943 resultados para Genetic and phenotypic correlation


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When noises considerations are made, nonredundant arrays (NRAs) are endowed with many advantages which other arrays e.g., uniformly redundant arrays (URAs) do not possess in applications of coded aperture imaging. However, lower aperture opening ratio limits the applications of NRA in practice. In this paper, we present a computer searching method based on a global optimization algorithm named DIRECT to design NRAs. Compared with the existing NRAs e.g., Golay's NRAs, which are well known and widely used in various applications, NRAs found by our method have higher aperture opening ratio and auto correlation compression ratio. These advantages make our aperture arrays be very useful for practical applications especially for which of aperture size are limited. Here, we also present some aperture arrays we found. These aperture arrays have an interesting property that they belong to both NRA and URA. (C) 2006 Elsevier GmbH. All rights reserved.

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The distal half of the bacteriophage T4 tail fiber interacts with the surface of the bacterium during adsorption. The largest polypeptide in this half fiber is the product of gene 37 (P37). During assembly of the tail fiber, P37 interacts with the product of gene 38 (P38). These two gene products are incompatible with the corresponding gene products from the related phage T2. T2 P37 does not interact with T4 P38 and T2 P38 does not interact with T4 P37. Crosses between T2 and T4 phages mutant in genes 37 and 38 have shown that the carboxyl end of P37 interacts with P38 and with the bacterial surface. In the corresponding region of gene 37 and in gene 38 there is no recombination between T2 and T4. In the rest of gene 37 there are two small regions with relatively high recombination and a region of low recombination.

When T2/T4 heteroduplex DNA molecules are examined in the electron microscope four nonhomologous loops appear in the region of genes 37 and 38. Heteroduplexes between hybrid phages which have part of gene 37 from T4 and part from T2 have roughly located gene 37 mutations in the heteroduplex pattern. For a more precise location of the , mutations a physical map of gene 37 was constructed by determining the molecular weights of amber polypeptide fragments on polyacrylamide gels in the presence of sodium dodecyl sulfate. When the physical and heteroduplex maps are aligned, the regions of low recombination correspond to regions of nonhomology between T2 and T4. Regions with relatively high recombination are homologous.

The molecular weight of T2 P37 is about 13,000 greater than that of T4 P37. Analysis of hybrid phage has shown that this molecular weight difference is all at the carboxyl end of P37.

An antiserum has been prepared which is specific for the distal half fiber of T4. Tests of the ability of gene 37 hybrids to block this antiserum show that there are at least 4 subclasses of antigen specified by different parts of P37.

Observations in the electron microscope of the tailfiber - anti- body complexes formed by the gene 37 hybrids and the specific anti- serum have shown that P37 is oriented linearly in the distal half fiber with its N-terminus near the joint between the two half fibers and its C-terminus near the tip of the fiber. These observations lead to a simple model for the structure of the distal half fiber.

The high recombination in T4 gene 34 was also investigated. A comparison of genetic and physical maps of gene 34 showed that there is a gradient of increasing recombination near one end of the gene.

