dataesr/scientific-paragraphs-categorization huggingface dataset:
Other data: Acoustic velocities and mechanical properties Acoustic velocities are available for relatively few samples in the database  (Franzson and Tulinius, 1999; Frolova et al. , 2005; Nono et al. , 2020; Lévy et al. , 2020b). Acoustic velocities express the propagation rate of mechanical waves -compressional P-waves and shear S-waves -in a bulk environment, composed of solid minerals and fluid in pores and fractures, either gas or liquid. While P-waves tend to travel faster in a water-saturated than dry environment, S-waves follow the reverse trend. For the samples from  Lévy et al. (2020b) , P-and S-wave velocities (  and   ) were measured at a frequency of 500 kHz for both dry and wet samples, using a digital oscilloscope, a pulse generator and coupled piezoelectric transducers, at University of Montpellier.
Data availability The database is archived at Zenodo at https://doi. org/10. 5281/zenodo. 6980232 (Scott et al. , 2022)  and is available under the Creative Commons Attribution 4. 0 International license. This repository includes an Excel file containing separate worksheets, one listing sample metadata and petrophysical properties, a second listing geochemical and petrographic data, a third listing the file names of photographs corresponding to the sample IDs, a fourth listing additional hyaloclastite data  (Frolova et al. , 2005) , and a fifth listing extended references. All worksheets are additionally included in the repository as csv files with the separator '|'. The photographs are also included in the Zenodo repository as a separate directory. We hope that the availability of this database will also stimulate future research into the petrophysical properties of Icelandic rocks.
Given the increasing emphasis on probabilistic (Bayesian) methods for geophysical inversions and numerical reservoir models, the data presented in this can be used to constrain the prior distributions assumed in geophysical inversions  (Scott et al. , 2019)  and numerical models (e. g. Scott et al. , 2022). The detailed sample descriptions, combined with the photographs of many of the sample sites included as a supplement to the dataset, should facilitate future research visits to the investigated areas. Moreover, the remaining cores from the Orkustofnun samples are now kept at Náttúrufraeðistofnun (the Icelandic Institute of Natural History) for interested parties to continue research. There are clear gaps in the database, including the lack of samples from the central or northern parts of Iceland, as well as the lack of mechanical data.
Gilbert et al. (2020) Samples obtained from IDDP-2 at ~3. 6-4. 6 km depth. Includes grain density and effective porosity (triple weight) as well as electrical conductivity and acoustic properties. 20 Present study Borehole samples from well ÞR-07 in Theistareykir. Effective porosity, grain density (triple weight), electrical properties, and acoustic velocities. Quantitative mineral characterization using XRD. 31 Present study Surface samples from the Austurhorn gabbro in SE Iceland. Effective porosity, grain density (triple weight), electrical properties, and acoustic velocities. the scope of the database, we only provide geochemical and mineralogical data for samples that also have petrophysical properties given in the first table.
The samples were analyzed for major, minor, and several trace elements (Zr, Y, Zn, Cu, Rb, Sr, Nb, Ga, Ce, V, Pb, U, Th and As). Major element analyses in the database are presented both in unnormalized form and after removing LOI (loss on ignition, see below) and renormalizing the composition to 100%. Figure7ashows the samples categorized by lithology plotted on a total alkali -silica diagram. Note that this diagram shows both altered and unaltered rocks. The vast majority of the samples plot in the basalt field, as expected. While it has been suggested that hydrothermal alteration in Icelandic rocks is close to an isochemical process (Franzson et al. , 2008) , the lava flows, hyaloclastites, and basaltic intrusions that plot outside of this field due to the effects of alteration, e. g. silicification in the upflow zones of geothermal systems.
https://doi. org/10. 5194/essd-2022-279 Preprint. Discussion started: 17 August 2022 c Author(s) 2022. CC BY 4. 0 License. 5 Concluding remarks & future status of the database Icelandic rocks are generally of igneous or volcanic origin and mostly basaltic. The efforts of geologists over the past 50+ years has resulted in a tremendous amount of data, spanning petrophysical, geochemical, and petrographic measurements of a wide range of basaltic rocks and associated silicic and intermediate rocks in Iceland. However, it has historically been commonthat after publication of a paper or report, the only remaining manifestations of the data are the figures contained in the publication, and much of the raw underlying data is not accessible or difficult to access. This practice is only starting to change in response to the increasing emphasis on data availability.
Cohort of unresolved MEN1 cases This study was performed on patients referred between March 2018 and March 2021 for MEN1 genetic testing to the molecular laboratory of Marseille La Conception Hospital. Patients presented with at least two MEN1-related tumors but without MEN1 pathogenic variants in the heterozygous state. Written informed consent for genetic analysis was obtained from all patients during one-on-one genetic counseling. NGS data produced during routine practice processes were retrospectively realigned and reanalyzed using the pipeline optimized for mosaic detection. All variants with an AF superior to 0. 5% were analyzed. The study was approved by the ethics committee of Aix-Marseille University (approval number: 2018-13-12-004).
