Tissue Phenomics for prognostic biomarker discovery in low- and intermediate-risk prostate cancer

Tissue Phenomics is the discipline of mining tissue images to identify patterns that are related to clinical outcome providing potential prognostic and predictive value. This involves the discovery process from assay development, image analysis, and data mining to the final interpretation and validation of the findings. Importantly, this process is not linear but allows backward steps and optimization loops over multiple sub-processes. We provide a detailed description of the Tissue Phenomics methodology while exemplifying each step on the application of prostate cancer recurrence prediction. In particular, we automatically identified tissue-based biomarkers having significant prognostic value for low-and intermediate-risk prostate cancer patients (Gleason scores 6-7b) after radical prostatectomy. We found that promising phenes were related to CD8(+) and CD68(+) cells in the microenvironment of cancerous glands in combination with the local micro-vascularization. Recurrence prediction based on the selected phenes yielded accuracies up to 83% thereby clearly outperforming prediction based on the Gleason score. Moreover, we compared different machine learning algorithms to combine the most relevant phenes resulting in increased accuracies of 88% for tumor progression prediction. These findings will be of potential use for future prognostic tests for prostate cancer patients and provide a proof-of-principle of the Tissue Phenomics approach

CANDELS/GOODS-S, CDFS, ECDFS: Photometric Redshifts For Normal and for X-Ray-Detected Galaxies

We present photometric redshifts and associated probability distributions for all detected sources in the Extended Chandra Deep Field South (ECDFS). The work makes use of the most up-to-date data from the Cosmic Assembly Near-IR Deep Legacy Survey (CANDELS) and the Taiwan ECDFS Near-Infrared Survey (TENIS) in addition to other data. We also revisit multi-wavelength counterparts for published X-ray sources from the 4Ms-CDFS and 250ks-ECDFS surveys, finding reliable counterparts for 1207 out of 1259 sources ($\sim 96\%$). Data used for photometric redshifts include intermediate-band photometry deblended using the TFIT method, which is used for the first time in this work. Photometric redshifts for X-ray source counterparts are based on a new library of AGN/galaxy hybrid templates appropriate for the faint X-ray population in the CDFS. Photometric redshift accuracy for normal galaxies is 0.010 and for X-ray sources is 0.014, and outlier fractions are $4\%$ and $5.4\%$ respectively. The results within the CANDELS coverage area are even better as demonstrated both by spectroscopic comparison and by galaxy-pair statistics. Intermediate-band photometry, even if shallow, is valuable when combined with deep broad-band photometry. For best accuracy, templates must include emission lines.Comment: The paper has been accepted by ApJ. The materials we provide are available under [Surveys] > [CDFS] through the portal http://www.mpe.mpg.de/XraySurvey

DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion

DNA cleavage by the Type III Restriction–Modification enzymes requires communication in 1D between two distant indirectly-repeated recognitions sites, yet results in non-specific dsDNA cleavage close to only one of the two sites. To test a recently proposed ATP-triggered DNA sliding model, we addressed why one site is selected over another during cleavage. We examined the relative cleavage of a pair of identical sites on DNA substrates with different distances to a free or protein blocked end, and on a DNA substrate using different relative concentrations of protein. Under these conditions a bias can be induced in the cleavage of one site over the other. Monte-Carlo simulations based on the sliding model reproduce the experimentally observed behaviour. This suggests that cleavage site selection simply reflects the dynamics of the preceding stochastic enzyme events that are consistent with bidirectional motion in 1D and DNA cleavage following head-on protein collision

The United Stamens of Rubiaceae. Morphology, Anatomy; Their Role in Pollination Ecology

Volume: 82Start Page: 357End Page: 38

Illustrated Pollen Terminology

This open access book offers a fully illustrated compendium of glossary terms and basic principles in the field of palynology, making it an indispensable tool for all palynologists. It is a revised and extended edition of “Pollen Terminology. An illustrated handbook,” published in 2009. This second edition, titled “Illustrated Pollen Terminology” shares additional insights into new and stunning aspects of palynology. In this context, the general chapters have been critically revised, expanded and restructured. The chapter “Misinterpretations in Palynology” has been extended with new research data and additional ambiguous terms, e.g., polyads vs. massulae; the chapter “Methods in Palynology” has been extensively enhanced with illustrated protocols showing the majority of the methods and techniques used when studying recent and fossil pollen with LM, SEM and TEM. Moreover, additional information about the description and publication of pollen data is provided in the chapter “How to Describe and Illustrate Pollen Grains.” Various other parts of the general chapters have now been updated and/or extended with more comprehensive textual passages and new illustrations. The chapter “Illustrated Pollen Terms” now features new and more appropriate examples of each term, including additional LM micrographs. Where necessary, the entries for selected pollen terms have been refined by rewording or adding definitions, illustrations, and new micrographs. Lastly, new terms are included, such as “suprasculpture” and the prefix “nano-“ for ornamentation features. The chapter “Illustrated Pollen Terms” is the main part of this book and comprises more than 300 widely used terms illustrated with over 1,000 high-quality images. It provides a detailed survey of the manifold ornamentation and structures of pollen, and offers essential insights into their stunning beauty

A serisi katı hal aydınlatma teknolojileri için pasif ısıl yönetimin sınırları

Thesis (M.A.)--Özyeğin University, Graduate School of Sciences and Engineering, Department of Mechanical Engineering, January 2015.Energy has been one of the most important problems for the last few decades. Efficient use of energy is as important as efficiency in energy production and transportation. Solid state lighting (SSL) technology may reduce consumed energy in buildings from 20 percent to less than 5 percent. Light emitting diodes (LEDs) have recently been evolved as a novel lighting technology that is over 7-10 times more efficient than conventional-old incandescent lamps. Although LED lighting systems have many other advantages as being more reliable and having longer lifetimes than conventional energy lighting systems like environmentally hazardous fluorescent lamps, they are based on solid state technology with thermal limitations. Low junction temperature requirement is one of the most important challenges for the high luminosity LED lighting systems, which also have high heat generation rates. Junction temperature of LEDs is directly related with reliability, lifetime, light output and quality. Therefore, thermal management is crucial for LED lighting systems. Passive thermal management of LED lighting systems has many advantages as simplicity, reliability, low cost and silent operation. Nevertheless high cooling capacity requirement means large passive cooling components, which push the limits of the form factor standards. Besides the size and weight limitations, tight interaction between thermal management and optical design obligate researchers to develop all components in a compact system. In this study, different passive air-cooling thermal management systems for high luminosity A-line LED lamps are investigated. Commercial A-line LED bulbs with various passive cooling approaches and designs are experimentally studied in order to bring thermal, optical and dimensional limitations of passively cooled A-line SSL systems into view. A new system level passive thermal management approach based on buoyancy driven chimney effect is computationally developed. The optical design of the system is also computationally developed at the same time. All computational results are validated with the experimental results. Computational and experimental results of the developed and manufactured system are analyzed, and the system is computationally optimized. Finally, several figure of merits (FOMs) are developed for SSL systems for the advancement of science and technology. Thus, various commercially available bulbs and developed prototypes are compared to bring various design options into view.Enerji son bir kaç on yıldır en önemli problemlerden biri olmuştur. Enerjinin verimli kullanılması enerjinin üretimindeki ve taşınmasındaki verimlilik kadar önemlidir. Katı hal aydınlatma (SSL) teknolojisi binalarda tüketilen enerjiyi yüzde 20'den yüzde 5'ten daha aşağıya düşürebilir. Geleneksel akkor lambalardan 7-10 kere daha verimli olan ışık yayan diyotlar (LED) son dönemde özgün bir aydınlatma teknoloji olarak gelişti. LED aydınlatma sistemleri, çevreye zararlı florasan lambalar gibi geleneksel aydınlatma sistemlerine nazaran daha güvenilir olma ve daha uzun kullanım ömrüne sahip olma gibi avantajlara sahip olsa da, termal limlitleri olan katı hal teknolojisine dayanırlar. Düşük jonksiyon sıcaklığı ihtiyacı yüksek aydınlatma gücüne ve ısı üretimine sahip LED aydınlatma sistemleri için en büyük problemlerden biridir. LED'lerin jonksiyon sıcaklığı, güvenilirlik kullanım ömrü, ışık çıkışı ve ışık kalitesi ile doğrudan ilgilidir. Bu yüzden, sistemin diğer gereksinimlerine de cevap vermesi gereken ısıl yönetim LED aydınlatma sistemleri için çok önemlidir. LED aydınlatma sistemlerinin pasif ısıl yönetimi basitlik, güvenilirlik, düsük maliyet ve sessiz çalışma gibi avantajlara sahiptir. Buna rağmen yüksek soğutma kapasitesi ihtiyacı, form faktör standartlarının sınırlarını zorlayan büyük pasif soğutma komponentleri anlamına gelmektedir. Boyut ve ağırlık limitlerinin yanında, ısıl yönetim ve optik dizayn arasındaki sıkı etkileşim araştırmacıları bütün komponentleri kompakt bir sistem olarak birlikte gelişitirmesine mecbur etmektedir. Bu çalışmada, yüksek ışık gücüne sahip sandart A serisi LED lambaları için olan farklı pasif hava-soğutma ısıl yönetim sistemleri araştırılmaktadır. Çeşitli pasif soğutma yaklaşımlarına ve tasarımlarına sahip ticari A serisi LED lambalar, pasif olarak soğutulan A serisi SSL sistemlerinin boyutsal, termal ve optik limitlerini ortaya çıkarmak için deneysel olarak çalışılmaktadır. Boyansi ile çalışan baca etkisine dayanan sistem seviyesindeki yeni bir ısıl yönetim yaklaşımı sayısal olarak geliştirildi. Sistemin optik dizaynı da aynı zamanda sayısal olarak geliştirilmiştir. Bütün sayısal sonuçlar deneysel sonuçlarla doğrulanmıştır. Geliştirilen ve üretilen sistemin sayısal ve deneysel sonuçlar analiz edilmiştir ve sayısal olarak optimize edilmiştir. Son olarak, bilim ve teknolojinin ilerlemisine katkı sağlayacak SSL sistemleri için çeşitli başarım ölçüleri (FOM) geliştirilmiştir. Böylece ticari olarak temin edilebilir çeşitli lambalar ve geliştirilen prototipler karşılaştırılarak çeşitli tasarım seçenekleri gözler önüne serilmiştir.İstanbul Development Agenc

