cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Resolving brain organoid heterogeneity by mapping single cell genomic data to a spatial reference
Creators: name: Fleck, Jonas S.
name: He, Zhisong
name: Boyle, Michael J.
name: Camp, J. Gray
name: Treutlein, Barbara
Publisher: name: ETH Zurich
Year: 2020

description: Self-organizing tissues resembling brain regions grown in vitro from human stem cells (so-called organoids or spheroids) offer exciting possibilities to study human brain development, disease, and evolution. Brain organoids or spheroids are complex and can contain cells at various stages of differentiation from different brain structures. Single-cell genomic methods provide powerful approaches to explore cell composition, differentiation trajectories, gene regulation, and genetic perturbations in brain organoid systems. However, it remains a major challenge to understand the cellular heterogeneity observed within and between individual organoids. Here, we have developed a computational approach (VoxHunt) to assess brain organoid patterning, developmental state, and cell composition through systematic comparisons to three-dimensional in situ hybridization data from the Allen Brain Atlas. Cellular transcriptomes as well as accessible chromatin landscapes can be compared to spatial transcript patterns in the developing mammalian brain, which enables characterization and visualization of organoid cell compositions. VoxHunt will be useful to assess novel organoid engineering protocols and to annotate cell fates that emerge in organoids during genetic and environmental perturbation experiments.
description: bioRxiv
Within-patient genetic diversity of SARS-CoV-2
Creators: name: Kuipers, Jack
name: Batavia, Aashil A.
name: Jablonski, Kim Philipp
name: Bayer, Fritz
name: Borgsmüller, Nico
name: Dondi, Arthur
name: Drăgan, Monica-Andreea
name: Ferreira, Pedro
name: Jahn, Katharina
name: Lamberti, Lisa
name: Pirkl, Martin
name: Posada Cespedes, Susana
name: Topolsky, Ivan
name: Nissen, Ina
name: Santacroce, Natascha
name: Burcklen, Elodie
name: Schär, Tobias
name: Capece, Vincenzo
name: Beckmann, Christiane
name: Kobel, Olivier
name: Noppen, Christoph
name: Redondo, Maurice
name: Nadeau, Sarah Ann
name: Seidel, Sophie
name: Santamaria de Souza, Noemie
name: Beisel, Christian
name: Stadler, Tanja
name: Beerenwinkel, Niko
Publisher: name: ETH Zurich
Year: 2020

description: SARS-CoV-2, the virus responsible for the current COVID-19 pandemic, is evolving into different genetic variants by accumulating mutations as it spreads globally. In addition to this diversity of consensus genomes across patients, RNA viruses can also display genetic diversity within individual hosts, and co-existing viral variants may affect disease progression and the success of medical interventions. To systematically examine the intra-patient genetic diversity of SARS-CoV-2, we processed a large cohort of 3939 publicly-available deeply sequenced genomes with specialised bioinformatics software, along with 749 recently sequenced samples from Switzerland. We found that the distribution of diversity across patients and across genomic loci is very unbalanced with a minority of hosts and positions accounting for much of the diversity. For example, the D614G variant in the Spike gene, which is present in the consensus sequences of 67.4% of patients, is also highly diverse within hosts, with 29.7% of the public cohort being affected by this coexistence and exhibiting different variants. We also investigated the impact of several technical and epidemiological parameters on genetic heterogeneity and found that age, which is known to be correlated with poor disease outcomes, is a significant predictor of viral genetic diversity.
description: bioRxiv
The Manin-Drinfeld theorem and the rationality of Rademacher symbols
Creators: name: Burrin, Claire
Publisher: name: ETH Zurich
Year: 2020

description: For any noncocompact Fuchsian group Γ, we show that periods of the canonical differential of the third kind associated to residue divisors of cusps are expressed in terms of Rademacher symbols for Γ - generalizations of periods appearing in the classical theory of modular forms. This result provides a relation between Rademacher symbols and the famous theorem of Manin and Drinfeld. On this basis, we present a straightforward group-theoretic argument to establish both the rationality of Rademacher symbols and the validity of the Manin-Drinfeld theorem for new families of Fuchsian groups and algebraic curves.
description: arXiv
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data
Creators: name: Posada Cespedes, Susana
name: Seifert, David
name: Topolsky, Ivan
name: Metzner, Karin J.
name: Beerenwinkel, Niko
Publisher: name: ETH Zurich
Year: 2020

description: High-throughput sequencing technologies are used increasingly, not only in viral genomics research but also in clinical surveillance and diagnostics. These technologies facilitate the assessment of the genetic diversity in intra-host virus populations, which affects transmission, virulence, and pathogenesis of viral infections. However, there are two major challenges in analysing viral diversity. First, amplification and sequencing errors confound the identification of true biological variants, and second, the large data volumes represent computational limitations. To support viral high-throughput sequencing studies, we developed V-pipe, a bioinformatics pipeline combining various state-of-the-art statistical models and computational tools for automated end-to-end analyses of raw sequencing reads. V-pipe supports quality control, read mapping and alignment, low-frequency mutation calling, and inference of viral haplotypes. For generating high-quality read alignments, we developed a novel method, called ngshmmalign, based on profile hidden Markov models and tailored to small and highly diverse viral genomes. V-pipe also includes benchmarking functionality providing a standardized environment for comparative evaluations of different pipeline configurations. We demonstrate this capability by assessing the impact of three different read aligners (Bowtie 2, BWA MEM, ngshmmalign) and two different variant callers (LoFreq, ShoRAH) on the performance of calling single-nucleotide variants in intra-host virus populations. V-pipe supports various pipeline configurations and is implemented in a modular fashion to facilitate adaptations to the continuously changing technology landscape. V-pipe is freely available at https://github.com/cbg-ethz/V-pipe.
description: bioRxiv
Contact Force Estimation for Minimally Invasive Robot-assisted Laser Osteotomy in the Human Knee
Creators: name: Eugster, Manuela
name: Zoller, Esther
name: Fasel, Lorin
name: Cattin, Philippe C.
name: Friederich, Niklaus
name: Zam, Azhar
name: Rauter, Georg
Publisher: name: ETH Zurich
Year: 2018
Subjects: force estimation
SURGERY (MEDICINE)
Endoscopy
KNEE JOINTS (ANATOMY AND PHYSIOLOGY)

