cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
title: Sitting in limbo: transformative change through drug and alcohol education at university
Creators: name: Fulton, Archie
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: Transformative change, drug and alcohol university education.

description: Transformative learning has been described as an important theory to understand how adults can develop and change their perspectives through education. Adopting longitudinal approach, this Study investigated perspective change in students’ beliefs about drugs and alcohol, through their experience of studying drugs and alcohol at university. The research involved a longitudinal study of 35 students at three universities, with a focus on those students with lived experience of drugs and alcohol. This involved multiple case studies with a mixed methods approach to the collection of data, mostly qualitative, at three time points during the students’ studies. In addition, data were analysed regarding the reflections of eleven teachers about the students’ change in perspectives. The findings indicate that students changed their perspectives with an increased willingness to accommodate different beliefs and became more flexible in their approach to drug and alcohol practice. One of the more significant findings suggests that students often retain personal beliefs about drugs and alcohol, which are contradictory to their changed practice beliefs. A feature for many students was that they frequently held contrary beliefs simultaneously, which over the time of the Study indicated a continuing accommodation of conflicting beliefs. The findings suggest this liminal state is more permanent than temporary. It was identified by both students and teachers that a supportive environment, in terms of a community of practice, and being challenged, contributed significantly toward facilitating perspective change. It was also indicated that the key subject of ‘Theories of Addiction’ facilitated both a challenge and a change of perspective. Resulting from their studies, students increased their confidence in practice and personal development. An important implication of this Study is the positive role university can contribute to the personal development of students and providing an educated, informed drug and alcohol workforce in the UK. What makes this study an original contribution to the literature is that it reports on the impact of a university experience in the UK on the perspective transformation of beliefs among students with lived experience of drugs and alcohol.
title: Programmable autonomous chemical robots for discovery and synthesis
Creators: name: Caramelli, Dario
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: Discovery, automation, algorithm, machine learning, organic synthesis, data sharing, isocyanide, Twitter.

description: The work presented in this thesis focuses on the development of a platform to explore chemical spaces for reaction discovery and a network of robots for automatic collaboration. We believe that in recent years scientific automated systems have become an invaluable asset in the laboratory, vastly improving the productivity and generally changing the approach to chemistry research in many fields. However, the current implementations are mostly for technical help in repetitive tasks or in optimisation of already known reactions. We envision a closed-loop platform pointed towards the unknown, able to automatically perform reactions, analyse them, and use the acquired data to navigate a chemical space and make discoveries. The platform configuration went through a series of gradual improvements and expansions: it started with a single reactor and 4 reagents to finish with 6 parallel reactors, 20 reagents, an inert atmosphere line and three LEDs for photochemical reactions. As analysis equipment we used three benchtop instruments: NMR, MS and IR. All of them were automatically controlled and the data produced was processed using two different algorithms for reactivity assessment: a features extractor and a neural network. Chemical space exploration was also simulated using a neural network correlating the reaction parameters with the reactivity. The system has been used for three applications of increasing complexity. The first one was a reaction optimization performed with two different approaches: a polynomial regressor model and a genetic algorithm. The second task was the exploration of a simple chemical space made of 6 organic molecules and a base. Lastly, the system explored a larger chemical space built to discover new photochemical reactions. By using real time analysis, it was possible to identify promising candidates and successfully discover a new multicomponent reaction, a new photochemical reaction, and re-discover various examples already known in literature. The most interesting reaction has also been investigated manually in order to test its robustness. As a parallel project this thesis will also tackle the science reproducibility problem. We believe that chemistry automation will ensure a better preservation of scientific data, since the experiments’ parameters will be exchanged as defined robotic operations instead of ambiguous manual procedures. Expanding this concept one step forward we imagine a future where laboratory machines are interconnected through the internet, allowing automatic collaboration and data sharing. As a proof of concept we built a network of physically separated robots and showed how it is possible to use internet communication to search an azo-dye chemical space in a fraction of time as well as encoding and decoding information into a network of oscillating reactions.
Automatisierte Zweipunktdiskrimination bei Phantomschmerzen
Creators: name: Koller, Thomas
name: Baumgartner, Daniel
Publisher: name: Springer
Year: 2017
Subjects: Amputation
Phantomschmerzen
Kortikale Repräsentation
Zweipunktdiskrimination
Intervention
615: Pharmakologie und Therapeutik

