Miracle-dz/UniFAR-FTUs huggingface dataset:
Description of a new long-snouted beaked whale from the Late Miocene of Denmark: evolution of suction feeding and sexual dimorphism in the Ziphiidae (Cetacea: Odontoceti)

A new genus and species of Ziphiidae, Dagonodum mojnum gen. nov., sp. nov., from the upper Miocene Gram Formation (c. 9.9–7.2 Ma) represents the first occurrence of the family in Denmark. This long-snouted ziphiid is characterized by two pairs of mandibular tusks, the Eustachian outlet that approximately levels with the dorsalmost margin of the posterior portion of the involucrum, and the left trapezoid nasal with a posteromedial projection into the frontal. A phylogenetic analysis including 25 species and 69 characters was conducted. Dagonodum mojnum is placed in a basal ziphiid clade as the sister taxon of Messapicetus. The specimen is probably a male, because it has enlarged tusks. Alternatively, females could also be involved in fights and develop erupted tusks as in the extant Berardius. Although less well supported, this interpretation proposes that aggressive interactions were not restricted to males in stem-ziphiids. With a thickened thyrohyal and the presence of a precoronoid crest, D. mojnum was able to use suction feeding, but was less specialized to it compared to extant ziphiids. The elongated neck of D. mojnum less optimized to perform deep dives, and the shallow depth at which the Gram Formation was deposited corroborates the hypothesis that at least part of the stem-ziphiids were not regular deep divers.
FLIM and PLIM in biomedical research – An innovative way to combine autofluorescence and oxygen measurements

Abstract: Fluorescence lifetime imaging microcopy (FLIM) is successfully used to image the intracellular fluorescent coenzymes NAD(P)H and FAD+. The redox state of these coenzymes is a parameter which helps to reveal the metabolic status of living cells and tissues. However, metabolic reactions are strongly dependent on the intracellular oxygen level. One promising optical method to monitor oxygen in biomedical samples is phosphorescence lifetime imaging microscopy (PLIM). PLIM is based on oxygen-dependent quenching of the phosphorescence of so-called “phosphors”. In this way, PLIM enables measurement of the oxygen partial pressure (pO2) within living cells. This review describes the FLIM and PLIM approaches used in biomedical research, drawing particular attention to the techniques of simultaneous FLIM and PLIM, which provide correlative imaging of both the fluorescence lifetime of metabolic coenzymes and pO2-sensitive phosphorescence lifetime.
Hepatitis C Virus Molecular Biology and Genetic Variability

The pathogenetic mechanisms of hepatitis C virus (HCV) infection are poorly known. An understanding of HCV biology and the potential clinical impact of HCV genetic variability is essential to managing, treating, and preventing HCV infections. HCV is a member of the Flaviviridae viral family. Its genome is a positive, single-strand RNA molecule. The structure of the HCV particles is poorly known due to the lack of an efficient cell culture system as well as a striking heterogeneity in density. The core protein may have a regulatory role on both viral and cellular gene expression. The mechanisms of HCV-RNA replication may include synthesis of negative strand intermediates, which drive synthesis of new positive RNA genomes. New procedures have been developed to better identify and characterize the HCV-RNA genome. The mechanisms of HCV persistence are currently unknown, although it is known that HCV chronicity develops despite humoral and cellular responses to HCV proteins. HCV-RNA shows s~gnificant genetic variability with an estimated rate of nucleotide change of approximately 10- substitutions/site/year. Currently, three major HCV genotypes and three to seven minor subtypes can be distinguished. The geographical distribution of these genotypes and subtypes varies significantly. It appears that poor clinical response to interferon (IFN) is more common with HCV genotype 1. In addition, some studies have shown an association between chronic infection, severe chronic hepatitis, and cirrhosis with subtype lb. Further, there is evidence for a potential direct effect of HCV in liver carcinogenesis, with subtype lb possibly being an independent risk factor for hepatic carcinoma development. HCV-RNA circulates as a population of RNA molecules, which creates a heterogeneity referred to as "quasispecies. " It is possible that some HCV strains might have direct clinical implications. It may be that highly heterogeneous populations observed prior to treatment might correlate with a lower rate of response to IFN therapy.
Spatially limited clonality and pollen and seed dispersal in a characteristic climber of Central African rain forests: Haumania danckelmaniana (Marantaceae)

