Miracle-dz/UniFAR-FTUs huggingface dataset:
Open-book Preparations from Chick Embryos and DiI Labeling of Commissural Axons

[Abstract] Successful neural circuit formation relies on the accurate navigation of axons towards their targets during development. Axons are guided by a combination of short-range and longrange, attractive and repulsive cues. The commissural axons of the developing spinal cord have provided an informative in vivo model for the identification of multiple axon guidance molecules and mechanisms. These axons extend ventrally from the dorsal spinal cord and cross the midline at the floor plate, before making a sharp rostral turn towards the head. This simple trajectory has facilitated the identification of many axon guidance molecules, because perturbation of the stereotypical guidance decisions as a result of genetic manipulations can be easily identified. The open-book assay is a method to assess the trajectory of spinal commissural axons. The spinal cord is dissected out, opened at the roof plate and pinned flat. Punctate injections of the lipophilic fluorescent dye, DiI, are used to trace commissural axon trajectories prior to microscopy and analysis.
The zoological contributions of Andrew Smith (1797–1872) with an annotated bibliography and a numerical analysis of newly described animal species

The army surgeon Andrew Smith studied South African fauna when he was the first Superintendent of the South African Museum in Cape Town. He visited some interior parts of the country, especially as commander of the Expedition for Exploring Central Africa in 1834–1836. His early work was published in rare and obscure journals printed in Cape Town, like the Cape Town Gazette and African Advertiser, the South African Commercial Advertiser and the South African Quarterly Journal. After his return to England in 1836, he exhibited animals found during his expeditions and he started to publish the Illustrations of the Zoology of South Africa, which appeared in 28 parts between 1838 and 1849 and was splendidly illustrated by George Henry Ford. The bibliography of all works authored by Smith is reconstructed here in detail, including for the first time items published in the Kaapstads Courant en Afrikaansche Berigter. It is found that he was the author of 142 works between 1819 and 1849. In these works, he described many new species. The name Accipiter selbyii A.Smith, 1829 was rediscovered. Some of the new names are now considered unavailable for purposes of zoological nomenclature, due to incorrect spellings, names without proper descriptions or emendations. However, he is known to be the first author of 76 generic names (67 available, 9 unavailable) and 558 specific names (460 available and 98 unavailable). At least 257 specific names are still in current use for mammals, birds, reptiles, amphibians and fishes. Andrew Smith was a true pioneer of South African zoology.
Limiting Dilution Assays to Determine Frequencies of Lymphohematopoietic Progenitors

[Abstract] This protocol is useful to determine the frequencies of lymphohematopoietic progenitors in tested samples. To effectively support the growth and differentiation of primitive lymphohematopoietic progenitors, complex signals from stromal cells are important. Several stromal cell lines are known to support both lymphoid and myeloid cells simultaneously in mouse. In this protocol, we introduce two stromal co-culture systems for murine lymphohematopoietic progenitors and their application for limiting dilution assays.
'Gap hunting' to identify multimodal distributions of DNA methylation

Background: The Illumina 450K array has been widely used in epigenetic association studies. Current quality-control (QC) pipelines typically remove certain sets of probes, such as those containing a SNP or with multiple mapping locations. An additional set of potentially problematic probes are those with multi-modal DNA methylation (DNAm) distributions characterized by two or more distinct clusters separated by gaps. Data-driven identification of such probes may offer additional insights for downstream analyses. Results: We developed a method, termed 9gap hunting9, to identify probes showing multi-modal distributions. Among 590 peripheral blood samples from the Study to Explore Early Development, we identified 11,007 9gap probes9. The vast majority (8,763) are likely attributed to an underlying SNP(s) in the probe, although SNP-affected probes exist that do not produce gap signals. Specific factors predict which SNPs lead to gap signals, including type of nucleotide change, probe type, DNA strand, and overall methylation state. These expected effects are demonstrated in paired genotype and 450k data on the same samples. Gap probes can also serve as a surrogate for the local genetic sequence on a haplotype scale and can be used to adjust for population stratification. Conclusions: The characteristics of gap probes reflect potentially informative biology. QC pipelines may benefit from an efficient data-driven approach that 9flags9 gap probes, rather than filtering such probes, followed by careful interpretation of downstream association analyses. Our results should translate directly to the recently released Illumina 850K EPIC array given the similar chemistry and content design.
Photosynthetic characteristics of seagrasses (Cymodocea serrulata, Thalassia hemprichii and Zostera capricornia) in a low-light environment, with a comparison of leaf-marking and lacunal-gas measurements of productivity

We describe the photosynthetic characteristics of three seagrasses and the relationship between their production and natural light intensities (photosynthesis-irradiance response, i.e. PI curves). Seagrass production (gross production minus shoot respiration) was measured in the field by the rate of gas release from the lacuna1 space of whole seagrass shoots and compared with net leaf production. Field work was carried out on the seagrasses Cymodocea serrulata (R. Br.) Aschers, and Magnus, Thalassia hemprichii (Ehrenb.) Aschers. , and Zostera capricornia Aschers. in the turbid, warm waters of Cairns Harbour, Queensland, Australia. The photosynthetic efficiencies (the initial slope of the PI curves) of all of the seagrass species were 10 times greater than any previously measured for the same species in higher-light environments. The high compensating light intensities (80-92 µE m-2 s-1) showed that the plants have high respiration rates that were probably due to the high water temperatures (29-33oC) of the harbour. The seagrasses responded to small increases of light at low light intensities by rapidly reaching saturating light intensities, and the maximum rates of production were between 0.4 and 0.6 mg C h-1 shoot-1. The average period of exposure to saturating light intensity was 2 h day-1. One-quarter of the gross production was lost to plant respiration. The net productivity and respiration of all three seagrasses was calculated from this photoperiod. Net leaf production in situ compared well with the seagrass production estimates that were measured with the lacunal-gas technique. Most of the production appeared to be allocated to the above-ground tissue, a feature consistent with seagrasses growing in low-light and terrigenous sediments.
Prevention of respiratory syncytial virus infection via methoxypoly(ethylene glycol)-modification of the virus or its host cell

Respiratory Syncytial Virus (RSV) causes significant morbidity and mortality in humans. To date, no vaccines or effective treatments exist for this serious respiratory disease. Current prophylactic therapy is limited to at-risk neonates due to its high cost, and involves the administration of anti-RSV immune globulins that are 5O% effective. To attenuate or inhibit RSV infection, we hypothesized that bioengineering of either the virus particle or host cell with methoxypoly(ethylene glycol) [mPEG] would prevent viral infection. Our specific objectives were to evaluate the effects of grafting concentration, linker chemistry, polymer length, and cell polarization on viral infection and propagation. Modification of either the virus or host cells with mPEG prevented RSV infection in a doseand size-dependent maimer. For virus modification, short chain polymers (2 kDa) were significantly more effective than long chain polymers (20 kDa). For example, plaque assays demonstrated that RSV modification with 5 mM, 2 or 20 kDa mPEG resulted in a 100 and -82% plaque reduction, respectively. In contrast, when small polymers were used to modify the host cell they provided no protection, while long chain polymers effectively prevented infection. For example, at 48 hours post-infection at a multiplicity of infection of 0.5 and grafting concentrations of 5, 7.5, and 15 mM, 20 kDa mPEG decreased infection by 45, 83, and 91%, respectively. However, these grafting concentrations of the 2 kDa mPEG resulted in 0% reduction. Importantly, with both viral and host cell PEGylation strategies, moderate to high grafting concentrations of the appropriate polymer species were able to provide near complete protection against infection in both non-polarized and polarized cells. In conclusion, mPEG-modification of RSV or the host cell are highly effective methods for preventing viral infection. Our findings indicate that the length of grafted polymer must be matched to the size of particle targeted for modification. Consequent to the high efficacy of both
Evidence for speciation with gene flow: an examination of the evolutionary genetics of blue-footed and Peruvian boobies

ii Co-Authorship . iv Acknowledgements . vii List of Figures. xvi List of Tables. xv Chapter 1 : General Introduction . 1 1.1 Population differentiation and speciation – models and advances . 2 1.2 Divergence without gene flow . 5 1.3 Divergence with gene flow . 6 1.4 Advances in analytical techniques . 9 1.5 Hybridization . 12 1.6 Hybridization and speciation in birds . 15 1.7 The study system. 17 1.8 Conservation and economic importance . 19 1.9 Thesis objectives and relevance . 20 1.10 Literature Cited . 22 Chapter 2 : Could specialization to cold-water upwelling systems influence gene flow and population differentiation in marine organisms? A case study using the blue-footed booby, Sula nebouxii . 32 2.1 Abstract . 32 2.2 Introduction . 33 2.3 Materials and Methods . 36 2.3. 1 Population genetic analysis of the mtDNA control region . 38 2.3. 2 Population genetic analysis of the microsatellites . 40 2.4 Results . 41 2.4. 1 Mitochondrial control region . 41 2.4. 2 Microsatellites . 48 2.5 Discussion . 50 2.5. 1 Blue-footed booby population differentiation compared to other sulids . 51 2.5. 2 Potential explanations for the observed pattern . 52
Toxicity Studies on Chloroform Extract of Solanum trilobatum: Effect on Drug Metabolizing and Antioxidant Enzymes in Rats

The aim of the study was to evaluate the effect of chloroform extract of Solanum trilobatum (CST) on drug metabolizing and antioxidant defense enzymes for assessing its chemo preventive potential and protection of tissues from oxidative damage. The CST was obtained by soxhlet extraction with chloroform. Animals (Male Sprague Dawley rats) were divided into three groups: Group I-normal control, group II-CST (200 mg kgG1 b.wt.), group III-CST (800 mg kgG1 b.wt.). The CST was given by oral gavage once daily for 15 days. At the end of the experimental period all the rats were sacrificed and the livers, lungs and kidneys were taken for estimating the phase I and II drug metabolizing and antioxidant enzyme activities. The gain in body weight and the levels of GSH and lipid peroxides in these tissues were also determined. The results showed that the administration of CST could modulate the phase I and phase II enzymes that are critical for cancer protection. Administration of CST at 200 and 800 mg kgG1 b.wt. to animals did not cause any apparent clinical signs as survivability or visible changes caused by toxicity in the liver, lungs and kidney. Administration of CST at a dose of (800 mg kgG1 b.wt.) was found to be ineffective in elevating the phase I enzymes suggesting that CST could possibly prevent the biotransformation of carcinogens. These results clearly indicate that CST with its biologically active components could be used as a chemo preventive agent in treating various cancers.
EPILEPTIC FOCUS LOCALIZATION BASED ON ENTROPY AND CONVOLUTIONAL NEURAL NETWORK

– Focal location is a necessary step before surgery in epileptic patients and directly affects the outcome of the surgery. However, this is a time-consuming and difficult process for clinical experts. Recent researches have shown that we can use machine learning approaches to reduce the workload of the focal location. In this paper, we proposed a method for extracting features by calculating the entropy of the intracranial electroencephalogram (iEEG) and use a one-dimensional convolutional neural network (1D-CNN) for classification, in this way, we can automatically locate the epileptic foci. More specifically, because epilepsy is caused by abnormal discharge of brain cells, entropy is a very suitable evaluation method. Experimental results show that our approach is effective for epilepsy localization and got an average test accuracy of 85.6%.
Multi-scale functional and taxonomic β-diversity of the macroinvertebrate communities in a Mediterranean coastal lagoon

Benthic macroinvertebrate communities form the basis of the intricate lagoonal food web. Understanding their functional and taxonomic response, from a β-diversity perspective, is essential to disclose underlying patterns with potential applicability in conservation and management actions. Within the central lagoon of Messolonghi we studied the main environmental components structuring the macroinvertebrate community. We analyzed the β-taxonomic and β-functional diversity across the main habitats and seasons, over a year time frame. Our results outline habitat type and vegetation biomass as the major factors structuring the communities. We found environmental variability to have a positive correlation with functional β-diversity, however no correlation was found with taxonomic β-diversity. Across the seasons an asynchronous response of the functional and taxonomic β-diversity was identified. The taxonomic composition displayed significant heterogeneity during the driest period and the functional during the rainy season. Across the habitats the unvegetated presented higher taxonomic homogeneity and functionally heterogeneity, contrary the vegetated habitats present higher taxonomic variability and functional homogeneity. Across the seasons and habitats a pattern of functional redundancy and taxonomic replacement was identified. Besides high functional turnover versus low taxonomic turnover was documented in an anthropogenic organically enriched habitat We conclude that habitats display independent functional and taxonomic seasonal patterns, thus different processes may contribute to their variability. The framework presented here highlights the importance of studying both β-diversity components framed in a multiscale approach to better understand ecological processes and variability patterns. These results are important to understand macroinvertebrate community assembly processes and are valuable for conservation purposes.
Polypore survey of Finland 5. The genus Polyporus

Distribution maps are presented for nine Polyporus species occurring in Finland. The commonest are P. brumalis (Pers.: Fr.) Fr. and P. ciliatus Fr. : Fr. A strictly southern species is P. badius (Pers.) Schw. , which has been found in two places only, and to a lesser extent P. umbellatus (Pers.: Fr.) Fr. ; both of these are classified as threatened. A widespread species with a southern emphasis is P. melanopus (Pers.: Fr.) Fr. , from which P. tubaeformis Karst has been separated. P. pseudobetulinus (Pi! .) Thorn, Kotiranta & Niemelli (syn. Piptoporus p.) has two localities in Finland and is considered to be threatened. P. squamosus (Huds.: Fr.) Fr. is sparsely distributed over the whole country and has two ecotypes, one growing on large park trees in old towns in the south, and the other a dwarfed kind inhabiting riparian thickets and having a northerly distribution. P. leptocephalus (Jacq.: Fr.) Fr. (P. varius (Pers.: Fr.) Fr. ) has a similar dual ecology, occurring both on dead, old-forest aspen trunks and on living park trees of various genera. All the species cause a white-rot, and, except for some questionable records from conifers, grow exclusively on hardwoods. Only P. squamosus does significant harm as a pathogen, causing decay in park trees.
Cooperative DNA Binding Activity

The biochemical activities that underlie the genetically defined activator and repressor functions of the VIVIPAROUSl (VP1) protein have resisted in vitro analysis. Here, we show that a glutathione S-transferase (GST) fusion protein, including only the highly conserved 83 domain of VP1, has a highly cooperative, sequence-specific DNA binding activity. GST fusion proteins that include larger regions of the VP1 protein have very low activity, indicating that removal of the flanking protein sequences is necessary to elicit DNA binding in vitro. DNA competition and DNase I footprinting analyses show that B3 binds specifically to the Sph element involved in VP1 activation of the Cf gene, whereas binding to the G-box-type VP1-responsive element is of low affinity and is nonspecific. Footprint analysis of the Cf promoter revealed that sequences flanking the core TCCATGCAT motif of Sph also contribute to the recognition of the Sph element in its native context. The salient features of the in vitro GST-B3 DNA interaction are in good agreement with the protein and DNA sequence requirements defined by the functional analyses of VP1 and VP1-responsive elements in maize cells.
Fast sex identification in wild mammals using PCR amplification of the Sry gene

Several primer sets were described for PCR amplification of the Sry gene that became very suitable method for sex identification in mammals. We tested applicability of two primer sets for sex identification in one bat and12 rodent species from Central Europe. Rapid DNA extraction with non-ionic detergents, which is very suitable for large-scale population studies, was used. Primers SRY-A from P o m p et al. (1995) did not amplify Sry fragment in males of Myotis myotis, four species of Microtus, and Clethrionomys glareolus, while amplification was successful in four species of Apodemus, two species of Mus, and Sciurus vulgaris. On the other hand, primers from S a n c h e z et al. (1996) gave clear Sry band in males of all tested species, only with one exception, i.e. male of Sciurus vulgaris.
Resistance against strongylid nematodes in two high prevalence Equine Recurrent Airway Obstruction families has a genetic basis

A recent study showed increased resistance against strongylid nematodes in offspring of a stallion affected by recurrent airway obstruction (RAG) compared with unrelated pasture mates. Resistance against strongylid nematodes was associated with RAG affection. Hypothesis: Resistance against strongylid nematodes has a genetic basis. The genetic variants influencing strongylid resistance also influence RAG susceptibility. Faecal samples from the half-sibling offspring of two RAG-affected Warmblood stallions 98 offspring from the first family (family 1) and 79 from the second family (family 2) were analysed using a combined sedimentation-flotation method. The phenotype was defined as a binary trait - either positive or negative for egg shedding. The influence of non-genetic factors on egg shedding was analysed using SAS, the mode of inheritance was investigated using PAP and iBay, and the association between shedding of strongyle eggs and RAG was estimated by odds ratios. Previously established genotypes for 315 microsatellite markers were used for QTL analyses using GRID QTL. The inheritance of "strongylid egg shedding" is influenced by major genes on ECA15 and ECA20. Shedding of strongylid eggs is associated with RAG in family 1 but not in family 2. Conclusions: The status of "shedding of strongyle eggs" has a genetic background. The results were inconclusive as to whether "egg shedding" and RAG share common genetic components. Our results suggest that it may be possible to select for resistance against strongylid nematodes.
Long‐term effects of vegetational restoration on soil microbial communities on the Loess Plateau of China

Soil microbial communities are important indicators for evaluating the effectiveness of vegetational restoration. The ability of soil microbial communities to recover under six types of restoration was examined using Biolog, phospholipid fatty acid (PLFA), and denaturing gradient gel electrophoresis (DGGE). Soil samples were collected from eroded loessial soils that had been restored for 30 years on the Loess Plateau with natural grass, black locust, korshinsk peashrub, Chinese pine, and mixed forest of Chinese pine‐indigo and black locust‐indigo. Part of sloped farmland that had not been restored represented pre‐restoration conditions. An 80‐year‐old forest of Chinese arborvitae represented the end point of restoration. Soils that were originally farmed but have been under restoration treatments for the past 30 years had significantly higher average well‐color development, total PLFAs, bacterial PLFAs, fungal PLFAs, and Shannon indices of catabolic diversity, structural diversity, and bacterial phylogenetic diversity. These indicators, though, were lower than those for the native forest. Principal component analysis significantly separated the sloped farmland, Chinese arborvitae, and the six types of restoration. Redundancy analysis indicated that pH, total organic carbon, total nitrogen, available nitrogen, and available phosphorus were the most important environment factors in affecting soil functional diversity, and C/N ratio and available nutrients were the main properties in determining microbial community structure. Vegetational restoration substantially increased microbial biomass and microbial physiological activity, and shifted microbial community structure, but the community structures and compositions did not recover to the status of the natural forest during the early stage (<30 years) of vegetational restoration.
Metabolic profiling using GC-MS to study biochemical changes during long-term storage of pears

Even though the storage disorder core breakdown in 'Conference' pears can be controlled quite well nowadays, its biochemical background remains unclear. In order to induce biochemical changes in pear fruit tissue, (1) late-harvested 'Conference' pears were stored at -1°C under browning-inducing conditions (1% O 2 , 10% CO 2 ) and (2) optimally picked pears were stored at -1°C under following CA conditions: 2.5% O 2 , 0.7% CO 2 ; 15% O 2 , 0.7% CO 2 ; 2.5% O 2 , 5% CO 2 ; 2.5% O 2 , 5% CO 2 . A simultaneous analysis of amino acids, organic acids and sugars was carried out using GC-MS. Multivariate statistics were used to reduce the complexity of the profiling data. All storage conditions were clearly separated. It was found that malic acid, succinic acid and fumaric acid were the most crucial metabolites, explaining most of the variance. Brown tissue is characterised by fumaric acid accumulation and malic and succinic acid depletion. High CO 2 conditions were characterised by enhanced levels of succinic acid whereas malic acid depletes. Depending on their degradation pathway and biosynthetic group, the concentration of certain amino acids increased while that of others decreased. An attempt was made to combine the biochemical observation with the known biochemistry of the Krebs cycle and its related pathways. Although core breakdown is considered as a CO 2 -injury, the biochemical profiles of brown pears were not equal to those of sound pears in high CO 2 conditions.