nils-herrmann/clean_scirepeval huggingface dataset:
Biodegradation of Fluoranthene by Basidiomycetes Fungal Isolate Pleurotus Ostreatus HP-1
Venue: Applied Biochemistry and Biotechnology

The biodegradation of fluoranthene, a high molecular weight polycyclic aromatic hydrocarbon (PAH), was investigated in submerged culture using the wood decaying fungus isolated from forest locality in Gujarat, India. The basidiomycete fungal isolate was found to have an ability to grow on sabaroud dextrose agar containing 50 mgl−1 of each naphthalene, anthracene, acenaphthene, benzo (a) anthracene, pyrene, flouranthene, carbazole, and biphenyl. The involvement of extracellular fungal peroxidases such as manganese peroxidase (MnP) and laccase (Phenol oxidase) in the degradation of fluoranthene was studied. On the eighth day of incubation 54.09% of 70 mg l−1 fluoranthene was removed. There after no PAHs removal was observed till the 20th day of the incubation period. The isolate was identified as Pleurotus ostreatus by 18S rRNA, 5.8S rRNA, and partial 28S rRNA gene sequencing. To the best of our knowledge this is the first time Pleurotus ostreatus have been reported to degrade such a high concentration of fluoranthene within much lower time period of incubation. Depletion in the residual fluoranthene in the culture medium was determined by HPLC. Attempts were made to identify the degradation product in the culture medium with the help of FT-IR, NMR, and HPTLC analysis. In the present study positive correlation between fluoranthene degradation and the ligninolytic enzyme (MnP and laccase) production is observed, thus this isolate can play an effective role for bioremediation of PAHs contaminated sites.
Arapaima Fish Scale: One of the Toughest Flexible Biological Materials
Venue: Matter

For fish scales to provide protection from predators without severely compromising mobility, they must be lightweight, flexible, and tough. The arapaima fish scale is a superb example of this, enabling its survival in piranha-infested lakes of the Amazon. These elasmoid scales comprise two layers: a laminate composite of parallel collagen fibrils arranged in a Bouligand-like pattern and a highly mineralized surface layer that prevents initial penetration damage. Here, we measure its J-integral fracture toughness and find that the crack-growth toughness is ∼100–200 kJ⋅m−2, representing a very high fracture resistance for a natural material. This toughness results from multiple deformation mechanisms acting in concert in the twisted plywood structure of the scale, involving the collagenous lamellae at varying orientations retarding crack advance through stretching, reorientation, delamination and shear, and fracture. The toughness values obtained for the arapaima scales indicate that they are among the toughest of nature's flexible biological materials.
Intestinal Myiasis Caused by Eristalis tenax
Venue: Journal of Clinical Microbiology

Myiasis is the infestation of live humans and other vertebrate animals with dipterous larvae which, at least for a certain period, feed on the host’s dead or living tissue, liquid body substances, or ingested food ([3][1]). Clinically, myiasis may be classified as cutaneous, atrial, wound,
Uptake of Water by the Lizard, Moloch horridus
Venue: Nature

Moloch horridusis an agamid lizard living in the desert regions of Western and South Australia. It weighs as much as 50 gm. and has been described by Buxton1 as “a repulsive animal with tubercles and spines, it has the power of absorbing water through the skin after showers of rain”. This ability of absorbing water through the skin is characteristic of many Amphibia and is correlated with a ready loss of water by the same route2. Reptiles living in arid conditions would find a water-permeable skin uneconomical for water conservation so that this mode of taking up water may be questioned for Moloch.
Aerodynamic force generation, performance and control of body orientation during gliding in sugar gliders (Petaurus breviceps)
Venue: The Journal of Experimental Biology

