Src- and Abl-family kinases activate spleen tyrosine kinase to maximize phagocytosis and Leishmania infection.

Leishmania spp. are obligate intracellular parasites that must be internalized by phagocytic cells to evade immune responses and cause disease. The uptake of both Leishmania promastigotes (insect-stage parasites) and amastigotes (proliferative-stage parasites in humans and mice) by phagocytes is thought to be mainly host cell driven, not parasite driven. Our previous work indicates that host Src- and Abl-family kinases facilitate Leishmania entry into macrophages and pathogenesis in murine cutaneous leishmaniasis. Here, we demonstrate that host spleen tyrosine kinase (SYK) is required for efficient uptake of Leishmania promastigotes and amastigotes. A Src-family kinase-Abl-family kinase-SYK signaling cascade induces Leishmania amastigote internalization. Finally, lesion size and parasite burden during Leishmania infection is significantly decreased in mice lacking SYK in monocytes or by treatment with the SYK inhibitor entospletinib. In summary, SYK is required for maximal Leishmania uptake by macrophages and disease in mice. Our results suggest potential for treating leishmaniasis using host cell-directed agents.

Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks.

BACKGROUND: Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of cellular processes in diseases such as cancer, although the functions of most remain poorly understood. To address this, here we apply a novel strategy to integrate gene expression profiles across 32 cancer types, and cluster human lncRNAs based on their pan-cancer protein-coding gene associations. By doing so, we derive 16 lncRNA modules whose unique properties allow simultaneous inference of function, disease specificity and regulation for over 800 lncRNAs. RESULTS: Remarkably, modules could be grouped into just four functional themes: transcription regulation, immunological, extracellular, and neurological, with module generation frequently driven by lncRNA tissue specificity. Notably, three modules associated with the extracellular matrix represented potential networks of lncRNAs regulating key events in tumour progression. These included a tumour-specific signature of 33 lncRNAs that may play a role in inducing epithelial-mesenchymal transition through modulation of TGFß signalling, and two stromal-specific modules comprising 26 lncRNAs linked to a tumour suppressive microenvironment and 12 lncRNAs related to cancer-associated fibroblasts. One member of the 12-lncRNA signature was experimentally supported by siRNA knockdown, which resulted in attenuated differentiation of quiescent fibroblasts to a cancer-associated phenotype. CONCLUSIONS: Overall, the study provides a unique pan-cancer perspective on the lncRNA functional landscape, acting as a global source of novel hypotheses on lncRNA contribution to tumour progression.

Genome-Wide Analysis of Circulating Cell-Free DNA Copy Number Detects Active Melanoma and Predicts Survival.

BACKGROUND: A substantial number of melanoma patients develop local or metastatic recurrence, and early detection of these is vital to maximise benefit from new therapies such as inhibitors of BRAF and MEK, or immune checkpoints. This study explored the use of novel DNA copy-number profiles in circulating cell-free DNA (cfDNA) as a potential biomarker of active disease and survival. PATIENTS AND METHODS: Melanoma patients were recruited from oncology and dermatology clinics in Sheffield, UK, and cfDNA was isolated from stored blood plasma. Using low-coverage whole-genome sequencing, we created copy-number profiles from cfDNA from 83 melanoma patients, 44 of whom had active disease. We used scoring algorithms to summarize copy-number aberrations and investigated their utility in multivariable logistic and Cox regression analyses. RESULTS: The copy-number aberration score (CNAS) was a good discriminator of active disease (odds ratio, 3.1; 95% CI, 1.5-6.2; P = 0.002), and CNAS above or below the 75th percentile remained a significant discriminator in multivariable analysis for active disease (P = 0.019, with area under ROC curve of 0.90). Additionally, mortality was higher in those with CNASs above the 75th percentile than in those with lower scores (HR, 3.4; 95% CI, 1.5-7.9; P = 0.005), adjusting for stage of disease, disease status (active or resected), BRAF status, and cfDNA concentration. CONCLUSIONS: This study demonstrates the potential of a de novo approach utilizing copy-number profiling of cfDNA as a biomarker of active disease and survival in melanoma. Longitudinal analysis of copy-number profiles as an early marker of relapsed disease is warranted.

