cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Dissemination and Public Engagement Plan including graphic design guidelines (release 3)
Creators: name: Santucci Raffaella
Publisher: name: Zenodo
Year: 2020
Subjects: Q-sort

description: This Dissemination and Public Engagement Plan provides an update of the dissemination strategy, activities,
 and materials that Q-SORT intends to use over the lifetime of the Project, with the goal of making it as visible
 as possible and of disseminating the Project’s results as widely as possible.
 The dissemination and engagement activities are targeted to reach:
 ● the scientific research community, including national research agencies
 ● science enthusiasts and people who want to know more about science
 ● audiences from projects similar to Q-SORT
 ● high-school students
 ● policy-group members
 ● private-enterprise scientists and managers .
 The Dissemination and Public Engagement Plan identifies the methods to be employed to reach each of
 these target groups, how to tune the messages accordingly, and the expected outcome of those activities.
 Central to the identity and presence of Q-SORT is the Project Website, whose role is described in this
 document and whose design is discussed in more detail in D6.1 Q-SORT Project Website.
 In addition, the current document describes how Q-SORT intends to capitalise on the potential of social
 media (SM) for informing and spreading awareness on the project, as well as engaging with a wider
 audience.
 Finally, a series of Conferences, Webinars, Science Bashes will also play an important role in the
 dissemination and engagement process, and, together with the Website and SM profiles, will ensure that the
 results will reach a broad range of pertinent audiences across Europe and beyond.
 This document serves as an easy-to-use internal guide for the project partners. In addition, it describes the
 dissemination methodologies and activities to be carried out by partners in the project and how these
 processes will be monitored.
 A further aim of this document is to improve, streamline, and standardise the procedures concerning the
 project’s dissemination activities and to provide Q-SORT partners with branding guidelines to be adopted.
 The standardisation of procedures will also help the project management in monitoring and reporting
 activities and outcomes.
 We acknowledge that the present document is built on the successful dissemination experiences and
 strategies of previous European projects such us Linked Heritage and EAGLE .
 For reasons of clarity, further additions in releases 2 and 3 of this document have been laid down mostly in
 specific dedicated extra chapters and paragraphs.
Genome-wide mapping of imprinted differentially methylated regions by DNA methylation profiling of human placentas from triploidies
Creators: name: Yuen, Ryan K.
name: Jiang, Ruby
name: Peñaherrera, Maria S.
name: McFadden, Deborah E.
name: Robinson, Wendy P.
Publisher: name: BioMed Central
Year: 2016

description: Background: Genomic imprinting is an important epigenetic process involved in regulating placental and foetal growth. Imprinted genes are typically associated with differentially methylated regions (DMRs) whereby one of the two alleles is DNA methylated depending on the parent of origin. Identifying imprinted DMRs in humans is complicated by species- and tissue-specific differences in imprinting status and the presence of multiple regulatory regions associated with a particular gene, only some of which may be imprinted. In this study, we have taken advantage of the unbalanced parental genomic constitutions in triploidies to further characterize human DMRs associated with known imprinted genes and identify novel imprinted DMRs. Results: By comparing the promoter methylation status of over 14,000 genes in human placentas from ten diandries (extra paternal haploid set) and ten digynies (extra maternal haploid set) and using 6 complete hydatidiform moles (paternal origin) and ten chromosomally normal placentas for comparison, we identified 62 genes with apparently imprinted DMRs (false discovery rate <0.1%). Of these 62 genes, 11 have been reported previously as DMRs that act as imprinting control regions, and the observed parental methylation patterns were concordant with those previously reported. We demonstrated that novel imprinted genes, such as FAM50B, as well as novel imprinted DMRs associated with known imprinted genes (for example, CDKN1C and RASGRF1) can be identified by using this approach. Furthermore, we have demonstrated how comparison of DNA methylation for known imprinted genes (for example, GNAS and CDKN1C) between placentas of different gestations and other somatic tissues (brain, kidney, muscle and blood) provides a detailed analysis of specific CpG sites associated with tissue-specific imprinting and gestational age-specific methylation. Conclusions: DNA methylation profiling of triploidies in different tissues and developmental ages can be a powerful and effective way to map and characterize imprinted regions in the genome.
title: Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson’s disease
Creators: name: Rémy Villette
name: Julia Ortis Sunyer
name: Polina Novikova
name: Velma Aho
name: Viacheslav Petrov
name: Oskar Hickl
name: Susheel Bhanu Busi
name: Charlotte De Rudder
name: Benoît Kunath
name: Anna Buschart
name: Jean-Pierre Trezzi
name: Rashi Halder
name: Christian Jäger
name: Laura Lebrun
name: Annegrät Daujeumont
name: Sebastian Schade
name: Annette Janzen
name: Nico Jehmlich
name: Martin Von Bergen
name: Cedric Christian Laczny
name: Patrick May
name: Claudia Trenkwalder
name: Wolfgang Oertel
name: Brit Mollenhauer
name: Paul Wilmes
Publisher: name: LCSB
Year: 2024

