Per-Pixel Forest Attribute Mapping and Error Estimation: The Google Earth Engine and R dataDriven Tool.

Remote sensing products are typically assessed using a single accuracy estimate for the entire map, despite significant variations in accuracy across different map areas or classes. Estimating per-pixel uncertainty is a major challenge for enhancing the usability and potential of remote sensing products. This paper introduces the dataDriven open access tool, a novel statistical design-based approach that specifically addresses this issue by estimating per-pixel uncertainty through a bootstrap resampling procedure. Leveraging Sentinel-2 remote sensing data as auxiliary information, the capabilities of the Google Earth Engine cloud computing platform, and the R programming language, dataDriven can be applied in any world region and variables of interest. In this study, the dataDriven tool was tested in the Rincine forest estate study area-eastern Tuscany, Italy-focusing on volume density as the variable of interest. The average volume density was 0.042, corresponding to 420 m3 per hectare. The estimated pixel errors ranged between 93 m3 and 979 m3 per hectare and were 285 m3 per hectare on average. The ability to produce error estimates for each pixel in the map is a novel aspect in the context of the current advances in remote sensing and forest monitoring and assessment. It constitutes a significant support in forest management applications and also a powerful communication tool since it informs users about areas where map estimates are unreliable, at the same time highlighting the areas where the information provided via the map is more trustworthy. In light of this, the dataDriven tool aims to support researchers and practitioners in the spatially exhaustive use of remote sensing-derived products and map validation.

Exciplex Formation in Lipid-bound Escherichia coli Flavohemoglobin.

Flavohemoglobins have the particular capability of binding unsaturated and cyclopropanated fatty acids as free acids or phospholipids. Fatty acid binding to the ferric heme results in a weak but direct bonding interaction. Ferrous and ferric protein, in presence or absence of a bound lipid molecule, have been characterized by transient absorption spectroscopy. Measurements have been also carried out both on the ferrous deoxygenated and on the CO bound protein to investigate possible long-range interaction between the lipid acyl chain moiety and the ferrous heme. After excitation of the deoxygenated derivatives the relaxation process reveals a slow dynamics (350 ps) in lipid-bound protein but is not observed in the lipid-free protein. The latter feature and the presence of an extra contribution in the absorption spectrum, indicates that the interaction of iron heme with the acyl chain moiety occurs only in the excited electronic state and not in the ground electronic state. Data analysis highlights the formation of a charge-transfer complex in which the iron ion of the lipid-bound protein in the expanded electronic excited state, possibly represented by a high spin Fe III intermediate, is able to bind to the sixth coordination ligand placed at a distance of at 3.5 Šfrom the iron. A very small nanosecond geminate rebinding is observed for CO adduct in lipid-free but not in the lipid-bound protein. The presence of the lipid thus appears to inhibit the mobility of CO in the heme pocket.

Addressing Charge-Transfer and Locally-Excited States in a Twisted Biphenyl Push-Pull Chromophore.

We present the synthesis and spectroscopic characterization of a twisted push-pull biphenyl molecule undergoing photoinduced electron transfer. Steady-state and transient absorption spectra suggest, in this rigid molecular structure, a subtle interplay between locally-excited and charge-transfer states, whose equilibrium and dynamics is only driven by solvation. A theoretical model is presented for the solvation dynamics and, with the support of quantum chemical calculations, we demonstrate the existence of two sets of states, having either local or charge-transfer character, that only "communicate" thanks to solvation, which is the sole driving force for the charge-separation process.

Photophysical properties and excited state dynamics of 4,7-dithien-2-yl-2,1,3-benzothiadiazole.

The relationships between the photophysics and structural properties of 4,7-dithien-2-yl-2,1,3-benzothiadiazole as a function of solvent polarity are investigated both experimentally and by computational methods. Stationary fluorescence measurements are consistent with a model envisaging the presence of three types of conformers in equilibrium in the ground state. They are characterized by different relative orientations of the thiophene rings. Due to a low rotational barrier, the sample in solution is characterized by a distribution of relative internal orientations. By applying the Kawski method, we evaluate the average dipole moment of ground and excited states of the three types of conformers. The ground state dipole moments are small and similar for the three types of conformers. On the contrary, dipole moments differ substantially in the excited state. X-ray diffraction of a single crystal confirms the presence of an orientational disorder of thiophene rings. Transient absorption UV-visible spectroscopy experiments allows the identification of the main mechanisms responsible for the large Stokes shift observed in this push-pull molecule. Time dependent spectra provide a picture of the relaxation processes occurring after excitation: the primary step is an internal charge transfer assisted by thiophene ring planarization which occurs on a time scale ranging from 0.88 to 1.3 picoseconds depending on solvent polarity. Moreover, time-resolved fluorescence measurements are consistent with a mechanism involving planarization accompanied by a stabilization of the charge transfer state as observed in polar solvents. In the latter, longer fluorescence lifetimes are observed along with a quantum yield decrease due to the activation of specific non-radiative relaxation channels. The photophysical behavior of 4,7-dithien-2-yl-2,1,3-benzothiadiazole in a solid matrix of polymethyl methacrylate is similar to that observed in solution, but the overall non-radiative process rate is slow with respect to that in the liquid phase. As a consequence, the radiative processes are enhanced giving rise to a fluorescence quantum yield of 90%. Such behavior is consistent with the proposed relaxation model.