Extracellular vesicle microRNA cargo is correlated with HPV status in oropharyngeal carcinoma.

BACKGROUND: The incidence of human papilloma virus positive (HPV+ ) oropharyngeal squamous cell carcinoma (OPSCC) has increased rapidly in recent decades. These tumours have a favourable outcome compared to HPV-negative (HPV- ) OPSCC. However, HPV+ tumours are more likely to metastasise to distant sites, suggesting a difference in how these tumour subtypes interact with the metastatic niche. Extracellular vesicles (EVs) have emerged as important players in cell-to-cell communication and are a potential source of biomarkers for cancer diagnosis. This study aims to characterise the microRNA cargo of small EVs released by HPV+ and HPV- OPSCC cell lines. METHODS: Extracellular vesicles produced by HPV+ (SCC2 and SCC90) and HPV- (SCC72 an SCC89) OPSCC cells were characterised by tunable resistive pulse sensing (TRPS) and western blotting. RNA was extracted from EVs and analysed by small RNA sequencing. A bioinformatics approach was used to identify EV miRNA signatures associated with HPV status. RESULTS: HPV- OPSCC cells produced more EVs than HPV+ OPSCC cells. EVs were positive for the common EV markers CD63, CD9 and TSG101. Unbiased hierarchical clustering analysis of EV miRNA cargo revealed that samples clustered based on HPV status. 14 miRNA were enriched in HPV+ cell-derived EVs, whereas 19 miRNA were enriched in EVs derived from HPV- cell lines. CONCLUSIONS: Here, we identify EV miRNA signatures indicative of the HPV status of the parent cell. This may provide a platform from which to validate salivary or blood-based biomarkers with utility for early detection and stratifying risk in OPSCC patients.

Multi-omic measurement of mutually exclusive loss-of-function enriches for candidate synthetic lethal gene pairs.

BACKGROUND: Identification of synthetic lethal interactions in cancer cells could offer promising new therapeutic targets. Large-scale functional genomic screening presents an opportunity to test large numbers of cancer synthetic lethal hypotheses. Methods enriching for candidate synthetic lethal targets in molecularly defined cancer cell lines can steer effective design of screening efforts. Loss of one partner of a synthetic lethal gene pair creates a dependency on the other, thus synthetic lethal gene pairs should never show simultaneous loss-of-function. We have developed a computational approach to mine large multi-omic cancer data sets and identify gene pairs with mutually exclusive loss-of-function. Since loss-of-function may not always be genetic, we look for deleterious mutations, gene deletion and/or loss of mRNA expression by bimodality defined with a novel algorithm BiSEp. RESULTS: Applying this toolkit to both tumour cell line and patient data, we achieve statistically significant enrichment for experimentally validated tumour suppressor genes and synthetic lethal gene pairings. Notably non-reliance on genetic loss reveals a number of known synthetic lethal relationships otherwise missed, resulting in marked improvement over genetic-only predictions. We go on to establish biological rationale surrounding a number of novel candidate synthetic lethal gene pairs with demonstrated dependencies in published cancer cell line shRNA screens. CONCLUSIONS: This work introduces a multi-omic approach to define gene loss-of-function, and enrich for candidate synthetic lethal gene pairs in cell lines testable through functional screens. In doing so, we offer an additional resource to generate new cancer drug target and combination hypotheses. Algorithms discussed are freely available in the BiSEp CRAN package at http://cran.r-project.org/web/packages/BiSEp/index.html .

Unbiased Detection of Somatic Copy Number Aberrations in cfDNA of Lung Cancer Cases and High-Risk Controls with Low Coverage Whole Genome Sequencing.

