cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 2: Figures S1-S8. of Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer
Creators: name: Hu, Zhi
name: Mao, Jian-Hua
name: Curtis, Christina
name: Huang, Ge
name: Shenda Gu
name: Heiser, Laura
name: Lenburg, Marc
name: Korkola, James
name: Bayani, Nora
name: Shamith Samarajiwa
name: Seoane, Jose
name: Dane, Mark
name: Esch, Amanda
name: Feiler, Heidi
name: Wang, Nicholas
name: Hardwicke, Mary
name: Laquerre, Sylvie
name: Jackson, Jeff
name: Wood, Kenneth
name: Weber, Barbara
name: Spellman, Paul
name: Aparicio, Samuel
name: Wooster, Richard
name: Caldas, Carlos
name: Gray, Joe
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Figure S1. The mitotic network is conserved across human malignancies including lung cancer [GEO:GSE3141] (Bild et al., 2006); ovarian cancer [GEO:GSE3149] (Bild et al., 2006); Wilms’ tumor [GEO:GSE10320] (Huang et al., 2009); prostate cancer [GEO:GSE8218]; glioblastomas [GEO:GSE13041] (Lee et al., 2008); acute lymphoblastic leukemia and acute myelogenous leukemia [GEO:GSE12417] (Metzeler et al., 2008); and lymphoblast cell lines [GEO:GSE11582] (Choy et al., 2008). Figure S2. Mitotic network activity is significantly higher in intraductal breast carcinoma (IDC) [GEO:GSE7307] as compared to normal tissues. Figure S3. A The activity of the mitotic network (MNAI) is significantly associated with pathological mitotic counts (p
Additional file 1: Tables S1, Tables S2, Tables S3 and Tables S4. of Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer
Creators: name: Hu, Zhi
name: Mao, Jian-Hua
name: Curtis, Christina
name: Huang, Ge
name: Shenda Gu
name: Heiser, Laura
name: Lenburg, Marc
name: Korkola, James
name: Bayani, Nora
name: Shamith Samarajiwa
name: Seoane, Jose
name: Dane, Mark
name: Esch, Amanda
name: Feiler, Heidi
name: Wang, Nicholas
name: Hardwicke, Mary
name: Laquerre, Sylvie
name: Jackson, Jeff
name: Wood, Kenneth
name: Weber, Barbara
name: Spellman, Paul
name: Aparicio, Samuel
name: Wooster, Richard
name: Caldas, Carlos
name: Gray, Joe
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology
subject: Computational Biology

description: Table S1. List of genes that are significantly correlated with either PLK1, CENPE or AURKB in breast cancer cell lines and used for constructing gene network. Table S2. Gene ontology (GO) analysis of genes significantly correlated with PLK1, CENPE or AURKB in human breast cancer cell lines. Table S3. Mitotic network gene list. Table S4. Pearson coefficients for correlation (and significance) between cell line responses across 53 breast cell lines derived from tumor and normal tissues. The number of lines used to establish the correlation is listed below each correlation in parentheses. (DOC 282 kb)
Additional file 10: Figure S4. of Expression of microRNAs and isomiRs in the porcine endometrium: implications for gene regulation at the maternal-conceptus interface
Creators: name: Krawczynski, Kamil
name: Bauersachs, Stefan
name: Zaneta Reliszko
name: Graf, Alexander
name: Kaczmarek, Monika
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Computational Biology

description: Cross-species comparison of 3â  UTRs of putative target genes of miR-140-3p and isomiR miR-140-3p 5â   DEL U. (PDF 95 kb)
Additional file 1: of Acupuncture for the treatment of phantom limb syndrome in lower limb amputees: a randomised controlled feasibility study
Creators: name: EsmĂŠ Trevelyan
name: Turner, Warren
name: Summerfield-Mann, Lynn
name: Robinson, Nicola
Publisher: name: Figshare
Year: 2016
Subjects: Space Science
Medicine
Cell Biology
Biotechnology
Developmental Biology
Science Policy

description: CONSORT 2010 checklist of information to include when reporting a randomised trial. (PDF 144 kb)
Additional file 2: of Acupuncture for the treatment of phantom limb syndrome in lower limb amputees: a randomised controlled feasibility study
Creators: name: EsmĂŠ Trevelyan
name: Turner, Warren
name: Summerfield-Mann, Lynn
name: Robinson, Nicola
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy

description: Acupuncture points used by practitioners during the feasibility study. (PDF 84 kb)
Leveraging rust types for modular specification and verification
Creators: name: Astrauskas, Vytautas
name: Müller, Peter
name: Poli, Federico
name: Summers, Alexander J.
Publisher: name: ETH Zurich
Year: 2018
Subjects: Rust
type systems
heap-manipulating programs
concurrency

