PARP14 is pro- and anti-viral host factor that promotes IFN production and affects the replication of multiple viruses.

PARP14 is a 203 kDa multi-domain protein that is primarily known as an ADP-ribosyltransferase, and is involved in a variety of cellular functions including DNA damage, microglial activation, inflammation, and cancer progression. In addition, PARP14 is upregulated by interferon (IFN), indicating a role in the antiviral response. Furthermore, PARP14 has evolved under positive selection, again indicating that it is involved in host-pathogen conflict. We found that PARP14 is required for increased IFN-I production in response to coronavirus infection lacking ADP-ribosylhydrolase (ARH) activity and poly(I:C), however, whether it has direct antiviral function remains unclear. Here we demonstrate that the catalytic activity of PARP14 enhances IFN-I and IFN-III responses and restricts ARH-deficient murine hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. To determine if PARP14's antiviral functions extended beyond CoVs, we tested the ability of herpes simplex virus 1 (HSV-1) and several negative-sense RNA viruses, including vesicular stomatitis virus (VSV), Ebola virus (EBOV), and Nipah virus (NiV), to infect A549 PARP14 knockout (KO) cells. HSV-1 had increased replication in PARP14 KO cells, indicating that PARP14 restricts HSV-1 replication. In contrast, PARP14 was critical for the efficient infection of VSV, EBOV, and NiV, with EBOV infectivity at less than 1% of WT cells. A PARP14 active site inhibitor had no impact on HSV-1 or EBOV infection, indicating that its effect on these viruses was independent of its catalytic activity. These data demonstrate that PARP14 promotes IFN production and has both pro- and anti-viral functions targeting multiple viruses.

Target Delineation in Postoperative Radiation Therapy for Head and Neck Cancer After Flap Reconstruction.

Delineation of the clinical target volume (CTV) after resection of head and neck cancer can be challenging, especially after flap reconstruction. The main area of contention is whether the entire flap should be included in the CTV. Several case series have reported marginal misses and intraflap failures when the entire flap was not routinely included in the CTV. On the other hand, available data have not convincingly demonstrated a detriment to long-term outcomes using intensity modulated radiotherapy after flap reconstruction. On the contrary, postoperative radiation can facilitate epilation and mucosalization of the flap tissue, reduce flap bulk, and improve long-term esthetic and functional outcomes. Therefore, our standard practice is to include the entire flap in the CTV. In certain scenarios, we may allow for a lower dose to part of flap distant from the resection bed than the flap-tumor bed junction, where recurrences are most likely. We provide three case vignettes describing such scenarios where sparing part of the flap, and more importantly, the nearby uninvolved native tissue, from high-dose radiation may be justified.

Risk of severe COVID-19 outcomes after autumn 2022 COVID-19 booster vaccinations: a pooled analysis of national prospective cohort studies involving 7.4 million adults in England, Northern Ireland, Scotland and Wales.

