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1
Apelblat, Alexander. "Dimerization and continuous association including formation of cyclic dimers." Canadian Journal of Chemistry 69, no. 4 (April 1, 1991): 638–47. http://dx.doi.org/10.1139/v91-097.
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New aspects of the theory of ideal associated mixtures related to a differentiation between formed cyclic and linear dimers are discussed. A mathematical analysis is presented for the dimerization model, A + B + A2, the continuous association (Mecke–Kempter) model, [Formula: see text], both coupled with the cyclic dimmer → linear dimer transformation and for the unsymmetrical (mixed) dimer formation model, A + B + A2 + B2 + AB. Introduction of the standard reaction enthalpies and volumes associated with transformations of dimers leads to a considerable change in behavior and symmetry properties of the excess thermodynamic functions. In terms of the modified Mecke–Kempter model, a consistent representation of the excess Gibbs energy of mixing GE, heat of mixing HE, and excess molar volume VE is reported for the acetic acid – water system at 298.15 K. Key words: association, dimerization, linear dimers, cyclic dimers, hydrogen bonding, carboxylic acids, alcohols, aqueous solutions.
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Huang, Dengchao, Shilin Liu, and Kang Yang. "Highly Unidirectional Radiation Enhancement Based on a Hybrid Multilayer Dimer." Nanomaterials 12, no. 4 (February 21, 2022): 710. http://dx.doi.org/10.3390/nano12040710.
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Dimers made of plasmonic particles support strong field enhancements but suffer from large absorption losses, while low-loss dielectric dimers are limited by relatively weak optical confinement. Hybrid dimers could utilize the advantages of both worlds. Here, we propose a hybrid nanoantenna that contains a dimer of core-dual shell nanoparticles known as the metal–dielectric–metal (MDM) structure. We discovered that the hybrid dimer sustained unidirectional forward scattering, which resulted in a nearly ideal Kerker condition in the frequency close to the resonance peak of the dimer due to enhancing the amplitude of the induced high-order electric multiples in the gap and effectively superimposing them with magnetic ones, which respond to the excitation of the plane wave in the dielectric layer of the dimer. Furthermore, when an electric quantum emitter is coupled to the dimer, our study shows that the optimal hybrid dimer simultaneously possesses high radiation directivity and low-loss features, which illustrates a back-to-front ratio of radiation 53 times higher than that of the pure dielectric dimer and an average radiation efficiency 80% higher than that of the pure metallic dimer. In addition, the unique structures of the hybrid hexamer direct almost decrease 75% of the radiation beamwidth, hence heightening the directivity of the nanoantenna based on a hybrid dimer.
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HUANG, YAN, XIAOYAN ZHU, and XIAOSHUANG CHEN. "SINGLE Si AD-DIMER DEPOSITION BEHAVIOR ON P(2×2)Si SURFACE." International Journal of Modern Physics B 20, no. 02 (January 20, 2006): 125–32. http://dx.doi.org/10.1142/s0217979206033140.
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The deposition of single Si ad-dimer on the p(2×2) reconstructed Si (100) surface has been simulated by an empirical tight-binding (ETB) method. Using the clean and defective Si surfaces as the deposition substrates, the deposition energies are mapped out around the clean surface and dimer vacancies. From the calculated energy plots, the binding sites and several possible diffusion paths are achieved. It is easy for the ad-dimer to form stable state A1 and metal stable state A2 on the clean surface. The change from A1 to A2 state appears as the rotation of the ad-dimer, which has been observed experimentally. The ad-dimers are found to prefer filling into the missing dimer vacancies. Finally, the diffusion traces of the ad-dimers on the surfaces have been simulated.
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Gould, Katherine A., Xiao-Su Pan, Robert J. Kerns, and L. Mark Fisher. "Ciprofloxacin Dimers Target Gyrase in Streptococcus pneumoniae." Antimicrobial Agents and Chemotherapy 48, no. 6 (June 2004): 2108–15. http://dx.doi.org/10.1128/aac.48.6.2108-2115.2004.
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ABSTRACT We have examined the antipneumococcal activities of novel quinolone dimers in which ciprofloxacin was tethered to itself or to pipemidic acid by linkage of C-7 piperazinyl rings. Symmetric 2,6-lutidinyl- and trans-butenyl-linked ciprofloxacin dimers (dimers 1 and 2, respectively) and a pipemidic acid-ciprofloxacin dimer (dimer 3) had activities against Streptococcus pneumoniae strain 7785 that were comparable to that of ciprofloxacin, i.e., MICs of 2, 1, and 4 to 8 μg/ml versus an MIC of 1 to 2 μg/ml, respectively. Surprisingly, unlike ciprofloxacin (which targets topoisomerase IV), several lines of evidence revealed that the dimers act through gyrase in S. pneumoniae. First, ciprofloxacin-resistant parC mutants of strain 7785 remained susceptible to dimers 1 to 3, whereas a gyrA mutation conferred a four- to eightfold increase in the dimer MIC but had little effect on ciprofloxacin activity. Second, dimer 1 selected first-step gyrA (S81Y or S81F) mutants (MICs, 8 to 16 μg/ml) that carried wild-type topoisomerase IV parE-parC genes. Third, dimers 1 and 2 promoted comparable DNA cleavage by S. pneumoniae gyrase and topoisomerase IV, whereas ciprofloxacin-mediated cleavage was 10-fold more efficient with topoisomerase IV than with gyrase. Fourth, the GyrA S81F and ParC S79F enzymes were resistant to dimers, confirming that the resistance phenotype is largely silent in parC mutants. Although a dimer molecule could bind very tightly by bridging quinolone binding sites in the enzyme-DNA complex, the greater potency of ciprofloxacin against gyrase and topoisomerase IV suggests that dimers 1 to 3 bind in a monomeric fashion. The bulky C-7 side chain may explain dimer targeting of gyrase and activity against efflux mutants. Tethered quinolones have potential as mechanistic tools and as novel antimicrobial agents.
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Ploegh, Hidde, and Philippe Benaroch. "MHC class II dimer of dimers." Nature 364, no. 6432 (July 1993): 16–17. http://dx.doi.org/10.1038/364016d0.
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Breslow, Ronald, Sandro Belvedere, Leland Gershell, and David Leung. "The chelate effect in binding, catalysis, and chemotherapy." Pure and Applied Chemistry 72, no. 3 (January 1, 2000): 333–42. http://dx.doi.org/10.1351/pac200072030333.
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Cyclodextrin (CD) dimers bind amino acid side chains, and such binding can dissociate aggregated proteins, including citrate synthase (dimer) and lactic dehydrogenase (tetramer). A CD dimer can bind a hydrophobic photosensitizer that, upon irradiation, generates singlet oxygen. This cleaves the dimer and releases the photosensitizer. CD dimers in a cytochrome P-450 mimic steer catalyzed hydroxylation to a bound steroid with geometric control. Chelate binding has also led to a group of cytodifferentiating agents whose mechanism has been recently established. They have promising anticancer properties, and are currently entering human trials as therapeutic agents.
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Caliezi, Holtz, and Wuillemin. "Case 16: Use of D-dimer assay in suspected deep vein thrombosis or pulmonary embolism." Therapeutische Umschau 56, no. 9 (September 1, 1999): 529–32. http://dx.doi.org/10.1024/0040-5930.56.9.529.
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D-Dimere sind Abbauprodukte des quervernetzten Fibrins nach fibrinolytischer Spaltung durch Plasmin. D-Dimere können im Plasma oder im Vollblut mittels gegen Epitope des D-Dimers gerichteter monoklonaler Antikörper nachgewiesen werden. Erhöhte D-Dimer-Werte finden sich bei Patienten mit tiefer Venenthrombose (TVT) oder Lungenembolie (LE), aber auch z.B. bei Patienten mit Infektionen, malignen Tumoren oder Herzinsuffizienz. Die Bestimmung der D-Dimere hat sich als früher Abklärungsschritt in der Diagnostik venöser Thromboembolien (TVT/LE) etabliert. Die hohe Sensitivität verschiedener ELISA-Teste ermöglicht es, die Diagnose einer TVT oder LE zuverlässig auszuschließen, falls die Konzentration der D-Dimere unterhalb einer kritischen Schwelle (sog. cut-off) liegt. Bei ambulanten Patienten gelingt es so, in rund 30% der Fälle mit Hilfe eines gut validierten Testes eine venöse Thromboembolie auszuschließen und auf weitere diesbezügliche Untersuchungen zu verzichten.
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Li, Wen-Tyng, John W. Shriver, and John N. Reeve. "Mutational Analysis of Differences in Thermostability between Histones from Mesophilic and Hyperthermophilic Archaea." Journal of Bacteriology 182, no. 3 (February 1, 2000): 812–17. http://dx.doi.org/10.1128/jb.182.3.812-817.2000.
