Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathogenesis of Rett syndrome and study of the role of meCP2 protein in neuronal function.

Rett syndrome (RTT) is a neurodevelopmental disorder that affects mainly girls. It features a period of apparently normal development during 6-18 months followed by an arrest in development with further deterioration of motor, autonomic and social and cognitive skills. RTT females present with a movement disorder (ataxia and apraxia), autistic behaviour, hand stereotypies and mental retardation. Besides this classical form of the syndrome, variant forms may comprise milder or more severe presentations, as well as the male phenotype, usually more severe due to hemizygosity of the X chromosome. Mutations in the methyl-CpG binding protein 2 gene (MECP2) are the primary cause of RTT (>90% in classical and 30% in atypical RTT cases). However, to a lower extent, mutations in MECP2 have also been identified in patients with other, partially overlapping neurodevelopmental disorders, such as autism, non-syndromic mental retardation and Angelman syndrome. MECP2 mutations occur throughout the entire gene and are of all types. Nevertheless, a significant proportion of RTT cases remain without a genetic explanation, which suggests the involvement of non-coding MECP2 regions or other genes in this pathology. The major role of MeCP2 protein is as a transcriptional repressor. MeCP2 binds to methylated DNA and acts through the recruitment of Sin3A and histone deacetylases to form a complex that will deacetylate histones in order to repress transcription. Mutations in the MeCP2 will cause a dysregulation in transcription of target genes. Nevertheless, other function(s) of MeCP2 may also be affected as some mutations in the MeCP2 that do not impair its repression capacity, occur in sites of MeCP2 binding to other proteins. Our goal in this study is to “map” specific mutations in the MECP2 gene with a specific phenotype in human and mice and to understand the pathogenic mechanism underneath this phenotypic variability, in particular in the motor impairment. In our Genetic study of Portuguese patients with RTT or with related neurodevelopmental disorders we identified different types of mutations in the MECP2 gene, distributed throughout the entire gene. Given the lack of a significant phenotype-genotype correlation in previous studies, we attempted an original approach to this question based on the predicted and observed functional effect of the different MECP2 mutations. We found an interestingly correlation between null alleles and mutations that completely abolish the repression capacity of MeCP2 with a more severe form of the disorder, where extrapyramidal signs predominate. On the other hand, mutations with a milder effect, such
Environmental and landscape effects on cross-pollination rates observed at long distance among French oilseed rape Brassica napus commercial fields

Summary 1 Evaluation of our ability to predict cross-pollination rates (CPR) at long distance using dispersal functions estimated in experimental set-ups differing by either their scale or their environmental conditions is crucial to establish appropriate management rules following the release of genetically modified (GM) crops. 2 From 1998 to 2004 we measured oilseed rape CPR in commercial fields for 44 donor-recipient couples separated by 220 up to 2000 m, from up to three different pollen donor cultivars in two French oilseed rape production areas. We followed the same sampling and screening designs and tested the effect of region, year, size, cultivar and distance on the observed CPR. 3 We then compared observed CPR to predictions from six empirical pollen dispersal models based on dispersal kernels that were fitted previously at the local and landscape scales. These predictions allowed us to test the possibility to extrapolate and up-scale dispersal kernels. 4 The observed CPR varied from 0% to 0·092%. They were higher in Champagne-Ardennes, where they depended negatively on distance, than in Bourgogne where they did not depend on distance. CPR also differed among years, being nil for the last 3 successive years, partly because of different environmental conditions and detection issues. CPR depended further on the source cultivars due to differences in pollen production. Dispersal kernels fitted at the local scale lead to systematic and huge underestimation of CPR, when observed. The power-law kernel fitted at the landscape scale under-estimated CPR by two orders of magnitude above 400 m but followed the rate of decrease of the observed pollination with distance. 5 Synthesis and applications. Caution should be taken when extrapolating and up-scaling dispersal kernels and models because predictions may differ greatly from observations. Models should rely at least upon dispersal kernels estimated from landscape-scale data obtained in different regions. Models should also integrate several phenomena at the agro-ecosystem scale including the dispersal by insects and become more mechanistic to account for variations observed among years, environments and distance to borders.
Technical Efficiency and Social Capital in Tilapia Aquaculture Production in Nueva Vizcaya, Philippines

This paper focuses on tilapia aquaculture production in Nueva Vizcaya, Philippines. Primary data were collected from a field survey. Apart from investigating the effects of technical efficiency variables (e.g., operatorâ€™s experience, age of fishpond owner, and frequency of visits of the manager) on the production frontier, this study also incorporated social capital variables (e.g., social network and trust) as additional factors affecting the frontier. A cross-sectional analysis of 202 fishpond operators from the 10 municipalities in the province was conducted using stochastic frontier analysis, where the error component consists of both the usual two-side random shocks and the one-side technical inefficiency shocks. Results suggest that social network has an indirect but significant relationship to aquaculture harvest. On the other hand, harvest is significantly influenced by community trustworthiness, which implies that fish farmers who do not readily lend money to members of their community are able to increase their harvest because they can devote their funds to production activities.
Sedimentology, geochemistry and reservoir properties of Upper Jurassic deep marine sediments (Hareelv Formation) in the Blokelv-1 borehole, Jameson Land Basin, East Greenland

