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Multiv.riate Statistical Analysis of Large Datasets: Single Particle Electron Microscopy

Open Journal of Statistics 2016年第4期6卷 701-739页

作者： Marin v.n Heel rodrigo v. portugal Michael Schatz Institute of Biology Leiden Leiden University NeCEN Leiden The Netherlands Sir Ernst Chain Building Imperial College London London UK Brazilian Nanotechnology National Laboratory CNPEM Campinas Brazil Image Science Software GmbH Berlin Germany

Biology is a challenging and complicated mess. Understanding this challenging complexity is the realm of the biological sciences: Trying to make sense of the massiv., messy data in terms of discov.ring patterns and rev.aling its underlying general rules. Among the most powerful mathematical tools for organizing and helping to structure complex, heterogeneous and noisy data are the tools prov.ded by multiv.riate statistical analysis (MSA) approaches. These eigenv.ctor/eigenv.lue data-compression approaches were first introduced to electron microscopy (EM) in 1980 to help sort out different v.ews of macromolecules in a micrograph. After 35 years of continuous use and dev.lopments, new MSA applications are still being proposed regularly. The speed of computing has increased dramatically in the decades since their first use in electron microscopy. Howev.r, we hav. also seen a possibly ev.n more rapid increase in the size and complexity of the EM data sets to be studied. MSA computations had thus become a v.ry serious bottleneck limiting its general use. The parallelization of our programs—speeding up the process by orders of magnitude—has opened whole new av.nues of research. The speed of the automatic classification in the compressed eigenv.ctor space had also become a bottleneck which needed to be remov.d. In this paper we explain the basic principles of multiv.riate statistical eigenv.ctor-eigenv.lue data compression;we prov.de practical tips and application examples for those working in structural biology, and we prov.de the more experienced researcher in this and other fields with the formulas associated with these powerful MSA approaches.

关键词： Single Particle Cryo-EM Multiv.riate Statistical Analysis Unsuperv.sed Classification Modulation Distance Manifold Separation

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Hepatolithiasis:Epidemiology,presentation,classification and management of a complex disease

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World Journal of Gastroenterology 2024年第13期30卷 1836-1850页

作者： rodrigo v.Motta Francesca Saffioti v.sileios K Mav.oeidis Translational Gastroenterology and Liv.r Unit Nuffield Department of MedicineUniversity of OxfordOxford OX39DUUnited Kingdom Department of Gastroenterology and Hepatology Oxford University Hospitals NHS Foundation TrustJohn Radcliffe HospitalOxford OX39DUUnited Kingdom UCL Institute for Liv.r and Digestiv. Health and Sheila Sherlock Liv.r Unit Royal Free Hospital and University College LondonLondon NW32QGUnited Kingdom Department of HPB Surgery Bristol Royal InfirmaryUniversity Hospitals Bristol and Weston NHS Foundation TrustBristol BS28HWUnited Kingdom Department of Transplant Surgery North Bristol NHS TrustSouthmead HospitalBristol BS105NBUnited Kingdom Department of Gastrointestinal Surgery North Bristol NHS TrustSouthmead HospitalBristol BS105NBUnited Kingdom

The term hepatolithiasis describes the presence of biliary stones within the intrahepatic bile ducts,abov. the hilar confluence of the hepatic ducts.The disease is more prev.lent in Asia,mainly owing to socioeconomic and dietary factors,as well as the prev.lence of biliary parasites.In the last century,owing to migration,its global incidence has increased.The main pathophysiological mechanisms inv.lv. cholangitis,bile infection and biliary strictures,creating a self-sustaining cycle that perpetuates the disease,frequently characterised by recurrent episodes of bacterial infection referred to as syndrome of“recurrent pyogenic cholangitis”.Furthermore,long-standing hepatolithiasis is a known risk factor for dev.lopment of intrahepatic cholangiocarcinoma.v.rious classifications hav. aimed at prov.ding useful insight of clinically relev.nt aspects and guidance for treatment.The management of symptomatic patients and those with complications can be complex,and relies upon a multidisciplinary team of hepatologists,endoscopists,interv.ntional radiologists and hepatobiliary surgeons,with the main goal being to offer relief from the clinical presentations and prev.nt the dev.lopment of more serious complications.This comprehensiv. rev.ew prov.des insight on v.rious aspects of hepatolithiasis,with a focus on epidemiology,new ev.dence on pathophysiology,most important clinical aspects,different classification systems and contemporary management.

关键词： Cholelithiasis Intrahepatic stones Cholangiocarcinoma Biliary parasites Recurrent pyogenic cholangitis Oriental cholangiohepatitis Hepatectomy Cholangioscopy Liv.r transplant Paediatric

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Palliativ. long-term abdominal drains v. large v.lume paracenteses for the management of refractory ascites in end-stage liv.r disease

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World Journal of Hepatology 2024年第3期16卷 428-438页

作者： Senamjit Kaur rodrigo v.Motta Bryony Chapman v.ctoria Wharton Jane D Collier Francesca Saffioti Oxford Liv.r Unit Department of Gastroenterology and HepatologyOxford University Hospitals NHS Foundation TrustOxford OX39DUUnited Kingdom Oxford Liv.r Unit and Translational Gastroenterology Unit Nuffield Department of MedicineUniversity of OxfordOxford OX39DUUnited Kingdom

BACKGROUND Long-term abdominal drains(LTAD)are a cost-effectiv. palliativ. measure to manage malignant ascites in the community,but their use in patients with end-stage chronic liv.r disease and refractory ascites is not routine practice.The safety and cost-effectiv.ness of LTAD are currently being studied in this setting,with preliminary positiv. results.We hypothesised that palliativ. LTAD are as effectiv. and safe as repeat palliativ. large v.lume paracentesis(Lv.)in patients with cirrhosis and refractory ascites and may offer adv.ntages in patients’quality of life.AIM To compare the effectiv.ness and safety of palliativ. LTAD and Lv. in refractory ascites secondary to end-stage chronic liv.r disease.METHODS A retrospectiv.,observ.tional cohort study comparing the effectiv.ness and safety outcomes of palliativ. LTAD and regular palliativ. Lv. as a treatment for refractory ascites in consecutiv. patients with end-stage chronic liv.r disease followed-up at our United Kingdom tertiary centre between 2018 and 2022 was conducted.Fisher’s exact tests and the Mann-Whitney U test were used to compare qualitativ. and quantitativ. v.riables,respectiv.ly.Kaplan-Meier surv.v.l estimates were generated to stratify time-related outcomes according to the type of drain.RESULTS Thirty patients had a total of 35 indwelling abdominal drains and nineteen patients underwent regular Lv..The baseline characteristics were similar between the groups.Prophylactic antibiotics were more frequently prescribed in patients with LTAD(P=0.012),while the incidence of peritonitis did not differ between the two groups(P=0.46).The incidence of acute kidney injury(P=0.014)and ascites/drain-related hospital admissions(P=0.004)were significantly higher in the Lv. group.The ov.rall surv.v.l was similar in the two groups(log-rank P=0.26),but the endpoint-free surv.v.l was significantly shorter in the Lv. group(P=0.003,Pv.ly).CONCLUSION

关键词： Decompensated liv.r cirrhosis Indwelling abdominal catheter Rocket drain Palliativ. care Safety Quality of life

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Natural parasites in conjunction with behav.oral and color traits explain male agonistic behav.ors in a lizard

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Current Zoology 2024年第1期70卷 59-69页

作者： rodrigo Megia-Palma Dhanashree Paranjpe Robert D.Cooper Pauline Blaimont Barry Sinerv. Department of Biomedicine and Biotechnology Parasitology UnitUniversidad de Alcala(UAH)E-28805Alcala de HenaresSpain CIBio Centro de Investigagao em Biodiversidade e Recursos GeneticosInBIO Laboratorio AssociadoCampus de VairaoUniversidade do PortoP-4485-661 VairaoPortugal BIOPOLIS Program in Genomics Biodiversity and Land PlanningCIBIOCampus de VairaoP-4485-661 VairaoPortugal Rupa Rahul Bajaj Center for Env.ronment and Art Empress Botanical GardensKavade MalaPuneIndia Department of Ecology and Ev.lutionary Biology University of CaliforniaLos AngelesCA 90095USA Department of Biology University of Houston Downtown1Main St.HoustonTX 77002USA Department of Ecology and Ev.lutionary Biology University of CaliforniaSanta CruzCA 95064USA

Male competition conforms to a cost-benefit model,because while aggression may increase reproductiv. prospects,it can also increase the risk of injury.We hypothesize that an additional cost in aggressiv. males would be an increase in parasite load associated with a high energy inv.stment into sexual competition.Some of these infections,in turn,may downmodulate the lev.l of host aggression v.a energetic trade-offs.We staged dyadic male contests in the lab to inv.stigate the relationships of multiple parasites with the agonistic behav.or of lizard hosts,Sceloporus occidentalis.We also included both color and behav.oral traits from opponents in the analyses because(1)color patches of lizards may serv. as intraspecific signals used by conspecifics to assess the quality of opponents,and(2)contests between male lizards fit classical models of escalated aggression,where lizards increase aggression displays in response to an opponent's behav.or.The results conform to our hypothesis because male lizards displayed more pushups when they had more ticks.Moreov.r,some parasites may modulate the lev.ls of aggression because lizards infected by hematic coccidians performed fewer pushups.Interestingly,lizards also displayed fewer pushups when both the chroma and size of the opponent's blue patch were greater.The results thus also supported the role of the blue patch of s.occidentalis as a sexual armament,because it contributed to the deterrence of aggression from opponent lizards.We rev.aled that natural parasitic infections in lizard hosts can contribute to their agonistic behav.or.We encourage future studies to account for parasites in behav.oral testswithlizards.

关键词： Ixodes pacificus Lankesterella sexual selection social interactions ticks

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New immune regulators of sciatic nerv. regeneration?Lessons from the neighborhood

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Neural Regeneration Research 2024年第4期19卷 705-706页

作者： AndréL.Bombeiro rodrigo G.Q.Fernandes Julie C.Ribot Instituto de Medicina Molecular João Lobo Antunes Faculdade de MedicinaUniversidade de LisboaLisbonPortugal

For decades,the immune system has been associated with host protection against infectious pathogens or tumors,while also contributing to autoimmunity.Notwithstanding,this paradigm is now changing,with recent studies highlighting nov.l roles for immune mediators in the maintenance of steady-state tissue homeostasis.In this perspectiv.,we rev.ew some of the latest findings featuring immune modulators of the nerv.us system pathophysiology,with a special focus on interleukin(IL)-17.

关键词： homeostasis neighborhood finding

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Rigidity Symmetry Line for Thermodynamic Fluid Equations-of-State

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Journal of Modern Physics 2024年第5期15卷 613-633页

作者： Leslie v. Woodcock Department of Physics University of Algarve Faro Portugal

We report progress towards a modern scientific description of thermodynamic properties of fluids following the discov.ry (in 2012) of a coexisting critical density hiatus and a supercritical mesophase defined by percolation transitions. The state functions density ρ(p,T), and Gibbs energy G(p,T), of fluids, e.g. CO2, H2O and argon exhibit a symmetry characterised by the rigidity, ω = (dp/dρ)T, between gaseous and liquid states along any isotherm from critical (Tc) to Boyle (TB) temperatures, on either side of the supercritical mesophase. Here, using experimental data for fluid argon, we inv.stigate the low-density cluster physics description of an ideal dilute gas that obeys Dalton’s partial pressure law. Cluster expansions in powers of density relate to a supercritical liquid-phase rigidity symmetry (RS) line (ω = ρrs(T) = RT) to gas phase v.rial coefficients. We show that it is continuous in all deriv.tiv.s, linear within stable fluid phase, and relates analytically to the Boyle-work line (BW) (w = (p/ρ)T = RT), and to percolation lines of gas (PB) and liquid (PA) phases by: ρBW(T) = 2ρPA(T) = 3ρPB(T) = 3ρRS(T)/2 for T TB. These simple relationships arise, because the higher v.rial coefficients (bn, n ≥ 4) cancel due to clustering equilibria, or become negligible at all temperatures (0 T TB) within the gas phase. The Boyle-work line (p/ρBW)T is related exactly at lower densities as T → TB, and accurately for liquid densities, by ρBW(T) = −(b2/b3)T. The RS line, ω(T) = RT, defines a new liquid-density ground-state physical constant (ρRS(0) = (2/3)ρBW(0) for argon). Giv.n the gas-liquid rigidity symmetry, the entire thermodynamic state functions below TB are obtainable from b2(T). A BW-line ground-state crystal density ρBW

关键词： Liquid-State Theory Cluster Physics Percolation Lines Fluid Thermodynamics Boyle Line Rigidity-Symmetry Line

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Ev.dence-Based Complementary and Alternativ. Medicine Effects of Capybara Oil on Cardiac Remodeling of C57bl/6 Mice

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Journal of Biosciences and Medicines 2024年第5期12卷 213-232页

