cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
title: Transcription d'un entretien auprès d’une femme âgée de 35 ans, mère de deux enfants dans la ville de Francfort-sur-le-Main en Allemagne
Creators: name: Knodel, Kathrin
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2017

description: Source: T-4945
description: Transcription en langue allemande
description: L’entretien débute par le récit du déroulement de la grossesse et poursuit sur l’accouchement par césarienne de son deuxième enfant qui a été difficile, l’informatrice est restée en fauteuil roulant durant quelques jours. Elle raconte qu’elle a été séparée de son enfant qui a été amené en service de néonatalité. Elle a pu avoir le premier contact avec son enfant plusieurs heures seulement après l’accouchement. Le soutien de son mari durant l’accouchement et à la maison est évoqué. L’informatrice se confie sur son ressenti suite à sa première rencontre avec son enfant. Elle compare le déroulement de sa première grossesse et son accouchement. L’informatrice a essayé de donner le sein une semaine après la naissance. Les premiers allaitements se sont bien passés et l’informatrice raconte qu’elle a utilisé une tétine pour habituer son enfant à la tétée. Elle a tiré son lait directement après l’accouchement. L’informatrice pense que l’allaitement est important car cela aide le système immunitaire de l’enfant. La durée de la période d’allaitement pour son premier enfant est évoquée. L’informatrice appelle le colostrum le premier lait, elle explique que pour son enfant prématuré, il a été conservé dans des seringues puis lorsqu’elle a eu sa montée de lait plus abondante, le lait a été conservé dans des flocons. Elle précise également que son enfant a reçu un sérum spécial pour les enfants prématurés. Elle raconte que son enfant est nourri au lait maternel et en complément il reçoit un lait maternisé qui renforce l’apport en calories. Les soins qui sont donnés à l’enfant prématuré dans les jours qui suivent la naissance sont évoqués. L’enquêtrice questionne ensuite l’informatrice sur ses connaissances sur le colostrum. Elle a remarqué qu’il est plus concentré et très bon pour l’enfant. Elle explique que c’est une sage-femme qui lui a appris le rôle du colostrum et ses qualités. L’informatrice décrit son utilisation du tire-lait, les problèmes et les blessures qu’elle rencontre liées à l'allaitement et les soins qu'elle fait pour protéger ses seins. Elle raconte le régime alimentaire qu’elle suit pour favoriser la production de lait maternel, en énonçant les aliments et les boissons qu’elle évite de consommer. L’informatrice consomme beaucoup de thé pour l’allaitement ainsi qu’une boisson à base de malte. L’informatrice compare ensuite son accouchement par voie naturelle pour son premier enfant et la césarienne pour le deuxième. L’allaitement en public est évoqué. L’informatrice se confie sur son ressentie au sujet de l’allaitement.
Gibberellic acid inhibitors control height growth and cone production in Abies fraseri
Creators: name: Crain, Brent A.
name: Cregg, Bert M.
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Developmental Biology
subject: Plant Biology

description: Precocious cone production in Fraser fir (Abies fraseri) results in substantial economic losses for Christmas tree growers in the United States. Cone removal often represents the second highest labor expense, after shearing. Gibberellins (GAs) regulate both reproductive development and shoot elongation, and are used to enhance cone production in conifer seed orchards. We identified plant growth regulators (PGRs) that inhibit GA biosynthesis—paclobutrazol, applied by foliar spray (PBZ-foliar) or soil injection (PBZ-soil), and chlormequat. We evaluated the effects of PGR treatments on cone production and vegetative growth in three tree size classes (small, medium, large) at four locations over a three-year period. PGRs were applied in spring 2013, but did not affect growth until 2014, nor did they affect cone production until 2015. In 2014, PBZ reduced leader length by 21 – 29% across size classes and sites, while also increasing bud density by 11 – 20%. In 2015, PBZ-soil reduced average cone density (cones/tree) in small, medium, and large trees by 33, 54, and 40%, respectively. PBZ-soil also reduced leader length by 20 – 29% and increased bud density by 16 – 25%, making it the most effective PGR at controlling height growth and cone production in Fraser fir.
Synthesis, characterization, and cytotoxic and antimicrobial activities of ruthenium(II) arene complexes with N,N-bidentate ligands
Creators: name: Gichumbi, Joel M.
name: Friedrich, Holger B.
name: Omondi, Bernard
name: Moganavelli Singh
name: Kovashnee Naicker
name: Hafizah Y. Chenia
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Three new complexes, [(η6-C6H6)RuCl(C5H4N-2-CH=N-Ar)]PF6 (Ar = phenylmethylene (1), (4-methoxyphenyl)methylene (2), and phenylhydrazone (3)), were prepared by reacting [(η6-C6H6)Ru(μ-Cl)Cl]2 with N,N′-bidentate ligands in a 1 : 2 ratio. Full characterization of the complexes was accomplished using 1H and 13C NMR, elemental and thermal analyses, UV–vis and IR spectroscopy and single crystal X-ray structures. Single crystal structures confirmed a pseudo-octahedral three-legged, piano-stool geometry around Ru(II), with the ligand coordinated to the ruthenium(II) through two N atoms. The cytotoxicity of the mononuclear complexes was established against three human cancer cell lines and selectivity was also tested against non-cancerous human epithelial kidney (HEK 293) cells. The compounds were selective toward the tumor cells in contrast to the known anti-cancer drug 5-fluoro uracil which was not selective between the tumor cells and non-tumor cells. All the compounds showed moderate activity against MCF7 (human breast adenocarcinoma), but showed low antiproliferative activity against Caco-2 and HepG2. Also, antimicrobial activities of the complexes were tested against a panel of antimicrobial-susceptible and -resistant Gram-negative and Gram-positive bacteria. Of special interest is the anti-mycobacterial activity of all three synthesized complexes against Mycobacterium smegmatis, and bactericidal activity against resistant Enterococcus faecalis and methicillin-resistant Staphylococcus aureus ATCC 43300.
On the Homotopy Perturbation Method for the Exact Solution of Fitzhugh–Nagumo Equation
Creators: name: S. Salman Nourazar
name: Soori, Mohsen
name: Nazari-Golshan, Akbar
Publisher: name: figshare
Year: 2016
Subjects: subject: 10299 Applied Mathematics not elsewhere classified
subject: FOS: Mathematics

