Miracle-dz/UniFAR-FTUs huggingface dataset:
THE PALEOBIOLOGICAL IMPLICATIONS OF HERBIVOROUS DINOSAUR COPROLITES FROM THE UPPER CRETACEOUS TWO MEDICINE FORMATION OF MONTANA: WHY EAT WOOD?

Abstract Rare assemblages of woody coprolites from different strata of the Two Medicine Formation provide surprising perspectives on the feeding behavior of Late Cretaceous ornithischian dinosaurs. Most of the irregularly shaped, calcareous specimens are largely composed of fragmented conifer wood (13%–85%) and can be identified as coprolites by the presence of distinctive backfilled dung beetle burrows. The large size (up to 7 L in volume), fibrous contents, and associated bones and eggshell strongly suggest that the source animals at one site were Maiasaura hadrosaurs. The wood-bearing coprolites occur in strata ranging in age from ∼74–80 Ma, revealing a recurring (possibly seasonal) habit of wood ingestion. The preponderance of wood in the specimens and the absence of recognizable small-diameter twig fragments suggest that wood ingestion was intentional—that the coprolite producers had not merely consumed wood inadvertently when feeding on the leaves and bark of terminal branches. Because undegraded wood provides inconsequential nutritive value for vertebrates, it is unlikely that ornithischians would have expended the energy to masticate intact wood for little benefit. Furthermore, patterns of tissue damage in the fecal wood fragments suggest fungal degradation. Thus, the most parsimonious explanation for the high fecal wood content is that the coprolite producers consumed decomposing wood to capitalize on resources released by fungal attack, along with the tissues of the decomposers and associated invertebrate detritivores. These multiple coprolite deposits provide direct fossil evidence of recurring dinosaur diets and suggest that some ornithischians at least occasionally tapped detrital resources. Although such feeding behavior is rare in large extant herbivores, utilization of rotting wood would have augmented the resource options of Cretaceous ecosystems that lacked fodder provided by grasses and other derived angiosperms.
Molecular characterization of ancient algal mats from the McMurdo Dry Valleys, Antarctica

Abstract The McMurdo Dry Valleys possess a cold and dry climate which favours biomolecular preservation, and present the possibility for preservation of biological materials over long timescales. We examined patterns of bacterial DNA abundance and diversity in algal mats from 8–26 539 years of age. Bacterial DNA abundance was inferred from extractable DNA quantity and quantitative polymerase chain reaction targeting the bacterial 16S rRNA gene. Because damage to bacterial DNA could limit its availability for polymerase chain reaction, the efficacy of DNA repair by a commercially available kit was also examined. Polymerase chain reaction amplicons of the bacterial 16S rRNA gene were obtained from seven of eight samples. Bulk DNA abundance and bacterial 16S rRNA gene copy number of template DNA declined with increasing sample age consistent with expectations of accumulation of DNA damage in ancient materials. Clone libraries revealed age related patterns of abundance for some bacterial phylogenetic groups. For example, Firmicutes and several other lineages were abundant in ancient samples, but Cyanobacteria were absent. This points to a biased persistence of bacterial lineages that change over time since photosynthesis was active.
Editorial

There is no single moment within the social process devoid of the capacity for transformative activity – a new imaginary; a new discourse arising out of some peculiar hybrid of others; new rituals or institutional configurations; new modes of social relating; new material practices and bodily experiences; new political power relations arising out of their internalised contradictions.Each and every one of these moments is full to the brim with transformative potentialities.
What is the effect of climate change on marine fish biodiversity in an area of low connectivity, the Baltic Sea?

Aim Climate change could result in an increase in species richness because large-scale biogeography suggests that more species could be gained from equatorial regions than may be lost pole-ward. However, the colonization of newly available habitat may lag behind the rate dictated by climatic warming if there exists of a lack of connectivity between ‘donor’ and receiving areas. The objective of this study was to compare how regional warming affected the biodiversity of marine fish in areas that differed in their connectivity in the Baltic Sea. Location North-east Atlantic, Kattegat and Baltic Sea. Methods The total species richness and the mean species richness from scientific surveys were related to changes in temperature and salinity. Changes in the extent of the distribution of individual fish species were related to the latitudinal distribution, salinity tolerance, maximum body size and exploitation status to assess to what extent climate change and fishing impacts could explain changes in species richness in the Baltic. Results Rising temperatures in the well-connected Kattegat correlated to an increase in the species richness of fish, due to an increase in low-latitude species. Unexpectedly, species richness in the poorly connected Baltic Sea also increased. However, the increase seems to be related to higher salinity rather than temperature and there was no influx of low-latitude species. Main conclusions These results do not support the hypothesis that low-connectivity areas are less likely to see increases in species richness in response to warming. This indicates that the effect of climate change on biodiversity may be more difficult to predict in areas of low connectivity than in well-connected areas.
Fish Assemblage Variability in a Florida Spring

