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Background: The use of stress ulcer prophylaxis (SUP) has risen in recent years, even in patients without a clear indication for therapy., Aim: To evaluate the efficacy of an electronic medical record (EMR)-based alarm to improve appropriate SUP use in hospitalized patients., Methods: We conducted an uncontrolled before-after study comparing SUP prescription in intensive care unit (ICU) patients and non-ICU patients, before and after the implementation of an EMR-based alarm that provided the correct indications for SUP., Results: 1627 patients in the pre-intervention and 1513 patients in the post-intervention cohorts were included. The EMR-based alarm improved appropriate (49.6% vs. 66.6%, p<0.001) and reduced inappropriate SUP use (50.4% vs. 33.3%, p<0.001) in ICU patients only. These differences were related to the optimization of SUP in low risk patients. There was no difference in overt gastrointestinal bleeding between the two cohorts. Unjustified costs related to SUP were reduced by a third after EMR-based alarm use., Conclusions: The use of an EMR-based alarm improved appropriate and reduced inappropriate use of SUP in ICU patients. This benefit was limited to optimization in low risk patients and associated with a decrease in SUP costs., (Copyright © 2018 Elsevier España, S.L.U. All rights reserved.)

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

The DNA-binding interfaces of the androgen (AR) and glucocorticoid (GR) receptors are virtually identical, yet these transcription factors share only about a third of their genomic binding sites and regulate similarly distinct sets of target genes. To address this paradox, we determined the intrinsic specificities of the AR and GR DNA-binding domains using a refined version of SELEX-seq. We developed an algorithm, SelexGLM , that quantifies binding specificity over a large (31-bp) binding site by iteratively fitting a feature-based generalized linear model to SELEX probe counts. This analysis revealed that the DNA-binding preferences of AR and GR homodimers differ significantly, both within and outside the 15-bp core binding site. The relative preference between the two factors can be tuned over a wide range by changing the DNA sequence, with AR more sensitive to sequence changes than GR. The specificity of AR extends to the regions flanking the core 15-bp site, where isothermal calorimetry measurements reveal that affinity is augmented by enthalpy-driven readout of poly(A) sequences associated with narrowed minor groove width. We conclude that the increased specificity of AR is correlated with more enthalpy-driven binding than GR. The binding models help explain differences in AR and GR genomic binding and provide a biophysical rationale for how promiscuous binding by GR allows functional substitution for AR in some castration-resistant prostate cancers., (© 2018 Zhang et al.; Published by Cold Spring Harbor Laboratory Press.)

Although DNA modifications play an important role in gene regulation, the underlying mechanisms remain elusive. We developed EpiSELEX-seq to probe the sensitivity of transcription factor binding to DNA modification in vitro using massively parallel sequencing. Feature-based modeling quantifies the effect of cytosine methylation ( 5 mC) on binding free energy in a position-specific manner. Application to the human bZIP proteins ATF4 and C/EBPβ and three different Pbx-Hox complexes shows that 5 mCpG can both increase and decrease affinity, depending on where the modification occurs within the protein-DNA interface. The TF paralogs tested vary in their methylation sensitivity, for which we provide a structural rationale. We show that 5 mCpG can also enhance in vitro p53 binding and provide evidence for increased in vivo p53 occupancy at methylated binding sites, correlating with primed enhancer histone marks. Our results establish a powerful strategy for dissecting the epigenomic modulation of protein-DNA interactions and their role in gene regulation., (Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: Venous thromboembolism (VTE) is a major health issue that may result in complications such as post-thrombotic syndrome, pulmonary hypertension, and death. Appropriate thromboprophylaxis in individuals undergoing kidney transplantation remains unclear. The aim of this study was to determine the prevalence of symptomatic VTE and major bleeding within 90 days after renal transplantation (RT)., Methods: This was a retrospective study on consecutive patients undergoing RT at Hospital Privado Córdoba, Argentina, from January 1, 2006, to December 31, 2013. Exclusion criteria were age <18 years and combined organ transplantation. Pharmacologic or mechanical thromboprophylaxis was not used routinely. Symptomatic VTE and major bleeding were documented., Results: A total of 511 RTs were performed; 62 patients received combined organ transplantation, and 8 patients (1.5%) were lost to follow-up. Overall, follow-up was completed on 441 patients, 4 (0.9%) of whom developed deep venous thrombosis and 14 (3%) of whom died. The most frequent causes of death were septic shock and severe hemorrhage. Duration of surgery >4 hours (P = .006) and a history of VTE (P < .001) were associated with VTE. Twenty-three patients (5.2%) had major bleeding, 2 (0.4%) died from bleeding complications, and 17 (3.85%) required a reoperation to control bleeding., Conclusions: This study shows a low prevalence of symptomatic VTE in patients undergoing RT despite not having used thromboprophylaxis routinely. Major bleeding was significant, and despite the high risk of VTE assigned by the Caprini score, which suggests pharmacologic prophylaxis, our data raise questions about the appropriate prophylaxis for these patients., (Copyright © 2016 Elsevier Inc. All rights reserved.)