Three-dimensional Clusters Research Articles

Highly Stable Three-Dimensional Silver (I) Chloride Cluster Based Coordination Polymer and Its Dye Removal Properties

A highly stable three-dimensional (3D) silver chloride cluster based coordination polymer (CP) with diphosphines ligand with the formula of [Ag4Cl4(L)2]n (1) (L = 1,3-bis(diphenylphosphino)propane, bdpp) has been prepared at room temperature. 1 was examined for the removal of Rhodamine B in aqueous solution, exhibiting potential for the removal of contaminants from wastewater.

QM study of interaction between arginine amino acid and Au clusters and the effects on arginine acidity

Understanding the various structures of gold clusters and the interaction modes between Au clusters and biomolecules is an important issue in material science such as biosensors and catalysts. The binding of small gold clusters (Aun n = 2–5) with neutral and anionic forms of arginine (Arg) amino acid is investigated in this study using density functional theory (DFT) and B3LYP level. The relative stability among different forms of Au clusters including linear, zigzag, planar, and three-dimensional Au clusters was estimated, initially. The calculated findings show that the zigzag structure for Au3 and the planar structure for Au4 and Au5 are the best form. Furthermore, the different modes of interaction were taken into account from thermodynamic view point between the most stable conformers of Arg and Arg− with gold clusters. Finally, the arginine is considered as a weak organic acid to investigate the impact of Au clusters on the gas phase acidity. The acidity of isolated arginine and the acidity of [Aun/Arg] complexes were also compared. Based on the obtained results, upon the complexation with Au clusters at 298 K, for the interaction of Au, Au2, Au3, Au4, and Au5 clusters with arginine, the gas phase acidity (GPA) of arginine alters from 342.12 to 314.17, 303.04, 299.42, 303.41, and 331.66 kcal/mol respectively. These calculated values predict that when a weak organic acid is complexed with Au clusters, it will be altered to super acid. Furthermore, for isolated and complexed species of Arg, pKa values were evaluated in water solvent.

Sn6 and Na4 Oxo Clusters Based Non-centrosymmetric Framework for Solution Iodine Absorption and Second Harmonic Generation Response.

A three-dimensional non-centrosymmetric cluster organic framework has successfully been built from the {Sn6} and {Na4} cluster units via the oxalate ligand, which belongs to the first 3D framework containing different cluster units in the field of tin-oxo clusters. Besides the interesting structural characteristics, the obtained 3D framework not only can efficiently adsorb the iodine molecules but also displays the second harmonic generation response under the 1064 nm Q-switch laser.

Two three-dimensional polyanionic clusters [M(P4Mo6)2] (M = Co, Zn) exhibiting excellent photocatalytic CO2 reduction performance.

Two captivating {P4Mo6}-based compounds, formulated as (H2bbi)2{[Co2(bbi)][Co2.33(H2O)4][H9.33CoP8Mo12O62]}·4H2O (1) and (H2bbi){[Zn(Hbbi)]2[Zn0.75(bbi)][K2Zn(H2O)4][H8.5ZnP8Mo12O62]} (2) [bbi = 1,1'-(1,4-butanediyl)bis(imidazole)], were successfully synthesized under hydrothermal conditions. Structural analysis demonstrates that compounds 1 and 2 are constructed from hourglass-shaped structures [M(P4Mo6O31)2]n- (M = Co, Zn), which are all made up of molybdophosphates and one transition metal ion as the central connecting node. Compounds 1 and 2 feature three-dimensional (3D) frameworks, which are all connected to form a 3D structure by metal ions and bbi ligands. More interestingly, compound 1 exhibits higher catalytic activity than 2 in CO2 photoreduction due to the suitable energy band structure of Co species in {P4Mo6} clusters. The CO yield was 3261 μmol g-1 with high selectivity in 8 h for compound 1 in photocatalytic CO2 reduction, which is highly promising in the photocatalytic field. Additionally, the photoluminescence properties of 2 were investigated.

Co-segmentation of three-dimensional shape clusters by shape similarity

Co-segmentation of three-dimensional shape clusters by shape similarity

Replating Protocol for Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes.

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) create an unlimited cell source for basic and translational cardiac research. Obtaining hiPSC-CM culture as a single-cell, monolayer or three-dimensional clusters for downstream applications can be challenging. Thus, it is critical to develop replating strategies for hiPSC-CMs by evaluating different enzymatic or nonenzymatic reagents for dissociation and seeding on different coating materials. To reseed hiPSC-CMs with high viability and at structures desirable for the downstream applications, here we defined optimized protocols to dissociate hiPSC-CMs by using collagenase A&B, Collagenase II, TrypLE, and EDTA and reseeding on various matrix materials including fibronectin, laminin, imatrix, Matrigel, and Geltrex. By the replating methods described here, a single cell or cluster-containing hiPSC-CM cultures can be generated effectively.

Three-dimensional clusters of peony-shaped CuO nanosheets as a high-rate anode for Li-ion batteries.

Copper oxide (CuO) has emerged as a promising anode material for lithium-ion batteries (LIBs) due to its high theoretical capacity, low cost and low toxicity to the natural environment. However, the low electronic/ionic conductivity and the imponderable volume expansion problem during the charge and discharge process hinder its practical applications. Herein, we introduced three-dimensional clusters of peony-shaped CuO nanosheets (TCP-CuO) to tackle these problems by increasing the surface of the active material. The unique three-dimensional peony-liked structure not only alleviates the volume expansion problem, but also enhances the electron/ion conductivity. As a result, the TCP-CuO electrode possesses a reversible high capacity of 641.1 mA h g−1 at 0.1 A g−1 after 80 cycles as well as an outstanding rate performance of 531.6 mA h g−1 at a rate of 5C (1C = 674 mA g−1) and excellent cycling durability of 441.1 mA h g−1 at 1 A g−1 after 100 cycles. This work demonstrated a novel strategy for the construction of a well-designed structure for other advanced energy-storage technologies.

Analysis of the plasmonic excitations in assemblies of three-dimensional electron clusters

In the quest to built novel metamaterials with unique optical properties, three-dimensional assemblies of metal clusters and nanoparticles are gathering significant attention. Organized geometries, such as tetrahedra and icosahedra, can be built, for example, by using DNA strands or virus capsids as templates. Here we use the jellium model and time-dependent density functional theory to study the plasmonic resonances in different arrangements of eight-electron clusters from the electronic perspective. A charge transfer ratio index based on the induced transition densities is used to quantify the charge transfer nature of the excitations at different energies. We vary the size, shape, and intercluster separation, building systems of four-cluster tetrahedra, 12-cluster icosahedra and cuboctahedra, and 20-cluster dodecahedra. All the studied systems are found to have charge transfer plasmon-type excitations at low energies. Analysis of the electron-hole transitions contributing to the transition dipole moment is further used to characterize these excitations, showing that they have significant screening contributions unlike the higher-energy excitations. The understanding gained for the optical response of these simple model systems can help in interpreting the properties of real, complex cluster systems.

Cluster of differentiation (CD) 9-positive mouse pituitary cells are adult stem/progenitor cells.

SOX2-positive cells are stem/progenitor cells that supply hormone-producing cells; they are found in the anterior lobe of the rodent pituitary gland. However, they are likely composed of several subpopulations. In rats, a SOX2-positive cell populations can be distinguished by the presence of S100β. We identified the novel markers cluster of differentiation (CD) CD9 and CD81, members of the tetraspanin superfamily, for the identification of S100β/SOX2-positive cells. Recently, CD9/CD81 double-knockout mice were generated. Although they grew normally until 3weeks after birth, they exhibited atrophy of the pituitary gland. These findings suggested that CD9/CD81/S100β/SOX2-positive cells in the mouse pituitary are adult stem/progenitor cells. To substantiate this hypothesis, we examined CD9 and CD81 expression in the adult and developing anterior lobe. Immunohistochemistry showed that CD9/CD81-positive cells began appearing from postnatal day 0 and settled in the stem cell niches (marginal cell layer and parenchyma) of the adult anterior lobe while expressing S100β. We next isolated CD9 -positive cells from the adult anterior lobe, using the anti-CD9 antibody for cell characterisation. The cells in culture formed free-floating three-dimensional clusters (pituispheres); moreover, induction into all types of hormone-producing cells was successful. Furthermore, reduction of CD9 and CD81 mRNAs by siRNAs inhibited cell proliferation. These findings indicate that CD9/CD81/S100β/SOX2-positive cells may play a role as adult stem/progenitor cells in SOX2-positive subpopulations, thus supplying hormone-producing cells in the postnatal anterior lobe. Furthermore, CD9 and CD81 are implicated in cell proliferation. The current findings provide novel insights into adult pituitary stem/progenitor cells.

The cytologic and immunohistochemical findings of pancreatic mixed acinar-endocrine carcinoma.

The classification of epithelioid pancreatic neoplasms based on fine-needle aspiration (FNA) is important for proper management, as distinction of pancreatic neuroendocrine neoplasms from other similar appearing lesions can result in significantly different treatment. Mixed acinar-endocrine carcinomas (MAEC) are genetically related to acinar carcinomas and are treated as such. We reviewed cases of MAEC to better characterize their cytologic and immunohistochemical features. Eight FNAs of MAECs were identified and reviewed. A chart review for each case was conducted. All patients were male, 42-68 years of age, and presented with either Stage 3 or 4 disease. Smear backgrounds of all cases showed naked nuclei without significant necrosis. The smears were cellular with cells arranged in either three-dimensional (3D) clusters with intervening capillaries or singly dispersed. Acinar formation was a prominent feature. Cells were round to oval with small to moderate amounts of delicate cytoplasm. The nuclei were round to oval with mild to moderate anisonucleosis with granular chromatin and small nucleoli. Apoptotic bodies and mitoses were noted in most cases, with Ki67 indices of 10%-48%. All tumors, by definition, demonstrated expression of trypsin and synaptophysin with variable chromogranin expression (50%). The cytology of acinar cell carcinoma shares features with aspirates of other nonductal adenocarcinoma neoplasms of the pancreas. A clue to the diagnosis is that tumors show high Ki67 indices and a diagnosis of MAEC should be excluded anytime a diagnosis of Grade 2 or 3 well-differentiated neuroendocrine tumor or high-grade neuroendocrine carcinoma is in the differential.

Mt. Etna Feeding System and Sliding Flank: A New 3D Image From Earthquakes Distribution in a Customisable GIS

High-resolution seismic imaging enables the reconstruction of ascending paths of magma and fluids, shallow molten accumulation and flank collapse areas, all crucial information for developing an efficient eruption forecasting strategy. Here, the Marching Cubes algorithm (MC - generally applied to medical visualisation and 3D modelling) is applied to 16 years of earthquake location data at Mt. Etna (Italy). The algorithm defines three-dimensional seismic clusters that take into account seismic location uncertainties and are embedded in a novel volcano-oriented GIS (VolGIS) offering an interpretational environment comprising tomographic images and alternative geophysical models. The results show that a volume of very-low-seismicity is embedded in a high-velocity body, and acts as a zone of transition between transient magmatic events (west) and eastern seismicity related to the sliding eastern flank. The eastern cluster represents the first 3D seismic signature of a deeper flank instability caused by a combination of magmatic and gravitational forces.

Natural and Synthetic Biomaterials for Engineering Multicellular Tumor Spheroids.

The lack of in vitro models that represent the native tumor microenvironment is a significant challenge for cancer research. Two-dimensional (2D) monolayer culture has long been the standard for in vitro cell-based studies. However, differences between 2D culture and the in vivo environment have led to poor translation of cancer research from in vitro to in vivo models, slowing the progress of the field. Recent advances in three-dimensional (3D) culture have improved the ability of in vitro culture to replicate in vivo conditions. Although 3D cultures still cannot achieve the complexity of the in vivo environment, they can still better replicate the cell–cell and cell–matrix interactions of solid tumors. Multicellular tumor spheroids (MCTS) are three-dimensional (3D) clusters of cells with tumor-like features such as oxygen gradients and drug resistance, and represent an important translational tool for cancer research. Accordingly, natural and synthetic polymers, including collagen, hyaluronic acid, Matrigel®, polyethylene glycol (PEG), alginate and chitosan, have been used to form and study MCTS for improved clinical translatability. This review evaluates the current state of biomaterial-based MCTS formation, including advantages and disadvantages of the different biomaterials and their recent applications to the field of cancer research, with a focus on the past five years.

