Multilevel competing risk models to evaluate the risk of nosocomial infection

Introduction Risk factor analyses for nosocomial infections (NIs) are complex. First, due to competing events for NI, the association between risk factors of NI as measured using hazard rates may not coincide with the association using cumulative probability (risk). Second, patients from the same intensive care unit (ICU) who share the same environmental exposure are likely to be more similar with regard to risk factors predisposing to a NI than patients from different ICUs. We aimed to develop an analytical approach to account for both features and to use it to evaluate associations between patient- and ICU-level characteristics with both rates of NI and competing risks and with the cumulative probability of infection. Methods We considered a multicenter database of 159 intensive care units containing 109,216 admissions (813,739 admission-days) from the Spanish HELICS-ENVIN ICU network. We analyzed the data using two models: an etiologic model (rate based) and a predictive model (risk based). In both models, random effects (shared frailties) were introduced to assess heterogeneity. Death and discharge without NI are treated as competing events for NI. Results There was a large heterogeneity across ICUs in NI hazard rates, which remained after accounting for multilevel risk factors, meaning that there are remaining unobserved ICU-specific factors that influence NI occurrence. Heterogeneity across ICUs in terms of cumulative probability of NI was even more pronounced. Several risk factors had markedly different associations in the rate-based and risk-based models. For some, the associations differed in magnitude. For example, high Acute Physiology and Chronic Health Evaluation II (APACHE II) scores were associated with modest increases in the rate of nosocomial bacteremia, but large increases in the risk. Others differed in sign, for example respiratory vs cardiovascular diagnostic categories were associated with a reduced rate of nosocomial bacteremia, but an increased risk. Conclusions A combination of competing risks and multilevel models is required to understand direct and indirect risk factors for NI and distinguish patient-level from ICU-level factors.

Female greater wax moths reduce sexual display behavior in relation to the potential risk of predation by echolocating bats

Female greater wax moths Galleria mellonella display by wing fanning in response to bursts of ultrasonic calls produced by males. The temporal and spectral characteristics of these calls show some similarities with the echolocation calls of bats that emit frequency-modulated (FM) signals. Female G. mellonella therefore need to distinguish between the attractive signals of male conspecifics, which may lead to mating opportunities, and similar sounds made by predatory bats. We therefore predicted that (1) females would display in response to playbacks of male calls; (2) females would not display in response to playbacks of the calls of echolocating bats (we used the calls of Daubenton's bat Myotis daubentonii as representative of a typical FM echolocating bat); and (3) when presented with male calls and bat calls during the same time block, females would display more when perceived predation risk was lower. We manipulated predation risk in two ways. First, we varied the intensity of bat calls to represent a nearby (high risk) or distant (low risk) bat. Second, we played back calls of bats searching for prey (low risk) and attacking prey (high risk). All predictions were supported, suggesting that female G. mellonella are able to distinguish conspecific male mating calls from bat calls, and that they modify display rate in relation to predation risk. The mechanism (s) by which the moths separate the calls of bat and moth must involve temporal cues. Bat and moth signals differ considerably in duration, and differences in duration could be encoded by the moth's nervous system and used in discrimination.

On the need for an international effort to capture, share and use crystallization screening data

When crystallization screening is conducted many outcomes are observed but typically the only trial recorded in the literature is the condition that yielded the crystal(s) used for subsequent diffraction studies. The initial hit that was optimized and the results of all the other trials are lost. These missing results contain information that would be useful for an improved general understanding of crystallization. This paper provides a report of a crystallization data exchange (XDX) workshop organized by several international large-scale crystallization screening laboratories to discuss how this information may be captured and utilized. A group that administers a significant fraction of the worlds crystallization screening results was convened, together with chemical and structural data informaticians and computational scientists who specialize in creating and analysing large disparate data sets. The development of a crystallization ontology for the crystallization community was proposed. This paper (by the attendees of the workshop) provides the thoughts and rationale leading to this conclusion. This is brought to the attention of the wider audience of crystallographers so that they are aware of these early efforts and can contribute to the process going forward. © 2012 International Union of Crystallography All rights reserved.

Using upper bounds on attainable discrimination to select discrete valued features

Selection of features that will permit accurate pattern classification is a difficult task. However, if a particular data set is represented by discrete valued features, it becomes possible to determine empirically the contribution that each feature makes to the discrimination between classes. This paper extends the discrimination bound method so that both the maximum and average discrimination expected on unseen test data can be estimated. These estimation techniques are the basis of a backwards elimination algorithm that can be use to rank features in order of their discriminative power. Two problems are used to demonstrate this feature selection process: classification of the Mushroom Database, and a real-world, pregnancy related medical risk prediction task - assessment of risk of perinatal death.