description: Individuals with Parkinson’s disease (PD) exhibit differences in their gut microbiomes’ composition compared to healthy controls (HC). The functional consequences of these differences remain unclear. Here we use an integrated multi-omics approach to resolve the functional activities of the gut microbiome in prodromal PD (idiopathic REM sleep behavior disorder, iRBD) and PD compared to HC. Meta-metabolomic analyses identified 11 metabolites that were differentially abundant in PD or iRBD. These differences guided our subsequent comparisons. Amongst the identified metabolites, β-glutamate was significantly increased in individuals with PD or iRBD, and correlated with the transcriptional activity of Akkermansia, Methanobrevibacter and Clostridium. We specifically identified differences in transcripts related to glutamate metabolism that were linked to a decrease in flagellar assembly and chemotaxis transcripts expressed by specific taxa in PD. Our integrated multi-omics data highlights multifactorial alterations of structure and function in PD with disrupted functions linked to disease pathways.
Echinacea—A Source of Potent Antivirals for Respiratory Virus Infections
Creators: name: Hudson, James
name: Vimalanathan, Selvarani
Publisher: name: Multidisciplinary Digital Publishing Institute
Year: 2019

description: Extracts of Echinacea species have been used traditionally in North America for the control of symptoms of colds, influenza, and other diseases, and some of them have become very popular as “herbal medicines”. Recent studies have revealed that preparations derived from certain species and plant parts, but not all of them, possess potent antiviral activities, at non-cytotoxic concentrations, particularly against membrane-containing viruses. Thus all strains of human and avian influenza viruses tested (including a Tamiflu-resistant strain), as well as herpes simplex virus, respiratory syncytial virus, and rhinoviruses, were very sensitive to a standardized Echinacea purpurea preparation. In mechanistic studies the influenza virus-specific hemagglutinin and neuraminidase were inhibited. In addition some extracts displayed anti-inflammatory activity in virus-infected cells, and numerous other effects on the expression of cellular genes. Multiple components, either discrete compounds or mixtures, appeared to be responsible for the various antiviral activities.
Considérations clés : santé mentale et soutien psychosocial dans la province du Nord-Kivu, en RDC
Creators: name: Jones, Theresa
name: Bedford, Juliet
name: Psychosocial, Le Groupe De Référence Du CPI Pour La Santé Mentale Et Le Soutien
name: Social Science In Humanitarian Action Platform
Publisher: name: F1000 Research Limited
Year: 2020

description: Cette note stratégique résume les considérations clés relatives à la santé mentale et au soutien psychosocial dans le contexte de la flambée épidémique de la maladie à virus Ébola (MVE) survenue dans la province du Nord-Kivu, en RDC.
Compilation de données en matière de sciences sociale et comportementales, No.5, Ebola, RDC
Creators: name: Bardosh, Kevin
name: Jones, Theresa
name: Tulloch, Olivia
name: Social Science In Humanitarian Action Platform
Publisher: name: F1000 Research Limited
Year: 2020

description: Cette brève compilation d’analyses de données fournit un « état des lieux » des données en matière de science sociale et comportementale liées à la flambée épidémique actuelle du virus Ébola dans les provinces du Nord-Kivu, du Sud-Kivu et de l’Ituri. Sur la base des données collectées et analysées par des organisations œuvrant à la riposte au virus Ébola et, de manière plus générale, au sein de la région, elle examine les convergences et les divergences entre les jeux de données. Dans la mesure du possible, cette note prend également en compte les différences par zone géographique, groupe démographique, période de temps et autres variables pertinentes. Les sources de données sont indiquées à la fin du document. Il s’agit de la cinquième compilation d’analyses de données élaborée par la Plateforme Social Science in Humanitarian Action (SSHAP) et elle est axée sur des données générées entre septembre et novembre 2019. Elle est fondée sur les quatre notes stratégiques de compilation de données précédentes, (#1 : août à octobre 2018 ; #2 : novembre 2018 à janvier 2019 ; #3 : février à mai 2019 ; #4 : juin à août 2019).
Difficult decisions in times of constraint: Criteria based Resource Allocation in the Vancouver Coastal Health Authority
Creators: name: Mitton, Craig, 1972-
name: Dionne, Francois
name: Damji, Rizwan
name: Campbell, Duncan
name: Bryan, Stirling
Publisher: name: BioMed Central
Year: 2016

