Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial.

Anthropogenic factors have impacted the diversity and evolutionary trajectory of various species. This can be through factors such as pressure on population size or range, habitat fragmentation, or extensive manipulation and translocation. Here we use time-calibrated data to better understand the pattern and processes of evolution in the heavily manipulated European fallow deer (Dama dama). During the Pleistocene, fallow deer had a broad distribution across Europe and were found as far north as Britain during the Eemian interglacial. The last glacial period saw fallow deer retreat to southern refugia and they did not disperse north afterwards. Their recolonisation was mediated by people and, from northern Europe and the British Isles, fallow deer were transported around the world. We use ancient and modern mitochondrial DNA (mtDNA) and mitogenomic data from Eemian Britain to assess the pattern of change in distribution and lineage structure across Europe over time. We find founder effects and mixed lineages in the northern populations, and stability over time for populations in southern Europe. The Eemian sample was most similar to a lineage currently in Italy, suggesting an early establishment of the relevant refuge. We consider the implications for the integration of anthropogenic and natural processes towards a better understanding of the evolution of fallow deer in Europe.

Cryptic lineage differentiation among Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the northwest Indian Ocean.

Phylogeography can provide insight into the potential for speciation and identify geographic regions and evolutionary processes associated with species richness and evolutionary endemism. In the marine environment, highly mobile species sometimes show structured patterns of diversity, but the processes isolating populations and promoting differentiation are often unclear. The Delphinidae (oceanic dolphins) are a striking case in point and, in particular, bottlenose dolphins (Tursiops spp.). Understanding the radiation of species in this genus is likely to provide broader inference about the processes that determine patterns of biogeography and speciation, because both fine-scale structure over a range of kilometers and relative panmixia over an oceanic range are known for Tursiops populations. In our study, novel Tursiops spp. sequences from the northwest Indian Ocean (including mitogenomes and two nuDNA loci) are included in a worldwide Tursiops spp. phylogeographic analysis. We discover a new 'aduncus' type lineage in the Arabian Sea (off India, Pakistan and Oman) that diverged from the Australasian lineage ∼261 Ka. Effective management of coastal dolphins in the region will need to consider this new lineage as an evolutionarily significant unit. We propose that the establishment of this lineage could have been in response to climate change during the Pleistocene and show data supporting hypotheses for multiple divergence events, including vicariance across the Indo-Pacific barrier and in the northwest Indian Ocean. These data provide valuable transferable inference on the potential mechanisms for population and species differentiation across this geographic range.

The effect of temperature on the autofluorescence of scattering and non-scattering tissue.

BACKGROUND AND OBJECTIVES: With the increasing use of fluorescence in medical applications, a comprehensive understanding of the effect of temperature on tissue autofluorescence is essential. The purpose of this study is to explore the effect of temperature on the fluorescence of porcine cornea and rat skin and determine the relative contributions of irreversible changes in optical properties and in fluorescence yield. STUDY DESIGN/MATERIALS AND METHODS: Fluorescence, diffuse reflectance, and temperature measurements were acquired from excised porcine cornea and rat skin over a temperature range of 0-80 °C. A dual excitation system was used with a 337 nm pulsed nitrogen laser for the fluorescence and a white light source for the diffuse reflectance measurements. A thermal camera measured tissue temperature. Optical property changes were inferred from diffuse reflectance measurements. The reversibility of the change in fluorescence was examined by acquiring measurements while the tissue sample cooled from the highest induced temperature to room temperature. RESULTS: The fluorescence intensity decreased with increasing tissue temperature. This fluorescence change was reversible when the tissue was heated to a temperature of 45 °C, but irreversible when heated to a temperature of 80 °C. CONCLUSION: Auto-fluorescence intensity dependence on temperature appears to be a combination of temperature-induced optical property changes and reduced fluorescence quantum yield due to changes in collagen structure. Temperature-induced changes in measured fluorescence must be taken into consideration in applications where fluorescence is used to diagnose disease or guide therapy.

Population divergence and gene flow in an endangered and highly mobile seabird.