Gene dispersal and clonality are important aspects of plant evolution affecting the spatial genetic structure (SGS) and the long‐term survival of species. In the tropics these parameters have mostly been investigated in trees and some herbs, but rarely in climbers which frequently: (1) show clonal growth leading to a patchy distribution pattern similar to that of understory herbs; and (2) flower in the canopy where they may have access to long‐distance dispersal like canopy trees. We thus hypothesize for climbers an intermediate genetic structure between herbs and trees. The study aims at assessing breeding system and spatial extent of clonality and gene dispersal in Haumania danckelmaniana (Marantaceae), a common climber in the tropical rain forests from western Central Africa. In eastern Cameroon, 330 ramets were sampled at three spatial scales and genotyped at seven microsatellite loci. Clonality was moderate (clonal extend: 15–25 m, clonal diversity 0.4–0.65) indicating the importance of recruitment from seeds at this locality. The low inbreeding (FIS) suggested predominant outcrossing. The rate of decay of the relatedness between individuals with distance indicated limited gene dispersal distance (σg = 9–50 m, neighborhood sizes Nb = 23–67) in accordance with narrowly gravity dispersed seeds and restricted pollen transfer distance in densely flowering populations. The marked SGS (Sp = 0.011–0.026) was similar to that reported in tropical trees, but might increase with augmented clonality as in many herbs, especially under more severe disturbance regimes.
Enamel Pathology Resulting from Loss of Function in the Cystic Fibrosis Transmembrane Conductance Regulator in a Porcine Animal Model

Cystic fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR), a phosphorylation- and ATP-regulated anion channel. CFTR expression and activity is frequently associated with an anion exchanger (AE) such as AE2 coded by the Slc4a2 gene. Mice null for Cftr and mice null for Slc4a2 have enamel defects, and there are some case reports of enamel anomalies in patients with CF. In this study we demonstrate that both Cftr and AE2 expression increased significantly during the rat enamel maturation stage versus the earlier secretory stage (5.6- and 2.9-fold, respectively). These qPCR data imply that there is a greater demand for Cl – and bicarbonate (HCO3 ) transport during the maturation stage of enamel formation, and that this is, at least in part, provided by changes in Cftr and AE2 expression. In addition, the enamel phenotypes of 2 porcine models of CF, CFTR- null, and CFTR- F508 have been examined using backscattered electron microscopy in a scanning electron microscope. The enamel of newborn CFTR- null and CFTR- F508 animals is hypomineralized. Together, these data provide a molecular basis for interpreting enamel disease associated with disruptions to CFTR and AE2 expression.
Seasonal shift in the taxonomic diversity of rocky reef fishes in the southwestern Gulf of California

"En el suroeste del Golfo de California se presentan capturas de peces de importancia comercial; sin embargo hay pocos estudios relacionados con la diversidad taxonomica de los peces en el area. Se determinaron los cambios en la diversidad taxonomica de la comunidad de peces en 8 localidades cercanas a Bahia de La Paz durante el periodo marzo 2002-abril 2003. Se analizaron los cambios estacionales en la diversidad de peces de arrecife rocoso considerando la distancia taxonomica entre especies de peces utilizando la diversidad alfa, promedio alfa, beta y gama, asi como la distintividad taxonomica (TD D*), y el indice promedio de distintividad taxonomica (AvTD D+). Se realizaron censos visuales submarinos en 48 transectos, de 100 × 5 m (500 m2) a 5 m de profundidad, en el horario diurno de 09:00 to 16:00 h. Se observaron 2 temporadas climaticas; una estacion fria con una temperatura de 22,57°C, y una temporada calida con temperatura promedio de 27,09°C. Se contabilizaron 24.633 peces de 92 especies y 67 generos. De acuerdo con los resultados del promedio de los indices de diversidad de alfa, beta y gama, agosto fue el mes con mayor diversidad (19,5, 40,5 y 60 especies, respectivamente), mientras que diciembre tuvo la menor diversidad (20,6, 27,4 y 48 especies, respectivamente). En los analisis espaciales del TD y AvTD no se presentaron diferencias significativas, mientras que en el analisis estacional de los indices, se presentaron diferencias significativas. Estas diferencias en ambos indices podrian ser debido a que la localidad El Guano tiene mayor impacto de actividades humanas. "
Fusion of microvascular endothelial cells induced by muramidase-released protein of Streptococcus suis type 2

