{"id":"https://openalex.org/W4319082101","doi":"https://doi.org/10.1101/2023.02.01.526705","title":"Quantification of gallium cryo-FIB milling damage in biological lamella","display_name":"Quantification of gallium cryo-FIB milling damage in biological lamella","publication_year":2023,"publication_date":"2023-02-03","ids":{"openalex":"https://openalex.org/W4319082101","doi":"https://doi.org/10.1101/2023.02.01.526705"},"language":"en","primary_location":{"id":"doi:10.1101/2023.02.01.526705","doi":"https://doi.org/10.1101/2023.02.01.526705","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1101/2023.02.01.526705","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/02/03/2023.02.01.526705.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2023/02/03/2023.02.01.526705.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045116847","display_name":"Bronwyn A. Lucas","orcid":"https://orcid.org/0000-0001-9162-0421","observed_orcids":["https://orcid.org/0000-0001-9162-0421"]},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bronwyn A. Lucas","raw_affiliation_strings":["RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA","RNA Therpeutics Institute, University of Msschusetts Chn Medicl School, Worcester, MA"],"raw_orcid":"https://orcid.org/0000-0001-9162-0421","affiliations":[{"raw_affiliation_string":"RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA","institution_ids":["https://openalex.org/I166722992"]},{"raw_affiliation_string":"RNA Therpeutics Institute, University of Msschusetts Chn Medicl School, Worcester, MA","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024079309","display_name":"Nikolaus Grigorieff","orcid":"https://orcid.org/0000-0002-1506-909X","observed_orcids":["https://orcid.org/0000-0002-1506-909X"]},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nikolaus Grigorieff","raw_affiliation_strings":["Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA","RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA","RNA Therpeutics Institute, University of Msschusetts Chn Medicl School, Worcester, MA"],"raw_orcid":"https://orcid.org/0000-0002-1506-909X","affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I166722992"]},{"raw_affiliation_string":"RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA","institution_ids":["https://openalex.org/I166722992"]},{"raw_affiliation_string":"RNA Therpeutics Institute, University of Msschusetts Chn Medicl School, Worcester, MA","institution_ids":["https://openalex.org/I166722992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5024079309","https://openalex.org/A5045116847"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I166722992"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13552","display_name":"Advanced Materials Characterization Techniques","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cryo-fib-milling","display_name":"cryo-FIB milling","score":0.7820000052452087},{"id":"https://openalex.org/keywords/electron-scattering","display_name":"electron scattering","score":0.7770000100135803},{"id":"https://openalex.org/keywords/radiation-damage","display_name":"radiation damage","score":0.6340000033378601},{"id":"https://openalex.org/keywords/lamellar-thickness","display_name":"lamellar thickness","score":0.3959999978542328},{"id":"https://openalex.org/keywords/cryo-em-sample-preparation","display_name":"cryo-EM sample preparation","score":0.5360000133514404}],"concepts":[{"id":"https://openalex.org/C136301237","wikidata":"https://www.wikidata.org/wiki/Q3247568","display_name":"Lamella (surface anatomy)","level":2,"score":0.841858446598053},{"id":"https://openalex.org/C550372918","wikidata":"https://www.wikidata.org/wiki/Q861","display_name":"Gallium","level":2,"score":0.7252306938171387},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.5114006400108337},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.38348594307899475},{"id":"https://openalex.org/C191897082","wikidata":"https://www.wikidata.org/wiki/Q11467","display_name":"Metallurgy","level":1,"score":0.22252124547958374},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.14319738745689392}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2023.02.01.526705","doi":"https://doi.org/10.1101/2023.02.01.526705","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1101/2023.02.01.526705","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/02/03/2023.02.01.526705.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2023.02.01.526705","doi":"https://doi.org/10.1101/2023.02.01.526705","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1101/2023.02.01.526705","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/02/03/2023.02.01.526705.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3765674710","display_name":null,"funder_award_id":"#2021-234617","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"},{"id":"https://openalex.org/G6209046298","display_name":null,"funder_award_id":"2021-234617 (5022","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"}],"funders":[{"id":"https://openalex.org/F4320315474","display_name":"Chan Zuckerberg Initiative","ror":"https://ror.org/02qenvm24"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4319082101.pdf","grobid_xml":"https://content.openalex.org/works/W4319082101.