Molecular profiling using low coverage whole genome sequencing of cell free DNA (cfDNA) represents a non-targeted approach to identify multiple somatic copy number alterations (SCNA) across different lung cancer subtypes. We aim to establish that SCNA can be detected in cfDNA of lung cancer cases.Standard protocols were followed to process matched cfDNA, formalin-fixed paraffin embedded (FFPE) tumour and lymphocyte DNA. Copy number profiles for cfDNA or FFPE DNA were normalised to profiles from matched lymphocyte DNA with the software CNAnorm. Technical sensitivity was determined by spiking different proportions of FFPE tumour DNA into cfDNA from controls.The median genome coverage was 0.26X (range 0.05X-0.97X). For two advanced stage cases there was a positive correlation between copy number ratio profiles of matched cfDNA and FFPE DNA (r = 0.62, p < 0.0001 and r = 0.75, p < 0.0001). There was no correlation for four advanced and two early stage cases. There were low magnitude copy number aberrations detected in high-risk controls (N = 5). We detected spiked FFPE DNA derived SCNAs with a tumour fraction as low as 10 % of cfDNA.Our preliminary results demonstrate non-invasive detection of tumour-derived copy number alterations in advanced lung cancer cases with low coverage whole genome sequencing. Clinical characteristics and treatment may influence whether SCNA are detected in cfDNA.

Statistical estimation of fatal and serious injuries saved by iRAP protocols in 74 countries.

OBJECTIVE: Road traffic crashes cause 1.19 million deaths and millions more injuries annually. The persistently high burden has drawn attention from national and international stakeholders worldwide. Unsafe road infrastructure is one of the major risk factors for traffic safety, particularly in low- and middle-income countries. METHODS: Aiming to eliminate high-risk roads in all countries, the International Road Assessment Programme (iRAP) developed a robust and evidence-based approach to support country transportation agencies. RESULTS: Thus far, the iRAP protocols have been used to collect 1.8 million kilometers of Crash Risk Mapping and 1.5 million kilometers of Star Rating and FSI estimations in 128 countries. Deploying an observational before-and-after (or pre-post) study design, this report estimated the fatal and series injuries (FSI) saved through use of the iRAP protocols. The study is based on 441,753 kilometers of assessed roads from 1,039 projects in 74 countries. Our results show that the implementation of iRAP's proposed countermeasures saves about 159,936 FSI annually. Throughout the lifetime of the implemented countermeasures, a total of 3.2 million FSI could be saved. CONCLUSION: While quantifying the success of the iRAP protocols, our results suggest an opportunity to save many millions more lives on the roads through expanding iRAP implementation to more regions and countries.

The difficult airway in trauma: What you need to know.

ABSTRACT: Airway evaluation and management is generally the first priority for treatment of trauma patients from the prehospital setting throughout their hospital stay. Delay in recognition of an airway problem, or inability to oxygenate or ventilate due to an inadequate airway, will lead to rapid death. Therefore, all clinicians involved in the care of trauma patients should have adequate knowledge of current best practices for airway evaluation and management. In addition, trauma providers should develop and maintain the skills needed to perform various airway maneuvers to establish and maintain an adequate airway. While elective airway management has the luxury of time for thorough airway evaluation, the airway management in the trauma setting does not allow this same opportunity. For this reason, all trauma airways should be presumed to be a difficult airway and teams should prepare accordingly. This review will summarize the best practices for airway evaluation and management for trauma patients from the prehospital setting through the emergency department.

Trends in prehospital cervical collar utilization in trauma patients: Closer, but not there yet.

OBJECTIVE: This study aims to assess the change in cervical spine (C-spine) immobilization frequency in trauma patients over time. We hypothesize that the frequency of unnecessary C-spine immobilization has decreased. METHODS: A retrospective chart review of adult trauma patients transported to our American College of Surgeons-verified Level I trauma center from January 1, 2014, to December 31, 2021, was performed. Emergency medical services documentation was manually reviewed to record prehospital physiology and the application of a prehospital cervical collar (c-collar). C-spine injuries were defined as cervical vertebral fractures and/or spinal cord injuries. Univariate and year-by-year trend analyses were used to assess changes in C-spine injury and immobilization frequency. RESULTS: Among 2906 patients meeting inclusion criteria, 12% sustained C-spine injuries, while 88% did not. Patients with C-spine injuries were more likely to experience blunt trauma (95% vs. 68%, p < 0.001), were older (46 years vs. 41 years, p < 0.001), and had higher Injury Severity Scores (31 vs. 18, p < 0.001). They also exhibited lower initial systolic blood pressures (108 mm Hg vs. 119 mm Hg, p < 0.001), lower heart rates (92 beats/min vs. 97 beats/min, p < 0.05), and lower Glasgow Coma Scale scores (9 vs. 11, p < 0.001). In blunt trauma, c-collars were applied to 83% of patients with C-spine injuries and 75% without; for penetrating trauma, c-collars were applied to 50% of patients with C-spine injuries and only 8% without. Among penetrating trauma patients with C-spine injury, all patients either arrived quadriplegic or did not require emergent neurosurgical intervention. The proportion of patients receiving a c-collar decreased in both blunt and penetrating traumas from 2014 to 2021 (blunt-82% in 2014 to 68% in 2021; penetrating-24% in 2014 to 6% in 2021). CONCLUSIONS: Unnecessary C-spine stabilization has decreased from 2014 to 2021. However, c-collars are still being applied to patients who do not need them, both in blunt and in penetrating trauma cases, while not being applied to patients who would benefit from them.

Nonoperative Management for Low-Grade Blunt Thoracic Aortic Injury.

BACKGROUND: Thoracic endovascular aortic repair (TEVAR) is the standard of care for the treatment of blunt thoracic aortic injury (BTAI) requiring intervention. Data suggest that low-grade BTAI (grade I [intimal tears] or grade II [intramural hematoma]) will resolve spontaneously if treated with nonoperative management (NOM) alone. There has been no comparison specifically between the use of NOM vs TEVAR for low-grade BTAI. We hypothesize that these low-grade injuries can be safely managed with NOM alone. STUDY DESIGN: Retrospective analysis of all patients with a low-grade BTAI in the Aortic Trauma Foundation Registry from 2016 to 2021 was performed. The study population was 1 primary outcome was mortality. Secondary outcomes included complications, ICU length of stay, and ventilator days. RESULTS: A total of 880 patients with BTAI were enrolled. Of the 269 patients with low-grade BTAI, 218 (81%) were treated with NOM alone (81% grade I, 19% grade II), whereas 51 (19%) underwent a TEVAR (20% grade I, 80% grade II). There was no difference in demographic or mechanism of injury in patients with low-grade BTAI who underwent NOM vs TEVAR. There was a difference in mortality between NOM alone and TEVAR (8% vs 18%, p = 0.009). Aortic-related mortality was 0.5% in the NOM group and 4% in the TEVAR group (p = 0.06). Hospital and ICU length of stay and ventilator days were not different between the 2 groups. CONCLUSIONS: NOM alone is safe and appropriate management for low-grade BTAI, with lower mortality and decreased rates of complication when compared with routine initial TEVAR.

Temporal changes in the prehospital management of trauma patients: 2014-2021.

INTRODUCTION: Aggressive prehospital interventions (PHI) in trauma may not improve outcomes compared to prioritizing rapid transport. The aim of this study was to quantify temporal changes in the frequency of PHI performed by EMS. METHODS: Retrospective chart review of adult patients transported by EMS to our trauma center from January 1, 2014 to 12/31/2021. PHI were recorded and annual changes in their frequency were assessed via year-by-year trend analysis and multivariate regression. RESULTS: Between the first and last year of the study period, the frequency of thoracostomy (6% vs. 9%, p â€‹= â€‹0.001), TXA administration (0.3% vs. 33%, p â€‹< â€‹0.001), and whole blood administration (0% vs. 20%, p â€‹< â€‹0.001) increased. Advanced airway procedures (21% vs. 12%, p â€‹< â€‹0.001) and IV fluid administration (57% vs. 36%, p â€‹< â€‹0.001) decreased. ED mortality decreased from 8% to 5% (p â€‹= â€‹0.001) over the study period. On multivariate regression, no PHI were independently associated with increased or decreased ED mortality. CONCLUSION: PHI have changed significantly over the past eight years. However, no PHI were independently associated with increased or decreased ED mortality.

Intraoperative factors associated with unplanned return to the operating room after emergent hemorrhage control surgery.

BACKGROUND: Unplanned return to the operating room (uROR) is associated with worse outcomes and increased mortality. Little is known regarding intraoperative factors associated with uROR after emergent surgery in trauma patients. The objective of this study was to identify intraoperative factors associated with uROR after emergent hemorrhage control procedures in bleeding trauma patients. METHODS: We used anesthetic record of intraoperative management to perform a retrospective study (2017-2022) of bleeding trauma patients who were taken for an emergent hemorrhage control operation. RESULTS: A total of 225 patients met the inclusion criteria, 46 (20%) had uROR, and 181 (80%) did not. While there was no difference in demographics, mechanism, admission physiology, or time from emergency department to operating room, the uROR patients had a higher Injury Severity Score (30 vs. 25, p = 0.007). While there was no difference in volume of crystalloid infused (3,552 ± 2,279 mL vs. 2,977 ± 2,817 mL, p = 0.20), whole blood (2.2 ± 0.9 vs. 2.0 ± 0.5, p = 0.20), or platelets (11.6 ± 8.6 vs. 9.2 ± 9.0, p = 0.14), the uROR group received more packed red blood cells (11.5 ± 10.6 vs. 7.8 ± 7.5, p = 0.006) and plasma (9.6 ± 8.3 vs. 6.5 ± 6.6, p = 0.01), and more uROR patients received ≥10 U of packed red blood cells (48% vs. 27%, p = 0.006). Damage-control surgery (DCS) was more common in uROR patients (78% vs. 45%, p < 0.0001). After logistic regression, ≥10 U of packed cells in the operating room (4.3 [1.5-12.8], p = 0.009), crystalloid (1.0 [1.0-1.001], p = 0.009), International Normalized Ratio (INR) (7.6 [1.3-45.7], p = 0.03), and DCS (5.7 [1.7-19.1], p = 0.005) were independently associated with uROR. CONCLUSION: Massive transfusion, crystalloid resuscitation, persistent coagulopathy, and DCS are the most significant risk factors for uROR. During hemorrhage control surgery in bleeding trauma patients who receive ≥10 U of blood, providers must maintain a keen focus on minimizing crystalloid and ongoing balanced resuscitation, particularly during damage-control procedures. LEVEL OF EVIDENCE: Retrospective/Descriptive; Level IV.

Structural Racism, Residential Segregation, and Exposure to Trauma: The Persistent Impact of Redlining.

INTRODUCTION: As part of New Deal era federal housing policy, the Home Owners Loan Corporation (HOLC) developed maps grading US neighborhoods by perceived financial security. Neighborhoods with high concentrations of racial and ethnic minorities were deemed financially unstable and denied federal investment, a practice colloquially known as redlining. The aim of this study was to assess the association of historical redlining within Austin, Texas to spatial patterns of penetrating traumatic injury. METHODS: Retrospective cross sectional study utilizing data from violent penetrating trauma admissions between January 1, 2014 - December 31, 2021, at the single Level 1 trauma center in Austin, Texas. Using ArcGIS, addresses where the injury took place were geocoded and spatial joining was used to match them to their corresponding census tract, for which 1935 HOLC financial designations are classified as: "Hazardous", "Definitely Declining", "Still Desirable", "Best", or "Non HOLC Graded". Tracts with designations of "Hazardous" and "Definitely Declining" were categorized as Redlined. The adjusted incidence rate ratio comparing rates of penetrating trauma among historically Redlined vs. Not Redlined and Not Graded census tracts was calculated. RESULTS: 1,404 violent penetrating trauma admissions were identified for the study period, of which 920 occurred within the county of interest. Among these, 5% occurred in census tracts that were Not Redlined, 13% occurred in Redlined tracts, and 82% occurred in non HOLC graded tracts. When adjusting for differences in current census tract demographics and social vulnerability, historically Redlined areas experienced a higher rate of penetrating traumatic injury (Not Redlined IRR = 0.42, 95% CI 0.19-0.94, p = 0.03; Not Graded IRR = 0.15, 95% CI 0.07-0.29, p < 0.001). CONCLUSIONS: Neighborhoods unfavorably classified by HOLC in 1935 continue to experience a higher incidence rate of violent penetrating trauma today. These results underscore the persistent impacts of structural racism and of historical residential segregation policies on exposure to trauma. LEVEL OF EVIDENCE: Level IV, Prognostic and Epidemiological.

When is it safe to start venous thromboembolism prophylaxis after blunt solid organ injury? A prospective American Association for the Surgery of Trauma multi-institutional trial.

BACKGROUND: The optimal time to initiate venous thromboembolism (VTE) chemoprophylaxis (VTEp) after blunt solid organ injury remains controversial, as VTE mitigation must be balanced against bleeding promulgation. Evidence from primarily small, retrospective, single-center work suggests that VTEp ≤48 hours is safe and effective. This study was undertaken to validate this clinical practice. METHODS: Blunt trauma patients presenting to 19 participating trauma centers in North America were screened over a 1-year study period beginning between August 1 and October 1, 2021. Inclusions were age older than 15 years; ≥1 liver, spleen, or kidney injury; and initial nonoperative management. Exclusions were transfers, emergency department death, pregnancy, and concomitant bleeding disorder/anticoagulation/antiplatelet medication. A priori power calculation stipulated the need for 1,158 patients. Time of VTEp initiation defined study groups: Early (≤48 hours of admission) versus Late (>48 hours). Bivariate and multivariable analyses compared outcomes. RESULTS: In total, 1,173 patients satisfied the study criteria with 571 liver (49%), 557 spleen (47%), and 277 kidney injuries (24%). The median patient age was 34 years (interquartile range, 25-49 years), and 67% (n = 780) were male. The median Injury Severity Score was 22 (interquartile range, 14-29) with Abbreviated Injury Scale Abdomen score of 3 (interquartile range, 2-3), and the median American Association for the Surgery of Trauma grade of solid organ injury was 2 (interquartile range, 2-3). Early VTEp patients (n = 838 [74%]) had significantly lower rates of VTE (n = 28 [3%] vs. n = 21 [7%], p = 0.008), comparable rates of nonoperative management failure (n = 21 [3%] vs. n = 12 [4%], p = 0.228), and lower rates of post-VTEp blood transfusion (n = 145 [17%] vs. n = 71 [23%], p = 0.024) when compared with Late VTEp patients (n = 301 [26%]). Late VTEp was independently associated with VTE (odd ratio, 2.251; p = 0.046). CONCLUSION: Early initiation of VTEp was associated with significantly reduced rates of VTE with no increase in bleeding complications. Venous thromboembolism chemoprophylaxis initiation ≤48 hours is therefore safe and effective and should be the standard of care for patients with blunt solid organ injury. LEVEL OF EVIDENCE: Therapeutic and Care Management; Level III.

Racial and Ethnic Disparity in Prehospital Pain Management for Trauma Patients.

BACKGROUND: Although evidence suggests that racial and ethnic minority (REM) patients receive inadequate pain management in the acute care setting, it remains unclear whether these disparities also occur during the prehospital period. The aim of this study is to assess the impact of race and ethnicity on prehospital analgesic use by emergency medical services (EMS) in trauma patients. STUDY DESIGN: Retrospective chart review of adult trauma patients aged 18 to 89 years old transported by EMS to our American College of Surgeons-verified level 1 trauma center from 2014 to 2020. Patients who identified as Black, Asian, Native American, or Other for race and/or Hispanic or Latino or Unknown for ethnicity were considered REM. Patients who identified as White, non-Hispanic were considered White. Groups were compared in univariate and multivariate analysis. The primary outcome was prehospital analgesic administration. RESULTS: A total of 2,476 patients were transported by EMS (47% White and 53% REM). White patients were older on average (46 years vs 38 years; p < 0.001) and had higher rates of blunt trauma (76% vs 60%; p < 0.001). There were no differences in Injury Severity Score (21 vs 20; p = 0.22). Although REM patients reported higher subjective pain rating (7.2 vs 6.6; p = 0.002), they were less likely to get prehospital pain medication (24% vs 35%; p < 0.001), and that difference remained significant after controlling for baseline characteristics, transport method, pain rating, prehospital hypotension, and payor status (adjusted odds ratio [95% CI], 0.67 [0.47 to 0.96]; p = 0.03). CONCLUSIONS: Patients from racial and ethnic minority groups were less likely to receive prehospital pain medication after traumatic injury than White patients. Forms of conscious and unconscious bias contributing to this inequity need to be identified and addressed.

The more you have, the more you lose: Muscle mass changes in trauma patients with prolonged hospitalizations.

INTRODUCTION: Sarcopenia is a clinically relevant loss of muscle mass with implications of increased morbidity and mortality in adult trauma populations.  Our study aimed to evaluate loss of muscle mass change in adult trauma patients with prolonged hospital stays. METHODS: Retrospective analysis using institutional trauma registry to identify all adult trauma patients with hospital length of stay >14 days admitted to our Level 1 center between 2010 and 2017. All CT images were reviewed, and cross-sectional area (cm2) of the left psoas muscle was measured at the level of the third lumbar vertebral body to determine total psoas area (TPA) and Total Psoas Index (TPI) normalized for patient stature.  Sarcopenia was defined as a TPI on admission below gender specific thresholds of 5.45(cm2/m2) in men and 3.85(cm2/m2) in women.  TPA, TPI, and rates of change in TPI were then evaluated and compared between sarcopenic and non-sarcopenic adult trauma patients. RESULTS: There were 81 adult trauma patients who met inclusion criteria. The average change in TPA was -3.8 cm2 and TPI was -1.3 cm2. On admission, 23% (n = 19) of patients were sarcopenic while 77% (n = 62) were not. Non-sarcopenic patients had a significantly greater change in TPA (-4.9 vs. -0.31, p<0.0001), TPI (-1.7 vs. -0.13, p<0.0001), and rate of decrease in muscle mass (p = 0.0002). 37% of patients who were admitted with normal muscle mass developed sarcopenia during admission.  Older age was the only risk factor independently associated with developing sarcopenia (OR: 1.04, 95%CI 1.00-1.08, p = 0.045). CONCLUSION: Over a third of patients with normal muscle mass at admission subsequently developed sarcopenia with older age as the primary risk factor. Patients with normal muscle mass at admission had greater decreases in TPA and TPI, and accelerated rates of muscle mass loss compared to sarcopenic patients.

Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe.

Strand-specific RNA sequencing of S. pombe revealed a highly structured programme of ncRNA expression at over 600 loci. Waves of antisense transcription accompanied sexual differentiation. A substantial proportion of ncRNA arose from mechanisms previously considered to be largely artefactual, including improper 3' termination and bidirectional transcription. Constitutive induction of the entire spk1+, spo4+, dis1+ and spo6+ antisense transcripts from an integrated, ectopic, locus disrupted their respective meiotic functions. This ability of antisense transcripts to disrupt gene function when expressed in trans suggests that cis production at native loci during sexual differentiation may also control gene function. Consistently, insertion of a marker gene adjacent to the dis1+ antisense start site mimicked ectopic antisense expression in reducing the levels of this microtubule regulator and abolishing the microtubule-dependent 'horsetail' stage of meiosis. Antisense production had no impact at any of these loci when the RNA interference (RNAi) machinery was removed. Thus, far from being simply 'genome chatter', this extensive ncRNA landscape constitutes a fundamental component in the controls that drive the complex programme of sexual differentiation in S. pombe.