The effectiveness of information-sharing interventions to reduce anxiety in families waiting for surgical patients undergoing an elective surgical procedure: A systematic review

Background Whilst waiting for patients undergoing surgery, a lack of information regarding the patient’s status and the outcome of surgery, can contribute to the anxiety experienced by family members. Effective strategies for providing information to families are therefore required. Objectives To synthesize the best available evidence in relation to the most effective information-sharing interventions to reduce anxiety for families waiting for patients undergoing an elective surgical procedure. Inclusion criteria Types of participants All studies of family members over 18 years of age waiting for patients undergoing an elective surgical procedure were included, including those waiting for both adult and pediatric patients.   Types of intervention All information-sharing interventions for families of patients undergoing an elective surgical procedure were eligible for inclusion in the review. Types of studies All randomized controlled trials (RCTs) quasi-experimental studies, case-controlled and descriptive studies, comparing one information-sharing intervention to another or to usual care were eligible for inclusion in the review. Types of outcomes Primary outcome: The level of anxiety amongst family members or close relatives whilst waiting for patients undergoing surgery, as measured by a validated instrument such as the S-Anxiety portion of the State-Trait Anxiety Inventory (STAI). Secondary outcomes: Family satisfaction and other measurements that may be considered indicators of stress and anxiety, such as mean arterial pressure (MAP) and heart rate. Search strategy A comprehensive search, restricted to English language only, was undertaken of the following databases from 1990 to May 2013: Medline, CINAHL, EMBASE, ProQuest, Web of Science, PsycINFO, Scopus, Dissertation and Theses PQDT (via ProQuest), Current Contents, CENTRAL, Google Scholar, OpenGrey, Clinical Trials, Science.gov, Current Controlled Trials and National Institute for Clinical Studies (NHMRC). Methodological quality Two independent reviewers critically appraised retrieved papers for methodological quality using the standardized critical appraisal instruments for randomized controlled trials and descriptive studies from the Joanna Briggs Institute Meta Analysis of Statistics Assessment and Review Instruments (JBI-MAStARI). Data extraction Two independent reviewers extracted data from included papers using a customized data extraction form. Data synthesis Statistical pooling was not possible, mainly due to issues with data reporting in two of the studies, therefore the results are presented in narrative form. Results Three studies with a total of 357 participants were included in the review. In-person reporting to family members was found to be effective in comparison with usual care in which no reports were provided. Telephone reporting was also found to be effective at reducing anxiety, in comparison with usual care, although not as effective as in-person reporting. The use of paging devices to keep family members informed were found to increase, rather than decrease anxiety. Conclusions Due to the lack of high quality research in this area, the strength of the conclusions are limited. It appears that in-person and telephone reporting to family members decreases anxiety, however the use of paging devices increases anxiety.

The BAD project: data mining, database and prediction of protein adsorption on surfaces

Protein adsorption at solid-liquid interfaces is critical to many applications, including biomaterials, protein microarrays and lab-on-a-chip devices. Despite this general interest, and a large amount of research in the last half a century, protein adsorption cannot be predicted with an engineering level, design-orientated accuracy. Here we describe a Biomolecular Adsorption Database (BAD), freely available online, which archives the published protein adsorption data. Piecewise linear regression with breakpoint applied to the data in the BAD suggests that the input variables to protein adsorption, i.e., protein concentration in solution; protein descriptors derived from primary structure (number of residues, global protein hydrophobicity and range of amino acid hydrophobicity, isoelectric point); surface descriptors (contact angle); and fluid environment descriptors (pH, ionic strength), correlate well with the output variable-the protein concentration on the surface. Furthermore, neural network analysis revealed that the size of the BAD makes it sufficiently representative, with a neural network-based predictive error of 5% or less. Interestingly, a consistently better fit is obtained if the BAD is divided in two separate sub-sets representing protein adsorption on hydrophilic and hydrophobic surfaces, respectively. Based on these findings, selected entries from the BAD have been used to construct neural network-based estimation routines, which predict the amount of adsorbed protein, the thickness of the adsorbed layer and the surface tension of the protein-covered surface. While the BAD is of general interest, the prediction of the thickness and the surface tension of the protein-covered layers are of particular relevance to the design of microfluidics devices.

