cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Towards supporting shared cognition in distributed multidisciplinary teams: design and evaluation of an AI-based affective recognition system for online collaboration
Creators: name: Nguyen, Mimi
Publisher: name: Imperial College London
Year: 2023

description: This thesis investigates the challenges and opportunities of multidisciplinary design collaboration in distributed teams, with a particular focus on creativity and shared under- standing. Using a Design Research Methodology (DRM) structure, this thesis leverages a literature review and qualitative research for the Descriptive Study, proposes a prototype for the Prescriptive Study, and provides an evaluation of the tool for the Descriptive study to help multidisciplinary teams improve distributed collaboration based on rigorous guidance on how to do so in practice: 1. What is our current understanding of multidisciplinary collaboration in relation to design teamwork? 2. How have previous studies been conducted through their experimental choices, and adopted setups? 3. How do we build a shared cognition with our teammates in distributed design collaboration? 4. How does affective recognition (including sentiment and emotion) affect shared understanding and creativity in text-based communication? To answer these, we conducted a systematic literature review that identifies the main patterns and discrepancies in previous studies on multidisciplinary design collaboration, followed by an interview-based qualitative study that investigates the use of virtual collaboration tools and their impact on distributed collaboration and shared cognition. We developed a prototype with a machine learning-based dynamic affective recognition feed-back system and conducted mixed-methods evaluation studies of the tool. Research shows that the prototype was effective in increasing both creativity and shared understanding in distributed multidisciplinary design collaboration. The work draws on the research at the intersection of design studies, human-computer interaction, and team management, providing a better understanding of multidisciplinary distributed collaboration and suggests directions for AI solution designers looking to augment decentralised teamwork. Key contributions of this research include findings from a systematic literature review of prior empirical studies, insights from a qualitative study for improving the use of virtual tools in multidisciplinary design, an evidence-based prototype with an affective recognition feedback system which increases shared understanding and creativity in distributed design collaboration, and a set of guidelines for designing future AI-based tools.
Trophic structure of shrimp-trawl catches in the Pearl River estuary in winter, using stable isotope analyses
Creators: name: Zhixin Ke
name: Yehui Tan
name: Liangmin Huang
name: Chunyu Zhao
name: Huajian Liu
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: Hematology

description: The Pearl River estuary is the second largest estuary in the South China Sea. The species composition and trophic structure of shrimp-trawl catches from this estuary were investigated using stable isotope analyses during the winter of 2012. Crabs dominated the catches, constituting 37% of the total biomass in the inner estuary and 45% in the outer estuary. The δ15N and δ13C values for particulate organic matter gradually changed from the inner to the outer estuary. δ15N of particulate organic matter was more enriched in the inner estuary, while δ13C was more enriched in the outer estuary. Higher δ15N values in the inner estuary suggested a stronger influence from anthropogenic eutrophication. The δ15N and δ13C values of shrimp-trawl catches showed the same trends as the particulate organic matter. Trophic structure and faunal composition of shrimp-trawl catches varied greatly between the inner and outer estuary areas. The trophic niches were clearly distinct among fishery groups in the outer estuary. Community-wide metrics of stable isotope values showed that there was greater diversity of food sources and more complex trophic interactions in the inner estuary, whereas trophic levels were more evenly distributed in the outer estuary.
title: 03_0397
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/
Nephelauxetic effect in the lanthanide complexes with methyl acetoacetate
Creators: name: Mishchenko, Artem M.
name: Trunova, Elena K.
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Plant Biology

description: The complexation between methyl acetoacetate and certain lanthanides was studied in the mixed ethanol–water solvent (90% ethanol) using electronic absorption spectroscopy. The formation of the cationic 1:2 type complexes was shown at alkalescent medium. Based on the energy of the f–f transitions, the interelectronic repulsion parameters (Slater integrals) were determined by a least-square fit using effective Hamiltonian comprised of electrostatic and spin–orbit components and the nephelauxetic ratio was calculated as a ratio of the second-order Slater integrals. The nephelauxetic ratio was found to be proportional to the relative shortening of the lanthanide–oxygen bond length when the geometry of the complexes was optimized by semiempirical Sparkle/Parametric Method 7.
Longevity interventions temporally scale healthspan in Caenorhabditis elegans
Creators: name: Statzer, Cyrill
name: Reichert, Peter
name: Dual, Jürg
name: Ewald, Collin
Publisher: name: ETH Zurich
Year: 2021
Subjects: Acoustophoresis
Microfluidics
Healthy aging
Maximum muscle strength
Healthspan
Sickspan
Aging biomarker
Lifespan machine