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ABSTRACT Amino acid residues responsible for the large difference in thermostability between HMfB and HFoB, archaeal histones from the hyperthermophile Methanothermus fervidus and the mesophileMethanobacterium formicicum, respectively, have been identified by site-specific mutagenesis. The thermal denaturation of ∼70 archaeal histone variants has been monitored by circular dichroism, and the data generated were fit to a two-state unfolding model (dimer→two random coil monomers) to obtain a standard-state (1M) melting temperature for each variant dimer. The results of single-, double-, and triple-residue substitutions reveal that the much higher stability of rHMfB dimers, relative to rHFoB dimers, is conferred predominantly by improved intermolecular hydrophobic interactions near the center of the histone dimer core and by additional favorable ion pairs on the dimer surface.
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Tholen, Inger, Christiane Weingart, and Barbara Kohn. "Concentration of D-dimers in healthy cats and sick cats with and without disseminated intravascular coagulation (DIC)." Journal of Feline Medicine and Surgery 11, no. 10 (October 2009): 842–46. http://dx.doi.org/10.1016/j.jfms.2009.04.008.
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The objective of this prospective study was to measure concentrations of D-dimers in 48 cats with various diseases and in 20 healthy cats to evaluate the sensitivity and specificity for D-dimers to diagnose disseminated intravascular coagulation (DIC). The cats were classified as having DIC if an underlying disease and at least three of the following criteria were present: thrombocytopenia, prolonged activated partial thromboplastin time, prothrombin time or thrombin time, schistocytes and/or a reduced antithrombin activity. D-dimer concentrations were measured using a semi-quantitative latex agglutination (LA) test (Accuclot D-Dimer, Sigma Diagnostics). The D-dimer test was positive for 8/12 cats with DIC and for 16/36 sick cats without DIC. D-dimers were negative for all healthy control cats. The comparison of the sick cats with DIC and those without DIC revealed a specificity and sensitivity of the D-dimer test of 56% and 67%; a comparison of the results for healthy cats and cats with DIC revealed a specificity and sensitivity of 100% and 67%, respectively. The D-dimer LA test is only of limited value for the diagnosis of DIC in cats.
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Lazaroff, Carolyn, David Peeney, Sadeechya Gurung, and William G. Stetler-Stevenson. "Abstract 3837: The physiological relevance of TIMP dimer formation." Cancer Research 82, no. 12_Supplement (June 15, 2022): 3837. http://dx.doi.org/10.1158/1538-7445.am2022-3837.
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Abstract Tissue inhibitors of metalloproteinases (TIMPs) are a family of four paralogous genes that modulate the activity of matrix metalloproteinases (MMPs) and are vital for tissue homeostasis. Additionally, TIMPs display activities that are independent of their MMP inhibitory activities. Dysregulation and perturbations within this system can lead to complex tissue-specific pathologies. TIMP2 is the most abundantly expressed member of the TIMP family and has been shown to display potential therapeutic uses in cancer and other diseases. We have noted the persistent presence of SDS-stable TIMP2 dimers/multimers in SDS-PAGE at a level of ~5% total protein. The goal of this study is to determine the stability and biological relevance of SDS-stable dimer formation of TIMP2 in in vitro and in vivo. We found that TIMP2 dimers display an enhanced ability to inhibit MMP2 activity in reverse zymography assays. Immunoblotting revealed gel extracted TIMP2 dimer entered an equilibrium with monomeric TIMP2, while the extracted monomer did not form new dimer. In addition, MMP2 activity assays do not corroborate the enhanced MMP2 inhibitory activity observed in reverse zymograms but are consistent with the observation that isolated TIMP2 dimers re-equilibrate with monomers. This implies that structural or sequence difference mediates the formation of dimers. Dimer/multimer formation is observed across the TIMP family. Mass spectrometry analysis of gel extracted TIMP monomers and dimers show that monomer and dimer forms of TIMPs display unique post-translation modification (PTM) profiles. We propose that understanding the interplay between TIMP multimers and PTMs will reveal new biological functions within this intriguing family of proteins. We are currently working to resolve the functional differences between monomer and dimer and reveal the underlying mechanisms at play. Citation Format: Carolyn Lazaroff, David Peeney, Sadeechya Gurung, William G. Stetler-Stevenson. The physiological relevance of TIMP dimer formation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3837.
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Seligmann, Jenny F., Peter Hall, Patrick Hamilton, Simon Richard Lord, Paul Baxter, Maria Marples, and Daniel P. Stark. "D-dimers as a tumor marker in GIST: Can it reduce the frequency of CT scanning in patients receiving palliative imatinib?" Journal of Clinical Oncology 30, no. 4_suppl (February 1, 2012): 119. http://dx.doi.org/10.1200/jco.2012.30.4_suppl.119.
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119 Background: Treatment with palliative imatinib has improved outcomes in advanced GISTs, with a reported 2 year PFS of 50%. Guidelines suggest monitoring during imatinib by CT scan at 12 week intervals. There are no validated biomarkers to assist in disease evaluation. High d-dimer levels are associated with poor prognosis in several cancers and are predictive of disease progression during chemotherapy. In the diagnosis of venous thromboembolism, low D-dimer levels have a high negative predictive value (npv) for thrombosis. We investigated whether low d-dimers have a clinically useful npv for GIST progression. Methods: We retrospectively identified all patients treated with palliative Imatinib for GIST in a single tertiary referral centre using a systematic search of an electronic clinical database. Every 12 weeks during treatment patients were assessed by clinical evaluation, CT and a d-dimer measurement (HemosIL HS assay). The prognostic value of d-dimers was assessed by Cox regression. The clinical utility of d-dimers as a biomarker for radiological progression (rPD) was evaluated using radio operator curve (ROC) analysis. Results: 50 patients treated between Jan 2002 and June 2011 met criteria for inclusion. D-dimers were prognostic for progression free survival and overall survival, when analysed by level or over time (p <0.05). Over 460 clinical observations with CT and d-dimer were analysed. Scans demonstrating rPD were associated with higher d-dimer levels and a rising trend (p <0.05). D-dimer levels <1000 had a npv for rPD of 85%. An asymptomatic patient with a d-dimer level <1000 and a falling level over time was seen in 32% of observations, and had a npv for rPD of 92%. Conclusions: D-dimers may have a useful role in disease monitoring for GIST patients treated with palliative imatinib, particularly as a negative predictor of progression. This may reduce the burden of CT scanning in a useful percentage of patients but will require further validation.
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Ren, Shi Wei. "The Spin Transport of the Coblt Dimers with Different Directions." Applied Mechanics and Materials 543-547 (March 2014): 3947–50. http://dx.doi.org/10.4028/www.scientific.net/amm.543-547.3947.
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In this paper, the spin transport properties of the coblt dimers parrallel to the transport direction and perpendicular to ransprot direction are investigated by using the first principle analysis. Calculation shows that both the coblt dimers parrallel to the transport direction and perpendicular to ransprot direction give obvious spin polarized density of states and current. It is found that the dimer parrallel to the transport direction have larger spin polarization current.The spin polarized efficiency for the parrallel dimer increase steadily with the increase of the bias voltage. But the the spin polarization for the transverse dimer changes greatly.
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Прасолов, Н. Д., А. А. Гуткин, and П. Н. Брунков. "Исследование с помощью молекулярной динамики образования димеров на поверхности (001) GaAs при низких температурах." Физика и техника полупроводников 55, no. 2 (2021): 134. http://dx.doi.org/10.21883/ftp.2021.02.50498.9516.
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The simulation of dimers formation during the low-temperature reconstruction of GaAs (001) surface terminated with Ga or As atoms was performed by the molecular dynamics method using the analytical Bond-Order Potential based on quantum mechanical theory incorporating both σ- and π- bonds between atoms. A decrease in values of potential energy of the atoms during formation of isolated surface dimer have been determined. It has been found that potential energy of an atom in As-dimer is several tenths of an eV lower than in Ga-dimer. Kinetics of the initial stages of Ga-dimers formation in the temperature range of 25 - 40 K was studied. It was found that the characteristic thermal activation energy of single isolated Ga-dimers formation is ~ 29 meV, which is lower than the same value for As-dimers (~ 38 meV). Time constants characterizing the average rate of transformation of one dimer into a chain of two dimers at temperature range of 28 - 37 K were estimated. Inverse values of these parameters for paired Ga- and As-dimers are in the ranges of 10^11 – 10^12 s^-1 and 10^9 – 10^10 s^-1, respectively, while corresponding parameters for the formation of single dimers are in the ranges of 4·10^6 – 10^8 s^-1 and 1.4·10^6 – 7.4·10^7 s^-1.
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Guseman, Alex J., Gerardo M. Perez Goncalves, Shannon L. Speer, Gregory B. Young, and Gary J. Pielak. "Protein shape modulates crowding effects." Proceedings of the National Academy of Sciences 115, no. 43 (October 9, 2018): 10965–70. http://dx.doi.org/10.1073/pnas.1810054115.