description: Objectives: The aim of the project was to develop a plan to address a forecasted deficit of approximately $4.65 million for fiscal year 2010/11 in the Vancouver Communities division of the Vancouver Coastal Health Authority. For disinvestment opportunities identified beyond the forecasted deficit, a commitment was made to consider options for resource re-allocation within the Vancouver Communities division. Methods: A standard approach to program budgeting and marginal analysis (PBMA) was taken with a priority setting working committee and a broader advisory panel. An experienced, non-vested internal project manager worked closely with the two-member external research team throughout the process. Face to face evaluation interviews were held with 10 decision makers immediately following the process. Results: The recommendations of the working committee included the implementation of 44 disinvestment initiatives with an annualized value of CAD $4.9 million, as well as consideration of possible investments if the realized savings match expectations. Overall, decision makers viewed the process favorably and the primary aim of addressing the deficit gap was met. Discussion: A key challenge was the tight timeline which likely lead to less evidence informed decision making then one would hope for. Despite this, decision makers felt that better decisions were made then had the process not been in place. In the end, this project adds value in finding that PBMA can be used to cover a deficit and minimize opportunity cost through systematic application of criteria whilst ensuring process fairness through focusing on communication, transparency and decision maker engagement.
H3K9me3-binding proteins are dispensable for SETDB1/H3K9me3-dependent retroviral silencing
Creators: name: Maksakova, Irina A
name: Goyal, Preeti
name: Bullwinkel, Jörn
name: Brown, Jeremy P
name: Bilenky, Misha
name: Mager, Dixie L
name: Singh, Prim B
name: Lorincz, Matthew C
Publisher: name: BioMed Central
Year: 2016

description: Background: Endogenous retroviruses (ERVs) are parasitic sequences whose derepression is associated with cancer and genomic instability. Many ERV families are silenced in mouse embryonic stem cells (mESCs) via SETDB1-deposited trimethylated lysine 9 of histone 3 (H3K9me3), but the mechanism of H3K9me3-dependent repression remains unknown. Multiple proteins, including members of the heterochromatin protein 1 (HP1) family, bind H3K9me2/3 and are involved in transcriptional silencing in model organisms. In this work, we address the role of such H3K9me2/3 "readers" in the silencing of ERVs in mESCs. Results: We demonstrate that despite the reported function of HP1 proteins in H3K9me-dependent gene repression and the critical role of H3K9me3 in transcriptional silencing of class I and class II ERVs, the depletion of HP1α, HP1β and HP1γ, alone or in combination, is not sufficient for derepression of these elements in mESCs. While loss of HP1α or HP1β leads to modest defects in DNA methylation of ERVs or spreading of H4K20me3 into flanking genomic sequence, respectively, neither protein affects H3K9me3 or H4K20me3 in ERV bodies. Furthermore, using novel ERV reporter constructs targeted to a specific genomic site, we demonstrate that, relative to Setdb1, knockdown of the remaining known H3K9me3 readers expressed in mESCs, including Cdyl, Cdyl2, Cbx2, Cbx7, Mpp8, Uhrf1 and Jarid1a-c, leads to only modest proviral reactivation. Conclusion: Taken together, these results reveal that each of the known H3K9me3-binding proteins is dispensable for SETDB1-mediated ERV silencing. We speculate that H3K9me3 might maintain ERVs in a silent state in mESCs by directly inhibiting deposition of active covalent histone marks.
Knowledge Management Strategies and Emerging Technologies -- An Overview Of the Underpinning Concepts
Creators: name: Tiwari, Siddhartha Paul
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computers and Society (cs.CY)
subject: FOS: Computer and information sciences
subject: K.4.1; K.4.3

description: Among the essential elements of knowledge management is the use of information and data, as well as the knowledge, skills, and abilities inherent within communities, as well as their ideas, commitments, and motivations for making good decisions as emerging technologies become more prevalent. Numerous leading social scientists in this field have asserted that organisational knowledge should be regarded as a strategic asset. There is a growing awareness of the importance of gathering, locating, capturing, and sharing collective knowledge and expertise of societies, and societies are urged to develop effective and efficient methods of gathering, locating, capturing, and sharing that knowledge in order to deal with problems and to benefit from opportunities. People living in many countries and regions are interested in implementing knowledge management processes and technologies, and many of them have included knowledge management as an integral part of their overall development strategies. The management of knowledge plays an increasingly important role in global economic development (Bell, 1973, 1978). In order to remain relevant in the modern world, organisations should not ignore knowledge management and emerging technologies.
Brief history of the pion-nucleon sigma term
Creators: name: Alarcón, J. M.
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Lattice (hep-lat)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The pion-nucleon sigma term is a quantity involved in many important aspects of particle and nuclear physics. In this review I show its origin and how it is connected to important questions as the origin of mass of the ordinary matter, studies of dark matter detection and nucleosynthesis. I mention the most common methods used to obtain the sigma term, and comment on the extracted values. As it is shown, the accepted value of the sigma term has been moving from relatively low ($\sim 40$ MeV) to larger ones ($\sim 60$ MeV) until today, where this controversy still persist.
description: Invited review for European Physical Journal Special Topics (REVTeX version). 34 pages, 5 figures. Accepted for publication on 10 May 2021
title: Journal of Technological Sciences, Vol. 1 No. 2 (2023): Zimbabwe Journal of Technological Sciences (JTS)
title: Zimbabwe Journal of Technological Sciences (JTS)
titleType: AlternativeTitle
Creators: name: Journal Of Technological Sciences
Publisher: name: Journal of Technological Sciences
Year: 2024

