LisBeth: New cladistics for phylogenetics and biogeography

Within phylogenetics, two methods are known to implement cladistics: parsimony or maximum parsimony (MP) and three-item analysis (3ia). Despite the lack of suitable software, 3ia is occasionally used in systematic, and more regularly, in historical biogeography. Here, we present LisBeth, the first and only phylogenetic/biogeographic program freely available that uses the 3ia approach and offer some insights into its theoretical propositions. LisBeth does not rely on the conventional taxon/character matrix. Instead, characters are represented as rooted trees. LisBeth performs 3ia analyses based on maximum congruence of three-item statements and calculates the intersection tree (which differs from usual consensus). In biogeography, it applies the transparent method to handle widespread taxa and implements paralogy-free subtree analysis to remove redundant distributions. For the sake of interoperability, LisBeth may import/export characters from/to matrix in NEXUS format, allowing comparison with other cladistic programs. LisBeth also imports phylogenetic characters from Xper² knowledge bases.     

Tracking the intermediate stages of epithelial-mesenchymal transition in epithelial stem cells and cancer

Epithelial-mesenchymal transition (EMT) is an essential developmental program that becomes reactivated in adult tissues to promote the progression of cancer. EMT has been largely studied by examining the beginning epithelial state or the ending mesenchymal state without studying the intermediate stages. Recent studies using trophoblast stem (TS) cells paused in EMT have defined the molecular and epigenetic mechanisms responsible for modulating the intermediate “metastable” stages of EMT. Targeted inactivation of MAP3K4, knockdown of CBP or overexpression of SNAI1 in TS cells induced similar metastable phenotypes. These TS cells exhibited epigenetic changes in the histone acetylation landscape that cause loss of epithelial maintenance while preserving self-renewal and multipotency. A similar phenotype was found in claudin-low breast cancer cells with properties of EMT and stemness. This intersection between EMT and stemness in TS cells and claudin-low metastatic breast cancer demonstrates the usefulness of developmental EMT systems to understand EMT in cancer.Key words: EMT, metastable EMT, TS cells, claudin-low breast cancer, EMT and stemness, epigenetics, MAP3K4, CBP, histone acetylation     

Genome Wide Association Study Identifies New Loci Associated with Undesired Coat Color Phenotypes in Saanen Goats

This paper reports a quantitative genetics and genomic analysis of undesirable coat color patterns in goats. Two undesirable coat colors have routinely been recorded for the past 15 years in French Saanen goats. One fifth of Saanen females have been phenotyped “pink” (8.0%) or “pink neck” (11.5%) and consequently have not been included in the breeding program as elite animals. Heritability of the binary “pink” and “pink neck” phenotype, estimated from 103,443 females was 0.26 for “pink” and 0.21 for “pink neck”. Genome wide association studies (using haplotypes or single SNPs) were implemented using a daughter design of 810 Saanen goats sired by 9 Artificial Insemination bucks genotyped with the goatSNP50 chip. A highly significant signal (-log10pvalue = 10.2) was associated with the “pink neck” phenotype on chromosome 11, suggesting the presence of a major gene. Highly significant signals for the “pink” phenotype were found on chromosomes 5 and 13 (-log10p values of 7.2 and, 7.7 respectively). The most significant SNP on chromosome 13 was in the ASIP gene region, well known for its association with coat color phenotypes. Nine significant signals were also found for both traits. The highest signal for each trait was detected by both single SNP and haplotype approaches, whereas the smaller signals were not consistently detected by the two methods. Altogether these results demonstrated a strong genetic control of the “pink” and “pink neck” phenotypes in French Saanen goats suggesting that SNP information could be used to identify and remove undesired colored animals from the breeding program.     

Wet-dry-wet drug screen leads to the synthesis of TS1, a novel compound reversing lung fibrosis through inhibition of myofibroblast differentiation

