Integrating remote sensing and a Markov-FLUS model to simulate future land use changes in Hokkaido, Japan

As the second largest island in Japan, Hokkaido provides precious land resources for the Japanese people. Meanwhile, as the food base of Japan, the gradual decrease of the agricultural population and more intensive agricultural practices on Hokkaido have led its arable land use to change year by year, which has also caused changes to the whole land use pattern of the entire island of Hokkaido. To realize the sustainable use of land resources in Hokkaido, past and future changes in land use patterns must be investigated, and target-based land use planning suggestions should be given on this basis. This study uses remote sensing and GIS technology to analyze the temporal and spatial changes of land use in Hokkaido during the past two decades. The types of land use include cultivated land, forest, waterbody, construction, grassland, and others, by using the satellite images of the Landsat images in 2000, 2010, and 2019 to achieve this goal to make classification. In addition, this study used the coupled Markov-FLUS model to simulate and analyze the land use changes in three different scenarios in Hokkaido in the next 20 years. Scenario-based situational analysis shows that the cultivated land in Hokkaido will drop by about 25% in 2040 under the natural development scenario (ND), while the cultivated land area in Hokkaido will remain basically unchanged in cultivated land protection scenario (CP). In forest protection scenario (FP), the area of forest in Hokkaido will increase by 1580.8 km2. It is believed that the findings reveal that the forest land in Hokkaido has been well protected in the past and will be protected well in the next 20 years. However, in land use planning for future, Hokkaido government and enterprises should pay more attention to the protection of cultivated land.</jats:p

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Stacking Interactions in Denaturation of DNA Fragments

A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the \emph{adenine-thymine} rich portions of the fragment. The harmonic stacking coupling shifts, along the $T$-axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.Comment: European Physical Journal E (2011) in pres

Assessing vulnerability for inhabitants of Dhaka City considering flood-hazard exposure

Globalna opasnost od poplave postupno se povećava. Iako ih je nemoguće izbjeći, gubici i šteta od opasnosti (npr. poplave, cikloni i potresi) mogu se učinkovito smanjiti smanjenjem ranjivosti kućanstava odgovarajućim mjerama. Cilj ove studije je kvantitativno mjerenje ranjivosti kućanstava obzirom na opasnosti od poplave kao alata za njihovo ublažavanje. Također je predložen jedinstveni pristup za kvantificiranje ugroženosti kućanstava obzirom na opasnosti od poplave, a kao primjer predstavljena je primjena u gradu Dhaki sklonom poplavama. Podaci su prikupljeni i sa siromašnih i bogatih područja kako bi bilo pokriveno cijelo urbano područje te kako bi se usporedila razina ugroženosti od poplava. Ukupno 300 kućanstava anketirano je strukturiranim upitnikom na temelju pet čimbenika (ekonomskih, socijalnih, okolišnih, strukturnih i institucionalnih) ugroženosti od poplava. Analitički hijerarhijski postupak (AHP) primijenjen je za mjerenje pojedinačnih rezultata ranjivosti kućanstva korištenjem relativne težine varijabli i pokazatelja uz pravilnu standardizaciju. Analitički rezultati pokazali su da je 63,06% siromašnih kućanstava i 20,02% bogatih kućanstava vrlo osjetljivo na poplave. Uz to, ovaj je rad utvrdio i procijenio čimbenike odgovorne za ranjivost kućanstava u Dhaki. Što se tiče strukturne ranjivosti, rezultati su pokazali da je 82% kućanstava u siromašnim krajevima bilo visoko ranjivo, a 95,3% kućanstava koja nisu iz siromašnih četvrti bilo je umjereno ranjivo. Društveno, 67,3% siromašnih i 78,7% kućanstava koja nisu iz siromašnih naselja bila su umjereno i slabo ranjiva. Većina kućanstava u siromašnoj i nesiromašnoj četvrti (84%, odnosno 59,3%) pokazala je visoku i umjerenu ekonomsku ranjivost. Štoviše, za 69,3% siromašnih i 65,3% nesiromašnih kućanstava institucionalna ranjivost je bila visoka. Od stanovnika siromašnih naselja, 63,3% je bilo izloženo ekološkom riziku, a 78% staništa koja nisu u siromašnim područjima bilo je u kategoriji niske ranjivosti. Uz odgovarajuću prilagodbu ovdje predložen učinkoviti alat za mjerenje ranjivosti koji je ovdje prilagođen specifičnoj lokaciji, primjenjiv je i za mjerenje ranjivosti drugih gradova u svijetu. Na temelju ove studije moglo bi se provesti buduće istraživanje s više čimbenika, varijabli i pokazatelja ljudske ranjivosti na prirodne ili umjetne opasnosti / katastrofe. Budući rad mogao bi pružiti bolju sliku stanja ranjivosti od pojedinačne / višestruke opasnosti / katastrofe.Global flood hazard is gradually increasing. Though it is impossible to avoid them, losses and damage of hazards (e.g., floods, cyclones, and earthquakes) could be efficiently reduced by reducing household vulnerability with appropriate measures. This study aims to quantitatively measure the household vulnerability of flood hazards as a mitigation tool. It also proposed a unique approach to quantify flood-hazard household vulnerability, and shows its application in the flood prone city of Dhaka as an example case. Data were collected from both slum and non-slum areas to cover the entire urban habitat, and to compare their level of flood vulnerability. A total of 300 households were surveyed by structured questionnaire on the basis of five factors (economic, social, environmental, structural, and institutional) of flood vulnerability. The analytical hierarchy process (AHP) was applied to measure individual household vulnerability scores by using the relative weightage of variables and indicators with proper standardisation. Analytical results demonstrated that 63.06% slum and 20.02% non-slum households were highly vulnerable to floods. In addition, this paper determined and assessed responsible factors for household flood vulnerability in Dhaka. For structural vulnerability, results exhibited that 82% of slum households were highly vulnerable, and 95.3% of non-slum households were moderately vulnerable. Socially, 67.3% of slum and 78.7% of non-slum households were moderately and low-vulnerable. The majority of slum and non-slum households (84% and 59.3%, respectively) showed high and moderate vulnerability with respect to economic vulnerability. Moreover, 69.3% of slum and 65.3% of nonslum household institutional vulnerability levels were high. Of slum inhabitants, 63.3% were environmentally at high risk, and 78% of non-slum habitats were in the low-vulnerability category. However, as an effective tool to measure location-specific vulnerability, it is applicable for the measuring vulnerability of other cities in the world with proper customisation. On the basis of this study, future research could be conducted with more factors, variables, and indicators of human vulnerability to natural or artificial hazards/disasters. Future work may provide a better reflection of the vulnerability status of single/multiple hazard(s)/disaster(s)