3D virtual histology of human pancreatic tissue by multiscale phase-contrast X-ray tomography.

A multiscale three-dimensional (3D) virtual histology approach is presented, based on two configurations of propagation phase-contrast X-ray tomography, which have been implemented in close proximity at the GINIX endstation at the beamline P10/PETRA III (DESY, Hamburg, Germany). This enables the 3D reconstruction of characteristic morphological features of human pancreatic normal and tumor tissue, as obtained from cancer surgery, first in the form of a large-scale overview by parallel-beam illumination, followed by a zoom into a region-of-interest based on zoom tomography using a Kirkpatrick-Baez mirror with additional waveguide optics. To this end 1 mm punch biopsies of the tissue were taken. In the parallel tomography, a volumetric throughput on the order of 0.01 mm3 s-1 was achieved, while maintaining the ability to segment isolated cells. With a continuous rotation during the scan, a total acquisition time of less than 2 min was required for a full tomographic scan. Using the combination of both setups, islets of Langerhans, a three-dimensional cluster of cells in the endocrine part of the pancreas, could be located. Cells in such an islet were segmented and visualized in 3D. Further, morphological alterations of tumorous tissue of the pancreas were characterized. To this end, the anisotropy parameter Ω, based on intensity gradients, was used in order to quantify the presence of collagen fibers within the entire biopsy specimen. This proof-of-concept experiment of the multiscale approach on human pancreatic tissue paves the way for future 3D virtual pathology.

Finite-Temperature Structures of Supported Subnanometer Catalysts Inferred via Statistical Learning and Genetic Algorithm-Based Optimization.

Single-atom catalysts (SACs) minimize noble metal utilization and can alter the activity and selectivity of supported metal nanoparticles. However, the morphology of active centers, including single atoms and subnanometer clusters of a few atoms, remains elusive due to experimental challenges. The computational cost to describe numerous cluster shapes and sizes makes direct first-principles calculations impractical. We present a computational framework to enable structure determination for single-atom and subnanometer cluster catalysts. As a case study, we obtained the low-energy structures of Pdn (n = 1-21) clusters supported on CeO2(111), which are critical components of automobile three-way catalysts. Trained on density functional theory data, a three-dimensional cluster expansion is established using statistical learning to describe the Hamiltonian and predict energies of supported Pdn clusters of any structure. Low-energy stable and metastable structures are identified using a Metropolis Monte Carlo-based genetic algorithm in the canonical ensemble at 300 K. We observe that supported single atoms sinter to form bilayer clusters, and large cluster isomers share similarities in both shape and energy. The findings elucidate the significance of the support and microstructure on cluster stability. We discovered a simple surrogate structure-energy model, where the energy per atom scales with the square root of the average first coordination number, which can be used to estimate energies and compare the stability of clusters. Our framework, applicable to any metal/support system, fills an important methodological gap to predict the stability of supported metal catalysts in the subnanometer regime.

Density functional study of gallium clusters on graphene: electronic doping and diffusion

Motivated by experimental results on transport properties of graphene covered by gallium atoms, the density functional theory study of clustering of gallium atoms on graphene (up to a size of 8 atoms) is presented. The paper explains a rapid initial increase of graphene electron doping by individual Ga atoms with Ga coverage, which is continually reduced to zero, when bigger multiple-atom clusters have been formed. According to density functional theory calculations with and without the van der Waals correction, gallium atoms start to form a three-dimensional cluster from five and three atoms, respectively. The results also explain an easy diffusion of Ga atoms while forming clusters caused by a small diffusion barrier of 0.11 eV. Moreover, the calculations show this barrier can be additionally reduced by the application of an external electric field, which was simulated by the ionization of graphene. This effect offers a unique possibility to control the cluster size in experiments only by applying a gate-voltage to the graphene in a field-effect transistor geometry and thereby without growth temperature assistance.

Gastric-type endocervical adenocarcinoma and cervical cytology: Experience at a general hospital and review of the literature.

Gastric-type endocervical adenocarcinoma (GAS) is an uncommon type of endocervical adenocarcinoma that is not associated with human papillomavirus infection. This diagnosis is relatively rare and may portend a worse prognosis than usual-type endocervical adenocarcinoma. Subtle morphological features make it an under-recognised diagnostic challenge. Study of the cytological features of individual cases is valuable in order to increase awareness of this entity. The pathology database of our institution was searched for the diagnosis of GAS and all cytological and surgical specimens for each patient were reviewed. The original cytological interpretation was compared to a retrospective central review interpretation. Clinical history and follow-up results were obtained from the electronic medical record. Four cases of GAS were identified. The findings on initial cervical cytology varied, with GAS found in both patients with negative cervical cytology and those with atypical glandular cells. Cytological findings included endocervical cells arranged in three-dimensional clusters and honeycomb sheets with abundant vacuolar cytoplasm, and in two patients, moderate nuclear atypia with irregular nuclear membranes, coarse chromatin, hyperchromatic nuclei, and prominent nucleoli. In one patient, GAS was incidentally discovered via thorough sampling of a cystic lesion in the superior portion of the endocervical canal. GAS is an aggressive human papillomavirus-independent type of endocervical adenocarcinoma with subtle morphological features and, as our study shows, varying clinical presentation. Given the aggressive nature of GAS and the difficulties in initial diagnosis, increased awareness of this entity among pathologists is crucial.

Ultrasensitive Electrochemiluminescence Immunosensor Based on a Three-Dimensional Flower-Like Manganese Dioxide–Polyethyleneimine–Palladium Nanocomposite as the Signal Label for Detection of Avian Leukosis Virus Subgroup J

A novel sandwich-type electrochemiluminescence (ECL) immunosensor was successfully fabricated for the ultrasensitive detection of avian leukosis virus subgroup J (ALV-J). The immunosensor used a glassy carbon electrode decorated with gold nanoparticles (Au NPs), primary antibodies (Ab1) and bovine serum albumin as the sensor platform. For the signal label, three-dimensional flower-like MnO2 clusters modified with polyethyleneimine and palladium nanoparticles (MnO2–PEI–Pd nanocomposite) were used as the novel carrier of Ru(bpy)3Cl2 and secondary antibodies (Ab2). Under optimal conditions, the ECL immunosensor offered a linear relationship between the ECL signal and the logarithm of the ALV-J concentration in the range from 101.98 to 104.30 TCID50/mL with a detection limit of 101.90 TCID50/mL (based upon a signal-to-noise ratio of 3). In addition, the immunosensor showed excellent stability, selectivity and reproducibility, thus offering an effective tool for the quantitative detection of ALV-J in clinical applications.

Temporal-mode continuous-variable three-dimensional cluster state for topologically protected measurement-based quantum computation

Measurement-based quantum computation with continuous variables in an optical setup shows the great promise towards implementation of large-scale quantum computation, where the time-domain multiplexing approach enables us to generate the large-scale cluster state used to perform measurement-based quantum computation. To make effective use of the advantage of the time-domain multiplexing approach, in this paper, we propose the method to generate the large-scale 3-dimensional cluster state which is a platform for topologically protected measurement-based quantum computation. Our method combines a time-domain multiplexing approach with a divide-and-conquer approach, and has the two advantages for implementing large-scale quantum computation. First, the squeezing level for verification of the entanglement of the 3-dimensional cluster states is experimentally feasible. The second advantage is the robustness against analog errors derived from the finite squeezing of continuous variables during topologically-protected measurement-based quantum computation. Therefore, our method is a promising approach to implement large-scale quantum computation with continuous variables.