Therapies halting the progression of fibrosis are ineffective and limited. Activated myofibroblasts are emerging as important targets in the progression of fibrotic diseases. Previously, we performed a high-throughput screen on lung fibroblasts and subsequently demonstrated that the inhibition of myofibroblast activation is able to prevent lung fibrosis in bleomycin-treated mice. High-throughput screens are an ideal method of repurposing drugs, yet they contain an intrinsic limitation, which is the size of the library itself. Here, we exploited the data from our “wet” screen and used “dry” machine learning analysis to virtually screen millions of compounds, identifying novel anti-fibrotic hits which target myofibroblast differentiation, many of which were structurally related to dopamine. We synthesized and validated several compounds ex vivo (“wet”) and confirmed that both dopamine and its derivative TS1 are powerful inhibitors of myofibroblast activation. We further used RNAi-mediated knock-down and demonstrated that both molecules act through the dopamine receptor 3 and exert their anti-fibrotic effect by inhibiting the canonical transforming growth factor β pathway. Furthermore, molecular modelling confirmed the capability of TS1 to bind both human and mouse dopamine receptor 3. The anti-fibrotic effect on human cells was confirmed using primary fibroblasts from idiopathic pulmonary fibrosis patients. Finally, TS1 prevented and reversed disease progression in a murine model of lung fibrosis. Both our interdisciplinary approach and our novel compound TS1 are promising tools for understanding and combating lung fibrosis.Subject terms: Drug discovery, Respiratory tract diseases     

Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing

Intrinsically disordered regions have been associated with various cellular processes and are implicated in several human diseases, but their exact roles remain unclear. We previously defined two classes of conserved disordered regions in budding yeast, referred to as “flexible” and “constrained” conserved disorder. In flexible disorder, the property of disorder has been positionally conserved during evolution, whereas in constrained disorder, both the amino acid sequence and the property of disorder have been conserved. Here, we show that flexible and constrained disorder are widespread in the human proteome, and are particularly common in proteins with regulatory functions. Both classes of disordered sequences are highly enriched in regions of proteins that undergo tissue-specific (TS) alternative splicing (AS), but not in regions of proteins that undergo general (i.e., not tissue-regulated) AS. Flexible disorder is more highly enriched in TS alternative exons, whereas constrained disorder is more highly enriched in exons that flank TS alternative exons. These latter regions are also significantly more enriched in potential phosphosites and other short linear motifs associated with cell signaling. We further show that cancer driver mutations are significantly enriched in regions of proteins associated with TS and general AS. Collectively, our results point to distinct roles for TS alternative exons and flanking exons in the dynamic regulation of protein interaction networks in response to signaling activity, and they further suggest that alternatively spliced regions of proteins are often functionally altered by mutations responsible for cancer.     

Direct Observation (DO) for Drug-Resistant Tuberculosis: Do We Really DO?

Introduction

Directly-observed therapy (DOT) is recommended for drug-resistant tuberculosis (DR-TB) patients during their entire treatment duration. However, there is limited published evidence on implementation of direct observation (DO) in the field. This study aims to detail whether DO was followed with DR-TB patients in a Médecins Sans Frontières (MSF) tuberculosis program in Mumbai, India.

Methods

This was a cross-sectional, mixed-methods study. Existing qualitative data from a purposively-selected subset of 12 patients, 5 DOT-providers and 5 family members, were assessed in order to determine how DO was implemented. A questionnaire-based survey of DR-TB patients, their DOT-providers and MSF staff was completed between June and August 2014. Patients were defined as”following Strict DO” and “following DO” if a DOT-provider had seen the patient swallow his/her medications “every day” or “most of the days” respectively. If DO was not followed, reasons were also recorded. The qualitative data were analysed for theme and content and used to supplement the questionnaire-based data.

Results

A total of 70 DR-TB patients, 65 DOT-providers and 21 MSF health staff were included. Fifty-five per cent of the patients were HIV-co-infected and 41% had multidrug-resistant-TB plus additional resistance to a fluoroquinolone. Among all patients, only 14% (10/70) and 20% (14/70) self-reported “following Strict DO” and “following DO” respectively. Among DOT-providers, 46% (30/65) reported that their patients “followed DO”. MSF health staff reported none of the patients “followed DO”. Reasons for not implementing DO included the unavailability of DOT-provider, time spent, stigma and treatment adverse events. The qualitative data also revealed that “Strict DO” was rarely followed and noted the same reasons for lack of implementation.

Conclusion

This mixed-methods study has found that a majority of patients with DR-TB in Mumbai did not follow DO, and this was reported by patients and care-providers. These data likely reflect the reality of DO implementation in many high-burden settings, since this relatively small cohort was supported and closely monitored by a skilled team with access to multiple resources. The findings raise important concerns about the necessity of DO as a “pillar” of DR-TB treatment which need further validation in other settings. They also suggest that patient-centred adherence strategies might be better approaches for supporting patients on treatment.     