description: Longer lived individuals, such as centenarians or longevity mutants of model organisms, have later onsets and lower incidence rates of late-life morbidities or disabilities than the average population. However, whether increased lifespan is caused by a compression of the portion of life spent in a state of morbidity, i.e., “sickspan,” is highly debated. It is unclear which health matrices are representative for measuring healthspan (time spent in good health); however, muscular performance is generally a good indicator for the health status in humans and a predictor for their mortality, regardless of the underlying cause. Here, we developed a novel microfluidic device that employs acoustophoretic force fields to quantify the maximum muscle strength and dynamic power in aging C. elegans populations. We found that longevity mutants have a delayed onset and lower declining rates in maximum muscle strength compared to wild type. Reconciling previous conflicting reports, we confirmed that certain longevity mutants exhibited a mild increase in relative sickspan measured by voluntary movement matrices, which is not the case when using our acoustophoretic force measurements, swim endurance, or other approaches. Using six different biomarkers for healthspan, we observed a time-dependent onset of morbidity, starting with a loss of stress resilience, a decline in dynamic power, and a decline in structural integrity, culminating finally in inactivity (lethargy) and a loss of mobility. We observed that a subset of aging biomarkers correlate with each other and maybe functionally interconnected. Surprisingly, we did not observe a compression of sickspan in longevity mutants but instead observed a temporal scaling of healthspan with diminishing returns for extreme lifespan extensions. Given the conservation of these longevity interventions, this raises the question of whether the healthspan of mammalian longevity interventions is temporally scaled as well.
description: bioRxiv
Nephelauxetic Effect in the Lanthanide Complexes with Methyl Acetoacetate
Creators: name: Mishchenko, Artem M.
name: Trunova, Elena K.
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Plant Biology

description: The complexation between methyl acetoacetate and certain lanthanides was studied in the mixed ethanol–water solvent (90% ethanol) using electronic absorption spectroscopy. The formation of the cationic 1:2 type complexes was shown at alkalescent medium. Based on the energy of the f–f transitions, the interelectronic repulsion parameters (Slater integrals) were determined by a least-square fit using effective Hamiltonian comprised of electrostatic and spin–orbit components and the nephelauxetic ratio was calculated as a ratio of the second-order Slater integrals. The nephelauxetic ratio was found to be proportional to the relative shortening of the lanthanide–oxygen bond length when the geometry of the complexes was optimized by semiempirical Sparkle/Parametric Method 7.
Inferring Transmission Fitness Advantage of SARS-CoV-2 Variants of Concern in Wastewater Using Digital PCR
Creators: name: Caduff, Lea
name: Dreifuss, David
name: Schindler, Tobias
name: Devaux, Alexander J.
name: Ganesanandamoorthy, Pravin
name: Kull, Anina
name: Stachler, Elyse
name: Fernandez-Cassi, Xavier
name: Beerenwinkel, Niko
name: Kohn, Tamar
name: Ort, Christoph
name: Julian, Timothy R.
Publisher: name: ETH Zurich
Year: 2021
Subjects: SARS-CoV-2
B.1.1.7
Digital PCR
Drop-off assays
Transmission fitness

description: Throughout the global COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterized by increased transmissibility, increased virulence, or reduced neutralization by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on sequencing, typically whole-genome sequencing of clinical samples. Wastewater surveillance is increasingly used to track the introduction and spread of SARS-CoV-2 variants through sequencing approaches. Here, we adapt and apply a rapid, high-throughput method for detection and quantification of the frequency of two deletions characteristic of the B.1.1.7, B.1.351, and P.1 VOCs in wastewater. We further develop a statistical approach to analyze temporal dynamics in drop-off RT-dPCR assay data to quantify transmission fitness advantage, providing data similar to that obtained from clinical samples. Digital PCR assays targeting signature mutations in wastewater offer near real-time monitoring of SARS-CoV-2 VOCs and potentially earlier detection and inference on transmission fitness advantage than clinical sequencing.
description: medRxiv
title: 03_0717
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/
Nitric oxide synthase neurons in the preoptic hypothalamus are sleep-active and contribute to regulating NREM and REM sleep and lowering body temperature
Creators: name: Harding, Edward C.
name: Ba, Wei
name: Zahir, Reesha
name: Yu, Xiao
name: Yustos, Raquel
name: Hsieh, Bryan
name: Lignos, Leda
name: Vyssotski, Alexei L.
name: Constandinou, Timothy
name: Franks, Nicholas P.
name: Wisden, William
Publisher: name: ETH Zurich
Year: 2021
Subjects: Preoptic hypothalamus
Nitric oxide
Sleep
Calcium photometry
Body temperature
Tetanus-toxin light-chain

