dataesr/scientific-paragraphs-categorization huggingface dataset:
Results Here, we establish the geology of the nodule occurrence, at and near the Groken site, and current compositions and mineralogies of the Groken nodules and their host rocks. The geologic relations of the nodules come from visual imaging by Mastcam, MAHLI, and ChemCam RMI. Chemical and mineralogical data come from APXS, ChemCam LIBS, CheMin, and relative reflectance spectra from ChemCam and Mastcam. We separate the chemical/mineralogical inferences into those related to rock surfaces and drilled materials. Analyses related to rock surfaces can be correlated with objects or locations on images, giving them geologic context in the finely laminated Mary Anning rock. Drilled samples are fine-grained mixtures of materials in the rock beneath the drill epicenter. After the drill anomaly of sol 1536, the drill material delivered to SAM and CheMin is not representative of the entire drilled core, but only of the final rock that was drilled, i.
[79, 80]. SU scores are unquantified but are in proper relative orde elemental abundance. Scores for P and Mn on graph axes, score for H in symbol color. Target Glasgow, rubbly material, and Hutton have low Mn and H scores and variable P scores. All tar on Mozie_Law (Groken/Mary Anning) have higher Mn scores and H scores that increase with t of P and Mn. The analyses of Table  4 , as with all LIBS analyses, typically represent the summations of results of the last 25 of 30 laser shots in a single location. Data from the first few laser shots are not included, being inferred to represent dust or coatings on the rock surface. Quantified results from the last 25 shots on a target can be used to assess the target's homogeneity with depth. Figure  8A ,B show profiles of MnO and SiO 2 abundances in LIBS observation points in the area of the Ayton APXS raster.
Unlike APXS spectra, XRF spectra from CheMin are not calibrated; there is no baseline for the counts at an element's Kα energy in the absence of that element, and no function to convert X-ray counts to elemental abundance. However, because the calibration function should be approximately linear in this limited range of compositions, we can use CheMin XRF data for the Mary_Annings to test whether the Groken sample delivered to CheMin was enriched in Mn relative to the surrounding nodule-free rock. The abundance of nodule material in the CheMin sample can be constrained by comparing APXS analyses of cuttings and surfaces with CheMin XRF data on the delivered material. As described above, CheMin collects XRF along with the XRD data; CheMin XRF spectra have much lower energy resolution than APXS spectra and have not been calibrated.
Here, we use them semi-quantitatively to show that the Groken sample analyzed in CheMin contained minimal Mn-rich nodule material. Figure  12A  shows the CheMin XRF spectra for Groken, Mary_Anning, and Mary_Anning3, which all have peaks at energies corresponding to Kα radiations from Fe, Ti, and Ca. The MnKα X-ray energy is on the low-energy shoulder of the FeKα peak and only appears as a distinct peak in the Groken spectrum (Figure  12A ). Unlike APXS spectra, XRF spectra from CheMin are not calibrated; there is no baseline for the counts at an element's Kα energy in the absence of that element, and no function to convert X-ray counts to elemental abundance. However, because the calibration function should be approximately linear in this limited range of compositions, we can use CheMin XRF data for the Mary_Annings to test whether the Groken sample delivered to CheMin was enriched in Mn relative to the surrounding nodule-free rock.
2 ). For this test of whether the Groken drill sample contained a significant proportion of Mn-rich nodules, we compare its MnKα X-ray counts from CheMin with the APXS analysis of the Groken drill cuttings. Because we lack a 'zero calibration' for CheMin MnKα, we look at the difference in its counts between the Mary_Anning sample and the others (i. e. , the difference value for Mary_Anning itself is zero). Data for this test are in Figure  12B , which graphs the difference in CheMin XRF counts at the MnKα peak energy against quantified MnO abundances (from APXS) of the drill cuttings for each sample. In Figure  12B , data for Mary_Anning and Mary_Anning3 define a linear relation between these quantities. Data for the Groken sample fall close to that linear relation, implying that the MnO abundance in the drill cuttings (by APXS) is a fair representation of the MnO abundance in the CheMin drill sample.
Drill Engineering Data Curiosity collects engineering data during drilling, including the progress of penetration as a function of time. Drill progress depends on the strength (i. e. , scratch hardness and fracture toughness) of the target, but also another parameter unrelated to rock properties (e. g. , pressure on the bit, percussion level, and side load on drill stem). With caution, then, drill progress can be used as a rough, qualitative indication of rock strength and the absence of other issues. For the Groken target, one might expect the dark nodules to be stronger than their host, given their resistance to aeolian abrasion; if the drill penetrated nodule material, one might then see a decrease in penetration rate. However, we cannot know if the nodules' resistance to aeolian abrasion translates to increased strength detectable during drilling.
