Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF.

Whereas oncogenes can potentially be inhibited with small molecules, the loss of tumour suppressors is more common and is problematic because the tumour-suppressor proteins are no longer present to be targeted. Notable examples include SMARCB1-mutant cancers, which are highly lethal malignancies driven by the inactivation of a subunit of SWI/SNF (also known as BAF) chromatin-remodelling complexes. Here, to generate mechanistic insights into the consequences of SMARCB1 mutation and to identify vulnerabilities, we contributed 14 SMARCB1-mutant cell lines to a near genome-wide CRISPR screen as part of the Cancer Dependency Map Project1-3. We report that the little-studied gene DDB1-CUL4-associated factor 5 (DCAF5) is required for the survival of SMARCB1-mutant cancers. We show that DCAF5 has a quality-control function for SWI/SNF complexes and promotes the degradation of incompletely assembled SWI/SNF complexes in the absence of SMARCB1. After depletion of DCAF5, SMARCB1-deficient SWI/SNF complexes reaccumulate, bind to target loci and restore SWI/SNF-mediated gene expression to levels that are sufficient to reverse the cancer state, including in vivo. Consequently, cancer results not from the loss of SMARCB1 function per se, but rather from DCAF5-mediated degradation of SWI/SNF complexes. These data indicate that therapeutic targeting of ubiquitin-mediated quality-control factors may effectively reverse the malignant state of some cancers driven by disruption of tumour suppressor complexes.

Mitotic bookmarking by SWI/SNF subunits.

For cells to initiate and sustain a differentiated state, it is necessary that a 'memory' of this state is transmitted through mitosis to the daughter cells1-3. Mammalian switch/sucrose non-fermentable (SWI/SNF) complexes (also known as Brg1/Brg-associated factors, or BAF) control cell identity by modulating chromatin architecture to regulate gene expression4-7, but whether they participate in cell fate memory is unclear. Here we provide evidence that subunits of SWI/SNF act as mitotic bookmarks to safeguard cell identity during cell division. The SWI/SNF core subunits SMARCE1 and SMARCB1 are displaced from enhancers but are bound to promoters during mitosis, and we show that this binding is required for appropriate reactivation of bound genes after mitotic exit. Ablation of SMARCE1 during a single mitosis in mouse embryonic stem cells is sufficient to disrupt gene expression, impair the occupancy of several established bookmarks at a subset of their targets and cause aberrant neural differentiation. Thus, SWI/SNF subunit SMARCE1 has a mitotic bookmarking role and is essential for heritable epigenetic fidelity during transcriptional reprogramming.

Acute prevention of a heart attack : Early identification of prodromal symptoms as the Rosetta Stone in decoding the heart attack problem.

Chest discomfort before severe chest pain represents a marker of clinical ischemia and indicates live myocardium in jeopardy and often precedes cardiac arrest or acute myocardial infarction (MI). The intermittent or "stuttering" symptoms that precede MI are referred to as "prodromal symptoms." These symptoms have been shown to correlate with cyclic ST changes and repeated episodes of spontaneous reperfusion and occlusion, occurring during a period of hours or days before the acute ischemia proceeds to death or heart damage. These symptoms of premonitory angina have been associated with improved outcomes due to ischemic pre-conditioning or opening of collateral vascular channels around the area of ischemia. Acute prevention of an MI through recognition of prodromal symptoms represents an opportunity to significantly reduce heart attack deaths. The Early Heart Attack Care (EHAC) program puts emphasis on prodromal symptom recognition and allows for a shift in time backward to prevent the ischemic process from proceeding to MI. This strategy has been shown to detect the 15% of patients with ischemia in the low-probability group and to reduce inappropriate admissions to hospital as well as to reduce the number of patients with missed MI being sent home from the emergency department.

Full-length nuclear receptor allosteric regulation.

Nuclear receptors are a superfamily of transcription factors regulated by a wide range of lipids that include phospholipids, fatty acids, heme-based metabolites, and cholesterol-based steroids. Encoded as classic two-domain modular transcription factors, nuclear receptors possess a DNA-binding domain (DBD) and a lipid ligand-binding domain (LBD) containing a transcriptional activation function. Decades of structural studies on the isolated LBDs of nuclear receptors established that lipid-ligand binding allosterically regulates the conformation of the LBD, regulating transcriptional coregulator recruitment and thus nuclear receptor function. These structural studies have aided the development of several FDA-approved drugs, highlighting the importance of understanding the structure-function relationships between lipids and nuclear receptors. However, there are few published descriptions of full-length nuclear receptor structure and even fewer descriptions of how lipids might allosterically regulate full-length structure. Here, we examine multidomain interactions based on the published full-length nuclear receptor structures, evaluating the potential of interdomain interfaces within these nuclear receptors to act as inducible sites of allosteric regulation by lipids.

