Large‐depth‐of‐field full‐field optical angiography

A large‐depth‐of‐field full‐field optical angiography (LD‐FFOA) method is developed to expand the depth‐of‐field (DOF) using a contrast pyramid fusion algorithm (CPFA). The absorption intensity fluctuation modulation effect is utilized to obtain full‐field optical angiography (FFOA) images at different focus positions. The CPFA is used to process these FFOA images with different focuses. By selecting high‐contrast areas, the CPFA can highlight the characteristics and details of blood vessels to obtain LD‐FFOA images. In the optimal case of the proposed method, the DOF for FFOA is more than tripled using 10 differently focused FFOA images. Both the phantom and animal experimental results show that the LD‐FFOA resolves FFOA defocusing issues induced by surface and thickness inhomogeneities in biological samples. The proposed method can be potentially applied to practical biological experiments.      

A Study on the Correlation Between Structure and Hole Transport in Semi‐Crystalline Regioregular P3HT

A correlation between the hole transport and corresponding structural properties of the bulk regioregular poly(3‐hexylthiophene) (rr‐P3HT) is studied as a function of temperature by the time‐of‐flight (TOF) and wide angle X‐ray diffraction (WAXD) techniques. The thermally‐reversible structural evolution along the (100) and (020) directions in a semi‐crystalline rr‐P3HT can be divided into two distinct temperature regions. At T > 120 °C, a large thermal expansion along the π–π stacking direction in the nanocrystals and a deteriorated ordering in the material result in negative slopes of temperature and electric field dependences of hole mobility. The WAXD data suggest that the hole transport is limited by a decrease in the crystallinity and by an increase in the hopping distance along the π‐π stacking direction, while the Gaussian Disorder Model (GDM) with temperature‐independent parameters cannot be applied. At T < 120 °C, the transport‐related structural changes are negligible and the temperature and electric field dependences of hole mobility can be described by the GDM with constant energetic (σ ～ 120 meV) and positional disorder parameters (Σ ～ 3.33). These values suggest that the hole transport is limited by the amorphous phase, as commonly seen in disordered polymers. Moreover, a regiorandom P3HT (rra‐P3HT), which shows a temperature‐independent intermolecular distance of ～15.3Å, provides a route for separate examination of the amorphous phase in rr‐P3HT.     

Stacking geometry for non‐canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion‐corrected DFT‐D study

Emergence of thousands of crystal structures of noncoding RNA molecules indicates its structural and functional diversity. RNA function is based upon a large variety of structural elements which are specifically assembled in the folded molecules. Along with the canonical Watson‐Crick base pairs, different orientations of the bases to form hydrogen‐bonded non‐canonical base pairs have also been observed in the available RNA structures. Frequencies of occurrences of different non‐canonical base pairs in RNA indicate their important role to maintain overall structure and functions of RNA. There are several reports on geometry and energetic stabilities of these non‐canonical base pairs. However, their stacking geometry and stacking stability with the neighboring base pairs are not well studied. Among the different non‐canonical base pairs, the G:U wobble base pair (G:U W:WC) is most frequently observed in the RNA double helices. Using quantum chemical method and available experimental data set we have studied the stacking geometry of G:U W:WC base pair containing dinucleotide sequences in roll‐slide parameters hyperspace for different values of twist. This study indicates that the G:U W:WC base pair can stack well with the canonical base pairs giving rise to large interaction energy. The overall preferred stacking geometry in terms of roll, twist and slide for the eleven possible dinucleotide sequences is seen to be quite dependent on their sequences. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 328–338, 2015.     

Freestanding stacked mesh‐like hydrogel sheets enable the creation of complex macroscale cellular scaffolds

Hydrogel‐based bottom‐up tissue engineering depends on assembly of cell‐laden modules for complex three‐dimensional tissue reconstruction. Though sheet‐like hydrogel modules enable rapid and controllable assembly, they have limitations in generating spatial microenvironments and mass transport. Here, we describe a simple method for forming large‐scale cell‐hydrogel assemblies via stacking cell‐embedded mesh‐like hydrogel sheets to create complex macroscale cellular scaffolds. Freestanding stacked hydrogel sheets were fabricated for long‐term cell culturing applications using a facile stacking process where the micropatterned hydrogel sheets (8.0 mm × 8.7 mm) were aligned using a polydimethylsiloxane drainage well. The stacked hydrogel sheets were precisely aligned so that the openings could facilitate mass transport through the stacked sheets. Despite the relatively large height of the stacked structure (400–700 μm), which is larger than the diffusion limit thickness of 150–200 μm, the freestanding cell‐ydrogel assemblies maintained cell viability and exhibited enhanced cellular function compared with single hydrogel sheets. Furthermore, a three‐dimensional co‐culture system was constructed simply by stacking different cell‐containing hydrogel sheets. These results show that stacked hydrogel sheets have significant potential as a macroscale cell‐culture and assay platform with complex microenvironments for biologically relevant in vitro tissue‐level drug assays and physiological studies.     

Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure

The crystal structure of d(CATGGGCCCATG)₂ shows unique stacking patterns of a stable B↔A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in the standard and crystal B-DNA geometries. Thus, naturally occurring stacking geometries were essentially isoenergetic while individual base pair steps differed substantially in the balance of intra-strand and inter-strand stacking terms. Also, relative dispersion, electrostatic and polarization contributions to the stability of different base pair steps were very sensitive to base composition and sequence context. A large stacking flexibility is most apparent for the CpA step, while the GpG step is characterized by weak intra-strand stacking. Hydration effects were estimated using the Langevin dipoles solvation model. These calculations showed that an aqueous environment efficiently compensates for electrostatic stacking contributions. Finally, we have carried out explicit solvent molecular dynamics simulation of the d(CATGGGCCCATG)₂ duplex in water. Here the DNA conformation did not retain the initial crystal geometry, but moved from the B↔A intermediate towards the B-DNA structure. The base stacking energy improved in the course of this simulation. Our findings indicate that intrinsic base stacking interactions are not sufficient to stabilize the local conformational variations in crystals.     

Back Cover: Large‐depth‐of‐field full‐field optical angiography (J. Biophotonics 5/2019)

A large‐depth‐of‐field full‐field optical angiography (LD‐FFOA) method is developed to expand the depth‐of‐field (DOF). The contrast pyramid fusion algorithm is used to fuse 10 FFOA images at different focus depth. Cover images of mouse ear shows LD‐FFOA image has higher contrast and more detailed features. The LD‐FFOA method solves the defocused problem caused by the limited DOF of lens, the curved surface and uneven thickness of the sample. Further details can be found in the article by Mingyi Wang, Nanshou Wu, Hongheng Huang, et al. ( e201800329 ).

     

Fish preference for hydraulic habitat in typical middle reaches of Yangtze River,China

This study presents a method of combining hydroacoustics and hydraulic data to estimate fish preference in a large and rapidly flowing river system. A typical middle reach of the Yangtze River with three islands and two wandering sections was taken as the research object to interpret schools of fish with different sizes and densities for their preference of physical habitat features such as water depth and velocity by using Geographic Information Systems (GIS). Fish density and size were determined based on the hydroacoustic data, and hydraulic variables were simultaneously collected using an Acoustic Doppler Current Profiler (ADCP) system. Results show that fish sizes are correlated with water depth and velocity and that fish density correlated only with water depth. Small fish prefer high water depth average velocity (WDAV), lower vertical average velocity (VAV), deep water, as well as a wide depth and velocity range; large fish prefer low WDAV, high VAV, deep water, and a narrow depth and velocity range. High fish densities appear around islands and areas with deep water. The results show that large fish may be sufficiently strong enough to select their preference for water depth and velocity. Areas of deep water can provide broad velocity diversity and more space to accommodate fish. The island littoral zone could provide a variety of habitats with a diverse pattern of depth and velocity for fish. This study provides a contributive method for the field habitat suitability assessment for fish.     

Coexistence of two similar copepod species, <Emphasis Type="Italic">Eudiaptomus gracilis</Emphasis> and <Emphasis Type="Italic">E. graciloides</Emphasis>: the role of differential predator avoidance

Habitat choice in relation to environmental factors of two coexisting calanoid copepod species, Eudiaptomus gracilis and E. graciloides, was studied in a mesotrophic lake and in large indoor mesocosms. Both species and sexes showed pronounced diel vertical migration (DVM) in the field. In 12 m deep mesocosms with free ranging fish DVM was observed and species increased day depth over time. No changes were observed in copepod day depth over time in experiments with fish kairomone. It is hypothesized that fish kairomone acts as an early warning system to copepods which respond by moving deeper, but only as far as the thermocline. For full DVM, a nearby mechanical stimulus is necessary. Thus, as fish go deeper to feed, copepods retreat. The response of copepods to fish predation, in the presence of low and high numbers of Daphnia,shows that copepods effectively use Daphniaas living shields to avoid predation. The two species adopt different vertical migration strategies depending on whether there are high or low numbers of Daphniapresent. A dominant feature of mesocosm experiments was the night time aggregating (lekking) of E. gracilis males at the surface. When the spring and autumn percentages of risk takers in the epilimnion were compared, E. gracilis, particularly males, suffered the greatest cost.     