description: When mice are exposed to external warmth, nitric oxide synthase (NOS1) neurons in the median and medial preoptic (MnPO/MPO) hypothalamus induce sleep and concomitant body cooling. However, how these neurons regulate baseline sleep and body temperature is unknown. Using calcium photometry, we show that NOS1 neurons in MnPO/MPO are predominantly NREM active. This is the first instance of a predominantly NREM-active population in the PO area, or to our knowledge, elsewhere in the brain. In addition to releasing nitric oxide, NOS1 neurons in MnPO/MPO can release GABA, glutamate and peptides. We expressed tetanus-toxin light-chain in MnPO/MPO NOS1 cells to reduce vesicular release of transmitters. This induced changes in sleep structure: over 24 hours, mice had less NREM sleep in their dark (active) phase, and more NREM sleep in their light (sleep) phase. REM sleep episodes in the dark phase were longer, and there were fewer REM transitions between other vigilance states. REM sleep had less theta power. Mice with synaptically blocked MnPO/MPO NOS1 neurons were also warmer. In particular, mice were warmer than control mice at the dark-light transition (ZT0), as well as during the dark phase siesta (ZT16-20), where there is usually a body temperature dip. Also, at this siesta point of cooled body temperature, mice usually have more NREM, but mice with synaptically blocked MnPO/MPO NOS1 cells showed reduced NREM sleep at this time. Overall, MnPO/MPO NOS1 neurons promote both NREM and REM sleep and contribute to chronically lowering body temperature, particularly at transitions where the mice normally enter NREM sleep.
description: bioRxiv
Рекомендации по лечению ВИЧ (EACS). Версия 8.0, Октябрь 2015 ( русский язык).pdf
Creators: name: Doe, Jonn
Publisher: name: figshare
Year: 2016
Subjects: subject: Uncategorized
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Лечение ВИЧ-инфекции у взрослых в Европе.«Рекомендации по лечению ВИЧ (EACS). Версия 8.0, Октябрь 2015 ( русский язык)»
Demineralization of Turkish Tosya lignite coal by boric acid leaching
Creators: name: Hacifazlioglu, Hasan
name: Uckan, Dilara
name: Sahin, Musa
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Space Science
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Boric acid is a weak inorganic acid type which is generally being used in glass, ceramics, detergents, agriculture, nuclear energy, and medicine fields, which has white crystal color and which can easily dissolve in water. Boric acid is being produced from colemanite which is a boron mineral having wide reserves in Turkey. In recent years, intense studies have been performed on the alternative usage areas of boric acid in Turkey. In this study, boric acid was used as a leaching reagent for the demineralization of coal with high ash content. For the accurate determination of the success of boric acid in dissolving mineral matter, first a series of leaching tests were performed with boric acid, and then studies for removing mineral matter with strong acids such as hydrofluoric acid (HF), HCl, and H2SO4 were performed.
Hierarchical model-based deep reinforcement learning for trading
Creators: name: Millea, Adrian
Publisher: name: Imperial College London
Year: 2023

