cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5688508
title: Supplemental Figures

description: Figures showing single session data for all sessions, in same format as the example session figures (8A, 8B and 9B) provided in the paper.<br>Each subdirectory of the figure is named as a session code of the form: IIYYMMDDlightness000N_SSSpx_Kcx_Lcy_F. In the code, II are the initials of the monkey (BR, JD, ST or SY), YY is the year of the session (20YY), MM is the month, and DD is the day. N is a session identifier. SSS gives the size of the stimulus in monitor pixels, K gives the x center location of the stimulus, L gives the y center location, and F is a code that indicates whether the image was flipped (g for not flipped, i for flipped). In some cases, K and L have more than one digit. On the display, one pixel was approximately 0.03 degrees of visual angle. Each subdirectory contains three figures in PDF format. Fig_extPaintShadowEffectDecodeBothDecoding.pdf matches 8A in format, Fig_extPaintShadowEffectDecodeBothInferredMatches.pdf matches 8B in format, and Fig_extPaintShadowEffectRMSEEnvelope.pdf matches 9B in format.<br>
DOI: 10.6084/m9.figshare.5688508.v3
title: Supplemental Figures

description: Figures showing single session data for all sessions, in same format as the example session figures (8A, 8B and 9B) provided in the paper.<br>Each subdirectory of the figure is named as a session code of the form: IIYYMMDDlightness000N_SSSpx_Kcx_Lcy_F. In the code, II are the initials of the monkey (BR, JD, ST or SY), YY is the year of the session (20YY), MM is the month, and DD is the day. N is a session identifier. SSS gives the size of the stimulus in monitor pixels, K gives the x center location of the stimulus, L gives the y center location, and F is a code that indicates whether the image was flipped (g for not flipped, i for flipped). In some cases, K and L have more than one digit. On the display, one pixel was approximately 0.03 degrees of visual angle. Each subdirectory contains three figures in PDF format. Fig_extPaintShadowEffectDecodeBothDecoding.pdf matches 8A in format, Fig_extPaintShadowEffectDecodeBothInferredMatches.pdf matches 8B in format, and Fig_extPaintShadowEffectRMSEEnvelope.pdf matches 9B in format.<br>
DOI: 10.6084/m9.figshare.5688337
title: Development of a microcomputed tomography scoring system to characterize disease progression in the Hartley guinea pig model of spontaneous osteoarthritis

description: <b><i>Aim</i></b>: There is potential discrepancy between human and laboratory animal studies of osteoarthritis (OA), as radiographic assessment is the hallmark of the former and histopathology the standard for the latter. This suggests a need to evaluate OA in animal models in a manner similar to that utilized in people. Our study aimed to develop a whole joint grading scheme for microcomputed tomography (microCT) images in Hartley guinea pigs, a strain that recapitulates joint changes highlighted in human spontaneous OA. <b><i>Materials and Methods</i></b>: Knees from animals aged 2, 3, 5, 9, and 15 months were evaluated via whole joint microCT and standard histologic scoring. Quantitative microCT parameters, such as bone volume/total volume were also collected. <b><i>Results</i></b>: Both whole joint microCT and histologic scores increased with advancing age and showed strong correlation (<i>r</i> = 0.89. <i>p</i> <i>Conclusions</i>: This work provides data that advocates the use of a whole joint microCT scoring system in guinea pig studies of OA, as it provides important information regarding bony changes that occur at a different rate than articular cartilage changes. This grading scheme, in conjunction with histology and quantitative microCT measurements, may enhance the translational value of this animal model as it pertains to human work.
DOI: 10.6084/m9.figshare.5688337.v1
title: Development of a microcomputed tomography scoring system to characterize disease progression in the Hartley guinea pig model of spontaneous osteoarthritis

description: <b><i>Aim</i></b>: There is potential discrepancy between human and laboratory animal studies of osteoarthritis (OA), as radiographic assessment is the hallmark of the former and histopathology the standard for the latter. This suggests a need to evaluate OA in animal models in a manner similar to that utilized in people. Our study aimed to develop a whole joint grading scheme for microcomputed tomography (microCT) images in Hartley guinea pigs, a strain that recapitulates joint changes highlighted in human spontaneous OA. <b><i>Materials and Methods</i></b>: Knees from animals aged 2, 3, 5, 9, and 15 months were evaluated via whole joint microCT and standard histologic scoring. Quantitative microCT parameters, such as bone volume/total volume were also collected. <b><i>Results</i></b>: Both whole joint microCT and histologic scores increased with advancing age and showed strong correlation (<i>r</i> = 0.89. <i>p</i> <i>Conclusions</i>: This work provides data that advocates the use of a whole joint microCT scoring system in guinea pig studies of OA, as it provides important information regarding bony changes that occur at a different rate than articular cartilage changes. This grading scheme, in conjunction with histology and quantitative microCT measurements, may enhance the translational value of this animal model as it pertains to human work.
DOI: 10.6084/m9.figshare.12888566
title: Killifish telomere data 2020

description: data used for analysis in a paper submitted to eLife: "<b>Environment and sex control</b><b> </b><b>lifespan and telomere length in wild-derived African killifish"</b><b></b>
DOI: 10.6084/m9.figshare.12888566.v1
title: Killifish telomere data 2020

description: data used for analysis in a paper submitted to eLife: "<b>Environment and sex control</b><b> </b><b>lifespan and telomere length in wild-derived African killifish"</b><b></b>
DOI: 10.6084/m9.figshare.5688199
title: Supplementary Tables from Deciphering pathogenicity and antibiotic resistance islands in methicillin-resistant <i>Staphylococcus aureus</i> genomes

description: Additional information on known and predicted genomic islands in MRSA
DOI: 10.6084/m9.figshare.5688199.v1
title: Supplementary Tables from Deciphering pathogenicity and antibiotic resistance islands in methicillin-resistant <i>Staphylococcus aureus</i> genomes

description: Additional information on known and predicted genomic islands in MRSA
DOI: 10.6084/m9.figshare.5688190
title: Postcranial measurements from Postcranial diversity and recent ecomorphic impoverishment of North American gray wolves

description: Raw data to be deposited in Dryad
DOI: 10.6084/m9.figshare.5688190.v1
title: Postcranial measurements from Postcranial diversity and recent ecomorphic impoverishment of North American gray wolves

description: Raw data to be deposited in Dryad
DOI: 10.6084/m9.figshare.5688127
title: Drilling Tools Ontology

description: Drilling tools ontology
DOI: 10.6084/m9.figshare.5688127.v1
title: Drilling Tools Ontology

description: Drilling tools ontology
DOI: 10.6084/m9.figshare.5688061
title: MMU_RandomEuclideanInstances.zip

description: A library of 40,000 random Euclidean travelling salesman problem instances (10,000 each of 100, 200, 500 and 1000 vertices), all solved to optimality using Concorde. Optimum values and optimum tours included.
DOI: 10.6084/m9.figshare.5688061.v1
title: MMU_RandomEuclideanInstances.zip

description: A library of 40,000 random Euclidean travelling salesman problem instances (10,000 each of 100, 200, 500 and 1000 vertices), all solved to optimality using Concorde. Optimum values and optimum tours included.
DOI: 10.6084/m9.figshare.5688040
title: Challenges in financing public sector low-carbon initiatives: lessons from private finance for a school district in British Columbia, Canada

description: Governments are major investors in climate change mitigation, but aversion to public indebtedness has led to reliance on private finance to deliver public assets. Compounding this challenge, financing through Energy Service Contracts is ruled out by accounting rules. With public and traditional private funding avenues closed, government departments have sought contracts that do not disclose the full cost of borrowing, such as the Public–Private Partnership (PPP) described in this case study. We unpack the utility contract filed with the provincial regulator to show that circumventing budgetary constraints cost the Delta School Board (DSB) 8.75% per annum on borrowed private funds while public finance would have cost 4%pa. All levels of the public sector are keen to play their role in climate mitigation. Climate policy is about not passing our burden of unbridled fossil fuel use and greenhouse gas emissions to future generations. If we do not exempt public sector capital investments for decarbonization from deficit regulations, we risk passing an unnecessary economic burden to future generations. <b>Key policy insights</b>Transition to a low-carbon economy requires public sector investments that exceed budget deficit regulations and political aversion in many jurisdictions;Private–Public Partnerships are currently viewed as the solution to this self-imposed fiscal constraint;PPPs without clear performance targets or contractual templates will expose less experienced public sector investors to high costs and emissions above expectations. Transition to a low-carbon economy requires public sector investments that exceed budget deficit regulations and political aversion in many jurisdictions; Private–Public Partnerships are currently viewed as the solution to this self-imposed fiscal constraint; PPPs without clear performance targets or contractual templates will expose less experienced public sector investors to high costs and emissions above expectations.
DOI: 10.6084/m9.figshare.5688040.v1
title: Challenges in financing public sector low-carbon initiatives: lessons from private finance for a school district in British Columbia, Canada

description: Governments are major investors in climate change mitigation, but aversion to public indebtedness has led to reliance on private finance to deliver public assets. Compounding this challenge, financing through Energy Service Contracts is ruled out by accounting rules. With public and traditional private funding avenues closed, government departments have sought contracts that do not disclose the full cost of borrowing, such as the Public–Private Partnership (PPP) described in this case study. We unpack the utility contract filed with the provincial regulator to show that circumventing budgetary constraints cost the Delta School Board (DSB) 8.75% per annum on borrowed private funds while public finance would have cost 4%pa. All levels of the public sector are keen to play their role in climate mitigation. Climate policy is about not passing our burden of unbridled fossil fuel use and greenhouse gas emissions to future generations. If we do not exempt public sector capital investments for decarbonization from deficit regulations, we risk passing an unnecessary economic burden to future generations. <b>Key policy insights</b>Transition to a low-carbon economy requires public sector investments that exceed budget deficit regulations and political aversion in many jurisdictions;Private–Public Partnerships are currently viewed as the solution to this self-imposed fiscal constraint;PPPs without clear performance targets or contractual templates will expose less experienced public sector investors to high costs and emissions above expectations. Transition to a low-carbon economy requires public sector investments that exceed budget deficit regulations and political aversion in many jurisdictions; Private–Public Partnerships are currently viewed as the solution to this self-imposed fiscal constraint; PPPs without clear performance targets or contractual templates will expose less experienced public sector investors to high costs and emissions above expectations.
DOI: 10.6084/m9.figshare.5688019
title: Early results of a phase-II study of modified short-course radiotherapy combined with capecitabine and delayed surgery for T3M0 lower rectal cancer

description: Early results of a phase-II study of modified short-course radiotherapy combined with capecitabine and delayed surgery for T3M0 lower rectal cancer
DOI: 10.6084/m9.figshare.5688019.v1
title: Early results of a phase-II study of modified short-course radiotherapy combined with capecitabine and delayed surgery for T3M0 lower rectal cancer

description: Early results of a phase-II study of modified short-course radiotherapy combined with capecitabine and delayed surgery for T3M0 lower rectal cancer
DOI: 10.6084/m9.figshare.5688016
title: Input assemblies

description: Transcript assemblies used for evaluating Mikado, divided by subsection:<br><br>- Input_assemblies_real_data.zip: assemblies derived from real data, see the "Performance of Mikado" section in the manuscript.<br>- Input_assemblies_simulated_data.zip: assemblies derived from simulated data, see the "Performance of Mikado" section in the manuscript.<br>- Input_assemblies_multiple_Isoform_Fraction.zip: StringTie and CLASS2 assemblies derived by varying the Minimum Isoform Fraction parameter. See the "Filtering lenient assemblies" section in the manuscript.<br>- Input_assemblies_multiple_samples.zip: assemblies derived from real data using multiple samples RNA-Seq of A. thaliana; see the "Multi-sample transcript reconstruction" section in the manuscript.<br>- Input_assemblies_pacbio.zip: alignments and assemblies of Illumina and PacBio reads; see the "Expansion to long read technologies" section in the manuscript.<br><br>Except for the PacBio alignments, which are GMAP gff alignments, all assemblies are in GTF format and follow the pattern:<br><br>-0---0.gtf<br><br>E.g. the file:<br><br>stringtie-0-tophat-err588042-0.gtf<br><br>is a StringTie assembly derived from a TopHat2 alignment of sample ERR588042.<br><br>Please see the manuscript and SnakeMake files in this repository for details on how these assemblies have been generated.<br><br><br><br>
DOI: 10.17637/rh.5687995
title: GIb04a 1948-2003.xlsx