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Protein−protein interactions are usually studied in dilute buffered solutions with macromolecule concentrations of <10 g/L. In cells, however, the macromolecule concentration can exceed 300 g/L, resulting in nonspecific interactions between macromolecules. These interactions can be divided into hard-core steric repulsions and “soft” chemical interactions. Here, we test a hypothesis from scaled particle theory; the influence of hard-core repulsions on a protein dimer depends on its shape. We tested the idea using a side-by-side dumbbell-shaped dimer and a domain-swapped ellipsoidal dimer. Both dimers are variants of the B1 domain of protein G and differ by only three residues. The results from the relatively inert synthetic polymer crowding molecules, Ficoll and PEG, support the hypothesis, indicating that the domain-swapped dimer is stabilized by hard-core repulsions while the side-by-side dimer shows little to no stabilization. We also show that protein cosolutes, which interact primarily through nonspecific chemical interactions, have the same small effect on both dimers. Our results suggest that the shape of the protein dimer determines the influence of hard-core repulsions, providing cells with a mechanism for regulating protein−protein interactions.
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Si, Tieyan. "Odd–even effect of melting finite polymer film on square lattice." International Journal of Modern Physics B 29, no. 09 (April 7, 2015): 1550062. http://dx.doi.org/10.1142/s0217979215500629.
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Two-dimensional film system bears many exotic thermodynamics behaviors. We proposed a mathematical physics model to explore how the melting temperature of a two-dimensional mathematical dimer film depends on the odd–evenness of the finite width of dimer film. A weak external bond between dimers is introduced into the classical dimer model in this dimer film. We derived a general equation of melting temperature and applied it for computing the melting temperature of a dimer film covering a finite square lattice. The melting temperature is proportional to the external bonding energy that we assume it binds neighboring dimers together and proportional to the inverse of entropy per site. Furthermore, it shows fusing two small rectangular dimer film with odd number of length into one big rectangular film gains more entropy than fusing two small rectangles with even number of length into the same big rectangle. Fusing two small toruses with even number of length into one big torus reduces entropy. Fusing two small toruses with odd number of length increases the entropy. Thus two dimer films with even number of length repel each other, two dimer films with odd length attract each other. The odd–even effect is also reflected on the correlation function of two topologically distinguishable loops in a torus surface. The entropy of finite system dominates odd–even effect. This model has straightforward extension to longer polymers and three-dimensional systems.
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Zawadzki, Paweł, Anita Nowak, and Lukasz Dzieciuchowicz. "Factors affecting D-dimer levels in patients with uncomplicated primary varicose veins." Polish Journal of Surgery 93, no. 5 (June 23, 2021): 1–5. http://dx.doi.org/10.5604/01.3001.0014.9658.
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Objectives The diagnosis of deep venous thrombosis (DVT) is hampered in patients with primary varicose veins due to similarity of symptoms of DVT and PVV and elevated levels of D-dimers. The purpose of this study was to analyze factors that influence the D-dimer concentration in patients with PVV in order to redefine its diagnostic value. Methods Forty- one patients with non-complicated PVV were enrolled in the study, in whom D-dimer level was determined by immunoturbidimetric assay. The influence of selected clinical factors on the concentration of D-dimers was determined with univariate and bivariate analysis. Besides descriptive statistics the D-dimers levels were compared to the age -adjusted cutoff values. Results The median concentration of D-dimer was 630.0 ng/ml (440.0-1140.0 ng/ml) and was above the age-adjusted level in 21 (52%) of patients. There was a positive correlation between the patient’s age and and D-dimer concentration (p = 0.035, Spearman correlation coefficient rs=0,33. The bivariate analysis showed a significant interaction between age and weight p=0,02. Conclusions In patients with PVV the diagnostic value of D-dimers is limited especially in older and overweight subjects.
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Yin, Ke, Shixin Mai, and Jun Zhao. "Atmospheric Sulfuric Acid Dimer Formation in a Polluted Environment." International Journal of Environmental Research and Public Health 19, no. 11 (June 3, 2022): 6848. http://dx.doi.org/10.3390/ijerph19116848.
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New particle formation (NPF) contributes significantly to atmospheric particle number concentrations and cloud condensation nuclei (CCN). In sulfur-rich environments, field measurements have shown that sulfuric acid dimer formation is likely the critical step in NPF. We investigated the dimer formation process based upon the measured sulfuric acid monomer and dimer concentrations, along with previously reported amine concentrations in a sulfur-rich atmosphere (Atlanta, USA). The average sulfuric acid concentration was in the range of 1.7 × 107–1.4 × 108 cm−3 and the corresponding neutral dimer concentrations were 4.1 × 105–5.0 × 106 cm−3 and 2.6 × 105–2.7 × 106 cm−3 after sub-collision and collision ion-induced clustering (IIC) corrections, respectively. Two previously proposed acid–base mechanisms (namely AA and AB) were employed to respectively estimate the evaporation rates of the dimers and the acid–amine complexes. The results show evaporation rates of 0.1–1.3 s−1 for the dimers based on the simultaneously measured average concentrations of the total amines, much higher than those (1.2–13.1 s−1) for the acid–amine complexes. This indicates that the mechanism for dimer formation is likely AA through the formation of more volatile dimers in the initial step of the cluster formation.
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GIANNOULOPOULOS (Γ.Δ. ΓΙΑΝΝΟΥΛΟΠΟΥΛΟΣ), G. D., L. V. ATHANASIOU (Λ.Β. ΑΘΑΝΑΣΙΟΥ), and Z. S. POLIZOPOULOU (Ζ.Σ. ΠΟΛΥΖΟΠΟΥΛΟΥ). "D-dimer as a diagnostic tool for canine thromboembolic disorders." Journal of the Hellenic Veterinary Medical Society 61, no. 1 (November 13, 2017): 49. http://dx.doi.org/10.12681/jhvms.14876.
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D-dimers are small protein fragments present in the blood after a blood clot is degraded by plasmin. During the fibrin(ogen) degradation, a number of products are produced called fibrin(ogen) degradation products (FDPs). D-dimers are part of the FDPs, formed as a result of plasmin activity on cross-linked fibrin. Thus, D-dimers indicate the activity of both thrombin and plasmin and are specific markers for fibrinolysis. D-dimer measurement is widely used in the diagnostic work-up of human patients as the most sensitive test to diagnose pulmonary thromboembolism (PTE) and disseminated intravascular coagulation (DIC) and it is, also, considered essential in the evaluation of antithrombotic therapy. During the last decade, there was considerable research regarding the potential utility of D-dimer in veterinary medicine, particularly in canine and equine species. In dogs, D-dimer plasma concentrations can be used to rapidly detect the thrombotic complications and DIC associated with many systemic diseases (high quantitative D-dimer levels). The symptoms of PTE are subtle and the confirmation of diagnosis with routine hematological tests can be difficult, thus jeopardizing the patient's survival. Several techniques have been employed for the detection of D-dimer; the immunoenzymatic assay (ELISA), the immuno-turbidimetric assay and several latex agglutination assays are more commonly used.
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Sawant, Kirti V., Renling Xu, Robert Cox, Hal Hawkins, Elena Sbrana, Deepthi Kolli, Roberto P. Garofalo, and Krishna Rajarathnam. "Chemokine CXCL1-Mediated Neutrophil Trafficking in the Lung: Role of CXCR2 Activation." Journal of Innate Immunity 7, no. 6 (2015): 647–58. http://dx.doi.org/10.1159/000430914.
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The chemokine CXCL1 and its receptor CXCR2 play a crucial role in host immune response by recruiting and activating neutrophils for microbial killing at the tissue site. Dysregulation in this process has been implicated in collateral tissue damage causing disease. CXCL1 reversibly exists as monomers and dimers, and it has been proposed that distinct monomer and dimer activities and the monomer-dimer equilibrium regulate the neutrophil function. However, the molecular mechanisms linking the CXCL1/CXCR2 axis and the neutrophil ‘beneficial' and ‘destructive' phenotypes are not known. In this study, we characterized neutrophil trafficking and its consequence in the mouse lung by the CXCL1 wild type (WT), which exists as monomers and dimers, and by a nondissociating dimer. Whereas the WT, compared to the dimer, was more active at low doses, both the WT and the dimer elicited a large neutrophil efflux at high doses. Importantly, robust neutrophil recruitment elicited by the WT or dimer was not detrimental to lung tissue integrity and, further, could not be correlated to surface CXCR2 levels. We conclude that the CXCL1 monomer-dimer distribution and receptor interactions are highly coupled and regulate neutrophil trafficking and that injury in the context of disease is a consequence of inappropriate CXCR2 activation at the target tissue and not due to mechanical forces exerted by neutrophils during recruitment.
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Hahne, Kathrin, Pia Lebiedz, and Frank Breuckmann. "Impact of D-Dimers on the Differential Diagnosis of Acute Chest Pain: Current Aspects besides the Widely Known." Clinical Medicine Insights: Cardiology 8s2 (January 2014): CMC.S15948. http://dx.doi.org/10.4137/cmc.s15948.
