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A gap-free genome assembly of Chlamydomonas reinhardtii anddetection of translocations induced by CRISPR-mediated mutagenesis

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Plant Communications 2023年第2期4卷 249-271页

作者： zachary l.payne Gervette M.Penny Tychele N.Turner Susan K.Dutcher Department of Genetics Washington University School of MedicineSaint LouisMO 63110USA

Genomic assemblies of the unicellular green alga Chlamydomonas reinhardtii have provided important resources for ***,assembly errors,large gaps,and unplaced scaffolds as well as strain-specific variants currently impede many types of *** combining PacBio HiFi and Oxford Nanopore long-read technologies,we generated a de novo genome assembly for strain CC-5816,derived from crosses of strains CC-125 and *** methods of evaluating genome completeness and base-pair error rate suggest that the final telomere-to-telomere assembly is highly *** CC-5816 assembly enabled previously difficult analyses that include characterization of the 17 centromeres,rDNA arrays on three chromosomes,and 56 insertions of organellar DNA into the nuclear *** Nanopore sequencing,we identified sites of cytosine(CpG)methylation,which are enriched at *** analyzed CRISPR-Cas9 insertional mutants in the PF23 *** of the three alleles produced progeny that displayed patterns of meiotic inviability that suggested the presence of a chromosomal *** Nanopore reads from pf23-2 and pf23-3 onto the CC-5816 genome showed that these two strains each carry a translocation that was initiated at the PF23 gene locus on chromosome 11 and joined with chromosomes 5 or 3,*** translocations were verified by demonstrating linkage between loci on the two translocated chromosomes in meiotic *** three pf23 alleles display the expected short-cilia phenotype,and immunoblotting showed that pf23-2 lacks the PF23 *** CC-5816 genome assembly will undoubtedly provide an important tool for the Chlamydomonas research community.

关键词： alga reference genome de novo PacBio Nanopore structural variation

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Phanerozoic co-evolution of O2-CO2 and ocean habitability

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National Science Review 2024年第06期 18-21页

作者： Zunli lu Rosalind E.M.Rickaby Jonathan l.payne Ashley N.Prow Department of Earth & Environmental Sciences Syracuse University Department of Earth Sciences University of Oxford Department of Earth and Planetary Sciences Stanford University

Atmospheric carbon dioxide and oxygen concentrations are partially linked via the geological cycle of organic carbon （Fig. 1A–C; e.g. CO2+H2O■CH2O+O2）. The history of these two biologically active components, controls on their concentrations, and implications for the complexity of the biosphere and habitability of Earth have been hotly debated, but are generally considered independently.

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Anneal-free ultra-low loss silicon nitride integrated photonics

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light(Science & Applications) 2024年第8期13卷 1565-1577页

作者： Debapam Bose Mark W.Harrington Andrei Isichenko Kaikai liu Jiawei Wang Nitesh Chauhan zachary l.Newman Daniel J.Blumenthal Department of Electrical and Computer Engineering University of California Santa BarbaraSanta BarbaraCA 93106USA Octave Photonics LouisvilleCO 80027USA

Heterogeneous and monolithic integration of the versatile low-loss silicon nitride platform with low-temperature materials such as silicon electronics and photonics,III–V compound semiconductors,lithium niobate,organics,and glasses has been inhibited by the need for high-temperature annealing as well as the need for different process flows for thin and thick *** techniques are needed to maintain the state-of-the-art losses,nonlinear properties,and CMOS-compatible processes while enabling this next generation of 3D silicon nitride *** report a significant advance in silicon nitride integrated photonics,demonstrating the lowest losses to date for an anneal-free process at a maximum temperature 250℃,with the same deuterated silane based fabrication flow,for nitride and oxide,for an order of magnitude range in nitride thickness without requiring stress mitigation or *** report record low anneal-free losses for both nitride core and oxide cladding,enabling 1.77 dBm-1 loss and 14.9 million Q for 80 nm nitride core waveguides,more than half an order magnitude lower loss than previously reported sub 300℃ *** 800 nm-thick nitride,we achieve as good as 8.66 dBm-1 loss and 4.03 million Q,the highest reported Q for a low temperature processed resonator with equivalent device area,with a median of loss and Q of 13.9 dBm-1 and 2.59 million each *** demonstrate laser stabilization with over 4 orders of magnitude frequency noise reduction using a thin nitride reference cavity,and using a thick nitride micro-resonator we demonstrate OPO,over two octave supercontinuum generation,and four-wave mixing and parametric gain with the lowest reported optical parametric oscillation threshold per unit resonator *** results represent a significant step towards a uniform ultra-low loss silicon nitride homogeneous and heterogeneous platform for both thin and thick waveguides capable of linear and nonlinear photonic circuits and integrat

