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Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915

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    Association of common and rare variants with Alzheimer's disease in more than 13,000 diverse individuals with whole-genome sequencing from the Alzheimer's Disease Sequencing Project.
    (Wiley Periodicals LLC on behalf of Alzheimer's Association, 2024-10-20) Lee W-P; Choi SH; Shea MG; Cheng P-L; Dombroski BA; Pitsillides AN; Heard-Costa NL; Wang H; Bulekova K; Kuzma AB; Leung YY; Farrell JJ; Lin H; Kunkle BW; Naj A; Blue EE; Nusetor F; Wang D; Boerwinkle E; Bush WS; Zhang X; De Jager PL; Dupuis J; Farrer LA; Fornage M; Martin E; Pericak-Vance M; Seshadri S; Wijsman EM; Wang L-S; Alzheimer's Disease Sequencing Project; Schellenberg GD; Destefano AL; Haines JL; Peloso GM
    INTRODUCTION Alzheimer's disease (AD) is a common disorder of the elderly that is both highly heritable and genetically heterogeneous. METHODS We investigated the association of AD with both common variants and aggregates of rare coding and non-coding variants in 13,371 individuals of diverse ancestry with whole genome sequencing (WGS) data. RESULTS Pooled-population analyses of all individuals identified genetic variants at apolipoprotein E (APOE) and BIN1 associated with AD (p < 5 × 10−8). Subgroup-specific analyses identified a haplotype on chromosome 14 including PSEN1 associated with AD in Hispanics, further supported by aggregate testing of rare coding and non-coding variants in the region. Common variants in LINC00320 were observed associated with AD in Black individuals (p = 1.9 × 10−9). Finally, we observed rare non-coding variants in the promoter of TOMM40 distinct of APOE in pooled-population analyses (p = 7.2 × 10−8). DISCUSSION We observed that complementary pooled-population and subgroup-specific analyses offered unique insights into the genetic architecture of AD. Highlights We determine the association of genetic variants with Alzheimer's disease (AD) using 13,371 individuals of diverse ancestry with whole genome sequencing (WGS) data. We identified genetic variants at apolipoprotein E (APOE), BIN1, PSEN1, and LINC00320 associated with AD. We observed rare non-coding variants in the promoter of TOMM40 distinct of APOE.
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    Decoupling of nutrient stoichiometry in Suaeda glauca (Bunge) senesced leaves under salt treatment
    (Frontiers Media S.A., 2023-09-04) Yang F; Liu S; Qian M; Wang D; Chen J; Li W
    The stoichiometry of senesced leaves is pivotal in nutrient cycling and can be significantly influenced by soil salinization, a rising global issue threatening the functionality of ecosystems. However, the impacts of soil salinization on senesced leaf stoichiometry are not fully understood. In this study, we conducted a pot experiment with varying soil salt concentrations to examine their influence on the concentrations and stoichiometric ratios of nitrogen (N), phosphorus (P), sodium (Na), potassium (K), calcium (Ca), magnesium (Mg), and zinc (Zn) in the senesced leaves of Suaeda glauca (Bunge). Compared to the control group, salt treatments significantly enhanced Na concentration while diminishing the concentrations of K, Ca, Mg, Zn, N, and P. Interestingly, as salinity levels escalated, N concentration maintained stability, whereas P concentration exhibited an increasing trend. Moreover, K, Ca, and Mg significantly declined as salt levels rose. Salt treatments brought about significant changes in stoichiometric ratios, with the N:P, K:Na, N:Na, N:Mg, and Ca : Mg ratios dropping and the N:Ca and N:K ratios rising, illustrating the varying nutrient coupling cycles under different salt conditions. These findings shed light on the plasticity of stoichiometric traits in S. glauca senesced leaves in response to soil salinization shifts, which could potentially offer insights into nutrient cycling reactions to soil salinization.
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    Efficacy of commercial peroxyacetic acid on Vibrio parahaemolyticus planktonic cells and biofilms on stainless steel and Greenshell™ mussel (Perna canaliculus) surfaces.