Chorioamnionitis and Patent Ductus Arteriosus: A Systematic Review and Meta-Analysis

Background

Chorioamnionitis has recently been reported as a risk factor for various neonatal diseases, including cerebral palsy, bronchopulmonary dysplasia, and necrotizing enterocolitis, but its effect on patent ductus arteriosus (PDA) is unclear. We performed a systematic review and meta-analysis to evaluate the effect of chorioamnionitis on PDA.

Methods

We searched PubMed, EMBASE, Cochrane Library, and KoreaMed databases using the terms: “intrauterine infection” or “maternal infection” or “antenatal infection” or “chorioamnionitis” or “placenta inflammation” or “placenta pathology” or “neonatal outcome” or “neonatal morbidity” or “PDA or patent ductus arteriosus” or “ductus arteriosus,” and “prematurity” or “very low birth weight infant.” Studies were included if they were randomized controlled trials, case–control studies, or cohort studies that included information relating to chorioamnionitis and PDA.

Results

Among 1,571 studies, a total of 23 studies (17,708 cases) were included in the meta-analysis to analyze the relationship between chorioamnionitis and PDA, except one study that only included PDA requiring surgical ligation. The association between chorioamnionitis and PDA was statistically significant (odds ratio [OR] 1.43; 95% confidence interval [CI] 1.19, 1.72; P < 0.0001). In subgroup analysis, clinical chorioamnionitis was not associated with PDA (OR 1.28; 95% CI 1.00, 1.64, 1.790; P = 0.05), whereas histologic chorioamnionitis (OR 1.54; 95% CI 1.10, 2.15; P = 0.01) and chorioamnionitis diagnosed from both clinical and histologic findings (OR 1.75; 95% CI 1.07, 2.86; P = 0.03) showed significant associations with PDA. Chorioamnionitis did not increase the risk of PDA requiring surgical ligation (OR 1.23; 95% CI 0.69, 2.17; P = 0.48), and antenatal steroid use reduced the risk of PDA (OR 0.62; 95% CI 0.42, 0.90; P = 0.01) after chorioamnionitis.

Conclusions

The results from this meta-analysis support an association between maternal chorioamnionitis and PDA in offspring.     

Differential Distribution of Genes Encoding the Virulence Factor Trans-Sialidase along Trypanosoma cruzi Discrete Typing Units

Trypanosoma cruzi the agent of Chagas disease is a monophyletic but heterogeneous group conformed by several Discrete Typing Units (DTUs) named TcI to TcVI characterized by genetic markers. The trans-sialidase (TS) is a virulence factor involved in cell invasion and pathogenesis that is differentially expressed in aggressive and less virulent parasite stocks. Genes encoding TS-related proteins are included in a large family divided in several groups but only one of them contains TS genes. Two closely related genes differing in a T/C transition encode the enzymatically active TS (aTS) and a lectin-like TS (iTS). We quantified the aTS/iTS genes from TcII and TcVI aggressive and TcI low virulent strains and found variable aTS number (1–32) per haploid genome. In spite of being low TS enzyme-expressers, TcI strains carry 28–32 aTS gene copies. The intriguing absence of iTS genes in TcI strains together with the presence of aTS/iTS in TcII and TcVI strains (virulent) were observed. Moreover, after sequencing aTS/iTS from 38 isolates collected along the Americas encompassing all DTUs, the persistent absence of the iTS gene in TcI, TcIII and TcIV was found. In addition, the sequence clustering together with T/C transition analysis correlated to DTUs of T. cruzi. The consistence of TS results with both evolutionary genome models proposed for T. cruzi, namely the “Two Hybridization” and the “Three Ancestor” was discussed and reviewed to fit present findings. Parasite stocks to attempt genetic KO or to assay the involvement of iTS in parasite biology and virulence are finally available.     

