nils-herrmann/clean_scirepeval huggingface dataset:
Helminths and the IBD hygiene hypothesis
Venue: Inflammatory Bowel Diseases

&NA; Helminths are parasitic animals that have evolved over 100,000,000 years to live in the intestinal track or other locations of their hosts. Colonization of humans with these organisms was nearly universal until the early 20th century. More than 1,000,000,000 people in less developed countries carry helminths even today. Helminths must quell their host's immune system to successfully colonize. It is likely that helminths sense hostile changes in the local host environment and take action to control such responses. Inflammatory bowel disease (IBD) probably results from an inappropriately vigorous immune response to contents of the intestinal lumen. Environmental factors strongly affect the risk for IBD. People living in less developed countries are protected from IBD. The “IBD hygiene hypothesis” states that raising children in extremely hygienic environments negatively affects immune development, which predisposes them to immunological diseases like IBD later in life. Modern day absence of exposure to intestinal helminths appears to be an important environmental factor contributing to development of these illnesses. Helminths interact with both host innate and adoptive immunity to stimulate immune regulatory circuitry and to dampen effector pathways that drive aberrant inflammation. The first prototype worm therapies directed against immunological diseases are now under study in the United States and various countries around the world. Additional studies are in the advanced planning stage.
Effect of natural root grafting on growth response of jack pine (Pinus banksiana; Pinaceae).
Venue: American Journal of Botany

Trees are traditionally considered as distinct entities even though they can share a communal root system through root grafts, which are morphological unions between two or more roots. Little is known regarding the ecological significance of natural root grafting, but because grafted trees can share resources and secondary compounds, growth of linked trees can be affected directly by the presence of root grafts. Traditional forest ecology concepts may have to be revised to include direct interactions between connected trees.



We hydraulically excavated six 30-50-m(2) plots (three natural stands and three plantations). We measured yearly radial growth and determined the influence of root grafting on radial growth of grafted trees.



During periods of root graft formation, root grafting tended to reduce radial growth of jack pine trees, after which growth generally increased. The influence of root grafting on growth was more significant in natural stands, where root grafting was more frequent than in plantations.



These results suggest that root grafting initially is an energetically costly process but that it is afterward nonprejudicial and maybe beneficial to tree growth. The use of a communal root system allows for a maximum use of resources by redistributing them among trees, leading to increased tree growth.
Nuthatches eavesdrop on variations in heterospecific chickadee mobbing alarm calls
Venue: Proceedings of the National Academy of Sciences of the United States of America

Many animals recognize the alarm calls produced by other species, but the amount of information they glean from these eavesdropped signals is unknown. We previously showed that black-capped chickadees (Poecile atricapillus) have a sophisticated alarm call system in which they encode complex information about the size and risk of potential predators in variations of a single type of mobbing alarm call. Here we show experimentally that red-breasted nuthatches (Sitta canadensis) respond appropriately to subtle variations of these heterospecific “chick-a-dee” alarm calls, thereby evidencing that they have gained important information about potential predators in their environment. This study demonstrates a previously unsuspected level of discrimination in intertaxon eavesdropping.
The role of granules within viscous capture threads of orb-weaving spiders
Venue: The Journal of Experimental Biology

Sticky viscous prey capture threads form the spiral elements of spider orb-webs and are responsible for retaining insects that strike a web. These threads are formed of regularly spaced aqueous droplets that surround a pair of supporting axial fibers. When a thread is flattened on a microscope slide a small, opaque granule can usually be seen within each droplet. These granules have been thought to be the glycoprotein glue that imparts thread adhesion. Both independent contrast and standard regressions showed that granule size is directly related to droplet volume and indicated that granule volume is about 15% of droplet volume. We attempted to find support for the hypothesized adhesive role of granules by establishing an association between the contact surface area and volume of these granules and the stickiness of the viscous threads of 16 species in the context of a six-variable model that describes thread stickiness. However, we found that granule size made either an insignificant or a small negative contribution to thread stickiness. Consequently, we hypothesize that granules serve to anchor larger, surrounding layers of transparent glycoprotein glue to the axial fibers of the thread, thereby equipping droplets to resist slippage on the axial fibers as these droplets generate adhesion, elongate under a load, and transfer force to the axial fibers.
Rethinking the value of high wood density
Venue: Functional Ecology