Gliding has often been discussed in the literature as a possible precursor to powered flight in vertebrates, but few studies exist on the mechanics of gliding in living animals. In this study I analyzed the 3D kinematics of sugar gliders (Petaurus breviceps) during short glides in an enclosed space. Short segments of the glide were captured on video, and the positions of marked anatomical landmarks were used to compute linear distances and angles, as well as whole body velocities and accelerations. From the whole body accelerations I estimated the aerodynamic forces generated by the animals. I computed the correlations between movements of the limbs and body rotations to examine the control of orientation during flight. Finally, I compared these results to those of my earlier study on the similarly sized and distantly related southern flying squirrel (Glaucomys volans). The sugar gliders in this study accelerated downward slightly (1.0±0.5 m s–2), and also accelerated forward (2.1±0.6 m s–2) in all but one trial, indicating that the body weight was not fully supported by aerodynamic forces and that some of the lift produced forward acceleration rather than just balancing body weight. The gliders used high angles of attack (44.15±3.12°), far higher than the angles at which airplane wings would stall, yet generated higher lift coefficients (1.48±0.18) than would be expected for a stalled wing. Movements of the limbs were strongly correlated with body rotations, suggesting that sugar gliders make extensive use of limb movements to control their orientation during gliding flight. In addition, among individuals, different limb movements were associated with a given body rotation, suggesting that individual variation exists in the control of body rotations. Under similar conditions, flying squirrels generated higher lift coefficients and lower drag coefficients than sugar gliders, yet had only marginally shallower glides. Flying squirrels have a number of morphological specializations not shared by sugar gliders that may help to explain their greater lift generating performance.
Light-harvesting mechanism of bacteria exploits a critical interplay between the dynamics of transport and trapping.
Venue: Physical Review Letters

Light-harvesting bacteria Rhodospirillum photometricum were recently found to adopt strikingly different architectures depending on illumination conditions. We present analytic and numerical calculations which explain this observation by quantifying a dynamical interplay between excitation transfer kinetics and reaction center cycling. High light-intensity membranes exploit dissipation as a photoprotective mechanism, thereby safeguarding a steady supply of chemical energy, while low light-intensity membranes efficiently process unused illumination intensity by channeling it to open reaction centers. More generally, our analysis elucidates and quantifies the trade-offs in natural network design for solar energy conversion.
Bristled shark skin: a microgeometry for boundary layer control?
Venue: Bioinspiration & Biomimetics

There exists evidence that some fast-swimming shark species may have the ability to bristle their scales during fast swimming. Experimental work using a water tunnel facility has been performed to investigate the flow field over and within a bristled shark skin model submerged within a boundary layer to deduce the possible boundary layer control mechanisms being used by these fast-swimming sharks. Fluorescent dye flow visualization provides evidence of the formation of embedded cavity vortices within the scales. Digital particle image velocimetry (DPIV) data, used to evaluate the cavity vortex formation and boundary layer characteristics close to the surface, indicate increased momentum in the slip layer forming above the scales. This increase in flow velocity close to the shark's skin is indicative of boundary layer control mechanisms leading to separation control and possibly transition delay for the bristled shark skin microgeometry.
Ecological impact of beavers Castor fiber and Castor canadensis and their ability to modify ecosystems
Venue: Mammal Review

The genus Castor comprises two species: the Eurasian beaver Castor fibre , and the North American beaver Castor canadensis . Both species suffered from overexploitation, but have seen a revival since the 1920s due to increased protection and reintroduction programmes. Increases in the populations and distributions of species that are able to modify ecosystems have generated much scientific interest. Here we review the available literature concerning the possible ecological impact of beaver species in the Old and New World. 2. Beavers, being ecosystem engineers, are among the few species besides humans that can significantly change the geomorphology, and consequently the hydrological characteristics and biotic properties of the landscape. In so doing, beavers increase heterogeneity, and habitat and species diversity at the landscape scale. Beaver foraging also has a considerable impact on the course of ecological succession, species composition and structure of plant commu- nities, making them a good example of ecologically dominant species (e.g. keystone species). 3. Nevertheless, the strength of beavers' impact varies from site to site, depending on the geographical location, relief and the impounded habitat type. Consequently, they may not be significant controlling agents of the ecosystem in all parts of their distribution, but have strong interactions only under certain circumstances. We suggest that beavers can create important management opportunities in the Holarctic, and this review will help land man- agers determine the likely outcome of beaver activity.
Induced production of antifungal naphthoquinones in the pitchers of the carnivorous plant Nepenthes khasiana
Venue: Journal of Experimental Botany