Metoclopramide Nasal Spray in Women with Symptomatic Diabetic Gastroparesis: A Randomized, Double-Blind, Placebo-Controlled Phase 3 Study.

BACKGROUND & AIMS: Metoclopramide nasal spray (MNS) was developed as an alternative to oral metoclopramide. Prior phase 2 studies demonstrated efficacy in reducing symptoms in women, but not men with diabetic gastroparesis. The aim of this phase 3 study was to further determine the safety and efficacy of MNS compared with placebo in reducing symptoms of diabetic gastroparesis in women. METHODS: This US multicenter, randomized, double-blind, parallel group study enrolled women aged 18-75 years with diabetic gastroparesis and delayed gastric emptying. Subjects were randomized 1:1 to receive placebo or MNS 10 mg. The primary efficacy end point was change in mean daily Gastroparesis Symptom Assessment total score from baseline to Week 4. The Gastroparesis Symptom Assessment daily diary is a validated patient-reported outcome instrument that averages scores of nausea, early satiety, prolonged fullness, bloating, and upper abdominal pain on a 5-point ordinal scale. RESULTS: Two hundred and five subjects were randomized to receive placebo (n = 103) or MNS (n = 102). Overall, the MNS group did not experience a significant reduction in symptoms compared with the placebo group from baseline to Week 4 (P = .881). However, subjects with moderate-to-severe symptoms at baseline had a significant treatment effect from Weeks 1 to 3 (P < .05) and experienced a significant reduction in nausea and upper abdominal pain for all 4 weeks versus placebo (P < .05). Treatment-emergent adverse events were primarily mild to moderate with headache and abdominal pain reported most frequently. CONCLUSIONS: Although the primary end point was not met using all enrolled patients, treatment with MNS provided significant relief for women with moderate-to-severe diabetic gastroparesis symptoms. MNS was well tolerated and demonstrated a similar safety profile to placebo. (ClinicalTrials.gov identifier: NCT02025725.).

Increased Fellow Scholarly Publication Rate After Implementation of a Comprehensive Research Curriculum and Milestone-Based Research Timeline for Pediatric Emergency Medicine Fellows.

OBJECTIVE: Pediatric subspecialty fellows are required to complete a scholarly product during training; however, many do not bring the work to publication. To amplify our fellows' publication success, our pediatric emergency medicine fellowship program implemented a comprehensive research curriculum and established a milestone-based research timeline for each component of a project. Our objective was to assess whether these interventions increased the publication rate and enhanced the graduated fellows' perceived ability to perform independent research. METHODS: Our study was conducted at a tertiary children's hospital affiliated with an academic university, enrolling 3 fellows each year in its pediatric emergency medicine program. A comprehensive research curriculum and a milestone-based research timeline were implemented in 2011. We analyzed the publication rate of our graduating fellows before (2004-2011) and after (2012-2016) our intervention. In addition, in 2017 we surveyed our previous fellows who graduated from 2004 to 2016 and analyzed factors favoring manuscript publication and confidence with various research skills. RESULTS: During the study period, 38 trainees completed the fellowship program. Publication rate increased from 26% ± 17% to 87% ± 30 % ( P < 0.05). When scoring the importance of various factors, fellows most valued mentorship (5 ± 0 vs 4.3 ± 1.0, P < 0.05, postintervention vs preintervention) for the completion of the fellowship study and manuscript. Fellows after the intervention reported greater confidence in performing an analysis of variance (89% vs 36%, odds ratio, 6.3; 95% confidence interval, 1.4-150.1). CONCLUSIONS: Implementation of a comprehensive research curriculum and a milestone-based research timeline was associated with an increase in the publication rate within 3 years of graduation of our pediatric emergency medicine fellows. After implementation, fellows reported an increased importance of mentorship and greater confidence in performing an analysis of variance. We provide a comprehensive curriculum and a research timeline that may serve as a model for other fellowship programs.

Vaping-Induced Proteolysis Causes Airway Surface Dehydration.

Proteases such as neutrophil elastase cleave and activate the epithelial sodium channel (ENaC), causing airway dehydration. Our current study explores the impact of increased protease levels in vapers' airways on ENaC activity and airway dehydration. Human bronchial epithelial cultures (HBECs) were exposed to bronchoalveolar lavage fluid (BALF) from non-smokers, smokers and vapers. Airway surface liquid (ASL) height was measured by confocal microscopy as a marker of hydration. ENaC cleavage was measured by Western blotting. Human peripheral blood neutrophils were treated with a menthol-flavored e-liquid (Juul), and the resulting secretions were added to HBECs. BALF from smokers and vapers significantly and equally increased ENaC activity and decreased ASL height. The ASL height decrease was attenuated by protease inhibitors. Non-smokers' BALF had no effect on ENaC or ASL height. BALF from smokers and vapers, but not non-smokers, induced ENaC cleavage. E-liquid-treated neutrophil secretions cleaved ENaC and decreased ASL height. Our study demonstrated that elevated protease levels in vapers' airways have functional significance since they can activate ENaC, resulting in airway dehydration. Lung dehydration contributes to diseases like cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD) and asthma. Thus, our data predict that vaping, like smoking, will cause airway surface dehydration that likely leads to lung disease.

From UAV to PlanetScope: Upscaling fractional cover of an invasive species Rosa rugosa.

Invasive plant species pose a direct threat to biodiversity and ecosystem services. Among these, Rosa rugosa has had a severe impact on Baltic coastal ecosystems in recent decades. Accurate mapping and monitoring tools are essential to quantify the location and spatial extent of invasive plant species to support eradication programs. In this paper we combined RGB images obtained using an Unoccupied Aerial Vehicle, with multispectral PlanetScope images to map the extent of R. rugosa at seven locations along the Estonian coastline. We used RGB-based vegetation indices and 3D canopy metrics in combination with a random forest algorithm to map R. rugosa thickets, obtaining high mapping accuracies (Sensitivity = 0.92, specificity = 0.96). We then used the R. rugosa presence/absence maps as a training dataset to predict the fractional cover based on multispectral vegetation indices derived from the PlanetScope constellation and an Extreme Gradient Boosting algorithm (XGBoost). The XGBoost algorithm yielded high fractional cover prediction accuracies (RMSE = 0.11, R2 = 0.70). An in-depth accuracy assessment based on site-specific validations revealed notable differences in accuracy between study sites (highest R2 = 0.74, lowest R2 = 0.03). We attribute these differences to the various stages of R. rugosa invasion and the density of thickets. In conclusion, the combination of RGB UAV images and multispectral PlanetScope images is a cost-effective method to map R. rugosa in highly heterogeneous coastal ecosystems. We propose this approach as a valuable tool to extend the highly local geographical scope of UAV assessments into wider areas and regional evaluations.

Chronic E-Cigarette Exposure Alters Human Alveolar Macrophage Morphology and Gene Expression.

INTRODUCTION: Alveolar macrophages (AMs) are lung-resident immune cells that phagocytose inhaled particles and pathogens, and help coordinate the lung's immune response to infection. Little is known about the impact of chronic e-cigarette use (ie, vaping) on this important pulmonary cell type. Thus, we determined the effect of vaping on AM phenotype and gene expression. AIMS AND METHODS: We recruited never-smokers, smokers, and e-cigarette users (vapers) and performed research bronchoscopies to isolate AMs from bronchoalveolar lavage fluid samples and epithelial cells from bronchial brushings. We then performed morphological analyses and used the Nanostring platform to look for changes in gene expression. RESULTS: AMs obtained from smokers and vapers were phenotypically distinct from those obtained from nonsmokers, and from each other. Immunocytochemistry revealed that vapers AMs had significantly elevated inducible nitric oxide synthase (M1) expression and significantly reduced CD301a (M2) expression compared with nonsmokers or smokers. Vapers' AMs and bronchial epithelia exhibited unique changes in gene expression compared with nonsmokers or smokers. Moreover, vapers' AMs were the most affected of all groups and had 124 genes uniquely downregulated. Gene ontology analysis revealed that vapers and smokers had opposing changes in biological processes. CONCLUSIONS: These data indicate that vaping causes unique changes to AMs and bronchial epithelia compared with nonsmokers and smokers which may impact pulmonary host defense. IMPLICATIONS: These data indicate that normal "healthy" vapers have altered AMs and may be at risk of developing abnormal immune responses to inflammatory stimuli.

Brief resolved unexplained events: a new diagnosis, with implications for evaluation and management.

