Photobodies: Light‐Activatable Single‐Domain Antibody Fragments

Photocaged antibody fragments, termed photobodies, have been developed that are impaired in their antigen‐binding capacity and can be activated by irradiation with UV light (365 nm). This rational design concept builds on the selective photocaging of a single tyrosine in a nanobody (a single‐domain antibody fragment). Tyrosine is a frequently occurring residue in central positions of the paratope region. o‐Nitrobenzyl‐protected tyrosine variants were incorporated into four nanobodies, including examples directed against EGFR and HER2, and photodeprotection restores the native sequence. An anti‐GFP photobody exhibited an at least 10 000‐fold impaired binding affinity before photodeprotection compared with the parent nanobody. A bispecific nanobody–photobody fusion protein was generated to trigger protein heterodimerization by light. Photoactivatable antibodies are expected to become versatile protein reagents and to enable novel approaches in diagnostic and therapeutic applications.     

A one-dimensional silver(I) coordination polymer with saccharin and pyrazine: synthesis,crystal structure,thermal analysis,FTIR spectra,and DFT studies

A silver(I) complex of saccharinate (sac) with pyrazine (pyz), [Ag(sac)(pyz)] _n , has been synthesized and characterized by elemental analysis, IR, thermal analysis, and single-crystal X-ray diffractometry. The complex crystallizes orthorhombic space group Pnma with unit cell parameters of a = 13.0073(9) Å, b = 6.4907(6) Å, c = 13.4007(9) Å, V = 1131.37(15) Å³, and Z = 4. [Ag(sac)(pyz)] _n is a one-dimensional coordination polymer, in which the sac ligand acts as a monodentate ligand through the N atom and the trigonal silver centers are linked by the bridging pyz ligands. The individual chains are connected into two-dimensional supramolemular network by aromatic π(sac)···π(pyz) stacking interactions. The FTIR spectrum of [Ag(sac)(pyz)] _n has been recorded in the region and 4,000–400 cm^?1. The optimized geometry, frequency, and intensity of the vibrational bands of [Ag(sac)(pyz)] _n were obtained by density functional theory (DFT) at the B3LYP level. The vibrational frequencies were calculated and the scaled values have been compared with the experimental FTIR data. The observed and calculated frequencies are found to be in good agreement.     

Application of differential quadrature to transport processes

The methodology and numerical solution of problems concerning transport processes via the method of differential quadrature are presented. Application of the method is demonstrated by solving a simple one-dimensional, time-dependent (transient) diffusion process involving an irreversible reaction without any flux across the end boundary. In addition, the same technique is used (for the first time to the authors' knowledge) to solve a steady-state problem. For this purpose, a convection-diffusion problem involving an irreversible reaction is considered. The demonstration is carried out in two ways, (1) using the Bellman et al. technique which employs approximation formulas for higher order partial derivatives derived by iterating the linear quadrature approximation for the first order partial derivative, and (2) using individual quadratures to approximate the partial derivatives of first, as well as higher orders, as suggested by Mingle. Both approaches give the same results; however, the latter saves an appreciable amount of iterative computing effort despite the fact that it requires separate weighting coefficients for each individual quadrature. Since the technique of differential quadrature can produce solutions with sufficient accuracy even when using as few as three discrete points, both the programming task and computational effort are alleviated considerably. For these reasons the differential quadrature approach appears to be very practical in solving a variety of problems related to transport phenomena.     

Validation and verification of social processes within agent-based computational organization models

The use of simulation modeling in computational analysis of organizations is becoming a prominent approach in social science research. However, relying on simulations to gain intuition about social phenomena has significant implications. While simulations may give rise to interesting macro-level phenomena, and sometimes even mimic empirical data, the underlying micro and macro level processes may be far from realistic. Yet, this realism may be important to infer results that are relevant to existing theories of social systems and to policy making. Therefore, it is important to assess not only predictive capability but also explanation accuracy of formal models in terms of the degree of realism reflected by the embedded processes. This paper presents a process-centric perspective for the validation and verification (V&V) of agent-based computational organization models. Following an overview of the role of V&V within the life cycle of a simulation study, emergent issues in agent-based organization model V&V are outlined. The notion of social contract that facilitates capturing micro level processes among agents is introduced to enable reasoning about the integrity and consistency of agent-based organization designs. Social contracts are shown to enable modular compositional verification of interaction dynamics among peer agents. Two types of consistency are introduced: horizontal and vertical consistency. It is argued that such local consistency analysis is necessary, but insufficient to validate emergent macro processes within multi-agent organizations. As such, new formal validation metrics are introduced to substantiate the operational validity of emergent macro-level behavior. Levent Yilmaz is Assistant Professor of Computer Science and Engineering in the College of Engineering at Auburn University and co-founder of the Auburn Modeling and Simulation Laboratory of the M&SNet. Dr. Yilmaz received his Ph.D. and M.S. degrees from Virginia Polytechnic Institute and State University (Virginia Tech). His research interests are on advancing the theory and methodology of simulation modeling, agent-directed simulation (to explore dynamics of socio-technical systems, organizations, and human/team behavior), and education in simulation modeling. Dr. Yilmaz is a member of ACM, IEEE Computer Society, Society for Computer Simulation International, and Upsilon Pi Epsilon. URL: http://www.eng.auburn.edu/~yilmaz     

Proton NMR relaxation in albumin solutions doped with Mn(II)

The aim of this study is to obtain further information about the source of proton relaxation in the Mn(II)-human serum albumin complex. For this purpose, proton relaxation rates in albumin solutions 1/T ₁ and 1/T ₂ were measured versus increasing amounts of manganese [Mn_t]. The fractions of manganese bound to albumin [Mn_b] and free manganese [Mn_f] were then determined from proton relaxation rate enhancement data. Paramagnetic contributions of bound manganese to the observed relaxation rates (1/T _1p^*)_b and (1/T _2p^*)_b were also determined. Finally, the (1/T _2p^*)_b/(1/T _1p^*)_b ratio was used in a derived equation to estimate an effective correlation time τ. Mean τ value of the complex was found to be in the order of 3 ns, while the hydration number of bound manganese q was estimated to be about 4. The 1/τ was found to be the sum of the inverse values of rotational correlation time 1/τ _r, mean residence time of water in hydration spheres of the complex 1/τ _m, and longitudinal electronic relaxation time of manganese 1/τ _s in the complex. In conclusion, the relaxation mechanism in albumin solutions containing Mn(II) can be interpreted through dipolar and scalar interactions modulated by τ _r, τ _m and τ _s. This analysis enables one to get reasonable figures for the τ _r and q of Mn(II) in albumin solution.     

Usage of deep eutectic solvents for the digestion and ultrasound-assisted liquid phase microextraction of copper in liver samples

In this study, we used deep eutectic solvents for digestion and ultrasound-assisted emulsification liquid phase microextraction (UA-ELPME) of copper in liver samples. Different types of DESs were prepared for digestion and microextraction steps. DESs consisting of lactic acid and choline chloride for the digestion step and DESs consisting of tetrabuthylamonium chloride and decanoic acid for ultrasound-assisted emulsification liquid phase microextraction were used in this method. The liver samples were digested by using DES-based digestion method. After digestion step, Cu(II) ions in aqueous phase were complexed with sodium dimethyl dithiocarbamate (NaDMDTC) and the obtained hydrophobic complex was extracted to tetrabuthylamonium chloride-decanoic acid DES phase. A microsample injection system coupled with flame atomic absorption spectrometer (MS-FAAS) was used in the detection of copper. LOD, LOQ, PF and % RSD were determined as 4.00, 13.2 µg L^??1, 10 and 3.2%, respectively. The proposed microextraction procedure was successfully applied to copper contents of the liver samples.     

Stress Dependency of Permeability Represented by an Elastic Cylindrical Pore-Shell Model: Comment on Zhu et al. (Transp Porous Med (2018) 122:235–252)

Transport in Porous Media - Stress dependency of permeability of porous rocks is described by means of a theoretical elastic cylindrical pore-shell model. This model is developed based on a bundle...     

On the number of eigenvalues for parameter‐dependent diffusion problem on time scales

In this study, we consider parameter‐dependent diffusion eigenvalue problem on time scales. An upper bound on the number of eigenvalues for this problem on a finite time scale is given.     

QCD sum rule analysis of the coupling constant g ωσγ

We employ QCD sum rules to calculate the coupling constant g by studying the three point -correlation function. Our result complements the analysis of this coupling constant utilizing the experimental value of the ⁰⁰ decay rate studied within the framework of chiral perturbation theory including vector meson and meson intermediate states.