description: Nourazar, S.S., Soori, M. and Nazari-Golshan, A., 2015. On the Homotopy Perturbation Method for the Exact Solution of Fitzhugh–Nagumo Equation. International Journal of Mathematics & Computation™, 27(1), pp.32-43.
In this paper the Homotopy Perturbation Method (HPM) is used to solve the Fitzhugh-Nagumo non-linear differential equations.
A multiplexed cell-free assay to screen for antimicrobial peptides in double emulsion droplets
Creators: name: Nuti, Nicola
name: Rottmann, Philipp
name: Stucki, Ariane
name: Koch, Philipp
name: Panke, Sven
name: Dittrich, Petra S.
Publisher: name: ETH Zurich
Year: 2021
Subjects: Analytical methods
Membranes
Antimicrobial peptides
Droplet microfluidics
Cell-free protein synthesis

description: The global surge in bacterial resistance against traditional antibiotics triggered intensive research for novel compounds, with antimicrobial peptides (AMPs) identified as a promising candidate. Automated methods to systematically generate and screen AMPs according to their membrane preference, however, are still lacking. We introduce a novel microfluidic system for the simultaneous cell-free production and screening of AMPs for their membrane specificity. On our device, AMPs are cell-free produced within water-in-oil-in-water double emulsion droplets, generated at high frequency. Within each droplet, the peptides can interact with different classes of co-encapsulated liposomes, generating a membrane-specific fluorescent signal. The double emulsions can be incubated and observed in a hydrodynamic trapping array or analysed via flow cytometry. Our approach provides a valuable tool for the discovery and development of membrane-active antimicrobials.
description: bioRxiv
title: 02_1089
Creators: name: Wesley Baldwin, John
name: Baldwin, John W.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2018
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: L'ensemble de ces notes ont été crée par John Baldwin lors d'une de ses premières périodes de résidence à Paris. Ces documents comprennent tous les magistri qu’il avait pu rencontrer dans ses sources. Aux XIIème et XIIIème siècles, les universités n'existant pas encore, le titre de magister s'il évoque certainement une compétence n'est pas rattaché de façon systématique au passage par les écoles. De surcroît, les magistris sont le plus souvent désignés par leur seul prénom. La lecture de ces données est donc difficile et suppose un long travail pour tenter d'identifier un individu auquel on pourrait rattacher plusieurs mentions. John Baldwin avait donc renoncé à utiliser ces données pour donner un prolongement à sa magnifique étude sur les gradués d'université et leur emploi par les Capétiens et les Plantagenêts. Néanmoins, il a conservé ces données et elles sont potentiellement très utile dans le cadre de Studium, comme le sont toutes les mentions dans les volumes des Fasti Ecclesiae Gallicanae de chanoines portant ce titre de magister sans autres précisions. L'ampleur des dépouillements rend ces données très utiles et nous devons une grande reconnaissance à John Baldwin pour avoir pris la peine de faire photocopier ses fiches et de nous les avoir transmises amicalement.
Les données ainsi que les images des fiches sont accessibles sur le site Internet à l'adresse suivante : http://studium-baldwin.lamop.fr/.
Les transcriptions des fiches ont été effectuées par des étudiants de Paris 1 Panthéon - Sorbonne mais elles n'ont pas été corrigées par la suite.
description: Relation: https://lamop.hypotheses.org/
Hingepoint emergence in mammalian spinal neurulation
Creators: name: de Goederen, Veerle
name: Vetter, Roman
name: McDole, Katie
name: Iber, Dagmar
Publisher: name: ETH Zurich
Year: 2021

