Quantum optimization of maximum independent set using Rydberg atom arrays

Realizing quantum speedup for practically relevant, computationally hard problems is a central challenge in quantum information science. Using Rydberg atom arrays with up to 289 qubits in two spatial dimensions, we experimentally investigate quantum algorithms for solving the Maximum Independent Set problem. We use a hardware-efficient encoding associated with Rydberg blockade, realize closed-loop optimization to test several variational algorithms, and subsequently apply them to systematically explore a class of graphs with programmable connectivity. We find the problem hardness is controlled by the solution degeneracy and number of local minima, and experimentally benchmark the quantum algorithm's performance against classical simulated annealing. On the hardest graphs, we observe a superlinear quantum speedup in finding exact solutions in the deep circuit regime and analyze its origins.

Probing topological spin liquids on a programmable quantum simulator

[Figure: see text].

A rare case of severe gastroenteritis caused by Aeromonas hydrophila after colectomy in a patient with anti-Hu syndrome: a case report

Background

Aeromonas hydrophila is a gram-negative facultative anaerobic coccobacillus, which is an environmental opportunistic pathogen. A. hydrophila are involved in several infectious diseases such as gastroenteritis, septicemia and wound infections. However, gastroenteritis caused by Aeromonas spp. are rare and the clinical relevance of Aeromonas species in stool specimens is still under debate.

Case presentation

Our case concerns a 32-year-old woman who presented at hospital with a worsening watery diarrhea and fever requiring intensive care. A cholera-like illness was diagnosed. The patient had a past history of an anti-Hu syndrome with a myenteric ganglionitis. A molecular multiplex RT-PCR (QIAstat-Dx Gastrointestinal Panel, QIAGEN) covering a broad spectrum of diverse gastrointestinal pathogens performed directly from the stool was negative but the stool culture revealed growth of A. hydrophila. Further investigations of the A. hydrophila strain in cell cultures revealed the presence of a cytotoxic enterotoxin.

Conclusions

Although A. hydrophila rarely causes gastroenteritis, Aeromonas spp. should be considered as a causative agent of severe gastroenteritis with a cholera-like presentation. This case highlights the need to perform culture methods from stool samples when PCR-based methods are negative and gastrointestinal infection is suspected.

Analyzing Nonequilibrium Quantum States through Snapshots with Artificial Neural Networks

Current quantum simulation experiments are starting to explore nonequilibrium many-body dynamics in previously inaccessible regimes in terms of system sizes and timescales. Therefore, the question emerges as to which observables are best suited to study the dynamics in such quantum many-body systems. Using machine learning techniques, we investigate the dynamics and, in particular, the thermalization behavior of an interacting quantum system that undergoes a nonequilibrium phase transition from an ergodic to a many-body localized phase. We employ supervised and unsupervised training methods to distinguish nonequilibrium from equilibrium data, using the network performance as a probe for the thermalization behavior of the system. We test our methods with experimental snapshots of ultracold atoms taken with a quantum gas microscope. Our results provide a path to analyze highly entangled large-scale quantum states for system sizes where numerical calculations of conventional observables become challenging.

Controlling quantum many-body dynamics in driven Rydberg atom arrays

The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science.

Noninferiority of Simplified Dolutegravir Monotherapy Compared to Continued Combination Antiretroviral Therapy That Was Initiated During Primary Human Immunodeficiency Virus Infection: A Randomized, Controlled, Multisite, Open-label, Noninferiority Trial

BACKGROUND

Patients who start combination antiretroviral therapy (cART) during primary human immunodeficiency virus type 1 (HIV-1) infection show a smaller HIV-1 latent reservoir, less immune activation, and less viral diversity compared to patients who start cART during chronic infection. We conducted a pilot study to determine whether these properties would allow sustained virological suppression after simplification of cART to dolutegravir monotherapy.

METHODS

EARLY-SIMPLIFIED is a randomized, open-label, noninferiority trial. Patients who started cART <180 days after a documented primary HIV-1 infection and had an HIV-1 RNA <50 copies/mL plasma for at least 48 weeks were randomized (2:1) to monotherapy with dolutegravir 50 mg once daily or to continuation of cART. The primary efficacy endpoint was the proportion of patients with <50 HIV-1 RNA copies/mL on or before week 48; noninferiority margin 10%.

