Prioritizing causal disease genes using unbiased genomic features

Background: Cardiovascular disease (CVD) is the leading cause of death in the developed world. Human genetic studies, including genome-wide sequencing and SNP-array approaches, promise to reveal disease genes and mechanisms representing new therapeutic targets. In practice, however, identification of the actual genes contributing to disease pathogenesis has lagged behind identification of associated loci, thus limiting the clinical benefits. Results: To aid in localizing causal genes, we develop a machine learning approach, Objective Prioritization for Enhanced Novelty (OPEN), which quantitatively prioritizes gene-disease associations based on a diverse group of genomic features. This approach uses only unbiased predictive features and thus is not hampered by a preference towards previously well-characterized genes. We demonstrate success in identifying genetic determinants for CVD-related traits, including cholesterol levels, blood pressure, and conduction system and cardiomyopathy phenotypes. Using OPEN, we prioritize genes, including FLNC, for association with increased left ventricular diameter, which is a defining feature of a prevalent cardiovascular disorder, dilated cardiomyopathy or DCM. Using a zebrafish model, we experimentally validate FLNC and identify a novel FLNC splice-site mutation in a patient with severe DCM. Conclusion: Our approach stands to assist interpretation of large-scale genetic studies without compromising their fundamentally unbiased nature. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0534-8) contains supplementary material, which is available to authorized users

Combinations of β-lactam or aminoglycoside antibiotics with plectasin are synergistic against methicillin-sensitive and methicillin-resistant Staphylococcus aureus.

Bacterial infections remain the leading killer worldwide which is worsened by the continuous emergence of antibiotic resistance. In particular, methicillin-sensitive (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) are prevalent and the latter can be difficult to treat. The traditional strategy of novel therapeutic drug development inevitably leads to emergence of resistant strains, rendering the new drugs ineffective. Therefore, rejuvenating the therapeutic potentials of existing antibiotics offers an attractive novel strategy. Plectasin, a defensin antimicrobial peptide, potentiates the activities of other antibiotics such as β-lactams, aminoglycosides and glycopeptides against MSSA and MRSA. We performed in vitro and in vivo investigations to test against genetically diverse clinical isolates of MSSA (n = 101) and MRSA (n = 115). Minimum inhibitory concentrations (MIC) were determined by the broth microdilution method. The effects of combining plectasin with β-lactams, aminoglycosides and glycopeptides were examined using the chequerboard method and time kill curves. A murine neutropenic thigh model and a murine peritoneal infection model were used to test the effect of combination in vivo. Determined by factional inhibitory concentration index (FICI), plectasin in combination with aminoglycosides (gentamicin, neomycin or amikacin) displayed synergistic effects in 76-78% of MSSA and MRSA. A similar synergistic response was observed when plectasin was combined with β-lactams (penicillin, amoxicillin or flucloxacillin) in 87-89% of MSSA and MRSA. Interestingly, no such interaction was observed when plectasin was paired with vancomycin. Time kill analysis also demonstrated significant synergistic activities when plectasin was combined with amoxicillin, gentamicin or neomycin. In the murine models, plectasin at doses as low as 8 mg/kg augmented the activities of amoxicillin and gentamicin in successful treatment of MSSA and MRSA infections. We demonstrated that plectasin strongly rejuvenates the therapeutic potencies of existing antibiotics in vitro and in vivo. This is a novel strategy that can have major clinical implications in our fight against bacterial infections

VEGFR2 Translocates to the Nucleus to Regulate Its Own Transcription

Vascular Endothelial Growth Factor Receptor-2 (VEGFR2) is the major mediator of the angiogenic effects of VEGF. In addition to its well known role as a membrane receptor that activates multiple signaling pathways, VEGFR2 also has a nuclear localization. However, what VEGFR2 does in the nucleus is still unknown. In the present report we show that, in endothelial cells, nuclear VEGFR2 interacts with several nuclear proteins, including the Sp1, a transcription factor that has been implicated in the regulation of genes needed for angiogenesis. By in vivo chromatin immunoprecipitation (ChIP) assays, we found that VEGFR2 binds to the Sp1-responsive region of the VEGFR2 proximal promoter. These results were confirmed by EMSA assays, using the same region of the VEGFR2 promoter. Importantly, we show that the VEGFR2 DNA binding is directly linked to the transcriptional activation of the VEGFR2 promoter. By reporter assays, we found that the region between -300/-116 relative to the transcription start site is essential to confer VEGFR2-dependent transcriptional activity. It was previously described that nuclear translocation of the VEGFR2 is dependent on its activation by VEGF. In agreement, we observed that the binding of VEGFR2 to DNA requires VEGF activation, being blocked by Bevacizumab and Sunitinib, two anti-angiogenic agents that inhibit VEGFR2 activation. Our findings demonstrate a new mechanism by which VEGFR2 activates its own promoter that could be involved in amplifying the angiogenic response

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Correction to: Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

The original version of this article unfortunately contained a mistake

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Multi-scale numerical simulations of thermal expansion properties of CNT-reinforced nanocomposites