description: Es gibt erste Hinweise dafür, dass Phantomschmerzen mit einer gestörten Organisation des sensorischen Kortex einhergehen und dass diese Organisation mit einem Training der Zweipunktdiskrimination (ZPD) normalisiert werden könnte. Bis jetzt bedurfte es immer einer ausführenden Person, die die ZPD beim Patienten anwendete. Mit einer automatisierten Zweipunktdiskrimination konnte in dieser Kasuistik bei einem unterschenkelamputierten Patienten während einer 19-tägigen Testphase eine Reduktion der anhaltenden Phantomschmerzen von m = 2,3/10 (VAS) auf 1,3/10 (VAS) und eine Reduktion der einschießenden Phantomschmerzen von m = 3,7/10 (VAS) auf 2,0/10 (VAS) beobachtet werden. Diese Resultate weisen eine erfreuliche Tendenz auf, sind aber (ausgenommen der nächtlichen Schmerzattacken) eher von eingeschränkter klinischer Relevanz.
How to Use Chipster for Bioinformatics Analysis of Nanomaterial-Based Omics Data
Creators: name: Nymark, Penny
name: Ehrhart, Friederike
name: Willighagen, Egon
name: Kohonen, Pekka
name: Korpelainen, Eija
name: Grafström, Roland
Publisher: name: figshare
Year: 2017
Subjects: subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 100708 Nanomaterials
subject: FOS: Nanotechnology
subject: 60408 Genomics
subject: FOS: Biological sciences

description: This tutorial will get you started on the basic use of the bioinformatics tool Chipster, an alternative to ArrayAnalysis.org described in other eNM tutorials. It will guide you through the import of microarray data (Affymetrix .CEL files), quality checks, normalization, pre-processing, basic statistical analyses methods and visualization of your data. Chipster is not specific to the nanosafety field, but this tutorial will be focused on the specific needs of nanotoxicological research. Chipster is an open source user-friendly analysis software for high-throughput data analysis. It offers over 350 bioinformatics tools and it is constantly updated according to the latest state-of-the-art tools and scripts. Users can analyse and visualize data interactively, and share complete analysis sessions and automatic workflows with colleagues. Chipster supports the analysis of over 120 different microarray platforms, including the most common types by Affymetrix, Agilent and Illumina. In addition, Chipster has extensive functions and tools for the analysis of NGS data. For additional and deeper guidance on how to use Chipster, beyond this tutorial, see the website with manuals and tutorials or contact the Chipster team. The website also includes guidance on how to analyze next-generation sequencing (NGS) data in Chipster.
title: Understanding the genomic relationship between nuclear DNA replication and genome plasticity in kinetoplastid genomes
Creators: name: Campbell, Samantha Jane
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: kinetoplastid, Leishmania, Trypanosoma, DNA replication, plasticity, genomics.

description: DNA replication is an essential process in all eukaryotes initiated from sites termed origins of replication. Recent studies in the kinetoplastid species Leishmania and Trypanosoma brucei have revealed striking differences in the process of DNA replication between the largely syntenic genomes. T. brucei replication origins are generally consistent with previous eukaryotic models while Leishmania chromosomes appears to contain a single major origin, as is observed in bacteria, although how the parasites can complete replication in this manner remains unknown. Sites of DNA replication co-localise to strand switch regions where transcription initiation and termination also occur. However, not every strand switch region contains an origin of replication and differences between those containing an origin and those without have not been identified. The use of a variety of computational approaches, including machine learning, allow the investigation of origins of replication in both Leishmania and Trypanosoma brucei at the DNA sequence level and within the structure of the surrounding genomic context and further characterization of the different classes of strand switch region. A significant feature of the Leishmania genome is its ability to adapt in response to environmental pressures through copy number variation of genes and chromosomes and the formation of episomes, allowing the parasites to evade the host immune system and rapidly develop drug resistance through modulation of gene expression. Analysis of the sequence and structure of the Leishmania mexicana genome in serial passage conditions provides insight into the mechanisms underlying genome plasticity and presents a novel hypothesis explaining the potential relationship with DNA replication.
Fringe Benefit Costs in Food Industries
Creators: name: Chumley, Toledo
name: Chumley, Toledo
Publisher: name: Unknown
Year: 1963
Subjects: Agribusiness
Labor and Human Capital
Production Economics

description: Excerpt from the report: During World War II when direct wage increases were not allowed, the War Labor Relations Board permitted companies to augment wages by indirect means, which it termed "fringe benefits." Because of the tight labor market, employers quickly took this cue and devised ingenious methods to attract workers. Premium pay for overtime was no longer sufficient to draw workers. Today, fringe benefits are so substantial that "fringe" seems a misnomer. Internal Revenue Service data show that the aggregate costs of pension plans and other fringe benefits reported by corporations manufacturing, wholesaling, and retailing food products was $474.7 million in 1960, about 114 percent more than in 1954. During the period the total bill for marketing farm-originated food products in the United States increased a third. Fringe benefits seem destined to become an increasingly important part of the food marketing bill.
description: Reprinted from the Marketing and Transportation Situation, August 1963
How to Use Chipster for Bioinformatics Analysis of Nanomaterial-Based Omics Data
Creators: name: Nymark, Penny
name: Ehrhart, Friederike
name: Willighagen, Egon
Publisher: name: figshare
Year: 2017
Subjects: subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 100708 Nanomaterials
subject: FOS: Nanotechnology
subject: 60408 Genomics
subject: FOS: Biological sciences