RESULTS

Of the 101 patients randomized, 68 were assigned to simplification to dolutegravir monotherapy and 33 to continuation of cART. At week 48 in the per-protocol population, 67/67 (100%) had virological response in the dolutegravir monotherapy group vs 32/32 (100%) in the cART group (difference, 0.00%; 95% confidence interval, -100%, 4.76%). This showed noninferiority of the dolutegravir monotherapy at the prespecified level.

CONCLUSION

In this pilot study consisting of patients who initiated cART during primary HIV-1 infection and had <50 HIV-1 RNA copies/mL for at least 48 weeks, monotherapy with once-daily dolutegravir was noninferior to cART. Our results suggest that future simplification studies should use a stratification according to time of HIV infection and start of first cART.

CLINICAL TRIALS REGISTRATION

NCT02551523.

Metagenomic Virome Sequencing in Living Donor and Recipient Kidney Transplant Pairs Revealed JC Polyomavirus Transmission

Background

Before kidney transplantation, donors and recipients are routinely screened for viral pathogens using specific tests. Little is known about unrecognized viruses of the urinary tract that potentially result in transmission. Using an open metagenomic approach, we aimed to comprehensively assess virus transmission in living-donor kidney transplantation.

Methods

Living kidney donors and their corresponding recipients were enrolled at the time of transplantation. Follow-up study visits for recipients were scheduled 4–6 weeks and 1 year thereafter. At each visit, plasma and urine samples were collected and transplant recipients were evaluated for signs of infection or other transplant-related complications. For metagenomic analysis, samples were enriched for viruses, amplified by anchored random polymerase chain reaction (PCR), and sequenced using high-throughput metagenomic sequencing. Viruses detected by sequencing were confirmed using real-time PCR.

Results

We analyzed a total of 30 living kidney donor and recipient pairs, with a follow-up of at least 1 year. In addition to viruses commonly detected during routine post-transplant virus monitoring, metagenomic sequencing detected JC polyomavirus (JCPyV) in the urine of 7 donors and their corresponding recipients. Phylogenetic analysis confirmed infection with the donor strain in 6 cases, suggesting transmission from the transplant donor to the recipient, despite recipient seropositivity for JCPyV at the time of transplantation.

Conclusions

Metagenomic sequencing identified frequent transmission of JCPyV from kidney transplant donors to recipients. Considering the high incidence rate, future studies within larger cohorts are needed to define the relevance of JCPyV infection and the donor’s virome for transplant outcomes.

Generation and manipulation of Schrödinger cat states in Rydberg atom arrays

Quantum entanglement involving coherent superpositions of macroscopically distinct states is among the most striking features of quantum theory, but its realization is challenging because such states are extremely fragile. Using a programmable quantum simulator based on neutral atom arrays with interactions mediated by Rydberg states, we demonstrate the creation of "Schrödinger cat" states of the Greenberger-Horne-Zeilinger (GHZ) type with up to 20 qubits. Our approach is based on engineering the energy spectrum and using optimal control of the many-body system. We further demonstrate entanglement manipulation by using GHZ states to distribute entanglement to distant sites in the array, establishing important ingredients for quantum information processing and quantum metrology.

[For Once Not Corona Virus - an Uncommon Cause of Fever and Hepatitis]

For Once Not Corona Virus - an Uncommon Cause of Fever and Hepatitis Abstract. Our case reports acute Q fever as uncommon cause of fever, typically accompanied by pneumonia and/or hepatitis. It is caused by Coxiella burnetii, a bacterium which is generally hosted by live stock and affects humans by inhaling aerosols of the animals' excrements. If detected, it may be treated effectively. It should be considered in patients living in a typical environment or with a typical history. The route of our patient's infection remains unclear since he plausibly denied contact with any animals.