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D-dimers are cleavage products of fibrin that occur during plasmin-mediated fibrinolysis of blood clots. In the emergency department, D-dimer measurement represents a valuable and cost-effective tool in the differential diagnosis of acute chest pain including the main life-threatening entities: acute coronary syndrome, pulmonary embolism, and acute aortic syndrome. Whereas the diagnostic and prognostic values of D-dimer testing in acute coronary syndrome is of less priority, increases of D-dimers are frequently found in venous thromboembolism and acute aortic syndromes, especially acute aortic dissection. As to the high negative predictive value of D-dimer in those disorders, patients with low to intermediate pretest probability may profit in terms of less necessity of further non-invasive or even invasive imaging, simultaneously reducing potential complications and healthcare-related costs. However, because of the low specificity of the different D-dimer tests in contrast to its frequent usage, adequate interpretation is required. Age-related adjustment of D-dimer levels may be used to increase its diagnostic power.
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Jang, Hyunbum, Serena Muratcioglu, Attila Gursoy, Ozlem Keskin, and Ruth Nussinov. "Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers." Biochemical Journal 473, no. 12 (June 10, 2016): 1719–32. http://dx.doi.org/10.1042/bcj20160031.
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Are the dimer structures of active Ras isoforms similar? This question is significant since Ras can activate its effectors as a monomer; however, as a dimer, it promotes Raf's activation and MAPK (mitogen-activated protein kinase) cell signalling. In the present study, we model possible catalytic domain dimer interfaces of membrane-anchored GTP-bound K-Ras4B and H-Ras, and compare their conformations. The active helical dimers formed by the allosteric lobe are isoform-specific: K-Ras4B-GTP favours the α3 and α4 interface; H-Ras-GTP favours α4 and α5. Both isoforms also populate a stable β-sheet dimer interface formed by the effector lobe; a less stable β-sandwich interface is sustained by salt bridges of the β-sheet side chains. Raf's high-affinity β-sheet interaction is promoted by the active helical interface. Collectively, Ras isoforms’ dimer conformations are not uniform; instead, the isoform-specific dimers reflect the favoured interactions of the HVRs (hypervariable regions) with cell membrane microdomains, biasing the effector-binding site orientations, thus isoform binding selectivity.
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Kuruvilla, John, Phil Wells, Bev Morrow, Karen MacKinnon, Michael Keeney, and Michael Kovacs. "Prospective assessment of the natural history of positive D-dimer results in persons with acute venous thromboembolism (DVT or PE)." Thrombosis and Haemostasis 89, no. 02 (2003): 284–87. http://dx.doi.org/10.1055/s-0037-1613444.
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SummaryThe natural history of initially positive D-dimers for venous thromboembolism is not known. If it returns to negative in the majority of patients, it would be potentially helpful to diagnose a recurrence. In this study, we prospectively measured D-dimer levels in outpatients with a diagnosis of venous thrombo-embolism. There were a total of 152 patients with an average age of 57. D-dimer results were performed at baseline and repeated at one week, one month and three months.At baseline 120 of 152 (79%) had a positive D-dimer result. Of those with an initially positive result, 80% were still positive at one week and 39% were still positive at one month. Finally at three months, 13% remained positive. Seven patients had recurrent events and all had persistently elevated D-dimers at one month. This study suggests that a persistently positive D-dimer result after one month of treatment may indicate a higher risk of recurrent venous thromboembolism. D-dimer testing for the diagnosis of recurrence of venous thromboembolism deserves further study.
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PUTUNGAN, DARWIN B., HENRY J. RAMOS, FENG-CHUAN CHUANG, and MARVIN A. ALBAO. "MODELING OF CO-DEPOSITION OF INDIUM AND TIN ON SILICON(100): A KINETIC MONTE CARLO STUDY." International Journal of Modern Physics B 25, no. 14 (June 10, 2011): 1889–98. http://dx.doi.org/10.1142/s0217979211100941.
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A growth model for co-deposition of Sn and In on Si (100) at room-temperature was simulated using Kinetic Monte Carlo methods to shed light on the chemical selectivity and lack of dimer ordering seen in [Jure et al., Appl. Surf. Sci.162, 638 (2000)], a Scanning Tunneling Microscopy (STM) study. In this work, the experimental observation that the number of mixed In – Sn dimers is unaffected even when the relative flux rates are adjusted to favor In over Sn (by 100:1) — a manifestation of some sort of chemical selectivity — was investigated. Our simulations reveal that this phenomenon is ultimately related to the fact that the number of Sn -terminated chains is largely unaffected by the relative flux rate. Finally, we found that the attraction between metal dimers (whether of the same or different species) within a Si dimer row has only negligible effect on the apparent lack of dimer ordering seen in the STM study. Instead, dimer ordering is controlled by the detachment barriers in dimer-terminated islands.
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Hegde, Gautam, Pranay Nayak, Ratheejit Ghosh, and Rejish Nath. "Soliton dimer–soliton scattering in coupled quasi-one-dimensional dipolar Bose–Einstein condensates." Journal of Physics B: Atomic, Molecular and Optical Physics 54, no. 20 (October 20, 2021): 205301. http://dx.doi.org/10.1088/1361-6455/ac3370.
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Abstract We discuss scattering between a bright soliton and a soliton dimer in coupled quasi-one-dimensional dipolar Bose–Einstein condensates. The dimer is formed by each soliton from both tubes due to the attractive inter-layer dipole–dipole interaction. The dipoles within each tube repel each other, and a stable, bright soliton is stabilized via attractive contact interactions. In general, the scattering is inelastic, transferring the kinetic energy into internal modes of both soliton dimer and single soliton. Our studies reveal rich scattering scenarios, including dimer–soliton repulsion at small initial velocities, exchange of atoms between dimer and single soliton and soliton fusion at intermediate velocities. Interestingly, for some particular initial velocities, the dimer–soliton scattering results in a state of two dimers. At large initial velocities, the scattering is elastic as expected.
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Wheater, John F., and P. D. Xavier. "The cylinder amplitude in the hard dimer model on 2D causal dynamical triangulations." Classical and Quantum Gravity 39, no. 7 (March 2, 2022): 075004. http://dx.doi.org/10.1088/1361-6382/ac50ec.
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Abstract We consider the model of hard dimers coupled to two-dimensional causal dynamical triangulations (CDT) with all dimer types present and solve it exactly subject to a single restriction. Depending on the dimer weights there are, in addition to the usual gravity phase of CDT, two tri-critical and two dense dimer phases. We establish the properties of these phases, computing their cylinder and disk amplitudes, and their scaling limits.
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Briz, Montserrat, Helen Marr, Kate Talks, John Hanley, and Patrick Kesteven. "Serial D-Dimer Measurements Are Useful in Predicting the Recurrence of Venous Thromboembolism after Discontinuation of Anticoagulation." Blood 112, no. 11 (November 16, 2008): 525. http://dx.doi.org/10.1182/blood.v112.11.525.525.
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Abstract The optimal duration of anticoagulation following a venous thromboembolism (VTE) is influenced by the site of the event and the presence of risk factors. After anticoagulation is discontinued, approximately 10% of patients will have a recurrent event. At present, there is no accurate method of identifying this group of patients, in whom the benefits of reanticoagulation may outweigh the bleeding risks. In 2006, Palaretti et al reported the use of a single qualitative d-dimer measurement, 4 weeks after stopping anticoagulation for a spontaneous VTE, to identify patients at increased risk of a recurrent VTE. Our observational study investigates whether serial quantitative d-dimer measurements, after the discontinuation of anticoagulation for VTE, are of use in identifying patients at higher risk of VTE recurrence. We followed an unselected group of patients attending a hospital based Thrombosis Clinic in whom anticoagulation for VTE was stopped. Over a 2 year period from July 2005 to July 2007, anticoagulation was discontinued in 216 patients (112 females, 104 males) after a median period of 6 months’ treatment (range 2–324 months). The patients ranged in age from 16–88 years, with a mean age of 54 years. Of the group, 146 had been anticoagulated for a deep vein thrombosis (DVT), 59 for pulmonary embolism (PE) +/− DVT, and 11 had been anticoagulated for VTE at other sites. Major risk factors for VTE (recent surgical procedure, malignancy, pregnancy) were present at diagnosis in 80 patients. Minor risk factors (minor trauma, prolonged travel or immobility, hormone therapy) were present in 61 patients, while no risk factors were identified in 69 patients. Presence of risk factors was unknown in the remaining 6 patients. After discontinuation of their anticoagulation, patients were followed up in the Thrombosis Clinic for a median of 14.5 months (range 0–41 months). D-dimer measurements were recorded at the point of stopping anticoagulation, 4 weeks later, and then on subsequent clinic visits. Quantitative d-dimer results were obtained using an automated latex immunoassay (Instrumentation Laboratories, d-dimers HS) on an ACL TOP CTS analyser. Recurrence of VTE occurred in 23 of the 216 (10.7%) patients. D-dimer results off anticoagulation were available in 207 patients. Forty six patients had repeatedly high d-dimer measurements (> 300ng/ml) off anticoagulation. D-dimers remained within the normal range in 112 patients. In 33 patients, d-dimers were initially normal, but subsequently became high, while the opposite was true in 16 patients, where initially high d-dimers later fell into the normal range. Of the recurrences, 8 occurred in the group who had repeatedly high d-dimers after anticoagulation was stopped (17.4%), whilst only 3 recurrences occurred in patients whose d-dimers were consistently normal (2.7%). In the group whose d-dimers were initially normal, but subsequently became high during follow up, there were 6 recurrences (18.2%). There was 1 recurrence in the group whose d-dimers were initially high, but then became normal. In the 9 patients in whom serial d-dimer results were not available, 5 recurrent VTE were observed: 4 of these occurred within 4 weeks of the patient stopping anticoagulation. After statistical analysis of the data, taking into account the nature of the original event, age, gender and d-dimer measurements, a high d-dimer off anticoagulation was the only significant independent variable predicting for recurrence of VTE (Chi-square 13.1 p<0.00001). This data supports a role for monitoring d-dimer measurements in identifying patients at increased risk of VTE recurrence. Further investigation is needed to establish the benefits of reanticoagulation in these patients.