    (Elsevier B.V., 2023-11-16) Wang D; Palmer JS; Fletcher GC; On SLW; Gagic D; Flint SH
    The potential of using commercial peroxyacetic acid (PAA) for Vibrio parahaemolyticus sanitization was evaluated. Commercial PAA of 0.005 % (v/v, PAA: 2.24 mg/L, hydrogen peroxide: 11.79 mg/L) resulted in a planktonic cell reduction of >7.00 log10 CFU/mL when initial V. parahaemolyticus cells averaged 7.64 log10 CFU/mL. For cells on stainless steel coupons, treatment of 0.02 % PAA (v/v, PAA: 8.96 mg/L, hydrogen peroxide: 47.16 mg/L) achieved >5.00 log10 CFU/cm2 reductions in biofilm cells for eight strains but not for the two strongest biofilm formers. PAA of 0.05 % (v/v, PAA: 22.39 mg/L, hydrogen peroxide: 117.91 mg/L) was required to inactivate >5.00 log10 CFU/cm2 biofilm cells from mussel shell surfaces. The detection of PAA residues after biofilm treatment demonstrated that higher biofilm production resulted in higher PAA residues (p < 0.05), suggesting biofilm is acting as a barrier interfering with PAA diffusing into the matrices. Based on the comparative analysis of genomes, robust biofilm formation and metabolic heterogeneity within niches might have contributed to the variations in PAA resistance of V. parahaemolyticus biofilms.
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    Comparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus.
    (Elsevier B.V., 2023-04-01) Wang D; Fletcher GC; Gagic D; On SLW; Palmer JS; Flint SH
    Vibrio parahaemolyticus biofilms on the seafood processing plant surfaces are a potential source of seafood contamination and subsequent food poisoning. Strains differ in their ability to form biofilm, but little is known about the genetic characteristics responsible for biofilm development. In this study, pangenome and comparative genome analysis of V. parahaemolyticus strains reveals genetic attributes and gene repertoire that contribute to robust biofilm formation. The study identified 136 accessory genes that were exclusively present in strong biofilm forming strains and these were functionally assigned to the Gene Ontology (GO) pathways of cellulose biosynthesis, rhamnose metabolic and catabolic processes, UDP-glucose processes and O antigen biosynthesis (p < 0.05). Strategies of CRISPR-Cas defence and MSHA pilus-led attachment were implicated via Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Higher levels of horizontal gene transfer (HGT) were inferred to confer more putatively novel properties on biofilm-forming V. parahaemolyticus. Furthermore, cellulose biosynthesis, a neglected potential virulence factor, was identified as being acquired from within the order Vibrionales. The cellulose synthase operons in V. parahaemolyticus were examined for their prevalence (22/138, 15.94 %) and were found to consist of the genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC. This study provides insights into robust biofilm formation of V. parahaemolyticus at the genomic level and facilitates: identification of key attributes for robust biofilm formation, elucidation of biofilm formation mechanisms and development of potential targets for novel control strategies of persistent V. parahaemolyticus.
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    Collective remembering of Confucianism in Chinese language textbooks: Official historical representations from 1949 to 2019
    (SAGE Publishing, 2021) Xie T; Chen S; Wang D; Liu JH
    This study focuses on the collective remembering of an ancient system of meaning, examining content and changes in the construction of Confucianism in Chinese textbooks. The data consists of 84 editions of Chinese language teaching textbooks published by the People’s Education Press from 1949 to 2019. Content analysis shows that Confucianism is and was barely represented in this corpus. Thematic analysis shows that: (i) Only Confucius and Mencius were recognized as Confucian masters. (ii) Representations of Confucianism in the textbooks come from The Analects, Mencius, The Book of Rites, and The Book of Poetry, all of which are more than 2000 years old. (iii) Except for the 1970s, Confucianism was represented in a positive or at least neutral way. (iv) Confucianism is represented in a distant, abstract, decontextualized, and apolitical way, disconnected from students’ daily life. This gives insight into how a core representation stripped of its peripheral elements can lose meaning, and lose its normative influence on behavior. Contributions to collective memory, and implications for how to edit Chinese language textbooks to be more engaging are discussed.
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    Global expansion of Vibrio parahaemolyticus threatens the seafood industry: Perspective on controlling its biofilm formation
    (Elsevier Ltd, 2022-03-15) Wang D; Flint SH; Palmer JS; Gagic D; Fletcher GC; On SLW
    As global warming increases the geographical range and frequency of Vibrio parahaemolyticus infections, its formation of biofilms providing bacteria greater resistance to stress and contributing to the persistence of pathogens, is threatening the seafood industry. V. parahaemolyticus has a number of advantages leading to biofilm formation. This study reviews recent advances in understanding V. parahaemolyticus biofilm formation on biotic and abiotic surfaces, discusses research gaps in the mechanism of biofilm formation and examines promising biofilm control strategies to overcome current limitations of chemical disinfectant. This information will deepen our understanding of V. parahaemolyticus biofilm formation, as well as help design and optimize V. parahaemolyticus biofilm control strategies for the seafood industry.
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    Biofilm formation, sodium hypochlorite susceptibility and genetic diversity of Vibrio parahaemolyticus
    (Elsevier BV, 2023-01-16) Wang D; Fletcher GC; On SLW; Palmer JS; Gagic D; Flint SH
    Vibrio parahaemolyticus is a marine oriented pathogen; and biofilm formation enables its survival and persistence on seafood processing plant, complicating the hygienic practice. The objectives of this study are to assess the ability of V. parahaemolyticus isolated from seafood related environments to form biofilms, to determine the effective sodium hypochlorite concentrations required to inactivate planktonic and biofilm cells, and to evaluate the genetic diversity required for strong biofilm formation. Among nine isolates, PFR30J09 and PFR34B02 isolates were identified as strong biofilm forming strains, with biofilm cell counts of 7.20, 7.08 log10 CFU/cm2, respectively, on stainless steel coupons after incubation at 25 °C. Free available chlorine of 1176 mg/L and 4704 mg/L was required to eliminate biofilm cells of 1.74-2.28 log10 CFU/cm2 and > 7 log10 CFU/cm2, respectively, whereas 63 mg/L for planktonic cells, indicating the ineffectiveness of sodium hypochlorite in eliminating V. parahaemolyticus biofilm cells at recommended concentration in the food industry. These strong biofilm-forming isolates produced more polysaccharides and were less susceptible to sodium hypochlorite, implying a possible correlation between polysaccharide production and sodium hypochlorite susceptibility. Genetic diversity in mshA, mshC and mshD contributed to the observed variation in biofilm formation between isolates. This study identified strong biofilm-forming V. parahaemolyticus strains of new multilocus sequence typing (MLST) types, showed a relationship between polysaccharide production and sodium hypochlorite resistance.
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    Roadmap on signal processing for next generation measurement systems
    (IOP Publishing, 2022-01-01) Iakovidis DK; Ooi M; Kuang YC; Demidenko S; Shestakov A; Sinitsin V; Henry M; Sciacchitano A; Discetti S; Donati S; Norgia M; Menychtas A; Maglogiannis I; Wriessnegger SC; Chacon LAB; Dimas G; Filos D; Aletras AH; Töger J; Dong F; Ren S; Uhl A; Paziewski J; Geng J; Fioranelli F; Narayanan RM; Fernandez C; Stiller C; Malamousi K; Kamnis S; Delibasis K; Wang D; Zhang J; Gao RX
    Signal processing is a fundamental component of almost any sensor-enabled system, with a wide range of applications across different scientific disciplines. Time series data, images, and video sequences comprise representative forms of signals that can be enhanced and analysed for information extraction and quantification. The recent advances in artificial intelligence and machine learning are shifting the research attention towards intelligent, data-driven, signal processing. This roadmap presents a critical overview of the state-of-the-art methods and applications aiming to highlight future challenges and research opportunities towards next generation measurement systems. It covers a broad spectrum of topics ranging from basic to industrial research, organized in concise thematic sections that reflect the trends and the impacts of current and future developments per research field. Furthermore, it offers guidance to researchers and funding agencies in identifying new prospects.
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    Transverse-momentum and pseudorapidity distributions of charged hadrons in pp collisions at square root of s = 7 TeV.
    (AMER PHYSICAL SOC, 9/07/2010) Khachatryan V; Sirunyan AM; Tumasyan A; Adam W; Bergauer T; Dragicevic M; Erö J; Fabjan C; Friedl M; Frühwirth R; Ghete VM; Hammer J; Hänsel S; Hoch M; Hörmann N; Hrubec J; Jeitler M; Kasieczka G; Kiesenhofer W; Krammer M; Liko D; Mikulec I; Pernicka M; Rohringer H; Schöfbeck R; Strauss J; Taurok A; Teischinger F; Waltenberger W; Walzel G; Widl E; Wulz C-E; Mossolov V; Shumeiko N; Suarez Gonzalez J; Benucci L; Ceard L; De Wolf EA; Hashemi M; Janssen X; Maes T; Mucibello L; Ochesanu S; Roland B; Rougny R; Selvaggi M; Van Haevermaet H; Van Mechelen P; Van Remortel N; Adler V; Beauceron S; Blyweert S; D'Hondt J; Devroede O; Kalogeropoulos A; Maes J; Maes M; Tavernier S; Van Doninck W; Van Mulders P; Villella I; Chabert EC; Charaf O; Clerbaux B; De Lentdecker G; Dero V; Gay APR; Hammad GH; Marage PE; Vander Velde C; Vanlaer P; Wickens J; Costantini S; Grunewald M; Klein B; Marinov A; Ryckbosch D; Thyssen F; Tytgat M; Vanelderen L; Verwilligen P; Walsh S; Zaganidis N; Basegmez S; Bruno G; Caudron J; De Favereau De Jeneret J; Delaere C; Demin P; Favart D; Giammanco A; Grégoire G; Hollar J; Lemaitre V; Militaru O; Ovyn S; Pagano D; Pin A; Piotrzkowski K; Quertenmont L; Schul N; Beliy N; Caebergs T; Daubie E; Alves GA; Pol ME; Souza MHG; Carvalho W; Da Costa EM; De Jesus Damiao D; De Oliveira Martins C; Fonseca De Souza S; Mundim L; Oguri V; Santoro A; Silva Do Amaral SM; Sznajder A; Torres Da Silva De Araujo F; Dias FA; Dias MAF; Fernandez Perez Tomei TR; Gregores EM; Marinho F; Novaes SF; Padula SS; Darmenov N; Dimitrov L; Genchev V; Iaydjiev P; Piperov S; Stoykova S; Sultanov G; Trayanov R; Vankov I; Dyulendarova M; Hadjiiska R; Kozhuharov V; Litov L; Marinova E; Mateev M; Pavlov B; Petkov P; Bian JG; Chen GM; Chen HS; Jiang CH; Liang D; Liang S; Wang J; Wang J; Wang X; Wang Z; Yang M; Zang J; Zhang Z; Ban Y; Guo S; Hu Z; Mao Y; Qian SJ; Teng H; Zhu B; Cabrera A; Carrillo Montoya CA; Gomez Moreno B; Ocampo Rios AA; Osorio Oliveros AF; Sanabria JC; Godinovic N; Lelas D; Lelas K; Plestina R; Polic D; Puljak I; Antunovic Z; Dzelalija M; Brigljevic V; Duric S; Kadija K; Morovic S; Attikis A; Fereos R; Galanti M; Mousa J; Nicolaou C; Papadakis A; Ptochos F; Razis PA; Rykaczewski H; Tsiakkouri D; Zinonos Z; Mahmoud M; Hektor A; Kadastik M; Kannike K; Müntel M; Raidal M; Rebane L; Azzolini V; Eerola P; Czellar S; Härkönen J; Heikkinen A; Karimäki V; Kinnunen R; Klem J; Kortelainen MJ; Lampén T; Lassila-Perini K; Lehti S; Lindén T; Luukka P; Mäenpää T; Tuominen E; Tuominiemi J; Tuovinen E; Ungaro D; Wendland L; Banzuzi K; Korpela A; Tuuva T; Sillou D; Besancon M; Dejardin M; Denegri D; Descamps J; Fabbro B; Faure JL; Ferri F; Ganjour S; Gentit FX; Givernaud A; Gras P; Hamel de Monchenault G; Jarry P; Locci E; Malcles J; Marionneau M; Millischer L; Rander J; Rosowsky A; Rousseau D; Titov M; Verrecchia P; Baffioni S; Bianchini L; Bluj M; Broutin C; Busson P; Charlot C; Dobrzynski L; Elgammal S; Granier de Cassagnac R; Haguenauer M; Kalinowski A; Miné P; Paganini P; Sabes D; Sirois Y; Thiebaux C; Zabi A; Agram J-L; Besson A; Bloch D; Bodin D; Brom J-M; Cardaci M; Conte E; Drouhin F; Ferro C; Fontaine J-C; Gelé D; Goerlach U; Greder S; Juillot P; Karim M; Le Bihan A-C; Mikami Y; Speck J; Van Hove P; Fassi F; Mercier D; Baty C; Beaupere N; Bedjidian M; Bondu O; Boudoul G; Boumediene D; Brun H; Chanon N; Chierici R; Contardo D; Depasse P; El Mamouni H; Fay J; Gascon S; Ille B; Kurca T; Le Grand T; Lethuillier M; Mirabito L; Perries S; Tosi S; Tschudi Y; Verdier P; Xiao H; Roinishvili V; Anagnostou G; Edelhoff M; Feld L; Heracleous N; Hindrichs O; Jussen R; Klein K; Merz J; Mohr N; Ostapchuk A; Perieanu A; Raupach F; Sammet J; Schael S; Sprenger D; Weber H; Weber M; Wittmer B; Actis O; Ata M; Bender W; Biallass P; Erdmann M; Frangenheim J; Hebbeker T; Hinzmann A; Hoepfner K; Hof C; Kirsch M; Klimkovich T; Kreuzer P; Lanske D; Magass C; Merschmeyer M; Meyer A; Papacz P; Pieta H; Reithler H; Schmitz SA; Sonnenschein L; Sowa M; Steggemann J; Teyssier D; Zeidler C; Bontenackels M; Davids M; Duda M; Flügge G; Geenen H; Giffels M; Haj Ahmad W; Heydhausen D; Kress T; Kuessel Y; Linn A; Nowack A; Perchalla L; Pooth O; Sauerland P; Stahl A; Thomas M; Tornier D; Zoeller MH; Aldaya Martin M; Behrenhoff W; Behrens U; Bergholz M; Borras K; Campbell A; Castro E; Dammann D; Eckerlin G; Flossdorf A; Flucke G; Geiser A; Hauk J; Jung H; Kasemann M; Katkov I; Kleinwort C; Kluge H; Knutsson A; Kuznetsova E; Lange W; Lohmann W; Mankel R; Marienfeld M; Melzer-Pellmann I-A; Meyer AB; Mnich J; Mussgiller A; Olzem J; Parenti A; Raspereza A; Schmidt R; Schoerner-Sadenius T; Sen N; Stein M; Tomaszewska J; Volyanskyy D; Wissing C; Autermann C; Draeger J; Eckstein D; Enderle H; Gebbert U; Kaschube K; Kaussen G; Klanner R; Mura B; Naumann-Emme S; Nowak F; Sander C; Schettler H; Schleper P; Schröder M; Schum T; Schwandt J; Stadie H; Steinbrück G; Thomsen J; Wolf R; Bauer J; Buege V; Cakir A; Chwalek T; Daeuwel D; De Boer W; Dierlamm A; Dirkes G; Feindt M; 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Albergo S; Cappello G; Chiorboli M; Costa S; Tricomi A; Tuve C; Barbagli G; Broccolo G; Ciulli V; Civinini C; D'Alessandro R; Focardi E; Frosali S; Gallo E; Genta C; Lenzi P; Meschini M; Paoletti S; Sguazzoni G; Tropiano A; Benussi L; Bianco S; Colafranceschi S; Fabbri F; Piccolo D; Fabbricatore P; Musenich R; Benaglia A; Cerati GB; De Guio F; Di Matteo L; Ghezzi A; Govoni P; Malberti M; Malvezzi S; Martelli A; Massironi A; Menasce D; Miccio V; Moroni L; Negri P; Paganoni M; Pedrini D; Ragazzi S; Redaelli N; Sala S; Salerno R; Tabarelli de Fatis T; Tancini V; Taroni S; Buontempo S; Cimmino A; De Cosa A; De Gruttola M; Fabozzi F; Iorio AOM; Lista L; Noli P; Paolucci P; Azzi P; Bacchetta N; Bellan P; Bellato M; Biasotto M; Bisello D; Carlin R; Checchia P; De Mattia M; Dorigo T; Fanzago F; Gasparini F; Giubilato P; Gresele A; Lacaprara S; Lazzizzera I; Margoni M; Maron G; Meneguzzo AT; Nespolo M; Perrozzi L; Pozzobon N; Ronchese P; Simonetto F; Torassa E; Tosi M; Triossi A; Vanini S; Zumerle G; 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CMS Collaboration
    Charged-hadron transverse-momentum and pseudorapidity distributions in proton-proton collisions at square root of s = 7  TeV are measured with the inner tracking system of the CMS detector at the LHC. The charged-hadron yield is obtained by counting the number of reconstructed hits, hit pairs, and fully reconstructed charged-particle tracks. The combination of the three methods gives a charged-particle multiplicity per unit of pseudorapidity dN(ch)/dη|(|η|<0.5) = 5.78 ± 0.01(stat) ± 0.23(syst) for non-single-diffractive events, higher than predicted by commonly used models. The relative increase in charged-particle multiplicity from square root of s = 0.9 to 7 TeV is [66.1 ± 1.0(stat) ± 4.2(syst)]%. The mean transverse momentum is measured to be 0.545 ± 0.005(stat) ± 0.015(syst)  GeV/c. The results are compared with similar measurements at lower energies.