Machine learning methods for assessing photosynthetic activity: environmental monitoring applications.

Monitoring of the photosynthetic activity of natural and artificial biocenoses is of crucial importance. Photosynthesis is the basis for the existence of life on Earth, and a decrease in primary photosynthetic production due to anthropogenic influences can have catastrophic consequences. Currently, great efforts are being made to create technologies that allow continuous monitoring of the state of the photosynthetic apparatus of terrestrial plants and microalgae. There are several sources of information suitable for assessing photosynthetic activity, including gas exchange and optical (reflectance and fluorescence) measurements. The advent of inexpensive optical sensors makes it possible to collect data locally (manually or using autonomous sea and land stations) and globally (using aircraft and satellite imaging). In this review, we consider machine learning methods proposed for determining the functional parameters of photosynthesis based on local and remote optical measurements (hyperspectral imaging, solar-induced chlorophyll fluorescence, local chlorophyll fluorescence imaging, and various techniques of fast and delayed chlorophyll fluorescence induction). These include classical and novel (such as Partial Least Squares) regression methods, unsupervised cluster analysis techniques, various classification methods (support vector machine, random forest, etc.) and artificial neural networks (multilayer perceptron, long short-term memory, etc.). Special aspects of time-series analysis are considered. Applicability of particular information sources and mathematical methods for assessment of water quality and prediction of algal blooms, for estimation of primary productivity of biocenoses, stress tolerance of agricultural plants, etc. is discussed.

Implementation of palliative care consult Service in Hungary - integration barriers and facilitators.

BACKGROUND: The Palliative Care Consult Service (PCCS) programme was among the first initiations in Hungary to provide palliative care for patients admitted to hospital. The PCCS team provides palliative care for mainly cancer patients and their family members and manages the patient pathway after being discharged from the hospital. The service started in 2014 with 300-400 patient visits per year. The aim of this study is to give a comprehensive overview of the PCCS programme guided by a conceptual framework designed by SELFIE ("Sustainable intEgrated chronic care modeLs for multi-morbidity: delivery, FInancing, and performancE"), a Horizon2020 funded EU project and to identify the facilitators and barriers to its wider implementation. METHODS: PCCS has been selected by the SELFIE consortium for in-depth evaluation as one of the Hungarian integrated care models for persons with multi-morbidity. The qualitative analysis of the PCCS programme was based on available documents of the care provider and interviews with different stakeholders related to the programme. RESULTS: The integrated, multidisciplinary and patient-centred approach was well-received among the patients, family members and clinical departments, as verified by the increasing number of requests for consultations. As a result of the patient pathway management across providers (e.g. from inpatient care to homecare) a higher level of coordination could be achieved in the continuity of care for seriously-ill patients. The regulatory framework has only partially been established, policies to integrate care across organizations and sectors and adequate financial mechanism to support the enhancement and sustainability of the PCCS are still missing. CONCLUSIONS: The service integration of palliative care could be implemented successfully in an academic hospital in Hungary. However, the continuation and enhancement of the programme will require further evidence on the performance of the integrated model of palliative care and a more systematic approach particularly regarding the evaluation, financing and implementation process.

Simulation of chlorophyll fluorescence rise and decay kinetics, and P700-related absorbance changes by using a rule-based kinetic Monte-Carlo method.

A model of primary photosynthetic reactions in the thylakoid membrane was developed and its validity was tested by simulating three types of experimental kinetic curves: (1) the light-induced chlorophyll a fluorescence rise (OJIP transients) reflecting the stepwise transition of the photosynthetic electron transport chain from the oxidized to the fully reduced state; (2) the dark relaxation of the flash-induced fluorescence yield attributed to the QA- oxidation kinetics in PSII; and (3) the light-induced absorbance changes near 820 or 705 nm assigned to the redox transitions of P700 in PSI. A model was implemented by using a rule-based kinetic Monte-Carlo method and verified by simulating experimental curves under different treatments including photosynthetic inhibitors, heat stress, anaerobic conditions, and very high light intensity.

Study of the effect of reducing conditions on the initial chlorophyll fluorescence rise in the green microalgae Chlamydomonas reinhardtii.

Incubation of Chlamydomonas reinhardtii cells under nutrient deficiency results in the faster initial rise in the light-induced chlorophyll fluorescence kinetic curve. We showed that short-term anaerobic incubation of algal cells altered initial fluorescence in a way similar to nutrient starvation, suggesting an important role of the plastoquinones redox state in the observed effect. Bi-component analysis of highly resolved initial fluorescence rise kinetics in sulfur- or oxygen-depleted C. reinhardtii cells suggested that one of the mechanisms underlying the observed phenomenon involves primary closure (photochemical inactivation via Qa reduction) of ß-type PSII as compared to α-PSII. Moreover, results of modeling of the fluorescence curve brought us to the conclusion that accumulation of closed centers in α-PSII supercomplexes may also cause a faster initial fluorescence rise. The observed correlations between nutrient supply rate and initial fluorescence rise pattern in green algae can serve to characterize culture nutritional status in vivo.

[Study of the effect of methylmercury and copper ions on primary photosynthesis processes in the green algae Chlamydomonas moevusii using the parameters of kinetic curves of the variable of chlorophyll fluorescence].

The effect of methylmercury and copper ions on the kinetics of light induction and dark relaxation of the variable of chlorophyll a fluorescence has been studied on cultures of the microalgae Chlamydomonas moevusii. It was shown that the toxicants added at concentrations that induce no decrease in photochemical activity of PS II (F(v)/F(M)) affect the electron transport on the acceptor side of PS II, the nonphotochemical quenching of excitation in the antenna, and the reoxidation of the quinone pool. At low concentrations, methylmercury produced a more toxic effect. The results obtained indicate that this approach can be used for detecting the changes in plant and algae cells at the early stages of the action of toxicants.

Probing of photosynthetic reactions in four phytoplanktonic algae with a PEA fluorometer.

High-resolution light-induced kinetics of chlorophyll fluorescence (OJIP transients) were recorded and analyzed in cultures of diatoms (Thalassiosira weissflogii, Chaetoceros mulleri) and dinoflagellates (Amphidinium carterae, Prorocentrum minimum). Fluorescence transients showed the rapid exponential initial rise from the point O indicating low connectivity between PS II units and high absorption cross-section of PS II antenna. Dark-adapted dinoflagellates revealed capability to maintain the PS I-mediated re-oxidation of the PQ pool at the exposure to strong actinic light that may lead to the underestimation of F(M) value. In OJIP transients recorded in phytoplanktonic algae the fluorescence yield at the point O exceeded F(O) level because Q(A) has been already partly reduced at 50 micros after the illumination onset. PEA was also employed to study the recovery of photosynthetic reactions in T. weissflogii during incubation of nitrogen starved cells in N-replete medium. N limitation caused the impairment of electron transport between Q(A) and PQs, accumulation of closed PS II centers, and the reduced ability to generate transmembrane DeltapH upon illumination, almost fully restored during the recovery period. The recovered cells showed much higher values of NPQ than control ones suggesting maximization of photoprotection mechanisms in the population with a 'stress history.'

Progenitor cell self-renewal and cyclic neutropenia.

OBJECTIVES: Cyclic neutropenia (CN) is a rare genetic disorder where patients experience regular cycling of numbers of neutrophils and various other haematopoietic lineages. The nadir in neutrophil count is the main source of problems due to risk of life-threatening infections. Patients with CN benefit from granulocyte colony stimulating factor therapy, although cycling persists. Mutations in neutrophil elastase gene (ELA2) have been found in more than half of patients with CN. However, neither connection between phenotypic expression of ELA2 and CN nor the mechanism of cycling is known. MATERIALS AND METHODS: Recently, a multicompartment model of haematopoiesis that couples stem cell replication with marrow output has been proposed. In the following, we couple this model of haematopoiesis with a linear feedback mechanism via G-CSF. RESULTS: We propose that the phenotypic effect of ELA2 mutations leads to reduction in self-renewal of granulocytic progenitors. The body responds by overall relative increase of G-CSF and increasing progenitor cell self-renewal, leading to cell count cycling. CONCLUSION: The model is compatible with available experimental data and makes testable predictions.

Exciting hard spheres.

We investigate the collision cascade that is generated by a single moving particle in a static and homogeneous hard-sphere gas. We argue that the number of moving particles at time t grows as t;{xi} and the number collisions up to time t grows as t;{eta} , with xi=2d(d+2) , eta=2(d+1)(d+2) , and d the spatial dimension. These growth laws are the same as those from a hydrodynamic theory for the shock wave emanating from an explosion. Our predictions are verified by molecular dynamics simulations in d=1 and 2. For a particle incident on a static gas in a half-space, the resulting backsplatter ultimately contains almost all the initial energy.

[Effect of dibromothymoquinone on chlorophyll a fluorescence in Chlamydomonas reinhardtii cells incubated in complete or sulfur-depleted medium].