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Meisinger, Christa, Inge Kirchberger, Tobias D. Warm, Alexander Hyhlik-Dürr, Yvonne Goßlau, and Jakob Linseisen. "Elevated Plasma D-Dimer Concentrations in Adults after an Outpatient-Treated COVID-19 Infection." Viruses 14, no. 11 (November 3, 2022): 2441. http://dx.doi.org/10.3390/v14112441.
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Elevated D-dimer plasma concentrations are common in hospitalized COVID-19 patients and are often associated with a worse prognosis, but it is not yet clear whether this also applies to outpatient cases. The present cross-sectional study evaluated D-dimer levels and their association with clinical parameters and inflammation biomarkers after a COVID-19 disease in individuals treated as outpatients. The study included 411 individuals (43.3% men) with an average age of 46.8 years (SD 15.2). Study participants who had acute COVID-19 disease at a median of 235 days (120; 323) ago were examined at the University Hospital Augsburg, Southern Germany, between 11/2020 and 05/2021. Plasma D-dimers were measured by a particle-enhanced immunoturbidimetric assay. Sixty-one subjects (15%) showed increased D-dimer concentrations (≥500 µg/L). Study participants with elevated D-dimer levels in comparison to subjects with levels in the reference range were significantly older, and more frequently reported a history of cardiovascular disease, hypertension, venous thromboembolism, and chronic venous insufficiency. In multivariable logistic regression analysis, CRP levels (OR 5.58 per mg/dL, 95% CI 1.77–17.60) and white blood cell count (OR 1.48 per nL, 95% CI 1.19–1.83) were significantly related to elevated D-dimers even after adjustment for multiple testing. However, acute or persistent symptoms were not significantly associated with increased D-dimers. Elevated D-dimer levels months after an acute COVID-19 disease seems to be associated with markers of inflammation. Further studies are needed to investigate the underlying pathophysiological mechanisms and consequences of prolonged D-dimer elevation in these patients.
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Mühleip, Alexander W., Friederike Joos, Christoph Wigge, Achilleas S. Frangakis, Werner Kühlbrandt, and Karen M. Davies. "Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria." Proceedings of the National Academy of Sciences 113, no. 30 (July 11, 2016): 8442–47. http://dx.doi.org/10.1073/pnas.1525430113.
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F1Fo-ATP synthases are universal energy-converting membrane protein complexes that synthesize ATP from ADP and inorganic phosphate. In mitochondria of yeast and mammals, the ATP synthase forms V-shaped dimers, which assemble into rows along the highly curved ridges of lamellar cristae. Using electron cryotomography and subtomogram averaging, we have determined the in situ structure and organization of the mitochondrial ATP synthase dimer of the ciliate Paramecium tetraurelia. The ATP synthase forms U-shaped dimers with parallel monomers. Each complex has a prominent intracrista domain, which links the c-ring of one monomer to the peripheral stalk of the other. Close interaction of intracrista domains in adjacent dimers results in the formation of helical ATP synthase dimer arrays, which differ from the loose dimer rows in all other organisms observed so far. The parameters of the helical arrays match those of the cristae tubes, suggesting the unique features of the P. tetraurelia ATP synthase are directly responsible for generating the helical tubular cristae. We conclude that despite major structural differences between ATP synthase dimers of ciliates and other eukaryotes, the formation of ATP synthase dimer rows is a universal feature of mitochondria and a fundamental determinant of cristae morphology.
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Mughal, Sabeeha, C. Grazia Bezzu, Emma Carter, Simon J. A. Pope, and Neil B. McKeown. "The tetratriptycenoporphyrazines revisited." Journal of Porphyrins and Phthalocyanines 17, no. 08n09 (August 2013): 778–84. http://dx.doi.org/10.1142/s1088424613500351.
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The spectroscopic behavior of octa-t-butyltetra-2,3-triptycenotetraazaporphyrin and some of its metal complexes ( Cu 2+, Zn 2+ and Co 2+) were examined. UV-visible and electron paramagnetic resonance spectroscopy indicate that these phthalocyanine derivatives form cofacial dimers in pentane solution. Modeling suggests that the lowest energy configuration of the dimer is a self-complementary embrace in which the two phthalocyanine cores are staggered at an angle of 45° relative to each other. This configuration results in a remarkably intense and sharp absorption band (~635 nm; ε = ~4.0 × 105 M-1.cm-1) arising from excitonic coupling within the dimer, a unique property for self-assembled dimers but analogous to the behavior of certain μ-oxo-dimers of silicon phthalocyanine. Introduction of methyl substituents into the bridgehead positions of the triptycene subunits prevents dimer formation.
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Westerlund, Kristina, Anders Myrhammar, Hanna Tano, Maxime Gestin, and Amelie Eriksson Karlström. "Stability Enhancement of a Dimeric HER2-Specific Affibody Molecule through Sortase A-Catalyzed Head-to-Tail Cyclization." Molecules 26, no. 10 (May 12, 2021): 2874. http://dx.doi.org/10.3390/molecules26102874.
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Natural backbone-cyclized proteins have an increased thermostability and resistance towards proteases, characteristics that have sparked interest in head-to-tail cyclization as a method to stability-enhance proteins used in diagnostics and therapeutic applications, for example. In this proof-of principle study, we have produced and investigated a head-to-tail cyclized and HER2-specific ZHER2:342 Affibody dimer. The sortase A-mediated cyclization reaction is highly efficient (>95%) under optimized conditions, and renders a cyclic ZHER3:342-dimer with an apparent melting temperature, Tm, of 68 °C, which is 3 °C higher than that of its linear counterpart. Circular dichroism spectra of the linear and cyclic dimers looked very similar in the far-UV range, both before and after thermal unfolding to 90 °C, which suggests that cyclization does not negatively impact the helicity or folding of the cyclic protein. The cyclic dimer had an apparent sub-nanomolar affinity (Kd ~750 pM) to the HER2-receptor, which is a ~150-fold reduction in affinity relative to the linear dimer (Kd ~5 pM), but the anti-HER2 Affibody dimer remained a high-affinity binder even after cyclization. No apparent difference in proteolytic stability was detected in an endopeptidase degradation assay for the cyclic and linear dimers. In contrast, in an exopeptidase degradation assay, the linear dimer was shown to be completely degraded after 5 min, while the cyclic dimer showed no detectable degradation even after 60 min. We further demonstrate that a site-specifically DyLight 594-labeled cyclic dimer shows specific binding to HER2-overexpressing cells. Taken together, the results presented here demonstrate that head-to-tail cyclization can be an effective strategy to increase the stability of an Affibody dimer.
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KARATAŞ KILIÇCIOĞLU, Gizem, Tezcan KAYA, Kubilay İŞSEVER, Ertuğrul GÜÇLÜ, and Oğuz KARABAY. "COVID-19 hastalarında koagülopati için C-reaktif protein/albumin oranının tanısal doğruluğu." Cukurova Medical Journal 47, no. 2 (June 30, 2022): 622–28. http://dx.doi.org/10.17826/cumj.1050419.
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Amaç: Bu çalışma, COVİD-19'da D-dimer yüksekliğini öngörmede C-reaktif proteinin (CRP) albümine oranının (CAR) tanısal faydasını değerlendirmek amaçlamıştır.
Gereç ve Yöntem: Bu retrospektif kohort çalışmasında, bir üniversite hastanesinde COVID-19 olduğu doğrulanmış 145 yatan hastadan veri topladık. Hastalar D-dimer düzeylerine göre D-dimer düzeyi yüksek olanlar ve D-dimer düzeyi normal olanlar olarak iki gruba ayrıldı. Hastaların tıbbi kayıtlarından demografik veriler, komorbiditeler, klinik semptomlar, CAR ve laboratuvar sonuçları elde edildi ve gruplar arasında kıyaslamalar yapıldı.
Bulgular: Hastaların yaş ortalaması 52,9±17,9 yıl olup, 76'sı erkek idi. CAR medyanı, D-dimer değeri yüksek olanlarda anlamlı olarak daha yüksekti (134,1'e karşı 20,7,). D-dimeri yüksek hastalarda CRP, prokalsitonin, lökosit, nötrofil, laktat dehidrojenaz, ferritin ve fibrinojen daha yüksekti. CAR ve D-Dimer arasında oldukça anlamlı pozitif korelasyon vardı. Lojistik regresyon analizi, CAR'ın D-dimer yüksekliği için önemli bir belirleyici olduğunu ortaya koydu. ROC eğrisi altında kalan alan (AUC) CAR için 0,741 idi. COVİD-19 hastalarında D-dimer yüksekliğini öngörmek için CAR'ın doğrulanmış eşik değeri, %58 duyarlılık ve %70 özgüllük ile 81,8 idi.
