Biotic Interactions in Soil are Underestimated Drivers of Microbial Carbon Use Efficiency

Microbial carbon use efficiency (CUE)-the balance between microbial growth and respiration-strongly impacts microbial mediated soil carbon storage and is sensitive to many well-studied abiotic environmental factors. However, surprisingly, little work has examined how biotic interactions in soil may impact CUE. Here, we review the theoretical and empirical lines of evidence exploring how biotic interactions affect CUE through the lens of life history strategies. Fundamentally, the CUE of a microbial population is constrained by population density and carrying capacity, which, when reached, causes species to grow more quickly and less efficiently. When microbes engage in interspecific competition, they accelerate growth rates to acquire limited resources and release secondary chemicals toxic to competitors. Such processes are not anabolic and thus constrain CUE. In turn, antagonists may activate one of a number of stress responses that also do not involve biomass production, potentially further reducing CUE. In contrast, facilitation can increase CUE by expanding species realized niches, mitigating environmental stress and reducing production costs of extracellular enzymes. Microbial interactions at higher trophic levels also influence CUE. For instance, predation on microbes can positively or negatively impact CUE by changing microbial density and the outcomes of interspecific competition. Finally, we discuss how plants select for more or less efficient microbes under different contexts. In short, this review demonstrates the potential for biotic interactions to be a strong regulator of microbial CUE and additionally provides a blueprint for future research to address key knowledge gaps of ecological and applied importance for carbon sequestration.

Listeria infection in young infants: results from a national surveillance study in the UK and Ireland

OBJECTIVES

To describe the epidemiology, age at infection, clinical characteristics and outcome of listeria infection in young infants to inform management and empiric antibiotic choice in young infants.

DESIGN

Prospective 2-year surveillance of Listeria monocytogenes infection in young infants detected through the British Paediatric Surveillance Unit 'orange card' system and triangulated with the public health laboratories.

SETTING

National population study (England, Wales, Scotland and the Ireland) PATIENTS: All infants under 90 days with proven or probable invasive listeriosis MAIN OUTCOME MEASURES: Incidence, mortality, age of infection, clinical characteristics and outcome RESULTS: During a 2-year period (2017-2019), 27 cases of listeriosis in infants <90 days of age were reported. The incidence of listeriosis in this study was 1.8 per 100 000 live births with 7% mortality (2/27). Nearly all cases presented within the first 24 hours of life (26/27). The majority (20/27, 74%) were born preterm and 16/24 (67%) were born to women from ethnic minority backgrounds.

CONCLUSIONS

Invasive listeriosis in young infants in the UK and Ireland is rare and presents early in the neonatal period. National guidelines that recommend the use of amoxicillin as part of empiric regimes for sepsis and meningitis in infants over 1 month of age should be modified.

Epidemiology and healthcare factors associated with neonatal enterococcal infections

OBJECTIVE

To investigate the epidemiology and healthcare factors associated with late-onset neonatal enterococcal infections.

DESIGN

Multicentre, multinational retrospective cohort study using prospectively collected infection data from a neonatal infection surveillance network between 2004 and 2016; this was supplemented with healthcare data from a questionnaire distributed to participating neonatal units.

SETTING

Sixty neonatal units across Europe (UK, Greece, Estonia) and Australia.

PATIENTS

Infants admitted to participating neonatal units who had a positive culture of blood, cerebrospinal fluid or urine after 48 hours of life.

RESULTS

In total, 414 episodes of invasive Enterococcus spp infection were reported in 388 infants (10.1% of a total 4083 episodes in 3602 infants). Enterococcus spp were the second most common cause of late-onset infection after coagulase-negative Staphylococcus spp and were strongly associated with necrotising enterocolitis (NEC) (adjusted OR 1.44, 95% CI 1.02 to 2.03, p=0.038), total parenteral nutrition (TPN) (adjusted OR 1.34, 95% CI 1.06 to 1.70, p=0.016), increasing postnatal age (per 1-week increase: adjusted OR 1.04, 95% CI 1.02 to 1.06, p<0.001) and decreasing birth weight (per 1 kg increase: adjusted OR 0.85, 95% CI 0.74 to 0.97, p=0.017). There was no evidence that inadequate nurse to patient staffing ratios in high-dependency units were associated with a higher risk of enterococcal infections.

CONCLUSIONS

Enterococcus spp were the second most frequent cause of late-onset infections. The association between enterococcal infections, NEC and TPN may inform empiric antimicrobial regimens in these contexts and provide insights into reducing these infections.

Increased surfactant protein-D levels in the airways of preterm neonates with sepsis indicated responses to infectious challenges

AIM

Sepsis is multifactorial and potentially devastating for preterm neonates. Changes in surfactant protein-D (SP-D), phosphatidylcholine (PC) and PC molecular species during infection may indicate innate immunity or inflammation during sepsis. We aimed to compare these important pulmonary molecules in ventilated neonates without or with sepsis.

METHODS

Endotracheal aspirates were collected from preterm neonates born at 23-35 weeks and admitted to the neonatal intensive care unit at the John Radcliffe Hospital, Oxford, UK, from October 2000 to March 2002. Samples were collected at one day to 30 days and analysed for SP-D, total PC and PC molecular species concentrations using enzyme-linked immunosorbent assay and mass spectrometry.

RESULTS

We found that 8/54 (14.8%) neonates developed sepsis. SP-D (p < 0.0001), mono- and di-unsaturated PC were significantly increased (p = 0.05), and polyunsaturated PC was significantly decreased (p < 0.01) during sepsis compared to controls. SP-D:PC ratios were significantly increased during sepsis (p < 0.001), and SP-D concentrations were directly related to gestational age in neonates with sepsis (r²  = 0.389, p < 0.01).

CONCLUSION

Increased SP-D levels and changes in PC molecular species during sepsis were consistent with direct or indirect pulmonary inflammatory processes. Very preterm neonates we able to mount an acute inflammatory innate immune response to infectious challenges, despite low levels of surfactant proteins at birth.

Constraining the Spin-Dependent WIMP-Nucleon Cross Sections with XENON1T

We report the first experimental results on spin-dependent elastic weakly interacting massive particle (WIMP) nucleon scattering from the XENON1T dark matter search experiment. The analysis uses the full ton year exposure of XENON1T to constrain the spin-dependent proton-only and neutron-only cases. No significant signal excess is observed, and a profile likelihood ratio analysis is used to set exclusion limits on the WIMP-nucleon interactions. This includes the most stringent constraint to date on the WIMP-neutron cross section, with a minimum of 6.3×10^{-42}  cm^{2} at 30  GeV/c^{2} and 90% confidence level. The results are compared with those from collider searches and used to exclude new parameter space in an isoscalar theory with an axial-vector mediator.

First Results on the Scalar WIMP-Pion Coupling, Using the XENON1T Experiment

We present first results on the scalar coupling of weakly interacting massive particles (WIMPs) to pions from 1  t yr of exposure with the XENON1T experiment. This interaction is generated when the WIMP couples to a virtual pion exchanged between the nucleons in a nucleus. In contrast to most nonrelativistic operators, these pion-exchange currents can be coherently enhanced by the total number of nucleons and therefore may dominate in scenarios where spin-independent WIMP-nucleon interactions are suppressed. Moreover, for natural values of the couplings, they dominate over the spin-dependent channel due to their coherence in the nucleus. Using the signal model of this new WIMP-pion channel, no significant excess is found, leading to an upper limit cross section of 6.4×10^{-46}  cm^{2} (90% confidence level) at 30  GeV/c^{2} WIMP mass.

Dark Matter Search Results from a One Ton-Year Exposure of XENON1T

We report on a search for weakly interacting massive particles (WIMPs) using 278.8 days of data collected with the XENON1T experiment at LNGS. XENON1T utilizes a liquid xenon time projection chamber with a fiducial mass of (1.30±0.01)  ton, resulting in a 1.0 ton yr exposure. The energy region of interest, [1.4,10.6]  keV_{ee} ([4.9,40.9] keV_{nr}), exhibits an ultralow electron recoil background rate of [82_{-3}^{+5}(syst)±3(stat)]  events/(ton yr keV_{ee}). No significant excess over background is found, and a profile likelihood analysis parametrized in spatial and energy dimensions excludes new parameter space for the WIMP-nucleon spin-independent elastic scatter cross section for WIMP masses above 6  GeV/c^{2}, with a minimum of 4.1×10^{-47}  cm^{2} at 30  GeV/c^{2} and a 90% confidence level.

First Dark Matter Search Results from the XENON1T Experiment

We report the first dark matter search results from XENON1T, a ∼2000-kg-target-mass dual-phase (liquid-gas) xenon time projection chamber in operation at the Laboratori Nazionali del Gran Sasso in Italy and the first ton-scale detector of this kind. The blinded search used 34.2 live days of data acquired between November 2016 and January 2017. Inside the (1042±12)-kg fiducial mass and in the [5,40]  keV_{nr} energy range of interest for weakly interacting massive particle (WIMP) dark matter searches, the electronic recoil background was (1.93±0.25)×10^{-4}  events/(kg×day×keV_{ee}), the lowest ever achieved in such a dark matter detector. A profile likelihood analysis shows that the data are consistent with the background-only hypothesis. We derive the most stringent exclusion limits on the spin-independent WIMP-nucleon interaction cross section for WIMP masses above 10  GeV/c^{2}, with a minimum of 7.7×10^{-47}  cm^{2} for 35-GeV/c^{2} WIMPs at 90% C.L.

Assessment of healthcare delivery in the early management of bacterial meningitis in UK young infants: an observational study

OBJECTIVE

To define early presenting features of bacterial meningitis in young infants in England and to review the adequacy of individual case management as compared with relevant national guidelines and an expert panel review.

DESIGN

Retrospective medical case note review and parental recall using standardised questionnaires.

SETTING

England and Wales.

PARTICIPANTS

Infants aged <90 days with bacterial meningitis diagnosed between July 2010 and July 2013.

RESULTS

Of the 97 cases recruited across England and Wales, 66 (68%) were admitted from home and 31 (32%) were in hospital prior to disease onset. Almost all symptoms reported by parents appeared at the onset of the illness, with very few new symptoms appearing subsequently. Overall, 20/66 (30%) infants were assessed to have received inappropriate prehospital management. The median time from onset of first symptoms to first help was 5 hours (IQR: 2-12) and from triage to receipt of first antibiotic dose was 2.0 hours (IQR: 1.0-3.3), significantly shorter in infants with fever or seizures at presentation compared with those without (1.7 (IQR: 1.0-3.0) vs 4.2 (IQR: 1.8-6.3) hours, p=0.02). Overall, 26 (39%) infants had a poor outcome in terms of death or neurological complication; seizures at presentation was the only significant independent risk factor (OR, 7.9; 95% CI 2.3 to 207.0). For cases in hospital already, the median time from onset to first dose of antibiotics was 2.6 (IQR: 1.3-9.8) hours, and 12/31 (39%) of infants had serious neurological sequelae at hospital discharge. Hearing test was not performed in 23% and when performed delayed by ≥4 weeks in 41%.

CONCLUSIONS

In young infants, the non-specific features associated with bacterial meningitis appear to show no progression from onset to admission, whereas there were small but significant differences in the proportion of infants with more specific symptoms at hospital admission compared with at the onset of the illness, highlighting the difficulties in early recognition by parents and healthcare professionals alike. A substantial proportion of infants received inappropriate prehospital and posthospital management. We propose a targeted campaign for education and harmonisation of practice with evidence-based management algorithms.

Search for Electronic Recoil Event Rate Modulation with 4 Years of XENON100 Data

We report on a search for electronic recoil event rate modulation signatures in the XENON100 data accumulated over a period of 4 yr, from January 2010 to January 2014. A profile likelihood method, which incorporates the stability of the XENON100 detector and the known electronic recoil background model, is used to quantify the significance of periodicity in the time distribution of events. There is a weak modulation signature at a period of 431_{-14}^{+16} day in the low energy region of (2.0-5.8) keV in the single scatter event sample, with a global significance of 1.9σ; however, no other more significant modulation is observed. The significance of an annual modulation signature drops from 2.8σ, from a previous analysis of a subset of this data, to 1.8σ with all data combined. Single scatter events in the low energy region are thus used to exclude the DAMA/LIBRA annual modulation as being due to dark matter electron interactions via axial vector coupling at 5.7σ.

Neonatal listeriosis in the UK 2004-2014

OBJECTIVE

To define the clinical features and outcomes of neonatal listeriosis, and identify the maternal risk factors to seek scope for improvement.

METHODS

Neonatal listeriosis was identified prospectively from a United Kingdom neonatal infection surveillance network (neonIN) between 2004 and 2014. The participating neonatal units completed a study-specific proforma.

RESULTS

The incidence of neonatal listeriosis was 3.4 per 100,000 live births. Of the 21 cases identified, 19 were confirmed with a median gestational age of 33 weeks and a median birth weight of 1960 g. The majority had clinical features (95%, 18/19), presented within the first 24 h (95%, 18/19), and received penicillin empirically (94%, 18/19). The neonatal case-fatality rate was 21% (24% if probable cases were included). A proportion of mothers were investigated (60%, 12/18) and diagnosed with listeriosis (58%, 7/12); 32% (6/19) were treated with antibiotics but only 33% (6/12) included penicillin.

DISCUSSION

Despite its rarity and the prompt and appropriate use of antibiotics neonatal listeriosis has a high case-fatality rate. There is room for improvement in the adherence to the empiric antibiotic choice for puerperal sepsis, according to the national guidelines as this, would target listeriosis. Strategies should be in place to prevent pregnancy-associated listeriosis in higher risk population.

ONCE DAILY GENTAMICIN DOSE BANDING IN NEWBORNS WITH SIGNS OF EARLY ONSET OF NEONATAL SEPSIS (EONS), BASED ON INITIAL BIRTH WEIGHT AND GESTATIONAL AGE

AIM

Prospective assessment of safety of dose banding of once daily gentamicin in newborns with signs of EONS in their first days of life.

METHOD

All neonates admitted on the level-3 neonatal unit, with at least three consecutive once daily gentamicin doses, started no later than 48 hrs after birth were included. The dose was based on initial birth weight and not adjusted to daily changes of the bodyweight(W). A gentamicin trough level of 2 mg/L was permitted. Neonates with hypoxic ischaemic encephalopathy at birth were not started on a gentamicin regimen. Data was taken from a database system registered as a service evaluation.Of more than 1200 admitted neonates eighty nine (60 boys, 29 girls; born between Feb 2014 and Jul 2015) received at least three consecutive gentamicin doses for EONS soon after birth (within first 24 hrs: 96.6%), while the majority of antibiotic courses started with a gentamicin regimen were stopped within 36 hrs. 23 (25.8%) neonates with a gestational age (GA) of less than 30 weeks started on 5 mg/kg 48-hourly. Neonates 30 weeks and older started on weight based dosing range: Up to 3 kg: 48 (53.9%) neonates on 5 mg/kg 24 hourly. Between 3-3.5 kg: 13 (14.6%) at fixed 15 mg 24 hourly; between 3.5-4 kg: 5 (5.6%) neonates at fixed 17.5 mg 24 hourly. The first trough level (95.5%) was taken before the third dose. Daily weight (W) was recorded. Routine blood samples was recorded including creatinine, C-reactive protein and a routine sample was sent for investigation of bacterial growth.

RESULTS

The first trough level for neonates up to 30 weeks on 48 hourly regimen (GA-mean 27, range 24-29; W-mean 0.96 kg, range 0.54-1.4 kg; W-change 3.9%) was for all less than 2 mg/L (mean 0.66 mg/L, range 0.2-1.3). For neonates 30 weeks and older, up to 3 kg: (GA-mean 34, range 30-41; W-mean 2.16 kg, range 1.09-2.86 kg; W-change 2.9%) on 24 hourly regimen the level was for 37(82%) up 2 mg/L (mean 1.6 mg/L, range 0.2-2; for 3 cases no level; eight cases 2 up to 3 mg/L of which 3 results cannot be explained with change of a disease status). Neonates between 3-3.5 kg: (GA-mean 38, range 33-42; W-mean 3.3 kg, range 3-3.48 kg; W-change 0.96%) on 24 hourly regimen: all except for one less than 2 mg/L (mean 1.3 mg/L, range 0.4-2; one at 2.7 with hyperinsulinaemia). Between 3.5-4 kg: (GA-mean 39, range 36-41; W-mean 3.78 kg, range 3.6-3.9 kg; W-change 1.3%) on 24 hourly regimen: all less than 2 mg/L (mean 1.1 mg/L, range 0.4-1.7). None of the samples for 73(82%) neonates sent for bacterial investigation showed bacterial growth over 5 days.

CONCLUSION

Dose banding for gentamicin in EONS is a promising safe option for dosing neonates. There needs to be a revision and re-evaluation in context of the disease profile of the population of a newborn unit as indicated by results for dosing neonates 30 weeks and older but less than 3 kg.

Search for Event Rate Modulation in XENON100 Electronic Recoil Data

We have searched for periodic variations of the electronic recoil event rate in the (2-6) keV energy range recorded between February 2011 and March 2012 with the XENON100 detector, adding up to 224.6 live days in total. Following a detailed study to establish the stability of the detector and its background contributions during this run, we performed an unbinned profile likelihood analysis to identify any periodicity up to 500 days. We find a global significance of less than 1σ for all periods, suggesting no statistically significant modulation in the data. While the local significance for an annual modulation is 2.8σ, the analysis of a multiple-scatter control sample and the phase of the modulation disfavor a dark matter interpretation. The DAMA/LIBRA annual modulation interpreted as a dark matter signature with axial-vector coupling of weakly interacting massive particles to electrons is excluded at 4.8σ.

Neonatal invasive fungal infection in England 2004-2010

Rates of invasive fungal infection are highest among neonates, especially those of low birthweight. This study aimed to describe the current epidemiology of invasive neonatal fungal infections in a UK neonatal infection surveillance network. From 2004 to 2010 prospective multicentre surveillance was conducted by 14 neonatal units using a web-based database. Clinicians then completed a standardized pro forma for each positive fungal blood and/or cerebrospinal fluid culture. The overall incidence was 2.4/1000 neonatal unit admissions and was highest among babies <1000 g (extreme low birthweight, 18.8/1000). Only five infants (6%) were >1500 g. The majority of infections were caused by Candida albicans (59; 69%) and Candida parapsilosis (17; 20%); 33% of infants had received antifungal prophylaxis. Known risk factors (use of central venous catheter, parenteral nutrition, previous antibiotic use) were common among cases. The attributable case fatality rate was 21% (18/84). Extreme low birthweight infants remain at highest risk of invasive fungal infection and prophylaxis should be particularly considered for this group. The number needing to receive prophylaxis to prevent one case varies significantly among units, hence unit-specific decisions are required. Further research is still needed into the optimal empiric and therapeutic strategies.

Characterization of lactate utilization and its implication on the physiology of Haemophilus influenzae

Haemophilus influenzae is a Gram-negative bacillus and a frequent commensal of the human nasopharynx. Earlier work demonstrated that in H. influenzae type b, l-lactate metabolism is associated with serum resistance and in vivo survival of the organism. To further gain insight into lactate utilization of the non-typeable (NTHi) isolate 2019 and laboratory prototype strain Rd KW20, deletion mutants of the l-lactate dehydrogenase (lctD) and permease (lctP) were generated and characterized. It is shown, that the apparent K_M of l-lactate uptake is 20.1 μM as determined for strain Rd KW20. Comparison of the COPD isolate NTHi 2019-R with the corresponding lctP knockout strain for survival in human serum revealed no lactate dependent serum resistance. In contrast, we observed a 4-fold attenuation of the mutant strain in a murine model of nasopharyngeal colonization. Characterization of lctP transcriptional control shows that the lactate utilization system in H. influenzae is not an inductor inducible system. Rather negative feedback regulation was observed in the presence of l-lactate and this is dependent on the ArcAB regulatory system. Additionally, for 2019 it was found that lactate may have signaling function leading to increased cell growth in late log phase under conditions where no l-lactate is metabolized. This effect seems to be ArcA independent and was not observed in strain Rd KW20. We conclude that l-lactate is an important carbon-source and may act as host specific signal substrate which fine tunes the globally acting ArcAB regulon and may additionally affect a yet unknown signaling system and thus may contribute to enhanced in vivo survival.

Managing and preventing outbreaks of Gram-negative infections in UK neonatal units

De novo guidance on the management of Gram-negative bacteria outbreaks in UK neonatal units was developed in 2012 by a Department of Health, England Antimicrobial Resistance and Healthcare Associated Infection working group. The recommendations included activation of an organisational response and establishing a control team when an outbreak is suspected; screening for the specific organism only during an outbreak; undertaking multidisciplinary reviews of cleaning routines, hand hygiene and Gram-negative bacteria transmission risks; considering deep-cleaning; cohorting colonised and infected babies preferably but not necessarily in isolation cubicles; and considering reducing beds or closing a unit to new admissions as a way of improving spacing and staff:patient ratios until the outbreak is under control. The group advised establishing mechanisms to communicate effectively across the network; informing parents of the outbreak as early as possible, and providing prewritten 'infection outbreak' information sheets. For prevention of outbreaks, the group advised meeting national staffing and cot-spacing requirements; following a Water Action Plan; using infection reduction care bundles and benchmarking; and introducing breast milk early and limiting antibiotic use.

Early onset group B streptococcus sepsis: guidelines review

Group B streptococcus (GBS) is the commonest cause of early onset sepsis in UK newborns. Several risk factors for early onset GBS sepsis (EOGBS) have been described. The presence of these risk factors provides an opportunity for intrapartum antibiotic prophylaxis (IAP) and forms the basis of current UK EOGBS prevention guidance. Having observed poor compliance with national guidelines in a review of EOGBS cases within the UK Neonatal Infection Surveillance Network (NeonIN), we reviewed 14 NeonIN unit guidelines. We found substantial variation in recommendations within and between units on indications for IAP and treatment of asymptomatic neonates, and discrepancies between obstetric and neonatal guidelines, potentially increasing infants’ risk of infection. The lack of high quality evidence in this area and related ambiguity in national guidance may have contributed to diverse local approaches. A common approach would permit prospective evaluation of an EOGBS prevention strategy, generating an evidence base to benefit future guidelines.

Cow's milk and the emergence of group B streptococcal disease in newborn babies

BACKGROUND

Group B streptococcus (GBS), the most significant cause of neonatal bacterial sepsis, is thought to have emerged in the 1960s. GBS also causes mastitis in cows, and there is indirect evidence that human GBS is derived from a bovine ancestor.

OBJECTIVE

A major change in the collection of milk from farms, using bulk tanks rather than churns, occurred in the 1960s. We sought to define the temporal relationship between this change in farming and the emergence of GBS neonatal disease.

METHODS

We searched PubMed for reports of GBS disease from 1930 until 1980 to more exactly determine the time of emergence of neonatal infection and supported this data with UK hospital admission statistics for GBS infections. We identified the dates of the change from churns to bulk tanks by searching the internet and books for information on the history of milk transportation, farming and milk collection in the UK.

RESULTS

There are no PubMed reports of neonatal GBS disease between 1930 and 1950, and reports from the UK only emerged in the mid-1960s, confirming the notion that GBS neonatal infection was a newly emergent disease in the 1960s. No national data on hospital admissions are available around this time, but the Oxford Record Linkage Study, with admission data available for Oxford from 1968, showed no cases of neonatal disease until 1974. Cow's milk collection in the UK switched to bulk tank between 1960 and 1979, and publications relating to GBS disease emerged soon after.

CONCLUSIONS

There is a temporal relationship between the emergence of neonatal GBS disease reports in the UK in the 1960s and a change in cow's milk collection. This finding may be a temporal coincidence or may add support to the notion that human GBS was historically derived from a bovine ancestor.

