cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8798378.v1
title: Proteomic signatures of neuroinflammation in Alzheimer’s disease, multiple sclerosis and ischemic stroke

description: <b>Introduction</b>: Inflammation is integral in the neuropathology of both chronic and acute neurological disorders. Knowing the inflammatory profile is important for clarification of disease mechanisms, diagnostic purposes, and ultimately treatment options. <b>Areas covered</b>: A systematic review was performed on literature from PubMed using the search terms ‘Alzheimer’s disease’ (AD) or ”multiple sclerosis” (MS) or ”ischemic stroke” and ‘proteomics’. Inflammatory proteins were assessed in blood, cerebrospinal fluid (CSF), and post-mortem brain tissue. Regulated inflammatory proteins across compartments and disorders mainly consisted of innate immune proteins, acute phase proteins and oxidative stress response proteins. In addition, immunoglobulin chains were signature proteins of MS, reflecting additional involvement of adaptive immunity. The Chitinase 3-like protein 1 was increased in ten original articles on MS and in three on AD supporting its implication in these diseases. Furthermore, CNS/CSF AD inflammatory proteins were matched to a CNS myeloid cell proteome implicating Alpha-2-Macroglobulin and Annexin A1 in AD pathogenesis. <b>Expert opinion</b>: Proteomics is an excellent technique for profiling inflammatory proteins in tissues and cells, but still targeted approaches are required for profiling of very low abundance proteins and peptides. Knowing the inflammatory signature of brain tissue, CSF, blood, and CNS myeloid cells holds the potential to point to novel mechanistic aspects of neurological diseases.
DOI: 10.6084/m9.figshare.8798345
title: AID1.rar

description: The images in this dataset are downloaded from Google Earth. It comprises 30 categories with a total of 10,000 images. It is a large datasets and is uploaded in parts. The entire dataset can be compiled by combining AID1, AID2, AID3, AID4 and AID 5 respectively.<br>Xia GS, Hu J, Hu F, Shi B, Bai X, Zhong Y, et al. AID: A benchmark data set for performance evaluation of aerial scene classification. IEEE Transactions on Geoscience and Remote Sensing. 2017;55(7):3965-3981.<br>
DOI: 10.6084/m9.figshare.8798357.v1
title: Untitled Item

description: Multiple sequence alignment used for phylogenetic reconstruction of the TPXL gene family in Arabidopsis.
DOI: 10.6084/m9.figshare.8798345.v1
title: AID1.rar

description: The images in this dataset are downloaded from Google Earth. It comprises 30 categories with a total of 10,000 images. It is a large datasets and is uploaded in parts.<br>Xia GS, Hu J, Hu F, Shi B, Bai X, Zhong Y, et al. AID: A benchmark data set for performance evaluation of aerial scene classification. IEEE Transactions on Geoscience and Remote Sensing. 2017;55(7):3965-3981.<br>
DOI: 10.6084/m9.figshare.8798345.v3
title: AID1.rar

description: The images in this dataset are downloaded from Google Earth. It comprises 30 categories with a total of 10,000 images. It is a large datasets and is uploaded in parts.<br>Xia GS, Hu J, Hu F, Shi B, Bai X, Zhong Y, et al. AID: A benchmark data set for performance evaluation of aerial scene classification. IEEE Transactions on Geoscience and Remote Sensing. 2017;55(7):3965-3981.<br>
DOI: 10.6084/m9.figshare.8798345.v4
title: AID1.rar

description: The images in this dataset are downloaded from Google Earth. It comprises 30 categories with a total of 10,000 images. It is a large datasets and is uploaded in parts. <br>Xia GS, Hu J, Hu F, Shi B, Bai X, Zhong Y, et al. AID: A benchmark data set for performance evaluation of aerial scene classification. IEEE Transactions on Geoscience and Remote Sensing. 2017;55(7):3965-3981.<br>
DOI: 10.6084/m9.figshare.8798111
title: MultiQC reports for Hymenolepis diminuta assembling project

description: MultiQC reports for Hymenolepis diminuta assembling project
DOI: 10.6084/m9.figshare.8798111.v1
title: MultiQC reports for Hymenolepis diminuta assembling project

description: MultiQC reports for Hymenolepis diminuta assembling project
DOI: 10.6084/m9.figshare.8798096
title: Proteogam02_Supplementary File 4__Transrate results