A steady-state and time-resolved photophysical study of CdTe quantum dots in water.

The exciton generation and recombination dynamics in semiconductor nanocrystals are very sensitive to small variations in dimensions, shape and surface capping. In the present work CdTe quantum dots are synthesized in water using 3-mercaptopropionic acid and 1-thioglycerol as stabilizers. Nanocrystals with an average dimension of 4.0 ± 1.0 and 3.7 ± 0.9 nm were obtained, when 3-mercaptopropionic acid or 1-thioglycerol, respectively, was used as a capping agent. The steady-state characterization shows that the two types of colloids have different luminescence behavior. In order to investigate the electronic structure and the dynamics of the exciton state, a combined study in the time domain has been carried out by using fluorescence time-correlated single photon counting and femtosecond transient absorption techniques. The electron-hole radiative recombination follows the non-exponential decay law for both colloids, which results in different average decay time values (of the order of tens of nanoseconds) for the two samples. The data demonstrate that the process is slower for 1-thioglycerol-stabilized colloids. The ultrafast transient absorption measurements are performed at two different excitation wavelengths (at the band gap and at higher energies). The spectra are dominated in both types of samples by the negative band-gap bleaching signals although transient positive absorption bands due to the electrons in the conduction band are observable. The analysis of the signals is affected by the different interactions with the defect states, due to ligand capping capacities. In particular, the data indicate that in 1-thioglycerol-stabilized colloids the non-radiative recombination processes are kinetically more competitive than the radiative recombination. Therefore the comparison of the data obtained from the two samples is interpreted in terms of the effects of the capping agents on the electronic relaxation of the colloids.

Excited-state absorption and ultrafast relaxation dynamics of protoporphyrin IX and hemin.

The transient evolution of protoporphyrin IX (PPIX) and hemin following the Soret band excitation was measured in the 410-600 nm spectral region with sub-picosecond time resolution. In PPIX the relaxation pathway was characterized in the femto- and picosecond time scale by two processes with time constants of 350 fs and ~6 ps, describing the evolution of the system through internal Q(y) → Q(x) conversion and vibrational relaxation and cooling in the Q(x) state. The lifetime of the Q(x) state was found to be 10.4 ns by time resolved fluorescence measurements. In hemin, the ground state is completely recovered in tens of picoseconds through pathways involving CT and (d,d) states. The experimentally observed vibrational dynamics is mainly due to "hot" ground state transitions.

Maturation of Aluminium Adsorbed Antigens Contributes to the Creation of Homogeneous Vaccine Formulations.

Although aluminium-based vaccines have been used for almost over a century, their mechanism of action remains unclear. It is established that antigen adsorption to the adjuvant facilitates delivery of the antigen to immune cells at the injection site. To further increase our understanding of aluminium-based vaccines, it is important to gain additional insights on the interactions between the aluminium and antigens, including antigen distribution over the adjuvant particles. Immuno-assays can further help in this regard. In this paper, we evaluated how established formulation strategies (i.e., sequential, competitive, and separate antigen addition) applied to four different antigens and aluminium oxyhydroxide, lead to formulation changes over time. Results showed that all formulation samples were stable, and that no significant changes were observed in terms of physical-chemical properties. Antigen distribution across the bulk aluminium population, however, did show a maturation effect, with some initial dependence on the formulation approach and the antigen adsorption strength. Sequential and competitive approaches displayed similar results in terms of the homogeneity of antigen distribution across aluminium particles, while separately adsorbed antigens were initially more highly poly-dispersed. Nevertheless, the formulation sample prepared via separate adsorption also reached homogeneity according to each antigen adsorption strength. This study indicated that antigen distribution across aluminium particles is a dynamic feature that evolves over time, which is initially influenced by the formulation approach and the specific adsorption strength, but ultimately leads to homogeneous formulations.