Acknowledgments We thank all the patients and their physicians:  Dr Albarel ,  Dr Alesandre ,  Dr Andrieu ,  Dr Barriquand ,  Dr Zatta ,  Dr Chevalier ,  Dr Corsini ,  Dr D'Anella ,  Dr Gall ,  Dr Grouthier ,  Dr Grulet ,  Dr Jelloul ,  Dr Julier ,  Dr Lagrave-Vergnet ,  Dr Lazoussinie ,  Dr Laveille ,  Dr Mallet ,  Dr Moreau ,  Dr Moutton ,  Dr Nassouri ,  Pr Niccoli ,  Dr Philippon ,  Dr Plas ,  Dr Priou Guesdon ,  Dr Puerto ,  Dr Radaoui ,  Dr Raingeard ,  Dr Morange ,  Dr Rigalleau ,  Dr Rochette ,  Dr Solmon ,  Dr Scheyer ,  Pr Taillard ,  Dr Tchknavorian ,  Dr Vermalle ,  Dr Vital. The authors thank  Ian Darby  from Editingbiomed for English revisions.
49 vavax (NVX-CoV2373). Novavax (NVX-CoV2373) efficacy has been evaluated in Phase II and Phase III trials. 4 The vaccine's efficacy against mild, moderate, and severe disease was found to be 90. 0% in Phase III trials. 4 The Strategic Advisory Group of Experts (SAGE) recommends administering the Novavax (NVX-CoV2373) vaccine in two doses (0. 5 ml) intramuscularly for those older than 18 years of age. 4  The two doses should be given three to four weeks apart. 4 Data on the safety and immunogenicity of vaccines for children under the age of 18 are currently being generated; therefore, vaccination of children under the age of 18 is not recommended until such data are sufficiently available and can be further reviewed. 4 There is currently no data on the safety and efficacy of the Novavax (NVX-CoV2373) vaccine in pregnant women.
Methods: The authors proactively collected clinical data from 20 institutions in different European countries for patients under the age of 16 treated with a PHA implant. The data were obtained by conducting an on-site interview with physicians in charge of the patients (Post-Marketing Surveillance, PMS group). The endpoints were the incidence of adverse events and related implant removal. The clinical data were compared to the company-based register including all patients under the age of 16 who received the same implant from January 1, 2004 to December 31, 2020, and the collecting complications voluntarily reported by surgeons (Database, DB group). Results: The two groups were similar in terms of demographic characteristics and rate of complications. In the PMS group, a total of 11 (16. 9%) complications were reported in the group of 65 patients that were proactively collected.
MATERIALS AND METHODS The study includes patients below the age of 16 years who underwent PHA cranioplasty (CustomBone Service, Finceramica Faenza Spa, Italy). To achieve the goal of the study, the complication rate in two groups of pediatric patients was compared: the first group included all PHA custom bone implanted patients from Custom Bone Service Fin-Ceramica, Faenza Database; whereas in the second group, a randomly collected group of patients from European Neurosurgical Centers underwent clinical follow-up. Details about the surgical methodology were already published elsewhere  (6). The current European Medical Device Regulation requires post-market clinical follow-up activities to be carried out by manufacturers to evaluate device performance and safety. For CustomBone Service, the activity of post-market clinical follow-up started in December 2018  (10).
For this activity, a specific protocol and a case report form (CRF) were produced for data collection. The protocol is included in the Supplementary Material. Among all institutions using custom-made PHA, 20 neurosurgical European centers have been randomly contacted for data to analyze their experience with this device in pediatric patients. Each center participating in the study was visited by one of the co-authors (IZ) before the coronavirus disease-2019 (COVID-19) restriction period, and CRFs were filled for each patient implanted in the institution with the aid of neurosurgeons involved in the procedure (Supplementary Material). The centers involved in this study are summarized in Table  1. Concerning the use of the database from the manufacturing company, an agreement was reached to allow the authors to use the company database for scientific purposes.
The database is web-based, and it contains general information, under a serialized number for privacy purposes, of all patients implanted with a PHA cranioplasty. The company agreed not to influence the collection of data, and the results of the study were not available to the company before study publication. Several variables were taken into consideration for this study, namely, demographic information (gender, age, and surgery date), initial pathology, reason for surgery, localization of the cranial lesion, date of surgery, and country. Concerning postoperative outcome, the authors collected all main types of complications related to PHA cranioplasty implantation (deep and superficial infection, device fracture or mobilization, or related to the procedure, i. e. , hydrocephalus, epidural, or subdural hematomas).
