High-throughput analysis suggests differences in journal false discovery rate by subject area and impact factor but not open access status.

BACKGROUND: A low replication rate has been reported in some scientific areas motivating the creation of resource intensive collaborations to estimate the replication rate by repeating individual studies. The substantial resources required by these projects limits the number of studies that can be repeated and consequently the generalizability of the findings. We extend the use of a method from Jager and Leek to estimate the false discovery rate for 94 journals over a 5-year period using p values from over 30,000 abstracts enabling the study of how the false discovery rate varies by journal characteristics. RESULTS: We find that the empirical false discovery rate is higher for cancer versus general medicine journals (p = 9.801E-07, 95% CI: 0.045, 0.097; adjusted mean false discovery rate cancer = 0.264 vs. general medicine = 0.194). We also find that false discovery rate is negatively associated with log journal impact factor. A two-fold decrease in journal impact factor is associated with an average increase of 0.020 in FDR (p = 2.545E-04). Conversely, we find no statistically significant evidence of a higher false discovery rate, on average, for Open Access versus closed access journals (p = 0.320, 95% CI - 0.015, 0.046, adjusted mean false discovery rate Open Access = 0.241 vs. closed access = 0.225). CONCLUSIONS: Our results identify areas of research that may need additional scrutiny and support to facilitate replicable science. Given our publicly available R code and data, others can complete a broad assessment of the empirical false discovery rate across other subject areas and characteristics of published research.

An approach to evaluating the reliability of diagnostic tests on pooled groups of infected individuals.

An experimental design and statistical analysis providing information on the reliability of pooled test procedures is described. It involves estimating the relationship between the probability of a positive pooled test result (dependent variable) and the expected number of infected individuals in a pool (explanatory variable). The intercept is an estimate of the proportion of false positives (1-pooled specificity) and pooled sensitivities can be estimated for indicative prevalences of infected individuals. Simulations for a theoretical infection are used to investigate the advantages and limitations of the approach. The approach is used to evaluate the reliability of a virus isolation and qRT-PCR test procedure detecting Salmonid alphavirus the pathogenic agent necessary for the development of Pancreas Disease in Atlantic salmon (Salmo salar).

The effect of Parkinson's disease and levodopa on adaptation of anticipatory postural adjustments.

Postural support alters anticipatory postural adjustments (APAs). Efficient adaptation to changes in postural support in reactive and centrally initiated postural synergies is impaired in Parkinson's disease (PD). This study examined whether APAs are affected differently by familiar and novel supports in people with PD, ON and OFF levodopa. The effect of PD and levodopa on the ability to immediately adapt APAs to changes in support and refine with practice was also investigated. Fourteen people with PD and 14 healthy control participants performed 20 single rapid leg lift tasks in four support conditions: unsupported, bilateral handgrip (familiar), bite plate (novel) and a combined handgrip+bite plate condition. APAs, identified from force plate data, were characterized by an increase in the vertical ground reaction force under the lifted leg as a result of a shift of weight toward the stance limb. Results showed the ability to incorporate familiar and novel external supports into the postural strategy was preserved in PD. Controls and PD patients in the OFF state further refined the postural strategy with practice as evidenced by changes in amplitude of vertical ground reaction forces and forces applied to support apparatus within conditions between the initial and final trials. In the ON state, people with PD failed to refine the use of postural supports in any condition. The results suggest that immediate postural adaptation is intact in people with PD and unaffected by levodopa administration but the ability to refine postural adaptations with task experience is compromised by dopamine therapy.

Pollen-mediated gene flow in flax (Linum usitatissimum L.): can genetically engineered and organic flax coexist?