Seabirds are highly vagile and can disperse up to thousands of kilometers, making it difficult to identify the factors that promote isolation between populations. The endemic Hawaiian petrel (Pterodroma sandwichensis) is one such species. Today it is endangered, and known to breed only on the islands of Hawaii, Maui, Lanai and Kauai. Historical records indicate that a large population formerly bred on Molokai as well, but this population has recently been extirpated. Given the great dispersal potential of these petrels, it remains unclear if populations are genetically distinct and which factors may contribute to isolation between them. We sampled petrels from across their range, including individuals from the presumably extirpated Molokai population. We sequenced 524 bp of mitochondrial DNA, 741 bp from three nuclear introns, and genotyped 18 microsatellite loci in order to examine the patterns of divergence in this species and to investigate the potential underlying mechanisms. Both mitochondrial and nuclear data sets indicated significant genetic differentiation among all modern populations, but no differentiation was found between historic samples from Molokai and modern birds from Lanai. Population-specific nonbreeding distribution and strong natal philopatry may reduce gene flow between populations. However, the lack of population structure between extirpated Molokai birds and modern birds on Lanai indicates that there was substantial gene flow between these populations and that petrels may be able to overcome barriers to dispersal prior to complete extirpation. Hawaiian petrel populations could be considered distinct management units, however, the dwindling population on Hawaii may require translocation to prevent extirpation in the near future.

New chemistry of 1,2-closo-P2B10H10 and 1,2-closo-As2B10H10; in silico and gas electron diffraction structures, and new metalladiphospha- and metalladiarsaboranes.

The molecular structures of 1,2-closo-P(2)B(10)H(10) (1) and 1,2-closo-As(2)B(10)H(10) (2) have been determined by gas electron diffraction and the results obtained compared with those from computation at the MP2/6-31G** level of theory. The level of agreement is good for 2 (root-mean-square [rms] misfit for As and B atoms 0.0297 Å) and very good for 1 (rms misfit for P and B atoms 0.0082 Å). In comparing the structures of 1 and 2 with that of 1,2-closo-C(2)B(10)H(12) (I) it is evident that expansion of the polyhedron from I to 1 to 2 is restricted only to the heteroatom vertices and the B(6) face to which these are bound. Following deboronation (at B3) and subsequent metallation, compounds 1 and 2 have been converted into the new metalladiheteroboranes 3-(η-C(9)H(7))-3,1,2-closo-CoAs(2)B(9)H(9) (4), 3-(η-C(10)H(14))-3,1,2-closo-RuAs(2)B(9)H(9) (5), 3-(η-C(5)H(5))-3,1,2-closo-CoP(2)B(9)H(9) (6), 3-(η-C(9)H(7))-3,1,2-closo-CoP(2)B(9)H(9) (7) and 3-(η-C(10)H(14))-3,1,2-closo-RuP(2)B(9)H(9) (8), the last three constituting the first examples of metalladiphosphaboranes. Together with the known compound 3-(η-C(5)H(5))-3,1,2-closo-CoAs(2)B(9)H(9) (3), compounds 4-8 have been analysed by NMR spectroscopy and (except for 8) single-crystal X-ray diffraction. The (11)B NMR spectra of analogous pairs of metalladiphosphaborane and metalladiarsaborane (6 and 3, 7 and 4, 8 and 5) reveal a consistently narrower (9-10 ppm) chemical shift range for the metalladiarsaboranes, the combined result of a deshielding of the lowest frequency resonance (B6) and an increased shielding of the highest frequency resonance (B8) via an antipodal effect. In crystallographic studies, compounds 3 and 5B (one of two crystallographically-independent molecules) suffer As/B disorder, but in both cases it was possible to refine distinct, ordered, components of the disorder, the first time this has been reported for metalladiarsaboranes. Moreover, whilst the Cp compounds 6 and 3 are disordered, their indenyl analogues 7 and 4 are either ordered or significantly less disordered, a consequence of both the reduced symmetry of an indenyl ligand compared to a Cp ligand and the preference of the former for a distinct conformation relative to the cage heteroatoms. Unexpectedly, whilst this conformation in the cobaltadiphosphaborane 7 is cis-staggered (similar to that previously established for the analogous cobaltadicarborane), in the cobaltadiarsaborane 4 the conformation is close to cis-eclipsed.