Current thinking holds that wood density mediates a tradeoff between strength and economy of construction, with higher wood density providing higher strength but at higher cost. 2. Yet the further away wood fibres are from the central axis of the trunk, the more they increase the strength of the trunk; thus, a fat trunk of low-density wood can achieve greater strength at lower construction cost than a thin trunk of high-density wood. 3. What then are the countervailing advantages of high wood density? 4. We hypothesize that high wood density is associated with lower maintenance costs due to lower trunk surface area, as surface area correlates with maintenance respiration. 5. This advantage would be particularly important to long-lived trees and could in part explain why they tend to have high wood density. 6. High wood density has also been associated with lower risk of trunk breakage, xylem implosion and pathogen invasion, but we argue that these relationships are not causal and instead reflect correlated selection on other traits of value to long-lived trees. 7. This revaluation of the costs and benefits of high wood density has important implications for understanding tree life-history evolution, functional diversity, forest carbon stocks and the impacts of global change.
The echinoderm collagen fibril: a hero in the connective tissue research of the 1990s
Venue: BioEssays

Collagen fibrils are some of the most‐abundant and important extracellular structures in our bodies, yet we are unsure of their shape and size. This is largely due to an inherent difficulty in isolating them from their surrounding tissues. Echinoderms have collagenous tissues that are similar to ours in many ways, yet they can be manipulated to easily relinquish their collagen fibrils, providing an excellent opportunity to study native fibrillar structure. In the early 1990s, they were found to defy the commonly accepted fibrillar model of the time in that they were much shorter, they were shaped like double‐ended spindles, and their centers exhibited a reversal in molecular polarity. Realization of these features helped to reform the questions that were being asked about vertebrate fibrils, shifting the focus toward shape and size. Since then, researchers working with both groups (echinoderms and vertebrates) have worked together to find the structure of native fibrils. This information will be fundamental in understanding what holds collagenous tissues together at the fibrillar level, and could have important implications for people with Ehlers‐Danlos syndrome. BioEssays 29:645–653, 2007.
Implications of the mesophyll conductance to CO2 for photosynthesis and water-use efficiency during long-term water stress and recovery in two contrasting Eucalyptus species.
Venue: Plant Cell and Environment

Water stress (WS) slows growth and photosynthesis (A(n)), but most knowledge comes from short-time studies that do not account for longer term acclimation processes that are especially relevant in tree species. Using two Eucalyptus species that contrast in drought tolerance, we induced moderate and severe water deficits by withholding water until stomatal conductance (g(sw)) decreased to two pre-defined values for 24 d, WS was maintained at the target g(sw) for 29 d and then plants were re-watered. Additionally, we developed new equations to simulate the effect on mesophyll conductance (g(m)) of accounting for the resistance to refixation of CO(2). The diffusive limitations to CO(2), dominated by the stomata, were the most important constraints to A(n). Full recovery of A(n) was reached after re-watering, characterized by quick recovery of gm and even higher biochemical capacity, in contrast to the slower recovery of g(sw). The acclimation to long-term WS led to decreased mesophyll and biochemical limitations, in contrast to studies in which stress was imposed more rapidly. Finally, we provide evidence that higher gm under WS contributes to higher intrinsic water-use efficiency (iWUE) and reduces the leaf oxidative stress, highlighting the importance of gm as a target for breeding/genetic engineering.
Evidence for an elastic projection mechanism in the chameleon tongue
Venue: Proceedings of The Royal Society B: Biological Sciences

To capture prey, chameleons ballistically project their tongues as far as 1.5 body lengths with accelerations of up to 500 m s⊃–2. At the core of a chameleon's tongue is a cylindrical tongue skeleton surrounded by the accelerator muscle. Previously, the cylindrical accelerator muscle was assumed to power tongue projection directly during the actual fast projection of the tongue. However, high–speed recordings of Chamaeleo melleri and C. pardalis reveal that peak powers of 3000 W kg⊃–1 are necessary to generate the observed accelerations, which exceed the accelerator muscle's capacity by at least five– to 10–fold. Extrinsic structures might power projection via the tongue skeleton. High–speed fluoroscopy suggests that they contribute less than 10% of the required peak instantaneous power. Thus, the projection power must be generated predominantly within the tongue, and an energy–storage–and–release mechanism must be at work. The key structure in the projection mechanism is probably a cylindrical connective–tissue layer, which surrounds the entoglossal process and was previously suggested to act as lubricating tissue. This tissue layer comprises at least 10 sheaths that envelop the entoglossal process. The outer portion connects anteriorly to the accelerator muscle and the inner portion to the retractor structures. The sheaths contain helical arrays of collagen fibres. Prior to projection, the sheaths are longitudinally loaded by the combined radial contraction and hydrostatic lengthening of the accelerator muscle, at an estimated mean power of 144 W kg⊃–1 in C. melleri. Tongue projection is triggered as the accelerator muscle and the loaded portions of the sheaths start to slide over the tip of the entoglossal process. The springs relax radially while pushing off the rounded tip of the entoglossal process, making the elastic energy stored in the helical fibres available for a simultaneous forward acceleration of the tongue pad, accelerator muscle and retractor structures. The energy release continues as the multilayered spring slides over the tip of the smooth and lubricated entoglossal process. This sliding–spring theory predicts that the sheaths deliver most of the instantaneous power required for tongue projection. The release power of the sliding tubular springs exceeds the work rate of the accelerator muscle by at least a factor of 10 because the elastic–energy release occurs much faster than the loading process. Thus, we have identified a unique catapult mechanism that is very different from standard engineering designs. Our morphological and kinematic observations, as well as the available literature data, are consistent with the proposed mechanism of tongue projection, although experimental tests of the sheath strain and the lubrication of the entoglossal process are currently beyond our technical scope.
Magnetoreception System in Honeybees (Apis mellifera)
Venue: PLOS ONE