Clinamen2: Functional-style evolutionary optimization in Python for atomistic structure searches

[Supplementary material]: Nature of problem: Find optimal atomistic structures retaining full flexibility in the choice of the optimization target, the methodological approach and its implementation (e.g. CPU- vs. GPU-heavy calculations). Enable interfacing with relevant software, including but not limited to density-functional-theory (DFT) codes and machine-learning (ML) solutions. [Solution method]: The covariance matrix adaptation evolution strategy (CMA-ES) algorithm is implemented using Cholesky decompositions for efficiency. The core algorithm and application examples for specific problems are implemented in functional-style Python free of side effects, with data classes to keep track of the state of the evolution. Dask is used for job control to enable highly distributed workflows. Advanced strategies like BI-Population CMA-ES are easy to implement and illustrated in the examples.Clinamen2 is a versatile functional-style Python implementation of the covariance matrix adaptation evolution strategy (CMA-ES) utilizing Cholesky decomposition. On top of a problem-agnostic core algorithm, the software package offers a suite of utilities and library code enabling applications to important atomistic structure searches. Features include massively distributed computation and the BI-Population restart scheme. This article details the general code structure and introduces examples that illustrate some relevant applications for the materials science and chemistry worlds, including interfacing to density-functional-theory codes and machine-learned surrogate models. The functional design renders the code modular and adaptable, and makes the creation of interfaces to other atomistic software straightforward.[Program summary]: Program Title: Clinamen2 CPC Library link to program files: https://doi.org/10.17632/x7syr2txsd.1 Developer's repository link: https://github.com/Madsen-s-research-group/clinamen2-public-releases Code Ocean capsule: https://codeocean.com/capsule/4950229 Licensing provisions: Apache-2.0 Programming language: PythonThis work was supported by the Austrian Science Fund (FWF) (SFB F81 TACO).Peer reviewe