description: Rust’s type system ensures memory safety: well-typed Rust programs are guaranteed to not exhibit problems such as dangling pointers, data races, and unexpected side effects through aliased references. Going beyond memory safety, for instance, to guarantee the absence of assertion failures or functional correctness, requires static program verification. Formal verification of system software is notoriously difficult and requires complex specifications and logics to reason about pointers, aliasing, and side effects on mutable state. This complexity is a major obstacle to a more widespread verification of system software.
In this paper, we present a novel verification technique that leverages Rust’s type system to greatly simplify the specification and verification of Rust programs. We analyse information from the Rust compiler and synthesise a corresponding core proof for the program in a flavour of separation logic tailored to automation. Crucially, our proofs are constructed and checked automatically; users of our work never work with the underlying formal logic. Users can add specifications at the abstraction level of Rust expressions; we show how to interweave these to extend our core proof to prove modularly whether these specifications are correct. We have implemented our technique for a subset of Rust; our initial evaluation on two thousand functions from widely-used Rust crates demonstrates its effectiveness.
Additional file 14: Table S8. of Expression of microRNAs and isomiRs in the porcine endometrium: implications for gene regulation at the maternal-conceptus interface
Creators: name: Krawczynski, Kamil
name: Bauersachs, Stefan
name: Zaneta Reliszko
name: Graf, Alexander
name: Kaczmarek, Monika
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: miRNA/isomiR names, sequences and assays ID of molecules validated by stem-loop real-time RT-PCR in the porcine endometrium. (DOCX 18 kb)
Additional file 15: Table S9. of Expression of microRNAs and isomiRs in the porcine endometrium: implications for gene regulation at the maternal-conceptus interface
Creators: name: Krawczynski, Kamil
name: Bauersachs, Stefan
name: Zaneta Reliszko
name: Graf, Alexander
name: Kaczmarek, Monika
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Names, Assay IDs, GenBank accession numbers and product length of selected genes analyzed in real-time PCR in an in vitro study. (DOCX 15 kb)
Equivalence of the catalytic entropy conjecture and the transitivity conjecture is plausible
Creators: name: Sergeev, Ivan
Publisher: name: ETH Zurich
Year: 2019

description: In essence, the catalytic entropy conjecture states that for a given initial state and a target state with higher entropy there exists a unitary operator acting on the tensor product of the initial state and a state of an auxiliary system such that the marginal states after the action of the unitary are precisely the target state and the same auxiliary state respectively. Since the state of the auxiliary system remains unchanged, we refer to the auxiliary system as the catalyst and to the whole operation as a catalytic transition. The primary aim of this work is to show that the catalytic entropy is equivalent to the transitivity conjecture: if there exist two catalytic transitions leading from one state to another through an intermediate state, then there exists a compound transition from the initial state directly to the target state. This goal is achieved partially: we outline a two-part proof of equivalence of the catalytic entropy conjecture and the transitivity conjecture, rigorously prove the first step, and provide numerical evidence of plausibility of the second step in the $3$-dimensional case for precision-based versions of the two conjectures. In addition, we generalize the family of catalytic transitions introduced in a paper by Sparaciari, Jennings, and Oppenheim to an arbitrary dimension, as well as show that the transitivity conjecture is a nontrivial statement by proving that a naive approach to proving it fails.
Additional file 4: Figure S2. of Expression of microRNAs and isomiRs in the porcine endometrium: implications for gene regulation at the maternal-conceptus interface
Creators: name: Krawczynski, Kamil
name: Bauersachs, Stefan
name: Zaneta Reliszko
name: Graf, Alexander
name: Kaczmarek, Monika
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Pre-miRNA sequences with assigned miRNAs/isomiRs not included in miRNA characterization. Reference/canonical miRNA found in miRBase, corresponding to specific pre-miRNA was marked in bold and underlined. All sequences found in our dataset were assigned to specific miRNA transcript and ambiguous sequences were underlined. (PDF 77 kb)
Automated point-of-care processing and interpretation of pulse oximetry for global health applications
Creators: name: Karlen, Walter
Publisher: name: ETH Zurich
Year: 2019
Subjects: Pulse oximetry
Global health