Coexistence allows growers and consumers the choice of producing or purchasing conventional or organic crops with known standards for adventitious presence of genetically engineered (GE) seed. Flax (Linum usitatissimum L.) is multipurpose oilseed crop in which product diversity and utility could be enhanced for industrial, nutraceutical and pharmaceutical markets through genetic engineering. If GE flax were released commercially, pollen-mediated gene flow will determine in part whether GE flax could coexist without compromising other markets. As a part of pre-commercialization risk assessment, we quantified pollen-mediated gene flow between two cultivars of flax. Field experiments were conducted at four locations during 2006 and 2007 in western Canada using a concentric donor (20 × 20 m) receptor (120 × 120 m) design. Gene flow was detected through the xenia effect of dominant alleles of high α-linolenic acid (ALA; 18:3(cisΔ9,12,15)) to the low ALA trait. Seeds were harvested from the pollen recipient plots up to a distance of 50 m in eight directions from the pollen donor. High ALA seeds were identified using a thiobarbituric acid test and served as a marker for gene flow. Binomial distribution and power analysis were used to predict the minimum number of seeds statistically required to detect the frequency of gene flow at specific α (confidence interval) and power (1-ß) values. As a result of the low frequency of gene flow, approximately 4 million seeds were screened to derive accurate quantification. Frequency of gene flow was highest near the source: averaging 0.0185 at 0.1 m but declined rapidly with distance, 0.0013 and 0.00003 at 3 and 35 m, respectively. Gene flow was reduced to 50% (O50) and 90% (O90) between 0.85 to 2.64 m, and 5.68 to 17.56 m, respectively. No gene flow was detected at any site or year > 35 m distance from the pollen source, suggesting that frequency of gene flow was ≤ 0.00003 (P = 0.95). Although it is not possible to eliminate all adventitious presence caused by pollen-mediated gene flow, through harvest blending and the use of buffer zones between GE and conventional flax fields, it could be minimized. Managing other sources of adventitious presence including seed mixing and volunteer populations may be more problematic.

Diversity of putative Tn5253-like elements in Streptococcus pneumoniae.

Pneumococcal resistance to tetracycline, chloramphenicol, erythromycin and clindamycin is often attributed to carriage of conjugative transposons of the Tn916 family. The less well studied conjugative transposon Tn5253 is a composite transposon consisting of a Tn916-like element inserted within the unrelated Tn5252 element, which has also been associated with chloramphenicol and tetracycline resistance. Here, carriage of the Tn5252 integrase (int(5252)), Tn5252-encoded umuC and umuD homologues and Tn916 integrase (int(916)) was examined among 55 clinical isolates of Streptococcus pneumoniae resistant to one or more of the above mentioned antibiotics. Tn5253-associated genes were common among the antibiotic-resistant S. pneumoniae examined, including members of international clones, although the spectrum of genes and resistances carried was diverse. Analysis of five isolates demonstrated insertion of a Tn5253-related element at the same chromosomal locus but sequence and restriction site diversity. This study shows for the first time a high degree of variability of Tn5253-related elements within clinical isolates of pneumococci. The fact that these elements are prevalent among internationally recognised pandemic clones warrants a more intensive investigation.

Sensitivity of an immunomagnetic-separation-based test for detecting Escherichia coli O26 in bovine feces.

The sensitivity of a test for cattle shedding Escherichia coli serogroup O26 was estimated using several fecal pats artificially inoculated at a range of concentrations with different E. coli O26 strains. The test involves the enrichment of fecal microflora in buffered peptone water, the selective concentration of E. coli O26 using antibody-coated immunomagnetic-separation beads, the identification of E. coli colonies on Chromocult tryptone bile X-glucuronide agar, and confirmation of the serogroup with E. coli serogroup O26-specific antisera using slide agglutination. The effective dose of E. coli O26 for an 80% test sensitivity (ED(80)) was 1.0 x 10(4) CFU g(-1) feces (95% confidence interval, 4.7 x 10(3) to 2.4 x 10(4)). Differences in test sensitivity between different E. coli O26 strains and fecal pats were also observed. Individual estimates of ED(80) for each strain and fecal pat combination ranged from 4.2 x 10(2) to 4.8 x 10(5) CFU g(-1). These results suggest that the test is useful for identifying individuals shedding a large number of E. coli O26 organisms or, if an appropriate number of individuals in a herd are sampled, for identifying affected herds. The study also provides a benchmark estimate of sensitivity that can be used to compare alternative tests for E. coli O26 and a methodological approach that can be applied to tests for other pathogenic members of the Enterobacteriaceae and other sample types.

Development of extended-spectrum activity in TEM beta-lactamases in hyper-mutable, mutS Escherichia coli.

TEM-1 and TEM(pUC19)beta-lactamases can gain activity against ceftazidime and other expanded-spectrum cephalosporins via point mutation. The frequency of emergent resistance to ceftazidime at 4 x MIC was elevated >or= 250-fold in hyper-mutable, MutS-deficient Escherichia coli harbouring these beta-lactamase genes on high- or low-copy plasmids. Moreover, although ceftazidime-resistant mutants, or those with reduced susceptibility, were selected in both the wild-type and mutS hosts, many more mutants in the mutS host showed ceftazidimase-type extended-spectrum beta-lactamase (ESBL) activity. This correlated with a G-A point mutation at position 484 in the bla(TEM-1) and bla(TEM-pUC19) genes, conferring the Arg164His amino-acid substitution found in the TEM-29 ESBL. Non-ESBL mutants lacked changes in bla(TEM).

QSAR modeling based on structure-information for properties of interest in human health.

The development of QSAR models based on topological structure description is presented for problems in human health. These models are based on the structure-information approach to quantitative biological modeling and prediction, in contrast to the mechanism-based approach. The structure-information approach is outlined, starting with basic structure information developed from the chemical graph (connection table). Information explicit in the connection table (element identity and skeletal connections) leads to significant (implicit) structure information that is useful for establishing sound models of a wide range of properties of interest in drug design. Valence state definition leads to relationships for valence state electronegativity and atom/group molar volume. Based on these important aspects of molecules, together with skeletal branching patterns, both the electrotopological state (E-state) and molecular connectivity (chi indices) structure descriptors are developed and described. A summary of four QSAR models indicates the wide range of applicability of these structure descriptors and the predictive quality of QSAR models based on them: aqueous solubility (5535 chemically diverse compounds, 938 in external validation), percent oral absorption (%OA, 417 therapeutic drugs, 195 drugs in external validation testing), AMES mutagenicity (2963 compounds including 290 therapeutic drugs, 400 in external validation), fish toxicity (92 substituted phenols, anilines and substituted aromatics). These models are established independent of explicit three-dimensional (3-D) structure information and are directly interpretable in terms of the implicit structure information useful to the drug design process.

Antibiotic resistance in bacteria from magpies (Pica pica) and rabbits (Oryctolagus cuniculus) from west Wales.

The prevalence of antibiotic-resistant bacteria in wild animal and bird populations is largely unknown, with little consistency among the few published reports. We therefore examined intestinal bacteria from magpies (Pica pica) and rabbits (Oryctolagus cuniculus) collected in rural west Wales. Escherichia coli isolates resistant to multiple antibiotics were grown from eight of 20 magpies trapped in spring, 1999 and one of 17 in spring, 2000; the most prevalent resistance trait among these isolates was to tetracycline, but resistances to ampicillin, chloramphenicol, kanamycin, sulphonamide, tetracycline and trimethoprim were also found. Tetracycline-resistant Enterococcus spp. were found in one of 20 magpies in 1999 and three of 17 in 2000. Only one resistant E. coli isolate was detected among gut bacteria from 13 rabbits, and this strain was resistant only to tetracycline. Differences in the prevalence of resistance between bacteria from rabbits and magpies may reflect differences in diet: rabbits graze field edges, whereas magpies are omnivorous and opportunistic. The resistance genes found in E. coli isolates from magpies mostly corresponded to those common among human isolates, but those conferring tetracycline resistance were unique.

SmtB-DNA and protein-protein interactions in the formation of the cyanobacterial metallothionein repression complex: Zn2+ does not dissociate the protein-DNA complex in vitro.

The synechococcal metallothionein locus smt consists of two divergent genes: smtA coding for the metallothionein SmtA, and smtB coding for the trans-acting regulator SmtB. The latter binds at two inverted repeats, designated S1/S2 and S3/S4, in the overlapping promoter/operator sites between the two genes. We have determined the binding stoichiometries to the entire operator/promoter DNA and to the separate S1/S2 and S3/S4 half-operator oligonucleotides using sedimentation equilibrium and sedimentation velocity measurements. The full promoter/operator DNA binds two SmtB dimers. The hydrodynamic behavior of this complex supports a compact nucleoprotein structure. Each separate S1/S2 and S3/S4 operator sequence also binds two dimers. An equal molar mixture of separate S1/S2 and S3/S4 operator sequences, in excess SmtB, forms a S1/S2-SmtB:SmtB-S3/S4 bridge complex. Combining these results with previously published binding interference data, which showed consecutive S1/S2 and S3/S4 SmtB occupancy on the operator/promoter DNA, we have developed a model for the establishment of the repression complex that appears to involve significant DNA compaction, presumably DNA bending, stabilized by SmtB-SmtB bridge interactions. DNase I footprinting titrations also showed consecutive S1/S2 and S3/S4 SmtB occupancy. The footprints expand considerably in the presence of Zn2+. Hence, SmtB remains bound to the operator sites when Zn2+ ions are present. This result is further supported by gel retardation assay. Failure of the metal ions to dissociate SmtB from the DNA points to a hitherto unknown function of SmtB in the regulation of the smt locus.

