cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12123168
title: Supplementary Material for: Long-Term Outcomes after Spleen-Preserving Distal Pancreatectomy for Pancreatic Neuroendocrine Tumors: Results from the US Neuroendocrine Study Group

description: <b><i>Background:</i></b> The adoption of spleen-preserving distal pancreatectomy (SPDP) for malignant disease such as pancreatic neuroendocrine tumors (pNETs) has been controversial. The objective of the current study was to assess the impact of SPDP on outcomes of patients with pNETs. <b><i>Methods:</i></b> Patients undergoing a distal pancreatectomy for pNET between 2002 and 2016 were identified in the US Neuroendocrine Tumor Study Group database. Propensity score matching (PSM) was used to compare short- and long-term outcomes of patients undergoing SPDP versus distal pancreatectomy with splenectomy (DPS). <b><i>Results:</i></b> Among 621 patients, 103 patients (16.6%) underwent an SPDP. Patients who underwent SPDP were more likely to have lower BMI (median, 27.5 [IQR 24.0–31.2] vs. 28.7 [IQR 25.7–33.6]; <i>p</i> = 0.005) and have undergone minimally invasive surgery (<i>n</i> = 56, 54.4% vs. <i>n</i> = 185, 35.7%; <i>p</i> &lt; 0.001). After PSM, while the median total number of lymph nodes examined among patients who underwent an SPDP was lower compared with DPS (3 [IQR 1–8] vs. 9 [5–13]; <i>p</i> &lt; 0.001), 5-year overall survival (OS) and recurrence-free survival (RFS) were comparable (OS: 96.8 vs. 92.0%, log-rank <i>p</i> = 0.21, RFS: 91.1 vs. 84.7%, log-rank <i>p</i> = 0.93). In addition, patients undergoing SPDP had less intraoperative blood loss (median, 100 mL [IQR 10–250] vs. 150 mL [IQR 100–400]; <i>p</i> = 0.001), lower incidence of serious complications (<i>n</i> = 13, 12.8% vs. <i>n</i> = 28, 27.5%; <i>p</i> = 0.014), and shorter length of stay (median: 5 days [IQR 4–7] vs. 6 days [IQR 5–13]; <i>p</i> = 0.049) compared with patients undergoing DPS. <b><i>Conclusion:</i></b> SPDP for pNET was associated with acceptable perioperative and long-term outcomes that were comparable to DPS. SPDP should be considered for patients with pNET.
DOI: 10.6084/m9.figshare.12123165.v1
title: The complex effect of heterogeneity and isolation in determining alpha and beta orchid diversity on islands in the Aegean archipelago

description: Knowledge of factors determining the distribution of plants on islands is of crucial importance in island biogeography. Here the drivers and mechanisms that best explain α- and β-diversity of orchids in the Aegean Archipelago were explored. The analyses were based on (a) matrix of the total number of orchid taxa recorded on each island, and (b) matrix containing the number of grid cells of each island in which each orchid has been recorded. Based on these matrices, generalized linear models (GLMs) were then used to determine the most important factors (geographical, climatic, geological) associated with orchid richness. Generalized dissimilarity modelling (GDM) was used to explore whether there are specific patterns in β-diversity and to evaluate contributions to individual factors to these patterns. To investigate the similarity of the Aegean islands in terms of their orchid flora, a β-diversity abundance matrix was analyzed using non-metric multidimensional scaling ordination method. GLM analysis revealed that maximum elevation, index of bioclimatic breadth (IBB), neighbour index (NI), island area, and the percentage of granite, limestone and quartz at each island were the best predictors of orchid α-diversity. Maximum elevation, habitat heterogeneity, IBB and island area were positively associated with α-diversity, whereas neighbour index and the percentage of granite, limestone and quartz at each island were negatively associated. Maximum elevation, NI, habitat heterogeneity and geographical distance were the best predictors of orchid turnover across the Aegean islands, whereas IBB, granite and limestone were less important. The NMDS ordination revealed that islands are structured from the southernmost to the northernmost, in a way that in general conforms to the phytogeographical division of the Aegean Archipelago. The drivers that account for the patterns in α- and β-diversity were associated with differences in the degrees of isolation and heterogeneity (climatic and habitat) of the islands. Among the predictors, elevation and IBB proved to be better surrogates of habitat heterogeneity than island area.
DOI: 10.6084/m9.figshare.12123168.v1
title: Supplementary Material for: Long-Term Outcomes after Spleen-Preserving Distal Pancreatectomy for Pancreatic Neuroendocrine Tumors: Results from the US Neuroendocrine Study Group