Validity of Antibodies in Lymphocyte Supernatant in Diagnosing Tuberculosis in Severely Malnourished Children Presenting with Pneumonia

BackgroundThe diagnosis of tuberculosis (TB) in young children can be challenging, especially in severely malnourished children. There is a critical need for improved diagnostics for children. Thus, we sought to evaluate the performance of a technique that measures antibodies in lymphocyte supernatant (ALS) for the diagnosis of TB in severely malnourished children presenting with suspected pneumonia.MethodsChildren less than 5 years with severe acute malnutrition and radiological features of pneumonia admitted to the Dhaka Hospital of International Centre for Diarrhoeal Disease Research, Bangladesh, were enrolled consecutively following informed written consent. In addition to clinical and radiological assessment, samples taken for TB diagnosis included gastric lavage fluid and induced sputum for microbiological confirmation. ALS was measured from venous blood, and results were evaluated in children classified as “confirmed”, “non-confirmed TB” or “not TB”.ResultsAmong 224 children who had ALS analysis, 12 (5.4%) children had microbiologically “confirmed TB”, a further 41 (18%) had clinically diagnosed “non-confirmed TB” and the remaining 168 (75%) were considered not to have TB. ALS was positive in 89 (40%) and negative in 85 (39%) of children, with a large number (47 or 21%) reported as “borderline”. These proportions were similar between the three diagnostic groups. The sensitivity and specificity of ALS when comparing “Confirmed TB” to “Not TB” was only 67% (95% CI: 31–91%) and 51% (95% CI: 42–60%), respectively.

Conclusions and Significance

Our data suggest that ALS is not sufficiently accurate to improve the diagnosis of TB in children with severe malnutrition.     

Influence of Inter-Training Intervals on Intermanual Transfer Effects in Upper-Limb Prosthesis Training: A Randomized Pre-Posttest Study

Improvement in prosthetic training using intermanual transfer (the transfer of motor skills from the trained, “unaffected” hand to the untrained, “affected” hand) has been shown in previous studies. The aim of this study is to determine the influence of the inter-training interval on the magnitude of the intermanual transfer effects. This was done using a mechanistic, randomized, single-blinded pretest-posttest design. Sixty-four able-bodied, right-handed participants were randomly assigned to the Short and Long Interval Training Groups and the Short and Long Interval Control Groups. The Short and Long Interval Training Groups used a prosthesis simulator in their training program. The Short and Long Interval Control Groups executed a sham training program, that is, a dummy training program in which the same muscles were trained as with the prosthesis simulator. The Short Interval Training Group and the Short Interval Control Groups trained on consecutive days, while the Long Interval Training Group and Long Interval Control Group trained twice a week. To determine the improvement in skills, a test was administered before, immediately after, and at two points in time after the training. Training was performed with the “unaffected” arm; tests were performed with the “affected” arm. The outcome measurements were: the movement time (the time from the beginning of the movement until completion of the task); the duration of maximum hand opening, (the opening of the prosthetic hand while grasping an object); and the grip-force control (the error from the required grip-force during a tracking task). Intermanual transfer was found in movement times, but not in hand opening or grip-force control. The length of the inter-training interval did not affect the magnitude of intermanual transfer effects. No difference in the intermanual transfer effect in upper-limb prosthesis training was found for training on a daily basis as compared to training twice a week.

Trial Registration

Nederlands Trial Register NTR3888     

How Do Tracking and Changes in Dietary Pattern during Adolescence Relate to the Amount of Body Fat in Early Adulthood?

Background

Few studies have addressed the influence of dietary patterns (DP) during adolescence on the amount of body fat in early adulthood.

Objective

To analyze the associations between DP tracking and changes in the period between 15 and 18 years of age and the percentage of body fat (%BF) at age 18 years.

Methods

We used data from 3,823 members of the 1993 Pelotas (Brazil) birth cohort. Body density was measured at age 18 years by air displacement plethysmograph (BOD POD) and the %BF was calculated applying the Siri equation. Based on the estimates from the FFQ, we identified DP at ages 15 (“Varied”, “Traditional”, “Dieting” and “Processed meats”) and 18 years (“Varied”, “Traditional”, “Dieting” and “Fish, fast food and alcohol”). The DP tracking was defined as the individual’s adherence to the same DP at both ages. Associations were tested using multiple linear regression models stratified by sex.

Results

The mean %BF was 25.0% (95% CI: 24.7 to 25.4), significantly greater for girls than boys (p<0.001). The adherence to any DP at age 15 years was not associated with the %BF at age 18 years. However, individuals who adhered to a “Dieting” DP at age 18 years showed greater %BF (1.30 and 1.91 percentage points in boys and girls, respectively) in comparison with those who adhered to a “Varied” DP. Boys who presented tracking of a “Dieting” DP presented greater average %BF in comparison with others DP, as well as girls who changed from the “Traditional” or “Processed meats” DP to a “Dieting” DP.

Conclusion

These results may support public health policies and strategies focused on improving dietary habits of adolescents and young adults and preventing accumulation of body fat, especially among the adolescents with restrictive dietary habits.     