Brief resolved unexplained events (BRUE) are concerning episodes of short duration (typically < 1 min) characterized by a change in breathing, consciousness, muscle tone (hyper- or hypotonia), and/or skin color (cyanosis or pallor). The episodes occur in a normal-appearing infant in the first year of life, self-resolve, and have no readily identifiable explanation for the cause of the event. Previously called apparent life-threatening events (ALTE), the term BRUE was first defined by the American Academy of Pediatrics (AAP) in 2016. The criteria for BRUE carry greater specificity compared to that of ALTE and additionally are indicative of a diagnosis of exclusion. While most patients with BRUE will have a benign clinical course, important etiologies, including airway, cardiac, gastrointestinal, genetic, infectious, neurologic, and traumatic conditions (including nonaccidental), must be carefully considered. A BRUE is classified as either lower- or higher-risk based on patient age, corrected gestational age, event duration, number of events, and performance of cardiopulmonary resuscitation at the scene. The AAP clinical practice guideline provides recommendations for the management of lower-risk BRUEs, advocating against routine admission, blood testing, and imaging for infants with these events, though a short period of observation and/or an electrocardiogram may be advisable. While guidance exists for higher-risk BRUE, more data are required to better identify proportions and risk factors for serious outcomes among these patients. Conclusion: BRUE is a diagnosis with greater specificity relative to prior definitions and is now a diagnosis of exclusion. Additional research is needed, particularly in the evaluation of higher-risk events. Recent data suggest that the AAP guidelines for the management of lower-risk infants can be safely implemented.This review article summarizes the history, definitional changes, current guideline recommendations, and future research needs for BRUE. What is Known: • BRUE, first described in 2016, is a diagnosis used to describe a well-appearing infant who presents with change in breathing, consciousness, muscle tone (hyper- or hypotonia), and/or skin color (cyanosis or pallor). • BRUE can be divided into higher- and lower-risk events. Guidelines have been published for lower-risk events, with expert recommendations for higher-risk BRUE. What is New: • BRUE carries a low rate of serious diagnoses (< 5%), with the most common representing seizures and airway abnormalities. • Prior BRUE events are associated with serious diagnoses and episode recurrence.

Trimethylamine N-oxide (TMAO): a new attractive target to decrease cardiovascular risk.

Cardiovascular disease (CVD) is one of the greatest disease burdens and takes the lives of many each year. There are many risk factors both modifiable and non-modifiable which contribute to the onset and progression of the disease. Trimethylamine N-oxide (TMAO) in recent years has been found to have a correlation with CVD onset. Those with increased levels of the metabolite have a markedly increased risk of future development of cardiometabolic disorders.This literature review aimed to critique past studies undertaken to find a consensus of the significance of the interrelationship between TMAO and cardiovascular risk. A definite link between TMAO levels and a CVD outcome was found. The majority of the literature stated the relationship with evidence; however, there is still some uncertainty as to why and how the correlation occurs. Further study needs to be done to further dissect and understand the relationship between TMAO and CVD risk.

ISCCM Guidelines on Acute Kidney Injury and Renal Replacement Therapy.

Acute kidney injury (AKI) is a complex syndrome with a high incidence and considerable morbidity in critically ill patients. Renal replacement therapy (RRT) remains the mainstay of treatment for AKI. There are at present multiple disparities in uniform definition, diagnosis, and prevention of AKI and timing of initiation, mode, optimal dose, and discontinuation of RRT that need to be addressed. The Indian Society of Critical Care Medicine (ISCCM) AKI and RRT guidelines aim to address the clinical issues pertaining to AKI and practices to be followed for RRT, which will aid the clinicians in their day-to-day management of ICU patients with AKI. How to cite this article: Mishra RC, Sodhi K, Prakash KC, Tyagi N, Chanchalani G, Annigeri RA, et al. ISCCM Guidelines on Acute Kidney Injury and Renal Replacement Therapy. Indian J Crit Care Med 2022;26(S2):S13-S42.

Competencies for Point-of-care Ultrasonography in ICU: An ISCCM Expert Panel Practice Recommendation.

How to cite this article: Srinivasan S, Kumar PG, Govil D, Gupta S, Kumar V, Pichamuthu K, et al. Competencies for Point-of-care Ultrasonography in ICU: An ISCCM Expert Panel Practice Recommendation. Indian J Crit Care Med 2022;26(S2):S7-S12.

The acyl chains of phosphoinositide PIP3 alter the structure and function of nuclear receptor steroidogenic factor-1.

Nuclear receptors are transcription factors that bind lipids, an event that induces a structural conformation of the receptor that favors interaction with transcriptional coactivators. The nuclear receptor steroidogenic factor-1 (SF-1, NR5A1) binds the signaling phosphoinositides PI(4,5)P2 (PIP2) and PI(3,4,5)P3 (PIP3), and our previous crystal structures showed how the phosphoinositide headgroups regulate SF-1 function. However, what role the acyl chains play in regulating SF-1 structure remains unaddressed. Here, we used X-ray crystallography with in vitro binding and functional assays to examine how the acyl chains of PIP3 regulate human SF-1 ligand-binding domain structure and function. Altering acyl chain length and unsaturation regulates apparent binding of all tested phosphoinositides to SF-1. Mass spectrometry-based lipidomics data suggest C16 and C18 phospholipids preferentially associate with SF-1 expressed ectopically in bacteria. We then solved the 2.5 Å crystal structure of SF-1 bound to dioleoyl PIP3(18:1/18:1) to compare it with a matched structure of SF-1 bound to dipalmitoyl PIP3(16:0/16:0). The dioleoyl-bound structure was severely disordered in a specific SF-1 region associated with pathogenic human polymorphisms and within the coactivator-binding region critical for SF-1 function while inducing increased sensitivity to protease digestion in solution. Validating these structural observations, in vitro functional studies showed dioleoyl PIP3 induced 6-fold poorer affinity of a peroxisome proliferator-activated receptor gamma coactivator 1-alpha coactivator peptide for SF-1 compared with dipalmitoyl PIP3. Together, these data suggest the chemical nature of the phosphoinositide acyl chains controls the ordered state of specific, clinically important structural regions in SF-1, regulating SF-1 function in vitro.

Alternative methods of viability determination in single cell mass cytometry.

The identification and discrimination of viable cells is important to understand how experimental variables may influence biochemical processes such as cell metabolism, cell cycle, and signaling pathways. Cisplatin is commonly used as a viability stain in mass cytometry studies, however, recent work by Mei et al. has demonstrated that cisplatin can also be used to label antibodies, complicating the simultaneous use of the platinum measurement channels for both antibody and viability staining. This study demonstrates that other metal salts (hafnium chloride, niobium chloride, and zirconium chloride) can serve as substitutes for cisplatin in viability staining. These stains yield similar fractions of live and dead cells and stain the same dead cells in parallel high parameter analyses. In addition, this study demonstrates how a variety of protein antigen viability markers (pRb, Ki-67, Histone H1, cleaved PARP, and GAPDH) can be used to discriminate live and dead cell populations, without the need for a separate viability staining step. As few as two of these protein antigen viability markers can help identify live and dead cell populations in fixed samples and can identify the same viable cells in high dimensional analyses with or without use of viability stain information. This study demonstrates several alternative approaches to mass cytometry viability assessment that can facilitate use of platinum isotopes for antibody staining and enables identification of live and dead cell populations in samples for which a separate viability stain is not practical.

A phase Ib open-label dose escalation study of the safety, pharmacokinetics, and pharmacodynamics of cobimetinib (GDC-0973) and ipatasertib (GDC-0068) in patients with locally advanced or metastatic solid tumors.

BACKGROUND: This Phase Ib study explored combination dosing of the allosteric MEK1/2 inhibitor cobimetinib and the ATP-competitive pan-AKT inhibitor ipatasertib. METHODS: Patients with advanced solid tumors were enrolled to two dose escalation arms, each using a 3 + 3 design in 28-day cycles. In Arm A, patients received concurrent cobimetinib and ipatasertib on days 1-21. In Arm B, cobimetinib was administered intermittently with ipatasertib for 21 days. Primary objectives evaluated dose-limiting toxicities (DLTs), maximum tolerated doses (MTD), and the recommended Phase II dose (RP2D). Secondary objectives included analysis of pharmacokinetic parameters, MAPK and PI3K pathway alterations, changes in tissue biomarkers, and preliminary anti-tumor efficacy. Expansion cohorts included patients with PTEN-deficient triple-negative breast cancer and endometrial cancer. RESULTS: Among 66 patients who received ≥1 dose of study drug, all experienced an adverse event (AE). Although no DLTs were reported, 6 patients experienced Cycle 1 DLT-equivalent AEs. The most common treatment-related AEs were diarrhea, nausea, vomiting, dermatitis acneiform, and fatigue. Thirty-five (53%) patients experienced drug-related AEs of ≥ grade 3 severity. Cobimetinb/ipatasertib MTDs were 60/200 mg on Arm A and 150/300 mg on Arm B; the latter was chosen as the RP2D. No pharmacokinetic interactions were identified. Biomarker analyses indicated pathway blockade and increases in IFNγ and PD-L1 gene expression following the combination. Three patients with endometrial or ovarian cancer achieved partial response, all with PTEN-low disease and two with tumor also harboring KRAS mutation. CONCLUSION: There was limited tolerability and efficacy for this MEK and AKT inhibitor combination. Nonetheless, pharmacodynamic analyses indicated target engagement and suggest rationale for further exploration of cobimetinib or ipatasertib in combination with other anticancer agents. ClinicalTrials.gov identifier: NCT01562275.

Early Antibiotic Administration Is Associated with a Reduced Infection Risk When Combined with Primary Wound Closure in Patients with Open Tibia Fractures.

BACKGROUND: Early administration of antibiotics and wound coverage have been shown to decrease the deep infection risk in all patients with Type 3 open tibia fractures. However, it is unknown whether early antibiotic administration decreases infection risk in patients with Types 1, 2, and 3A open tibia fractures treated with primary wound closure. QUESTIONS/PURPOSES: (1) Does decreased time to administration of the first dose of antibiotics decrease the deep infection risk in all open tibia fractures with primary wound closure? (2) What patient demographic factors are associated with an increased deep infection risk in Types 1, 2, and 3A open tibia fractures with primary wound closure? METHODS: We identified 361 open tibia fractures over a 5-year period at a Level I regional trauma center that receives direct admissions and transfers from other hospitals which produces large variation in the timing of antibiotic administration. Patients were excluded if they were younger than 18 years, had associated plafond or plateau fractures, associated with compartment syndrome, had a delay of more than 24 hours from injury to the operating room, underwent repeat débridement procedures, had incomplete data, and were treated with negative-pressure dressings or other adjunct wound management strategies that would preclude primary closure. Primary closure was at the descretion of the treating surgeon. We included patients with a minimum follow-up of 6 weeks with assessment at 6 months and 12 months. One hundred forty-three patients with were included in the analysis. Our primary endpoint was deep infection as defined by the CDC criteria. We obtained chronological data, including the time to the first dose of antibiotics and time to surgical débridement from ambulance run sheets, transferring hospital records, and the electronic medical record to answer our first question. We considered demographics, American Society of Anesthesiologists classification, mechanism of injury, smoking status, presence of diabetes, and Injury Severity Score in our analysis of other factors. These were compared using one-way ANOVA, chi-square, or Fisher's exact tests. Binary regression was used to to ascertain whether any factors were associated with postoperative infection. Receiver operator characteristic curves were used to identify threshold values. RESULTS: Increased time to first administration of antibiotics was associated with an increased infection risk in patients who were treated with primary wound closure; the greatest inflection point on that analysis occurred at 150 minutes, when the increased infection risk was greatest (20% [8 of 41] versus 4% [3 of 86]; odds ratio 5.6 [95% CI 1.4 to 22.2]; p = 0.01). After controlling for potential confounding variables like age, diabetes and smoking status, none of the variables we evaluated were associated with an increased risk of deep infection in Type 1, 2, and 3A open tibia fractures in patients treated with primary wound closure. CONCLUSION: Our findings suggest that in open tibia fractures, which receive timely antibiotic administration, primary wound closure is associated with a decreased infection risk. We recognize that more definitive studies need to be performed to confirm these findings and confirm feasibility of early antibiotic administration, especially in the pre-hospital context. LEVEL OF EVIDENCE: Level III, therapeutic study.

Procalcitonin (in COVID-19): The Incessant Quest.

How to cite this article: Savio RD. Procalcitonin (in COVID-19): The Incessant Quest. Indian J Crit Care Med 2021;25(1):1-2.

Detection of long repeat expansions from PCR-free whole-genome sequence data.

Identifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step toward integrating WGS into precision medicine. We developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2786/2789, 95% CI [0.997, 1.00]) of the wild-type samples were correctly classified as wild type by this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a set of 152 samples in which every sample had one of eight different pathogenic repeat expansions, including those associated with fragile X syndrome, Friedreich's ataxia, and Huntington's disease, and correctly flagged all but one of the known repeat expansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions.