cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4225/03/58b8dcf8ee9dc
title: MicroRNA-21 in diabetic nephropathy and a cross-sectional analysis of the role of TGFβ in proximal tubule epithelial cells and mesangial cells

description: Diabetic nephropathy (DN) is the leading cause of renal failure in much of the world. It is a complex disease resulting in pathological changes in various cell types and ultimately culminating in end-stage renal disease. Specifically, mesangial cells (MC) undergo hyperplasia and hypertrophy leading to destruction of the glomerular ultrastructure while also contributing to podocytes loss. Proximal tubule epithelial cells (PTC) undergo similar processes leading to tubulointerstitial fibrosis and also interstitial inflammation. Although these changes are initially propagated by chronic hyperglycaemia, the changes in cellular physiology are elicited via activation and modulation of a wide range of pathways and their products. A central and potent mediator cellular pathophysiology in diabetic nephropathy is TGFβ which is itself upregulated by hyperglycaemia.
   TGFβ influences many cellular processes and signalling networks. It has becoming increasingly clear that TGFβ mediates its effects in the diabetic kidney through dysregulation of microRNA particularly in MC and PTC, although the extent of these relationships has not been investigated. Despite this, there is still a lack of system biology approaches available for the study of microRNA. Also gaining attention in recent years is the role of mitochondrial dysfunction in the propagation of DN. Although links have been made between TGFβ and mitochondrial function or microRNA expression and mitochondrial function, little has been reported on the influence of TGFβ-mediated microRNA dysregulation on mitochondria.
   To this end, this thesis has demonstrates and explores the wide reaching effects of TGFβ upon both PTC and MC. The genome wide effect of TGFβ-mediated miRNA dysregulation of the cell wide signalling landscape is also explored. miR-21 is highly dysregulated in PTC and its role in TGFβ-mediated fibrotic signalling is clarified. This effect is clearly defined in regard to the relative contribution of SMAD7 and PTEN. The significance of miR-21 in human DN is also demonstrated. Finally, the role of miR-21 in mitochondrial dysfunction in PTC is proposed to occur at least in part through ACAT1 and AK2. This work adds valuable knowledge to the growing recognition of the importance of microRNA in DN. Furthermore, the development of in silico pipelines may aid those who endeavour to undertake similar projects with the data garnered from such experiments providing an important reference for future investigations. The findings from this thesis are likely to aid in the development of future therapies focusing on retarding the development and progression of DN, not least of all in the rectification of mitochondrial dysfunction and preventing the relentless cycle of fibrotic tissue damage that ultimately results in renal failure. Additional material(s) submitted with thesis.
DOI: 10.4225/03/58b8dd088631d
title: Assembly of multimeric outer membrane proteins in Escherichia coli

description: Gram-negative bacterial outer membranes incorporate proteins of at least three well characterized architectures: β-barrel proteins, lipoproteins and multimeric secretion pores. Assembly of β-barrel proteins into the outer membrane is mediated by the β-barrel assembly machinery (BAM), consisting of an essential core β-barrel BamA and four accessory lipoproteins (BamBCDE). Lipoproteins are targeted and subsequently anchored to the outer membrane by covalently attached lipid modifications by the localization of lipoproteins (Lol) machinery. Secretins are amongst the most characterized multimeric outer membrane proteins, and often rely on a small lipoprotein, termed pilotin, to catalyze the efficient translocation of secretin monomers to the outer membrane for assembly into a functional secretion pore. Through the use of cryo-EM and X-ray crystallography it has become clear that oligomeric outer membrane proteins can adopt either α-helical or β-stranded transmembrane conformations, yet their mechanism of assembly remains unclear.

Chapter two describes the identification and characterisation of a novel pilotin AspS for the secretin GspD from the type 2 secretion system of enteropathogenic Escherichia coli. Sucrose density fractionation and novel time course assays show that AspS is required for the targeting of GspD to the outer membrane and for the efficient assembly of GspD multimers. The structure of AspS was solved, demonstrating convergent evolution wherein AspS is functionally equivalent and yet structurally unrelated to pilotins from other secretion syetems.

