Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the role of T-cells in chronic lymphocytic leukemia

Abstract ! T-cells appear to have multiple conflicting roles in CLL. On the one hand tumour-specific T-cells could be used to deliver effective immunotherapy; on the other hand, certain T-cell populations may enhance CLL survival and disease progression. The aim of this thesis was to address these contradictory aspects and to provide a deeper understanding of the role of T-cells in CLL. Firstly, candidate peptides from the pro-apoptotic protein Bax were used to activate potential CLL specific T-cells from HLA-A2 patients. A CD8 T-cell clone (6C5) was isolated and it’s specificity was initially mapped to (Bax161-170; LLSYFGTPT) and (Bax160–170; GLLSYFGTPT). However, 6C5 failed to recognise HLA-A2 + CLL cells in vitro, T-cells appear to have multiple conflicting roles in CLL. On the one hand tumour-specific T-cells could be used to deliver effective immunotherapy; on the other hand, certain T-cell populations may enhance CLL survival and disease progression. The aim of this thesis was to address these contradictory aspects and to provide a deeper understanding of the role of T-cells in CLL. Firstly, candidate peptides from the pro-apoptotic protein Bax were used to activate potential CLL specific T-cells from HLA-A2 patients. A CD8 T-cell clone (6C5) was isolated and it’s specificity was initially mapped to (Bax161-170; LLSYFGTPT) and (Bax160–170; GLLSYFGTPT). However, 6C5 failed to recognise HLA-A2 + CLL cells in vitro, and failed to recognise highly purified forms of the peptides. Further characterisation, involving mass spectrometry and HPLC, mapped T-cell specificity to a modified peptide (LLSY(3-tBu)FGTPT). A second strand of this project involved detailed phenotypic analysis of T-cells from CLL patients (n=97) in order to investigate the basis for immune dysfunction. This analysis indicated that patients with an inverted CD4:CD8 ratio (CLL), displayed a skewing towards a highly differentiated T-cell phenotype, as well as expression of markers associated with replicative senescence (CD57, CD27) within CD4 and CD8 T-cell compartments. In addition, CD4 T-cells expressing markers associated with immunosuppression (PD-1, TIM-3) were also increased in CLL. Importantly, the inversion of the CD4:CD8 ratio was associated with shorter progression-free survival. Furthermore, the frequencies of distinct T-cell populations were also shown to have prognostic impact in both univariate analysis (CD4PD-1, CD4CD57, CD8CD57 and CD8CD27) and multivariate analysis (CD4CD27PD-1LAG-3 and CD8CD27 CD57PD-1). To further evaluate the differences between CLL and CLL patients, preliminary transcriptional analysis was performed, focusing on genes associated with T-cell function.
An Antimicrobial Diterpene from Chrysanthemum Coronarium

The CHCl3 extract of the air-dried leaves of Chrysanthemum coronarium afforded ent-kaurane-3β,16β-diol (1). The structure of 1 was determined by extensive 1D and 2D NMR spectroscopy. Antimicrobial tests on 1 by the agar cup method indicated that it has low antimicrobial activity against B. subtilis, S. aureus, C. albicans and T. mentagrophytes and is inactive against . F aernginosa and E. coli.
Prevalence of Salmonella in Swine and Pork: A Farm to Consumer Study

and Implications Fecal, tissue, and environmental cultures and serological tests were performed on 100 swine on a multiÐ site farrow to finish production facility. Salmonella of 10 types were identified in the swine herd and environment but none were recovered from rodents or flies caught in the production units. At slaughter, 52% (24 of 46) of swine were serologically positive for Salmonella antibodies, while 9% (4 of 46) were positive by culture. Although clinical salmonellosis was not detected in the study herd, multiple serotypes of Salmonella were causing endemic infections in the study herd.
Handbook on Metalloproteins

Interaction of sodium and potassium with proteins structure and function of sodium and potassium channel proteins in membranes magnesium-activated enzyme systems calcium and its enzymes vanadium in proteins and enzymes are there proteins containing chromium? manganese-containing enzymes and proteins iron in heme and related proteins iron-sulfur proteins structure-function of non-heme iron proteins with oxygen and nitrogen dominated coordination iron storage and transport cobalt in vitamin B12 and its enzymes nickel-containing enzymes copper proteins in the transport and activation of dioxygen, and the reduction of inorganic molecules multi-copper oxidases copper in electron transfer proteins proteins of various functions containing copper zinc sites in metalloenzymes and related proteins zinc finger proteins other zinc proteins -metallthioneins and insulin enzymes and proteins containing molybdenum or tungsten emerging themes and patterns among metalloproteins one and three letter symbols for the amino acids the standard genetic code.
Impacts of deficit irrigaton applied at different growth stages on vitamin contents of broccoli.

