Miracle-dz/UniFAR-FTUs huggingface dataset:
On Asian ornithopods (Dinosauria: Ornithischia). 4. Probactrosaurus Rozhdestvensky, 1966

The genus Probactrosaurus was first established for material discovered by a joint Russian/Chinese expedition to the Chinese autonomous region of Neimongol (Inner Mongolia). Fossils were collected at a site named Maorty (= Maortu). Material attributable to ornithopod dinosaurs was considered sufficiently distinct to permit the definition of two species of the new genus: Probactrosaurus gobiensis and P. alashanicus. The former species was based on a considerable quantity of skeletal material, much of which is still to be found in the collections of the Palaeontological Institute (PIN), Moscow. The latter was based on far less well-preserved specimens, including a holotype (a posterior skull roof) that can no longer be found in the collections of the PIN and which, along with other materials, was reportedly returned to the Institute of Vertebrate Palaeontology and Palaeoanthropology, Beijing. Some remnants of the original material attributed to P. alashanicus have been located in the PIN collections. Both taxa, established by A. K. Rozhdestvensky, are re-described using all of the available material collected during the early Sino-Soviet expeditions. Probactrosaurus alashanicus is considered to be a junior subjective synonym of P. gobiensis. Further comparisons are made with the recently described species Probactrosaurus mazongshanensis Lu, 1997. The latter does not appear to be referable to the genus Probactrosaurus. Probactrosaurus is a gracile ornithopod (ranging between 4 and 6 m in length). The skull is unadorned by any form of cranial crest; however, the premaxillary beak is deflected ventrally and the dentition is similar to that seen in more derived hadrosaurid ornithopods. The postcranial skeleton is notable for its gracility, in particular the elongate forearm and manus, and the retention of a small, conical pollex spine. Systematic analysis suggests that P. gobiensis is a derived non-hadrosaurid iguanodontian ornithopod and the basal sister-taxon to the clade Hadrosauridae. The phylogeny of currently known iguanodontians is reviewed. © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society, 2002, 136, 113–144.
Mass spectrometric analysis of pilus assembly, amyloid fibril formation, and membrane proteins in their native state

Structural analysis of proteins and their complexes is crucial to understanding protein function. This thesis demonstrates the application of mass spectrometry (MS) to the study of pilus assembly on Gram-negative bacteria and amyloid formation in dialysisrelated amyloidosis. In addition, it also tackles the challenging area of membrane protein analysis by MS. Pili are hair-like appendages located on the outer membrane of bacteria that are involved in the transmission of infection. A periplasmic chaperone and an outer membrane usher protein coordinate pilin subunit assembly. Electrospray ionisation (ESI)-MS was used to elucidate the mechanism of subunit assembly. Experiments revealed the specific amino acids on the N-terminal extension of the pilus subunits that are important in catalysing the subunit assembly process. Further MS/MS analysis indicated differences in the stability of the chaperone-subunit-usher ternary complexes formed, providing new insights into the role of the usher in orchestrating pilus biogenesis. Ion mobility spectrometry (IMS)-MS was next used to characterise oligomeric intermediates formed during beta-2 microglobulin (β2m) assembly into amyloid fibrils. Analysis of the oligomers formed by a range of β2m point mutants that affect the kinetics of amyloid fibril formation highlighted the complexity of this fibril-forming process. Further detailed characterisation of the β2m mutant H51A revealed subtle differences in the subunit exchange dynamics of the oligomers involved in fibril formation. Finally, this thesis shows a novel method for solubilising membrane proteins for MS analysis. Amphipathic polymers, termed amphipols, were used to fold and enhance the stability of two bacterial outer membrane proteins, OmpT and PagP. The utility of amphipols to study the structural and functional properties of membrane proteins by ESI-IMS-MS was then developed. Together these data show the power of ESI-IMS-MS in separating conformationally-distinct populations of amphipathic polymers from the amphipol-membrane complex whilst maintaining a ‘native-like’ membrane protein structure in the gas phase.
SELECTING ANGORA GOATS TO CONSUME MORE JUNIPER

This research project was initiated in 2003 to develop a more effective tool for biological management of invading juniper species on rangelands through herbivory by Angora goats. After we had established that juniper consumption in free-ranging goats has a genetic component (heritability = 13%) , male and female goats were bred selectively for above- (high) and below-average (low) juniper consumption that was estimated by fecal near-infrared reflectance spectroscopy. Divergent lines are being produced to facilitate the identification of physiological mechanisms that permit some goats to consume considerably more juniper than others as a regular component of their diet. Because diet is known to affect growth and fiber production, another objective of the project is to establish the effects of the selection protocol on body weights, fleece weights, and fiber characteristics. Mature females (age > 1.5 yr) and kids were maintained on rangeland and shorn twice a year. Extreme high- and low-consuming yearling males (10 of each per year) were evaluated annually in a central performance test. The selection protocol resulted in average EBV for percentage juniper consumption of 3.9 and -0.4 ( P A physiological difference in bioavailability of monoterpenes between high and low consumers was recently detected. Fiber data for 2006-born 12-mo-old kid goats indicated no significant differences ( P > 0.1) in body weight, mohair production and properties between high and low consumers. However, the adult data for the extreme males indicated that high consuming males have lower body weights than low consumers (53.8 vs. 57.9 kg, P = 0.01). Differences in body weight and several mohair production and quality traits have also been detected in the mature females but at this early stage of the selection program, no substantial differences have been observed and certainly none that would have an economic impact for producers. Ultimately, we expect to demonstrate that the high-consuming line controls juniper more effectively than either the low-consuming line or unselected Angora goats. Subsequently, we plan to release high juniper-consuming genetics to commercial breeders for use in range management.
Reevaluating the self-thinning boundary line for ponderosa pine (Pinus ponderosa) forests

The self-thinning rule has been used extensively to predict population dynamics under intraspecific and interspecific competition. In forestry, it is an important silvicultural concept for maintaining stand health in the face of climate change and biotic stress, but uncertainty exists because traditional self-thinning limits were set subjectively without regard to site quality. We addressed this by analyzing ponderosa pine (Pinus ponderosa Lawson & C. Lawson) data from 109 research plots measured repeatedly and 59 inventory plots measured once across California. Self-thinning boundaries were fitted to the data with quantile regression and stochastic frontier function (SFF) techniques with and without site index (SI) as a covariate. The models from both methods fitted the data well with either research plots or all plots. Slopes for size-density trajectories were –0.45 with the 0.99 quantile and –0.47 for SFF. Maximum stand density indices (SDI) were 1250 trees per hectare (TPH) with the 0.99 quantile and .
PHYLOGENETIC ANALYSIS AMONG FOUR SECTIONS OF GENUS DENDROBIUM SW. (ORCHIDACEAE) IN PENINSULAR MALAYSIA USING RBCL SEQUENCE DATA

Phylogenetic analysis using chloroplast DNA, the ribulose-bisphosphate carboxylase gene (rbcL), was conducted to examine relationship among four sections of the genus Dendrobium (Orchidaceae): Aporum, Crumenata, Strongyle, and Bolbidium in Peninsular Malaysia. Classifications based on morphological characters have not been able to clearly divide these four sections, therefore deeper and detailed analyses are required to ascertain their status. In this study, the phylogenetic relationships among species of the four sections were investigated to clarify their relations either to lump them into one section or reduce them into two.
Chromosome aberrations in human lymphocytes irradiated with heavy ions

Because of the increasing use of heavy ions in cancer therapy and for the planning of manned space travels, a realistic estimate of the health risks associated with particle exposure is indispensable. The standard method to quantify the exposed dose and to assess the health risks of radiation is the analysis of chromosome aberrations in peripheral blood lymphocytes at the first post-irradiation mitosis at one fixed time, 48 h, after in vitro stimulation. Using this procedure very low RBE values for high LET particles are reported. However, evidence is accumulating that high LET induced cell cycle delays and apoptosis may influence the aberration yield observable in metaphase cells. To address these questions, lymphocytes obtained from a healthy donor were irradiated with X-rays, C-, Fe- and Fe-like particles with LETs ranging from 2-3160 keV/microm and chromosome aberrations were measured in first cycle metaphase cells at multiple 3 h collection intervals from 48 to 84 h post-irradiation. In parallel, aberrations were determined in G2-phase cells and cell cycle progression as well as radiation-induced apoptosis were examined. Analysis of the data sets shows that high LET-induced apoptosis does not affect the observable aberration yield. However, a relationship between high LET induced cell cycle delays and the number of aberrations carried by a cell was found: the delayed entry of heavily damaged cells into mitosis results from a prolonged arrest in G2 and the delay is dose- and LET-dependent. Detailed statistical analysis of the frequency distributions of aberrations among cells revealed a correlation between the selective delay of heavily damaged cells and the number of particle hits per cell nucleus. Altogether, the data demonstrate that the application of the standard metaphase assay 48 h post-irradiation results in an underestimation of the RBE of high LET particles. Application of alternative cytogenetic approaches (G2-PCC analysis, the integration analysis) confirmed this conclusion.
Status, ecological attributes and conservation of native rodents in Queensland

In total, 41 species of native rodents have been recorded from Queensland, more than for any other State or Territory in Australia. Assessments of status for these species, using information on patterns of distribution and abundance, indicate that 21 species remain common, 3 are rare, 2 are vulnerable, 7 are endangered and 8 are presumed extinct. Comparisons of body weights, habits and habitats revealed no differences between common and threatened species, but species with broad diets have tended to remain common compared with dietary specialists. South-eastern Queensland has relatively more threatened and extinct species combined than the richer north-east, while species that occur or occurred in two or more regions are more likely to have remained common than those that occurred in one region only. All 12 extant rare and threatened species appear to be afflicted by one or more threatening processes, with only seven of these having ranges that coincide with reserved land. Although native rodents have fared better in Queensland than in other, principally southern States, their status leaves no room for complacency for future management. We propose several measures for survey, research, management and education to assist progress toward conservation goals.
EFFECTS OF TEMPERATURE AND SUBSTRATE QUALITY ON ELEMENT MINERALIZATION IN SIX ARCTIC SOILS

We compared the effects of temperature on rates of microbial respiration, N mineralization, nitrification, and P mineralization in soils from six arctic ecosystems located along a toposequence on Alaska's North Slope. Soils from these ecosystems were incubated aerobically in the laboratory for 13 wk and at temperatures representative of field values during a typical growing season. Rates of C and N mineralization were insen- sitive to temperature between 30 and 90C but increased by factors of 2 or more between 90 and 15? For both C and N, differences in mineralization rates among soils were greater than differences due to incubation temperature within single soils. This suggests that the quality of soil organic matter varies widely among these ecosystems and is more important than soil temperature differences in controlling rates of these processes in the field. Nitri- fication occurred in all soils, even at 30, but there were large differences among soils in nitrification potentials. Overall differences in P mineralization between soils were small. Rates of P mineralization, however, decreased with increasing temperature in soils from some sites and increased with temperature in others. Carbon respired during the 1 3-wk incubations ranged between 1.5 and 8% of total soil organic C across soil types and incubation temperatures. In contrast to the relatively high C mineralization rates in these soils, net N and P mineralization rates were very low and were likely due to high microbial demands for these nutrients. High microbial demand for mineral nutrients can severely limit plant N and P availability in arctic soils.
Endogenous amino acid flow in the stomach and small intestine of the young growing pig

Endogenous ileal amino acid flows were determined in the young growing pig given an enzymically hydrolysed casein (EHC)-based diet with subsequent treatment of the digesta by ultrafiltration. Comparison was made with endogenous excretions obtained from pigs fed an EHC-based or a protein-free diet but without treatment of the digesta. Ten entire male pigs of 15 kg liveweight were fed either an EHC-based diet or a protein-free diet, and samples of digesta were collected following euthanasia. The digesta from the EHC-fed pigs were divided into two equal portions. One portion was untreated, and the second portion was ultrafiltered after centrifugation with the retentate (high-molecular-weight fraction) being added to the precipitate. Endogenous ileal amino acid flows were determined for the untreated digesta and for the digesta following the centrifugation plus ultrafiltration treatment. Except for arginine, glycine, leucine and phenylalanine, the endogenous amino acid flows were significantly (P < 0.05) higher for the untreated digesta than for the digesta following the centrifugation plus ultrafiltration treatment. Except for arginine, glycine, leucine and phenylalanine, the endogenous amino acid flows were significantly (P < 0.05) highter for the untreated digesta than for the digesta following the centrifugation plus ultrafiltration treatment. The pigs fed a protein-free diet generally had lower amino acid flows than those fed the EHC-based diet (ultrafiltration treatment). significantly (P < 0.05) so for lysine, aspartic acid, threonine, serine, glutamic acid, glycine, valine, isoleucine and leucine. The endogenous flows in different segments of the upper digestive tract of the young growing pig were also determined in the animals fed the protein-free diet. The endogenous amino acid flow was highest in the second third of the upper digestive tract. There was a significant (P < 0.05) difference between the amino acid flows determined in the first and second thirds of the small intestine for most of the amino acids.
Generalisation Methods for Control-Flow Oriented IC3 Algorithms

IC3 is a bit-level formal verification method for hardware systems. Given the program in terms of a finite-state transition system, the IC3 algorithm tries to infer an inductive invariant strong enough to prove the correctness of the program. Therefore, it incrementally derives a sequence of overapproximations of the reachable program states. The IC3 generalisation function is a key component of the entire algorithm, because it abstracts from the concrete counterexamples. This abstraction is computed by applying Boolean SAT-solving techniques, such that the resulting generalisation blocks multiple states simultaneously. IC3CFA is based on the idea to lift the principles of Boolean IC3 to software model checking, i.e. SMT. Thereby, the program is given in terms of a control flow automaton (CFA). This thesis presents several approaches to improve the IC3CFA generalisation algorithm, where these approaches try to avoid unnecessary or redundant computations. More precise, since the SMT calls are usually considered to be time consuming and badly scalable, the SMT queries are as far as possible replaced by equivalent syntactical checks. The experimental results show the effectiveness of the presented improvements regarding runtime and memory requirements.
Molecular phylogenetics evidence for a novel lineage of amoebae within Discosea (Amoebozoa: Lobosa)

Some amoebae were recovered from freshwater samples on agar plates. Due to a fungal contamination tightly associated with these amoebae, it was impossible to correctly characterize them on a morphological base, but sequences of the small subunit ribosomal RNA gene (SSU rDNA) were successfully obtained from three strains. Phylogenetic analysis performed on these SSU rDNA allowed to identify these amoebae as members of a new lineage, related to the Dermamoebida, which includes also several other environmental SSU sequences.
Salinity Induces Granal Development in Bundle Sheath Chloroplasts of NADP-Malic Enzyme Type C4 Plants

Abstract In NADP-malic enzyme (NADP-ME) type C4 plants, MC chloroplasts have well-developed grana, whereas BSC chloroplasts are generally characterized by highly reduced grana. In the previous study, salt treatment induced granal development in BSC chloroplasts of Zea mays, an NADP-ME type C4 plant. Therefore, we examined the effects of salinity stress on the granal structure of BSC chloroplasts in seven other C4 species belonging to the NADP-ME type. The plants were grown in soil and after a certain period of time, they were treated with 3% NaCl for 5 d. Ultrastructure and quantitative properties of chloroplasts at the middle part of leaf tissues were investigated. In BSC chloroplasts of all the C4 species, almost no structural damage was observed, but the development of granal stacking was induced under salinity condition. Granal indices and appressed thylakoid density of BSC chloroplasts in the salt-treated plants were higher than those in the control plants. In all the species, the structure of MC chloroplasts was more or less damaged by salt stress; thylakoids were swollen and chloroplast envelope was disorganized. These results suggest that the granal development in BSC chloroplasts and the high damage of MC chloroplasts are common features of NADP-ME type C4 plants under salinity stress.
Cellular and Molecular Mechanisms regulating Cell Proliferation during the Forebrain Development of the Mouse

The predominant precursor cell type during cortical neurogenesis are radial glia cells, which receive extrinsic and intrinsic signals that might influence cell proliferation and neurogenesis. These radial glia cells have direct contact to the growth factor rich basement membrane throughout cell division. However, it is not known, how the signals received from the basal cell attachment influence the behavior of radial glia cells in regard to the regulation of cell proliferation and neurogenesis. Therefore, I examined the lamininγ1 (LNγ1) mutant, lacking the contact of radial glial endfeet to the basement membrane, and the α6 integrin-/- with a disturbed assembly of the basement membrane. The analysis of the LNγ1 mutant and the α6 integrin-/- showed no defects in the radial glia progeny, cell proliferation or their orientation of cell division. Thus, these results strongly suggest that the direct contact of radial glia cells to the basement membrane is not required for these aspects. Radial glia cells of the dorsal telencephalon are also known to be specified by the expression of the transcription factor Pax6, which plays a pivotal role in the regulation of cell proliferation, neurogenesis and regionalisation during development of the telencephalon. In order to understand how Pax6 coordinates these diverse functions at the molecular level, the roles of the different DNA-binding domains of Pax6, the paired domain (PD), the splice variant of the paired domain (PD5a) and the homeodomain (HD) were analyzed in loss- and gain-of-function approaches. The analysis of the specific paired domain mutant Pax6Aey18-/-, that lacks large parts of the paired domain, but contains an intact homeodomain and transactivating domain (TAD), showed that the paired domain is required for the regulation of neurogenesis, cell proliferation and regionalisation in the developing telencephalon and eye. The homeodomain plays only a minor role during telencephalic development, in contrast to its function in the eye, as shown by the analysis of Pax64Neu-/- mice, which have a point mutation in the DNA-binding domain of the homeodomain, while paired domain and transactivating domain are still functional. Moreover retrovirus-mediated overexpression of Pax6 and Pax6(5a) in cortical cells showed that splicing of the paired domain regulates between a Pax6 form that affects neurogenesis, and cell proliferation, while the other Pax6 form, containing exon5a, regulates exclusively cell proliferation.