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We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.

UL20, an essential herpes simplex virus 1 (HSV-1) protein, is involved in cytoplasmic envelopment of virions and virus egress. We reported recently that UL20 can bind to a host protein encoded by the zinc finger DHHC-type containing 3 (ZDHHC3) gene (also known as Golgi-specific DHHC zinc finger protein [GODZ]). Here, we show for the first time that HSV-1 replication is compromised in murine embryonic fibroblasts (MEFs) isolated from GODZ-/- mice. The absence of GODZ resulted in blocking palmitoylation of UL20 and altered localization and expression of UL20 and glycoprotein K (gK); the expression of gB and gC; and the localization and expression of tegument and capsid proteins within HSV-1-infected MEFs. Electron microscopy revealed that the absence of GODZ limited the maturation of virions at multiple steps and affected the localization of virus and endoplasmic reticulum morphology. Virus replication in the eyes of ocularly HSV-1-infected GODZ-/- mice was significantly lower than in HSV-1-infected wild-type (WT) mice. The levels of UL20, gK, and gB transcripts in the corneas of HSV-1-infected GODZ-/- mice on day 5 postinfection were markedly lower than in WT mice, whereas only UL20 transcripts were reduced in trigeminal ganglia (TG). In addition, HSV-1-infected GODZ-/- mice showed notably lower levels of corneal scarring, and HSV-1 latency reactivation was also reduced. Thus, normal HSV-1 infectivity and viral pathogenesis are critically dependent on GODZ-mediated palmitoylation of viral UL20.IMPORTANCE HSV-1 infection is widespread. Ocular infection can cause corneal blindness; however, approximately 70 to 90% of American adults exposed to the virus show no clinical symptoms. In this study, we show for the first time that the absence of a zinc finger protein called GODZ affects primary and latent infection, as well as reactivation, in ocularly infected mice. The reduced virus infectivity is due to the absence of the GODZ interaction with HSV-1 UL20. These results strongly suggest that binding of UL20 to GODZ promotes virus infectivity in vitro and viral pathogenesis in vivo.

ABSTRACT: History of present illness: A 64-year-old female presented to the emergency department feeling like she had “pills stuck in [her] throat,” specifically calcium and a multivitamin, which she tried to relieve with drinking, eating and sticking two fingers down her throat. She was sitting upright, speaking in full sentences but had a hoarse voice. She was tolerating her secretions but had frothy sputum in the posterior oropharynx. Significant findings: Soft tissue lateral X-ray of neck was performed. The lateral soft tissue X-ray of the neck showed a metallic foreign body at the level cricoid. Discussion: Most swallowed foreign bodies enter the esophagus. Larger foreign bodies tend to obstruct proximally and may cause airway compromise in addition to esophageal trauma.1 Foreign bodies tend to lodge at areas of anatomic narrowing, most commonly the upper and lower esophageal sphincters, physiologic angulation, and areas of pathologic stricture.2,3 Ensuring airway patency and ability to manage secretions is paramount and any concern for compromise should prompt emergent consultation with otolaryngology and/or gastrointestinal. Determination of which service to consult should be made based on the suspected location of obstruction and associated symptoms. In addition to obtaining a complete history of the ingestion including type of foreign body, size, and shape, it is prudent to ask what measures, if any, the patient has already taken to remove the object.In this case, flexible fiberoptic laryngoscopy revealed swollen arytenoids and some small abrasions proximal to the vocal cords, which themselves appeared normal. She had copious secretions with no foreign bodies seen. On endoscopy, a metallic finger ring was found at the cricopharyngeus muscle along with non- obstructing laryngeal edema. The ring was removed with rat-toothed forceps. No pills were found. The patient had no recollection of swallowing the ring, but presumably, it slipped off her finger in the process of attempting to make herself vomit. After brief observation, she passed a bedside swallow assessment and was discharged in good condition. Repeat upper endoscopy 8 days later revealed a tortuous esophagus but was otherwise unremarkable. Topics: Foreign body, laryngoscopy, endoscopy, airway management.

Honey bees exhibit an elaborate social structure based in part on an age-related division of labor. Young workers perform tasks inside the hive, while older workers forage outside the hive, tasks associated with distinct diets and metabolism. Critical to colony fitness, the work force can respond rapidly to changes in the environment or colony demography and assume emergency tasks, resulting in young foragers or old nurses. We hypothesized that both task and age affect the gut microbiota consistent with changes to host diet and physiology. We performed two experiments inducing precocious foragers and reverted nurses, then quantified tissue-specific gut microbiota and host metabolic state associated with nutrition, immunity and oxidative stress. In the precocious forager experiment, both age and ontogeny explained differences in midgut and ileum microbiota, but host gene expression was best explained by an interaction of these factors. Precocious foragers were nutritionally deficient, and incurred higher levels of oxidative damage relative to age-matched nurses. In the oldest workers, reverted nurses, the oxidative damage associated with age and past foraging was compensated by high Vitellogenin expression, which exceeded that of young nurses. Host-microbial interactions were evident throughout the dataset, highlighted by an age-based increase of Gilliamella abundance and diversity concurrent with increased carbonyl accumulation and CuZnSOD expression. The results in general contribute to an understanding of ecological succession of the worker gut microbiota, defining the species-level transition from nurse to forager.

