cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10635618
title: HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology - Model Weights

description: This repository contains trained weights for:

HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology

(Under review at MIDL2024)

More information and code are available at https://github.com/digitalpathologybern/hover_next_inference

lizard_convnextv2_large,lizard_convnextv2_base and lizard_convnextv2_tiny correspond to HoVer-NeXt_Large,HoVer-NeXt_Base and HoVer-NeXt_Tiny.

pannuke_convnextv2_tiny_* corresponds to the weights trained on the specific pannuke split.
DOI: 10.34740/kaggle/dsv/7610049
title: AutoXGB
DOI: 10.5281/zenodo.10636591
title: HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology - Datasets

description: This repository contains training and validation data for

HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology 

(Under review at MIDL2024)

More information and code are available at https://github.com/digitalpathologybern/hover_next_inference

Modified Lizard dataset to include mitosis (lizard_mitosis.zip), mitosis dataset (mitosis_ds.zip) and a holdout eosinophil validation set (eos_eval.zip)

mitosis_ds.zip also contains the hold-out H&E mitosis test set.

The original lizard dataset was createdy by Simon Graham et al. and was shared under CC BY-NC-SA 4.0. The tile-based dataset can be downloaded from https://conic-challenge.grand-challenge.org/Data/ after registering for the challenge. We modify the dataset by including an additional mitosis class, however note that there are a number of mitosis which are still not (correctly annotated).
DOI: 10.34740/kaggle/dsv/7610050
title: OnlineFree
DOI: 10.6084/m9.figshare.14289385
title: In vivo and in vitro study of co-expression of LMP1 and Cripto-1 in nasopharyngeal carcinoma

description: Abstract Introduction: Nasopharyngeal carcinoma, an epithelial-derived malignant tumor which because of its anatomical location and atypical early symptoms, when diagnosed invasion and metastasis often have occurred. This requires a better understanding of the development mechanism, identifying diagnostic markers, and developing new treatment strategies. Objective: To study the relationship of LMP1 and Cripto-1 in nasopharyngeal carcinoma. Methods: The expression of LMP1 and Cripto-1 in specimens obtained from nasopharyngeal carcinoma patients (n = 42) and nasopharyngitis patients (n = 22) were examined. The expression of LMP1 and Cripto-1 in LMP1-negative and LMP1-positive (CNE1-LMP1) cells were also examined. Results: The expression of LMP1 and Cripto-1 was significantly higher in nasopharyngeal carcinoma than in nasopharyngitis (p &lt; 0.05). Their expression in nasopharyngeal carcinoma with metastasis were significantly higher than that without metastasis (p &lt; 0.05), which was correlated with TNM staging (p &lt; 0.05). High Cripto-1 expression and high proliferation rate were seen in CNE1-LMP1 cells. Conclusions: The expression of LMP1 and Cripto-1 in nasopharyngeal carcinoma is positively related. Their co-expression might contribute to the proliferation and metastasis of nasopharyngeal carcinoma.
DOI: 10.6084/m9.figshare.14289365
title: Which risk factors are associated with stomal recurrence after total laryngectomy for laryngeal cancer? A meta-analysis of the last 30 years

description: Abstract Introduction Stomal recurrence is a troublesome complication after total laryngectomy. Despite a large number of studies having been performed, there is still controversy about which risk factors are most significant for the development of stomal recurrence. Objective The objective of the present meta-analysis was to analyze the potential factors leading to stomal recurrence after total laryngectomy. Methods PubMed, Web of Science, Cochrane Library, and Ovid databases were systematically searched using multiple search terms. Eighteen studies with 6462 patients were identified. The quality of evidence was assessed by The National Institute for Health and Clinical Excellence. Results The results showed that, tumor subsite (supraglottic vs. subglottic, RR = 0.292, 95% CI 0.142–0.600, p = 0.001; glottic vs. subglottic, RR = 0.344, 95% CI 0.175–0.676, p = 0.002), T stage (RR = 0.461, 95% CI 0.286–0.742, p = 0.001), preoperative tracheotomy (RR = 1.959, 95% CI 1.500–2.558, p &lt; 0.001) were the high-risk factors associated with the development of stomal recurrence. Conclusion From the results of our study, tumor subsite, T stage and preoperative tracheotomy were the significant risk factors for stomal recurrence. Methodologically high-quality comparative investigations are needed for further evaluation.
DOI: 10.6084/m9.figshare.14289385.v1
title: In vivo and in vitro study of co-expression of LMP1 and Cripto-1 in nasopharyngeal carcinoma

description: Abstract Introduction: Nasopharyngeal carcinoma, an epithelial-derived malignant tumor which because of its anatomical location and atypical early symptoms, when diagnosed invasion and metastasis often have occurred. This requires a better understanding of the development mechanism, identifying diagnostic markers, and developing new treatment strategies. Objective: To study the relationship of LMP1 and Cripto-1 in nasopharyngeal carcinoma. Methods: The expression of LMP1 and Cripto-1 in specimens obtained from nasopharyngeal carcinoma patients (n = 42) and nasopharyngitis patients (n = 22) were examined. The expression of LMP1 and Cripto-1 in LMP1-negative and LMP1-positive (CNE1-LMP1) cells were also examined. Results: The expression of LMP1 and Cripto-1 was significantly higher in nasopharyngeal carcinoma than in nasopharyngitis (p &lt; 0.05). Their expression in nasopharyngeal carcinoma with metastasis were significantly higher than that without metastasis (p &lt; 0.05), which was correlated with TNM staging (p &lt; 0.05). High Cripto-1 expression and high proliferation rate were seen in CNE1-LMP1 cells. Conclusions: The expression of LMP1 and Cripto-1 in nasopharyngeal carcinoma is positively related. Their co-expression might contribute to the proliferation and metastasis of nasopharyngeal carcinoma.
DOI: 10.6084/m9.figshare.14289365.v1
title: Which risk factors are associated with stomal recurrence after total laryngectomy for laryngeal cancer? A meta-analysis of the last 30 years

description: Abstract Introduction Stomal recurrence is a troublesome complication after total laryngectomy. Despite a large number of studies having been performed, there is still controversy about which risk factors are most significant for the development of stomal recurrence. Objective The objective of the present meta-analysis was to analyze the potential factors leading to stomal recurrence after total laryngectomy. Methods PubMed, Web of Science, Cochrane Library, and Ovid databases were systematically searched using multiple search terms. Eighteen studies with 6462 patients were identified. The quality of evidence was assessed by The National Institute for Health and Clinical Excellence. Results The results showed that, tumor subsite (supraglottic vs. subglottic, RR = 0.292, 95% CI 0.142–0.600, p = 0.001; glottic vs. subglottic, RR = 0.344, 95% CI 0.175–0.676, p = 0.002), T stage (RR = 0.461, 95% CI 0.286–0.742, p = 0.001), preoperative tracheotomy (RR = 1.959, 95% CI 1.500–2.558, p &lt; 0.001) were the high-risk factors associated with the development of stomal recurrence. Conclusion From the results of our study, tumor subsite, T stage and preoperative tracheotomy were the significant risk factors for stomal recurrence. Methodologically high-quality comparative investigations are needed for further evaluation.
DOI: 10.6084/m9.figshare.14289376
title: Efficacy of nasal irrigation with hypertonic saline on chronic rhinosinusitis: systematic review and meta-analysis

description: Abstract Introduction: Currently, several different concentrations of saline are recommended for use in nasal irrigation. Increasing studies show that nasal irrigation with hypertonic saline is more effective than traditional saline in the treatment of rhinosinusitis, but there have been few systematic analyses of the effect of nasal irrigation with hypertonic saline on chronic rhinosinusitis. Objective: We sought to compare the effects of hypertonic saline and isotonic saline in the treatment of rhinosinusitis in order to provide a reference for clinical nasal irrigation for chronic rhinosinusitis treatment. Methods: Medline, cochrane library, EMBASE, PubMed, Chinese biomedical journal database, China national knowledge infrastructure, Wanfang database, and other databases were searched, and the searching was supplemented by manual searches for relevant references to treatment of rhinosinusitis by saline nasal irrigation. The last retrieval date was March 2018. The included studies were evaluated for quality, and data were extracted for meta-analysis using RevMan 5.3. Results: Seven studies were included. Effects favoring hypertonic saline on nasal symptoms were greater in 4 subgroups. These were (1) patients with nasal secretion (SMD = 1.52; 95% CI: 1.04, 2.00; p &lt; 0.01), (2) patients with congestion (SMD = 1.52; 95% CI: 1.04, 2.00; p &lt; 0.01), (3) patients with headache (SMD = 0.82; 95% CI: 0.38, 1.26; p &lt; 0.01), (4) patients with overall symptomatic relief (SMD = 1.63; 95% CI: 0.83, 2.44; p &lt; 0.01). However, no difference was shown in smell improvement (SMD = 0.47; 95% CI: −0.65, 1.59; p = 0.41) and radiologic scores improvement (SMD = 2.44; 95% CI: -3.14, 8.02; p &lt; 0.01). Besides, hypertonic saline showed greater improvement in mucociliary clearance time scores than did the isotonic saline group (SMD = 1.19; 95% CI: 0.78, 1.60; p &lt; 0.01). Hypertonic saline brought greater minor adverse effects. Conclusion: Compared with isotonic saline, hypertonic saline nasal irrigation for the treatment of chronic rhinosinusitis is significantly more effective and has mild side effects in improving nasal symptoms and ciliary movement, but there is no significant difference in imaging findings and smell improvement. Although hypertonic saline is worthy of widespread use in clinical practice, it is still necessary to further study the exact manner and concentration of nasal irrigation.
DOI: 10.6084/m9.figshare.14289376.v1
title: Efficacy of nasal irrigation with hypertonic saline on chronic rhinosinusitis: systematic review and meta-analysis