description: This tutorial will get you started on the basic use of the bioinformatics tool Chipster, an alternative to ArrayAnalysis.org described in other eNM tutorials. It will guide you through the import of microarray data (Affymetrix .CEL files), quality checks, normalization, pre-processing, basic statistical analyses methods and visualization of your data. Chipster is not specific to the nanosafety field, but this tutorial will be focused on the specific needs of nanotoxicological research. Chipster is an open source user-friendly analysis software for high-throughput data analysis. It offers over 350 bioinformatics tools and it is constantly updated according to the latest state-of-the-art tools and scripts. Users can analyse and visualize data interactively, and share complete analysis sessions and automatic workflows with colleagues. Chipster supports the analysis of over 120 different microarray platforms, including the most common types by Affymetrix, Agilent and Illumina. In addition, Chipster has extensive functions and tools for the analysis of NGS data. For additional and deeper guidance on how to use Chipster, beyond this tutorial, see the website with manuals and tutorials or contact the Chipster team. The website also includes guidance on how to analyze next-generation sequencing (NGS) data in Chipster.
title: Perception and reality: an exploration of domestic abuse victims' experiences of the criminal justice process in Scotland
Creators: name: Forbes, Emma Elizabeth
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: Domestic abuse, gender-based violence, criminal justice response, law, feminist methodology.

description: This thesis is a feminist critique of Scotland’s investigation and prosecution of domestic abuse through the lens of tackling domestic abuse as a gendered offence. It tells two stories: Scotland’s policy and legislative response to this issue and the experience of female victims who report domestic abuse to the police. The apparent sweep of progress on the public stage is juxtaposed with the private struggle of individuals who continue to face barriers to justice. Drawing on in-depth interviews with women who have experienced domestic abuse and those who support them, the data identifies a number of enduring challenges. The data from these interviews is contextualised within a 40-year perspective of Scotland’s policy, legal, social and academic responses to victims of gender violence in general, and domestic abuse in particular. The web of public and private priorities is examined in a temporal analysis which highlights multiple misalignments, a complex hierarchy of timescales and identifies obstacles to effective justice. Recognising the consequences of these tensions and the traumatic impact on victims highlights the ways in which aspects of the justice response could be reconfigured to provide them with greater agency. This thesis argues that legislative change has limited potential until structural inequalities are addressed, the full implications of the public and private dimensions of domestic abuse are understood, and appropriate procedural justice is consistently delivered.
title: Development of a divergent synthetic strategy for the asbestinins
Creators: name: Campbell, Angus
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: Total synthesis, asbestinins, natural products.

description: Asbestinins are the most complex of the ether bridged 2,11-cyclised cembranoids, isolated from the gorgonian octocoral species Briareum asbestinum. They have a complex rigid tetracyclic framework with nine or more contiguous stereocentres and a highly substituted tetrahydrofuran, for example in 11-acetoxy-4-deoxyasbestinin D and asbestinin 12. The asbestinins have been shown to possess significant biological activities including antimicrobial and anticancer properties. The significant synthetic challenge presented by the asbestinins structures combined with their biological activity make them an interesting target for total synthesis. There have been numerous syntheses of the structurally related cladiellin family but only two previous syntheses of the asbestinins which were reported by Crimmins in 2005 and 2008. Previous work in the Clark group had established methodology for the synthesis of multiple members of the cladiellin family (>10 members synthesised) from a common tricyclic intermediate which could be utilised in the synthesis of the asbestinins. This involved a few key transformations including a tandem oxonium ylide formation, [2,3]-sigmatropic rearrangement to construct the bicyclic core followed by a Stille/Diels–Alder sequence to give a common tricyclic intermediate. In this thesis, the first total syntheses of five members of the 4-deoxyasbestinin family are reported as well as the second total synthesis of 11 acetoxy 4 deoxyasbestinin D. The syntheses were completed utilising the common tricyclic intermediate previously reported during the synthesis of multiple members of the cladiellin family. The reported total syntheses have allowed for confirmation or re-evaluation of the reported revised structures of members of the asbestinin family.
title: Characterisation of terrestrial weathering products in ordinary and CM carbonaceous chondrites
Creators: name: Floyd, Cameron James
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: Chondrites, ordinary chondrites, carbonaceous chondrites, CM Chondrites, terrestrial weathering, Raman spectroscopy, planetary science, mineralogy, meteoritics.

description: Research investigating the terrestrial weathering experienced by ordinary and CM chondrites at high spatial resolution is sparse, with most published work using either bulk mineralogical or chemical analysis techniques. With asteroid sample return missions, Hayabusa 2 and OSIRIS-REx expected to return samples in near future, understanding the effects of terrestrial contamination and weathering in fine detail is of paramount importance. The research presented here sets out to investigate terrestrial weathering by analysing the alteration products found around Fe,Ni metal grains by coupled chemical and mineralogical analysis for the first time. Analysis is conducted using a suite of high spatial resolution imaging and spectroscopic techniques including EDS spectroscopy and Raman spectroscopy, an approach with very limited previous use in this field. Initially characterisation of the effects of terrestrial weathering on ordinary chondrites, which should have only experienced significant aqueous alteration in the terrestrial environment, is conducted. The effects of weathering in three climates (the Antarctic, Sahara and Western Australia) are investigated to compare the intensity of alteration between typical find environments. The results of ordinary chondrite analysis reveal Cl-bearing akaganeite is the first terrestrial alteration product to form, followed by goethite and a poorly crystallised hydrated iron III oxide or oxyhydroxide. Analysis also reveals that terrestrial weathering was least intense in cold desert environments (Antarctica) and most intense in semi-arid environments (Western Australia). Having characterised the terrestrial weathering products which form around Fe,Ni metal the effects of terrestrial weathering on CM chondrites, which have experienced significant aqueous alteration both terrestrially and on their parent bodies, is investigated. Analysis of the weathering products in CM chondrites revealed the terrestrial alteration products akaganeite and goethite eroding/replacing parent body alteration products tochilinite and magnetite. The work presented here highlights the need for high resolution, chemical and mineralogical analysis of the alteration products found in ordinary and CM chondrites in order to prevent misinterpretation of terrestrially derived alteration products as evidence of parent body alteration.
Additional file 1 of Exosomal long noncoding RNA HOTTIP as potential novel diagnostic and prognostic biomarker test for gastric cancer
Creators: name: Zhao, Rui
name: Zhang, Yanli
name: Zhang, Xin
name: Yang, Yongmei
name: Zheng, Xin
name: Li, Xiaohui
name: Liu, Yingjie
name: Zhang, Yi
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Figure S1. Levels of exosomal HOTTIP expressed in cell culture medium. (PDF 561 kb)
Additional file 1: of The first-in-class alkylating deacetylase inhibitor molecule tinostamustine shows antitumor effects and is synergistic with radiotherapy in preclinical models of glioblastoma
Creators: name: Festuccia, Claudio
name: Mancini, Andrea
name: Colapietro, Alessandro
name: Gravina, Giovanni
name: Vitale, Flora
name: Marampon, Francesco
name: Monache, Simona Delle
name: Pompili, Simona
name: Cristiano, Loredana
name: Vetuschi, Antonella
name: Tombolini, Vincenzo
name: Chen, Yi
name: Mehrling, Thomas
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: Figure S1. Radiosensitizing effects of TINO on tumor weight and time to progression in U87MG xenograft model. (A) Analysis of tumor weights harvested at the end of experiment (50th day from randomization) in U251MG xenografts; (B) Kaplan-Meier curves generated for time to progression in U251: comparisons amongst RT, TMZ and TINO single therapies; (C) Kaplan-Meier curves generated for time to progression: analysis of radio-sensitizing effects of TINO for U251G xenografts in comparison with TMZ and RTâ +â TMZ; (D) Forest plots (U87MG) for the comparison of TTP distribution in different treatments with untreated animals (vehicle); (E) Forest plots (U87MG) for comparison of TTP in the different combination regimens. (PDF 126 kb)
title: Investigating the mechanisms and modifiers of disease resulting from mutations in COL4A1 and COL4A2
Creators: name: Fleming, Lauren Kaye
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: Basement membrane, COL4A1, COL4A2, extracellular matrix, genetic disease.