关键词： resonator thick free

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Impact of COVID-19-related lifestyle changes on diabetic macular edema

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International Journal of Ophthalmology(English edition) 2024年第1期17卷 97-106页

作者： Bryce P.Johnson Yu-Guang He zachary M.Robertson Angeline Wang Rafael l.Ufret-Vincenty Department of Ophthalmology UT Southwestern Medical CenterDallasTexas 75390-9057USA

AIM:To assess diabetic macular edema(DME)progression during the early phases of the COVID-19 pandemic,when severe societal restrictions raised the concern of possible deterioration of health in patients with systemic conditions,particularly those requiring frequent office ***:This is a multicenter retrospective chart review of 370 patients(724 eyes)with an established diagnosis of DME seen on 3 separate visits between January 2019 and July *** 1 was January 2019 to February 2020(considered pre-COVID-19),period 2 was March 2020 to December 2020(considered the height of the pandemic;highest level of pandemic-related clinical and societal regulations)and period 3 was January 2021 to July 2021(re-adjustment to the new“pandemic norms”).Main outcome measures included visual acuity,body mass index(BMI),blood pressure(BP),hemoglobin A1c(HbA1c),macular thickness,patient adherence to scheduled ophthalmology visits,and DME treatment(s)received at each *** facilitate measurement of macular thickness,each macula was divided into 9 Early Treatment Diabetic Retinopathy Study(ETDRS)-defined macular sectors as measured by OCT ***:There was no change of BMI,systolic BP,and diastolic BP between any of the time ***1c showed a very small increase from period 1(7.6%)to period 2(7.8%,P=0.015)and decreased back to 7.6%at period 3(P=0.12).Macular thickness decreased for 100%of macular *** central macular thickness decreased across all 3 periods from 329.5 to 316.6μm(P=0.0045).After analysis of multiple variables including HbA1c,BMI,adherence to scheduled appointments,different clinic centers,and treatment interventions,there was no easily identifiable subgroup of patients that experienced the increase in ***:DME doesn’t worsen during the COVID-19 pandemic,instead sustaining a very small but statistically significant *** identifying a mechanism behind our findings is beyond the scope of this study,potential explanat

关键词： COVID-19 diabetic macular edema diabetic retinopathy optical coherence tomography

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Utilization of RNA sequencing to investigate olfactory dysfunction in chronic rhinosinusitis without nasal polyps:A pilot study

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World Journal of Otorhinolaryngology-Head and Neck Surgery 2024年第1期10卷 29-36页

作者： Jorge A.Gutierrez III Jeremy l.Barth Rodney J.Schlosser Thomas S.Edwards Timothy l.Smith zachary M.Soler Department of Otolaryngology-Head and Neck Surgery Medical University of South CarolinaCharlestonSouth CarolinaUSA Department of Regenerative Medicine&Cell Biology Medical University of South CarolinaCharlestonSouth CarolinaUSA Department of Otolaryngology-Head and Neck Surgery Oregon Health&Science UniversityPortlandOregonUSA