description: Editorial for the Journal of Technological Sciences Volume 2...i
The Design of an IoT based automatic pollution monitoring system ...151-183
Advances in Heat Storage(HS) Schemes for Concentrated Solar Power Plants(CSPPs)–A Technical Paper ...120-150
A Systematic Investigation of Microwave Heating in Oxidised Platinum Group Metal Ores...90-119
COVID-19 spread regulator robot - An automatic robot that detects face mask, check human body temperature, and hand sanitizes people at entrance point ...75-89
Determinants of Economic Growth for SADC Nations: A Fixed Effects Approach...53-74
A Multilevel Approach to Measuring Revenue Collection Efficiency in Local Governments. ...33-52
Natural mating versus artificial insemination on reproductive performance of cattle in Zimbabwe’s smallholder sector: A review...15-32
Use of ethnoveterinary medicines for poultry health management in Southern Africa Development Community (SADC) countries: A review ...1-14
A Multilevel Approach to Measuring Revenue Collection Efficiency in Local Governments...1-5
The Stereochemistry of Complex Polyketide Biosynthesis by Modular Polyketide Synthases
Creators: name: Kwan, David H.
name: Schulz, Frank
Publisher: name: Multidisciplinary Digital Publishing Institute
Year: 2019

description: Polyketides are a diverse class of medically important natural products whose biosynthesis is catalysed by polyketide synthases (PKSs), in a fashion highly analogous to fatty acid biosynthesis. In modular PKSs, the polyketide chain is assembled by the successive condensation of activated carboxylic acid-derived units, where chain extension occurs with the intermediates remaining covalently bound to the enzyme, with the growing polyketide tethered to an acyl carrier domain (ACP). Carboxylated acyl-CoA precursors serve as activated donors that are selected by the acyltransferase domain (AT) providing extender units that are added to the growing chain by condensation catalysed by the ketosynthase domain (KS). The action of ketoreductase (KR), dehydratase (DH), and enoylreductase (ER) activities can result in unreduced, partially reduced, or fully reduced centres within the polyketide chain depending on which of these enzymes are present and active. The PKS-catalysed assembly process generates stereochemical diversity, because carbon–carbon double bonds may have either cis- or trans- geometry, and because of the chirality of centres bearing hydroxyl groups (where they are retained) and branching methyl groups (the latter arising from use of propionate extender units). This review shall cover the studies that have determined the stereochemistry in many of the reactions involved in polyketide biosynthesis by modular PKSs.
Task Force Open Science: Research Data Management at CESAER Universities
Creators: name: Kraft, Angelina
name: Martinez-Lavanchy, Paula
Publisher: name: Zenodo
Year: 2020
Subjects: Research Data Management
CESAER
Task Force Open Science
Technical Universities
FAIRdata
Engineering Sciences
STEM

description: Presentation given by Angelina Kraft and Paula Martinez Lavanchy at the 'STM’s FREE Multi-stakeholder webinar on Research Data' on the 19. May 2020. The presentation summarizes the main results of the CESAER white paper 'Advancing Research Data Management in universities of Science and Technology' - http://doi.org/10.5281/zenodo.3665372
title: Journal of Technological Sciences, Vol. 1 No. 1 (2022): Journal of Technological sciences (JTS)
title: Journal of Technological sciences (JTS)
titleType: AlternativeTitle
Creators: name: Journal Of Technological Sciences
Publisher: name: Journal of Technological Sciences
Year: 2022

description: CUT's  Journal of Technological sciences (JTS) (formerly Zimbabwe Journal of Technological Sciences) is proud to publish the first issue online in August 2022. The focus of the journal is in the following subject areas:


• Health Sciences & Technology

• ICT, Materials and Engineering Sciences &Technology

• Life Sciences & Technology

• Physical Sciences & Technology
description: The design of an automated CO emission control system for automobiles using activated carbon.
Poultry endogenous biosurfactants based feed additive, a potential counter to Antimicrobial resistance (AMR) challenge
Modelling of hourly solar radiation collected on a tilted surface at Banket in Mashonaland West, Zimbabwe for optimum design of off-grid solar systems.
Design and performance assessment of an automatic grain moisture measuring system for use in Zimbabwe
Editorial for Journal of Technological Sciences
Pit silos require hermeticity to serve as an alternative low cost storage facility for maize grain by smallholder farmers
Establishing the most cost effective reliability for off-grid solar systems in Zimbabwe
Establishing the most cost effective reliability for off-grid solar systems in Zimbabwe
Establishing the most cost effective reliability for off-grid solar systems in Zimbabwe
the
Client satisfaction among participants in a randomized trial comparing oral methadone and injectable diacetylmorphine for long-term opioid-dependency
Creators: name: Marchand, Kirsten
name: Oviedo-Joekes, Eugenia
name: Guh, Daphne
name: Brissette, Suzanne
name: Marsh, David C.
name: Schechter, Martin T.
Publisher: name: BioMed Central
Year: 2015