his research was conducted in order to determine the impacts of deficit irrigation applied at different growth stages on some vitamin contents of broccoli during 2010 growing season. Variations in L-ascorbic acid (vitamin C), retinol (vitamin A) and α-tocopherol (vitamin E) contents were determined by using high-pressure liquid chromatography (HPLC) method. Maraton Broccoli was grown as the plant material of the study and 5 different water deficit levels (80, 60, 40, 20%, and a control treatment with 100%) were applied during 3 different growth stages (early vegetative, late vegetative and flowering periods) of broccoli plants. Results revealed significant variations in L-ascorbic acid (vitamin C), retinol (vitamin A) and α-tocopherol (vitamin E) contents of broccoli heads with deficit irrigation applications at different growth stages. Results revealed significant variations in L-ascorbic acid (vitamin C), retinol (vitamin A) and α-tocopherol (vitamin E) contents of broccoli heads with deficit irrigation applications at different growth stages.
Influence of way of farming and types of food on the morphometric characteristics of the small and large intestines in broiler turkey.

Morphological characteristics of the digestive systems in birds are direct reflection of evolutionary adaptations of these animals to different type and way of diet. The research conducted on domestic and some wild birds indicate that besides the evolutionary factors, time of start of food intake after the hatching, and amount and composition of food in the period of intensive growth also influence morphological characteristics of digestive systems in birds. The aim of this study was to determine the influence of extensive and intensive way of farming, and different types and amount of food on the morphometric characteristics of the small and large intestines in 45 broiler turkeys (BIG BUT 600). Statistical analysis shows that the way of breeding and the type and quantity of food all have significant impact on the body weight in turkeys but do not influence the length of the intestinal tract in these animals. Key words: turkey, digestive system, morphology
Terrestrial Ecosystems in Changing Environments

Preface 1. The importance of understanding ecosystem change 2. The omnipresence of change 3. Temporal scale, spatial scale and the ecosystem 4. An introduction to ecological modelling 5. Niche theory 6. Vegetation and environment relations 7. The mosaic theory of natural landscapes 8. Individual-based models 9. Consequences of gap models 10. Landscape models 11. Mosaic landscape models 12. Spatially interactive landscapes 13. Homogeneous landscape models 14. Global change References Index.
Evaluation of Common Bean Cultivars for their Resistance Against Xanthomonas Axonopodis Pv. Phaseoli

Common bacterial blight (CBB) caused by the bacterium Xanthomonas axonopodis pv.phaseoli (Xap), is an economically important disease of beans worldwide. Since there wasno satisfactory chemical control for the disease, use of resistant cultivars is an important management strategy. The main objective of this study was to determine CBB reaction oftwenty different bean genotypes breed and/or maintained by Melkassa Agricultural Research Center. The genotypes were evaluated under field and greenhouse conditions for their reaction to Xap following leaf-spray inoculation with bacterial suspension of 10 8cfu/ml. Disease was ratted with 0 - 9 visual scale and the percent severity index (PSI)was calculated. The results revealed that the evaluated genotypes showed various levelof reaction to Xap. Three genotypes GLP-2, ECAB005 and Gobe Rasha were showed resistant reaction against Xap. Eleven genotypes showed moderately susceptible disease reaction with mean disease severity rating values ranging from 3.57- 5.00 while sixgenotypes were categorized as susceptible and one genotype Mexcan-142 showed highsusceptibility. The study results were in a conclusion that there is a resistant gene in theresistant and moderately susceptible genotypes. Therefore, the resistant genotypesshould be promoted in bean production system to increase common bean production and productivity in reducing CBB epidemics and associated yield loss. Moreover, theresistant and moderately susceptible genotypes identified can be used as possible sources of resistance for breeding program against CBB to improve the susceptibility ofcommercial bean cultivars commonly cultivated in the study area.
Collagen hydrolysates derived from Yezo sika deer (Cervus nippon yesoensis) tendon have highly health-promoting potentials.

Hydrolysis was applied to collagen of Yezo sika deer tendon using six proteases (pepsin, trypsin, papain, chymotrypsin, pronase E, and thermolysin). The yields of hydrolysates and its protein contents ranged from 69 to 96% (w/w) and 185.7 to 260.6 μg/mg lyophilized powder, respectively. Next, the functional properties of hydrolysates were demonstrated using a different four systems. Antioxidative activities were moderate; the hydrolysates prepared by pepsin, trypsin, chymotrypsin, and pronase E showed the same activities as 1 mM ascorbic acid. Reactive oxygen species scavenging activities were also measured. Highly scavenging activities were observed in pronase E, papain, and chymotrypsin hydrolysates. On the other hand, thermolysin hydrolysate strongly inhibited ACE activity. From the above investigation, Yezo sika deer tendon can be used as an easily accessible underutilized bioresource of natural antioxidants, ACE inhibitors, and as a possible food supplement or in biomedical fields and pharmaceutical industry.
Inhibitors of N-linked glycosylation induce systemic acquired resistance in cucumber.

Abstract Localized treatment of cucumber ( Cucumis sativus L. cv. Wisonsin) cotyledons with inhibitors of N-glycosylation such as tunicamycin or amphomycin resulted in systemic acquired resistance in the first leaf to the fungal pathogen Colletotrichum lagenarium . Resistance was maximal as early as 2 days after application and best results were observed when the inhibitor was used at 100 μ M . The same treatment also induced salicylic acid accumulation as well as the expression of chitinase and a PR1-like protein. The systemic effect is not caused by the transport of tunicamycin, since tunicamycin was not detected in the leaves. Within 2 h after application tunicamycin inhibited N-glycosylation, but not protein synthesis as indicated by labelling experiments. The amount of large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase decreased after tunicamycin treatment and after pathogen inoculation and the expression of BiP, a protein localized in the endoplasmic reticulum was enhanced. The activation of defense reactions seems to be dependent and sensitive to N-linked glycosylation.
Clostridium perfringens: spores & cells, media & modeling

Clostridium perfringens is one of the five major food borne pathogens in the western world (expressed as cases per year). Symptoms of C. perfringens food poisoning are caused by an enterotoxin, which is released when ingested cells sporulate in the intestines. To increase knowledge on this bacterium, it was tried to optimize sporulation of a variety of strains, but only strain dependent effects were noted. Since many media are available to isolate C. perfringens from foods, a selection of these media was compared and it was shown that these media performed equally well. Cooling and storage of food are often the cause of gastro enteritis. Therefore, the behavior of this microorganism was studied at low temperatures and a model was designed to predict the effect of various cooling procedures applied to food on growth of C. perfringens . The model can be used to set up Good Manufacturing Procedures (GMP).
Animal Tracks and Signs

PREFACE HOW TO USE THIS BOOK FOREWORD BY RAY MEARS INTRODUCTION FOOTPRINTS BIRD TRACKS FEEDING SIGNS FEEDING SIGNS ON SEEDS, FRUIT AND HERBACEOUS PLANTS ANIMAL REMAINS OTHER FEEDING SIGNS DROPPINGS URINE PELLETS OTHER SIGNS INDEX
Occurrence of Clubroot in Cruciferous Vegetable Crops and Races of the Pathogen in Korea

Cruciferous vegetable crops grown in several locations in Korea were surveyed from 1996 to 2000. Clubroot severely occurred up to a maximum of 100％ in Chinese cabbage fields in 15 out of 42 locations, and in cabbage fields in 5 out of 13 locations surveyed. The disease also severely occurred up to a maximum of 40％ in radish fields in 6 out of 35 locations, and up to a maximum of 40% and 100％ in turnip and brown mustard fields in one each out of the few locations surveyed, respectively. The disease occurred less than l％ in one kale field in one out of two locations surveyed. A total of 268 isolates of Plasmodiophora brassicae was obtained from six cruciferous vegetable crops. The isolates were classified into 13 races based on their pathogenicity to the differential varieties of cabbage and rutabaga. There were 13 races found in isolates from Chinese cabbage, while 6 races each were found in isolates from cabbage and radish. There were five and three races found in turnip and brown mustard isolates, respectively. One isolate from kale was identified as race 8. Race 8 was the most frequently isolated from five cruciferous vegetable crops, except brown mustard. Races 3 and 14 were isolated only from Chinese cabbage.
The effect of growth conditions on the surface properties of Listeria monocytogenes

Due to the recent persistence of Listeria monocytogenes in food factory environments and an increase in outbreaks of Listeriosis, in particular some associated with duck meat products, an investigation was carried out to establish the potential effects of different growth conditions on the hydrophobicity of L. monocytogenes cells and to determine the behaviour of the cells in a minimal nutrient environment. It was found that duck meat extracts increased growth rate but did not alter the surface charge of the cells and when grown in minimal 010 and MCDB202 media the cells flocculated and showed more hydrophobicity than when grown in the rich media BHI. The modified surface of the organism behaved like an emulsifier and this led to the discovery for the first time, that there was formation of capsular exopolymeric substances (EPS) on the surface of planktonic cells of L. monocytogenes. After confirmation of the capsular EPS by two capsule stains, namely Nigrosin and Giemsa, the EPS was purified and proved to play a role in holding the cells together. It was also found to absorb water rapidly and can retain water for long periods suggesting that the EPS can contribute to the desiccation tolerance of L. monocytogenes cells embedded in a biofilm matrix. Chemical characterization of the EPS showed high levels of glycerol and phosphate indicating that the EPS is amphiphatic and may contain mainly glycerolphosphates.
Mechanisms of Experience-dependent Prevention of Plasticity in Visual Circuits

Development of brain function is instructed by both genetically-determined processes (nature) and environmental stimuli (nurture). The relative importance of nature and nurture is a major question in developmental neurobiology. In this dissertation, I investigated the role of visual experience in the development and plasticity of the visual pathway. Each neuron that receives visual input responds to a specific area of the visual fieldtheir receptive field (RF). Developmental refinement reduces RF size and underlies visual acuity, which is important for survival. By rearing Syrian hamsters (Mesocricetus auratus) in constant darkness (dark rearing, DR) from birth, I investigated the role of visual experience in RF refinement and plasticity. Previous work in this lab has shown that developmental refinement of RFs occurs in the absence of visual experience in the superior colliculus (SC), but that RFs unrefine and thus enlarge in adulthood during chronic DR. Using an in vivo electrophysiological approach, I show that, contrary to a widely held view, visual experience is not necessary for refinement of RFs in primary visual cortex (V1). In both SC and V1, RFs refine by postnatal day (P) 60, but enlarge by P90 with chronic DR. One week of visual experience was sufficient to prevent RF enlargement in SC and V1. How normal sensory experience prevents plasticity in mature circuits is not well understood. Using an in vitro electrophysiological approach, I demonstrated that GABAergic inhibition is reduced in DR SC, which in turn affects short-term (but not long-term) synaptic plasticity. The level of GABABR-mediated short-term synaptic depression (STD) that occurs during high-frequency afferent stimulation, such as occurs during vision, is reduced by DR. Using a computational model of RF size, I propose that, in addition to the effect of reduced inhibition, reduced STD of excitation could contribute to enlarged RFs. This work provides insight into mechanisms of development and plasticity of the nervous system. How plasticity is restricted in mature circuits is of fundamental importance in neuroscience and could instruct therapies to prevent maladaptive plasticity in disease and to enhance recovery of function in adults. INDEX WORDS: Superior colliculus, Visual cortex, Adult plasticity, Receptive field, Inhibitory plasticity, Rodent, Critical period, Visual deprivation MECHANISMS OF EXPERIENCE-DEPENDENT PREVENTION OF PLASTICITY IN VISUAL CIRCUITS
Improving biosecurity: a necessity for aquaculture sustainability.

M. Hine1 (*), S. Adams2, J.R. Arthur3, D. Bartley4, M.G. Bondad-Reantaso5, C. Chavez6, J.H. Clausen7, A. Dalsgaard8, T. Flegel9, R. Gudding10, E. Hallerman11, C. Hewitt12, I. Karunasagar13, H. Madsen14, C.V. Mohan15, D. Murrell16, R. Perera17, P. Smith18, R. Subasinghe19, P.T. Phan20 and R. Wardle21 1 73, rue de la Fee au Bois, 17450, Fouras, Charente Maritime, France. E-mail: vinet.hine@orange.fr 2 Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, Scotland, UK. E-mail: alexandra.adams@stir.ac. uk 3 Box 1216, Barriere, B.C., Canada V0E 1E0. E-mail: jraconsulting@xplornet.ca 4,5,13,19 Department of Fisheries and Aquaculture, Food and Agriculture Organization of the United Nations (FAO), Viale delle Terme di Caracalla, Rome, Italy. Devin.Bartley@fao.org, Melba.Reantaso@fao.org, Iddya.Karunasagar@fao.org, Rohana.Subasinghe@fao.org 6 Unidad Mazatlan en Acuicultura y Manejo Ambiental del CIAD, A.C. Av. Sabalo Cerritos s/n, Mazatlan, Sinaloa, Mexico. E-mail: marcris@ciad.mx 7, 8, 14, 16 Department of Veterinary Pathobiology, Royal Veterinary and Agricultural University, Groennegaardsvej 15, 1870 Frederiksberg, Denmark. E-mail: jehc@life.ku. dk ; ad@life.ku. dk ; hm@life.ku. dk ; hm@life.ku. dk 9 Centex Shrimp and Dept. Biotechnology, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok 10400, Thailand. E-mail: sctwf@mahidol.ac. th 10 National Veterinary Institute, POBox 750, 0106 Oslo, Norway. E-mail: roar.gudding@vetinst.no 11 Department of Fisheries and Wildlife Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0321, United States. E-mail: ehallerm@vt.edu 12 National Centre for Marine and Coastal Conservation, Australian Maritime College, University of Tasmania, Australia. E-mail: chewitt@amc.edu. au 15 Network of Aquaculture Centres in Asia and the Pacific, Bangkok, Thailand. E-mail: mohan@enaca.org 17 Biosecurity Australia, Australian Government Department of Agriculture Fisheries and Forestry, GPO Box 858, Canberra ACT 2601, Australia. E-mail: Ramesh.Perera@daff.gov. au 18 Department of Microbiology, National University of Ireland, Galway, Ireland. E-mail: peter.smith@nuigalway.ie 20 Centre for Environment Disease Monitoring in Aquaculture-Research Institute for Aquaculture, No. 1. Bac Ninh, Vietnam. E-mail: phanvan@ria1.org 21 Intervet Schering-Plough Animal Health, 24-26 Gold Street, Saffron Walden, Essex CB10 1EJ. E-mail: Robin.wardle@sp.intervet. com
Antisense RNA and DNA.

Partial table of contents: ANTISENSE RNA Regulation of Gene Expression and Function by Antisense RNA in Bacteria (C. Thomas) Use of Antisense RNA to Study Gene Expression in the Mammalian Preimplantation Embryo (B. Levy, et al.) Manipulation of Myelin Formation in Transgenic Mice (M. Kimura, et al.) Use of Antisense RNA Technology to Engineer Virus Resistance in Plants (E. Bejarano, et al.) The Double-Stranded RNA Unwinding/Modifying Activity (B. Bass) ANTISENSE DNA Anticancer Drug Design Using Modified Antisense Oligonucleotides (D. Tidd) Transmembrane Passage and Cell Targeting of Antiviral Synthetic Oligonucleotides (G. Degols, et al.) CASE STUDIES Alternative Antiviral Approaches to Influenza Virus: Antisense RNA and DNA (S. Agrawal & J. Leiter) RIBOZYMES Selective Amplification Techniques for Optimization of Ribozyme Function (G. Joyce) Index.
Moritella viscosa Virulence. Extracellular Products and Host-Pathogen Interaction

Moritella viscosa is the causative agent of winter ulcer disease of marine fish. Knowledge of its pathogenicity is limited and there are no reports comparing the virulence properties of a collection of bacterial isolates. The in vivo and in vitro virulence of the extracellular products (ECP) of 22 M. viscosa isolates was screened. Two non-virulent Canadian isolates and a Norwegian isolate with reduced vir- ulence produced non-lethal ECP. Correlation was obtained between cytotoxin and haemolysin pro- duction of M. viscosa. Isolates from salmon pro- duced ECP with lower cytotoxic and haemolytic activities than ECP of isolates originating from other hosts. Correlation was not found between lethality of ECPs in salmon and cytotoxic or hae- molytic activities. All isolates secreted esterases and a metallopeptidase (MvP1), degraded starch and produced siderophores. Variable levels of ECP protein concentration, different enzymatic activities and siderophore production could not explain dif- ferences in virulence. The results show that virulent M. viscosa isolates secrete a lethal toxic factor of unknown nature and that cytotoxin production may reflect host adaptation. Cell-culture models may not be optimal for determining the virulence of M. viscosa, as no association between cytotoxicity and bacterial virulence was obtained. Non-virulent strains may be useful in future research on M. vis- cosa virulence, as construction of mutants has not been successful.