The fully cored Blokelv-1 borehole was drilled through Upper Jurassic strata in the central part of the Jameson Land Basin, central East Greenland. The borehole reached a total depth of 233.8 m with nearly 100% recovery of high-quality core. An extensive analytical programme was undertaken on the core; sedimentological interpretation and reservoir characterisation were based on facies analysis combined with conventional core analysis, bulk geochemistry and spectral gamma and density scanning of the core. The Upper Jurassic Hareelv Formation was deposited in relatively deep water in a slope-to-basin setting where background sedimentation was dominated by suspension settling of organic-rich mud in oxygen-depleted conditions. Low- and high-density gravity-flow sandstone interbeds occur throughout the cored succession. About two-thirds of the high-density turbidite sandstones were remobilised and injected into the surrounding mud-rock. The resulting succession comprises nearly equal amounts of mudstones and sandstones in geometrically complex bodies. Ankerite cementation occurs in 37% of the analysed sandstones in varying amounts from minor to pervasive. Such ankerite-cemented sandstones can be identified by their bulk geochemistry where Ca > 2 wt%, Mg > 1 wt% and C > 1 wt%. The analysed mudstones are rich in Al, Fe, Ti and P and poor in Ca, Mg, Na and Mn. The trace-metal content shows a general increase in the upper part of the core reflecting progressive oxygen depletion at the sea floor. The reservoir properties of the Blokelv-1 sandstones were evaluated by both conventional core analysis and using log-derived porosity and permeability curves. The high-density turbidite beds and injectite bodies are a few centimetres to several metres thick and show large variations in porosity and permeability, in the range of 6–26 % for porosity and 0.05–400 mD for permeability. Individual sandstone units that are 1–7 m thick yield a net vertical reservoir thickness of 40 m with porosities of 15–26% and permeabilities of 1–200 mD. Heterolithic sandstone–mudstone units are generally characterised by poor reservoir quality with porosities of 2–14% and permeabilities of 0.1–0.6 mD.
Composição do zooplâncton em cinco lagos da Amazônia Central

A study of the species composition, satnding-stock and diversity of the zooplancton groups Rotifera. Cladocera and Copepoda. was conducted in five lakes In the Central Amazonian region. The lakes present distinct physical, chemical and biological parameters which allows for distinguishing two groups: On the first group, caracterized by the lakes which present greater concentration of ions, greater availability of nutrients, and greater diversity of zooplancton species are the "varzea" lakes. Castanho, Redondo and Jacaretinga. On the second group, caracterized by the lakes which present low concentrations of ions, few nutrients, and a low diversity of zooplancton species are the "terra-firme" lakes, Cristalino and taruma-Mirim. The structure of the zooplancton comunities in Amazonian lakes is periodically altered by the inundation of the rivers.
The toxic effects of ammonia on growth rate and some blood parameters in common carp (Cyprinus carpio L.)

This study was performed to know the effect of ammonia on the blood picture and the weight of common carp fish. 50 fish were used at the age of 6 months and were divided into two groups. Each group included 25 fish. The first group represented the treatment group with ammonia at a concentration of 1.0 mg/ L. and the second group represented control group. It is grown in plastic basins with dimensions of 1.5 × 2 meters and continued treatment for four weeks. It was observed that the weight in the ammonium treatment group had the lowest significant value (p≤0.05) compared to the control group. It was also observed in this study that the ammonia group had the lowest significant values in (white blood cells, red blood cells, hemoglobin concentration and Packed cell volume) compared with control group. As for the biochemical parameters, it was observed that the Glucose concentration and each of the enzymes Alanine Aminotransferase (ALT) and Aspartate Aminotransferase (AST) had a record the highest value in the group treated with ammonia compared with the control group while the total protein recorded the lowest significant value in the group treated with ammonia Compared to control group. We conclude from this study that increasing the concentration of ammonia in the aquatic environment has a negative impact on fish breeding and health.
Activity, molecular mass and hydrolysis on baker's yeast protein of extracellular proteases from the putative probiotic bacteria Microbacterium sp. strain 8L and Exiguobacterium mexicanum strain 8N

The bacteria Microbacterium sp. 8L and Exiguobacterium mexicanum 8N are known to improve the culture of Artemia franciscana using baker's yeast as food. Using spectrophotometry, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), substrate-SDS-PAGE and pH-stat in vitro-digestibility assays, the activity, molecular mass and hydrolysis on baker's yeast protein of proteases from extracellular polymeric substances (EPS) of the strains 8L and 8N along with the pathogenic strains Microbacterium sp. 8R and Vibrio parahaemolyticus 588 CECT (Vp) were studied. The EPSs of 8L and 8R showed one activity band, on which the serine inhibitor phenylmethylsulphonyl fluoride (PMSF) had no effect. The EPSs of 8N showed four bands; two were unaffected by PMSF, whereas one was affected, and the other was partially affected. The EPSs of Vp showed two bands, one partially inhibited by PMSF. No inhibitory effects from 1-chloro-3-tosylamido-7-amino-2-heptanone (trypsin inhibitor) were observed in the protease bands of the studied bacteria. The EPSs of 8L and 8N showed a similar degree of hydrolysis (pH-stat). The EPSs of 8L had the lowest Dice index of similarity of yeast protein profiles at 1 h of reaction. We conclude that the strain 8L could benefit A. franciscana by providing bacterial proteases for digestion of baker's yeast.
Exploring the relationship between restored ecosystem function and species composition: a meta-analysis

iv Acknowledgements v Chapter 1 – Measuring ecological composition, structure and function in assessing restoration success 1 Chapter 2 – The relationship between restored ecosystem function and species composition: a meta-analysis 15 Introduction 15 Methods 17 Results 25 Discussion 37 Chapter 3 – Broader implications and future research directions 42 Appendix 46 Literature cited 57 Un ive rsi ty of Ca pe To wn
Association between noise annoyance and hearing loss caused by chronic exposure to noise among the workers of an automotive industry

Background: As a physical pollutant in the workplace, noise has physiological and psychological consequences for people. Objective: The aim of this study was to investigate the relationship between annoyance and hearing loss in the people exposed to chronic noise in the automotive industry. Methods: 250 workers exposed to sound pressure in the work environment were randomly selected. The DANPLEX-AS54 audiometry device was also used to measure the workers’ hearing levels. Furthermore, an annoyance inventory containing questions numbered 1 to 11 to indicate the level of annoyance was used as well. Results: using Pearson correlation coefficient to evaluate hearing levels and annoyance, we found out a significant positive relationship between annoyance and hearing level at frequencies of 2000, 4000 and 8000 in the left ear, and frequency of 6000 in the right ear (P <0.001). Also, there was a significant relationship between annoyance and NIHL (noise-induced hearing loss) in the left ear, and general conditions (both ears) (P <0.001). Conclusion: The results of this study, showed that there was a significant positive relationship between noise annoyance and hearing loss among the workers, and the likelihood of noise annoyance increased with the incidence of hearing loss. *Correspondence to: Fakhradin Ahmadi kanrash, MSc Student, Department of Occupational Health Engineering, Student Research Committee, School of Public Health, Iran University of Medical Sciences, Tehran, Iran, E-mail: F_ahmadi1367@yahoo.com
A Yeast Genomic Screen to Identify Effectors of Kir2.1 Plasma Membrane Residence

Protein quality control is important for the disposal of toxic misfolded proteins. Ion channels represent a class of proteins that are suited for the study of protein quality control within the secretory pathway. The inward rectifying potassium channel, Kir2.1, functions at the plasma membrane in several tissues to maintain membrane potential and osmotic homeostasis, and not surprisingly defects in Kir2.1 lead to a host of diseases. To identify Kir2.1 regulators, a yeast Kir2.1 expression system was established. Although a small population appeared to localize to the plasma membrane, Kir2.1 primarily localized to the ER and a significant fraction was targeted for ER associated-degradation (ERAD). To identify the spectrum of factors that maintain Kir2.1 plasma membrane residence, the expression plasmid was introduced into a potassium transporter deficient strain in which Kir2.1 restores growth on low potassium, and the strain was crossed to the deletion collection to obtain haploid progeny. Among the mutated genes that significantly increased cell growth on low potassium were those encoding members of the Endosomal Sorting Complex Required for Transport (ESCRT). ESCRT also regulated Kir2.1 stability in HeLa cells. These data indicate that Kir2.1 function is controlled by later steps in secretory pathway quality control, but not ERAD. The screen described represents a model that can be used for other ion channels.
MELOIDOGYNE SPP. INFECTING ORNAMENTAL PLANTS IN FLORIDA

Brito, J. A. , R. Kaur, R. Cetintas, J. D. Stanley, M. L. Mendes, T. O. Powers, and D. W. Dickson. 2010. Meloidogyne spp. infecting ornamental plants in Florida. Nematropica 40:87-103. A total of 206 root samples were collected from ornamental plants growing in ornamental nurseries and various landscapes in Florida. Isozyme phenotypes, especially esterase (EST) and malate dehydrogenase (MDH) were the main methods used to identify the root-knot nematode species. When needed, the morphology of female perineal patterns, morphometric characters and mitochondrial DNA were used to aid in the identification. Six Meloidogyne spp. , M. arenaria, M. floridensis, M. graminis, M. incognita, M. javanica and M. mayaguensis were found infecting ornamental plants in Florida. As previously reported EST activity was of highest diagnostic value to identify Meloidogyne spp. found in this study; however, MDH was helpful to distinguish M. mayaguensis and M. graminis from the other root-knot nematode species identified. Five new EST phenotypes were detected associated with 17 unidentified root-knot nematode populations. To our knowledge, this is the first report of ornamental plants in the genera Dracena and Hibiscus, and Ligustrum and Washingtonia being host of M. floridensis and M. mayaguensis, respectively. New plant species host records for M. mayaguensis were Ajuga reptans, Amaranthus tricolor, Buddleja davidii, Caryopteris x clandonensis, Clerodendrum x ugandense, Hibiscus grandiflorus, Lagerstroemia indica, Penta lanceolata, Plectranthus scutellarioides, and Solandra maxima.
Evolution of acquiescence to manipulation

A productive framework to study phenotypic evolution is based on the notion of “inclusive fitness”, which considers how an individual’s phenotype affects the fitness of other individuals. A promising extension of the notion of inclusive fitness is that of the “extended phenotype”, which considers how an individual’s phenotype affects its environment, including the phenotype of other individuals. Affecting another individual’s phenotype is sometimes referred to as manipulation (which introduces indirect genetic effects). However, manipulated individuals may evolve resistance to manipulation, possibly reducing or eliminating the manipulated behavior (and the indirect genetic effects). In this dissertation I use mathematical modeling to identify different ways in which acquiescence (i.e., no resistance) to manipulation evolves. In Chapter 1, I show how costs of resistance may cause the evolution of acquiescence. In Chapter 2, I find that manipulation may cause the evolution of social efficiency, which can eliminate selection for resistance. In Chapter 3, I obtain that manipulation causes the evolutionofmaternal exploitation,which can also eliminate selection for resistance. In Appendices I-III, I present population genetics models of maternal manipulation that prompted the general models of chapters 1-3. Together, the results presented in this dissertation suggest that manipulationmay be a particularly powerful promoter of stable social behavior.
Origins of Sex: Three Billion Years of Genetic Recombination

A fascinating and detailed examination of the evolution-and occasional devolution-of sexuality in microorganisms and more complex forms of life. Margulis and Sagan trace sex from its inauspicious beginnings in bacteria threatened by ultraviolet radiation to its intimate relation with the origin of mitotic division of nucleated cells. The origin of meiotic sex through cannibalism followed by centriole reproductive tardiness and the connection of cell symbiosis to sex and differentiation are explored. "The authors have not only given us a new and exiting scenario for the evolution of sex, but have also provided us with critical ways in which we can test their hypotheses.This is a stimulating book that is sure to invoke criticism and discussion; I strongly recommend it. "-Symbiosis "The book is well organized and well written, leading the reader from one thought to another almost effortlessly. Background information is presented to aid those of us who are not experts in this field, and a glossary is appended. The book could be used at all levels of study, from interested undergraduates in general biology though postdoctoral students of genetics and evolution. I recommend this thought-provoking book to you for both your enjoyment and your enlightenment. "-Richard W. Cheney, Jr., Journal of College Science Teaching "This book, undoubtedly controversial, is a thoughtful and original contribution to an important aspect of cellular biology. "-John Langridge
Persistence of Northern Pacific Rattlesnakes masks the impact of human disturbance on weight and body condition

Species may remain present on developed landscapes over extended periods, suggesting viability, while in reality, populations may be indirectly affected in subtle and significant ways. We investigated indirect effects of human disturbance and habitat development on a population of the threatened Northern Pacific Rattlesnake Crotalus oreganus oreganus in British Columbia, Canada. We used mark‐recapture (n = 623 males and non‐gravid females, 2002–2011) and radio‐telemetry (n = 100 males, n = 4 non‐gravid females, 2004–2011) to examine weight, length, body condition, ecdysis and exposure risk in habitats of varying disturbance levels. Snakes in the most disturbed areas (<10 m to the nearest source of human activity or development) had lower weights and body condition, and they lost significantly more weight during the active season. Mean body condition of all snakes was stable or even increasing up to 2008 whereafter declines occurred in all categories, but particularly so for animals using disturbed habitat. Although there was some indication that ecdysis rates were affected by disturbance, we found no evidence that animals in disturbed habitat tended to be more exposed (i.e. distant from cover). Our findings indicate that there are consequences of occupying disturbed habitats, even though outward changes in behaviour or declines in density on the landscape are not detected.