description: Pulse oximetry is an essential monitoring tool for global health applications, but widely underused. Reasons include, besides the high costs and low robustness of existing devices, the difficulty for health care staff to correctly interpret the obtained measurements. Technology for automated interpretation of blood oxygen saturation could bridge this gap.
Additional file 1: Table S1. of Expression of microRNAs and isomiRs in the porcine endometrium: implications for gene regulation at the maternal-conceptus interface
Creators: name: Krawczynski, Kamil
name: Bauersachs, Stefan
name: Zaneta Reliszko
name: Graf, Alexander
name: Kaczmarek, Monika
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Average values representing read counts after subsequent steps of pre-analysis of raw data obtained from Illumina sequencing. Letters indicate pregnancy (P) and the estrous cycle (C), whereas numbers a day (n = 5 for all groups, except P12 [n = 4] and P20 [n = 6]). Valid sequences were obtained by subtracting number of reads with length <17 nt and reads with unknown bases from reads with found adaptor sequences. (DOCX 17 kb)
Privacy Loss Classes: The Central Limit Theorem in Differential Privacy
Creators: name: Sommer, David
name: Meiser, Sebastian
name: Mohammadi, Esfandiar
Publisher: name: ETH Zurich
Year: 2018
Subjects: Differential privacy
Privacy Loss

description: In recent years, privacy enhancing technologies have gained tremendous momentum and they are expected to keep a sustained importance. Quantifying the degree of privacy offered by any mechanism working on potentially sensitive data is a complex and well-researched topic; epsilon-differential privacy (DP) and its slightly weaker and more versatile variant (epsilon,delta)-approximate differential privacy (ADP) have become the de-facto standard for privacy measures in the literature. Recently, novel variants of (A)DP focused on giving tighter privacy bounds under continual observation. In this paper, we unify many of these previous works in a common core theory, focused on the privacy loss of a mechanism. We show that in sequential composition of the mechanism, the privacy loss (represented as a distribution) undergoes a convolution, which in turn enables us to show the central limit theorem for differential privacy: the privacy loss of any mechanism will converge to a Gauss distribution. This observation leads us to several practically relevant insights: 1) we show that several of the novel DP-variants are equally expressive as ADP, 2) we improve existing bounds, such as the moments accountant bound, 3) we derive exact ADP guarantees for the Gauss mechanism, i.e., an analytical and simple formula to directly calculate ADP (not an over-approximating bound), 4) we derive exact ADP guarantees for the Randomized Response, and, 5) we characterize the privacy guarantees of a mechanism by the Gauss distribution to which it converges, its privacy class, and using normal approximation theorems derive novel upper and lower ADP bounds for arbitrary mechanisms.
Additional file 6: Figure S3. of Expression of microRNAs and isomiRs in the porcine endometrium: implications for gene regulation at the maternal-conceptus interface
Creators: name: Krawczynski, Kamil
name: Bauersachs, Stefan
name: Zaneta Reliszko
name: Graf, Alexander
name: Kaczmarek, Monika
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Computational Biology

description: miRNAs and isomiRs classified to the miR-23 (A) and miR-148 (B) families, harboring the same seed sequences. Reference/canonical miRNA found in miRBase, corresponding to specific pre-miRNA was marked in bold and underlined. Underlined sequence of miR-23a/b isomiR could not be uniquely assigned to one member of given family. (PDF 149 kb)
Surrogate modelling meets machine learning
Creators: name: Sudret, Bruno
name: Lataniotis, Christos
name: Lüthen, Nora
name: Marelli, Stefano
name: Torre, Emiliano
Publisher: name: ETH Zurich
Year: 2019

description: Complex computational models are used nowadays in all fields of applied sciences to predict the behaviour of natural, economic and engineering systems. High-fidelity simulators are able to capture more and more realistic features by including multi-scale or multi-physics aspects in their governing equations, which can result in high complexity. Although computer power has attained unprecedented levels, it is still not possible to use brute force approaches such as Monte Carlo simulation for solving uncertainty propagation, sensitivity or optimization problems with those models. This is the reason why surrogate models such as polynomial chaos expansions (PCE) or Gaussian processes (GP), among others, have gained a lot of attention in the past two decades.
In parallel, machine learning and in particular deep neural networks have shown tremendous performance in solving dedicated problems such as image classification or natural language processing. This has raised a lot of interest in the uncertainty quantification community, too. In this lecture, we advocate a sound cross-fertilization of the two worlds.
The links between surrogate modelling and supervised learning are first underlined. We show that sparse polynomial chaos expansions can be used as a supervised learning technique in a pure data-driven sense. Through various examples, we show that their predicting capabilities are comparable to, or in some cases better, than neural networks and support vector regression, especially in the context of small data sets.
In a second part, we address problems with high-dimensional input vectors for which standard PCE or GP techniques cannot be straightforwardly applied. In this context, we devise an optimal coupling strategy between dimensionality reduction techniques borrowed from machine learning  and standard surrogate modelling. This allows us to develop surrogates for computational models where inputs are large time series or maps. We illustrate the performance of this approach on examples in heat conduction and wind turbine dynamics.
Additional file 11: Table S7. of Expression of microRNAs and isomiRs in the porcine endometrium: implications for gene regulation at the maternal-conceptus interface
Creators: name: Krawczynski, Kamil
name: Bauersachs, Stefan
name: Zaneta Reliszko
name: Graf, Alexander
name: Kaczmarek, Monika
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Primers, GenBank accession numbers and product lengths of miRNA synthesis/transport-related genes studied in real-time RT-PCR analysis. (DOCX 17 kb)
Surrogate models for uncertainty quantification and design optimization
Creators: name: Sudret, Bruno
name: Mai, Chu V.
name: Marelli, Stefano
name: Schöbi, Roland
name: Wagner, Paul-Remo
Publisher: name: ETH Zurich
Year: 2019
Subjects: uncertainty quantification
Surrogate models
Polynomial chaos expansions
Kriging

