Miracle-dz/UniFAR-FTUs huggingface dataset:
Spectral correction algorithm for multispectral CdTe x-ray detectors

Abstract. Compared to the dual-energy scintillator detectors widely used today, energy-resolved photon-counting x-ray detectors show the potential to improve material identification in various radiography and tomography applications used for industrial and security purposes. However, detector effects, such as charge sharing and photon pileup, distort the measured spectra in pixelated, photon-counting detectors operating under high flux. These effects result in a significant performance degradation of the detectors when used for material identification where accurate spectral measurements are required. We have developed a semianalytical, postdata acquisition, computational algorithm that corrects the measured attenuation curve for severe spectral distortions caused by the detector. The calibration of the algorithm is based on simple attenuation measurements of commercially available materials using standard laboratory sources, enabling the algorithm to be used in any x-ray setup. The algorithm is developed for correcting spectral data acquired with the MultiX ME100 CdTe x-ray detector but could be adapted with small adjustments to other photon-counting, energy-resolved detectors with CdTe sensors. The validation of the algorithm has been done using experimental data acquired with both a standard laboratory source and synchrotron radiation. The experiments show that the algorithm is fast, reliable at x-ray flux up to 5 Mph / s / mm2 and greatly improves the accuracy of the measured spectrally resolved linear attenuation, making the algorithm useful for both security and industrial applications where photon-counting detectors are used.
Phytophthora infestans population structure: a worldwide scale

Phytophthora infestans, the causal agent of late blight disease in potato and other members of the Solanaceae family, is responsible for causing the Irish potato famine and, even today, it causes enormous economic losses all over the world. For the establishment of an adequate pest management strategy, the determination of population structure is required. To characterize P. infestans populations worldwide two allozymes, Gpi (Glucose-6-phospate isomerase) and Pep (Peptidase), the RG57 DNA RFLP fingerprinting probe, as well as resistance to the fungicide metalaxyl and the mating type, have been used as markers. P. infestans populations in Mexico have been one of the main focuses of research in the population biology of this pathogen because this country has been considered as one of the possible centers of origin of this oomycete. In this review we present the population structure of P. infestans in Mexico, Europe, Africa, Asia, North America, and South America expanding on the present situation of P. infestans in Colombia. Finally, we will discuss different lines of research that are being carried out today with respect to P. infestans in Colombia, which have shown the importance of continuing the study of this devastating plant pathogen in our country.
The origin and early evolution of animals

Find the secret to improve the quality of life by reading this origin and early evolution of animals. This is a kind of book that you need now. Besides, it can be your favorite book to read after having this book. Do you ask why? Well, this is a book that has different characteristic with others. You may not need to know who the author is, how well-known the work is. As wise word, never judge the words from who speaks, but make the words as your good value to your life.
Adenocarcinoma insitu presenting as extensive crazy paving pattern: HRCT findings and review of literature

The crazy-paving pattern seen on HRCT is comprised of diffuse areas of ground glass attenuation. This imaging finding has numerous differentials including idiopathic, infectious, neoplastic and other miscellaneous entities. A 52-year-old non-smoker presented with mild to moderate dyspnoea with occasional cough and restrictive pattern on PFT. Chest radiograph showed bilateral diffuse air space opacities with crazy paving pattern on High resolution CT of the lung. This pattern has numerous differentials with pattern of lung involvement, the patient’s history and clinical findings being helpful in narrowing the diagnosis.
Phylogenetics of Thysanoptera (Insecta: Paraneoptera)

