cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7525341
title: Test-Retest Reliability of the Human Connectome: An OPM-MEG study

description: OPM-MEG data was acquired during naturalistic viewing of a 600s clip from the film "Dog Day Afternoon".


Two sets of MEG data were acquired in each of the 10 scanned subjects.


Defaced, T1 weighted MRIs are available for each subject and OPM sensor locations and orientations are given relative to subject anatomy to allow for source reconstruction.


An example of MATLAB code used to analyse these data can be found on GitHub, which includes all code used to produce the results described in "Test-Retest Reliability of the Human Connectome: An OPM-MEG study" (biorxiv.org/cgi/content/short/2022.12.21.521184v1)
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Updates:
v1.0.1
Added missing meshes and AAL source location files


v1.1.0
Added video file used in the experiment
description: This work was supported by an Engineering and Physical Sciences Research Council (EPSRC) Healthcare Impact Partnership Grant (EP/V047264/1) and an Innovate UK germinator award (Grant number 1003346). We acknowledge support from the UK Quantum Technology Hub in Sensing and Timing, funded by EPSRC (EP/T001046/1). Sensor development was made possible by funding from the National Institutes of Health (R44MH110288). S.M. is funded by Deutsche Forschungsgemeinschaft (DFG), project 437219953. We also express thanks to Cerca Magnetics Ltd., Metamorphic AM and Added Scientific Ltd. for the useful and productive discussions that led to the design of the lightweight helmet used for paediatric measurements.
DOI: 10.6084/m9.figshare.11937648
title: Additional file 9 of Evolution of PHAS loci in the young spike of Allohexaploid wheat

description: Additional file 9: Supplementary Table 1. Identified 21- and 24-PHAS with phased scores greater than 15, 20, 25 and 30 in 261 small RNA samples.
DOI: 10.6084/m9.figshare.11937648.v1
title: Additional file 9 of Evolution of PHAS loci in the young spike of Allohexaploid wheat

description: Additional file 9: Supplementary Table 1. Identified 21- and 24-PHAS with phased scores greater than 15, 20, 25 and 30 in 261 small RNA samples.
DOI: 10.14473/csda/vtt61j/ilt9xi
title: tazatele_data_bez_diakritiky_w3_chps_v1.0_ENG_FIN.tab

description: Data
DOI: 10.6084/m9.figshare.25259899
title: Supplementary Material for: No efficacy with non-invasive brain stimulation 1 for painful legs and moving toes: A Case report

description: Introduction: Painful legs and moving toes (PLMT) is a rare neurological disorder characterized by neuropathic pain and involuntary movements in the lower limbs. The pathophysiological mechanisms are unclear but central mechanisms might be involved suggesting that non-invasive brain stimulation might be helpful. Thus far no reports have been published on non-invasive brain stimulation to treat PLMT. Case presentation: a 70-year old female had a one year history of PLMT. After several unsuccessful medical attempts the patient received repetitive transcranial magnetic stimulation and transcranial direct current stimulation to alleviate the pain and involuntary movements with no benefit. Conclusion: This is a first report on non-invasive brain stimulation in a PLMT patient. Although ineffective in our patient non-invasive brain stimulation should be further studied in this often difficult to treat and debilitating syndrome.
DOI: 10.6084/m9.figshare.6694814
title: MOESM1 of Quantifying spatial accessibility in public health practice and research: an application to on-premise alcohol outlets, United States, 2013

description: Additional file 1: Population-weighted spatial access to 7 nearest on-premise alcohol outlets by U.S. states, counties and census tracts, 2013.
DOI: 10.6084/m9.figshare.11937702
title: Additional file 6 of Linker histone variant H1t is closely associated with repressed repeat-element chromatin domains in pachytene spermatocytes

description: Additional file 6. ChIP-sequencing peaks of H1t in P20 mouse testicular cells.
DOI: 10.6084/m9.figshare.11937702.v1
title: Additional file 6 of Linker histone variant H1t is closely associated with repressed repeat-element chromatin domains in pachytene spermatocytes

description: Additional file 6. ChIP-sequencing peaks of H1t in P20 mouse testicular cells.
DOI: 10.6084/m9.figshare.8791991
title: Antifungal activity and functional components of cell-free supernatant from <i>Bacillus amyloliquefaciens</i> LZN01 inhibit <i>Fusarium oxysporum</i> f. sp. <i>niveum</i> growth