Chapter three describes the optimization of a bamA depletion strain of E. coli to monitor outer membrane protein assembly. Assays were performed to analyse bacterial viability, morphology and functionality of the BAM after bamA depletion. Chapter four focusses on analysing the role of BamA in assembling secretion channels GspD, Wza and CsgG, using the depletion regime described in Chapter three. Assembly assays demonstrate that GspD, Wza and CsgG can assemble into the outer membrane in the absence of BamA. These assays also showed that periplasmic proteins CsgE and CsgF could enhance the assembly efficiency of both the mature CsgG multimer and a possible CsgG assembly intermediate.
DOI: 10.4225/03/58b8dd19ea9da
title: Challenging traditional notions of value:
how Australian companies are navigating sustainable hybrid value creation

description: Abstract
The purpose of this study is to understand how organizations that wish to create multiple forms of value, e.g. social, environmental and financial, are able to deliver potentially conflicting forms of value. Drawing upon institutional logics and value theories, I explore what is meant by value and frame the possible challenges and tensions that arise in the pursuit of different types of value that draw upon different rationalities and ideologies. This thesis addresses a gap in understanding how hybrid organizations manage multiple logics to create complex forms of value that reflect the disparate ideologies associated with sustainable development goals.

I undertake exploratory qualitative research with a multiple embedded case study design of six Australian hybrid organizations. I engage 49 participants in semi-structured interviews, focus groups and a survey and analyse these results using thematic analysis to identify patterns in the data that are then organized into categories and themes to explain how and why organizations pursue hybrid forms of value. I find that my case studies draw on six organizing concepts to interpret what is meant by hybrid value, which is underpinned by four value components (social, environmental, financial and internal value) and four institutional logics (market, community, social welfare, and intrinsic logic). I also find that the reasons that they define value as a hybrid construct is due to individual values coupled with perceived organizational ‘need,’ as the pursuit of ‘additional’ or bonus value, and/or due to legislative and normative pressures. Additionally, I uncover 200 examples of organizational practices that lead to hybrid value outcomes.

This thesis makes substantial contributions to the hybrid value, hybrid organization, value theories and institutional logics literatures. Specifically I build upon the extant literature by providing examples and evidence of extant hybrid value concepts, examples of how organizations are overcoming the issues raised by value plurality, evidence of why organizations pursue hybrid value, and examples of how organizations manage the tensions that arise due to plural logics. Finally, I make new contributions to the literature by developing a taxonomy and typology of hybrid value, uncovering five new hybrid value concepts and a new type of institutional logic and develop a conceptual model of how institutional logics inform the meaning of hybrid value. My conceptual model holds practical implications demonstrating how organizations can map their value ‘footprints’ and develop practice-to-outcome models.
DOI: 10.14457/cmu.res.2004.370
title: คุณภาพการนอนหลับและปัจจัยที่รบกวนการนอนหลับของผู้ป่วยในระยะ 72 ชั่วโมงแรก หลังทำผ่าตัดใหญ่ /
DOI: 10.14457/cmu.res.2004.371
title: คุณภาพการนอนหลับและปัจจัยรบกวนการนอนหลับของผู้ป่วย ในหอผู้ป่วยหนักอายุรกรรม โรงพยาบาลลำปาง /
DOI: 10.14457/cmu.the.2007.584
title: คุณค่าทางโภชนะและการใช้ประโยชน์ได้ ของหญ้าเนเปียร์หมักสำหรับโค /
DOI: 10.14457/cmu.the.2008.784
title: คุณค่าทางโภชนะ และการใช้ประโยชน์ของต้นข้าวโพดฝักอ่อน เป็นแหล่งอาหารหยาบสำหรับโคนม /
DOI: 10.14457/cmu.the.2009.635
title: คำสี่พยางค์ในภาษาไทลื้อ /
DOI: 10.4225/03/58b8ddaf9db1d
title: What is a poem worth? an investigation of poetry participation in Australia