description: Nowadays computational models are used in virtually all fields of applied sciences and engineering to predict the behaviour of complex natural or man-made systems. Also known as simulators, they allow the engineer to assess the performance of a system in-silico, and then optimize its design or operating. 
Realistic models (e.g. finite element models) usually feature tens of parameters and are costly to run, even when taking full advantage of the available computer power. In parallel, the more complex the system, the more uncertainty in its governing parameters, environmental and operating conditions. In this respect, uncertainty quantification methods used to solve reliability, sensitivity or optimal design problems may require thousands to millions of model runs when using brute force techniques such as Monte Carlo simulation, which is not affordable with high-fidelity simulators. 
In contrast, surrogate models allow one to tackle the problem by constructing an accurate approximation of the simulator’s response from a limited number of runs at selected values (the so-called experimental design) and some learning algorithm. In this lecture, two types of efficient surrogate models will be presented in details, namely polynomial chaos expansions (including sparse approaches for high-dimensional problems) and Kriging (a.k.a. Gaussian process modelling). Recent extensions to dynamics and supervised learning will be addressed. Various applications in sensitivity and reliability analysis as well as model calibration (Bayesian inversion) and reliability-based design optimization will be shown as an illustration.
Data-based sparse polynomial chaos expansions: applications in dynamics and machine learning
Creators: name: Sudret, Bruno
Publisher: name: ETH Zurich
Year: 2019
Subjects: Machine learning
Polynomial chaos expansions
Uncertainty quantification

description: The links between uncertainty quantification and classical machine learning (ML) have tightened in the past few years. On the one hand, uncertainty propagation techniques are nowadays mainly based on the use of surrogate models such as polynomial chaos expansions (PCE), Gaussian processes or low-rank tensor representations that are constructed in a non-intrusive manner using a batch of computer experiments and dedicated algorithms. On the other hand, in the context of supervised learning, artificial intelligence algorithms are used to build predictive models from input/output data sets. 
In this talk we will emphasize the links between the two fields, and present more specifically recent developments on sparse polynomial chaos expansions that allow one to handle problems with functional output quantities (e.g. trajectories of a dynamical system). 
As a second application, sparse PCEs will be used in a purely data-driven approach to handle benchmark data sets that are commonly used in the machine learning community. It is shown that sparse PCEs give as good as, or even better results than the (ad-hoc tuned) ML ones presented in the literature.
Sparse polynomial chaos expansions for uncertainty quantification  and sensitivity analysis
Creators: name: Sudret, Bruno
Publisher: name: ETH Zurich
Year: 2019

description: Computational models are used nowadays in virtually all fields of applied sciences and engineering to predict the behaviour of complex natural or man-made systems. These so-called simulators usually feature dozens of parameters and are expensive to run, even when taking full advantage of the available computer power. In this respect, uncertainty quantification techniques used to solve reliability, sensitivity, model calibration/inversion or optimal design problems would require thousands to millions of runs with different values of the model input parameters, which is not affordable with high-fidelity, costly simulators. 

Polynomial chaos expansions (PCE) have emerged two decades ago to solve partial differential equations with random coefficients [1]. In the last decade, with the development of so-called non intrusive methods [2], they have become a mature tool for building surrogate models of complex simulators, which is nowadays applied in civil, mechanical and electrical engineering but also in economics, and recently in astrophysics. Sparse PCE, which are  based on statistical learning and compressive sensing approaches nowadays allow to use PCEs also in high-dimensions [3]. 

