Search

Background/AimsClinical fellows support the hospital workforce while gaining experience in different specialities, research, leadership and teaching. The authors aimed to assess the impact of clinical fellow programmes in an acute teaching hospital trust.MethodsAn anonymous electronic service evaluation was sent to clinical fellows to investigate their views on whether the programme had improved patient safety, doctors' clinical performance, training and wellbeing. Thematic analysis was used to analyse the free-text responses.ResultsA total of 95 out of 144 clinical fellows responded to the evaluation survey. The clinical fellows believed that the programme had improved patient safety, clinical performance (time to manage acute patients), foundation and internal medicine training, undergraduate teaching and junior doctors' wellbeing. Four similar themes emerged from the free-text responses: career development, patient safety, training and doctors' wellbeing.ConclusionsClinical fellow programmes may improve patient safety, clinical performance, training, undergraduate education and doctors' wellbeing.

Breast cancer results in a three‐ to four‐fold increased risk of venous thromboembolism (VTE), which is associated with reduced patient survival. Despite this, the mechanisms underpinning breast cancer‐associated thrombosis remain poorly defined. Tumor cells can trigger endothelial cell (EC) activation resulting in increased von Willebrand factor (VWF) secretion. Importantly, elevated plasma VWF levels constitute an independent biomarker for VTE risk. Moreover, in a model of melanoma, treatment with low molecular weight heparin (LMWH) negatively regulated VWF secretion and attenuated tumor metastasis. To investigate the role of VWF in breast cancer metastasis and examine the effect of LMWH in modulating EC activation and breast tumor transmigration. von Willebrand factor levels were measured by ELISA. Primary ECs were used to assess tumor‐induced activation, angiogenesis, tumor adhesion, and transendothelial migration. Patients with metastatic breast cancer have markedly elevated plasma VWF:Ag levels that also correlate with poorer survival. MDA‐MB‐231 and MCF‐7 breast cancer cells induce secretion of VWF, angiopoietin‐2, and osteoprotegerin from ECs, which is further enhanced by the presence of platelets. Vascular endothelial growth factor‐A (VEGF‐A) plays an important role in modulating breast cancer‐induced VWF release. Moreover, VEGF‐A from breast tumor cells also contributes to a pro‐angiogenic effect on ECs. VWF multimers secreted from ECs, in response to tumor‐VEGF‐A, mediate adhesion of breast tumor cells along the endothelium. LMWH inhibits VWF‐breast tumor adhesion and transendothelial migration. Our findings highlight the significant crosstalk between tumor cells and the endothelium including increased VWF secretion which may contribute to tumor metastasis.

Breast cancer results in a three‐ to four‐fold increased risk of venous thromboembolism (VTE), which is associated with reduced patient survival. Despite this, the mechanisms underpinning breast cancer‐associated thrombosis remain poorly defined. Tumor cells can trigger endothelial cell (EC) activation resulting in increased von Willebrand factor (VWF) secretion. Importantly, elevated plasma VWF levels constitute an independent biomarker for VTE risk. Moreover, in a model of melanoma, treatment with low molecular weight heparin (LMWH) negatively regulated VWF secretion and attenuated tumor metastasis.

Glioblastoma is an aggressive brain tumor, thus early detection and immunotherapy may improve survival. This study includes large-scale analyses of the peptidome of the plasma-soluble HLA molecules of Glioblastoma patients and healthy controls, and the membranal HLA of the patients' tumors. These HLA peptidomes contain many HLA peptides derived from tumor antigens, providing potential opportunities for early diagnosis, and possibly also for personalized immunotherapy. The results emphasize the usefulness of the plasma-soluble HLA peptidomes as a source for biomarkers.

Patients with glioblastoma currently do not sufficiently benefit from recent breakthroughs in cancer treatment that use checkpoint inhibitors1,2. For treatments using checkpoint inhibitors to be successful, a high mutational load and responses to neoepitopes are thought to be essential3. There is limited intratumoural infiltration of immune cells4in glioblastoma and these tumours contain only 30–50 non-synonymous mutations5. Exploitation of the full repertoire of tumour antigens—that is, both unmutated antigens and neoepitopes—may offer more effective immunotherapies, especially for tumours with a low mutational load. Here, in the phase I trial GAPVAC-101 of the Glioma Actively Personalized Vaccine Consortium (GAPVAC), we integrated highly individualized vaccinations with both types of tumour antigens into standard care to optimally exploit the limited target space for patients with newly diagnosed glioblastoma. Fifteen patients with glioblastomas positive for human leukocyte antigen (HLA)-A*02:01 or HLA-A*24:02 were treated with a vaccine (APVAC1) derived from a premanufactured library of unmutated antigens followed by treatment with APVAC2, which preferentially targeted neoepitopes. Personalization was based on mutations and analyses of the transcriptomes and immunopeptidomes of the individual tumours. The GAPVAC approach was feasible and vaccines that had poly-ICLC (polyriboinosinic-polyribocytidylic acid-poly-l-lysine carboxymethylcellulose) and granulocyte–macrophage colony-stimulating factor as adjuvants displayed favourable safety and strong immunogenicity. Unmutated APVAC1 antigens elicited sustained responses of central memory CD8+T cells. APVAC2 induced predominantly CD4+T cell responses of T helper 1 type against predicted neoepitopes.

Glioblastoma multiforme (GBM) is the most aggressive brain tumor with poor prognosis to most patients. Immunotherapy of GBM is a potentially beneficial treatment option, whose optimal implementation may depend on familiarity with tumor specific antigens, presented as HLA peptides by the GBM cells. Furthermore, early detection of GBM, such as by a routine blood test, may improve survival, even with the current treatment modalities. This study includes large-scale analyses of the HLA peptidome (immunopeptidome) of the plasma-soluble HLA molecules (sHLA) of 142 plasma samples, and the membranal HLA of GBM tumors of 10 of these patients' tumor samples. Tumor samples were fresh-frozen immediately after surgery and the plasma samples were collected before, and at multiple visits after surgery. In total, this HLA peptidome analysis involved 52 different HLA allotypes and resulted in the identification of more than 35,000 different HLA peptides. Strong correlations were observed in the signal intensities and in the repertoires of identified peptides between the tumors and plasma-soluble HLA peptidomes of the individual patients, whereas low correlations were observed between these HLA peptidomes and the tumors' proteomes. HLA peptides derived from Cancer/Testis Antigens (CTAs) were selected based on their presence among the HLA peptidomes of the patients and absence of expression of their source genes from any healthy and essential human tissues, except from immune-privileged sites. Additionally, peptides were selected as potential biomarkers if their levels in the plasma-sHLA peptidome were significantly reduced after the removal of tumor mass. The CTAs identified among the analyzed HLA peptidomes provide new opportunities for personalized immunotherapy and for early diagnosis of GBM.

A personal narrative is presented which explores the author's experience of searching for the remains of a crashed bomber with metal detectors and finding some valuable objects.

This article relates a story about the Heinkel 111P, a German bomber aircraft, during the second world war between the British and the Germans. The event took place in April 1941 over Great Britain when the Germans attacked its cities and towns in retaliation to their defeat in the Battle of Britain. The Heinkel 111P was brought down by the British Boulton-Paul Defiant fighters in a counter attack. The combat report of Flight Sergeant E. R. Thorn, who piloted the British aircraft, is also presented.

The cAMP-specific phosphodiesterase-4 (PDE4) gene family is the target of several potential selective therapeutic inhibitors. The four PDE4 genes generate several distinct protein-coding isoforms through the use of alternative promoters and 5'-coding exons. Using mouse transcripts, we identified a novel, super-short isoform of human PDE4B encoding a novel 5' terminus, which we label PDE4B5. The protein-coding region of the novel 5' exon is conserved across vertebrates, chicken, zebrafish, and fugu. Reverse-transcription-polymerase chain reaction (PCR) and quantitative (PCR) measurements show that this isoform is brain-specific. The novel protein is 58 +/- 2 kDa; it has cAMP hydrolyzing enzymatic activity and is inhibited by PDE4-selective inhibitors rolipram and cilomilast (Ariflo). Confocal and subcellular fractionation analyses show that it is distributed predominantly and unevenly within the cytosol. The 16 novel N-terminal residues of PDE4B5 are identical to the 16 N-terminal residues of the super-short isoform of PDE4D (PDE4D6), which is also brain-specific. PDE4B5 is able to bind the scaffold protein DISC1, whose gene has been linked to schizophrenia. Microarray expression profiling of the PDE4 gene family shows that specific PDE4 genes are enriched in muscle and blood fractions; however, only by monitoring the individual isoforms is the brain specificity of the super-short PDE4D and PDE4B isoforms revealed. Understanding the distinct tissue specificity of PDE4 isoforms will be important for understanding phosphodiesterase biology and opportunities for therapeutic intervention.

Describes several main campaign medals issued during World War I. 1914 Star, Territorial Force War and British War medals; On War Service badge; Brooches.

The fires that burned the Greater Yellowstone Area (GYA) during the summer of 1988 were the largest ever recorded for the region. Wildfire can have profound indirect effects on associated aquatic ecosystems by increased nutrient loading, sediment erosion and runoff. Satellite remote sensing and water quality sampling was used to compare pre- versus post-fire conditions in the GYA's large oligotrophic (high transparency, low productivity) lakes. Inputs of suspended sediment to Jackson Lake appear to have increased. Yellowstone Lake has not shown any discernable shift in water quality. The insights gained separately from the Landsat Thematic and NOAA AVHRR remote sensing systems, along with conventional in-situ sampling, can be combined into a useful water quality monitoring tool.

Along the Kamchatka-Kuril-Japan-Izu-Bonin-Mariana subduction zones, the old age of the subducting Pacific Plate and the rapid subduction rate together suggest that earthquakes should occur to the bottom of the transition zone. However, the seismicity cutoff varies in depth between 350 km and 650 km. Along these subduction zones, the largest deep-focus earthquakes invariably occur near the depth of the local seismicity cutoff regardless of its depth. The events near the seismicity cutoffs also have systematically different focal mechanisms than shallower events. Furthermore, data from S660Parrivals, residual sphere analysis, and tomographic studies all show that the slab dip consistently steepens to a near-vertical orientation at the seismicity cutoff. This change in slab dip indicates a strength loss in the slab. We hypothesize the following causal connection among all these observations: The cold temperatures in the slab kinetically hinder the olivine to spinel phase change and allow the olivine to persist metastably to depths well below its equilibrium pressure. When the phase transition occurs, it nucleates very fine-grained spinel which acts as a lubricant, allowing the initiation of earthquake faulting at high confining pressures which further nucleates additional fine-grained spinel. The cold anomaly of the slab severely inhibits the growth of the nucleated spinel crystals. The presence of the fine-grained spinel crystals reduces the strength of the coldest part of the slab by several orders of magnitude, allowing high slab deformation rates. Additionally, the phase change, by increasing the density, provides a negative buoyancy force. Combined, these processes reduce the slab membrane strength and allow the slab to descend at a steeper dip.

Ten riverine fish species were tested at 10, 20, and 30 C to determine their resistance to monochloramine. The exposure regime consisted of four 40-minute exposures administered at 5-hour intervals over 24 hours. All species exhibited an inverse relationship between temperature and median lethal (LC50) concentrations. LC50 values generally decreased by a factor of two as the exposure temperature increased from 10 to 30 C. LC50 values ranged from 0.35 mg/liter at 30 C for the emerald shiner to 3.00 mg/liter at 10 C for the bluegill. Based on their resistance to monchloramine at 30 C the fish were separated into sensitive and resistant groups. The sensitive group, which included (in decreasing order of sensitivity) the emerald shiner (Notropis atherinoides), spotfin shiner (Notropis spilopterus), common shiner (Notropis cornutus), channel catfish (Ictalurus punctatus), white sucker (Catastomus commersoni), and sauger (Stizostedion canadense), had LC50 values ranging from 0.35 to 0.71 mg/liter. The resistant group, freshwater drum (Aplodinotus grunniens), white bass (Morone chrysops), bluegill (Lepomis macrochirus), and carp (Cyprinus carpio) had LC50 values of 1.0–1.50 mg/liter.

ABSTRACT: We analyzed the spatial heterogeneity in vegetation indices among 13 North American landscapes by using full Landsat Thematic Mapper images. Landscapes varied broadly in the statistical distribution of vegetation indices, but were successfully ordinated by using a measure of central tendency (the mean) and a measure of dispersion (the standard deviation or the coefficient of variation). Differences in heterogeneity among landscapes were explained by their topographic relief and their land cover. Landscape heterogeneity (standard deviation of the Normalized Difference Vegetation Index, NDVI) tended to increase linearly with topographic relief (standard deviation of elevation), but landscapes with low relief were much more heterogeneous than expected from this relationship. The latter were characterized by a large proportion of agricultural land. Percent agriculture, in turn, was inversely related to topographic relief. The strength of these relationships was evaluated against changes in image spatial resolution (grain size). Aggregation of NDVI images to coarser grain size resulted in steady decline of their standard deviation. Although the relationship between landscape heterogeneity and explanatory variables was generally preserved, rates of decrease in heterogeneity with grain size differed among landscapes. A spatial autocorrelation analysis showed that rates of decrease were related to the scale at which pattern is manifested. On one end of the spectrum are agricultural, low-relief landscapes with low spatial autocorrelation and small-scale heterogeneity associated with fields; their heterogeneity decreased sharply as grain size increased. At the other end, desert landscapes were characterized by low small-scale heterogeneity, high spatial autocorrelation, and almost no change in heterogeneity as grain sized was increased—their heterogeneity, associated with land forms, was present at a large scale.