description: <i>Bacillus amyloliquefaciens</i> LZN01 shows antagonistic behaviour against <i>Fusarium oxysporum</i> f. sp. <i>niveum</i> (<i>Fon</i>). This study aimed to analyze the antifungal activity and the functional components of cell-free supernatant from <i>B. amyloliquefaciens</i> LZN01 that inhibited <i>Fon</i> growth. The results showed that the cell-free supernatant (CFS) from the death phase had stronger antifungal activity against <i>Fon</i> compared to those from the exponential stage and stationary phase. The analyses from scanning and transmission electron microscopy demonstrated that treatment with CFS led to cellular morphological changes, including concave formations on the conidial surface, the disruption of cell walls and membranes, the leakage of intracellular contents and the aggregation of organelles. Confocal laser scanning microscopy revealed that the CFS damaged membrane integrity. Myriocin, sphingofungin E, sphingofungin F, 3-methyl-2-oxovaleric acid, gabapentin and sphingofungin C were confirmed as the major differential metabolites by ultra-high-performance liquid chromatography-LTQ orbitrap (UHPLC-LTQ Orbitrap) MS analysis. Quantitative analysis showed that the myriocin content in the CFS was 0.6 μg/mL, and its minimum inhibitory concentration (MIC) was 1.25 μg/mL. It can be speculated that some antifungal compounds in the CFS, including myriocin, sphingofungin E, sphingofungin F and sphingofungin C, play major roles in inhibiting the growth of <i>Fon</i> and the synergistic effects among these antifungal compounds are important in suppressing <i>Fon</i> reproduction. This study suggests that <i>B. amyloliquefaciens</i> LZN01 is a promising biological agent against <i>Fon</i> as its CFS exerts antifungal activity by deforming conidial structures and damaging membranes and myriocin was one of the major functional components of the CFS.
DOI: 10.6084/m9.figshare.8791991.v1
title: Antifungal activity and functional components of cell-free supernatant from <i>Bacillus amyloliquefaciens</i> LZN01 inhibit <i>Fusarium oxysporum</i> f. sp. <i>niveum</i> growth

description: <i>Bacillus amyloliquefaciens</i> LZN01 shows antagonistic behaviour against <i>Fusarium oxysporum</i> f. sp. <i>niveum</i> (<i>Fon</i>). This study aimed to analyze the antifungal activity and the functional components of cell-free supernatant from <i>B. amyloliquefaciens</i> LZN01 that inhibited <i>Fon</i> growth. The results showed that the cell-free supernatant (CFS) from the death phase had stronger antifungal activity against <i>Fon</i> compared to those from the exponential stage and stationary phase. The analyses from scanning and transmission electron microscopy demonstrated that treatment with CFS led to cellular morphological changes, including concave formations on the conidial surface, the disruption of cell walls and membranes, the leakage of intracellular contents and the aggregation of organelles. Confocal laser scanning microscopy revealed that the CFS damaged membrane integrity. Myriocin, sphingofungin E, sphingofungin F, 3-methyl-2-oxovaleric acid, gabapentin and sphingofungin C were confirmed as the major differential metabolites by ultra-high-performance liquid chromatography-LTQ orbitrap (UHPLC-LTQ Orbitrap) MS analysis. Quantitative analysis showed that the myriocin content in the CFS was 0.6 μg/mL, and its minimum inhibitory concentration (MIC) was 1.25 μg/mL. It can be speculated that some antifungal compounds in the CFS, including myriocin, sphingofungin E, sphingofungin F and sphingofungin C, play major roles in inhibiting the growth of <i>Fon</i> and the synergistic effects among these antifungal compounds are important in suppressing <i>Fon</i> reproduction. This study suggests that <i>B. amyloliquefaciens</i> LZN01 is a promising biological agent against <i>Fon</i> as its CFS exerts antifungal activity by deforming conidial structures and damaging membranes and myriocin was one of the major functional components of the CFS.
DOI: 10.6084/m9.figshare.11937720
title: Additional file 9 of Linker histone variant H1t is closely associated with repressed repeat-element chromatin domains in pachytene spermatocytes

description: Additional file 9. H1t and associated heterochromatin-related proteins.
DOI: 10.6084/m9.figshare.11937720.v1
title: Additional file 9 of Linker histone variant H1t is closely associated with repressed repeat-element chromatin domains in pachytene spermatocytes

description: Additional file 9. H1t and associated heterochromatin-related proteins.
DOI: 10.6084/m9.figshare.23098232
title: Table S1 sn-multiome-seq metrics

description: <strong>Table S1</strong>: sn-multiome-seq samples reads and mapping statistics.
DOI: 10.6084/m9.figshare.23098232.v2
title: Table S1 sn-multiome-seq metrics

description: <strong>Table S1</strong>: sn-multiome-seq samples reads and mapping statistics.
DOI: 10.6084/m9.figshare.6694859
title: Additional file 8: of Identification and characterization of long noncoding RNAs and mRNAs expression profiles related to postnatal liver maturation of breeder roosters using Ribo-zero RNA sequencing

description: Table S8. GO enrichment analysis (Pâ &lt;â 0.05) of differentially expressed protein-coding genes targeted by differentially expressed lncRNAs in either trans- or cis- regulatory roles. S gene number: the number of significant differentially expressed lncRNAs whose cis- or trans-regulated mRNAs match to a GO term; TS gene number: the number of significant differentially expressed mRNAs lncRNAs whose cis- or trans-regulated mRNAs have GO annotations; B gene number: the number of detected lncRNAs whose cis- or trans-regulated mRNAs match to a GO term; TB gene number: the number of all detected lncRNAs whose cis- or trans-regulated mRNAs have GO annotations. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.6694859.v1
title: Additional file 8: of Identification and characterization of long noncoding RNAs and mRNAs expression profiles related to postnatal liver maturation of breeder roosters using Ribo-zero RNA sequencing

description: Table S8. GO enrichment analysis (Pâ &lt;â 0.05) of differentially expressed protein-coding genes targeted by differentially expressed lncRNAs in either trans- or cis- regulatory roles. S gene number: the number of significant differentially expressed lncRNAs whose cis- or trans-regulated mRNAs match to a GO term; TS gene number: the number of significant differentially expressed mRNAs lncRNAs whose cis- or trans-regulated mRNAs have GO annotations; B gene number: the number of detected lncRNAs whose cis- or trans-regulated mRNAs match to a GO term; TB gene number: the number of all detected lncRNAs whose cis- or trans-regulated mRNAs have GO annotations. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.23098259
title: TableS2_Clusters.xlsx

description: <strong>Table S2</strong>: sn-multiome-seq cluster annotations with differentially expressed genes and differentially accessible chromatin.
DOI: 10.6084/m9.figshare.23098259.v2
title: Table S2 Clusters

description: <strong>Table S2</strong>: sn-multiome-seq cluster annotations with differentially expressed genes and differentially accessible chromatin.
DOI: 10.6084/m9.figshare.23098253
title: Table S3 Bulk RIN and concentrations

description: <strong>Table S3:</strong> Bulk kidney RNA-seq RNA integrity numbers and concentration.
DOI: 10.6084/m9.figshare.23098253.v2
title: Table S3 Bulk RIN and concentrations

description: <strong>Table S3:</strong> Bulk kidney RNA-seq RNA integrity numbers and concentration.
DOI: 10.6084/m9.figshare.23098262
title: Table S4 DEG.xlsx

description: <strong>Table S4</strong>: Differentially expressed genes (Dehydrated/ad lib) for the kidney sn-multiome-seq.
DOI: 10.6084/m9.figshare.23098262.v2
title: Table S4 DEG

description: <strong>Table S4</strong>: Differentially expressed genes (Dehydrated/ad lib) for the kidney sn-multiome-seq.
DOI: 10.6084/m9.figshare.23098268.v2
title: Table S5 DAC

description: Table S5: Differentially accessible chromatin (Dehydrated/ad lib) for the kidney sn-multiome-seq.
DOI: 10.6084/m9.figshare.23098268
title: Table S5 DAC

description: Table S5: Differentially accessible chromatin (Dehydrated/ad lib) for the kidney sn-multiome-seq.
DOI: 10.6084/m9.figshare.23098271
title: Table S6 Bulk Kidney RNA-seq DEG.

description: <strong>Table S6</strong>: Differentially expressed genes from the bulk kidney RNA-seq.
DOI: 10.6084/m9.figshare.23098271.v2
title: Table S6 Bulk Kidney RNA-seq DEG.

