cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7910549.v2
title: Adaptive Incremental Mixture Markov Chain Monte Carlo

description: We propose adaptive incremental mixture Markov chain Monte Carlo (AIMM), a novel approach to sample from challenging probability distributions defined on a general state-space. While adaptive MCMC methods usually update a parametric proposal kernel with a global rule, AIMM locally adapts a semiparametric kernel. AIMM is based on an independent Metropolis–Hastings proposal distribution which takes the form of a finite mixture of Gaussian distributions. Central to this approach is the idea that the proposal distribution adapts to the target by locally adding a mixture component when the discrepancy between the proposal mixture and the target is deemed to be too large. As a result, the number of components in the mixture proposal is not fixed in advance. Theoretically, we prove that there exists a stochastic process that can be made arbitrarily close to AIMM and that converges to the correct target distribution. We also illustrate that it performs well in practice in a variety of challenging situations, including high-dimensional and multimodal target distributions. Finally, the methodology is successfully applied to two real data examples, including the Bayesian inference of a semiparametric regression model for the Boston Housing dataset. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7904942.v1
title: Influence Diagnostics for High-Dimensional Lasso Regression

description: The increased availability of high-dimensional data, and appeal of a “sparse” solution has made penalized likelihood methods commonplace. Arguably the most widely utilized of these methods is l1 regularization, popularly known as the lasso. When the lasso is applied to high-dimensional data, observations are relatively few; thus, each observation can potentially have tremendous influence on model selection and inference. Hence, a natural question in this context is the identification and assessment of influential observations. We address this by extending the framework for assessing estimation influence in traditional linear regression, and demonstrate that it is equally, if not more, relevant for assessing model selection influence for high-dimensional lasso regression. Within this framework, we propose four new “deletion methods” for gauging the influence of an observation on lasso model selection: df-model, df-regpath, df-cvpath, and df-lambda. Asymptotic cut-offs for each measure, even when p→∞, are developed. We illustrate that in high-dimensional settings, individual observations can have a tremendous impact on lasso model selection. We demonstrate that application of our measures can help reveal relationships in high-dimensional real data that may otherwise remain hidden.
DOI: 10.6084/m9.figshare.7887842.v1
title: Distributed Generalized Cross-Validation for Divide-and-Conquer Kernel Ridge Regression and its Asymptotic Optimality

description: Tuning parameter selection is of critical importance for kernel ridge regression. To this date, data driven tuning method for divide-and-conquer kernel ridge regression (d-KRR) has been lacking in the literature, which limits the applicability of d-KRR for large data sets. In this paper, by modifying the Generalized Cross-validation (GCV, Wahba, 1990) score, we propose a distributed Generalized Cross-Validation (dGCV) as a data-driven tool for selecting the tuning parameters in d-KRR. Not only the proposed dGCV is computationally scalable for massive data sets, it is also shown, under mild conditions, to be asymptotically optimal in the sense that minimizing the dGCV score is equivalent to minimizing the true global conditional empirical loss of the averaged function estimator, extending the existing optimality results of GCV to the divide-and-conquer framework.
DOI: 10.6084/m9.figshare.7862876.v1
title: Damped Anderson acceleration with restarts and monotonicity control for accelerating EM and EM-like algorithms

description: The expectation-maximization (EM) algorithm is a well-known iterative method for computing maximum likelihood estimates in a variety of statistical problems. Despite its numerous advantages, a main drawback of the EM algorithm is its frequently observed slow convergence which often hinders the application of EM algorithms in high-dimensional problems or in other complex settings. To address the need for more rapidly convergent EM algorithms, we describe a new class of acceleration schemes that build on the Anderson acceleration technique for speeding fixed-point iterations. Our approach is effective at greatly accelerating the convergence of EM algorithms and is automatically scalable to high dimensional settings. Through the introduction of periodic algorithm restarts and a damping factor, our acceleration scheme provides faster and more robust convergence when compared to un-modified Anderson acceleration, while also improving global convergence. Crucially, our method works as an “off-the-shelf” method in that it may be directly used to accelerate any EM algorithm without relying on the use of any model-specific features or insights. Through a series of simulation studies involving five representative problems, we show that our algorithm is substantially faster than the existing state-of-art acceleration schemes.
DOI: 10.6084/m9.figshare.14510127.v1
title: Brood production by the dung beetles and physico-chemical characteristics of the cattle dung

