The test of independence of two groups of variables is addressed in the case where the sample size N is considered randomly distributed. This assumption may lead to a more realist testing procedure since in many situations the sample size is not known in advance. Three sample schemes are considered where N may have a Poisson, Binomial or Hypergeometric distribution. For the case of two groups with p1 and p2 variables, it is shown that when either p1 or p2 (or both) are even the exact distribution corresponds to a finite or an infinite mixture of Exponentiated Generalized Integer Gamma distributions. In these cases a computational module is made available for the cumulative distribution function of the test statistic. When both p1 and p2 are odd, the exact distribution of the test statistic may be represented as a finite or an infinite mixture of products of independent Beta random variables whose density and cumulative distribution functions do not have a manageable closed form. Therefore, a computational approach for the evaluation of the cumulative distribution function is provided based on a numerical inversion formula originally developed for Laplace transforms. When the exact distribution is represented through infinite mixtures, an upper bound for the error of truncation of the cumulative distribution function is provided. Numerical studies are developed in order to analyze the precision of the results and the accuracy of the upper bounds proposed. A simulation study is provided in order to assess the power of the test when the sample size N is considered randomly distributed. The results are compared with the ones obtained for the fixed sample size case.

Protein crystallization still remains mostly an empirical science, as the production of crystals with the required quality for X-ray analysis is dependent on the intensive screening of the best protein crystallization and crystal’s derivatization conditions. Herein, this demanding step was addressed by the development of a high-throughput and low-budget microfluidic platform consisting of an ion exchange membrane (117 Nafion® membrane) sandwiched between a channel layer (stripping phase compartment) and a wells layer (feed phase compartment) forming 75 independent micro-contactors. This microfluidic device allows for a simultaneous and independent screening of multiple protein crystallization and crystal derivatization conditions, using Hen Egg White Lysozyme (HEWL) as the model protein and Hg2+ as the derivatizing agent. This microdevice offers well-regulated crystallization and subsequent crystal derivatization processes based on the controlled transport of water and ions provided by the 117 Nafion® membrane. Diffusion coefficients of water and the derivatizing agent (Hg2+) were evaluated, showing the positive influence of the protein drop volume on the number of crystals and crystal size. This microfluidic system allowed for crystals with good structural stability and high X-ray diffraction quality and, thus, it is regarded as an efficient tool that may contribute to the enhancement of the proteins’ crystals structural resolution.

Abstract Fiber reinforced polymer (FRP) composites can be efficient for flexural strengthening of flat slabs if debonding of the FRP is postponed. However, with the increase of the flexural capacity, the flat slab becomes more susceptible to punching shear failure. In this context, four flexural or simultaneous flexural and punching shear retrofitting systems are investigated in this study to strengthen a flexure-deficient flat slab. Externally Bonded Reinforcement on Grooves (EBROG) and externally bonded reinforcement (EBR) methods are used for flexural strengthening in two cases: slabs without punching shear reinforcement and with post-installed shear bolts as shear reinforcement. According to the results, flexural strengthening of the slab using the EBR and EBROG techniques increased its load capacity by 12% and 21%, respectively. Simultaneous flexural and shear strengthening of the slab using the EBROG technique was the most effective, leading to a 57% enhancement of the load capacity. For specimens whose failure was governed by punching, comparing the results with code predictions showed that Eurocode and ACI (and the respective guide documents fib bulletin 90 and ACI 440.2R) overestimated the capacity of these specimens. In cases where failure was governed by flexure, a simple application of the yield line theory predicted reasonably well the load capacity of the specimens.

Microstructured transparent conductive oxides (TCOs) have shown great potential as photonic electrodes in photovoltaic (PV) applications, providing both optical and electrical improvements in the solar cells’ performance due to: (1) strong light trapping effects that enhance broadband light absorption in PV material and (2) the reduced sheet resistance of the front illuminated contact. This work developed a method for the fabrication and optimization of wavelength-sized indium zinc oxide (IZO) microstructures, which were soft-patterned on flexible indium tin oxide (ITO)-coated poly(ethylene terephthalate) (PET) substrates via a simple, low-cost, versatile, and highly scalable colloidal lithography process. Using this method, the ITO-coated PET substrates patterned with IZO micro-meshes provided improved transparent electrodes endowed with strong light interaction effects—namely, a pronounced light scattering performance (diffuse transmittance up to  50%). In addition, the photonic-structured IZO mesh allowed a higher volume of TCO material in the electrode while maintaining the desired transparency, which led to a sheet resistance reduction (by  30%), thereby providing further electrical benefits due to the improvement of the contact conductance. The results reported herein pave the way for a new class of photonic transparent electrodes endowed with mechanical flexibility that offer strong potential not only as advanced front contacts for thin-film bendable solar cells but also for a much broader range of optoelectronic applications.