description: <strong>Table S6</strong>: Differentially expressed genes from the bulk kidney RNA-seq.
DOI: 10.6084/m9.figshare.23098280.v2
title: Table S7 DEG_Sex

description: <strong>Table S7</strong>: Gene Ontology analyses for the sn-multiome-seq based upon sex of the mouse.
DOI: 10.6084/m9.figshare.23098280
title: Table S7 DEG_Sex

description: <strong>Table S7</strong>: Gene Ontology analyses for the sn-multiome-seq based upon sex of the mouse.
DOI: 10.5519/qd.h56iyuxq
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5519/qd.9jxjrd5x
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (128 records)
DOI: 10.6084/m9.figshare.14559223
title: Additional file 5 of Metabolome and transcriptome profiling reveals anthocyanin contents and anthocyanin-related genes of chimeric leaves in Ananas comosus var. bracteatus

description: Additional file 5: Table S3: Characteristics of all genes in GR and RE samples of Ananas comosus var. bracteatus chimeric leaves.
DOI: 10.6084/m9.figshare.14559223.v1
title: Additional file 5 of Metabolome and transcriptome profiling reveals anthocyanin contents and anthocyanin-related genes of chimeric leaves in Ananas comosus var. bracteatus

description: Additional file 5: Table S3: Characteristics of all genes in GR and RE samples of Ananas comosus var. bracteatus chimeric leaves.
DOI: 10.6084/m9.figshare.12986401
title: Additional file 5 of Mining and evolution analysis of lateral organ boundaries domain (LBD) genes in Chinese white pear (Pyrus bretschneideri)

description: Additional file 5: Table S2. The synteny block contained PbrLBD duplicated gene pairs.
DOI: 10.6084/m9.figshare.12986401.v1
title: Additional file 5 of Mining and evolution analysis of lateral organ boundaries domain (LBD) genes in Chinese white pear (Pyrus bretschneideri)

description: Additional file 5: Table S2. The synteny block contained PbrLBD duplicated gene pairs.
DOI: 10.6084/m9.figshare.25259938
title: Supplementary Material for: Optical biopsies using probe-based confocal laser endomicroscopy for autoimmune pulmonary alveolar proteinosis

description: Introduction: Increasing numbers of cases of mild asymptomatic pulmonary alveolar proteinosis (PAP) are being reported with the recent increase in chest computed tomography (CT). Bronchoscopic diagnosis of mild PAP is challenging because of the patchy distribution of lesions, which makes it difficult to obtain sufficient biopsy samples. Additionally, the pathological findings of mild PAP, particularly those that differ from severe PAP, have not been fully elucidated. This study aimed to clarify the pathological findings of mild PAP and the usefulness of optical biopsy using probe-based confocal laser endomicroscopy (pCLE).
Methods: We performed bronchoscopic optical biopsy using pCLE and tissue biopsy in five consecutive patients with PAP (three with mild PAP and two with severe PAP). We compared the pCLE images of mild PAP with those of severe PAP by integrating clinical findings, tissue pathology, and chest computed tomography images.
Results: pCLE images of PAP showed giant cells with strong fluorescence, amorphous substances, and thin alveolar walls. Images of affected lesions in mild PAP were equivalent to those obtained in arbitrary lung lesions in severe cases. All three patients with mild PAP spontaneously improved or remained stable after ≥3 years of follow-up. Serum autoantibodies to granulocyte-macrophage colony-stimulating factor were detected in all five cases. 
Conclusion: Optical biopsy using pCLE can yield specific diagnostic findings, even in patients with mild PAP. pCLE images of affected areas in mild and severe PAP showed similar findings, indicating that the dysfunction level of pathogenic alveolar macrophages in affected areas is similar between both disease intensities.
DOI: 10.6084/m9.figshare.7286084.v1
title: Safety of insertion of the copper IUD and LNG-IUS in nulliparous women: a systematic review

description: <b>Objective:</b> Intrauterine contraception (IUC) is one of the more effective contraceptive methods for women at highest risk of unintended pregnancy. This includes younger, often nulliparous, women; however, uptake has been relatively low in this group. <b>Methods:</b> In February 2017 we conducted a systematic review of randomised controlled trials, prospective and retrospective observational studies to identify barriers to IUC use in nulliparous women. <b>Results:</b> Study quality was poor. No differences in rates of infection or expulsions between nulliparous and parous were seen. Fertility rates following removal appeared no different from the general population. Higher rates insertion difficulty, insertion failure and pain during insertion were observed in nulliparous women. <b>Conclusion:</b> A long-acting reversible contraceptive method such as IUC reduces the risk of unintended pregnancy since user failure is minimised. Evidence-based information about the advantages and disadvantages of IUC is required to inform decision-making and dispel any myths and misperceptions. Potential barriers to IUC use in nulliparous women, particularly concerns around infection, significantly higher rates of device expulsion and adverse effects on fertility, do not appear to be justified. IUC is appropriate for all medically-eligible women, including nulliparous women, and should be included in the range of contraceptive options discussed during counselling.
DOI: 10.6084/m9.figshare.25259938.v1
title: Supplementary Material for: Optical biopsies using probe-based confocal laser endomicroscopy for autoimmune pulmonary alveolar proteinosis

description: Introduction: Increasing numbers of cases of mild asymptomatic pulmonary alveolar proteinosis (PAP) are being reported with the recent increase in chest computed tomography (CT). Bronchoscopic diagnosis of mild PAP is challenging because of the patchy distribution of lesions, which makes it difficult to obtain sufficient biopsy samples. Additionally, the pathological findings of mild PAP, particularly those that differ from severe PAP, have not been fully elucidated. This study aimed to clarify the pathological findings of mild PAP and the usefulness of optical biopsy using probe-based confocal laser endomicroscopy (pCLE).
Methods: We performed bronchoscopic optical biopsy using pCLE and tissue biopsy in five consecutive patients with PAP (three with mild PAP and two with severe PAP). We compared the pCLE images of mild PAP with those of severe PAP by integrating clinical findings, tissue pathology, and chest computed tomography images.
Results: pCLE images of PAP showed giant cells with strong fluorescence, amorphous substances, and thin alveolar walls. Images of affected lesions in mild PAP were equivalent to those obtained in arbitrary lung lesions in severe cases. All three patients with mild PAP spontaneously improved or remained stable after ≥3 years of follow-up. Serum autoantibodies to granulocyte-macrophage colony-stimulating factor were detected in all five cases. 
Conclusion: Optical biopsy using pCLE can yield specific diagnostic findings, even in patients with mild PAP. pCLE images of affected areas in mild and severe PAP showed similar findings, indicating that the dysfunction level of pathogenic alveolar macrophages in affected areas is similar between both disease intensities.
DOI: 10.6084/m9.figshare.23642946
title: Combining Historical Maps, Travel Itineraries and Least-Cost Path Modelling to Reconstruct Pre-Modern Travel Routes and Locations in Northern Tigray (Ethiopia)

description: Investigating long-distance travelling routes is crucial for understanding both historical decision-making processes as well as possible regional points of interest that may have been lost in the course of time. Located in the northern Ethiopian highlands, the city of Aksum was the starting and return point for both, Ethiopian, Arabian, and European travellers on the north-south passage to Cairo, Jerusalem or Europe, at least from the fifteenth century onwards. We extracted locations from travel itineraries from the fifteenth and sixteenth centuries and analysed historical maps from the fifteenth to the twentieth centuries. This data was used to calculate several least-cost paths (LCPs). Results suggest that route planning in historical times was in some cases very cost effective, while in others, visiting specific locations may have played a major role in path selection. Additionally, LCPs based on historical waypoints reveal several remarkable historical locations along their way.
DOI: 10.6084/m9.figshare.7286084
title: Safety of insertion of the copper IUD and LNG-IUS in nulliparous women: a systematic review

description: <b>Objective:</b> Intrauterine contraception (IUC) is one of the more effective contraceptive methods for women at highest risk of unintended pregnancy. This includes younger, often nulliparous, women; however, uptake has been relatively low in this group. <b>Methods:</b> In February 2017 we conducted a systematic review of randomised controlled trials, prospective and retrospective observational studies to identify barriers to IUC use in nulliparous women. <b>Results:</b> Study quality was poor. No differences in rates of infection or expulsions between nulliparous and parous were seen. Fertility rates following removal appeared no different from the general population. Higher rates insertion difficulty, insertion failure and pain during insertion were observed in nulliparous women. <b>Conclusion:</b> A long-acting reversible contraceptive method such as IUC reduces the risk of unintended pregnancy since user failure is minimised. Evidence-based information about the advantages and disadvantages of IUC is required to inform decision-making and dispel any myths and misperceptions. Potential barriers to IUC use in nulliparous women, particularly concerns around infection, significantly higher rates of device expulsion and adverse effects on fertility, do not appear to be justified. IUC is appropriate for all medically-eligible women, including nulliparous women, and should be included in the range of contraceptive options discussed during counselling.