description: Haemorrhagic stroke accounts for 15% of adult stroke. Mutations within COL4A1 and COL4A2 (collagen IV alpha chain 1/2) cause familial forms of cerebrovascular disease, including intracerebral haemorrhage (ICH). Collagen IV is a major component of the basement membrane and provides structural support within blood vessel walls. Cerebrovascular disease caused by mutations inCOL4A1/COL4A2 exhibit reduced penetrance, indicating that genetic modifiers can prevent disease development, and their identification will highlight putative therapeutic targets. We aimed to shed light on the underlying molecular mechanism of COL4A1/COL4A2 disease and the identity of genetic modifiers by performing proteomics analysis (LC/MS) on cells from both an ICH patient and his unaffected father who both carry the same pathogenic COL4A2+/G702D mutation. Candidate modifier pathways were then verified using functional analyses. Pharmacological mimicking of one particular candidate modifier pathway in patient dermal fibroblasts revealed that the molecular phenotype associated with disease severity, namely COL4A2 accumulation within the ER, could be reduced. Lastly, there is a growing pool of patients presenting with disease phenotypes resultant from atypical mutations in COL4A1/COL4A2, however, molecular analysis of these individuals has thus far been largely unreported. Through collaborations, we gained access to fibroblast samples from patients with various COL4A1/COL4A2 mutations who exhibit cerebral small vessel disease, including a different glycine mutation, 3’UTR mutations in COL4A1 and a 13q33.2q34 duplication. Investigation of their pathomolecular mechanisms and efficacy of our candidate modifier on those mutations in which a downstream intracellular phenotype occurs, was performed. In summary, BM fragility owed to mutations in COL4A1 and COL4A2 is likely mediated by multiple independent molecular influences. Further studies unpicking the relative contributions of these processes may shed light on the pleiotropic effects of COL4A1/COL4A2 mutations in human disease, which will enable the identification of therapeutic agent that specifically targets one pathway, without indirectly aggravating other pathways, to achieve the greatest therapeutic potential.
Additional file 2 of Exosomal long noncoding RNA HOTTIP as potential novel diagnostic and prognostic biomarker test for gastric cancer
Creators: name: Zhao, Rui
name: Zhang, Yanli
name: Zhang, Xin
name: Yang, Yongmei
name: Zheng, Xin
name: Li, Xiaohui
name: Liu, Yingjie
name: Zhang, Yi
Publisher: name: figshare
Year: 2018
Subjects: Biochemistry
Cell Biology
Molecular Biology
Biological Sciences not elsewhere classified
Mathematical Sciences not elsewhere classified
Developmental Biology
Cancer

description: Figure S2. The expression levels of exosomal HOTTIP were upregulated in gastric cancers serum. (PDF 732 kb)
Contract Production of Truck Crops, 12 Selected Areas, United States
Creators: name: Mighell, Ronald L.
name: Jones, Lawrence A.
name: Gavett, Earle E.
name: Mighell, Ronald L.
name: Jones, Lawrence A.
name: Gavett, Earle E.
Publisher: name: Unknown
Year: 1964
Subjects: subject: Agricultural Finance
subject: Crop Production/Industries
subject: Farm Management
subject: Labor and Human Capital
subject: Marketing
subject: FOS: Economics and business
subject: Production Economics

description: Excerpts from the Introduction: Information on truck crop production reported in this study was obtained from nearly 2,500 vegetable growers in 12 selected areas by personal interview. This report is primarily concerned with the extent and nature of contracting and vertical integration in the production of truck crops. It is part of a larger study of the same sample of farms made in 1959 for the crop year 1958-59. The other parts of the overall study were concerned with an analysis of labor and material inputs used in the production of truck crops. As defined here, contracting and integration have the following meanings. Contracting refers to arrangements between independent firms for providing goods or services. Vertical integration means the joining in one firm of two or more stages of production. More specifically, contracting is between vegetable growers and processors or dealers; vertical integration occurs when a processor or dealer is also a grower.
Additional file 3 of Exosomal long noncoding RNA HOTTIP as potential novel diagnostic and prognostic biomarker test for gastric cancer
Creators: name: Zhao, Rui
name: Zhang, Yanli
name: Zhang, Xin
name: Yang, Yongmei
name: Zheng, Xin
name: Li, Xiaohui
name: Liu, Yingjie
name: Zhang, Yi
Publisher: name: figshare
Year: 2018
Subjects: Cell Biology
Molecular Biology
Biotechnology
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Mathematical Sciences not elsewhere classified
Developmental Biology
Cancer

description: Figure S3. Stability of exosomal HOTTIP levels. Exosomal HOTTIP levels remained stable when treated with a prolonged exposure to room temperature, b and multiple freeze-thaw cycles. (PDF 1778 kb)
Additional file 2: of The first-in-class alkylating deacetylase inhibitor molecule tinostamustine shows antitumor effects and is synergistic with radiotherapy in preclinical models of glioblastoma
Creators: name: Festuccia, Claudio
name: Mancini, Andrea
name: Colapietro, Alessandro
name: Gravina, Giovanni
name: Vitale, Flora
name: Marampon, Francesco
name: Monache, Simona Delle
name: Pompili, Simona
name: Cristiano, Loredana
name: Vetuschi, Antonella
name: Tombolini, Vincenzo
name: Chen, Yi
name: Mehrling, Thomas
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Table S1. Additional hazard ratio analyses in xenograt models. Table S2 Additional hazard ratio analyses in orthotopic U251models. Table S3 Additional hazard ratio analyses in orthotopic CSCs-5model. (DOCX 23 kb)
Alterations in amygdala–prefrontal circuits in infants exposed to prenatal maternal depression
Creators: name: J Posner
name: Jiook Cha
name: AK Roy
name: BS Peterson
name: R Bansal
name: HC Gustafsson
name: E Raffanello
name: J Gringrich
name: C Monk
Publisher: name: figshare
Year: 2017
Subjects: Neuroscience