Chirality driven self-assembly in a fluorescent organogel.

In this work, we present the characterization of an enantiomeric pair of fluorescent dye organogelators and the properties of their stable gel at low concentration in organic solvents. The gels of both enantiomers and of their mixtures were analyzed by differential scanning calorimetry, circular dichroism (CD), atomic force microscopy, UV-vis absorption, and fluorescence. The acquired data were supported by molecular modeling of the helical assembly of the gelators and by the simulation of their CD spectra by means of DeVoe method, and suggested the occurrence of an enantiomeric discrimination process during the formation of the gels.

Pyrene-excimers-based antenna systems.

A series of dendrimeric compounds bearing pyrene units were synthesized to afford light-harvesting antennae based on the formation of intramolecular excimers. The synthetic plan profited from the efficiency of the Huisgen reaction, the 1,3-dipolar cycloaddition of azides and terminal alkynes, which allowed ready assembly of the different building blocks. The three molecular antennae obtained, of increasing generation, revealed efficient energy transfer both in solution and in the solid state.

Förster resonance energy transfer (FRET) with a donor-acceptor system adsorbed on silver or gold nanoisland films.

We observed Förster resonance energy transfer (FRET) with a covalently linked donor-acceptor pair D-A consisting of two naphthalene groups acting as the donors and a benzofurazan group acting as the acceptor and adsorbed onto Ag or Au nanoisland films. The use of metal nanoisland films, which caused a strong enhancement of the Raman signal, permitted description of the adsorption mechanism onto the two metals. The intense fluorescence response of molecular adsorbates and the different behavior of the antenna on Ag and Au nanoislands are partly explained in terms of the radiating plasmon model.

Excited-state absorption and ultrafast relaxation dynamics of porphyrin, diprotonated porphyrin, and tetraoxaporphyrin dication.

The relaxation dynamics of unsubstituted porphyrin (H2P), diprotonated porphyrin (H4P2+), and tetraoxaporphyrin dication (TOxP2+) has been investigated in the femtosecond-nanosecond time domain upon photoexcitation in the Soret band with pulses of femtosecond duration. By probing with spectrally broad femtosecond pulses, we have observed transient absorption spectra at delay times up to 1.5 ns. The kinetic profiles corresponding with the band maxima due to excited-state absorption have been determined for the three species. Four components of the relaxation process are distinguished for H2P: the unresolvably short B --> Qy internal conversion is followed by the Qy --> Qx process, vibrational relaxation, and thermalization in the Qx state with time constant approximately 150 fs, 1.8 ps, and 24.9 ps, respectively. Going from H2P to TOxP2+, two processes are resolved, i.e., B --> Q internal conversion and thermal equilibration in the Q state. The B --> Q time constant has been determined to be 25 ps. The large difference with respect to the B --> Qy time constant of H2P has been related to the increased energy gap between the coupled states, 9370 cm-1 in TOxP2+ vs 6100 cm-1 in H2P. The relaxation dynamics of H4P2+ has a first ultrafast component of approximately 300 fs assigned as internal conversion between the B (or Soret) state and charge-transfer (CT) states of the H4P2+ complex with two trifluoroacetate counterions. This process is followed by internal CT --> Q conversion (time constant 9 ps) and thermalization in the Q state (time constant 22 ps).

Excited states of porphyrin macrocycles.

S1 --> S(n) spectra of porphyrin, diprotonated porphyrin, and tetraoxaporphyrin dication have been measured in the energy range 2-3 eV above S1 at room temperature in solution by means of transient absorption spectroscopy exciting with femtosecond pulses. Highly excited pi pi* states not active in the conventional S0 --> S(n) spectrum have been observed. The experimental data are discussed on the basis of the time dependent density functional theory taking advantage of large scale calculations of configuration interaction between singly excited configurations (DF/SCI). The DF/SCI calculation on porphyrin has allowed to assign g states active in the S1 --> S(n) spectrum. Applying the same calculation method to tetraoxaporphyrin dication the S0 --> S(n) spectrum is reproduced relatively to the Q and B (Soret) bands as well as to the weaker E(u) bands at higher energy. According to our calculation the S1 --> S(n) transient spectrum is related to states of g symmetry mainly arising from excitations between doubly degenerate pi and pi* orbitals such as 2e(g) --> 4e(g). In the case of diprotonated porphyrin it is shown that the complex of the macrocycle with two trifluoroacetate anions plays a significant role for absorption. Charge transfer excitations from the anions to the macrocycle contribute to absorption above the Soret band, justifying the intensity enhancement of the S0 --> S(n) spectrum with respect to the other two macrocyclic systems.