In this talk, the basic machinery of PCEs will be presented, as well algorithms to compute sparse expansions at low cost (typically, a few dozens to hundreds of runs of the original model, for problems with up to 100 parameters). These sparse PCEs allow for the most efficient computation of the well-established Sobol’ (global) sensitivity indices, but can also be use in the context of Bayesian model calibration and rare event estimation. Application to subsurface flow [4] and other engineering problems will be presented as an illustration.
Additional file 3 of Multi-objective optimization for RNA design with multiple target secondary structures
Creators: name: Taneda, Akito
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Supplementary Figures S1 â   S3. Figure S1. Boltzmann probabilities of the designed RNA sequences by MODENA, Frnakenstein, and RNAdesign for the two-target RNAtabupath dataset. Figure S2. An example of the ribozyme-based RNA device design which takes energy barrier height into account. Figure S3. Boltzmann probabilities of the RNA sequences designed by MODENA with and without the crossover operator for the two-target RNAtabupath dataset. (PDF 557 kb)
Additional file 1: of The impact of item-writing flaws and item complexity on examination item difficulty and discrimination value
Creators: name: Rush, Bonnie
name: Rankin, David
name: White, Brad
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Examples of select item-writing flaws. (PDF 244 kb)
Valuing meteorological services in resource-constrained settings: Application to smallholder farmers in the Peruvian Altiplano
Creators: name: Brausmann, Alexandra
name: Flubacher, Moritz
name: Lechthaler, Filippo
Publisher: name: ETH Zurich
Year: 2019
Subjects: Valuation
meteorological information
uncertainty
agriculture
quinoa farming
climate change

description: Economics Working Paper Series, 19/324
Additional file 3: of Evaluation of Salvadora persica L. and green tea anti-plaque effect: a randomized controlled crossover clinical trial
Creators: name: Abdulbaqi, Hayder
name: Himratul-Aznita, Wan
name: Nor Baharuddin
Publisher: name: Figshare
Year: 2016
Subjects: subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology

description: Raw data and statistics of means Pl of participants for placebo, test and chlorhexidine mouth rinses. (PDF 158 kb)
Additional file 1: of Evaluation of Salvadora persica L. and green tea anti-plaque effect: a randomized controlled crossover clinical trial
Creators: name: Abdulbaqi, Hayder
name: Himratul-Aznita, Wan
name: Nor Baharuddin
Publisher: name: Figshare
Year: 2016
Subjects: subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology

description: Raw data of sample size, power and effect size of the study. (PDF 226 kb)
Additional file 2: of Evaluation of Salvadora persica L. and green tea anti-plaque effect: a randomized controlled crossover clinical trial
Creators: name: Abdulbaqi, Hayder
name: Himratul-Aznita, Wan
name: Nor Baharuddin
Publisher: name: Figshare
Year: 2016
Subjects: subject: Cell Biology
subject: Molecular Biology
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology
subject: FOS: Biological sciences

description: Raw data and statistics of intra-examiner calibration. (PDF 127 kb)
Additional file 1: Table S1. of Maternal history of childhood sexual abuse and preterm birth: an epidemiologic review
Creators: name: Adaeze Wosu
name: Bizu Gelaye
name: Williams, Michelle
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Science Policy

description: Search terms used to identify relevant publications. (DOCX 14 kb)
Elatine alsinastrum L.
Creators: name: Konrad Lauber
name: Gerhart Wagner
name: Andreas Gygax
Publisher: name: Haupt Verlag
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Malpighiales
Elatinaceae
Elatine
Elatine alsinastrum

description: Elatine alsinastrum L.
Artbeschreibung: Schlammpflanze mit 2-30(-100) cm langen, niederliegenden Stängeln und +/- sitzenden, quirlständigen Blättern. Diese über Wasser meist zu 3, eiförmig bis lanzettlich, 1-3 cm lang, unter Wasser bis 16 im Quirl, schlaff, bis 5 cm lang und höchstens 1,5 mm breit. Blüten +/- sitzend in den Blattwinkeln, grünlich, 4 zählig, Kronblätter 1-1,5 mm lang, wenig länger als die Kelchblätter. Staubblätter 8. Griffel 4. Frucht rund, abgeflacht.
Blütezeit: 6-9
Standort und Verbreitung in der Schweiz: Zeitweise überschwemmte, schlammige Ufer / kollin / Früher MZ (BE) und TI
Verbreitung global: Eurasiatisch
Ökologische Zeigerwerte nach Landolt & al. (2010)
BodenfaktorenKlimafaktorenSalztoleranzFeuchtezahl Fnass; Feuchtigkeit stark wechselnd (mehr als ± 2 Stufen)Lichtzahl LhellSalzzeichen1Reaktionszahl Rsauer (pH 3.5-6.5)Temperaturzahl Twarm-kollinNährstoffzahl NnährstoffreichKontinentalitätszahl Ksubozeanisch (hohe Luftfeuchtigkeit, geringe Temperaturschwankungen, eher milde Winter)
Volksname Deutscher Name: Quirliger Tännel Nom français: Elatine verticillée Nome italiano: Pepe d'acqua maggiore
description: Published as part of Konrad Lauber, Gerhart Wagner & Andreas Gygax, 2018, Flora Helvetica - Elatinaceae, pp. 408 in Flora Helvetica, Bern :Haupt Verlag on page 408
Elatine hexandra DC.
Creators: name: Konrad Lauber
name: Gerhart Wagner
name: Andreas Gygax
Publisher: name: Haupt Verlag
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Malpighiales
Elatinaceae
Elatine
Elatine hexandra

