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https://www.readbyqxmd.com/read/28319747/integration-of-in-silico-methods-and-computational-systems-biology-to-explore-endocrine-disrupting-chemical-binding-with-nuclear-hormone-receptors
#1
P Ruiz, A Sack, M Wampole, S Bobst, M Vracko
Thousands of potential endocrine-disrupting chemicals present difficult regulatory challenges. Endocrine-disrupting chemicals can interfere with several nuclear hormone receptors associated with a variety of adverse health effects. The U.S. Environmental Protection Agency (U.S. EPA) has released its reviews of Tier 1 screening assay results for a set of pesticides in the Endocrine Disruptor Screening Program (EDSP), and recently, the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP) data...
March 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28317055/electronic-and-relativistic-contributions-to-ion-pairing-in-polyoxometalate-model-systems
#2
Dylan J Sures, Stefano A Serapian, Károly Kozma, Pedro I Molina, Carles Bo, May Nyman
Ion pairs and solubility related to ion-pairing in water influence many processes in nature and in synthesis including efficient drug delivery, contaminant transport in the environment, and self-assembly of materials in water. Ion pairs are difficult to observe spectroscopically because they generally do not persist unless extreme solution conditions are applied. Here we demonstrate two advanced techniques coupled with computational studies that quantify the persistence of ion pairs in simple solutions and offer explanations for observed solubility trends...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28306666/new-biomarkers-and-imaging-approaches-for-the-diagnosis-of-deep-venous-thrombosis
#3
Jordan K Schaefer, Benjamin Jacobs, Thomas W Wakefield, Suman L Sood
PURPOSE OF REVIEW: Symptoms suggestive of deep vein thrombosis (DVT) are extremely common in clinical practice, but unfortunately nonspecific. In both ambulatory and inpatient settings, clinicians are often tasked with evaluating these concerns. Here, we review the most recent advances in biomarkers and imaging to diagnose lower extremity DVT. RECENT FINDINGS: The modified Wells score remains the most supported clinical decision rule for risk stratifying patients...
March 16, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28302851/structural-basis-of-the-day-night-transition-in-a-bacterial-circadian-clock
#4
Roger Tseng, Nicolette F Goularte, Archana Chavan, Jansen Luu, Susan E Cohen, Yong-Gang Chang, Joel Heisler, Sheng Li, Alicia K Michael, Sarvind Tripathi, Susan S Golden, Andy LiWang, Carrie L Partch
Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. In cyanobacteria, timing is generated by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA and CikA, which transduce this rhythm to control gene expression. Here, we describe crystal and nuclear magnetic resonance structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how the metamorphic properties of KaiB, a protein that adopts two distinct folds, and the post-adenosine triphosphate hydrolysis state of KaiC create a hub around which nighttime signaling events revolve, including inactivation of KaiA and reciprocal regulation of the mutually antagonistic signaling proteins, SasA and CikA...
March 17, 2017: Science
https://www.readbyqxmd.com/read/28298123/caesium-hydride-ms-caspt2-potential-energy-curves-and-a-1-%C3%AE-%C3%A2-x-1-%C3%AE-absorption-emission-spectroscopy
#5
Ján Škoviera, Pavel Neogrády, Florent Louis, Michal Pitoňák, Ivan Černušák
Correlated ab initio methods (CASPT2 and CCSD(T)) in conjunction with the ANO-RCC basis sets were used to calculate potential energy curves (PECs) of the ground, valence, and Rydberg electronic states of CsH with the inclusion of the scalar relativistic effects. The spectroscopic constants of bound states were calculated from the PECs and compared with previous theoretical and/or available experimental data. Absorption and emission spectra arising from the transition between X(1)Σ(+) and A(1)Σ(+) states were modelled using vibrational and rotational energy levels and corresponding nuclear wave functions obtained via the direct numerical integration of one-dimensional rovibrational Schrödinger equation in the CASPT2/ANO-RCC electronic potentials...