The homodimeric GBS1074 from Streptococcus agalactiae

ESAT-6 is a well characterized secreted protein from Mycobacterium tuberculosis and represents the archetype of the WXG100 family of proteins. Genes encoding ESAT-6 homologues have been identified in the genome of the human pathogen Streptococcus agalactiae; one of these genes, esxA, has been cloned and the recombinant protein has been crystallized. In contrast to M. tuberculosis ESAT-6, the crystal structure of GBS1074 reveals a homodimeric structure similar to homologous structures from Staphylococcus aureus and Helicobacter pylori. Intriguingly, GBS1074 forms elongated fibre-like assemblies in the crystal structure.

Effects of phyto-oestrogens on tissues

Recent investigations on the effects of phyto-oestrogens on various tissues have revealed that these diverse molecules may improve human health, particularly by protecting against certain chronic diseases. After a brief examination of the food sources, structures, and general cellular actions of the major phyto-oestrogens, current research findings on cardiovascular disease, skeletal tissues, and reproductive cancers are reviewed. Phyto-oestrogen concentrations in blood may be maintained at high levels in those consuming soyabean (Glycine max)-based food daily at several meals and exert their effects on target cells through either genomic effects via the classical oestrogen receptors or non-genomic effects mediated by membrane-bound oestrogen receptors or other cellular proteins. The expression of oestrogen receptor (OR) subtypes alpha (a) and beta (beta) varies across tissues, and cells that preferentially express OR-beta, which may include bone cells, are more likely to respond to phyto-oestrogens. Conversely, reproductive tissues contain relatively more OR-a and may, thus, be differently affected by phyto-oestrogens. Soyabean phyto-oestrogens appear to prevent the progression of atherosclerosis through multiple interactions, including lowering of plasma lipids and lipoproteins, increased vasodilatation and, possibly, decreased activation of blood platelets and vascular smooth muscle cells. However, a favourable impact on cardiovascular disease morbidity and mortality by a soyabean-enriched western-type diet remains to be shown, and unresolved questions remain regarding dose and form of the phyto-oestrogens in relation to risks and benefits. The isoflavones of soyabean have been shown consistently to have bone-retentive effects in animal studies by several investigators using rodent models, although intakes must be above a relatively high threshold level for a lengthy period of time, and little or no extra benefit is observed with intakes above this threshold level. The reports of modest or no effects on prevention of bone loss in human and non-human primate studies respectively, may be due to the limited doses tested so far. The relationship between soyabean-food intake and cancer risk has been more extensively investigated than for any other disease, but with less certainty about the benefits of long-term consumption of phyto-oestrogen-containing foods on prevention of cancer. The observations that breast and prostate cancer rates are lower in Asian countries, where soyabean foods are consumed at high levels, and the high isoflavone content of soyabeans have led to examination of the potential protective effects of phyto-oestrogens. Establishing diet-cancer relationships has proved difficult, in part because of the conflicting data from various studies of effects of soyabean-diets on cancer. Epidemiological evidence, though not impressive, does suggest that soyabean intake reduces breast cancer risk. The isoflavone genistein has a potent effect on breast cancer cells in vitro, and early exposure of animals to genistein has been effective in reducing later development of mammary cancer. Thus, continuous consumption of soyabean foods in early life and adulthood may help explain the low breast cancer mortality rates in Asian countries. Although the evidence for a protective effect against prostate cancer may be slightly more supportive, more research is needed before any firm conclusions can be made about the phyto-oestrogen-cancer linkages.

The Coalition Against Major Diseases: developing tools for an integrated drug development process for Alzheimer's and Parkinson's diseases

Aiming to emulate the successful accelerated development of HIV/AIDS drugs, the Critical Path Institute (C-Path), in collaboration with the Engelberg Center for Health Care Reform at the Brookings Institution, has formed the Coalition Against Major Diseases (CAMD). Members include 6 nonprofit groups representing patients' interests, 15 leading pharmaceutical companies, the US Food and Drug Administration (FDA), the European Medicines Agency (EMEA), 2 institutes of the National Institutes of Health (NIH)-the National Institute on Aging (NIA) and the National Institute of Neurological Disorders and Stroke (NINDS)-and representatives from academia. The coalition's purpose is to transform the drug development paradigm for neurodegenerative diseases and serve as a model for other major diseases.

Transposon insertion in a serine-specific minor tRNA coding sequence affects intraperitoneal survival of Haemophilus influenzae in the infant rat model

Due to its lifestyle as a commensal and occasional pathogen in the upper and lower respiratory tracts of humans, Haemophilus influenzae needs to protect itself from endogenously and exogenously generated reactive oxygen species. To better understand the oxygen radical resistance and to investigate a correlation with virulence, randomly generated paraquat-sensitive H. influenzae transposon mutants were analyzed in an infant rat model of infection. Among 25 different paraquat-sensitive mutants only one mutant harbouring a Tn-insertion within the tRNA-Ser1 gene specific for the rare serine codon UCC, was highly attenuated for intraperitoneal infectivity. Compared to the wild-type strain, the tRNA-Ser1 mutant was also more sensitive to neutrophil-mediated killing, deficient for DNA transformation but showed similar growth rates under laboratory conditions. However, by comparative analysis using an oxyR mutant strain, we could show that neutrophil-mediated killing might not be relevant for intraperitoneal infectivity. Therefore, the increased ROS sensitivity observed for tRNA-Ser1 mutant may not be directly responsible for the observed virulence deficiency in the intraperitoneal infection. We speculate that a reduced translation efficiency of several UCC containing mRNAs results in a delay of protein synthesis and consequently in the loss of cellular mechanisms which are necessary for ROS resistance and virulence.

Warfarin interactions with substances listed in drug information compendia and in the FDA-approved label for warfarin sodium

Interactions of warfarin with other drugs or substances can pose a serious problem. We assessed three drug information compendia-Clinical Pharmacology, ePocrates, and Micromedex-and the warfarin sodium (Coumadin) product label (August 2007) approved by the US Food and Drug Administration for listings of interactions between warfarin and drugs, biologics, foods, and dietary supplements. The drug information compendia and warfarin label differed greatly as to the total number of substances that interact with warfarin. Of a total of 648 entries from the four sources, only 50 were common to all the sources. The types of substances listed as interacting with warfarin were entire classes of drugs, individual drugs, and combinations; biologics; dietary supplements; foods; alcohol; and tobacco. These sources were then examined for classification by severity of interaction and the underlying evidence base. This study provides evidence that there is little concordance among commonly used drug compendia and product labels with respect to interactions involving warfarin.

Using a similarity measure for credible classification

This paper concerns classification by Boolean functions. We investigate the classification accuracy obtained by standard classification techniques on unseen points (elements of the domain, {0, 1}(n), for some n) that are similar, in particular senses, to the points that have been observed as training observations. Explicitly, we use a new measure of how similar a point x in {0, 1}(n) is to a set of such points to restrict the domain of points on which we offer a classification. For points sufficiently dissimilar, no classification is given. We report on experimental results which indicate that the classification accuracies obtained on the resulting restricted domains are better than those obtained without restriction. These experiments involve a number of standard data-sets and classification techniques. We also compare the classification accuracies with those obtained by restricting the domain on which classification is given by using the Hamming distance.

Design of the POSSIBLE UStrade mark Study: postmenopausal women's compliance and persistence with osteoporosis medications

Failure to take prescribed medication is common. The POSSIBLE US study is evaluating the impact of physician and patient characteristics on patient-reported compliance and persistence with osteoporosis medications. We report our study design and the baseline characteristics of 4,994 postmenopausal women recruited from primary care physician offices in 33 states.

INTRODUCTION

The Prospective Observational Scientific Study Investigating Bone Loss Experience (POSSIBLE US) is a longitudinal cohort study of osteoporosis therapy in primary care.

METHODS

Between 2004 and 2007, 134 physicians (in 33 states) enrolled postmenopausal women initiating, changing, or continuing osteoporosis medications. After completing a baseline questionnaire, participants will provide data semi-annually for up to 3 years through 2008. Physicians provide patient data at baseline and routine follow-up visits. Participants from 23 sites also signed a release regarding administrative claims data for economic analyses and validation of self-reported data.

BASELINE RESULTS

Four thousand nine hundred and ninety-four evaluable women were recruited from internal medicine (n = 1,784), family practice (n = 1,556), obstetrics/gynecology (n = 1,556), and from one rheumatology practice (n = 98). Mean participant age was 64.3 years (SD = 9.97); 89% were Caucasian; 59% had some college education. Sixty-three percent used a single osteoporosis agent, usually a bisphosphonate. For monotherapy patients, concordance between clinic- and patient-reported medication use was lowest for patients prescribed estrogen therapy (70%) or calcium/vitamin D (72%). Obstetrician/gynecologists enrolled younger women, who were more likely to use estrogen therapy than patients enrolled by other physicians. The 934 women (19%) prescribed only calcium/vitamin D were younger than women prescribed pharmacologic therapy.

CONCLUSIONS

POSSIBLE US provides a unique foundation for evaluating longitudinal use of osteoporosis medications and related outcomes.

A study of the Indian valve for ventriculo-atrial shunts in the treatment of hydrocephalus

Because of the high costs of importing commercially-available shunts, a hand-made ventriculo-atrial shunt was devised in India for the treatment of hydrocephalus. Modifications have been made to the original design and these shunts are now being produced commercially at a fraction of the cost of other available shunts. Hydrodynamic testing indicates that they compare favourably with the other shunts at present in use.

Risk of renal failure associated with IV bisphosphonate use in patients with multiple myeloma

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Background: IV Bisphosphonates including zoledronic acid (ZA) and pamidroniate are frequently used to delay time to skeletal related events in patients with multiple myeloma. The risk of renal toxicity with these agents is well known and regular monitoring of kidney function is required. Despite regular monitoring of creatinine, patients taking IV bisphosphonates may experience decreased renal functioning and renal failure. The purpose of this study was to determine the relative risk of renal failure in patients with multiple myeloma treated with ZA or pamidronate relative to patients whose lytic lesions remained untreated with medications. Methods: Commercially insured adults newly diagnosed with multiple myeloma 7/1/2002–6/2006 were identified using ICD-9 codes within the PHARMetrics Integrated Outcomes Database. Patients were stratified based on evidence of IV bisphosphonate use (treated) or no such evidence (untreated) following initial qualifying diagnosis. For treated patients, the date of first administration of an IV bisphosphonate was the patient's index date. Treated patients were matched to untreated patients based on use of radiation therapy or chemotherapy, year of cancer diagnosis, and health plan enrollment duration.The incidence rate (IR) for renal failure defined using ICD-9 codes was based on number of incident cases identified among the total person-years at risk and expressed as a rate per patient year. IRs and incidence rate ratios (IRR) (comparing the treated to untreated cohorts), with corresponding 95% confidence intervals are reported. Results: Treated (n=401) and untreated (n=431) patients were similar with respect to age (mean 56 years in both cohorts), but treated patients were more likely to be female (54% vs. 47%; p = 0.04) and less likely to have a history of anemia (48% vs. 51%; p=0.002). IV bisphosphonate use was associated with an 8.5% incidence of developing renal failure per patient year versus 4.9% in the untreated cohort (IRR 1.72; 95% CI 1.22–2.42). The risk was similar whether patients were treated with ZA or pamidronate. Conclusions: IV bisphosphonate use was associated with a significantly increased risk (72%) of developing renal failure in patients with multiple myeloma.

No significant financial relationships to disclose.

Soy, isoflavones and atherosclerosis

Consumption of soy protein is associated with a lower risk of cardiovascular disease in man, and reduced atherosclerosis in a variety of experimental animals. Although a portion of the cardiovascular protective effects appears to be due to reductions in plasma lipoprotein concentration, in most people the magnitude of this effect is relatively small. In many, but not all studies using animal models, the reduction in atherosclerosis is in part independent of changes in plasma lipids and lipoproteins. This implies that there may be a direct effect on the arterial wall of one or more of the components in soyprotein that reduces susceptibility to atherosclerosis. The most actively studied components of soy protein that may be responsible for these anti-atherogenic effects are the isoflavones and various protein factions. Extraction of isoflavones and other alcohol-soluble components from soy protein lowers, but does not eliminate its ability to reduce atherosclerosis. Surprisingly, in most studies, adding back the isoflavone-rich alcohol extract to the previously extracted soy protein, or to another protein, does not restore its lipoprotein lowering or anti-atherogenic properties. This implies that alcohol extraction either destroys an active component of soy, alters the structural integrity of the soy proteins, or disassociates a required isoflavone-soy protein complex. Understanding the mechanism of this effect is an important goal for future research. Likewise, the sites of action on the arterial wall, and the mechanisms by which various soy components act to reduce atherosclerosis are just now being studied. The recent demonstration that expression of estrogen receptor alpha is required for atheroprotection by soy protein provides important new mechanistic insight. Other properties of soy, including antioxidant, anti-inflammatory and potentially antithrombogenic properties need to be explored more mechanistically before the full potential of dietary soy protein for the protection from cardiovascular disease will be known.

Defining benefits and risks for SERMs in clinical trials and clinical practice

Differences between clinical trials and clinical practice with respect to defining benefits and benefit/risk ratios for SERMs are discussed. These differences stem from the perception that there is discordance between the statistical significance and the "clinical meaningfulness" of research data in the minds of the practitioner and patient. One way that we can obtain data that are more clinically meaningful is to solicit input in the planning stages of clinical trials from practicing community clinicians and their patients. However, there are drawbacks to community input, such as potentially unrealistic expectations. A further issue is the need to characterize clinically meaningful drug benefits and acceptable benefit/risk ratios for a drug. Individual patients have differences regarding their views of optimal benefits and acceptable risks, so a method or tool for determining what is clinically meaningful would be helpful in presenting comprehensive information to the patient. To present useful information to clinicians, head-to-head comparisons of a new drug with a standard agent should be undertaken. NIH's support in this area of comparator trials is critical to their implementation. Estrogen has been considered the standard for comparison of agents for conditions associated with menopause in clinical trials. Estrogen has been the "gold standard" in clinical practice as well. In fact, challenging the position of estrogen, even where scientifically supported, has proven to be an uphill battle. In the practice setting, we elaborate the challenges of keeping up with the scientific literature and of then communicating this information in a fashion that is relevant to the individual patient.