Nepenthes spp. are carnivorous plants that have developed insect capturing traps, evolved by specific modification of the leaf tips, and are able to utilize insect degradation products as nutritional precursors. A chitin-induced antifungal ability, based on the production and secretion to the trap liquid of droserone and 5-O-methyldroserone, is described here. Such specific secretion uniquely occurred when chitin injection was used as the eliciting agent and probably reflects a certain kind of defence mechanism that has been evolved for protecting the carnivory-based provision of nutritional precursors. The pitcher liquid containing droserone and 5-O-methyldroserone at 3:1 or 4:1 molar ratio, as well as the purified naphthoquinones, exerted an antifungal effect on a wide range of plant and human fungal pathogens. When tested against Candida and Aspergillus spp., the concentrations required for achieving inhibitory and fungicidal effects were significantly lower than those causing cytotoxicity in cells of the human embryonic kidney cell line, 293T. These naturally secreted 1,4-naphthoquinone derivatives, that are assumed to act via semiquinone enhancement of free radical production, may offer a new lead to develop alternative antifungal drugs with reduced selectable pressure for potentially evolved resistance.
Organic solutes in freezing tolerance.
Venue: Comparative Biochemistry and Physiology Part A: Physiology

The accumulation of high levels of low-molecular-weight solutes (polyhydric alcohols, saccharides) provides cryoprotection to freeze-tolerant animals by minimizing, via colligative effects, the percentage of body water converted to extracellular ice and the extent of cell volume reduction. Many freeze-tolerant insects accumulate high levels of polyols during autumn cold hardening, whereas freeze-tolerant frogs respond to ice formation in peripheral tissues by synthesizing large amounts of glucose in the liver and rapidly distributing the sugar throughout the body. Seasonal patterns of enzymatic change occur in cold-hardy insects; activities associated with cryoprotectant synthesis rise in the fall, whereas enzymes associated with polyol degradation dominate in the spring. Enzyme profiles also revealed the route of glycerol degradation via polyol dehydrogenase and the novel enzyme, glyceraldehyde kinase. Proton magnetic resonance imaging of freezing and thawing in whole frogs showed a new adaptive effect of the very high glucose levels in core organs; during thawing, organs such as liver and heart melted first, allowing recovery of their vital functions to begin while the rest of the frog thawed. New studies have examined signal transduction in the stimulation of glucose production by wood frog liver, revealing the key role of beta-adrenergic receptors and cAMP-mediated activation of glycogenolysis for cryoprotectant synthesis. The seasonal elevation of plasma membrane glucose transporters was also shown to be key to cryoprotectant distribution during freezing. Other new work has shown that frog freeze tolerance probably grew out of preexisting mechanisms of amphibian dehydration tolerance and that both freeze-tolerant and -intolerant frogs show a hyperglycemic response to desiccation at 5 degrees C.
Current challenges in traditional design verification and its application in flip-chip devices
Venue: International Electronics Manufacturing Technology Symposium

The acceleration of new developments in semiconductor design and manufacturing technology in keeping up with Moore's Law has introduced significant new challenges for device designers as well as manufacturing organizations. Short channel effects, multi-level interconnect cross talk problems, and new materials such as low K dielectric, copper, and silicon on insulator have made modeling and simulation of semiconductor devices and processes extremely difficult. Many times this results in failure to meet performance targets in first silicon introduction. The high cost of mask sets, together with the opportunity costs related to time-to-market, drives the need for shorter and fewer redesign cycles, making effective transistor level design debug a necessity. To make things even more difficult, the transition to flip chip packaging and multiple interconnect metal layers makes backside probing the only effective way to perform node level analysis. This paper describes these new challenges in detail, and the use of photon probing technology as an effective way to address them. The use of a time resolved photon emission microscope allows measuring performance at the critical node level. This is done by collecting the photons, emitted by carriers that are accelerated in the pinch off region during CMOS transistor switching. This enables optimization of device speed paths, and resolution of problems such as race conditions and contentions, encountered during design debug and failure analysis cycles.
Chemical niche differentiation among sympatric species of orchid bees.
Venue: Ecology