description: An actively growing speleothem sampled from New St. Michaels Cave in 2004 is composed of paired laminae consisting of light columnar calcite and a darker microsparitic calcite. Stable isotope analysis of samples micromilled in 100 μm steps at the equivalent of bi-monthly intervals reveals fabric-correlated annual cycles in carbon isotopes, oxygen isotopes and trace elements responding to seasonal changes in cave microclimate, hydrology and ventilation patterns. Calcite δ13C values reach a minimum in the light columnar fabric and evidence from trace element behaviour and cave monitoring indicates that this grows under cave ‘winter’ conditions of highest pCO2, whereas the dark microsparitic calcite, characterised by elevated δ13C and δ18O values grows under low ‘summer’ pCO2 conditions. Drip water δ13CDIC reaches a minimum in March–April, at which time the attenuated δ18O signal becomes most representative of winter precipitation. An age model based on cycle counting and the position of the 14C bomb carbon spike yields a precisely dated winter oxygen isotope proxy of cave seepage water for comparison with the GNIP and instrumental climate record for Gibraltar. The δ18O characteristics of calcite deposited from drip water representing winter precipitation for each year can be derived from the seasonally resolved record and allows reconstruction of the δ18O drip water representing winter precipitation for each year from 1951–2004. These data show an encouraging level of correspondence (r2 =0.47) with the δ18O of rainfall falling each year between October and March and on a decadal scale the δ18O of reconstructed winter drip water mirrors secular change in mean winter temperatures.
DOI: 10.6084/m9.figshare.5687944
title: beta 2 Adrenergic receptor expression analysis by flow cytometry on CD4+ T cells isolated from mPGES-1 KO or WT mouse splenocytes

description: Flow cytometric data from five experiments analyzing beta-2-adrenergic receptor expression on CD4+ T cells (MACS positive selection from spleen) from mPGES-1 ko (-/-) or WT (+/+) mice subjected to vagus nerve stimulation (VNS) and intraperitoneal LPS injection 30 min prior to sample collection.<br><br>Panel (<i>more detailed info can be found in the "FCS file identification list" document</i>):<br>FITC-Viability<br>PE-b2AR<br>PCPCy5.5-CD69<br>PECy7-CD62L<br>APC-CD44<br>APCCy7-CD3<br>BV421-CD25<br>BV510-CD4<br><br>The protocol for staining, cell extraction VNS etc. is described in the publication "Microsomal prostaglandin E synthase-1 gene deletion impairs neuro-immune circuitry of the cholinergic anti-inflammatory pathway in endotoxaemic mpuse spleen" published in <b>PLOS ONE 2017</b> by the authors: Priya Revathikumar, Johanna Estelius, Utsa Karmakar, Erwan LeMaître, Marina Korotkova, Per-Johan Jakobsson and Jon Lampa. <br><br><br>
DOI: 10.6084/m9.figshare.5687929
title: Immunofluorescent staining of Choline Acetyltransferase (ChAT) in splenocytes from mPGES-1 ko or wt mice treated with LPS

description: Microscopy images of immunofluorescent staining of choline acetyltransferase (ChAT) in splenocytes from mPGES-1 ko (-/-) or WT (+/+) mice following 20h cultures with or without 10ng/ml LPS. (2 experiments)<br><br>Green (L5) = ChAT, Blue (A4) = DAPI, Red (N21) = CD3*<br><br>*CD3 staining gave signal in negative control samples so should be disregarded.<br><br>The protocol for staining and cell culture is described in the publication "Microsomal prostaglandin E synthase-1 gene deletion impairs neuro-immune circuitry of the cholinergic anti-inflammatory pathway in endotoxaemic mpuse spleen" published in <b>PLOS ONE 2017</b> by the authors: Priya Revathikumar, Johanna Estelius, Utsa Karmakar, Erwan LeMaître, Marina Korotkova, Per-Johan Jakobsson and Jon Lampa.
DOI: 10.6084/m9.figshare.5687929.v1
title: Immunofluorescent staining of Choline Acetyltransferase (ChAT) in splenocytes from mPGES-1 ko or wt mice treated with LPS

description: Microscopy images of immunofluorescent staining of choline acetyltransferase (ChAT) in splenocytes from mPGES-1 ko (-/-) or WT (+/+) mice following 20h cultures with or without 10ng/ml LPS. (2 experiments)<br><br>Green (L5) = ChAT, Blue (A4) = DAPI, Red (N21) = CD3*<br><br>*CD3 staining gave signal in negative control samples so should be disregarded.<br><br>The protocol for staining and cell culture is described in the publication "Microsomal prostaglandin E synthase-1 gene deletion impairs neuro-immune circuitry of the cholinergic anti-inflammatory pathway in endotoxaemic mpuse spleen" published in <b>PLOS ONE 2017</b> by the authors: Priya Revathikumar, Johanna Estelius, Utsa Karmakar, Erwan LeMaître, Marina Korotkova, Per-Johan Jakobsson and Jon Lampa.
DOI: 10.6084/m9.figshare.5687926
title: EDiP: the Epitope Dilution Phenomenon. Lessons learnt from a malaria vaccine antigen and its applicability to polymorphic antigens