The Mary_Anning and Mary_Anning3 drill samples contain siderite and hematite in quantities detectable by CheMin  [36] , suggesting that their chemical conditions might be described by the latter equilibrium. It is possible that early siderite in these rocks was partially oxidized to hematite after deposition, and even under present-day exposure to Mars' atmosphere. However, the Groken drill sample contains Fe-bearing carbonate but no detectable hematite, suggesting slightly more reduced conditions. If the Fe-bearing carbonate was ankerite, CaFe(CO 3 ) 2 , somewhat higher oxidation states would be possible, but cannot be quantified because the GWB thermochemical database does not include ankerite. It still is not obvious how much of the iron mineralogy of the Groken drill sample is also present in the nodules.
The diagrams of Figure  14  must be taken only as guides and not as quantitative representations of mineral stabilities. The thermochemical parameters for laueite and strunzite are estimated (see Supplementary Materials), and this estimation method yielded unreasonable stability fields for other minerals (reddingite, rockbridgeite, and vivianite-Mn). The thermochemical database does not include a few possible minerals (e. g. , ludlamite). Also, calculations for the figures do not include possible solid solutions, especially that of Mn in vivianite. Natural vivianites commonly contain significant Mn, so the stability fields of natural vivianites are likely larger than in the figures. Recognizing these shortcomings, we press onward.
Localization The final question is why the Mn-Fe-P nodules are so localized, having been found only at one location and there only in a few sedimentary laminae. Why only here at Groken, and nowhere else in Glen Torridon? And, elsewhere, why only at Jones_Marsh and Maple_Spring on Vera Rubin ridge? These questions cannot be answered with certainty, and perhaps could not even if Curiosity could return to the Knockfarfill Hill for extensive Earth-style field study. Yet, the available data allow us to reject some hypotheses, and terrestrial analogs suggest some possible reasons for the limited distribution of Grokenstyle nodules. The Mn-Fe-P nodules cannot be related to the widely-distributed pervasive diagenetic processes that affected Glen Torridon rocks  [8, 34]. Those processes are marked mostly by enrichments in Ca-sulfates and/or iron oxides (nodules or cement), rarely by manganese, and never by phosphorus (as noted so far).
Implications: Speculative History For the Groken nodules, the Curiosity rover was unable to collect sufficient data to allow a complete, well-justified history of their origin and development. Unfortunately, the Groken drill sample contained minimal to no nodule material; a full study of the dark nodules would have required more time than was available and additional analytical instruments. Even so, the data in hand and terrestrial analogs allow a speculative selfconsistent story. At the time the Mozie_Law (Knockfarrill Hill) sediments were deposited (Figure  2 ), Mn and P were locally enriched in the water of the shallow Gale crater lake or its nearsurface sediments, perhaps from a spring or seep of alkaline, reduced groundwater. These conditions allowed Mn-rich vivianite to crystallize in the freshly deposited sediments, filling pore spaces among the sediment grains.
Acknowledgments: The authors acknowledge the support they received, and have received, from  NASA 's  Mars Exploration Program  through the  Mars Science Laboratory  project, and their respective instrument PIs and the  MSL participating scientist program  ( J. R. Johnson ,  80NSSC22K0779 ). Part of this research was carried out at the  Jet Propulsion Laboratory, California Institute of Technology , under a contract with the  National Aeronautics and Space Administration (NASA). Treiman is grateful for contract support through the  CheMin instrument. The  Lunar and Planetary Institute (LPI)  is operated by  Universities Space Research Association (USRA)  under a cooperative agreement with the  Science Mission Directorate of NASA. We are grateful for corrections and comments from two anonymous reviewers.
Data Availability Statement: All data reported here are available through the NASA Planetary Data System (PDS). ChemCam relative reflectance spectra can be found here: https://pds-geosciences. wustl. edu/msl/urn-nasa-pds-msl_chemcam_psv_calibrated/. CheMin data are also available at https://odr. io/chemin (all accessed 7 July 2023).
WHAT THIS STUDY ADDS ⇒ Here, we systematically evaluated the performance of EURbased BC PRS on Ashkenazi Jewish (AJ) women from Israel. Our results demonstrate that extant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC. women: 1437 cases and 724 controls. According to the 'ethnOt' field in the BCAC phenotype file, all the women in the BCAC-IL cohort are tagged as 'Jewish Ashkenazi'. In addition, there are 73 samples in the EUR cohort that are tagged as AJ. All samples analysed were genotyped using the OncoArray chip. In our analysis, we used an imputed version of the data provided by BCAC. The imputation was done against the 1000 Genomes Project imputation panel. In BCAC-IL, 119 (5. 5%) BRCA1/2 mutation carriers were identified by a self-reporting field provided by the BCAC.