Male Neotropical orchid bees (Euglossini) collect volatile substances (fragrances) from flowers and other sources (e.g., decaying wood) and store them in specialized hind tibial pockets. The accumulated chemicals are later emitted during courtship display, presumably to lure conspecific females for mating. We analyzed tibial fragrances of males of 15 sympatric Panamanian species in the genus Euglossa to test whether communities of euglossine bees are chemically structured, and to elucidate whether male fragrance signals evolve to convey premating isolation. Our analysis revealed substantial chemical disparity among all lineages. Disparity was mediated by compounds that were exclusive to certain species but also by differences in relative quantity of shared compounds. We mapped tibial fragrance compounds present in each species on a DNA-based phylogeny (reconstructed using partial sequences of COI, EF1-alpha, ArgK, and Pol-II) and found that most dominant compounds were highly homoplasious. In an analysis of chemical differentiation in relation to phylogenetic divergence through time, disparity was greater than expected from a null model at any point during evolutionary history, suggesting that diversifying selection has shaped fragrance phenotypes. Notably, chemical disparity was greater within recently diverged lineages than among them, suggesting that chemical preferences in orchid bees evolved rapidly in the early stages of species divergence. We postulate communication interference as the possible mechanism behind the observed fragrance differentiation, which may be the product of reproductive character (fragrance) displacement. Our findings are consistent with the hypothesis that male fragrance signals evolve to convey premating isolation.
Do desert ants smell the scenery in stereo?
Venue: Animal Behaviour

Desert ants, Cataglyphis fortis, navigate individually in the inhospitable saltpans of Tunisia using path integration for long-distance navigation, and visual and olfactory landmarks for fine-scale orientation in the vicinity of the nest entrance. Here, we show in a field experiment that the ants are able to locate the nest entrance within a two-dimensional olfactory array. Ants were trained to forage in an open channel and to memorize the nest entrance relative to four odours that were applied at the corners of an invisible quadratic array. In a test situation, the ants pinpointed the fictive nest only when the odours were present at their learned positions. Our results suggest that the ants had learned the olfactory scenery around their nest. Furthermore, unilaterally antennectomized ants could not pinpoint the nest within a two-dimensional array. Hence, this kind of orientation depends on the simultaneous input of both antennae, that is, on a stereo sense of smell. Until now, insects and mammals, including humans, have only been known to use bilateral sensory input to follow a concentration gradient of an odour. Our evidence suggests that desert ants require a stereo sense of smell to make use of the olfactory scenery around their nest for homing.
Sidewinding with minimal slip: Snake and robot ascent of sandy slopes
Venue: Science

Limbless organisms such as snakes can navigate nearly all terrain. In particular, desert-dwelling sidewinder rattlesnakes (Crotalus cerastes) operate effectively on inclined granular media (such as sand dunes) that induce failure in field-tested limbless robots through slipping and pitching. Our laboratory experiments reveal that as granular incline angle increases, sidewinder rattlesnakes increase the length of their body in contact with the sand. Implementing this strategy in a physical robot model of the snake enables the device to ascend sandy slopes close to the angle of maximum slope stability. Plate drag experiments demonstrate that granular yield stresses decrease with increasing incline angle. Together, these three approaches demonstrate how sidewinding with contact-length control mitigates failure on granular media. Robots based on sidewinder rattlesnakes are used to understand motion on sloped granular terrain.
Cellular and molecular biology of the aquaporin water channels.
Venue: Annual Review of Biochemistry