Heterogeneity assessment of functional T cell avidity.

The potency of cellular immune responses strongly depends on T cell avidity to antigen. Yet, functional avidity measurements are rarely performed in patients, mainly due to the technical challenges of characterizing heterogeneous T cells. The mean functional T cell avidity can be determined by the IFN-γ Elispot assay, with titrated amounts of peptide. Using this assay, we developed a method revealing the heterogeneity of functional avidity, represented by the steepness/hillslope of the peptide titration curve, documented by proof of principle experiments and mathematical modeling. Our data show that not only natural polyclonal CD8 T cell populations from cancer patients, but also monoclonal T cells differ strongly in their heterogeneity of functional avidity. Interestingly, clones and polyclonal cells displayed comparable ranges of heterogeneity. We conclude that besides the mean functional avidity, it is feasible and useful to determine its heterogeneity (hillslope) for characterizing T cell responses in basic research and patient investigation

A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen

Experimental work has shown that T cells of the immune system rapidly and specifically respond to antigenic molecules presented on the surface of antigen-presenting-cells and are able to discriminate between potential stimuli based on the kinetic parameters of the T cell receptor-antigen bond. These antigenic molecules are presented among thousands of chemically similar endogenous peptides, raising the question of how T cells can reliably make a decision to respond to certain antigens but not others within minutes of encountering an antigen presenting cell. In this theoretical study, we investigate the role of localized rebinding between a T cell receptor and an antigen. We show that by allowing the signaling state of individual receptors to persist during brief unbinding events, T cells are able to discriminate antigens based on both their unbinding and rebinding rates. We demonstrate that T cell receptor coreceptors, but not receptor clustering, are important in promoting localized rebinding, and show that requiring rebinding for productive signaling reduces signals from a high concentration of endogenous pMHC. In developing our main results, we use a relatively simple model based on kinetic proofreading. However, we additionally show that all our results are recapitulated when we use a detailed T cell receptor signaling model. We discuss our results in the context of existing models and recent experimental work and propose new experiments to test our findings

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

A large topographic feature on the surface of the trans-Neptunian object (307261) 2002 MS4_4 measured from stellar occultations

This work aims at constraining the size, shape, and geometric albedo of the dwarf planet candidate 2002 MS4 through the analysis of nine stellar occultation events. Using multichord detection, we also studied the object's topography by analyzing the obtained limb and the residuals between observed chords and the best-fitted ellipse. We predicted and organized the observational campaigns of nine stellar occultations by 2002 MS4 between 2019 and 2022, resulting in two single-chord events, four double-chord detections, and three events with three to up to sixty-one positive chords. Using 13 selected chords from the 8 August 2020 event, we determined the global elliptical limb of 2002 MS4. The best-fitted ellipse, combined with the object's rotational information from the literature, constrains the object's size, shape, and albedo. Additionally, we developed a new method to characterize topography features on the object's limb. The global limb has a semi-major axis of 412 $\pm$ 10 km, a semi-minor axis of 385 $\pm$ 17 km, and the position angle of the minor axis is 121 $^\circ$ $\pm$ 16$^\circ$. From this instantaneous limb, we obtained 2002 MS4's geometric albedo and the projected area-equivalent diameter. Significant deviations from the fitted ellipse in the northernmost limb are detected from multiple sites highlighting three distinct topographic features: one 11 km depth depression followed by a 25$^{+4}_{-5}$ km height elevation next to a crater-like depression with an extension of 322 $\pm$ 39 km and 45.1 $\pm$ 1.5 km deep. Our results present an object that is $\approx$138 km smaller in diameter than derived from thermal data, possibly indicating the presence of a so-far unknown satellite. However, within the error bars, the geometric albedo in the V-band agrees with the results published in the literature, even with the radiometric-derived albedo

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its ‘Minimal Information for Studies of Extracellular Vesicles’, which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly