Biomechanics of circulating cellular and subcellular bioparticles: beyond separation.

Biomechanical attributes have emerged as novel markers, providing a reliable means to characterize cellular and subcellular fractions. Numerous studies have identified correlations between these factors and patients' medical status. However, the absence of a thorough overview impedes their applicability in contemporary state-of-the-art therapeutic strategies. In this context, we provide a comprehensive analysis of the dimensions, configuration, rigidity, density, and electrical characteristics of normal and abnormal circulating cells. Subsequently, the discussion broadens to encompass subcellular bioparticles, such as extracellular vesicles (EVs) enriched either from blood cells or other tissues. Notably, cell sizes vary significantly, from 2 µm for platelets to 25 µm for circulating tumor cells (CTCs), enabling the development of size-based separation techniques, such as microfiltration, for specific diagnostic and therapeutic applications. Although cellular density is relatively constant among different circulating bioparticles, it allows for reliable density gradient centrifugation to isolate cells without altering their native state. Additionally, variations in EV surface charges (-6.3 to -45 mV) offer opportunities for electrophoretic and electrostatic separation methods. The distinctive mechanical properties of abnormal cells, compared to their normal counterparts, present an exceptional opportunity for diverse medical and biotechnological approaches. This review also aims to provide a holistic view of the current understanding of popular techniques in this domain that transcend conventional boundaries, focusing on early harvesting of malignant cells from body fluids, designing effective therapeutic options, cell targeting, and resonating with tissue and genetic engineering principles.

Grid: A Python library for molecular integration, interpolation, differentiation, and more.

Grid is a free and open-source Python library for constructing numerical grids to integrate, interpolate, and differentiate functions (e.g., molecular properties), with a strong emphasis on facilitating these operations in computational chemistry and conceptual density functional theory. Although designed, maintained, and released as a stand-alone Python library, Grid was originally developed for molecular integration, interpolation, and solving the Poisson equation in the HORTON and ChemTools packages. Grid is designed to be easy to use, extend, and maintain; this is why we use Python and adopt many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. We leverage popular scientific packages, such as NumPy and SciPy, to ensure high efficiency and optimized performance in grid development. This article is the official release note of the Grid library showcasing its unique functionality and scope.

The tale of HORTON: Lessons learned in a decade of scientific software development.

HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade.

Refractory and Recurrent Idiopathic Granulomatous Mastitis Treatment: Adaptive, Randomized Clinical Trial.

BACKGROUND: Idiopathic granulomatous mastitis (IGM) is mostly described as an autoimmune disease with higher prevalence among Middle Eastern childbearing-age women. This study aimed to evaluate the best treatment of choice in patients with resistant or recurrent IGM. STUDY DESIGN: Patients with established recurrent or resistant IGM who were referred to the Breast Cancer Research Center from 2017 to 2020 were randomly assigned to either one of the following treatment groups: A (best supportive care), B (corticosteroids: prednisolone), and C (methotrexate and low-dose corticosteroids). This adaptive clinical trial evaluated radiological and clinical responses, as well as the potential side effects, on a regular basis in each group, with patients followed up for a minimum of 2 years. RESULTS: A total of 318 participants, with a mean age of 33.52 ± 6.77 years, were divided into groups A (10 patients), B (78 patients), and C (230 patients). In group A, no therapeutic response was observed; group B exhibited a mixed response, with 14.1% experiencing complete or partial responses, 7.7% maintaining stability, and 78.2% experiencing disease progression. Accordingly, groups A and B were terminated due to inadequate response. In group C, 94.3% achieved complete response, 3% showed partial remission, and 2.7% had no response to therapy. Among the entire patient cohort, 11.6% tested positive for antinuclear antibodies, 3.5% for angiotensin-converting enzyme, and 12.3% for erythema nodosum. Notably, hypothyroidism was a prevalent condition among the patients, affecting 7.2% of the cohort. The incidence of common side effects was consistent across all groups. CONCLUSIONS: The most effective treatment option for patients with recurrent or resistant IGM is a combination therapy involving steroids and disease-modifying antirheumatic drugs such as methotrexate.

An information-theoretic approach to basis-set fitting of electron densities and other non-negative functions.

