Exon Array Analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer

<p>Abstract</p> <p>Background</p> <p>Treatment of non-small cell lung cancer with novel targeted therapies is a major unmet clinical need. Alternative splicing is a mechanism which generates diverse protein products and is of functional relevance in cancer.</p> <p>Results</p> <p>In this study, a genome-wide analysis of the alteration of splicing patterns between lung cancer and normal lung tissue was performed. We generated an exon array data set derived from matched pairs of lung cancer and normal lung tissue including both the adenocarcinoma and the squamous cell carcinoma subtypes. An enhanced workflow was developed to reliably detect differential splicing in an exon array data set. In total, 330 genes were found to be differentially spliced in non-small cell lung cancer compared to normal lung tissue. Microarray findings were validated with independent laboratory methods for <it>CLSTN1</it>, <it>FN1</it>, <it>KIAA1217</it>, <it>MYO18A</it>, <it>NCOR2</it>, <it>NUMB</it>, <it>SLK</it>, <it>SYNE2</it>, <it>TPM1</it>, (in total, 10 events) and <it>ADD3</it>, which was analysed in depth. We achieved a high validation rate of 69%. Evidence was found that the activity of FOX2, the splicing factor shown to cause cancer-specific splicing patterns in breast and ovarian cancer, is not altered at the transcript level in several cancer types including lung cancer.</p> <p>Conclusions</p> <p>This study demonstrates how alternatively spliced genes can reliably be identified in a cancer data set. Our findings underline that key processes of cancer progression in NSCLC are affected by alternative splicing, which can be exploited in the search for novel targeted therapies.</p

a combined ecological momentary assessment and fMRI study

Regulation of emotions is necessary for successful attainment of short-term and long-term goals. However, over-regulation may also have its costs. In anorexia nervosa (AN), forgoing food intake despite emaciation and endocrine signals that promote eating is an example of “too much” self-control. Here we investigated whether voluntary emotion regulation in AN patients comes with associated disorder-relevant costs. Thirty-five patients with acute AN and thirty-five age-matched healthy controls (HCs) performed an established emotion regulation paradigm during functional magnetic resonance imaging after an overnight fast. The task required reducing emotions induced by positively valenced pictures via distancing. We calculated a neural regulation score from responses recorded in a reward-related brain region of interest (ventral striatum; VS) by subtracting activation measured on “positive distance” trials from that elicited under the “positive watch” (baseline) condition. Complementing the imaging data, we used ecological momentary assessment (EMA) to probe disorder-related rumination and affect six times/day for 2 weeks following the scanning session. The neural regulation score indicating reduced VS activation during emotion regulation was used as a predictor in hierarchical linear models with EMA measures as outcomes. No group differences in neural activity were found for the main contrasts of the task. However, regulation of VS activity was associated with increased body-related rumination and increased negative affect in AN, but not in HC. In line with this finding, correlational analysis with longitudinal BMI measurements revealed a link between greater VS regulation and poorer treatment outcome after 60 and 90 days. Together, these results identify a neural correlate of altered emotion regulation in AN, which seems to be detrimental to psychological well-being and may interfere with recovery

Terrestrial laser scanning in forest inventories

AbstractDecision making on forest resources relies on the precise information that is collected using inventory. There are many different kinds of forest inventory techniques that can be applied depending on the goal, scale, resources and the required accuracy. Most of the forest inventories are based on field sample. Therefore, the accuracy of the forest inventories depends on the quality and quantity of the field sample. Conventionally, field sample has been measured using simple tools. When map is required, remote sensing materials are needed. Terrestrial laser scanning (TLS) provides a measurement technique that can acquire millimeter-level of detail from the surrounding area, which allows rapid, automatic and periodical estimates of many important forest inventory attributes. It is expected that TLS will be operationally used in forest inventories as soon as the appropriate software becomes available, best practices become known and general knowledge of these findings becomes more wide spread. Meanwhile, mobile laser scanning, personal laser scanning, and image-based point clouds became capable of capturing similar terrestrial point cloud data as TLS. This paper reviews the advances of applying TLS in forest inventories, discusses its properties with reference to other related techniques and discusses the future prospects of this technique

Structural evolution and disintegration of oceanic intraplate volcanoes: The Bathymetrists Seamounts and its relation to Sierra Leona Rise (eastern equatorial Atlantic) - Cruise No. M152/2, 03.01. – 12.02.2019, Las Palmas (Spain) – Walvis Bay (Namibia), SEDIS