Strategies for teaching evidence-based practice to undergraduate health students: A systematic review protocol

Review question/objective The objective of this review is to find, critically appraise and synthesize the available quantitative evidence on the effectiveness of interventions that promote successful teaching of the evidence-based practice process in undergraduate health students, in preparation for them to become professional evidence-based practitioners. More specifically, the question that this review seeks to answer is: What is the effectiveness of teaching strategies for evidence-based practice for undergraduate health students? Inclusion criteria Types of participants This review will consider studies that include undergraduate health students from any undergraduate health discipline, including but not limited to medicine, nursing and allied health. Post graduate and post-registration students will not be included. Types of interventions This review will consider studies that evaluate strategies or interventions aimed at teaching any or all of the five steps of evidence-based practice, namely asking a structured clinical question; collecting the best evidence available; critically appraising the evidence to ensure validity, relevance and applicability; applying or integrating the results into clinical practice, and evaluating outcomes. The strategy may take place solely within a tertiary education environment or may be combined with a clinical setting. Types of outcomes This review will consider studies that include the following outcome measures: evidence-based practice behavior, knowledge, skills, attitudes, self-efficacy (or self-confidence), beliefs, values, intention to use evidence-based practice (future use) and confidence levels. Tools used to measure these outcomes will be assessed for reported validity, reliability and generalizability. Outcomes will be measured during the student’s education period up to graduation. If studies are conducted across different year levels this will be taken into account during analysis and reported accordingly.

Searching for semantic person queries using channel representations

It is not uncommon to hear a person of interest described by their height, build, and clothing (i.e. type and colour). These semantic descriptions are commonly used by people to describe others, as they are quick to relate and easy to understand. However such queries are not easily utilised within intelligent surveillance systems as they are difficult to transform into a representation that can be searched for automatically in large camera networks. In this paper we propose a novel approach that transforms such a semantic query into an avatar that is searchable within a video stream, and demonstrate state-of-the-art performance for locating a subject in video based on a description.

Napping, development and health from 0 to 5 years : a systematic review

Background Duration and quality of sleep affect child development and health. Encouragement of napping in preschool children has been suggested as a health-promoting strategy. Objectives The aim of this study is to assess evidence regarding the effects of napping on measures of child development and health. Design This study is a systematic review of published, original research articles of any design. Subjects Children aged 0–5 years. Method Electronic database search was performed following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and assessment of research quality was carried out following a Grading of Recommendations, Assessment, Development and Evaluations (GRADE) protocol. Results Twenty-six articles met inclusion criteria. These were of heterogeneous quality; all had observational designs (GRADE-low). Development and health outcomes included salivary cortisol, night sleep, cognition, behaviour, obesity and accidents. The findings regarding cognition, behaviour and health impacts were inconsistent, probably because of variation in age and habitual napping status of the samples. The most consistent finding was an association between napping and later onset, shorter duration and poorer quality of night sleep, with evidence strongest beyond the age of 2 years. Limitations Studies were not randomised. Most did not obtain data on the children's habitual napping status or the context of napping. Many were reliant on parent report rather than direct observation or physiological measurement of sleep behaviour. Conclusions The evidence indicates that beyond the age of 2 years napping is associated with later night sleep onset and both reduced sleep quality and duration. The evidence regarding behaviour, health and cognition is less certain. There is a need for more systematic studies that use stronger designs. In preschool children presenting with sleep problems clinicians should investigate napping patterns.

Machine learning approaches to analysing textual injury surveillance data: A systematic review

Objective To synthesise recent research on the use of machine learning approaches to mining textual injury surveillance data. Design Systematic review. Data sources The electronic databases which were searched included PubMed, Cinahl, Medline, Google Scholar, and Proquest. The bibliography of all relevant articles was examined and associated articles were identified using a snowballing technique. Selection criteria For inclusion, articles were required to meet the following criteria: (a) used a health-related database, (b) focused on injury-related cases, AND used machine learning approaches to analyse textual data. Methods The papers identified through the search were screened resulting in 16 papers selected for review. Articles were reviewed to describe the databases and methodology used, the strength and limitations of different techniques, and quality assurance approaches used. Due to heterogeneity between studies meta-analysis was not performed. Results Occupational injuries were the focus of half of the machine learning studies and the most common methods described were Bayesian probability or Bayesian network based methods to either predict injury categories or extract common injury scenarios. Models were evaluated through either comparison with gold standard data or content expert evaluation or statistical measures of quality. Machine learning was found to provide high precision and accuracy when predicting a small number of categories, was valuable for visualisation of injury patterns and prediction of future outcomes. However, difficulties related to generalizability, source data quality, complexity of models and integration of content and technical knowledge were discussed. Conclusions The use of narrative text for injury surveillance has grown in popularity, complexity and quality over recent years. With advances in data mining techniques, increased capacity for analysis of large databases, and involvement of computer scientists in the injury prevention field, along with more comprehensive use and description of quality assurance methods in text mining approaches, it is likely that we will see a continued growth and advancement in knowledge of text mining in the injury field.