Honeybees (Apis mellifera) undergo iron biomineralization, providing the basis for magnetoreception. We showed earlier the presence of superparamagnetic magnetite in iron granules formed in honeybees, and subscribed to the notion that external magnetic fields may cause expansion or contraction of the superparamagnetic particles in an orientation-specific manner, relaying the signal via cytoskeleton (Hsu and Li 1994). In this study, we established a size-density purification procedure, with which quantitative amount of iron granules was obtained from honey bee trophocytes and characterized; the density of iron granules was determined to be 1.25 g/cm3. While we confirmed the presence of superparamagnetic magnetite in the iron granules, we observed changes in the size of the magnetic granules in the trophycytes upon applying additional magnetic field to the cells. A concomitant release of calcium ion was observed by confocal microscope. This size fluctuation triggered the increase of intracellular Ca+2 , which was inhibited by colchicines and latrunculin B, known to be blockers for microtubule and microfilament syntheses, respectively. The associated cytoskeleton may thus relay the magnetosignal, initiating a neural response. A model for the mechanism of magnetoreception in honeybees is proposed, which may be applicable to most, if not all, magnetotactic organisms.
The structural basis of water permeation and proton exclusion in aquaporins (Review)
Venue: Molecular Membrane Biology

Aquaporins (AQPs) represent a ubiquitous class of integral membrane proteins that play critical roles in cellular osmoregulations in microbes, plants and mammals. AQPs primarily function as water-conducting channels, whereas members of a sub-class of AQPs, termed aquaglyceroporins, are permeable to small neutral solutes such as glycerol. While AQPs facilitate transmembrane permeation of water and/or small neutral solutes, they preclude the conduction of protons. Consequently, openings of AQP channels allow rapid water diffusion down an osmotic gradient without dissipating electrochemical potentials. Molecular structures of AQPs portray unique features that define the two central functions of AQP channels: effective water permeation and strict proton exclusion. This review describes AQP structures known to date and discusses the mechanisms underlying water permeation, proton exclusion and water permeability regulation.
POSITIVE AND NEGATIVE EFFECTS OF ORGANISMS AS PHYSICAL ECOSYSTEM ENGINEERS
Venue: Ecology

Physical ecosystem engineers are organisms that directly or indirectly control the availability of resources to other organisms by causing physical state changes in biotic or abiotic materials. Physical ecosystem engineering by organisms is the physical modification, maintenance, or creation of habitats. Ecological effects of engineers on many other species occur in virtually all ecosystems because the physical state changes directly create nonfood resources such as living space, directly control abiotic resources, and indirectly modulate abiotic forces that, in turn, affect resource use by other organisms. Trophic interactions and resource competition do not constitute engineering. Engineering can have significant or trivial effects on other species, may involve the physical structure of an organism (like a tree) or structures made by an organism (like a beaver dam), and can, but does not invariably, have feedback effects on the engineer. We argue that engineering has both negative and positive effects on species richness and abundances at small scales, but the net effects are probably positive at larger scales encompassing engineered and nonengineered environments in ecological and evolutionary space and time. Models of the population dynamics of engineers suggest that the engineer/habitat equilibrium is often, but not always, locally stable and may show long-term cycles, with potential ramifications for community and ecosystem stability. As yet, data adequate to parameterize such a model do not exist for any engineer species. Because engineers control flows of energy and materials but do not have to participate in these flows, energy, mass, and stoichiometry do not appear to be useful in predicting which engineers will have big effects. Empirical observations suggest some potential generalizations about which species will be important engineers in which ecosystems. We point out some of the obvious, and not so obvious, ways in which engineering and trophic relations interact, and we call for greater research on physical ecosystem engineers, their impacts, and their interface with trophic relations.
Blue luminescence of ripening bananas.
Venue: Angewandte Chemie