Streptococcus suis type 2 (SS2) mainly causes meningitis of human and pigs. Muramidase-released protein (MRP) is one of the key virulence factors of SS2. However,the pathogenic effects of MRP on microvascular endothelial cells (MEC) which makes up of brain blood barrier (BBB) is unknown to date. So the spleen microvascular endothelial cells (SMEC) from neonatal rabbit were isolated, purified, immortalized by SV40-T antigen, and used as cell model in present study. After co-incubation with electrophoretically purified MRP, two principal morphologic changes of SMEC confluent layer were revealed by light microscopy. Firstly, the confluent cell layer turned into a riddle-like structure full of giant hole. Secondly, cells were fused into syncytia which scattered in the hole, containing 10～30 nuclei. The nuclei were then released from the syncytia after an extreme condensation. And finally, the syncytia disappeared. Results of present study suggest that MRP alone is sufficient to destroy the brain blood barrier.
A novel approach for the assembly of complex genomic DNA cloned into bacterial artificial chromosome vectors: assembly and analysis of Triticum aestivum chromosome arm 7DS

Next generation DNA sequencing technologies have led to an exponential growth in the number of genomes being sequenced. While generating whole genome shotgun (WGS) assemblies using next generation sequencing (NGS) is relatively fast and inexpensive, the application of this approach to the assembly of highly repetitive and complex genomes such as wheat results in inferior assemblies thus slowing efforts in identifying markers for
Effect of native dominant AM fungus and PGPRs on growth and biochemical characteristics of medicinally important Indigofera aspalathoides Vahl. ex. DC.

The effect of native dominant AM fungus Glomus aggregatum isolated from the rhizosphere soil of Indigofera aspalathoides Vahl. Ex DC and plant growth promoting rhizo-microorganisms (PGPRs) viz., Bacillus coagulans and Trichoderma viride on the growth and biochemical parameters of the medicinally important I. aspalathoides was studied in pot culture. Infection percentage and number of spores in the rhizosphere soil were higher in plants treated with triple inoculation (Glomus aggregatum + Bacillus coagulans + Trichoderma viride). Dry matter content of I. aspalathoides was high in dual inoculation (G. aggregatum + B. coagulans) whereas plant height, protein and amino acid contents were higher in triple inoculation. The macroand micronutrients of the test plant except manganese were also higher in G. aggregatum and PGPRs treated plants than the uninoculated control. Total chlorophyll, carotenoids, lipid and phenol contents were higher in triple inoculation of I. aspalathoides than the other treatments. The inoculation of efficient AM fungus in combination with the two PGPRs had positively influenced the growth and biochemical constituents of I. aspalathoides whereas B. coagulans and T. viride as individual inoculations did not show significant effect on the test plants.
The evolutionary history of bears is shaped by gene flow across species

Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to the closely related polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using three different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains numerous uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to massive amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. The increasing evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.
Dietary source and availibility of fatty acids to manipulate ruminal protozoa, metabolism of fat, and milk fatty acid profile in lactating dairy cows