Sonuç: Çalışmamız, CAR'ın D-dimer ile önemli ölçüde korele olduğunu ve COVİD-19’u olan hastalarda D-dimer yüksekliğini öngörmek için kullanılabileceğini göstermiştir.
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Grela, Przemysław, Xiao-Ping Li, Marek Tchórzewski, and Nilgun E. Tumer. "Functional divergence between the two P1–P2 stalk dimers on the ribosome in their interaction with ricin A chain." Biochemical Journal 460, no. 1 (April 25, 2014): 59–69. http://dx.doi.org/10.1042/bj20140014.
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Wild-type yeast ribosomes and ribosomes bearing only the P1B–P2A dimer bound to the ricin A chain better and were more susceptible to depurination and toxicity than ribosomes bearing only the P1A–P2B dimer, indicating that the two stalk dimers differ in their function.
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Nagpal, Anushka, Dinesh Dhankhar, Thomas C. Cesario, Runze Li, Jie Chen, and Peter M. Rentzepis. "Thymine dissociation and dimer formation: A Raman and synchronous fluorescence spectroscopic study." Proceedings of the National Academy of Sciences 118, no. 6 (February 1, 2021): e2025263118. http://dx.doi.org/10.1073/pnas.2025263118.
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In this study, absorption, fluorescence, synchronous fluorescence, and Raman spectra of nonirradiated and ultraviolet (UV)-irradiated thymine solutions were recorded in order to detect thymine dimer formation. The thymine dimer formation, as a function of irradiation dose, was determined by Raman spectroscopy. In addition, the formation of a mutagenic (6-4) photoproduct was identified by its synchronous fluorescence spectrum. Our spectroscopic data suggest that the rate of conversion of thymine to thymine dimer decreases after 20 min of UV irradiation, owing to the formation of an equilibrium between the thymine dimers and monomers. However, the formation of the (6-4) photoproduct continued to increase with UV irradiation. In addition, the Raman spectra of nonirradiated and irradiated calf thymus DNA were recorded, and the formation of thymine dimers was detected. The spectroscopic data presented make it possible to determine the mechanism of thymine dimer formation, which is known to be responsible for the inhibition of DNA replication that causes bacteria inactivation.
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Číčel, Blahoslav, Peter Komadel, and Miloš Nigrin. "Catalytic Activity of Smectites on Dimerization of Oleic Acid." Collection of Czechoslovak Chemical Communications 57, no. 8 (1992): 1666–71. http://dx.doi.org/10.1135/cccc19921666.
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A series of dimerization experiments were conducted to investigate the relationship between dimerization yield and crystallochemical composition of five smectite minerals used as catalysts. Effect of interlayer cations and acid treatement of one montmorillonite was also investigated. The maximum dimer yield was obtained with magnesium as interlayered cation. Aluminium and calcium varieties yielded lower amounts of dimers. Addition of sodium carbonate (natrification) was detrimental to dimer production. Dimer recovery was increased by the use of montmorillonite partially decomposed by hydrochloric acid. Variations in the crystallochemical composition of smectites had little effect on the amount of dimer produced. High iron content in the catalyst lowered the quality of the dimerization products.
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Geissenberger, Fabian, Florian Schwarz, Michael Probst, Sabine Haberl, Stefanie Gruetzner, Thomas Kroencke, Wolfgang von Scheidt, and Thomas M. Berghaus. "D-Dimer Predicts Disease Severity but Not Long-Term Prognosis in Acute Pulmonary Embolism." Clinical and Applied Thrombosis/Hemostasis 25 (January 1, 2019): 107602961986349. http://dx.doi.org/10.1177/1076029619863495.
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D-dimer might be correlated with prognosis in pulmonary embolism (PE). The predictive value of plasma D-dimer for disease severity and survival was investigated in the lowest and highest D-dimer quartile among 200 patients with PE. Patients with high D-dimers were significantly more often hypotensive ( P = .001), tachycardic ( P = .016), or hypoxemic ( P = .001). Pulmonary arterial obstruction index (PAOI) values were significantly higher in the high D-dimer quartile ( P < .001). Elevated troponin I (TNI) levels ( P < .001), simplified PE severity indices ≥1 ( P < .001), right-to-left ventricular (RV/LV) diameter ratios ≥1 ( P < .001), and thrombolysis ( P = .001) were more frequent in the high D-dimer quartile. D-dimer was associated with RV/LV ratios ≥1 ( P = .021), elevated PAOI ( P < .001) or TNI levels ( P < .001), hypotension ( P < .001), tachycardia ( P = .003), and hypoxemia ( P < .001), but not with long-term all-cause mortality. D-dimer predicts disease severity but not long-term prognosis in acute PE, possibly due to a more aggressive treatment strategy in severely affected patients.
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Favaloro, Emmanuel J., and Jecko Thachil. "Reporting of D-dimer data in COVID-19: some confusion and potential for misinformation." Clinical Chemistry and Laboratory Medicine (CCLM) 58, no. 8 (July 28, 2020): 1191–99. http://dx.doi.org/10.1515/cclm-2020-0573.
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AbstractCoronavirus disease 2019 (COVID-19) represents a new pandemic caused by severe acute respiratory syndrome virus coronavirus 2 (SARS-CoV-2). A previous pooled analysis clearly identified elevated D-dimer levels as being associated with severity of COVID-19. Since then, several other studies have provided clearer support for this initial evidence. However, potentially under-recognized by those reporting on D-dimer is the considerable variation in reporting units for D-dimer, and thus also the potential for misreporting of D-dimer data based on poor or incomplete reporting. A PubMed search was used to identify recent papers reporting on D-dimers in COVID-19-based studies. We report that: (1) most publications did not identify either the manufacturer or D-dimer product used; (2) most did not identify whether D-dimer values were reported as D-dimer units (DDU) or fibrinogen equivalent units (FEU) (~2 × differences); (3) nearly half did not identify normal cut-off values; (4) some did not report numerical findings or units for D-dimer; (5) where reported, most identified units as either mg/L or μg/mL; (6) we identified at least four errors in reporting from 21 papers. It may not be possible to truly standardize D-dimer assays, but it should be feasible to harmonize D-dimer assays to a single unit of measurement.
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Roy, Sujayita, Ran He, Arun Kapoor, Michael Forman, Jennifer R. Mazzone, Gary H. Posner, and Ravit Arav-Boger. "Inhibition of Human Cytomegalovirus Replication by Artemisinins: Effects Mediated through Cell Cycle Modulation." Antimicrobial Agents and Chemotherapy 59, no. 7 (April 13, 2015): 3870–79. http://dx.doi.org/10.1128/aac.00262-15.
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ABSTRACTArtemisinin-derived monomers and dimers inhibit human cytomegalovirus (CMV) replication in human foreskin fibroblasts (HFFs). The monomer artesunate (AS) inhibits CMV at micromolar concentrations, while dimers inhibit CMV replication at nanomolar concentrations, without increased toxicity in HFFs. We report on the variable anti-CMV activity of AS compared to the consistent and reproducible CMV inhibition by dimer 606 and ganciclovir (GCV). Investigation of this phenomenon revealed that the anti-CMV activity of AS correlated with HFFs synchronized to the G0/G1stage of the cell cycle. In contact-inhibited serum-starved HFFs or cells arrested at early/late G1with specific checkpoint regulators, AS and dimer 606 efficiently inhibited CMV replication. However, in cycling HFFs, in which CMV replication was productive, virus inhibition by AS was significantly reduced, but inhibition by dimer 606 and GCV was maintained. Cell cycle analysis in noninfected HFFs revealed that AS induced early G1arrest, while dimer 606 partially blocked cell cycle progression. In infected HFFs, AS and dimer 606 prevented the progression of cell cycle toward the G1/S checkpoint. AS reduced the expression of cyclin-dependent kinases (CDK) 2, 4, and 6 in noninfected cycling HFFs, while the effect of dimer 606 on these CDKs was moderate. Neither compound affected CDK expression in noninfected contact-inhibited HFFs. In CMV-infected cells, AS activity correlated with reduced CDK2 levels. CMV inhibition by AS and dimer 606 also correlated with hypophosphorylation (activity) of the retinoblastoma protein (pRb). AS activity was strongly associated with pRb hypophosphorylation, while its reduced anti-CMV activity was marked by pRb phosphorylation. Roscovitine, a CDK2 inhibitor, antagonized the anti-CMV activities of AS and dimer 606. These data suggest that cell cycle modulation through CDKs and pRb might play a role in the anti-CMV activities of artemisinins. Proteins involved in this modulation may be identified and targeted for CMV inhibition.