Objectives:Prior research on olfactory dysfunction in chronic rhinosinusitis(CRS)has focused on patients with polyps and suggests that direct inflammation of the olfactory cleft mucosa plays a contributory *** purpose of this study was to evaluate gene expression in superior turbinate mucosal specimens,comparing normosmic and dysosmic CRS patients without polyps(CRSsNP).Methods:Tissue samples were obtained from the superior turbinates of patients with CRSsNP at the time of endoscopic sinus *** subsequently underwent RNA sequencing and functional analysis to investigate biological pathways associated with differentially expressed genes between dysosmic(n=7)and normosmic(n=4)***:Differential gene expression analysis comparing dysosmic and normosmic CRSsNP patients showed upregulation of 563 genes and downregulation of 327 *** stringent criteria for multiple comparisons,one upregulated gene(Immediate Early Response 3[IER3])had an false discovery rate(FDR)correction adjustedP value considered statistically significant(Pld change 2.69).Reactome functional analysis revealed eight biological pathways significantly different between dysosmic and normosmic patients(Pluding Il-4 and Il-13 signaling,Il-10 signaling,and rhodopsin-like ***:RNA sequencing of the superior turbinates in patients with CRSsNP can provide valuable information regarding biological pathways and genes involved in olfactory *** study supports literature suggesting that Type 2 inflammation may play a role in olfactory dysfunction in at least some patients with *** study also prompts questions regarding the role of Il-10,rhodopsin-like receptors,andIER3 in the pathogenesis of olfactory dysfunction.

关键词： chronic rhinosinusitis without nasal polyps olfactory dysfunction RNA sequencing

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Tracking the Cretaceous transcontinental Ceduna River through Australia:The hafnium isotope record of detrital zircons from offshore southern Australia

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Geoscience Frontiers 2016年第2期7卷 237-244页

作者： Jarred lloyd Alan S.Collins Justin l.payne Stijn Glorie Simon Holford Anthony J.Reid Centre for Tectonics Resources and Exploration(TRaX)Department of Earth SciencesThe University of Adelaide Centre for Tectonics Resources and Exploration(TRaX)School of Built and Natural EnvironmentsThe University of South Australia Centre for Tectonics Resources and Exploration(TRaX)Australian School of PetroleumThe University of Adelaide Geological Survey of South Australia Department of State DevelopmentGovernment of South Australia

The middle-upper Cretaceous Ceduna River system traversed continental Australia from the NE coast to the centre of the southern coast. At its mouth, it formed a vast delta system that is similar in scale to the Niger delta of West Africa. The delta system is composed of two main lobes that represent different phases of delta construction. A recent hypothesis has challenged the traditional idea that both lobes of the delta were derived from a transcontinental river system by suggesting that the upper lobe （Santonian -Maastrichtian） is instead derived from a restricted catchment within southern Australia. Hf isotopic data presented here fingerprint the original source of the upper delta lobe zircons to NE Australia, with data comparing well with similar U-Pb and lu-Hf isotopic data from the lachlan Orogen, the New England Orogen, the eastern Musgraves Province and the northern Flinders Ranges. These data do not preclude a model where the lobe is derived from recycled Eromanga Basin sediments during a phase of late Cretaceous inland Australian uplift, but when coupled with reconnaissance low-temperature thermochronometry from the region of the Ceduna River course indicating widespread Triassic-Jurassic exhumation, and comparisons with detrital zircon data from the Winton Formation upstream of any proposed uplift, we suggest that both lobes of the Ceduna Delta are likely to be derived from a transcontinental Ceduna River.

