bluuebunny/crossref_metadata_2025 huggingface dataset:
Laser frequency offset locking using electromagnetically induced transparency
Authors: Bell S. C. , Heywood D. M. , White J. D. , Close J. D. , Scholten R. E.
Published: April 2007

The authors have used an electromagnetically induced transparency resonance in rubidium as a dispersive reference to lock the relative frequency of two lasers to the atomic ground-state hyperfine splitting. The beat frequency between the two lasers directly generates a microwave signal at 3.036GHz (Rb85) or 6.835GHz (Rb87). High bandwidth (600kHz) feedback was achieved with only low-frequency (10MHz) electronics using the frequency modulation sideband method. The spectral width of the microwave beat frequency was reduced to less than 1kHz. The technique offers a convenient and low-cost method suitable for many topical two-frequency experiments, including coherent population trapping, slow light, lasing without inversion, and Raman sideband cooling.
Determination of transit time distribution and Rabi frequency by applying regularized inverse on Ramsey spectra
Authors: Park Young-Ho , Lee Soo Heyong , Park Sang Eon , Lee Ho Seong , Kwon Taeg Yong
Published: April 2007

The authors report on a method to determine the Rabi frequency and transit time distribution of atoms that are essential for proper operation of atomic beam frequency standards. Their method, which employs alternative regularized inverse on two Ramsey spectra measured at different microwave powers, can be used for the frequency standards with short Ramsey cavity as well as long ones. The authors demonstrate that uncertainty in Rabi frequency obtained from their method is 0.02%.
Broadband super-resolving lens with high transparency in the visible range
Authors: Bloemer M. , D’Aguanno G. , Mattiucci N. , Scalora M. , Akozbek N.
Published: April 2007

The authors present a theoretical analysis of a super-resolving lens based on one-dimensional metal-dielectric photonic band gap composed of Ag∕GaP multilayers. The lens contains a total of ten optical skin depths of Ag, yet maintains a normal incidence transmittance of ∼50% for propagating waves over the super-resolving wavelength range of 500–650nm. The individual Ag layers are 22nm thick and can be readily fabricated in conventional deposition systems. The importance of antireflection coatings for the transmission of evanescent and propagating waves is illustrated by comparison to periodic and symmetric structures without the coatings.
Dynamics of charge transfer: Rate processes formulated with nonequilibrium Green’s functions
Authors: Yeganeh Sina , Ratner Mark A. , Mujica Vladimiro
Published: April 2007

The authors examine the connection between electron transport under bias in a junction and nonadiabatic intramolecular electron transfer (ET). It is shown that under certain assumptions it is possible to define a stationary current that allows the computation of the intramolecular transfer rate using the same formalism that is employed in the description of transport. They show that the nonequilibrium Green’s function formalism of quantum transport can be used to calculate the ET rate. The formal connection between electron transport and electron transfer is made, and they work out the simple case of an electronic level coupled to a vibrational mode representing a thermal bath and show that the result is the same as expected from a Fermi golden rule treatment, and in the high-temperature limit yields the Marcus electron transfer theory. The usefulness of this alternative formulation of rates is discussed.
Does Contour Classification Precede Contour Grouping in Perception of Partially Visible Figures?
Authors: Scheessele Michael R , Pizlo Zygmunt
Published: April 2007

When a figure is only partially visible and its contours represent a small fraction of total image contours (as when there is much background clutter), a fast contour classification mechanism may filter non-figure contours in order to restrict the size of the input to subsequent contour grouping mechanisms. The results of two psychophysical experiments suggest that the human visual system can classify figure from non-figure contours on the basis of a difference in some contour property (eg length, orientation, curvature, etc). While certain contour properties (eg orientation, curvature) require only local analysis for classification, other contour properties (eg length) may require more global analysis of the retinal image. We constructed a pyramid-based computational model based on these observations and performed two simulations of experiment 1: one simulation with classification enabled and the other simulation with classification disabled. The classification-based simulation gave the superior account of human performance in experiment 1. When a figure is partially visible, with few contours relative to the number of non-figure contours, contour classification followed by contour grouping can be more efficient than contour grouping alone, owing to smaller input to grouping mechanisms.
Conceptual Set as a Top — Down Constraint on Visual Object Identification
Authors: Balcetis Emily , Dale Rick
Published: April 2007

Four studies are reported which demonstrate that indirectly, loosely related information, otherwise known as conceptual set, modulates object identification. Studies 1A and 1B demonstrate the impact of indirect, nonspecific, non-perceptual, conceptual primes on the interpretation of ambiguous visual figures. Study 2 demonstrates that indirect, conceptual information (category of farm animals) biases identification without requiring the activation of direct perceptual information (here the image of a horse). Study 3 uses a non-linguistic dependent measure to address the alternative explanation that language and not perception mediates the relationship between incidental conceptual prime and biased object identification. These results suggest that conceptual set constrains object identification.
Parasite-intrinsic factors can explain ordered progression of trypanosome antigenic variation
Authors: Lythgoe Katrina A. , Morrison Liam J. , Read Andrew F. , Barry J. David
Published: April 2007