description: The kernel of this thesis posits that a hierarchical reinforcement learning (RL) system, with specialized agents, some of them being deep RL (DRL) agents, trained on distinct market data or employing diverse decision-making models, will surpass single-agent approaches in adapting to varying market conditions, optimizing risk-adjusted returns, and maintaining robust performance across different financial markets without frequent retraining. We first develop a single-asset approach consisting of a hierarchical reinforcement learning (RL) architecture which employs different low-level agents to act in the environment, i.e. the market. The highest level agent selects among a group of different specialised agents, which then act on the market. We add two simple decision-making models to the set of low-level agents, which diversify the pool of available agents, thus increasing overall behaviour flexibility. We also use a risk-based reward at the high-level which transforms the overall problem into a risk--return optimization. This shows significant reduction in risk while minimally reducing profits. We then devise a hierarchical decision-making architecture for portfolio optimization. At the highest level a DRL agent selects among a number of discrete actions, representing low-level agents. For the low-level agents, we use a set of Hierarchical Risk Parity (HRP) and Hierarchical Equal Risk Contribution (HERC) models with different hyperparameters, which all run in parallel, off-market (in a simulation). The modelling resembles a statefull, non-stationary, multi-arm bandit, where the performance of the individual arms changes with time and is assumed to be dependent on the recent history. We perform experiments on the cryptocurrency market (117 assets), on the stock market (46 assets) and on the foreign exchange market (28 pairs) showing the excellent robustness and performance of the overall system. Moreover, we eliminate the need for retraining and are able to deal with large testing sets successfully.
A complete biomimetic iron-sulfur cubane redox series
Creators: name: Grunwald, Liam
name: Clémancey, Martin
name: Klose, Daniel
name: Dubois, Lionel
name: Gambarelli, Serge
name: Jeschke, Gunnar
name: Wörle, Michael
name: Blondin, Geneviève
name: Mougel, Victor
Publisher: name: ETH Zurich
Year: 2021

description: Synthetic iron-sulfur cubanes are essential models for biological cofactors in the more complex enzymatic environments. However, a complete series of [Fe4S4]n complexes spanning all biorelevant oxidation states (n = 0-3+) has never been prepared. Here, we demonstrate that the use of a bulky arylthiolate ligand promoting the encapsulation of alkali-metal cations in the vicinity of the cubane enables the synthesis of such a series. Characterization by EPR, 57Fe Mössbauer spectroscopy, UV-Vis electronic absorption and variable-temperature X-ray diffraction analysis reveals key trends for the Fe4S4 core’s geometry as well as for the Mössbauer isomer shift, which both correlate systematically with oxidation state. Furthermore, we confirm the S=4 electronic ground state of the most reduced member, [Fe4S4]0, in agreement with that proposed for the all-ferrous cubanes in Nature.
description: ChemRxiv
description: ISSN:2573-2293
Functional assessment for elimination of mismatches in nuclear and whole cell extracts obtained from mouse and human blastocysts
Creators: name: Pinar Tulay
name: Jaroudi, Souraya
name: Alpesh Doshi
name: Sioban B. SenGupta
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Preimplantation embryos may have an increased risk of having mismatches due to the rates of cell proliferation and DNA replication. Elimination of mismatches in human gametes and embryos has not been investigated. In this study we developed a sensitive functional assay to examine the repair or elimination of mismatches in both commercially available cell extracts and extracts obtained from preimplantation embryos. Heteroduplex molecules were constructed using synthetic oligonucleotides. Efficiency of the repair of mismatches was semi-quantitatively analysed by exposure to nuclear/whole cell extracts (as little as 2.5 µg) and extracts obtained from pooled mouse and human blastocysts to investigate the repair capacity in human embryos. A cell free in vitro assay was successfully developed to analyze the repair of mismatches using heteroduplex complexes. The assay was further optimized to analyze repair of mismatches in cell extracts obtained from oocytes and blastocysts using minute amounts of protein. The efficiency of mismatch repair was examined in both mouse and human blastocysts (2.5 µg). The blastocysts were observed to have a lower repair efficiency compared to commercially available nuclear and whole cell extracts. In conclusion, a sensitive, easy, and fast in vitro technique was developed to detect the repair of mismatch efficiency in embryos.
Electrocatalytic metal hydride generation using concerted proton electron transfer mediators
Creators: name: Dey, Subal
name: Masero, Fabio
name: Brack, Enzo
name: Fontecave, Marc
name: Mougel, Victor
Publisher: name: ETH Zurich
Year: 2021

description: The electrochemical generation of metal hydride (M H) species remains one of the major hurdles for a wide range of catalytic reactions to be carried out electrochemically. We introduce here a new strategy for electrocatalytic M H generation using concerted proton electron transfer (CPET) mediators. We investigate the combination of a series of CPET mediators with the CO2 electroreduction catalyst [MnI(bpy)(CO)3Br] (bpy = 2,2’-bipyridine), probing the reversal of the product selectivity from CO to HCOOH to evaluate the efficiency of the M H generation step. We demonstrate the formation of the manganese-hydride by in-situ spectroscopic techniques and determine the thermodynamic boundary conditions for this mechanism to occur. A synthetic iron-sulfur cluster is identified as the best CPET-mediator for that system, enabling the preparation of a benchmark catalytic system for HCOOH generation.
description: ChemRxiv
description: ISSN:2573-2293
Temperature effects on the structure and mechanical properties of vapor deposited a-SiO2
Creators: name: Jambur, Vrishank
name: Molina-Ruiz, Manel
name: Dauer, Tom
name: Horton-Bailey, Donez
name: Vallery, Richard
name: Gidley, David
name: Metcalf, Thomas
name: Liu, Xiao
name: Hellman, Frances
name: Szlufarska, Izabela
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Amorphous silica (a-SiO2) exhibits unique thermo-mechanical behaviors that set it apart from other glasses. However, there is still limited understanding of how this mechanical behavior is related to the atomic structure and to the preparation conditions of a-SiO2. Here, we used electron beam (e-beam) physical vapor deposition (PVD) to prepare a series of a-SiO2 films grown at different substrate temperatures and then combined molecular simulations with Positronium Annihilation Lifetime Spectroscopy and nanoindentation experiments to establish relations among processing, structure, and mechanical response of the films. Specifically, we found that increase in the growth temperature leads to increase in the elastic moduli and hardness of the films. The relative porosity in the films also increases while the a-SiO2 network itself becomes denser, resulting in an overall increase in density despite increased porosity. In addition, we found that the a-SiO2 films exhibit the same anomalous temperature dependence of elastic modulus as bulk a-SiO2. However, the rate of increase in the elastic modulus with the measurement temperature was found to depend on the density of the a-SiO2 network and therefore on the growth temperature. Our findings provide new insights into the influence of the atomic network structure on the anomalous thermomechanical behavior of a-SiO2 and in turn guidance to control the mechanical properties of a-SiO2 films.
Detection and surveillance of SARS-CoV-2 genomic variants in wastewater
Creators: name: Jahn, Katharina
name: Dreifuss, David
name: Topolsky, Ivan
name: Kull, Anina
name: Ganesanandamoorthy, Pravin
name: Fernandez-Cassi, Xavier
name: Bänziger, Carola
name: Devaux, Alexander J.
name: Stachler, Elyse
name: Caduff, Lea
name: Cariti, Federica
name: Corzón, Alex Tuñas
name: Fuhrmann, Lara
name: Chen, Chaoran
name: Jablonski, Kim Philipp
name: Nadeau, Sarah Ann
name: Feldkamp, Mirjam
name: Beisel, Christian
name: Aquino, Catharine
name: Stadler, Tanja
name: Ort, Christoph
name: Kohn, Tamar
name: Julian, Timothy R.
name: Beerenwinkel, Niko
Publisher: name: ETH Zurich
Year: 2021

description: The emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance of genomic variants. Wastewater samples provide an opportunity to assess circulating viral lineages in the community. We performed genomic sequencing of 122 wastewater samples from three locations in Switzerland to analyze the B.1.1.7, B.1.351, and P.1 variants of SARS-CoV-2 on a population level. We called variant-specific signature mutations and monitored variant prevalence in the local population over time. To enable early detection of emerging variants, we developed a bioinformatics tool that uses read pairs carrying multiple signature mutations as a robust indicator of low-frequency variants. We further devised a statistical approach to estimate the transmission fitness advantage, a key epidemiological parameter indicating the speed at which a variant spreads through the population, and compared the wastewater-based findings to those derived from clinical samples. We found that the local outbreak of the B.1.1.7 variant in two Swiss cities was observable in wastewater up to 8 days before its first detection in clinical samples. We detected a high prevalence of the B.1.1.7 variant in an alpine ski resort popular among British tourists in December 2020, a time when the variant was still very rare in Switzerland. We found no evidence of local spread of the B.1.351 and P.1 variants at the monitored locations until the end of the study (mid February) which is consistent with clinical samples. Estimation of local variant prevalence performs equally well or better for wastewater samples as for a much larger number of clinical samples. We found that the transmission fitness advantage of B.1.1.7, i.e. the relative change of its reproductive number, can be estimated earlier and based on substantially fewer wastewater samples as compared to using clinical samples. Our results show that genomic sequencing of wastewater samples can detect, monitor, and evaluate genetic variants of SARS-CoV-2 on a population level. Our methodology provides a blueprint for rapid, unbiased, and cost-efficient genomic surveillance of SARS-CoV-2 variants.
description: medRxiv
title: Memories and fragments
title: resource management in Central Maluku, Eastern Indonesia
titleType: Subtitle
Creators: name: Soselisa, Hermien
Publisher: name: Charles Darwin University
Year: 2002