description: Neurulation is the process in early vertebrate embryonic development during which the neural plate folds to form the neural tube. Spinal neural tube folding in the posterior neuropore changes over time, first showing a median hingepoint, then both the median hingepoint and dorsolateral hingepoints, followed by dorsolateral hingepoints only. The biomechanical mechanism of hingepoint formation in the mammalian neural tube is poorly understood. Here, we employ a mechanical finite element model to study neural tube formation. The computational model mimics the mammalian neural tube using microscopy data from mouse and human embryos. While intrinsic curvature at the neural plate midline has been hypothesized to drive neural tube folding, intrinsic curvature was not sufficient for tube closure in our simulations. We achieved neural tube closure with an alternative model combining mesoderm expansion, non-neural ectoderm expansion and neural plate adhesion to the notochord. Dorsolateral hingepoints emerged in simulations with low mesoderm expansion and zippering. We propose that zippering provides the biomechanical force for dorsolateral hingepoint formation in settings where the neural plate lateral sides extend above the mesoderm. Together, these results provide a new perspective on the biomechanical and molecular mechanism of mammalian spinal neurulation.
description: bioRxiv
On the Exact Solution of Burgers-Huxley Equation Using the Homotopy Perturbation Method
Creators: name: S. Salman Nourazar
name: Soori, Mohsen
name: Nazari-Golshan, Akbar
Publisher: name: figshare
Year: 2016
Subjects: subject: 10299 Applied Mathematics not elsewhere classified
subject: FOS: Mathematics

description: Nourazar, S.S., Soori, M. and Nazari-Golshan, A., 2015. On the Exact Solution of Burgers-Huxley Equation Using the Homotopy Perturbation Method. Journal of Applied Mathematics and Physics, 3(3), pp.285-295.
The Homotopy perturbation Method (HPM) is used to solve the Burgers-Huxley non-linear differential equations.
Development of a 3D atlas of the embryonic pancreas for topological and quantitative analysis of heterologous cell interactions
Creators: name: Glorieux, Laura
name: Sapala, Aleksandra
name: Willnow, David
name: Moulis, Manon
name: Edri, Shlomit
name: Darrigrand, Jean-Francois
name: Schonblum, Anat
name: Sakhneny, Lina
name: Schaumann, Laura
name: Gómez, Harold F.
name: Lang, Christine
name: Conrad, Lisa
name: Guillemot, Fabien
name: Levenberg, Shulamit
name: Landsman, Limor
name: Iber, Dagmar
name: Pierreux, Christophe
name: Spagnoli, Francesca M.
Publisher: name: ETH Zurich
Year: 2021
Subjects: Cell-cell interactions
Endothelial cells
Light-sheet fluorescence microscopy
Mesenchyme
Mouse embryo
Pancreas

description: Generating comprehensive image maps, while preserving spatial 3D context, is essential to quantitatively assess and locate specific cellular features and cell-cell interactions during organ development. Despite the recent advances in 3D imaging approaches, our current knowledge of the spatial organization of distinct cell types in the embryonic pancreatic tissue is still largely based on 2D histological sections. Here, we present a light-sheet fluorescence microscopy approach to image the pancreas in 3D and map tissue interactions at key development time points in the mouse embryo. We used transgenic mouse models and antibodies to visualize the three main cellular components within the developing pancreas, including epithelial, mesenchymal and endothelial cell populations. We demonstrated the utility of the approach by providing volumetric data, 3D distribution of distinct progenitor populations and quantification of relative cellular abundance within the tissue. Lastly, our image data were combined in an open source online repository (referred to as Pancreas Embryonic Cell Atlas). This image dataset will serve the scientific community by enabling further investigation on pancreas organogenesis but also for devising strategies for the in vitro generation of transplantable pancreatic tissue for regenerative therapies.
description: bioRxiv
Fairleigh Dickinson University's PublicMind: December 2013 Poll
Creators: name: Fairleigh Dickinson University's PublicMind
Publisher: name: Roper Center for Public Opinion Research
Year: 2020

description: Registered to vote (1); President Barack Obama job performance (1); direction country is headed (1); Congress job performance (1); Democrats/Republicans best address needs of average Americans (1); congressional inaction good/bad for society (1); who is most responsible for congressional inaction (1); news sources (9); US Supreme Court cases (6); professional football (5); kids should/should not be allowed to play football (1); Mixed Martial Arts (MMA) (6); agree/disagree with various statements about how we celebrate Christmas in America today (5); opinion on various birth control policy issues (3); political partisanship (2); Democratic candidate for president (1); Republican candidate for president (1); political ideology (1); religious service attendance (1).
Synthesis, characterization, cytotoxic and antimicrobial activity of ruthenium(II) arene complexes with N,N-bidentate ligands
Creators: name: Gichumbi, Joel M.
name: Friedrich, Holger B.
name: Omondi, Bernard
name: Moganavelli Singh
name: Kovashnee Naidoo
name: Hafizah Y. Chenia
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer

description: Three new complexes, [(η6-C6H6)RuCl(C5H4N-2-CH=N-Ar)]PF6 (Ar = phenylmethylene (1), (4-methoxyphenyl)methylene (2), phenylhydrazone (3)), are prepared by reacting [(η6-C6H6)Ru(μ-Cl)Cl]2 with N,Nʹ-bidentate ligands in a 1:2 ratio. Full characterization of the complexes was accomplished using 1H and 13C NMR, elemental and thermal analyses, UV-Vis and IR spectroscopy and single crystal X-ray structures. Single crystal structures confirmed a pseudo-octahedral three-legged, piano-stool geometry around Ru(II), with the ligand coordinated to the ruthenium(II) through two N atoms. The cytotoxicity of the mononuclear complexes was established against the human ovarian cancer cell lines and selectivity was also tested against non-cancerous human epithelial kidney (HEK 293) cells. The compounds were selective towards the tumor cells in contrast to the known anti-cancer drug 5-flouro uracil which was not selective between the tumor cells and non-tumor cells. All the compounds showed moderate activity against MCF7 (human breast adenocarcinoma), but showed low antiproliferative activity against Caco-2 and HepG2. Also, antimicrobial activities of the complexes were tested against a panel of antimicrobial-susceptible and -resistant Gram-negative and Gram-positive bacteria. Of special interest is the anti-mycobacterial activity of all three synthesized complexes against M. smegmatis, and bactericidal activity against resistant E. faecalis and methicillin-resistant S. aureus ATCC 43300.
De Finetti Theorems for Quantum Conditional Probability Distributions with Symmetry
Creators: name: Jandura, Sven
name: Tan, Ying Zhe Ernest
Publisher: name: ETH Zurich
Year: 2021

description: The aim of device-independent quantum key distribution (DIQKD) is to study protocols that allow the generation of a secret shared key between two parties under minimal assumptions on the devices that produce the key. These devices are merely modeled as black boxes and mathematically described as conditional probability distributions. A major obstacle in the analysis of DIQKD protocols is the huge space of possible black box behaviors. De Finetti theorems can help to overcome this problem by reducing the analysis to black boxes that have an iid structure. Here we show two new de Finetti theorems that relate conditional probability distributions in the quantum set to de Finetti distributions (convex combinations of iid distributions), that are themselves in the quantum set. We also show how one of these de Finetti theorems can be used to enforce some restrictions onto the attacker of a DIQKD protocol. Finally we observe that some desirable strengthenings of this restriction, for instance to collective attacks only, are not straightforwardly possible.
description: arXiv
Enumeration of fully parked trees
Creators: name: Chen, Linxiao
Publisher: name: ETH Zurich
Year: 2021

description: We enumerate a class of fully parked trees. In a probabilistic context, this means computing the partition function F(x,y) of the parking process where an i.i.d. number of cars arrives at each vertex of a Galton-Watson tree with a geometric offspring distribution, conditioned to leave no vertex unoccupied at the end. The variables x and y count the number of vertices in the tree and the number of cars exiting from the root, respectively.
For any car arrival distribution b, we obtain an explicit parametric expression of F(x,y) in terms of the probability generating function B(y) of b. We show that the model has a generic phase where the singular behavior of F(x,y) is essentially independent of B(y), and a non-generic phase where it depends sensitively on the singular behavior of B(y). The non-generic phase is further divided into two cases, which we call dilute and dense. We give a simple algebraic description of the phase diagram, and, under mild additional assumptions on b, carry out detailed singularity analysis of F(x,y) in the generic and the dilute phases. The singularity analysis uses the classical transfer theorem, as well as its generalization for bivariate asymptotics. In the process, we develop a variational method for locating the dominant singularity of the inverse of an analytic function, which is of independent interest.
The phases defined in this paper are closely related to, but not the same as, the phases in the transition of macroscopic runoff described in arXiv:1912.06012 and related works.
description: arXiv
title: Anthocercis ilicifolia subsp. ilicifolia
title: Version 1
titleType: Subtitle
Creators: name: L.Haegi, R.W.Purdie
Publisher: name: Flora of Australia
Year: 2020
Subjects: Anthocercis ilicifolia subsp. ilicifolia

description: Taxonomic treatment for Anthocercis ilicifolia subsp. ilicifolia
On The Exact Solution of Newell-Whitehead-Segel Equation Using the Homotopy Perturbation Method
Creators: name: S. Salman Nourazar
name: Soori, Mohsen
name: Nazari-Golshan, Akbar
Publisher: name: figshare
Year: 2016
Subjects: subject: 10299 Applied Mathematics not elsewhere classified
subject: FOS: Mathematics

description: In the present work, we used the homotopy perturbation method (HPM) to solve the Newell-Whihihead-Segel non-linear differential equations.
Genome editing
Creators: name: Schuermann-Kaelin, Irene
name: Rosakis, Alexandra
name: Schumacher, Ralph
name: Dahinden, Manuela
Publisher: name: ETH Zurich
Year: 2021
Subjects: Open Educational Resources für Sekundarstufe und Gymnasium