description: Prenatal exposure to maternal depression is common and puts offspring at risk for developing a range of neuropsychiatric disorders. Despite its prevalence and adverse associations, neurobiological processes by which prenatal maternal depression (PMD) confers risk remain poorly understood. Maternal mood and fetal behavior were assessed between 34 and 37 gestational weeks. Using resting-state functional magnetic resonance imaging (fMRI) and diffusion MRI, we examined functional and structural connectivity within amygdala–prefrontal circuits in 64 infants (mean age = 5.8 ± 1.7 weeks) with (n = 20) and without (n = 44) in utero exposure to PMD. Resting fMRI and diffusion MRI both indicated atypical amygdala–prefrontal connectivity in PMD-exposed infants: Resting fMRI indicated increased inverse, or negative, functional connectivity between the amygdala and the dorsal prefrontal cortex (PFC), bilaterally, and diffusion MRI indicated decreased structural connectivity between the right amygdala and the right ventral PFC. Spectral dynamic causal modeling supported these findings suggesting altered amygdala–PFC effective (or directed) connectivity in PMD-exposed infants. Last, path analyses supported a mechanistic account relating PMD to a third-trimester fetal behavior: PMD alters amygdala–PFC connectivity, which in turn, is associated with an increase in fetal heart rate reactivity to in utero perturbation. These data suggest that the maturation and coordination of central and peripheral physiology are altered by prenatal exposure to maternal depression. To the best of our knowledge, this is the first study to directly associate infant MRI measures with a behavior—fetal heart rate response, and supports hypotheses that PMD-associated variations in the development of amygdala– PFC circuits are relevant for future neurobehavioral maturation.
Additional file 4 of Exosomal long noncoding RNA HOTTIP as potential novel diagnostic and prognostic biomarker test for gastric cancer
Creators: name: Zhao, Rui
name: Zhang, Yanli
name: Zhang, Xin
name: Yang, Yongmei
name: Zheng, Xin
name: Li, Xiaohui
name: Liu, Yingjie
name: Zhang, Yi
Publisher: name: figshare
Year: 2018
Subjects: Space Science
Cell Biology
Pharmacology
Biological Sciences not elsewhere classified
Mathematical Sciences not elsewhere classified
Cancer
Virology

description: Table S1. The sensitivity of biomarkers when the specificity was 95%. (PDF 7 kb)
title: Improved dendritic cell therapy for cancer by enhancing in vivo lymph node migration using a novel chemokine-based sorting method
Creators: name: Burgoyne, Paul
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: dendritic cell, chemokine, CCR7, immunotherapy, cancer therapy.

description: Dendritic cells (DCs) are potent antigen presenting cells and are crucially involved in the induction of the adaptive immune response. Multiple DC subsets exist in the body at rest and during inflammation with unique tissue origins and development. The main function of DCs is the uptake of antigen from the peripheral tissue by endocytosis, and the transfer of this antigen to T cells within the lymph nodes (LNs) to generate an immune response against the antigen. Given the potency of the potential T cell response, DCs are an attractive cell type for therapeutic use in contexts such as cancer. Over 20 years of clinical trials have developed DCs for this purpose: although significant progress has been made, DC clinical trials still show subclinical and variable T cell responses in patients. Numerous strategies have been tested to improve this, including use of specific DC subsets, ex vivo activation and maturation of the cells using cytokines, different antigen loading strategies and different routes of injection. These, however, do not sufficiently take into consideration the migration capability of these injected cells, which severely limits the potential cell function. CCR7 is the chemokine receptor crucially involved in DC homing to LNs and is a marker of DC maturity, but it has been shown that ex vivo-generated cells do not consistently express this receptor. Using a novel sorting methodology to isolate DCs expressing CCR7, it is possible to improve the maturity and function of the injected cells, as well as in vivo migration. CCR7 expressing cells are more capable of generating mature T cell responses in vitro due to the expression of co-stimulatory molecules such as CD80 and CD86 and the production of T cell-attracting chemokines. The B16F10 mouse melanoma was used to assess the potential improvement in therapeutic DC use following CCR7-sorting. In the subcutaneous model after a single injection, or multiple prophylactic injections, of CCR7- sorted DCs there was significant control of the tumour growth and this resulted in a longer survival duration. This was attributed to the increased T cell response induced by DCs reaching the LN, as more antigen-specific T cells were present in the CCR7-expressing DC-receiving animals and that the T cell phenotype was more mature by surface marker expression. In the metastatic model, however, there was no difference in the overall tumour burden between groups despite having a significantly improved antigen-specific T cell response following injection of the CCR7-sorted DCs. Finally, it was shown that this CCR7-sorting methodology is directly translatable to clinical use using the clinical grade MACSQuant Tyto cell sorter, and that CCR7-sorted human monocyte-derived DCs were also more potent activators of T cells in vitro.
MOESM1 of The structural and functional contributions of Î˛-glucosidase-producing microbial communities to cellulose degradation in composting
Creators: name: Zang, Xiangyun
name: Liu, Meiting
name: Fan, Yihong
name: Xu, Jie
name: Xu, Xiuhong
name: Li, Hongtao
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Computational Biology