description: <b>Introduction</b>: Polymorphism in vaccine antigens poses major challenges to vaccinologists. The <i>Plasmodium falciparum</i> Apical Membrane Antigen 1 (AMA1) poses such a challenge. We found that immunization with a mixture of three variants yielded functional antibody levels to all variants comparable to levels induced by monovalent immunization. The mechanism behind the observed broadening was shown to be an increase in the fraction of cross-reactive antibodies, most likely because strain-specific epitopes are present at lower frequency relative to conserved epitopes. <b>Areas covered</b>: We hereby introduce the Epitope Dilution Phenomenon (EDiP) as a practical strategy for the induction of broad, cross-variant antibody responses against polymorphic antigens and discuss the utility and applicability of this phenomenon for the development of vaccines against polymorphic antigens of pathogens like Influenza, HIV, Dengue and <i>Plasmodium</i>. <b>Expert commentary</b>: EDiP can be used to broaden antibody responses by immunizing with a mixture of at least 3 antigenic variants, where the variants included can differ, yet yield broadened responses.
DOI: 10.6084/m9.figshare.5687926.v2
title: EDiP: the Epitope Dilution Phenomenon. Lessons learnt from a malaria vaccine antigen and its applicability to polymorphic antigens

description: <b>Introduction</b>: Polymorphism in vaccine antigens poses major challenges to vaccinologists. The <i>Plasmodium falciparum</i> Apical Membrane Antigen 1 (AMA1) poses such a challenge. We found that immunization with a mixture of three variants yielded functional antibody levels to all variants comparable to levels induced by monovalent immunization. The mechanism behind the observed broadening was shown to be an increase in the fraction of cross-reactive antibodies, most likely because strain-specific epitopes are present at lower frequency relative to conserved epitopes. <b>Areas covered</b>: We hereby introduce the Epitope Dilution Phenomenon (EDiP) as a practical strategy for the induction of broad, cross-variant antibody responses against polymorphic antigens and discuss the utility and applicability of this phenomenon for the development of vaccines against polymorphic antigens of pathogens like Influenza, HIV, Dengue and <i>Plasmodium</i>. <b>Expert commentary</b>: EDiP can be used to broaden antibody responses by immunizing with a mixture of at least 3 antigenic variants, where the variants included can differ, yet yield broadened responses.
DOI: 10.6084/m9.figshare.5687890
title: <i>In silico</i> evaluation of the resistance of the T790M variant of epidermal growth factor receptor kinase to cancer drug Erlotinib

description: Epidermal growth factor receptor kinase is implicated in cancer development due to either overexpression or activation variants in its functional intracellular kinase domain. Threonine to methionine (Thr 790 Met) is one such variant observed commonly in patients showing resistance to kinase inhibitor drug Erlotinib. Two mechanisms for resistance have been proposed (1) steric hindrance and (2) enhanced binding to ATP. In this study, we employed molecular dynamics simulations and studied both the mechanisms. Extensive simulations and free energy of binding analyses has shown that steric hindrance does not explain appropriately the mechanism for resistance against Erlotinib therapy for this variant. It has been observed that conformational switching from an intermediate intrinsically disordered C-helix conformation is required for completion of the kinase’s catalytic cycle. Our study substantiates that T790M variant has greater tendency for early transition to this intrinsically disordered C-helix intermediate state. We propose that enhanced catalytic efficiency in addition to enhanced ATP binding explains mechanism of T790M resistance to drug Erlotinib.
DOI: 10.6084/m9.figshare.5687890.v1
title: <i>In silico</i> evaluation of the resistance of the T790M variant of epidermal growth factor receptor kinase to cancer drug Erlotinib

description: Epidermal growth factor receptor kinase is implicated in cancer development due to either overexpression or activation variants in its functional intracellular kinase domain. Threonine to methionine (Thr 790 Met) is one such variant observed commonly in patients showing resistance to kinase inhibitor drug Erlotinib. Two mechanisms for resistance have been proposed (1) steric hindrance and (2) enhanced binding to ATP. In this study, we employed molecular dynamics simulations and studied both the mechanisms. Extensive simulations and free energy of binding analyses has shown that steric hindrance does not explain appropriately the mechanism for resistance against Erlotinib therapy for this variant. It has been observed that conformational switching from an intermediate intrinsically disordered C-helix conformation is required for completion of the kinase’s catalytic cycle. Our study substantiates that T790M variant has greater tendency for early transition to this intrinsically disordered C-helix intermediate state. We propose that enhanced catalytic efficiency in addition to enhanced ATP binding explains mechanism of T790M resistance to drug Erlotinib.