description: Die Lerneinheit «Genome Editing – Zur Erzeugung von genetischer Vielfalt im landwirtschaftlichen Anbau» besteht aus drei Teilen. Der erste und dritte Teil enthalten theoretische Lektionen, welche den zweiten Teil (einen Workshop mit dem Zurich-Basel Plant Science Center) einbetten und die gesellschaftliche Relevanz des Themas verdeutlichen. Lektion 1 thematisiert die Herausforderungen an die heutige Pflanzenzucht. Anhand von Beispielen wird diskutiert, welche Bedeutung eine hohe genetische Vielfalt einer Kulturpflanze hat. In Lektion 2 wird CRISPR/Cas9 vorgestellt, ein Werkzeug, mit dem Kultursorten mit gewünschten Eigenschaften ausgestattet werden können. Zum Beispiel können Wildsorten mit nützlichen Eigenschaften von Kultursorten ausgestattet werden und so für den landwirtschaftlichen Anbau nutzbar werden. Lektion 3 erklärt den Ursprung des CRISPR/Cas9-Systems. Damit wird die Funktion des Systems in Bakterien erklärt. In Lektion 4 werden die verschiedenen Züchtungsmethoden in Bezug auf ihre Einsatzmöglichkeiten in der Pflanzenzucht miteinander verglichen – dies v.a. im Zusammenhang mit den aktuellen Regulierungen in der Schweiz.
description: Lerneinheit, 8
On the Exact Solution of Burgers-Huxley Equation Using the Homotopy Perturbation Method
Creators: name: S. Salman Ourazar
name: Soori, Mohsen
name: Nazari-Golshan, Akbar
Publisher: name: figshare
Year: 2016
Subjects: subject: 10299 Applied Mathematics not elsewhere classified
subject: FOS: Mathematics

description: The Homotopy perturbation Method (HPM) is used to solve the Burgers-Huxley non-linear differential equations.
CD8+ T cell signature in acute SARS-CoV-2 infection identifies memory precursors
Creators: name: Adamo, Sarah
name: Michler, Jan
name: Zurbuchen, Yves
name: Cervia, Carlo
name: Taeschler, Patrick
name: Raeber, Miro E.
name: Baghai Sain, Simona
name: Nilsson, Jakob
name: Moor, Andreas
name: Boyman, Onur
Publisher: name: ETH Zurich
Year: 2021

description: Immunological memory is a hallmark of adaptive immunity and facilitates an accelerated and enhanced immune response upon re-infection with the same pathogen1,2. Since the outbreak of the ongoing coronavirus disease 19 (COVID-19) pandemic, a key question has focused on whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells stimulated during acute infection give rise to long-lived memory T cells3. Using spectral flow cytometry combined with cellular indexing of transcriptomes and T cell receptor (TCR) sequencing we longitudinally characterize individual SARS-CoV-2-specific CD8+ T cells of COVID-19 patients from acute infection to one year into recovery and find a distinct signature identifying long-lived memory CD8+ T cells. SARS-CoV-2-specific memory CD8+ T cells persisting one year after acute infection re-express CD45RA and interleukin-7 receptor α (CD127), upregulate T cell factor-1 (TCF1), and maintain low CCR7, thus resembling CD45RA+ effector-memory T (TEMRA) cells. Tracking individual clones of SARS-CoV-2-specific CD8+ T cells, we reveal that an interferon signature marks clones giving rise to long-lived cells, whereas prolonged proliferation and mammalian target of rapamycin (mTOR) signaling are associated with clone contraction and disappearance. Collectively, we identify a transcriptional signature differentiating short-from long-lived memory CD8+ T cells following an acute virus infection in humans.
description: bioRxiv
Local contrastive loss with pseudo-label based self-training for semi-supervised medical image segmentation
Creators: name: Chaitanya, Krishna
name: Erdil, Ertunc
name: Karani, Neerav
name: Konukoglu, Ender
Publisher: name: ETH Zurich
Year: 2021
Subjects: Contrastive learning
Self-supervised learning
Semi-supervised learning
Machine learning
Deep learning
Medical image segmentation

description: Supervised deep learning-based methods yield accurate results for medical image segmentation. However, they require large labeled datasets for this, and obtaining them is a laborious task that requires clinical expertise. Semi/self-supervised learning-based approaches address this limitation by exploiting unlabeled data along with limited annotated data. Recent self-supervised learning methods use contrastive loss to learn good global level representations from unlabeled images and achieve high performance in classification tasks on popular natural image datasets like ImageNet. In pixel-level prediction tasks such as segmentation, it is crucial to also learn good local level representations along with global representations to achieve better accuracy. However, the impact of the existing local contrastive loss-based methods remains limited for learning good local representations because similar and dissimilar local regions are defined based on random augmentations and spatial proximity; not based on the semantic label of local regions due to lack of large-scale expert annotations in the semi/self-supervised setting. In this paper, we propose a local contrastive loss to learn good pixel level features useful for segmentation by exploiting semantic label information obtained from pseudo-labels of unlabeled images alongside limited annotated images. In particular, we define the proposed loss to encourage similar representations for the pixels that have the same pseudo-label/ label while being dissimilar to the representation of pixels with different pseudo-label/label in the dataset. We perform pseudo-label based self-training and train the network by jointly optimizing the proposed contrastive loss on both labeled and unlabeled sets and segmentation loss on only the limited labeled set. We evaluated on three public cardiac and prostate datasets, and obtain high segmentation performance.
description: arXiv
Structured hierarchical models for probabilistic inference from perturbation screening data
Creators: name: Dirmeier, Simon
name: Beerenwinkel, Niko
Publisher: name: ETH Zurich
Year: 2019
Subjects: Probabilistic models
Hierarchical model
Markov random fields
Biological network
Genetic perturbation screen
Interventional data
Python
PyMC3