A dizinc complex for selective fluorescence sensing of uridine and uridine-containing dinucleotides.

A dizinc complex with a polyamine macrocycle is able to selectively bind and sense uridine (U) as well as the uridine-containing ribodinucleotides U(3'-5')pU and U(3'-5')pA, thanks to an exciplex emission arising from a pi-stacked complex involving the dipyridine unit and Zn(II)-bound uridine moieties.

Role of local structure and dynamics of small ligand migration in proteins: a study of a mutated truncated hemoprotein from Thermobifida fusca by time resolved MIR spectroscopy.

Carbon monoxide recombination dynamics in a mutant of the truncated hemoglobin from Thermobida fusca (3F-Tf-trHb) has been analyzed by means of ultrafast Visible-pump/MidIR-probe spectroscopy and compared with that of the wild-type protein. In 3F-Tf-trHb, three topologically relevant amino acids, responsible for the ligand stabilization through the formation of a H-bond network (TyrB10 TyrCD1 and TrpG8), have been replaced by Phe residues. X-ray diffraction data show that Phe residues in positions B10 and G8 maintain the same rotameric arrangements as Tyr and Trp in the wild-type protein, while Phe in position CD1 displays significant rotameric heterogeneity. Photodissociation of the ligand has been induced by exciting the sample with 550 nm pump pulses and the CO rebinding has been monitored in two mid-IR regions respectively corresponding to the ν(CO) stretching vibration of the iron-bound CO (1880-1980 cm(-1)) and of the dissociated free CO (2050-2200 cm(-1)). In both the mutant and wild-type protein, a significant amount of geminate CO rebinding is observed on a subnanosecond time scale. Despite the absence of the distal pocket hydrogen-bonding network, the kinetics of geminate rebinding in 3F-Tf-trHb is very similar to the wild-type, showing how the reactivity of dissociated CO toward the heme is primarily regulated by the effective volume and flexibility of the distal pocket and by caging effects exerted on the free CO on the analyzed time scale.

Ligand uptake modulation by internal water molecules and hydrophobic cavities in hemoglobins.

Internal water molecules play an active role in ligand uptake regulation, since displacement of retained water molecules from protein surfaces or cavities by incoming ligands can promote favorable or disfavorable effects over the global binding process. Detection of these water molecules by X-ray crystallography is difficult given their positional disorder and low occupancy. In this work, we employ a combination of molecular dynamics simulations and ligand rebinding over a broad time range to shed light into the role of water molecules in ligand migration and binding. Computational studies on the unliganded structure of the thermostable truncated hemoglobin from Thermobifida fusca (Tf-trHbO) show that a water molecule is in the vicinity of the iron heme, stabilized by WG8 with the assistance of YCD1, exerting a steric hindrance for binding of an exogenous ligand. Mutation of WG8 to F results in a significantly lower stabilization of this water molecule and in subtle dynamical structural changes that favor ligand binding, as observed experimentally. Water is absent from the fully hydrophobic distal cavity of the triple mutant YB10F-YCD1F-WG8F (3F), due to the lack of residues capable of stabilizing it nearby the heme. In agreement with these effects on the barriers for ligand rebinding, over 97% of the photodissociated ligands are rebound within a few nanoseconds in the 3F mutant case. Our results demonstrate the specific involvement of water molecules in shaping the energetic barriers for ligand migration and binding.

A comparative study on bulk and nanoconfined water by time-resolved optical Kerr effect spectroscopy.

The low frequency (nu < 500 cm(-1)) vibrational spectra of hydrated porous silica are specifically sensitive to the hydrogen bond interactions and provide a wealth of information on the structural and dynamical properties of the water contained in the pores of the matrix. We investigate systematically this spectral region for a series of Vycor porous silica samples (pore size approximately equal 4 nm) at different levels of hydration, from the dry matrix to completely filled pores. The spectra are obtained as the Fourier transforms of time-resolved heterodyne detected optical Kerr effect (HD-OKE) measurements. The comparison of these spectra with that of bulk water enables us to separately extract and analyze the spectral contributions of the first and second hydration layers, as well as that of bulk-like inner water. We conclude that the extra water entering the pores above approximately equal 10% water/silica weight ratio behaves very similarly to bulk water. At lower levels of hydration, corresponding to two complete superficial water layers or less, the H-bond bending and stretching bands, characteristic of the tetrahedral coordination of water in the bulk phase, progressively disappear: clearly in these conditions the H-bond connectivity is very different from that of liquid water. A similar behavior is observed for the structural relaxation times measured from the decay of the time-dependent HD-OKE signal. The value for the inner water is very similar to that of the bulk liquid; that of the first two water layers is definitely longer by a factor approximately equal 4. These findings should be carefully taken into account when employing pore confinement to extend towards lower temperatures the accessible temperature range of supercooled water.