Investigations on laser hard tissue ablation under various environments.

The purpose of this study was to investigate the effect of liquid environments upon laser bone ablation. A long-pulsed Er,Cr:YSGG laser was employed to ablate bovine bone tibia at various radiant exposures under dry, wet (using water or perfluorocarbon) and spray environmental conditions. Energy loss by the application of liquid during laser irradiation was evaluated, and ablation performance for all conditions was quantitatively measured by optical coherence tomography (OCT). Microscope images were also used to estimate thermal side effects in tissue after multiple-pulse ablation. Wet using water and spray conditions equally attenuated the 2.79 microm wavelength laser beam. Higher transmission efficiency was obtained utilizing a layer of perfluorocarbon. Dry ablation exhibited severe carbonization due to excessive heat accumulation. Wet condition using water resulted in similar ablation volume to the dry case without carbonization. The perfluorocarbon layer produced the largest ablation volume but some carbonization due to the poor thermal conductivity. Spray induced clean cutting with slightly reduced efficiency. Liquid-assisted ablation provided significant beneficial effects such as augmented material removal and cooling/cleaning effects during laser osteotomy.

Hard tissue ablation with a spray-assisted mid-IR laser.

The objective of this study was to understand the dominant mechanism(s) for dental enamel ablation with the application of water spray. A free-running Er,Cr:YSGG (yttrium, scandium, gallium, garnet) laser was used to ablate human enamel tissue at various radiant exposures. During dental ablation, distilled water was sprayed on the sample surface, and these results were compared to ablation without a spray (dry ablation). In order to identify dominant ablation mechanisms, transient acoustic waves were compared to ablation thresholds and the volume of material removed. The ablation profile and depth were measured using optical coherence tomography (OCT). Irregular surface modification, charring and peripheral cracks were associated with dry ablation, whereas craters for spray samples were relatively clean without thermal damage. In spite of a 60% higher ablation threshold for spray associated irradiations owing to water absorption, acoustic peak pressures were six times higher and ablation volume was up to a factor of 2 larger compared to dry ablation. The enhanced pressure and ablation performance of the spray-assisted process was the result of rapid water vaporization, material ejection with recoil stress, interstitial water explosion and possibly liquid-jet formation. With water cooling and abrasive/disruptive mechanical effects, the spray ablation can be a safe and efficient modality for dental treatment.

Porcine skin visible lesion thresholds for near-infrared lasers including modeling at two pulse durations and spot sizes.

With the advent of such systems as the airborne laser and advanced tactical laser, high-energy lasers that use 1315-nm wavelengths in the near-infrared band will soon present a new laser safety challenge to armed forces and civilian populations. Experiments in nonhuman primates using this wavelength have demonstrated a range of ocular injuries, including corneal, lenticular, and retinal lesions as a function of pulse duration. American National Standards Institute (ANSI) laser safety standards have traditionally been based on experimental data, and there is scant data for this wavelength. We are reporting minimum visible lesion (MVL) threshold measurements using a porcine skin model for two different pulse durations and spot sizes for this wavelength. We also compare our measurements to results from our model based on the heat transfer equation and rate process equation, together with actual temperature measurements on the skin surface using a high-speed infrared camera. Our MVL-ED50 thresholds for long pulses (350 micros) at 24-h postexposure are measured to be 99 and 83 J cm(-2) for spot sizes of 0.7 and 1.3 mm diam, respectively. Q-switched laser pulses of 50 ns have a lower threshold of 11 J cm(-2) for a 5-mm-diam top-hat laser pulse.

Dehydration mechanism of optical clearing in tissue.

Previous studies identified various mechanisms of light scattering reduction in tissue induced by chemical agents. Our results suggest that dehydration is an important mechanism of optical clearing in collagenous and cellular tissue. Photographic and optical coherence tomography images indicate that air-immersed skin and tendon specimens become similarly transparent to glycerol-immersed specimens. Transmission electron microscopy images reveal that dehydration causes individual scattering particles such as collagen fibrils and organelles to become more densely packed, but does not significantly alter size. A heuristic particle-interaction model predicts that the scattering particle volume fraction increase can contribute substantially to optical clearing in collagenous and cellular tissue.