description: CRAS 2018 Proceedings of the 8th Joint Workshop on New Technologies for Computer/Robot Assisted Surgery
AStarix: Fast and Optimal Sequence-to-Graph Alignment
Creators: name: Ivanov, Pesho
name: Bichsel, Benjamin
name: Mustafa, Harun
name: Kahles, André
name: Rätsch, Gunnar
name: Vechev, Martin
Publisher: name: ETH Zurich
Year: 2020
Subjects: Next-generation sequencing
Optimal alignment
Genome graph
Shortest path
A* algorithm

description: We present an algorithm for the optimal alignment of sequences to genome graphs. It works by phrasing the edit distance minimization task as finding a shortest path on an implicit alignment graph. To find a shortest path, we instantiate the A* paradigm with a novel domain-specific heuristic function that accounts for the upcoming sub-sequence in the query to be aligned, resulting in a provably optimal alignment algorithm called AStarix.Experimental evaluation of AStarix shows that it is 1–2 orders of magnitude faster than state-of-the-art optimal algorithms on the task of aligning Illumina reads to reference genome graphs. Implementations and evaluations are available at https://github.com/eth-sri/astarix.
description: bioRxiv
title: Mise en place d'un dispositif de carnet créatif et d'expression libre auprès de trois élèves du primaire à besoins éducatifs particuliers dans un contexte ordinaire : recherche exploratoire de l'engagement dans cette activité et de ses effets.
title: Mise en place d'un dispositif de carnet créatif et d'expression libre auprès de trois élèves du primaire à besoins éducatifs particuliers dans un contexte ordinaire : recherche exploratoire de l'engagement dans cette activité et de ses effets.
titleType: AlternativeTitle
Creators: name: Mondonneix, Yannick
name: Viret, Lysianne
Publisher: name: Unknown
Year: 0
Subjects: subject: Engagement
subject: carnet
subject: créativité
subject: expression libre
subject: émotions

description: Ce mémoire explore la mise en place d'un dispositif de carnet créatif et d'expression libre auprès de trois élèves du primaire ayant des besoins éducatifs particuliers dans un contexte ordinaire. Les enseignantes spécialisées impliquées dans deux contextes différents souhaitaient offrir à leurs élèves un espace de création et d'expression libre. L'objectif principal est d'évaluer de manière qualitative et quantitative l'engagement de ces élèves dans cette activité et d'observer les effets perçus. À travers une approche compréhensive, la recherche s'appuie sur trois outils : un questionnaire individuel, une observation au moyen d'un journal et des entretiens individuels. L'analyse inductive, par cas et inter-cas, permet d'explorer les dimensions comportementale, cognitive et affective de l'engagement scolaire dans le contexte du carnet créatif créatif d’expression libre. Ce dernier a permis aux élèves d'expérimenter sans jugement, d'exprimer leur créativité et de gagner confiance en leurs compétences. Leur engagement dans cette activité a révélé une mobilisation d'émotions positives et un enthousiasme important pour le carnet. Les observations et les entretiens ont confirmé ces résultats.
Supplementary Material from Coastal ocean and shelf-sea biogeochemical cycling of trace elements and isotopes: lessons learned from GEOTRACES
Creators: name: Charette, Matthew A.
name: Lam, Phoebe J.
name: Lohan, Maeve C.
name: Kwon, Eun Young
name: Hatje, Vanessa
name: Jeandel, Catherine
name: Shiller, Alan M.
name: Cutter, Gregory A.
name: Thomas, Alex
name: Boyd, Philip W.
name: Homoky, William B.
name: Milne, Angela
name: Thomas, Helmuth
name: Andersson, Per S.
name: Porcelli, Don
name: Tanaka, Takahiro
name: Geibert, Walter
name: Dehairs, Frank
name: Garcia-Orellana, Jordi
Publisher: name: The Royal Society
Year: 2016
Subjects: subject: Geochemistry
subject: FOS: Earth and related environmental sciences
subject: Oceanography

description: Description and derivation of equation used to derive trace element and isotope fluxes from the continental margin
Molting incidents of Hyalomma spp. carrying human pathogens in Germany under different weather conditions
Creators: name: Chitimia-Dobler, Lidia
name: Springer, Andrea
name: Lang, Daniel
name: Lindau, Alexander
name: Fachet, Katrin
name: Dobler, Gerhard
name: Nijhof, Ard M.
name: Strube, Christina
name: Mackenstedt, Ute
Publisher: name: Freie Universität Berlin
Year: 2024
Subjects: subject: Hyalomma marginatum
subject: Hyalomma rufipes
subject: Weather conditions
subject: Tick-borne pathogens
subject: Germany
subject: 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::630 Landwirtschaft und verwandte Bereiche