description: Genetic perturbation screening is an experimental method in biology to study cause and effect relationships between different biological entities. However, knocking out or knocking down genes is a highly error-prone process that complicates estimation of the effect sizes of the interventions. Here, we introduce a family of generative models, called the structured hierarchical model (SHM), for probabilistic inference of causal effects from perturbation screens. SHMs utilize classical hierarchical models to represent heterogeneous data and combine them with categorical Markov random fields to encode biological prior information over functionally related biological entities. The random field induces a clustering of functionally related genes which informs inference of parameters in the hierarchical model. The SHM is designed for extremely noisy data sets for which the true data generating process is difficult to model due to lack of domain knowledge or high stochasticity of the interventions. We apply the SHM to a pan-cancer genetic perturbation screen in order to identify genes that restrict the growth of an entire group of cancer cell lines and show that incorporating prior knowledge in the form of a graph improves inference of parameters.
description: bioRxiv
On the Exact Solution of Burgers-Huxley Equation Using the Homotopy Perturbation Method
Creators: name: S. Salman Nourazar
name: Soori, Mohsen
name: Nazari-Golshan, Akbar
Publisher: name: figshare
Year: 2016
Subjects: subject: 10299 Applied Mathematics not elsewhere classified
subject: FOS: Mathematics

description: The Homotopy perturbation Method (HPM) is used to solve the Burgers-Huxley non-linear differential equations.
Modeling and Control of an Omnidirectional Micro Aerial Vehicle Equipped with a Soft Robotic Arm
Creators: name: Szász, Róbert
name: Allenspach, Mike
name: Han Minghao
name: Tognon, Marco
name: Katzschmann, Robert K.
Publisher: name: ETH Zurich
Year: 2021

description: Flying manipulators are aerial drones with attached rigid-bodied robotic arms and belong to the latest and most actively developed research areas in robotics. The rigid nature of these arms often lack compliance, flexibility, and smoothness in movement. This work proposes to use a soft-bodied robotic arm attached to an omnidirectional micro aerial vehicle (OMAV) to leverage the compliant and flexible behavior of the arm, while remaining maneuverable and dynamic thanks to the omnidirectional drone as the floating base. The unification of the arm with the drone poses challenges in the modeling and control of such a combined platform; these challenges are addressed with this work. We propose a unified model for the flying manipulator based on three modeling principles: the Piecewise Constant Curvature (PCC) and Augmented Rigid Body Model (ARBM) hypotheses for modeling soft continuum robots and a floating-base approach borrowed from the traditional rigid-body robotics literature. To demonstrate the validity and usefulness of this parametrisation, a hierarchical model-based feedback controller is implemented. The controller is verified and evaluated in simulation on various dynamical tasks, where the nullspace motions, disturbance recovery, and trajectory tracking capabilities of the platform are examined and validated. The soft flying manipulator platform could open new application fields in aerial construction, goods delivery, human assistance, maintenance, and warehouse automation.
description: arXiv
The black hole information puzzle and the quantum de Finetti theorem
Creators: name: Renner, Renato
name: Wang, Jinzhao
Publisher: name: ETH Zurich
Year: 2021

description: The black hole information puzzle arises from a discrepancy between conclusions drawn from general relativity and quantum theory about the nature of the radiation emitted by a black hole. According to Hawking's original argument, the radiation is thermal and its entropy thus increases monotonically as the black hole evaporates. Conversely, due to the reversibility of time evolution according to quantum theory, the radiation entropy should start to decrease after a certain time, as predicted by the Page curve. This decrease has been confirmed by new calculations based on the replica trick, which also exhibit its geometrical origin: spacetime wormholes that form between the replicas. Here we analyse the discrepancy between these and Hawking's original conclusions from a quantum information theory viewpoint, using in particular the quantum de Finetti theorem. The theorem implies the existence of extra information, W, which is neither part of the black hole nor the radiation, but plays the role of a reference. The entropy obtained via the replica trick can then be identified to be the entropy S(R|W) of the radiation conditioned on the reference W, whereas Hawking's original result corresponds to the non-conditional entropy S(R). The entropy S(R|W), which mathematically is an ensemble average, gains an operational meaning in an experiment with N independently prepared black holes: For large N, it equals the normalised entropy of their joint radiation, S(R1⋯RN)/N. The discrepancy between this entropy and S(R) implies that the black holes are correlated. The replica wormholes may thus be interpreted as the geometrical representation of this correlation. Our results also suggest a many-black-hole extension of the widely used random unitary model, which we support with non-trivial checks.
description: arXiv
Safety profile of the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV)
Creators: name: Silfverdal, Sven Arne
name: Coremans, Vanessa
name: François, Nancy
name: Borys, Dorota
name: Cleerbout, Jan
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: FOS: Biological sciences