Using sandpaper for noninvasive transepidermal optical skin clearing agent delivery.

We present a gentle mechanical method for the noninvasive transepidermal delivery of topically applied optical skin clearing agents. Optical skin clearing reduces light scattering in highly turbid skin with the aid of hyperosmotic chemicals such as glycerol, polyethylene glycol, and solutions of dextrose. Transepidermal delivery of such agents is believed to be most patient compliant and most likely to be used in a clinical environment. Optical skin clearing has the potential to expand the current limited use of laser light in medicine for diagnostic and therapeutic applications. Light scattering limits the penetration depth of collimated light into skin. In order to increase the diffusion of topically applied optical skin clearing agents into skin, we present a gentle mechanical delivery method involving glycerol and dextrose as optical skin clearing agents and fine 220-grit sandpaper to rub the clearing agent into the tissue. Gentle rubbing causes abrasion of the superficial skin layer including the stratum corneum, which otherwise prevents these optical skin clearing agents from freely diffusing into skin. Results indicate very fast optical skin clearing rates. In vivo hamster skin turned transparent within 2 min. The 1e light penetration depth increased by 36+/-3.75% for dextrose and 43+/-8.24% for glycerol. Optical skin clearing was reversed using phosphate buffered saline solution. Skin viability was observed 70 h post-treatment and showed scabbing and erythema on a few percent of the total optically cleared skin surface.

Enhancement of transepidermal skin clearing agent delivery using a 980 nm diode laser.

BACKGROUND AND OBJECTIVES: Patient compliant optical skin clearing requires non-invasive topical delivery of clearing agents such as glycerol. This requires reducing the skin barrier function by disrupting stratum corneum integrity, which was achieved using a 980 nm diode laser with artificial absorption substrates on the skin surface. Reduction of light scattering has the potential to improve many current and novel diagnostic and therapeutic applications of lasers in medicine. STUDY DESIGN/MATERIALS AND METHODS: In vivo hamster and rat skin was used to test optical skin clearing. Absorption substrates were applied to the skin after shaving. These included black ink, dark children's rub-on tattoo, and carbon paper. 980 nm cw laser light was used to ablate these substrates and to heat the skin surface to enhance the diffusion of topically applied glycerol for optical skin clearing. Increased light penetration was determined from amplitude optical coherence tomography data. RESULTS: Results indicate an improvement of the ability to measure an OCT signal at a wavelength of 1,290 nm up to 42% deeper into in vivo rodent skin using a 980 nm laser with a fluence of less than 0.96 J/mm(2) to alter the stratum corneum. CONCLUSIONS: The use of an inexpensive diode laser can significantly enhance the delivery of topically applied glycerol for optical skin clearing. The laser use involves application of an absorption substrate onto the skin surface. Using carbon paper left no unwanted residue behind and is considered optimal for this purpose.

Dependence of calculus retropulsion dynamics on fiber size and radiant exposure during Ho:YAG lithotripsy.

During pulsed laser lithotripsy, the calculus is subject to a strong recoil momentum which moves the calculus away from laser delivery and prolongs the operation. This study was designed to quantify the recoil momentum during Ho:YAG laser lithotripsy. The correlation among crater shape, debris trajectory, laser-induced bubble and recoil momentum was investigated. Calculus phantoms made from plaster of Paris were ablated with free running Ho:YAG lasers. The dynamics of recoil action of a calculus phantom was monitored by a high-speed video camera and the laser ablation craters were examined with Optical Coherent Tomography (OCT). Higher radiant exposure resulted in larger ablation volume (mass) which increased the recoil momentum. Smaller fibers produced narrow craters with a steep contoured geometry and decreased recoil momentum compared to larger fibers. In the presence of water, recoil motion of the phantom deviated from that of phantom in air. Under certain conditions, we observed the phantom rocking towards the fiber after the laser pulse. The shape of the crater is one of the major contributing factors to the diminished recoil momentum of smaller fibers. The re-entrance flow of water induced by the bubble collapse is considered to be the cause of the rocking of the phantom.

Calculus fragmentation in laser lithotripsy.

The intracorporeal treatment of urinary calculi with lasers is presented, which describes laser-calculus interactions associated with lithotripsy. Reliable fragmentation of calculi with diverse compositions and minimal collateral tissue damage are primarily contingent upon laser parameters (wavelength, pulse duration, and pulse energy) and physical properties of calculi (optical, mechanical, and chemical). The pulse duration governs the dominant mechanism in calculi fragmentation, which is either photothermal or photoacoustical/photomechanical. Lasers with long pulse durations (i.e. > tens of micros) induce a temperature rise in the laser-affected zone with minimal acoustic waves; material is removed by means of vaporization, melting, mechanical stress, and/or chemical decomposition. Short-pulsed laser ablation (i.e. < 10 micros), on the other hand, produces shock waves, and the resultant mechanical energy fragments calculi. Work continues throughout the world to evaluate the feasibility of advanced lasers in lithotripsy and to optimize laser parameters and light delivery systems pertinent to efficient fragmentation of calculi.

Midinfrared optical breakdown in transparent dielectrics.

Optical breakdown measurements for transparent dielectrics are reported for 1 ps laser pulses as a function of mid-IR wavelength from 4.7 to 7.8 microm. For wide-gap dielectrics seed electrons are generated by tunnel ionization with subsequent avalanche ionization and laser absorption by dense plasma. For narrow-gap dielectrics tunnel ionization alone leads to dense plasma formation.

Effect of lithotripsy on holmium:YAG optical beam profile.

PURPOSE: To determine the effect of holmium:YAG lithotripsy on the optical beam profile. MATERIALS AND METHODS: Beam profiles of the laser light from holmium:YAG optical fiber systems were characterized with a pyroelectric camera. Beam profiles were measured with 272-microm and 365-microm optical fibers both straight and bent to simulate lower-pole ureteronephroscopy. Struvite calculi were irradiated. Beam profiles and energy outputs were characterized for the fibers before and after ablation. Ablation crater geometry was characterized with optical coherence tomography. RESULTS: Undamaged, straight fibers produced a near-Gaussian beam profile. Craters showed a similar near-Gaussian shape. Undamaged, bent 272-microm fibers produced a near-Gaussian beam but slightly flatter profile than the straight fiber. The bent 272-microm fiber transmitted 99% to 100% of the energy, similar to the 100% transmission of the straight fibers. After ablation, measured energy output dropped by 30% within 50 pulses at 0.2 J pulse energy. The damaged fibers produced irregular beam profiles with hot spots. Craters showed irregular contours. CONCLUSIONS: During Ho:YAG lithotripsy, the beam profile at the optical fiber tip approaches a Gaussian distribution. This shape corresponds to the crater produced on the stone surface. With further ablation, the beam profile becomes erratic and unpredictable, with loss of lithotripsy efficiency. The findings provide further insight into the photothermal mechanism of Ho:YAG lithotripsy.

Stone retropulsion during holmium:YAG lithotripsy.

PURPOSE: We modeled retropulsion during holmium:YAG lithotripsy on the conservation of momentum, whereby the force of ejected fragment debris off of the calculous surface should equal the force of retropulsion displacing the stone. We tested the hypothesis that retropulsion occurs as a result of ejected stone debris. MATERIALS AND METHODS: Uniform calculous phantoms were irradiated with holmium:YAG energy in air and in water. Optical fiber diameter and pulse energy were varied. Motion of the phantom was monitored with high speed video imaging. Laser induced crater volume and geometry were characterized by optical coherence tomography. To determine the direction of plume laser burn paper was irradiated at various incident angles. RESULTS: Retropulsion was greater for phantoms irradiated in air versus water. Retropulsion increased as fiber diameter increased and as pulse energy increased (p <0.001). Crater volumes increased as pulse energy increased (p <0.05) and generally increased as fiber diameter increased. Crater geometry was wide and shallow for larger fibers, and narrow and deeper for smaller fibers. The ejected plume propagated in the direction normal to the burn paper surface regardless of the laser incident angle. CONCLUSIONS: Retropulsion increases as pulse energy and optical fiber diameter increase. Vector analysis of the ejected plume and crater geometry explains increased retropulsion using larger optical fibers. Holmium:YAG lithotripsy should be performed with small optical fibers to limit retropulsion.