description: This is the raw dataset for the manuscript.
DOI: 10.25345/c5h819
title: MassIVE MSV000087336 - Fungus-QIII9-CE and Beauvericin-20210429
title: t uses the same login and password. To manipulate MS data files in GNPS, they must first be uploaded to MassIVE, which is an online repository for mass spectrometry datasets hosted by the UCSD Center for Computational Mass Spectrometry (CCMS). The user workspace in GNPS/MassIVE provides a personalized location where researchers can curate m
DOI: 10.6084/m9.figshare.14510073
title: Supplementary Material for: Association of Phosphate Containing Solutions with Incident Hypophosphatemia in Critically Ill Patients Requiring Continuous Renal Replacement Therapy

description: <b><i>Background:</i></b> Hypophosphatemia in critically ill patients is a common electrolyte disturbance associated with a myriad of adverse effects. Critically ill patients requiring continuous renal replacement therapy (CRRT) are at high risk of hypophosphatemia and often require phosphate supplementation during therapy. The aim of this study was to evaluate the association of phosphate versus non-phosphate containing CRRT solutions with incident hypophosphatemia in critically ill patients requiring CRRT. <b><i>Materials and Methods:</i></b> This is a single-center, retrospective, cohort study at a tertiary academic medical center of 1,396 adult patients requiring CRRT during their intensive care unit stay comprising 7,529 (phosphate containing) and 4,821 (non-phosphate containing) cumulative days of CRRT. Multivariable logistic regression was used to model the primary outcome of hypophosphatemia during CRRT according to exposure to phosphate versus non-phosphate containing CRRT solutions. <b><i>Results:</i></b> Incident hypophosphatemia during CRRT, serum phosphate &lt;2.5 mg/dL or 0.81 mmol/L, was significantly higher in the non-phosphate versus phosphate containing solution group: 304/489 (62%) versus 175/853 (21%) (<i>p</i> &lt; 0.001). Cumulative phosphate supplementation was also significantly higher in the non-phosphate versus phosphate containing solution group: 79 (IQR: 0–320) versus 0 (0–16) mmol (<i>p</i> &lt; 0.001). Non-phosphate solutions were associated with an 8-fold increase in the incidence of hypophosphatemia (adjusted OR 8.05; 95% CI 5.77, 11.26; <i>p</i> &lt; 0.001). <b><i>Discussion/Conclusions:</i></b> The use of phosphate containing CRRT solutions was independently associated with reduced risk of incident hypophosphatemia and decreased phosphate supplementation during CRRT. Interventional studies to confirm these findings are needed.
DOI: 10.6084/m9.figshare.14510073.v1
title: Supplementary Material for: Association of Phosphate Containing Solutions with Incident Hypophosphatemia in Critically Ill Patients Requiring Continuous Renal Replacement Therapy

description: <b><i>Background:</i></b> Hypophosphatemia in critically ill patients is a common electrolyte disturbance associated with a myriad of adverse effects. Critically ill patients requiring continuous renal replacement therapy (CRRT) are at high risk of hypophosphatemia and often require phosphate supplementation during therapy. The aim of this study was to evaluate the association of phosphate versus non-phosphate containing CRRT solutions with incident hypophosphatemia in critically ill patients requiring CRRT. <b><i>Materials and Methods:</i></b> This is a single-center, retrospective, cohort study at a tertiary academic medical center of 1,396 adult patients requiring CRRT during their intensive care unit stay comprising 7,529 (phosphate containing) and 4,821 (non-phosphate containing) cumulative days of CRRT. Multivariable logistic regression was used to model the primary outcome of hypophosphatemia during CRRT according to exposure to phosphate versus non-phosphate containing CRRT solutions. <b><i>Results:</i></b> Incident hypophosphatemia during CRRT, serum phosphate &lt;2.5 mg/dL or 0.81 mmol/L, was significantly higher in the non-phosphate versus phosphate containing solution group: 304/489 (62%) versus 175/853 (21%) (<i>p</i> &lt; 0.001). Cumulative phosphate supplementation was also significantly higher in the non-phosphate versus phosphate containing solution group: 79 (IQR: 0–320) versus 0 (0–16) mmol (<i>p</i> &lt; 0.001). Non-phosphate solutions were associated with an 8-fold increase in the incidence of hypophosphatemia (adjusted OR 8.05; 95% CI 5.77, 11.26; <i>p</i> &lt; 0.001). <b><i>Discussion/Conclusions:</i></b> The use of phosphate containing CRRT solutions was independently associated with reduced risk of incident hypophosphatemia and decreased phosphate supplementation during CRRT. Interventional studies to confirm these findings are needed.
DOI: 10.5281/zenodo.4726637
title: Composer name cross-links across resources: Delpher, CDR/Muziekweb, Wikidata, and the IMSLP