Outcomes for patients with the same disease treated inside and outside of randomized trials: a systematic review and meta-analysis

Background:

It is unclear whether participation in a randomized controlled trial (RCT), irrespective of assigned treatment, is harmful or beneficial to participants. We compared outcomes for patients with the same diagnoses who did (“insiders”) and did not (“outsiders”) enter RCTs, without regard to the specific therapies received for their respective diagnoses.

Methods:

By searching the MEDLINE (1966–2010), Embase (1980–2010), CENTRAL (1960–2010) and PsycINFO (1880–2010) databases, we identified 147 studies that reported the health outcomes of “insiders” and a group of parallel or consecutive “outsiders” within the same time period. We prepared a narrative review and, as appropriate, meta-analyses of patients’ outcomes.

Results:

We found no clinically or statistically significant differences in outcomes between “insiders” and “outsiders” in the 23 studies in which the experimental intervention was ineffective (standard mean difference in continuous outcomes −0.03, 95% confidence interval [CI] −0.1 to 0.04) or in the 7 studies in which the experimental intervention was effective and was received by both “insiders” and “outsiders” (mean difference 0.04, 95% CI −0.04 to 0.13). However, in 9 studies in which an effective intervention was received only by “insiders,” the “outsiders” experienced significantly worse health outcomes (mean difference −0.36, 95% CI −0.61 to −0.12).

Interpretation:

We found no evidence to support clinically important overall harm or benefit arising from participation in RCTs. This conclusion refutes earlier claims that trial participants are at increased risk of harm.When people are asked to participate in a randomized controlled trial (RCT), it is natural for them to ask several questions in return. How safe are these treatments? How many extra visits and tests must I undergo? Will the researchers keep my family doctor informed about what’s going on? What outcomes are to be measured, and do they include ones that are of interest to me as a patient?These multiple questions can be summarized as follows: Would I fare better being treated within the trial (as an “insider”) or in routine clinical care outside it (as an “outsider”)? Patients may ask this question in 1 of 2 ways. The first is highly specific: “Am I better off receiving this specific treatment as an insider or as an outsider?” Alternatively, they might ask a more general question: “Am I better off having my illness managed, regardless of the specific treatment I would receive, as an insider or as an outsider?” These questions are highly appropriate, and both deserve to be asked and answered,^1,2 especially given that nonsystematic reviews have suggested a possible “inclusion benefit” from participating in trials.³These 2 specific patient questions are analogous to those posed by researchers asking whether treatments do more good than harm when applied under “ideal” circumstances (in explanatory trials) or in the “real world” of routine health care (in pragmatic trials). Vist and colleagues answered the explanatory question when their earlier review⁴ found no advantage or disadvantage from receiving the same treatment inside or outside an RCT. Left unanswered, however, was the broader, more pragmatic question. In our experience, trial participants are often offered new, as-yet-untested treatments that would not be available to them outside the trial. This review looks at the dilemma faced by these patients, which needs to be addressed before general conclusions can be drawn about trial safety.     

Prognostic Value of Tissue Inhibitor of Metalloproteinase-2 Expression in Patients with Non–Small Cell Lung Cancer: A Systematic Review and Meta-Analysis

Background and Objectives

Tissue inhibitor of metalloproteinase-2 (TIMP-2) is a small secretory glycoprotein with anti–matrix metalloproteinase activity. Data on the value of TIMP-2 as a prognostic factor in non–small cell lung cancer (NSCLC) are discordant and remain controversial. A systematic review and meta-analysis was performed to explore this issue.

Methods

We identified the relevant literature by searching the PubMed, EMBASE, Web of Science, China National Knowledge Infrastructure, SinoMed, and Wanfang Data databases (search terms: “non-small cell lung cancer” or “NSCLC” or “Lung Carcinoma, Non-Small-Cell”, “Tissue Inhibitor of Metalloproteinase-2” or “TIMP-2”, and “prognosis” or “prognostic” or “survive”) for updates prior to March 1, 2014. The pooled hazard ratio (HR) of overall survival with a 95% confidence interval (95% CI) was used to evaluate the strength of the association between positive TIMP-2 expression and survival in patients with NSCLC.

Results

We included 12 studies in our systematic review; five studies involving 399 patients with NSCLC were meta-analyzed. The pooled HR of all included patients was 0.57 (95% CI: 0.43–0.77), and the HRs of subgroup analysis according to stage (I–IV), testing method (immunohistochemistry) and high TIMP-2 expression percentage (<50%) were 0.63 (95% CI: 0.43–0.92), 0.55 (95% CI: 0.41–0.74), and 0.50 (95% CI: 0.28–0.88), respectively. These data suggested that high TIMP-2 expression is associated with favorable prognosis in NSCLC. The meta-analysis did not reveal heterogeneity or publication bias.

Conclusions

TIMP-2 expression indicates favorable prognosis in patients with NSCLC; as a protective factor, it could help predict outcome and may guide clinical therapy in the future.     

Demography and Population Dynamics of Massive Coral Communities in Adjacent High Latitude Regions (United Arab Emirates)

Individual massive coral colonies, primarily faviids and poritids, from three distinct assemblages within the southeastern Arabian Gulf and northwestern Gulf of Oman (United Arab Emirates) were studied from 2006–2009. Annual photographic censuses of approximately 2000 colonies were used to describe the demographics (size class frequencies, abundance, area cover) and population dynamics under “normal” environmental conditions. Size class transitions included growth, which occurred in 10–20% of the colonies, followed in decending order by partial mortality (3–16%), colony fission (<5%) and ramet fusion (<3%). Recruitment and whole colony mortality rates were low (<0.7 colonies/m²) with minimal interannual variation. Transition matrices indicated that the Arabian Gulf assemblages have declining growth rates (λ<1) whereas the massive coral population is stable (λ = 1) in the Gulf of Oman. Projection models indicated that (i) the Arabian Gulf population and area cover declines would be exacerbated under 10-year and 16-year disturbance scenarios as the vital rates do not allow for recovery to pre-disturbance levels during these timeframes, and (ii) the Gulf of Oman assemblage could return to its pre-disturbance area cover but its overall population size would not fully recover under the same scenarios.     

The Association between the Use of Proton Pump Inhibitors and the Risk of Hypomagnesemia: A Systematic Review and Meta-Analysis

Background

Although many case reports have described patients with proton pump inhibitor (PPI)-induced hypomagnesemia, the impact of PPI use on hypomagnesemia has not been fully clarified through comparative studies. We aimed to evaluate the association between the use of PPI and the risk of developing hypomagnesemia by conducting a systematic review with meta-analysis.

Methods

We conducted a systematic search of MEDLINE, EMBASE, and the Cochrane Library using the primary keywords “proton pump,” “dexlansoprazole,” “esomeprazole,” “ilaprazole,” “lansoprazole,” “omeprazole,” “pantoprazole,” “rabeprazole,” “hypomagnesemia,” “hypomagnesaemia,” and “magnesium.” Studies were included if they evaluated the association between PPI use and hypomagnesemia and reported relative risks or odds ratios or provided data for their estimation. Pooled odds ratios with 95% confidence intervals were calculated using the random effects model. Statistical heterogeneity was assessed with Cochran’s Q test and I ² statistics.

Results

Nine studies including 115,455 patients were analyzed. The median Newcastle-Ottawa quality score for the included studies was seven (range, 6–9). Among patients taking PPIs, the median proportion of patients with hypomagnesemia was 27.1% (range, 11.3–55.2%) across all included studies. Among patients not taking PPIs, the median proportion of patients with hypomagnesemia was 18.4% (range, 4.3–52.7%). On meta-analysis, pooled odds ratio for PPI use was found to be 1.775 (95% confidence interval 1.077–2.924). Significant heterogeneity was identified using Cochran’s Q test (df = 7, P<0.001, I ² = 98.0%).

Conclusions

PPI use may increase the risk of hypomagnesemia. However, significant heterogeneity among the included studies prevented us from reaching a definitive conclusion.     

The Risks of Sleeping “Too Much”. Survey of a National Representative Sample of 24671 Adults (INPES Health Barometer)

Background

A significant U-shaped association between sleep duration and several morbidity (obesity, diabetes or cardiovascular disease) and mortality risks has been regularly reported. However, although the physiological pathways and risks associated with “too short sleep” (<5 hours/day) have been well demonstrated, little is known about “too much sleeping”.

Purpose

To explore socio-demographic characteristics and comorbidities of “long sleepers” (over 10 hours/day) from a nationally representative sample of adults.