description: <b><i>Background:</i></b> The adoption of spleen-preserving distal pancreatectomy (SPDP) for malignant disease such as pancreatic neuroendocrine tumors (pNETs) has been controversial. The objective of the current study was to assess the impact of SPDP on outcomes of patients with pNETs. <b><i>Methods:</i></b> Patients undergoing a distal pancreatectomy for pNET between 2002 and 2016 were identified in the US Neuroendocrine Tumor Study Group database. Propensity score matching (PSM) was used to compare short- and long-term outcomes of patients undergoing SPDP versus distal pancreatectomy with splenectomy (DPS). <b><i>Results:</i></b> Among 621 patients, 103 patients (16.6%) underwent an SPDP. Patients who underwent SPDP were more likely to have lower BMI (median, 27.5 [IQR 24.0–31.2] vs. 28.7 [IQR 25.7–33.6]; <i>p</i> = 0.005) and have undergone minimally invasive surgery (<i>n</i> = 56, 54.4% vs. <i>n</i> = 185, 35.7%; <i>p</i> &lt; 0.001). After PSM, while the median total number of lymph nodes examined among patients who underwent an SPDP was lower compared with DPS (3 [IQR 1–8] vs. 9 [5–13]; <i>p</i> &lt; 0.001), 5-year overall survival (OS) and recurrence-free survival (RFS) were comparable (OS: 96.8 vs. 92.0%, log-rank <i>p</i> = 0.21, RFS: 91.1 vs. 84.7%, log-rank <i>p</i> = 0.93). In addition, patients undergoing SPDP had less intraoperative blood loss (median, 100 mL [IQR 10–250] vs. 150 mL [IQR 100–400]; <i>p</i> = 0.001), lower incidence of serious complications (<i>n</i> = 13, 12.8% vs. <i>n</i> = 28, 27.5%; <i>p</i> = 0.014), and shorter length of stay (median: 5 days [IQR 4–7] vs. 6 days [IQR 5–13]; <i>p</i> = 0.049) compared with patients undergoing DPS. <b><i>Conclusion:</i></b> SPDP for pNET was associated with acceptable perioperative and long-term outcomes that were comparable to DPS. SPDP should be considered for patients with pNET.
DOI: 10.6084/m9.figshare.12123111
title: Clinical results and microbiota changes after faecal microbiota transplantation for chronic pouchitis: a pilot study

description: <b>Objectives:</b> Research evidence suggests that chronic pouchitis is associated with intestinal dysbiosis. Faecal microbiota transplantation (FMT) has been proposed as a possible treatment. We performed a 6-month prospective, open-label, single-centre cohort pilot-study (NCT03538366) to investigate if FMT could improve clinical outcome and alter gut microbiota in patients with chronic pouchitis. <b>Materials and methods:</b> Nine adult patients with chronic pouchitis were included and allocated to 14 days FMT by enemas from five faecal donors, with a 6-month follow-up. Pouchitis severity was assessed using pouchitis disease activity index (PDAI) before and after FMT. Changes in gut microbiota, and engraftment of donor’s microbiota were assessed in faecal samples. <b>Results:</b> All patients were treated with FMT for 14 continuous days. Overall, four of nine patients receiving FMT were in clinical remission at 30-day follow-up, and three patients remained in remission until 6-month follow-up. Clinical symptoms of pouchitis improved significantly between inclusion and 14-day follow-up (<i>p</i> = .02), but there was no improvement in PDAI between inclusion (mean 8.6) and 30-day follow-up (mean 5.2). Treatment with FMT caused a substantial shift in microbiota and increased microbial diversity in six patients, resembling that of the donors, with a high engraftment of specific donor microbiota. <b>Conclusions:</b> Symptomatic benefit in FMT treatment was found for four of nine patients with chronic pouchitis with increased microbial diversity and high engraftment of donor’s microbiota. A larger, randomised controlled study is required to fully evaluate the potential role of FMT in treating chronic pouchitis.
DOI: 10.6084/m9.figshare.12123111.v1
title: Clinical results and microbiota changes after faecal microbiota transplantation for chronic pouchitis: a pilot study