description: Raw results from Transrate
DOI: 10.6084/m9.figshare.8798090
title: MP NxTrim

description: MP NxTrim
DOI: 10.6084/m9.figshare.8798051
title: Proteogam02_Supplementary File 5_COI.pdf

description: COI Sequences and Phylogenetic tree
DOI: 10.6084/m9.figshare.8797934
title: Direct evidence for toxin production by <i>Pseudo-nitzschia plurisecta</i> (Bacillariophyceae) and extension of its distribution area

description: We confirm an amnesic shellfish poisoning risk associated with domoic acid production by the species <i>Pseudo-nitzschia plurisecta</i> and determine the toxin profile, which includes three domoic acid isomers. Although the species was reported once in European waters, along the Spanish Atlantic coast, here we describe and characterize <i>P. plurisecta</i> collected during the first occurrence in French Atlantic waters. Three strains (IFR-PPL-15.1, 15.2 and 15.3) were isolated from French coastal water samples in June 2015. These strains were identified and characterized by microscopic observation, molecular (ITS region sequencing and phylogenetic analysis) and metabolite (toxins and pigments) analyses. The cell shape is lanceolate and the valve contains a central interspace with uniseriate stria of oval-square poroids, each divided into 3–10 sectors. The ITS gene sequence is homologous to the original sequence available for the Spanish strain <i>P. plurisecta</i>. The pigment profile contains chl <i>a, c<sub>3</sub>, c<sub>2</sub></i>, fucoxanthin, diatoxanthin, diadinoxanthin and traces of β,β-carotene. Results on morphology, phylogeny and pigments led to the identification of <i>P. plurisecta</i> and confirmed its first occurrence in French waters.
DOI: 10.6084/m9.figshare.8797967
title: Outcome of treatment in patients with small cell lung cancer in poor performance status

description: <b>Background:</b> Patients with small cell lung cancer (SCLC) with poor performance status (PS) especially in the elderly may not benefit from chemotherapy. The aim of this study was to compare survival of treated patients with PS 3-4 with untreated patients. <b>Material and methods:</b> We reviewed the medical records and pathology data for 448 patients diagnosed with small cell carcinoma from 2010 to 2015 and selected all patients in PS 3-4 for review. <b>Results:</b> A total of 87 patients fulfilled the inclusion criteria. Of these, 53 (61%) received chemotherapy (CT), while 34 (39%) did not. The median overall survival (OS) was 5.1 months for the treated patients and 0.7 month for the untreated (<i>p</i> <b>Conclusion:</b> CT was associated with improved survival in patients with SCLC with PS 3-4 independent of age and stage of disease. Neither ED, high age, nor poor PS should be used as criteria for omitting CT.
DOI: 10.6084/m9.figshare.8797901
title: Museums and digital memory: from creation and curation to digital preservation. Conference programme 2018. Twitter Hashtags Data

description: This dataset documents the Twitter hashtags data (#MADM2018) from the 'Museums and digital memory: from creation and curation to digital preservation' conference 2018. The event was the first digital preservation conference held in the Museum sector in the United Kingdom. It was held in the British Museum on 3 September 2018. This dataset was created by Glenn Cumiskey, Digital Preservation Resource Manager, the British Museum from Twitter following the conference close. <b>Additional Information:</b> In 2018 the British Museum's National Programmes team hosted its free annual conference in partnership with the Digital Preservation Coalition, thanks to the generous support of the Vivmar Foundation. The conference explored the subject of digital content and its preservation in museums, with a range of lively workshops, discussion and debate shaped by contributions from colleagues across the UK. <b>Conference Scope:</b> The UK museum sector is making increasingly creative use of digital technologies in the way it records and disseminates information about its collections. These technologies and advances in museum practice offer dynamic and exciting new ways of engaging people with collections, but they also provoke urgent questions about how we manage and preserve all the digital content we’re creating. Looking after physical assets in archives and collections is at the heart of museum work, but how do we do the same for our digital assets? What are the new skills museums need to safeguard digital content and how will we develop them? This conference aimed to explore best practice in how we as a sector create, curate and preserve digital content – not just the exciting outward-facing side of digital technology in museums, but the often overlooked back-of-house digital preservation work that is essential to ensure the long-term viability and sustainability of these efforts. Central to the day was the question: if museums are memory institutions, how do we ensure that we maintain access to the digital memory that we’re creating now for our future audiences Twitter hashtag: #MADM2018
DOI: 10.6084/m9.figshare.8797934.v1
title: Direct evidence for toxin production by <i>Pseudo-nitzschia plurisecta</i> (Bacillariophyceae) and extension of its distribution area

