Detecting mutually exclusive interactions in protein-protein interaction maps

Comprehensive protein interaction maps can complement genetic and biochemical experiments and allow the formulation of new hypotheses to be tested in the system of interest. The computational analysis of the maps may help to focus on interesting cases and thereby to appropriately prioritize the validation experiments. We show here that, by automatically comparing and analyzing structurally similar regions of proteins of known structure interacting with a common partner, it is possible to identify mutually exclusive interactions present in the maps with a sensitivity of 70% and a specificity higher than 85% and that, in about three fourth of the correctly identified complexes, we also correctly recognize at least one residue (five on average) belonging to the interaction interface. Given the present and continuously increasing number of proteins of known structure, the requirement of the knowledge of the structure of the interacting proteins does not substantially impact on the coverage of our strategy that can be estimated to be around 25%. We also introduce here the Estrella server that embodies this strategy, is designed for users interested in validating specific hypotheses about the functional role of a protein-protein interaction and it also allows access to pre-computed data for seven organisms.     

“The 3/3 Strategy”: A Successful Multifaceted Hospital Wide Hand Hygiene Intervention Based on WHO and Continuous Quality Improvement Methodology

Background

Only multifaceted hospital wide interventions have been successful in achieving sustained improvements in hand hygiene (HH) compliance.

Methodology/Principal Findings

Pre-post intervention study of HH performance at baseline (October 2007– December 2009) and during intervention, which included two phases. Phase 1 (2010) included multimodal WHO approach. Phase 2 (2011) added Continuous Quality Improvement (CQI) tools and was based on: a) Increase of alcohol hand rub (AHR) solution placement (from 0.57 dispensers/bed to 1.56); b) Increase in frequency of audits (three days every three weeks: “3/3 strategy”); c) Implementation of a standardized register form of HH corrective actions; d) Statistical Process Control (SPC) as time series analysis methodology through appropriate control charts. During the intervention period we performed 819 scheduled direct observation audits which provided data from 11,714 HH opportunities. The most remarkable findings were: a) significant improvements in HH compliance with respect to baseline (25% mean increase); b) sustained high level (82%) of HH compliance during intervention; c) significant increase in AHRs consumption over time; c) significant decrease in the rate of healthcare-acquired MRSA; d) small but significant improvements in HH compliance when comparing phase 2 to phase 1 [79.5% (95% CI: 78.2–80.7) vs 84.6% (95% CI:83.8–85.4), p<0.05]; e) successful use of control charts to identify significant negative and positive deviations (special causes) related to the HH compliance process over time (“positive”: 90.1% as highest HH compliance coinciding with the “World hygiene day”; and “negative”:73.7% as lowest HH compliance coinciding with a statutory lay-off proceeding).

Conclusions/Significance

CQI tools may be a key addition to WHO strategy to maintain a good HH performance over time. In addition, SPC has shown to be a powerful methodology to detect special causes in HH performance (positive and negative) and to help establishing adequate feedback to healthcare workers.     

Energy,Water and Fish: Biodiversity Impacts of Energy-Sector Water Demand in the United States Depend on Efficiency and Policy Measures

Rising energy consumption in coming decades, combined with a changing energy mix, have the potential to increase the impact of energy sector water use on freshwater biodiversity. We forecast changes in future water use based on various energy scenarios and examine implications for freshwater ecosystems. Annual water withdrawn/manipulated would increase by 18–24%, going from 1,993,000–2,628,000 Mm³ in 2010 to 2,359,000–3,271,000 Mm³ in 2035 under the Reference Case of the Energy Information Administration (EIA). Water consumption would more rapidly increase by 26% due to increased biofuel production, going from 16,700–46,400 Mm³ consumption in 2010 to 21,000–58,400 Mm³ consumption in 2035. Regionally, water use in the Southwest and Southeast may increase, with anticipated decreases in water use in some areas of the Midwest and Northeast. Policies that promote energy efficiency or conservation in the electric sector would reduce water withdrawn/manipulated by 27–36 m³GJ⁻¹ (0.1–0.5 m³GJ⁻¹ consumption), while such policies in the liquid fuel sector would reduce withdrawal/manipulation by 0.4–0.7 m³GJ⁻¹ (0.2–0.3 m³GJ⁻¹ consumption). The greatest energy sector withdrawal/manipulation are for hydropower and thermoelectric cooling, although potential new EPA rules that would require recirculating cooling for thermoelectric plants would reduce withdrawal/manipulation by 441,000 Mm³ (20,300 Mm³ consumption). The greatest consumptive energy sector use is evaporation from hydroelectric reservoirs, followed by irrigation water for biofuel feedstocks and water used for electricity generation from coal. Historical water use by the energy sector is related to patterns of fish species endangerment, where water resource regions with a greater fraction of available surface water withdrawn by hydropower or consumed by the energy sector correlated with higher probabilities of imperilment. Since future increases in energy-sector surface water use will occur in areas of high fish endemism (e.g., Southeast), additional management and policy actions will be needed to minimize further species imperilment.     

An acenocoumarol dosing algorithm using clinical and pharmacogenetic data in spanish patients with thromboembolic disease

Appropriate dosing of coumarins is difficult to establish, due to significant inter-individual variability in the dose required to obtain stable anticoagulation. Several genetic and other clinical factors have been associated with the coumarins dose, and some pharmacogenetic-guided dosing algorithms for warfarin and acenocoumarol have been developed for mixed populations. We recruited 147 patients with thromboembolic disease who were on stable doses and with an international normalized ratio (INR) between 2 and 3. We ascertained the influence of clinical and genetic variables on the stable acenocoumarol dose by multiple linear regression analysis in a derivation cohort (DC; n = 117) and developed an algorithm for dosing that included clinical factors (age, body mass index and concomitant drugs) and genetic variations of VKORC1, CYP2C9, CYP4F2 and APOE. For purposes of comparison, a model including only clinical data was created. The clinical factors explained 22% of the dose variability, which increased to 60.6% when pharmacogenetic information was included (p<0.001); CYP4F2 and APOE variants explained 4.9% of this variability. The mean absolute error of the predicted acenocoumarol dose (mg/week) obtained with the pharmacogenetic algorithm was 3.63 vs. 5.08 mg/week with the clinical algorithm (95% CI: 0.88 to 2.04). In the testing cohort (n = 30), clinical factors explained a mere 7% of the dose variability, compared to 39% explained by the pharmacogenetic algorithm. Considering a more clinically relevant parameter, the pharmacogenetic algorithm correctly predicted the real stable dose in 59.8% of the cases (DC) vs. only 37.6% predicted by the clinical algorithm (95% CI: 10 to 35). Therefore the number of patients needed to genotype to avoid one over- or under-dosing was estimated to be 5.     

African Perceptions of Female Attractiveness

Little is known about mate choice preferences outside Western, educated, industrialised, rich and democratic societies, even though these Western populations may be particularly unrepresentative of human populations. To our knowledge, this is the first study to test which facial cues contribute to African perceptions of African female attractiveness and also the first study to test the combined role of facial adiposity, skin colour (lightness, yellowness and redness), skin homogeneity and youthfulness in the facial attractiveness preferences of any population. Results show that youthfulness, skin colour, skin homogeneity and facial adiposity significantly and independently predict attractiveness in female African faces. Younger, thinner women with a lighter, yellower skin colour and a more homogenous skin tone are considered more attractive. These findings provide a more global perspective on human mate choice and point to a universal role for these four facial cues in female facial attractiveness.     

Response to Arsenate Treatment in Schizosaccharomyces pombe and the Role of Its Arsenate Reductase Activity

Arsenic toxicity has been studied for a long time due to its effects in humans. Although epidemiological studies have demonstrated multiple effects in human physiology, there are many open questions about the cellular targets and the mechanisms of response to arsenic. Using the fission yeast Schizosaccharomyces pombe as model system, we have been able to demonstrate a strong activation of the MAPK Spc1/Sty1 in response to arsenate. This activation is dependent on Wis1 activation and Pyp2 phosphatase inactivation. Using arsenic speciation analysis we have also demonstrated the previously unknown capacity of S. pombe cells to reduce As (V) to As (III). Genetic analysis of several fission yeast mutants point towards the cell cycle phosphatase Cdc25 as a possible candidate to carry out this arsenate reductase activity. We propose that arsenate reduction and intracellular accumulation of arsenite are the key mechanisms of arsenate tolerance in fission yeast.     