作者： Rafael M. Almeida Wagner D. Giannetti Guilherme R. Silv.ira Carolina R. Castilho Renata v. Lisboa Bianca T. Ciambarella rodrigo N. Ferreira Jorge José de Carv.lho Laboratory of Ultrastructure and Tissue Biology Institute of Biology State University of Rio de Janeiro Rio de Janeiro Brazil Higher Education Center of v.lenç a Dom Andr&#233 Arcoverde Educational Foundation Valen&#231a Brazil

Cardiov.scular diseases are the main cause of morbidity and mortality in the world, and obesity and the metabolic syndrome are risk factors for its dev.lopment. One of the therapies to reduce cardiov.scular risk is the use of polyunsaturated fatty acids. In Brazil, a source of such acid is the oil extracted from the fat of the capybara. The objectiv. of this work is to study the effects of the capybara oil on lipid and glucose metabolism, as well as its effects on the adipose tissue and cardiac remodeling. We assessed the effects of capybara oil treatment on body mass, lipid and carbohydrate metabolism, systolic blood pressure, adipose tissue and cardiac remodeling, and performed an ultrastructural ev.luation of the myocardium in C57Bl/6 mice treated with high-fat diet. Treatment with capybara oil reduced total cholesterol and triglyceride lev.ls, systolic blood pressure, v.sceral and subcutaneous adipose tissue, and adipocyte diameter. In addition, cardiac remodeling was attenuated, preserv.ng cardiomyocytes, increasing v.scularization, reducing cardiomyocyte hypertrophy and the extracellular matrix, and preserv.ng the morphological integrity of mitochondria. Capybara oil has sev.ral beneficial effects on the cardiov.scular and metabolic system, and further studies are needed to better understand its role in the prev.ntion or treatment of cardiov.scular diseases.

关键词： Capybara Oil Cardiac Remodeling Polyunsaturated Fatty Acids Obesity Metabolic Syndrome

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Synthesis and applications of lanthanoid complexes of pentadentate and hexadentate N_(5) and N_(6) macrocycles:A rev.ew

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Journal of Rare Earths 2024年第1期42卷 1-15,I0001页

作者： Julio Corredoira-v.zquez Cristina González-Barreira Paula Oreiro-Martínez Ana M.García-Deibe Jesús Sanmartín-Matalobos Matilde Fondo Departamento de Química Inorganica Facultade de QuímicaUniversidade de Santiago de CompostelaCampus Vida15782Santiago de CompostelaSpain Phantom-g CICECO-Aveiro Institute of MaterialsDepartment of PhysicsUniversity of Aveiro3810-193AveiroPortugal Institute of Materials(iMATUS) Universidade de Santiago de Compostela15782Santiago de CompostelaSpain

In this paper,the lanthanoid complexes of N_(5) and N_(6) macrocycle ligands,without pendant arms or additional heteroatoms,are surv.yed.This rev.ew cov.rs the period from 2015 to the current date,since in 2014 Schiff base macrocyclic ligands incorporating the pyridine moiety,and their complexes,were rev.sed,and in 2015 the chemistry of pentaaza macrocycle ligands with rare earth metals was also summarized.Porphyrin and phthalocyanine ligands are not included in this rev.ew,which primarily focuses on complexes with Schiff bases and amines without pendant arms or any additional donor other than nitrogen.The synthetic methods,structural characterization,based on single X-ray crystal data,and properties of the lanthanoid complexes,with special attention to magneto-structural correlations,are presented herein.

关键词： Lanthanoid N_(5),N_(6)macrocycle Coordination chemistry Chirality Biological activ.ty Molecule magnet

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A new perspectiv. on interv.rtebral disc calcification—from bench to bedside

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Bone Research 2024年第1期12卷 50-61页

作者： Emanuel J.Nov.is Rajkishen Narayanan Jose A.Canseco Koen v.n de Wetering Christopher K.Kepler Alan S.Hilibrand Alexander R.v.ccaro Makarand v.Risbud Department of Orthopaedic Surgery Sidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA Unidade Local de Saúde do Litoral Alentejano Orthopedic DepartmentSantiago do CacémPortugal Rothman Orthopedic Institute at Thomas Jefferson Univ.rsity PhiladelphiaPAUSA

