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https://www.readbyqxmd.com/read/29679847/deep-learning-in-mammography-and-breast-histology-an-overview-and-future-trends
#1
Azam Hamidinekoo, Erika Denton, Andrik Rampun, Kate Honnor, Reyer Zwiggelaar
Recent improvements in biomedical image analysis using deep learning based neural networks could be exploited to enhance the performance of Computer Aided Diagnosis (CAD) systems. Considering the importance of breast cancer worldwide and the promising results reported by deep learning based methods in breast imaging, an overview of the recent state-of-the-art deep learning based CAD systems developed for mammography and breast histopathology images is presented. In this study, the relationship between mammography and histopathology phenotypes is described, which takes biological aspects into account...
March 26, 2018: Medical Image Analysis
https://www.readbyqxmd.com/read/29674784/bat-wing-biometrics-using-collagen-elastin-bundles-in-bat-wings-as-a-unique-individual-identifier
#2
Sybill K Amelon, Sarah E Hooper, Kathryn M Womack
The ability to recognize individuals within an animal population is fundamental to conservation and management. Identification of individual bats has relied on artificial marking techniques that may negatively affect the survival and alter the behavior of individuals. Biometric systems use biological characteristics to identify individuals. The field of animal biometrics has expanded to include recognition of individuals based upon various morphologies and phenotypic variations including pelage patterns, tail flukes, and whisker arrangement...
May 29, 2017: Journal of Mammalogy
https://www.readbyqxmd.com/read/29671837/analysis-of-17-genes-detects-mutations-in-81-of-811-patients-with-lissencephaly
#3
Nataliya Di Donato, Andrew E Timms, Kimberly A Aldinger, Ghayda M Mirzaa, James T Bennett, Sarah Collins, Carissa Olds, Davide Mei, Sara Chiari, Gemma Carvill, Candace T Myers, Jean-Baptiste Rivière, Maha S Zaki, Joseph G Gleeson, Andreas Rump, Valerio Conti, Elena Parrini, M Elizabeth Ross, David H Ledbetter, Renzo Guerrini, William B Dobyns
PurposeTo estimate diagnostic yield and genotype-phenotype correlations in a cohort of 811 patients with lissencephaly or subcortical band heterotopia.MethodsWe collected DNA from 756 children with lissencephaly over 30 years. Many were tested for deletion 17p13.3 and mutations of LIS1, DCX, and ARX, but few other genes. Among those tested, 216 remained unsolved and were tested by a targeted panel of 17 genes (ACTB, ACTG1, ARX, CRADD, DCX, LIS1, TUBA1A, TUBA8, TUBB2B, TUBB, TUBB3, TUBG1, KIF2A, KIF5C, DYNC1H1, RELN, and VLDLR) or by whole-exome sequencing...
April 19, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29671337/non-histone-targets-of-kat2a-and-kat2b-implicated-in-cancer-biology
#4
Emma Bondy-Chorney, Alix Denoncourt, Yuka Sai, Michael Downey
Lysine acetylation is a critical post-translation modification that can impact a protein's localization, stability and function. Originally thought to only occur on histones, we now know thousands of non-histone proteins are also acetylated. In conjunction with many other proteins, lysine acetyltransferases (KATs) are incorporated into large protein complexes that carry out these modifications. In this review we focus on the contribution of two KATs, KAT2A and KAT2B, and their potential roles in the development and progression of cancer...
April 19, 2018: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/29669861/informational-limits-of-biological-organisms
#5
Jussi Taipale
Genomic analyses have revealed that free-living biological organisms carry between 107 and 1011 bits of information in their genomes. In large organisms with relatively small population sizes, such as humans, only in the order of 1% of the genomic information is shaped by the environment via natural selection. A much larger amount of information than this is routinely being generated by biomedical researchers, and the rapidly accumulating data is often interpreted to mean that biological systems are extremely complex...
April 18, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29666752/pathways-of-topological-rank-analysis-potra-a-novel-method-to-detect-pathways-involved-in-hepatocellular-carcinoma
#6
Chaoxing Li, Li Liu, Valentin Dinu
Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway's topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs...
2018: PeerJ
https://www.readbyqxmd.com/read/29665411/iterative-genome-editing-of-escherichia-coli-for-3-hydroxypropionic-acid-production
#7
Rongming Liu, Liya Liang, Alaksh Choudhury, Marcelo C Bassalo, Andrew D Garst, Katia Tarasava, Ryan T Gill
Synthetic biology requires strategies for the targeted, efficient, and combinatorial engineering of biological sub-systems at the molecular level. Here, we report the use of the iterative CRISPR EnAbled Trackable genome Engineering (iCREATE) method for the rapid construction of combinatorially modified genomes. We coupled this genome engineering strategy with high-throughput phenotypic screening and selections to recursively engineer multiple traits in Escherichia coli for improved production of the platform chemical 3-hydroxypropionic acid (3HP)...
April 14, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29665344/sepsis-diagnostics-in-the-era-of-omics-technologies
#8
REVIEW
Miroslav Průcha, Roman Zazula, Stefan Russwurm
Sepsis is a multifactorial clinical syndrome with an extremely dynamic clinical course and with high diverse clinical phenotype. Early diagnosis is crucial for the final clinical outcome. Previous studies have not identified a biomarker for the diagnosis of sepsis which would have sufficient sensitivity and specificity. Identification of the infectious agents or the use of molecular biology, next gene sequencing, has not brought significant benefit for the patient in terms of early diagnosis. Therefore, we are currently searching for biomarkers, through "omics" technologies with sufficient diagnostic specificity and sensitivity, able to predict the clinical course of the disease and the patient response to therapy...
2018: Prague Medical Report
https://www.readbyqxmd.com/read/29665035/challenges-of-comprehensive-taxon-sampling-in-comparative-biology-wrestling-with-rosids
#9
Ryan A Folk, Miao Sun, Pamela S Soltis, Stephen A Smith, Douglas E Soltis, Robert P Guralnick
Using phylogenetic approaches to test hypotheses on a large scale, in terms of both species sampling and associated species traits and occurrence data-and doing this with rigor despite all the attendant challenges-is critical for addressing many broad questions in evolution and ecology. However, application of such approaches to empirical systems is hampered by a lingering series of theoretical and practical bottlenecks. The community is still wrestling with the challenges of how to develop species-level, comprehensively sampled phylogenies and associated geographic and phenotypic resources that enable global-scale analyses...
April 17, 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29663162/functional-defects-of-treg-cells-new-targets-in-rheumatic-diseases-including-ankylosing-spondylitis
#10
REVIEW
Jinlin Miao, Ping Zhu
PURPOSE OF REVIEW: This study aims to review the advances of Treg cell biology, the functional defects of Treg cells, and the potential strategies for the experimental, preclinical or clinical application of Treg cell therapy in the context of autoimmune/immune-mediated rheumatic diseases. RECENT FINDINGS: CD4+ CD25+ regulatory T (Treg) cells are a phenotypically and functionally heterogeneous subset of lymphocytes that prevent a variety of autoimmune diseases. As in many autoimmune diseases, the functional defects of Treg cells are supposed to play relevant roles in the pathogenesis and development of systemic lupus erythematosus, rheumatoid arthritis, ankylosing spondylitis, and other autoimmune/immune-mediated rheumatic diseases...
April 16, 2018: Current Rheumatology Reports
https://www.readbyqxmd.com/read/29660923/haemochromatosis-pathophysiology-and-the-red-blood-cell1
#11
Kieran J Richardson, Antony P McNamee, Michael J Simmonds
Haemochromatosis remains the most prevalent genetic disorder of Caucasian populations in Australia and the United States, occurring in ∼1 of 200 individuals and having a carrier frequency of 10-14%. Hereditary haemochromatosis is an autosomal recessive condition, that is phenotypically characterised by a gradual accumulation of iron, above and beyond that required for biological function. Once the binding capacity of iron carriers reaches saturation, the highly reactive free iron generates radicals that may lead to widespread cellular dysfunction...
April 7, 2018: Clinical Hemorheology and Microcirculation
https://www.readbyqxmd.com/read/29657985/the-chlamydia-muridarum-plasmid-revisited-new-insights-into-growth-kinetics
#12
Rachel J Skilton, Yibing Wang, Colette O'Neill, Simone Filardo, Peter Marsh, Angèle Bénard, Nicholas R Thomson, Kyle H Ramsey, Ian N Clarke
Background: Research in chlamydial genetics is challenging because of its obligate intracellular developmental cycle. In vivo systems exist that allow studies of different aspects of basic biology of chlamydiae, the murine Chlamydia muridarum model is one of great importance and thus an essential research tool. C. muridarum carries a plasmid that has a role in virulence.  Our aim was to compare and contrast the C. muridarum plasmid-free phenotype with that of a chromosomally isogenic plasmid-bearing strain, through the inclusion phase of the developmental cycle...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29657963/hologenomics-systems-level-host-biology
#13
Kevin R Theis
The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations...
March 2018: MSystems
https://www.readbyqxmd.com/read/29657091/injectable-polypeptide-hydrogels-via-methionine-modification-for-neural-stem-cell-delivery
#14
A L Wollenberg, T M O'Shea, J H Kim, A Czechanski, L G Reinholdt, M V Sofroniew, T J Deming
Injectable hydrogels with tunable physiochemical and biological properties are potential tools for improving neural stem/progenitor cell (NSPC) transplantation to treat central nervous system (CNS) injury and disease. Here, we developed injectable diblock copolypeptide hydrogels (DCH) for NSPC transplantation that contain hydrophilic segments of modified l-methionine (Met). Multiple Met-based DCH were fabricated by post-polymerization modification of Met to various functional derivatives, and incorporation of different amino acid comonomers into hydrophilic segments...
April 5, 2018: Biomaterials
https://www.readbyqxmd.com/read/29656881/fundamentals-of-functional-imaging-i-current-clinical-techniques
#15
A Luna, T Martín Noguerol, L Alcalá Mata
Imaging techniques can establish a structural, physiological, and molecular phenotype for cancer, which helps enable accurate diagnosis and personalized treatment. In recent years, various imaging techniques that make it possible to study the functional characteristics of tumors quantitatively and reproducibly have been introduced and have become established in routine clinical practice. Perfusion studies enable us to estimate the microcirculation as well as tumor angiogenesis and permeability using ultrafast dynamic acquisitions with ultrasound, computed tomography, or magnetic resonance (MR) imaging...
April 12, 2018: Radiología
https://www.readbyqxmd.com/read/29656345/update-on-the-treatment-of-early-stage-triple-negative-breast-cancer
#16
REVIEW
Priyanka Sharma
Triple-negative breast cancer (TNBC) accounts for 15% of all breast cancers and is associated with poor long-term outcomes compared to other breast cancer subtypes. Currently, chemotherapy remains the main modality of treatment for early-stage TNBC, as there is no approved targeted therapy for this subtype. The biologic heterogeneity of TNBC has hindered the development and evaluation of novel agents, but recent advancements in subclassifying TNBC have paved the way for further investigation of more effective systemic therapies, including cytotoxic and targeted agents...
April 14, 2018: Current Treatment Options in Oncology
https://www.readbyqxmd.com/read/29650809/-molecular-targeted-therapies-for-hereditary-cancer-syndrome
#17
Hideki Shimodaira
Development of molecular targeted drugs has achieved remarkable improvement of systemic cancer therapy. Recently, the several molecular targeted drugs have become available which associated with the status of responsible genes for hereditary cancer syndrome. These drugs would allow to establish specific strategy for hereditary cancer syndrome or sporadic cancers with similar biological phenotype with hereditary cancer. Genetic tests for the diagnosis of hereditary cancer syndrome will have the meaning of biomarker for predicting the efficacy of these molecular targeted drugs...
April 2018: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/29649100/targeting-the-adenosinergic-axis-in-chronic-lymphocytic-leukemia-a-way-to-disrupt-the-tumor-niche
#18
REVIEW
Tiziana Vaisitti, Francesca Arruga, Silvia Deaglio
Targeting adenosine triphosphate (ATP) metabolism and adenosinergic signaling in cancer is gaining momentum, as increasing evidence is showing their relevance in tumor immunology and biology. Chronic lymphocytic leukemia (CLL) results from the expansion of a population of mature B cells that progressively occupies the bone marrow (BM), the blood, and peripheral lymphoid organs. Notwithstanding significant progress in the treatment of these patients, the cure remains an unmet clinical need, suggesting that novel drugs or drug combinations are needed...
April 12, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29644800/defining-cell-identity-with-single-cell-omics
#19
REVIEW
Laura Mincarelli, Ashleigh Lister, James Lipscombe, Iain C Macaulay
Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviours of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variation - most notably in the emergence and evolution of tumours...
April 12, 2018: Proteomics
https://www.readbyqxmd.com/read/29643813/skull-development-ossification-pattern-and-adult-shape-in-the-emerging-lizard-model-organism-pogona-vitticeps-a-comparative-analysis-with-other-squamates
#20
Joni Ollonen, Filipe O Da Silva, Kristin Mahlow, Nicolas Di-Poï
The rise of the Evo-Devo field and the development of multidisciplinary research tools at various levels of biological organization have led to a growing interest in researching for new non-model organisms. Squamates (lizards and snakes) are particularly important for understanding fundamental questions about the evolution of vertebrates because of their high diversity and evolutionary innovations and adaptations that portrait a striking body plan change that reached its extreme in snakes. Yet, little is known about the intricate connection between phenotype and genotype in squamates, partly due to limited developmental knowledge and incomplete characterization of embryonic development...
2018: Frontiers in Physiology
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