Focuses on the advantages of private equity financing. Absence of fixed obligatory interest and principal payments; Access to additional management expertise and deep pockets; Opportunities for owners to cash out.

The case of a female patient alive and well nine years after she suffered a perforated carcinoma of the colon is recorded and discussed. In the treatment of patients with a malignant growth who survive for long periods of time, there is an overwhelming desire to call the patient cured, combined with an increasing reluctance to take any such presumption. This patient's continuing survival over ten years since the known start of the bowel cancer, and over nine years since its rupture and known dissemination, combined with recent knowledge of the apparent lack of local disease, has inspired the report of this case as an encouragement to others involved in this continuing struggle.

The additional author support information was erroneously omitted from the Supplementary Information. This has been corrected online.

ABSTRACTImmune checkpoint blockade (ICB) is currently evaluated in patients with glioblastoma (GBM), based on encouraging clinical data in other cancers, and results from studies with the methylcholanthrene-induced GL261 mouse glioma. In this paper, we describe a novel model faithfully recapitulating some key human GBM characteristics, including low mutational load, a factor reported as a prognostic indicator of ICB response. Consistent with this observation, SB28 is completely resistant to ICB, contrasting with treatment sensitivity of the more highly mutated GL261. Moreover, SB28 shows features of a poorly immunogenic tumor, with low MHC-I expression and modest CD8+T-cell infiltration, suggesting that it may present similar challenges for immunotherapy as human GBM. Based on these key features for immune reactivity, SB28 may represent a treatment-resistant malignancy likely to mirror responses of many human tumors. We therefore propose that SB28 is a particularly suitable model for optimization of GBM immunotherapy.

ABSTRACTThe B16F10 murine melanoma cell line displays a low expression of MHC class I molecules favoring immune evasion and metastases in immunocompetent C57 BL/6 wild-type mice. Here, we generated metastases to the liver, an organ that is skewed towards immune tolerance, by intrasplenic injection of B16F10 cells in syngeneic C57 BL/6 compared to allogeneic Balb/c mice. Surprisingly, Balb/c mice, which usually display a pronounced M2 macrophage and Th2 T cell polarization, were ∼3 times more susceptible to metastasis than C57 BL/6 mice, despite a much higher M1 and Th1 T cell immune response. The anti-metastatic advantage of C57 BL/6 mice could be attributed to a more potent NK-cell mediated cytotoxicity against B16F10 cells. Our findings highlight the role of NK cells in innate anti-tumor immunity in the context of the liver – particularly against highly aggressive MHC I-deficient cancer cells. Moreover, the B16F10 model of melanoma liver metastasis is suited for developing novel therapies targeting innate NK cell related immunity in liver metastases and liver cancer.

Cancer immunotherapies such as immune checkpoint inhibitors (CI) are approved for a broad range of solid tumors and selected hematologic malignancies. Clinical response to CIs has been shown to be associated with mutation burden and is predicated on the presence of T cells specific to tumor-associated antigens. Therefore, increasing the frequency of such T cell responses should increase the efficacy of anti-tumor immunity. Individualized neoantigen peptide vaccines are a promising strategy to activate tumor-specific T cell immunity. Next generation sequencing of tumor specimens is now widely available and novel computational algorithms provide the means for the prediction and selection of neoantigens.

Next generation sequencing enables identification of immunogenic tumor mutations targetable by individualized vaccines. In the B16F10 melanoma system as pre-clinical proof-of-concept model, we found a total of 563 non-synonymous expressed somatic mutations. Of the mutations we tested, one third were immunogenic. Immunization conferred in vivo tumor control, qualifying mutated epitopes as source for effective vaccines.