In this work, the thermal expansion properties of carbon nanotube (CNT)-reinforced nanocomposites with CNT content ranging from 1 to 15 wt% were evaluated using a multi-scale numerical approach, in which the effects of two parameters, i.e., temperature and CNT content, were investigated extensively. For all CNT contents, the obtained results clearly revealed that within a wide low-temperature range (30°C ~ 62°C), thermal contraction is observed, while thermal expansion occurs in a high-temperature range (62°C ~ 120°C). It was found that at any specified CNT content, the thermal expansion properties vary with temperature - as temperature increases, the thermal expansion rate increases linearly. However, at a specified temperature, the absolute value of the thermal expansion rate decreases nonlinearly as the CNT content increases. Moreover, the results provided by the present multi-scale numerical model were in good agreement with those obtained from the corresponding theoretical analyses and experimental measurements in this work, which indicates that this multi-scale numerical approach provides a powerful tool to evaluate the thermal expansion properties of any type of CNT/polymer nanocomposites and therefore promotes the understanding on the thermal behaviors of CNT/polymer nanocomposites for their applications in temperature sensors, nanoelectronics devices, etc

Prioritizing causal disease genes using unbiased genomic features

BACKGROUND: Cardiovascular disease (CVD) is the leading cause of death in the developed world. Human genetic studies, including genome-wide sequencing and SNP-array approaches, promise to reveal disease genes and mechanisms representing new therapeutic targets. In practice, however, identification of the actual genes contributing to disease pathogenesis has lagged behind identification of associated loci, thus limiting the clinical benefits. RESULTS: To aid in localizing causal genes, we develop a machine learning approach, Objective Prioritization for Enhanced Novelty (OPEN), which quantitatively prioritizes gene-disease associations based on a diverse group of genomic features. This approach uses only unbiased predictive features and thus is not hampered by a preference towards previously well-characterized genes. We demonstrate success in identifying genetic determinants for CVD-related traits, including cholesterol levels, blood pressure, and conduction system and cardiomyopathy phenotypes. Using OPEN, we prioritize genes, including FLNC, for association with increased left ventricular diameter, which is a defining feature of a prevalent cardiovascular disorder, dilated cardiomyopathy or DCM. Using a zebrafish model, we experimentally validate FLNC and identify a novel FLNC splice-site mutation in a patient with severe DCM. CONCLUSION: Our approach stands to assist interpretation of large-scale genetic studies without compromising their fundamentally unbiased nature

The 100 Most Mentioned Glaucoma Articles Online with Highest Altmetric Attention Scores

Precis: Characteristics of the most mentioned glaucoma articles on the internet were analyzed, allowing a better understanding of the dissemination of glaucoma research to the general public. Purpose: To determine the 100 most mentioned articles on the internet in the field of glaucoma and analyze their characteristics. Materials and Methods: We identified the top 100 glaucoma articles with the highest Altmetric Attention Score (AAS), an automatically calculated metric for monitoring social media. Each article was evaluated for several characteristics including year of publication, title, journal name, journal impact factor (IF), article topic, article type, affiliation, and online mentions (news, blog, policy, Twitter, Facebook, etc). Correlation analysis was conducted for AAS with these characteristics. Results: The selected 100 articles came from 44 journals with more than half (56%) published in ophthalmology-specific journals. There was no significant correlation between IF and number of articles in a specific journal or AAS (P\u3e0.1), but the number of articles in the top 100 was higher for ophthalmology journals with a higher IF (P\u3c0.05). Original study was the most common study type (87%), of which clinical observation study was the most common subgroup (40%). Epidemiology/risk factor and basic science were the most common article topics (each 24%), followed by medical treatment (13%). Article topics regarding medical treatment had a significantly greater AAS than other topics (P\u3c0.05). Of the top 5 articles, more than half (60%) were related to Lifestyle choice topics. Conclusions: There was no association between journal IF and AAS, consistent with previous studies. 90% of journals that had articles in the top 100 had a Twitter page. Lifestyle choice activities and other modifiable risk factors attracted significant online attention regarding glaucoma studies, with two of the top three most mentioned articles related to dietary intake. The present study thus provides a better understanding of online engagement with glaucoma research and the dissemination of this research to the general public

Soypeptide supplementation attenuates weight loss and improves quality of life among brain cancer patients in a pilot study

Abstract Inability to meet nutrition needs resulting from multiple diseases‐related, and individual factors contribute significantly to malnutrition and poor disease outcome among cancer patients. Strategies capable of delivering metabolically efficient nutrients with less digestive and metabolic stress without adding bulk to the diet of patients may be suitable for dealing with cancer‐related malnutrition and quality of life (QoL). We sought to test the hypothesis that peptide supplementation could attenuate weight loss and improve QoL among brain cancer patients compared to conventionally treated controls. In a non‐blind pilot study, brain cancer patients received 9 g soybean peptide supplementation twice per day (peptide group, n = 9) and compared with conventional treatment (control group, n = 10) over two chemotherapy cycles of 42 days. Compared to the controls, soypeptide supplementation attenuated weight loss with 5.4% increase in weight. Moreover, QoL, assessed using the European Organization for Research and Treatment of Cancer QLQ‐C30, revealed that physical (8.1 ± 15.6, p < .047) and emotional (7.5 ± 3.5, p < .033) functioning as well as summary scores (7.1 ± 2.4, p < .048) improved, whereas others remain stable. Molecular docking simulation suggested that the peptides could induce body weight through the inhibition of angiotensin‐converting enzyme (ACE) upon digestion. Daily soypeptide supplementation could enhance weight gain and improve QoL among brain cancer patients possibly by inhibiting ACE activity. However, a follow‐up study with a larger sample size in a double‐blind randomized trial is required to validate these preliminary findings