March 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28298110/near-infrared-overtone-voh-2-%C3%A2-0-spectroscopy-of-ne-h2o-clusters
#6
Michael P Ziemkiewicz, Christian Pluetzer, Michael Wojcik, Jérôme Loreau, Ad van der Avoird, David J Nesbitt
Vibrationally state selective overtone spectroscopy and dynamics of weakly bound Ne-H2O complexes (D0((para)) = 31.67 cm(-1), D0((ortho)) = 34.66 cm(-1)) are reported for the first time, based on near infrared excitation of van der Waals cluster bands correlating with vOH = 2 ← 0 overtone transitions (|02(-)⟩←|00(+)⟩ and |02(+)⟩←|00(+)⟩) out of the ortho (101) and para (000) internal rotor states of the H2O moiety. Quantum theoretical calculations for nuclear motion on a high level ab initio potential energy surface (CCSD(T)/VnZ-f12 (n = 3,4), corrected for basis set superposition error and extrapolated to the complete basis set limit) are employed for assignment of Σ←Σ,Π←Σ, and Σ←Π infrared bands in the overtone spectra, where Σ(K = 0) and Π (K = 1) represent approximate projections (K) of the body angular momentum along the Ne-H2O internuclear axis...
March 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28297668/mutually-exclusive-cbc-containing-complexes-contribute-to-rna-fate
#7
Simone Giacometti, Nour El Houda Benbahouche, Michal Domanski, Marie-Cécile Robert, Nicola Meola, Michal Lubas, Jakob Bukenborg, Jens S Andersen, Wiebke M Schulze, Celine Verheggen, Grzegorz Kudla, Torben Heick Jensen, Edouard Bertrand
The nuclear cap-binding complex (CBC) stimulates processing reactions of capped RNAs, including their splicing, 3'-end formation, degradation, and transport. CBC effects are particular for individual RNA families, but how such selectivity is achieved remains elusive. Here, we analyze three main CBC partners known to impact different RNA species. ARS2 stimulates 3'-end formation/transcription termination of several transcript types, ZC3H18 stimulates degradation of a diverse set of RNAs, and PHAX functions in pre-small nuclear RNA/small nucleolar RNA (pre-snRNA/snoRNA) transport...
March 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28297282/volumetric-modulated-arc-therapy-using-multicriteria-optimization-for-body-and-extremity-sarcoma
#8
Michael R Young, David L Craft, Caroline M Colbert, Kyla Remillard, Liam Vanbenthuysen, Yi Wang
This study evaluates the implementation of volumetric-modulated arc therapy (VMAT) using multicriteria optimization (MCO) in the RayStation treatment planning system (TPS) for complex sites, namely extremity and body sarcoma. The VMAT-MCO algorithm implemented in RayStation is newly developed and requires an integrated, comprehensive analysis of plan generation, delivery, and treatment efficiency. Ten patients previously treated by intensity-modulated radiation therapy (IMRT) with MCO were randomly selected and replanned using VMAT-MCO...
November 2016: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28295484/who-2016-classification-changes-and-advancements-in-the-diagnosis-of-miscellaneous-primary-cns-tumours
#9
Felix Sahm, David E Reuss, Caterina Giannini
This short review highlights significant changes and recent findings incorporated to varying extent in the WHO 2016 definition of a variety of tumours, including peripheral nerve sheath tumours, meningiomas, mesenchymal non-meningothelial tumours, melanocytic tumours, lymphomas and histiocytic tumours, germ cell tumours and non-neuroendocrine pituitary tumours. Most notable classification changes include: adding "hybrid nerve sheath tumours" to the spectrum of benign nerve sheath tumours; an updated definition of atypical meningioma (WHO grade II), including cases with brain invasion; recognizing dural solitary fibrous tumour (SFT) and haemangiopericytoma (HPC) as a single tumour entity characterized by NAB2 and STAT6 gene fusions for which the term solitary SFT/HPC was chosen; recognizing that pituitary granular cell tumour, spindle cell oncocytoma, and pituicytoma all share nuclear expression of TTF-1, possibly representing a spectrum of a single nosological entity derived from posterior pituitary glial cells...
March 12, 2017: Neuropathology and Applied Neurobiology
https://www.readbyqxmd.com/read/28294943/a-team-of-heterochromatin-factors-collaborates-with-small-rna-pathways-to-combat-repetitive-elements-and-germline-stress
#10
Alicia N McMurchy, Przemyslaw Stempor, Tessa Gaarenstroom, Brian Wysolmerski, Yan Dong, Darya Aussianikava, Alex Appert, Ni Huang, Paulina Kolasinska-Zwierz, Alexandra Sapetschnig, Eric A Miska, Julie Ahringer
Repetitive sequences derived from transposons make up a large fraction of eukaryotic genomes and must be silenced to protect genome integrity. Repetitive elements are often found in heterochromatin; however, the roles and interactions of heterochromatin proteins in repeat regulation are poorly understood. Here we show that a diverse set of C. elegans heterochromatin proteins act together with the piRNA and nuclear RNAi pathways to silence repetitive elements and prevent genotoxic stress in the germ line. Mutants in genes encoding HPL-2/HP1, LIN-13, LIN-61, LET-418/Mi-2, and H3K9me2 histone methyltransferase MET-2/SETDB1 also show functionally redundant sterility, increased germline apoptosis, DNA repair defects, and interactions with small RNA pathways...
March 15, 2017: ELife
https://www.readbyqxmd.com/read/28293858/thyroglossal-duct-cyst-carcinomas-in-pediatric-patients-report-of-two-cases-with-a-comprehensive-literature-review
#11
Lester D R Thompson, Hannah B Herrera, Sean K Lau
Thyroglossal duct cyst (TGDC) carcinomas are rarely encountered in the pediatric population. The clinical behavior of these tumors in the pediatric setting is unclear and management is not well defined. Two cases of pediatric thyroglossal duct cyst carcinoma were identified in a review of all thyroglossal duct cysts diagnosed over a ten year period. These two cases were analyzed along with 57 cases of thyroglossal duct cyst carcinoma affecting patients less than 21 years of age compiled from the English literature...
March 14, 2017: Head and Neck Pathology
https://www.readbyqxmd.com/read/28293120/glucocorticoid-receptor-expression-in-20-solid-tumor-types-using-immunohistochemistry-assay
#12
Thaddeus S Block, Tiffany I Murphy, Pamela N Munster, Dat P Nguyen, Frank J Lynch
BACKGROUND: Glucocorticoid receptor (GR) activity plays a role in many aspects of human physiology and may play a crucial role in chemotherapy resistance in a wide variety of solid tumors. A novel immunohistochemistry (IHC) based assay has been previously developed and validated in order to assess GR immunoreactivity in triple-negative breast cancer. The current study investigates the standardized use of this validated assay to assess GR expression in a broad range of solid tumor malignancies...
2017: Cancer Management and Research
https://www.readbyqxmd.com/read/28292899/fission-yeast-myosin-i-facilitates-pi-4-5-p2-mediated-anchoring-of-cytoplasmic-dynein-to-the-cortex
#13
Jerrin Mathew Thankachan, Stephen Sukumar Nuthalapati, Nireekshit Addanki Tirumala, Vaishnavi Ananthanarayanan
Several key processes in the cell, such as vesicle transport and spindle positioning, are mediated by the motor protein cytoplasmic dynein, which produces force on the microtubule. For the functions that require movement of the centrosome and the associated nuclear material, dynein needs to have a stable attachment at the cell cortex. In fission yeast, Mcp5 is the anchor protein of dynein and is required for the oscillations of the horsetail nucleus during meiotic prophase. Although the role of Mcp5 in anchoring dynein to the cortex has been identified, it is unknown how Mcp5 associates with the membrane as well as the importance of the underlying attachment to the nuclear oscillations...
March 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28292441/spop-mutation-drives-prostate-tumorigenesis-in%C3%A2-vivo-through-coordinate-regulation-of-pi3k-mtor-and-ar-signaling
#14
Mirjam Blattner, Deli Liu, Brian D Robinson, Dennis Huang, Anton Poliakov, Dong Gao, Srilakshmi Nataraj, Lesa D Deonarine, Michael A Augello, Verena Sailer, Lalit Ponnala, Michael Ittmann, Arul M Chinnaiyan, Andrea Sboner, Yu Chen, Mark A Rubin, Christopher E Barbieri
Recurrent point mutations in SPOP define a distinct molecular subclass of prostate cancer. Here, we describe a mouse model showing that mutant SPOP drives prostate tumorigenesis in vivo. Conditional expression of mutant SPOP in the prostate dramatically altered phenotypes in the setting of Pten loss, with early neoplastic lesions (high-grade prostatic intraepithelial neoplasia) with striking nuclear atypia and invasive, poorly differentiated carcinoma. In mouse prostate organoids, mutant SPOP drove increased proliferation and a transcriptional signature consistent with human prostate cancer...
March 13, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28290475/the-development-of-loop-mediated-isothermal-amplification-lamp-assays-for-the-rapid-authentication-of-five-forbidden-vegetables-in-strict-vegetarian-diets
#15
Meng-Shiou Lee, Ting-Ying Su, Yi-Yang Lien, Shyang-Chwen Sheu
Plant-based food ingredients such as garlic, Chinese leek, Chinese onion, green onion and onion are widely used in many cuisines around the world. However, these ingredients known as the "five forbidden vegetables" (FFVs) are not allowed in some vegetarian diets. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed for the detection of FFVs using five respective LAMP primer sets. The specific primers targeted the ITS1-5.8S-ITS2 nuclear ribosomal DNA sequence regions among the five vegetables...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28290098/cardiac-sympathetic-nervous-system-imaging-with-123-i-meta-iodobenzylguanidine-perspectives-from-japan-and-europe
#16
Kenichi Nakajima, Arthur J H A Scholte, Tomoaki Nakata, Aukelien C Dimitriu-Leen, Taishiro Chikamori, João V Vitola, Keiichiro Yoshinaga
Cardiac sympathetic nervous system dysfunction is closely associated with risk of serious cardiac events in patients with heart failure (HF), including HF progression, pump-failure death, and sudden cardiac death by lethal ventricular arrhythmia. For cardiac sympathetic nervous system imaging, (123)I-meta-iodobenzylguanidine ((123)I-MIBG) was approved by the Japanese Ministry of Health, Labour and Welfare in 1992 and has therefore been widely used since in clinical settings. (123)I-MIBG was also later approved by the Food and Drug Administration (FDA) in the United States of America (USA) and it was expected to achieve broad acceptance...
March 13, 2017: Journal of Nuclear Cardiology: Official Publication of the American Society of Nuclear Cardiology
https://www.readbyqxmd.com/read/28289275/epigenetic-programming-by-stress-and-glucocorticoids-along-the-human-lifespan
#17
A S Zannas, G P Chrousos
Psychosocial stress triggers a set of behavioral, neural, hormonal, and molecular responses that can be a driving force for survival when adaptive and time-limited, but may also contribute to a host of disease states if dysregulated or chronic. The beneficial or detrimental effects of stress are largely mediated by the hypothalamic-pituitary axis, a highly conserved neurohormonal cascade that culminates in systemic secretion of glucocorticoids. Glucocorticoids activate the glucocorticoid receptor, a ubiquitous nuclear receptor that not only causes widespread changes in transcriptional programs, but also induces lasting epigenetic modifications in many target tissues...
March 14, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28287963/a-dataset-and-a-technique-for-generalized-nuclear-segmentation-for-computational-pathology
#18
Neeraj Kumar, Ruchika Verma, Sanuj Sharma, Surabhi Bhargava, Abhishek Vahadane, Amit Sethi
Nuclear segmentation in digital microscopic tissue images can enable extraction of high-quality features for nuclear morphometrics and other analysis in computational pathology. Conventional image processing techniques such as Otsu thresholding and watershed segmentation do not work effectively on challenging cases, such as chromatin-sparse and crowded nuclei. In contrast, machine learning-based segmentation can generalize across various nuclear appearances. However, training machine learning algorithms require datasets of images in which a vast number of nuclei have been annotated...
March 6, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28286206/simplified-qpcr-method-for-detecting-excessive-mtdna-damage-induced-by-exogenous-factors
#19
Artem P Gureev, Ekaterina A Shaforostova, Anatoly A Starkov, Vasily N Popov
Damage to mitochondrial DNA (mtDNA) is a meaningful biomarker for evaluating genotoxicity of drugs and environmental toxins. Existing PCR methods utilize long mtDNA fragments (∼8-10kb), which complicates detecting exact sites of mtDNA damage. To identify the mtDNA regions most susceptible to damage, we have developed and validated a set of primers to amplify ∼2kb long fragments, while covering over 95% of mouse mtDNA. We have modified the detection method by greatly increasing the enrichment of mtDNA, which allows us solving the problem of non-specific primer annealing to nuclear DNA...
March 9, 2017: Toxicology
https://www.readbyqxmd.com/read/28283903/detection-of-esr1-mutations-in-plasma-and-tumors-from-metastatic-breast-cancer-patients-using-next-generation-sequencing
#20
Takehiro Yanagawa, Naofumi Kagara, Tomohiro Miyake, Tomonori Tanei, Yasuto Naoi, Masafumi Shimoda, Kenzo Shimazu, Seung Jin Kim, Shinzaburo Noguchi
PURPOSE: Liquid biopsy using digital PCR (dPCR) has been widely used for the screening of ESR1 mutations, since they are frequently identified in the hotspot. However, dPCR is limited to the known mutations. Therefore, we aimed to analyze the utility of next-generation sequencing (NGS) to discover novel ESR1 mutations. METHODS: Whole exon sequencing of the ESR1 gene using NGS was performed in 16 primary and 47 recurrent tumor samples and 38 plasma samples from hormone receptor-positive metastatic breast cancer patients...
March 10, 2017: Breast Cancer Research and Treatment
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