description: <b>Objectives:</b> Research evidence suggests that chronic pouchitis is associated with intestinal dysbiosis. Faecal microbiota transplantation (FMT) has been proposed as a possible treatment. We performed a 6-month prospective, open-label, single-centre cohort pilot-study (NCT03538366) to investigate if FMT could improve clinical outcome and alter gut microbiota in patients with chronic pouchitis. <b>Materials and methods:</b> Nine adult patients with chronic pouchitis were included and allocated to 14 days FMT by enemas from five faecal donors, with a 6-month follow-up. Pouchitis severity was assessed using pouchitis disease activity index (PDAI) before and after FMT. Changes in gut microbiota, and engraftment of donor’s microbiota were assessed in faecal samples. <b>Results:</b> All patients were treated with FMT for 14 continuous days. Overall, four of nine patients receiving FMT were in clinical remission at 30-day follow-up, and three patients remained in remission until 6-month follow-up. Clinical symptoms of pouchitis improved significantly between inclusion and 14-day follow-up (<i>p</i> = .02), but there was no improvement in PDAI between inclusion (mean 8.6) and 30-day follow-up (mean 5.2). Treatment with FMT caused a substantial shift in microbiota and increased microbial diversity in six patients, resembling that of the donors, with a high engraftment of specific donor microbiota. <b>Conclusions:</b> Symptomatic benefit in FMT treatment was found for four of nine patients with chronic pouchitis with increased microbial diversity and high engraftment of donor’s microbiota. A larger, randomised controlled study is required to fully evaluate the potential role of FMT in treating chronic pouchitis.
DOI: 10.6084/m9.figshare.12123015
title: Dataset Matare T study

description: This stata dta file contains the dataset for MarareT et al study on changes in ART uptake, delays and retention before-during Treat All in Harare, Zimbabwe
DOI: 10.6084/m9.figshare.12122991
title: Supplementary Material for: Integrative Analysis of Long Noncoding RNAs in Patients with Graft-versus-Host Disease

description: <b><i>Background:</i></b> Chronic graft-versus-host disease (cGVHD) remains a major cause of late non-recurrence mortality despite remarkable improvements in the field of allogeneic hematopoietic stem cell transplantation. Although recent studies have found that B-cell receptor (BCR)-activated B cells contribute to pathogenesis in cGVHD, the specific molecular mechanisms of B cells in this process remain unclear. <b><i>Methods:</i></b> In our study, human long noncoding RNA (lncRNA) microarrays and bioinformatic analysis were performed to identify different expressions of lncRNAs in peripheral blood B cells from cGVHD patients compared with healthy ones. The differential expression of lncRNA was confirmed in additional samples by quantitative real-time polymerase chain reaction (qRT-PCR). <b><i>Results:</i></b> The microarray analysis revealed that 106 of 198 differentially expressed lncRNAs were upregulated and 92 were downregulated in cGVHD patients compared with healthy controls. Intergenic lncRNAs accounted for the majority of differentially expressed lncRNAs. A KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that the differentially expressed mRNAs, which were coexpressed with lncRNA, between the cGVHD group and the healthy group were significantly enriched in the BCR signaling pathway. Further analysis of the BCR signaling pathway and its coexpression network identified three lncRNAs with the strongest correlation with BCR signaling and cGVHD, as well as a series of protein-coding genes and transcription factors associated with them. The three candidate lncRNAs were further validated in another group of cGVHD patients by qRT-PCR. <b><i>Conclusions:</i></b> This is the first study on the correlation between lncRNA and cGVHD using lncRNA microarray analysis. Our study provides novel enlightenment in exploring the molecular pathogenesis of cGVHD.
DOI: 10.6084/m9.figshare.12123015.v2
title: Dataset Matare T study

description: This stata dta file contains the dataset for MarareT et al study on changes in ART uptake, delays and retention before-during Treat All in Harare, Zimbabwe
DOI: 10.6084/m9.figshare.12122973
title: Supplementary Material for: Seasonal Variation in Activity Budget of Assamese Macaques in Limestone Forest of Southwest Guangxi, China

description: The activity budget is important for understanding behavioural variability and adaptation in primates. Assamese macaques (<i>Macaca assamensis</i>) found in the limestone forest of Guangxi Nonggang National Nature Reserve, Southwest China, primarily feed on young leaves of <i>Bonia saxatilis</i> (a shrubby, karst-endemic bamboo). To understand how a specific bamboo leaf-based diet and ecological factors affect activity budget, one group of Assamese macaques was studied using instantaneous scan sampling for 1 year. The macaques spent most of their time feeding (32.7 ± 5.4%), followed by resting (28.6 ± 6.3%), moving (28.6 ± 5.3%), grooming (8.0 ± 3.0%), playing (1.7 ± 1.6%) and other activities (0.4 ± 0.2%). Their activity budget was similar to that of typical frugivorous primates and bamboo-dominated primates, which spent more time on active behaviours (feeding and moving, 61.3 ± 6.0%) than on inactive behaviours (resting and grooming, 36.6 ± 6.4%). The macaques spent significantly more time resting during the fruit-lean season and more time moving during the fruit-rich season. Their activity budget was significantly affected by diet. Resting time increased with decreased fruit consumption, whereas moving time decreased with the increasing mature leaf consumption. Playing time decreased when the macaques consumed more young bamboo leaves. The activity budget was also influenced by food availability and climatic factors. Resting time increased with decreasing temperature, whereas moving time increased with increasing day length and young leaf availability. Grooming time increased with decreasing day length and increasing temperature, and playing time increased with increasing day length. Our findings provide evidence of the importance of diet, food availability, temperature and day length in coping with seasonal variation in ecological factors, highlighting the need to increase knowledge of the behavioural ecology of the Assamese macaques living in the unique limestone forest and to understand the influence of a bamboo-dominated diet and ecological factors on their survival.
DOI: 10.6084/m9.figshare.12123015.v1
title: Dataset Matare T study

description: This stata dta file contains the dataset for MarareT et al study on changes in ART uptake, delays and retention before-during Treat All in Harare, Zimbabwe
DOI: 10.25392/leicester.data.12122952
title: Flexible Parafoveal Encoding of Character Order Supports Word Predictability Effects in Chinese Reading: Evidence from Eye Movements

description: These are data for an eye movement experiment investigating the influence of contextual predictability on parafoveal processing of character transpositions during Chinsese reading. The files include an excel file containing the eye movement data and a file containing the code used to conduct linear mixed-effects analyses of these data in R.
DOI: 10.6084/m9.figshare.12122967
title: faded_test_002.tar.gz

description: 2/2 test data
DOI: 10.6084/m9.figshare.12122862
title: Supplementary Material for: Modulation of Airway Epithelial Innate Immunity and Wound Repair by M(GM-CSF) and M(M-CSF) Macrophages

description: Airway epithelial cells and macrophages participate in inflammatory responses to external noxious stimuli, which can cause epithelial injury. Upon injury, epithelial cells and macrophages act in concert to ensure rapid restoration of epithelial integrity. The nature of the interactions between these cell types during epithelial repair is incompletely understood. We used an in vitro human coculture model of primary bronchial epithelial cells cultured at the air-liquid interface (ALI-PBEC) and polarized primary monocyte-derived macrophages. Using this coculture, we studied the contribution of macrophages to epithelial innate immunity, wound healing capacity, and epithelial exposure to whole cigarette smoke (WCS). Coculture of ALI-PBEC with lipopolysaccharide (LPS)-activated M(GM-CSF) macrophages increased the expression of <i>DEFB4A</i>, <i>CXCL8</i>, and <i>IL6</i> at 24 h in the ALI-PBEC, whereas LPS-activated M(M-CSF) macrophages only increased epithelial <i>IL6</i> expression. Furthermore, wound repair was accelerated by coculture with both activated M(GM-CSF) and M(M-CSF) macrophages, also following WCS exposure. Coculture of ALI-PBEC and M(GM-CSF) macrophages resulted in increased <i>CAMP</i> expression in M(GM-CSF) macrophages, which was absent in M(M-CSF) macrophages. <i>CAMP</i> encodes LL-37, an antimicrobial peptide with immune-modulating and repair-enhancing activities. In conclusion, dynamic crosstalk between ALI-PBEC and macrophages enhances epithelial innate immunity and wound repair, even upon concomitant cigarette smoke exposure.
DOI: 10.6084/m9.figshare.12122934
title: faded_test_001.tar.gz

description: 1/2 test data CAPTCHA.
DOI: 10.6084/m9.figshare.12122967.v1
title: faded_test_002.tar.gz

description: 2/2 test data
DOI: 10.25392/leicester.data.12122952.v1
title: Flexible Parafoveal Encoding of Character Order Supports Word Predictability Effects in Chinese Reading: Evidence from Eye Movements