Increased microparticle production and impaired microvascular endothelial function in aldosterone-salt-treated rats: protective effects of polyphenols

We aimed to characterize circulating microparticles in association with arterial stiffness, inflammation and endothelial dysfunction in aldosterone-salt-induced hypertension in rats and to investigate the preventive effects of red wine polyphenols. Uninephrectomized male Sprague-Dawley rats were treated with aldosterone-salt (1 µg.h⁻¹), with or without administration of either red wine polyphenols, Provinols™ (20 mg.kg⁻¹.day⁻¹), or spironolactone (30 mg.kg⁻¹.day⁻¹) for 4 weeks. Microparticles, arterial stiffness, nitric oxide (NO) spin trapping, and mesenteric arterial function were measured. Aldosterone-salt rats showed increased microparticle levels, including those originating from platelets, endothelium and erythrocytes. Hypertension resulted in enhanced aortic stiffness accompanied by increased circulating and aortic NO levels and an upregulation of aortic inducible NO-synthase, NFκB, superoxide anions and nitrotyrosine. Flow-induced dilatation was reduced in mesenteric arteries. These effects were prevented by spironolactone. Provinols™ did not reduce arterial stiffness or systolic hypertension but had effects similar to those of spironolactone on endothelial function assessed by flow-mediated vasodilatation, microparticle generation, aortic NO levels and oxidative stress and apoptosis in the vessel wall. Neither the contractile response nor endothelium-dependent relaxation in mesenteric arteries differed between groups. The in vivo effects of Provinols™ were not mediated by mineralocorticoid receptors or changes in shear stress. In conclusion, vascular remodelling and endothelial dysfunction in aldosterone-salt-mediated hypertension are associated with increased circulating microparticles. Polyphenols prevent the enhanced release of microparticles, macrovascular inflammation and oxidative stress, and microvascular endothelial dysfunction independently of blood pressure, shear stress and mineralocorticoid receptor activation in a model of hyperaldosteronism.     

Believing and perceiving: authorship belief modulates sensory attenuation

Sensory attenuation refers to the observation that self-generated stimuli are attenuated, both in terms of their phenomenology and their cortical response compared to the same stimuli when generated externally. Accordingly, it has been assumed that sensory attenuation might help individuals to determine whether a sensory event was caused by themselves or not. In the present study, we investigated whether this dependency is reciprocal, namely whether sensory attenuation is modulated by prior beliefs of authorship. Participants had to judge the loudness of auditory effects that they believed were either self-generated or triggered by another person. However, in reality, the sounds were always triggered by the participants' actions. Participants perceived the tones' loudness attenuated when they believed that the sounds were self-generated compared to when they believed that they were generated by another person. Sensory attenuation is considered to contribute to the emergence of people's belief of authorship. Our results suggest that sensory attenuation is also a consequence of prior belief about the causal link between an action and a sensory change in the environment.     

Ethnic differences in tissue creatine kinase activity: an observational study

Background

Serum creatine kinase (CK) levels are reported to be around 70% higher in healthy black people, as compared to white people (median value 88 IU/L in white vs 149 IU/L in black people). As serum CK in healthy people is thought to occur from a proportional leak from normal tissues, we hypothesized that the black population subgroup has a generalized higher CK activity in tissues.

Methodology/Principal Findings

We compared CK activity spectrophotometrically in tissues with high and fluctuating energy demands including cerebrum, cerebellum, heart, renal artery, and skeletal muscle, obtained post-mortem in black and white men. Based on serum values, we conservatively estimated to find a 50% greater CK activity in black people compared with white people, and calculated a need for 10 subjects of one gender in each group to detect this difference. We used mixed linear regression models to assess the possible influence of ethnicity on CK activity in different tissues, with ethnicity as a fixed categorical subject factor, and CK of different tissues clustered within one person as the repeated effect response variable. We collected post-mortem tissue samples from 17 white and 10 black males, mean age 62 y (SE 4). Mean tissue CK activity was 76% higher in tissues from black people (estimated marginal means 107.2 [95% CI, 76.7 to 137.7] mU/mg protein in white, versus 188.6 [148.8 to 228.4] in black people, p = 0.002).

Conclusion

We found evidence that black people have higher CK activity in all tissues with high and fluctuating energy demands studied. This finding may help explain the higher serum CK levels found in this population subgroup. Furthermore, our data imply that there are differences in CK-dependent ATP buffer capacity in tissue between the black and the white population subgroup, which may become apparent with high energy demands.