description: Safety and reactogenicity data were reviewed following 10 years of experience with the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) in clinical development and from post-licensure settings. Analyses of pooled clinical trial data and post-marketing reports provided an overview of its safety profile and allowed assessment of rare adverse events that might not have been identified previously. The safety of PHiD-CV was also evaluated in children at higher risk for pneumococcal infection (preterm and HIV-infected or HIV-exposed infants), for different vaccination schedules and co-administered pediatric vaccines, and with a focus on special categories of adverse events (febrile convulsions, apnea, Kawasaki disease and sudden deaths). Following the distribution of over 235 million doses, PHiD-CV has been well tolerated when co-administered with other pediatric vaccines to children aged less than 5 years from diverse ethnic and geographic backgrounds. Detailed examination of various aspects has confirmed its favorable benefit: risk profile.
Single-cell RNA sequencing unveils intestinal eosinophil development and specialization
Creators: name: Gurtner, Alessandra
name: Borrelli, Costanza
name: Núñez, Nicolás G.
name: Gonzalez-Perez, Ignacio
name: Crepaz, Daniel
name: Handler, Kristina
name: Valenta, Tomas
name: Basler, Konrad
name: Becher, Burkhard
name: Moor, Andreas
name: Arnold, Isabelle C.
Publisher: name: ETH Zurich
Year: 2021

description: Eosinophils are an integral part of the gastrointestinal (GI) immune system that contribute to homeostatic and inflammatory processes. Here, we investigated the existence of functional subsets that carry out specialized tasks in health and disease. We used single-cell transcriptomics and high-dimensional flow cytometry to delineate murine eosinophil subpopulations and their ontogenetic relationship in the steady state and during infection and inflammation. Profiling of eosinophils from bone marrow, blood, spleen and several GI tissues revealed five distinct subsets representing consecutive developmental and maturation stages across organs, each controlled by a specific set of transcription factors. Furthermore, we discovered a highly adapted PD-L1+CD80+ eosinophil subset in the GI tract, characterized by its immune regulatory properties, bactericidal activity upon challenge infection and tissue-protective function during inflammation. Our data provide a framework for the characterization of eosinophil subsets in GI diseases and highlight their crucial contribution to homeostasis, immune regulation and host defense.
description: bioRxiv
Optimisation of nutritional requirements for dopamine synthesis by calcium alginate-entrapped mutant strain of Aspergillus oryzae EMS-6
Creators: name: Sikander Ali
name: Wajeeha Nawaz
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: The optimisation of nutritional requirements for dopamine (DA) synthesis by calcium alginate-entrapped mutant variant of Aspergillus oryzae EMS-6 using submerged fermentation technique was investigated. A total of 13 strains were isolated from soil. Isolate I-2 was selected as a better producer of DA and improved by exposing with ethyl methylsulphonate (EMS). EMS-6 was selected as it exhibited 43 μg/mL DA activity. The mutant variable was further treated with low levels of l-cysteine HCl to make it resistant against diversion and environmental stress. The conidiospores of mutant variant were entrapped in calcium alginate beads for stable product formation. EMS-6 gave maximum DA activity (124 μg/mL) when supplemented with 0.1% peptone and 0.2% sucrose, under optimised parameters viz. pH 3, temperature of 55 °C and incubation time of 70 min. The study involves the high profile of DA activity and is needed, as DA is capable to control numerous neurogenic disorders.
Tool Deflection Error of Three-Axis Computer Numerical Control Milling Machines, Monitoring and Minimizing by a Virtual Machining System
Creators: name: Soori, Mohsen
name: Behrooz Arezoo
name: Habibi, Mohsen
Publisher: name: figshare
Year: 2017
Subjects: subject: 91001 CAD/CAM Systems
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Soori, M., Arezoo, B. and Habibi, M., 2016. Tool Deflection Error of Three-Axis Computer Numerical Control Milling Machines, Monitoring and Minimizing by a Virtual Machining System. Journal of Manufacturing Science and Engineering, 138(8), pp.081005.
Virtual machining system carry out the simulation of manufacturing processes in digital environments in order to increase accuracy as well as productivity in part production.
Declining soil-root hydraulic conductance drives stomatal closure of tomato under drought 
Creators: name: Abdalla, Mohanned
name: Carminati, Andrea
name: Cai, Gaochao
name: Javaux, Mathieu
name: Ahmed, Mutez
Publisher: name: ETH Zurich
Year: 2021

description: The fundamental question as to what triggers stomatal closure during soil drying remains contentious. Thus, we urgently need to improve our understanding of stomatal response to water deficits in soil and atmosphere. Here, we investigated the role of soil-plant hydraulic conductance (Ksp) on transpiration (E) and stomata regulation. We used a root pressure chamber to measure the relation between E, leaf xylem water potential (ψleaf-x) and soil water potential (ψsoil) in tomato. Additional measurements of ψleaf-x were performed with unpressurized plants. A soil-plant hydraulic model was used to simulate E(ψleaf-x) for decreasing ψsoil. In wet soils, E(ψleaf-x) had a constant slope while in dry soils the slope decreased, with ψleaf-x rapidly and nonlinearly decreasing for moderate increases in E. The ψleaf-x measured in pressurized and unpressurized plants matched well, which indicates that the shoot hydraulic conductance did not decrease during soil drying and that the decrease in Ksp is caused by a decrease in soil-root conductance. The decrease of E matched well the onset of hydraulic nonlinearity. Our findings demonstrate that stomatal closure prevents the drop in ψleaf-x caused by a decrease in Ksp and elucidate a strong correlation between stomatal regulation and belowground hydraulic limitation.
description: EGUsphere
Rx TimeMachine: A global pseudoprospective earthquake forecast database for training and ranking predictive algorithms
Creators: name: Kamer, Yavor
name: Nandan, Shyam
name: Hiemer, Stefan
name: Ouillon, Guy
name: Sornette, Didier
Publisher: name: ETH Zurich
Year: 2021

description: Recent advances in machine learning and pattern recognition methods have propagated into various applications in seismology. Phase picking, earthquake location, anomaly detection and classification applications have benefited also from the increased availability of cloud computing and open-source software libraries. However, applications of these new techniques to the problems of earthquake forecasting and prediction have remained relatively stagnant.