ii Dedication. v Acknowledgments. vi Vita. viii List of tables. xiv List of figures. xvi Abbreviations. xvii Chapters 1. General introduction. 1 2. Literature review. 4 Importance of protein nutrition in dairy cows. 4 Nitrogen and the environment. 4 Protein nutrition in dairy cows. 5 Efficiency of microbial protein synthesis. 7 Microbial efficiency. 7 Mechanisms of ruminal N degradation. 9 Mechanisms of microbial protein synthesis. 11 Dietary manipulation of EMPS. 14 Ionophores. 14 Fat source and availability. 17 Unsaturated fat and MFD. 17 Medium chain FA and protozoal inhibition. 19 Coconut oil (CO) and protozoal inhibition. 20 Reduction of methanogenesis with fat. 21 Potential pitfalls. 22 3. Processing whole cottonseed moderates fatty acid metabolism and improves performance by dairy cows. 24 Abstract. 24 Introduction. 26 Materials and methods. 28 xii Experiment 1: Digestibility Trial. 28 Animals and diets. 28 Ruminal metabolism. 30 Disappearance of alfalfa hay NDF and CS products in situ. 31 Total tract digestibility. 33 Milk production and composition. 34 Statistical analysis. 35 Experiment 2: Lactation Trial. 36 Animals and diets. 36 Milk production and composition. 37 Statistical analysis. 37 Results and discussion. 38 Experiment 1: Digestibility Trial. 38 Diets. 38 Ruminal fermentation. 39 Disappearance of alfalfa hay NDF and CS products in situ. 40 Apparent total tract digestibility. 43 Milk production and composition. 44 Experiment 2: Lactation Trial. 46 Milk production and composition. 46 Conclusions. 48 4. Interaction of unsaturated fat or coconut oil with Rumensin on protozoal abundance, nutrient digestibility, and microbial protein flow to the omasum in lactating dairy cows fed twelve times daily. 60 Abstract. 60 Introduction. 61 Materials and methods. 65 Animal and diets. 65 Milking. 67 Feed sampling and analysis. 68 Ruminal evacuation. 70 Omasal flow markers. 71 Omasal sampling. 75 Marker measurements. 76 Total tract digestibility. 77 Statistical analysis. 78 Results. 79 Diet composition. 79 Protozoal abundance. 79 Ruminal fermentation. 79 Pool size and passage kinetics. 80 OM and NDF digestibility. 81 N digestibility. 81 Lactation performance. 82 xiii Discussion. 83 Protozoal abundance. 83 Ruminal fermentation. 85 Pool size and passage kinetics. 86 Digesta flow and digestibility. 87 Intake. 90 Milk composition. 91 Conclusion. 92 5. Interaction of unsaturated fat or coconut oil with Rumensin on fatty acid flow to the omasum and milk fatty acid profile in lactating dairy cows fed twelve times daily. 101 Abstract. 10
Fibrinogen-to-prealbumin ratio: A new prognostic marker of resectable pancreatic cancer

Background The fibrinogen-to-prealbumin ratio (FPR), a novel immune-nutritional biomarker, has been reported to be associated with prognosis in several types of cancer, but the role of FPR in the prognosis of resectable pancreatic cancer has not been elucidated. Methods A total of 263 patients with resectable pancreatic cancer were enrolled in this study and were randomly divided into a training cohort (n = 146) and a validation cohort (n = 117). Receiver operating characteristic curve (ROC) was used to calculate the cut-off values of immune-nutritional markers. The least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression were performed in the training cohort to identify the independent risk factors, based on which the nomogram was established. The performance of the nomogram was evaluated and validation by the training and validation cohort, respectively. Results The optimal cutoff value for FPR was 0.29. Multivariate analysis revealed that FPR, controlling nutritional status (CONUT), carbohydrate antigen 19-9 (CA19-9), carcinoembryonic antigen (CEA), and tumor node metastasis (TNM) stage were independent predictors of overall survival (OS). The nomogram was established by involving the five factors above. The C-index of the training cohort and validation cohort were 0.703 (95% CI: 0.0.646-0.761) and 0.728 (95% CI: 0.671-0.784). Decision curve analysis and time-dependent AUC showed that the nomogram had better predictive and discriminative ability than the conventional TNM stage. Conclusion FPR is a feasible biomarker for predicting prognosis in patients with resectable pancreatic cancer. The nomogram based on FPR is a useful tool for clinicians in making individualized treatment strategies and survival predictions.
Divergent reproductive allocation trade‐offs with canopy exposure across tree species in temperate forests