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Resumen Background: Nitric oxide can be measured at multiple flow rates to determine proximal (maximum airway nitric oxide flux; Jaw(NO)) and distal inflammation (alveolar nitric oxide concentration; CA(NO)). The main aim was to study the association among symptoms, lung function, proximal (maximum airway nitric oxide flux) and distal (alveolar nitric oxide concentration) airway inflammation in asthmatic children treated and not treated with inhaled glucocorticoids. Methods: A cross-sectional study with prospective data collection was carried out in a consecutive sample of girls and boys aged between 6 and 16 years with a medical diagnosis of asthma. Maximum airway nitric oxide flux and alveolar nitric oxide concentration were calculated according to the two-compartment model. In asthmatic patients, the asthma control questionnaire (CAN) was completed and forced spirometry was performed. In controls, differences between the sexes in alveolar nitric oxide concentration and maximum airway nitric oxide flux and their correlation with height were studied. The correlation among the fraction of exhaled NO at 50 ml/s (FENO50), CA(NO), Jaw(NO), forced expiratory volume in 1 second (FEV1) and the CAN questionnaire was measured and the degree of agreement regarding asthma control assessment was studied using Cohen's kappa. Results: We studied 162 children; 49 healthy (group 1), 23 asthmatic participants without treatment (group 2) and 80 asthmatic patients treated with inhaled corticosteroids (group 3). CA(NO) (ppb) was 2.2 (0.1-4.5), 3 (0.2-9.2) and 2.45 (0.1-24), respectively. Jaw(NO) (pl/s) was 516 (98.3-1470), 2356.67 (120-6110) and 1426 (156-11805), respectively. There was a strong association (r = 0.97) between FENO50 and Jaw(NO) and the degree of agreement was very good in group 2 and was good in group 3. There was no agreement or only slight agreement between the measures used to monitor asthma control (FEV1, CAN questionnaire, CA(NO) and Jaw(NO)). Conclusions: The results for CA(NO) and Jaw(NO) in controls were similar to those found in other reports. There was no agreement or only slight agreement among the three measure instruments analyzed to assess asthma control. In our sample, no additional information was provided by CA(NO) and Jaw(NO).

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A Neuromielite Óptica (NMO), anteriormente considerada como um subtipo de Esclerose Múltipla, é uma doença autoimune, inflamatória do sistema nervoso central, na qual o sistema imune ataca a mielina dos neurônios localizados nos nervos ópticos e medula espinhal, produzindo, então, mielite e neurite óptica simultânea ou sequenciais. A patogênese da neuromielite óptica é influenciada pela combinação de fatores genéticos e ambientais, incluindo agentes infecciosos. Diferentes doenças infecciosas podem tanto desencadear como exacerbar a autoimunidade. Portanto, o objetivo do presente estudo foi de analisar a responsividade imune in vitro a Escherichia coli, Staphylococcus aureus e Candida albicans em pacientes com NMO recorrente-remitente, e a correlacionar ao nível de incapacidade neurológica. Nesse contexto, a extensão da linfoproliferação e perfil de citocinas em resposta a S. aureus e C. albicans, em culturas de células mononucleares do sangue periférico (CMSP) foram similares entre pacientes com NMO e indivíduos saudáveis. Entretanto, maior proliferação de células T associada à elevada liberação de IL-1β, IL-6 e IL-17 foi observada em culturas de células derivadas de pacientes com NMO quando estimuladas com E. coli. Ademais, nessas culturas, a produção de IL-10 foi significativamente menor quando comparada ao grupo controle. Ensaios conduzidos em culturas de CMSP depletadas de diferentes subtipos de linfócitos demonstraram que, enquanto células T CD4+ e T CD8+ produzem IL-6 em resposta a E. coli, a produção de IL-17 foi praticamente restrita às células T CD4+. Os níveis de IL-6 e IL-17 in vitro induzidos por E. coli foram correlacionados positivamente às incapacidades neurológicas. Essa maior tendência a produzir citocinas relacionadas ao perfil Th17 foi diretamente associada aos níveis de IL-23 produzidos por monócitos ativados com LPS. De modo interessante, níveis elevados de LPS foram quantificados no plasma de pacientes com NMO e estes foram correlacionados aos níveis plasmáticos de IL-6. Em conclusão, nossos resultados sugerem que uma maior responsividade a E. coli poderia estar envolvida na patogênese da NMO. Esse tipo de investigação é muito importante pois inibidores da ligação ou sinalização do TLR poderiam ser considerados terapias com grande potencial como adjuvantes no tratamento de pacientes com NMO.

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The m-plane GaN films grown on LiAlO2(100) by metal-organic chemical vapor deposition exhibit anisotropic crystallographic properties. The Williamson-Hall plots point out they are due to the different tilts and lateral correlation lengths of mosaic blocks parallel and perpendicular to GaN[0001] in the growth plane. The symmetric and asymmetric reciprocal space maps reveal the strain of m-plane GaN to be biaxial in-plane compress epsilon(xx)=-0.79% and epsilon(zz)=-0.14% with an out-of-plane dilatation epsilon(yy)=0.38%. This anisotropic strain further separates the energy levels of top valence band at Gamma point. The energy splitting as 37 meV as well as in-plane polarization anisotropy for transitions are found by the polarized photoluminescence spectra at room temperature. (c) 2008 American Institute of Physics.