Cancer cell lines are a tremendous resource for cancer biology and therapy development. These multipurpose tools are commonly used to examine the genetic origin of cancers, to identify potential novel tumor targets, such as tumor antigens for vaccine devel­opment, and utilized to screen potential therapies in preclinical studies. Mutations, gene expression, and drug sensitivity have been determined for many cell lines using next-generation sequencing (NGS). However, the human leukocyte antigen (HLA) type and HLA expression of tumor cell lines, characterizations necessary for the development of cancer vaccines, have remained largely incomplete and, such information, when available, has been distributed in many publications. Here, we determine the 4-digit HLA type and HLA expression of 167 cancer and 10 non-cancer cell lines from publically available RNA-Seq data. We use standard NGS RNA-Seq short reads from “whole transcriptome” sequencing, map reads to known HLA types, and statistically determine HLA type, heterozygosity, and expression. First, we present previously unreported HLA Class I and II genotypes. Second, we determine HLA expression levels in each cancer cell line, providing insights into HLA downregulation and loss in cancer. Third, using these results, we provide a fundamental cell line “barcode” to track samples and prevent sample annotation swaps and contamination. Fourth, we integrate the cancer cell-line specific HLA types and HLA expression with available cell-line specific mutation information and existing HLA binding prediction algorithms to make a catalog of predicted antigenic mutations in each cell line. The compilation of our results are a fundamental resource for all researchers selecting specific cancer cell lines based on the HLA type and HLA expression, as well as for the development of immunotherapeutic tools for novel cancer treatment modalities.

ABSTRACTStudies of the host response to virus infection typically focus on protein-coding genes. However, non-protein-coding RNAs (ncRNAs) are transcribed in mammalian cells, and the roles of many of these ncRNAs remain enigmas. Using next-generation sequencing, we performed a whole-transcriptome analysis of the host response to severe acute respiratory syndrome coronavirus (SARS-CoV) infection across four founder mouse strains of the Collaborative Cross. We observed differential expression of approximately 500 annotated, long ncRNAs and 1,000 nonannotated genomic regions during infection. Moreover, studies of a subset of these ncRNAs and genomic regions showed the following. (i) Most were similarly regulated in response to influenza virus infection. (ii) They had distinctive kinetic expression profiles in type I interferon receptor and STAT1 knockout mice during SARS-CoV infection, including unique signatures of ncRNA expression associated with lethal infection. (iii) Over 40% were similarly regulated in vitroin response to both influenza virus infection and interferon treatment. These findings represent the first discovery of the widespread differential expression of long ncRNAs in response to virus infection and suggest that ncRNAs are involved in regulating the host response, including innate immunity. At the same time, virus infection models provide a unique platform for studying the biology and regulation of ncRNAs.IMPORTANCEMost studies examining the host transcriptional response to infection focus only on protein-coding genes. However, there is growing evidence that thousands of non-protein-coding RNAs (ncRNAs) are transcribed from mammalian genomes. While most attention to the involvement of ncRNAs in virus-host interactions has been on small ncRNAs such as microRNAs, it is becoming apparent that many long ncRNAs (>200 nucleotides [nt]) are also biologically important. These long ncRNAs have been found to have widespread functionality, including chromatin modification and transcriptional regulation and serving as the precursors of small RNAs. With the advent of next-generation sequencing technologies, whole-transcriptome analysis of the host response, including long ncRNAs, is now possible. Using this approach, we demonstrated that virus infection alters the expression of numerous long ncRNAs, suggesting that these RNAs may be a new class of regulatory molecules that play a role in determining the outcome of infection.

Background Interpretation of lists of genes or proteins with altered expression is a critical and time-consuming part of microarray and proteomics research, but relatively little attention has been paid to methods for extracting biological meaning from these output lists. One powerful approach is to examine the expression of predefined biological pathways and gene sets, such as metabolic and signaling pathways and macromolecular complexes. Although many methods for measuring pathway expression have been proposed, a systematic analysis of the performance of multiple methods over multiple independent data sets has not previously been reported.Results Five different measures of pathway expression were compared in an analysis of nine publicly available mRNA expression data sets. The relative sensitivity of the metrics varied greatly across data sets, and the biological pathways identified for each data set are also dependent on the choice of pathway activation metric. In addition, we show that removing incoherent pathways prior to analysis improves specificity. Finally, we create and analyze a public map of pathway expression in human tissues by gene-set analysis of a large compendium of human expression data.Conclusion We show that both the detection sensitivity and identity of pathways significantly perturbed in a microarray experiment are highly dependent on the analysis methods used and how incoherent pathways are treated. Analysts should thus consider using multiple approaches to test the robustness of their biological interpretations. We also provide a comprehensive picture of the tissue distribution of human gene pathways and a useful public archive of human pathway expression data.

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.