Persistence of sulphonamide resistance in Escherichia coli in the UK despite national prescribing restriction.

BACKGROUND: There is a clear association between heavy antimicrobial consumption within a population and the frequent recovery of resistant bacteria, but whether a reduction in antimicrobial use can reverse this process is less clear. We investigated the effect of a national restriction of sulphonamide prescribing in the UK on the prevalence of sulphonamide resistance in Escherichia coli. METHODS: Consecutive clinical isolates of E coli were collected at the Royal London Hospital in 1991 and 1999. These collections, each of more than 350 isolates, were compared. Minimum inhibitory concentrations of sulphamethoxazole and eight other antimicrobials were determined. The presence and locations of sulphonamide-resistance genes were examined by PCR, plasmid extraction, Southern hybridisation, and transconjugation. FINDINGS: Despite a huge decrease in sulphonamide prescriptions (from 3,208,000 [corrected] prescriptions per year in 1991 to 77,000 [corrected] in 1999), the frequency of resistance remained high in 1999 (165/359 [46.0%] vs 143/360 [39.7%] in 1991; difference 6.2% [95% CI 20.9 to 13.3]). Integron-borne sulI was present in 16.4% of isolates in 1991 and 17.5% in 1999. The prevalence of sulII increased from 26.7% in 1991 to 36.5% in 1999 (difference 9.8% [3.1 to 16.5] p=0.0046). SulII was located on large plasmids, at least some of which were conjugative multiresistance determinants. INTERPRETATION: These results show that a huge decrease in antibiotic prescribing does not necessarily reduce resistance within a useful time. The main reason seems to be the genetic linkage of the index resistance to other resistance determinants.

Multiple mutations modulate the function of dihydrofolate reductase in trimethoprim-resistant Streptococcus pneumoniae.

Trimethoprim resistance in Streptococcus pneumoniae can be conferred by a single amino acid substitution (I100-L) in dihydrofolate reductase (DHFR), but resistant clinical isolates usually carry multiple DHFR mutations. DHFR genes from five trimethoprim-resistant isolates from the United Kingdom were compared to susceptible isolates and used to transform a susceptible control strain (CP1015). All trimethoprim-resistant isolates and transformants contained the I100-L mutation. The properties of DHFRs from transformants with different combinations of mutations were compared. In a transformant with only the I100-L mutation (R12/T2) and a D92-A mutation also found in the DHFRs of susceptible isolates, the enzyme was much more resistant to trimethoprim inhibition (50% inhibitory concentration [IC50], 4.2 microM) than was the DHFR from strain CP1015 (IC50, 0.09 microM). However, Km values indicated a lower affinity for the enzyme's natural substrates (Km for dihydrofolate [DHF], 3.1 microM for CP1015 and 27.5 microM for R12/T2) and a twofold decrease in the specificity constant. In transformants with additional mutations in the C-terminal portion of the enzyme, Km values for DHF were reduced (9.2 to 15.2 microM), indicating compensation for the lower affinity generated by I100-L. Additional mutations in the N-terminal portion of the enzyme were associated with up to threefold-increased resistance to trimethoprim (IC50 of up to 13.7 microM). It is postulated that carriage of the mutation M53-I-which, like I100-L, corresponds to a trimethoprim binding site in the Escherichia coli DHFR-is responsible for this increase. This study demonstrates that although the I100-L mutation alone may give rise to trimethoprim resistance, additional mutations serve to enhance resistance and modulate the effects of existing mutations on the affinity of DHFR for its natural substrates.

Amino acid repetitions in the dihydropteroate synthase of Streptococcus pneumoniae lead to sulfonamide resistance with limited effects on substrate K(m).

