Avian ecological studies in a sagebrush community: bird responses to fire and territory dynamics in a sparrow population

In 1980-1985, I documented the responses of nongame birds to a prescribed fire in an Idaho sagebrush (Artemisia spp.) community, and I tested the hypothesis that territory shifts by sage sparrows (Amphispiza belli) represented adaptive adjustments in site use. The burn was incomplete (45%) but altered major components of the vegetation. Burned plots supported 1 more bird species than controls, and although total bird densities declined the year after fire, they were greater on burned plots than on controls by the fourth postburn year. Sage sparrow numbers were unaffected by fire; Brewer\u27s sparrow (Spizella breweri) numbers declined in the 2 breeding seasons immediately after fire but increased dramatically thereafter. Sage thrashers (Oreoscoptes montanus) showed no response to fire; horned larks (Eremophila alpestris) and vesper sparrows (Pooecetes gramineus) colonized burned areas. Return rate of male sage sparrows was somewhat reduced 2 years after fire, nest survival probability was greater on burned plots than on controls the first year after fire, and nestling growth rate increased the first year postburn. Sage sparrow mating success, clutch size, and fledgling production were not influenced by fire. Brewer\u27s sparrow return rate, mating success, clutch size, nest survival probability, fledgling production, and nestling growth were unaffected by fire. Burning altered nest-site characteristics of both sparrows;I predicted that territory shifts by sage sparrows should (1) result in changes in territory characteristics, (2) be influenced by previous reproductive success and result in greater success, and (3) decline in magnitude for individual males over time. Habitat features of territories changed little as a result of shifts, and were unrelated to reproductive success. Territory size increased after shifts, and was positively related to reproductive success. The magnitude of territory shifts was negatively correlated with preshift fledgling success, and after shifts, males experienced greater reproductive success than before. Successive territory shifts by individual males became progressively smaller. Thus, territory shifting by sage sparrows seems to be adaptive behavior aimed primarily at increasing territory size

Automated cardiovascular magnetic resonance image analysis with fully convolutional networks

Background: Cardiovascular magnetic resonance (CMR) imaging is a standard imaging modality for assessing cardiovascular diseases (CVDs), the leading cause of death globally. CMR enables accurate quantification of the cardiac chamber volume, ejection fraction and myocardial mass, providing information for diagnosis and monitoring of CVDs. However, for years, clinicians have been relying on manual approaches for CMR image analysis, which is time consuming and prone to subjective errors. It is a major clinical challenge to automatically derive quantitative and clinically relevant information from CMR images. Methods: Deep neural networks have shown a great potential in image pattern recognition and segmentation for a variety of tasks. Here we demonstrate an automated analysis method for CMR images, which is based on a fully convolutional network (FCN). The network is trained and evaluated on a large-scale dataset from the UK Biobank, consisting of 4,875 subjects with 93,500 pixelwise annotated images. The performance of the method has been evaluated using a number of technical metrics, including the Dice metric, mean contour distance and Hausdorff distance, as well as clinically relevant measures, including left ventricle (LV) end-diastolic volume (LVEDV) and end-systolic volume (LVESV), LV mass (LVM); right ventricle (RV) end-diastolic volume (RVEDV) and end-systolic volume (RVESV). Results: By combining FCN with a large-scale annotated dataset, the proposed automated method achieves a high performance in segmenting the LV and RV on short-axis CMR images and the left atrium (LA) and right atrium (RA) on long-axis CMR images. On a short-axis image test set of 600 subjects, it achieves an average Dice metric of 0.94 for the LV cavity, 0.88 for the LV myocardium and 0.90 for the RV cavity. The mean absolute difference between automated measurement and manual measurement was 6.1 mL for LVEDV, 5.3 mL for LVESV, 6.9 gram for LVM, 8.5 mL for RVEDV and 7.2 mL for RVESV. On long-axis image test sets, the average Dice metric was 0.93 for the LA cavity (2-chamber view), 0.95 for the LA cavity (4-chamber view) and 0.96 for the RA cavity (4-chamber view). The performance is comparable to human inter-observer variability. Conclusions: We show that an automated method achieves a performance on par with human experts in analysing CMR images and deriving clinically relevant measures

Genetic and Epigenetic Factors at COL2A1 and ABCA4 Influence Clinical Outcome in Congenital Toxoplasmosis