Abstract Florida springs are generally characterized as static ecosystems with unique faunal and floral assemblages that persist under relatively stable physical and chemical conditions. We sampled the fish fauna of Volusia Blue Spring to determine whether this presumption would withstand scrutiny at a higher temporal resolution and over time. We sampled by seining or snorkeling at five stations along the 320-m run weekly or bimonthly from October 2000 to September 2004. This four-year study consisted of 1152 samples that produced approximately 164,000 observations of 30 species of fish on 72 sampling trips. Concurrent water quality samples were collected at 14 sites along the center of the run and at each of the seine sites. Virtually anoxic water discharged from the spring head, but this water accumulated oxygen as it traveled the run. Fish density and species composition also changed dramatically along the length of the run. Species that tolerate low oxygen concentrations, such as poeciliids, dominated the assemblage at the spring head. Species that use patches of algae or small backwater areas, such as fundulids, were prominent in the middle reach of the run. Larger species, such as centrarchids and Lepisosteus spp. , were abundant in the lower reach of the run. Within these broad patterns, most species exhibited great variability in density, probably due to the influence of variable emigration of potential predators, and also perhaps smaller species, from the St. Johns River.
Cell Division and Expansion in the Growth of the Shoot Apex

The number and the total volume of cells produced in small portions of the apical region of the shoot have been measured at different stages of development. In non-vernalized seedlings of winter rye, grown in July, the cells in the portions examined divided about once every i-8 days during the first week of growth, and there was about a 2-2-fold increase in the volume of each cell genera tion. Four weeks later the apices were still vegetative, but the rate of division in the portions then examined had fallen to once every 5-8 days and there was slightly less than a 2 2-fold increase in the volume of each generation. The average cell volume decreased as the apices developed. In vernalized seedlings more cells were produced in unit time during the first 4 days of growth than in non-vernalized seedlings, but, as in the latter, the rate of production fell during vegetative development. The rate of cell expansion in the vernalized seedlings was probably slightly lower than in the non-vernalized seed lings during the first 4 days of growth and tended to increase during vegetative development. At the time of transition to reproductive growth the cells were dividing about once every 2-0 days and there was about a 2 2-fold increase in the volume of each succeeding generation. After transition the rates increased. From 4 to 8 days after transition the cells divided once every 1-4 days and there was then a 2 4-fold increase in the volume of each succeeding generation. Subsequently, the rate of division changed little but the rate of expansion decreased. Higher rates of division and expansion were found in the apices of lupin seed lings grown in July than in November. In the portions of the meristem examined during the first 5 days of growth the cells divided about once every 1-3 days in July, but only once every i-8 days in November. The increase in volume of each generation in the same time was slightly higher in July than in November. Both the rates of division and expansion decreased until transition to reproductive growth occurred, and then increased. About 5 days after transition the cells divided once every 1 -4 days in July and once every 2-0 days in November. In both experiments there was a 2 4-fold increase in the volume of each generation. Both the rates of division and expansion decreased subsequently. The data are discussed in relation to the changes in size which accompany the development of the shoot apex.
The amino‐acid composition of processed bones and meat

Quantitative amino-acid analyses were made by ion-exchange chromatography on two samples of commercial feeding meals containing high contents of meat and bone, respectively, after processing in an Iwel cooker and acid hydrolysis. The processed bones had an amino-acid composition close to that of collagen with slightly larger amounts of most essential amino-acids. The meat material contained significantly higher amounts of essential amino-acids than the processed bones and had an overall composition intermediate between whole muscle protein and collagen. The hydroxyproline contents, supported by values for other amino-acids, indicated that the protein from processed bones contained about 83%, and the meat protein some 58%, of collagen, and that in commercial meat and meat-and-bone meals 50 to 65% of the total protein was collagen. Since collagen is deficient in several essential amino-acids, its presence in large amounts may be expected significantly to reduce the nutritional value of the total protein of feeding meal. It is suggested that the determination of hydroxyproline could form the basis of a simple method for the assessment of protein quality in meat and bone meals.
Basic quantitative morphological methods applied to the central nervous system