The numerical ill-conditioning associated with approximating an electron density with a convex sum of Gaussian or Slater-type functions is overcome by using the (extended) Kullback-Leibler divergence to measure the deviation between the target and approximate density. The optimized densities are non-negative and normalized, and they are accurate enough to be used in applications related to molecular similarity, the topology of the electron density, and numerical molecular integration. This robust, efficient, and general approach can be used to fit any non-negative normalized functions (e.g., the kinetic energy density and molecular electron density) to a convex sum of non-negative basis functions. We present a fixed-point iteration method for optimizing the Kullback-Leibler divergence and compare it to conventional gradient-based optimization methods. These algorithms are released through the free and open-source BFit package, which also includes a L2-norm squared optimization routine applicable to any square-integrable scalar function.

Pumpless deterministic lateral displacement separation using a paper capillary wick.

Deterministic lateral displacement (DLD) is a passive separation method that separates particles by hydrodynamic size. This label-free method is a promising technique for cell separation because of its high size resolution and insensitivity to flow rate. Development of capillary-driven microfluidic technologies allows microfluidic devices to be operated without any external power for fluid pumping, lowering their total cost and complexity. Herein, we develop and test a DLD-based particle and cell sorting method that is driven entirely by capillary pressure. We show microchip self-filling, flow focusing, flow stability, and capture of separated particles. We achieve separation efficiency of 92% for particle-particle separation and more than 99% efficiency for cell-particle separation. The high performance of driven flow and separation along with simplicity of the operation and setup make it a valuable candidate for point-of-care devices.

Effect of process parameters on separation efficiency in a deterministic lateral displacement device.

Deterministic lateral displacement (DLD) is a hydrodynamic method known for its high-resolution sorting of particles. It achieves this through a periodic array of obstacles and laminar flow that passively directs particles along in two different directions depending on the particles' diameter. Many prior publications have been dedicated to the structural and geometrical development of DLD arrays to improve separation performance; however, a successful separation requires much more than a well-designed array. This paper shows how separation performance is affected by process parameters. For this purpose, the design and fabrication of a DLD device are described. Then three experiments show how process parameters affect the performance of the device. The first experiment uses dye solutions to visualize the formation of a hydrodynamically focused sample stream. The second experiment shows that the particle separation performance (of 7- & 15-µm particles) is affected by the way output fluids are collected. Finally, the third experiment looks at the particle separation efficiency as the input flow rates and the ratio of buffer to sample are changed. The results show that the proper range for buffer and sample flow rate in this device is 1-10 and 0.1-1 (µl/min), respectively. The buffer to sample flow rate ratio of 10 gives the highest separation efficiency, but at a lower sample throughput. The optimized values are specific for our device but demonstrate processes that we believe are universal for DLD separations.

Intramedullary nail holes laser indicator, a non-invasive technique for interlocking of intramedullary nails.

Interlocking of intramedullary nails is a challenging procedure in orthopedic trauma surgery. Numerous methods have been described to facilitate this process. But they are exposed patient and surgical team to X-rays or involves trial and error. An accurate and non-invasive method has been provided to easily interlocking intramedullary nails. By transferring a safe visible light inside the nail, a drilling position appears which use to drilling bone toward the nail hole. The wavelength of this light was obtained from ex-vivo spectroscopy on biological tissues which has optimal transmission, reflectance, and absorption properties. Moreover, animal and human experiments were performed to evaluate performance of the proposed system. Ex-vivo performance experiments were performed successfully on two groups of cow and sheep samples. Output parameters were procedure time and drilling quality which there were significant differences between the two groups in procedure time (P < 0.05). But no significant differences were observed in drilling quality (P > 0.05). Moreover, an In-vivo performance experiment was performed successfully on a middle-aged man. To compare the provided method, targeting-arm, and free-hand techniques, two human experiments were performed on a middle-aged and a young man. The results indicate the advantage of the proposed technique in the procedure time (P < 0.05), while the drilling quality is equal to the free-hand technique (P = 0.05). Intramedullary nail holes laser indicator is a safe and accurate method that reduced surgical time and simplifies the process. This new technology makes it easier to interlocking the intramedullary nail which can have good clinical applications.

Phenolic nitroaromatics detection by fluorinated metal-organic frameworks: Barrier elimination for selective sensing of specific group of nitroaromatics.