The main challenges in this regard have been the testing and validation of the proposed methods. While there are established metrics to quantify the performance of algorithms in common pattern recognition and classification problems, the earthquake prediction problem requires a properly defined reference (null) model to establish the information gain of a proposed algorithm. This complicates the development of new methods, as researchers are required to develop not only a novel algorithm but also a sufficiently robust null model to test it against.

We propose a solution to this problem. We have recently introduced a global real-time earthquake forecasting model that can provide occurrence probabilities for a user defined time-space-magnitude window anywhere on the globe (Nandan et al. 2020). In addition, we have proposed the Information Ratio (IR) metric that can rank algorithms producing alarm based deterministic predictions as well as those producing probabilistic forecasts (Kamer et al. 2020). To provide the community with a retrospective benchmark, we have run our model in a pseudoprospective fashion for the last 30 years (1990-2020). We have calculated and stored the earthquake occurrence probabilities for each day, for the whole globe (at ~40km resolution) for various time-space windows (7 to 30 days, 75 to 300 km). These can be queried programmatically via an Application Programmable Interface (API) allowing model developers to train and test their algorithms retrospectively. Here we shall present how the Rx TimeMachine API is used for the training of a simple pattern recognition algorithm and show the algorithm's prospective predictive performance.
description: EGUsphere
Does Education Improve Health? Evidence from Indonesia
Creators: name: Rasyad A. Parinduri
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Medicine
subject: Biotechnology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: I examine the effects of education on health in Indonesia using an exogenous variation in education induced by an extension of Indonesia’s school term length in 1978–1979, a natural experiment that fits a regression discontinuity design. I find the longer school year increases educational attainment and wages, but I do not find evidence that education improves health. I explore some mechanisms through which education may affect health, but education does not seem to promote healthy lifestyles, increase the use of modern healthcare services, or improve access to health insurance; if anything, education improves only cognitive capacity.
How small can ground movements be to be detectable with GNSS?
Creators: name: Hohensinn, Roland
name: Ruttner, Pia
name: Soja, Benedikt
name: Rothacher, Markus
Publisher: name: ETH Zurich
Year: 2021

description: High-precision GNSS (Global Navigation Satellite System) positioning can reach an accuracy at the millimeter level, and by collecting these data over years, very small ground movements can be resolved. These data can be used to study geodynamics, like continental drifts, tidal- and non-tidal loading effects, or earthquakes, for example. Here we focus on the sensitivity of GNSS for resolving these different types of movements. We derive minimal detectable displacements for linear drift rates, annual- and semiannual periodic motions, and offsets – these are main parameters of the so-called standard linear trajectory model for GNSS station motions. For our analysis, our data comes from several hundreds of permanent GNSS stations across Europe– the GNSS stations’ coordinates are obtained at a daily sampling rate, with almost 25 years of data available for some stations. Based on cleaned residual GNSS time series we calibrate a “power-law plus white noise” stochastic model for each station. Together with the functional trajectory model we compute the formal errors of the movement parameters based on a least-squares adjustment. Based on these errors we then introduce the statistics to derive minimum detectable displacements for the movement parameters.

Our analysis shows that the minimum detectable trends can be as low as few tenth of millimeters per year. The minimum detectable amplitudes at the annual and semiannual periods are at the millimeter level or lower, and the detectable offset is few millimeters on average, too. As expected, the minimum detectable displacements depend strongly on the length of the datasets and on the noise characteristics. Another important parameter is the number of discontinuities and offsets for each station – it impacts the minimum detectable trend. We conclude that such an analysis can be very useful for sensitivity studies in climate change monitoring. Furthermore, the methodology cannot only be applied in the field of GNSS time series analysis, but also to any other time series data in geosciences.
description: EGUsphere
Tool Deflection Error of Three-Axis Computer Numerical Control Milling Machines, Monitoring and Minimizing by a Virtual Machining System
Creators: name: Soori, Mohsen
name: Behrooz Arezoo
name: Habibi, Mohsen
Publisher: name: figshare
Year: 2016
Subjects: subject: 91001 CAD/CAM Systems
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Soori, M., Arezoo, B. and Habibi, M., 2016. Tool Deflection Error of Three-Axis Computer Numerical Control Milling Machines, Monitoring and Minimizing by a Virtual Machining System. Journal of Manufacturing Science and Engineering, 138(8), pp.081005.
Virtual machining system carry out the simulation of manufacturing processes in digital environments in order to increase accuracy as well as productivity in part production.