关键词： Detrital zircon Hf U-Pb Ceduna sub-basin Bight basin Australia

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Magmatism and metamorphism at ca. 1.45 Ga in the northern Gawler Craton: The Australian record of rifting within Nuna(Columbia)

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Geoscience Frontiers 2019年第1期10卷 175-194页

作者： laura J.Morrissey Karin M.Barovich Martin Hand Katherine E.Howard Justin l.payne School of Natural and Built Environments University of South Australia Department of Earth Sciences School of Physical Sciences University of Adelaide

U-Pb monazite and zircon geochronology and calculated metamorphic phase diagrams from drill holes in the northern Gawler Craton, southern Australia, reveal the presence of ca. 1.45 Ga magmatism and metamorphism. Magmatism and granulite facies metamorphism of this age has not previously been recognised in the Gawler Craton. The magmatic rocks have steep lREE-enriched patterns and high Ga/Al values, suggesting they are A-type granites. Calculated metamorphic forward models suggest that this event was associated with high apparent thermal gradients and reached pressures of 3.2 -5.4 kbar and temperatures of 775-815℃. The high apparent thermal gradients may reflect pluton-enhanced metamorphism, consistent with the presence of A-type granites. The recognition of ca. 1.45 Ga tectonism in the northern Gawler Craton is added to a compilation of ca. 1.50 -1.40 Ga magmatism, shear zone reactivation, rift basin development and isotope resetting throughout the South and North Australian Cratons that shows that this event was widespread in eastern Proterozoic Australia. This event is stylistically similar to ca. 1.45 Ga A-type magmatism and high thermal gradient metamorphism in laurentia in this interval and provides further support for a connection between Australia and laurentia during the Mesoproterozoic. The tectonic setting of the 1.50-1.40 Ga event is unclear but may record rifting within the Nuna(or Columbia) supercontinent, or a period of intracontinental extension within a long-lived convergent setting.

关键词： Gawler Craton laurentia Metamorphism U-Pb geochronology Paleogeographic reconstruction

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Conservative management of spinal pathology with autologous conditioned serum: A systematic review of the literature

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World Journal of Orthopedics 2024年第9期15卷 870-881页

作者： Christian J Rajkovic Matthew l Merckling Alyssa W lee Galadu Subah Aryan Malhotra zachary D Thomas Sabrina l Zeller John V Wainwright Merritt D Kinon Department of Neurosurgery Westchester Medical CenterValhallaNY 10595United States

BACKGROUND Chronic inflammatory pain is associated with increased expression of interleukin(Il)-1,an inflammatory cytokine,and activity on its receptor(Il-1R).In response,the body produces Il-1R antagonist(Il-1Ra)to reduce this *** conditioned serum(ACS)is the only biologic therapy for spinal pathologies that enhances the action of endogenous Il-1Ra reserves to improve *** systematic review investigates the effectiveness of ACS in treating pain and dis-ability caused by spinal *** To evaluate the use of ACS as a conservative management option for spinal *** A systematic review of PubMed/Medline was performed to identify studies inve-stigating administration of ACS for treatment of any spinal *** Six articles were included,comprising 684 patients treated with epidural(n=133)or transforaminal(n=551)ACS *** had an average age of 54.0 years with slight female predominance(53.2%).The lumbar spine was most com-monly treated,with 567 patients(82.9%)receiving injections for lumbar radicu-lopathy(n=67),degenerative disc disease(DDD)(n=372),or spinal stenosis(n=128);cervical injections were performed in 109 patients(15.9%).Mean(SD)follow-up was 21.7(4.8)weeks from first ACS *** studies investigating mecha-nical lumbar and lumbar or cervical radicular pain reported significant pain re-duction at final follow-up compared to *** achieved comparable or su-perior results to lumbar epidural steroid *** events were reported in 21 patients(3.1%),with no serious adverse *** ACS injection is a safe and effective intervention for pain reduction in many spinal pathologies,including cervical and lumbar radiculopathies.