description: Elatine hexandra (Lapierre) DC.
Artbeschreibung: Unterscheidet sich von E. hydropipe r durch folgende Merkmale: Blattstiel kürzer als die Spreite, Blüten 3 zählig, 0,5-5 mm lang gestielt, Kronblätter weiss oder rötlich, 1-1,5 mm lang, länger als die Kelchblätter, Staubblätter 6, Griffel 3, Samen wenig gebogen.
Blütezeit: 6-9
Standort und Verbreitung in der Schweiz: Zeitweise überschwemmte, schlammige Ufer / kollin / J, MW
Verbreitung global: Europäisch
Ökologische Zeigerwerte nach Landolt & al. (2010)
BodenfaktorenKlimafaktorenSalztoleranzFeuchtezahl Fnass; Feuchtigkeit stark wechselnd (mehr als ± 2 Stufen)Lichtzahl LhellSalzzeichen--Reaktionszahl Rschwach sauer bis neutral (pH 4.5-7.5)Temperaturzahl Tkollin (Laubmischwälder mit Eichen)Nährstoffzahl NnährstoffreichKontinentalitätszahl Ksubozeanisch (hohe Luftfeuchtigkeit, geringe Temperaturschwankungen, eher milde Winter)
Volksname Deutscher Name: Sechsmänniger Tännel Nom français: Elatine à six étamines Nome italiano: Pepe d'acqua a sei stami
description: Published as part of Konrad Lauber, Gerhart Wagner & Andreas Gygax, 2018, Flora Helvetica - Elatinaceae, pp. 408 in Flora Helvetica, Bern :Haupt Verlag on page 408
Additional file 6: Table S5. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response
Creators: name: Lips, Esther
name: Michaut, Magali
name: Hoogstraat, Marlous
name: Mulder, Lennart
name: Besselink, Nicolle
name: Koudijs, Marco
name: Cuppen, Edwin
name: Voest, Emile
name: Bernards, Rene
name: Nederlof, Petra
name: Wesseling, Jelle
name: Rodenhuis, Sjoerd
name: Wessels, Lodewyk
Publisher: name: Figshare
Year: 2015
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Association between relapse and pathway mutations. This table shows the top five pathways associated with relapse. No significant associations were found. (DOCX 14 kb)
Elatine hydropiper L.
Creators: name: Konrad Lauber
name: Gerhart Wagner
name: Andreas Gygax
Publisher: name: Haupt Verlag
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Malpighiales
Elatinaceae
Elatine
Elatine hydropiper

description: Elatine hydropiper L.
Artbeschreibung: Sehr kleine, schlaffe Schlammpflanze mit 2-15 cm langen, niederliegenden Stängeln und gegenständigen Blättern. Diese oval oder spatelförmig, höchstens 5 mm lang, in einen Stiel verschmälert, dieser 1-3mal so lang wie die Spreite. Blüten 4 zählig, in den Blattwinkeln +/- sitzend, rötlich, Kronblätter ca. 0,5 mm lang, gleich lang wie die Kelchblätter. Staubblätter 8. Griffel 4. Frucht rund, abgeflacht. Samen hakenförmig gebogen (nur bei dieser E.- Art).
Blütezeit: 6-9
Standort und Verbreitung in der Schweiz: Zeitweise überschwemmte, schlammige Ufer / kollin / Südliches TI
Verbreitung global: Eurosibirisch
Ökologische Zeigerwerte nach Landolt & al. (2010)
BodenfaktorenKlimafaktorenSalztoleranzFeuchtezahl Fnass; Feuchtigkeit stark wechselnd (mehr als ± 2 Stufen)Lichtzahl LhellSalzzeichen--Reaktionszahl Rschwach sauer bis neutral (pH 4.5-7.5)Temperaturzahl Tkollin (Laubmischwälder mit Eichen)Nährstoffzahl NnährstoffreichKontinentalitätszahl Ksubozeanisch (hohe Luftfeuchtigkeit, geringe Temperaturschwankungen, eher milde Winter)
Volksname Deutscher Name: Wasserpfeffer-Tännel Nom français: Elatine poivre d'eau Nome italiano: Pepe d'acqua ad otto stami
description: Published as part of Konrad Lauber, Gerhart Wagner & Andreas Gygax, 2018, Flora Helvetica - Elatinaceae, pp. 408 in Flora Helvetica, Bern :Haupt Verlag on page 408
Additional file 1: Figure S1. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response
Creators: name: Lips, Esther
name: Michaut, Magali
name: Hoogstraat, Marlous
name: Mulder, Lennart
name: Besselink, Nicolle
name: Koudijs, Marco
name: Cuppen, Edwin
name: Voest, Emile
name: Bernards, Rene
name: Nederlof, Petra
name: Wesseling, Jelle
name: Rodenhuis, Sjoerd
name: Wessels, Lodewyk
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: BRCA1 gene expression, measured by RT-PCR, for BRCA1-methylated, mutated and non-mutated/non-methylated triple negative breast cancer (TNBC) samples. This figure shows the association between BRCA proficiency/deficiency and BRCA1 gene expression, as measured by RT-PCR. Samples with either BRCA1 promoter methylation or a BRCA1 mutation all had low gene expression values. (DOCX 134 kb)
Additional file 10: Table S7. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response
Creators: name: Lips, Esther
name: Michaut, Magali
name: Hoogstraat, Marlous
name: Mulder, Lennart
name: Besselink, Nicolle
name: Koudijs, Marco
name: Cuppen, Edwin
name: Voest, Emile
name: Bernards, Rene
name: Nederlof, Petra
name: Wesseling, Jelle
name: Rodenhuis, Sjoerd
name: Wessels, Lodewyk
Publisher: name: Figshare
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: Cancer
subject: Science Policy