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Liang, Xu, Li Xu, Minzhi Li, John Mack, Justin Stone, Tebello Nyokong, Yu Jiang, Nagao Kobayashi, and Weihua Zhu. "Facile synthesis, spectroscopic and electrochemical properties, and theoretical calculations of porphyrin dimers with a bridging amide-bonded xanthene moiety." Journal of Porphyrins and Phthalocyanines 19, no. 07 (July 2015): 819–29. http://dx.doi.org/10.1142/s1088424615500492.
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A free base porphyrin dimer bridged by a flexible amide-bonded xanthene moiety and its binuclear zinc(II) complex zinc(II) complex were synthesized and characterized. Structural characterization by MS and 1 H NMR spectroscopy confirmed the bridged porphyrin dimer structure. The properties of the dimers were characterized by IR, UV-visible absorption, fluorescence and magnetic circular dichroism (MCD) spectroscopy, and electrochemistry studies. Theoretical calculations were carried out to analyze the electronic structures of porphyrin dimers with a bridging amide-bonded xanthene moiety.
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Bloomfield, Hannah R., and Jamie S. Ritch. "A new polymorph of phenylselenium trichloride." Acta Crystallographica Section C Structural Chemistry 75, no. 11 (October 4, 2019): 1471–74. http://dx.doi.org/10.1107/s2053229619013019.
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A second polymorph of phenylselenium trichloride, PhSeCl3 or C6H5Cl3Se, is disclosed, which is comprised of asymmetric chlorine-bridged noncovalent dimer units rather than polymeric chains. These dimers are each weakly bound to an adjacent dimer through noncovalent Se...Cl bonding interactions. Phenyl rings within each dimer are oriented in a syn fashion. Density functional theory (DFT) calculations reveal that the putative anti isomer is within 5 kJ mol−1 of the experimentally observed form. This structure represents the first additional polymorph discovered for an organoselenium trihalide compound.
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Rhoads, Tim L., Alfred T. Mikell Jr., and Michael H. Eley. "Investigation of the lignin-degrading activity of Serratia marcescens: biochemical screening and ultrastructural evidence." Canadian Journal of Microbiology 41, no. 7 (July 1, 1995): 592–600. http://dx.doi.org/10.1139/m95-079.
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Forty-one morphologically distinct bacterial isolates were developed from six lignin-containing environments. Each isolate was initially screened for potential lignin-degrading activity using relative growth on a lignocellulosic substrate and relative decolorization of a polymeric dye. Screened isolates were then tested for the ability to oxidize various lignin-related monomers, and the dimers anisoin and veratrylglycerol-β-guaiacyl ether. Although most of the isolates oxidized the monomers, only two successfully oxidized the dimers. The dimer-degrading isolates were tested for extracellular activity against the β-O-4 dimer veratryl-glycerol-β-guaiacyl ether. No activity was detected for the isolates. Phanerochaete chrysosporium Burds used as a positive control demonstrated a high degree of activity in each assay. Extensive ultrastructural studies of lignocellulose alteration by the dimer-degrading isolates were conducted via light and transmission electron microscopy. These studies indicate that one of the isolates, identified as Serratia marcescens, is capable of degrading highly lignified secondary cell wall components. This activity is localized, apparently requiring direct contact between cells and substrate, which could be facilitated by an associated glycocalix. The results of the dimer degradation assays concur with the characterization of the responsible enzyme system as being membrane associated.Key words: lignin, β-O-4 dimer, bacteria, Serratia, ultrastructure.
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Jiang, Wangshu, Glareh Askarieh, Alexander Shkumatov, My Hedhammar, and Stefan D. Knight. "Structure of the N-terminal domain of Euprosthenops australis dragline silk suggests that conversion of spidroin dope to spider silk involves a conserved asymmetric dimer intermediate." Acta Crystallographica Section D Structural Biology 75, no. 7 (June 26, 2019): 618–27. http://dx.doi.org/10.1107/s2059798319007253.
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Spider silk is a biomaterial with exceptional mechanical toughness, and there is great interest in developing biomimetic methods to produce engineered spider silk-based materials. However, the mechanisms that regulate the conversion of spider silk proteins (spidroins) from highly soluble dope into silk are not completely understood. The N-terminal domain (NT) of Euprosthenops australis dragline silk protein undergoes conformational and quaternary-structure changes from a monomer at a pH above 7 to a homodimer at lower pH values. Conversion from the monomer to the dimer requires the protonation of three conserved glutamic acid residues, resulting in a low-pH `locked' dimer stabilized by symmetric electrostatic interactions at the poles of the dimer. The detailed molecular events during this transition are still unresolved. Here, a 2.1 Å resolution crystal structure of an NT T61A mutant in an alternative, asymmetric, dimer form in which the electrostatic interactions at one of the poles are dramatically different from those in symmetrical dimers is presented. A similar asymmetric dimer structure from dragline silk of Nephila clavipes has previously been described. It is suggested that asymmetric dimers represent a conserved intermediate state in spider silk formation, and a revised `lock-and-trigger' mechanism for spider silk formation is presented.
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Jovanović, Saša, Elek Zlatan, Dušan Petrović, Gojko Igrutinović, Danijela Vićentijević, and Aleksandar Božović. "SIGNIFICANCE OF INCREASED D-DIMER VALUES IN FRESH FRACTURES IN ORTHOPEDICS AND CORRELATIONS WITH THROMBOEMBOLIC COMPLICATIONS." MEDIS – International Journal of Medical Sciences and Research 1, no. 2 (May 31, 2022): 17–22. http://dx.doi.org/10.35120/medisij010217j.
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Background/aim. At the end of the process of separating clots composed of fibrin we have a D-dimer. This process involves thrombin, which is formed during the process where fibrinogen is converted into fibrin, a factor whose role is to bind the basic units of clots and plasmin, the final participant in the breakdown of fibrin. In medicine, we should not use value of D-dimers as the only parameter for thrombosis. The aims of are research is to investigate correlation between clinical signs of venous thrombosis and D-dimer values in fresh bone fractures and demonstrate, that there is momentous correlation between high values of D-dimers and clinical signs of venous thrombosis, which is often a contraindication for surgical treatment of fractures. Methods: D-dimer levels of 211 patients with fresh bone fractures. They are classified into groups based on D-dimer values as follows: <250 ng/ml, 250–1000 ng/ml, 1000-5000 ng/ml, 5000-10 000ng/ml. Results: D-dimer values are not statistically significant with clinical symptoms of venous thrombosis in recent fractures in orthopedics. Discussion: D-dimer is an indicator related to fibrin degradation that has been used in the past as a prevalence in patients with chances of venous thrombosis. In inflammatory processes, we also have increased values of this parameter, which suggests the existence of some inflammatory change in the body or infection. Оur research is among the first to compare D-dimer values in recent fractures in orthopedics and thromboembolic complications. In our research, we showed that there is no significant correlation between elevated D-dimer values in hospitalizations of fresh fractures with clinical signs and a diagnosis of vascular thrombosis. We showed that there is no significant correlation between elevated D-dimer values in hospitalizations of fresh fractures with clinical signs and a diagnosis of vascular thrombosis. With this study, we proved that elevated D dimer is a consequence of trauma and disruption of the continuity and integrity of bone blood vessels, both endosteal and periosteal, which results in thrombosis of small blood vessels. Conclusions: There is no momentous correlation between elevated D-dimer values in fresh fractures and venous thrombosis. High values of D-dimer are not a contraindication for surgical treatment of fresh fractures.
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Kuznetsov, Aleksey E. "Computational design of ZnP(P)4 stacks: Three modes of binding." Journal of Theoretical and Computational Chemistry 15, no. 05 (August 2016): 1650043. http://dx.doi.org/10.1142/s0219633616500437.
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A large variety of metalloporphyrin arrays, including stacks, have been synthesized and extensively explored for their numerous applications in molecular devices. Motivated by the phenomenon of formation of stacks by regular metalloporphyrins, we performed the computational check of the stack formation between the MP(P)4 species without any linkers or substituents. For this we chose the ZnP(P)4 species as the simplest MP(P)4 compound. Three modes of binding or coordination were found to be possible between the monomeric ZnP(P)4 units. The “convexity-to-convexity” dimer I generally is the most stable compound with the highest binding energy. The dimers II and III are generally bound significantly weaker than the “convexity-to-convexity” dimer I. In the dimer I, the strongly convex shape of both monomer units was demonstrated. The Zn–Zn distances in the dimer I, ca. 3.5[Formula: see text]Å, were computed to be significantly shorter than in two other dimers. This could lead to additional interactions between the metal centers with unpaired d-electrons involved in the formation of such a dimer. In the dimer I significant decrease of the charge was found on the Zn-centers, along with slight decrease of the positive charge on the P-centers coordinated to the Zn-centers of another monomer, and slight buildup of the positive charge on the P-centers not coordinated to the Zn-centers of another monomer.
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Bolden, Nicholas, Verna Van, Canessa Swanson, Sarah Monti, and Michael Summers. "Using gel centrifugation to determine the monomer-dimer equilibrium of the HIV-1 5’-leader (VIR9P.1162)." Journal of Immunology 194, no. 1_Supplement (May 1, 2015): 215.28. http://dx.doi.org/10.4049/jimmunol.194.supp.215.28.
