Constrained Markovian dynamics of random graphs

We introduce a statistical mechanics formalism for the study of constrained graph evolution as a Markovian stochastic process, in analogy with that available for spin systems, deriving its basic properties and highlighting the role of the `mobility' (the number of allowed moves for any given graph). As an application of the general theory we analyze the properties of degree-preserving Markov chains based on elementary edge switchings. We give an exact yet simple formula for the mobility in terms of the graph's adjacency matrix and its spectrum. This formula allows us to define acceptance probabilities for edge switchings, such that the Markov chains become controlled Glauber-type detailed balance processes, designed to evolve to any required invariant measure (representing the asymptotic frequencies with which the allowed graphs are visited during the process). As a corollary we also derive a condition in terms of simple degree statistics, sufficient to guarantee that, in the limit where the number of nodes diverges, even for state-independent acceptance probabilities of proposed moves the invariant measure of the process will be uniform. We test our theory on synthetic graphs and on realistic larger graphs as studied in cellular biology.Comment: 28 pages, 6 figure

Electrochemical methods for speciation of trace elements in marine waters. Dynamic aspects

The contribution of electrochemical methods to the knowledge of dynamic speciation of toxic trace elements in marine waters is critically reviewed. Due to the importance of dynamic considerations in the interpretation of the electrochemical signal, the principles and recent developments of kinetic features in the interconversion of metal complex species will be presented. As dynamic electrochemical methods, only stripping techniques (anodic stripping voltammetry and stripping chronopotentiometry) will be used because they are the most important for the determination of trace elements. Competitive ligand ex- change-adsorptive cathodic stripping voltammetry, which should be considered an equilibrium technique rather than a dynamic method, will be also discussed because the complexing parameters may be affected by some kinetic limitations if equilibrium before analysis is not attained and/or the flux of the adsorbed complex is in fluenced by the lability of the natural complexes in the water sample. For a correct data interpretation and system characterization the comparison of results obtained from different techniques seems essential in the articulation of a serious discussion of their meaning

Effects of Climate and Atmospheric Nitrogen Deposition on Early to Mid-Term Stage Litter Decomposition Across Biomes

