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https://www.readbyqxmd.com/read/29134679/prediction-of-protein-structure-with-the-coarse-grained-unres-force-field-assisted-by-small-x-ray-scattering-data-and-knowledge-based-information
#1
Agnieszka S Karczyńska, Magdalena A Mozolewska, Paweƚ Krupa, Artur Gieƚdoń, Adam Liwo, Cezary Czaplewski
A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment...
November 14, 2017: Proteins
https://www.readbyqxmd.com/read/28964503/is-procedural-memory-enhanced-in-tourette-syndrome-evidence-from-a-sequence-learning-task
#2
Ádám Takács, Andrea Kóbor, Júlia Chezan, Noémi Éltető, Zsanett Tárnok, Dezso Nemeth, Michael T Ullman, Karolina Janacsek
Procedural memory, which is rooted in the basal ganglia, underlies the learning and processing of numerous automatized motor and cognitive skills, including in language. Not surprisingly, disorders with basal ganglia abnormalities have been found to show impairments of procedural memory. However, brain abnormalities could also lead to atypically enhanced function. Tourette syndrome (TS) is a candidate for enhanced procedural memory, given previous findings of enhanced TS processing of grammar, which likely depends on procedural memory...
September 9, 2017: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/28963129/trapped-sweat-in-basketball-uniforms-and-the-effect-on-sweat-loss-estimates
#3
Lindsay B Baker, Adam J Reimel, Bridget C Sopeña, Kelly A Barnes, Ryan P Nuccio, Peter John D De Chavez, John R Stofan, James M Carter
The aims of this study were to determine: (1) trapped sweat (TS) in basketball uniforms and the effect on sweat loss (SL) estimates during a laboratory-based basketball simulation protocol; (2) the impact of exercise intensity, body mass, age, and SL on TS; and (3) TS during on-court training to assess the ecological validity of the laboratory-based results. Twenty-four recreational/competitive male basketball players (23 ± 10 years, 77.0 ± 16.7 kg) completed three randomized laboratory-based trials (Low, Moderate, and High intensity) consisting of 150-min intermittent exercise...
September 2017: Physiological Reports
https://www.readbyqxmd.com/read/28958271/operative-outcomes-after-open-abdominal-wall-reconstruction-with-retromuscular-mesh-fixation-using-fibrin-glue-versus-transfascial-sutures
#4
COMPARATIVE STUDY
Adam S Weltz, Udai S Sibia, H Reza Zahiri, Alexa Schoeneborn, Adrian Park, Igor Belyansky
Ideal fixation techniques have not been fully elucidated at the time of complex open abdominal wall reconstruction (AWR). We compared operative outcomes and quality of life with retromuscular mesh fixation using fibrin glue (FG) versus transfascial sutures (TS). Retrospective review identified complex hernia patients who underwent open AWR with mesh from November 2012 through April 2016. Multivariate analysis examined postoperative outcomes between groups. Quality of life was assessed using the Carolinas Comfort Scale...
September 1, 2017: American Surgeon
https://www.readbyqxmd.com/read/28809726/clinical-and-laboratory-associations-with-persistent-hyperferritinemia-in-373-black-hemochromatosis-and-iron-overload-screening-study-participants
#5
James C Barton, J Clayborn Barton, Paul C Adams
BACKGROUND: 373 black participants had elevated screening and post-screening serum ferritin (SF) (> 300 μg/L men; > 200 μg/L women). MATERIAL AND METHODS: We retrospectively studied SF and post-screening age; sex; body mass index; transferrin saturation (TS); ALT; AST; GGT; elevated C-reactive protein; ß-thalassemia; neutrophils; lymphocytes; monocytes; platelets; metacarpophalangeal joint hypertrophy; hepatomegaly; splenomegaly; diabetes; HFE H63D positivity; iron/alcohol intakes; and blood/erythrocyte transfusion units...