As revealed in the last two decades, chlorophyll breakdown in senescent leaves appears to occur by a largely common and well-controlled catabolic path, which rapidly furnishes non-fluorescent, colorless chlorophyll catabolites (NCCs) as “final” products.[1,2] Recently NCCs detected in ripe apples and pears were found to be the same as those in degreened leaves, suggesting chlorophyll catabolism in leaf senescence and fruit ripening to be similar (Scheme 1).[3,4]
Contributions of feather microstructure to eider down insulation properties
Venue: Journal of Avian Biology

Insulation is an essential component of nest structure that helps provide incubation requirements for birds. Many species of waterfowl breed in high latitudes where rapid heat loss can necessitate a high energetic input from parents and use down feathers to line their nests. Common eider Somateria mollissima nest down has exceptional insulating properties but the microstructural mechanisms behind the feather properties have not been thoroughly examined. 
 
Here, we hypothesized that insulating properties of nest down are correlated to down feather (plumule) microstructure. We tested the thermal efficiency (fill power) and cohesion of plumules from nests of two Icelandic colonies of wild common eiders and compared them to properties of plumules of wild greylag goose Anser anser. We then used electron microscopy to examine the morphological basis of feather insulating properties. We found that greylag goose down has higher fill power (i.e. traps more air) but much lower cohesion (i.e. less prone to stick together) compared to common eider down. These differences were related to interspecific variation in feather microstructure. Down cohesion increased with the number of barbule microstructures (prongs) that create strong points of contact among feathers. Eider down feathers also had longer barbules than greylag goose down feathers, likely increasing their air-trapping capacity. Feather properties of these two species might reflect the demands of their contrasting evolutionary history. In greylag goose, a temperate, terrestrial species, plumule microstructure may optimize heat trapping. In common eiders, a diving duck that nests in arctic and subarctic waters, plumule structure may have evolved to maximize cohesion over thermal insulation, which would both reduce buoyancy during their foraging dives and enable nest down to withstand strong arctic winds.
²⁶Mg labeling of the sea urchin regenerating spine: Insights into echinoderm biomineralization process.
Venue: Journal of Structural Biology

This paper reports the results of the first dynamic labeling experiment with regenerating spines of sea urchins Paracentrotus lividus using the stable isotope ²⁶Mg and NanoSIMS high-resolution isotopic imaging, which provide a direct information about the growth process. Growing spines were labeled twice (for 72 and 24 h, respectively) by increasing the abundance of ²⁶Mg in seawater. The incorporation of ²⁶Mg into the growing spines was subsequently imaged with the NanoSIMS ion microprobe. Stereom trabeculae initially grow as conical micro-spines, which form within less than 1 day. These micro-spines fuse together by lateral outgrowths and form a thin, open meshwork (inner stereom), which is subsequently reinforced by addition of layered thickening deposits (outer stereom). The (longitudinal) growth rate of the inner stereom is ca. 125 μm/day. A single (ca. 1 μm) thickening layer in the stereom trabeculae is deposited during 24h. The thickening process is contemporaneous with the formation micro-spines and involves both longitudinal trabeculae and transverse bridges to a similar degree. Furthermore, the skeleton-forming cells remain active in the previously formed open stereom for at least 10 days, and do not migrate upwards until the end of the thickening process. The experimental capability presented here provides a new way to obtain detailed information about the skeleton formation of a multitude of marine, calcite producing organisms.
Microbiology of the Oil Fly, Helaeomyia petrolei
Venue: Applied and Environmental Microbiology

Helaeomyia petrolei larvae isolated from the asphalt seeps of Rancho La Brea in Los Angeles, Calif., were examined for microbial gut contents. Standard counts on Luria-Bertani, MacConkey, and blood agar plates indicated ca. 2 × 105 heterotrophic bacteria per larva. The culturable bacteria represented 15 to 20% of the total population as determined by acridine orange staining. The gut itself contained large amounts of the oil, had no observable ceca, and maintained a slightly acidic pH of 6.3 to 6.5. Despite the ingestion of large amounts of potentially toxic asphalt by the larvae, their guts sustained the growth of 100 to 1,000 times more bacteria than did free oil. All of the bacteria isolated were nonsporeformers and gram negative. Fourteen isolates were chosen based on representative colony morphologies and were identified by using the Enterotube II and API 20E systems and fatty acid analysis. Of the 14 isolates, 9 were identified as Providencia rettgeriand 3 were likely Acinetobacter isolates. No evidence was found that the isolates grew on or derived nutrients from the asphalt itself or that they played an essential role in insect development. Regardless, any bacteria found in the oil fly larval gut are likely to exhibit pronounced solvent tolerance and may be a future source of industrially useful, solvent-tolerant enzymes.