Investigation of the transduction mechanism of infrared detection in Melanophila acuminata: photo-thermal-mechanical hypothesis.

Differential phase optical low coherence reflectometry (OLCR) was used to detect sub-wavelength displacements in the infrared-sensitive thoracic pit organ of Melanophila acuminata (Coleoptera: Buprestidae) upon absorption of infrared radiation at 3.39 microm. The displacement had more complex morphology but similar amplitude ( approximately 100 nm at 1 W cm(-2)) when compared to the displacement measured from the exocuticle in an alternate region on the beetle's body. In addition, a simplified finite difference model was developed to predict the temperature distribution and resultant thermal expansion in the pit organ tissue. The experimental and model results were interpreted to help clarify the mechanism by which the sensilla in the pit organ convert infrared radiation to neural signals. The results of this paper are discussed in relation to the photo-thermal-mechanical transduction hypothesis. This is the first experimental examination of the transduction mechanism in Melanophila acuminata.

Are halocarboranes suitable for substitution reactions? The case for 3-I-1,2-closo-C(2)B(10)H(11): molecular orbital calculations, aryldehalogenation reactions, (11)B NMR interpretation of closo-carboranes, and molecular structures of 1-Ph-3-Br-1,2-closo-C(2)B(10)H(10) and 3-Ph-1,2-closo-C(2)B(10)H(11).

In this paper, the chemistry of 3-X-1,2-closo-C(2)B(10)H(11) (X = halogen) derivatives is extended. Molecular orbital and (11)B and (13)C NMR calculations on these species are presented. A qualitative interpretation of the (11)B NMR spectra of closo o-carborane derivatives is also provided. The synthesis of 3-X-1-R-o-carborane (X = I, Br and R = Me, Ph) derivatives is reported, and aryldehalogenation at the B3 position is reported for the first time. The molecular and crystal structures of 1-phenyl-3-bromo-1,2-dicarba-closo-dodecaborane and 3-phenyl-1,2-dicarba-closo-dodecaborane are described.

Analysis of thermal relaxation during laser irradiation of tissue.

BACKGROUND AND OBJECTIVE: Thermal relaxation time (tau(r)) is a commonly-used parameter for estimating the time required for heat to conduct away from a directly-heated tissue region. Previous studies have demonstrated that temperature superposition can occur during multiple-pulse irradiation, even if the interpulse time is considerably longer than tau(r). The objectives of this study were (1) to analyze tissue thermal relaxation following laser-induced heating, and (2) to calculate the time required for a laser-induced temperature rise to decrease to near-baseline values. STUDY DESIGN/MATERIALS AND METHODS: One-dimensional (1-D) analytical and numerical and 2-D numerical models were designed and used for calculations of the time tau(eff) required for the peak temperature (T(peak)) to decrease to values slightly over baseline (DeltaT(base)). Temperature values included T(peak)=65 and 100 degrees C, and DeltaT(base) = 5, 10, and 20 degrees C. To generalize the calculations, a wide range of optical and thermal properties was incorporated into the models. Flattop and gaussian spatial beam profiles were also considered. RESULTS: 2-D model calculations of tau(eff) demonstrated that tau(eff) (2-D) was as much as 40 times longer than tau(r). For a given combination of T(peak) and DeltaT(base), a linear relationship was calculated between tau(eff) (1-D) and tau(r) and was independent of optical and thermal properties. A comparison of 1-D and 2-D models demonstrated that 1-D models generally predicted longer values of tau(eff) than those predicted with a 2-D geometry when the laser spot diameter was equal to or less than the optical penetration depth. CONCLUSION: Relatively simple calculations can be performed to estimate tau(eff) for known values of tau(r), T(peak) and DeltaT(base). The parameter tau(eff) may be a better estimate than tau(r) of tissue thermal relaxation during multiple-pulse laser irradiation.