Flexible wide‐field optical micro‐angiography based on Fourier‐domain multiplexed dual‐beam swept source optical coherence tomography

Wide‐field optical coherence tomography angiography (OCTA) is gaining interest in clinical imaging applications. In this pursuit, it is challenging to maintain the imaging resolution and sensitivity throughout the wide field of view (FoV). Here, we propose a novel method/system of dual‐beam arrangement and Fourier‐domain multiplexing to achieve wide‐field OCTA when imaging the uneven surface samples. The proposed system provides 2 separate FoVs, with flexibility that the imaging area, focus of the imaging beam and imaging depth range can be individually adjusted for each FoV, leading to either (1) increased system imaging FoV or (2) capability of targeting 2 regions of interests that locate at depths with large difference between each other. We demonstrate this novel method by employing 100 kHz laser source in a swept source OCTA to achieve an effective 200 kHz sweeping rate, covering a 22 × 22 mm FoV. The results are verified by a SS‐OCTA system employing a 200 kHz laser source, together with the experimental demonstrations when imaging whole brain vasculature in rodent models and skin blood perfusion in human fingers, show‐casing the capability of proposed system to image live large samples with complex surface topography.      

High‐Quality Graphene Microflower Design for High‐Performance Li–S and Al‐Ion Batteries

Poor quality and insufficient productivity are two main obstacles for the practical application of graphene in electrochemical energy storage. Here, high‐quality crumpled graphene microflower (GmF) for high‐performance electrodes is designed. The GmF possesses four advantages simultaneously: highly crystallized defect‐free graphene layers, low stacking degree, sub‐millimeter continuous surface, and large productivity with low cost. When utilized as carbon host for sulfur cathode, the GmF‐sulfur hybrid delivers decent areal capacities of 5.2 mAh cm^?2 at 0.1 C and 3.8 mAh cm^?2 at 0.5 C. When utilized as cathode of Al‐ion battery, the GmF affords a high capacity of 100 mAh g^?1 with 100% capacity retention after 5000 cycles and excellent rate capability from 0.1 to 20 A g^?1. This facile and large‐scale producible GmF represents a meaningful high‐quality graphene powder for practical energy storage technology. Meanwhile, this unique high‐quality graphene design provides an effective route to improve electrochemical properties of graphene‐based electrodes.     

On the stability of nucleic acid structures in solution: enthalpy-entropy compensations, internal rotations and reversibility.

The thermodynamics of self-association (stacking) of free bases and nucleotides, intramolecular stacking in dinucleotides, nearest-neighbour base pair stacking interactions in duplex DNA and RNA, and the formation of hairpin loops illustrate enthalpy/entropy compensations. Large stacking exothermicities are associated with large negative entropy changes that ensure that delta G is small, permitting readily reversible associations in solution. We rationalise enthalpy/entropy compensations with reference to residual motions and torsional vibrations which make a larger entropic contribution to binding when - delta H approximately kT (thermal energy at room temperature), than when - delta H >> kT. We present a factorisation of experimental free energies for helix formation in terms of approximate contributions from the restriction of rotations, hydrophobic interactions, electrostatic interactions due to base stacking, and contributions from hydrogen bonding, and estimate the adverse free energy cost per rotor (mainly entropy) of ordering the phosphate backbone as between 1.9 and 5.4 kJ mol-1 [averaged over 12 rotors per base pair for A-U on A-U stacking (lower limit), and G-C on C-G stacking (upper limit)]. The largest cost is associated with the most exothermic stacking interactions, while the range of values is consistent with earlier conclusions from data on the fusion of hydrocarbon chains (lower value), and with entropy changes in covalent isomerisations of small molecules involving severe restrictions (upper value).     