description: This thesis explores the pattern of Central Malukan livelihood and its ecological consequences over four hundred years. Using historical, ecological, and regional approaches, and local actors' perceptions, I explore the strategic choices of Central Malukan people in making a living, using resources and shaping their environment. The core of the study, therefore, examines changes over time in local livelihoods and the landscape as results of human-environmental relations. The change in a local community and environment is very much related to their encapsulation into wider socio-cultural, economic, and political systems from pre-colonial through colonial to contemporary situations. The recent sectarian conflict in Maluku also demonstrates the interconnection of local elements and wider systems that affects local livelihood, resources and environment as well as inter-community social systems. Local livelihood, in using and modifying the environment, is constructed and constrained by culture. The story from Buano Island as an extended ethnographic study demonstrates how different religious cosmology may cause difference in livelihood choices, adaptation and shaping landscape. Through a historical perspective, this study develops an account of how the Central Maluku social and cultural system and its impact on the landscape can be understood. This account of the region illustrates variety and flexibility in historical context. The analysis of Central Maluku shows short and long-term changes and transformations of patterns of livelihood and environmental relations. From the perspective of longer-term changes, and larger centre-periphery relations, the current unrest in Maluku can be interpreted as a stage in the ongoing pattern of local adaptation to regional circumstances. While the particular events of the present are historically unique, they are consistent with the recurrent events within the long history of Central Maluku society presented in this thesis.
Predictive profiling of SARS-CoV-2 variants by deep mutational learning
Creators: name: Taft, Joseph M.
name: Weber, Cédric
name: Gao, Beichen
name: Ehling, Roy A.
name: Han, Jiami
name: Frei, Lester
name: Metcalfe, Sean
name: Yermanos, Alexander
name: Kelton, William
name: Reddy, Sai T.
Publisher: name: ETH Zurich
Year: 2021

description: The continual evolution of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and the emergence of variants that show resistance to vaccines and neutralizing antibodies (1–4) threaten to prolong the coronavirus disease 2019 (COVID-19) pandemic (5). Selection and emergence of SARS-CoV-2 variants are driven in part by mutations within the viral spike protein and in particular the ACE2 receptor-binding domain (RBD), a primary target site for neutralizing antibodies. Here, we develop deep mutational learning (DML), a machine learning-guided protein engineering technology, which is used to interrogate a massive sequence space of combinatorial mutations, representing billions of RBD variants, by accurately predicting their impact on ACE2 binding and antibody escape. A highly diverse landscape of possible SARS-CoV-2 variants is identified that could emerge from a multitude of evolutionary trajectories. DML may be used for predictive profiling on current and prospective variants, including highly mutated variants such as omicron (B.1.1.529), thus supporting decision making for public heath as well as guiding the development of therapeutic antibody treatments and vaccines for COVID-19.
description: bioRxiv
5G International Standardisation efforts from EU experts: Insights from StandICT 2023 funded fellows
Creators: name: de Majo, Claudio
name: Giuffrida, Maria
Publisher: name: Zenodo
Year: 2024
Subjects: 5G
Standardisation

description: This paper explores the contributions to European and global 5G standardisation, drawing from the StandICT.eu 2023 project. The analysis focuses on insights from the “fellows” of the StandICT.eu 2023 project, examining how these efforts have influenced the development and integration of 5G technologies, highlighting the key role of interoperability in promoting technological harmony and maximising the societal and economic benefits of these innovations.
A Framework for Applying Digital Technologies to Enhance Advance Directives
Creators: name: Biller-Andorno, Nikola
name: Gloeckler, Sophie
name: Ferrario, Andrea
Publisher: name: ETH Zurich
Year: 2021
Subjects: advance directives
digital technologies
informed decision-making
goal concordant care
biomedical ethics

description: Commentary on the use of digital technologies to enhance Advance Directives and support informed decision-making. This, in turn, promotes the ultimate end of goal concordant care.
description: Zenodo
Supporting Information for Reply to Bryan et al.: Variation in context unlikely explanation of non-robustness of noun versus verb results
Creators: name: Alan.Gerber@Yale.Edu
name: Gregory.Huber@Yale.Edu
name: Daniel.Biggers@Ucr.Edu
name: Hendry, David J.
Publisher: name: figshare
Year: 2016
Subjects: Applied Psychology

description: Supporting Information for:
"Reply to Bryan et al.: Variation in context unlikely explanation of non-robustness of noun versus verb results" by Alan S. Gerber, Gregory A. Huber, Daniel R. Biggers, and David J. Hendry, Proceedings of the National Academy of Sciences.
Modeling Choice in Co-Design
Creators: name: Furter, Marius
Publisher: name: ETH Zurich
Year: 2021
Subjects: codesign

description: This report describes a method for modeling free and forced choice within Co-Design. In a free choice among a set, one has control over which option is selected, while in a forced choice one does not. Given a preorder P describing resources or functionalities, a free choice among a subset of P acts like a meet. Dually, a forced choice acts like a join. Moreover, the two types of choice distribute over one another. Based on this, we construct a universal model for choice on a preorder using the free completely distributive lattice ULP. Feasibility relations are then extended to these models. Along the way, we illustrate how to work within ULP and provide results that simplify calculations. The definitions presented here have been implemented in Haskell.
GerberEtAl-PNASResponseToBryanEtAl-SI.pdf
Creators: name: Alan.Gerber@Yale.Edu
name: Gregory.Huber@Yale.Edu
name: Daniel.Biggers@Ucr.Edu
name: Hendry, David J.
Publisher: name: figshare
Year: 2016
Subjects: Applied Psychology

description: Supporting Information for:
"Reply to Bryan et al.: Variation in context unlikely explanation of non-robustness of noun versus verb results" by Alan S. Gerber, Gregory A. Huber, Daniel R. Biggers, and David J. Hendry, Proceedings of the National Academy of Sciences.
Discovery of Antimicrobials By Mex : Massively Parallelized Growth Assays
Creators: name: Koch, Philipp
name: Schmitt, Steven
name: Cardner, Mathias
name: Beerenwinkel, Niko
name: Panke, Sven
name: Held, Martin
Publisher: name: ETH Zurich
Year: 2021

description: The number of newly approved antimicrobial compounds has been steadily decreasing over the past 50 years emphasizing the need for novel antimicrobial substances. Here we present Mex, a method for the high-throughput discovery of novel antimicrobials, that relies on E.coli self-screening to determine the bioactivity of more than ten thousand naturally occurring peptides. Analysis of thousands of E. coli growth curves using next-generation sequencing enables the identification of more than 1,000 previously unknown antimicrobial peptides. Additionally, by incorporating the kinetics of growth inhibition, a first indication of the mode of action is obtained, which has implications for the ultimate usefulness of the peptides in question. The most promising peptides of the screen are chemically synthesized and their activity is determined in standardized susceptibility assays. Ten out of 15 investigated peptides efficiently eradicate bacteria at a minimal inhibitory concentration in the lower µm or upper nm range. This work represents a step-change in the high-throughput discovery of functionally diverse antimicrobials.
description: Research Square
description: ISSN:2693-5015
Fairleigh Dickinson University's PublicMind: April 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); US Supreme Court cases (6); opinion of various issues pertaining to mothers (7); opinion of various issues pertaining to fathers (4); mom/dad has played most positive role in life (1); mothers/fathers blamed more when children get into trouble (1); news sources (1); agree/disagree with various statements about federal government (3); political partisanship (2); political ideology (1); own a firearm (1); Democratic candidate for president (1); Republican candidate for president (1).
Incorporación de la perspectiva de género en la docencia y la investigación
Creators: name: García-Holgado, Alicia
name: Verdugo-Castro, Sonia
Publisher: name: Zenodo
Year: 2023
Subjects: brecha de género
perspectiva de género
coeducación
igualdad de género
investigación
docencia
educación superior

description: Material del taller realizado en el marco de la estancia internacional de investigación en la Universidad Andrés Bello, Chile, en la sede Concepción, con el apoyo del proyecto "Ciencia e Innovación para el 2030".
title: 01_0765
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/
Transatlantic patterns: The relexification of locative constructions in Sranan
Creators: name: Yakpo, Kofi
name: Bruyn, Adrienne
Publisher: name: Zenodo
Year: 2015
Subjects: Creole