Finally, an explantation and follow-up data were also collected. No sensitive information was collected during the research, which was limited to the processing of data regarding adverse events and was according to the biomedical device surveillance norms in force (MEDDEV 2. 7/1 rev. 4)  (10). To reduce the risk of selection bias, despite randomized collection, representativeness of the collected data from the selected centers was compared with the general series of pediatric patients implanted, which was retrieved with the manufacturer's web portal database, an up-to-date, highly protected, and secure ordering platform and working tool in which all the produced devices are regularly recorded (DB group). The DB group included all pediatric patients who received PHA cranioplasty in different neurosurgical centers from Europe and the United States from January 2004 to December 2020.
RESULTS The PMS group comprehended clinical data from 65 pediatric patients below the age of 16 (for a total of 76 implanted devices) that were collected from the different hospitals visited by the authors. Among all, 36 (55%) of the patients were male and 29 (45%) were female, with a mean age of 9. 1 years (1-16 years ± 4. 67). They were stratified into four different groups based on the age ranges: there was 1 (1. 5%) child in the range 0-2 years old, which has been implanted off-label, 18 (27. 7%) children between 2-7 years old, 25 (38. 5%) of them were included in the range 8-12 years old, and, finally, 21 (32. 3%) patients were in the last group  (12-16 years). The DB group included data from 725 patients (below the age of 16), who received a CustomBone device from January 1, 2004 to December 31, 2020.
Furthermore, the present rates of complications and explantation (16. 9 and 4. 5%, respectively) are comparable to the rates previously reported in children 7-13 years old (14. 5 and 6. 58%, respectively)  (1). Moreover, the rate of explantation (4. 5%) is similar to the rate recently reported in a large adult series of PHA CP (4. 25%) (6), although the present study also included patients under 7 years of age at higher risk of complications  (23). The 65 pediatric cases reported here were randomly collected from 20 clinical sites. These cases were treated in most recent years but show similar clinical features of the total pediatric population collected by the manufacturer's database, as confirmed by the comparison between the two groups. The two cohorts of patients were indeed comparable in terms of age, gender, cause of decompression, line of treatment (first-or second-line of treatment), revision rate, and explantation rate  (24) (25) (26).
PATIENTS AND METHODS Indonesia, Malaysia, Singapore and Thailand were selected as the countries for the study following meetings with representatives from respective clinical oncology societies and cancer registries. In July 2019, a study protocol was developed to assess the feasibility of collecting clinical information on newly diagnosed lung cancer patients. Before the commencement of data collection, a 2-day in-person training workshop on the definitions and methods with representatives from each participating site was held in September 2019. Ethics approval for the study was obtained through the IARC's institutional review board and locally from each participating site. Implementation of the study was overseen by local principal investigators and by an advisory committee comprising representatives from ESMO and IARC.
17 The second method of case finding was specific to Singapore, where the national PBCR was not accessible to the study. Rather, inclusion was restricted to consenting patients participating in the Lung Cancer Consortium Singapore National Lung Cancer Research Study, an open-based clinical research platform. 18  request to the National Registry of Diseases Office in Singapore was made to obtain aggregate data during the study period from the Singapore Cancer Registry. Chart reviews conducted by trained personnel from each PBCR were used to abstract the required clinical data elements. Vital status and cause of death were obtained by Lampang, Penang and Yogyakarta and linked to the PBCR, while aggregate mortality data were available in Singapore. A set of indicators were developed using an iterative process led by the authors.
0] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]  The list was refined through clinical input from the study representatives to examine relevance and feasibility. A final set of 38 indicators were selected that were grouped into six major themes: (i) process and diagnostic; (ii) staging; (iii) treatment; (iv) outcomes; (v) comorbidity; and (vi) palliative care. Indicators for the study included many additional data items than those normally collected by a PBCR, necessitating chart reviews by trained staff to obtain the required clinical information. An online data collection tool was developed in English using REDCap  39  to electronically capture information from two filesdan incident file and a clinical file. The incident dataset, consisted of 19 fields that are commonly collected by PBCRs, such as patient demographics, diagnoses and tumor characteristics.
40 The clinical dataset was designed to capture the remaining required data fields (n ¼ 60). The incidence and clinical files were transferred separately to IARC for centralized data quality review and analyses. Personal information on patients was removed at each center before the files were being sent to IARC. A unique study identification number was created in order to combine files and communicate with each site about queries of specific records. To help ensure the accuracy of the linkage, records were cross-checked through a common set of variables on each fileddate of birth, date of diagnosis, sex and ICD-O topography and morphology diagnosis. Records with the same study identification number that had differing values on common fields were rechecked with each study site to correct potential mismatches.