September 2017: Annals of Hepatology
https://www.readbyqxmd.com/read/28731701/model-for-the-enantioselectivity-of-asymmetric-intramolecular-alkylations-by-bis-quaternized-cinchona-alkaloid-derived-catalysts
#6
Cyndi Qixin He, Adam Simon, Yu-Hong Lam, Andrew P J Brunskill, Nobuyoshi Yasuda, Jiajing Tan, Alan M Hyde, Edward C Sherer, K N Houk
A model for the stereoselectivity of intramolecular alkylations by N,N'-disubstituted cinchona alkaloids reported by Xiang et al. was established using density functional theory (DFT) calculations. The stereocontrol is based on the minimal distortion of the transition state (TS) and catalyst required to achieve favorable electrostatic interactions in the favored TS. Counterions must be included in computational modeling of ion-paired catalysis in order to reproduce experimental enantioselectivity.
August 18, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28718513/the-fine-needle-aspiration-of-translocation-sarcomas
#7
C J VandenBussche, C L Adams, O G McDonald, S A Whitworth, S Z Ali
INTRODUCTION: Soft tissue sarcomas comprise a heterogeneous group of clinically aggressive cancers that are often hard to classify on limited cytological samples. "Translocation sarcomas" (TS) are a diverse subset of such cancers, different from pleomorphic sarcomas, and characterised by unique single chromosomal translocations in each sarcoma subtype. Interestingly, despite their high-grade biological behaviour, TS have deceptively monotonous and bland cytomorphology, therefore creating diagnostic issues on limited samples...
July 17, 2017: Cytopathology: Official Journal of the British Society for Clinical Cytology
https://www.readbyqxmd.com/read/28710940/procedural-learning-in-tourette-syndrome-adhd-and-comorbid-tourette-adhd-evidence-from-a-probabilistic-sequence-learning-task
#8
Ádám Takács, Yuval Shilon, Karolina Janacsek, Andrea Kóbor, Antoine Tremblay, Dezső Németh, Michael T Ullman
Procedural memory, which is rooted in the basal ganglia, plays an important role in the implicit learning of motor and cognitive skills. Few studies have examined procedural learning in either Tourette syndrome (TS) or Attention Deficit Hyperactivity Disorder (ADHD), despite basal ganglia abnormalities in both of these neurodevelopmental disorders. We aimed to assess procedural learning in children with TS (n=13), ADHD (n=22), and comorbid TS-ADHD (n=20), as well as in typically developing children (n=21). Procedural learning was measured with a well-studied implicit probabilistic sequence learning task, the alternating serial reaction time task...
July 12, 2017: Brain and Cognition
https://www.readbyqxmd.com/read/28298437/riding-the-metalloproteinase-roller-coaster
#9
Gillian Murphy
To many of us in the field, working on matrix metalloproteinases (MMPs) has felt like riding a roller coaster, traveling through times of both excitement and despair. I was fortunate to join the ride when it was a mere carousel of three activities thought to target the proteins that comprise the extracellular matrix (ECM). New technologies brought the thrills of discovery as we uncovered specific proteinase genes and defined specialized activities in different cellular processes. The MMPs and the sister families of "adisintegrin and metalloproteinase" (ADAMs), ADAMs with thrombospondin domains (ADAM-TS), and Astacins are now recognized as key signaling "scissors" that drive rapid changes in a plethora of cellular pathways...
May 12, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28294193/characteristics-of-ferroelectric-ferroelastic-domains-in-n%C3%A3-el-type-skyrmion-host-gav4s8
#10
Ádám Butykai, Sándor Bordács, István Kézsmárki, Vladimir Tsurkan, Alois Loidl, Jonathan Döring, Erik Neuber, Peter Milde, Susanne C Kehr, Lukas M Eng
GaV4S8 is a multiferroic semiconductor hosting Néel-type magnetic skyrmions dressed with electric polarization. At Ts = 42 K, the compound undergoes a structural phase transition of weakly first-order, from a non-centrosymmetric cubic phase at high temperatures to a polar rhombohedral structure at low temperatures. Below Ts, ferroelectric domains are formed with the electric polarization pointing along any of the four 〈111〉 axes. Although in this material the size and the shape of the ferroelectric-ferroelastic domains may act as important limiting factors in the formation of the Néel-type skyrmion lattice emerging below TC = 13 K, the characteristics of polar domains in GaV4S8 have not been studied yet...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27807143/hif-kdm3a-mmp12-regulatory-circuit-ensures-trophoblast-plasticity-and-placental-adaptations-to-hypoxia
#11
Damayanti Chakraborty, Wei Cui, Gracy X Rosario, Regan L Scott, Pramod Dhakal, Stephen J Renaud, Makoto Tachibana, M A Karim Rumi, Clifford W Mason, Adam J Krieg, Michael J Soares
The hemochorial placenta develops from the coordinated multilineage differentiation of trophoblast stem (TS) cells. An invasive trophoblast cell lineage remodels uterine spiral arteries, facilitating nutrient flow, failure of which is associated with pathological conditions such as preeclampsia, intrauterine growth restriction, and preterm birth. Hypoxia plays an instructive role in influencing trophoblast cell differentiation and regulating placental organization. Key downstream hypoxia-activated events were delineated using rat TS cells and tested in vivo, using trophoblast-specific lentiviral gene delivery and genome editing...
November 15, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27749055/use-of-restraints-from-consensus-fragments-of-multiple-server-models-to-enhance-protein-structure-prediction-capability-of-the-unres-force-field
#12
Magdalena A Mozolewska, Paweł Krupa, Bartłomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
Recently, we developed a new approach to protein-structure prediction, which combines template-based modeling with the physics-based coarse-grained UNited RESidue (UNRES) force field. In this approach, restrained multiplexed replica exchange molecular dynamics simulations with UNRES, with the C(α)-distance and virtual-bond-dihedral-angle restraints derived from knowledge-based models are carried out. In this work, we report a test of this approach in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11), in which we used the template-based models from early-stage predictions by the LEE group CASP11 server (group 038, called "nns"), and further improvement of the method...
November 28, 2016: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/27651465/validating-genetic-markers-of-response-to-recombinant-human-growth-hormone-in-children-with-growth-hormone-deficiency-and-turner-syndrome-the-predict-validation-study
#13
MULTICENTER STUDY
Adam Stevens, Philip Murray, Jerome Wojcik, John Raelson, Ekaterina Koledova, Pierre Chatelain, Peter Clayton
OBJECTIVE: Single-nucleotide polymorphisms (SNPs) associated with the response to recombinant human growth hormone (r-hGH) have previously been identified in growth hormone deficiency (GHD) and Turner syndrome (TS) children in the PREDICT long-term follow-up (LTFU) study (Nbib699855). Here, we describe the PREDICT validation (VAL) study (Nbib1419249), which aimed to confirm these genetic associations. DESIGN AND METHODS: Children with GHD (n = 293) or TS (n = 132) were recruited retrospectively from 29 sites in nine countries...
December 2016: European Journal of Endocrinology
https://www.readbyqxmd.com/read/27552837/effect-of-instrument-design-and-access-outlines-on-the-removal-of-root-canal-obturation-materials-in-oval-shaped-canals
#14
Tuomas K Niemi, Melissa A Marchesan, Adam Lloyd, Robert J Seltzer
INTRODUCTION: The aim of this study was to compare the effectiveness of TRUShape (TS) instruments with ProFile Vortex Blue (VB) instruments for the removal of obturation materials during retreatment of single-canal mandibular premolars performed through 2 access outlines. METHODS: Initial root canal treatment was completed through a contracted endodontic cavity (CEC) design. Canals were instrumented to an F2 ProTaper instrument, obturated with warm lateral condensation of gutta-percha with AH Plus sealer, and allowed to set for 30 days at 37°C and 100% humidity...
October 2016: Journal of Endodontics
https://www.readbyqxmd.com/read/27491848/insight-into-the-kinetics-and-thermodynamics-of-the-hydride-transfer-reactions-between-quinones-and-lumiflavin-a-density-functional-theory-study
#15
Clorice R Reinhardt, Tanner C Jaglinski, Ashly M Kastenschmidt, Eun H Song, Adam K Gross, Alyssa J Krause, Jonathan M Gollmar, Kristin J Meise, Zachary S Stenerson, Tyler J Weibel, Andrew Dison, Mackenzie R Finnegan, Daniel S Griesi, Michael D Heltne, Tom G Hughes, Connor D Hunt, Kayla A Jansen, Adam H Xiong, Sanchita Hati, Sudeep Bhattacharyya
The kinetics and equilibrium of the hydride transfer reaction between lumiflavin and a number of substituted quinones was studied using density functional theory. The impact of electron withdrawing/donating substituents on the redox potentials of quinones was studied. In addition, the role of these substituents on the kinetics of the hydride transfer reaction with lumiflavin was investigated in detail under the transition state (TS) theory assumption. The hydride transfer reactions were found to be more favorable for an electron-withdrawing substituent...