description: Background Hyalomma marginatum and H. rufipes are two-host tick species, which are mainly distributed in southern Europe, Africa to central Asia but may also be found in Central and Northern Europe through introduction by migratory birds. Methods Ticks were collected while feeding or crawling on animals and humans, or from the environment, in different regions in Germany, between 2019 and 2021 in a citizen science study and from 2022 to 2023 in the wake of this study. Results From 2019 to 2023, a total of 212 Hyalomma adult ticks were detected in Germany. This included 132 H. marginatum and 43 H. rufipes ticks sent to research institutions and 37 photographic records that were only identified to genus level. The number of detected ticks varied over the years, with the highest number of 119 specimens recorded in 2019, followed by 57 in 2020. Most of the specimens were collected from horses, while some were collected from other animals, humans or found crawling on human clothes or other objects inside or outside houses. The screening of 175 specimens for Crimean-Congo hemorrhagic fever virus and of 132 specimens for Babesia/Theileria spp. by PCR gave negative results, while human-pathogenic Rickettsia were detected in 44% (77/175) of the total samples. Subsequent amplicon sequencing and phylogenetic analysis of representative samples determined the species of 41 Rickettsia aeschlimannii and one R. slovaca sequences. Conclusions Analysis of climatic factors indicated a significantly higher probability of Hyalomma occurrence at locations with higher average spring temperature during the years 2019 and 2020 compared to randomly generated pseudo-absence locations. Dry and hot conditions probably facilitated Hyalomma nymphs’ survival and molting into adults during these years.
Gland Segmentation in Colon Histology Images: The GlaS Challenge Contest
Creators: name: Sirinukunwattana, Korsuk
name: Pluim, Josien P.W.
name: Chen, Hao
name: Qi, Xiaojuan
name: Heng, Pheng-Ann
name: Guo, Yun B.
name: Wang, Li Y.
name: Matuszewski, Bogdan J.
name: Bruni, Elia
name: Sanchez, Urko
name: Böhm, Anton
name: Ronneberger, Olaf
name: Cheikh, Bassem B.
name: Racoceanu, Daniel
name: Kainz, Philipp
name: Pfeiffer, Michael
name: Urschler, Martin
name: Snead, David R.J.
name: Rajpoot, Nasir M.
Publisher: name: ETH Zurich
Year: 2016

description: Colorectal adenocarcinoma originating in intestinal glandular structures is the most common form of colon cancer. In clinical practice, the morphology of intestinal glands, including architectural appearance and glandular formation, is used by pathologists to inform prognosis and plan the treatment of individual patients. However, achieving good inter-observer as well as intra-observer reproducibility of cancer grading is still a major challenge in modern pathology. An automated approach which quantifies the morphology of glands is a solution to the problem. This paper provides an overview to the Gland Segmentation in Colon Histology Images Challenge Contest (GlaS) held at MICCAI'2015. Details of the challenge, including organization, dataset and evaluation criteria, are presented, along with the method descriptions and evaluation results from the top performing methods.
description: arXiv
Comparison of RNA extraction methods for the detection of SARS-CoV-2 by RT-PCR
Creators: name: Eichhoff, Ossia M.
name: Bellini, Elisa
name: Lienhard, Reto
name: Stark, Wendelin J.
name: Bechtold, Philippe
name: Grass, Robert N.
name: Bosshard, Philipp P.
name: Levesque, Mitchell P.
Publisher: name: ETH Zurich
Year: 2020

description: medRxiv
Augmenting Printed School Atlases with Thematic 3D Maps
Creators: name: Schnürer, Raimund
name: Dind, Cédric
name: Schalcher, Stefan
name: Tschudi, Pascal
name: Hurni, Lorenz
Publisher: name: ETH Zurich
Year: 2020
Subjects: Augmented reality
Atlases
3D cartography
Thematic maps
Education
Usability

description: Digitalization in schools requires a rethinking of teaching materials and methods in all subjects. This upheaval also
concerns traditional print media, like school atlases used in geography classes. In this work, we examine the cartographic
technological feasibility of extending a printed school atlas with digital content by augmented reality (AR). While
previous research rather focused on topographic three-dimensional (3D) maps, our prototypical application for Android
tablets complements map sheets of the Swiss World Atlas with thematically related data. We follow a natural marker
approach using the AR engine Vuforia and the game engine Unity. We compare two workflows to insert geo-data, being
correctly aligned with the map images, into the game engine. Next, the imported data are transformed into partly animated
3D visualizations, such as a dot distribution map, curved lines, pie chart billboards, stacked cuboids, extruded bars, and
polygons. Additionally, we implemented legends, elements for temporal and thematic navigation, a screen capture
function, and a touch-based feature query for the user interface. We evaluated our prototype in a usability experiment,
which showed that secondary school students are as effective, interested, and sustainable with printed as with augmented
maps when solving geographic tasks.
description: Abstracts of the ICA, 2
description: ISSN:2570-2106
description: Central European Cartographic Conference and 68th German Cartography Congress – EuroCarto 2020
Raw data of the ASV titration and Zn uptake experiments from The effect of acidification on the bioavailability and electrochemical lability of zinc in seawater
Creators: name: Ja-Myung Kim
name: Baars, Oliver
name: Morel, François M. M.
Publisher: name: The Royal Society
Year: 2016
Subjects: subject: Geochemistry
subject: FOS: Earth and related environmental sciences
subject: Oceanography
subject: 30199 Analytical Chemistry not elsewhere classified
subject: FOS: Chemical sciences

