TASK DEFINITION: Given a passage classify if the passage has a definite objective/aim/goal or not. Output '1' if the passage has a defininte objective/aim/goal and output '0' if the passage does not have a definite objective/aim/goal.
PROBLEM: Inflammation triggered by infection or injury is tightly controlled by glucocorticoid hormones which signal via a dedicated transcription factor, the Glucocorticoid Receptor (GR), to regulate hundreds of genes. However, the hierarchy of transcriptional responses to GR activation and the molecular basis of their oftentimes non-linear dynamics are not understood.', 'We investigated early glucocorticoid-driven transcriptional events in macrophages, a cell type highly responsive to both pro- and anti-inflammatory stimuli. Using whole transcriptome analyses in resting and acutely lipopolysaccharide (LPS)-stimulated macrophages, we show that early GR target genes form dense networks with the majority of control nodes represented by transcription factors. The expression dynamics of several glucocorticoid-responsive genes are consistent with feed forward loops (FFL) and coincide with rapid GR recruitment. Notably, GR binding sites in genes encoding members of the KLF transcription factor family colocalize with KLF binding sites. Moreover, our gene expression, transcription factor binding and computational data are consistent with the existence of the GR-KLF9-KLF2 incoherent FFL. Analysis of LPS-downregulated genes revealed striking enrichment in multimerized Zn-fingers- and KRAB domain-containing proteins known to bind nucleic acids and repress transcription by propagating heterochromatin. This raises an intriguing possibility that an increase in chromatin accessibility in inflammatory macrophages results from broad downregulation of negative chromatin remodelers.

SOLUTION: 0

PROBLEM: Indoleamine 2,3 dioxygenase (IDO) degrades the essential amino acid tryptophan and has been shown to minimize rejection in animal models of renal transplantation. Ischemia-reperfusion injury (IRI) is unavoidable in renal transplantation and correlates with shorter graft survival times. Despite its favorable effects on rejection, there is evidence that IDO may facilitate renal IRI. Differentiating the negative impact of IDO on IRI from its pro-tolerant effects in allograft rejection is of clinical relevance. In these studies we hypothesized that constitutive IDO activity may influence renal genes associated with recovery from IRI, and that IDO inhibition may unmask these effects.', 'We examined the renal transcriptome in a rat model of IRI with and without IDO inhibition with 1-methyl-d-tryptophan (1-MT), and assessed for alterations in the gene expression signature.', 'These studies demonstrated that during recovery from renal IRI, pre-treatment with 1-MT alleviated alterations in 105 coding sequences associated with IRI, and in turn triggered new changes in 66 non-coding transcripts, the majority of which were represented by small nucleolar RNA.

SOLUTION: 0

PROBLEM: We hypothesized that myocardial scar characterization using cardiac magnetic resonance imaging (CMR) may be associated with the occurrence of ventricular tachyarrhythmia (VT), appropriate implantable cardioverter-defibrillator (ICD) therapy and mortality.', 'Since a minority of patients with prophylactic ICD implantation receive appropriate ICD therapy, there is a need for more effective risk stratification for primary prevention in patients with ischemic cardiomyopathy.', "In 99 patients with ischemic cardiomyopathy, CMR was performed prior to ICD implantation. We assessed if CMR indices (cardiac mass, LVEF) and CMR scar characteristics (infarct core mass, peri-infarction mass and the ratio's between left ventricular mass, infarct core mass and peri-infarction mass) were associated with outcome. The primary endpoint was sustained VT and/or appropriate ICD therapy. The secondary endpoint was all-cause mortality. During a median follow-up of 5.4 years (IQR 4.5-6.6 years), 34 patients reached the primary end-point (17 appropriate ICD shocks) and 26 patients died. In multivariable Cox regression analysis, peri-infarction to core-infarction ratio (HR 2.01, 95%CI: 1.17-3.44, p=0.01) was independently and significantly associated with the primary endpoint, whereas NYHA-class and lower LVEF were not. Conversely, age (HR 1.06, 95% CI: 1.01-1.12, p=0.02) and lower LVEF (HR 0.95, 95% CI: 0.91-1.00, p=0.04) were independently associated with all-cause mortality, mainly due to heart failure.

SOLUTION:
1