description: Comparison of top alterations listed by Balko et al. (reference [30]) (A) and our study (B) for TCGA [3], Balko et al. [31] and our study. Part A shows the top alterations as listed by Balko (reference [30]) in our study and TCGA (reference [3]), part B shows the top alterations in our study. (DOCX 17 kb)
Additional file 5: Table S4. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response
Creators: name: Lips, Esther
name: Michaut, Magali
name: Hoogstraat, Marlous
name: Mulder, Lennart
name: Besselink, Nicolle
name: Koudijs, Marco
name: Cuppen, Edwin
name: Voest, Emile
name: Bernards, Rene
name: Nederlof, Petra
name: Wesseling, Jelle
name: Rodenhuis, Sjoerd
name: Wessels, Lodewyk
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: Plant Biology
subject: 60506 Virology

description: Association between mutations and chemotherapy response or relapse. This table shows the top five genes associated with either response or relapse. No significant associations were found. (DOCX 18 kb)
Additional file 9: Figure S3. of Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response
Creators: name: Lips, Esther
name: Michaut, Magali
name: Hoogstraat, Marlous
name: Mulder, Lennart
name: Besselink, Nicolle
name: Koudijs, Marco
name: Cuppen, Edwin
name: Voest, Emile
name: Bernards, Rene
name: Nederlof, Petra
name: Wesseling, Jelle
name: Rodenhuis, Sjoerd
name: Wessels, Lodewyk
Publisher: name: Figshare
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Plant Biology

description: Validation of TTK, TP53BP2 and genome-wide copy number profiles with Nimblegen 135Â K aCGH arrays. aCGH and exome data, for the samples for which aCGH data were available (three cases for TTK, five cases for TP53BP2). Arrow indicates respectively the TTK and TP53BP2 locus. From page 3 on we show all 14 samples for which we have both exome and aCGH data, irrespective of TTK and TP53BP2 status. In these rainbow plots, the samples containing a TTK or TP53BP2 gain are indicated with an arrow at the respective genomic location. (PDF 1639 kb)
Additional file 2: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy
Creators: name: Groof, Aurélie De
name: Ducreux, Julie
name: Humby, Frances
name: Toukap, Adrien Nzeusseu
name: Badot, Valérie
name: Pitzalis, Costantino
name: Houssiau, Frédéric
name: Durez, Patrick
name: Lauwerys, Bernard
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology

description: Patients’ characteristics (immunohistochemistry studies on ultrasound (US)-guided biopsies). Characteristics of the patients with early rheumatoid arthritis (RA) included in the immunohistochemistry studies on US-guided biopsies. (DOCX 47 kb)
Additional file 1: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy
Creators: name: Groof, Aurélie De
name: Ducreux, Julie
name: Humby, Frances
name: Toukap, Adrien Nzeusseu
name: Badot, Valérie
name: Pitzalis, Costantino
name: Houssiau, Frédéric
name: Durez, Patrick
name: Lauwerys, Bernard
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: 60506 Virology

description: Patients’ characteristics (immunohistochemistry studies on needle arthroscopic biopsies). Characteristics of the patients with early rheumatoid arthritis (RA) included in the immunohistochemistry studies on needle arthroscopic biopsies. (DOCX 56 kb)
Additional file 1: Table S1. of Effect of mineralocorticoid receptor antagonists on proteinuria and progression of chronic kidney disease: a systematic review and meta-analysis
Creators: name: Currie, Gemma
name: Taylor, Alison
name: Fujita, Toshiro
name: Ohtsu, Hiroshi
name: Lindhardt, Morten
name: Rossing, Peter
name: Boesby, Lene
name: Edwards, Nicola
name: Ferro, Charles
name: Townend, Jonathan
name: Meiracker, Anton Van Den
name: Saklayen, Mohammad
name: Oveisi, Sonia
name: Jardine, Alan
name: Delles, Christian
name: Preiss, David
name: Mark, Patrick
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Assessment of bias. Table S2. Baseline characteristics for individual study groups. Table S3. Comparison of baseline data in meta-analyses. Table S4. Events reported in trials analysed CVA- cerebrovascular accident; MI- myocardial infarction; CABG- coronary artery bypass graft. Figure S1. Plot of percentage reduction in proteinuria/albuminuria (any measure) SBP (mmHg) at final visit across all studies. Each study is represented by a single circle, scaled to number of participants in the study. Figure S2. Effect of addition of MRA on all-cause mortality in RRT studies. Figure S3. Funnel plot (pseudo 95 % confidence limits) showing no evidence of publication bias for GFR (Egger test p = 0.89). Figure S4. Funnel plot (pseudo 95 % confidence limits) showing no evidence of publication bias for hyperkalaemia (Egger test p = 0.81). Appendix 1. Search strategy. Appendix 2. Sample data extraction form. (DOCX 192 kb)
Representation of blocking anticyclones in the new numerical weather prediction model ICON
Creators: name: Attinger, Roman
Publisher: name: ETH Zurich
Year: 2016
Subjects: atmospheric blocking
Model evaluation

description: Atmospheric blocking describes an important part of the weather variability inherent to the mid-latitudes imposing an anomalous strong, quasi stationary anticyclonic circulation on the upper-level flow. Blocking leads to a reversal of the customary upper-level westerly flow and deflects the jet stream as well as migratory weather systems north and southward. Owing to the long persistence and anomalous flow regime, blocking is associated with severe heat waves in summer and cold spells in winter. Despite its vast impact on regional weather and society, average skills in predicting blocking initiation and continuation are observed across many numerical weather prediction models. In this study, the representation of atmospheric blocking in the new general circulation model ICON is investigated by means of a blocking climatology, an analysis of blocking characteristics
and a mean state assessment. To this end, a Northern Hemisphere blocking climatology is derived by identifying blocking as regions of anomalous low vertically averaged potential vorticity (PV) values directly below the tropopause. Three 5-year model runs forced with sea surface temperatures and sea ice fields from the
ERA-Interim reanalysis for the period of 2001 to 2005 are integrated (AMIP setup). Results from increasing horizontal resolutions (80, 40 and 20 km) are considered and compared to ERA-Interim observations for the period of 1979 to 2014. Three preferred regions of blocking activity are identified, two at the end of the Atlantic
and Pacific storm track and a third over northern Russia. Good agreement of the spatial blocking patterns is found, especially in the core region of blocking activity. Main regions of deviation are confined to the mid-latitudes ranging from the Pacific to the Atlantic ocean. Statistics show that blocking duration is overestimated,
while blocking size is systematically underestimated in ICON. The atmospheric mean state of the troposphere is generally simulated well, whereas large biases emerge in the stratosphere. A cool bias in the lower stratosphere leads to a PV dipole which is responsible for globally lifting the tropopause north of 50° N. A potential link between the Madden-Julian oscillation and the PV distribution in the Pacific region is suggested, leading to a shift of the customary Pacific PV trough. The strong mean state bias as well as the overestimated duration of blocking in the low resolution configuration are mainly responsible for the mediocre blocking representation in the mid-latitude Pacific sector. An improved mean state with increasing horizontal resolution is observed in the Pacific, resulting in better blocking depiction. However, in the Atlantic sector, no improvement of the 20 km run
over the intermediate configuration is found. This points to the importance of different processes in blocking representation such as orographic or diabatic effects in the Atlantic sector.
Additional file 2: of Opportunity costs and local health service spending decisions: a qualitative study from Wales
Creators: name: Schaffer, Sarah Karlsberg
name: Sussex, Jon
name: Dyfrig Hughes
name: Devlin, Nancy
Publisher: name: Figshare
Year: 2016
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy

description: COREQ checklist. (DOCX 20 kb)