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W171520057","https://openalex.org/W1971080731","https://openalex.org/W1996074267","https://openalex.org/W2016314394","https://openalex.org/W2037744310","https://openalex.org/W2045671533","https://openalex.org/W2100455255","https://openalex.org/W2142161929","https://openalex.org/W2148941629","https://openalex.org/W2165629370","https://openalex.org/W2213948507","https://openalex.org/W2222956998","https://openalex.org/W2273597373","https://openalex.org/W2475510374","https://openalex.org/W2611333828","https://openalex.org/W2791354025","https://openalex.org/W2887254425","https://openalex.org/W2897254286","https://openalex.org/W2899321578","https://openalex.org/W2924025784","https://openalex.org/W2953032371","https://openalex.org/W2953320394","https://openalex.org/W2990910340","https://openalex.org/W3008923011","https://openalex.org/W3011024809","https://openalex.org/W3018000103","https://openalex.org/W3083406432","https://openalex.org/W3127722007","https://openalex.org/W3154498115","https://openalex.org/W3202179996","https://openalex.org/W4221119125","https://openalex.org/W4289356783","https://openalex.org/W4293102039","https://openalex.org/W4309160136","https://openalex.org/W4319333664"],"related_works":["https://openalex.org/W4377291231","https://openalex.org/W7130558806","https://openalex.org/W4387376589","https://openalex.org/W4412908770","https://openalex.org/W7171059552","https://openalex.org/W3114465990","https://openalex.org/W4411988939","https://openalex.org/W4385431160","https://openalex.org/W2619349075","https://openalex.org/W3024513041"],"abstract_inverted_index":{"Abstract":[0],"Cryogenic":[1],"electron":[2,209,275],"microscopy":[3,276],"(cryo-EM)":[4],"has":[5,50,93],"the":[6,10,80,88,132,144,180,192,221,247,295],"potential":[7,222],"to":[8,30,39,87,123,140,163,277,284,300,314,325,333],"reveal":[9],"molecular":[11,128,232],"details":[12],"of":[13,36,53,67,70,75,82,113,151,158,166,182,194,234,252,291,297,317,328,331],"biological":[14,152,235],"processes":[15],"in":[16,110,185,280,335],"their":[17,238,257],"native,":[18],"cellular":[19,54,258],"environment":[20],"at":[21,282],"atomic":[22,285],"resolution.":[23],"However,":[24,79,246,294],"few":[25],"cells":[26,38,114,281,302],"are":[27],"sufficiently":[28],"thin":[29,90,289],"permit":[31],"imaging":[32],"with":[33,56,340],"cryo-EM.":[34,57],"Thinning":[35],"frozen":[37,292,301],"<500":[40],"nm":[41,168,319,337],"lamellae":[42,150],"by":[43,85,287],"cryogenic":[44,274],"focused":[45],"ion":[46,269],"beam":[47,270],"(FIB)":[48,271],"milling":[49,272],"enabled":[51],"visualization":[52],"structures":[55],"FIB-milling":[58,86,154,195,212,217,298,311,339],"represents":[59],"a":[60,101,127,156,164,315,326],"significant":[61],"advance":[62],"over":[63],"prior":[64],"approaches":[65],"because":[66],"its":[68],"ease":[69],"use,":[71],"scalability,":[72],"and":[73,106,131,178,211,237,250,260,348],"lack":[74],"large-scale":[76],"sample":[77],"distortions.":[78],"amount":[81],"damage":[83,160,196,201,218,299,313],"caused":[84],"generated":[89],"cell":[91,353],"section":[92],"not":[94],"yet":[95],"been":[96],"determined.":[97],"We":[98,189],"recently":[99],"described":[100],"new":[102],"approach":[103],"for":[104,148,184,207,351],"detecting":[105],"identifying":[107],"single":[108],"molecules":[109],"cryo-EM":[111,203],"images":[112],"using":[115,243],"2D":[116],"template":[117],"matching":[118],"(2DTM).":[119],"2DTM":[120,139],"is":[121,197,240,303],"sensitive":[122],"small":[124],"differences":[125],"between":[126],"model":[129],"(template)":[130],"detected":[133],"structure":[134],"(target).":[135],"Here":[136,305],"we":[137,214,306],"use":[138],"demonstrate":[141],"that":[142,161,191,216,308],"under":[143],"standard":[145],"conditions":[146],"used":[147],"machining":[149],"samples,":[153],"introduces":[155,312],"layer":[157],"variable":[159],"extends":[162],"depth":[165,316],"60":[167],"from":[169,199,224,320],"each":[170,321],"lamella":[171,225,322],"surface.":[172],"This":[173],"thickness":[174],"exceeds":[175],"previous":[176],"estimates":[177],"limits":[179],"recovery":[181],"information":[183,330],"situ":[186],"structural":[187,352],"biology.":[188,354],"find":[190,215],"mechanism":[193],"distinct":[198],"radiation":[200],"during":[202],"imaging.":[204],"By":[205],"accounting":[206],"both":[208,345],"scattering":[210],"damage,":[213],"will":[219],"negate":[220],"improvements":[223],"thinning":[226],"beyond":[227],"90":[228],"nm.":[229],"Significance":[230],"The":[231],"mechanisms":[233],"macromolecules":[236,254,279],"assemblies":[239],"often":[241],"studied":[242,265],"purified":[244],"material.":[245],"composition,":[248],"conformation":[249],"function":[251],"most":[253],"depend":[255],"on":[256],"context,":[259],"therefore,":[261],"must":[262],"also":[263],"be":[264],"inside":[266],"cells.":[267,293],"Focused":[268],"enables":[273],"visualize":[278],"close":[283],"resolution":[286],"generating":[288],"sections":[290],"extent":[296],"unknown.":[304],"show":[307],"Ga":[309,341],"+":[310,342],"\u223c60":[318],"surface,":[323],"leading":[324],"loss":[327],"recoverable":[329],"up":[332],"20%":[334],"100":[336],"samples.":[338],"therefore":[343],"presents":[344],"an":[346,349],"opportunity":[347],"obstacle":[350]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3}],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2023-02-04T00:00:00"}