description: A poorly studied but potentially important consequence of the CO2-induced acidification of the surface ocean is a possible change in the bioavailability of trace metals, which play a critical role in the productivity and population dynamics of marine ecosystems. We report laboratory and field experiments designed to compare quantitatively the effects of acidification on the bioavailability of Zn, a metal essential to the growth of phytoplankton and on the extent of its complexation by model and natural ligands. We observed a good correspondence between the effects of pH on the rate of Zn uptake by a model diatom and the chemical lability of Zn measured by anodic stripping voltammetry (ASV). In model laboratory systems, the chemical lability and the bioavailability of Zn could either increase or decrease at low pH depending on the mix of complexing ligands. In a sample of coastal surface water, we observed similar increases in the ASV-labile and bioavailable Zn concentrations upon acidification, a result contrary to previous observations. These results, which can likely be generalized to other bioactive trace metals, mutatis mutandis, demonstrate the intricacy of the effects of ocean acidification on the chemistry and the ecology of surface seawater.
Unsupervised clustering of catalogue-driven features for characterizing temporal evolution of labquake stress
Creators: name: Karimpouli, Sadegh
name: Kwiatek, Grzegorz
name: Martínez-Garzón, Patricia
name: Dresen, Georg
name: Bohnhoff, Marco
Publisher: name: Freie Universität Berlin
Year: 2024
Subjects: subject: Machine learning
subject: Acoustic properties
subject: Earthquake interaction
subject: forecasting and prediction
subject: 500 Naturwissenschaften und Mathematik::550 Geowissenschaften, Geologie::550 Geowissenschaften

description: Earthquake forecasting poses significant challenges, especially due to the elusive nature of stress states in fault systems. To tackle this problem, we use features derived from seismic catalogues obtained from acoustic emission (AE) signals recorded during triaxial stick-slip experiments on natural fractures in three Westerly granite samples. We extracted 47 physically explainable features from AE data that described spatio-temporal evolution of stress and damage in the vicinity of the fault surface. These features are then subjected to unsupervised clustering using the K-means method, revealing three distinct stages with a proper agreement with the temporal evolution of stress. The recovered stages correspond to the mechanical behaviour of the rock, characterized as initial stable (elastic) deformation, followed by a transitional stage leading to an unstable deformation prior to failure. Notably, AE rate, clustering-localization features, fractal dimension, b-value, interevent time distribution, and correlation integral are identified as significant features for the unsupervised clustering. The systematically evolving stages can provide valuable insights for characterizing preparatory processes preceding earthquake events associated with geothermal activities and waste-water injections. In order to address the upscaling issue, we propose to use the most important features and, in case of normalization challenge, removing non-universal features, such as AE rate. Our findings hold promise for advancing earthquake prediction methodologies based on laboratory experiments and catalogue-driven features.
Décimas nuevas. Disputa entre un moro y un cristiano sobre los mandamientos de la ley de Dios: Digital edition
Creators: name: Leblanc Elina
Publisher: name: Zenodo
Year: 2021
Subjects: Spanish literature
Digital edition
XML-TEI

description: Digital edition of a Spanish pliego de cordel, published by the Andalusian printer José María Moreno (19th c.). It contains the XML-TEI file of the edition, as well as the files that led to this edition, i.e. the digital facsimiles (raw and retouched), and the transcription produced by the OCR tool Transkribus (PAGE-XML). This digital edition is a part of the research project Desenrollando el cordel / Untangling the cordel / Démêler le cordel (2020-2022), led by the professor Constance Carta at the University of Geneva and supported by the philanthropic Sandoz-Monique de Meuron Family Foundation.
Décimas nuevas. Disputa entre un moro y un cristiano sobre los mandamientos de la ley de Dios: Digital edition
Creators: name: Leblanc Elina
Publisher: name: Zenodo
Year: 2024
Subjects: Spanish literature
Digital edition
XML-TEI

description: Digital edition of a Spanish pliego de cordel, published by the Andalusian printer José María Moreno (19th c.). It contains the XML-TEI file of the edition, as well as the files that led to this edition, i.e. the digital facsimiles (raw and retouched), and the transcription produced by the OCR tool Transkribus (PAGE-XML). This digital edition is a part of the research project Desenrollando el cordel / Untangling the cordel / Démêler le cordel (2020-2024), led by professor Constance Carta at the University of Geneva and supported by the philanthropic Sandoz-Monique de Meuron Family Foundation.
Décimas nuevas. Disputa entre un moro y un cristiano sobre los mandamientos de la ley de Dios: Digital edition
Creators: name: Leblanc Elina
Publisher: name: Zenodo
Year: 2022
Subjects: Spanish literature
Digital edition
XML-TEI