Variation in tree reproduction can alter forest community dynamics, especially if reproductive output is costly for other functions like growth. However, empirical studies reach conflicting conclusions about the constraints on reproductive allocation relative to growth and how they vary through time, across species, and between environments. Here, we test the hypothesis that a critical resource, canopy exposure to light availability, limits reproductive allocation by comparing longterm relationships between reproduction and growth for trees from 21 species in forests throughout the Southeastern United States. We found that species have divergent responses to light availability, with shadeintolerant species experiencing an alleviation of tradeoffs at high lightand shadetolerant species showing no changes in reproductive output across light environments. Correlations between temporal variation in individual growth and reproduction were weak and generally insensitive to canopy exposure, but changed when considering time lags. The diversity of responses across species indicates that reproductive allocation for trees in these forests is strongly influenced by both species’ life history and environmental heterogeneity in space and time.
Genome-resolved analyses of oligotrophic groundwater microbial communities along phenol pollution in a continuous-flow biodegradation model system

Groundwater pollution is one of the major environmental concerns. The entrance of pollutants into the oligotrophic groundwater ecosystems alters native microbial community structure and metabolism. This study investigated the application of innovative Small Bioreactor Chambers and CaO2 nanoparticles for phenol removal within continuous-flow sand-packed columns for 6 months. Scanning electron microscopy and confocal laser scanning microscopy analysis were conducted to indicate the impact of attached biofilm on sand surfaces in bioremediation columns. Then, the influence of each method on the microbial biodiversity of the column’s groundwater was investigated by next-generation sequencing of the 16S rRNA gene. The results indicated that the simultaneous application of biostimulation and bioaugmentation completely eliminated phenol during the first 42 days. However, 80.2% of phenol remained in the natural bioremediation column at the end of the experiment. Microbial diversity was decreased by CaO2 injection while order-level groups known for phenol degradation such as Rhodobacterales and Xanthomonadales dominated in biostimulation columns. Genome-resolved comparative analyses of oligotrophic groundwater prokaryotic communities revealed that Burkholderiales, Micrococcales, and Cytophagales were the dominant members of the pristine groundwater. Six-month exposure of groundwater to phenol shifted the microbial population towards increasing the heterotrophic members of Desulfobacterales, Pseudomonadales, and Xanthomonadales with the degradation potential of phenol and other hydrocarbons.
Proliferation, cell death and reelin expression during development of the retina in a teleost, the common trout

We have analysed the spatiotemporal pattern of cell proliferation and apoptosis during the development of the retina in a teleost. Distribution of proliferating cells in different develop- mental stages (embryos, alevins, and juveniles) was analysed with an antibody against proliferating cell nuclear antigen (PCNA). After establishment of the retinal lamination, PCNA-immunoreactive (PCNA-ir) cells were frequently observed in all cell layers, with a high majority of proliferating cells located at the marginal (growing) retina. Clusters of PCNA-ir cells were characteristic of the inner nuclear layer (INL). The distribution of apoptotic cells was studied by the TUNEL method, which has revealed significant cell death before completion of the retinal lamination. We have also used an antibody against Reelin (RELN) as a marker for retinal cells that secrete this glycoprotein to the extracellular space. The pattern of RELN expression, as well as that of proliferating and dying cells was very similar to that described in tetrapods, suggesting that this protein regulates the cell migration and synaptogenesis in the different developmental stages of the retina. Development is a complex process based in a spatiotemporal control of cell proliferation, cells migration to their definitive posi- tion and programmed cell death in specific regions. We have analysed the distribution of proliferating and dying cells during the development of the retina in trout to evidence their spatiotemporal patterning. We have correlated these results with the distribution of immunoreactivity to RELN, a glycoprotein that appears to act at short distance as an instructive signal in the regulation of cell distribution. Heads of embryos (5 to 14 mm in length), alevins (15 to 26 mm in length), and juveniles (without vitelin sac) of trout were used for this study. Paraffin sections of retinas fixed with Bouin's fluid were immunohistochemically treated with anti-PCNA as a marker of cell proliferation (it marks cells in the S phase of the cell cycle). Cryostat sections of retinas fixed with 4% paraformaldehyde were pro- cessed with the TUNEL method to detect apoptotic cells, or treated immunohistochemically with an antibody against RELN (gift by Dr. Goffinet, Univ. Namur, Belgium) as a marker of cells that regulate the cell migration.