Methods

A cross-sectional nationally representative sample of 24,671 subjects from 15 to 85-year-old. An estimated total sleep time (TST) on non-leisure days was calculated based on a specifically designed sleep log which allows to distinguish “long sleepers” from “short sleepers” (<5 hours/day). Insomnia was assessed according to the International classification of sleep disorders (ICSD-2).

Results

The average TST was 7 hours and 13 minutes (+/− 17 minutes). Six hundred and twelve subjects were “long sleepers” (2.7%) and 1969 “short sleepers” (7.5%). Compared to the whole group, “long sleepers” were more often female, younger (15–25 year-old) or older (above 65 year-old), with no academic degree, mostly clerks and blue collar workers. “Long sleepers” were significantly more likely to have psychiatric diseases and a greater body mass index (BMI). However, long sleep was not significantly associated with the presence of any other chronic medical disease assessed. Conversely, short sleep duration was significantly associated with almost all the other chronic diseases assessed.

Conclusions

In the general population, sleeping too much was associated with psychiatric diseases and higher BMI, but not with other chronic medical diseases.     

Task Shifting Routine Inpatient Pediatric HIV Testing Improves Program Outcomes in Urban Malawi: A Retrospective Observational Study

Background

This study evaluated two models of routine HIV testing of hospitalized children in a high HIV-prevalence resource-constrained African setting. Both models incorporated “task shifting,” or the allocation of tasks to the least-costly, capable health worker.

Methods and Findings

Two models were piloted for three months each within the pediatric department of a referral hospital in Lilongwe, Malawi between January 1 and June 30, 2008. Model 1 utilized lay counselors for HIV testing instead of nurses and clinicians. Model 2 further shifted program flow and advocacy responsibilities from counselors to volunteer parents of HIV-infected children, called “patient escorts.” A retrospective review of data from 6318 hospitalized children offered HIV testing between January-December 2008 was conducted. The pilot quarters of Model 1 and Model 2 were compared, with Model 2 selected to continue after the pilot period. There was a 2-fold increase in patients offered HIV testing with Model 2 compared with Model 1 (43.1% vs 19.9%, p<0.001). Furthermore, patients in Model 2 were younger (17.3 vs 26.7 months, p<0.001) and tested sooner after admission (1.77 vs 2.44 days, p<0.001). There were no differences in test acceptance or enrollment rates into HIV care, and the program trends continued 6 months after the pilot period. Overall, 10244 HIV antibody tests (4779 maternal; 5465 child) and 453 DNA-PCR tests were completed, with 97.8% accepting testing. 19.6% of all mothers (n = 1112) and 8.5% of all children (n = 525) were HIV-infected. Furthermore, 6.5% of children were HIV-exposed (n = 405). Cumulatively, 72.9% (n = 678) of eligible children were evaluated in the hospital by a HIV-trained clinician, and 68.3% (n = 387) successfully enrolled into outpatient HIV care.

Conclusions/Significance

The strategy presented here, task shifting from lay counselors alone to lay counselors and patient escorts, greatly improved program outcomes while only marginally increasing operational costs. The wider implementation of this strategy could accelerate pediatric HIV care access in high-prevalence settings.     

Categorizing Ideas about Trees: A Tree of Trees

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a “tree of trees.” Then, we categorize schools of tree-representations. Classical schools like “cladists” and “pheneticists” are recovered but others are not: “gradists” are separated into two blocks, one of them being called here “grade theoreticians.” We propose new interesting categories like the “buffonian school,” the “metaphoricians,” and those using “strictly genealogical classifications.” We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization.     

I Choose,Therefore I Like: Preference for Faces Induced by Arbitrary Choice

Behavioral choice alters one’s preference rather than simply reflecting it. This effect to fit preferences with past choice, is known as “choice-induced preference change.” After making a choice between two equally attractive options, one tends to rate the chosen option better than they initially did and/or the unchosen option worse. The present study examined how behavioral choice changes subsequent preference, using facial images for the choice options as well as blind choice techniques. Participants rated their facial preference for each face, and chose between two equally preferred faces and subsequently rated their facial preference. Results from four experiments demonstrated that randomly chosen faces were more preferred only after participants were required to choose “a preferred face,” (in Experiment 1) but not “an unpreferred face,” (in Experiment 2) or “a rounder face” (in Experiment 3). Further, preference change was still observed after participants were informed that choices were actually random (in Experiment 4). Our findings provide new and important implications characterizing the conditions under which random choice changes preference, and show that people are tempted to make a biased evaluation even after they know that they did not make the choice for themselves.