Phylogeny of Thysanoptera (Insecta: Paraneoptera) Rebecca S. Buckman Department of Biology, BYU Master of Science The order Thysanoptera (Insecta: Paraneoptera), commonly known as thrips, includes organisms that exhibit a wide range of social and feeding behaviors that are of particular interest in evolutionary studies. These studies within thrips have been inhibited by the lack of knowledge of thrips relationships. The recognized classification scheme strives to reflect evolutionary relationships and is based upon morphology. Molecular data is next as morphology alone is not enough to resolve relationships. Few molecular studies have been conducted and all were limited in their taxon sampling and genetic sampling. To provide a foundation of future evolutionary studies, the objectives of this study are to (1) test the monophyly of the suborders Terebrantia and Tubulifera, (2) test the monophyly of the families and decipher their relationships, and (3) test the monophyly of the recognized subfamilies. Phylogenies were reconstructed based upon 5299 bp, from five genetic loci: 18S ribosomal DNA, 28S ribosomal DNA, Histone 3 (H3), Tubulin-alpha (TubA) and cytochrome oxidase c subunit I (COI). 99 thrips species from seven of the nine families, all six subfamilies and 70 genera were sequenced. Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian analysis all strongly support a monophyletic Tubulifera and Terebrantia. Phlaeothripidae, Aeolothripidae, Melanthripidae and Thripidae are all monophyletic families. The relationship between Aeolothripidae and Merothripidae to the rest of Terebrantia is equivocal. Morphological and molecular data suggest Aeolothripidae or Merothripidae could be the basal lineage of Terebrantia. Four of the six subfamilies are recovered as monophyletic. The two largest subfamilies, Phlaeothripinae and Thripinae, are paraphyletic and require further study to understand relationships within them.
Biological studies on a number of Moorland Tipulidae

The life-history and ecology of Tipula subnodicornis Zetterstedt have been studied on the Moor House National Nature Reserve, an area of upland blanket-bog with an altitude range of 1300-278oft (396-845m). The annual life-cycle is maintained under different temperature conditions by adaptive responses to temperature and photoperiod during development. The optimum temperature for growth and the magnitude of response in growth rate to change in temperature both decrease during larval development. The growth phase is followed by an overwintering stage which is probably temperature independent but cannot be considered as a diapause as the metabolic rate does not drop. This phase can be ended by subjecting the larvae to an increased day length (l8hr). In the field the increasing day length in spring synchronises pupation. In the autumn emerging species, T. pagana, which has a summer diapause, decrease in day length breaks the diapause and promotes development towards pupation. In this case it has been shown that the degree of synchronisation is directly related to the shortness of day length. The population dynamics of T. subnodicornis have been studied and it was shown, by the method of k factor analysis, that overwinter mortality in the field is density dependent. Experimental manipulation of density in enclosures in the field and in culture indicated that the same was true for the early instars. A multi variate analysis on the factors affecting wing length, which was used as an indication of size and fecundity, showed that site and year were the most important influences in both sexes and that the effect of density was significant for the males. Wing length was not significantly correlated with altitude in either sex.
Bee pollination biology: buzzing, behavior, and biomechanics

For millions of years, flowering plants have relied on animals to transfer pollen among flowers; this leads to fertilization, seed set, and ultimately the passing of genetic information to the next generation. The relationships among pollinators and plants are complex. Pollinators generally visit flowers to collect food rewards. Plants have evolved a variety of mechanisms that manipulate pollinator behavior and increase the probability of successful fertilization. Plants can influence the evolution of pollinators, and pollinators can influence the evolution of plants. In this work, I characterize some of the relationships between plants and pollinators. First, I focus on buzz pollination (or floral sonication). When a bee performs this behavior, it usually grasps the anthers of the flower and, using its flight muscles, vibrates. When the vibration is transferred to the flower, pollen is released. This behavior is particularly useful when bees collect pollen from plants that have poricidal anthers that release pollen only from small pores. When bees vibrate these anthers, pollen is released, like salt coming out of a saltshaker. Buzz pollination is important for a variety of human foods (e.g. tomatoes). Honeybees, notably, cannot perform buzz pollination, and thus other pollinators, like bumblebees, are more effective at pollinating some plant species. I answer the following questions about buzz pollination: How do bumblebees change their buzz pollination behavior in different environmental conditions and on different species of plants? How do different species of bees perform buzz pollination differently?
Chinese overseas contracted projects and economic diversification in Angola and Ethiopia 2000-2017

This paper looks at Chinese construction projects in Angola and Ethiopia, which receive disproportionately little research attention compared to Chinese FDI, despite the fact that Chinese construction projects are much more important in terms of magnitude. This paper shows that Chinese construction projects have important economic spill-over effects by way of providing critical infrastructure for productive sector activities. What is more, the construction deals, often financed by Chinese state banks, have created profitable markets for building materials and spurred the production of building materials in Angola and Ethiopia thereby contributing to economic diversification in both countries. The growth of these industries is supported by policy incentives on the Chinese side and but also faces various challenges that ultimately have to be addressed by domestic industrial policy.
Immobilisation of Lactate Oxidase and Deoxyribonuclease I for use within a Bio-Artificial Liver Assist Device for the Treatment of Acute Liver Failure

Constraints of cell supply indicate that proliferating cell lines are likely to be essential components of Bio-Artificial Liver support devices (BAL) for the treatment of acute liver failure. The Liver Group BAL employs clones of cells derived from the HepG2 cell line, which in common with many tumour derived cells, are predominantly dependent on anaerobic glycolysis for energy supply, leading to production of lactate within the bioreactor. The BAL system requires prolonged culture of alginate encapsulated HepG2 cells, and lactate accumulation presents a potential hazard in this system: at ~15 mM, accumulated lactate becomes toxic to the cells in the bioreactor, and also compromises alginate bead integrity by chelating the calcium ions necessary for alginate polymerisation. Furthermore, the tumour lineage of the cells could prove a potential threat to patient safety should any HepG2 DNA enter the patient’s system. It was hypothesised that inclusion of immobilised Lactate oxidase (LOx) to catalyse degradation of lactate into pyruvate could offset these limitations whilst simultaneously providing a potential energy source utilisable by HepG2 cells. In a similar fashion, immobilised Deoxyribonuclease I (DNase I) could be utilised to remove non-patient DNA during the treatment phase of the BAL system. Here it is demonstrated that functionalised glass beads are a feasible method of immobilising LOx and DNase I. Enzymatic activity was retained even after prolonged incubation at 37°C in the presence of human plasma, offering a means of reducing lactate levels during HepG2 culture, and potentially removing circulating DNA below practically detectable levels, thus facilitating cellular performance and BAL efficiency as a safe and effective potential therapy for acute liver failure.
Inferring animal size from the unidentified long bones from the Middle Stone Age layers at Blombos Cave, South Africa

Zooarchaeological studies are generally based on analyses of faunal remains identified to family, genus or species. Middle Stone Age faunal assemblages, however, are usually highly fragmented with the majority of remains unidentified. We measured the cortical thickness of a sample of unidentified long bone fragments from the Middle Stone Age layers at Blombos Cave to investigate whether the unidentified specimens mimic the identified assemblage in terms of animal sizes represented. For reference samples, cortical thicknesses of goat (Capra hircus) bones from Gobabeb in Namibia were measured, in addition to the long bones from a sample of identified fauna from the M3 phase at Blombos Cave. Based on these comparative samples, cortical thickness measurements were used to group unidentified long bones from the M1 and upper and lower M2 phases into small, medium and large size classes. Our results suggest that medium-sized animals were more prevalent in the Blombos assemblage than indicated by the identified specimens. The size discrepancy between the identified and unidentified specimens may be the result of analytical or taphonomic processes, or human behaviour. The results also confirm previous analyses that larger animals were more common in the M1 than the upper and lower M2 at Blombos Cave.
Identifying common genetic variants associated with disease risk and clinical outcome in epithelial ovarian cancer

Combinations of common germline low-moderate susceptibility alleles may be responsible for some of the 90% of ovarian cancer (OC) cases not explained by known risk genes. These alleles may also affect survival of OC patients. The effects of 34 tagging single nucleotide polymorphisms (tSNPs) from candidate oncogenes (BRAF, ERBB2, KRAS, NMI and PIK3CA) and 63 tSNPs from “functionally” relevant genes (AIFM2, AKTIP, AXIN2, CASP5, FILIP1L, RBBP8, RGC32, RUVBL1 and STAG3) on the risk and survival of OC sufferers were evaluated with ~1,800 cases and 3,045 controls. Associations were found between disease risk and NMI rs11683487 (P-dominant=0.004) and RUVBL1 rs13063604 (P-trend=0.0192). These associations were not independently validated with additional samples, however, they remained significant when the results from both stages of genotyping were combined (P<0.05). Global tests of association with OC risk were significant for BRAF, ERBB2, CASP5 and RUVBL1 (P-global<0.05). However, there was no evidence of an excess of significant associations from 340 SNPs investigated with the admixture maximum likelihood test (P-trend=0.068). BRAF, FILIP1L, KRAS, RBBP8 and RUVBL1 were also associated with the survival of all OC cases (P<0.05). When analysis was restricted to the 4 main histological subtypes of OC, additional associations were identified. Although these results are of particular interest, they were based on relatively small numbers of samples and have not been corrected for multiple testing, therefore they should be treated with caution. The results from the secondary objective of the project, to evaluate whole genome amplification (WGA) of DNA and SNP multiplex platforms, are also described. To conclude, associations were identified between candidate oncogenes and functionally relevant genes on the survival and susceptibility of ovarian cancer. The performance of WGA DNA on SNP multiplex genotyping platforms highlighted the importance of comparing WGA DNA with corresponding gDNA in order to ascertain quality of genotyping on the platform.
The functional biology of IL-25

CD4+ T helper (Th) 2 cells secrete interleukin (IL)-4, IL-5 and IL-13 and promote immunity to gastrointestinal helminth infections and chronic inflammation associated with asthma and allergic disorders. However, the innate immune pathways that promote Th2 cell responses remain poorly characterized. The non-hematopoietic cell-derived cytokines thymic stromal lymphopoietin (TSLP), IL-33 and IL-25 (IL-17E) have been implicated in promoting Th2 cell-dependent inflammation at mucosal sites [1-4], but how these cytokines influence innate immune responses are less well defined. Studies in Chapter 2 and 3 examined the cellular mechanisms through which IL-25 promotes Th2 cell responses and demonstrated that IL-25 promotes the accumulation of a previously unrecognized non-B/non-T cell (NBNT) c-kit+ cell population in the gut-associated lymphoid tissue (GALT). Adoptive transfer of IL-25-elicited c-kit+ cells promoted Th2 cytokine responses and conferred protective immunity to helminth infection in normally susceptible Il17e-/mice. In Chapter 3, characterization of the IL-25-elicited c-kit+ cells revealed these cells to be a lineage negative (Linneg) multi-potent progenitor (MPP) cell population. This cell population, termed MPPtype2 cells, exhibited multi-potent capacity, giving rise to cells of monocyte/macrophage and granulocyte lineages both in vitro and in vivo. These data indicate the IL-25-elicited MPPtype2 cells may contribute to extramedullary hematopoiesis in vivo. The relationships between MPPtype2 cells and other recently identified innate cell populations, including natural helper cells (NHCs), nuocytes, and innate type 2 helper (Ih2) cells were examined in Chapter 4. MPPtype2 cells were found to be phenotypically distinct from nuocytes, NHCs and Ih2 cells. Further, stimulation of IL-25-elicited MPPtype2 cells with TSLP and IL-33 resulted in the differentiation of these cells into a T1/ST2+ IL7Rα+ NHC/nuocyte-like cell population, indicating that MPPtype2 cells could be progenitors of NHC/nuocytes. Combined, the results presented in this thesis demonstrate that IL-25 induces the emergence of a previously unrecognized multi-potent progenitor cell population and suggests that extramedullary hematopoiesis is an evolutionary conserved pathway that promotes Th2 cytokine responses at mucosal sites. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor David Artis
Establishing a cell biology platform: isolation and preservation of human blood products

presented to the “XXXVIII Jornadas Portuguesas de Genética”: Cell Biology Services at CEDOC/FCM Graça S. Marques, Inês Iria, Zélia Silva and Paula A. Videira The Cell Biology Services at CEDOC is a non-profitable Cell Biology Platform that offers a range of affordable, custom-made services to the research community. The Platform offers isolation of various types of human blood products (cells and sera). Primary blood cells such as mononuclear cells, monocytes, B cells and T cells are delivered on time either fresh or frozen. Haematopoietic progenitor’s differentiation into dendritic cells and macrophages is also available. The Platform is now expanding its services so as to offer genetic manipulation of primary cells. The products are processed under rigorous sterile conditions and observing strict standard operation procedures resulting from our improved, time-tested team methodologies. During and after isolation procedures, the products are analyzed and quality-tested. This service makes use of assay techniques such as Flow Cytometry, Microscopy, among others. Here, we will give an overview of our standard techniques and present our recent data comparing different methods of cell isolation, and methods for transducing non-dividing primary cells. The impact of those methodologies will be evaluated regarding cell yield, purity, and cell functional characteristics. A highly qualified and experienced team works, with gold standard criteria, to help researchers of several fields such as Immunology, Oncobiology or Genetics. With this Service we expect to establish collaborations with several Biotech companies and research groups, also to offer unique Cell Biology training to students and to develop in-house technology that may in the future lead to the setting of spin-off companies.
Characterization of Phytophthora nicotianae Pathogenic to Chamaerops humilis in Iran

Phytophthora nicotianae was isolated and identified using standard taxonomic criteria fro m Chamaerops humilis var. argentea showing inner basal leaves rot in Markazi province of Iran. Disease symptoms appeared as discoloration, water soaking on interior basal leaves. Collapse of an affected plant occurs less than one month. Lesion expands from the inner basal leaf to the tip. A ll affected plants turned to pale gray or silvery in advanced stage of disease. In pathogenicity test with insertion of mycelial plug of respective isolates, similar sympto ms produced as naturally infection. This is the first report of P. nicotianae in C. humilis fro m Iran.
Systematic studies of the South African Campanulaceae sensu stricto with and emphasis on generic delimitations

The South African Campanulaceae sensu stricto, comprising 10 genera, represent the most diverse lineage of the family in the southern hemisphere. In this study two phylogenies are reconstructed using parsimony and Bayesian methods. A family-level phylogeny was estimated to test the monophyly and time of divergence of the South African lineage. This analysis, based on a published ITS phylogeny and an additional ten South African taxa, showed a strongly supported South African clade sister to the campanuloids. Assessment of divergence times using a secondary calibration point suggests that this clade started to diversify during the Oligocene (28 mya), which coincided with global climatic changes from hot wet to cold dry conditions. A phylogenetic analysis of the South African lineage was undertaken based on morphological and DNA sequence data from the chloroplast trnL-F and the nuclear ITS regions. These data sets were analyzed separately and in combination. The phylogenetic hypothesis was used to re-assess the questionable generic boundaries in the family. The ITS data produced poor resolution under parsimony and poor support under Bayesian methods. The resulting phylogenies show five species assemblages that contradict traditional generic circumscriptions, which have primarily been based on the mode of capsule dehiscence. The date estimated for the South African clade was used as calibration point to estimate the age of the clades revealed by the molecular data. Radiation of the Campanulaceae in southern Africa seems to correlate with dramatic climatic and topographical changes such as aridification and continental uplift on the subcontinent that started during the Oligocene. The phylogenetic hypothesis was also used to trace the evolution of nine characters considered important in the circumscription of genera. An uncontradicted synapomorphy was found for the RhigiophyllumSiphocodon clade. The fruit character was found to be taxonomically unreliable at the generic level. The phylogeny of the South African clade was further used to focus on the closely related genera, Roella, Merciera and Prismatocarpus – a group forming a well supported clade in most analyses. The total evidence analysis was used to evaluate the status of each of these genera. Several options were explored to translate the phylogeny into a classification. This process was guided by the primary criterion of monophyly followed by stability in nomenclature, strong statistical support for the taxon, maximum phylogenetic information and ease of identification of the taxon. The results favour retaining of Roella, Prismatocarpus and Merciera as separate genera. A synopsis of these three is provided. Un ive rsi ty of Ca pe To wn