description: Background: Substitution with opioid-agonists (e.g., methadone) has shown to be an effective treatment for chronic long-term opioid dependency. Patient satisfaction with treatment has been associated with improved addiction treatment outcomes. However, there is a paucity of studies evaluating patients' satisfaction with Opioid Substitution Treatment (OST). In the present study, participants' satisfaction with OST was evaluated at 3 and 12 months. We sought to test the relationship between satisfaction and patients' characteristics, the treatment modality received and treatment outcomes. Methods Data from a randomized controlled trial, the North American Opiate Medication Initiative (NAOMI), conducted in Vancouver and Montreal (Canada) between 2005-2008, was analyzed. The NAOMI study compared the effectiveness of oral methadone vs. injectable diacetylmorphine over 12 months. A small sub-group of patients received injectable hydromorphone on a double blind basis with diacetylmorphine. The Client Satisfaction Questionnaire (CSQ-8) was used to measure satisfaction with treatment. CSQ-8 scores, as well as retention and response to treatment, did not differ between those receiving hydromorphone and diacetylmorphine at 3 or 12 months assessments; therefore, these two groups were analyzed together as the 'injectable' treatment group. Results A total of 232 (92%) and 237 (94%) participants completed the CSQ-8 at 3 and 12 months, respectively. Participants in both groups were highly satisfied with treatment. Independent of treatment group, participants satisfied with treatment at 3 months were more likely to be retained at 12 months. Multivariate analysis indicated that satisfaction was greater among those randomized to the injection group after controlling for treatment effectiveness. Participants who were retained, responded to treatment, and had fewer psychological symptoms were more satisfied with treatment. Finally, open-ended comments were made by 149 (60.3%) participants; concerns about the randomization process and the study ending were most commonly reported by participants receiving the oral and injectable medications, respectively. Conclusions The higher satisfaction among those receiving medically prescribed injectable diacetylmorphine (or hydromorphone) supports current evidence regarding the attractiveness of this treatment for long-term, opioid-dependent individuals not benefiting sufficiently from other treatments. In addition, the measurement of treatment satisfaction provides valuable information about participants at risk of relapse and in need of additional services. Trial Registration ClinicalTrials.gov Identifier: NCT00175357
The pedagogical value of the four-dimensional picture II: Another way of looking at the electromagnetic field
Creators: name: Kosyakov, B. P.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: The concept of electromagnetic field can be neatly formulated by recognizing that the simplest form of the four-force is indeed feasible. We show that Maxwell's equations almost entirely stem from the properties of spacetime, notably from the fact that our world has dimension d = 4. Their complete reconstruction requires three additional assumptions which are seemingly divorced from geometry, but, actually, may have much to do with the spacetime properties.
description: 10 pages
The pedagogical value of the four-dimensional picture I: Relativistic mechanics of point particles
Creators: name: Kosyakov, B. P.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: We outline two subjects of relativistic mechanics: (i) the set of allowable world lines, and (ii) the origin of the relativistic law of dynamics governing point particles. We show that: (i) allowable world lines in the classical theory of particles and fields are quite simple geometric objects as opposed to their associated three-dimensional trajectories, and (ii) Newton's second law requires neither modification nor generalization, it should be only smoothly embedded in the four-dimensional geometry of Minkowski spacetime to yield the dynamical law for relativistic particles.
description: 10 pages
Human health and the indoor environment : an analysis of building materials and sustainable architecture
Creators: name: Esslinger, Grace Elizabeth
Publisher: name: The University of Texas at Austin
Year: 2020
Subjects: Sustainable design
Sustainable architecture
Indoor air quality
Indoor environmental quality
Human health
Toxicity

description: In our modern industrial world, humans have migrated from the outdoors to indoor environments. Americans on average spend 93% of their time indoors and indoor air quality is a top threat to human health according to the U.S. Environmental Protection Agency. While energy reduction is often the most well-known aspect of sustainable design, human health is also significant because of our indoor lifestyles. One aspect of sustainable design is the selection of building materials that are safe for both humans and the environment. The lifecycle of a building product is important, but the lifecycle of humans should also be a design priority. This thesis explores the relationship between indoor environmental quality and building materials and aims to address points in architecture that are beneficial for human health and the indoor environment. Since the indoor environment is influenced by a variety of factors, there are many areas for opportunity. While healthy homes do exist, most homes in America are made using materials that may pose risks to human health. This thesis addresses which methods of sustainability are most appropriate to meet the current demands of new construction. As humans continue to spend more time indoors, the importance of materials decision is amplified. Designers and architects have the ability to choose materials that can protect human health indoors
Combined logical and data-driven models for linking signalling pathways to cellular response
Creators: name: Melas, Ioannis N
name: Mitsos, Alexander
name: Messinis, Dimitris E
name: Weiss, Thomas S.
name: Alexopoulos, Leonidas G
Publisher: name: Universität Regensburg
Year: 2011
Subjects: subject: Hepatocyte Growth Factor Tumor Necrosis Factor Alpha Lapatinib Integer Linear Program Partial Little Square Regression
subject: 610 Medizin

description: Abstract
Background

Signalling pathways are the cornerstone on understanding cell function and predicting cell behavior. Recently, logical models of canonical pathways have been optimised with high-throughput phosphoproteomic data to construct cell-type specific pathways. However, less is known on how signalling pathways can be linked to a cellular response such as cell growth, death, cytokine secretion, or transcriptional activity.
Results