Many piesce of research have been performed to detect nitroaromatic-compounds (NACs) by metal-organic frameworks (MOFs). Despite extensive studies, there are still significant challenges like selective detection of specific NAC group in presence of other NACs. Here, we have integrated two functionalization strategies through decoration of pore-walls of the MOFs with trifluoromethyl groups and extension in π-conjugated system. Based on this idea, trifluoromethyl TMU-44 (with the formula [Zn2(hfipbb)2(L1)]n.DMF, H2hfipbb = 4,4'-(hexafluoroisopropylidene) bis(benzoic acid), L1 = N,N'-bis-pyridin-4-ylmethylene-benzene-1,4-diamine) and TMU-45 (with formula [Zn2(hfipbb)2(L2)]n.DMF, L2 = N,N'-bis-pyridin-4-ylmethylene-naphthalene-1,5-diamine) frameworks have been synthesized. The aromatic skeleton of TMU-44 is based on phenyl rings while TMU-45 aromatic skeleton is extended by replacement of phenyl with naphthyl core. Measurements reveal that these MOFs are highly sensitive to phenolic NACs especially 2,4,6-trinitrophenol (TNP) with high quenching efficiency of 90% for TMU-44 (KSV = 10,652 M-1, LOD = 6.9 ppm) and 99% for TMU-45 (KSV = 34,741 M-1, LOD = 2.07 ppm). The proposed detection mechanism can be associated with hydrogen bonding between OH group of phenolic NACs and trifluoromethyl groups of TMU-MOFs as well as π(rich)∙∙∙π(deficient) interaction between π-conjugated backbone of TMU-frameworks and π-deficient ring of NACs.

IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files.

IOData is a free and open-source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane-wave density-functional-theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand-alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third-party) molecular quantum chemistry and solid-state density-functional-theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library.

Size-Selective Urea-Containing Metal-Organic Frameworks as Receptors for Anions.

Anion recognition by neutral hosts that function in aqueous solution is an emerging area of interest in supramolecular chemistry. The design of neutral architectures for anion recognition still remains a challenge. Among neutral anion receptor systems, urea and its derivatives are considered as "privileged groups" in supramolecular anion recognition, since they have two proximate polarized N-H bonds exploitable for anion recognition. Despite promising advancements in urea-based structures, the strong hydrogen bond drives detrimental self-association. Therefore, immobilizing urea fragments onto the rigid structures of a metal-organic framework (MOF) would prevent this self-association and promote hydrogen-bond-accepting substrate recognition. With this aim, we have synthesized two new urea-containing metal-organic frameworks, namely [Zn(bpdc)(L2)]n·nDMF (TMU-67) and [Zn2(bdc)2(L2)2]n·2nDMF (TMU-68) (bpdc = biphenyl-4,4'-dicarboxylate; bdc = terephthalate; L2 = 1,3-bis(pyridin-4-yl)urea), and we have assessed their recognition ability toward different anions in water. The two MOFs show good water stability and anion affinity, with a particular selectivity toward dihydrogen arsenate for TMU-67 and toward fluoride for TMU-68. Crystal structure characterizations reveal 3-fold and 2-fold interpenetrated 3D networks for TMU-67 and TMU-68, respectively, where all single interpenetrated networks are hydrogen bonded to each other in both cases. Despite the absence of self-quenching, the N-H urea bonds are tightly hydrogen bonded to the oxygen atoms of the dicarboxylate ligands and cannot be directly involved in the recognition process. The good performance in anion sensing and selectivity of the two MOFs can be ascribed to the network interpenetration that, shaping the void, creates monodimensional channels, decorated by exposed oxygen atom sites selective for arsenate sensing in TMU-67 and isolated cavities, covered by phenyl groups selective for fluoride recognition in TMU-68.

Preparing a New Class of Ultrathin Graphene Nanostructure by Chemical Vapor Deposition and Its Lasing Ability.

In this paper, we report a new method to grow graphene monolayers directly on a quartz substrate using chemical vapor deposition (CVD), without using any catalyst. For this purpose, ethanol as the precursor and a quartz substrate were used for growth, which controlled the growth process and the formation of an ultrathin layer of graphene. In this project, with use of plasma-enhanced chemical vapor deposition (PECVD), the substrate was cleaned by applying the cold plasma with the aim of improving the quality of the graphene monolayer grown. Atomic force microscopy (AFM) and Raman spectroscopy confirm that the graphene layer in regular triangular pieces grew to 200 nm in size. Photoluminescence spectroscopy (PL) of the samples showed a sharp peak in the blue spectrum, which indicates lasing emission in the graphene nanostructure. Finally, at a lower cost than other CVD methods, we have formed an ultrathin graphene layer on a dielectric substrate that can have many applications in the laser and photonics fields.

Ultrasonic assisted synthesis of two urea functionalized metal organic frameworks for phenol sensing: A comparative study.

Two pillared metal-organic frameworks containing urea functional groups were synthesized by a sonochemical method and characterized by scanning electron microscopy, X-ray powder diffraction, IR spectroscopy and elemental analysis. The time of sonication and concentration of starting materials have been optimized to synthesize nanoparticles of TMU-31 and TMU-32. These two frameworks are interesting candidates for a comparative fluorescence study. Thus, their potential abilities for phenol sensing were investigated. This investigation revealed the prominent roles of hydrogen bond donating urea groups inside the pore cavity in the ability of these structures in phenol sensing.

Ultrasound-assisted synthesis of nano-structured Zinc(II)-based metal-organic frameworks as precursors for the synthesis of ZnO nano-structures.

A 3D, porous Zn(II)-based metal-organic framework {[Zn2(oba)2(4-bpmn)]·(DMF)1.5}n (TMU-21), (4-bpmn=N,N'-Bis-pyridin-4-ylmethylene-naphtalene-1,5-diamine, H2oba=4,4'-oxybis(benzoic acid)) with nano-rods morphology under ultrasonic irradiation at ambient temperature and atmospheric pressure was prepared and characterized by scanning electron microscopy. Sonication time and concentration of initial reagents effects on the size and morphology of nano-structured MOFs were studied. Also {[Zn2(oba)2(4-bpmn)] (TMU-21) and {[Zn2(oba)2(4-bpmb)] (TMU-6), 4-bpmb=N,N'-(1,4-phenylene)bis(1-(pyridin-4-yl)methanimine) were easily prepared by mechanochemical synthesis. Nanostructures of Zinc(II) oxide were obtained by calcination of these compounds and their de-solvated analogue as activated MOFs, at 550°C under air atmosphere. As a result of that, different Nanostructures of Zinc(II) oxide were obtained. The ZnO nanoparticles were characterized by powder X-ray diffraction (XRD), scanning electron microscopy (SEM) and FT-IR spectroscopy.

Urea Metal-Organic Frameworks for Nitro-Substituted Compounds Sensing.

Urea groups are known to form strong hydrogen bonds with molecules containing atom(s) that can act as hydrogen bond acceptor(s). Thus, urea is a particularly interesting building block for designing receptors for neutral or charged guests. In the quest for new sensors with enhanced performance for the detection of nitro-substituted compounds, two pillared metal-organic frameworks containing urea functional groups were synthesized and structurally characterized. The sensing properties of these frameworks toward nitro-analytes were investigated and compared to each other. The study clearly reveals the importance of urea groups orientation inside the pore cavity of MOFs, as well as the supramolecular interactions between the interpenetrated networks. This work is interesting as it represents the first example of urea-functionalized MOFs for nitro-analytes recognition.

Microfluidic integrated acoustic waving for manipulation of cells and molecules.

Acoustophoresis with its simple and low-cost fabrication, rapid and localized fluid actuation, compatibility with microfluidic components, and biocompatibility for cellular studies, has been extensively integrated into microfluidics to provide on-chip microdevices for a variety of applications in biology, bioengineering and chemistry. Among different applications, noninvasive manipulation of cells and biomolecules are significantly important, which are addressed by acoustic-based microfluidics. Here in this paper, we briefly explain the principles and different configurations of acoustic wave and acoustic streaming for the manipulation of cells and molecules and overview its applications for single cell isolation, cell focusing and sorting, cell washing and patterning, cell-cell fusion and communication, and tissue engineering. We further discuss the application of acoustic-based microfluidic systems for the mixing and transport of liquids, manipulation of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) molecules, followed by explanation on the present challenges of acoustic-based microfluidics for the handling of cells and molecules, and highlighting the future directions.

Lanthanide metal-organic frameworks as selective microporous materials for adsorption of heavy metal ions.

Four microporous lanthanide metal-organic frameworks (MOFs), namely Ln(BTC)(H2O)(DMF)1.1 (Ln = Tb, Dy, Er and Yb, DMF = dimethylformamide, H3BTC = benzene-1,3,5-tricarboxylic acid), have been used for selective adsorption of Pb(ii) and Cu(ii). Among these MOFs, the Dy-based MOF shows better adsorption property and selectivity toward Pb(ii) and Cu(ii) ions. Adsorption isotherms indicate that sorption of Pb(ii) and Cu(ii) on MOFs is via monolayer coverage. Preconcentration is based on solid-phase extraction in which MOFs were rapidly injected into water samples and adsorption of metal ions was rapid because of good contact with analyte; then adsorbed Pb(ii) and Cu(ii) ions were analyzed by FAAS. The optimized methodology represents good linearity between 1 and 120 µg L(-1) and detection limit of 0.4 and 0.26 µg L(-1) for Pb(ii) and Cu(ii), respectively. Subsequently the method was evaluated for preconcentration of target metal ions in some environmental water samples.