Carbon monoxide recombination dynamics in truncated hemoglobins studied with visible-pump midIR-probe spectroscopy.

Carbon monoxide recombination dynamics upon photodissociation with visible light has been characterized by means of ultrafast visible-pump/MidIR probe spectroscopy for the truncated hemoglobins from Thermobifida fusca and Bacillus subtilis. Photodissociation has been induced by exciting the sample at two different wavelengths: 400 nm, corresponding to the heme absorption in the B-band, and 550 nm, in the Q-bands. The bleached iron-CO coordination band located at 1850-1950 cm(-1) and the free CO absorption band in the region 2050-2200 cm(-1) have been observed by probe pulses tuned in the appropriate infrared region. The kinetic traces measured at 1850-1950 cm(-1) reveal multiexponential subnanosecond dynamics that have been interpreted as arising from fast geminate recombination of the photolyzed CO. A compared analysis of the crystal structure of the two proteins reveals a similar structure of their distal heme pocket, which contains conserved polar and aromatic amino acid residues closely interacting with the iron ligand. Although fast geminate recombination is observed in both proteins, several kinetic differences can be evidenced, which can be interpreted in terms of a different structural flexibility of the corresponding heme distal pockets. The analysis of the free CO band-shape and of its dynamic evolution brings out novel features about the nature of the docking site inside the protein cavity.

Following ligand migration pathways from picoseconds to milliseconds in type II truncated hemoglobin from Thermobifida fusca.

CO recombination kinetics has been investigated in the type II truncated hemoglobin from Thermobifida fusca (Tf-trHb) over more than 10 time decades (from 1 ps to ∼100 ms) by combining femtosecond transient absorption, nanosecond laser flash photolysis and optoacoustic spectroscopy. Photolysis is followed by a rapid geminate recombination with a time constant of ∼2 ns representing almost 60% of the overall reaction. An additional, small amplitude geminate recombination was identified at ∼100 ns. Finally, CO pressure dependent measurements brought out the presence of two transient species in the second order rebinding phase, with time constants ranging from ∼3 to ∼100 ms. The available experimental evidence suggests that the two transients are due to the presence of two conformations which do not interconvert within the time frame of the experiment. Computational studies revealed that the plasticity of protein structure is able to define a branched pathway connecting the ligand binding site and the solvent. This allowed to build a kinetic model capable of describing the complete time course of the CO rebinding kinetics to Tf-trHb.

Relaxation properties of porphyrin, diprotonated porphyrin, and isoelectronic tetraoxaporphyrin dication in the S2 state.

The fluorescence spectra of unsubstituted porphyrin (H2P), diprotonated porphyrin (H4P2+), and isoelectronic tetraoxaporphyrin dication (TOxP2+) have been measured in solution at room temperature. The S2-->S0 fluorescence has been observed, much more intense for TOxP2+ than for H4P2+ and H2P. In the TOxP2+ case, the S2-->S0 fluorescence spectrum is remarkably sharp and shows an excellent mirror symmetry with respect to S0-->S2 absorption. On the contrary, the spectra of H4P2+ and H2P are shifted and more extended with respect to the absorption counterparts. The differences have been attributed primarily to the change of the equilibrium geometry upon excitation, larger in H2P and H4P2+ than in TOxP2+ and in the case of H4P2+ to the nonplanar conformation of the macrocycle. Also the S1-->S0 spectra of H2P, H4P2+, and TOxP2+ have been measured and more qualitatively discussed. The S1 and S2 fluorescence decays have been observed for H4P2+ and TOxP2+ exciting with ultrashort pulses. The S2 lifetime of TOxP2+ is of the order of the temporal resolution of our experimental apparatus, whereas that of H4P2+ is shorter. The S2-->S0 quantum yield of TOxP2+ has been estimated to be 0.035, approximately 3 orders of magnitude higher than that of H4P2+. It is proposed on the basis of ab initio model calculations that excited states of the H4P2+(CF3COO-)2 complex with charge-transfer character are responsible of the increased extension of the S2-->S0 spectrum with respect to that of H2P.