In this work, we measure the signalling activity (phosphorylation levels) and phenotypic behavior (cytokine secretion) of normal and cancer hepatocytes treated with a combination of cytokines and inhibitors. Using the two datasets, we construct "extended" pathways that integrate intracellular activity with cellular responses using a hybrid logical/data-driven computational approach. Boolean logic is used whenever a priori knowledge is accessible (i.e., construction of canonical pathways), whereas a data-driven approach is used for linking cellular behavior to signalling activity via non-canonical edges. The extended pathway is subsequently optimised to fit signalling and behavioural data using an Integer Linear Programming formulation. As a result, we are able to construct maps of primary and transformed hepatocytes downstream of 7 receptors that are capable of explaining the secretion of 22 cytokines.
Conclusions

We developed a method for constructing extended pathways that start at the receptor level and via a complex intracellular signalling pathway identify those mechanisms that drive cellular behaviour. Our results constitute a proof-of-principle for construction of "extended pathways" that are capable of linking pathway activity to diverse responses such as growth, death, differentiation, gene expression, or cytokine secretion.
Perturbation theory and thermal transport in mass-disordered alloys: Insights from Green's function methods
Creators: name: Thébaud, Simon
name: Berlijn, Tom
name: Lindsay, Lucas
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Lowest-order quantum perturbation theory (Fermi's golden rule) for phonon-disorder scattering has been used to predict thermal conductivities in several semiconducting alloys with surprising success given its underlying hypothesis of weak and dilute disorder. In this paper, we explain how this is possible by focusing on the case of maximally mass-disordered Mg$_2$Si$_{1-x}$Sn$_x$. We use a Chebyshev polynomials Green's function method that allows a full treatment of disorder on very large systems (tens of millions of atoms) to probe individual phonon linewidths and frequency-resolved thermal transport. We demonstrate that the success of perturbation theory originates from the specific form of mass disorder terms in the phonon Green's function and from the interplay between anharmonic and disorder scattering.
Adapting to informality: multistory housing driven by a co-productive process and the People’s Plans in Metro Manila, Philippines
Creators: name: Galuszka, Jakub
Publisher: name: Technische Universität Berlin
Year: 2020
Subjects: subject: 710 Städtebau, Raumplanung, Landschaftsgestaltung
subject: co-production
subject: multistorey housing
subject: Metro Manila
subject: resettlement
subject: public sector
subject: civil society
subject: climate change
subject: People’s Plan

description: Faced with an ever-increasing demand for land in Metro Manila, as well as with the domination of standardised low-income housing models, the local civil society and the urban-poor sector embarked on the development of an alternative shelter approach in-city multistorey housing delivered through the People’s Plan. The article documents the emergence of the approach, interrogates its main assumptions and takes a closer look at the implementation process through two case studies, in Pasig and San Jose Del Monte. The article analyses the modality as an attempt to create a hybrid approach between formal and informal delivery systems within the built form conventionally associated with the imaginaries of the ‘formal’ city. The findings underscore the role of co-production in enabling the urban-poor sector to leverage their approach, while documenting the need to move beyond a formal–informal dichotomy in both theory and urban development practice.
The state of stress and strain adjacent to notches in a new class of nonlinear elastic bodies
Creators: name: Kulvait, Vojtěch
name: Málek, Josef
name: Rajagopal, K. R.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Numerical Analysis (math.NA)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: In this paper we study the deformation of a body with a notch subject to an anti-plane state of stress within the context of a new class of elastic models. These models stem as approximations of constitutive response functions for an elastic body that is defined within the context of an implicit constitutive relation between the stress and the deformation gradient. Gum metal and many metallic alloys are described well by such constitutive relations. We consider the state of anti-plane stress of a body with a smoothened V-notch within the context of constitutive relations for the linearized strain in terms of a power-law for the stretch. The problem is solved numerically and the convergence and the stability of the solution is studied.
description: This version of the article has been accepted for publication, after peer review and is subject to Springer Nature's AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: https://doi.org/10.1007/s10659-019-09724-0
title: Production atypique enfantine - morphologie dérivationnelle : "terminage"
Creators: name: LIEGEOIS, Loic
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2025
Subjects: subject: corpucit
subject: corli

description: Extrait permettant d'illustrer une création enfantine en lien avec la morphologie dérivationnelle ("terminer" + "-age").
 Extrait généré via la plateforme Corpucit.
description: thumbnail
Retrieval-Enhanced Machine Learning
Creators: name: Zamani, Hamed
name: Diaz, Fernando
name: Dehghani, Mostafa
name: Metzler, Donald
name: Bendersky, Michael
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Computation and Language (cs.CL)
subject: Information Retrieval (cs.IR)
subject: FOS: Computer and information sciences