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Staphylococcus coagulase-negativo (SCN) estão frequentemente envolvidos em infecções nosocomiais associadas com o uso de cateteres e outros procedimentos médicos invasivos. A habilidade de aderir às superfícies abióticas e de produzir biofilme tem sido reconhecida entre os principais fatores de virulência dos SCN, especialmente de S. epidermidis, a principal espécie responsável por infecções relacionadas à assistência a saúde - IRASs. Dentre as demais espécies de SCN capazes de produzir biofilme, S. haemolyticus tem sido relacionado com quadros de infecções em recém-nascidos (RNs). O presente estudo teve como objetivo principal investigar aspectos microbiológicos e epidemiológicos dos processos infecciosos invasivos relacionados com SCN em neonatos internados em unidade de terapia intensiva neonatal (UTIN) de um hospital universitário do município do Rio de Janeiro (2008-2010). A técnica de PCR multiplex-mPCR foi empregada na determinação das espécies de 40 amostras de SCN isoladas de hemoculturas de RNs fazendo uso de cateteres intravenosos e submetidos à terapia antimicrobiana empírica com vancomicina e/ou gentamicina. A fenotipagem foi realizada por três métodos distintos: Simplificado em microplaca, Vitek 2 e API-Staph. Os perfis de resistência aos antimicrobianos foram verificados através do teste de disco-difusão, determinação de CIM (Oxacilina) e presença do gene mecA. A capacidade de produção de biofilme foi investigada pelos testes do Ágar Vermelho do Congo e ensaios de aderência em superfícies abióticas (poliestireno e vidro) além da PCR para os genes icaAB, atlE e aap. O perfil genômico dos micro-organismos foi determinado pela técnica de PFGE. Os resultados demonstraram o isolamento de S. haemolyticus (77%), S. epidermidis (15%), S. captis (5%) e S. warneri (3%). A análise comparativa dos resultados obtidos pelo m-PCR com métodos fenotípicos demonstrou uma concordância de 97,5% com o esquema simplificado e de ~40% Vitek 2 e o API Staph. A maioria (82,5%) das amostras apresentou perfis variados de multiresistência aos 16 antimicrobianos testados e resistência a oxacilina, apesar de 25% destas não apresentarem o gene mecA. Apesar da maioria das amostras de SCN ter apresentado capacidade de produzir slime e/ou biofilme não foi observada total correlação com a presença dos genes mecA, icaAB, aap, atlE, enfatizando a natureza multifatorial da produção de biofilme de SCN. Diferente do observado para as demais espécies, algumas amostras de S. haemolyticus foram incapazes de aderir ao vidro e ao poliestireno e/ou apresentaram os genes aap (38,7%), atlE (42%) além de icaAB (71%). Na UTIN foi detectada a presença de seis diferentes tipos clonais da espécie prevalente, indicando a disseminação de S. haemolyticusnesta unidade hospitalar e a endemicidade em nossa comunidade.

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Rockfish (Sebastes spp.) juveniles are often difficult to identify by using morphological characters. This study independently applies morphological characters and a key based on mitochondrial restriction site variation to identify juvenile rockf ishes collected in southern California during juvenile rockfish surveys. Twenty-four specimens of Sebastes were examined genetically without knowledge of the morphological assignment. Seventeen fish were identified genetically as S. semicinctus, S. goodei, S. auriculatus, S. jordani, S. levis, S. rastrelliger, and S. saxicola. Identities for the remaining fish were narrowed to two or three species: 1) three fish were either S. carnatus or S. chrysomelas; 2) one fish was either S. chlorosticus, S. eos, or S. rosenblatti; and 3) three fish could have been either S. hopkinsi or S. ovalis, the latter for which we now have distinguishing mitochondrial markers. The genetic and morphological assignments concurred except for the identity of one fish that could only be narrowed down to S. hopkinsi or S. semicinctus by using morphological characters. Genetics excluded more species from multispecies groupings than did the morphological approach, especially species within the subgenus Sebastomus. Species in the genetically unresolvable groups may be similar because of recent divergence or because of interspecies introgression.

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Background: The impact of nano-scaled materials on photosynthetic organisms needs to be evaluated. Plants represent the largest interface between the environment and biosphere, so understanding how nanoparticles affect them is especially relevant for environmental assessments. Nanotoxicology studies in plants allude to quantum size effects and other properties specific of the nano-stage to explain increased toxicity respect to bulk compounds. However, gene expression profiles after exposure to nanoparticles and other sources of environmental stress have not been compared and the impact on plant defence has not been analysed. Results: Arabidopsis plants were exposed to TiO2-nanoparticles, Ag-nanoparticles, and multi-walled carbon nanotubes as well as different sources of biotic (microbial pathogens) or abiotic (saline, drought, or wounding) stresses. Changes in gene expression profiles and plant phenotypic responses were evaluated. Transcriptome analysis shows similarity of expression patterns for all plants exposed to nanoparticles and a low impact on gene expression compared to other stress inducers. Nanoparticle exposure repressed transcriptional responses to microbial pathogens, resulting in increased bacterial colonization during an experimental infection. Inhibition of root hair development and transcriptional patterns characteristic of phosphate starvation response were also observed. The exogenous addition of salicylic acid prevented some nano-specific transcriptional and phenotypic effects, including the reduction in root hair formation and the colonization of distal leaves by bacteria. Conclusions: This study integrates the effect of nanoparticles on gene expression with plant responses to major sources of environmental stress and paves the way to remediate the impact of these potentially damaging compounds through hormonal priming.

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A comparison of Mycobacterium tuberculosis complex isolates from seals (pinnipeds) in Australia, Argentina, Uruguay, Great Britain and New Zealand was undertaken to determine their relationships to each other and their taxonomic position within the complex. Isolates from 30 cases of tuberculosis in six species of pinniped and seven related isolates were compared to representative and standard strains of the M. tuberculosis complex. The seal isolates could be distinguished from other members of the M. tuberculosis complex, including the recently defined ‘Mycobacterium canettii’ and ‘Mycobacterium caprae’, on the basis of host preference and phenotypic and genetic tests. Pinnipeds appear to be the natural host for this ‘seal bacillus’, although the organism is also pathogenic in guinea pigs, rabbits, humans, Brazilian tapir (Tapirus terrestris) and, possibly, cattle. Infection caused by the seal bacillus is predominantly associated with granulomatous lesions in the peripheral lymph nodes, lungs, pleura, spleen and peritoneum. Cases of disseminated disease have been found. As with other members of the M. tuberculosis complex, aerosols are the most likely route of transmission. The name Mycobacterium pinnipedii sp. nov. is proposed for this novel member of the M. tuberculosis ...

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Os bastonetes Gram positivos irregulares (BGPIs) compõem um grupo de espécies bacterianas com ampla diversidade fenotípica e que podem estar presente no meio ambiente, na microbiota humana e de animais. A identificação acurada de BGPIs em nível de gênero e espécie empregando métodos bioquímicos convencionais é bastante limitada, sendo recomendado, portanto, o uso de técnicas moleculares. No presente estudo, foram identificadas amostras de BGPIs oriundas de espécimes clínicos de humanos, de produtos farmacêuticos e de áreas limpas através da análise de sequencias do gene 16S rRNA e de outros genes conservados (housekeeping genes). Os resultados obtidos pelo sequenciamento dos genes 16S rRNA e rpoB demonstraram C. striatum multi-resistente (MDR) como responsável por surto epidêmico em ambiente hospitalar da cidade do Rio de Janeiro. Quinze cepas de C. striatum foram isoladas em cultura pura a partir de secreção traqueal de pacientes adultos submetidos a procedimentos de entubação endotraqueal. A análise por eletroforese em gel de campo pulsado (PFGE) indicou a presença de quatro perfis moleculares, incluindo dois clones relacionados com cepas MDR (PFGE I e II). Os dados demonstram a predominância de PFGE I entre cepas MDR isoladas de unidades de terapia intensiva e enfermarias cirúrgicas. Uma potencial ligação causal entre a morte e a infecção por C. striatum MDR (PFGE tipos I e II) foi observada em cinco casos. Adicionalmente, acreditamos que este seja o primeiro estudo de identificação de espécies de Nocardia relacionadas com infecções humanas pela análise da sequencia multilocus (MLSA) no Brasil. Diferente dos dados observados na literatura (1970 a 2013) e obtidos pelos testes fenotípicos convencionais, a caracterização molecular de quatro lócus (gyrB-16S-secA1-hsp65) permitiu a identificação das espécies N. nova, N. cyriacigeorgica, N. asiatica e N. exalbida/gamkensis relacionadas com quadros de nocardiose em humanos. Cepas de N. nova isoladas de diferentes materiais clínicos de um único paciente apresentaram padrões de susceptibilidade antimicrobianos idênticos e dois perfis PFGE, indicando a possibilidade de quadros de co-infecção por N. nova em humanos. Em outra etapa da investigação, amostras de BGPIs obtidos de ambientes de salas limpas que não puderam ser identificadas por critérios convencionais foram submetidas a análise da sequência do gene 16S rRNA e caracterizadas 95,83% em nível de gênero e 35,42% em espécies. Para gêneros mais encontrados no estudo, foram analisados os genes rpoB e recA de dezessete cepas de Microbacterium e utilizado o MLSA para a identificação de sete cepas identificadas como Streptomyces. Os ensaios permitiram a identificação de três cepas de Microbacterium e de uma única amostra de Streptomyces ao nível de espécie. A análise da sequencia do gene rpoB também se mostrou eficaz na identificação de espécies de cepas de Corynebacterium. Finalmente, para as cepas ambientais pertencentes à classe Actinobacteria os dados morfológicos, bioquímicos e genotípicos permitiram documentar a cepa 3117BRRJ como representante de uma nova espécie do gênero Nocardioides, para o qual o nome Nocardioides brasiliensis sp. nov. e as cepas 3712BRRJ e 3371BRRJ como representante de um novo gênero e espécie para o qual o nome Guaraldella brasiliensis nov. foi proposto.

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MOTIVATION: Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from synthetic lethality interaction networks. RESULTS: In this article, we present a novel technique called kernelROD for gene function prediction from synthetic lethal interaction networks based on kernel machines. We apply our novel algorithm to Gene Ontology functional annotation prediction in yeast. Our experiments show that our method leads to improved gene function prediction compared with state-of-the-art competitors and that combining genetic and congruence networks leads to a further improvement in prediction accuracy.

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NOAA’s National Centers for Coastal Ocean Science (NCCOS)-Center for Coastal Monitoring and Assessment’s (CCMA) Biogeography Branch, National Park Service (NPS), US Geological Survey, and the University of Hawaii used acoustic telemetry to quantify spatial patterns and habitat affinities of reef fishes around the island of St. John, US Virgin Islands. The objective of the study was to define the movements of reef fishes among habitats within and between the Virgin Islands Coral Reef National Monument (VICRNM), the Virgin Islands National Park (VIIS), and Territorial waters surrounding St. John. In order to better understand species’ habitat utilization patterns among management regimes, we deployed an array of hydroacoustic receivers and acoustically tagged reef fishes. Thirty six receivers were deployed in shallow near-shore bays and across the shelf to depths of approximately 30 m. One hundred eighty four individual fishes were tagged representing 19 species from 10 different families with VEMCO V9-2L-R64K transmitters. The array provides fish movement information at fine (e.g., day-night and 100s meters within a bay) to broad spatial and temporal scales (multiple years and 1000s meters across the shelf). The long term multi-year tracking project provides direct evidence of connectivity across habitat types in the seascape and among management units. An important finding for management was that a number of individuals moved among management units (VICRNM, VINP, Territorial waters) and several snapper moved from near-shore protected areas to offshore shelf-edge spawning aggregations. However, most individuals spent the majority of their time with VIIS and VICRNM, with only a few wide-ranging species moving outside the management units. Five species of snappers (Lutjanidae) accounted for 31% of all individuals tagged, followed by three species of grunts (Haemulidae) accounting for an additional 23% of the total. No other family had more than a single species represented in the study. Bluestripe grunt (Haemulon sciurus) comprised 22% of all individuals tagged, followed by lane snappers (Lutjanus synagris) at 21%, bar jack (Carangoides ruber) at 11%, and saucereye porgy (Calamus calamus) at 10%. The largest individual tagged was a 70 cm TL nurse shark (Ginglymostoma cirratum), followed by a 65 cm mutton snapper (Lutjanus analis), a 47 cm bar jack, and a 41 cm dog snapper (Lutjanus jocu). The smallest individuals tagged were a 19 cm blue tang (Acanthurus coeruleus) and a 19.2 cm doctorfish (Acanthurus chirurgus). Of the 40 bluestriped grunt acoustically tagged, 73% were detected on the receiver array. The average days at large (DAL) was 249 (just over 8 months), with one individual detected for 930 days (over two and a half years). Lane snapper were the next most abundant species tagged (N = 38) with 89% detected on the array. The average days at large (DAL) was 221 with one individual detected for 351 days. Seventy-one percent of the bar jacks (N = 21) were detected on the array with the average DALs at 47 days. All of the mutton snapper (N = 12) were detected on the array with an average DAL of 273 and the longest at 784. The average maximum distance travelled (MDT) was ca. 2 km with large variations among species. Grunts, snappers, jacks, and porgies showed the greatest movements. Among all individuals across species, there was a positive and significant correlation between size of individuals and MDT and between DAL and MDT.

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Studies on genetic improvement of penaeid prawns for the character higher tail weight using methods of selective breeding were undertaken. Prior to the actual breeding experiments it was necessary to find out the quantum of available variability in the character tail weight amongst the natural populations of Penaeus merguiensis from the Indian waters. Thirteen morphometric variables were measured and various statistical analyses were carried out. The tail weight showed almost double values of coefficient of variation in the females than the males (C.V. 20.37 and 11.08 respectively). The combination of the characters viz. sixth segment length (SSL), sixth segment depth (SSD) and posterior abdominal circumference (PAC) gave the highest R super(2) values. These variables were easy to measure and gave maximum variation in the character tail weight without sacrificing the breeders in the brood stock. The quantitative character tail weight was influenced by both genetic and environmental factors was statistically ascertained by applying 2-Factor analysis.

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Thirteen morphometric and seven meristic characters, length-weight relationship and food and feeding habits of Otolithoides biauritus of Bombay coast (Maharashtra, India) were studied. Compared morphometric characters revealed positive allometric growth and high correlation ("r" ranging 0.898 - 0.996) between each other. Meristic characters were observed to be B sub(vii), D sub(1) 8-10, D sub(2) 27-31, P 17-20, V 5-7 and 7-10. Number of gill rackers on the first left gill arch ranged from 15 to 19. Length-weight relationship for both sexes together worked out to be W = 0.026, L super(2.646). The species is a predator, feeding mainly on motile Acetes, small fish and Loligo in order of preference.

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Fecundity of threatened catfish Mystus montanus was estimated from a collection of gravid females, which ranged from 290 to 27,972 according to body length and weight. The relationship between fecundity and BL, BW, GL and GW was analyzed by linear regression, which showed both positive and negative correlation. Gonado-somatic index (GSI), hepato-somatic index (HSI) and spleen-somatic index (SSI) ranged from 0.135 to 21.28, 0.358 to 21.33 and 0.126 to 1.08 in females and the corresponding values for males were 0.17 to 10.68, 0.619 to 3.25 and 1.25 to 2.33 respectively.