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BackgroundTo reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.ResultsLog::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.AvailabilityThe source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).ConclusionUsing Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research.

O-GlcNAcase (OGA) is the only human enzyme that catalyzes the hydrolysis (deglycosylation) of O-linked beta-N-acetylglucosaminylation (O-GlcNAcylation) from numerous protein substrates. OGA has broad implications in many challenging diseases including cancer. However, its role in cell malignancy remains mostly unclear. Here, we report that a cancer-derived point mutation on the OGA's noncatalytic stalk domain aberrantly modulates OGA interactome and substrate deglycosylation toward a specific set of proteins. Interestingly, our quantitative proteomic studies uncovered that the OGA stalk domain mutant preferentially deglycosylated protein substrates with +2 proline in the sequence relative to the O-GlcNAcylation site. One of the most dysregulated substrates is PDZ and LIM domain protein 7 (PDLIM7), which is associated with the tumor suppressor p53. We found that the aberrantly deglycosylated PDLIM7 suppressed p53 gene expression and accelerated p53 protein degradation by promoting the complex formation with E3 ubiquitin ligase MDM2. Moreover, deglycosylated PDLIM7 significantly up-regulated the actin-rich membrane protrusions on the cell surface, augmenting the cancer cell motility and aggressiveness. These findings revealed an important but previously unappreciated role of OGA's stalk domain in protein substrate recognition and functional modulation during malignant cell progression. [ABSTRACT FROM AUTHOR]

Background and Aims In this systematic review we summarise existing scoring indices for assessing disease activity and quality of life in perianal fistulising Crohn's disease [PFCD], and highlight gaps in the literature. Methods MEDLINE, EMBASE, and CENTRAL were searched from August 24, 2022, to identify studies evaluating clinical, radiological, or patient-reported outcome measures [PROMS] in PFCD. The primary objective was to identify all available scoring indices and describe the operating properties of these indices. Results A total of 53 studies reported on the use of one clinical index [Perianal Disease Activity Index: PDAI], three PROMs, and 10 radiological indices; 25 studies evaluated the operating properties of these indices. The PDAI demonstrated content validity, construct validity, and responsiveness but criterion validity or reliability were not assessed. The Van Assche Index [VAI], modified VAI, and the Magnetic Resonance Index for Assessing Fistulas in Patients with CD [MAGNIFI-CD] were the most studied radiological indices. These indices demonstrated responsiveness and reliability. The VAI and MAGNIFI-CD demonstrated construct validity; criterion and content validity and feasibility have not been assessed. Among the three PROMs, the Crohn's Anal Fistula Quality of Life index demonstrated content and construct validity, inter-observer reliability, and responsiveness; criterion validity, intra-observer reliability, and feasibility have not been assessed for this index. Conclusions There are no fully valid, reliable, and responsive clinical disease or radiological indices for PFCD. Although the radiological indices demonstrated responsiveness and reliability, well-defined cut-offs for response and remission are lacking. Future research should focus on establishing standardised definitions and thresholds for outcomes. [ABSTRACT FROM AUTHOR]

Background Fistulas are a debilitating complication of Crohn's disease [CD]. We conducted a systematic review to assess the efficacy of medical therapies for fistulizing CD. Methods MEDLINE, Embase, and CENTRAL were searched on May 26, 2022, for randomized controlled trials [RCTs] of pharmacological therapy in adults with fistulizing CD. The primary outcome was induction and maintenance of fistula response. Pooled risk ratios [RRs] and 95% confidence intervals [CIs] were calculated. GRADE was used to assess the certainty of evidence. Results Thirty-eight RCTs were included. Nineteen trials [50%] exclusively involved perianal fistula. The remaining studies included some participants with non-perianal fistula. Pooled RRs for anti-tumour necrosis factor [TNF] agents were not statistically significant for induction [RR 1.36, 95% CI 0.97–1.91] or maintenance of fistula response [RR 1.48, 95% CI 0.97–2.27]. However, in a sensitivity analysis of studies with fistula response as the primary outcome, anti-TNFs were superior to placebo for induction [RR 1.94, 95% CI 1.10–3.41] and maintenance [RR 1.88, 95% CI 1.23–2.88] of fistula response. Oral small molecules [RR 2.56, 95% CI 1.18–5.53] and mesenchymal stem cell [MSC] therapy [RR 1.26, 95% CI 1.01–1.57] were effective for induction of fistula response. Ustekinumab was associated with maintenance of fistula response [RR 1.80, 95% CI 1.04–3.11]. Vedolizumab was not superior to placebo. The certainty of evidence ranged from very low to moderate. Conclusion Very low- to moderate-certainty evidence suggests that anti-TNF therapy, oral small molecules, ustekinumab, and MSCs are effective for perianal fistulizing CD. Dedicated fistula studies evaluating biologics and small molecules are needed. [ABSTRACT FROM AUTHOR]

The negative impact of vacant and abandoned housing in city neighborhoods is extreme, affecting health and quality of life, promoting violence, and leading to further abandonment. One approach to addressing abandoned housing is to intervene with low-cost interventions that provide a visual sense of ownership. We tested whether a low-cost remediation of abandoned and vacant houses or a trash cleanup intervention would make a noticeable difference in the levels of nearby disrepair, disorder, and public safety. The abandoned housing remediation and trash cleanup interventions were a test of compliance with municipal ordinances. We used an experimental design to test the causal effects of the ordinances and because the scale of abandonment was too large to provide treatment to all abandoned houses in the city. We used systematic social observation methods to rate changes in disrepair, disorder, and litter at housing sites and on the city blocks they were located and police-reported data on gun violence and illegal substance use. Our experimental design allowed us to see whether observed disrepair, disorder, and public safety improved after working windows and doors were installed on abandoned houses compared with a trash cleanup around properties or a no-intervention control condition. Our results showed significant changes in observed disrepair, disorder, and gun violence and illustrate the benefits of experimental evaluations of place-based changes to the built environment. Improving compliance with ordinances to remediate abandoned housing can make a noticeable difference in disrepair in neighborhoods and contribute to improved public safety. We illustrate how planners can use field experiments in partnership with city agencies, nonprofit community groups, and local universities to discover novel approaches to advance place-based changes to the built environment that can help economically disadvantaged communities abate problems of physical disorder. [ABSTRACT FROM AUTHOR]