Egfl7 promotes tumor escape from immunity

Egfl7 is an endothelial-specific gene which expression is deregulated in human cancers. We showed that Egfl7 promotes tumor escape from immunity by downregulating the expression of leukocyte adhesion molecules in endothelial cells, thus repressing immune cell extravasation into tumors

Risk factors for poor outcomes of children with acute acalculous cholecystitis

BACKGROUND: Acute acalculous cholecystitis (AAC) is generally considered to be a mild disease in children; however, if left untreated or treated without caution, AAC can lead to severe outcomes, such as death. The objectives of this study were to present the clinical features and identify the predictors of mortality in pediatric AAC. METHODS: Patients diagnosed with AAC between 2005 and 2012 were enrolled. AAC was defined by the presence of fever and an echo-proven thickened gallbladder wall exceeding 4 mm. A poor health outcome was defined as death. Further information related to the demographics, clinical manifestations, laboratory results, ultrasound findings, and pathogens present in the AAC patients was also collected. Predictors of mortality were identified by association analyses and confirmed by multivariate logistic regression. RESULTS: A total of 147 pediatric AAC patients (male/female = 1.01, mean age = 5.2 years) were included in this retrospective study. The most common clinical presentation was an elevated C-reactive protein level (84%) followed by hepatomegaly (80%) and anorexia (78%). AAC in children was associated with various diseases, including infectious diseases (70%), systemic diseases (13%), and malignancy (11%). Fourteen of the 147 (9.25%) patients died during the study period. The presences of thrombocytopenia, anemia, gallbladder sludge, hepatitis, and/or sepsis plus hepatitis were found to be the important predictors of AAC mortality. CONCLUSIONS: The factors associated with AAC mortality were anemia, thrombocytopenia, gallbladder sludge, hepatitis, and sepsis plus hepatitis. These predictors are likely to help clinicians identify patients who are at a high risk of poor prognoses and make appropriate clinical decisions

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society

Penetration of the Optic Nerve or Chiasm by Anterior Communicating Artery Aneurysms: Three Case Reports

Although large and giant aneurysms can induce visual disturbance by compression of the anterior visual pathway, splitting and penetration of the optic apparatus are extremely rare. The authors describe three patients who underwent clipping surgery for anterior communicating artery aneurysm infiltrating into the optic nerve or chiasm. These findings were suspected on preoperative magnetic resonance imaging and confirmed at surgery. Two aneurysms were ruptured and one unruptured. The authors review the literature and discuss the mechanism of cranial nerve penetration by an aneurysm.ArticleNEURO-OPHTHALMOLOGY. 35(3):128-132 (2011)journal articl

Vascular phenotypes in primary non-small cell lung carcinomas and matched brain metastases

BACKGROUND: Anti-angiogenic therapy with bevacizumab (an anti-vascular endothelial growth factor (VEGF) antibody) predominantly targets immature blood vessels. Bevacizumab has shown a survival benefit in non-small cell lung carcinoma (NSCLC) and has recently been demonstrated to be safe in patients with brain metastases. However, it is not known whether bevacizumab is effective against brain metastases or whether metastases are representative of their primary in terms of VEGF expression, hypoxia, proliferation and vascular phenotype. The aim of this study was to evaluate these factors in a series of matched primary NSCLCs and brain metastases. METHODS AND RESULTS: Immunohistochemistry showed strong correlation of carbonic anhydrase 9 expression (a marker of hypoxia) in primary and secondary cancers (P=0.0002). However, the proliferation index, VEGF expression, microvessel density and the proportion of mature vessels were discordant between primary and secondary cancers. The mean proportion of mature vessels was 63.2% higher in the brain metastases than the primary tumours (P=0.004). Moreover, the vascular pattern of the primary tumour was not representative of the metastasis. CONCLUSIONS: Brain metastases have a significantly higher proportion of mature vasculature, suggesting that they may be refractory to anti-VEGF therapy. These findings may have implications for clinical trials and biomarker studies evaluating anti-angiogenic agents in brain metastases

Attacking a smartphone biometric fingerprint system:a novice’s approach

Biometric systems on mobile devices are an increasingly ubiquitous method for identity verification. The majority of contemporary devices have an embedded fingerprint sensor which may be used for a variety of transactions including unlock a device or sanction a payment. In this study we explore how easy it is to successfully attack a fingerprint system using a fake finger manufactured from commonly available materials. Importantly our attackers were novices to producing the fingers and were also constrained by time. Our study shows the relative ease that modern devices can be attacked and the material combinations that lead to these attacks

Scoring docking conformations using predicted protein interfaces

BACKGROUND: Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a complex is especially useful for drug design, limitations of experimental techniques have restricted their practical use. Despite progress in docking predictions, there is still room for improvement. In this study, we contribute to this topic by proposing T-PioDock, a framework for detection of a native-like docked complex 3D structure. T-PioDock supports the identification of near-native conformations from 3D models that docking software produced by scoring those models using binding interfaces predicted by the interface predictor, Template based Protein Interface Prediction (T-PIP). RESULTS: First, exhaustive evaluation of interface predictors demonstrates that T-PIP, whose predictions are customised to target complexity, is a state-of-the-art method. Second, comparative study between T-PioDock and other state-of-the-art scoring methods establishes T-PioDock as the best performing approach. Moreover, there is good correlation between T-PioDock performance and quality of docking models, which suggests that progress in docking will lead to even better results at recognising near-native conformations. CONCLUSION: Accurate identification of near-native conformations remains a challenging task. Although availability of 3D complexes will benefit from template-based methods such as T-PioDock, we have identified specific limitations which need to be addressed. First, docking software are still not able to produce native like models for every target. Second, current interface predictors do not explicitly consider pairwise residue interactions between proteins and their interacting partners which leaves ambiguity when assessing quality of complex conformations

Assessment of protein-protein interfaces in cryo-EM derived assemblies

Structures of macromolecular assemblies derived from cryo-EM maps often contain errors that become more abundant with decreasing resolution. Despite efforts in the cryo-EM community to develop metrics for map and atomistic model validation, thus far, no specific scoring metrics have been applied systematically to assess the interface between the assembly subunits. Here, we comprehensively assessed protein–protein interfaces in macromolecular assemblies derived by cryo-EM. To this end, we developed Protein Interface-score (PI-score), a density-independent machine learning-based metric, trained using the features of protein–protein interfaces in crystal structures. We evaluated 5873 interfaces in 1053 PDB-deposited cryo-EM models (including SARS-CoV-2 complexes), as well as the models submitted to CASP13 cryo-EM targets and the EM model challenge. We further inspected the interfaces associated with low-scores and found that some of those, especially in intermediate-to-low resolution (worse than 4 Å) structures, were not captured by density-based assessment scores. A combined score incorporating PI-score and fit-to-density score showed discriminatory power, allowing our method to provide a powerful complementary assessment tool for the ever-increasing number of complexes solved by cryo-EM