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Abstract An estimated 35 million people live with Human Immunodeficiency Virus (HIV-1), with approximately 1.7 million associated deaths per year. HIV-1 is a retrovirus that infects the T cells of the host’s immune system. After infection, the virus reverse-transcribes its RNA genome into DNA and integrates the viral DNA into the host DNA, which is eventually transcribed into RNA by the host cell. The 5’ untranslated region (UTR) of the RNA, is the most conserved region of the genome. It exists in equilibrium between a monomeric form, important for translation, and a dimeric form, important for genome packaging. While gel electrophoresis is usually used to determine the equilibrium of monomer and dimer, we have developed a new technique that uses gel centrifugation. We are developing this technique as it may allow us to look at the monomer-dimer equilibria of different RNAs, such as HIV-2, which have weaker “kissing” dimer interactions. When gel electrophoresis is used on these dimers, the magnesium that stabilizes the dimer is drawn towards the opposite pole as the RNA, providing inaccurate data by dissociating the dimers and causing more monomer to be visualized. Magnesium containing gels are used to combat this, but it is difficult to determine how much magnesium is needed to obtain accurate results. Future work includes testing this method on retroviruses with a “kissing dimer” interaction and eventually determining a way to quantify the amount of monomer and dimer present.
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Lim, Wilber, Ferdinando Randisi, Jonathan P. K. Doye, and Ard A. Louis. "The interplay of supercoiling and thymine dimers in DNA." Nucleic Acids Research 50, no. 5 (February 21, 2022): 2480–92. http://dx.doi.org/10.1093/nar/gkac082.
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Abstract Thymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here, we introduce a model of thymine dimers in the oxDNA forcefield, parametrized by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.
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Joseph, Prem Raj B., Kirti V. Sawant, and Krishna Rajarathnam. "Heparin-bound chemokine CXCL8 monomer and dimer are impaired for CXCR1 and CXCR2 activation: implications for gradients and neutrophil trafficking." Open Biology 7, no. 11 (November 2017): 170168. http://dx.doi.org/10.1098/rsob.170168.
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Chemokine CXCL8 plays a pivotal role in host immune response by recruiting neutrophils to the infection site. CXCL8 exists as monomers and dimers, and mediates recruitment by interacting with glycosaminoglycans (GAGs) and activating CXCR1 and CXCR2 receptors. How CXCL8 monomer and dimer interactions with both receptors and GAGs mediate trafficking is poorly understood. In particular, both haptotactic (mediated by GAG-bound chemokine) and chemotactic (mediated by soluble chemokine) gradients have been implicated, and whether it is the free or the GAG-bound CXCL8 monomer and/or dimer that activates the receptor remains unknown. Using solution NMR spectroscopy, we have now characterized the binding of heparin-bound CXCL8 monomer and dimer to CXCR1 and CXCR2 receptor N-domains. Our data provide compelling evidence that heparin-bound monomers and dimers are unable to bind either of the receptors. Cellular assays also indicate that heparin-bound CXCL8 is impaired for receptor activity. Considering dimer binds GAGs with higher affinity, dimers will exist predominantly in the GAG-bound form and the monomer in the free form. We conclude that GAG interactions determine the levels of free CXCL8, and that it is the free, and not GAG-bound, CXCL8 that activates the receptors and mediates recruitment of blood neutrophils to the infected tissue.
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Troyanovsky, Regina B., Eugene P. Sokolov, and Sergey M. Troyanovsky. "Endocytosis of Cadherin from Intracellular Junctions Is the Driving Force for Cadherin Adhesive Dimer Disassembly." Molecular Biology of the Cell 17, no. 8 (August 2006): 3484–93. http://dx.doi.org/10.1091/mbc.e06-03-0190.
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The adhesion receptor E-cadherin maintains cell–cell junctions by continuously forming short-lived adhesive dimers. Here mixed culture cross-linking and coimmunoprecipitation assays were used to determine the dynamics of adhesive dimer assembly. We showed that the amount of these dimers increased dramatically minutes after the inhibition of endocytosis by ATP depletion or by hypertonic sucrose. This increase was accompanied by the efficient recruitment of E-cadherin into adherens junctions. After 10 min, when the adhesive dimer amount had reached a plateau, the assembly of new dimers stalled completely. These cells, in a striking difference from the control, became unable to disintegrate both their intercellular contacts and adhesive dimers in response to calcium depletion. The same effects, but after a slightly longer time course, were obtained using acidic media, another potent approach inhibiting endocytosis. These data suggest that endocytosis is the main pathway for the dissociation of E-cadherin adhesive dimers. Its inhibition blocks the replenishment of the monomeric cadherin pool, thereby inhibiting new dimer formation. This suggestion has been corroborated by immunoelectron microscopy, which revealed cadherin-enriched coated pit-like structures in close association with adherens junctions.
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Sánchez-Pérez, Gabino Francisco, and María Ángeles Pajares. "Polar Interactions at the Dimer–Dimer Interface of Methionine Adenosyltransferase MAT I Control Tetramerization." International Journal of Molecular Sciences 22, no. 24 (December 8, 2021): 13206. http://dx.doi.org/10.3390/ijms222413206.
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Catalytic MATα1 subunits associate into kinetically distinct homo-dimers (MAT III) and homo-tetramers (MAT I) that synthesize S-adenosylmethionine in the adult liver. Pathological reductions in S-adenosylmethionine levels correlate with MAT III accumulation; thus, it is important to know the determinants of dimer–dimer associations. Here, polar interactions (<3.5 Å) at the rat MAT I dimer–dimer interface were disrupted by site-directed mutagenesis. Heterologous expression rendered decreased soluble mutant MATα1 levels that appeared mostly as dimers. Substitutions at the B1–B2 or B3–C1 β-strand loops, or changes in charge on helix α2 located behind, induced either MAT III or MAT I accumulation. Notably, double mutants combining neutral changes on helix α2 with substitutions at either β-strand loop further increased MAT III content. Mutations had negligible impact on secondary or tertiary protein structure, but induced changes of 5–10 °C in thermal stability. All mutants preserved tripolyphosphatase activity, although AdoMet synthesis was only detected in single mutants. Kinetic parameters were altered in all purified proteins, their AdoMet synthesis Vmax and methionine affinities correlating with the association state induced by the corresponding mutations. In conclusion, polar interactions control MATα1 tetramerization and kinetics, diverse effects being induced by changes on opposite β-sheet loops putatively leading to subtle variations in central domain β-sheet orientation.
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Acharya, R., N. Pant, V. K. Jha, and M. K. Yadav. "Adsorption and dissociation of dinitrogen on mono-metallic and bimetallic dimers." International Journal of Modern Physics B 34, no. 26 (September 17, 2020): 2050236. http://dx.doi.org/10.1142/s0217979220502367.
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This paper deals with Density Functions Theory (DFT) based theoretical investigation of the dissociation of strong N–N triple bond of dinitrogen (N2). Mono-metallic and bimetallic dimers of selected transition metals (Zr, Nb, Hf, and Ta) are used as adsorbent. The dissociation of N–N bond is found to be strongly dependent on orientation of N–N axis with respect to the axis of the adsorbent dimer. N–N axis perpendicular to dimer axis has been found to be suitable for dissociative adsorption of dinitrogen. Apart from orientation the combination of two different transition metal atoms in the dimer also has significant effect in the elongation and dissociation of N–N bond. Our study shows even 2-atom clusters (dimers) of these transition metals are capable of breaking N–N triple bond.
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Małecka-Giełdowska, Milena, Karolina Nowak, Aleksandra Leszczyńska, and Olga Ciepiela. "A comparison of D-dimer concentration determination using different methods in automated hemostatis analyzers ACL TOP 500 CTS, ACL TOP 700 CTS, and VIDAS." Diagnostyka Laboratoryjna 58, no. 2 (December 7, 2022): 38–50. http://dx.doi.org/10.5604/01.3001.0016.1351.
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<br>Introduction: D-dimer is a product of stabilized fibrin degradation under the influence of plasmin. Evaluation of D-dimer concentration is crucial in exclusion of thromboembolism as well as in monitoring of coagulation and fibrinolysis processes in affected patients. Concentration of D-dimer corresponds with dynamics of clot formation and degradation in vessels.</br> <br>Aim: The aim of the study was to evaluate interchangeability of different analysers: ACL TOP 500 CTS, ACL TOP 700 CTS and VIDAS 3 in D-dimer assessment.</br> <br>Material and methods: Study included D-dimer measurements in 4476 patients. There were statistically significant differences in D-dimer concentration obtained with reference ELFA method and immunoturbidymetric method, both in women and men groups.</br> <br>Results: There were also significant differences in D-dimers concentration when studying samples with D-dimer of 500-1500 mg/L obtained with ACL TOP, with lower values obtained with VIDAS 3.</br> <br>Conclusions: Basing on our results it can be stated, that ELFA and immunoturbidymetric method are not interchangeable and should not be used in assessment of D-dimer concentration in one patient interchangeably.</br>