The REFLECT statement: methods and processes of creating reporting guidelines for randomized controlled trials for livestock and food safety

The conduct of randomized controlled trials in livestock with production, health, and food-safety outcomes presents unique challenges that may not be adequately reported in trial reports. The objective of this project was to modify the CONSORT (Consolidated Standards of Reporting Trials) statement to reflect the unique aspects of reporting these livestock trials. A two-day consensus meeting was held on November 18-19, 2008 in Chicago, IL, United States of America, to achieve the objective. Prior to the meeting, a Web-based survey was conducted to identify issues for discussion. The 24 attendees were biostatisticians, epidemiologists, food-safety researchers, livestock-production specialists, journal editors, assistant editors, and associate editors. Prior to the meeting, the attendees completed a Web-based survey indicating which CONSORT statement items may need to be modified to address unique issues for livestock trials. The consensus meeting resulted in the production of the REFLECT (Reporting Guidelines For Randomized Control Trials) statement for livestock and food safety (LFS) and 22-item checklist. Fourteen items were modified from the CONSORT checklist, and an additional sub-item was proposed to address challenge trials. The REFLECT statement proposes new terminology, more consistent with common usage in livestock production, to describe study subjects. Evidence was not always available to support modification to or inclusion of an item. The use of the REFLECT statement, which addresses issues unique to livestock trials, should improve the quality of reporting and design for trials reporting production, health, and food-safety outcomes.

Statistical evaluation of test accuracy studies for Toxoplasma gondii in food animal intermediate hosts

The availability of accurate diagnostic tests is essential for the detection and control of Toxoplasma gondii infections in both definitive and intermediate hosts. Sensitivity, specificity and the area under the receiver-operating characteristic (ROC) curve are commonly used measures of test accuracy for infectious diseases such as toxoplasmosis. These test performance characteristics are important considerations when selecting from among a group of tests for a specific testing purpose. In this study, we reviewed statistical approaches to evaluation of tests for toxoplasmosis with and without a gold-standard (reference) test, including use of ROC analysis and likelihood ratios which retain the diagnostic information inherent in a quantitative test result. We use previously published data from a comparison of the accuracy of serological tests for swine toxoplasmosis to demonstrate suggested methods of data analysis. We make recommendations for statistical analysis and reporting of test evaluation studies for T. gondii in food animals based on our own experiences and those of others.

Functions and pathologies of BiP and its interaction partners

The endoplasmic reticulum (ER) is involved in a variety of essential and interconnected processes in human cells, including protein biogenesis, signal transduction, and calcium homeostasis. The central player in all these processes is the ER-lumenal polypeptide chain binding protein BiP that acts as a molecular chaperone. BiP belongs to the heat shock protein 70 (Hsp70) family and crucially depends on a number of interaction partners, including co-chaperones, nucleotide exchange factors, and signaling molecules. In the course of the last five years, several diseases have been linked to BiP and its interaction partners, such as a group of infectious diseases that are caused by Shigella toxin producing E. coli. Furthermore, the inherited diseases Marinesco-Sjögren syndrome, autosomal dominant polycystic liver disease, Wolcott-Rallison syndrome, and several cancer types can be considered BiP-related diseases. This review summarizes the physiological and pathophysiological characteristics of BiP and its interaction partners.

A retrospective study of the clinical presentation of 140 dogs and 39 cats with bacteraemia

OBJECTIVES

To evaluate retrospective data from 140 dogs and 39 cats with positive blood cultures that were presented to the Clinic for Small Animal Medicine in Munich from 1995 to 2004.

METHODS

The identity of bacteria isolated from blood cultures of dogs and cats with bacteraemia was determined, and clinical and laboratory findings and outcome of animals with Gram-negative versus Gram-positive bacteraemia were compared.

RESULTS

Sepsis was diagnosed in 81.7 per cent of dogs and 59.5 per cent of cats with bacteraemia. Escherichia coli was isolated in one third of the animals. Dogs with bacteraemia more often showed monocytosis and increased alkaline phosphatase activity, while in cats, hyperglycaemia was found more commonly. Dogs with Gram-negative bacteraemia had hypoalbuminaemia significantly more often than dogs with Gram-positive bacteraemia, while among the remaining parameters, there were no statistically significant differences.

CLINICAL SIGNIFICANCE

Not all dogs and cats with a positive blood culture met the criteria for sepsis. Bacteraemia caused by Gram-positive versus Gram-negative bacteria cannot be distinguished based on clinical or laboratory parameters, and bacterial culture and susceptibility testing have to be performed for the right choice of antibiotic treatment.

Quantitative assessment of the likelihood of the introduction of classical swine fever virus into the Danish swine population

Classical swine fever virus (CSFV) is a major infectious-disease agent of livestock and causes production losses through increased morbidity and mortality, particularly of young pigs. We identified the pathways for introduction of CSFV into Denmark and assessed the annual probability of introduction (based on a US Department of Agriculture model). We developed pathways based on material from scientific articles, reports from veterinary agencies and custom officers, and consultations with experts in the field. Returning livestock trucks and legal meat imports were the most important pathways for CSFV introduction to Denmark from other EU states with predicted overall likelihood of one or more introductions of CSFV within a median of 130 years (46-280) provided mitigating steps, such as cleaning trucks, were maintained to a very high standard. The likelihood would increase dramatically if these activities were abandoned: one or more introductions within a median of 5.2 years (2-14). The predicted risks from live-animal imports and semen were extremely low given the very few imports of these products. The most important countries for Denmark's CSFV risk are Germany and the Netherlands, though this risk is again predicted to be dramatically reduced as long as mitigating activities are maintained. We predicted the risk from illegal movements of pork into Denmark to be low because little pork enters through this route and only a small fraction of this pork would be fed to pigs.

Coherent quantum optical control with subwavelength resolution

We suggest a new method for quantum optical control with nanoscale resolution. Our method allows for coherent far-field manipulation of individual quantum systems with spatial selectivity that is not limited by the wavelength of radiation and can, in principle, approach a few nanometers. The selectivity is enabled by the nonlinear atomic response, under the conditions of electromagnetically induced transparency, to a control beam with intensity vanishing at a certain location. Practical performance of this technique and its potential applications to quantum information science with cold atoms, ions, and solid-state qubits are discussed.

Risk Factors for Changing Test Classification in the Danish Surveillance Program for Salmonella in Dairy Herds

A surveillance program in which all cattle herds in Denmark are classified into Salmonella infection categories has been in place since 2002. Dairy herds were considered test negative and thus most likely free of infection if Salmonella antibody measurements were consistently low in bulk tank milk samples collected every 3 mo. Herds were considered test positive and thus most likely infected if the 4-quarter moving average bulk tank milk antibody concentration was high or if there was a large increase in the most recent measurement compared with the average value from the previous 3 samples. The objective of this study was to evaluate risk factors for changing from test negative to positive, which was indicative of herds becoming infected from one quarter of the year to the next, and risk factors for changing from test positive to negative, which was indicative of herds recovering from infection between 2 consecutive quarters of the year. The Salmonella serotypes in question were Salmonella Dublin or other serotypes that cross-react with the Salmonella Dublin antigen in the ELISA (e.g., some Salmonella Typhimurium types). Two logistic regression models that accounted for repeated measurements at the herd level and controlled for herd size and regional effects were used. Data from 2003 was used for the analyses. A change from test negative to positive occurred in 2.0% of the quarterly observations (n = 21,007) from test negative dairy herds. A change from test positive to negative occurred in 10.0% of quarterly observations (n = 6,168) available from test positive dairy herds. The higher the number of test-positive neighbor herds in the previous year-quarter, the more likely herds were to become test positive for Salmonella. The number of purchased cattle from test-positive herds was also associated with changing from test negative to positive. The bigger the herd, the more likely it was to change from negative to test positive. The effect of herd size on recovery was less clear. Large herds consisting mainly of large breeds or having test-positive neighbors in a 2-km radius were less likely to change from test positive to negative, whereas the breed and neighbor factors were not found to be important for small herds. Organic production was associated with remaining test positive, but not with becoming test positive. The results emphasize the importance of external and internal biosecurity measures to control Salmonella infections.

Recrystallization of tungsten wire for fabrication of sharp and stable nanoprobe and field-emitter tips

Atomically sharp tungsten tips made from single crystal tungsten wire are superior to those made from cold-drawn polycrystalline wire but are rarely used due to their high price. We have devised a method of obtaining highly crystalline tungsten wire by recrystallizing cold-drawn wire. The effect of various heat treatments on the wire microstructure was observed using scanning electron microscopy and x-ray diffraction. A dramatic difference in the shapes of tips etched from cold-drawn and recrystallized wires was observed using transmission electron microscopy. The described annealing process is an inexpensive alternative to using single crystal wires.

Demonstrating freedom from disease using multiple complex data sources 2: case study--classical swine fever in Denmark

A method for quantitative evaluation of surveillance for disease freedom has been presented in the accompanying paper (Martin et al., 2007). This paper presents an application of the methods, using as an example surveillance for classical swine fever (CSF) in Denmark in 2005. A scenario tree model is presented for the abattoir-based serology component of the Danish CSF surveillance system, in which blood samples are collected in an ad hoc abattoir sampling process, from adult pigs originating in breeding herds in Denmark. The model incorporates effects of targeting (differential risk of seropositivity) associated with age and location (county), and disease clustering within herds. A surveillance time period of one month was used in the analysis. Records for the year 2005 were analysed, representing 25,332 samples from 3528 herds; all were negative for CSF-specific antibodies. Design prevalences of 0.1-1% of herds and 5% of animals within an infected herd were used. The estimated mean surveillance system component (SSC) sensitivities (probability that the SSC would give a positive outcome given the animals processed and that the country is infected at the design prevalences) per month were 0.18, 0.63 and 0.86, for among-herd design prevalences of 0.001, 0.005 and 0.01. The probabilities that the population was free from CSF at each of these design prevalences, after a year of accumulated negative surveillance data, were 0.91, 1.00 and 1.00. Targeting adults and herds from South Jutland was estimated to give approximately 1.9, 1.6 and 1.4 times the surveillance sensitivity of a proportionally representative sampling program for these three among-herd design prevalences.

Demonstrating freedom from disease using multiple complex data sources 1: a new methodology based on scenario trees

Current methods to demonstrate zone or country freedom from disease are based on either quantitative analysis of the results of structured representative surveys, or qualitative assessments of multiple sources of evidence (including complex non-representative sources). This paper presents a methodology for objective quantitative analysis of multiple complex data sources to support claims of freedom from disease. Stochastic scenario tree models are used to describe each component of a surveillance system (SSC), and used to estimate the sensitivity of each SSC. The process of building and analysing the models is described, as well as techniques to take into account any lack of independence between units at different levels within a SSC. The combination of sensitivity estimates from multiple SSCs into a single estimate for the entire surveillance system is also considered, again taking into account lack of independence between components. A sensitivity ratio is used to compare different components of a surveillance system. Finally, calculation of the probability of country freedom from the estimated sensitivity of the surveillance system is illustrated, incorporating the use and valuation of historical surveillance evidence.

Comparative evaluation of six ELISAs for the detection of antibodies to the non-structural proteins of foot-and-mouth disease virus

To validate the use of serology in substantiating freedom from infection after foot-and-mouth disease (FMD) outbreaks have been controlled by measures that include vaccination, 3551 sera were tested with six assays that detect antibodies to the non-structural proteins of FMD virus. The sera came from naïve, vaccinated, infected and vaccinated-and-infected animals; two-thirds from cattle, the remainder from sheep and pigs. The assays were covariant for sensitivity, but not necessarily for specificity. A commercial kit from Cedi-diagnostics and an in-house assay from IZS-Brescia were comparable to the NCPanaftosa-screening index method described in the Diagnostic Manual of the World Animal Health Organisation. Using these three tests the specificity and sensitivity for the detection of carriers in vaccinated cattle approaches or exceeds 99% and 90%, respectively.

Simulation model estimates of test accuracy and predictive values for the Danish Salmonella surveillance program in dairy herds

The Danish government and cattle industry instituted a Salmonella surveillance program in October 2002 to help reduce Salmonella enterica subsp. enterica serotype Dublin (S. Dublin) infections. All dairy herds are tested by measuring antibodies in bulk tank milk at 3-month intervals. The program is based on a well-established ELISA, but the overall test program accuracy and misclassification was not previously investigated. We developed a model to simulate repeated bulk tank milk antibody measurements for dairy herds conditional on true infection status. The distributions of bulk tank milk antibody measurements for infected and noninfected herds were determined from field study data. Herd infection was defined as having either >or=1 Salmonella culture-positive fecal sample or >or=5% within-herd prevalence based on antibody measurements in serum or milk from individual animals. No distinction was made between Dublin and other Salmonella serotypes which cross-react in the ELISA. The simulation model was used to estimate the accuracy of herd classification for true herd-level prevalence values ranging from 0.02 to 0.5. Test program sensitivity was 0.95 across the range of prevalence values evaluated. Specificity was inversely related to prevalence and ranged from 0.83 to 0.98. For a true herd-level infection prevalence of 15%, the estimate for specificity (Sp) was 0.96. Also at the 15% herd-level prevalence, approximately 99% of herds classified as negative in the program would be truly noninfected and 80% of herds classified as positive would be infected. The predictive values were consistent with the primary goal of the surveillance program which was to have confidence that herds classified negative would be free of Salmonella infection.

Network analysis of Danish cattle industry trade patterns as an evaluation of risk potential for disease spread

Trade patterns of animal movements in a specific industry are complex and difficult to study because there are many stakeholders, premises that are heterogeneously spread over the country, and a highly dynamic flow of animals exists among them. The Danish cattle industry was defined as a network of animal movements and graph theory was used to analyse the movements of cattle within this network. A premise was defined as a farm, an abattoir or a market. These premises constituted the network nodes in the graph and the animal movements between them were the links. In this framework, each premise had a sub-network of other premises to which it was linked by these animal movements. If no movement of animals were registered for a specific farm, then the sub-network for that premise consisted of only that premise. Otherwise, the sub-network linked the premise of interest to all premises from which and to which animals were moved, as long as there was a path linking animal movements to that specific premise. This approach allowed visualization and analyses of four levels of organization that existed in Denmark animal registers: (1) the animal that was moved, (2) the movements of all animals between two premises, (3) the specific premise network, and (4) the overall industry network. When contagious animals are moved from one premise to another, then to a third and so forth, these movements create a path for potential transfer of pathogens. The paths within which pathogens are present identify the transmission risks. A network of animal movements should provide information about pathogen transmission and disease spread. The network of the Danish cattle industry network was a directed scale-free graph (the direction of a movement was known), with an in-degree power of 2 an out-degree power of 1.46, consisted of 29,999 nodes, and 130,265 movements during a 6-month period. The in clustering coefficient was calculated to be 0.52 for the inward direction (movement to), while it was 0.02 for the outward direction (movement from). In Denmark, the cattle movements between premises demonstrated a large degree of heterogeneity. This heterogeneity in movements between farms should be used to evaluate the risk potential of disease transmission for each premise and must be considered when modelling disease spread between premises. The objective of this research was to describe the network of animal movements and not just the animal movements per se.

ERj1p has a basic role in protein biogenesis at the endoplasmic reticulum

ERj1p is a membrane protein of the endoplasmic reticulum (ER) that can recruit the ER lumenal chaperone BiP to translating ribosomes. ERj1p can also modulate protein synthesis at initiation and is predicted to be a membrane-tethered transcription factor. Here we attribute the various functions of ERj1p to distinct regions within its cytosolic domain. A highly positively charged nonapeptide within this domain is necessary and sufficient for binding to ribosomes. Binding of ERj1p to ribosomes involves the 28S ribosomal RNA and occurs at the tunnel exit. Additionally, ERj1p has a dual regulatory role in gene expression: ERj1p inhibits translation in the absence of BiP, and another charged oligopeptide within the cytosolic domain of ERj1p mediates binding of the nuclear import factor importin beta and import into the nucleus, thereby paving the way for subsequent action on genomic DNA.

Kap120 functions as a nuclear import receptor for ribosome assembly factor Rpf1 in yeast

The nucleocytoplasmic exchange of macromolecules is mediated by receptors specialized in passage through the nuclear pore complex. The majority of these receptors belong to the importin beta protein family, which has 14 members in Saccharomyces cerevisiae. Nine importins carry various cargos from the cytoplasm into the nucleus, whereas four exportins mediate nuclear export. Kap120 is the only receptor whose transport cargo has not been found previously. Here, we characterize Kap120 as an importin for the ribosome maturation factor Rpf1, which was identified in a two-hybrid screen. Kap120 binds directly to Rpf1 in vitro and is released by Ran-GTP. At least three parallel import pathways exist for Rpf1, since nuclear import is defective in strains with the importins Kap120, Kap114, and Nmd5 deleted. Both kap120 and rpf1 mutants accumulate large ribosomal subunits in the nucleus. The nuclear accumulation of 60S ribosomal subunits in kap120 mutants is abolished upon RPF1 overexpression, indicating that Kap120 does not function in the actual ribosomal export step but rather in import of ribosome maturation factors.

Momentum distribution of a Fermi gas of atoms in the BCS-BEC crossover

We observe dramatic changes in the atomic momentum distribution of a Fermi gas in the crossover region between the BCS theory superconductivity and Bose-Einstein condensation (BEC) of molecules. We study the shape of the momentum distribution and the kinetic energy as a function of interaction strength. The momentum distributions are compared to a mean-field crossover theory, and the kinetic energy is compared to theories for the two weakly interacting limits. This measurement provides a unique probe of pairing in a strongly interacting Fermi gas.

Production efficiency of ultracold feshbach molecules in bosonic and fermionic systems

We investigate the production efficiency of ultracold molecules in bosonic 85Rb and fermionic 40K when the magnetic field is swept across a Feshbach resonance. For adiabatic sweeps of the magnetic field, our novel model shows that the conversion efficiency of both species is solely determined by the phase space density of the atomic cloud, in contrast with a number of theoretical predictions. In the nonadiabatic regime our measurements of the 85Rb molecule conversion efficiency follow a Landau-Zener model.

Probing pair-correlated fermionic atoms through correlations in atom shot noise

Pair-correlated fermionic atoms are created through dissociation of weakly bound molecules near a magnetic-field Feshbach resonance. We show that correlations between atoms in different spin states can be detected using the atom shot noise in absorption images. Furthermore, using time-of-flight imaging we have observed atom pair correlations in momentum space.

Probing the excitation spectrum of a fermi gas in the BCS-BEC crossover regime

We measure excitation spectra of an ultracold gas of fermionic (40)K atoms in the BCS-Bose-Einstein-condensation (BEC) crossover regime. The measurements are performed with a novel spectroscopy that employs a small modulation of the B field close to a Feshbach resonance to give rise to a modulation of the interaction strength. With this method we observe both a collective excitation as well as the dissociation of fermionic atom pairs in the strongly interacting regime. The excitation spectra reveal the binding energy or excitation gap for pairs in the crossover region.

Risk factors for dairy cow mastitis in the central highlands of Ethiopia

This study, with the objective of assessing the effect of risk factors on dairy cow mastitis in the central highlands of Ethiopia, was undertaken between February and September 2001 in the urban and peri-urban areas of Addis Ababa, Ethiopia. A prevalence study and questionnaire survey were carried out simultaneously. Clinical examination of lactating udders and California mastitis test (CMT) determined clinical and subclinical mastitis, respectively. Risk factors for subclinical and clinical mastitis were identified from data on animals and farm management by chi-square analysis and subsequent logistic regression. Cows aged at least 8 years, with poor body condition, with at least 8 parities and in at least the eighth month of lactation had a significantly higher risk for subclinical mastitis (p < 0.05). The risk was reduced for cows up to their third parity in good body condition and for cows receiving dry cow therapy. Cows aged at least 4 years, or with at least 8 parities, cows in at least the fourth month of lactation, cows with poor body condition, leaking milk or previous udder infections had a significantly higher risk of clinical mastitis (p <0.05). The risk was reduced by the use of separate towels for udder cleaning and by drying off at the end of lactation. Most of the risk factors were in agreement with previous reports. However, stage of lactation and drying-off style were in contrast to others. Further research is needed to identify the interrelationship between production level, specific pathogens and management risk factors.

State selective production of molecules in optical lattices

We demonstrate quantum control over both internal and external quantum degrees of freedom in a high number of identical "chemical reactions," carried out in an array of microtraps in a 3D optical lattice. Starting from a Mott insulating phase of an ultracold atomic quantum gas, we use two-photon Raman transitions to create molecules on lattice sites occupied by two atoms. In the atom-molecule conversion process, we can control both the internal rovibronic and external center of mass quantum state of the molecules. The lattice isolates the microscopic chemical reactions from each other, thereby allowing photoassociation spectra without collisional broadening even at high densities of up to 2 x 10(15) cm(-3).

Effects of caspofungin (MK-0991) and anidulafungin (LY303366) on phagocytosis, oxidative burst and killing of Candida albicans by human phagocytes

The objective of the present study was to investigate the influence of the new echinocandins caspofungin (MK-0991) and anidulafungin (LY303366) on human phagocytes. Phagocytosis, oxidative burst and intracellular killing of Candida albicans were analyzed by flow cytometry. Neither caspofungin nor anidulafungin significantly influenced phagocytosis. Only caspofungin significantly influenced oxidative burst after 15 min of incubation ( P<0.05). Both caspofungin and anidulafungin improved intracellular killing rates of C. albicans after 2 h of incubation (42.4% and 43.2%, respectively, compared to 37.9% in controls; P<0.05). In conclusion, caspofungin significantly improves oxidative burst and intracellular killing, which may be advantageous for clinical therapy.

Entanglement interferometry for precision measurement of atomic scattering properties

We report on a matter wave interferometer realized with entangled pairs of trapped 87Rb atoms. Each pair of atoms is confined at a single site of an optical lattice potential. The interferometer is realized by first creating a coherent spin superposition of the two atoms and then tuning the interstate scattering length via a Feshbach resonance. The selective change of the interstate scattering length leads to an entanglement dynamics of the two-particle state that can be detected in a Ramsey interference experiment. This entanglement dynamics is employed for a precision measurement of atomic interaction parameters. Furthermore, the interferometer allows us to separate lattice sites with one or two atoms in a nondestructive way.