BACKGROUND: Pediatric brain tumors are the leading cause of death for children with cancer in the U.S. Incorporating next-generation sequencing data for both pediatric low-grade (pLGGs) and high-grade gliomas (pHGGs) can inform diagnostic, prognostic, and therapeutic decision-making. MATERIALS AND METHODS: We performed comprehensive genomic profiling on 282 pediatric gliomas (157 pHGGs, 125 pLGGs), sequencing 315 cancer-related genes and calculating the tumor mutational burden (TMB; mutations per megabase [Mb]). RESULTS: In pLGGs, we detected genomic alterations (GA) in 95.2% (119/125) of tumors. BRAF was most frequently altered (48%; 60/125), and FGFR1 missense (17.6%; 22/125), NF1 loss of function (8.8%; 11/125), and TP53 (5.6%; 7/125) mutations were also detected. Rearrangements were identified in 35% of pLGGs, including KIAA1549-BRAF, QKI-RAF1, FGFR3-TACC3, CEP85L-ROS1, and GOPC-ROS1 fusions. Among pHGGs, GA were identified in 96.8% (152/157). The genes most frequently mutated were TP53 (49%; 77/157), H3F3A (37.6%; 59/157), ATRX (24.2%; 38/157), NF1 (22.2%; 35/157), and PDGFRA (21.7%; 34/157). Interestingly, most H3F3A mutations (81.4%; 35/43) were the variant K28M. Midline tumor analysis revealed H3F3A mutations (40%; 40/100) consisted solely of the K28M variant. Pediatric high-grade gliomas harbored oncogenic EML4-ALK, DGKB-ETV1, ATG7-RAF1, and EWSR1-PATZ1 fusions. Six percent (9/157) of pHGGs were hypermutated (TMB >20 mutations per Mb; range 43-581 mutations per Mb), harboring mutations deleterious for DNA repair in MSH6, MSH2, MLH1, PMS2, POLE, and POLD1 genes (78% of cases). CONCLUSION: Comprehensive genomic profiling of pediatric gliomas provides objective data that promote diagnostic accuracy and enhance clinical decision-making. Additionally, TMB could be a biomarker to identify pediatric glioblastoma (GBM) patients who may benefit from immunotherapy. IMPLICATIONS FOR PRACTICE: By providing objective data to support diagnostic, prognostic, and therapeutic decision-making, comprehensive genomic profiling is necessary for advancing care for pediatric neuro-oncology patients. This article presents the largest cohort of pediatric low- and high-grade gliomas profiled by next-generation sequencing. Reportable alterations were detected in 95% of patients, including diagnostically relevant lesions as well as novel oncogenic fusions and mutations. Additionally, tumor mutational burden (TMB) is reported, which identifies a subpopulation of hypermutated glioblastomas that harbor deleterious mutations in DNA repair genes. This provides support for TMB as a potential biomarker to identify patients who may preferentially benefit from immune checkpoint inhibitors.

Abstract Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative option for many hematologic conditions and is associated with considerable morbidity and mortality. Therefore, prognostic tools are essential to navigate the complex patient, disease, donor, and transplant characteristics that differentially influence outcomes. We developed a novel, comprehensive composite prognostic tool. Using a lasso-penalized Cox regression model (n = 273), performance status, HCT-CI, refined disease-risk index (rDRI), donor and recipient CMV status, and donor age were identified as predictors of disease-free survival (DFS). The results for overall survival (OS) were similar except for recipient CMV status not being included in the model. Models were validated in an external dataset (n = 378) and resulted in a c-statistic of 0.61 and 0.62 for DFS and OS, respectively. Importantly, this tool incorporates donor age as a variable, which has an important role in HSCT outcomes. This needs to be further studied in prospective models. An easy-to-use and a web-based nomogram can be accessed here: https://allohsctsurvivalcalc.iowa.uiowa.edu/ .