Habitat quality and among-population differentiation in reproductive effort and flowering phenology in the perennial herb <Emphasis Type="Italic">Primula farinosa</Emphasis>

In heterogeneous environments, selection on life-history traits and flowering time may vary considerably among populations because of differences in the extent to which mortality is related to age or size, and because of differences in the seasonal patterns of resource availability and intensity of biotic interactions. Spatial variation in optimal reproductive effort and flowering time may result in the evolution of genetic differences in life-history traits, but also in the evolution of adaptive phenotypic plasticity. The perennial herb Primula farinosa occurs at sites that differ widely in soil depth and therefore in water-holding capacity, vegetation cover, and frost-induced soil movement in winter. We used data from eight natural populations and a common-garden experiment to test the predictions that reproductive allocation is negatively correlated with soil depth while age at first reproduction and first flowering date among reproductive individuals are positively correlated with soil depth. In the common-garden experiment, maternal families collected in the field were grown from seed and monitored for 5 years. In the field, reproductive effort (number of flowers in relation to rosette area) varied among populations and was negatively related to soil depth. In the common-garden experiment, among-population differences in age at first reproduction, and reproductive effort were statistically significant, but relatively small and not correlated with soil depth at the site of origin. Flowering time varied considerably among populations, but was not related to soil depth at the site of origin. Taken together, the results suggest that among-population variation in reproductive effort observed in the field largely reflects phenotypic plasticity. They further suggest that among-population differentiation in flowering time cannot be attributed to variation in environmental factors correlated with soil depth.     

Habitat selection by larvae of a fluvial lamprey, <Emphasis Type="Italic">Lethenteron reissneri</Emphasis>, in a small stream and an experimental aquarium

Habitat selection by fluvial lamprey larvae, Lethenteron reissneri (Petromyzontidae), was studied in a natural stream and an experimental aquarium to clarify microhabitat requirements for future conservation of natural populations. A gross collection survey of lamprey larvae in the Monbetsu River, southeastern Hokkaido, Japan, revealed a remarkable bias toward distribution in sandy-mud beds. An analysis using Jacobs' electivity index showed that the larvae selectively utilized spaces having regard to shallow water, weak current, deep sandy-mud, and fine substrate particles. A comparison of microhabitat use between small- (≤5 cm) and large-sized larvae (>5 cm) indicated that the latter utilized the space with greater ranges in both water depth and substrate particle size than the former. Both the field survey and laboratory experiments on larval selectivity of physical habitat variables clearly demonstrated that substrate particle size was the most important variable for small-sized larvae whereas both water depth and substrate depth were more important for large larvae. These findings should be applicable in directing attempts at fluvial habitat restoration for conservation of this endangered lamprey species. Received: November 1, 2000 / Revised: September 12, 2001 / Accepted: October 18, 2001     

Sex allocation in the polydomous leaf-cutting ant <Emphasis Type="Italic">Acromyrmex</Emphasis><Emphasis Type="Italic">balzani</Emphasis>

Logistic regression analysis was used to analyse sex allocation in a population of the leaf-cutting ant Acromyrmex balzani occurring in a pasture in southern Brazil. The field sample consisted of 151 fungus-garden chambers (18 queenright and 133 queenless), belonging to 50 nests with three vertically stacked chambers per nest on average. Taking nest chamber as the unit of analysis, seven predictor variables were considered: sampling date, chamber depth, chamber volume, weight of fungus garden, presence of a queen, number of large workers, and number of small to medium workers. The population-level numerical proportion of females was 0.548 and the inferred proportional energetic investment in females 0.672. The former was not significantly different from 0.5 (P=0.168), but the latter was (P=0.0003). The proportional investment in females per fungus garden increased with the number of large workers present (P=0.0002) and decreased with the dry weight of the fungus garden (P=0.012). This implies that resource acquisition through foraging is likely to be a major proximate determinant of sex allocation. The negative correlation between female bias and fungus garden weight might be due to developing adult females requiring more food than males, but this hypothesis could not be confirmed by direct statistical evidence.     

DNA polymorphism and local variation in base-pair orientation: a theoretical rationale.

