direct electrical stimulation, real-time functional mapping of the brain can be used to prevent the resection of essential areas near the tumor. Simple clinical observations of patients with a resection of slow-growing tumors have demonstrated substantial recovery within a few days of such 'awake surgery'. The aim of this study was to investigate the kinetics of recovery following the resection of slow-growing tumors invading the left parietal area and to focus mainly on its rapidity. Two patients were assessed by standard line bisection tests and compared with eight healthy individuals. Independently of the pure nature of the symptoms, we report that the patients rapidly and substantially recovered from pronounced right neglect. They were tested 48 hours after the surgery and the recovery was significant for both patients after less than 4 hours. Strikingly, for one patient, recovery was ultra fast and substantial in the first practice session within less than 7 minutes: it occurred without verbal feedback and was substantially retained during the following testing session. Its rapidity suggests a process of unmasking redundant networks. With the slow growth of the lesion, the contralesional hemisphere is probably progressively prepared for rapid unmasking of homologue networks. These results have major clinical implications. For patients with an invading left-side tumor, it is now clear that line bisections are required before, during, and after awake surgery to: plan the surgery, control the quality of the resection, and also optimize the rehabilitation of the patient

Growth and characterization of CoO ultra thin films

In this report we present the growth process of the cobalt oxide system using reactive electron beam deposition. In that technique, a target of metallic cobalt is evaporated and its atoms are in-flight oxidized in an oxygen rich reactive atmosphere before reaching the surface of the substrate. With a trial and error procedure the deposition parameters have been optimized to obtain the correct stoichiometry and crystalline phase. The evaporation conditions to achieve the correct cobalt oxide salt rock structure, when evaporating over amorphous silicon nitride, are: 525 K of substrate temperature, 2.5·10-4 mbar of oxygen partial pressure and 1 Å/s of evaporation rate. Once the parameters were optimized a set of ultra thin film ranging from samples of 1 nm of nominal thickness to 20nm thick and bulk samples were grown. With the aim to characterize the samples and study their microstructure and morphology, X-ray diffraction, transmission electron microscopy, electron diffraction, energy dispersive X-ray spectroscopy and quasi-adiabatic nanocalorimetry techniques are utilised. The final results show a size dependent effect of the antiferromagnetic transition. Its Néel temperature becomes depressed as the size of the grains forming the layer decreases.