Background: UK COVID-19 vaccination policy has evolved to offering COVID-19 booster doses to individuals at increased risk of severe Illness from COVID-19. Building on our analyses of vaccine effectiveness of first, second and initial booster doses, we aimed to identify individuals at increased risk of severe outcomes (i.e., COVID-19 related hospitalisation or death) post the autumn 2022 booster dose. Methods: We undertook a national population-based cohort analysis across all four UK nations through linked primary care, vaccination, hospitalisation and mortality data. We included individuals who received autumn 2022 booster doses of BNT162b2 (Comirnaty) or mRNA-1273 (Spikevax) during the period September 1, 2022 to December 31, 2022 to investigate the risk of severe COVID-19 outcomes. Cox proportional hazard models were used to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (CIs) for the association between demographic and clinical factors and severe COVID-19 outcomes after the autumn booster dose. Analyses were adjusted for age, sex, body mass index (BMI), deprivation, urban/rural areas and comorbidities. Stratified analyses were conducted by vaccine type. We then conducted a fixed-effect meta-analysis to combine results across the four UK nations. Findings: Between September 1, 2022 and December 31, 2022, 7,451,890 individuals ≥18 years received an autumn booster dose. 3500 had severe COVID-19 outcomes (2.9 events per 1000 person-years). Being male (male vs female, aHR 1.41 (1.32-1.51)), older adults (≥80 years vs 18-49 years; 10.43 (8.06-13.50)), underweight (BMI <18.5 vs BMI 25.0-29.9; 2.94 (2.51-3.44)), those with comorbidities (≥5 comorbidities vs none; 9.45 (8.15-10.96)) had a higher risk of COVID-19 hospitalisation or death after the autumn booster dose. Those with a larger household size (≥11 people within household vs 2 people; 1.56 (1.23-1.98)) and from more deprived areas (most deprived vs least deprived quintile; 1.35 (1.21-1.51)) had modestly higher risks. We also observed at least a two-fold increase in risk for those with various chronic neurological conditions, including Down's syndrome, immunodeficiency, chronic kidney disease, cancer, chronic respiratory disease, or cardiovascular disease. Interpretation: Males, older individuals, underweight individuals, those with an increasing number of comorbidities, from a larger household or more deprived areas, and those with specific underlying health conditions remained at increased risk of COVID-19 hospitalisation and death after the autumn 2022 vaccine booster dose. There is now a need to focus on these risk groups for investigating immunogenicity and efficacy of further booster doses or therapeutics. Funding: National Core Studies-Immunity, UK Research and Innovation (Medical Research Council and Economic and Social Research Council), Health Data Research UK, the Scottish Government, and the University of Edinburgh.

Burden and risk factors for Achilles tendinopathy in the military population from 2006 to 2015. A retrospective cohort study.

CONTEXT: Ankle-foot injuries are ubiquitous in the US military, with Achilles tendinopathy (AT) a common condition that affects function and health-related quality of life. OBJECTIVE: To evaluate the burden and associated factors of AT. DESIGN: Descriptive Epidemiology Study. SETTING: The Defense Medical Epidemiological Database was utilized to identify relevant healthcare encounters. PATIENTS OR OTHER PARTICIPANTS: All active duty and reserve military members who served between 2006 to 2015 (officers: n= 2 149 887; enlisted: n= 9 503 995). MAIN OUTCOME MEASURES: Multi-year prevalence of AT care episodes were calculated and compared by year, service branch, and military rank. Unadjusted and adjusted assessment of injury burden were calculated. RESULTS: Officers incurred 37,939 episodes at a prevalence of 17.65 per 1000 servicemembers (male officers: 18.20 per 1000 servicemembers; female officers: 14.80 per 1000 servicemembers). Among enlisted personnel, there were 116,122 episodes of AT that occurred in 12.22 per 1000 servicemembers (male enlisted: 12.07 per 1000 servicemembers; female enlisted: 13.22 per 1000 servicemembers). All officer specialties had significantly higher burden of AT episodes compared to the ground and naval gunfire officers (prevalence ratio [PR]: 1.04-1.43), except for aviation that demonstrated a significantly lower burden (PR: 0.65). Among enlisted occupations, maritime/naval specialties had lower burden of AT compared to infantry (PR: 0.82) and all other specialties, except for aviation, had significantly higher burden (PR: 1.07-1.71). There were multiple associated factors identified, to include sex, age, rank, military occupation, and service branch. CONCLUSION: AT was ubiquitous in the US military, with a progressive increase in prevalence during the study epoch. There were multiple associated factors identified, to include sex, age, rank, military occupation, and service branch. These findings highlight both the need for prophylactic interventions and identification of the populations with the greatest need.

Exceptional response to cetuximab monotherapy after failure of immunotherapy with a checkpoint inhibitor in a patient with metastatic head and neck squamous cell cancer: case report and review of the literature.

Immunotherapy with PD-1 inhibitors monotherapy or combined with chemotherapy comprises the first-line palliative treatment for patients with recurrent or metastatic head and neck squamous cell cancers (R/M HNSCC). The established survival advantage among responders is overshadowed by the high percentage of patients failing the standard PD-1 inhibitor-based treatments. Salvage therapies are direly needed. However, no current standards are available. We present the case of a 65-year-old patient with heavily pretreated laryngeal squamous cell carcinoma who had an exceptional response to cetuximab monotherapy following the failure of immunotherapy with the PD-1 inhibitor nivolumab. We reviewed the literature for other cases of exceptional response to cetuximab, clinical studies investigating the combined or sequential administration of cetuximab and PD-1 inhibitors, and the mechanistic rationale for consideration of cetuximab as a potential salvage treatment after immunotherapy with PD-1 inhibitors. In addition to the specific epidermal growth factor receptor inhibitory effect, cetuximab, as an immunoglobulin G1 isotype, binds NK cells and elicits antibody-dependent cellular toxicity, triggering a domino of immunostimulatory, and immunoinhibitory effects that actually might decrease the cetuximab anticancer efficacy. However, in a tumor microenvironment exposed to previous treatment with a PD-1 inhibitor, the effects of the PD-1 inhibitor followed by cetuximab on innate and adaptative immune response appear to synergize. Specifically, persistent immune checkpoint inhibitors' consequences may negate downstream immunosuppressive effects of cetuximab caused through PD-1/PD-L1 upregulation, making it a more potent treatment option. Besides the potential synergistic effect on antitumor immune response with previous immune checkpoint inhibitors therapy, cetuximab is the only targeted agent approved for treating R/M HNSCC, making it a most advantageous candidate for further treatment validation studies as salvage treatment post-immunotherapy.

Computational immunohistochemical mapping adds immune context to histological phenotypes in mouse models of colitis.

Inflammatory bowel disease (IBD) is characterized by chronic, dysregulated inflammation in the gastrointestinal tract. The heterogeneity of IBD is reflected through two major subtypes, Crohn's Disease (CD) and Ulcerative Colitis (UC). CD and UC differ across symptomatic presentation, histology, immune responses, and treatment. While colitis mouse models have been influential in deciphering IBD pathogenesis, no single model captures the full heterogeneity of clinical disease. The translational capacity of mouse models may be augmented by shifting to multi-mouse model studies that aggregate analysis across various well-controlled phenotypes. Here, we evaluate the value of histology in multi-mouse model characterizations by building upon a previous pipeline that detects histological disease classes in hematoxylin and eosin (H&E)-stained murine colons. Specifically, we map immune marker positivity across serially-sectioned slides to H&E histological classes across the dextran sodium sulfate (DSS) chemical induction model and the intestinal epithelium-specific, inducible Villin-CreERT2;Klf5fl/fl (Klf5ΔIND) genetic model. In this study, we construct the beginning frameworks to define H&E-patch-based immunophenotypes based on IHC-H&E mappings.

The histologic outcomes of indeterminate thyroid nodules with rat sarcoma mutations: A case series.

Molecular testing is an adjunct test for thyroid fine needle aspirations with indeterminate diagnoses, with certain mutations showing a greater risk of malignancy (ROM). Rat sarcoma (RAS) point mutations are the most common alterations in indeterminate thyroid nodules. While they can have a high ROM, they are also found in benign disease. This study describes the histologic outcomes of indeterminate nodules with RAS mutations. Bethesda III and IV thyroid nodules with ThyroSeq results showing RAS mutations (NRAS, KRAS, and HRAS) were identified between November 1, 2018 and February 28, 2023. Baseline patient characteristics, ThyroSeq results, and surgical diagnoses were collected. We identified 18 nodules with RAS mutations from 17 patients. Fourteen were NRAS (isolated NRAS in 6; NRAS with other abnormalities [NRAS+] in 8); one was isolated KRAS; and three were HRAS with other abnormalities (HRAS+). NRAS Q16R was the most common amino acid change. Twelve cases had follow-up. Two were malignant, a minimally invasive follicular carcinoma (NRAS+) and a papillary thyroid carcinoma, follicular variant (HRAS+). Three were noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP), 2 HRAS+ and 1 NRAS+. Four were follicular adenomas, one being atypical (3 NRAS+ and one isolated NRAS). One was an oncocytic adenoma (isolated NRAS). Two were nodular hyperplasias (isolated NRAS and NRAS+, respectively). Twenty-eight percent of our RAS-mutated nodules were malignant or NIFTP. All three HRAS-mutated nodules were malignant or NIFTP. The three isolated RAS mutations with follow up were benign (adenomas or nodular hyperplasia). These findings were in line with the literature.

Time to treatment patterns of head and neck cancer patients before and during the Covid-19 pandemic.

OBJECTIVES: The delivery of healthcare has changed significantly over the past decades. This study analyzes the clinicodemographic factors and treatment patterns of head and neck squamous cell carcinoma (HNSCC) patients between 2004 and 2020. MATERIALS AND METHODS: Retrospective cohort analysis of HNSCC patients from the National Cancer Data Base from 2004 to 2020. RESULTS: A total of 164,290 patients were included. Increased times from diagnosis to definitive surgery (TTS) were seen across all facility types (academic centers, AC; non-academic centers, NAC) between 2004 and 2019, with NAC affected more. TTS < 15 days (RR = 1.05, 95%CI:1.05-1.09) and > 75 days (1.07, 95%CI:1.05-1.09) were associated with increased mortality risk. This association was more prominent among HPV + HNSCC (RR = 1.45; 95%CI:1.18-1.78). Treatment in AC was associated with a decreased mortality risk (RR = 0.94, 95%CI:0.93-0.95). Despite the universal increase in wait times from 2004 to 2019, short-term mortality was significantly decreased from 2016 to 2019, relative to 2004-2007 (3-month mortality: RR = 0.77, 95%CI:0.70-0.85; 12-month mortality: RR = 0.80, 95%CI:0.77-0.84). Wait times decreased in 2020. CONCLUSIONS: TTS increased between 2004 and 2019, with NAC affected more. However, despite longer wait times, short-term survival increased significantly. Very short (<15 days) and very long (>75 days) TTS were associated with increased mortality risk. Patients with HPV + HNSCC have the highest increase among those treated > 75 days from diagnosis. Treatment at AC was associated with improved survival, which could be explained by the presence of multidisciplinary teams and subspecialists that may be less available at NAC. The 2021 NCDB data are required for a comprehensive analysis of wait times in 2020.

Predictors of incomplete COVID-19 vaccine schedule among adults in Scotland: Two retrospective cohort analyses of the primary schedule and third dose.

BACKGROUND: Vaccination continues to be the key public health measure for preventing severe COVID-19 outcomes. Certain groups may be at higher risk of incomplete vaccine schedule, which may leave them vulnerable to COVID-19 hospitalisation and death. AIM: To identify the sociodemographic and clinical predictors for not receiving a scheduled COVID-19 vaccine after previously receiving one. METHODS: We conducted two retrospective cohort studies with ≥3.7 million adults aged ≥18 years in Scotland. Multivariable logistic regression was used to estimate adjusted odds ratios (aOR) of not receiving a second, and separately a third dose between December 2020 and May 2022. Independent variables included sociodemographic and clinical factors. RESULTS: Of 3,826,797 people in the study population who received one dose, 3,732,596 (97.5%) received two doses, and 3,263,153 (86.5%) received all doses available during the study period. The most strongly associated predictors for not receiving the second dose were: being aged 18-29 (reference: 50-59 years; aOR:4.26; 95% confidence interval (CI):4.14-4.37); hospitalisation due to a potential vaccine related adverse event of special interest (AESI) (reference: not having a potential AESI, aOR:3.78; 95%CI: 3.29-4.35); and living in the most deprived quintile (reference: least deprived quintile, aOR:3.24; 95%CI: 3.16-3.32). The most strongly associated predictors for not receiving the third dose were: being 18-29 (reference: 50-59 years aOR:4.44; 95%CI: 4.38-4.49), living in the most deprived quintile (reference: least deprived quintile aOR:2.56; 95%CI: 2.53-2.59), and Black, Caribbean, or African ethnicity (reference: White ethnicity aOR:2.38; 95%CI: 2.30-2.46). Pregnancy, previous vaccination with mRNA-1273, smoking history, individual and household severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity, and having an unvaccinated adult in the household were also associated with incomplete vaccine schedule. CONCLUSION: We observed several risk factors that predict incomplete COVID-19 vaccination schedule. Vaccination programmes must take immediate action to ensure maximum uptake, particularly for populations vulnerable to severe COVID-19 outcomes.

Y-Chromosome-Linked Genes Are Associated With Sex-Related Head-Neck Squamous Cell Carcinoma Survival.

OBJECTIVE: To define novel gene biomarkers for prognosis of head and neck squamous cell carcinoma (HNSCC) patients' survival. STUDY DESIGN: Retrospective study. SETTING: The Cancer Genome Atlas (TCGA) HNSCC RNA-Seq dataset. METHODS: Coexpressed gene clusters were extracted from TCGA RNA-seq data using our previously published method (EPIG). Kaplan-Meier estimator was then used for overall survival-relevant analysis, with patients partitioned into 3 groups based on gene expression levels: female, male_low, and male_high. RESULTS: Male had better overall survival than female and male with higher expression level of Y-chromosome-linked (Y-linked) genes had significantly better survival than those with lower expression levels. In addition, male with a higher expression level of Y-linked genes showed even better survival when they have a higher level of coexpressed cluster of genes related to B or T cell immune response. Other clinical conditions related to immune responses also consistently showed favorable effects on the Y-linked genes for survival estimation. Male patients with higher expression level of Y-linked genes also have significantly higher tumor/normal tissue (T/N) ratio of those genes and higher level of several immune responses related clinical measurements (eg, lymphocyte and TCR related). Male patients with lower expression level of Y-linked genes benefited from radiation-only treatment. CONCLUSIONS: The favorable role of a cluster of coexpressed Y-linked genes in HNSCC patients' survival is potentially associated with elevated level of immune responses. These Y-linked genes could serve as useful prognostic biomarkers for HNSCC patients' survival estimation and treatment.

Camera traps reveal that terrestrial predators are pervasive at riverscape cold-water thermal refuges.

Perceived predation risks by terrestrial predators are major ecological forces in aquatic systems, particularly for aggregating fish. Riverscape thermal refuges are discrete, localized cold-water patches where fish temporarily aggregate to buffer against heat events. Predation pressures by terrestrial predators at thermal refuges may decrease the thermoregulatory benefits of refuge use, but quantifying such effects can be challenging and controversial when sampling can impose additional stress on fish. We passively monitored terrestrial predator visitation patterns and predation at four thermal refuges in the Housatonic River, Connecticut, USA, between May 18th and September 29th, 2022, with camera traps, a common wildlife monitoring method. Specifically, we (1) assessed diel visitation patterns by different categories of terrestrial predators at thermal refuges and determined if patterns varied among predator categories or with prevailing environmental conditions, and (2) estimated the probability of predation by hour of the day combined across all predator categories, quantifying general predation pressures at refuges. We detected at least one terrestrial predator at a thermal refuge each day, and mean hourly visitation rates (count/h) were highly variable across predator categories and sampling dates. The most supported generalized additive mixed model indicated that terrestrial predator visitation rates (count/h/day) varied with mean daily river discharge and water temperature differential, and relationships differed across categories of terrestrial predators. We observed 22 separate predation attempts on thermoregulating salmonids and predicted that the probability of predation by any terrestrial predator increased from 0.002 to 0.017 throughout a 24 h day (p = .004). Camera traps provided novel evidence that terrestrial predators are pervasive at riverine thermal refuges, which is relevant for refuge conservation and management globally. We recommend the implementation of a coordinated monitoring network across riverine thermal refuges using camera traps, further enriching our ecological understanding of cumulative predator effects in refuges across complex riverscapes.

The Impact of Medicaid Expansion on Head and Neck Malignancies Presentation and Survival.

OBJECTIVE: Under the Affordable Care Act (ACA), Medicaid expansion became effective in states that have adopted it. We aim to examine its impact on head and neck cancers. METHODS: A retrospective study that utilizes the Surveillance, Epidemiology, and End Results database, 2010-2016. Study population included patients with head and neck squamous cell carcinoma (HNSCC), differentiated thyroid carcinoma, and head and neck cutaneous melanoma. The objective is to examine disease-specific survival before and after Medicaid expansion. RESULTS: In states that adopted Medicaid expansion, the ratio of Medicaid: uninsured patients increased from 3:1 to 9:1 (p < 0.001). In states that did not adopt Medicaid expansion, the ratio increased from 1:1 to 2:1 (p < 0.001), making the increase in Medicaid coverage in states that adopted the expansion significantly higher (p < 0.001). Patients diagnosed with HNSCC before the expansion had worse survival (hazard ratio [HR]: 1.24, 95% confidence interval: 1.11, 1.39, p < 0.001) in states that adopted Medicaid expansion. CONCLUSIONS: Early data indicate that implementation of ACA improved disease-specific survival of patients with HNSCC. LEVEL OF EVIDENCE: 3 Laryngoscope, 133:1409-1414, 2023.

Spatiotemporal changes in largemouth bass mercury concentrations from Connecticut waterbodies, 1995-2021.

We evaluated spatiotemporal changes in the mean and variation in largemouth bass (Micropterus salmoides) mercury concentrations over three discrete time periods (1995, 2005-2006, and 2019-2021) across 56 Connecticut waterbodies. We detected largemouth bass raw mercury concentrations that exceeded the US Environmental Protection Agency (USEPA) Fish Tissue Residue Criterion (≥ 0.30 µg g-1 ww) in 75.1%, 63.3%, and 47.7% of all fish sampled during 1995, 2005-2006, and 2019-2021, respectively. Total length (TL)-adjusted largemouth bass mercury concentrations declined across all ecoregions in Connecticut between subsequent sampling periods but increased between 2005-2006 and 2019-2021 in the Northwest Hills/Uplands ecoregion. The coefficient of variation (CV) of largemouth bass TL-adjusted mercury concentrations increased through time, increasing from 25.78% during 1995 to 36.47% during 2019-2021. The probability of a largemouth bass having a raw mercury concentration > 0.30 µg g-1 ww increased with total length (TL), but the TL with a 50% probability varied across ecoregions and periods. The variation in largemouth bass mercury concentrations highlights the roles that changes to individual behaviors, food web structure, lake properties, and legacy mercury may play in shaping broad patterns and trends in mercury consumption risks.

Retrospective Review of Antecustodial Deaths Referred for Medicolegal Autopsy at the Medical University of South Carolina.

Deaths occurring in police custody have dominated public discourse over recent years. However, deaths occurring after law enforcement have initiated nonphysical contact but before active restraint or containment lie outside the strict definition of "in custody." These "antecustodial" deaths demonstrate a unique population and interaction with law enforcement. A retrospective analysis of medicolegal cases referred to the Medical University of South Carolina from September 1, 2012, to April 28, 2022 was performed. Deaths during nonphysical interaction with or during evasion of law enforcement occurred in 78 cases and were categorized by demographic data, cause of death, manner of death, the presence of drugs and/or alcohol, and circumstances surrounding the interaction. Antecustodial deaths occurred primarily during law enforcement pursuit and deescalation scenarios. Decedents were predominantly male (92.3%) with a Black-to-White ratio of 1.1:1. The average age of male and female decedents was 35.7 and 32.2 years, respectively. The most common causes of death were gunshot wounds and blunt trauma sustained in motor vehicle crashes. The most common manner of death was homicide (43.6%), followed by suicide (28.2%) and accident (28.2%).

A Pseudomonas aeruginosa small RNA regulates chronic and acute infection.

The ability to switch between different lifestyles allows bacterial pathogens to thrive in diverse ecological niches1,2. However, a molecular understanding of their lifestyle changes within the human host is lacking. Here, by directly examining bacterial gene expression in human-derived samples, we discover a gene that orchestrates the transition between chronic and acute infection in the opportunistic pathogen Pseudomonas aeruginosa. The expression level of this gene, here named sicX, is the highest of the P. aeruginosa genes expressed in human chronic wound and cystic fibrosis infections, but it is expressed at extremely low levels during standard laboratory growth. We show that sicX encodes a small RNA that is strongly induced by low-oxygen conditions and post-transcriptionally regulates anaerobic ubiquinone biosynthesis. Deletion of sicX causes P. aeruginosa to switch from a chronic to an acute lifestyle in multiple mammalian models of infection. Notably, sicX is also a biomarker for this chronic-to-acute transition, as it is the most downregulated gene when a chronic infection is dispersed to cause acute septicaemia. This work solves a decades-old question regarding the molecular basis underlying the chronic-to-acute switch in P. aeruginosa and suggests oxygen as a primary environmental driver of acute lethality.

Viral predation pressure on coral reefs.

BACKGROUND: Predation pressure and herbivory exert cascading effects on coral reef health and stability. However, the extent of these cascading effects can vary considerably across space and time. This variability is likely a result of the complex interactions between coral reefs' biotic and abiotic dimensions. A major biological component that has been poorly integrated into the reefs' trophic studies is the microbial community, despite its role in coral death and bleaching susceptibility. Viruses that infect bacteria can control microbial densities and may positively affect coral health by controlling microbialization. We hypothesize that viral predation of bacteria has analogous effects to the top-down pressure of macroorganisms on the trophic structure and reef health. RESULTS: Here, we investigated the relationships between live coral cover and viruses, bacteria, benthic algae, fish biomass, and water chemistry in 110 reefs spanning inhabited and uninhabited islands and atolls across the Pacific Ocean. Statistical learning showed that the abundance of turf algae, viruses, and bacteria, in that order, were the variables best predicting the variance in coral cover. While fish biomass was not a strong predictor of coral cover, the relationship between fish and corals became apparent when analyzed in the context of viral predation: high coral cover (> 50%) occurred on reefs with a combination of high predator fish biomass (sum of sharks and piscivores > 200 g m-2) and high virus-to-bacteria ratios (> 10), an indicator of viral predation pressure. However, these relationships were non-linear, with reefs at the higher and lower ends of the coral cover continuum displaying a narrow combination of abiotic and biotic variables, while reefs at intermediate coral cover showed a wider range of parameter combinations. CONCLUSIONS: The results presented here support the hypothesis that viral predation of bacteria is associated with high coral cover and, thus, coral health and stability. We propose that combined predation pressures from fishes and viruses control energy fluxes, inhibiting the detrimental accumulation of ecosystem energy in the microbial food web.

Müllerian Cysts of the Posterior Mediastinum: A Case Report and Review of the Literature.

Cysts can be segregated according to their embryonic backgrounds. The cysts that were found in the mediastinum are usually divided into bronchogenic cysts, enteric cysts, esophageal cysts, and nonspecific cysts. We add to the relatively small body of literature that exists on this topic by reporting a case of a Müllerian cyst occurring in the posterior mediastinum of a 60-year-old female, showing diffuse nuclear positivity for estrogen receptor (ER) and PAX-8. We examined and summarized the findings of the unique reported cases in the literature. Lastly, an institutional retrospective review of all posterior mediastinal lesions in the last 38.5 years was performed. This revealed that out of 135 candidates within our own healthcare system, the only case consistent with the diagnosis of a mediastinal Müllerian cyst is the report included herein.

Interpreting and de-noising genetically engineered barcodes in a DNA virus.

The concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy, especially when growing through multiple generations or assaying the pathogen long-term. The potential problems include: the barcode might alter fitness, the barcode may accumulate mutations, and construction of the marked pathogens may result in unintended barcodes that are not as designed. Here, we generate approximately 5,000 randomized barcodes in the genome of the prototypic small DNA virus murine polyomavirus. We describe the challenges faced with interpreting the barcode sequences obtained from the library. Our Illumina NextSeq sequencing recalled much greater variation in barcode sequencing reads than the expected 5,000 barcodes-necessarily stemming from the Illumina library processing and sequencing error. Using data from defined control virus genomes cloned into plasmid backbones we develop a vetted post-sequencing method to cluster the erroneous reads around the true virus genome barcodes. These findings may foreshadow problems with randomized barcodes in other microbial systems and provide a useful approach for future work utilizing nucleic acid barcoded pathogens.