The high water permeability characteristic of mammalian red cell membranes is now known to be caused by the protein AQP1. This channel freely permits movement of water across the cell membrane, but it is not permeated by other small, uncharged molecules or charged solutes. AQP1 is a tetramer with each subunit containing an aqueous pore likened to an hourglass formed by obversely arranged tandem repeats. Cryoelectron microscopy of reconstituted AQP1 membrane crystals has revealed the three-dimensional structure at 3-6 A. AQP1 is distributed in apical and basolateral membranes of renal proximal tubules and descending thin limbs as well as capillary endothelia. Ten mammalian aquaporins have been identified in water-permeable tissues and fall into two groupings. Orthodox aquaporins are water-selective and include AQP2, a vasopressin-regulated water channel in renal collecting duct, in addition to AQP0, AQP4, and AQP5. Multifunctional aquaglyceroporins AQP3, AQP7, and AQP9 are permeated by water, glycerol, and some other solutes. Aquaporins are being defined in numerous other species including amphibia, insects, plants, and microbials. Members of the aquaporin family are implicated in numerous physiological processes as well as the pathophysiology of a wide range of clinical disorders.
The physical state of water in bacterial spores
Venue: Proceedings of the National Academy of Sciences of the United States of America

The bacterial spore, the hardiest known life form, can survive in a metabolically dormant state for many years and can withstand high temperatures, radiation, and toxic chemicals. The molecular basis of spore dormancy and resistance is not understood, but the physical state of water in the different spore compartments is thought to play a key role. To characterize this water in situ, we recorded the water 2H and 17O spin relaxation rates in D2O-exchanged Bacillus subtilis spores over a wide frequency range. The data indicate high water mobility throughout the spore, comparable with binary protein–water systems at similar hydration levels. Even in the dense core, the average water rotational correlation time is only 50 ps. Spore dormancy therefore cannot be explained by glass-like quenching of molecular diffusion but may be linked to dehydration-induced conformational changes in key enzymes. The data demonstrate that most spore proteins are rotationally immobilized, which may contribute to heat resistance by preventing heat-denatured proteins from aggregating irreversibly. We also find that the water permeability of the inner membrane is at least 2 orders of magnitude lower than for model membranes, consistent with the reported high degree of lipid immobilization in this membrane and with its proposed role in spore resistance to chemicals that damage DNA. The quantitative results reported here on water mobility and transport provide important clues about the mechanism of spore dormancy and resistance, with relevance to food preservation, disease prevention, and astrobiology.
Comparative jet wake structure and swimming performance of salps
Venue: The Journal of Experimental Biology

Salps are barrel-shaped marine invertebrates that swim by jet propulsion. Morphological variations among species and life-cycle stages are accompanied by differences in swimming mode. The goal of this investigation was to compare propulsive jet wakes and swimming performance variables among morphologically distinct salp species (Pegea confoederata, Weelia (Salpa) cylindrica, Cyclosalpa sp.) and relate swimming patterns to ecological function. Using a combination of in situ dye visualization and particle image velocimetry (PIV) measurements, we describe properties of the jet wake and swimming performance variables including thrust, drag and propulsive efficiency. Locomotion by all species investigated was achieved via vortex ring propulsion. The slow-swimming P. confoederata produced the highest weight-specific thrust (T=53 N kg–1) and swam with the highest whole-cycle propulsive efficiency (ηwc=55%). The fast-swimming W. cylindrica had the most streamlined body shape but produced an intermediate weight-specific thrust (T=30 N kg–1) and swam with an intermediate whole-cycle propulsive efficiency (ηwc=52%). Weak swimming performance variables in the slow-swimming C. affinis, including the lowest weight-specific thrust (T=25 N kg–1) and lowest whole-cycle propulsive efficiency (ηwc=47%), may be compensated by low energetic requirements. Swimming performance variables are considered in the context of ecological roles and evolutionary relationships.