RESUMO O artigo apresenta resultados do projeto desenvolvido pelo Grupo de Pesquisa em Governança Energética no contexto da Macrometrópole Paulista em face da Variabilidade Climática. Com base numa abordagem qualitativa suportada por análise documental e dados quantitativos e qualitativos produzidos pelo grupo de pesquisa, o presente trabalho combina os conceitos de “estilo de política” e “ciência pós-normal”, considerando a transição energética por um lado e a mitigação e adaptação às mudanças climáticas por outro. Esse arcabouço conceitual é confrontado com três estudos de caso: a) a geopolítica da energia na América do Sul, no nível macro; b) o Plano Decenal de Energia no Brasil, no nível meso; e, c) as políticas de mitigação e adaptação frente às mudanças climáticas na cidade de São Paulo, no nível micro. Embora nos três níveis sejam identificadas proposições institucionais para tratar do manejo de fontes energéticas e redução de emissões, as práticas demonstram contextos multifacetados, que dificultam o alcance das metas preconizadas pelas políticas públicas.

In February 2021, routine sentinel surveillance for influenza-like illness in Cambodia detected a human avian influenza A(H9N2) virus infection. Investigations identified no recent H9N2 virus infections in 43 close contacts. One chicken sample from the infected child’s house was positive for H9N2 virus and genetically similar to the human virus.

Abstract Background The majority of surgical wounds are closed (for example with sutures or staples) and so heal by primary intention. Where closure is not possible, or the wound subsequently breaks down, wounds may be left to heal from the bottom up (healing by secondary intention). Surgical wound healing by secondary intention (SWHSI) frequently presents a significant management challenge. Additional treatments are often required during the course of healing, and thus a significant financial burden is associated with treating these wounds. Increasingly, negative pressure wound therapy (NPWT) is used in the management of SWHSI. This wound dressing system provides a negative pressure (vacuum) to the wound, removing fluid into a canister, which is believed to be conducive to wound healing. Despite the increasing use of NPWT, there is limited robust evidence for the effectiveness of this device. A well-designed and conducted randomised controlled trial is now required to ascertain if NPWT is a clinically and cost-effective treatment for SWHSI. Methods SWHSI-2 is a pragmatic, multi-centre, cross surgical specialty, two arm, parallel group, randomised controlled superiority trial. Adult patients with a SWHSI will be randomised to receive either NPWT or usual care (no NPWT) and will be followed up for 12 months. The primary outcome will be time to healing (defined as full epithelial cover in absence of a scab) in number of days since randomisation. Secondary outcomes will include key clinical events (hospital admission or discharge, treatment status, reoperation, amputation, antibiotic use and death), wound infection, wound pain, health-related quality of life, health utility and resource use. Discussion Given the increasing use of NPWT, despite limited high-quality supporting evidence, the SWHSI-2 Trial will provide robust evidence on the clinical and cost-effectiveness of NPWT in the management of SWHSI. The SWHSI-2 Trial opened to recruitment in May 2019 and is currently recruiting across 20 participating centres. Trial registration ISRCTN 26277546 . Prospectively registered on 25 March 2019

Rhabdomyosarcoma is extremely rare in adults. Metastatic rhabdomyosarcoma can resemble other malignancies, which can delay diagnosis and prompt treatment. This case illustrates an example of metastatic alveolar rhabdomyosarcoma with concurrent bone marrow infiltration. A 67-year-old woman presented with epistaxis and diffuse bone pain. She developed progressive thrombocytopenia requiring platelet transfusions. The patient was initially thought to have leukemia. She was found to have a large sinonasal mass with extensive metastatic disease and bone marrow infiltration. The patient was ultimately diagnosed with metastatic alveolar rhabdomyosarcoma. She was started on chemotherapy with vincristine, actinomycin, and cyclophosphamide. Unfortunately, she died prior to discharge home. Alveolar rhabdomyosarcoma can resemble a primary bone marrow malignancy when it infiltrates the bone marrow. Further investigation is needed to clarify its clinical behavior and expedite diagnosis and treatment.

The most prevalent pathogen in bone infections is Staphylococcus aureus; its incidence and severity are partially determined by host factors. Prior studies showed that anti-glucosaminidase (Gmd) antibodies are protective in animals, and 93.3 % of patients with culture-confirmed S. aureus osteomyelitis do not have anti-Gmd levels > 10 ng/mL in serum. Infection in patients with high anti-Gmd remains unexplained. Are anti-Gmd antibodies in osteomyelitis patients of the non-opsonising, non-complement-fixing IgG4 isotype? The relative amounts of IgG4 and total IgG against Gmd and 7 other S. aureus antigens: iron-surface determinants (Isd) IsdA, IsdB, and IsdH, amidase (Amd), α-haemolysin (Hla), chemotaxis inhibitory protein from S. aureus (CHIPS), and staphylococcal-complement inhibitor (SCIN) were determined in sera from healthy controls (Ctrl, n = 92), osteomyelitis patients whose surgical treatment resulted in infection control (IC, n = 95) or an adverse outcome (AD, n = 40), and post-mortem (PM, n = 7) blood samples from S. aureus septic-death patients. Anti-Gmd IgG4 levels were generally lower in infected patients compared to controls; however, levels among the infected were higher in AD than IC patients. Anti-IsdA, IsdB and IsdH IgG4 levels were increased in infected patients versus controls, and Jonckheere-Terpstra tests of levels revealed an increasing order of infection (Ctrl < IC < AD < PM) for anti-Isd IgG4 antibodies and a decreasing order of infection (Ctrl > IC > AD > PM) for anti-autolysin (Atl) IgG4 antibodies. Collectively, this does not support an immunosuppressive role of IgG4 in S. aureus osteomyelitis but is consistent with a paradigm of high anti-Isd and low anti-Atl responses in these patients.

BackgroundSarcomas are a diverse group of neoplasms that vary greatly in clinical presentation and responsiveness to treatment. Given the differences in the sites of involvement, rarity, and treatment modality, a multidisciplinary approach is required. Previous literature suggests patients with sarcoma suffer from poorer quality of life (QoL) especially physical and functional wellbeing. Adolescent and young adult (AYA) patients are an underrepresented population in cancer research and have differing factors influencing QoL.MethodsRetrospective analysis of Young Adult patients (age 18–39) enrolled in the Sarcoma Tissue Repository at University of Iowa. QoL was assessed using the self-report FACT-G questionnaire at enrollment and 12 months post-diagnosis; overall scores and the 4 wellbeing subscales (Physical, Emotional, Social, Functional) were calculated. Linear mixed effects models were used to measure the association between the rate of change in FACT-G subscale scores and baseline clinical, comorbidity, and treatment characteristics.Results49 patients were identified. 57.1% of patients had a malignancy involving an extremity. Mean FACT-G scores of overall wellbeing improved from baseline to 12 months (76.4 vs. 85.4, p < 0.01). Social and emotional wellbeing did not differ significantly between baseline and 12 months. Physical wellbeing (18.8 vs. 23.9, p < 0.01) and functional wellbeing (16.8 vs. 20.0, p< 0.01) scores improved from baseline to 12 months. No difference was seen for FACT-G overall scores for age, sex, laterality, marital status, performance status, having children, clinical stage, limb surgery, chemotherapy, or tumor size. A difference was demonstrated in physical wellbeing scores for patients with baseline limitation (ECOG 1-3) compared to those with no baseline limitation (ECOG 0) (p = 0.03). A difference was demonstrated in social wellbeing based on anatomical site (p = 0.02).ConclusionYoung adults with sarcoma treated at a tertiary center had improvements in overall reported QoL at 12 months from diagnosis. Overall baseline QoL scores on FACT-G were lower than the general adult population for YA patients with sarcoma but at 12 months became in line with general population norms. The improvements seen merit further investigation to evaluate how these change over the continuum of care. Quality of life changes may be useful outcomes of interest in sarcoma trials.

Abstract Background Recent shifts from radiation to chemotherapy‐based treatment for acute lymphoblastic leukemia (ALL) have contributed to reduced long‐term morbidity. Despite this, ALL survivors remain at increased risk for long‐term cognitive impairments. Aim To identify demographic and treatment factors associated with school performance in pediatric survivors of ALL. Methods We collected standardized test scores for reading, math, and science obtained in a school setting from grades 3–11 in 63 ALL survivors (46.0% boys). Most participants were assessed across multiple grades (median number of grades n = 5, range 1–7), and 269 observations were considered in the analyses. Treatment exposures were extracted from medical records. Socio‐economic status was estimated using participation in free/reduced lunch programs at school. Mixed effects linear regression models were conducted to determine factors associated with school performance. Results ALL survivors' scores were comparable to state norms on reading, math, and science performances. On multivariable analysis, participation in free/reduced lunch programs was significantly associated with lower reading scores (β = −12.52; 95% CI −22.26:−2.77, p = .01). Exposure to radiation during treatment was also associated with lower reading test scores (β = −30.81, 95% CI −52.00:−9.62, p = .01). No significant associations between demographics and treatment parameters were observed for math and science test scores. Conclusions We utilized population‐based achievement tests conducted from grades 3–11 to characterize school performance in ALL survivors. Our results imply that survivors with low socio‐economic status and those exposed to radiation during treatment could benefit from early monitoring and intervention to maximize academic success.

As United States farmers adapt soybean (Glycine max) production methods from oilseed to vegetable (edamame), key management practices will need to be considered. The key objective of this study was to determine the optimal nitrogen (N) rate and N application timing for edamame in the mid-Atlantic coastal plain system. The study was conducted for three years in Painter, VA, USA on sandy loam soils. A factorial arrangement of four N rates was applied with two application timing strategies: at-planting, and split application. Leaf tissue samples were collected and analyzed at R1. At harvest, the Normalized Difference Vegetation Index (NDVI) was measured, whole pods were mechanically collected, and yield was recorded. Additionally, pod and bean physical and chemical quality were assessed. Nitrogen fertilization significantly increased pod yield in two out of three years. R1 leaf N and sulfur (S) concentrations correlated to the yield, and R1 leaf and R6 whole-plant N concentrations correlated to the total N uptake. None of the tested parameters indicated that N fertilizer decreased yield or quality. In conclusion, we found that N fertilizer applied at planting may aid edamame yield and profit for sandy loam soils in the mid-Atlantic, USA.

Increasing size, severity, and human proximity to fires in the western US are driving a need for more effective ecosystem restoration in the immediate post-fire period. Surface treatments, such as mastication of logging slash, reduce erosion and improve soil nutrient and water retention on steep slopes. However, few studies have investigated the impact of these treatments on arthropod communities over time. Our objective was to determine which insect communities return to these treated areas and if the mulch changes the community structure over time. We surveyed arthropod abundance using pitfall traps in mulch treatments in a landscape-scale fire near Flagstaff, Arizona, and a controlled split-plot experiment outside of the larger fire footprint. Predatory beetles were more abundant in mulch in the large landscape treatment, with no differences in abundance in the split plots. Fungivores had no significant mulch preference, and several native bark beetles were more abundant in the untreated sites. We found that the size of the fire footprint and distance to the intact forest matrix likely impact arthropod community composition over time. We were unable to fully evaluate vegetation recovery, but further work will allow us to understand how surface treatments impact the interaction of arthropods and vegetation.

Visceral artery pseudoaneurysms are rare and potentially fatal unless recognized and treated immediately. Here we present to our mind the first documented case of a ruptured pseudoaneurysm involving the left gastric artery giving rise to Michels’ Type II replaced left hepatic artery. An 84-year-old female presented with an acute rupture of such an aneurysm post radical cystectomy. CT Angiogram prior to intervention was key for appropriate catheter selection. Endovascular embolization proved effective, and the patient recovered unremarkably. The case report includes a brief discussion regarding the investigation and management of such ruptures, as well as the rarity of the variant anatomy described.

Introduction: We evaluated knowledge, attitudes, and practices (KAP) related to influenza and influenza vaccination among pregnant women in three selected countries. Methods: During 2017, pregnant women seeking antenatal care at hospitals at participating sites were enrolled. We described characteristics and responses to KAP questions. We also evaluated predictors associated with influenza vaccination during pregnancy at sites with substantial influenza vaccine uptake by multivariable logistic regression. Results: Overall, 4,648 pregnant women completed the survey. There were substantial differences among the three survey populations; only 8% of the women in Nagpur had heard of influenza, compared to 90% in Lima and 96% in Bangkok (p-value

Abstract Background Familial adenomatous polyposis is an inherited genetic disease, characterized by colorectal polyps. It is caused by inactivating mutations in the Adenomatous polyposis coli (Apc) gene. Mice carrying a nonsense mutation in the Apc gene at R850, which is designated Apc Min/+ (Multiple intestinal neoplasia), develop intestinal adenomas. Several genetic modifier loci of Min (Mom) were previously mapped, but so far, most of the underlying genes have not been identified. To identify novel modifier loci associated with Apc Min/+ , we performed quantitative trait loci (QTL) analysis for polyp development using 49 F1 crosses between different Collaborative Cross (CC) lines and C57BL/6 J-Apc Min/+ mice. The CC population is a genetic reference panel of recombinant inbred lines, each line independently descended from eight genetically diverse founder strains. C57BL/6 J-Apc Min/+ males were mated with females from 49 CC lines. F1 offspring were terminated at 23 weeks and polyp counts from three sub-regions (SB1–3) of small intestinal and colon were recorded. Results The number of polyps in all these sub-regions and colon varied significantly between the different CC lines. At 95% genome-wide significance, we mapped nine novel QTL for variation in polyp number, with distinct QTL associated with each intestinal sub-region. QTL confidence intervals varied in width between 2.63–17.79 Mb. We extracted all genes in the mapped QTL at 90 and 95% CI levels using the BioInfoMiner online platform to extract, significantly enriched pathways and key linker genes, that act as regulatory and orchestrators of the phenotypic landscape associated with the Apc Min/+ mutation. Conclusions Genomic structure of the CC lines has allowed us to identify novel modifiers and confirmed some of the previously mapped modifiers. Key genes involved mainly in metabolic and immunological processes were identified. Future steps in this analysis will be to identify regulatory elements – and possible epistatic effects – located in the mapped QTL.

BackgroundRindopepimut (also known as CDX-110), a vaccine targeting the EGFR deletion mutation EGFRvIII, consists of an EGFRvIII-specific peptide conjugated to keyhole limpet haemocyanin. In the ACT IV study, we aimed to assess whether or not the addition of rindopepimut to standard chemotherapy is able to improve survival in patients with EGFRvIII-positive glioblastoma.MethodsIn this randomised, double-blind, phase 3 trial, we recruited patients aged 18 years and older with glioblastoma from 165 hospitals in 22 countries. Eligible patients had newly diagnosed glioblastoma confirmed to express EGFRvIII by central analysis, and had undergone maximal surgical resection and completion of standard chemoradiation without progression. Patients were stratified by European Organisation for Research and Treatment of Cancer recursive partitioning analysis class, MGMT promoter methylation, and geographical region, and randomly assigned (1:1) with a prespecified randomisation sequence (block size of four) to receive rindopepimut (500 μg admixed with 150 μg GM-CSF) or control (100 μg keyhole limpet haemocyanin) via monthly intradermal injection until progression or intolerance, concurrent with standard oral temozolomide (150-200 mg/m2 for 5 of 28 days) for 6-12 cycles or longer. Patients, investigators, and the trial funder were masked to treatment allocation. The primary endpoint was overall survival in patients with minimal residual disease (MRD; enhancing tumour

Breast cancer is a complex and multifactorial disease. Tumors have a heterogeneous microenvironment, which have multiple interactions with other cell types, greatly influencing the behavior of tumor cells and response to therapy. The 3D culture mimics the microenvironment better found in vivo and is more appropriated than the traditional 2D culture made from plastic to test the cellular response to drugs. To investigate the effects of [10]-gingerol on breast tumor cells, we used physiologically relevant three-dimensional (3D) cultures of malignant and non-malignant human breast cells grown in laminin-rich extracellular matrix gels (lr-ECM). Our results showed selective cytotoxicity of [10]-gingerol against the malignant T4-2 breast cancer cell line compared to non-malignant S1 cells. The compound reverted the malignant phenotype of the cancer cells, downregulating the expression of epidermal growth factor receptor (EGFR) and β1-integrin. Moreover, [10]-gingerol induced apoptosis in this cell line. These results suggest that [10]-gingerol may be an effective compound to use as adjuvant therapy in breast cancer treatment. J. Cell. Biochem. 118: 2693-2699, 2017. © 2017 Wiley Periodicals, Inc.

BackgroundPlatelet clumping is a common occurrence during peripheral blood hematopoietic stem cell (HSC) collection using the Spectra Optia mononuclear cell (MNC) protocol. If clumping persists, it may prevent continuation of the collection and interfere with proper MNC separation. This study is the first to report the incidence of clumping, identify precollection factors associated with platelet clumping, and describe the degree to which platelet clumping interferes with HSC product yield.Study design and methodsIn total, 258 HSC collections performed on 116 patients using the Optia MNC protocol were reviewed. Collections utilized heparin in anticoagulant citrate dextrose to facilitate large-volume leukapheresis. Linear and logistic regression models were utilized to determine which precollection factors were predictive of platelet clumping and whether clumping was associated with product yield or collection efficiency.ResultsPlatelet clumping was observed in 63% of collections. Multivariable analysis revealed that a lower white blood cell count was an independent predictor of clumping occurrence. Chemotherapy mobilization and a lower peripheral blood CD34+ cell count were predictors of the degree of clumping. Procedures with clumping had higher collection efficiency but lower blood volume processed on average, resulting in no difference in collection yields. Citrate toxicity did not correlate with clumping.ConclusionAlthough platelet clumping is a common technical problem seen during HSC collection, the total CD34+ cell-collection yields were not affected by clumping. WBC count, mobilization approach, and peripheral blood CD34+ cell count can help predict clumping and potentially drive interventions to proactively manage clumping.

In 2010, when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.

In 2010, when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.

The role of sex in biomedical studies has often been overlooked, despite evidence of sexually dimorphic effects in some biological studies. Here, we used high-throughput phenotype data from 14,250 wildtype and 40,192 mutant mice (representing 2,186 knockout lines), analysed for up to 234 traits, and found a large proportion of mammalian traits both in wildtype and mutants are influenced by sex. This result has implications for interpreting disease phenotypes in animal models and humans.

ABSTRACT The highly social honey bee has dense populations but a significantly reduced repertoire of immune genes relative to solitary species, suggesting a greater reliance on social immunity. Here we investigate immune gene expression and gut microbial succession in queens during colony introduction. Recently mated queens were placed into an active colony or a storage hive for multiple queens: a queen-bank. Feeding intensity, social context, and metabolic demand differ greatly between the two environments. After 3 weeks, we examined gene expression associated with oxidative stress and immunity and performed high-throughput sequencing of the queen gut microbiome across four alimentary tract niches. Microbiota and gene expression in the queen hindgut differed by time, queen breeder source, and metabolic environment. In the ileum, upregulation of most immune and oxidative stress genes occurred regardless of treatment conditions, suggesting postmating effects on gut gene expression. Counterintuitively, queens exposed to the more social colony environment contained significantly less bacterial diversity indicative of social immune factors shaping the queens microbiome. Queen bank queens resembled much older queens with decreased Alpha 2.1, greater abundance of Lactobacillus firm5 and Bifidobacterium in the hindgut, and significantly larger ileum microbiotas, dominated by blooms of Snodgrassella alvi. Combined with earlier findings, we conclude that the queen gut microbiota experiences an extended period of microbial succession associated with queen breeder source, postmating development, and colony assimilation. IMPORTANCE In modern agriculture, honey bee queen failure is repeatedly cited as one of the major reasons for yearly colony loss. Here we discovered that the honey bee queen gut microbiota alters according to early social environment and is strongly tied to the identity of the queen breeder. Like human examples, this early life variation appears to set the trajectory for ecological succession associated with social assimilation and queen productivity. The high metabolic demand of natural colony assimilation is associated with less bacterial diversity, a smaller hindgut microbiome, and a downregulation of genes that control pathogens and oxidative stress. Queens placed in less social environments with low metabolic demand (queen banks) developed a gut microbiota that resembled much older queens that produce fewer eggs. The queens key reproductive role in the colony may rely in part on a gut microbiome shaped by social immunity and the early queen rearing environment.

Purpose: Platinum-based chemotherapy with or without immunotherapy is the mainstay of treatment for advanced stage non-small cell lung cancer (NSCLC) lacking a molecular driver alteration. Pre-clinical studies have reported that pharmacological ascorbate (P-AscH-) enhances NSCLC response to platinum-based therapy. We conducted a phase II clinical trial combining P-AscH- with carboplatin-paclitaxel chemotherapy. Experimental design: Chemotherapy naïve advanced stage NSCLC patients received 75 g ascorbate twice per week intravenously with carboplatin and paclitaxel every three weeks for four cycles. The primary endpoint was to improve tumor response per Response Evaluation Criteria in Solid Tumors (RECIST) v1.1 compared to the historical control of 20%. The trial was conducted as an optimal Simon's two-stage design. Blood samples were collected for exploratory analyses. Results: The study enrolled 38 patients and met its primary endpoint with an objective response rate of 34.2% (p = 0.03). All were confirmed partial responses (cPR). The disease control rate was 84.2% (stable disease + cPR). Median progression-free and overall survival were 5.7 months and 12.8 months, respectively. Treatment-related adverse events (TRAE) included one grade 5 (neutropenic fever) and five grade 4 events (cytopenias). Cytokine and chemokine data suggest that the combination elicits an immune response. Immunophenotyping of peripheral blood mononuclear cells demonstrated an increase in effector CD8 T-cells in patients with a progression-free survival (PFS) ≥ 6 months. Conclusions: The addition of P-AscH- to platinum-based chemotherapy improved tumor response in advanced stage NSCLC. P-AscH- appears to alter the host immune response and needs further investigation as a potential adjuvant to immunotherapy.

Background Research waste is prevalent in many scientific fields despite a number of initiatives to improve research practices. Interventions to improve practice are often implemented without evaluating their effectiveness. It is therefore important to identify the interventions that have been evaluated, assess how they have been evaluated and to identify areas where further research is required. Objectives A scoping review will be undertaken to assess what interventions, aimed at researchers or research teams, to improve research design and conduct have been evaluated. This review will also consider when in the research pathway these interventions are implemented; what aspects of research design or conduct are being targeted; and who is implementing these interventions. Methods Interventions which aim to improve the design or conduct of research will be eligible for inclusion. The review will not include interventions aimed at hypothetical research projects or interventions implemented without evaluation. The following sources will be searched: MEDLINE, EMBASE, ERIC, HMIC, EconLit, Social Policy and Practice, ProQuest theses, and MetaArXiv. Hand searching of references and citations of included studies will also be undertaken. Searches will be limited to articles published in the last 10 years. Data extraction will be completed using a data extraction template developed for this review. Results will be tabulated by type of intervention, research stage, and outcome. A narrative review will also be provided addressing each of the objectives.

Gadfly petrels (genus Pterodroma) are one of the most threatened groups of birds. They are exceptionally well adapted to forage over enormous areas to maximize chances of encountering prey. Their wide-ranging travel, extensive use of oceanic habitats beyond national jurisdictions (the high seas), and limited information on their at-sea distributions and foraging ecology pose several management challenges. Here, we examined the foraging distributions and habitat preferences of three gadfly petrels that breed on Phillip Island (Norfolk Island Group), in the southwest Pacific Ocean, and tested the ability of species distribution models (SDMs) to predict important marine habitats. GPS loggers were deployed in 2018 and 2019 on chick-provisioning black-winged petrels (P. nigripennis) and white-necked petrels (P. cervicalis) and in 2020 on Kermadec petrels (P. neglecta), and hidden Markov models (HMMs) were used to estimate behavioral states across 387 foraging trips. SDMs were built using six algorithms and the predictive performance of models constructed using conventional random cross-validation (CV) was compared to those constructed with spatially independent CV. All three species demonstrated dual-foraging strategies with short trips closer to the colony and longer, presumably self-provisioning, trips with maximum distances from the colony of several thousand kilometers for black-winged and white-necked petrels. Foraging areas of each species were distinctly partitioned across the Tasman Sea during long trips, but there was high overlap during short trips. Black-winged and white-necked petrels exhibited area-restricted search foraging behavior throughout their foraging ranges which spanned almost the entire Tasman Sea and into the western Pacific, whereas the foraging range of Kermadec petrels was restricted closer to the colony. Approximately half of each species’ foraging range extended into the high seas. Response curves and variable importance between the two SDM CV approaches were similar, suggesting that model fitting was robust to the CV approach. However, evaluation using spatially independent CV indicated that generalizability of ensemble SDMs to new data ranged from poor to fair for all three species. This suggests that the maximal-area foraging strategy of gadfly petrels (whereby they search opportunistically for resources across expansive oceanic habitats) results in weak or wide associations with environmental features making predicting important habitats extremely challenging.

Abstract Background Selection has dramatically shaped genetic and phenotypic variation in bread wheat. We can assess the genomic basis of historical phenotypic changes, and the potential for future improvement, using experimental populations that attempt to undo selection through the randomizing effects of recombination. Results We bred the NIAB Diverse MAGIC multi-parent population comprising over 500 recombinant inbred lines, descended from sixteen historical UK bread wheat varieties released between 1935 and 2004. We sequence the founders’ genes and promoters by capture, and the MAGIC population by low-coverage whole-genome sequencing. We impute 1.1 M high-quality SNPs that are over 99% concordant with array genotypes. Imputation accuracy only marginally improves when including the founders’ genomes as a haplotype reference panel. Despite capturing 73% of global wheat genetic polymorphism, 83% of genes cluster into no more than three haplotypes. We phenotype 47 agronomic traits over 2 years and map 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Around half of these overlap known quantitative trait loci. Most traits exhibit extensive polygenicity, as revealed by multi-locus shrinkage modelling. Conclusions Our results are consistent with a gene pool of low haplotypic diversity, containing few novel loci of large effect. Most past, and projected future, phenotypic changes arising from existing variation involve fine-scale shuffling of a few haplotypes to recombine dozens of polygenic alleles of small effect. Moreover, extensive pleiotropy means selection on one trait will have unintended consequences, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break unfavorable trait-trait associations.

Objectives: Pediatric thyroid cancer is rare. Most cases are well-differentiated thyroid cancers (WDTCs). However, gross laryngotracheal invasion of WDTCs is unusual. This report details the first case in English medical literature of a pediatric WDTC invading the trachea. Methods: Thyroid stimulating hormone, free triiodothyronine, free thyroxine, thyroglobulin, parathyroid hormone, calcitonin, thyroglobulin antibody, chest magnetic resonance imaging, neck ultrasound, neck computed tomography, and fine needle aspiration were performed. Results: A 9-year-old boy with moderate persistent asthma presented with increasing upper respiratory symptoms. Spirometry suggested a fixed upper airway obstruction. Chest x-ray revealed a left tracheal shift, and chest magnetic resonance imaging identified a right thyroid mass. Thyroglobulin level was 809 ng/mL (normal, ≤33 ng/mL). Results of thyroid stimulating hormone, free triiodothyronine, free thyroxine, parathyroid hormone, calcitonin, and thyroglobulin antibody were normal. Neck ultrasound revealed 2 right thyroid lobe nodules. Neck computed tomography revealed tracheal compression. Fine needle aspiration of the largest nodule yielded atypia of undetermined significance. Bronchoscopy findings at his local hospital were concerning for tracheal invasion. He underwent total thyroidectomy, cricotracheal resection, reconstruction, and radioactive iodine therapy (220 mCi). Pathology demonstrated a well-differentiated papillary thyroid carcinoma without solid or diffuse sclerosing subtype components. Tumor cytogenetic and single nucleotide polymorphism microarray studies showed normal findings. One year postoperatively, neck ultrasound demonstrated no recurrence, and thyroglobulin levels were undetectable while on levothyroxine therapy. Conclusion: Pediatric WDTC invading the trachea has not been reported.