description: These are data for an eye movement experiment investigating the influence of contextual predictability on parafoveal processing of character transpositions during Chinsese reading. The files include an excel file containing the eye movement data and a file containing the code used to conduct linear mixed-effects analyses of these data in R.
DOI: 10.6084/m9.figshare.12122853
title: faded_train_008.tar.gz

description: 8/8 train faded captcha dataset
DOI: 10.6084/m9.figshare.12122850
title: MinimalDataset_BSEM_ComorbidityLD.sav

description: This is the minimal dataset used for data analysis in our manuscript.
DOI: 10.6084/m9.figshare.12122853.v1
title: faded_train_008.tar.gz

description: 8/8 train faded captcha dataset
DOI: 10.6084/m9.figshare.12122934.v1
title: faded_test_001.tar.gz

description: 1/2 test data CAPTCHA.
DOI: 10.6084/m9.figshare.12122850.v1
title: MinimalDataset_BSEM_ComorbidityLD.sav

description: This is the minimal dataset used for data analysis in our manuscript.
DOI: 10.18119/n9jk5h
title: IMEx/IntAct Coronavirus Dataset: SARS-CoV-2 + human context
DOI: 10.6084/m9.figshare.12122277
title: Supplementary Material for: Application of 17 Contrast-Induced Acute Kidney Injury Risk Prediction Models

description: <b><i>Introduction:</i></b> Contrast-induced acute kidney injury (CI-AKI) is a frequent complication of percutaneous coronary interventions (PCI). Various groups have developed and validated risk scores for CI-AKI. Although the majority of these risk scores achieve an adequate accuracy, their usability in clinical practice is limited and greatly debated. <b><i>Objective:</i></b> With the present study, we aimed to prospectively assess the diagnostic performance of recently published CI-AKI risk scores (up to 2018) in a cohort of patients undergoing PCI. <b><i>Methods:</i></b> We enrolled 1,247 consecutive patients (80% men, mean age 62 ± 10 years) treated with elective or urgent PCI. For each patient, we calculated the individual CI-AKI risk score based on 17 different risk models. CI-AKI was defined as an increase of ≥25% (liberal) or ≥0.5 mg/dL (strict) in pre-PCI serum creatinine 48 h after PCI. <b><i>Results:</i></b> CI-AKI definition and, therefore, CI-AKI incidence have a significant impact on risk model performance (median negative predictive value increased from 85 to 99%; median c-statistic increased from 0.516 to 0.603 using more strict definition criteria). All of the 17 published models were characterized by a weak-to-moderate discriminating ability mainly based on the identification of “true-negative” cases (median positive predictive value 19% with liberal criterion and 3% with strict criterion). In none of the models, c-statistic was &gt;0.800 with either CI-AKI definition. Novel, different combinations of the &gt;35 independent variables used in the published models either by down- or by up-scaling did not result in significant improvement in predictive performance. <b><i>Conclusions:</i></b> The predictive ability of all models was similar and only modest, derived mainly by identifying true-negative cases. A new approach is probably needed by adding novel markers or periprocedural characteristics.
DOI: 10.6084/m9.figshare.12122010
title: Supplementary Material for: Neoadjuvant Radio(chemo)therapy for Breast Cancer: An Old Concept Revisited

description: <b><i>Background:</i></b> The international standard of care for the treatment of high-risk breast cancer (BC) consists of neoadjuvant chemotherapy (NACT) and surgery followed by adjuvant whole breast/chest wall irradiation. In this setting, the time interval from the start of NACT to the end of radiotherapy (RT) is usually postponed to 6 months or longer. In addition to this, a high percentage of capsular fibrosis may occur when breast implants are irradiated. Most of these disadvantages could be avoided by using preoperative RT (PRT). PRT is already the standard of care in several other tumor entities (rectal cancer, esophagus carcinoma, lung cancer, and soft tissue sarcoma). Nevertheless, PRT in BC has been tested in several trials, but randomized prospective trials using modern radiation technology and systemic therapies are lacking. The available evidence summarized in this review indicates that PRT may improve survival and reduce long-term toxicity in patients with a higher risk of recurrence and should be consequently tested in a randomized trial. <b><i>Summary:</i></b> Prospective, randomized trials concerning PRT in high-risk BC are needed. We plan to conduct a NeoRad trial (NACT followed by PRT in high-risk BC). <b><i>Key Messages:</i></b> Prospective, randomized studies concerning PRT in high-risk BC are needed.