description: Additional file 1: Figure S1. Differences in the abundance and expression of GH1B and GH3E genes in the natural compost and the inoculated compost.
Effects of Intermittent Fasting on Cerebral Hypoperfusion-Induced Inflammatory and Neurodegenerative Gene Expression
Creators: name: Jasim, Dalal
Publisher: name: La Trobe
Year: 2024

description: Submitted in total fulfilment of the requirements for the degree of Master of Science to the School of Agriculture, Biomedicine and Environment, La Trobe University, Victoria, Australia.
Additional file 5 of Exosomal long noncoding RNA HOTTIP as potential novel diagnostic and prognostic biomarker test for gastric cancer
Creators: name: Zhao, Rui
name: Zhang, Yanli
name: Zhang, Xin
name: Yang, Yongmei
name: Zheng, Xin
name: Li, Xiaohui
name: Liu, Yingjie
name: Zhang, Yi
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology

description: Table S2. Univariate and multivariate analysis of clinicopathological parameters influencing prognosis. (PDF 90 kb)
title: Crosstalk between EZH2 and BCL6 in regulating chronic myeloid leukaemia (CML) stem cell survival: from epigenomics to novel therapeutic approaches
Creators: name: Bugler, Jane
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: chronic myeloid leukaemia, CML, leukaemia stem cells, epigenetics.

description: Chronic Myeloid Leukaemia (CML) is a haematopoietic stem cell disorder characterised by the presence of the BCR-ABL1 fusion gene, which produces a constitutively active tyrosine kinase responsible for disease progression. Despite the introduction of tyrosine kinase inhibitors (TKIs) to target this overactive tyrosine kinase, the low cure rate and risk of disease recurrence and progression remains a major clinical issue. This is thought to occur due to a pool of TKIpersistent leukaemia stem cells (LSCs). Thus, understanding how LSCs evade TKI therapy and maintain their survival is important to identify novel drug targets and eradicate residual disease. Evidence suggests that the epigenetic regulator EZH2, is required for LSC survival. A combination of EZH2 inhibitors and TKIs targeted LSCs in vitro and in vivo, and resulted in the re-activation of several targets involved in cell cycle and apoptosis, including those normally regulated by the transcription factor BCL6. BCL6 is a survival factor in CML cells upregulated following TKI treatment, driving an anti-apoptotic phenotype. The hypothesis of this project was that BCL6 and EZH2 work through similar survival pathways that underpin an important network in CML which is therapeutically targetable. Genetic knockdowns of BCL6 and EZH2 in CML cell lines ± TKI significantly decreased cell expansion and increased apoptosis, and dual targeting of BCL6 and EZH2 resulted in additional effects on cell expansion. CML and non-CML CD34+ primary cells were treated with varying concentrations of a BCL6 inhibitor ± TKI or EZH2i, significantly decreasing colony forming cell (CFC) and long-term cultureinitiating cell (LTC-IC) outputs, suggesting targeting of more primitive CML cells. To further examine this relationship, chromatin immunoprecipitation (ChIP) was performed in CML cell lines and CD34+ cells. Whilst BCL6 and EZH2 targets were predominantly mutually exclusive, sets of their targets were enriched in many of the same downstream pathways. Moreover, a coordinated pattern of occupancy was observed when BCL6 and EZH2 shared targets. RNA-sequencing revealed strong enrichment for c-MYC and differentiation gene signatures following targeting of BCL6 and EZH2. Integrating these pathways with ChIP-seq data generated a network map highlighting the importance of c-MYC in the BCL6 and EZH2 network, as well as identifying putative targets mediating LSC survival that require further investigation as potential novel therapies in CML.
Enhancing the Machine Learning Pipeline for a Sustainable Future
Creators: name: Islam, Ashhadul
Publisher: name: Manara - Qatar Research Repository
Year: 2024
Subjects: classificationCode: 40
subject: Engineering