Ultrasonic-assisted synthesis and structural characterization of two new nano-structured Hg(II) coordination polymers.

Two new Hg(II) coordination polymers containing N,N'-Bis-pyridin-3-ylmethylene-naphtalene-1,5-diamine ligand were synthesized by conventional and sonochemical methods, characterized by spectroscopic techniques (FT-IR and elemental analysis), and their X-ray crystallographic structures were determined. The crystal packing and supramolecular features of these coordination polymers were studied using geometrical analysis and Hirshfeld surface analysis. The crystal structure analysis revealed that H⋯H contacts, C-H⋯π and C-H⋯X (X = Cl for 1 and X = Br for 2) hydrogen bonding interactions are strong enough to govern the supramolecular architecture. The BFDH analysis helps us to compare the predicted morphology to that obtained under ultrasonication. This study may provide further insight into discovering the role of weak intermolecular interactions in the context of nano-supramolecular assembly.

The role of weak hydrogen and halogen bonding interactions in the assembly of a series of Hg(II) coordination polymers.

A series of eight new Hg(II) complexes based on the L4-X ligands, where L is (E) -4-halo-N-(pyridin-4-ylmethylene)aniline, were synthesized and characterized and their supramolecular crystal structures were studied by different geometrical and theoretical methods. Our study reveals the role of weak intermolecular interactions involving halogens, such as C­H∙∙∙X hydrogen bonds (in the cases of 1, 2, 3, 5, 6 and 7) and C­X∙∙∙X'­M halogen bonds (in the cases of 4 and 8), in the structural changes of supramolecular assemblies of coordination compounds. Complexes 1­8 were also synthesized by sonochemical irradiation and the morphology of the prepared complexes was investigated using FE-SEM. The BFDH analysis helps us to compare the predicted morphology to that obtained under ultrasonication. This study may provide further insight into discovering the role of weak intermolecular interactions in the context of metallosupramolecular assembly.

Influence of halogen bonding interaction on supramolecular assembly of coordination compounds; head-to-tail N···X synthon repetitivity.

In this study, N-(3-halophenyl)-2-pyrazinecarboxamide ligands, L(3-F), L(3-Cl), L(3-Br), and L(3-I), carrying a different halogen atom on the phenyl meta-position and N-phenyl-2-pyrazinecarboxamide ligand, L(H), have been employed for the synthesis of 12 mercury(II) complexes, [HgCl2(L(H))]n, 1, [HgCl2(L(3-Cl))]n, 2, [Hg2Cl4(L(3-Br))2], 3, [Hg2Cl4(L(3-I))2], 4, [Hg2Br4(L(H))2], 5, [HgBr2(L(3-F))], 6, [HgBr2(L(3-Cl))], 7, [HgBr2(L(3-Br))], 8, [HgBr2(L(3-I))], 9, [Hg2I4(L(H))2], 10, [HgI2(L(3-Br))], 11, and [HgI2(L(3-I))]n, 12. Interestingly, structural analysis clearly shows that, by the replacing of coordinated anions from chloride with bromide and iodide in each series containing the same ligand, the coordination geometry and structural motif of the resulting compounds have been dramatically affected. One of the common features in the crystal structures of these complexes is that there is a strong tendency to form halogen bonding synthons between adjacent halophenyl and pyrazine rings. The influence of these halogen bonding interactions on the supramolecular assemblies has been discussed with the help of geometrical analysis and theoretical calculations. The X···N halogen bonding distances are 2.5-9.4% shorter than the sum of the van der Waals radii of nitrogen and halogen atoms. Theoretical methods also show the halogen bonding energies within a range of -27.86 to -46.15 kJ·mol(-1). In all complexes synthesized here, the pyrazine ring is coordinated to the mercury(II) ion through the N atom syn to the carbonyl. Therefore, the second common feature of the crystal structures for complexes studied here is the selectivity of the metal ion coordination site. The halogen bond synthon repetitivity across these compounds and selectivity in the mercury(II) ion coordination site further point to application in the coordination crystal engineering research field.