Basepair stacking calculations have been carried out to understand the conformational polymorphism of DNA and its sequence dependence. The recently developed self-consistent parameter set, which is specially suitable for describing irregular DNA structures, has been used to describe the geometry of a basepair doublet. While for basepairs without any propeller, the favourable stacking patterns do not appear to have very strong features, much more noticeable sequence dependent stacking patterns emerge once a propeller is applied to the basepairs. The absolute minima for most sequences occurs for a doublet geometry close to the B-DNA fibre models. Hence in the B-DNA region, no strong sequence dependent features are found, but the range of doublet geometries observed in the crystal structures generally lie within the low energy contours, obtained from stacking energy calculations. The doublet geometry corresponding to the A-DNA fibre model is not energetically favourable for the purine-pyrimidine sequences, which prefer small roll angle values when the slide has a large negative value as in A-DNA. However positive roll with large negative slide is allowed for GG, GA, AG and the pyrimidine-purine steps. This is consistent with the observed geometries of various steps in A-DNA crystals. Thus the general features of the basepair doublets predicted from these theoretical studies agree very well with the results from crystal structure analysis. However, since most sequences show an overall preference for B-type doublet geometry, the B----A transition for random sequence DNA cannot be explained on the basis of basepair stacking interactions.     

Distribution and Population Dynamics of Nematodes in a Rice Field and Pasture in India

Ecological studies on soil nematodes were made in a tropical rice field and pasture. Parasitic species were more diversified in the pasture than in the rice field. Eighty-six and sixty percent of total nematodes occurred in the top 10 cm in rice field and pasture, respectively. Nematodes were not randomly or uniformly dispersed but aggregated. Parasitic forms were most abundant and correlated with root biomass in the 0-15-cm soil layer, the greatest number usually occurring at the 10-15-cm depth at both sites. In summer, however, they were densest at the 15-30-cm depth. Microbivores were most frequent in the top 5 cm of both sites. Micellaneous feeders (food sources uncertain) usually occurred in highest densities at the 15-30-cm depth. Predators showed no distinct depth preference. Temperature and moisture of the soil apparently played an important role in regulating nematode population. Peak densities of 31.3 × 10⁴/m² and 21.6 × 10⁴/m² at a 30-cm depth occurred in January, while minimum densities of 5.0-5.3 × 10⁴/m² and 4.1 × 10⁴/m² occurred in July-October and April in rice field and pasture, respectively. Monthly mean biomass of nematodes was 23.8 ± 4.5 mg/m² in rice field and 11.5 ± 1.5 mg/m² in pasture.     

Interlayer energy-optimum stacking registry for two curved graphene sheets of nanometre dimensions

The interlayer energy between two circular graphene sheets of nanometre scale, which is curved into cylindrical shape with different curvature radius, is investigated by a molecular force field based on a registry-dependent interlayer interaction potential. It is found that there is a special interlayer stacking angle near which the interlayer energy is significantly lower. This interlayer energy-minimum stacking registry angle shifts away from the original Bernal (AB) stacking orientation when the curvature radius of curved graphene sheets is less than 20 nm, and increases with decreasing curvature radius beyond this point. The stability of interlayer energy-minimum stacking of the curved graphene sheets decreases with decreasing curvature radius.     

Base-stacking interactions in double-helical DNA structures: experiment versus theory

Atom-atom potential energy calculations have been undertaken for deriving stacking energies in double-helical structures. A comparison between the energy patterns of A- and B-type double-helical fragments determined by single-crystal X-ray diffraction methods versus idealized uniform models based on fibre diffraction data shows that the van der Waals stacking energy is largely sensitive to local changes in the relative orientation of adjacent base pairs. The sequence-dependent conformational variability observed in the high-resolution structures appears to be a consequence of the equipartitioning of the stacking energy along the double helix. The large energy variations expected for a uniform structure are dampened considerably in the observed structures by means of local changes in conformational features such as helix rotation and roll angles between base pairs.     

Achieving zT > 2 in p‐Type AgSbTe2−xSex Alloys via Exploring the Extra Light Valence Band and Introducing Dense Stacking Faults

Through simultaneously enhancing the power factor by engineering the extra light band and enhancing phonon scatterings by introducing a high density of stacking faults, a record figure‐of‐merit over 2.0 is achieved in p‐type AgSbTe_2?xSe_x alloys. Density functional theory calculations confirm the presence of the light valence band with large degeneracy in AgSbTe₂, and that alloying with Se decreases the energy offset between the light valence band and the valence band maximum. Therefore, a significantly enhanced power factor is realized in p‐type AgSbTe_2?xSe_x alloys. In addition, transmission electron microscopy studies indicate the appearance of stacking faults and grain boundaries, which together with grain boundaries and point defects significantly strengthen phonon scatterings, leading to an ultralow thermal conductivity. The synergetic strategy of simultaneously enhancing power factor and strengthening phonon scattering developed in this study opens up a robust pathway to tailor thermoelectric performance.