Anharmonic force constant calculations

The relationship of the anharmonic force constants in curvilinear internal coordinates to the observed vibration-rotation spectrum of a molecule is reviewed. A simplified method of setting up the required non-linear coordinate transformations is described: this makes use of an / tensor, which is a straightforward generalization of the / matrix used in the customary description of harmonic force constant calculations. General formulae for the / tensor elements, in terms of the familiar L matrix elements, are presented. The use of non-linear symmetry coordinates and redundancies are described. Sample calculations on the water and ammonia molecules are reported.

ASYM20: a program for force constant and normal coordinate calculations, with a critical review of the theory involved

The theory of harmonic force constant refinement calculations is reviewed, and a general-purpose program for force constant and normal coordinate calculations is described. The program, called ASYM20. is available through Quantum Chemistry Program Exchange. It will work on molecules of any symmetry containing up to 20 atoms and will produce results on a series of isotopomers as desired. The vibrational secular equations are solved in either nonredundant valence internal coordinates or symmetry coordinates. As well as calculating the (harmonic) vibrational wavenumbers and normal coordinates, the program will calculate centrifugal distortion constants, Coriolis zeta constants, harmonic contributions to the α′s. root-mean-square amplitudes of vibration, and other quantities related to gas electron-diffraction studies and thermodynamic properties. The program will work in either a predict mode, in which it calculates results from an input force field, or in a refine mode, in which it refines an input force field by least squares to fit observed data on the quantities mentioned above. Predicate values of the force constants may be included in the data set for a least-squares refinement. The program is written in FORTRAN for use on a PC or a mainframe computer. Operation is mainly controlled by steering indices in the input data file, but some interactive control is also implemented.

Ranking efficiency units in DEA using bootstrapping an applied analysis for Slovenian farm data

This article explores how data envelopment analysis (DEA), along with a smoothed bootstrap method, can be used in applied analysis to obtain more reliable efficiency rankings for farms. The main focus is the smoothed homogeneous bootstrap procedure introduced by Simar and Wilson (1998) to implement statistical inference for the original efficiency point estimates. Two main model specifications, constant and variable returns to scale, are investigated along with various choices regarding data aggregation. The coefficient of separation (CoS), a statistic that indicates the degree of statistical differentiation within the sample, is used to demonstrate the findings. The CoS suggests a substantive dependency of the results on the methodology and assumptions employed. Accordingly, some observations are made on how to conduct DEA in order to get more reliable efficiency rankings, depending on the purpose for which they are to be used. In addition, attention is drawn to the ability of the SLICE MODEL, implemented in GAMS, to enable researchers to overcome the computational burdens of conducting DEA (with bootstrapping).

Change in the effect of constant photoperiods on the rate of sexual maturation in modern genotypes of domestic pullet

1. Data for modern egg-type hybrids reared on constant daylengths show that, as expected, they mature more quickly than earlier genotypes. However, the constant photoperiod which gives earliest sexual maturity has not changed as a result of selection and is 10 h for both early and modern genotypes. 2. Further analysis showed that the rate of delay in sexual maturity for constant photoperiods above 10 h is similar for modern and for early hybrids ( +0.29 d for each incremental one hour of photoperiod), the response of modern hybrids below 10 h ( +4.22 d for each one-hour reduction in photoperiod) is more than double that of early hybrids ( +1.71 d/h).

In vitro cumulative gas production techniques: History, methodological considerations and challenges

Methodology used to measure in vitro gas production is reviewed to determine impacts of sources of variation on resultant gas production profiles (GPP). Current methods include measurement of gas production at constant pressure (e.g., use of gas tight syringes), a system that is inexpensive, but may be less sensitive than others thereby affecting its suitability in some situations. Automated systems that measure gas production at constant volume allow pressure to accumulate in the bottle, which is recorded at different times to produce a GPP, and may result in sufficiently high pressure that solubility of evolved gases in the medium is affected, thereby resulting in a recorded volume of gas that is lower than that predicted from stoichiometric calculations. Several other methods measure gas production at constant pressure and volume with either pressure transducers or sensors, and these may be manual, semi-automated or fully automated in operation. In these systems, gas is released as pressure increases, and vented gas is recorded. Agitating the medium does not consistently produce more gas with automated systems, and little or no effect of agitation was observed with manual systems. The apparatus affects GPP, but mathematical manipulation may enable effects of apparatus to be removed. The amount of substrate affects the volume of gas produced, but not rate of gas production, provided there is sufficient buffering capacity in the medium. Systems that use a very small amount of substrate are prone to experimental error in sample weighing. Effect of sample preparation on GPP has been found to be important, but further research is required to determine the optimum preparation that mimics animal chewing. Inoculum is the single largest source of variation in measuring GPP, as rumen fluid is variable and sampling schedules, diets fed to donor animals and ratios of rumen fluid/medium must be selected such that microbial activity is sufficiently high that it does not affect rate and extent of fermentation. Species of donor animal may also cause differences in GPP. End point measures can be mathematically manipulated to account for species differences, but rates of fermentation are not related. Other sources of inocula that have been used include caecal fluid (primarily for investigating hindgut fermentation in monogastrics), effluent from simulated rumen fermentation (e.g., 'Rusitec', which was as variable as rumen fluid), faeces, and frozen or freeze-dried rumen fluid (which were both less active than fresh rumen fluid). Use of mixtures of cell-free enzymes, or pure cultures of bacteria, may be a way of increasing GPP reproducibility, while reducing reliance on surgically modified animals. However, more research is required to develop these inocula. A number of media have been developed which buffer the incubation and provide relevant micro-nutrients to the microorganisms. To date, little research has been completed on relationships between the composition of the medium and measured GPP. However, comparing GPP from media either rich in N or N-free, allows assessment of contributions of N containing compounds in the sample. (c) 2005 Published by Elsevier B.V.

Differential effects of temperature on fruit development and bean quality of contrasting genotypes of cacao (Theobroma cacao)

The effects of temperature and light integral on fruit growth and development of five cacao genotypes (Amelonado, AMAZ 15/15, SCA 6, SPEC 54/1 and UF 676) were studied in semi-controlled environment glasshouses in which the thermal regimes of cacao-growing regions of Brazil, Ghana and Malaysia were simulated. Fruit losses because of physiological will (cherelle will) were greater at higher temperatures and also differed significantly between genotypes, reflecting genetic differences in competition for assimilates between vegetative and reproductive components. Short-term measurements of fruit growth indicated faster growth rates at higher temperatures. In addition, a significant negative linear relationship between temperature and development time was observed. There was an effect of genotype on this relationship, such that time to fruit maturation at a given temperature was greatest for the clone UF 676 and least for AMAZ 15/15. Analysis of base temperatures, derived from these relationships indicated genetic variability in sensitivity of cacao fruit growth to temperature (base temperatures ranged from 7.5 degrees C for Amelonado and AMAZ 15/15 to 12.9 for SPEC 54/1). Final fruit size was a positive function of beam number for all genotypes and a positive function of light integral for Amelonado in the Malaysia simulated environment (where the temperature was almost constant). In simulated environments where temperature was the main variable (Brazil and Ghana) increases in temperature resulted in a significant decrease in final pod size for one genotype (Amelonado) in Brazil and for two genotypes (SPEC 54/1 and UF 676) in Ghana. It was hypothesised that pod growth duration (mediated by temperature), assimilation and beam number are all determinants of final pod size but that under specific conditions one of these factors may override the others. There was variability between genotypes in the response of beam size and beam lipid content to temperature. Negative relationships between temperature and bean size were found for Amelonado and UF 676. Lipid concentration was a curvilinear function of temperature for Amelonado and UF 676, with optimal temperatures of 23 degrees C and 24 degrees C, respectively. The variability observed here of different cacao genotypes to temperature highlights the need and opportunities for appropriate matching of planting material with local environments.

Declining survival rates in a reintroduced population of the Mauritius kestrel: evidence for non-linear density dependence and environmental stochasticity

1. We studied a reintroduced population of the formerly critically endangered Mauritius kestrel Falco punctatus Temmink from its inception in 1987 until 2002, by which time the population had attained carrying capacity for the study area. Post-1994 the population received minimal management other than the provision of nestboxes. 2. We analysed data collected on survival (1987-2002) using program MARK to explore the influence of density-dependent and independent processes on survival over the course of the population's development. 3.We found evidence for non-linear, threshold density dependence in juvenile survival rates. Juvenile survival was also strongly influenced by climate, with the temporal distribution of rainfall during the cyclone season being the most influential climatic variable. Adult survival remained constant throughout. 4. Our most parsimonious capture-mark-recapture statistical model, which was constrained by density and climate, explained 75.4% of the temporal variation exhibited in juvenile survival rates over the course of the population's development. 5. This study is an example of how data collected as part of a threatened species recovery programme can be used to explore the role and functional form of natural population regulatory processes. With the improvements in conservation management techniques and the resulting success stories, formerly threatened species offer unique opportunities to further our understanding of the fundamental principles of population ecology.

Designs for an adaptive tuned vibration absorber with variable shape stiffness element

An adaptive tuned vibration absorber (ATVA) with a smart variable stiffness element is capable of retuning itself in response to a time-varying excitation frequency., enabling effective vibration control over a range of frequencies. This paper discusses novel methods of achieving variable stiffness in an ATVA by changing shape, as inspired by biological paradigms. It is shown that considerable variation in the tuned frequency can be achieved by actuating a shape change, provided that this is within the limits of the actuator. A feasible design for such an ATVA is one in which the device offers low resistance to the required shape change actuation while not being restricted to low values of the effective stiffness of the vibration absorber. Three such original designs are identified: (i) A pinned-pinned arch beam with fixed profile of slight curvature and variable preload through an adjustable natural curvature; (ii) a vibration absorber with a stiffness element formed from parallel curved beams of adjustable curvature vibrating longitudinally; (iii) a vibration absorber with a variable geometry linkage as stiffness element. The experimental results from demonstrators based on two of these designs show good correlation with the theory.

Fecal microbiota in patients receiving enteral feeding are highly variable and may be altered in those who develop diarrhea

Background: The pathogenesis of diarrhea in patients receiving enteral feeding includes colonic water secretion, antibiotic prescription, and enteropathogenic colonization, each of which involves an interaction with the gastrointestinal microbiota. Objective: The objective was to investigate temporal changes in the concentrations of fecal microbiota and short-chain fatty acids (SCFAs) in patients starting 14-d of enteral feeding and to compare these changes between patients who do and do not develop diarrhea. Design: Twenty patients starting exclusive nasogastric enteral feeding were monitored for 14 d. Fecal samples were collected at the start, middle, and end of this period and were analyzed for major bacterial groups by using culture independent fluorescence in situ hybridization and for SCFAs by using gas-liquid chromatography. Results: Although no significant changes in fecal microbiota or SCFAs were observed during enteral feeding, stark alterations occurred within individual patients. Ten patients (50%) developed diarrhea, and these patients had significantly higher concentrations of clostridia (P = 0.026) and lower concentrations (P = 0.069) and proportions (P = 0.029) of bifidobacteria. Patients with and without diarrhea had differences in the proportion of bifidobacteria (median: 0.4% and 3.7%; interquartile range: 0.8 compared with 4.3; P = 0.035) and clostridia (median: 10.4% and 3.7%; interquartile range: 14.7 compared with 7.0; P = 0.063), respectively, even at the start of enteral feeding. Patients who developed diarrhea had higher concentrations of total fecal SCFAs (P = 0.044), acetate (P = 0.029), and butyrate (P = 0.055). Conclusion: Intestinal dysbiosis occurs in patients who develop diarrhea during enteral feeding and may be involved in its pathogenesis. Am J Clin Nutr 2009; 89: 240-7.