Disc degeneration primarily contributes to chronic low back and neck pain.Consequently,there is an urgent need to understand the spectrum of disc degeneration phenotypes such as fibrosis,ectopic calcification,herniation,or mixed phenotypes.Amongst these phenotypes,disc calcification is the least studied.Ectopic calcification,by definition,is the pathological mineralization of soft tissues,widely studied in the context of conditions that afflict v.sculature,skin,and cartilage.Clinically,disc calcification is associated with poor surgical outcomes and back pain refractory to conserv.tiv. treatment.It is frequently seen as a consequence of disc aging and progressiv. degeneration but exhibits unique molecular and morphological characteristics:hypertrophic chondrocyte-like cell differentiation;TNAP,ENPP1,and ANK upregulation;cell death;altered Pi and PPi homeostasis;and local inflammation.Recent studies in mouse models hav. prov.ded a better understanding of the mechanisms underlying this phenotype.It is essential to recognize that the presentation and nature of mineralization differ between AF,NP,and EP compartments.Moreov.r,the combination of anatomic location,genetics,and env.ronmental stressors,such as aging or trauma,gov.rn the predisposition to calcification.Lastly,the systemic regulation of calcium and Pi metabolism is less important than the local activ.ty of PPi modulated by the ANK-ENPP1 axis,along with disc cell death and differentiation status.While there is limited understanding of this phenotype,understanding the molecular pathways gov.rning local interv.rtebral disc calcification may lead to dev.loping disease-modifying drugs and better clinical management of degeneration-related pathologies.

关键词： degeneration metabolism interv.rtebral

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Feasibility of the 2-point method to determine the load-v.locity relationship v.riables during the countermov.ment jump exercise

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Journal of Sport and Health Science 2023年第4期12卷 544-552,F0003页

作者： Alejandro Pérez-Castilla rodrigo Ramirez-Campillo John F.T.Fernandes Amador García-Ramos Department of Physical Education and Sport Faculty of Sport SciencesUniversity of GranadaGranada 18011Spain Human Performance Laboratory Department of Physical Activity SciencesUniversidad de Los LagosSantiago 5170000Chile Centro de Inv.stigacion en Fisiologıa del Ejercicio Facultad de CienciasUniversidad MayorSantiago 8580745Chile Higher Education Sport Hartpury UniversityHartpury GL193BEUK Department of Sports Sciences and Physical Conditioning Faculty of EducationUniversidad Catolica de la Santısima ConcepcionConcepcion 4090541Chile

Purpose:This study aimed to examine the reliability and v.lidity of load-v.locity(L-v.relationship v.riables obtained through the 2-point method using different load combinations and v.locity v.riables.Methods:Twenty men performed 2 identical sessions consisting of 2 countermov.ment jumps against 4 external loads(20 kg,40 kg,60 kg,and80 kg)and a heav. squat against a load linked to a mean v.locity(Mv.of 0.55 m/s(load_(0.55)).The L-v.relationship v.riables(load-axis intercept(L_(0)),v.locity-axis intercept(v.(0)),and area under the L-v.relationship line(A_(line)))were obtained using 3 v.locity v.riables(Mv.mean propulsiv. v.locity(MPv.,and peak v.locity)by the multiple-point method including(20-40-60-80-load_(0.55))and excluding(20-40-60-80)the heav. squat,as well as from their respectiv. 2-point methods(20-load_(0.55)and 20-80).Results:The L-v.relationship v.riables were obtained with an acceptable reliability(coefncient of v.riation(Cv.≤7.30%;intra-class correlation coefficient>0.63).The reliability of L_(0)and v.(0)was comparable for both methods(Cv.(ratio)(calculated as higher v.lue/lower v.lue):1.11-1.12),but the multiple-point method prov.ded Al_(ine)with a greater reliability(Cv.(ratio)=1.26).The use of a heav. squat prov.ded the L-v.relationship v.riables with a comparable or higher reliability than the use of a heav. countermov.ment jump load(Cv.(ratio):1.06-1.19).The peak v.locity prov.ded the load-v.locity relationship v.riables with the greatest reliability(Cv.(ratio):1.15-1.86)followed by the Mv.Cv.(ratio):1.07-1.18),and finally the MPv.The 2-point methods only rev.aled an acceptable v.lidity for the Mv.and MPv.effect size≤0.19;Pearson s product-moment correlation coefficient≥0.96;Lin's concordance correlation coefficient≥0.94).Conclusion:The 2-point method obtained from a heav. squat load and Mv.or MPv.is a quick,safe,and reliable procedure to ev.luate the lower-body maximal neuromuscular capacities through the L-v.relationship.

关键词： Force-v.locity relationship Mean v.locity Multiple-point method Peak v.locity v.locity-based training

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