Detection of NDM-19, a novel variant of the New Delhi metallo-β-lactamase with increased carbapenemase activity under zinc-limited conditions, in Switzerland

A novel New Delhi metallo-β-lactamase (NDM) variant, NDM-19, was identified in a carbapenem-resistant E. coli strain isolated from a subcutaneous infection of a laparotomy scar from an Egyptian patient in a Swiss hospital. NDM-19 is a derivative of NDM-7, from which it differs by a single amino acid substitution (Ala233Val). Under zinc-limiting growth conditions, E. coli DH5α transformants producing NDM-19 displayed reduced susceptibility towards expanded-spectrum cephalosporins and carbapenems as compared to transformants producing NDM-1 or NDM-7.

Terebratulide brachiopod shell biomineralization by mantle epithelial cells

To understand mineral transport pathways for shell secretion and to assess differences in cellular activity during mineralization, we imaged with TEM and FE-SEM ultrastructural characteristics of outer mantle epithelium (OME) cells. Imaging was carried out on Magellania venosa shells embedded/etched, chemically fixed/decalcified and high-pressure frozen/freeze-substituted samples from the commissure, central shell portions and from puncta. Imaging results are complemented with morphometric evaluations of volume fractions of membrane-bound organelles. At the commissure the OME consists of several layers of cells. These cells form oblique extensions that, in cross-section, are round below the primary layer and flat underneath fibres. At the commissure the OME is multi-cell layered, in central shell regions it is single-cell layered. When actively secreting shell carbonate extrapallial space is lacking, because OME cells are in direct contact with the calcite of the forming fibres. Upon termination of secretion, OME cells attach via apical hemidesmosomes to extracellular matrix membranes that line the proximal surface of fibres. At the commissure volume fractions for vesicles, mitochondria and lysosomes are higher relative to single-cell layered regions, whereas for endoplasmic-reticulum and Golgi apparatus there is no difference. FE-SEM, TEM imaging reveals the lack of extrapallial space between OME cells and developing fibres. In addition, there is no indication for an amorphous precursor within fibres when these are in active secretion mode. Accordingly, our results do not support transport of minerals by vesicles from cells to sites of mineralization, rather by transfer of carbonate ions via transport mechanisms associated with OME cell membranes.

Implementation of a stable, high-power optical lattice for quantum gas microscopy

We describe the design and implementation of a stable high-power 1064 nm laser system to generate optical lattices for experiments with ultracold quantum gases. The system is based on a low-noise laser amplified by an array of four heavily modified, high-power fiber amplifiers. The beam intensity is stabilized and controlled with a nonlinear feedback loop. Using real-time monitoring of the resulting optical lattice, we find the stability of the lattice site positions to be well below the lattice spacing over the course of hours. The position of the harmonic trap produced by the Gaussian envelope of the lattice beams is stable to about one lattice spacing and the long-term (six-month) relative root-mean-square stability of the lattice spacing itself is 0.5%.

Abstract P4-09-08: Shared-patient physician networks and their impact on the uptake of genomic testing in early-stage breast cancer

Background: Oncotype DX (ODX) or 21-gene recurrence score genomic testing is used to stratify risk and determine appropriate treatment in women with early-stage breast cancer (BC). Diffusion of ODX by way of physician networks has not been studied.

Objective: To determine the association between physician network connections, defined by shared patients, and the use of ODX testing.

Methods: SEER-Medicare claims from 2008-2012 were used to identify a cohort of woman with a diagnosis of BC from registry/ICD codes, continuously enrolled in Medicare fee-for-service Part A and B one year prior to and one year following diagnosis. We identify receipt of ODX from the associated CPT code, claim reimbursement, and performing NPI. To look at the influence of network connections on ODX use, we split the study into two time periods: early adoption from 2008-2009, and late from 2010-2012. Medical oncologists with a BC-related claim in the cohort above, and any rendered BC-related service are considered 'connected' if they shared two or more BC patients. Analyses describe these connections and explore the association between connectedness to an early adopting medical oncologist and ODX use in parallel physician and patient-level analyses using generalized linear mixed models with a hospital referral region-specific random effect. Models control for physician and patient-level characteristics where applicable.

Results:24,463 women met study criteria; 12,874 were diagnosed with BC in the early adoption time period (1,790 received ODX) and 11,589 were diagnosed in the late period (2,334 received ODX). 2,073 medical oncologists treated these patients from 2008-2009. The mean number of BC patients treated per medical oncologist was 86.8 during the early adoption period, and medical oncologists had a median number of peer connections of 11 (IQR: 7-18). Early adopting medical oncologists had higher numbers of peer connections and higher average patient counts than non-early adopters. A higher percentage of female medical oncologists were early adopters (39%) then male medical oncologists (33%) (p&lt;0.02). Among non-early adopting oncologists, peer connection to at least two early adopting providers in 2008-2009 is associated with a 3.2 (95% CI: 2.0-4.9) times increase in the odds of ordering ODX in 2010-2012 after adjustment for physician gender and time in practice. In patient-level models with controls for physician and patient characteristics, seeing a medical oncologist with connections to at least two early adopting physicians is associated with a 1.6 times (95% CI: 1.1-2.2) increase in the odds of receiving ODX testing in 2010-2012.

Conclusions: We observe a positive adjusted association between connectedness to an early-adopting physician and ODX prescribing/use in both physician-level and patient-level analyses. These results suggest that provider networks may help diffuse new technologies, and that BC genomic testing is likely to be an area of shared practices between providers. Efforts to increase testing, where appropriate, may benefit from a range of peer-to-peer connection strategies.

Citation Format: Rotter J, Wilson L, Greiner M, Pollack C, Dinan M. Shared-patient physician networks and their impact on the uptake of genomic testing in early-stage breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-09-08.

Abstract P6-09-10: Provider characteristics and receipt of oncotype Dx testing in women diagnosed with early stage breast cancer using SEER-Medicare data

Background: Oncotype DX (ODX) genomic testing to evaluate recurrence risk and benefit of adjuvant chemotherapy in patients with ER-positive, node-negative breast cancers was approved for Medicare reimbursement in 2006. We previously examined patient-level factors associated with utilization of ODX testing from 2005-2009 in the SEER-Medicare population; ODX testing occurred most frequently in patients with ER+, node negative disease, with 80% of all tests occurring in patients aged 66-75. In our current study, we examined potential provider factors associated with patient-level ODX testing from 2008 to 2012.

Methods: Using a retrospective cohort design, we identified all individuals who had a SEER diagnosis of breast cancer from 2008-2011 and were enrolled in fee-for-service Medicare parts A and B for one year before and one year after diagnosis. We limited our analysis to individuals who had surgical resection of their breast tumor within 4 months of diagnosis and had a breast tumor which was ER+, invasive, and non-metastatic to capture the eligible patient population. Using Medicare claims data linked with the AMA physician dataset (which includes AMA members and non-members), we identified physician characteristics of the primary breast surgeon and medical oncologist including specialty, gender, years in practice, case volume, utilization of chemotherapy, and whether they serve rural populations. For patients with an ODX test, we used the identification on the claim to link to the performing provider. We examined the associations between provider characteristics and patient receipt of ODX testing using unadjusted and adjusted logistic regression models. Adjusted models included patient demographic and clinical characteristics.

Results: We identified 24,463 eligible breast cancer patients who received their care from 3172 primary surgeons and 2475 medical oncologists. Of 4124 ODX tests ordered for patients in the study, 70% were ordered by the assigned medical oncologist and 16% were ordered by the breast surgeon. In multivariable regression models, multiple physician characteristics were associated with receipt of ODX testing including having an assigned medical oncologist (OR 2.77, 95% CI 2.00-3.82), having a surgeon with a specialty of surgical oncology (OR 1.20, 95% CI 1.09-1.31), having a female medical oncologist (OR 1.10 95% CI 1.02-1.20). Having a medical oncologist with ≥5 years in practice was associated with lower odds of testing (OR 0.83 95% CI 0.76-0.92). Breast surgery performed at an academic hospital was associated with higher odds of ODX testing (OR 1.11 95% CI 1.02-1.20).

Conclusion: The majority of ODX testing for indicated breast cancer patients is ordered by medical oncologists, though surgeons and physicians of other specialties also order the tests in practice. Physician characteristics including gender and time in practice appear to affect a patient's likelihood of receiving ODX testing, creating opportunities for targeting interventions to help women with breast cancer receive optimal care.

Citation Format: Dinan MA, Wilson LE, Greiner M, Pollack CE. Provider characteristics and receipt of oncotype Dx testing in women diagnosed with early stage breast cancer using SEER-Medicare data [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-09-10.

Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection

Background

Lung transplant patients are a vulnerable group of immunosuppressed patients that are prone to frequent respiratory infections. We studied 60 episodes of respiratory symptoms in 71 lung transplant patients. Almost half of these episodes were of unknown infectious etiology despite extensive routine diagnostic testing.

Methods

We re-analyzed respiratory samples of all episodes with undetermined etiology in order to detect potential viral pathogens missed/not accounted for in routine diagnostics. Respiratory samples were enriched for viruses by filtration and nuclease digestion, whole nucleic acids extracted and randomly amplified before high throughput metagenomic virus sequencing. Viruses were identified by a bioinformatic pipeline and confirmed and quantified using specific real-time PCR.

Results

In completion of routine diagnostics, we identified and confirmed a viral etiology of infection by our metagenomic approach in four patients (three Rhinovirus A, one Rhinovirus B infection) despite initial negative results in specific multiplex PCR. Notably, the majority of samples were also positive for Torque teno virus (TTV) and Human Herpesvirus 7 (HHV-7). While TTV viral loads increased with immunosuppression in both throat swabs and blood samples, HHV-7 remained at low levels throughout the observation period and was restricted to the respiratory tract.

Conclusion

This study highlights the potential of metagenomic sequencing for virus diagnostics in cases with previously unknown etiology of infection and in complex diagnostic situations such as in immunocompromised hosts.

Applicability and feasibility of systematic review for performing evidence-based risk assessment in food and feed safety

Food and feed safety risk assessment uses multi-parameter models to evaluate the likelihood of adverse events associated with exposure to hazards in human health, plant health, animal health, animal welfare, and the environment. Systematic review and meta-analysis are established methods for answering questions in health care, and can be implemented to minimize biases in food and feed safety risk assessment. However, no methodological frameworks exist for refining risk assessment multi-parameter models into questions suitable for systematic review, and use of meta-analysis to estimate all parameters required by a risk model may not be always feasible. This paper describes novel approaches for determining question suitability and for prioritizing questions for systematic review in this area. Risk assessment questions that aim to estimate a parameter are likely to be suitable for systematic review. Such questions can be structured by their "key elements" [e.g., for intervention questions, the population(s), intervention(s), comparator(s), and outcome(s)]. Prioritization of questions to be addressed by systematic review relies on the likely impact and related uncertainty of individual parameters in the risk model. This approach to planning and prioritizing systematic review seems to have useful implications for producing evidence-based food and feed safety risk assessment.

Stringent adherence to a cytomegalovirus-prevention protocol is associated with reduced overall costs in the first 6 months after kidney transplantation

BACKGROUND

We previously documented that a stringent implementation of a preemptive cytomegalovirus (CMV) prevention protocol reduced the number of CMV disease episodes after kidney transplantation, when compared with a routine preemptive protocol. The impact on overall costs was assessed.

METHODS

Cost comparisons were made for inpatient and outpatient costs and overall costs, using costs provided by the financial department. Variables were analyzed using the Wilcoxon rank-sum test. A multivariable global linear model evaluated the effect of all co-variables on cost differences. In Cohort 1 (n = 84), 74% were followed with a standard CMV preemptive protocol, and 26% received prophylaxis. In Cohort 2 (n = 74), an intensified CMV surveillance protocol was applied in 74% of patients, and 26% were given prophylaxis.

RESULTS

Overall, Cohort 1 had significantly higher treatment costs as compared with Cohort 2 (mean Swiss francs [CHF] 104,548 and CHF 76,983, respectively, P = 0.0005). Excluding patients who received prophylaxis reduced these costs to CHF 89,318 in Cohort 1 and CHF 73,652 in Cohort 2. Outcome between Cohort 1 and 2 was comparable.

CONCLUSION

A stringent adherence to the CMV prevention protocol was associated with a significant reduction in overall costs. Whether this benefit is because of the demonstrated reduction in the rate of CMV disease needs to be assessed in a randomized trial.

Single-mode master-oscillator power amplifier at 647 nm with more than 500 mW output power

Using an AlGaInP-based truncated tapered power amplifier, it was possible to boost the output power of a 647-nm distributed Bragg reflector laser from 50 mW to more than 500 mW. The light source has the potential to replace bulky Kr ion lasers still in use at this wavelength.

How Does the Pathophysiology Influence the Treatment of Pelvic Congestion Syndrome and is the Result Long-lasting?

The objectives of this study are to consider the influence of pathophysiology in the treatment of pelvic congestion syndrome (PCS) and to determine the criteria which impact on the long-term results. A classification of venous pathology including three types of pathophysiological conditions, independent of the location of the pelvic venous pathology, is developed and illustrated. These types, diagnosed by cross-sectional imaging and confirmed by phlebography, are associated with a specific therapeutic plan. The long-term results are dependent on the quality of the initial Phlebographic mapping that must be selective and complete, the angiographic findings, in particular the study of collaterals feeding the venous anomalies, the treatment of all venous anomalies, the respect of contraindications, the use of appropriate materials and the occurrence of new pregnancies. In conclusion, the feasibility and satisfactory short-term results of endovascular treatment of PCS are admitted. Questions remain regarding the effectiveness of the different embolic agents and the long-term results of this treatment.

Inducing vortices in a Bose-Einstein condensate using holographically produced light beams

In this paper we demonstrate a technique that can create non-equilibrium vortex configurations with almost arbitrary charge and geometry in a Bose-Einstein condensate. We coherently transfer orbital angular momentum from a holographically generated light beam to a 87Rb condensate using a two-photon stimulated Raman process. Using matter wave interferometry, we verify the phase pattern imprinted onto the atomic wave function for a single vortex and a vortex-antivortex pair. In addition to their phase winding, the vortices created with this technique have an associated hyperfine spin texture.

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 might 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 2-day consensus meeting was held on November 18-19, 2008 in Chicago, IL, to achieve the objective. Before 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. Before the meeting, the attendees completed a Web-based survey indicating which CONSORT statement items would 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 and 22-item checklist. Fourteen items were modified from the CONSORT checklist, and an additional subitem 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.

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, Ill, 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.

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.

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.

Variance of Landmarks in Digital Evaluations: Comparison between CT-based and Conventional Digital Lateral Cephalometric Radiographs

AIM

The aim of this study was to examine whether bony, dental and soft tissue landmarks could be placed in CT-based lateral cephalograms with the same precision as in conventional digital lateral cephalograms.

MATERIALS AND METHODS

Nine patients without craniofacial dysplasia (2 female, 7 male, aged 12.8-32.3) who had undergone a lateral cephalogram and CT examination within an interval of a maximum of 6.5 months were selected in retrospect. The lateral cephalograms were done with the ORTHOPHOS Plus DS Ceph, and the CT examination with the SOMATOM Sensation 16 or 64 scanner. The CT-based cephalograms were generated with the VoXim 4.3 program based on axial CT reconstructions in the bone window. The cephalograms were analyzed using the Onyx Ceph 2.7 software by 2 orthodontists and 5 postgraduate students, each cephalogram being examined five times by each examiner on different days. Statistics were compiled with SPSS 13.0 and 14.0 based on the deviation from the individual mean value of each landmark.

RESULTS

The descriptive statistics showed in the conventional cephalogram, averaged over all 61 landmarks, a mean quartile range of on average 0.62 mm in the horizontal and 0.67 mm in the vertical axes. The CT-based cephalograms ranged between 0.64 mm horizontally and 0.74 mm vertically. The statistics comparing the two types of images with the Wilcoxon test for paired samples showed no significant difference.

CONCLUSION

When a CT scan is necessary for assessment of complex craniofacial dysplasias, an orthodontic-specific diagnosis is possible without having to resort to conventional X-rays of the skull. The data from this study demonstrate that it is possible to construct a cephalogram from CT data, which can be analyzed in the same way as a conventional cephalogram provided that the CT's field of view is large enough.

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.

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.