The influence of dibromothymoquinone on chlorophyll fluorescence was studied in Chlamydomonas reinhardtii cells using PAM and PEA fluorometers. The reagent affected differently control cells incubated in complete medium and S-starved cells. Thus, the fluorescence yield in the control essentially increased in the presence of dibromothymoquinone, which can be due to the inactivation of light-harvesting complex II protein kinase, followed by the suppression of membrane transition from high-fluorescence state 1 to low-fluorescence state 2. On the contrary, S-starved cells with membranes in state 2 showed a lower fluorescence yield in the presence of dibromothymoquinone than without it. The JIP test of OJIP fluorescence transients suggests that dibromothymoquinone inhibits both light-harvesting complex II kinase and photosynthetic electron transport when added to control, while in starved cells, it acts predominantly as an electron acceptor.

In vivo analysis of chlorophyll a fluorescence induction.

Quantitative characteristics of photosynthetic electron transport were evaluated in vivo on the basis of the multi-exponential analysis of OJIP fluorescence transients induced by saturating actinic light. The OJIP fluorescence curve F(t), measured in Chlamydomonas reinhardtii cells, was transformed into the (1 - F(O)/F(t)) x (F(V)/F(M))(-1) transient, which is shown to relate to PS 2 closure. We assumed that kinetics of PS 2 closure during OJIP rise reflects time-separated processes related to the establishment of redox equilibrium at the PS 2 acceptor side (OJ), PQ pool (JI), and beyond Cyt b/f (IP). Three-exponential fitting was applied to (1 - F(O)/F(t)) x (F(V)/F(M))(-1) transient to obtain lifetimes and amplitudes of the OJ, JI, and IP components of PS 2 closure, which were used to calculate overall rates of reduction and re-oxidation of the PS 2 acceptor side, PQ pool, and intermediates beyond Cyt b/f complex. The results, obtained in the presence of inhibitors, oxidative reagents, and under different stress conditions prove the suggested model and characterize the introduced parameters as useful indicators of photosynthetic function.

Logarithmic current fluctuations in nonequilibrium quantum spin chains.

We study zero-temperature quantum spin chains, which are characterized by a nonvanishing current. For the XX model starting from the initial state mid R:cdots, three dots, centered upward arrow upward arrow upward arrow downward arrow downward arrow downward arrowcdots, three dots, centered we derive an exact expression for the variance of the total spin current. We show that asymptotically the variance exhibits an anomalously slow logarithmic growth; we also extract the subleading constant term. We then argue that the logarithmic growth remains valid for the XXZ model in the critical region.

Dynamics of an idealized model of microtubule growth and catastrophe.

We investigate a simple dynamical model of a microtubule that evolves by attachment of guanosine triphosphate (GTP) tubulin to its end, irreversible conversion of GTP to guanosine diphosphate (GDP) tubulin by hydrolysis, and detachment of GDP at the end of a microtubule. As a function of rates of these processes, the microtubule can grow steadily or its length can fluctuate wildly. In the regime where detachment can be neglected, we find exact expressions for the tubule and GTP cap length distributions, as well as power-law length distributions of GTP and GDP islands. In the opposite limit of instantaneous detachment, we find the time between catastrophes, where the microtubule shrinks to zero length, and determine the size distribution of avalanches (sequence of consecutive GDP detachment events). We obtain the phase diagram for general rates and verify our predictions by numerical simulations.

Guiding fields for phase separation: controlling Liesegang patterns.

Liesegang patterns emerge from precipitation processes and may be used to build bulk structures at submicrometer length scales. Thus they have significant potential for technological applications provided adequate methods of control can be devised. Here we describe a simple, physically realizable pattern control based on the notion of driven precipitation, meaning that the phase separation is governed by a guiding field such as, for example, a temperature or pH field. The phase separation is modeled through a nonautonomous Cahn-Hilliard equation whose spinodal is determined by the evolving guiding field. Control over the dynamics of the spinodal gives control over the velocity of the instability front that separates the stable and unstable regions of the system. Since the wavelength of the pattern is largely determined by this velocity, the distance between successive precipitation bands becomes controllable. We demonstrate the above ideas by numerical studies of a one-dimensional system with a diffusive guiding field. We find that the results can be accurately described by employing a linear stability analysis (pulled-front theory) for determining the velocity-local-wavelength relationship. From the perspective of the Liesegang theory, our results indicate that the so-called revert patterns may be naturally generated by diffusive guiding fields.

Aging and immortality in a cell proliferation model.

We investigate a model of cell division in which the length of telomeres within a cell regulates its proliferative potential. At each division, telomeres undergo a systematic length decrease as well as a superimposed fluctuation due to exchange of telomere DNA between the two daughter cells. A cell becomes senescent when one or more of its telomeres become shorter than a critical length. We map this telomere dynamics onto a biased branching-diffusion process with an absorbing boundary condition whenever any telomere reaches the critical length. Using first-passage ideas, we find a phase transition between finite lifetime and immortality (infinite proliferation) of the cell population as a function of the influence of telomere shortening, fluctuations, and cell division.

