Identification of Driver Epistatic Gene Pairs Combining Germline and Somatic Mutations in Cancer.

Cancer arises from the complex interplay of various factors. Traditionally, the identification of driver genes focuses primarily on the analysis of somatic mutations. We describe a new method for the detection of driver gene pairs based on an epistasis analysis that considers both germline and somatic variations.

A novel in situ passive heating method for evaluating whole-tree responses to daytime warming in remote environments.

Background: Many significant ecosystems, including important non-forest woody ecosystems such as the Cerrado (Brazilian savannah), are under threat from climate change, yet our understanding of how increasing temperatures will impact native vegetation remains limited. Temperature manipulation experiments are important tools for investigating such impacts, but are often constrained by access to power supply and limited to low-stature species, juvenile individuals, or heating of target organs, perhaps not fully revealing how entire or mature individuals and ecosystems will react to higher temperatures.

Results: We present a novel, modified open top chamber design for in situ passive heating of whole individuals up to 2.

Incidence and characteristics of transient St-segment elevation during transseptal puncture.

Purpose: Delineate retrospectively and prospectively the incidence and characteristics of transient ST-segment elevation during transseptal puncture.

Methods: The study retrospectively evaluated 307 patients from January 1, 2015, to December 31, 2017, and prospectively evaluated 231 patients from January 1, 2018, to July 31, 2019.

Results: The presence of ST-segment elevation was significantly higher in the prospective sample than in the retrospective sample (5.

The acetabulum as an adult age marker and the new IDADE2 (the IDADE2 web page).

Objective: In 2006, an age estimation method was proposed utilizing Bayesian inference to interpret age-progressive changes in the acetabulum. This was accompanied by the IDADE2 software to facilitate calculations. However, the MS-DOS operating system on which the software was based became obsolete.

Correction: Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations.

[This corrects the article DOI: 10.1371/journal.pone.

Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations.

Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity.

Comparison of a shortened isosorbide dinitrate-potentiated head-up tilt testing with the conventional protocol: tolerance and diagnostic accuracy.

Background: The head-up tilt test (HUT) is widely used to investigate unexplained syncope; however, in clinical practice, it is long and sometimes not well tolerated.

Objectives: To compare the sensitivity, specificity, accuracy, and patients' tolerance of a conventional and shortened HUT.

Methods: Patients with a history of vasovagal syndrome (VVS) were randomized to a conventional HUT (group I) consisting of 20-minute passive tilt followed by 25 minutes after administration of sublingual isosorbide dinitrate (ISDN), or a shortened HUT (group II) where ISDN was given immediately after tilt and observed for 25 minutes.

The significance of the ProtDeform score for structure prediction and alignment.

Background: When a researcher uses a program to align two proteins and gets a score, one of her main concerns is how often the program gives a similar score to pairs that are or are not in the same fold. This issue was analysed in detail recently for the program TM-align with its associated TM-score. It was shown that because the TM-score is length independent, it allows a P-value and a hit probability to be defined depending only on the score.

[Oral anticoagulation in patients with atrial fibrillation: from guidelines to bedside].

Objective: Although oral anticoagulation has proved beneficial for patients with atrial fibrillation (AF) and embolic risk factors, it is still underused. The objective of this study was to evaluate the adequacy of anticoagulation therapy in patients with AF followed in a private clinic specialized in cardiology, in accordance with the American and European societies of cardiology guidelines/2006 and with the Brazilian Guidelines/2003.

Methods: Between November 2005 and August 2006, we evaluated 7,486 electrocardiograms and selected 53 patients with AF and complete chart records.

Flexible structural protein alignment by a sequence of local transformations.

Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use.

Results: We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation.

On the ancestral compatibility of two phylogenetic trees with nested taxa.

Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree of life. The notion of ancestral compatibility of phylogenetic trees with nested taxa was recently introduced. In this paper we analyze in detail the meaning of this compatibility from the points of view of the local structure of the trees, of the existence of embeddings into a common supertree, and of the joint properties of their cluster representations.