description: We confirm an amnesic shellfish poisoning risk associated with domoic acid production by the species <i>Pseudo-nitzschia plurisecta</i> and determine the toxin profile, which includes three domoic acid isomers. Although the species was reported once in European waters, along the Spanish Atlantic coast, here we describe and characterize <i>P. plurisecta</i> collected during the first occurrence in French Atlantic waters. Three strains (IFR-PPL-15.1, 15.2 and 15.3) were isolated from French coastal water samples in June 2015. These strains were identified and characterized by microscopic observation, molecular (ITS region sequencing and phylogenetic analysis) and metabolite (toxins and pigments) analyses. The cell shape is lanceolate and the valve contains a central interspace with uniseriate stria of oval-square poroids, each divided into 3–10 sectors. The ITS gene sequence is homologous to the original sequence available for the Spanish strain <i>P. plurisecta</i>. The pigment profile contains chl <i>a, c<sub>3</sub>, c<sub>2</sub></i>, fucoxanthin, diatoxanthin, diadinoxanthin and traces of β,β-carotene. Results on morphology, phylogeny and pigments led to the identification of <i>P. plurisecta</i> and confirmed its first occurrence in French waters.
DOI: 10.6084/m9.figshare.8797898
title: Soil and groundwater salinization in Siwa Oasis and management opportunities: twenty year change detection and assessment

description: The use of saline groundwater in irrigation due to the limited availability of fresh water is one of the main causes of land degradation in arid and semi-arid environments. The agro-ecosystem of Siwa Oasis was monitored over a period of two decades. A stable isotope study, oxygen-18 and deuterium, indicated that Siwa groundwater is of meteoric origin. Siwa has two groundwater aquifers: a shallow limestone aquifer, LA, with highly saline water (Total Dissolved Solids, TDS, up to 6848 mg/L), and a deep Nubian sandstone aquifer, NSA, containing fresh water (TDS 192–256 mg/L). The sodium adsorption ratio, SAR, of LA water is high with an average value of 13.9 while the SAR of NSA water is low with an average value of 2.1. Schoeller and Piper’s diagrams showed that LA water was of sodium, chloride-sulfate type, while the NSA water was classified as sodium carbonate and bicarbonate water type. Saturation Index (SI) calculations showed that both the LA and NSA water were undersaturated to halite minerals. Consequently, there is room to accommodate extra Na<sup>+</sup> and Cl<sup>−</sup> from halite. Most Siwa land is irrigated with LA water due to low drilling costs. LA groundwater and Siwa soils were found to be deteriorating dramatically and the average water and soil salinity increased by 30–36% per decade. No change in NSA water quality was recorded over the same period. Interventions for the restoration of the deteriorated Siwa ecosystem are summarized. The approach conducted in this study can be repeated in similar ecosystems.
DOI: 10.6084/m9.figshare.8797901.v1
title: Museums and digital memory: from creation and curation to digital preservation. Conference programme 2018. Twitter Hashtags Data

description: This dataset documents the Twitter hashtags data (#MADM2018) from the 'Museums and digital memory: from creation and curation to digital preservation' conference 2018. The event was the first digital preservation conference held in the Museum sector in the United Kingdom. It was held in the British Museum on 3 September 2018. This dataset was created by Glenn Cumiskey, Digital Preservation Resource Manager, the British Museum from Twitter following the conference close. <b>Additional Information:</b> In 2018 the British Museum's National Programmes team hosted its free annual conference in partnership with the Digital Preservation Coalition, thanks to the generous support of the Vivmar Foundation. The conference explored the subject of digital content and its preservation in museums, with a range of lively workshops, discussion and debate shaped by contributions from colleagues across the UK. <b>Conference Scope:</b> The UK museum sector is making increasingly creative use of digital technologies in the way it records and disseminates information about its collections. These technologies and advances in museum practice offer dynamic and exciting new ways of engaging people with collections, but they also provoke urgent questions about how we manage and preserve all the digital content we’re creating. Looking after physical assets in archives and collections is at the heart of museum work, but how do we do the same for our digital assets? What are the new skills museums need to safeguard digital content and how will we develop them? This conference aimed to explore best practice in how we as a sector create, curate and preserve digital content – not just the exciting outward-facing side of digital technology in museums, but the often overlooked back-of-house digital preservation work that is essential to ensure the long-term viability and sustainability of these efforts. Central to the day was the question: if museums are memory institutions, how do we ensure that we maintain access to the digital memory that we’re creating now for our future audiences Twitter hashtag: #MADM2018
DOI: 10.6084/m9.figshare.8797967.v2
title: Outcome of treatment in patients with small cell lung cancer in poor performance status