description: Digital edition of a Spanish pliego de cordel, published by the Andalusian printer José María Moreno (19th c.). It contains the XML-TEI file of the edition, as well as the files that led to this edition, i.e. the digital facsimiles (raw and retouched), and the transcription produced by the OCR tool Transkribus (PAGE-XML). This digital edition is a part of the research project Desenrollando el cordel / Untangling the cordel / Démêler le cordel (2020-2022), led by the professor Constance Carta at the University of Geneva and supported by the philanthropic Sandoz-Monique de Meuron Family Foundation.
Supplementary Tables from Southern Ocean biological iron cycling in the pre-whaling and present ecosystems
Creators: name: Maldonado, Maria T.
name: Surma, Szymon
name: Pakhomov, Evgeny A.
Publisher: name: The Royal Society
Year: 2016
Subjects: subject: Oceanography
subject: FOS: Earth and related environmental sciences

description: This study aimed to create the first model of biological iron (Fe) cycling in the Southern Ocean food web. Two biomass-balanced Ecopath models were built to represent pre- and post-whaling ecosystem states (1900 and 2008). Functional group biomasses (tonnes wet weight km-2) were converted to biogenic Fe pools (kg Fe km-2) using published Fe content ranges. In both models, biogenic Fe pools and consumption in the pelagic Southern Ocean were highest for plankton and small nektonic groups. The production of plankton biomass, particularly unicellular groups, accounted for the highest annual Fe demand. Microzooplankton contributed most to biological Fe recycling, followed by carnivorous zooplankton and krill. Biological Fe recycling matched previous estimates, and under most conditions, could entirely meet the Fe demand of bacterioplankton and phytoplankton. Iron recycling by large baleen whales was reduced 10-fold by whaling between 1900 and 2008. However, even under the 1900 scenario, the contribution of whales to biological Fe recycling was negligible compared with that of planktonic consumers. These models are a first step in examining oceanic-scale biological Fe cycling, highlighting gaps in our present knowledge and key questions for future research on the role of marine food webs in the cycling of trace elements in the sea.
The role of long non-coding RNA in hepatocellular carcinoma
Creators: name: Liang, Weizheng
name: Zhao, Yan
name: Meng, Qingxue
name: Jiang, Wenjie
name: Deng, Shoulong
name: Xue, Jun
Publisher: name: Freie Universität Berlin
Year: 2024
Subjects: subject: hepatocellular carcinoma
subject: long non -coding RNA
subject: prognosis
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Hepatocellular carcinoma (HCC) is a prevalent liver malignancy with complex etiology and generally poor prognosis. Recently, long non-coding RNAs (lncRNAs), non-protein-coding RNA molecules exceeding 200 nucleotides, have emerged as pivotal players in HCC, influencing its initiation, progression, invasion, and metastasis. These lncRNAs modulate gene expression at epigenetic, transcriptional, and post-transcriptional levels, actively participating in the pathological and physiological processes of HCC. Understanding the intricate relationship between lncRNAs and HCC is important for improving prognosis and reducing mortality. This review summarizes advancements in elucidating the role of lncRNAs in HCC pathogenesis.
Sequence characterization and expression analysis of a PDGF/VEGF related factor gene in swimming crab Portunus trituberculatus
Creators: name: Gu, Y
name: Qu, Z
name: Hu, J-J
name: Wang, M-Q
Publisher: name: Invertebrate Survival Journal
Year: 2024

description:  

PDGF/VEGF factors are closely associated with immune defense systems. In this study, a PDGF/VEGF related factor gene (designated as PtPVF) from swimming crab Portunus trituberculatus was identified and analyzed. Its full-length cDNA is 1320 bp, containing an open reading frame (ORF) of 582 bp, 5’ untranslated regions (UTR) of 105 bp and 3’ UTR of 633 bp, which encoded a polypeptide of 193 amino acid residues. The deduced amino acid sequence of PtPVF contained a signal peptide, a typical PDGF/VEGF domain, and a cysteine knot motif (CXCXC). Quantitative real-time PCR analysis demonstrated that the mRNA of PtPVF was detectable in gills, gonads, heart, hemocytes, hepatopancreas, intestines, muscles, optic stalk, stomach, and the highest level was found in hemocytes, followed by gill and hepatopancreas. After stimulation by Vibrio alginolyticus, pentachlorophenol (PCP) or cadmium chloride (CdCl2), the relative mRNA expression levels of PtPVF in hemocytes reached their respective peaks at 3 h, 6 h and 6 h, and 36.61-fold, 3.06-fold and 21.26-fold compared with the original level, respectively, and the respond to V. alginolyticus and CdCl2 is earlier than to PCP, while under the challenge of V. alginolyticus and CdCl2, the mRNA expression level of PtPVF was significantly higher than that of PCP stimulation. Furthermore, the mRNA expression level of PtPVF first decreased at 3 h and then increased rapidly to a peak at 6 h after PCP challenge. All these results demonstrated that PtPVF might be involved in the response to invading pathogens and environmental pollution stimulants of P. trituberculatus.
description: Invertebrate Survival Journal, Vol. 21 No. 1 (2024)
title: 11. Chant bati par Adisé Mändäfro
Creators: name: Wion, Anaïs
name: Bolay, Anne
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020

description: Une tierce personne donne des poèmes à chanter à l'azmari.
libMBD: A general-purpose package for scalable quantum many-body dispersion calculations
Creators: name: Hermann, Jan
name: Stohr, Martin
name: Góger, Szabolcs
name: Chaudhuri, Shayantan
name: Aradi, Bálint
name: Maurer, Reinhard J.
name: Tkatchenko, Alexandre
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: general-purpose package
subject: scalable quantum many-body dispersion calculations
subject: libMBD
subject: 500 Naturwissenschaften und Mathematik::530 Physik::530 Physik

