CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues.

BACKGROUND: Cis-regulatory elements (CREs) play a pivotal role in gene expression regulation, allowing cells to serve diverse functions and respond to external stimuli. Understanding CREs is essential for personalized medicine and disease research, as an increasing number of genetic variants associated with phenotypes and diseases overlap with CREs. However, existing databases often focus on subsets of regulatory elements and present each identified instance of element individually, confounding the effort to obtain a comprehensive view. To address this gap, we have created CREdb, a comprehensive database with over 10 million human regulatory elements across 1,058 cell types and 315 tissues harmonized from different data sources. We curated and aligned the cell types and tissues to standard ontologies for efficient data query. RESULTS: Data from 11 sources were curated and mapped to standard ontological terms. 11,223,434 combined elements are present in the final database, and these were merged into 5,666,240 consensus elements representing the combined ranges of the individual elements informed by their overlap. Each consensus element contains curated metadata including the number of elements supporting it and a hash linking to the source databases. The inferred activity of each consensus element in various cell-type and tissue context is also provided. Examples presented here show the potential utility of CREdb in annotating non-coding genetic variants and informing chromatin accessibility profiling analysis. CONCLUSIONS: We developed CREdb, a comprehensive database of CREs, to simplify the analysis of CREs by providing a unified framework for researchers. CREdb compiles consensus ranges for each element by integrating the information from all instances identified across various source databases. This unified database facilitates the functional annotation of non-coding genetic variants and complements chromatin accessibility profiling analysis. CREdb will serve as an important resource in expanding our knowledge of the epigenome and its role in human diseases.

SARS-CoV-2 viral load assessment in respiratory samples.

Real-time reverse transcriptase polymerase chain reaction (rRTPCR) has been the main method for diagnosis of SARS-CoV-2 infection in the early stages of the COVID-19 pandemic. De-identified results from upper and lower respiratory samples submitted to a reference laboratory demonstrated a positivity rate of 14.9 % (4428 of 29,713 samples tested). Distribution of results by birth year cohort and specimen type suggested general consistency in mean, median and peak values but higher positivity rates in individuals born from 1964 to 1974. Female patients had a significantly lower positivity rate (P < 0.0001), although similar load mean and median values, compared to males. Overall, 15.3 % (676 of 4428 positive results) of positive results had viral loads greater than 8 log10 copies/mL, with occasional samples exceeding 10 log10 copies/mL. These results support quantitative assessment of SARS-CoV-2 viral load in patient testing and efforts to control viral transmission.

Management of severe traumatic flexion-distraction injuries in a multisystem trauma patient: A case report.

STUDY DESIGN: Case report and relevant literature review. OBJECTIVE: To discuss the management of severe flexion-distraction injury of the subaxial cervical spine in a multisystem trauma patient. SUMMARY OF BACKGROUND DATA: Traumatic cervical spine injury from flexion-distraction injury can cause significant instability requiring extensive instrumentation complicated by vascular and soft tissue injuries. METHODS: The medical record of a patient who suffered traumatic flexion-distraction injury was reviewed for relevant clinical and radiology data. A literature review on the management of traumatic cervical injuries was performed using the PubMed database. RESULTS: We report a case of 21-year-old woman who suffered a C5-C6 flexion-distraction injury. After she underwent anterior cervical discectomy and fusion (ACDF), her care was transferred to the senior author (S.K.) due to the severity of the distraction. The patient returned to the OR the next day and underwent removal of implants at C5 and corpectomy with anterior and posterior instrumentation. CONCLUSION: There are many ways to manage a flexion-distraction injury of the cervical spine. In a polytrauma patient, the surgical strategy can become complex. We present a surgical option with an acceptable outcome.