description: <b>Background:</b> Patients with small cell lung cancer (SCLC) with poor performance status (PS) especially in the elderly may not benefit from chemotherapy. The aim of this study was to compare survival of treated patients with PS 3-4 with untreated patients. <b>Material and methods:</b> We reviewed the medical records and pathology data for 448 patients diagnosed with small cell carcinoma from 2010 to 2015 and selected all patients in PS 3-4 for review. <b>Results:</b> A total of 87 patients fulfilled the inclusion criteria. Of these, 53 (61%) received chemotherapy (CT), while 34 (39%) did not. The median overall survival (OS) was 5.1 months for the treated patients and 0.7 month for the untreated (<i>p</i> <b>Conclusion:</b> CT was associated with improved survival in patients with SCLC with PS 3-4 independent of age and stage of disease. Neither ED, high age, nor poor PS should be used as criteria for omitting CT.
DOI: 10.6084/m9.figshare.8797898.v1
title: Soil and groundwater salinization in Siwa Oasis and management opportunities: twenty year change detection and assessment

description: The use of saline groundwater in irrigation due to the limited availability of fresh water is one of the main causes of land degradation in arid and semi-arid environments. The agro-ecosystem of Siwa Oasis was monitored over a period of two decades. A stable isotope study, oxygen-18 and deuterium, indicated that Siwa groundwater is of meteoric origin. Siwa has two groundwater aquifers: a shallow limestone aquifer, LA, with highly saline water (Total Dissolved Solids, TDS, up to 6848 mg/L), and a deep Nubian sandstone aquifer, NSA, containing fresh water (TDS 192–256 mg/L). The sodium adsorption ratio, SAR, of LA water is high with an average value of 13.9 while the SAR of NSA water is low with an average value of 2.1. Schoeller and Piper’s diagrams showed that LA water was of sodium, chloride-sulfate type, while the NSA water was classified as sodium carbonate and bicarbonate water type. Saturation Index (SI) calculations showed that both the LA and NSA water were undersaturated to halite minerals. Consequently, there is room to accommodate extra Na<sup>+</sup> and Cl<sup>−</sup> from halite. Most Siwa land is irrigated with LA water due to low drilling costs. LA groundwater and Siwa soils were found to be deteriorating dramatically and the average water and soil salinity increased by 30–36% per decade. No change in NSA water quality was recorded over the same period. Interventions for the restoration of the deteriorated Siwa ecosystem are summarized. The approach conducted in this study can be repeated in similar ecosystems.
DOI: 10.6084/m9.figshare.8798045.v1
title: Enzyme replacement therapy with recombinant pro-CTSD (cathepsin D) corrects defective proteolysis and autophagy in neuronal ceroid lipofuscinosis

description: CTSD (cathepsin D) is one of the major lysosomal proteases indispensable for the maintenance of cellular proteostasis by turning over substrates of endocytosis, phagocytosis and autophagy. Consequently, CTSD deficiency leads to a strong impairment of the lysosomal-autophagy machinery. In mice and humans CTSD dysfunction underlies the congenital variant (CLN10) of neuronal ceroid lipofuscinosis (NCL). NCLs are distinct lysosomal storage disorders (LSDs) sharing various hallmarks, namely accumulation of protein aggregates and ceroid lipofuscin leading to neurodegeneration and blindness. The most established and clinically approved approach to treat LSDs is enzyme replacement therapy (ERT) aiming to replace the defective hydrolase with an exogenously applied recombinant protein. Here we reveal that recombinant human pro-CTSD produced in a mammalian expression system can be efficiently taken up by a variety of cell models, is correctly targeted to lysosomes and processed to the active mature form of the protease. In proof-of-principle experiments we provide evidence that recombinant human CTSD (rhCTSD) can improve the biochemical phenotype of CTSD-deficient hippocampal slice cultures <i>in vitro</i> and retinal cells <i>in vivo</i>. Furthermore, we demonstrate that dosing of rhCTSD in the murine CLN10 model leads to a correction of lysosomal hypertrophy, storage accumulation and impaired autophagic flux in the viscera and central nervous system (CNS). We establish that direct delivery of the recombinant protease to the CNS is required for improvement of neuropathology and lifespan extension. Together these data support the continuation of the pre-clinical studies for the application of rhCTSD in the treatment of NCL.
DOI: 10.6084/m9.figshare.8797967.v1
title: Outcome of treatment in patients with small cell lung cancer in poor performance status

