Miracle-dz/UniFAR-FTUs huggingface dataset:
Handbook of Meta-analysis in Ecology and Evolution

"Meta-analysis is a powerful statistical methodology for synthesizing research evidence across independent studies. This is the first comprehensive handbook of meta-analysis written specifically for ecologists and evolutionary biologists, and it provides an invaluable introduction for beginners as well as an up-to-date guide for experienced meta-analysts. The chapters, written by renowned experts, walk readers through every step of meta-analysis, from problem formulation to the presentation of the results. The handbook identifies both the advantages of using meta-analysis for research synthesis and the potential pitfalls and limitations of meta-analysis (including when it should not be used). Different approaches to carrying out a meta-analysis are described, and include moment and least-square, maximum likelihood, and Bayesian approaches, all illustrated using worked examples based on real biological datasets. This one-of-a-kind resource is uniquely tailored to the biological sciences, and will provide an invaluable text for practitioners from graduate students and senior scientists to policymakers in conservation and environmental management. Walks you through every step of carrying out a meta-analysis in ecology and evolutionary biology, from problem formulation to result presentation Brings together experts from a broad range of fields Shows how to avoid, minimize, or resolve pitfalls such as missing data, publication bias, varying data quality, nonindependence of observations, and phylogenetic dependencies among species Helps you choose the right software Draws on numerous examples based on real biological datasets "--
Structure and function of K ATP -channels in inspiratory neurons of mice

The respiratory center within the brainstem is one of the most active neuronal networks in the brain that generates rhythmic activity for lifetime. Such extreme stability requires efficient processes for activity-dependent adjustment of neuronal excitability. A regulatory factor securing stability comprises ATP-dependent K+-channels (KATP-channels), which link cell metabolism with electrical activity and continuously adjust the excitability of respiratory neurons during normoxia and hypoxia.Here, KATP-channels are investigated in respiratory neurons in vitro using the rhythmic brainstem slice preparation, which allows simultaneous recordings of respiratory output activity from hypoglossal nerve rootlets, patch-clamp data from respiratory neurons, and microfluorometric measurements. Single channel measurements on rhythmically active inspiratory neurons reveal that KATP-channels are persistently active and are periodically modulated. Parameters that quantitatively describe this behavior are defined and used as criterions to test the channels under conditions affecting the respiratory output (hypoxia, elevation of extracellular [K+]). The data indicate that the periodic modulation of KATP-channels is due to submembrane [ATP]-fluctuations of amplitude 5-40 microM following Na+/K+-pump activity during rhythmic respiratory bursting. Model simulations based on the signal of the fluorometric dye mag-fura-2 give an estimate of approximately 500 microM for ATP-depletion during hypoxia. As revealed by single cell polymerase chain reaction (PCR) analysis of amplified aRNA, KATP-channels of inspiratory neurons are composed of Kir6.2 and SUR1 subunits and thus correspond to the pancreatic beta-cell type. Their gating behavior, however, more closely resembles the channel kinetics described for the smooth muscle cell type as it displays at least three closed states and two open states. Finally, the intrinsic optical signal (IOS), which has previously been utilized as an indirect sensor for neuronal activity changes, is investigated. Evidence is presented that mechanisms other than cell volume changes, e.g. mitochondrial volume changes, contribute to the IOS response specifically after application of KATP-channel drugs.
Nitrogen efficiency of wheat cultivars in a Mediterranean environment

Summary. Experiments were conducted at 3 sites in Western Australia in 1993 using 33 wheat cultivars and crossbreds. Two rates of applied nitrogen fertiliser (0 and 40 kg/ha of nitrogen) were used to screen the lines for efficiency of nitrogen uptake, grain yield and grain protein production per unit of nitrogen applied, and nitrogen translocation to the grain. This information can be useful in determining nitrogen fertiliser strategies for wheat cultivars in the field. Nitrogen uptake in the plant tops was measured during the season and in the grain and straw at maturity. Grain yield, grain protein and nitrogen efficiency parameters were not markedly different between grain quality grades which are largely based on grain hardness. Yield efficient lines (high net yield increase per unit of applied nitrogen) were characterised by greater net uptake and net utilisation efficiencies but had similar yields and grain protein percentages as yield inefficient lines. Protein efficient lines (high net grain protein increase per unit of applied nitrogen) also had greater uptake efficiencies but lower utilisation efficiencies than protein inefficient lines. No lines were both yield and protein efficient suggesting that lines either use fertiliser nitrogen preferentially in yield production or in production of protein. The results indicate that in nitrogen-responsive situations it will be more profitable to use yield-efficient lines. Further investigation is needed to examine the suggestion that where soil nitrogen levels are higher (and yield responses to nitrogen are less) a greater economic return may come from using protein efficient lines. Some wheat lines had a high ability to recover fertiliser nitrogen applied to the crop. Others had a high ability to take up soil nitrogen. It is postulated that these differences may be due to differences in root systems. Some mid- and long-season lines that had high concentrations of nitrogen in the tops at anthesis metabolised that nitrogen poorly into grain yield or protein. This suggests that nitrogen efficiency may be partly related to maturity relative to length of growing season.
Genotyping of Sarawak rice cultivars using microsatellite markers.

Genetic diversity of 53 Sarawak rice cultivars, originating from Southern Sarawak, was assessed using 54 microsatellite markers. Initial polymorphism detection was conducted using 54 primer pairs distributed on 12 rice chromosomes. Polymorphic markers were chosen from the initial screening results in order to obtain microsatellite marker panels that can differentiate the rice cultivars undertaken in the study. The chosen microsatellite marker panel consisted of RM1, RM240, RM489, RM252, RM413, RM204, RM11, RM404, RM316, RM271, RM206, and RM19, with one representative from each chromosome. A total of 43 alleles were detected with an average of 3.58 alleles per locus. The polymorphism information content (PIC) values obtained from the microsatellite marker panels ranged from 0.306 to 0.730, with an average of 0.622. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram (r = 0.789) revealed 2 major groups with 6 sub-clusters and the wide range of similarity values (0.24-1.0) obtained showed a high degree of diversity among the cultivars. The results suggest microsatellite markers as a useful tool for the estimation of genetic diversity and cultivar differentiation and present invaluable genetic information for future breeding and association mapping efforts.
The role of idiotype-specific immunity in antigen receptor diversity

Lymphocytes express antigen receptors which are formed by re-arrangement of gene segments. Mutations acquired during this process, predominantly in the complementarity determining regions (CDRs), result in generation of non-germline sequences. Through analysing the CDR3 sequence, this study attempts to determine whether editing of the lymphocyte repertoire is present in an HLA-dependant manner. Data presented demonstrates a decrease frequency of CDR3-derived HLA-A2 binding peptides in HLA-A2+ donors (0.03% (SYFPEITHI) and 0.35% (BIMAS)) compared with HLA-A2- donors (0.24% (SYFPEITHI, p=0.01) and 0.54% (BIMAS, p=0.19)). Trends similar to those seen in HLA-A2 were observed in other HLA alleles as well suggesting that there may be a process by which potentially dangerous B cell populations are edited from the B cell repertoire. Similar analysis of the TCR CDR3 did not reveal any such process in all of the HLA alleles tested suggesting that there is no immunoediting of the T cell repertoire. Simultaneously, this study attempts to determine the processing and presentation of CDR3-derived peptides at the cell surface using lymphocyte antigen receptor models containing CDR3-encoded viral epitopes. The apparent presence of these peptides on the cell surface leads to the hypothesis that antibodies enter the antigen processing pathway and potentially deliver an immunogenic peptide to a target cell. Using antibodies specific for B cells, this study has shown that cells labelled with an antibody-peptide complex are targeted and lysed by cytotoxic CD4+ T cells in a peptide-specific manner. The use of such technology in antibody immunotherapy may be of considerable therapeutic benefit.
Using Recombinant PCR to Study Sequence Polymorphisms in a Family of Compact Albumin Binding Domains

Title of Document: USING RECOMBINANT PCR TO STUDY SEQUENCE POLYMORPHISMS IN A FAMILY OF COMPACT ALBUMIN BINDING DOMAINS David Anthony Rozak, Doctor of Philosophy, 2005 Directed By: Dr. Philip N. Bryan, Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute. Sixteen homologs of a compact albumin binding domain were previously identified in six proteins and four bacterial species. These domains, which exhibit varied affinities for different albumins, have been shown to support bacterial growth in vitro, and may contribute to host specificity. This dissertation describes the development of a robust PCR-based recombination technique, which is applied to representatives of the albumin binding domain to identify and understand the impact of sequence polymorphisms on domain stability and function. Analysis of phage-selected recombinants highlights the potential impact of multiple mutations in stabilizing the selected domains and improving albumin binding through gains in hydrophilic surface area, direct modifications to the binding interface, and subtle changes in the position of the third helix. The most common mutant was encoded by three fourths of the selected phage and exhibited 5 and 10 fold increases in human and guinea pig albumin binding constants compared to the wild type streptococcal domain (G148GA3). This study serves to validate further the application of in vitro recombination and phage display in the analysis of sequence polymorphisms. The recombination technique itself is shown to be well suited for producing multiple recombination events among compact heterologous domains and appears to offer several advantages over traditional DNA shuffling techniques.
Biochemical constituents of Gracilaria edulis cultured from spores

Gracilaria edulis was cultivated in west coast of India off Narakkal by reproductive method using the carpospores. The culture period was from November to March with regular sampling of growing plants for the estimation of biochemical constituents, quantitative and qualitative estimation of agar. The biochemical constituents like protein and carbohydrate content increased corresponding to the age of the plant whereas the lipid content declined. Harvesting of the crop can be determined from the qualitative and the quantitative estimation of agar along with other biochemical constituents. It was found out that crop harvested after 121 days of culture period had better quality of agar and also high protein content
Contribution à l'étude de la diversité biochimique et biologique des agents des encéphalopathies spongiformes transmissibles

Les encephalopathies spongiformes transmissibles (EST) sont caracterisees par l'accumulation d'une proteine, la PrPSc, dans le systeme nerveux central des individus malades. Selon le concept du prion, la PrPSc serait l'agent infectieux responsable des EST. La capacite des typages biologique (in vivo) et biochimique (etude des proprietes de la PrPSc) des souches de prion a refleter la reelle diversite des agents des EST reste incertaine. La premiere partie de notre travail a consiste a etudier le phenotype biochimique de la PrPSc au sein d'un panel d'isolats de maladie de Creutzfeldt-Jakob (MCJ) prealablement classes sur la base de criteres genetiques et clinico-lesionnels. Nous avons pu definir quatre groupes biochimiques distincts ne correspondant que partiellement aux categories de la classification pre-etablie et pouvant potentiellement correspondre a differentes souches de prion. Dans le deuxieme volet de nos travaux, nous avons etudie la capacite d'isolats de tremblante a se propager dans divers modeles de souris transgeniques exprimant une PrP heterologue ainsi que les consequences de ces transmissions interspecifiques sur leurs proprietes biologiques et biochimiques. Nous avons pu demontrer que le franchissement des barrieres d'especes porcine et bovine par l'agent de la tremblante atypique entrainait l'emergence de nouveaux prions, dont celui responsable de l'encephalopathie spongiforme bovine. Par ailleurs, nous avons reussi a transmettre plusieurs isolats de tremblante classique a deux lignees de souris transgeniques exprimant la PrP humaine. Dans l'une de ces lignees, la signature biochimique de l'agent propage etait similaire a celle d'isolats de MCJ sporadique.
Evolution of MHC diversity in cetacean species environment: implications for the role of a pathogen

Previous studies have indicated that the evolution of diversity in the immune system genes responsible for antigen presentation in terrestrial mammals is driven by selection. However, it is not clear whether mammals in the marine environment would experience the same selective pressures as terrestrial mammals, given their different pathogen environment. The diversity and pattern of radiation of exon-2 (peptide binding region) of the DQBl locus of Class II MHC molecule was investigated in a broad range of cetacean species, including an extended sample of six focal species (three Mysticeti and three Odontoceti species). The role of natural selection and of the evolutionary history of this locus was evaluated based on phylogenetic and genetic distance analyses, in order to assess the following hypotheses: i) the marine pathogen environment presents comparable selection pressures to those of the terrestrial environment, ii) social behaviour and structure will affect pathogenic pressure and iii) populations of cetacean species with a world-wide distribution across different habitats and geographic regions are under differential selective pressure. The phylogenetic comparison of the cetacean species was consistent with the trans-species evolution pattern described for terrestrial mammals. Furthermore, high non-synonymous to synonymous substitution rates suggest that polymorphism at this locus in cetaceans is maintained by natural selection. The higher number of trans- species lineages and non-synonymous substitution rates exhibited by social species suggest that social behaviour and social structure may affect pathogenic pressure. Population differentiation according to DQBl locus reveals a contrasting pattern to that inferred by neutral markers (microsatellite DNA) supporting the hypothesis that habitat and geographic regions may place populations under differential selection pressure. The results of the present investigation suggest that the pattern of evolution of the immune response in cetaceans is similar to that in terrestrial mammal species.
In Vitro Digestion for Pigs and Poultry

There is now widespread interest in the development of in vitro methods for assessing the digestibility of feedstuffs for monogastric farm animals, i.e. pigs and poultry. In vivo methods require the use of surgically modified animals, which is becoming less favoured due to increased awareness of animal welfare, and are expensive and slow. A number of research groups around the world are now developing in vitro methods, and this book, based on a workshop held at the Rowett Research Institute in October 1990, presents current knowledge of the subject. The book should be of interest to research workers in animal nutrition in both academic institutions and the feedstuff industry.
Assessing the risk of boat strike on Dugongs Dugong dugon at Burrum Heads, Queensland, Australia

The risk of mortality due to boat strike is increasingly being recognized as an important management issue for marine wildlife, including Dugongs Dugong dugan. Ameliorating the effects of boat strike requires assessment of how that risk varies over the management area. This is dependent on the distribution and movements of both Dugongs and boats and on the physical characteristics of the area, particularly depth. In this study we assess these features for a small community that is dependent on tourism centred around recreational fishing and which is home to a regionally significant Dugong population. During one of the most popular holiday times, boats accessing the favoured fishing site pass directly through the core area of Dugong activity. Our data show that boat strike risk to Dugongs can be lowered significantly with minimal imposition on boaters. Boaters can avoid the area of highest risk by travelling around it in deeper water. However, this straightforward solution is only possible because of the restricted spatial scale of Dugong activity and the proximity of a deepwater channel enabling boaters to easily avoid shallow areas where boat strike risk is highest.
Colostral transfer of rinderpest neutralizing antibody to offspring of vaccinated dams.

Abstract The transfer of maternal antibodies to Friesian and buffalo calves born of dams vaccinated against rinderpest was through colostrum only. Colostral antibody titers at the time of parturition were higher than the serum titer. Two hours after suckling, a high level of rinderpest neutralizing antibodies was detected in the sera of newborn animals. The half-life of maternal antibodies in buffalo and Friesian calves was found to be approximately 33 and 29 days respectively. By the age of 7-8 months, 60 per cent of buffalo calves and 80 per cent of Friesian calves had no detectable levels of rinderpest neutralizing antibody.
Five new species of jawfishes ( Opistognathus : Opistognathidae) from the western Atlantic Ocean

Synonymies, diagnoses, descriptions, illustrations, and spot distribution maps are given for ten species of Opistognathus, including all western Atlantic species that have a cirrus on their anterior nostrils. Three deep-water species lacking nasal cirri are also treated, including O. leprocarus n. sp. (Bahamas and Lesser Antilles), O. melachasme (Yucatan), and O. nothus n. sp. (North Carolina, Gulf of Mexico and Cuba); the latter two species were originally thought to represent different sexes of the same species. The O. macrognathus species group is diagnosed primarily by having sexually dimorphic jaws and sexually dichromatic maxillary markings, and includes the eastern Pacific O. scops and the following five western Atlantic species: O. macrognathus (Florida, Gulf of Mexico, and Bahamas to northern South America), O. brasiliensis n. sp. (southern Brazil), O. cuverii (southern Brazil), O. robinsi n. sp. (South Carolina, Florida, Bahamas, and Gulf of Mexico), and O. signatus n. sp. (Nicaragua, Panama, and northern South America). Opistognathus robinsi and O. signatus are very similar morphologically and here recognized as allopatric sister-species but the possibility exists that their disjunct continental distributions may be a collecting artifact. The broadly distributed and shallow-water species Opistognathus whitehurstii and O. maxillosus are superficially similar to some members of the O. macrognathus species group, including having cirri on their anterior nostrils, but differ most obviously in having non-sexually dimorphic jaws and more numerous cephalic sensory pores. An identification key is provided for all known western Atlantic species of Opistognathus.
Estudios genómicos y funcionales en Anaplasma marginale y en bacterias intracelulares de la clase alfa-proteobacteria y su relación con la reducción del genoma

La subdivision α- de la clase proteobacteria representa un grupo sumamente diverso y heterogeneo de bacterias con una gran variabilidad en sus caracteristicas genomicas, biologicas y ecologicas. Dentro de esta subdivision se encuentra el orden Rickettsiales que ha cobrado gran importancia durante los ultimos anos por agrupar a diversos patogenos [. ]
Importance of marine prey to growth of estuarine tern chicks: Evidence from an energetic balance model

We assessed the effects of quality and quantity of prey species on the growth of Little Tern Sterna albifrons chicks raised in salinas (salt-pans), Algarve, Portugal. An energetic balance model was developed, which estimated the total amount of energy ingested by all chicks in a nest and the energy expenditure by the chicks when either growing alone or in groups of two and three per nest. Energy intake per chick depended on the energy available per nest and a competition value for food between chicks. Energy expenditure was defined by the basal metabolic rate (BMR), which depends on chick's weight, plus a multiple of BMR, obtained by calibration and accounting for unspecified energetic losses. Prey species ingested by Little Tern chicks were mainly the fishes sand-smelt Atherina spp. , Sardine Sardina pilchardus, Garfish Belone belone and mummichog Fundulus spp. , but also two types of shrimp (Paleomonetes spp. and Paleomon spp.). Although prey species more abundant in salinas (shrimps and Fundulus spp.) were delivered at a higher rate, and Fundulus spp. had the greatest calorific content, chick growth was more sensitive to alterations in the ingestion of typically marine fish species, such as Sardina pilchardus and Belone belone. Model predictions were in agreement with data obtained in the field, as adults breeding in salinas foraged regularly at sea. Practical considerations from the present results are: (1) birds breeding in salinas rely on a sufficient amount of typically marine prey to ensure the growth of their chicks; (2) in some years foraging conditions in the salinas can be favourable, apparently because high food abundance (plus proximity to nests) may compensate for relatively poor quality of food types encountered.
Molecular investigation of tick-borne protozoan parasites at the livestock- wildlife interface in Kenya and evaluation of a candidate anti-tick vaccine antigen [an abstract of entire text]

Title Molecular investigation of tick-borne protozoan parasites at the livestockwildlife interface in Kenya and evaluation of a candidate anti-tick vaccine antigen [an abstract of entire text] Author(s) Githaka, Naftaly Wang'ombe Citation 北海道大学. 博士(獣医学) 甲第11071号 Issue Date 2013-09-25 Doc URL http://hdl.handle. net/2115/53836 Type theses (doctoral abstract of entire text) File Information Naftaly_Githaka_summary. pdf