open263siWe acknowledge support by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (FZT 118), Scientific Grant Agency VEGA(GrantNo.2/0101/18), as well as by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Program (Grant Agreement No. 677232)Litter decomposition is a key process for carbon and nutrient cycling in terrestrial ecosystems and is mainly controlled by environmental conditions, substrate quantity and quality as well as microbial community abundance and composition. In particular, the effects of climate and atmospheric nitrogen (N) deposition on litter decomposition and its temporal dynamics are of significant importance, since their effects might change over the course of the decomposition process. Within the TeaComposition initiative, we incubated Green and Rooibos teas at 524 sites across nine biomes. We assessed how macroclimate and atmospheric inorganic N deposition under current and predicted scenarios (RCP 2.6, RCP 8.5) might affect litter mass loss measured after 3 and 12 months. Our study shows that the early to mid-term mass loss at the global scale was affected predominantly by litter quality (explaining 73% and 62% of the total variance after 3 and 12 months, respectively) followed by climate and N deposition. The effects of climate were not litter-specific and became increasingly significant as decomposition progressed, with MAP explaining 2% and MAT 4% of the variation after 12 months of incubation. The effect of N deposition was litter-specific, and significant only for 12-month decomposition of Rooibos tea at the global scale. However, in the temperate biome where atmospheric N deposition rates are relatively high, the 12-month mass loss of Green and Rooibos teas decreased significantly with increasing N deposition, explaining 9.5% and 1.1% of the variance, respectively. The expected changes in macroclimate and N deposition at the global scale by the end of this century are estimated to increase the 12-month mass loss of easily decomposable litter by 1.1-3.5% and of the more stable substrates by 3.8-10.6%, relative to current mass loss. In contrast, expected changes in atmospheric N deposition will decrease the mid-term mass loss of high-quality litter by 1.4-2.2% and that of low-quality litter by 0.9-1.5% in the temperate biome. Our results suggest that projected increases in N deposition may have the capacity to dampen the climate-driven increases in litter decomposition depending on the biome and decomposition stage of substrate.openKwon T.; Shibata H.; Kepfer-Rojas S.; Schmidt I.K.; Larsen K.S.; Beier C.; Berg B.; Verheyen K.; Lamarque J.-F.; Hagedorn F.; Eisenhauer N.; Djukic I.; Caliman A.; Paquette A.; Gutierrez-Giron A.; Petraglia A.; Augustaitis A.; Saillard A.; Ruiz-Fernandez A.C.; Sousa A.I.; Lillebo A.I.; Da Rocha Gripp A.; Lamprecht A.; Bohner A.; Francez A.-J.; Malyshev A.; Andric A.; Stanisci A.; Zolles A.; Avila A.; Virkkala A.-M.; Probst A.; Ouin A.; Khuroo A.A.; Verstraeten A.; Stefanski A.; Gaxiola A.; Muys B.; Gozalo B.; Ahrends B.; Yang B.; Erschbamer B.; Rodriguez Ortiz C.E.; Christiansen C.T.; Meredieu C.; Mony C.; Nock C.; Wang C.-P.; Baum C.; Rixen C.; Delire C.; Piscart C.; Andrews C.; Rebmann C.; Branquinho C.; Jan D.; Wundram D.; Vujanovic D.; Adair E.C.; Ordonez-Regil E.; Crawford E.R.; Tropina E.F.; Hornung E.; Groner E.; Lucot E.; Gacia E.; Levesque E.; Benedito E.; Davydov E.A.; Bolzan F.P.; Maestre F.T.; Maunoury-Danger F.; Kitz F.; Hofhansl F.; Hofhansl G.; De Almeida Lobo F.; Souza F.L.; Zehetner F.; Koffi F.K.; Wohlfahrt G.; Certini G.; Pinha G.D.; Gonzlez G.; Canut G.; Pauli H.; Bahamonde H.A.; Feldhaar H.; Jger H.; Serrano H.C.; Verheyden H.; Bruelheide H.; Meesenburg H.; Jungkunst H.; Jactel H.; Kurokawa H.; Yesilonis I.; Melece I.; Van Halder I.; Quiros I.G.; Fekete I.; Ostonen I.; Borovsk J.; Roales J.; Shoqeir J.H.; Jean-Christophe Lata J.; Probst J.-L.; Vijayanathan J.; Dolezal J.; Sanchez-Cabeza J.-A.; Merlet J.; Loehr J.; Von Oppen J.; Loffler J.; Benito Alonso J.L.; Cardoso-Mohedano J.-G.; Penuelas J.; Morina J.C.; Quinde J.D.; Jimnez J.J.; Alatalo J.M.; Seeber J.; Kemppinen J.; Stadler J.; Kriiska K.; Van Den Meersche K.; Fukuzawa K.; Szlavecz K.; Juhos K.; Gerhtov K.; Lajtha K.; Jennings K.; Jennings J.; Ecology P.; Hoshizaki K.; Green K.; Steinbauer K.; Pazianoto L.; Dienstbach L.; Yahdjian L.; Williams L.J.; Brigham L.; Hanna L.; Hanna H.; Rustad L.; Morillas L.; Silva Carneiro L.; Di Martino L.; Villar L.; Fernandes Tavares L.A.; Morley M.; Winkler M.; Lebouvier M.; Tomaselli M.; Schaub M.; Glushkova M.; Torres M.G.A.; De Graaff M.-A.; Pons M.