A merged study file was created and processed using the IARC-Check program to assess inconsistency in reporting. 41 Results of the edit check were sent to each site asking that they correct errors before inclusion in the final analyses. Results were grouped by histology. NSCLC was classified into squamous cell and non-squamous cell, with the latter further divided into adenocarcinoma, large cell carcinoma and 'not otherwise specified'. Grouped TNM (tumore nodeemetastasis) stage was captured as a field in data abstraction. When this was missing, stage was derived by combining the individual components of tumor, node and metastasis beginning with clinical elements followed by pathology. The UICC TNM seventh edition was used in Yogyakarta, while Penang and Singapore used the UICC TNM eighth edition to classify stage; Lampang used a mixture of the two editions and had three cases classified in the sixth edition.
42 When neither was available, grouped TNM codes supplied by the cancer registry were used. EGFR and BRAF mutation, and ALK and ROS1 fusion status from pre-treatment tumor samples were collected. Also captured were the use of next-generation sequencing (NGS) and the determination of PD-L1 expression by immunohistochemistry. A response of 'unknown' was given when no record of a test being administered was found in the patient's chart. We reported molecular test results by grouping together 'unknown', 'no test administered' and 'missing' responses. PD-L1 test results were recorded as positive if the percentage of cells positive was greater or equal to one. Treatment data collected were limited to the first 6 months after diagnosis. Specific anticancer agents used for first-line therapy were collected based on a pre-established selected list of agents.
0%. The rate of testing varied between the regions, being lowest in Lampang and highest in Singapore. During the study period, EGFR TKIs were available in Penang, Singapore and Yogyakarta; however, unaffordability was reported as obstacles to wider testing by Yogyakarta and Penang. In Lampang, EGFR TKIs were available only to Thai patients who were under the Civil Servant Medical Benefit Scheme. 44 Testing rates in the same time frame were 75% for the United States based on the flatiron database and ranged from 73% to 85% in selected European countries. 45, 46 esting for ALK gene rearrangement was reported as the next most commonly carried out followed closely by ROS1  gene rearrangement testing. With the exception of Singapore, test rates for ALK gene rearrangement were low, ranging from 0.
A subnational PBCR was the source in Lampang, Penang and Yogyakarta. Notwithstanding challenges due to COVID-19, a comparison of observed versus expected cases yielded a high degree of completeness. The unique features of a PBCR that include all cases in the targeted population, allowing for findings to be more easily generalized, have contributed to its importance in cancer control. 52 While data from Singapore was from a single hospital and should be interpreted with caution, when compared with aggregated data obtained from the Singapore Cancer Registry, the distribution of cases was found to be similar. The high rates of testing and treatment patterns in Singapore may be in part due to their increased availability at the National Cancer Centre Singapore, while in the other settings, high patient costs were likely the main deterrent.
47 In the case of Yogyakarta, the PBCR was newly established. Additional data quality assessments were conducted to ensure comparability of results with the other PBCRs. In many low-and middle-income settings, cancer registries face challengesdin particular, the overall quality of medical records available, together with specific issues of access to private institutions. 53 These challenges were largely overcome in this study through the selection of sites where co-operation with local data sources had been secured. To capture the movement of patients between private and public treatment and diagnostic centers, data from the PBCR are brought together to form one record for the patient. This aspect of PBCR lessens the likelihood of missing relevant information for the study when a patient is seen at multiple institutions during their care.
Data collection for the study was hampered by the emergence of the COVID-19 outbreak. A slow-down began in January 2020, culminating with a temporary stoppage of all data collection activities from March to May 2020 due to strict restrictions imposed on movement and outdoor activities. Cancer registries worldwide had similar experiences. 54 Data collection resumed in June 2020 but remained limited as staff at centers had restrictions on work hours and where they could visit, as COVID-19 management became the priority. To compensate for the impact of COVID-19, centers were asked to prioritize data collection for 2017-2018 incident cases. Despite these limitations, the study was successful to gather real-word data from an estimated 80. 5% of the expected lung cancer cases in the respective regions where PBCRs were used.
This study has provided new evidence on lung cancer treatment and diagnostic work-up in diverse settings across Southeast Asia. The design has demonstrated that it is possible to obtain more detailed data than normally collected by PBCR but that approaches required flexibility to account for variation in the hospital systems within these areas. The findings call other cancer sites to be studied in light of the advances in biomarker-defined targeted treatments. The need to address issues at the health systems level to improve outcomes in lower resource settings has been well documented. 55 This disparity is a call for action for the communities to not only focus on implementing scientific advances, but also consider how we could act together to bring clinical advances to cancer patients at large, in particular situations such as EGFR mutations, where the prevalence in lung adenocarcinoma is 50% or higher.