Pathogens often persist during infection because of antigenic variation in which they evade immunity by switching between distinct surface antigen variants. A central question is how ordered appearance of variants, an important determinant of chronicity, is achieved. Theories suggest that it results directly from a complex pattern of transition connectivity between variants or indirectly from effects such as immune cross-reactivity or differential variant growth rates. Using a mathematical model based only on known infection variables, we show that order in trypanosome infections can be explained more parsimoniously by a simpler combination of two key parasite-intrinsic factors: differential activation rates of parasite variant surface glycoprotein (VSG) genes and density-dependent parasite differentiation. The model outcomes concur with empirical evidence that several variants are expressed simultaneously and that parasitaemia peaks correlate withVSGgenes within distinct activation probability groups. Our findings provide a possible explanation for the enormity of the recently sequencedVSGsilent archive and have important implications for field transmission.
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
Authors: Lowe Craig B. , Bejerano Gill , Haussler David
Published: April 2007

At least 5% of the human genome predating the mammalian radiation is thought to have evolved under purifying selection, yet protein-coding and related untranslated exons occupy at most 2% of the genome. Thus, the majority of conserved and, by extension, functional sequence in the human genome seems to be nonexonic. Recent work has highlighted a handful of cases where mobile element insertions have resulted in the introduction of novel conserved nonexonic elements. Here, we present a genome-wide survey of 10,402 constrained nonexonic elements in the human genome that have all been deposited by characterized mobile elements. These repeat instances have been under strong purifying selection since at least the boreoeutherian ancestor (100 Mya). They are most often located in gene deserts and show a strong preference for residing closest to genes involved in development and transcription regulation. In particular, constrained nonexonic elements with clear repetitive origins are located near genes involved in cell adhesion, including all characterized cellular members of the reelin-signaling pathway. Overall, we find that mobile elements have contributed at least 5.5% of all constrained nonexonic elements unique to mammals, suggesting that mobile elements may have played a larger role than previously recognized in shaping and specializing the landscape of gene regulation during mammalian evolution.
GATA6
is an astrocytoma tumor suppressor gene identified by gene trapping of mouse glioma model
Authors: Kamnasaran Deepak , Qian Baoping , Hawkins Cynthia , Stanford William L. , Guha Abhijit
Published: April 2007

Malignant astrocytomas are the most common and lethal adult primary brain tumor. Retroviral gene trapping of nontransformed neonatal astrocytes from a glial fibrillary acidic protein (GFAP):
V12
Ha-Ras murine astrocytoma model led to isolation of the transcription factor
Gata6
. Loss of Gata6 resulted in enhanced proliferation and transformation of astrocytes. Human malignant astrocytoma cell lines, explant xenografts, and operative specimens demonstrated loss of GATA6 expression. Loss-of-function
GATA6
mutations with loss of heterozygosity of the
GATA6
locus were found in human malignant astrocytoma specimens but not in lower-grade astrocytomas or normal adult astrocytes. Knockdown of Gata6 expression in
V12
Ha-Ras or p53−/− astrocytes, but not in parental murine or human astrocytes, led to acceleration of tumorgenesis. Knockin GATA6 expression in human malignant astrocytoma cells reduced their tumorgenic growth with decreased VEGF expression. Collectively, these data demonstrate that
GATA6
, isolated from a murine astrocytoma model, is a novel tumor suppressor gene that is a direct target of mutations during malignant progression of murine and human astrocytomas. This work also demonstrates the utility of random mutagenesis strategies, such as gene trapping, on murine cancer models toward discovery of novel genetic alterations in corresponding human cancers.
Cell proliferation and survival induced by Toll-like receptors is antagonized by type I IFNs
Authors: Hasan Uzma A. , Caux Christophe , Perrot Ivan , Doffin Anne-Claire , Menetrier-Caux Christine , Trinchieri Giorgio , Tommasino Massimo , Vlach Jaromir
Published: April 2007

TRIF is an adaptor protein associated with the signaling by Toll-like receptor (TLR)3 and TLR4 for the induction of type I IFNs. Here, we demonstrate a mechanism by which TLR signaling controls cell proliferation and survival. We show that TLR3 and TLR4 can induce cell cycle entry via TRIF, which targets the cell cycle inhibitor p27kip1for relocalization, phosphorylation by cyclin/cdk complexes, and proteasome degradation. These events are antagonized by type I IFN induced by the TRIF pathway. Furthermore, in human dendritic cells treated with TLR3, TLR4, or TLR5 ligands, we demonstrate that IFN signaling modulates p27kip1degradation and apoptosis, identifying an immunoregulatory “switching” function of type I IFNs. These findings reveal a previously uncharacterized function of TLR signaling in cell proliferation and survival.
Metabolic engineering of
Escherichia coli
for the production of
l
-valine based on transcriptome analysis and
in silico
gene knockout simulation
Authors: Park Jin Hwan , Lee Kwang Ho , Kim Tae Yong , Lee Sang Yup
Published: April 2007