description: In Melbourne, poems are everywhere. They are in lounge rooms, hotels, festivals, toilets, wedding ceremonies and funerals. Poems are pasted in alleyways, spray-painted on walls, emailed and facebooked and blogged. In this research project, by applying Bourdieu’s concept of a symbolic good, I track the exchange of symbolic and commodity values in the cultural field of poetry participation in Melbourne. I focus on two public domains of reception. The first domain is where poems are presented in hard-copy journals and books, and the second is where poems are seen and heard in public performance. I do not assume that a poet who presents their poems in performance made a decision during the composition process to present their poem in performance only. I define the dominant categories of page poetry and performance poetry as presentations of poems and acts of participation in poetry as a literary genre. I argue that the nomenclature of literary categories, which are given orthodoxy in arts funding, journal submission, prize entry and book solicitation guidelines in the cultural field of Australian poetry, constitutes symbolic violence. In current means of evaluation, poems presented in performance are often excluded from the literary genre of poetry. The conditions of access to the evaluation of a poem perpetuate this exclusion, as I find in the research setting of Melbourne, 2013 to 2015. The thesis has two parts, a written component and a performance component. The written component outlines the investigation and findings of the research project. I locate the means, terms and categories of poetry evaluation within international, national and local public settings and present the analysis as a series of contextual landscapes. The exegesis explores the practice-led investigation which is the last and overarching landscape. The production and presentation of poems is another approach to the research questions, and another way to further investigate previous findings. Yet even here, the poem drives the inquiry. I suggest that, in order to more closely evaluate poetry, the poem remain the object of evaluation and, in this case, the research subject. Additional material(s) submitted with thesis.
DOI: 10.5281/zenodo.345321
title: Large Dppc Monolayer Simulations With Charmm36+Opc @ 298 K (Part 1/2)

description: DPPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. 

The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a POPC monolayer system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. Next, POPC was replaced by DPPC, and the systems were energy minimized. Systems with area smaller than 51 Å^2 were generated by compressing the DPPC monolayer system with PLUMED.

All trajectories, 100–200 ns long (until convergence of surface tension), are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .

Part 2 of this upload is available at https://doi.org/10.5281/zenodo.838635

Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855

[1] DOI: 10.1021/jp101759q<br>
[2] DOI: 10.1021/jz501780a<br>
[3] DOI: 10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.345364
title: New Leads For Fragment Based Design Of Re/Tc Radiopharmaceutical Agents: Raw Diffraction Images

description: Multiple coordination possibilities of <em>fac</em>-[Re(CO)<sub>3</sub>]<sup>+</sup> to a protein, were found bound to the  Asp, Glu, Arg and His amino acid residues as well as to the C-terminal carboxylate in the vicinity of Leu and Pro and are described in the publication titled " <em>New leads for fragment based design of Re/Tc radiopharmaceutical agents</em>" written by Brink & Helliwell, <em>IUCrJ</em>, 2017

The raw diffraction images for the DLS and Cu Kalpha data sets are made available at the Zenodo research data archive, as specified in the publication.
DOI: 10.6073/pasta/82435aa71ebfb5f0c82fcdeb529ee17e
title: El Yunque Chronosequence Tree Census data 2011-2015
DOI: 10.7487/2017.65.1.1037
title: Issie Kelly HAB sub set

description: new list of taxa
DOI: 10.14457/cmu.the.2008.783
title: ความแปรปรวนทางพันธุกรรมของยีนอาร์วายอาร์ 1 และความสัมพันธ์ของยีนอาร์วายอาร์ 1 ต่อคุณภาพเนื้อในสุกรลูกผสม /
DOI: 10.3886/e4356v1
title: High-intensity therapist-guided internet-based cognitive behavior therapy for alcohol use disorders – a pilot study.

description: Background: A large proportion of people
with alcohol
problems do
not seek psychological treatment, but access to such treatment could
potentially be increased by delivering it over the Internet. Cognitive behavior
therapy (CBT) is widely regarded as one of the psychological treatments for
alcohol problems for which evidence is most robust. This study piloted a new, therapist-guided
internet-based CBT program (entitled ePlus), directed towards people with
alcohol use disorders. 