Background: Primary Toxoplasma gondii infection during pregnancy can be transmitted to the fetus. At birth, infected infants may have intracranial calcification, hydrocephalus, and retinochoroiditis, and new ocular lesions can occur at any age after birth. Not all children who acquire infection in utero develop these clinical signs of disease. Whilst severity of disease is influenced by trimester in which infection is acquired by the mother, other factors including genetic predisposition may contribute.Methods and Findings: In 457 mother-child pairs from Europe, and 149 child/parent trios from North America, we show that ocular and brain disease in congenital toxoplasmosis associate with polymorphisms in ABCA4 encoding ATP-binding cassette transporter, subfamily A, member 4. Polymorphisms at COL2A1 encoding type II collagen associate only with ocular disease. Both loci showed unusual inheritance patterns for the disease allele when comparing outcomes in heterozygous affected children with outcomes in affected children of heterozygous mothers. Modeling suggested either an effect of mother's genotype, or parent-of-origin effects. Experimental studies showed that both ABCA4 and COL2A1 show isoform-specific epigenetic modifications consistent with imprinting.Conclusions: These associations between clinical outcomes of congenital toxoplasmosis and polymorphisms at ABCA4 and COL2A1 provide novel insight into the molecular pathways that can be affected by congenital infection with this parasite

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Clínica e cirurgia de equinos

O presente relatório pretende descrever as atividades desenvolvidas no âmbito do estágio curricular do Mestrado Integrado em Medicina Veterinária da Universidade de Évora. Este relatório está separado em duas partes. Numa primeira parte apresenta-se a casuística acompanhada nos quatros meses de estágio nas diversas áreas da clínica geral de equinos, descrevendo-se alguns casos clínicos de forma mais específica. Na segunda parte é apresentada uma revisão bibliográfica sobre feridas contendo tecido de granulação, nas extremidades distais dos membros e o seu tratamento. Para terminar discutem-se três casos clínicos com diferente evolução do tecido de granulação. As feridas são das afeções mais comuns na clínica de equinos e, nesta espécie, umas das principais complicações é a formação excessiva de tecido de granulação. Desbridamento cirúrgico, corticosteroides, enxerto de pele e laser são alguns dos tratamentos a que se pode recorrer, embora algumas vezes nenhum deles seja eficaz; Equine clinic and surgery Abstract: The current report prentends to describe the activities developed in the ambit integrated internship of the master's degree in Veterinary Medicine of the University of Evora. This report is separated in two parts. In the first part it will be presented the casuistics followed in the four months of internship in the various areas of general equine practice, with some clinical cases being described more specifically. In the second part is presented a literature review about wounds with granulation tissue in the distal extremities of the limbs and their treatment. To finish, three clinical cases with diferent granulation tissue evolution are discussed. Wounds are the most common affections in the horse clinic, and in this specie, one of the main complications is the excessive formation of granulation tissue. Surgical debridement, corticosteroids, skin grafts and laser are some of the treatments that can be used, although sometimes none of them is effective

Fully-automated left ventricular mass and volume MRI analysis in the UK Biobank population cohort: evaluation of initial results

Funding was provided by British Heart Foundation (PG/14/89/31194), and by the National Institutes of Health (USA) 1R01HL121754. SN, SKP acknowledge the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre based at The Oxford University Hospitals Trust at the University of Oxford, and the British Heart Foundation Centre of Research Excellence. Aaron Lee and Steffen Petersen acknowledge support from the NIHR Biomedical Research Centre at Barts Health NHS Trust and from the “SmartHeart” EPSRC programme grant (EP/ P001009/1)

Resistance Exercise Reverses Aging in Human Skeletal Muscle

Human aging is associated with skeletal muscle atrophy and functional impairment (sarcopenia). Multiple lines of evidence suggest that mitochondrial dysfunction is a major contributor to sarcopenia. We evaluated whether healthy aging was associated with a transcriptional profile reflecting mitochondrial impairment and whether resistance exercise could reverse this signature to that approximating a younger physiological age. Skeletal muscle biopsies from healthy older (N = 25) and younger (N = 26) adult men and women were compared using gene expression profiling, and a subset of these were related to measurements of muscle strength. 14 of the older adults had muscle samples taken before and after a six-month resistance exercise-training program. Before exercise training, older adults were 59% weaker than younger, but after six months of training in older adults, strength improved significantly (P<0.001) such that they were only 38% lower than young adults. As a consequence of age, we found 596 genes differentially expressed using a false discovery rate cut-off of 5%. Prior to the exercise training, the transcriptome profile showed a dramatic enrichment of genes associated with mitochondrial function with age. However, following exercise training the transcriptional signature of aging was markedly reversed back to that of younger levels for most genes that were affected by both age and exercise. We conclude that healthy older adults show evidence of mitochondrial impairment and muscle weakness, but that this can be partially reversed at the phenotypic level, and substantially reversed at the transcriptome level, following six months of resistance exercise training