The
l
-valine production strain of
Escherichia coli
was constructed by rational metabolic engineering and stepwise improvement based on transcriptome analysis and gene knockout simulation of the
in silico
genome-scale metabolic network. Feedback inhibition of acetohydroxy acid synthase isoenzyme III by
l
-valine was removed by site-directed mutagenesis, and the native promoter containing the transcriptional attenuator leader regions of the
ilvGMEDA
and
ilvBN
operon was replaced with the
tac
promoter. The
ilvA
,
leuA
, and
panB
genes were deleted to make more precursors available for
l
-valine biosynthesis. This engineered Val strain harboring a plasmid overexpressing the
ilvBN
genes produced 1.31 g/liter
l
-valine. Comparative transcriptome profiling was performed during batch fermentation of the engineered and control strains. Among the down-regulated genes, the
lrp
and
ygaZH
genes, which encode a global regulator Lrp and
l
-valine exporter, respectively, were overexpressed. Amplification of the
lrp
,
ygaZH
, and
lrp-ygaZH
genes led to the enhanced production of
l
-valine by 21.6%, 47.1%, and 113%, respectively. Further improvement was achieved by using
in silico
gene knockout simulation, which identified the
aceF
,
mdh
, and
pfkA
genes as knockout targets. The VAMF strain (Val Δ
aceF
Δ
mdh
Δ
pfkA
) overexpressing the
ilvBN
,
ilvCED
,
ygaZH
, and
lrp
genes was able to produce 7.55 g/liter
l
-valine from 20 g/liter glucose in batch culture, resulting in a high yield of 0.378 g of
l
-valine per gram of glucose. These results suggest that an industrially competitive strain can be efficiently developed by metabolic engineering based on combined rational modification, transcriptome profiling, and systems-level
in silico
analysis.
Mapping the return on investment (ROI) of QTL: a progress report on animal genomics.
Authors: Schook L. B.
Published: April 2007

After more than 20 years of targeted investment, genomics is now on the verge of widespread adoption across many animal industries. Public-financed genome sequencing projects and the development of related technologies to lower the costs of genotyping continue to stimulate adoption of genomics by the animal industries and companion animal health providers. Early adoption in the livestock industry has initially involved improving existing breeding and traceability systems. The virtual or literal vertically integrated dairy, pig and chicken industries are well positioned to be early adopters. The integrated structures provide the business model to capture value generated by the incorporation of genomic information and technologies into their production systems. The major challenges will continue to be the costs of sample collection, processing and reporting, and how to integrate information into a real-time management system. Underpinning future research will be the availability of sequenced genomes for each of the production species (cattle, pigs and chickens) and large-scale DNA-arrays or 'single nucleotide polymorphism (SNP) chips' to perform low-cost genome scans. Such emerging technologies permit the identification and mapping of allelic variants affecting animal performance in existing commercial populations. The utility of markers to predict performance and genetic worth will expand from specialized tests for specific traits to 'whole genome selection', where segments of DNA are tracked and sold based on predicted genetic merit (for a specific management scheme). The implications are positive both for producers and consumers. Producers can address lower production costs associated with feed efficiencies and diseases, whereas consumers will witness the emergence of branded products that are safer with increased nutritional value, reduced environmental impacts and greater animal welfare. Finally, the application of genomics for companion animals (cats, dogs and horses) will focus on developing new nutritional approaches to improving health and wellness. Companion animal health and nutrition companies will use genomic information to develop specific diets for specific breeds and ages of animals. They have also developed diagnostic tests for parentage and breeding to eliminate genetic diseases in specific breeds. In conclusion, genomic information and related technologies are already providing 'quantitative' returns on research investments to livestock and healthcare industries and further promise to make 'qualitative' impacts on the nutritional value of foods, their safety, the wellness of our animals while decreasing environmental impacts. The future waits for further validation studies demonstrating the utility of genetic markers identified in experimental crosses in commercial operations. The creation of SNP haplomaps will also permit the use of SNPs across animal populations overcoming the current limitation of genetic marker utilization within families.
Selenium supplementation in heat-stressed poultry.
Authors: Sahin k. , Kucuk O.
Published: April 2007

Stress evoked by high ambient temperature results in economic loss through reducing feed intake while decreasing nutrient utilization, growth rate, egg production, egg quality and feed efficiency. Moreover, environmental stress leads to oxidative stress and reduces the antioxidant status of the bird
in vivo
, resulting in increased oxidative damage and lowered plasma concentrations of antioxidant vitamins (vitamin C, vitamin E) and minerals (zinc and selenium). Selenium is an essential trace element for animals and humans because of its role in the antioxidant enzyme glutathione peroxidase which protects cell membranes from damage caused by lipid peroxidation. Selenium deficiency causes several disorders in animal species and severe health problems in humans. Selenium supplementation has been found to eliminate selenium deficiency problems. Selenium is also used in the diets of heat-stressed poultry because of its reported benefits. This review deals with the effects of dietary selenium supplementation in poultry maintained at a high ambient temperature.
The potential of
Lysobacter
spp. as bacterial biological control agents for plant diseases.
Authors: Kobayashi D. Y. , Yuen G. Y.
Published: April 2007

The genus
Lysobacter
was established in the late 1970s to encompass strains of gliding bacteria that are morphologically and genetically distinct from other groups of myxobacteria. Strains were known to produce an impressive array of extracellular lytic enzymes and novel antibiotics that were associated with antagonistic activity towards a broad range of micro-organisms including fungi, nematodes and other bacteria. Characterization of these features was the subject of early research with
Lysobacter
strains, with the primary objective of identifying novel pharmaceuticals. Over the past decade, however, increased recognition of microbial antagonism displayed by
Lysobacter
spp. has led to investigations into their use as biological control agents of plant diseases. As a result,
Lysobacter
spp. are seen as valuable resources for biorationale approaches to plant disease control. In this review, we discuss: (i) the historical background of the
Lysobacter
group; (ii) the characterization of mechanisms contributing to microbial antagonism displayed by its members; (iii) our current knowledge of biocontrol by specific strains, including their ecological and biological behaviours; and (iv) the relationship of various mechanisms to biocontrol activity.
Regulation of the intestinal immune system by commensal microbiota in avian and ruminant species.
Authors: Brisbin J. T. , Haghighi H. R. , Kulkarni R. , Sharif S.
Published: April 2007

Maintenance of intestinal immune system homeostasis requires the host to distinguish commensal bacteria, which are members of the gut microbiota, from pathogenic micro-organisms and respond accordingly. Although the mechanisms that maintain this homeostasis are not completely understood, evidence, particularly from studies of rodents and humans, has enabled the unravelling of the finely tuned balance that exists between the host and its microbiota. Commensal bacteria, which are in close contact with cells of the intestinal immune system, have been shown to play an important role in regulation of innate and adaptive immune mechanisms. The anatomy of the gut-associated lymphoid tissue in avian and ruminant species differs from that of monogastric animal species. However, many of the mechanisms that are used to identify and respond to commensal bacteria are highly conserved among species and are, therefore, thought to function similarly. In recent years, interest in the area of gut microbiota interactions with the host immune system has significantly increased. This is partly because of the implications of these interactions for the development of novel strategies for improving gut health in animals.
Temperate forage legumes for adverse conditions.
Authors: Frame J. , Laidlaw A. S.
Published: April 2007

The suitability of temperate forage legumes for adverse physical conditions is considered. The ability of the major forage legumes i.e. lucerne, white and red clover and birdsfoot trefoil and the 'minor' species, many originating from Mediterranean-type climatic zones, to withstand soil acidity, alkalinity and salinity and drought, waterlogging and extreme temperatures is compared. As many of the references cited involve direct comparison between species in response to a given adverse environmental factor, species are ranked for tolerance to that factor in some instances. Both annual and perennial species are included in the review. Conclusions from comparisons are conditioned by cultivars or ecotypes chosen to represent the species and the method of evaluation. Nevertheless, species at either end of the tolerance spectrum to a specific adverse factor are generally clearly identified. There is no definite rule in deciding whether the most appropriate approach to improving tolerance in the legume component of a forage or pasture is either to search and replace the existing species with another or improve the existing species. In the latter case, molecular and transformation technology is becoming increasingly important. Increasing emphasis on international cooperation is urged as marginal areas are not restricted to any one country. The economic case for reliance on legumes, especially in marginal areas where response to nitrogenous fertilizer is poorest, remains strong.
Host resistance to infectious disease: immunogenetics of Mareks disease in chickens.
Authors: Sarson A. J. , Abdul-Careem M. F. , Parvizi P. , Sharif S.
Published: April 2007

It has been known for centuries that in epidemics of infectious diseases, some species, strains, families, and individuals are more resistant or susceptible than others. Since these early observations, the role of the inherent parameters in determining an individual's relative resistance to infectious diseases has been speculated upon. In the past few decades, with improvements in prevention, diagnosis and treatment of disease, as well as successful national and international eradication programmes, the incidence rate of infectious diseases in human and domestic animal populations has dropped drastically. However, the process of controlling infectious diseases remains hampered by the cost of eradication programmes, the need for an intimate collaboration between national and international organizations, lack of knowledge regarding the genetic interplay between the host and parasite, constant evolution of parasites and the risk of resurgence of old pathogens or even those presumed to be eradicated. In the case of domestic animals, genetically based approaches for enhancement of disease resistance may provide a complementary or an alternative approach to the currently available strategies for control of disease, such as vaccination and the use of antimicrobials. This review describes the current status of research in the area of genetic regulation of host response and disease resistance in domestic animals. Various approaches for dissecting out genetics of host response and disease resistance, including phenotypic selection, genetic markers, candidate genes and gene expression profiling will be discussed. Finally, genetics of resistance and susceptibility to Marek's disease in chickens will be explored in detail.
Risk assessment for plant-made pharmaceuticals.
Authors: Wolt J. D. , Karaman S. , Wang Kan Wang Kan
Published: April 2007

Plant-made pharmaceuticals (PMPs) offer great promise as efficacious and cost-effective products for the treatment of human and animal disease. The benefits of this technology must be balanced against potential health and environmental risks that may be associated with its use. Risks associated with human and animal health and environmental impacts of PMPs can be minimized through adoption of production confinement and product channelling processes that have stringencies consistent with the degree of hazard or uncertainty associated with a specific product. Risk assessment considers the probability for harm to occur as a consequence of exposure in the production, processing, and use of a given PMP. Risk assessment focused on the intended uses of PMPs involves manufacturing and medicinal use scenarios that consider workers and consumers of the PMP; whereas the risk assessment for unintended occurrence in food or feeds considers a differing nature of exposure (in terms of the route, intensity, frequency and duration of exposure). The consequences of intended and unintended use both must be considered and managed for comprehensive understanding of risk. Regardless, because PMPs presently have no provision for regulatory tolerances, their inadvertent occurrence in foods or feeds remains an important economic consideration, even when the health and environmental risks are low. Various production options may be utilized to account for uncertainties in order to mitigate the risks of PMPs.
The use of computer-based decision support systems in horticulture.
Authors: Collier R. H.
Published: April 2007

The horticulture industry is highly dependent on the weather, which affects not only crop yields, but also maturity times, nutrient supply and the onset of pest and disease problems. The ready availability of computers has led to the development of computer-based Decision Support Systems (DSS) for horticulture. DSS are systems designed to help users make more effective decisions by providing the information in a way which actively supports the decision process. Many horticultural DSS use weather data as a major input and for these, the frequency of data collection and the level of recording accuracy required depend on the process modelled. Potential sources of weather data range from weather stations run as part of national networks to automatic weather stations recording climatic conditions within individual crops. Computer-based DSS and their output are distributed to users in several ways. Some DSS can be run directly on the web or downloaded from the web. However, managed services are popular with growers because they are often accompanied by an interpretation from an expert. Output may be distributed by fax, email, the Internet or mobile phone. The uptake of DSS has, in general, been slower than might have been expected at the outset and can be attributed, at least in part, to the failure of scientists to understand and identify the 'market' sufficiently. Barriers to uptake include the gap between the processing power and capability of users' hardware and that expected by the software, and access to, and the cost of, up-to-date data, particularly weather data. There is also a perceived threat to the livelihood of agronomists and consultants. However, they are likely to be the main users of DSS rather than growers.
Equine influenza in India.
Authors: Gupta A. K. , Virmani N.
Published: April 2007

In the year 1987, India experienced a severe epizootic of equine influenza in which more than 83 000 equids were involved. The virus was isolated from various parts of the country and A/Equi-2 was confirmed to be the main causative agent, while A/Equi-1 was reported only in a few cases. By adopting adequate preventive and management practices, the disease was put under control. Although the incidence of respiratory disease causing problems 'similar to influenza' was reported in 1965 on the basis of haemagglutination titre and clinical symptoms, systematic studies (including the isolation of the virus and its characterization) were carried out only after the outbreak of 1987. Most of the characterization work and vaccine preparation was done with A/Equi-2 isolate of influenza virus (A/Equi-2/Ludhiana/87), as it was involved in majority of the affected equines. Nucleotide sequencing of haemagglutinin-1 (HA1), neuraminidase (NA) and nonstructural gene-1 (NS1) genes revealed that the Indian isolate had co-linearity with circulating isolates at that time. However, another isolate, A/Equi-2/Bhiwani/87 (H3N8), was observed to be a vaccine strain. Monoclonal antibodies, along with a number of diagnostic tests, namely single radial haemolysis (SRH), enzyme linked immunosorbent assay (ELISA), reverse transcriptase-polymerase chain reaction (RT-PCR) and RNA:DNA-hybridization-based DNA probes, were developed for detection of this virus. A low-cost equine influenza vaccine was also developed indigenously which contained 20 mg HA protein in the killed whole-virus vaccine. The efficacy and immunogenicity of this vaccine have already been tested successfully. Though no major equine influenza outbreak has been reported after 1987, the country should remain fully prepared to combat any such unforeseen situation in future, with up-to-date facilities for virus isolation, its characterization and development of new vaccine with emerging isolates, if any, at a very short notice.
Folate and health.
Authors: Picciano M. F. , Yetley E. A. , Coates P. M.
Published: April 2007

The B vitamin, folate, functions as a coenzyme in single-carbon transfer reactions. Dietary sources include a family of derivatives found naturally in foods and the synthetic form (folic acid) used in fortified foods and dietary supplements. The role of folate in treating and preventing the megaloblastic anaemia of pregnancy has long been recognized. Recent documentation of its beneficial role in preventing pregnancies affected by neural tube defects provided the basis for recommendations that women of child-bearing age take a dietary supplement containing 400 mg folic acid daily and, in some countries, for implementation of national folic acid fortification programmes. Relatively new hypotheses for a possible role of folate status in several health outcomes (e.g. cardiovascular disease, cancer, cognitive function and osteoporosis) and related research activities are described. Discussions of the tools and challenges in assessing and monitoring folate status are included. The US experience is used to illustrate the issues in designing and monitoring a national folic acid fortification programme. Future research and monitoring needs are identified.
Practical recommendations on the control of helminth parasites in organic sheep production systems.
Authors: Cabaret J.
Published: April 2007

Helminth infections are one of the major preoccupations in organic sheep farming. The present control strategy is two-fold; aiming to reduce intake of parasites by using proper grazing management or adult parasite load in the lambs. Uninfected pastures (following grazing, pasture newly sown or grazed previously by cattle) are often available and should be dedicated to lambs, which are more susceptible than ewes. The grazing of certain leguminous forages and herbs may reduce parasitic infestation in sheep but further studies are required prior to large-scale utilization in organic farms. The recommended treatments of lambs and/or ewes are based on phytotherapy and homeopathy. At present, claims of efficacy are not backed with hard facts, although the approaches are widely used in organic sheep farms. Shepherds also rely on synthetic chemical drugs, since several anthelmintic drenches are compatible with organic production. The use of different categories of products may prove costly in poorly managed farms. A targeted selective treatment (e.g. selection of animals or groups to be treated) is a proposal that will attract organic farmers, provided that they are given indicators for treatment decisions. At present, several indicators are available (laboratory analyses, pathophysiological indicators (anaemia or diarrhoea), and production traits (weight gains)) but they are costly or time-consuming and there is a need for their optimization. Their acceptance by farmers is also a prerequisite for their promotion.
Group SCAD regression analysis for microarray time course gene expression data
Authors: Wang Lifeng , Chen Guang , Li Hongzhe
Published: April 2007

Motivation: Since many important biological systems or processes are dynamic systems, it is important to study the gene expression patterns over time in a genomic scale in order to capture the dynamic behavior of gene expression. Microarray technologies have made it possible to measure the gene expression levels of essentially all the genes during a given biological process. In order to determine the transcriptional factors (TFs) involved in gene regulation during a given biological process, we propose to develop a functional response model with varying coefficients in order to model the transcriptional effects on gene expression levels and to develop a group smoothly clipped absolute deviation (SCAD) regression procedure for selecting the TFs with varying coefficients that are involved in gene regulation during a biological process.

Results: Simulation studies indicated that such a procedure is quite effective in selecting the relevant variables with time-varying coefficients and in estimating the coefficients. Application to the yeast cell cycle microarray time course gene expression data set identified 19 of the 21 known TFs related to the cell cycle process. In addition, we have identified another 52 TFs that also have periodic transcriptional effects on gene expression during the cell cycle process. Compared to simple linear regression (SLR) analysis at each time point, our procedure identified more known cell cycle related TFs.

Conclusions: The proposed group SCAD regression procedure is very effective for identifying variables with time-varying coefficients, in particular, for identifying the TFs that are related to gene expression over time. By identifying the TFs that are related to gene expression variations over time, the procedure can potentially provide more insight into the gene regulatory networks.

Contact:  hli@cceb.upenn.edu

Supplementary information:  http://www.cceb.med.upenn.edu/~hli/gSCAD-Appendix.pdf
An efficient method for the detection and elimination of systematic error in high-throughput screening
Authors: Makarenkov Vladimir , Zentilli Pablo , Kevorkov Dmytro , Gagarin Andrei , Malo Nathalie , Nadon Robert
Published: April 2007

Motivation: High-throughput screening (HTS) is an early-stage process in drug discovery which allows thousands of chemical compounds to be tested in a single study. We report a method for correcting HTS data prior to the hit selection process (i.e. selection of active compounds). The proposed correction minimizes the impact of systematic errors which may affect the hit selection in HTS. The introduced method, called a well correction, proceeds by correcting the distribution of measurements within wells of a given HTS assay. We use simulated and experimental data to illustrate the advantages of the new method compared to other widely-used methods of data correction and hit selection in HTS.

Contact: makarenkov.vladimir@uqam.ca

Supplementary information: Supplementary data are available at Bioinformatics online.
Petrous Apex Aspergillosis as a Long‐Term Complication of Cholesterol Granuloma
Authors: Eloy Jean Anderson , Bederson Joshua B. , Smouha Eric E.
Published: April 2007

Aspergillus infection of the petrous apex is a rare and devastating condition. To date, only two such cases have been reported, which resulted from direct extension of chronic Aspergillus otitis media. We present a case of petrous apex aspergillosis occurring years after surgical drainage of a petrous apex granuloma cyst. Because of the potential lethal nature of this condition, aggressive surgical therapy should be considered early in this illness and may provide the best chance for survival.
The Transnasal Esophagoscopy Documentation Dilemma
Authors: Garner Justin , Schweinfurth John , May Warren , Faust John
Published: April 2007

Objective: To determine radiographically the anatomic length difference between the nasal and oral aerodigestive tracts and to clarify gaps in the literature regarding standardized landmark measurements and documentation techniques in transnasal esophagoscopy, as opposed to traditional transoral esophagoscopy.

Study Design: This is a prospective radiographic cohort study.

Methods: Digital computerized tomography measurement techniques were used to determine the difference in length between the nasal and oral aerodigestive tracts. Using sagittal plane images from consecutive patients, the mean nares‐cricoid (NC) distance, upper incisor‐cricoid (IC) distance, and their mean differences were determined. Male, female, and overall distances and differences were calculated. Standard deviations, 95% confidence intervals, and 90% prediction intervals were also calculated. Mean difference data were applied to reported standard oral esophagoscopy landmark measurements to convert to standard landmark measurements from the nares.

Results: Overall mean NC and IC distances were 175.4 mm and 147.5 mm, respectively. For males, these mean distances were 185.5 mm and 155.0 mm, respectively. For females, these mean distances were 165.3 mm and 140.0 mm, respectively. Overall mean NC to IC difference was 27.9 mm. The mean NC to IC difference for males and females was 30.5 mm and 25.2 mm, respectively.

Conclusions: Historically, landmark and report measurements in esophagoscopy have been measured and standardized from the upper incisor. This study demonstrates and clarifies the inherent anatomic length difference of the nasal and oral aerodigestive tracts and the resultant documentation dilemma produced by transnasal esophagoscopy techniques. These data provide easy conversion of esophagoscopy measurements reported from the incisors or nares, providing better communication between endoscopists of different disciplines and techniques.
Otopathology in Mohr‐Tranebjærg Syndrome
Authors: Bahmad Fayez , Merchant Saumil N. , Nadol Joseph B. , Tranebjærg Lisbth
Published: April 2007

Background: Mohr‐Tranebjærg syndrome (MTS) is an X‐linked, recessive, syndromic sensorineural hearing loss (HL) characterized by onset of deafness in childhood followed later in adult life by progressive neural degeneration affecting the brain and optic nerves. MTS is caused by mutations in the DDP/TIMM8A gene, which encodes for a 97 amino acid polypeptide; this polypeptide is a translocase of the inner mitochondrial membrane.

Objectives: To describe the otologic presentation and temporal bone histopathology in four affected individuals with MTS.

Material and Methods: All four subjects belonged to a large, multigenerational Norwegian family and were known to carry a frame shift mutation in the TIMM8A gene. Temporal bones were removed at autopsy and studied by light microscopy. Cytocochleograms were constructed for hair cells, stria vascularis, and cochlear neuronal cells. Vestibular neurons were also counted.

Results: All four subjects developed progressive HL in early childhood, becoming profoundly deaf by the age of 10 years. All four developed language, and at least one subject used amplification in early life. Audiometric evaluation in two subjects showed 80‐ to 100‐dB HL by the age of 10 years. The subjects died between the ages of 49 and 67. The otopathology was strikingly similar in that all bones examined showed near‐total loss of cochlear neuronal cells and severe loss of vestibular neurons. When compared with age‐matched controls, there was 90% to 95% loss of cochlear neurons and 75% to 85% loss of vestibular neurons.

Conclusions: We infer that the HL in MTS is likely to be the result of a postnatal and progressive degeneration of cochlear neurons and that MTS constitutes a true auditory neuropathy. Our findings have implications for clinical diagnosis of patients with MTS and management of the HL.
Comparison of differential neuronal responsiveness for different regions of the prefrontal cortex in a conditional visual discrimination task
Authors: Xiang J.‐Z. , Brown M. W.
Published: April 2007

To investigate neuronal processing during monkeys' performance of a visual conditional discrimination task, recordings were made from four areas of prefrontal cortex (ventromedial, orbitofrontal, dorsolateral and anterior cingulate) where lesions have been shown to produce impairment of such tasks. Of 1911 recorded neurons, 573 (31%) responded to elements of the task. This proportion was less than the 50% previously reported as responsive in temporal cortex under the same conditions, suggesting sparser encoding in prefrontal than temporal cortex. Of the responsive prefrontal neurons, 165 (29%) responded differently on the different types of trial, so signalling various types of information relevant to task performance and cognition. In line with recent lesion findings, in the dorsolateral region the incidence of such differentially responsive neurons was only an eighth that in the other regions. The relatively high incidence of neuronal responses that encoded a potential instruction cue rather than specific individual stimulus arrangements was consistent with the animals solving the task by using such information, though other neuronal responses could have enabled the task to have been solved by rote learning. Compared to temporal neurons, prefrontal responses more frequently coded information relating to the planned behavioural response rather than perceptual aspects of the task. Population differential response latencies were long (> ∼ 225 ms) in prefrontal cortex. A comparison of such differential latencies between temporal and prefrontal cortex indicated that potential information flow was likely to be primarily from temporal to prefrontal cortex rather than vice versa.
Kynurenic acid blocks nicotinic synaptic transmission to hippocampal interneurons in young rats
Authors: Stone Trevor W.
Published: April 2007

The tryptophan metabolite kynurenic acid can block glutamate at ionotropic receptors, but recent evidence suggests a more potent antagonistic action at α7 nicotinic receptors for acetylcholine on cultured neurons. The present study examines activity of kynurenic acid at those nicotinic receptors, which mediate cholinergic neurotransmission onto interneurons in the rat hippocampus. Intracellular recordings were made from pyramidal cells and interneurons in the presence of atropine, bicuculline methobromide, (3‐aminopropyl)(diethoxymethyl)‐phosphinic acid [CGP35348, to block γ‐aminobutyric acid (GABA)B receptors] and 3‐tropanyl‐3,5‐dichlorobenzoate (MDL 72222, to block 5‐HT3 receptors). In the added presence of glutamate antagonists 2‐amino‐5‐phosphono‐pentanoic acid and 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione, interneurons exhibited a residual excitatory postsynaptic potential (EPSP) that could be blocked by the nicotinic α7 receptor blocker methyl‐lycaconitine, but not by dihydro‐β‐erythroidine which blocks α4β2 receptors. Kynurenic acid reduced the amplitude of these EPSPs with an EC50 of 136 µm. The amplitudes of nicotinic spontaneous miniature EPSPs were also reduced by methyl‐lycaconitine and kynurenic acid. The results show that kynurenic acid is more potent in blocking nicotinic EPSPs compared with the full, glutamate‐mediated EPSPs, but it was substantially less potent than has been reported in cultures, possibly because of differences in the accessibility of synaptic and extrasynaptic receptors. It is suggested that blockade of nicotinic synaptic transmission may be relevant to the actions of kynurenic acid in the hippocampus, but that in the intact brain this activity is likely to be comparable in importance to the blockade of glutamate‐mediated transmission.
Custom and the Courts: Ensuring Women's Rights to Land, Jharkhand, India
Authors: Rao Nitya
Published: April 2007

Based on field research in Dumka district, Jharkhand, this article examines the mechanisms through which women operationalize their rights to land. It questions the polarization of legitimation systems into statutory codes and customary practices, as operating independent of each other, and demonstrates the political and temporal situatedness of ‘law’, and the processes of hybridization that allow for the actualization of a legal right, by providing it social recognition and validity. The article explores the choice of different arenas by women for making their claims, with the choice of a particular arena depending not just on access and resource availability, but also on the women's social positionality.
Optimal Commodity Taxation with a Representative Agent
Authors: Kemp Murray C. , Shimomura Koji
Published: April 2007

It is argued that the task of describing the optimal vector of commodity taxes is trivialized by the traditional assumption of a price‐taking representative agent; that, in particular, the assumption of a representative agent ensures that the null vector is optimal.
School Choice and the Intergenerational Poverty Trap
Authors: Nishimura Kazuo , Raut Lakshmi K.
Published: April 2007

This paper formulates a dynamic altruistic model of parental choice of school quality and intergenerational social mobility. It shows that when there are many school qualities, the earnings of children as a function of parental schooling investment is a non‐concave function, which leads to multiple steady‐state equilibria. The paper studies the intergenerational dynamics of parental schooling investment and gives conditions on the rate of return from parental schooling investment under which some families are stuck in an intergenerational poverty trap. The policy implications are also discussed.
Exchange Rates, Expectations, and Monetary Policy: a NOEM Perspective*
Authors: Pierdzioch Christian , Stadtmann Georg
Published: April 2007

We use a dynamic general‐equilibrium optimizing two‐country model to analyze how the formation of exchange rate expectations shapes the effects of a monetary policy shock in an open economy. We also provide empirical evidence on how traders in foreign exchange markets form exchange rate expectations. Our model implies that the short‐run output effect of a permanent monetary policy shock diminishes if “technical traders” form the type of regressive exchange rate expectations we find in our empirical analysis. If the influence of technical traders is strong enough, a permanent expansionary monetary policy shock can result in a temporary decline of the output in the country in which it takes place. The output effect of a temporary monetary policy shock is magnified when technical traders form regressive exchange rate expectations.
Cartel Stability and Economic Integration
Authors: Schröder Philipp J. H.
Published: April 2007

This paper revisits the notion that economic integration—modeled as a reduction of trade costs—may be anticompetitive, in the sense that it may reinforce the ability of an international cartel to maintain a collusive understanding about staying out of each other’s markets. The paper is novel in terms of introducing ad valorem and fixed trade costs in addition to the customary unit trade costs. It is shown that an anticompetitive effect, found for reductions in unit trade costs, may disappear once trade costs are ad valorem or fixed.
Trade, Human Capital, and Technology Spillovers: an Industry‐level Analysis
Authors: Wang Yanling
Published: April 2007

This paper studies whether trade promotes North–South and South–South technology spillovers at the industry level, and how the absorptive capacity of the South affects the impact of the technology spillovers. Using data from 16 manufacturing industries in 25 developing countries from 1976 to 1998, the paper shows: (i) North–South trade‐related R&D has a substantial impact on total factor productivity in the South; (ii) South–South trade‐related R&D also promotes technology spillovers but with a smaller magnitude; and (iii) human capital is very important in facilitating North–South and South–South technology spillovers: an increase in human capital could lead to over three times the size of technology spillovers from an increase in trade‐related foreign R&D.