description: Spatial relations in Sranan are expressed through a broad range of constructions. Some of these reflect the influence of the Dutch superstrate, others clearly reflect the influence of the substrate languages of Sranan. These “Niger-Congo” structures are markedly different from equivalent “Indo-European” ones. Pattern relexification is held responsible for the wholesale carry-over of substrate semantics plus morpho-syntactic specifications into Sranan locative constructions. The synchronic variation in Sranan is partially explained by the equally broad variety of constructions found within and across the African languages and language families that participated in the creation of Sranan. However, much of the apparent diversity is superficial in nature, for it chiefly concerns constituent order. In contrast, morphosyntactic features like the nature of dependency, as well as the semantic structure of spatial descriptions remain highly similar in Sranan and the substrates.
A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons
Creators: name: Mikl, Martin
name: Eletto, Davide
name: Lee, Minkyoung
name: Lafzi, Atefeh
name: Mhamedi, Farah
name: Baghai Sain, Simona
name: Handler, Kristina
name: Moor, Andreas
Publisher: name: ETH Zurich
Year: 2021
Subjects: RNA localization
MPRA
Neurites

description: Asymmetric subcellular localization of mRNA is a common cellular phenomenon that is thought to contribute to spatial gene regulation. In highly polar neurons, subcellular transcript localization and translation are thought to enhance cellular efficiency and timely responses to external cues. Although mRNA localization has been observed in many tissues and numerous examples of the functional importance of this process exist, we still lack a systematic understanding of how the transcript sorting machinery works in a sequence-specific manner.

Here, we addressed these gaps by combining subcellular transcriptomics and rationally designed sequence libraries. We developed a massively parallel reporter assay (MPRA) for mRNA localization and tested ~50,000 sequences for their ability to drive RNA localization to neurites of neuronal cell lines. By scanning the 3’UTR of >300 genes we identified many previously unknown localization regions and mapped the localization potential of endogenous sequences. Our data suggest two ways the localization potential can be encoded in the 3’UTR: focused localization motifs and broadly encoded localization potential based on small contributions.

We identified sequence motifs enriched in dendritically localized transcripts and tested the potential of these motifs to affect the localization behavior of an mRNA. This assay revealed sequence elements with the ability to bias localization towards neurite as well as soma. Depletion of RNA binding proteins predicted or experimentally shown to bind these motifs abolished the effect on localization, suggesting that these motifs act by recruiting specific RNA-binding proteins.

Based on our dataset we developed machine learning models that accurately predict the localization behavior of novel sequences. Testing this predictor on native mRNA sequencing data showed good agreement between predicted and observed localization potential, suggesting that the rules uncovered by our MPRA also apply to the localization of native transcripts.

Applying similar systematic high-throughput approaches to other cell types will open the door for a comparative perspective on RNA localization across tissues and reveal the commonalities and differences of this crucial regulatory mechanism.
description: bioRxiv
Inferring and perturbing cell fate regulomes in human cerebral organoids
Creators: name: Fleck, Jonas S.
name: Jansen, Sophie M.J.
name: Wollny, Damian
name: Seimiya, Makiko
name: Zenk, Fides
name: Santel, Malgorzata
name: He, Zhisong
name: Camp, J. Gray
name: Treutlein, Barbara
Publisher: name: ETH Zurich
Year: 2021

description: Self-organizing cerebral organoids grown from pluripotent stem cells combined with single-cell genomic technologies provide opportunities to explore gene regulatory networks (GRNs) underlying human brain development. Here we acquire single-cell transcriptome and accessible chromatin profiling data over a dense time course covering multiple phases of organoid development including neuroepithelial formation, patterning, brain regionalization, and neurogenesis. We identify temporally dynamic and brain region-specific regulatory regions, and cell interaction analysis reveals emergent patterning centers associated with regionalization. We develop Pando, a flexible linear model-based framework that incorporates multi-omic data and transcription binding site predictions to infer a global GRN describing organoid development. We use pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoid. We find that certain factors regulate the abundance of cell fates, whereas other factors impact neuronal cell states after differentiation. We show that the zinc finger protein GLI3 is required for cortical fate establishment in humans, recapitulating previous work performed in mammalian model systems. We measure transcriptome and chromatin accessibility in normal or GLI3-perturbed cells and identify a regulome central to the dorsoventral telencephalic fate decision. This regulome suggests that Notch effectors HES4/5 are direct GLI3 targets, which together coordinate cortex and ganglionic eminence diversification. Altogether, we provide a framework for how multi-brain region model systems and single-cell technologies can be leveraged to reconstruct human brain developmental biology.
description: bioRxiv