Hadassah Medical Center (HMC) cohort The HMC dataset contains 181 Israeli AJ women, of whom 118 are BC cases under the age of 45 years and 63 are controls older than 75 years. We validated either by sequencing or genotyping that none of the women carried one of the three AJ founder mutations in BRCA1/2. Samples were genotyped using the Axiom PMDA chip. Likely pathogenic variants in selected genes are covered by this chip. Three women carried such variants in BRCA1/2, and none bore pathogenic variants in other BC susceptibility genes. We phased the data using SHAPEIT2  21  and imputed it using IMPUTE2. 22  The imputation reference panel was generated using SHAPEIT2 from the EUR samples from the 1000 Genomes Project (n=503). Using PLINK, we filtered out SNPs with uncertainty greater than 0. 1.
RESULTS We set to build and evaluate EUR-based BC PRS for AJ women from Israel. For this task, we used an Israeli cohort of 2161 AJ women (1437 BC cases and 724 controls) that is a part of the BCAC (Methods). We refer to the Israeli sub-cohort of the BCAC as BCAC-IL. In order to avoid inflation of the predictive performance, the target set should be independent of the discovery set. Therefore, we could not reliably assess how the commonly used EUR BC 313-SNP PRS  12  performs on the BCAC-IL cohort since this PRS was derived from BCAC GWAS, which included the BCAC-IL cohort. Therefore, we first removed the Israeli women from the EUR BCAC cohort and recomputed GWAS summary statistics using only data from the 132 335 non-Israeli EUR women (72 899 cases and 59 436 controls; Methods). A PCA on the BCAC genotype data confirmed the close genetic relatedness of AJ to the EUR population (figure  2 ).
Acknowledgements We thank all the individuals who took part in these studies and all the researchers, clinicians, technicians and administrative staff who enabled this work to be carried out. ABCFS thanks  Maggie Angelakos ,  Judi Maskiell  and  Gillian Dite. ABCS  thanks the  Blood bank Sanquin, The Netherlands. ABCTB investigators:  Christine Clarke ,  Deborah Marsh ,  Rodney Scott ,  Robert Baxter ,  Desmond Yip ,  Jane Carpenter ,  Alison Davis ,  Nirmala Pathmanathan ,  Peter Simpson ,  J. Dinny Graham  and  Mythily Sachchithananthan. Samples are made available to researchers on a non-exclusive basis. BBCS thanks  Eileen Williams ,  Elaine Ryder-Mills  and  Kara Sargus. BCEES  thanks  Allyson Thomson ,  Christobel Saunders ,  Terry Slevin ,  BreastScreen Western Australia ,  Elizabeth Wylie  and  Rachel Lloyd.
MCS is an NHMRC senior research fellow. The ABCS study was supported by the Dutch Cancer Society (grants NKI 2007-3839 and 2009 4363) and an institutional grant of the Dutch Cancer Society and of the Dutch Ministry of Health, Welfare and Sport. The Australian Breast Cancer Tissue Bank was supported by the National Health and Medical Research Council of Australia, The Cancer Institute NSW and the National Breast Cancer Foundation. The AHS study is supported by the intramural research program of the National Institutes of Health, the National Cancer Institute (grant number Z01-CP010119), and the National Institute of Environmental Health Sciences (grant number Z01-ES049030). The work of the BBCC was partly funded by ELAN-Fond of the University Hospital of Erlangen. The BBCS is funded by Cancer Research UK and Breast Cancer Now and acknowledges NHS funding to the NIHR Biomedical Research Centre, and the National Cancer Research Network (NCRN).
The BCEES was funded by the National Health and Medical Research Council, Australia and the Cancer Council Western Australia and acknowledges funding from the National Breast Cancer Foundation (JS). For the BCFR-NY, BCFR-PA, BCFR-UT this work was supported by grant UM1 CA164920 from the National Cancer Institute. The content of this manuscript does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the BCFR, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government or the BCFR. The BCINIS study is supported in part by the Breast Cancer Research Foundation (BCRF). For BIGGS, ES is supported by NIHR Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust in partnership with King's College London, United Kingdom.