An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression.

The transcriptional repressor B lymphocyte-induced maturation protein-1 (BLIMP1) regulates gene expression and cell fate. The DNA motif bound by BLIMP1 in vitro overlaps with that of interferon regulatory factors (IRFs), which respond to inflammatory/immune signals. At such sites, BLIMP1 and IRFs can antagonistically regulate promoter activity. In vitro motif selection predicts that only a subset of BLIMP1 or IRF sites is subject to antagonistic regulation, but the extent to which antagonism occurs is unknown, since an unbiased assessment of BLIMP1 occupancy in vivo is lacking. To address this, we identified an extended set of promoters occupied by BLIMP1. Motif discovery and enrichment analysis demonstrate that multiple motif variants are required to capture BLIMP1 binding specificity. These are differentially associated with CpG content, leading to the observation that BLIMP1 DNA-binding is methylation sensitive. In occupied promoters, only a subset of BLIMP1 motifs overlap with IRF motifs. Conversely, a distinct subset of IRF motifs is not enriched amongst occupied promoters. Genes linked to occupied promoters containing overlapping BLIMP1/IRF motifs (e.g. AIM2, SP110, BTN3A3) are shown to constitute a dynamic target set which is preferentially activated by BLIMP1 knock-down. These data confirm and extend the competitive model of BLIMP1 and IRF interaction.

GO-At: in silico prediction of gene function in Arabidopsis thaliana by combining heterogeneous data.

Despite recent advances, accurate gene function prediction remains an elusive goal, with very few methods directly applicable to the plant Arabidopsis thaliana. In this study, we present GO-At (gene ontology prediction in A. thaliana), a method that combines five data types (co-expression, sequence, phylogenetic profile, interaction and gene neighbourhood) to predict gene function in Arabidopsis. Using a simple, yet powerful two-step approach, GO-At first generates a list of genes ranked in descending order of probability of functional association with the query gene. Next, a prediction score is automatically assigned to each function in this list based on the assumption that functions appearing most frequently at the top of the list are most likely to represent the function of the query gene. In this way, the second step provides an effective alternative to simply taking the 'best hit' from the first list, and achieves success rates of up to 79%. GO-At is applicable across all three GO categories: molecular function, biological process and cellular component, and can assign functions at multiple levels of annotation detail. Furthermore, we demonstrate GO-At's ability to predict functions of uncharacterized genes by identifying ten putative golgins/Golgi-associated proteins amongst 8219 genes of previously unknown cellular component and present independent evidence to support our predictions. A web-based implementation of GO-At (http://www.bioinformatics.leeds.ac.uk/goat) is available, providing a unique resource for plant researchers to make predictions for uncharacterized genes and predict novel functions in Arabidopsis.

Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasite Plasmodium falciparum.

MOTIVATION: Functional genomics data provides a rich source of information that can be used in the annotation of the thousands of genes of unknown function found in most sequenced genomes. However, previous gene function prediction programs are mostly produced for relatively well-annotated organisms that often have a large amount of functional genomics data. Here, we present a novel method for predicting gene function that uses clustering of genes by semantic similarity, a naïve Bayes classifier and 'enrichment analysis' to predict gene function for a genome that is less well annotated but does has a severe effect on human health, that of the malaria parasite Plasmodium falciparum. RESULTS: Predictions for the molecular function, biological process and cellular component of P.falciparum genes were created from eight different datasets with a combined prediction also being produced. The high-confidence predictions produced by the combined prediction were compared to those produced by a simple K-nearest neighbour classifier approach and were shown to improve accuracy and coverage. Finally, two case studies are described, which investigate two biological processes in more detail, that of translation initiation and invasion of the host cell. AVAILABILITY: Predictions produced are available at http://www.bioinformatics.leeds.ac.uk/∼bio5pmrt/PAGODA.