description: Many-body dispersion (MBD) is a powerful framework to treat van der Waals (vdW) dispersion interactions in density-functional theory and related atomistic modeling methods. Several independent implementations of MBD with varying degree of functionality exist across a number of electronic structure codes, which both limits the current users of those codes and complicates dissemination of new variants of MBD. Here, we develop and document libMBD, a library implementation of MBD that is functionally complete, efficient, easy to integrate with any electronic structure code, and already integrated in FHI-aims, DFTB+, VASP, Q-Chem, CASTEP, and Quantum ESPRESSO. libMBD is written in modern Fortran with bindings to C and Python, uses MPI/ScaLAPACK for parallelization, and implements MBD for both finite and periodic systems, with analytical gradients with respect to all input parameters. The computational cost has asymptotic cubic scaling with system size, and evaluation of gradients only changes the prefactor of the scaling law, with libMBD exhibiting strong scaling up to 256 processor cores. Other MBD properties beyond energy and gradients can be calculated with libMBD, such as the charge-density polarization, first-order Coulomb correction, the dielectric function, or the order-by-order expansion of the energy in the dipole interaction. Calculations on supramolecular complexes with MBD-corrected electronic structure methods and a meta-review of previous applications of MBD demonstrate the broad applicability of the libMBD package to treat vdW interactions.
Digital Totem Poles: Experimental Computer Graphics By Rick Doble
Creators: name: Doble, Rick
Publisher: name: figshare
Year: 2016
Subjects: subject: Art
subject: Design
subject: Digital Humanities
subject: Entertainment
subject: 200104 Media Studies
subject: FOS: Media and communications
subject: 80103 Computer Graphics
subject: FOS: Computer and information sciences

description: Very tall narrow digital pictures inspired by the art and craft of both modern and traditional totem poles. The pictures cannot be viewed all at one time, but are interactive and must be scrolled. The patterns on these poles were derived from natural and man made patterns. With each totem pole you must scroll down its page. You will only be able to see a portion at one time.
BANKLARDA MUAMMOLI KREDITLAR BILAN ISHLASH SAMARADORLIGINI OSHIRISH YO'LLARI (ATB "KAPITALBANK" M.ULUGBEK FILIALI MISOLIDА
Creators: name: Qahhorov, Shohruh
Publisher: name: Zenodo
Year: 2025

description: Tijorat banklari faoliyatining asosiy ko‘rsatkichlaridan biri — ularning kredit portfeli sifati va muammoli kreditlar ulushining past darajada saqlanishidir. Muammoli kreditlar banklarning moliyaviy barqarorligiga, foydalilik darajasiga va iqtisodiy faoliyatga ko‘rsatadigan salbiy ta’siri sababli, ular bilan samarali ishlash tizimi bank sektorining rivojlanishida ustuvor yo‘nalish sanaladi. O‘zbekiston moliyaviy tizimida, xususan ATB "Kapitalbank" M.Ulug‘bek filiali misolida olib borilgan tahlillar shuni ko‘rsatadiki, muammoli kreditlarning vujudga kelish sabablari ko‘p omilli va murakkabdir. Ushbu omillar ichida qarz oluvchilarning moliyaviy ahvolining yomonlashuvi, kredit ajratish jarayonidagi tahlil va baholashdagi kamchiliklar, kredit monitoringining sustligi, shuningdek, iqtisodiy muhitdagi o‘zgarishlar asosiy o‘rin tutadi.
Detecting Corticospinal Tract Impairment in Tumor Patients With Fiber Density and Tensor-Based Metrics
Creators: name: Fekonja, Lucius Samo
name: Wang, Ziqian
name: Aydogan, Dogu Baran
name: Roine, Timo
name: Engelhardt, Melina
name: Dreyer, Felix
name: Vajkoczy, Peter
name: Picht, Thomas
Publisher: name: Humboldt-Universität zu Berlin
Year: 2021
Subjects: subject: tractography
subject: corticospinal tract
subject: diffusion magnetic resonance imaging
subject: motor function
subject: apparent diffusion coefficient
subject: tumor
subject: transcranial magnetic stimulation
subject: 610 Medizin und Gesundheit

description: Tumors infiltrating the motor system lead to significant disability, often caused by corticospinal tract injury. The delineation of the healthy-pathological white matter (WM) interface area, for which diffusion magnetic resonance imaging (dMRI) has shown promising potential, may improve treatment outcome. However, up to 90% of white matter (WM) voxels include multiple fiber populations, which cannot be correctly described with traditional metrics such as fractional anisotropy (FA) or apparent diffusion coefficient (ADC). Here, we used a novel fixel-based along-tract analysis consisting of constrained spherical deconvolution (CSD)-based probabilistic tractography and fixel-based apparent fiber density (FD), capable of identifying fiber orientation specific microstructural metrics. We addressed this novel methodology’s capability to detect corticospinal tract impairment. We measured and compared tractogram-related FD and traditional microstructural metrics bihemispherically in 65 patients with WHO grade III and IV gliomas infiltrating the motor system. The cortical tractogram seeds were based on motor maps derived by transcranial magnetic stimulation. We extracted 100 equally distributed cross-sections along each streamline of corticospinal tract (CST) for along-tract statistical analysis. Cross-sections were then analyzed to detect differences between healthy and pathological hemispheres. All metrics showed significant differences between healthy and pathologic hemispheres over the entire tract and between peritumoral segments. Peritumoral values were lower for FA and FD, but higher for ADC within the entire cohort. FD was more specific to tumor-induced changes in CST than ADC or FA, whereas ADC and FA showed higher sensitivity. The bihemispheric along-tract analysis provides an approach to detect subject-specific structural changes in healthy and pathological WM. In the current clinical dataset, the more complex FD metrics did not outperform FA and ADC in terms of describing corticospinal tract impairment.
The distribution of plasmid fitness effects explains plasmid persistence in bacterial communities
Creators: name: Alonso-del Valle, Aida
name: Leon-Sampedro, Ricardo
name: Rodríguez-Beltrán, Jerónimo
name: DelaFuente, Javier
name: Hernández-García, Marta
name: Ruiz-Garbajosa, Patricia
name: Cantón, Rafael
name: Peña-Miller, Rafael
name: San Millán, Álvaro
Publisher: name: ETH Zurich
Year: 2020

description: Plasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the distribution of fitness effects (DFE) for the major antibiotic resistance plasmid pOXA-48 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results show that although pOXA-48 produced an overall reduction in bacterial fitness, the DFE was dominated by quasi-neutral effects, and beneficial effects were observed in several isolates. Incorporating these data into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. Moreover, genomic results showed a link between plasmid fitness effects and bacterial phylogeny, helping to explain pOXA-48 epidemiology. Our results provide a simple and general explanation for plasmid persistence in natural bacterial communities.
description: bioRxiv
Safety and Tolerability of Accelerated Low-Frequency Repetitive Transcranial Magnetic Stimulation Over the Primary Motor Cortex–A Pilot Study
Creators: name: Engelhardt, Melina
name: Kimmel, Jana
name: Raffa, Giovanni
name: Conti, Alfredo
name: Picht, Thomas
Publisher: name: Humboldt-Universität zu Berlin
Year: 2022
Subjects: subject: transcranial magnetic stimulation
subject: neuromodulation
subject: accelerated
subject: low-frequency
subject: motor cortex
subject: 610 Medizin und Gesundheit

description: Low-frequency repetitive transcranial magnetic stimulation (rTMS) is capable of inducing changes in the functional organization of underlying brain regions, however, often at the cost of long stimulation protocols over several weeks. As these protocols can be difficult to implement in clinical settings, the aim of the present pilot study was to show the feasibility and safety of an accelerated low-frequency rTMS protocol applying multiple sessions daily. To this purpose, nine healthy subjects received 14 sessions of rTMS (1 Hz, 30 min, 110% RMT) to the hand motor hotspot. Subjects received stimulation for either 14 days once daily [classical rTMS (c-rTMS)], 7 days twice daily (accelerated rTMS; a-rTMS), or sham stimulation for 14 days once daily (s-rTMS). Daily stimulation sessions in the a-rTMS group were delivered with a 90-min break in between. In total, 74% of rTMS sessions in the c-rTMS group, 89% in the a-rTMS group, and 98% in the s-rTMS group were free of any side effects. Brief headaches and fatigue in stimulated muscle groups were the most frequent side effects. All side effects were reported to be at maximum mild and of short duration. Thus, accelerated low-frequency rTMS of the motor cortex seems to be a safe and feasible method, previously shown to induce a functional reorganization of the motor system. By shortening treatment duration in days, this approach can potentially make rTMS protocols more accessible to a wider range of patients.
Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting
Creators: name: Leon-Sampedro, Ricardo
name: DelaFuente, Javier
name: Díaz-Agero, Cristina
name: Crellen, Thomas
name: Musicha, Patrick
name: Rodríguez-Beltrán, Jerónimo
name: de la Vega, Carmen
name: Hernández-García, Marta
name: R-GNOSIS WP5 Study Group
name: López-Fresneña, Nieves
name: Ruiz-Garbajosa, Patricia
name: Cantón, Rafael
name: Cooper, Ben S.
name: San Millan, Alvaro
Publisher: name: ETH Zurich
Year: 2020

description: Infections caused by carbapenemase-producing enterobacteria (CPE) are a major concern in clinical settings worldwide. Two fundamentally different processes shape the epidemiology of CPE in hospitals: the dissemination of CPE clones from patient to patient (between-patient transfer), and the transfer of carbapenemase-encoding plasmids between enterobacteria in the gut microbiota of individual patients (within-patient transfer). The relative contribution of each process to the overall dissemination of carbapenem resistance in hospitals remains poorly understood. Here, we used mechanistic models combining epidemiological data from more than 9,000 patients with whole genome sequence information from 250 enterobacteria clones to characterise the dissemination routes of the carbapenemase-encoding plasmid pOXA-48 in a hospital setting over a two-year period. Our results revealed frequent between-patient transmission of high-risk pOXA-48-carrying clones, mostly of Klebsiella pneumoniae and sporadically Escherichia coli. The results also identified pOXA-48 dissemination hotspots within the hospital, such as specific wards and individual rooms within wards. Using high-resolution plasmid sequence analysis, we uncovered the pervasive within-patient transfer of pOXA-48, suggesting that horizontal plasmid transfer occurs in the gut of virtually every colonised patient. The complex and multifaceted epidemiological scenario exposed by this study provides new insights for the development of intervention strategies to control the in-hospital spread of CPE.
description: bioRxiv
Futurism, Geometry of “Photodynamism” and Digital Photography
Creators: name: Doble, Rick
name: Lorenzi, Marcella
Publisher: name: figshare
Year: 2016
Subjects: subject: Art
subject: Design
subject: Digital Humanities
subject: Entertainment
subject: History
subject: Philosophy
subject: FOS: Philosophy, ethics and religion