IT is supported by the Oxford Biomedical Research Centre. BOCS is supported by funds from Cancer Research UK (C8620/A8372/A15106) and the Institute of Cancer Research (UK). BOCS acknowledges NHS funding to the Royal Marsden / Institute of Cancer Research NIHR Specialist Cancer Biomedical Research Centre. The Breast Oncology GAlician Network is funded by Acción Estratégica de Salud del Instituto de Salud Carlos III FIS PI12/02125/Cofinanciado and FEDER PI17/00918/Cofinanciado FEDER; Acción Estratégica de Salud del Instituto de Salud Carlos III FIS Intrasalud (PI13/01136); Programa Grupos Emergentes, Cancer Genetics Unit, Instituto de Investigacion Biomedica Galicia Sur. Xerencia de Xestion Integrada de Vigo-SERGAS, Instituto de Salud Carlos III, Spain; Grant 10CSA012E, Consellería de Industria Programa Sectorial de Investigación Aplicada, PEME I + D e I + D Suma del Plan on August 8, 2023 by guest.
Protected by copyright. http://jmg. bmj. com/ J Med Genet: first published as 10. 1136/jmg-2023-109185 on 14 July 2023. Downloaded from Cancer genetics Gallego de Investigación, Desarrollo e Innovación Tecnológica de la Consellería de Industria de la Xunta de Galicia, Spain; Grant EC11-192. Fomento de la Investigación Clínica Independiente, Ministerio de Sanidad, Servicios Sociales e Igualdad, Spain; and Grant FEDER-Innterconecta. Ministerio de Economia y Competitividad, Xunta de Galicia, Spain. The BSUCH study was supported by the Dietmar-Hopp Foundation, the Helmholtz Society and the German Cancer Research Center (DKFZ). CBCS is funded by the Canadian Cancer Society (grant # 313404) and the CIHR. CCGP is supported by funding from the University of Crete. The CECILE study was supported by Fondation de France, Institut National du Cancer, Ligue Nationale contre le Cancer, Agence Nationale de Sécurité Sanitaire, de l'Alimentation, de l'Environnement et du Travail and Agence Nationale de la Recherche.
The opinions, findings and conclusions expressed herein are those of the author(s) and do not necessarily reflect the official views of the State of California, Department of Public Health, the National Cancer Institute, the National Institutes of Health, the Centers for Disease Control and Prevention or their Contractors and Subcontractors, or the Regents of the University of California or any of its programmes. The University of Westminster curates the DietCompLyf database funded by Against Breast Cancer Registered Charity No. 1121258 and the NCRN. The coordination of EPIC is financially supported by the European Commission (DG-SANCO) and the International Agency for Research on Cancer. The national cohorts are supported by Ligue Contre le Cancer, Institut Gustave Roussy, Mutuelle Générale de l'Education Nationale, Institut National de la Santé et de la Recherche Médicale (France); German Cancer Aid, DKFZ, Federal Ministry of Education and Research (BMBF) (Germany); the Hellenic Health Foundation, the Stavros Niarchos Foundation (Greece); Associazione Italiana per la Ricerca sul Cancro (AIRC) Italy and National Research Council (Italy); Dutch Ministry of Public Health, Welfare and Sports, Netherlands Cancer Registry, LK Research Funds, Dutch Prevention Funds, Dutch ZON (Zorg Onderzoek Nederland), World Cancer Research Fund, Statistics Netherlands (The Netherlands); Health Research Fund (FIS), PI13/00061 to Granada, PI13/01162 to EPIC-Murcia, regional governments of Andalucía, Asturias, Basque Country, Murcia and Navarra, ISCIII RETIC (RD06/0020) (Spain); Cancer Research UK (14136 to EPIC-Norfolk; C570/ A16491 and C8221/A19170 to EPIC-Oxford), Medical Research Council (1000143 to EPIC-Norfolk, MR/M012190/1 to EPIC-Oxford) (UK).
The ESTHER study was supported by a grant from the Baden Württemberg Ministry of Science, Research and Arts. Additional cases were recruited in the context of the VERDI study, which was supported by a grant from the German Cancer Aid (Deutsche Krebshilfe). FHRISK and PROCAS are funded from NIHR (grant PGfAR 0707-10031). DGE, AH and WGN were supported by the NIHR Manchester Biomedical Research Centre (IS-BRC-1215-20007). The GC-HBOC (German Consortium of Hereditary Breast and Ovarian Cancer) was supported by the German Cancer Aid (grant numbers 110837 and 70114178, coordinator: Rita K Schmutzler, Cologne) and the Federal Ministry of Education and Research, Germany (grant number 01GY1901). This work was also funded by the European Regional Development Fund and Free State of Saxony, Germany (LIFE -Leipzig Research Centre for Civilization Diseases, project numbers 713-241202, 713-241202, 14505/2470 and 14575/2470).