Summary The Bathymetrists Seamounts (BSM) are located north of the volcanic Sierra Leone Rise in the eastern Atlantic between 6° and 9°N. The three W-E, N-S and NE-SW striking directions of the seamounts indicate a clear structural control for the emplacement of these volcanoes. The origin of the melts, their relationship to the Sierra Leone Rise and the role of the faults in the formation of the melts are unknown as the BSM could be explained by plume related volcanism or decompression melting beneath deep (transform) faults. The SEDIS-cruise M152/2 of RV METEOR strove for a better understanding of the life cycle of submarine volcanoes and their effect on the oceanic lithosphere in the oceanic intraplate setting of the BSM and the relationship to the Sierra Leone Rise. The aims were: 1) to understand the interaction between crustal thickness, tectonics and volcanic phases, 2) to investigate the structural, chronological and petrological evolution of individual seamounts and seamount chains, 3) to review slope failures and resulting mass flow processes. We addressed these objectives by more than 4000 km highresolution reflection seismic and more than 5000 km of parametric echosounder, multi-beam, and gravity and magnetic profiles. Rock samples for ground truthing and geochemical research have been collected during 14 dredge stations. We further determined the concentrations in surface seawater and air and the state of air-sea exchange of a number of nowadays globally banned pesticides, polychlorinated biphenyls, brominated flame retardants, polycyclic aromatic hydrocarbons and their derivatives. Zusammenfassung Die Bathymetrists Seeberge liegen nördlich der Sierra Leone Schwelle, einer vulkanischen Plattform im östlichen Atlantik zwischen 6° und 9° N. Diese submarinen Vulkane gruppieren sich entlang W-E, N-S und NE-SW Trends, was eine strukturelle Kontrolle der Vulkanentstehung indiziert. Die Schmelzentstehung sind unbekannt und können mit PlumeVulkanismus oder Dekompressionsschmelzen unter bisher nicht untersuchten Störungen und tiefen Transformstörungen zusammenhängen. Der Bezug zur Sierra Leone Schwelle ist ebenfalls unbekannt. Im Zuge der SEDIS-Expedition M152/2 mit FS METEOR wurde der Lebenszyklus von Unterwasservulkanen und deren geochemischen Einfluss auf die ozeanische Lithosphäre der Bathymetrists Seeberge untersucht. Anhand der profilhaften geophysikalischer Messungen und Dredge-Proben wollen wir 1) die Wechselwirkung zwischen Krustenmächtigkeit, Tektonik und Vulkanismus verstehen, 2) die strukturelle, chronologische und petrologische Entwicklung von Vulkanen und Vulkanketten untersuchen, und 3) Auslösemechanismen, Transportprozesse und Volumina von Hangrutschungen studieren. Zur Bearbeitung der wissenschaftlichen Fragen sammelten wir mehr als 4000 km mehrkanal-reflexionsseismischer und mehr als 5000 km parametrische Sedimentecholot, Fächerlot, Schwere und Magnetik-Profile. Für die geochemischen Arbeiten sammelten wir an 14 Stationen Gesteinsproben unter Einsatz einer Dredge. Die regelmäßige Beprobung der Luft und des Oberflächenwassers diente der Bestimmung der Konzentration von heute weltweit verbotenen Pestiziden, polychlorierten Biphenylen, bromierten Flammschutzmitteln, polyzyklischen aromatischen Kohlenwasserstoffen und deren Derivaten und um den Austausch zwischen Luft und Meer weiter zu verstehen

A quantitative comparison of different methods to detect cardiorespiratory coordination during night-time sleep

BACKGROUND: The univariate approaches used to analyze heart rate variability have recently been extended by several bivariate approaches with respect to cardiorespiratory coordination. Some approaches are explicitly based on mathematical models which investigate the synchronization between weakly coupled complex systems. Others use an heuristic approach, i.e. characteristic features of both time series, to develop appropriate bivariate methods. OBJECTIVE: In this study six different methods used to analyze cardiorespiratory coordination have been quantitatively compared with respect to their performance (no. of sequences with cardiorespiratory coordination, no. of heart beats coordinated with respiration). Five of these approaches have been suggested in the recent literature whereas one method originates from older studies. RESULTS: The methods were applied to the simultaneous recordings of an electrocardiogram and a respiratory trace of 20 healthy subjects during night-time sleep from 0:00 to 6:00. The best temporal resolution and the highest number of coordinated heart beats were obtained with the analysis of 'Phase Recurrences'. Apart from the oldest method, all methods showed similar qualitative results although the quantities varied between the different approaches. In contrast, the oldest method detected considerably fewer coordinated heart beats since it only used part of the maximum amount of information available in each recording. CONCLUSIONS: The method of 'Phase Recurrences' should be the method of choice for the detection of cardiorespiratory coordination since it offers the best temporal resolution and the highest number of coordinated sequences and heart beats. Excluding the oldest method, the results of the heuristic approaches may also be interpreted in terms of the mathematical models

Recommended reading list of early publications on atomic layer deposition-Outcome of the "Virtual Project on the History of ALD"

Atomic layer deposition (ALD), a gas-phase thin film deposition technique based on repeated, self-terminating gas-solid reactions, has become the method of choice in semiconductor manufacturing and many other technological areas for depositing thin conformal inorganic material layers for various applications. ALD has been discovered and developed independently, at least twice, under different names: atomic layer epitaxy (ALE) and molecular layering. ALE, dating back to 1974 in Finland, has been commonly known as the origin of ALD, while work done since the 1960s in the Soviet Union under the name "molecular layering" (and sometimes other names) has remained much less known. The virtual project on the history of ALD (VPHA) is a volunteer-based effort with open participation, set up to make the early days of ALD more transparent. In VPHA, started in July 2013, the target is to list, read and comment on all early ALD academic and patent literature up to 1986. VPHA has resulted in two essays and several presentations at international conferences. This paper, based on a poster presentation at the 16th International Conference on Atomic Layer Deposition in Dublin, Ireland, 2016, presents a recommended reading list of early ALD publications, created collectively by the VPHA participants through voting. The list contains 22 publications from Finland, Japan, Soviet Union, United Kingdom, and United States. Up to now, a balanced overview regarding the early history of ALD has been missing; the current list is an attempt to remedy this deficiency. (C) 2016 Author(s).Peer reviewe

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.info:eu-repo/semantics/publishedVersio

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics

The era of reference genomes in conservation genomics

info:eu-repo/semantics/publishedVersio

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics