Non-Arrhenius ionic conductivities in glasses due to a distribution of activation energies.

Previously observed non-Arrhenius behavior in fast ion conducting glasses [J. Kincs and S. W. Martin, Phys. Rev. Lett. 76, 70 (1996)] occurs at temperatures near the glass transition temperature, T(g), and is attributed to changes in the ion mobility due to ion trapping mechanisms that diminish the conductivity and result in a decreasing conductivity with increasing temperature. It is intuitive that disorder in glass will also result in a distribution of the activation energies (DAE) for ion conduction, which should increase the conductivity with increasing temperature, yet this has not been identified in the literature. In this Letter, a series of high precision ionic conductivity measurements are reported for 0.5Na(2)S + 0.5[xGeS(2) + (1-x)PS(5/2)] glasses with compositions ranging from 0 ≤ x ≤ 1. The impact of the cation site disorder on the activation energy is identified and explained using a DAE model. The absence of the non-Arrhenius behavior in other glasses is explained and it is predicted which glasses are expected to accentuate the DAE effect on the ionic conductivity.

Is moving from targeted culling to BCG-vaccination of badgers (Meles meles) associated with an unacceptable increased incidence of cattle herd tuberculosis in the Republic of Ireland? A practical non-inferiority wildlife intervention study in the Republic of Ireland (2011-2017).

Bovine tuberculosis (BTB) remains as a costly disease of cattle-herds in the Republic of Ireland (ROI). This persistence is partially attributable to the presence of M. bovis infection in a wildlife reservoir, the European badger (Meles meles). Thus, both area-wide and limited-area targeted-badger-culling have been part of the ROI-BTB control/eradication program to help reduce the future incidence of a cattle-herd BTB breakdown (i.e. a "new herd-level occurrence of BTB"). However, neither badger-culling practice can be sustained as a major component in the ongoing BTB eradication program in the ROI. Vaccination of badgers with Bacille Calmette-Guérin (BCG) has been proposed as an alternative to badger culling. Thus, in 2011, a five-year non-inferiority study was implemented in seven counties in the ROI. This study was designed to compare and contrast the cattle-herd-BTB-incidence in areas where intramuscular badger vaccination would be implemented versus the cattle-herd-BTB-incidence in the remaining area of the same county where targeted-badger-culling was maintained as the standard treatment response to probable badger-sourced BTB breakdowns. Our outcome of interest was a new cattle-herd-BTB-episode (breakdown) with a total of >2 standard skin-test (SICTT) reactors detected during the episode. Treatments (badger vaccination or targeted badger culling) were cluster allocated based on where the majority of the herd owner's land was located. To assess the impact of the two treatments, we compared the incidence-risk, of our defined outcome, for cattle herds in the area under vaccination to the outcome incidence-risk for cattle herds in the remainder of the same county after 4 and 5 years of having implemented badger vaccination. A random-effects logit model with adjustment for clustering by treatment, and statistical control of herd-type, herd-size and five-year prior-BTB-episode history was used for our analyses. Although not included in the logistic model, a relative badger density metric based on the annual number of badgers captured-per-sett-night of capturing effort was developed for each treatment area; this metric indicated that relative badger density was approximately 40 % higher in vaccination areas than in the targeted badger-culling areas during our study. Overall, our study results indicated that vaccination was not inferior to targeted badger-culling in four counties and badger vaccination was deemed to produce ambivalent results in one (County Cork North) of the seven study sites in the ROI. A post-study investigation, in County Galway, where vaccination was deemed inferior to target culling, revealed that widespread purchases of cattle from a nearby cattle mart, by herd owners in the vaccination-area, was associated with the increased herd and vaccination-area risk of BTB. No single "biasing hypothesis" was evident for the apparent vaccine inferiority in the second study site (County Monaghan) where vaccination was deemed inferior to targeted culling; hence no further investigations were conducted.

Targeted badger removal and the subsequent risk of bovine tuberculosis in cattle herds in county Laois, Ireland.

We investigated the impact of targeted removal of badgers on the subsequent bovine tuberculosis (BTB) risk in cattle herds in county Laois, Ireland. The study period was 1989-2005. For each of 122 targeted badger-removal licenses (permit to remove badgers in the proximity of cattle herds undergoing a serious BTB episode), the herd number (index herd) for which the license was given was obtained. The herds in the proximity of the index herd were identified from another database. The main "exposure" in our study was the geographical location of herds relative to the area in which targeted badger removal was conducted. We categorized herds into five different exposure groups: herds were classified as non-exposed and denoted as group 0 (reference group) if they were located 500 m or more from the edge of any parcel of land of the index herd; group 1, was the index herds, group 2 the immediate (contiguous) neighbors of the index herd, group 3 herds were not immediate neighbors but within 150 m and group 4 herds were between 150 m and 500 m distance from the edge of any parcel of land of the index herd, respectively. We conducted a survival analysis (allowing multiple failures per herd) to compare the hazard of having a BTB episode in any of the four groups of exposed herds vs. the hazard in herds in the reference group. We controlled for other known risk factors as well taking into account a temporal component. Our analysis showed that the hazard ratio for the index herds (group 1) were non-significantly increased, indicating that there was no difference in the hazard of failing a BTB test (after the targeted badger removal was conducted) between index herds and reference herds. For the rest of the herds farther away from badger removal activities the hazards were lower than herds in areas not under badger removal. The hazard in the reference group decreased over the study period.

Development of a polymerase chain reaction assay for specific identification of Clostridium colinum.

Clostridium colinum is the causative agent of ulcerative enteritis, a serious disease of the bobwhite quail (Colinus virginianus) and sporadically of young chickens. The aim of the present study was to develop a polymerase chain reaction (PCR) assay specific for C. colinum identification. The 16S rDNA sequence of C. colinum was analysed and two species-specific primers were designed. The specificity of these primers was tested with closely related Clostridium species and the expected amplified product (935 base pairs) was observed only with DNA from samples containing C. colinum. Results from performing PCR assays on faecal samples from quails spiked with different concentrations of C. colinum, showed that the detection limit of the assay was 1.6 x 10(4) colony-forming units per gram of faecal material. This PCR assay can be used in diagnostic laboratories to confirm the presence of C. colinum in pure cultures and could be used to screen enriched samples or faecal samples for the presence of this pathogen.

Typing of Clostridium perfringens by multiple-locus variable number of tandem repeats analysis.

Clostridium perfringens is a well-characterized bacterial species which can be both commensal and pathogenic in humans and many animals. Genetic typing of the bacterium is often used for molecular epidemiological purposes, and can be useful for observing population structures as well. Analysis of the variable number of tandem repeats (VNTRs) within the genome, called multiple-locus VNTR analysis (MLVA) provides genetic information useful for molecular typing. A MLVA typing method has been developed recently by Sawires and Songer [Sawires, Y.S., Songer, J.G., 2005. Multiple-locus variable-number tandem repeat analysis for strain typing of Clostridium perfringens. Anaerobe 11, 262-272] for C. perfringens. A novel MLVA protocol is described here, with the aim of investigating the discriminatory potential of the method, and to obtain preliminary data on the population structure of C. perfringens from a wide variety of C. perfringens sources. This protocol uses new loci in noncoding regions of the chromosome, and also makes use of capillary electrophoresis for more precise results and for high-throughput typing. DNA sequencing of amplicons was performed to ensure inclusion of conserved tandem repeats within each locus. Fifty-four epidemiologically unrelated isolates from a local collection obtained from 11 different animal species were typed at 6 loci. Thirty-five unique MLVA types were obtained, resulting in a Simpson's index of diversity of 0.975. Epidemiologically related isolates (n=27) previously typed by pulsed-field gel electrophoresis (PFGE) were also examined with MLVA and the congruency of the two methods was found to be very high. All 81 isolates were successfully typed with MLVA, and polymerase chain reactions (PCR) were automated using robotics and 96-well plates, with PCR product sizes determined using capillary electrophoresis. Reproducibility was also shown to be very high.

Genetic diversity of Clostridium perfringens isolated from healthy broiler chickens at a commercial farm.

Clostridium perfringens is an important commensal and bacterial pathogen of many animal species. It has particular significance in poultry, where it may cause necrotic enteritis. Our objective was to characterize the population diversity of C. perfringens colonizing healthy birds, and to observe how diversity changed over time. Isolates were obtained from broiler chicken cecal samples in two barns on a single farm, on days 7, 14, 22, 27, 30 and 34 of a single 42-day rearing cycle. Bacitracin was used as a feed additive in one of the barns and withdrawn from the second barn for the duration of the experiment. Each isolate was typed using pulsed-field gel electrophoresis (PFGE) using SmaI restriction endonuclease. A total of 205 cecal isolates from 49 birds were typed, as well as 93 isolates from the barn environment (bedding, drinking water and feces). Eight major PFGE types and 17 subtypes were found in the 298 total isolates. The results show that an optimal sampling strategy would involve a large number of birds, with only a few isolates sampled per bird. The diversity of C. perfringens in this study appears to be low within a single bird, and increases as the bird matures. There was no significant difference in genetic diversity between the two barns. In addition, isolates from fresh fecal samples appear to represent the cecal C. perfringens population accurately, although this was not proven statistically. Antimicrobial susceptibility testing was performed on selected isolates (n=41) representing a cross-section of PFGE types. Based on minimum inhibitory concentration distributions, 95% of the isolates tested were deemed resistant to bacitracin, with a 16 microg/mL breakpoint. Three new cpb2 (beta2 toxin gene) variants were found in the study.

Risk factors for disclosure of additional tuberculous cattle in attested-clear herds that had one animal with a confirmed lesion of tuberculosis at slaughter during 2003 in Ireland.

All the Irish cattle herds considered "clear" of bovine tuberculosis (BTB) having a single animal with a tuberculous lesion at slaughter during 2003 were identified. We performed a descriptive and logistic regression analysis to investigate whether selected risk factors had an association with the result of the herd test immediately after the tuberculous lesion was found ("Factory Lesion Test", FLT). At the FLT, only 19.7% (n=338) of these 1713 herds had 1 or more standard reactors. The lesioned animal was home-bred in 46% of the "source" herds; these herds had an increased risk (23.4%) of having at least 1 standard reactor animal relative to herds with a purchased-lesioned animal (16.6%) (RR=1.41). Our logistic models identified a number of important risk factors; two that appeared most important in predicting the FLT outcome were the time spent (residency) by the lesioned animal in the "source" herd, and the presence, or not, of the lesioned animal in a previous BTB episode in either the "source" herd, or the seller's herd in the case the lesioned animal was purchased. Our models fit the data well based on the Hosmer-Lemeshow test, however their sensitivity and specificity were very low (57% and 61% respectively). Surveillance of the cattle population for BTB using lesions found at slaughter is an essential component of an overall control program. Nonetheless, due to the poor predictability of the variables we measured, complete herd investigations are needed to help explain the FLT outcome of a herd.

Temperature-related risk factors associated with the colonization of broiler-chicken flocks with Campylobacter spp. in Iceland, 2001-2004.

Our objective was to identify temperature-related risk factors associated with the colonization of broiler-chicken flocks with Campylobacter spp. in Iceland, with an underlying assumption that at minimum ambient temperatures, flies (Musca domestica) play a role in the epidemiology and seasonality of Campylobacter. At slaughter, pooled caecal samples were obtained from 792 flocks that hatched between March 15 and September 15 each year from 2001 to 2004, and cultured for Campylobacter. Daily temperature data (average, maximum and minimum temperatures) were obtained from the Icelandic Meteorological Office. We determined the closest weather station to each farm using ArcGIS 9. We then used logistic-regression models (with a random-effects term for farm) to examine associations between flock positivity and temperature-related predictors. The overall prevalence of Campylobacter was 27.4%, and the month with the highest prevalence (54.4%) was August. The final model included cumulative degree-days (CDD) above an average temperature of 4.4 degrees C and the presence of 1 or more days below a maximum temperature of 8.9 degrees C (threshold below which fly activity was expected to be substantially reduced and egg laying was not expected to occur) during the period 2-4 weeks (i.e. days 8-28) before slaughter. Below 79 CDD, the risk of flock Campylobacter colonization was generally low. Between 79 and 139 CDD, the risk increased gradually, but was lower for flocks raised during periods with 1 or more days <8.9 degrees C than flocks raised without days <8.9 degrees C. The risk increased sharply under conditions of high CDD (>139) and when the maximum temperature remained >8.9 degrees C during the period 2-4 weeks before slaughter.

Molecular Dynamics Modeling of the Structure and Na+-Ion Transport in Na2S + SiS2 Glassy Electrolytes.

Solid-state sodium batteries, a relatively safe and potentially cost-effective energy-storage technology, have attracted increasing scientific attention recently for application in stationary grid-scale energy storage. Identifying solid electrolytes with high electrochemical stability and high Na+-ion conductivity at room temperature is critically important to enable high energy densities with enhanced rate capabilities. We evaluated sodium sulfide-silicon sulfide, xNa2S + (1- x)SiS2, glasses as potential glassy solid electrolytes (GSEs) using molecular dynamics (MD) simulations. We employed ab initio MD to determine ion conduction mechanisms, to calculate energy barriers for ion hops, and to correlate these to the local short-range structure of 0.50Na2S + 0.50SiS2 glass. To simulate much larger systems for accurately calculating the ionic conductivity, we parameterized empirical Buckingham-type potential and performed classical MD simulations. After validating these calculations by comparing the structure obtained from MD to that from X-ray scattering data, we calculated the ionic conductivity of these glasses for the range of 0.33 ≤ x ≤ 0.67 compositions. The calculated ionic conductivities at room temperature were in the range of ∼10-5 S/cm for the x = 0.50 composition and increased significantly with sodium sulfide ( x) content. These calculations provide theoretical insights into the role of Na2S content on the ionic conductivity of GSEs aiding in the selection of specific compositions to enhance the ionic conductivity.

Membrane type matrix metalloproteinases (MMPs) show differential expression in non-small cell lung cancer (NSCLC) compared to normal lung: correlation of MMP-14 mRNA expression and proteolytic activity.

Improved understanding of the involvement of matrix metalloproteinases (MMPs), including membrane-type MMPs (MT-MMPs), in human tumours has potential diagnostic, prognostic and therapeutic implications. We assessed the relationship between MT-MMP expression and clinicopathological parameters in human non-small cell lung cancer (NSCLC) and histologically normal lung tissue by quantitative Real Time PCR (qRT-PCR). All MT-MMPs (MMPs 14-17, 24 and 25) were detected by qRT-PCR with significantly higher MMP-14, -15 and -17 expression observed in tumour relative to normal lung specimens. MMP-16 was undetectable in normal lung but expressed in 8% tumours. MMP-15 demonstrated significant overexpression in adenocarcinomas relative to squamous cell carcinomas and normal lung tissue. MMP-14 mRNA expression strongly correlated to MMP-14 proteolytic activity in preclinical tumour models, indicating that qRT-PCR may predict MMP-14 activity levels in NSCLC. These data suggest that MMP-14, -15 and -17 may be good markers of disease, or therapeutic targets for treatment of human NSCLC.

Quantification of the relative efficiency of factory surveillance in the disclosure of tuberculosis lesions in attested Irish cattle.

In Ireland, factory surveillance of cattle for gross lesions is an important supplementary method for detecting herds infected with bovine tuberculosis (tb), and in recent years between 27 and 46 per cent of all new herd breakdowns in any year have been detected by this method. The aim of this study was to determine the relative efficiency of factories in detecting lesions among attested cattle slaughtered during 2003 and 2004. National databases were available on animal slaughter, programmes of tuberculin testing for bovine tb and laboratory confirmation of suspected lesions. Factories were ranked according to their submission risk (number of animals submitted with lesions/number of attested animals killed) and confirmation risk (number of animals with laboratory-confirmed lesions/number of animals submitted with lesions), adjusting for the risk profile of the animals slaughtered, including potential confounding factors such as their age and sex, whether they were purchased or homebred, the test history of their herd, the prevalence of bovine tb in the area and the season of slaughter. Approximately 3.7 million cattle were slaughtered in 42 Irish export-licensed factories during the two years. Complete data were available for 2,374,987 animals from 84,510 attested herds in 2845 District Electoral Divisions. Samples from 7398 animals with suspected tb lesions were submitted for laboratory examination; 4767 (64.4 per cent) were positive, 2011 were negative and 620 were inconclusive. The average unadjusted submission risk for all the factories was 22 per 10,000, ranging from 0 to 58 per 10,000. The unadjusted factory confirmation risk (excluding factories that had sent in fewer than 10 lesions) varied between 34.3 per cent and 86.3 per cent. The unadjusted and adjusted submission and confirmation risks were highly correlated, and animal-related factors (including their characteristics and origin) therefore did not contribute to the variations in factory-level submission and confirmation risks.

Phosphorylation sites on calcium channel alpha1 and beta subunits regulate ERK-dependent modulation of neuronal N-type calcium channels.

Voltage-dependent calcium channels (VDCCs) in sensory neurones are tonically up-regulated via Ras/extracellular signal regulated kinase (ERK) signalling. The presence of putative ERK consensus sites within the intracellular loop linking domains I and II of neuronal N-type (Ca(v)2.2) calcium channels and all four neuronal calcium channel beta subunits (Ca(v)beta), suggests that Ca(v)2.2 and/or Ca(v)betas may be ERK-phosphorylated. Here we report that GST-Ca(v)2.2 I-II loop, and to a lesser extent Ca(v)beta1b-His(6), are substrates for ERK1/2 phosphorylation. Serine to alanine mutation of Ser-409 and/or Ser-447 on GST-Ca(v)2.2 I-II loop significantly reduced phosphorylation. Loss of Ser-447 reduced phosphorylation to a greater extent than mutation of Ser-409. Patch-clamp recordings from wild-type Ca(v)2.2,beta1b,alpha2delta1 versus mutant Ca(v)2.2(S447A) or Ca(v)2.2(S409A) channels revealed that mutation of either site significantly reduced current inhibition by UO126, a MEK (ERK kinase)-specific inhibitor that down-regulates ERK activity. However, no additive effect was observed by mutating both residues together, suggesting some functional redundancy between these sites. Mutation of both Ser-161 and Ser-348 on Ca(v)beta1b did not significantly reduce phosphorylation but did reduce UO126-induced current inhibition. Crucially, co-expression of Ca(v)2.2(S447A) with Ca(v)beta1b(S161,348A) had an additive effect, abolishing the action of UO126 on channel current, an effect not seen when Ca(v)beta1b(S161,348A) was co-expressed with Ca(v)2.2(S409A). Thus, Ser-447 on Ca(v)2.2 and Ser-161 and Ser-348 of Ca(v)beta1b appear to be both necessary and sufficient for ERK-dependent modulation of these channels. Together, our data strongly suggest that modulation of neuronal N-type VDCCs by ERK involves phosphorylation of Ca(v)2.2alpha1 and to a lesser extent possibly also Ca(v)beta subunits.

Targeting peptide nucleic acid (PNA) oligomers to mitochondria within cells by conjugation to lipophilic cations: implications for mitochondrial DNA replication, expression and disease.

The selective manipulation of mitochondrial DNA (mtDNA) replication and expression within mammalian cells has proven difficult. One promising approach is to use peptide nucleic acid (PNA) oligomers, nucleic acid analogues that bind selectively to complementary DNA or RNA sequences inhibiting replication and translation. However, the potential of PNAs is restricted by the difficulties of delivering them to mitochondria within cells. To overcome this problem we conjugated a PNA 11mer to a lipophilic phosphonium cation. Such cations are taken up by mitochondria through the lipid bilayer driven by the membrane potential across the inner membrane. As anticipated, phosphonium-PNA (ph-PNA) conjugates of 3.4-4 kDa were imported into both isolated mitochondria and mitochondria within human cells in culture. This was confirmed by using an ion-selective electrode to measure uptake of the ph-PNA conjugates; by cell fractionation in conjunction with immunoblotting; by confocal microscopy; by immunogold-electron microscopy; and by crosslinking ph-PNA conjugates to mitochondrial matrix proteins. In all cases dissipating the mitochondrial membrane potential with an uncoupler prevented ph-PNA uptake. The ph-PNA conjugate selectively inhibited the in vitro replication of DNA containing the A8344G point mutation that causes the human mtDNA disease 'myoclonic epilepsy and ragged red fibres' (MERRF) but not the wild-type sequence that differs at a single nucleotide position. Therefore these modified PNA oligomers retain their selective binding to DNA and the lipophilic cation delivers them to mitochondria within cells. When MERRF cells were incubated with the ph-PNA conjugate the ratio of MERRF to wild-type mtDNA was unaffected, even though the ph-PNA content of the mitochondria was sufficient to inhibit MERRF mtDNA replication in a cell-free system. This unexpected finding suggests that nucleic acid derivatives cannot bind their complementary sequences during mtDNA replication. In summary, we have developed a new strategy for targeting PNA oligomers to mitochondria and used it to determine the effects of PNA on mutated mtDNA replication in cells. This work presents new approaches for the manipulation of mtDNA replication and expression, and will assist in the development of therapies for mtDNA diseases.

A model of contagious bovine pleuropneumonia transmission dynamics in East Africa.

The dynamics of contagious bovine pleuropneumonia (CBPP) transmission vary widely between livestock production systems. This paper describes the development of a homogeneous, stochastic, compartmental model for CBPP transmission in pastoral herds of East Africa. The model was built using parameter estimates based on data published in the literature and on observations of livestock owners obtained through participatory research. The basic reproduction number for CBPP in southern Sudan was estimated to range from 3.2 to 4.6. The homogeneous model indicates that the critical community size for the persistence of CBPP falls within the typical herd sizes for pastoral communities in East Africa suggesting that individual isolated herds are capable of maintaining infection indefinitely. Vaccination alone with currently available vaccines was unlikely to eradicate the disease.

A heterogeneous population model for contagious bovine pleuropneumonia transmission and control in pastoral communities of East Africa.

Pastoral cattle live in highly structured communities characterized by complex contact patterns. The present paper describes a spatially heterogeneous model for the transmission of contagious bovine pleuropneumonia (CBPP) developed specifically for pastoral communities of East Africa. The model is validated against serological data on the prevalence of CBPP infection in several communities of southern Sudan and against livestock owner information on community structure, livestock contact and cattle exchange. The model is used to assess the impact of alternative control strategies including mass and elective vaccination programmes, potential treatment regimes and the combination of vaccination and treatment in a single unified strategy. The results indicate that the eradication of CBPP using mass vaccination with currently available vaccines is unlikely to succeed. On the other hand, elective control programmes based on herd level vaccination, treatment of clinical cases or a combination of both vaccination and treatment enabled individual livestock owners to capture a large benefit in terms of reduced animal-level prevalence and mortality experience. The most promising intervention scenario was a programme which combined the vaccination of healthy animals with treatment of clinical cases.

Quantifying badger exposure and the risk of bovine tuberculosis for cattle herds in county Kilkenny, Ireland.

The objectives of the study were to quantify the levels of badger exposure for cattle and to test the hypothesis that increased badger exposure does not increase the risk of bovine tuberculosis (BTB) in a herd. Information that became available from the targeted removal of badgers over the study period, and from a badger-removal project in county Kilkenny, during 1996-1999 was used. The specific location of cattle within each farm, and the length of time that cattle spent in each farm field during the grazing season, and in the barnyard during winter, was used to build an exposure coefficient to quantify the amount of badger exposure that cattle encountered either on pasture or in the barn. The study design was a matched case-control study in which the control herds were selected using incidence density sampling. During the 4-year study period, 543 badgers were removed and of these 96 badgers were classified as tuberculosis positive; 96 BTB herd breakdowns occurred. There was a significant association between case herds and having a higher badger sett exposure coefficient during 1996-1998. No significant association between case herds and having a higher exposure coefficient based on the number of badgers, or the number of tuberculous badgers, during September 1997-December 1999 was found.

A model-based longitudinal meta-analysis of FEV1 in randomized COPD trials.

A model-based, longitudinal meta-analysis of the efficacy on morning trough forced expiratory volume in 1 second (FEV1 ) in chronic obstructive pulmonary disease (COPD) is presented. Literature data from 142 randomized maintenance trials were included, comprising 106,422 patients who received 19 compounds. 1982 morning trough FEV1 observations were available, each representing the mean FEV1 for a study arm at a specific timepoint. The final model for absolute FEV1 included baseline, disease progression, placebo effect, and drug effect estimates for all compounds, with interstudy variability on all model components and additional interarm variability on baseline. A dose-response relationship was identifiable for 10 of the 19 compounds. Drug-drug interactions among direct bronchodilators and the effect of concomitant background COPD treatment were included. Covariates were identified on baseline. Disease progression was proportional to the baseline FEV1 , and a mean baseline of <1.2 L resulted in a lower efficacy, in particular for antiinflammatory treatments.

A quantitative systems pharmacology model of blood coagulation network describes in vivo biomarker changes in non-bleeding subjects.

Essentials Baseline coagulation activity can be detected in non-bleeding state by in vivo biomarker levels. A detailed mathematical model of coagulation was developed to describe the non-bleeding state. Optimized model described in vivo biomarkers with recombinant activated factor VII treatment. Sensitivity analysis predicted prothrombin fragment 1 + 2 and D-dimer are regulated differently. SUMMARY: Background Prothrombin fragment 1 + 2 (F1 + 2 ), thrombin-antithrombin III complex (TAT) and D-dimer can be detected in plasma from non-bleeding hemostatically normal subjects or hemophilic patients. They are often used as safety or pharmacodynamic biomarkers for hemostatis-modulating therapies in the clinic, and provide insights into in vivo coagulation activity. Objectives To develop a quantitative systems pharmacology (QSP) model of the blood coagulation network to describe in vivo biomarkers, including F1 + 2 , TAT, and D-dimer, under non-bleeding conditions. Methods The QSP model included intrinsic and extrinsic coagulation pathways, platelet activation state-dependent kinetics, and a two-compartment pharmacokinetics model for recombinant activated factor VII (rFVIIa). Literature data on F1 + 2 and D-dimer at baseline and changes with rFVIIa treatment were used for parameter optimization. Multiparametric sensitivity analysis (MPSA) was used to understand key proteins that regulate F1 + 2 , TAT and D-dimer levels. Results The model was able to describe tissue factor (TF)-dependent baseline levels of F1 + 2 , TAT and D-dimer in a non-bleeding state, and their increases in hemostatically normal subjects and hemophilic patients treated with different doses of rFVIIa. The amount of TF required is predicted to be very low in a non-bleeding state. The model also predicts that these biomarker levels will be similar in hemostatically normal subjects and hemophilic patients. MPSA revealed that F1 + 2 and TAT levels are highly correlated, and that D-dimer is more sensitive to the perturbation of coagulation protein concentrations. Conclusions A QSP model for non-bleeding baseline coagulation activity was established with data from clinically relevant in vivo biomarkers at baseline and changes in response to rFVIIa treatment. This model will provide future mechanistic insights into this system.

Explanation and Elaboration Document for the STROBE-Vet Statement: Strengthening the Reporting of Observational Studies in Epidemiology - Veterinary Extension.

The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) statement was first published in 2007 and again in 2014. The purpose of the original STROBE was to provide guidance for authors, reviewers and editors to improve the comprehensiveness of reporting; however, STROBE has a unique focus on observational studies. Although much of the guidance provided by the original STROBE document is directly applicable, it was deemed useful to map those statements to veterinary concepts, provide veterinary examples and highlight unique aspects of reporting in veterinary observational studies. Here, we present the examples and explanations for the checklist items included in the STROBE-Vet Statement. Thus, this is a companion document to the STROBE-Vet Statement Methods and process document, which describes the checklist and how it was developed.

Methods and Processes of Developing the Strengthening the Reporting of Observational Studies in Epidemiology - Veterinary (STROBE-Vet) Statement.

The reporting of observational studies in veterinary research presents many challenges that often are not adequately addressed in published reporting guidelines. A consensus meeting of experts was organized to develop an extension of the STROBE statement to address observational studies in veterinary medicine with respect to animal health, animal production, animal welfare and food safety outcomes. The consensus meeting was held 11-13 May 2014 in Mississauga, Ontario, Canada. Seventeen experts from North America, Europe and Australia attended the meeting. The experts were epidemiologists and biostatisticians, many of whom hold or have held editorial positions with relevant journals. Prior to the meeting, 19 experts completed a survey about whether they felt any of the 22 items of the STROBE statement should be modified and whether items should be added to address unique issues related to observational studies in animal species with health, production, welfare or food safety outcomes. At the meeting, the participants were provided with the survey responses and relevant literature concerning the reporting of veterinary observational studies. During the meeting, each STROBE item was discussed to determine whether or not re-wording was recommended, and whether additions were warranted. Anonymous voting was used to determine whether there was consensus for each item change or addition. The consensus was that six items needed no modifications or additions. Modifications or additions were made to the STROBE items numbered as follows: 1 (title and abstract), 3 (objectives), 5 (setting), 6 (participants), 7 (variables), 8 (data sources/measurement), 9 (bias), 10 (study size), 12 (statistical methods), 13 (participants), 14 (descriptive data), 15 (outcome data), 16 (main results), 17 (other analyses), 19 (limitations) and 22 (funding). Published literature was not always available to support modification to, or inclusion of, an item. The methods and processes used in the development of this statement were similar to those used for other extensions of the STROBE statement. The use of this extension to the STROBE statement should improve the reporting of observational studies in veterinary research related to animal health, production, welfare or food safety outcomes by recognizing the unique features of observational studies involving food-producing and companion animals, products of animal origin, aquaculture and wildlife.