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https://www.readbyqxmd.com/read/29240581/cutaneous-melanocytoma-with-crtc1-trim11-fusion-report-of-5-cases-resembling-clear-cell-sarcoma
#1
Lucie Cellier, Emilie Perron, Daniel Pissaloux, Marie Karanian, Veronique Haddad, Laurent Alberti, Arnaud de la Fouchardière
We report 5 cases of primary intradermal nodular unpigmented tumors with a melanocytic immunophenotype associated with a novel CRTC1-TRIM11 fusion. Clinically, the cutaneous nodules were slowly growing in 3 women and 2 men (25 to 82 y old, median, 28 y) with no specific topography. Lesion size ranged from 4 to 12 mm (median, 5 mm). The tumors were strictly located in the dermis with a nodular pattern. The cells were arranged in confluent nests and fascicules. Central fibronecrotic areas were present in 2 cases...
December 7, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29239568/spatiotemporal-transmission-and-socio-climatic-factors-related-to-paediatric-tuberculosis-in-north-western-ethiopia
#2
Kefyalew Addis Alene, Kerri Viney, Emma S McBryde, Archie C A Clements
The burden of tuberculosis (TB) in children reflects continuing and recent transmission within a population. This study aimed to identify spatiotemporal and socio-climatic factors associated with paediatric TB in north-western Ethiopia. Multivariate Poisson regression models were computed using a Bayesian framework. Estimates of parameters were generated using Markov chain Monte Carlo simulation. A total of 2,240 children aged under 15 years diagnosed with TB during the years 2013- 2016 were included in the analysis...
November 27, 2017: Geospatial Health
https://www.readbyqxmd.com/read/29239565/spatio-temporal-analysis-and-visualisation-of-the-anthrax-epidemic-situation-in-livestock-in-kazakhstan-over-the-period-1933-2016
#3
Sarsenbay K Abdrakhmanov, Yersyn Y Mukhanbetkaliyev, Fedor I Korennoy, Bolat Sh Karatayev, Aizada A Mukhanbetkaliyeva, Aruzhan S Abdrakhmanova
An analysis of the anthrax epidemic situation among livestock animals in the Republic of Kazakhstan over the period 1933-2016 is presented. During this time, 4,064 anthrax outbreaks (mainly in cattle, small ruminants, pigs and horses) were recorded. They fall into five historical periods of increase and decrease in the annual anthrax incidence (1933-1953; 1954-1968; 1969-1983; 1984- 2001; and 2002-2016), which has been associated with changes in economic activity and veterinary surveillance. To evaluate the temporal trends of incidence variation for each of these time periods, the following methods were applied: i) spatio-temporal analysis using a space-time cube to assess the presence of hotspots (i...
November 13, 2017: Geospatial Health
https://www.readbyqxmd.com/read/29239561/spatial-analysis-of-cutaneous-leishmaniasis-in-an-endemic-area-of-iran-based-on-environmental-factors
#4
Roghieh Ramezankhani, Nooshin Sajjadi, Roya Nezakati Esmaeilzadeh, Seyed Ali Jozi, Mohammad Reza Shirzadi
Leishmaniasis is a parasitic disease caused by different species of protozoan parasites. Cutaneous leishmaniasis (CL) is still a great public health problem in Iran, especially in Isfahan Province. Distribution and abundance of vectors and reservoirs of this disease is affected by different factors such as climatic, socioeconomic and cultural. This study aimed to identify the hotspot areas for CL in Isfahan and assess the relations between the climatic and topographic factors with CL incidence using spatial analysis...
November 8, 2017: Geospatial Health
https://www.readbyqxmd.com/read/29239555/analytical-report-of-the-2016-dengue-outbreak-in-c%C3%A3-rdoba-city-argentina
#5
Camilo Rotela, Laura Lopez, María Frías Céspedes, Gabriela Barbas, Andrés Lighezzolo, Ximena Porcasi, Mario A Lanfri, Carlos M Scavuzzo, David E Gorla
After elimination of the Aedes aegypti vector in South America in the 1960s, dengue outbreaks started to reoccur during the 1990s; strongly in Argentina since 1998. In 2016, Córdoba City had the largest dengue outbreak in its history. In this article we report this outbreak including spatio-temporal analysis of cases and vectors in the city. A total of 653 dengue cases were recorded by the laboratory-based dengue surveillance system and georeferenced by their residential addresses. Case maps were generated from the epidemiological week 1 (beginning of January) to week 19 (mid-May)...
November 6, 2017: Geospatial Health
https://www.readbyqxmd.com/read/29239553/detecting-space-time-disease-clusters-with-arbitrary-shapes-and-sizes-using-a-co-clustering-approach
#6
Sami Ullah, Hanita Daud, Sarat C Dass, Habib Nawaz Khan, Alamgir Khalil
Ability to detect potential space-time clusters in spatio-temporal data on disease occurrences is necessary for conducting surveillance and implementing disease prevention policies. Most existing techniques use geometrically shaped (circular, elliptical or square) scanning windows to discover disease clusters. In certain situations, where the disease occurrences tend to cluster in very irregularly shaped areas, these algorithms are not feasible in practise for the detection of space-time clusters. To address this problem, a new algorithm is proposed, which uses a co-clustering strategy to detect prospective and retrospective space-time disease clusters with no restriction on shape and size...
November 6, 2017: Geospatial Health
https://www.readbyqxmd.com/read/29237855/sex-specific-adaptation-and-genomic-responses-to-y-chromosome-presence-in-female-reproductive-and-neural-tissues
#7
Alan T Branco, Rute M Brito, Bernardo Lemos
Y chromosomes typically harbour a small number of genes and an abundance of repetitive sequences. In Drosophila, the Y chromosome comprises multimegabase long segments of repetitive DNA and a handful of protein-coding genes. In mammals, the Y chromosome also harbours a disproportionally high abundance of repeats. Here, we built on a Drosophila melanogaster model in which the Y chromosome is decoupled from sexual determination. Genotypes were genetically identical for the autosomes, X chromosome, and mitochondria, but differ by the presence or dose of the Y chromosome...
December 20, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29235850/a-digital-protocol-for-chemical-analysis-at-ultra-low-concentrations-by-surface-enhanced-raman-scattering
#8
Carlos Diego L de Albuquerque, Regivaldo Gomes Sobral Filho, Ronei Jesus Poppi, Alexandre G Brolo
Single molecule surface-enhanced Raman Spectroscopy (SM-SERS) has the potential to revolutionize quantitative analysis at ultra-low concentrations (less than 1 nM). However, there are no established protocols to generalize the application of this technique in analytical chemistry. Here, a protocol for quantification at ultra-low concentrations using SM-SERS is proposed. The approach aims to take advantage of the stochastic nature of the single-molecule regime to achieved lower limits of detection (LOD) and quantification (LOQ)...
December 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29235352/systems-approaches-to-understanding-and-designing-allosteric-proteins
#9
Srivatsan Raman
The study of allostery has a central place in biology due to the myriad roles of allosteric proteins in cellular function. As technologies to probe spatiotemporal resolution of biomolecules have become increasingly sophisticated, so has our understanding of the diverse structural and molecular mechanisms of allosteric proteins. Studies have shown that allosteric signal is transmitted a through a network of residue-residue interactions connecting distal sites on a protein. Linking structural and dynamical changes to the functional role of individual residues will give a more complete molecular view of allostery...
December 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/29234324/long-non-coding-rnas-emerging-and-versatile-regulators-in-host-virus-interactions
#10
REVIEW
Xing-Yu Meng, Yuzi Luo, Muhammad Naveed Anwar, Yuan Sun, Yao Gao, Huawei Zhang, Muhammad Munir, Hua-Ji Qiu
Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules, which are involved in various biological processes, including chromatin modification, cell differentiation, pre-mRNA transcription and splicing, protein translation, etc. During the last decade, increasing evidence has suggested the involvement of lncRNAs in both immune and antiviral responses as positive or negative regulators. The immunity-associated lncRNAs modulate diverse and multilayered immune checkpoints, including activation or repression of innate immune signaling components, such as interleukin (IL)-8, IL-10, retinoic acid inducible gene I, toll-like receptors 1, 3, and 8, and interferon (IFN) regulatory factor 7, transcriptional regulation of various IFN-stimulated genes, and initiation of the cell apoptosis pathways...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29233960/multiplexed-in-vivo-homology-directed-repair-and-tumor-barcoding-enables-parallel-quantification-of-kras-variant-oncogenicity
#11
Ian P Winters, Shin-Heng Chiou, Nicole K Paulk, Christopher D McFarland, Pranav V Lalgudi, Rosanna K Ma, Leszek Lisowski, Andrew J Connolly, Dmitri A Petrov, Mark A Kay, Monte M Winslow
Large-scale genomic analyses of human cancers have cataloged somatic point mutations thought to initiate tumor development and sustain cancer growth. However, determining the functional significance of specific alterations remains a major bottleneck in our understanding of the genetic determinants of cancer. Here, we present a platform that integrates multiplexed AAV/Cas9-mediated homology-directed repair (HDR) with DNA barcoding and high-throughput sequencing to simultaneously investigate multiple genomic alterations in de novo cancers in mice...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233099/pronounced-strain-specific-chemosensory-receptor-gene-expression-in-the-mouse-vomeronasal-organ
#12
Kyle Duyck, Vasha DuTell, Limei Ma, Ariel Paulson, C Ron Yu
BACKGROUND: The chemosensory system plays an important role in orchestrating sexual behaviors in mammals. Pheromones trigger sexually dimorphic behaviors and different mouse strains exhibit differential responses to pheromone stimuli. It has been speculated that differential gene expression in the sensory organs that detect pheromones may underlie sexually-dimorphic and strain-specific responses to pheromone cues. RESULTS: We have performed transcriptome analyses of the mouse vomeronasal organ, a sensory organ recognizing pheromones and interspecies cues...
December 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29232695/integrative-assessment-of-climate-change-for-fast-growing-urban-areas-measurement-and-recommendations-for-future-research
#13
Sebastian Scheuer, Dagmar Haase, Martin Volk
Over the 20th century, urbanization has substantially shaped the surface of Earth. With population rapidly shifting from rural locations towards the cities, urban areas have dramatically expanded on a global scale and represent crystallization points of social, cultural and economic assets and activities. This trend is estimated to persist for the next decades, and particularly the developing countries are expected to face rapid urban growth. The management of this growth will require good governance strategies and planning...
2017: PloS One
https://www.readbyqxmd.com/read/29232568/prior-systemic-treatment-increased-the-incidence-of-somatic-mutations-in-metastatic-breast-cancer
#14
Takeo Fujii, Naoko Matsuda, Miho Kono, Kenichi Harano, Huiqin Chen, Rajyalakshmi Luthra, Sinchita Roy-Chowdhuri, Aysegul A Sahin, Chetna Wathoo, Aron Y Joon, Debu Tripathy, Funda Meric-Bernstam, Naoto T Ueno
BACKGROUND: Understanding the biology of breast cancer is important for guiding treatment strategies and revealing resistance mechanisms. Our objectives were to investigate the relationship between previous systemic therapy exposure and mutational spectrum in metastatic breast cancer and to identify clinicopathological factors associated with identified frequent somatic mutations. METHODS: Archival tissues of patients with metastatic breast cancer were subjected to hotspot molecular testing by next-generation sequencing...
December 9, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/29232381/effects-of-experimental-nitrogen-fertilization-on-planktonic-metabolism-and-co2-flux-in-a-hypereutrophic-hardwater-lake
#15
Matthew J Bogard, Kerri Finlay, Marley J Waiser, Vijay P Tumber, Derek B Donald, Emma Wiik, Gavin L Simpson, Paul A Del Giorgio, Peter R Leavitt
Hardwater lakes are common in human-dominated regions of the world and often experience pollution due to agricultural and urban effluent inputs of inorganic and organic nitrogen (N). Although these lakes are landscape hotspots for CO2 exchange and food web carbon (C) cycling, the effect of N enrichment on hardwater lake food web functioning and C cycling patterns remains unclear. Specifically, it is unknown if different eutrophication scenarios (e.g., modest non point vs. extreme point sources) yield consistent effects on auto- and heterotrophic C cycling, or how biotic responses interact with the inorganic C system to shape responses of air-water CO2 exchange...
2017: PloS One
https://www.readbyqxmd.com/read/29232370/spatio-temporal-variations-of-conservation-hotspots-based-on-ecosystem-services-in-xishuangbanna-southwest-china
#16
Shiliang Liu, Yijie Yin, Fangyan Cheng, Xiaoyun Hou, Shikui Dong, Xue Wu
Integrating biodiversity and ecosystem services (BES) has been viewed as an appropriate approach to identifying conservation priorities. Taking Xishuangbanna tropical region in Southwest China, different BESs (habitat quality [used as a proxy for biodiversity], carbon storage, and water yield) were quantified using the InVEST model and conservation hotspots from 1976, 1990, and 2010 were identified by overlapping and ranking the service layers. Results showed that BESs areas were unevenly distributed. High habitat quality and carbon storage areas located in the eastern part of the region were mainly occupied by broad-leaved forest, while high water yield areas were covered by grassland and tropical forests...
2017: PloS One
https://www.readbyqxmd.com/read/29231959/causal-somatic-mutations-in-urine-dna-from-persons-with-the-cloves-subgroup-of-the-pik3ca-related-overgrowth-spectrum-pros
#17
M E Michel, D J Konczyk, K S Yeung, R Murillo, M P Vivero, A M Hall, D Zurakowski, D Adams, A Gupta, A Y Huang, B H Y Chung, M L Warman
Congenital Lipomatous Overgrowth with Vascular, Epidermal, and Skeletal anomalies (CLOVES) and Klippel-Trenaunay (KTS) syndromes are caused by somatic gain-of-function mutations in PIK3CA, encoding a catalytic subunit of phosphoinositide 3-kinase. Affected tissue is needed to find mutations, since mutant alleles are not detectable in blood. Because some patients with CLOVES develop Wilms tumor, we tested urine as a source of DNA for mutation detection. We extracted DNA from the urine of 17 and 24 individuals with CLOVES and KTS, respectively, and screened 5 common PIK3CA mutation hotspots using droplet digital PCR...
December 12, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29230887/integration-of-molecular-dynamics-simulation-and-hotspot-residues-grafting-for-de-novo-scfv-design-against-salmonella-typhi-tolc-protein
#18
Siew Wen Leong, Theam Soon Lim, Asma Ismail, Yee Siew Choong
With the development of de novo binders for protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design...
December 12, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29229825/network-analysis-identifies-chromosome-intermingling-regions-as-regulatory-hotspots-for-transcription
#19
Anastasiya Belyaeva, Saradha Venkatachalapathy, Mallika Nagarajan, G V Shivashankar, Caroline Uhler
The 3D structure of the genome plays a key role in regulatory control of the cell. Experimental methods such as high-throughput chromosome conformation capture (Hi-C) have been developed to probe the 3D structure of the genome. However, it remains a challenge to deduce from these data chromosome regions that are colocalized and coregulated. Here, we present an integrative approach that leverages 1D functional genomic features (e.g., epigenetic marks) with 3D interactions from Hi-C data to identify functional interchromosomal interactions...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229583/integrative-genomic-analysis-of-coincident-cancer-foci-implicates-ctnnb1-and-pten-alterations-in-ductal-prostate-cancer
#20
Marc Gillard, Justin Lack, Andrea Pontier, Divya Gandla, David Hatcher, Adam G Sowalsky, Jose Rodriguez-Nieves, Donald Vander Griend, Gladell Paner, David VanderWeele
BACKGROUND: Ductal adenocarcinoma of the prostate is an aggressive subtype, with high rates of biochemical recurrence and overall poor prognosis. It is frequently found coincident with conventional acinar adenocarcinoma. The genomic features driving evolution to its ductal histology and the biology associated with its poor prognosis remain unknown. OBJECTIVE: To characterize genomic features distinguishing ductal adenocarcinoma from coincident acinar adenocarcinoma foci from the same patient...
December 8, 2017: European Urology Focus
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