cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16616041
title: Supplementary Material for: A 3-Gene-Based Diagnostic Signature in Alzheimer’s Disease

description: <b><i>Background:</i></b> Alzheimer’s disease (AD) is a chronic neurodegenerative disease. In this study, potential diagnostic biomarkers were identified for AD. <b><i>Methods:</i></b> All AD samples and healthy samples were collected from 2 datasets in the GEO database, in which differentially expressed genes (DEGs) were analyzed by using the limma package of R language. GO and KEGG pathway enrichment was conducted basing on the DEGs via the clusterProfiler package of R. And, the PPI network construction and gene prediction were performed using the STRING database and Cytoscape. Then, a logistic regression model was constructed to predict the sample type. <b><i>Results:</i></b> Bioinformatic analysis of GEO datasets revealed 2,063 and 108 DEGs in GSE5281 and GSE4226 datasets, separately, and 15 overlapping DEGs were found. GO and KEGG enrichment analysis revealed terms associated with neurodevelopment. Then, we built a logistic regression model based on the hub genes from the PPI network and optimized the model to 3 genes (ALDOA, ENC1, and NFKBIA). The values of area under the curve of the training set GSE5281 and testing set GSE4226 were 0.9647 and 0.7857, respectively, which implied the efficacy of this model. <b><i>Conclusion:</i></b> The comprehensive bioinformatic analysis of gene expression in AD patients and the effective logistic regression model built in our study may provide promising research value for diagnostic methods of AD.
DOI: 10.6084/m9.figshare.16616041.v1
title: Supplementary Material for: A 3-Gene-Based Diagnostic Signature in Alzheimer’s Disease

description: <b><i>Background:</i></b> Alzheimer’s disease (AD) is a chronic neurodegenerative disease. In this study, potential diagnostic biomarkers were identified for AD. <b><i>Methods:</i></b> All AD samples and healthy samples were collected from 2 datasets in the GEO database, in which differentially expressed genes (DEGs) were analyzed by using the limma package of R language. GO and KEGG pathway enrichment was conducted basing on the DEGs via the clusterProfiler package of R. And, the PPI network construction and gene prediction were performed using the STRING database and Cytoscape. Then, a logistic regression model was constructed to predict the sample type. <b><i>Results:</i></b> Bioinformatic analysis of GEO datasets revealed 2,063 and 108 DEGs in GSE5281 and GSE4226 datasets, separately, and 15 overlapping DEGs were found. GO and KEGG enrichment analysis revealed terms associated with neurodevelopment. Then, we built a logistic regression model based on the hub genes from the PPI network and optimized the model to 3 genes (ALDOA, ENC1, and NFKBIA). The values of area under the curve of the training set GSE5281 and testing set GSE4226 were 0.9647 and 0.7857, respectively, which implied the efficacy of this model. <b><i>Conclusion:</i></b> The comprehensive bioinformatic analysis of gene expression in AD patients and the effective logistic regression model built in our study may provide promising research value for diagnostic methods of AD.
DOI: 10.5519/qd.ayvyvcx6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1001 records)
DOI: 10.5519/qd.sxgotat0
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (997 records)
DOI: 10.6084/m9.figshare.16616062
title: Supplementary Material for: Platelet Decreases following Continuous Renal Replacement Therapy Initiation as a Novel Risk Factor for Renal Nonrecovery

description: <b><i>Background:</i></b> Continuous renal replacement therapy (CRRT) is a form of dialysis used in critically ill patients, and has recently been associated with renal nonrecovery. Decreases in platelets following CRRT initiation are common and are associated with mortality, but associations with renal recovery are unclear. Our objective was to determine if platelet nadir or the degree of platelet decrease following CRRT initiation was associated with renal nonrecovery. <b><i>Methods:</i></b> This is a secondary analysis of the Randomized Evaluation of Normal versus Augmented Level (RENAL) trial. Primary predictors were platelet nadir discretized by median value and percent platelet decrease following CRRT initiation, with cut points evaluated by decile from 30 to 60%. The 2 primary outcomes were time to RRT-independence and RRT-free days. Secondary outcomes were 28-day mortality, 90-day mortality, intensive care unit (ICU)-free, and hospital-free days. <b><i>Results:</i></b> Time to RRT independence censored for death was achieved less frequently in patients with low platelet nadir (hazard ratio [HR] 0.77, confidence interval [CI] 0.66–0.91) and in those with &gt;50% platelet decrease (HR 0.84, CI 0.72–0.97). RRT-free days were lower in both low platelet nadir (odds ratio [OR] 0.94, CI 0.90–0.97) and &gt;50% platelet decrease (OR 0.91, CI 0.88–0.95). These groups also had higher rates of 28- and 90-day mortality and fewer ICU-free and hospital-free days. Thrombocytopenia at CRRT initiation was also associated with renal nonrecovery, although the clinical effect was small. <b><i>Conclusions:</i></b> Platelet nadir &lt;100 × 10<sup>3</sup>/µL and platelet decrease by &gt;50% following CRRT initiation were both associated with lower rates of renal recovery. Further research is needed to evaluate mechanisms-linking platelet changes and renal nonrecovery in CRRT.
DOI: 10.6084/m9.figshare.14994210.v2
title: Improved chromosome-level genome assembly and annotation of Chinese shrimp (Fenneropenaeus chinensis)

description: A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp <i>Fenneropenaeus chinensis</i> was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled <i>F. chinensis</i> genome was 1.47 Gb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. <br>
DOI: 10.5281/zenodo.5506594
title: Observation of Pauli blocking in light scattering from quantum degenerate fermions

description: The experimental data and code required to calculate the modelling results.
DOI: 10.5281/zenodo.5506593
title: Observation of Pauli blocking in light scattering from quantum degenerate fermions

description: The experimental data and code required to calculate the modelling results.
DOI: 10.5281/zenodo.5506598
title: Photogrammetry-derived bathymetry for the Penghu Islands

description: Photogrammetry-derived bathymetry for the Penghu Islands
DOI: 10.5281/zenodo.5506597
title: Photogrammetry-derived bathymetry for the Penghu Islands

description: Photogrammetry-derived bathymetry for the Penghu Islands
DOI: 10.6084/m9.figshare.16616107
title: Supplementary Material for: Attitude Matters! How Attitude towards Bariatric Surgery Influences the Effects of Behavioural Weight Loss Treatment

description: <b><i>Introduction:</i></b> Multidisciplinary obesity services at university hospitals usually treat patients with more complex and severe obesity. In addition, patients with Class 3 obesity, in particular, have different attitudes regarding the choices of therapy. <b><i>Methods:</i></b> This explorative study investigated the effect of patient attitudes towards bariatric surgery on body weight change (primary outcome) and psychological improvement (secondary outcomes: quality of life, depression, anxiety, and eating behaviour) in a 6-month moderate behavioural weight loss (BWL) programme in a university outpatient setting. <b><i>Results:</i></b> 297 patients with mostly Class 3 obesity participated in the programme. The patients did not yet have any indications for bariatric surgery. Of the participants, 37% had a positive attitude towards bariatric surgery (POS), whereas 38% had a negative attitude (NEG). The drop-out rate was 8%. NEG participants lost significantly more body weight than the POS participants (intention-to-treat population: 4.5 [SD: 6.3] kg versus 0.4 [SD: 5.8] kg; <i>p</i> &lt; 0.001). In both subgroups, anxiety, depression, the mental score for quality of life, and eating behaviour improved. <b><i>Conclusion:</i></b> A BWL treatment in a clinical setting identified 2 distinct groups with different attitudes towards bariatric surgery that were associated with different body weight change outcomes. These groups may require differently targeted programmes to achieve the best body weight loss results.
DOI: 10.6084/m9.figshare.15052765
title: Bisphosphonate treatment in children with acute lymphoblastic leukemia and osteonecrosis – radiological and clinical findings in a national cohort

description: <b>Background: </b>Osteonecrosis (ON) is a recognized complication of childhood ALL, but its optimal management remains unestablished. This study evaluated the effect of bisphosphonate (BP) treatment on the evolution of ON lesions in childhood ALL. <b>Material and Methods: </b>We included a national cohort of ALL patients diagnosed with symptomatic ON before 18 years of age and treated with BPs (<i>N</i> = 10; five males). Patients were followed both clinically and with serial MRIs. ON lesions were graded according to the Niinimäki classification. <b>Results: </b>The 10 patients had a total of 55 ON lesions. The median age was 13.3 years at ALL diagnosis and 14.8 years at ON diagnosis. Four patients had received HSCT before the ON diagnosis. BPs used were pamidronate (<i>N</i> = 7), alendronate (<i>N</i> = 2) and ibandronate (<i>N</i> = 1). The duration of BP treatment varied between 4 months and 4 years. In 4/10 patients, BP treatment was given during the chemotherapy. BPs were well-tolerated, with no severe complications or changes in kidney function. At the end of follow up 13/55 (24%) ON lesions were completely healed both clinically and radiographically; all these lesions were originally graded 3 or less. In contrast, ON lesions originally classified as grade 5 (joint destruction; <i>N</i> = 4) remained at grade 5. All grade 5 hip joint lesions needed surgical treatment. During BP treatment, the pain was relieved in 7/10 patients. At the end of follow-up, none of the patients reported severe or frequent pain. <b>Conclusion: </b>BP treatment was safe and seemed effective in relieving ON-induced pain in childhood ALL. After articular collapse (grade 5) lesions did not improve with BP treatment. Randomized controlled studies are needed to further elucidate the role of BPs in childhood ALL-associated ON.
DOI: 10.6084/m9.figshare.14737595
title: High density of cytotoxic T-lymphocytes is linked to tumoral PD-L1 expression regardless of the mismatch repair status in colorectal cancer

description: Immune checkpoint-inhibitors targeting the PD-1/PD-L1 system are FDA approved in microsatellite instable (MSI) or mismatch repair deficient (dMMR) colorectal cancer (CRC). PD-L1 expression is tightly linked to features connected to immune checkpoint inhibitor response, but studies on large subsets of cancers analyzing the correlation between different status of MSI/dMMR, tumor infiltrating lymphocytes and PD-L1 expression are still lacking. More than 1800 CRC were analyzed for PD-L1 by immunohistochemistry in a tissue microarray format. Data were compared to MMR, the number of intratumoral CD8<sup>+</sup> cytotoxic T-cells, and adverse clinico-pathological parameters. Different cutoff levels for defining PD-L1 positivity in tumor cells (1%, 5%, 10%, and 50%) yielded comparable results. At a cutoff level of 5%, PD-L1 positivity was seen in 5.1% of tumors. PD-L1 was more often positive in dMMR (18.6%) than in MMR proficient (pMMR) cancers (4.1%; <i>p</i> + lymphocytes was strikingly higher in PD-L1 positive (939.5 ± 118.2) than in PD-L1 negative cancers (310.5 ± 24.8). A higher number of intratumoral CD8<sup>+</sup> lymphocytes was found in dMMR CRC (PD-L1 positive: 1999.7 ± 322.0; PD-L1 negative: 398.6 ± 128.0; <i>p</i> p +, low tumor stage, and absence of lymph node metastasis and lymphatic/venous invasion (<i>p</i> The data support the previously suggested fact that PD-L1 expression in tumor cells is driven by extensive cytotoxic T-cell infiltration in highly immunogenic dMMR and pMMR CRC. Frequent and intense PD-L1 expression in tumor cells of dMMR CRC may contribute to the high response rates of dMMR CRC to immune checkpoint-inhibitors.
DOI: 10.6084/m9.figshare.15052765.v1
title: Bisphosphonate treatment in children with acute lymphoblastic leukemia and osteonecrosis – radiological and clinical findings in a national cohort

description: <b>Background: </b>Osteonecrosis (ON) is a recognized complication of childhood ALL, but its optimal management remains unestablished. This study evaluated the effect of bisphosphonate (BP) treatment on the evolution of ON lesions in childhood ALL. <b>Material and Methods: </b>We included a national cohort of ALL patients diagnosed with symptomatic ON before 18 years of age and treated with BPs (<i>N</i> = 10; five males). Patients were followed both clinically and with serial MRIs. ON lesions were graded according to the Niinimäki classification. <b>Results: </b>The 10 patients had a total of 55 ON lesions. The median age was 13.3 years at ALL diagnosis and 14.8 years at ON diagnosis. Four patients had received HSCT before the ON diagnosis. BPs used were pamidronate (<i>N</i> = 7), alendronate (<i>N</i> = 2) and ibandronate (<i>N</i> = 1). The duration of BP treatment varied between 4 months and 4 years. In 4/10 patients, BP treatment was given during the chemotherapy. BPs were well-tolerated, with no severe complications or changes in kidney function. At the end of follow up 13/55 (24%) ON lesions were completely healed both clinically and radiographically; all these lesions were originally graded 3 or less. In contrast, ON lesions originally classified as grade 5 (joint destruction; <i>N</i> = 4) remained at grade 5. All grade 5 hip joint lesions needed surgical treatment. During BP treatment, the pain was relieved in 7/10 patients. At the end of follow-up, none of the patients reported severe or frequent pain. <b>Conclusion: </b>BP treatment was safe and seemed effective in relieving ON-induced pain in childhood ALL. After articular collapse (grade 5) lesions did not improve with BP treatment. Randomized controlled studies are needed to further elucidate the role of BPs in childhood ALL-associated ON.
DOI: 10.6084/m9.figshare.14737595.v1
title: High density of cytotoxic T-lymphocytes is linked to tumoral PD-L1 expression regardless of the mismatch repair status in colorectal cancer

description: Immune checkpoint-inhibitors targeting the PD-1/PD-L1 system are FDA approved in microsatellite instable (MSI) or mismatch repair deficient (dMMR) colorectal cancer (CRC). PD-L1 expression is tightly linked to features connected to immune checkpoint inhibitor response, but studies on large subsets of cancers analyzing the correlation between different status of MSI/dMMR, tumor infiltrating lymphocytes and PD-L1 expression are still lacking. More than 1800 CRC were analyzed for PD-L1 by immunohistochemistry in a tissue microarray format. Data were compared to MMR, the number of intratumoral CD8<sup>+</sup> cytotoxic T-cells, and adverse clinico-pathological parameters. Different cutoff levels for defining PD-L1 positivity in tumor cells (1%, 5%, 10%, and 50%) yielded comparable results. At a cutoff level of 5%, PD-L1 positivity was seen in 5.1% of tumors. PD-L1 was more often positive in dMMR (18.6%) than in MMR proficient (pMMR) cancers (4.1%; <i>p</i> + lymphocytes was strikingly higher in PD-L1 positive (939.5 ± 118.2) than in PD-L1 negative cancers (310.5 ± 24.8). A higher number of intratumoral CD8<sup>+</sup> lymphocytes was found in dMMR CRC (PD-L1 positive: 1999.7 ± 322.0; PD-L1 negative: 398.6 ± 128.0; <i>p</i> p +, low tumor stage, and absence of lymph node metastasis and lymphatic/venous invasion (<i>p</i> The data support the previously suggested fact that PD-L1 expression in tumor cells is driven by extensive cytotoxic T-cell infiltration in highly immunogenic dMMR and pMMR CRC. Frequent and intense PD-L1 expression in tumor cells of dMMR CRC may contribute to the high response rates of dMMR CRC to immune checkpoint-inhibitors.
DOI: 10.6084/m9.figshare.14732143.v1
title: Plasma circulating cell free messenger RNA as a potential biomarker of melanoma

description: Blood borne cell free nucleic acids are increasingly emerging as significant non-invasive adjuncts to current methods of disease status evaluation in cancer patients. In this study, we sought to examine whether significant differences exist in the plasma transcriptomic profile of advanced melanoma patients with a high disease burden compared to patients with a low disease burden or therapeutic response. Pathway focussed gene expression analysis was performed using cDNA derived from the plasma circulating cell free messenger ribonucleic acid (ccfmRNA) samples of twenty-two patients with advanced melanoma. Patients were assessed with paired blood sample collection and CT scan assessments at baseline and at 3 months follow up. We identified several genes which were significantly over-expressed in patients with a low disease burden or therapeutic response; BCL2L1, CXCL9, IDO1, IL13, MIF, MYD88 and TLR4 (<i>p</i> ≤ 0.001, versus high disease burden). There was an increase in the magnitude of fold change (2^ (-dd CT)) of BCL2L1 (<i>p</i> = 0.031), CCL4 (<i>p</i> = 0.001), CCL5 (<i>p</i> = 0.043), CXCL9 (<i>p</i> = 0.012), GZMB (<i>p</i> = 0.023) and TNFSF10 (<i>p</i> = 0.039) genes in patients with therapeutic response at 3 months follow up assessment relative to baseline assessment. Moreover, in stage IV melanoma patients with brain metastases, CCL18, CCR1, CCR4, CD274, CSF2, EGF, and PTGS2 genes were significantly over-expressed (<i>p</i> Significant differences were observed in the plasma transcriptomic profile between the various melanoma patient groups, and we postulate that these differences may be exploited to identify novel therapeutic targets or biomarkers relevant to melanoma.
DOI: 10.6084/m9.figshare.14798019
title: Purchase of prophylactic topical corticosteroids is associated with improved survival in NSCLCs treated with EGFR TKI: real-world cohort study