EK was supported by the mega grant from the Government of Russian Federation (2020-220-08-2197), and the study was performed as part of the assignment of the Ministry of Science and Higher Education of the Russian Federation (№АААА-А16-116020350032-1). ICICLE was supported by Breast Cancer Now, CRUK and Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London. Financial support for KARBAC was provided through the regional agreement on medical training and clinical research (ALF) between Stockholm County Council and Karolinska Institutet, the Swedish Cancer Society, The Gustav V Jubilee foundation and Bert von Kantzows foundation. The KARMA study was supported by Märit and Hans Rausings Initiative Against Breast Cancer. The KBCP was financially supported by the special Government Funding (VTR) of Kuopio University Hospital grants, Cancer Fund of North Savo, the Finnish Cancer Organizations, and by the strategic funding of the University of Eastern Finland.
kConFab is supported by a grant from the National Breast Cancer Foundation, and previously by the NHMRC, the Queensland Cancer Fund, the Cancer Councils of New South Wales, Victoria, Tasmania and South Australia, and the Cancer Foundation of Western Australia. Financial support for the AOCS was provided by the United States Army Medical Research and Materiel Command (DAMD17-01-1-0729), Cancer Council Victoria, Queensland Cancer Fund, Cancer Council New South Wales, Cancer Council South Australia, The Cancer Foundation of Western Australia, Cancer Council Tasmania and the NHMRC (400413, 400281 and 199600). GCT and PW were supported by the  NHMRC. RB was a  Cancer Institute NSW   Clinical Research Fellow. LMBC was supported by the ' Stichting tegen Kanker '. DL was supported by the  FWO. The  MABCS  study is funded by the  Research Centre for Genetic Engineering and Biotechnology 'Georgi D.
Efremov', MASA. The MARIE study was supported by the  Deutsche Krebshilfe e. V. ( 70-2892-BR I ,  106332 ,  108253 ,  108419 ,  110826  and  110828 ), the  Hamburg Cancer Society , the  German Cancer Research Center (DKFZ)  and the  BMBF Germany  ( 01KH0402 ). MBCSG was supported by grants from the  AIRC. The MCBCS was supported by the  NIH  (grants  R35CA253187 ,  R01CA192393 ,  R01CA116167  and  R01CA176785 ), an  NIH Specialized Program of Research Excellence (SPORE) in Breast Cancer  ( P50CA116201 ) and the  Breast Cancer Research Foundation. The  Melbourne Collaborative Cohort Study (MCCS) cohort  recruitment was funded by  VicHealth and Cancer Council Victoria. The MCCS was further augmented by the  Australian National Health and Medical Research Council  (grants  209057 ,  396414  and  1074383 ) and by infrastructure provided by  Cancer Council Victoria.
Cases and their vital status were ascertained through the Victorian Cancer Registry and the  Australian Institute of Health and Welfare , including the  National Death Index  and the Australian Cancer Database. The MEC was supported by  NIH  (grants  CA63464 ,  CA54281 ,  CA098758 ,  CA132839  and  CA164973 ). The MISS study was supported by funding from  ERC-2011-294576  Advanced grant,  Swedish Cancer Society   CAN 2018/675 ,  Swedish Research Council , local hospital funds,  Berta Kamprad Foundation   FBKS 2021-19 ,  Gunnar Nilsson. MSKCC is supported by grants from the  Breast Cancer Research Foundation and Robert and Kate Niehaus Clinical Cancer Genetics Initiative. The work of MTLGEBCS was supported by the  Quebec Breast Cancer Foundation , the  Canadian Institutes of Health Research  for the ' CIHR Team in Familial Risks of Breast Cancer' programme  (grant number  CRN-87521 ) and the  Ministry of Economic Development, Innovation and Export Trade  (grant number  PSR-SIIRI-701 ).
Cancer genetics Familial Breast Cancer  Registry were supported by grant  U01CA164920  from the  USA National Cancer Institute of the National Institutes of Health. The content of this article does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the BCFR, nor does mention of trade names, commercial products or organisations imply endorsement by the  USA Government  or the BCFR. The  Carolina Breast Cancer Study (NCBCS)  was funded by  Komen Foundation , the  National Cancer Institute  ( P50 CA058223 ,  U54 CA156733  and  U01 CA179715 ) and the  North Carolina University Cancer Research Fund. The NGOBCS was supported by the  National Cancer Center Research and Development Fund (Japan). The NHS was supported by  NIH  (grants  P01 CA87969 ,  UM1 CA186107  and  U19 CA148065 ).