description: This folder contains links found in the Delpher newspaper portal, for queries of names of composers that: are known in the catalogue of CDR/Muziekweb; are known to have a Wikidata ID; are known to have sheet music entries in the Petrucci Music Library (IMSLP). The links are offered in *.csv format. For each article, we include: the Delpher article permalink; where available, the article appearance date, in the format ‘yyyymmdd’; where available, the article type, employing the Dutch article class namings as used in Delpher: ‘artikel’ for newspaper articles; ‘advertentie’ for advertisements; ‘familiebericht’ for family announcements; ‘Illustratie met onderschrift’ for illustrations with captions. The (possible composer) name occurring in this article, in standardized Wikidata name spelling; the Wikidata ID of the composer with this name. We used the standardized Wikidata name spelling as plain text queries to Delpher’s API. As a consequence, this list may be over-complete, as names may not only belong to a composer, but also (partially) to other persons with the same name (e.g. Martin Luther vs. Martin Luther King). The date and article type of the article may give useful information for further post-processing and filtering of this information. The Delpher collection, CDR/Muziekweb, Wikidata, and the IMSLP are all living collections, to which more content is added regularly. The current dataset reflects the status of October 1, 2020.
DOI: 10.5281/zenodo.4726636
title: Composer name cross-links across resources: Delpher, CDR/Muziekweb, Wikidata, and the IMSLP

description: This folder contains links found in the Delpher newspaper portal, for queries of names of composers that: are known in the catalogue of CDR/Muziekweb; are known to have a Wikidata ID; are known to have sheet music entries in the Petrucci Music Library (IMSLP). The links are offered in *.csv format. For each article, we include: the Delpher article permalink; where available, the article appearance date, in the format ‘yyyymmdd’; where available, the article type, employing the Dutch article class namings as used in Delpher: ‘artikel’ for newspaper articles; ‘advertentie’ for advertisements; ‘familiebericht’ for family announcements; ‘Illustratie met onderschrift’ for illustrations with captions. The (possible composer) name occurring in this article, in standardized Wikidata name spelling; the Wikidata ID of the composer with this name. We used the standardized Wikidata name spelling as plain text queries to Delpher’s API. As a consequence, this list may be over-complete, as names may not only belong to a composer, but also (partially) to other persons with the same name (e.g. Martin Luther vs. Martin Luther King). The date and article type of the article may give useful information for further post-processing and filtering of this information. The Delpher collection, CDR/Muziekweb, Wikidata, and the IMSLP are all living collections, to which more content is added regularly. The current dataset reflects the status of October 1, 2020.
DOI: 10.6084/m9.figshare.14510076.v1
title: sustainability-1187163_data

description: Data used in paper <br>Gene Editing for Improved Animal Welfare and Production<br>Traits in Cattle: Will This Technology Be Embraced or Rejected<br>by the Public?<br>Maria Cristina Yunes, Zimbábwe Osório‐Santos, Marina A. G. von Keyserlingk and Maria José Hötzelhttps://doi.org/10.3390/su13094966<br>
DOI: 10.11583/dtu.14387480
title: Resource data and turbulence array measurements from the 3 Vindeby masts

description: This dataset consists of time series and run statistics of wind speed and wind direction measurements from one onshore and two offshore masts near the Vindeby offshore wind farm in Denmark (Decommissioned 2017). The period includes more than 2300 hours of measurements, which starts in 1994. Furthermore, the Vindeby resource dataset (Vindeby2) consists of 30-minute statistics of wind speed and wind direction measurements from he three mast. The period includes more than 5 years of measurements from 1993.<br>Detailed site documentation is available here.<br><br>Public data Run statistics (NetCDF format): 1) vindeby_all.nc (NetCDF) 2) vindeby_concurrent.nc (NetCDF) Raw time series (ascii) each with a duration of 1800 sec, sampled with 2.5, 5, 10 and 20 Hz.: 3) vindeby_1994.zip 4) vindeby_1995.zip Wind resource data (NetCDF format), as 30-minutes statistics representing 5 years: 5) vindeby2_all.nc 6) vindeby2_concurrent.nc<br>
DOI: 10.1285/i26113775n5pi
title: Copertina
DOI: 10.6084/m9.figshare.14410811
title: Metadata record for the article: Next-generation sequencing revealed recurrent ZFPM1 mutations in encapsulated papillary carcinoma of the breast

description: <b>Summary</b><br> This metadata record provides details of the data supporting the claims of the related article: “Next-generation sequencing revealed recurrent ZFPM1 mutations in encapsulated papillary carcinoma of the breast”. The related study aimed to gain further insight into encapsulated papillary carcinoma (EPC) mutation profile. Type of data: whole exome sequencing; gene targeted sequencing Subject of data: <i>Homo sapiens</i> Population characteristics: patients had been diagnosed with encapsulated papillary carcinoma of the breast Recruitment: EPCs diagnosed from 2015 to 2018 were retrospectively retrieved from the surgical pathology files, then patients were contacted by phone and email. <b>Data access</b> The raw sequencing data are openly available in the NCBI <i>Sequence Read Archive</i>, and can be accessed via the following <i>BioProject</i> accession: https://identifiers.org/bioproject:PRJNA685582. These data have also been deposited in the <i>Genome Sequence Archive</i> (Genomics, Proteomics & Bioinformatics 2017) in the National Genomics Data Center (Nucleic Acids Res 2020), Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences. The accession code is HRA000480. The <i>TCGA</i> dataset used in the related article is from https://tcga-data.nci.nih.gov/docs/publications/brca_2012/ . Additional data underlying the figures of the related article are openly available in the files included with this <i>figshare </i>data record. Details of these files are as follows: - Supplementary Data 1: The clinicopathologica information and feature of 41 EPCs. - Supplementary Data 2: Somatic mutations detected by whole-exome sequencing in 26 EPCs - Supplementary Data 3: Somatic mutations detected by targeted sequencing in 41 EPCs - Supplementary Data 4: ZFPM1 mutations in breast cancer from COSMIC datesets. - Supplementary Table 3 and Supplementary Figure 4 were included in the Supplementary Information file. <b>Corresponding author(s) for this study</b> Zhiyong Liang, Department of Pathology, Peking Union Medical College Hospital, Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, China 100730, liangzhiyong1220@yahoo.com<br> <br> <b></b> <b>Study approval </b> The study protocol was approved by the Ethical Committee of Peking Union Medical University Hospital.
DOI: 10.6084/m9.figshare.14410811.v1
title: Metadata record for the article: Next-generation sequencing revealed recurrent ZFPM1 mutations in encapsulated papillary carcinoma of the breast

description: <b>Summary</b><br> This metadata record provides details of the data supporting the claims of the related article: “Next-generation sequencing revealed recurrent ZFPM1 mutations in encapsulated papillary carcinoma of the breast”. The related study aimed to gain further insight into encapsulated papillary carcinoma (EPC) mutation profile. Type of data: whole exome sequencing; gene targeted sequencing Subject of data: <i>Homo sapiens</i> Population characteristics: patients had been diagnosed with encapsulated papillary carcinoma of the breast Recruitment: EPCs diagnosed from 2015 to 2018 were retrospectively retrieved from the surgical pathology files, then patients were contacted by phone and email. <b>Data access</b> The raw sequencing data are openly available in the NCBI <i>Sequence Read Archive</i>, and can be accessed via the following <i>BioProject</i> accession: https://identifiers.org/bioproject:PRJNA685582. These data have also been deposited in the <i>Genome Sequence Archive</i> (Genomics, Proteomics & Bioinformatics 2017) in the National Genomics Data Center (Nucleic Acids Res 2020), Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences. The accession code is HRA000480. The <i>TCGA</i> dataset used in the related article is from https://tcga-data.nci.nih.gov/docs/publications/brca_2012/ . Additional data underlying the figures of the related article are openly available in the files included with this <i>figshare </i>data record. Details of these files are as follows: - Supplementary Data 1: The clinicopathologica information and feature of 41 EPCs. - Supplementary Data 2: Somatic mutations detected by whole-exome sequencing in 26 EPCs - Supplementary Data 3: Somatic mutations detected by targeted sequencing in 41 EPCs - Supplementary Data 4: ZFPM1 mutations in breast cancer from COSMIC datesets. - Supplementary Table 3 and Supplementary Figure 4 were included in the Supplementary Information file. <b>Corresponding author(s) for this study</b> Zhiyong Liang, Department of Pathology, Peking Union Medical College Hospital, Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, China 100730, liangzhiyong1220@yahoo.com<br> <br> <b></b> <b>Study approval </b> The study protocol was approved by the Ethical Committee of Peking Union Medical University Hospital.
DOI: 10.1285/i26113775n5p1
title: Frontespizio e pagine iniziali
DOI: 10.1285/i26113775n5p5
title: Contents
DOI: 10.1285/i26113775n5p7
title: Author
DOI: 10.1285/i26113775n5p9
title: Introduction
DOI: 10.1285/i26113775n5p19
title: LEADER approach: a starting point for review
DOI: 10.1285/i26113775n5p31
title: LEADER: basic features for a territorial approach
DOI: 10.1285/i26113775n5p41
title: Reading LEADER through the key features: European cases compared
DOI: 10.1285/i26113775n5p59
title: Reading LEADER through the key features: the regional case of Puglia
DOI: 10.6084/m9.figshare.14125391
title: Metadata record for the manuscript: Modulation of the immune microenvironment of high-risk breast ductal carcinoma in situ by intralesional injection of pembrolizumab

description: <b>Summary</b><br> This metadata record provides details of the data supporting the claims of the related manuscript: “Modulation of the immune microenvironment of high-risk breast ductal carcinoma in situ by intralesional injection of pembrolizumab”. The primary objective of this trial described in the related study was to establish the safety and feasibility of intralesional immunotherapy in patients with DCIS. A secondary objective was to evaluate changes in the tumour immune microenvironment pre- vs. post-therapy. Exploratory objectives included an evaluation of tumour volume measured using MRI pre- versus post-pembrolizumab therapy as well as an evaluation of markers of apoptosis (cleaved caspase 3) and proliferation (Ki67), pre- versus post-therapy. Type of data: clinical data; immune infiltrates data—Excel spreadsheet format Subject of data: <i>Homo sapiens</i> Sample size: 9 Population characteristics: Patients with pathologically-confirmed breast ductal carcinoma in situ (DCIS) were eligible for enrollment if they possessed at least two of the following high-risk features: young age (&lt; 45 years), large size (&gt; 5cm), high-grade (grade II or III), a palpable mass, hormone receptor (HR) negativity, and/or HER2 positivity. Recruitment: Participants were recruited from the University of California San Francisco (UCSF) Breast Care Center when evaluated by one of the breast surgical oncologists participating in this study. Date of data collection: Patients were recruited between March 2017 and June 2018. Trial registration number: NCT02872025 <b>Data access</b> The data generated and analysed in the related studyare openly available as part of this <i>figshare </i>metadata record in the file ‘Immune Infiltrates Data.xls’. This spreadsheet contains 6 tabs labelled according to the figure of the related article that it underlies. <b>Corresponding author(s) for this study</b> Michael J. Campbell PhD, Department of Surgery, University of California- San Francisco, 2330 Sutter St, N321, San Francisco CA 94115. michael.campbell@ucsf.edu. <br> <b>Study approval </b> This study was approved by the Institutional Review Board of the University of California, San Francisco, and all patients signed written informed consent.