description: Abstract Introduction: Currently, several different concentrations of saline are recommended for use in nasal irrigation. Increasing studies show that nasal irrigation with hypertonic saline is more effective than traditional saline in the treatment of rhinosinusitis, but there have been few systematic analyses of the effect of nasal irrigation with hypertonic saline on chronic rhinosinusitis. Objective: We sought to compare the effects of hypertonic saline and isotonic saline in the treatment of rhinosinusitis in order to provide a reference for clinical nasal irrigation for chronic rhinosinusitis treatment. Methods: Medline, cochrane library, EMBASE, PubMed, Chinese biomedical journal database, China national knowledge infrastructure, Wanfang database, and other databases were searched, and the searching was supplemented by manual searches for relevant references to treatment of rhinosinusitis by saline nasal irrigation. The last retrieval date was March 2018. The included studies were evaluated for quality, and data were extracted for meta-analysis using RevMan 5.3. Results: Seven studies were included. Effects favoring hypertonic saline on nasal symptoms were greater in 4 subgroups. These were (1) patients with nasal secretion (SMD = 1.52; 95% CI: 1.04, 2.00; p &lt; 0.01), (2) patients with congestion (SMD = 1.52; 95% CI: 1.04, 2.00; p &lt; 0.01), (3) patients with headache (SMD = 0.82; 95% CI: 0.38, 1.26; p &lt; 0.01), (4) patients with overall symptomatic relief (SMD = 1.63; 95% CI: 0.83, 2.44; p &lt; 0.01). However, no difference was shown in smell improvement (SMD = 0.47; 95% CI: −0.65, 1.59; p = 0.41) and radiologic scores improvement (SMD = 2.44; 95% CI: -3.14, 8.02; p &lt; 0.01). Besides, hypertonic saline showed greater improvement in mucociliary clearance time scores than did the isotonic saline group (SMD = 1.19; 95% CI: 0.78, 1.60; p &lt; 0.01). Hypertonic saline brought greater minor adverse effects. Conclusion: Compared with isotonic saline, hypertonic saline nasal irrigation for the treatment of chronic rhinosinusitis is significantly more effective and has mild side effects in improving nasal symptoms and ciliary movement, but there is no significant difference in imaging findings and smell improvement. Although hypertonic saline is worthy of widespread use in clinical practice, it is still necessary to further study the exact manner and concentration of nasal irrigation.
DOI: 10.6084/m9.figshare.14289398
title: The characteristic of otoacoustic emissions in full-term neonates according to ABO blood groups

description: Abstract Introduction: Previous research has suggested that individuals with different blood groups show varied incidences of noise-induced hearing loss. The reduced otoacoustic emissions amplitudes indicate the higher possibilities of outer hair cell damage for noise exposure. Objective: The objective is to analyze the characteristics of otoacoustic emissions, including the occurrence of spontaneous otoacoustic emission and the amplitudes of distortion product otoacoustic emission at certain frequencies in full term neonates with different ABO blood groups. Methods: A total of 80 selected full-term female neonates who passed the initial newborn hearing screen were enrolled into the study, with equal number of participants in four ABO blood groups (Blood Group A, Blood Group B, Blood Group AB, Blood Group O). Measurements of spontaneous otoacoustic emission and distortion product otoacoustic emission were performed in both ears for all participants. Results: (1) The blood group O participants showed significantly fewer spontaneous otoacoustic emission occurrences than the other three blood groups (A = 70%, B = 80%, AB = 67%, O = 25%, p &lt; 0.05). (2) The blood group O participants showed lower DPOAE amplitudes at 1257 Hz (M = 4.55 dB, SD = 8.36), 1587 Hz (M = 11.60 dB, SD = 6.57), 3174 Hz (M = 7.25 dB, SD = 5.99), 5042 Hz (M = 13.60, SD = 6.70) than participants with the other three blood groups in left ears (p &lt; 0.05). In right ears, the blood group O participants showed reduced amplitudes at 1257 Hz (M = 6.55 dB, SD = 8.36), 1587 Hz (M = 13.60 dB, SD = 6.57), 3174 Hz (M = 7.65 dB, SD = 6.43), 5042 Hz (M = 13.65 dB, SD = 6.50) than participants from non-O blood groups (p &lt; 0.05). Conclusion: Female individuals with blood group O have lower otoacoustic emissions values than individuals with the other three blood groups. We need to further investigate the possible relationships between ABO blood group and cochlear function, including the potential influences of noise damage on cochlear outer hair cells.
DOI: 10.6084/m9.figshare.14289398.v1
title: The characteristic of otoacoustic emissions in full-term neonates according to ABO blood groups

description: Abstract Introduction: Previous research has suggested that individuals with different blood groups show varied incidences of noise-induced hearing loss. The reduced otoacoustic emissions amplitudes indicate the higher possibilities of outer hair cell damage for noise exposure. Objective: The objective is to analyze the characteristics of otoacoustic emissions, including the occurrence of spontaneous otoacoustic emission and the amplitudes of distortion product otoacoustic emission at certain frequencies in full term neonates with different ABO blood groups. Methods: A total of 80 selected full-term female neonates who passed the initial newborn hearing screen were enrolled into the study, with equal number of participants in four ABO blood groups (Blood Group A, Blood Group B, Blood Group AB, Blood Group O). Measurements of spontaneous otoacoustic emission and distortion product otoacoustic emission were performed in both ears for all participants. Results: (1) The blood group O participants showed significantly fewer spontaneous otoacoustic emission occurrences than the other three blood groups (A = 70%, B = 80%, AB = 67%, O = 25%, p &lt; 0.05). (2) The blood group O participants showed lower DPOAE amplitudes at 1257 Hz (M = 4.55 dB, SD = 8.36), 1587 Hz (M = 11.60 dB, SD = 6.57), 3174 Hz (M = 7.25 dB, SD = 5.99), 5042 Hz (M = 13.60, SD = 6.70) than participants with the other three blood groups in left ears (p &lt; 0.05). In right ears, the blood group O participants showed reduced amplitudes at 1257 Hz (M = 6.55 dB, SD = 8.36), 1587 Hz (M = 13.60 dB, SD = 6.57), 3174 Hz (M = 7.65 dB, SD = 6.43), 5042 Hz (M = 13.65 dB, SD = 6.50) than participants from non-O blood groups (p &lt; 0.05). Conclusion: Female individuals with blood group O have lower otoacoustic emissions values than individuals with the other three blood groups. We need to further investigate the possible relationships between ABO blood group and cochlear function, including the potential influences of noise damage on cochlear outer hair cells.
DOI: 10.6084/m9.figshare.21629388
title: Additional file 6 of NLRP3 inflammasome regulates astrocyte transformation in brain injury induced by chronic intermittent hypoxia

description: Additional file 6: Table S1. The primer sequences uesd in RT-qPCR.
DOI: 10.6084/m9.figshare.20056597
title: Additional file 1 of Essential role for STAT3/FOXM1/ATG7 signaling-dependent autophagy in resistance to Icotinib

description: Additional file 1.
DOI: 10.6084/m9.figshare.25144466
title: Overview of interviews.pdf

description: Overview of conducted interviews constituting the empirical material reported in the submitted article Artistic expression as a property of resonant musical experience
DOI: 10.6084/m9.figshare.25144463
title: Interview guide.pdf

description: Interview guide used in collection of data reported in the article Artistic expression as a property of resonant musical experience
DOI: 10.6084/m9.figshare.25144463.v1
title: Interview guide.pdf

description: Interview guide used in collection of data reported in the article Artistic expression as a property of resonant musical experience
DOI: 10.6084/m9.figshare.25144466.v1
title: Overview of interviews.pdf

description: Overview of conducted interviews constituting the empirical material reported in the submitted article Artistic expression as a property of resonant musical experience
DOI: 10.6084/m9.figshare.14292487
title: A Generalized Framework of Optimal Two-Stage Designs for Exploratory Basket Trials

description: The primary goal of an exploratory oncology clinical trial is to identify an effective drug for further development. To expedite the drug development process and increase the chance of finding active tumor indications where the treatment works, multiple tumor cohorts are often investigated simultaneously in a basket trial. In this article, we propose a generalized framework of an optimal basket trial design in the exploratory setting where tumor indications can be homogeneous (objective response rates of all indications are the same under both the null and alternative hypotheses) or heterogeneous (objective response rates are not the same under at least one of the null or alternative hypotheses). The proposed design prunes the inactive tumor indication in Stage 1 and pools the remaining tumor indications at the end of Stage 2 to evaluate the overall effectiveness of whether the treatment works in at least one tumor indication. The design parameters are optimized to minimize the expected sample size while explicitly controlling the global Type I and Type II error rates. In addition, we consider reallocating the planned Stage 2 sample size of pruned indications to achieve a higher power when the total planned sample size is fixed. Simulation studies are conducted to show the favorable operating characteristics of the proposed design under certain scenarios.
DOI: 10.24403/jp.1322193
title: Ehlers, M.: Baum und Strauch in der Gestaltung und Pflege der Landschaft. - 2. Aufl. - Berlin und Hamburg : Verlag Paul Parey, 1986 / [rezensiert von] H. Manitz
DOI: 10.24403/jp.1322200
title: Exkursion an die Steppenhügel der Schwellenburg bei Kühnhausen und in die kontinentalen Eichenwälder der Fahnerschen Höhen am 28. April 1985 / F. K. Meyer
DOI: 10.24403/jp.1322202
title: Exkursion ins Obere Saaletal am 19. Mai 1985 / H.-J. Zündorf
DOI: 10.24403/jp.1322204
title: Exkursion in die Umgebung von Schwarzburg am 2. Juni 1985 / L. Meinunger
DOI: 10.24403/jp.1322210
title: Exkursion ins südthüringische Muschelkalkgebiet südlich Themar am 9. Juni 1985 / P. Heerlein
DOI: 10.6084/m9.figshare.20584484
title: Tumor mutational burden in non-immunotherapy patients with heavily pretreated metastatic breast cancer: long-term outcomes from a single institution

description: Patients with heavily pretreated (≥3<sup>rd</sup>-line treatment) metastatic breast cancer (MBC) had poor outcomes and lack prognostic biomarkers. Tumor mutational burden (TMB) was a prognostic biomarker for immunotherapy, but is not well defined in non-immunotherapy. Forty-nine heavily pretreated MBC not received immunotherapy were enrolled between March 2016 and September 2018. TMB of metastatic tumor tissue was evaluated by targeted next-generation sequencing of a 247-genes panel. CBRs (clinical benefit rates) were 47.7% (9 months), 36.2% (12 months) in high TMB patients, higher than 16.1% (9 months), 8.1% (12 months) in low TMB patients, respectively. After a median follow-up of 38 months, patients with high TMB had a longer mPFS (median progress-free survival) compared to low TMB patients in 3<sup>rd</sup>-line treatment group (13.5 versus 7 months, HR 0.32, <i>p</i> = 0.019) but not in &gt;3<sup>rd</sup>-line treatment group. Cox regression showed TMB and line of treatment were the two independent prognostic factors for prolonged mPFS in heavily pretreated MBC, with a HR of 0.34 (<i>p</i> = 0.009) for high TMB and 0.37 (<i>p</i> = 0.013) for 3<sup>rd</sup>-line treatment. In luminal subtype, mPFS was longer with endocrine therapy (ET) alone than with endocrine therapy + chemotherapy (ET + CT) in high TMB cohort (<i>p</i> = 0.037) but shorter mPFS with ET alone than with ET + CT in low TMB cohort (<i>p</i> = 0.047). High TMB and line of treatment are two independent prognostic factors for prolonged mPFS in heavily pretreated MBC patients. TMB may be a predictive biomarker of efficacy with ET alone or ET + CT in luminal subtype.