description: Although information access systems have long supported people in accomplishing a wide range of tasks, we propose broadening the scope of users of information access systems to include task-driven machines, such as machine learning models. In this way, the core principles of indexing, representation, retrieval, and ranking can be applied and extended to substantially improve model generalization, scalability, robustness, and interpretability. We describe a generic retrieval-enhanced machine learning (REML) framework, which includes a number of existing models as special cases. REML challenges information retrieval conventions, presenting opportunities for novel advances in core areas, including optimization. The REML research agenda lays a foundation for a new style of information access research and paves a path towards advancing machine learning and artificial intelligence.
description: To appear in proceedings of ACM SIGIR 2022
Structural transition of skyrmion quasiparticles under compression
Creators: name: Zhang, Xichao
name: Xia, Jing
name: Liu, Xiaoxi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The competition between external drives and interparticle interactions are important for the static and dynamic properties of topological quasiparticles in confined geometries. Here, we study the dynamics of particlelike skyrmions under a current-induced compression, where skyrmions are stabilized in a confined space and form a skyrmion solid. We find that a lattice structural transition of nanoscale skyrmions could be induced by the compression, which depends on the initial lattice configuration and the compression level. The compression effect in the skyrmion solid with strong skyrmion-skyrmion repulsion could produce a wave front showing an abrupt change of the skyrmion density, which may propagate through the skyrmion solid depending on the compression level. Besides, a chain of skyrmions on the surface of the compressed skyrmion solid could show a fast and stable motion along the surface as long as it remains within the driving region. Some skyrmions may collapse during the compression due to the destructive skyrmion-skyrmion collision, which mainly happens in the area around the skyrmion injection boundary between the driving and compressive regions. Our results are useful for understanding the compression physics of quasiparticles carrying nontrivial topology.
description: 10 pages, 8 figures
Quantum steganography with large payload based on dense coding and entanglement swapping of GHZ states
Creators: name: Ye, Tian-Yu
name: Jiang, Li-Zhen
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A quantum steganography protocol with large payload is proposed, based on dense coding and entanglement swapping of GHZ states. Its super quantum channel is formed by building up the hidden channel within the original quantum secure direct communication (QSDC) scheme. Based on the original QSDC, secrets messages are transmitted by integrating dense coding of GHZ states and entanglement swapping of GHZ states. Its capacity of super quantum channel achieves six bits per round covert communication, much higher than the previous quantum steganography protocols. Its imperceptibility is good, since the information and secrets messages can be regarded to be random or pseudo-random. Moreover, its security is proved to be reliable.
description: 8 pages, 1 table
Improving Dual-Microphone Speech Enhancement by Learning Cross-Channel Features with Multi-Head Attention
Creators: name: Xu, Xinmeng
name: Gu, Rongzhi
name: Zou, Yuexian
Publisher: name: arXiv
Year: 2022
Subjects: subject: Audio and Speech Processing (eess.AS)
subject: Sound (cs.SD)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Hand-crafted spatial features, such as inter-channel intensity difference (IID) and inter-channel phase difference (IPD), play a fundamental role in recent deep learning based dual-microphone speech enhancement (DMSE) systems. However, learning the mutual relationship between artificially designed spatial and spectral features is hard in the end-to-end DMSE. In this work, a novel architecture for DMSE using a multi-head cross-attention based convolutional recurrent network (MHCA-CRN) is presented. The proposed MHCA-CRN model includes a channel-wise encoding structure for preserving intra-channel features and a multi-head cross-attention mechanism for fully exploiting cross-channel features. In addition, the proposed approach specifically formulates the decoder with an extra SNR estimator to estimate frame-level SNR under a multi-task learning framework, which is expected to avoid speech distortion led by end-to-end DMSE module. Finally, a spectral gain function is adopted to further suppress the unnatural residual noise. Experiment results demonstrated superior performance of the proposed model against several state-of-the-art models.
description: Accepted by ICASSP 2022
Scalable Private Decision Tree Evaluation with Sublinear Communication
Creators: name: Bai, Jianli
name: Song, Xiangfu
name: Cui, Shujie
name: Chang, Ee-Chien
name: Russello, Giovanni
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Private decision tree evaluation (PDTE) allows a decision tree holder to run a secure protocol with a feature provider. By running the protocol, the feature provider will learn a classification result. Nothing more is revealed to either party. In most existing PDTE protocols, the required communication grows exponentially with the tree's depth $d$, which is highly inefficient for large trees. This shortcoming motivated us to design a sublinear PDTE protocol with $O(d)$ communication complexity. The core of our construction is a shared oblivious selection (SOS) functionality, allowing two parties to perform a secret-shared oblivious read operation from an array. We provide two SOS protocols, both of which achieve sublinear communication and propose optimizations to further improve their efficiency. Our sublinear PDTE protocol is based on the proposed SOS functionality and we prove its security under a semi-honest adversary. We compare our protocol with the state-of-the-art, in terms of communication and computation, under various network settings. The performance evaluation shows that our protocol is practical and more scalable over large trees than existing solutions.
The International Collaboration on Air Pollution and Pregnancy Outcomes : initial results
Creators: name: Parker, Jennifer D.
name: Rich, David Q.
name: Glinianaia, Svetlana V.
name: Leem, Jong Han
name: Wartenberg, Daniel
name: Bell, Michelle L.
name: Bonzini, Matteo
name: Brauer, Michael (Of University Of British Columbia)
name: Darrow, Lyndsey
name: Gehring, Ulrike
name: Gouveia, Nelson
name: Grillo, Paolo
name: Ha, Eunhee
name: Van Den Hooven, Edith H.
name: Jalaludin, Bin
name: Jesdale, Bill M.
name: Lepeule, Johanna
name: Morello-Frosch, Rachel
name: Morgan, Geoffrey G.
name: Slama, Rémy
name: Pierik, Frank H.
name: Pesatori, Angela Cecilia
name: Sathyanarayana, Sheela
name: Seo, Juhee
name: Strickland, Matthew
name: Tamburic, Lillian
name: Woodruff, Tracey J.
Publisher: name: The University of British Columbia
Year: 2015

description: BACKGROUND: The findings of prior studies of air pollution effects on adverse birth outcomes are difficult to synthesize because of differences in study design. OBJECTIVES: The International Collaboration on Air Pollution and Pregnancy Outcomes was formed to understand how differences in research methods contribute to variations in findings. We initiated a feasibility study to a) assess the ability of geographically diverse research groups to analyze their data sets using a common protocol and b) perform location-specific analyses of air pollution effects on birth weight using a standardized statistical approach. METHODS: Fourteen research groups from nine countries participated. We developed a protocol to estimate odds ratios (ORs) for the association between particulate matter ≤ 10 μm in aerodynamic diameter (PM₁₀) and low birth weight (LBW) among term births, adjusted first for socioeconomic status (SES) and second for additional location-specific variables. RESULTS: Among locations with data for the PM₁₀ analysis, ORs estimating the relative risk of term LBW associated with a 10-μg/m³ increase in average PM₁₀ concentration during pregnancy, adjusted for SES, ranged from 0.63 [95% confidence interval (CI), 0.30–1.35] for the Netherlands to 1.15 (95% CI, 0.61–2.18) for Vancouver, with six research groups reporting statistically significant adverse associations. We found evidence of statistically significant heterogeneity in estimated effects among locations. CONCLUSIONS: Variability in PM₁₀–LBW relationships among study locations remained despite use of a common statistical approach. A more detailed meta-analysis and use of more complex protocols for future analysis may uncover reasons for heterogeneity across locations. However, our findings confirm the potential for a diverse group of researchers to analyze their data in a standardized way to improve understanding of air pollution effects on birth outcomes.
Pathological heterogeneity in amyotrophic lateral sclerosis with FUS mutations : two distinct patterns correlating with disease severity and mutation
Creators: name: Mackenzie, Ian
name: Ansorge, Olaf
name: Strong, Michael
name: Bilbao, Juan
name: Zinman, Lorne
name: Ang, Lee-Cyn Ang
name: Baker, Matt
name: Stewart, Heather
name: Eisen, Andrew, 1936-
name: Rademakers, Rosa
name: Neumann, Manuela
Publisher: name: Acta Neuropathologica
Year: 2012

description: Mutations in the gene encoding the fused in sarcoma (FUS) protein are responsible for ~3% of familial amyotrophic lateral sclerosis (ALS) and <1% of sporadic ALS (ALS-FUS). Descriptions of the associated neuropathology are few and largely restricted to individual case reports. To better define the neuropathology associated with FUS mutations, we have undertaken a detailed comparative analysis of six cases of ALS-FUS that include sporadic and familial cases, with both juvenile and adult onset, and with four different FUS mutations. We found significant pathological heterogeneity among our cases, with two distinct patterns that correlated with the disease severity and the specific mutation. Frequent basophilic inclusions and round FUS-immunoreactive (FUS-ir) neuronal cytoplasmic inclusions (NCI) were a consistent feature of our early-onset cases, including two with the p.P525L mutation. In contrast, our late-onset cases, that included two with the p.R521C mutation, had tangle-like NCI and numerous FUS-ir glial cytoplasmic inclusions. Double-labeling experiments demonstrated that many of the glial inclusions were in oligodendrocytes. Comparison with the neuropathology of cases of frontotemporal lobar degeneration with FUS-ir pathology showed significant differences and suggests that FUS mutations are associated with a distinct pathobiology.
Stability of user satisfaction prediction in software projects - supplementary materials
Creators: name: Radliński, Łukasz
Publisher: name: Zenodo
Year: 2020
Subjects: User satisfaction
Software projects
Prediction stability
Machine learning
ISBSG

description: This is a supplementary material for the paper Stability of user satisfaction prediction in software projects to be published in the Proceedings of the 24th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems (KES) 2020 conference. Details on experimental part of data preparation and model learning and evaluation. According to the ISBSG licence terms the raw ISBSG dataset cannot be published. That is why attached documents only explain the use of the dataset without revealing its content.