description: With the first- and second-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), clinical benefit and rash correlate together. EGFR TKI-induced rash can be alleviated with topical corticosteroids and tetracyclines. This study investigates whether prophylaxis with topical corticosteroids is associated with improved survival among the EGFR TKI-treated non-small cell lung cancers (NSCLCs). We collected all the patients (<i>n</i> = 1271) who had received reimbursement for the first- or second-generation EGFR TKIs in Finland 2011–2016, had purchased TKIs, and had data available at the Finnish Cancer Registry (FCR). Survival was analyzed from the first EGFR TKI purchase to death or the end of follow-up, and patients were stratified according to the TKIs, purchases of topical corticosteroids, and their timing. A total of 270 (21%) patients had corticosteroid purchases −14 to +200 d (all), and 196 (15%) had purchased corticosteroids as prophylaxis (−14 to +14 d) from the first EGFR TKI purchase. Corticosteroid purchases were associated with improved survival in all (0.64 95% CI 0.56–0.74) and prophylactic (0.78, 95% CI 0.66–0.92) groups when compared to non-purchasers, although these results were limited to the erlotinib users only. The survival benefit of prophylactic corticosteroids among the erlotinib users remained in multivariate analysis including sex, stage, histology, and tetracycline prophylaxis (HR 0.78, 95% CI 0.64–0.95). The prophylactic use of corticosteroids was associated with a longer erlotinib treatment duration (HR 0.75, 95% CI 0.64–0.90). Prophylactic topical corticosteroids may improve the survival of NSCLC patients treated with EGFR TKIs, and they should be considered as prophylaxis when initiating EGFR TKIs with a high incidence of rash.
DOI: 10.6084/m9.figshare.14798019.v1
title: Purchase of prophylactic topical corticosteroids is associated with improved survival in NSCLCs treated with EGFR TKI: real-world cohort study

description: With the first- and second-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), clinical benefit and rash correlate together. EGFR TKI-induced rash can be alleviated with topical corticosteroids and tetracyclines. This study investigates whether prophylaxis with topical corticosteroids is associated with improved survival among the EGFR TKI-treated non-small cell lung cancers (NSCLCs). We collected all the patients (<i>n</i> = 1271) who had received reimbursement for the first- or second-generation EGFR TKIs in Finland 2011–2016, had purchased TKIs, and had data available at the Finnish Cancer Registry (FCR). Survival was analyzed from the first EGFR TKI purchase to death or the end of follow-up, and patients were stratified according to the TKIs, purchases of topical corticosteroids, and their timing. A total of 270 (21%) patients had corticosteroid purchases −14 to +200 d (all), and 196 (15%) had purchased corticosteroids as prophylaxis (−14 to +14 d) from the first EGFR TKI purchase. Corticosteroid purchases were associated with improved survival in all (0.64 95% CI 0.56–0.74) and prophylactic (0.78, 95% CI 0.66–0.92) groups when compared to non-purchasers, although these results were limited to the erlotinib users only. The survival benefit of prophylactic corticosteroids among the erlotinib users remained in multivariate analysis including sex, stage, histology, and tetracycline prophylaxis (HR 0.78, 95% CI 0.64–0.95). The prophylactic use of corticosteroids was associated with a longer erlotinib treatment duration (HR 0.75, 95% CI 0.64–0.90). Prophylactic topical corticosteroids may improve the survival of NSCLC patients treated with EGFR TKIs, and they should be considered as prophylaxis when initiating EGFR TKIs with a high incidence of rash.
DOI: 10.6084/m9.figshare.14732143
title: Plasma circulating cell free messenger RNA as a potential biomarker of melanoma

description: Blood borne cell free nucleic acids are increasingly emerging as significant non-invasive adjuncts to current methods of disease status evaluation in cancer patients. In this study, we sought to examine whether significant differences exist in the plasma transcriptomic profile of advanced melanoma patients with a high disease burden compared to patients with a low disease burden or therapeutic response. Pathway focussed gene expression analysis was performed using cDNA derived from the plasma circulating cell free messenger ribonucleic acid (ccfmRNA) samples of twenty-two patients with advanced melanoma. Patients were assessed with paired blood sample collection and CT scan assessments at baseline and at 3 months follow up. We identified several genes which were significantly over-expressed in patients with a low disease burden or therapeutic response; BCL2L1, CXCL9, IDO1, IL13, MIF, MYD88 and TLR4 (<i>p</i> ≤ 0.001, versus high disease burden). There was an increase in the magnitude of fold change (2^ (-dd CT)) of BCL2L1 (<i>p</i> = 0.031), CCL4 (<i>p</i> = 0.001), CCL5 (<i>p</i> = 0.043), CXCL9 (<i>p</i> = 0.012), GZMB (<i>p</i> = 0.023) and TNFSF10 (<i>p</i> = 0.039) genes in patients with therapeutic response at 3 months follow up assessment relative to baseline assessment. Moreover, in stage IV melanoma patients with brain metastases, CCL18, CCR1, CCR4, CD274, CSF2, EGF, and PTGS2 genes were significantly over-expressed (<i>p</i> Significant differences were observed in the plasma transcriptomic profile between the various melanoma patient groups, and we postulate that these differences may be exploited to identify novel therapeutic targets or biomarkers relevant to melanoma.