description: The energy appetite of AI is a growing environmental concern. Training large machine learning models requires a lot of computational resources, which in turn needs significant energy. This leads to the emission of greenhouse gases that contribute to climate change. Furthermore, the amount of water used to cool GPU clusters is also under scrutiny in addition to carbon emissions. Although the amount of data in the world is finite, AI models can be as large as the memory capacity and computational power used to train them. As these models become larger, there is an associated increase in the costs of computation, carbon emissions, and water consumption. Consequently, there is a need to develop more energy-efficient machine learning algorithms and computational infrastructure in order to minimize the impact on environment. In this thesis, the focus is on pruning neural networks to produce faster and more compact models that are many times smaller in size but still retain the same level of discrimination capability. This approach also improves the model’s resistance to adversarial attacks and reduces data requirements during transfer learning. The methods presented were tested against existing compression techniques using standard models and datasets, which resulted in impressive compression rates and accuracy performance. The thesis also addresses the problem of imbalance in datasets by broaching a novel data oversampling algorithm that is capable of creating new data points to enhance the decision capability of the discriminators. The approach is extended to regression data as well as image data. We compare the efficacy of our algorithm with the state-of-art data oversamplers on benchmark datasets to show the superiority of our algorithm. This method also gives better results in comparison to Generative Adversarial Networks in some cases. The pruning algorithm is made open source at https://github.com/ashhadulislam/SmartPruningDeepNN while the oversampling technique is published as a python library at https://pypi.org/project/knnor/.
AfterSSHOC: synergies along the journey to EOSC and a view into the future
Creators: name: Versic, Ivana Ilijasic
name: De Jong, Franciska
name: Lamanna, Giovanni
name: Gunsenheimer, Ute
name: Dekker, Ron
name: Morales, Laura
Publisher: name: Zenodo
Year: 2022
Subjects: SSHOC
Social Sciences and Humanities Open Cloud
European Open Science Cloud
EOSC
ESCAPE
EOSC Future

description: Moderator: Ivana Ilijasic Versic (CESSDA, SSHOC) Reporting back on Policy Discussions. Collaboration opportunities after SSHOC and Agreements - Franciska de Jong (CLARIN) ESFRI Cluster projects - Giovanni Lamanna (ESCAPE) EOSC Association - Ute Gunsenheimer (EOSC Association) EOSC Future - Ron Dekker (Technopolis Group, EOSC Future) Data Communities - Laura Morales (SciencesPo, SSHOC, Member of EOSC Researcher Engagement & Adoption Task Force, EOSC Future User Group) Panel discussion with: Franciska de Jong (CLARIN), Giovanni Lamanna (ESCAPE), Rudolf Dimper (PANOSC), Ute Gunsenheimer (EOSC Association), Ron Dekker (Technopolis Group, EOSC Future) and (Laura Morales, SciencesPo, SSHOC, Member of EOSC Researcher Engagement & Adoption Task Force, EOSC Future User Group)
MOESM2 of The structural and functional contributions of Î˛-glucosidase-producing microbial communities to cellulose degradation in composting
Creators: name: Zang, Xiangyun
name: Liu, Meiting
name: Fan, Yihong
name: Xu, Jie
name: Xu, Xiuhong
name: Li, Hongtao
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 2: Figure S2. Differences in the abundance and expression of family 1 Î˛-glucosidase genes from bacteria (GH1) in the natural compost and the inoculated compost.
Additional file 1: of Xiangbin prescription for the recovery of gastrointestinal function after abdominal surgery (the XBPRS trial): study protocol for a randomized controlled trial
Creators: name: Gan, Huachan
name: Lin, Jinxuan
name: Jiang, Zhi
name: Chen, Qicheng
name: Cao, Lixing
name: Chen, Zhiqiang
Publisher: name: figshare
Year: 2018
Subjects: subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy
subject: Mental Health

description: Statistical Analysis Plan. (DOCX 130 kb)
MOESM3 of The structural and functional contributions of Î˛-glucosidase-producing microbial communities to cellulose degradation in composting
Creators: name: Zang, Xiangyun
name: Liu, Meiting
name: Fan, Yihong
name: Xu, Jie
name: Xu, Xiuhong
name: Li, Hongtao
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 3: Figure S3. Differences in the abundance and expression of family 3 Î˛-glucosidase genes from fungi (GH3) in the natural compost and the inoculated compost.
Additional file 2: of Xiangbin prescription for the recovery of gastrointestinal function after abdominal surgery (the XBPRS trial): study protocol for a randomized controlled trial
Creators: name: Gan, Huachan
name: Lin, Jinxuan
name: Jiang, Zhi
name: Chen, Qicheng
name: Cao, Lixing
name: Chen, Zhiqiang
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy
subject: Mental Health

description: SPIRIT Checklist for the XBPRS trial protocol. (DOC 150 kb)
title: 01_0841
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/