Improved accuracy of U-series and radiocarbon dating of ostrich eggshell using a sample preparation method based on microstructure and geochemistry: A study from the Middle Stone Age of Northwestern Ethiopia

The Middle Stone Age (MSA) is important to studies of human evolution because it witnessed the origin of modern Homo sapiens and its dispersal out of Africa and across the rest of the Old World. Obtaining accurate ages for these and other events that occurred during this time interval is of critical importance. Ostrich eggshell (OES) is commonly found in MSA sites, and OES calcite can be dated by radiocarbon and U-series geochronologic techniques. It is important to understand how both techniques are potentially compromised when the eggshell’s pore clusters and intercrystalline microporosity are infilled with younger calcite and/or soil-derived detrital materials. We investigated this question by using high-resolution X-ray computed tomography (HRXCT) to reveal the extent and three-dimensional structure of the pore clusters, and element mapping to evaluate concentrations of detrital elements in modern versus ancient OES within the pore clusters and the crystal (outer) and cone (inner) layers relative to the palisade (central) layer. HRXCT results support earlier findings that OES pores are generally composed of one to several openings on the cone surface that develop into a complex three-dimensional cluster of anastomosing and branching pores that extend through the palisade layer to exit on the crystal surface. These hollow pore clusters provide a considerable total volume for the potential ingress of detrital materials. Element mapping revealed high concentrations of detrital mineral indicator elements (Al, Mg) in ancient relative to modern OES, and in the cone and crystal layers relative to the palisade layer. Within the palisade layer of ancient OES, there are relatively high detrital mineral indicator element concentrations within filled pore clusters. Extracted pore cluster infill from the palisade layer yields significantly higher and more variable concentrations of 232Th (2,200-10,000 ppt) and 238U (35–54 ppb) relative to the non-porous palisade layer (150–3,100 ppt 232Th, and 19–25 ppb 238U). Based on these results, we developed a mechanical preparation method that combines the removal of the pore cluster infill with the more common removal of the cone and crystal layers. Using this method, U–Th analyses of four OES from an MSA archaeological site in NW Ethiopia yielded a mean age of 75.7±4.7 ka (2 SD). The inclusion of the pore cluster infill with the palisade in a different OES from the same site produced a much younger age of 53±1.2 ka (1 SE). Splits of several of these same OES samples prepared by this new method yield AMS 14C ages that are beyond the range of 14C dating (∼50 ka), while ∼60% of the OES analyses of the palisade layer that retained the pore cluster infill yielded much younger ages (27–38 ka). Our results demonstrate that dating OES that retains the pore cluster infill shifts both U–Th and 14C analyses to younger ages. In order to obtain more precise and accurate ages, we recommend that preparation of OES for both U-series and 14C dating include the mechanical removal of both the pore cluster infill and the cone and crystal layers in order to more fully account for the incorporation of Th, U, and C from detrital and authigenic minerals within the OES structure.

Task-Specific Synthesis of 3D Porous Carbon Nitrides from the Cycloaddition Reaction and Sequential Self-Assembly Strategy toward Photocatalytic Hydrogen Evolution.

Carbon nitride has drawn widespread attention as a low-cost alternative to metal-based materials in the field of photocatalysis. However, the traditionally synthesized carbon nitrides always suffer a bulky architecture, which limits their intrinsic activities. Here, a cycloaddition reaction is proposed to synthesize a triazine-based precursor with implanted sodium and cyano groups, which are mostly retained in the resulting carbon nitride after the following polymerization. Incorporated sodium and cyano defects can not only tune the band structure of the carbon nitride but also provide more additive active sites. The optimized properties enable it an adorable photocatalytic hydrogen evolution rate of 1070 μmol h-1 g-1, varying by almost an order of magnitude from the pristine carbon nitride (79 μmol h-1 g-1). Moreover, a sequential self-assembly strategy has been adopted to further improve its architecture. As a consequence, a three-dimensional (3D) porous carbon nitride microtube cluster is constructed, indicating abundant exposed active sites and the faster separation of charge carriers. The corresponding photocatalytic hydrogen evolution rate is 1681 μmol h-1 g-1, which is very competitive compared with the reported pure carbon nitride photocatalysts. Briefly, this new approach may offer opportunities to fabricate task-specific carbon- and nitrogen-based materials from the molecular level.