Examination of chlorophyll fluorescence decay kinetics in sulfur deprived algae Chlamydomonas reinhardtii.

Chlorophyll fluorescence decay kinetics was measured in sulfur deprived cells of green alga Chlamydomonas reinhardtii with a home made picosecond fluorescence laser spectrometer. The measurements were carried out on samples either shortly adapted to the dark ('Fo conditions') or treated to reduce Qa ('Fm conditions'). Bi-exponential fitting of decay kinetics was applied to distinguish two components one of them related to energy trapping (fast component) and the other to charge stabilization and recombination in PS 2 reaction centers (slow component). It was found that the slow component yield increased by 2.0 and 1.2 times when measured under 'Fo' and 'Fm conditions', respectively, in sulfur deprived cells as compared to control ones. An additional rapid rise of the slow component yield was observed when incubation was carried out in a sealed bioreactor and cell culture turned to anaerobic conditions. The obtained results strongly indicate the existence of the redox control of PS 2 activity during multiphase adaptation of C. reinhardtii to sulfur deficiency stress. Probable mechanisms responsible for the observed increased recombinant fluorescence yield in starved cells are discussed.

Dynamics of Microtubule Instabilities.

We investigate an idealized model of microtubule dynamics that involves: (i) attachment of guanosine triphosphate (GTP) at rate λ, (ii) conversion of GTP to guanosine diphosphate (GDP) at rate 1, and (iii) detachment of GDP at rate µ. As a function of these rates, a microtubule can grow steadily or its length can fluctuate wildly. For µ = 0, we find the exact tubule and GTP cap length distributions, and power-law length distributions of GTP and GDP islands. For µ = ∞, we argue that the time between catastrophes, where the microtubule shrinks to zero length, scales as e(λ). We also discuss the nature of the phase boundary between a growing and shrinking microtubule.

Evolutionary dynamics on degree-heterogeneous graphs.

The evolution of two species with different fitness is investigated on degree-heterogeneous graphs. The population evolves either by one individual dying and being replaced by the offspring of a random neighbor (voter model dynamics) or by an individual giving birth to an offspring that takes over a random neighbor node (invasion process dynamics). The fixation probability for one species to take over a population of N individuals depends crucially on the dynamics and on the local environment. Starting with a single fitter mutant at a node of degree k, the fixation probability is proportional to k for voter model dynamics and to 1/k for invasion process dynamics.

[Examination of chlorophyll fluorescence in sulfur-deprived cells of Chlamydomonas reinhardtii].

Modulated fluorometry (PAM) was applied for probing the photosynthesis in cells of C. reinhardtii during sulfur deprivation. A significant (up to a fourfold) increase in chlorophyll fluorescence yield (parameters F(o) and F(m)) normalized to chlorophyll concentration was shown for deprived cells. An analysis of nonphotochemical quenching of chlorophyll fluorescence indicated a considerable modification of the energy deactivation pathways in PS II of sulfur-deprived cells. Thus, starved cells exhibited a lower deltapH-dependent quenching of excited states and a higher thermal dissipation of excess light energy in reaction centers of PS II, as well as the transition of the photosynthetic apparatus primarily to state 2. However, these changes cannot cause the elevation of chlorophyll fluorescence in the cells under sulfur limitation. The phenomenon observed may be due to a partial dissociation of light-harvesting complexes from reaction centers of PS II and/or dysfunction of the dissipative cycle in PS II with cytochrome b559 as an intermediate.

Flows on graphs with random capacities.

We investigate flows on graphs whose links have random capacities. For binary trees we derive the probability distribution for the maximal flow from the root to a leaf, and show that for infinite trees it vanishes beyond a certain threshold that depends on the distribution of capacities. We then examine the maximal total flux from the root to the leaves. Our methods generalize to simple graphs with loops, e.g., to hierarchical lattices and to complete graphs.

"Burnt-bridge" mechanism of molecular motor motion.

Motivated by a biased diffusion of molecular motors with the bias dependent on the state of the substrate, we investigate a random walk on a one-dimensional lattice that contains weak links (called "bridges") which are affected by the walker. Namely, a bridge is destroyed with probability when p the walker crosses it; the walker is not allowed to cross it again and this leads to a directed motion. The velocity of the walker is determined analytically for equidistant bridges. The special case of p = 1 is more tractable--both the velocity and the diffusion constant are calculated for uncorrelated locations of bridges, including periodic and random distributions.