Methods: Participants in the study
(n=13) were recruited through an alcohol self-help web site and were, after
initial internet screening, diagnostically assessed by telephone. Eligible participants
were offered access to the therapist-guided 12-week program. The main outcomes
were treatment
usage data and standard
drinks consumed the preceding week, measured with the self-rated Timeline Followback
(TLFB). Participant data were collected at screening, immediately
pre-treatment, post-treatment and three months post-treatment. 

Results: Most participants were active
throughout the treatment and found it highly acceptable. Significant reductions
in alcohol consumption with a large within-group effect size were found 
at the three-month follow-up. Secondary outcome measures of craving and self-efficacy,
as well as depression and quality of life, also showed significant improvements
with moderate to large within-group effect sizes. 

Conclusions: Therapist-guided internet-based
CBT may be a feasible and effective alternative for people with alcohol use
disorders. In view of the high acceptability and the large within-group effect
sizes found in this small pilot, a randomized controlled trial investigating treatment
efficacy is warranted. Trial registration: ClinicalTrials.gov (NCT02384278).









<br>
DOI: 10.5281/zenodo.311651
title: Single Molecule, Full-Length Transcript Sequencing Provides Insight Into The Extreme Metabolism Of Ruby-Throated Hummingbird Archilochus Colubris

description: Hummingbirds can support their high metabolic rates exclusively by oxidizing ingested sugars, which is unsurprising given their sugar-rich nectar diet and use of energetically expensive hovering flight. However, they cannot rely on dietary sugars as a fuel during fasting periods, such as during the night, at first light, or when undertaking long-distance migratory flights, and must instead rely exclusively on onboard lipids. This metabolic flexibility is remarkable both in that the birds can switch between exclusive use of each fuel type within minutes and in that de novo lipogenesis from dietary sugar precursors is the principle way in which fat stores are built, sometimes at exceptionally high rates, such as during the few days prior to a migratory flight. The hummingbird hepatopancreas is the principle location of de novo lipogenesis and likely plays a key role in fuel selection, fuel switching, and glucose homeostasis. Yet understanding how this tissue, and the whole organism, achieves and moderates high rates of energy turnover is hampered by a fundamental lack of information regarding how genes coding for relevant enzymes differ in their sequence, expression, and regulation in these unique animals. To address this knowledge gap, we generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding a total of 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, including classification of reads and clustering of isoforms (ICE) followed by error-correction (Arrow). We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. We also aligned our transcriptome against the Calypte anna genome where possible. Finally, we closely examined homology of critical lipid metabolic genes between our transcriptome data and avian and human genomes. We confirmed high levels of sequence divergence within hummingbird lipogenic enzymes, suggesting a high probability of adaptive divergent function in the lipogenic liver pathways. Our results have leveraged cutting-edge technology and a novel bioinformatics pipeline to provide a compelling first direct look at the transcriptome of this incredible organism.
description: This dataset contains high quality Arrow-polished Pacbio Iso-seq data (HQD), Cogent dataset for gene family prediction and redundancy reduction, and ANGEL predictions for coding sequence (.cds), protein sequence (.pep), and untranslated region (.utr) from both HQD and Cogent. Additionally, Cogent annotations predicted using BLAST best match are included.

Pacific Biosciences for reagents and SMRTcells as well as technical support. M. Schatz, E. Jarvis, J. Korlach, Y. Guo for discussion. HFSP grant #RGP0062/2016. Natural Sciences and Engineering Research Council of Canada Discovery Grant (#386466) to KCW.
DOI: 10.5281/zenodo.345338
title: Large Dppc Monolayer Simulations With Charmm36+Opc @ 310 K (Part 1/2)

description: DPPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. 

The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a POPC monolayer system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. Next, POPC was replaced by DPPC, and the systems were energy minimized. Systems with area smaller than 51 Å^2 were generated by compressing the DPPC monolayer system with PLUMED.

All trajectories, 100–200 ns long (until convergence of surface tension), are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .

Part 2 of this upload is available at https://doi.org/10.5281/zenodo.838641

Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855

[1] DOI: 10.1021/jp101759q<br>
[2] DOI: 10.1021/jz501780a<br>
[3] DOI: 10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.345791
title: Dataset Of Soil, Climatic And Stand Variables In Pinus Sylvestris And Pinus Halepensis Plantations In Spain

description: Soil, climatic and stand variables measured in 35 <em>Pinus sylvestris</em> and 32 <em>Pinus halepensis </em>plantations in Castilla y León region (Spain)
DOI: 10.5517/ccdc.csd.cc1nk97r
title: CCDC 1535964: Experimental Crystal Structure Determination

description: Related Article: James A. Miranda, Eric Martin, Marilyn M. Olmstead|2017|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1nk98s
title: CCDC 1535965: Experimental Crystal Structure Determination

description: Related Article: James A. Miranda, Eric Martin, Marilyn M. Olmstead|2017|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1nk99t
title: CCDC 1535966: Experimental Crystal Structure Determination

description: Related Article: James A. Miranda, Eric Martin, Marilyn M. Olmstead|2017|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.14457/cmu.the.2003.613
title: ความแปลกแยกทางการเมืองของชาวไทยมุสลิมในจังหวัดปัตตานี /
DOI: 10.14457/cmu.the.2004.581
title: ความแปรปรวนและสัดส่วนทางพันธุกรรมของการสะสมไขมันในข้าว /
DOI: 10.14457/cmu.the.2005.325
title: ความไม่เสมอภาคทางการศึกษาของไทย /
DOI: 10.14457/cmu.the.2006.553
title: ความแปรปรวนในปริมาณและการสะสมธาตุเหล็กของเมล็ดในข้าวพันธุ์ไทย /
DOI: 10.14457/cmu.res.2005.189
title: ความแปลกแยกในองค์การ : กรณีศึกษาพนักงานสำนักงานประปาเขต 9 เชียงใหม่ การประปาส่วนภูมิภาค /
DOI: 10.14457/cmu.res.2005.190
title: ความไม่สุขสบายของผู้ป่วยจากการได้รับการรักษาด้วยไฟฟ้า ที่โรงพยาบาลสวนปรุง /
DOI: 10.14457/cmu.res.2010.329
title: ความแปลกแยกทางการเมืองของชนชั้นกลางในจังหวัดเชียงใหม่ ภายหลังวิกฤตการเมืองเมษายน - พฤษภาคม [พ.ศ.2553] /
DOI: 10.14457/cmu.res.2010.330
title: ความไม่พึงพอใจของลูกค้าต่อการให้บริการของ ธนาคารกสิกรไทย จำกัด [มหาชน] สาขานิคมอุตสาหกรรมลำพูน /
DOI: 10.14457/cmu.the.1997.173
title: คำสอนเรื่องพรหมจรรย์ในพุทธศาสนา /
DOI: 10.14457/cmu.the.2010.703
title: คำยืมภาษาอัสสัมในภาษาไทอาหม /
DOI: 10.14457/cmu.res.2003.391
title: คอมพิวเตอร์ช่วยสอนกลศาสตร์ โดยแมโครมีเดียแฟลช MX /
DOI: 10.14457/cmu.res.2005.191
title: คอมพิวเตอร์เพื่อช่วยงานศัลยกรรมตกแต่งกะโหลกศีรษะ (ขั้นที่ 1) /
DOI: 10.14457/ubu.res.2013.20
title: การจัดเส้นทางของการเก็บขยะในเขตเทศบาลนครอุบลราชธานี
DOI: 10.14457/cu.res.2012.90
title: การวิเคราะห์การยับยั้งการเพิ่มจำนวนของไวรัสเอชไอวีโดยทีเซลล์: การทดสอบที่ใช้วิเคราะห์ภูมิคุ้มกันที่ได้จากการกระตุ้นด้วยวัคซีนป้องกัน HIV
DOI: 10.14457/cu.res.2014.21
title: การสังเคราะห์อนุพันธ์ของคาร์เพสเตอรอลและฤทธิ์ยับยั้งไลเพส