description: Under the light of new scientific discoveries of XX Century (Relativity, Quantum Mechanics, Fractality) we discuss how Digital Photography (and in particular the technique known as “Painting with Light”) can give a new “Future to Futurism”, incidentally implementing what the father of “Futuristic Photodynamism” (Anton Giulio Bragaglia) called the “Algebra of Movement”
Authigenic minerals reflect microbial control on pore waters in a ferruginous analogue
Creators: name: Vuillemin, A.
name: Morlock, M.
name: Paskin, A.
name: Benning, Liane G.
name: Henny, C.
name: Kallmeyer, J.
name: Russell, J. M.
name: Vogel, H.
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: authigenic minerals
subject: microbial control
subject: pore waters
subject: 500 Naturwissenschaften und Mathematik::550 Geowissenschaften, Geologie::550 Geowissenschaften

description: Ferruginous conditions prevailed in the oceans through much of Earth’s history. However, minerals recording these conditions remain difficult to interpret in terms of biogeochemical processes prior to lithification. In Lake Towuti, Indonesia, ferruginous sediments are deposited under anoxic sulfate-poor conditions similar to the Proterozoic oceans, allowing the study of mineralogical (trans)formations during microbial diagenesis. Comprehensive pore water geochemistry, high resolution geochemical core profiles, and electron microscopy of authigenic minerals revealed in situ formation of magnetite, millerite, and abundant siderite and vivianite along a 100 m long sequence. Framboidal magnetites represent primary pelagic precipitates, whereas millerite, a sulfide mineral often overlooked under sulfate-poor conditions, shows acicular aggregates entangled with siderite and vivianite resulting from saturated pore waters and continuous growth during burial. These phases act as biosignatures of microbial iron and sulfate reduction, fermentation and methanogenesis, processes clearly traceable in pore water profiles. Variability in metal and organic substrates attests to environment driven processes, differentially sustaining microbial processes along the stratigraphy. Geochemical profiles resulting from microbial activity over 200 kyr after deposition provide constraints on the depth and age of mineral formation within ferruginous records.
Quantified Self – Schnittstelle zwischen Lifestyle und Medizin
Creators: name: Meidert, Ursula
name: Scheermesser, Mandy
name: Prieur, Yvonne
name: Hegyi, Stefan
name: Stockinger, Kurt
name: Eyyi, Gabriel
name: Evers-Wölk, Michaela
name: Jacobs, Mattis
name: Oertel, Britta
name: Becker, Heidrun
Publisher: name: ETH Zurich
Year: 2018

description: TA-Swiss
description: ISBN:978-3-7281-3892-7
description: ISBN:978-3-7281-3891-0
Navigating the drought: upstream migration of a small-sized Cypriniformes (Telestes muticellus) in response to drying in a partially intermittent mountain stream
Creators: name: Schiavon, Alfredo
name: Comoglio, Claudio
name: Candiotto, Alessandro
name: Spairani, Michele
name: Hölker, Franz
name: Tarena, Fabio
name: Watz, Johan
name: Nyqvist, Daniel
Publisher: name: Freie Universität Berlin
Year: 2024
Subjects: subject: Climate change
subject: fluvial connectivity
subject: ires
subject: pit telemetry
subject: vairone
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: River flow intermittence is a natural phenomenon intensified by human activities, such as water abstraction and the effects of climate change. A growing number of rivers are predicted to experience intermittent flows, which may impact the diversity and abundance of freshwater species. Dry riverbeds directly diminish the availability of habitats for freshwater organisms, and suitable environments can turn into ecological traps with reduced survival rates, posing a significant threat to population persistence. Even though fish movements can enable drought-affected populations to persist, little is known about individual fish movement between intermittent and perennial reaches. Here, we study the movement of individual PIT-tagged Italian riffle dace (Telestes muticellus) in an intermittent and perennial river reach before, during and after two severe drying events. A high proportion of fish from the intermittent reach survived the drying riverbed through directed upstream migration. This was manifested in fish living in the intermittent reach of the river displaying significantly higher linear ranges, and net travelled distances during the monitoring period than fish in the perennial reach, which remained resident with limited linear range and net distances travelled. This finding underscores the importance of conserving longitudinal river connectivity in the face of increased water scarcity and intermittent flow patterns.
Truth-To-Materials in Photography: An Early Essay About the Potential of Digital Photography By Rick Doble
Creators: name: Doble, Rick
Publisher: name: figshare
Year: 2016
Subjects: subject: Art
subject: Design
subject: Digital Humanities
subject: Entertainment
subject: History
subject: 200104 Media Studies
subject: FOS: Media and communications
subject: Philosophy
subject: FOS: Philosophy, ethics and religion

description: Written in 2003 this early essay about digital photography draws on the age old idea of truth-to-materials. This essay suggests that digital photography could use its new abilities to 'draw with light' (photo = light, graph = draw) in a more expressive and unconventional manner.