-N.; Bauters M.; Mazn M.; Frenzel M.; Wagner M.; Didion M.; Hamid M.; Lopes M.; Apple M.; Weih M.; Mojses M.; Gualmini M.; Vadeboncoeur M.; Bierbaumer M.; Danger M.; Scherer-Lorenzen M.; Ruek M.; Isabellon M.; Di Musciano M.; Carbognani M.; Zhiyanski M.; Puca M.; Barna M.; Ataka M.; Luoto M.; H. Alsafaran M.; Barsoum N.; Tokuchi N.; Korboulewsky N.; Lecomte N.; Filippova N.; Hlzel N.; Ferlian O.; Romero O.; Pinto-Jr O.; Peri P.; Dan Turtureanu P.; Haase P.; Macreadie P.; Reich P.B.; Petk P.; Choler P.; Marmonier P.; Ponette Q.; Dettogni Guariento R.; Canessa R.; Kiese R.; Hewitt R.; Weigel R.; Kanka R.; Cazzolla Gatti R.; Martins R.L.; Ogaya R.; Georges R.; Gaviln R.G.; Wittlinger S.; Puijalon S.; Suzuki S.; Martin S.; Anja S.; Gogo S.; Schueler S.; Drollinger S.; Mereu S.; Wipf S.; Trevathan-Tackett S.; Stoll S.; Lfgren S.; Trogisch S.; Seitz S.; Glatzel S.; Venn S.; Dousset S.; Mori T.; Sato T.; Hishi T.; Nakaji T.; Jean-Paul T.; Camboulive T.; Spiegelberger T.; Scholten T.; Mozdzer T.J.; Kleinebecker T.; Runk T.; Ramaswiela T.; Hiura T.; Enoki T.; Ursu T.-M.; Di Cella U.M.; Hamer U.; Klaus V.; Di Cecco V.; Rego V.; Fontana V.; Piscov V.; Bretagnolle V.; Maire V.; Farjalla V.; Pascal V.; Zhou W.; Luo W.; Parker W.; Parker P.; Kominam Y.; Kotrocz Z.; Utsumi Y.Kwon T.; Shibata H.; Kepfer-Rojas S.; Schmidt I.K.; Larsen K.S.; Beier C.; Berg B.; Verheyen K.; Lamarque J.-F.; Hagedorn F.; Eisenhauer N.; Djukic I.; Caliman A.; Paquette A.; Gutierrez-Giron A.; Petraglia A.; Augustaitis A.; Saillard A.; Ruiz-Fernandez A.C.; Sousa A.I.; Lillebo A.I.; Da Rocha Gripp A.; Lamprecht A.; Bohner A.; Francez A.-J.; Malyshev A.; Andric A.; Stanisci A.; Zolles A.; Avila A.; Virkkala A.-M.; Probst A.; Ouin A.; Khuroo A.A.; Verstraeten A.; Stefanski A.; Gaxiola A.; Muys B.; Gozalo B.; Ahrends B.; Yang B.; Erschbamer B.; Rodriguez Ortiz C.E.; Christiansen C.T.; Meredieu C.; Mony C.; Nock C.; Wang C.-P.; Baum C.; Rixen C.; Delire C.; Piscart C.; Andrews C.; Rebmann C.; Branquinho C.; Jan D.; Wundram D.; Vujanovic D.; Adair E.C.; Ordonez-Regil E.; Crawford E.R.; Tropina E.F.; Hornung E.; Groner E.; Lucot E.; Gacia E.; Levesque E.; Benedito E.; Davydov E.A.; Bolzan F.P.; Maestre F.T.; Maunoury-Danger F.; Kitz F.; Hofhansl F.; Hofhansl G.; De Almeida Lobo F.; Souza F.L.; Zehetner F.; Koffi F.K.; Wohlfahrt G.; Certini G.; Pinha G.D.; Gonzlez G.; Canut G.; Pauli H.; Bahamonde H.A.; Feldhaar H.; Jger H.; Serrano H.C.; Verheyden H.; Bruelheide H.; Meesenburg H.; Jungkunst H.; Jactel H.; Kurokawa H.; Yesilonis I.; Melece I.; Van Halder I.; Quiros I.G.; Fekete I.; Ostonen I.; Borovsk J.; Roales J.; Shoqeir J.H.; Jean-Christophe Lata J.; Probst J.-L.; Vijayanathan J.; Dolezal J.; Sanchez-Cabeza J.-A.; Merlet J.; Loehr J.; Von Oppen J.; Loffler J.; Benito Alonso J.L.; Cardoso-Mohedano J.-G.; Penuelas J.; Morina J.C.; Quinde J.D.; Jimnez J.J.; Alatalo J.M.; Seeber J.; Kemppinen J.; Stadler J.; Kriiska K.; Van Den Meersche K.; Fukuzawa K.; Szlavecz K.; Juhos K.; Gerhtov K.; Lajtha K.; Jennings K.; Jennings J.; Ecology P.; Hoshizaki K.; Green K.; Steinbauer K.; Pazianoto L.; Dienstbach L.; Yahdjian L.; Williams L.J.; Brigham L.; Hanna L.; Hanna H.; Rustad L.; Morillas L.; Silva Carneiro L.; Di Martino L.; Villar L.; Fernandes Tavares L.A.; Morley M.; Winkler M.; Lebouvier M.; Tomaselli M.; Schaub M.; Glushkova M.; Torres M.G.A.; De Graaff M.-A.; Pons M.-N.; Bauters M.; Mazn M.; Frenzel M.; Wagner M.; Didion M.; Hamid M.; Lopes M.; Apple M.; Weih M.; Mojses M.; Gualmini M.; Vadeboncoeur M.; Bierbaumer M.; Danger M.; Scherer-Lorenzen M.; Ruek M.; Isabellon M.; Di Musciano M.; Carbognani M.; Zhiyanski M.; Puca M.; Barna M.; Ataka M.; Luoto M.; H. Alsafaran M.; Barsoum N.; Tokuchi N.; Korboulewsky N.; Lecomte N.; Filippova N.; Hlzel N.; Ferlian O.; Romero O.; Pinto-Jr O.; Peri P.; Dan Turtureanu P.; Haase P.; Macreadie P.; Reich P.B.; Petk P.; Choler P.; Marmonier P.; Ponette Q.; Dettogni Guariento R.; Canessa R.; Kiese R.; Hewitt R.; Weigel R.; Kanka R.; Cazzolla Gatti R.; Martins R.L.; Ogaya R.; Georges R.; Gaviln R.G.; Wittlinger S.; Puijalon S.; Suzuki S.; Martin S.; Anja S.; Gogo S.; Schueler S.; Drollinger S.; Mereu S.; Wipf S.; Trevathan-Tackett S.; Stoll S.; Lfgren S.; Trogisch S.; Seitz S.; Glatzel S.; Venn S.; Dousset S.; Mori T.; Sato T.; Hishi T.; Nakaji T.; Jean-Paul T.; Camboulive T.; Spiegelberger T.; Scholten T.; Mozdzer T.J.; Kleinebecker T.; Runk T.; Ramaswiela T.; Hiura T.; Enoki T.; Ursu T.-M.; Di Cella U.M.; Hamer U.; Klaus V.; Di Cecco V.; Rego V.; Fontana V.; Piscov V.; Bretagnolle V.; Maire V.; Farjalla V.; Pascal V.; Zhou W.; Luo W.; Parker W.; Parker P.; Kominam Y.; Kotrocz Z.; Utsumi Y