description: <b>Background:</b> Patients with small cell lung cancer (SCLC) with poor performance status (PS) especially in the elderly may not benefit from chemotherapy. The aim of this study was to compare survival of treated patients with PS 3-4 with untreated patients. <b>Material and methods:</b> We reviewed the medical records and pathology data for 448 patients diagnosed with small cell carcinoma from 2010 to 2015 and selected all patients in PS 3-4 for review. <b>Results:</b> A total of 87 patients fulfilled the inclusion criteria. Of these, 53 (61%) received chemotherapy (CT), while 34 (39%) did not. The median overall survival (OS) was 5.1 months for the treated patients and 0.7 month for the untreated (<i>p</i> <b>Conclusion:</b> CT was associated with improved survival in patients with SCLC with PS 3-4 independent of age and stage of disease. Neither ED, high age, nor poor PS should be used as criteria for omitting CT.
DOI: 10.6084/m9.figshare.8798045
title: Enzyme replacement therapy with recombinant pro-CTSD (cathepsin D) corrects defective proteolysis and autophagy in neuronal ceroid lipofuscinosis

description: CTSD (cathepsin D) is one of the major lysosomal proteases indispensable for the maintenance of cellular proteostasis by turning over substrates of endocytosis, phagocytosis and autophagy. Consequently, CTSD deficiency leads to a strong impairment of the lysosomal-autophagy machinery. In mice and humans CTSD dysfunction underlies the congenital variant (CLN10) of neuronal ceroid lipofuscinosis (NCL). NCLs are distinct lysosomal storage disorders (LSDs) sharing various hallmarks, namely accumulation of protein aggregates and ceroid lipofuscin leading to neurodegeneration and blindness. The most established and clinically approved approach to treat LSDs is enzyme replacement therapy (ERT) aiming to replace the defective hydrolase with an exogenously applied recombinant protein. Here we reveal that recombinant human pro-CTSD produced in a mammalian expression system can be efficiently taken up by a variety of cell models, is correctly targeted to lysosomes and processed to the active mature form of the protease. In proof-of-principle experiments we provide evidence that recombinant human CTSD (rhCTSD) can improve the biochemical phenotype of CTSD-deficient hippocampal slice cultures <i>in vitro</i> and retinal cells <i>in vivo</i>. Furthermore, we demonstrate that dosing of rhCTSD in the murine CLN10 model leads to a correction of lysosomal hypertrophy, storage accumulation and impaired autophagic flux in the viscera and central nervous system (CNS). We establish that direct delivery of the recombinant protease to the CNS is required for improvement of neuropathology and lifespan extension. Together these data support the continuation of the pre-clinical studies for the application of rhCTSD in the treatment of NCL. <b>Abbreviations:</b> AIF1/IBA1: allograft inflammatory factor 1; BBB: blood brain barrier; CNS: central nervous system; CTSB: cathepsin B; CTSD: cathepsin D; CTSL: cathepsin L; ERT: enzyme replacement therapy; GFAP: glial fibrillary acidic protein; INL: inner nuclear layer; LAMP1: lysosomal-associated membrane protein 1; LAMP2: lysosomal-associated membrane protein 2; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; LDL: low-density lipoprotein; LRP1: low density lipoprotein receptor-related protein 1; LSD: lysosomal storage disorder; MEFs: mouse embryonic fibroblasts; M6P: mannose 6-phosphate; mCTSD: mature CTSD; NCL: neuronal ceroid lipofuscinosis; ONL: outer nuclear layer; PB: phosphate buffer; proCTSD: pro-cathepsin D; LRPAP1: low density lipoprotein receptor-related protein associated protein 1; rhCTSD: human recombinant CTSD; SAPC: saposin C; SAPD: saposin D; ATP5G1: ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9); SQSTM1/p62: sequestosome 1; TPP1: tripeptidyl peptidase I.