This paper deals with the determination of upper and lower bounds for the three-dimensional undrained stability of shallow tunnels. The tunnel is circular and a distance between its face and its lining is considered. The soil shear strength is modeled using the Tresca criterion. Results of the upper and lower bounds of the stability number are presented, for several geometrical and resistance configurations and their comparison with previous results is made, showing the clear improvement obtained. Finally, equations approaching the stability number are proposed.

Journal of Trace Elements in Medicine and Biology, 68 (2021) 126837. doi:10.1016/j.jtemb.2021.126837

Ion beam analysis of fluorine has applications in research on teeth and bones, materials science, geochemistry and archaeometry. A novel PIGE (particle induced gamma-ray emission) standard free methodology for fluorine content determination for in-depth heterogeneous samples based on the excitation function of the 19F(p,p’$\gamma$)19F nuclear reaction is presented. New precise cross section measurements of this reaction in the proton energy range 2.1 to 4.1 MeV have been performed. In addition, the ERYA-Profiling code, a computer program specially developed for PIGE analysis of in-depth heterogeneous samples, employed this new excitation function in a case study where different fluorine simulated depth profiles probed the capability of insight into fluorine distributions in a given sample, showing the potential of PIGE analysis.

We present relativistic ab initio calculations of fundamental parameters for atomic selenium, based on the Multiconfiguration Dirac-Fock method. In detail, fluorescence yields and subshell linewidths, both of K shell, as well as K$\beta$ to K$\alpha$ intensity ratio are provided, showing overall agreement with previous theoretical calculations and experimental values. Relative intensities were evaluated assuming the same ionization cross-section for the K-shell hole states, leading to a statistical distribution of these initial states. A method for estimating theoretical linewidths of X-ray lines, where the lines are composed by a multiplet of fine-structure levels that are spread in energy, is proposed. This method provides results that are closer to K$\alpha$1,2 experimental width values than the usual method, although slightly higher discrepancies occur for the K$\beta$1,3 lines. This indicates some inaccuracies in the calculation of Auger rates that have a higher contribution for partial linewidths of the subshells involved in the K$\beta$1,3 profile. Apart from this, the calculated value of K$\beta$ to K$\alpha$ intensity ratio, which is less sensitive to Auger rates issues, is in excellent agreement with recommended values.

Nuclear Inst. and Methods in Physics Research, A, 1014 (2021) 165701. doi:10.1016/j.nima.2021.165701

The SOUL, or heme-binding protein HBP/SOUL, family represents a group of evolutionary conserved putative heme-binding proteins that contains a number of members in animal, plant andbacterial species. The structures of the murine form of HEBP1, or p22HBP, and the human form of HEBP2, or SOUL, have been determined in 2006 and 2011 respectively. In this work we discuss the structures of HEBP1 and HEBP2 in light of new X-ray data for heme bound murine HEBP1. The interaction between tetrapyrroles and HEBP1, initially proven to be hydrophobic in nature, was thought to also involve electrostatic interactions between heme propionate groups and positively charged amino acid side chains. However, the new X-ray structure, and results from murine HEBP1 variants and human HEBP1, confirm the hydrophobic nature of the heme-HEBP1 interaction, resulting in Kd values in the low nanomolar range, and rules out any electrostatic stabilization. Results from NMR relaxation time measurements for human HEBP1 describe a rigid globular protein with no change in motional regime upon heme binding. X-ray structures deposited in the PDB for human HEBP2 are very similar to each other and to the new heme-bound murine HEBP1 X-ray structure (backbone rmsd ca. 1 {\AA}). Results from a HSQC spectrum centred on the histidine side chain N$δ$-proton region for HEBP2 confirm that HEBP2 does not bind heme via H42 as no chemical shift differences were observed upon heme addition for backbone NH and N$δ$ protons. A survey of the functions attributed to HEBP1 and HEBP2 over the last 20 years span a wide range of cellular pathways. Interestingly, many of them are specific to higher eukaryotes, particularly mammals and a potential link between heme release under oxidative stress and human HEBP1 is also examined using recent data. However, at the present moment, trying to relate function to the involvement of heme or tetrapyrrole binding, specifically, makes little sense with our current biological knowledge and can only be applied to HEBP1, as HEBP2 does not interact with heme. We suggest that it may not be justified to call this very small family of proteins, heme-binding proteins. The family may be more correctly called “the SOUL family of proteins related to cellular fate” as, even though only HEBP1 binds heme tightly, both proteins may be involved in cell survival and/or proliferation.