Elective Cancer Surgery in COVID-19-Free Surgical Pathways During the SARS-CoV-2 Pandemic: An International, Multicenter, Comparative Cohort Study.

PURPOSE: As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19-free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS: This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19-free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS: Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19-free surgical pathways. Patients who underwent surgery within COVID-19-free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19-free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score-matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19-free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION: Within available resources, dedicated COVID-19-free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

Elective cancer surgery in COVID-19-free surgical pathways during the SARS-CoV-2 pandemic: An international, multicenter, comparative cohort study

PURPOSE As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19–free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19–free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19–free surgical pathways. Patients who underwent surgery within COVID-19–free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19–free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score–matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19–free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION Within available resources, dedicated COVID-19–free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Building connectomes using diffusion MRI: why, how and but

Why has diffusion MRI become a principal modality for mapping connectomes in vivo? How do different image acquisition parameters, fiber tracking algorithms and other methodological choices affect connectome estimation? What are the main factors that dictate the success and failure of connectome reconstruction? These are some of the key questions that we aim to address in this review. We provide an overview of the key methods that can be used to estimate the nodes and edges of macroscale connectomes, and we discuss open problems and inherent limitations. We argue that diffusion MRI-based connectome mapping methods are still in their infancy and caution against blind application of deep white matter tractography due to the challenges inherent to connectome reconstruction. We review a number of studies that provide evidence of useful microstructural and network properties that can be extracted in various independent and biologically-relevant contexts. Finally, we highlight some of the key deficiencies of current macroscale connectome mapping methodologies and motivate future developments

Outcomes from elective colorectal cancer surgery during the SARS-CoV-2 pandemic

This study aimed to describe the change in surgical practice and the impact of SARS-CoV-2 on mortality after surgical resection of colorectal cancer during the initial phases of the SARS-CoV-2 pandemic

Persistent Gastric Colonization with Burkholderia pseudomallei and Dissemination from the Gastrointestinal Tract following Mucosal Inoculation of Mice

Melioidosis is a disease of humans caused by opportunistic infection with the soil and water bacterium Burkholderia pseudomallei. Melioidosis can manifest as an acute, overwhelming infection or as a chronic, recurrent infection. At present, it is not clear where B. pseudomallei resides in the mammalian host during the chronic, recurrent phase of infection. To address this question, we developed a mouse low-dose mucosal challenge model of chronic B. pseudomallei infection and investigated sites of bacterial persistence over 60 days. Sensitive culture techniques and selective media were used to quantitate bacterial burden in major organs, including the gastrointestinal (GI) tract. We found that the GI tract was the primary site of bacterial persistence during the chronic infection phase, and was the only site from which the organism could be consistently cultured during a 60-day infection period. The organism could be repeatedly recovered from all levels of the GI tract, and chronic infection was accompanied by sustained low-level fecal shedding. The stomach was identified as the primary site of GI colonization as determined by fluorescent in situ hybridization. Organisms in the stomach were associated with the gastric mucosal surface, and the propensity to colonize the gastric mucosa was observed with 4 different B. pseudomallei isolates. In contrast, B. pseudomallei organisms were present at low numbers within luminal contents in the small and large intestine and cecum relative to the stomach. Notably, inflammatory lesions were not detected in any GI tissue examined in chronically-infected mice. Only low-dose oral or intranasal inoculation led to GI colonization and development of chronic infection of the spleen and liver. Thus, we concluded that in a mouse model of melioidosis B. pseudomallei preferentially colonizes the stomach following oral inoculation, and that the chronically colonized GI tract likely serves as a reservoir for dissemination of infection to extra-intestinal sites