September 2016: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/27187663/human-dihydrofolate-reductase-and-thymidylate-synthase-form-a-complex-in-vitro-and-co-localize-in-normal-and-cancer-cells
#16
Anna Antosiewicz, Adam Jarmuła, Dorota Przybylska, Grażyna Mosieniak, Joanna Szczepanowska, Anna Kowalkowska, Wojciech Rode, Joanna Cieśla
Enzymes involved in thymidylate biosynthesis, thymidylate synthase (TS), and dihydrofolate reductase (DHFR) are well-known targets in cancer chemotherapy. In this study, we demonstrated for the first time, that human TS and DHFR form a strong complex in vitro and co-localize in human normal and colon cancer cell cytoplasm and nucleus. Treatment of cancer cells with methotrexate or 5-fluorouracil did not affect the distribution of either enzyme within the cells. However, 5-FU, but not MTX, lowered the presence of DHFR-TS complex in the nucleus by 2...
May 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/26942946/pregnancy-after-oocyte-donation-in-45-x-turner-syndrome-women-complicated-by-gestational-diabetes-and-polyhydramnios-case-report-and-mini-review-of-literature
#17
REVIEW
Adam Czyzyk, Agnieszka Podfigurna-Stopa, Krzysztof Katulski, Grzegorz H Breborowicz, Andrea R Genazzani, Blazej Meczekalski
Patients suffering from Turner syndrome (TS) demonstrate characteristic clinical features, with a short stature and gonadal dysgenesis causing infertility in most patients. Spontaneous pregnancies in women with TS are quite rare and pregnancy outcomes involving an increased risk of miscarriage and stillbirths are observed. In this case report, we present a 28 years old pregnant woman with the diagnosis of TS. Due to hypergonadotrophic hypogonadism, she was proposed an in vitro fertilization (IVF) program with an oocyte donor from unrelated anonymous women...
August 2016: Gynecological Endocrinology
https://www.readbyqxmd.com/read/26925858/development-of-a-true-transition-state-force-field-from-quantum-mechanical-calculations
#18
Ádám Madarász, Dénes Berta, Robert S Paton
Transition state force fields (TSFF) treated the TS structure as an artificial minimum on the potential energy surface in the past decades. The necessary parameters were developed either manually or by the Quantum-to-molecular mechanics method (Q2MM). In contrast with these approaches, here we propose to model the TS structures as genuine saddle points at the molecular mechanics level. Different methods were tested on small model systems of general chemical reactions such as protonation, nucleophilic attack, and substitution, and the new procedure led to more accurate models than the Q2MM-type parametrization...
April 12, 2016: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/26916840/phosphorylation-of-thymidylate-synthase-affects-slow-binding-inhibition-by-5-fluoro-dump-and-n-4-hydroxy-dcmp
#19
Jan Ludwiczak, Piotr Maj, Piotr Wilk, Tomasz Frączyk, Tomasz Ruman, Borys Kierdaszuk, Adam Jarmuła, Wojciech Rode
Endogenous thymidylate synthases, isolated from tissues or cultured cells of the same specific origin, have been reported to show differing slow-binding inhibition patterns. These were reflected by biphasic or linear dependence of the inactivation rate on time and accompanied by differing inhibition parameters. Considering its importance for chemotherapeutic drug resistance, the possible effect of thymidylate synthase inhibition by post-translational modification was tested, e.g. phosphorylation, by comparing sensitivities to inhibition by two slow-binding inhibitors, 5-fluoro-dUMP and N(4)-hydroxy-dCMP, of two fractions of purified recombinant mouse enzyme preparations, phosphorylated and non-phosphorylated, separated by metal oxide/hydroxide affinity chromatography on Al(OH)3 beads...
April 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/26663830/desmoplastic-melanoma-c-ts-and-nf-%C3%AE%C2%BAb
#20
COMMENT
Roy Rabbie, David J Adams
No abstract text is available yet for this article.
March 2016: Pigment Cell & Melanoma Research
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