关键词： Spine Autologous conditioned serum Orthokine Regenokine Epidural steroid injection Interleukin-1 Inter-leukin-1 receptor antagonist

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late syn-to post-collisional magmatism in Madagascar:The genesis of the Ambalavao and Maevarano Suites

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Geoscience Frontiers 2019年第6期10卷 2063-2084页

作者： Donnelly B.Archibald Alan S.Collins John D.Foden Justin l.payne Peter Holden Théodore Razakamanana Department of Earth Sciences St.Francis Xavier UniversityPhysical Sciences Complex5009 Chapel SquareAntigonishNSB2G 2W5Canada Centre for Tectonics Resources and Exploration(TRaX)Department of Earth SciencesThe University of AdelaideAdelaide 5005SAAustralia Centre for Tectonics Resources and Exploration(TRaX)School of Built and Natural EnvironmentsUniversity of South AustraliaMawson LakesSA5001Australia Research School of Earth Sciences The Australian National UniversityCanberraACT2601Australia Departement des Sciences de la Terre Universitede ToliaraToliara601Madagascar

The East African Orogen involves a collage of Proterozoic microcontinents and arc terranes that became wedged between older cratonic blocks during the assembly of *** Ediacaran-Cambrian Ambalavao and Maevarano Suites in Madagascar were emplaced during the waning orogenic stages and consist of weakly deformed to undeformed plutonic rocks and dykes of mainly porphyritic granite but also gabbro,diorite and charnockite.U-Pb geochronological data date emplacement of the Ambalavao Suite to between ca.580 Ma and 540 Ma and the Maevarano Suite to between ca.537 Ma and522 *** and trace element concentrations are consistent with emplacement in a syn-to postcollisional tectonic setting as A-type(anorogenic) ***(δ^(18)O of 5.27‰-7.45‰) and hafnium(ε(Hf)(t) of-27.8 to-12.3) isotopic data from plutons in the Itremo and Antananarivo Domains are consistent with incorporation of an ancient crustal *** primitive δ^(18)O(5.27‰-5.32‰) andε(Hf)(t)(+0.0 to+0.2) isotopic values recorded in samples collected from the Ikalamavony Domain demonstrate the isotopic variation of basement sources present in the Malagasy *** Hf isotopic composition of Malagasy zircon are unlike more juvenile Ediacaran-Cambrian zircon sou rces elsewhere in the East African Orogen and,as such,Madagascar represents a distinct and identifiable detrital zircon source region in Phanerozoic sedimentary provenance *** together,these data indicate that high-T crustal anatexis,crustal assimilation and interaction of crustal material with mantle-derived melts were the processes operating during magma *** magmatism was coeval with polyphase deformation throughout Madagascar during the amalgamation of Gondwana and magmatism is interpreted to reflect lithospheric delamination of an extensive orogenic plateau.

关键词： Madagascar geology East African orogen Zircon geochronology Zircon oxygen and hafnium isotopes Post-collisional magmatism

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A Rare Case of Aortic Valve Endocarditis and Acute Meningitis Due to Haemophilus influenzae

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Case Reports in Clinical Medicine 2024年第6期13卷 207-211页

作者： zachary M. Visinoni Justin D. Tse Christopher F. Pease Department of Graduate Medical Education Internal Medicine Residency Sutter Roseville Medical Center Roseville USA Sutter Medical Group Roseville USA

HACEK organisms represent a rare but important group of causative pathogens in endocarditis. These bacteria have historically been associated with culture-negative endocarditis;however, modern laboratory techniques have made this less common. In this case, we present a 74-year-old man who presented with acute onset altered mentation, fever, and sepsis. He was ultimately found to have Haemophilus influenzae meningitis, cerebral empyema, aortic valve endocarditis, psoas myositis, and l2 - l3 diskitis with osteomyelitis. Although HACEK organisms are commonly found in the oropharynx and upper respiratory tract in humans, our patient did not report recent preceding dental or ENT procedures. H. influenzae is responsible for approximately 0.16% of all cases of bacterial endocarditis, representing a very limited subset. Although generally considered low virulent pathogens, this case demonstrates the unusual extent of infection from a HACEK organism, H. influenzae, causing aortic valve endocarditis as well as atypical non-cardiac sequelae, including acute meningitis.

关键词： HACEK Haemophilus influenzae Aortic Valve Endocarditis Bacterial Meningitis Cerebral Empyema

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