Generating numbers has become an almost inevitable task associated with studies of the morphology of the nervous system. Numbers serve a desire for clarity and objectivity in the presentation of results and are a prerequisite for the statistical evaluation of experimental outcomes. Clarity, objectivity, and statistics make demands on the quality of the numbers that are not met by many methods. This review provides a refresher of problems associated with generating numbers that describe the nervous system in terms of the volumes, surfaces, lengths, and numbers of its components. An important aim is to provide comprehensible descriptions of the methods that address these problems. Collectively known as design‐based stereology, these methods share two features critical to their application. First, they are firmly based in mathematics and its proofs. Second and critically underemphasized, an understanding of their mathematical background is not necessary for their informed and productive application. Understanding and applying estimators of volume, surface, length or number does not require more of an organizational mastermind than an immunohistochemical protocol. And when it comes to calculations, square roots are the gravest challenges to overcome. Sampling strategies that are combined with stereological probes are efficient and allow a rational assessment if the numbers that have been generated are “good enough. ” Much may be unfamiliar, but very little is difficult. These methods can no longer be scapegoats for discrepant results but faithfully produce numbers on the material that is assessed. They also faithfully reflect problems that associated with the histological material and the anatomically informed decisions needed to generate numbers that are not only valid in theory. It is within reach to generate practically useful numbers that must integrate with qualitative knowledge to understand the function of neural systems.
Specialized pro-resolving mediators: wiring the circuitry of effector immune and tissue homeostasis

Inflammation when uncontrolled is associated with prevalent disorders such as arthritis and periodontal disease, diabetes and cardiovascular diseases. Hence mechanisms to dampen the inflammatory response and promote resolution are of immense interest. Recent evidence has prompted a paradigm shift whereby the resolution of acute inflammation is now considered a biochemically active process regulated in part by endogenous PUFA (polyunsaturated fatty acid)-derived autacoids. Among these are specialized pro-resolving mediators (SPMs) that comprise lipoxins, resolvins, protectins and maresins. SPMs are endogenous stereoselective, potent mediators that temper both the magnitude and duration of inflammatory responses. Moreover, an appreciation of these endogenous mediators and pathways that control timely resolution opens a new terrain for therapeutic approaches targeted at stimulating resolution of local inflammation. The focus of this review is to depict recent advances on the biosynthesis and actions of these novel pro-resolving and protective lipid mediators. Collectively, these findings indicate that defective mechanisms and pathways in resolution may underlie the unchecked inflammatory phenotype(s) that characterize some prevalent human diseases.
A Comprehensive Coexpression Network Analysis in Vibrio cholerae

Cholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae, the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite the importance of this pathogen, roughly one-third of V. cholerae genes are functionally unannotated, leaving large gaps in our understanding of this microbe. Through coexpression network analysis of existing RNA sequencing data, this work develops an approach to uncover novel gene-gene relationships and contextualize genes with no known function, which will advance our understanding of V. cholerae virulence and evolution. ABSTRACT Research into the evolution and pathogenesis of Vibrio cholerae has benefited greatly from the generation of high-throughput sequencing data to drive molecular analyses. The steady accumulation of these data sets now provides a unique opportunity for in silico hypothesis generation via coexpression analysis. Here, we leverage all published V. cholerae RNA sequencing data, in combination with select data from other platforms, to generate a gene coexpression network that validates known gene interactions and identifies novel genetic partners across the entire V. cholerae genome. This network provides direct insights into genes influencing pathogenicity, metabolism, and transcriptional regulation, further clarifies results from previous sequencing experiments in V. cholerae (e.g., transposon insertion sequencing [Tn-seq] and chromatin immunoprecipitation sequencing [ChIP-seq]), and expands upon microarray-based findings in related Gram-negative bacteria. IMPORTANCE Cholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae, the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite the importance of this pathogen, roughly one-third of V. cholerae genes are functionally unannotated, leaving large gaps in our understanding of this microbe. Through coexpression network analysis of existing RNA sequencing data, this work develops an approach to uncover novel gene-gene relationships and contextualize genes with no known function, which will advance our understanding of V. cholerae virulence and evolution.
Ahamulina n. gen. (Cestoda: Diphyllidea) from the polkadot catshark, Scyliorhinus besnardi (Carcharhiniformes: Scyliorhinidae), off Brazil

A new genus and species of diphyllidean, Ahamulina catarina n. gen. n. sp. , is described from the polkadot catshark, Scyliorhi- nus besnardi, from Santa Catarina, Brazil. The new genus exhibits apical organ armature that is unique among diphyllideans inthe arrangement and shape of the apical hooks as well as in the lack of lateral hooklets. The taxon also exhibits a bipartite cirrussac. This is the seventh diphyllidean reported from a shark, and the third reported from a catshark suggesting that the dearth of cestode data for these particular sharks belies the true extent of diphyllidean diversity they host.
Eastern Wood-Pewees as Brown-headed Cowbird hosts: accepters but infrequently parasitized

Abstract Brown-headed Cowbird (Molothrus ater) parasitism on pewees (Contopus spp.) is uncommon or rare in North America, suggesting that pewees sympatric with cowbirds either reject cowbird eggs or are not selected by cowbirds for parasitism, or that cowbirds are unable to parasitize pewee nests. At Delta Marsh, Manitoba, we inspected Eastern Wood-Pewee (C. virens) nests to determine parasitism frequency and experimentally parasitized pewee nests with real and artificial Brown-headed Cowbird eggs to assess their response to parasitism. No parasitism was recorded at 20 unmanipulated nests or at 12 experimentally parasitized nests, whereas all real and artificial cowbird eggs were accepted. The lack of observed parasitism, therefore, was not an artifact of cowbird egg rejection. We suggest the lack of parasitism on Eastern Wood-Pewees at Delta Marsh reflects a partial asynchrony between the parasite's and host's laying seasons and possibly the high placement of pewee nests. However, these factors may not explain the lack of parasitism at all other sites in North America or on other Contopus species.
Introduction of non-native freshwater fish: is it all bad

Riskperceptionsareimportanttothepolicyprocess,butthereisoftenawell-established pattern of small risks being over assessed. This is also true with the issue of non-native freshwater fish introductions, where a great majority of research focuses on the few negativecases.Theattitudetowards‘non-natives’isacontinuallyevolvingprocessand varies according to current societal values. Here I show that on the global scale, the majority of freshwater fish introductions are not identified as having an ecological impact while having great societal benefits. Case studies from the African lakes are discussed in order to illustrate contrasting outcomes following fish introductions. Looking into the future, the environmental changes that freshwater ecosystems may encounter will have inevitable implications on the distribution of our native freshwater fish species and the need to rely on non-native introductions may become a growing reality. Aquaculture production is regularly increasing and our dependence on it is likely to become greater as it provides an important substitute for the declining production of capture fisheries. With it the number of freshwater fish introductions will increase and a more realistic attitude, albeit controversial, will need to be debated. This would mean protecting some introductions that present beneficial outcomes for biodiversity alongside a more systematic ban of species or families of fish presenting a higher historical ecological risk. The public perception of risk is something which cannotbeignoredbyanygovernmentorrulingbody,butinordertogainpublicsupport in the fight for conservation of freshwater fish biodiversity, the message needs to be clear, detailed and educational.
Purification and Characterization of Flagella from the Alkalophile Bacillus firmus RAB

Summary: Flagella from Bacillus firmus RAB, an alkalophilic bacterium, were purified to homogeneity. The flagella were shown to consist of a single protein subunit (flagellin) with an apparent molecular weight of 40000. The amino acid composition of B. firmus RAB flagellin was similar to that of other bacilli except that the former had far fewer basic amino acids. The paucity of basic amino acics may render the flagella more stable at external pH values as high as 11.0.
Elektrophoretische Untersuchungen an europaischen Arten der Gattungen Lacerta und Podarcis: Die Podarcis-Formen der griechischen Inseln Milos und Skiros

Zusammenfassung Anhand proteinelektrophoretischer Daten uber 18 Genloci wurden Kleinlacerten der griechischen Inseln Milos und Skiros mit Festiandspopulationen von Podarcis taurica ionica, Podarcis muralis albanica und Podarcis erhardii verglichen. Die Genfrequenzen der polymorphen Loci werden ange-geben und die genetischen Distanzen nach Neierrechnet. Die Grosen der genetischen Distanzen werden diskutierc und Podarcis milensis als Art bestatigt. Die Populationen von Milos und Skiros erwiesen sich als nachstverwandt, beide sind in die nahe Verwandtschaft von Podarcis taurica und nicht von Podarcis muralis zu stellen. Summary Electrophoretic investigations on European species of the genus Lacerta and Podarcis. I. The Podarcis forms from the Greek islands Milos and Skiros Small-lizards from the Greek islands Milos and Skiros are compared with populations from the continent of Podarcis taurica ionica, Podarcis muralis albanica and Podarcis erhardii by employing protein-electrophoretic data for 18 genloci. The gen frequencies of the polymorph loci are given and the genetic distances are calulated according to Nei. Extension of genetic distances is discussed. Podarcis milensis can be confirmed as a species. Populations of Milos and Skiros have shown to be closest related, both have to be considered as closely related to Podarcis taurica and not to Podarcis muralis. Resume Recbercbes elemophoretiques concernant les especes europeennes dn genre Lucerta et Podarcis. I. Les formes de Podarcis des iles greques Milos et Skiros On a compare les dates proteino-electrophoretiques de 18 locus generiques des petites laceftes des iles greques Milos et Skiros et des populations continentales des Podarcis taurica ionica, Podarcis muralir albanica et Podarcis erhardii. Apres avoir evalue les frequences des locus polymorphes, les distances genetiques ont ete calculees avec la formule de Nei. Elles ont ete l'objet de discussion et on peut affirmer ue Podarcis milemis est une espece autonome. Il se montra que les populations des iles Milos et Skiros sont tres apparantees et que toutes les deux sont proches parentes de Podarcis taurica mais point de Podarcis muralis.