The effectiveness of education or behavioral interventions on adherence to phosphate control in adults receiving hemodialysis: A systematic review protocol

The objective of this review is to identify the effectiveness of education or behavioral interventions on adherence to phosphate control in adults with end stage kidney disease (ESKD) receiving hemodialysis (HD).

LIS investigations: Let's not forget how to walk...

Last December Natural Language Processing and academic literature searching came into the spotlight in online conversations. Katherine Howard took a look at where and how this rapidly evolving technology fits with core competencies.

Common variants in the CYP2C19 gene are associated with susceptibility to endometriosis

Objective: To follow-up previous studies highlighting a possible role for cytochrome P450, family 2, subfamily C, 19 (CYP2C19) in susceptibility to endometriosis by searching for additional variants in the CYP2C19 gene that may be associated with the disease. Design Case-control study. Setting Academic research. Subject(s) The cases comprised 2,271 women with surgically confirmed endometriosis; the controls comprised 939 women with self-report of no endometriosis and 1,770 unscreened population samples. Intervention(s) Sequencing of the CYP2C19 region and follow-up of 80 single nucleotide polymorphisms (SNPs) in two case-control samples. Main Outcome Measure(s) Allele frequency differences between cases and controls. Result(s) Sequencing of the CYP2C19 gene region resulted in the detection of a large number of known and novel SNPs. Genotyping of 80 polymorphic SNPs in 901 endometriosis cases and 939 controls resulted in study-wide significant association signals for SNPs in moderate or complete linkage disequilibrium with rs4244285, a functional SNP in exon 5 that abrogates CYP2C19 function through the creation of an alternative splice site. Evidence of association was also detected for another functional SNP in the CYP2C19 promoter, rs12248560, which was highlighted in our previous study. Conclusion(s) Functional variants in CYP2C19 may contribute to endometriosis susceptibility in both familial and sporadic cases. © 2014 by American Society for Reproductive Medicine.

Preoperative bathing or showering with skin antiseptics to prevent surgical site infection

Background Surgical site infections (SSIs) are wound infections that occur after invasive (surgical) procedures. Preoperative bathing or showering with an antiseptic skin wash product is a well-accepted procedure for reducing skin bacteria (microflora). It is less clear whether reducing skin microflora leads to a lower incidence of surgical site infection. Objectives To review the evidence for preoperative bathing or showering with antiseptics for preventing hospital-acquired (nosocomial) surgical site infections. Search methods For this fifth update we searched the Cochrane Wounds Group Specialised Register (searched 18 December 2014); the Cochrane Central Register of Controlled Trials (The Cochrane Library 2014 Issue 11); Ovid MEDLINE (2012 to December Week 4 2014), Ovid MEDLINE (In-Process & Other Non-Indexed Citations December 18, 2014); Ovid EMBASE (2012 to 2014 Week 51), EBSCO CINAHL (2012 to December 18 2014) and reference lists of articles. Selection criteria Randomised controlled trials comparing any antiseptic preparation used for preoperative full-body bathing or showering with non-antiseptic preparations in people undergoing surgery. Data collection and analysis Two review authors independently assessed studies for selection, risk of bias and extracted data. Study authors were contacted for additional information. Main results We did not identify any new trials for inclusion in this fifth update. Seven trials involving a total of 10,157 participants were included. Four of the included trials had three comparison groups. The antiseptic used in all trials was 4% chlorhexidine gluconate (Hibiscrub/Riohex). Three trials involving 7791 participants compared chlorhexidine with a placebo. Bathing with chlorhexidine compared with placebo did not result in a statistically significant reduction in SSIs; the relative risk of SSI (RR) was 0.91 (95% confidence interval (CI) 0.80 to 1.04). When only trials of high quality were included in this comparison, the RR of SSI was 0.95 (95%CI 0.82 to 1.10). Three trials of 1443 participants compared bar soap with chlorhexidine; when combined there was no difference in the risk of SSIs (RR 1.02, 95% CI 0.57 to 1.84). Three trials of 1192 patients compared bathing with chlorhexidine with no washing, one large study found a statistically significant difference in favour of bathing with chlorhexidine (RR 0.36, 95%CI 0.17 to 0.79). The smaller studies found no difference between patients who washed with chlorhexidine and those who did not wash preoperatively. Authors' conclusions This review provides no clear evidence of benefit for preoperative showering or bathing with chlorhexidine over other wash products, to reduce surgical site infection. Efforts to reduce the incidence of nosocomial surgical site infection should focus on interventions where effect has been demonstrated.