Physics Letters B, 809 (2020) 135748. 10.1016/j.physletb.2020.135748

Siglec-15 is a conserved sialic acid-binding Ig-like lectin expressed on osteoclast progenitors that plays an important role in osteoclast development and function. It is also expressed by tumor-associated macrophages and by some tumors, where it is thought to contribute to the immunosuppressive microenvironment. It was shown previously that engagement of macrophage-expressed Siglec-15 with tumor cells expressing its ligand, sialyl Tn (sTn), triggered production of TGF-$\beta$. In the present study, we have further investigated the interaction between Siglec-15 and sTn on tumor cells and its functional consequences. Based on binding assays with lung and breast cancer cell lines and glycan-modified cells, we failed to see evidence for recognition of sTn by Siglec-15. However, using a microarray of diverse, structurally-defined glycans, we show that Siglec-15 binds with higher avidity to sialylated glycans other than sTn or related antigen sequences. In addition, we were unable to demonstrate enhanced TGF-$\beta$ secretion following co-culture of Siglec-15-expressing monocytic cells lines with tumor cells expressing sTn, or following Siglec-15 cross-linking with monoclonal antibodies. However, we did observe activation of the SYK/MAPK signaling pathway following antibody cross-linking of Siglec-15 that may modulate the functional activity of macrophages.

Understanding the specific molecular interactions between proteins and $\beta$1,3-1,4-mixed-linked d-glucans is fundamental to harvest the full biological and biotechnological potential of these carbohydrates and of proteins that specifically recognize them. The family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11) is known for its binding preference for $\beta$1,3-1,4-mixed-linked over $\beta$1,4-linked glucans. Despite the growing industrial interest of this protein for the biotransformation of lignocellulosic biomass, the molecular determinants of its ligand specificity are not well defined. In this report, a combined approach of methodologies was used to unravel, at a molecular level, the ligand recognition of CtCBM11. The analysis of the interaction by carbohydrate microarrays and NMR and the crystal structures of CtCBM11 bound to $\beta$1,3-1,4-linked glucose oligosaccharides showed that both the chain length and the position of the $\beta$1,3-linkage are important for recognition, and identified the tetrasaccharide Glc$\beta$1,4Glc$\beta$1,4Glc$\beta$1,3Glc sequence as a minimum epitope required for binding. The structural data, along with site-directed mutagenesis and ITC studies, demonstrated the specificity of CtCBM11 for the twisted conformation of $\beta$1,3-1,4-mixed-linked glucans. This is mediated by a conformation-selection mechanism of the ligand in the binding cleft through CH-$π$ stacking and a hydrogen bonding network, which is dependent not only on ligand chain length, but also on the presence of a $\beta$1,3-linkage at the reducing end and at specific positions along the $\beta$1,4-linked glucan chain. The understanding of the detailed mechanism by which CtCBM11 can distinguish between linear and mixed-linked $\beta$-glucans strengthens its exploitation for the design of new biomolecules with improved capabilities and applications in health and agriculture. DATABASE: Structural data are available in the Protein Data Bank under the accession codes 6R3M and 6R31.

The simulation of atomic relaxation relies on data libraries with tabulated partial fluorescence yield values of radiative transitions, commonly derived from the Evaluated Atomic Data Library (EADL)....

In this work, we aim at achieving the most accurate quantitative determination of elements in human tissues by means of X-ray Fluorescence spectrometry using the external calibration approach. A calibration curve built using a set of certified reference materials (CRM) of animal tissue was compared with the one obtained with a set of CRMs of plants and leaves with lower atomic number Z but with correction of the matrix using the scattering peaks of the X-ray tube anode. Finally, a calibration curve combining the two sets of CRMs was built and the accuracy of the quantification using the three methods was compared and a more precise method of quantification was obtained. This improved approach was tested on five paired samples of normal and tumour human tissue. Despite the high heterogeneity of the samples, and given the improvement in accuracy of the measurements, significant differences were found in the elemental concentration of low-Z elements. This journal is