Sulfonamide resistance in Streptococcus pneumoniae is due to changes in the chromosomal folP (sulA) gene coding for dihydropteroate synthase (DHPS). The first reported laboratory-selected sulfonamide-resistant S. pneumoniae isolate had a 6-bp repetition, the sul-d mutation, leading to a repetition of the amino acids Ile(66) and Glu(67) in the gene product DHPS. More recently, clinical isolates showing this and other repetitions have been reported. WA-5, a clinical isolate from Washington State, contains a 6-bp repetition in the folP gene, identical to the sul-d mutation. The repetition was deleted by site-directed mutagenesis. Enzyme kinetic measurements showed that the deletion was associated with a 35-fold difference in K(i) for sulfathiazole but changed the K(m) for p-aminobenzoic acid only 2.5-fold and did not significantly change the K(m) for 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine pyrophosphate. The enzyme characteristics of the deletion variant were identical to those of DHPS from a sulfonamide-susceptible strain. DHPS from clinical isolates with repetitions of Ser(61) had very similar enzyme characteristics to the DHPS from WA-5. The results confirm that the repetitions are sufficient for development of a resistant enzyme and suggest that the fitness cost to the organism of developing resistance may be very low.

SHV-14, a novel beta-lactamase variant in Klebsiella pneumoniae isolates from Nijmegen, The Netherlands.

Four ceftazidime-resistant isolates of a Klebsiella pneumoniae strain were collected from intensive care unit patients in Nijmegen, The Netherlands. These isolates had TEM-29 and SHV-14 beta-lactamases. SHV-14 is a novel variant, with two substitutions compared with the sequence of SHV-1: Ile8Phe and Arg43Ser. Its gene also had a silent C-->T mutation at nucleotide 481. The SHV-14 enzyme had slightly higher V(max) rates than SHV-1 for oxyimino-aminothiazolyl cephalosporins, but this activity was insufficient for the enzyme to count as an extended-spectrum beta-lactamase.

Complexity and diversity of Klebsiella pneumoniae strains with extended-spectrum beta-lactamases isolated in 1994 and 1996 at a teaching hospital in Durban, South Africa.

beta-Lactamase production was investigated in cultures of 25 Klebsiella pneumoniae isolates isolated at a hospital in Durban, South Africa, in 1994 and 1996. Twenty of these isolates gave ceftazidime MIC/ceftazidime plus clavulanate MIC ratios of >/=8, implying production of extended-spectrum beta-lactamases (ESBLs), and DNA sequencing identified an ESBL gene (bla(TEM-53)) in a further two isolates. Pulsed-field gel electrophoresis (PFGE) defined 4 distinct strains among the 12 isolates collected in 1994 and 9 distinct strains among the 13 isolates collected in 1996. In three cases, multiple isolates from single patients varied in their PFGE profiles and antibiograms, implying mixed colonization or infection. Isoelectric focusing and DNA hybridization found both TEM and SHV enzymes and their genes in all 25 isolates. Many isolates had multiple identical or different beta-lactamase gene variants, with at least 84 bla(SHV) and bla(TEM) gene copies among the 25 organisms. Sequencing identified the genes for the SHV-1, -2, and -5 enzymes and for four new SHV types (SHV-19, -20, -21, and -22). These new SHV variants had novel mutations remote from sites known to affect catalytic activity. Sequencing also found the genes for TEM-1, TEM-53, and one novel type, TEM-63. All the isolates had multiple and diverse plasmids. These complex and diverse patterns of ESBL production and strain epidemiology are far removed from the concept of an ESBL outbreak and suggest a situation in which ESBL production has become endemic and in which evolution is generating a wide range of enzyme combinations. This complexity and diversity complicates patient management and the design of antibiotic use policies.

Redesigning nursing work in long-term care environments.

The authors present a highly statistically oriented argument for examining work attitudes and activities among three groups of caregivers [RNs, RPNs, and HCAs] working in long-term care. The investigators used both work sampling, written surveys, and interviews with a sample of 46 caregivers in a large university-affiliated LTC facility in Toronto, Canada. While RNs stated their strong affinity for direct patient care activities, they perform the lowest percentage of direct care, chiefly due to their accountability for planning and coordinating the care provided by others. The HCAs who provided the bulk of direct patient care "valued it the least," apparently finding little gratification with this aspect of their role. This study suggests that there is a need to examine and clarify work roles and perceptions for all caregivers as part of any work redesign process. A higher level of RN involvement in direct patient care activities, along with "attention to enhancing the importance" of these activities for staff employed in the HCA role, could be beneficial.

Development of a nursing management practice atlas. Part 2, Variation in use of nursing and financial resources.

Developing mechanisms for making benchmark comparisons among hospital organization is a challenge that has been embraced by nurse executives. A methodologic approach for ensuring data congruency when using available secondary data bases for making benchmark comparisons was detailed in part one (July/August) of this two-part series. This second article analyzes nursing management data using a set of nursing and financial resource variables identified by senior nurse executives of the hospital sites involved in this study.