Biclustering Research Articles

Bi Cluster Engineering for Tunable Broadband NIR Optical Response

AbstractNear‐infrared (NIR) broadband active photonic materials play a crucial role in various domains such as optical communication, phototherapy, and medical imaging. However, the construction of NIR photonic materials with tunable optical response still remains a great challenge. This manuscript proposes a topological structure engineering strategy in Bi‐activated glass for the realization of the controllable NIR emission. By manipulating the topological structure of glass, the Bi cluster configuration can be precisely control, with the cluster size from 2.78 to 1.64 nm. Correspondingly, various optical properties including broadband emission, excited state absorption (ESA), and even unsaturable loss (UL) can be rationally switched. Based on the above findings, Bi cluster‐activated bulk glasses, optical fibers, and the derived NIR active devices with notably improved performance can be successfully fabricated. Their application potentials in optical communication and NIR imaging are also demonstrated. The study highlights the promise of Bi cluster‐activated materials in advancing NIR photonic materials and devices. Furthermore, the topological‐mediated cluster regulation strategy may also provide new insights into the fundamental science and cutting technology of other cluster‐activated materials.

Microstructure and coupling mechanisms in MnBi–FeSiB nanocomposites obtained by spark plasma sintering

Fabrication and extensive characterization of hard-soft nanocomposites composed of hard magnetic low-temperature phase LTP-MnBi and amorphous Fe70Si10B20 soft magnetic phase for bulk magnets are reported. Samples with compositions Mn55Bi45 + x⋅(Fe70Si10B20) (x = 0, 3, 5, 10, 20 wt.%) were prepared by spark plasma sintering of powder mixtures. Characterization has been performed by X-ray diffraction, scanning and transmission electron microscopy, magnetometry and 57Fe Mӧssbauer spectroscopy. It was shown that samples contain crystallized and nanometric LTP-MnBi phases with various elemental compositions depending on the degree of Bi clustering. Complex correlations between starting compositions, processes during fabrication, and functional magnetic characteristics were observed. Unexpected special situations of the relation between microstructure and magnetic coupling mechanisms are discovered. Exchange spring effects of different strengths occur, being very sensitive to morpho-structural and compositional features, which in turn are controlled by processing conditions. An in-depth analysis of related microscopic characteristics is provided. Results of this work suggest that fabrication by powder metallurgy routes, such as spark plasma sintering of hard and soft magnetic powder mixtures, of MnBi-based composites with exchange spring phenomena have a high potential in designing and optimization of suitable materials with tunable magnetic properties towards rare-earth–free permanent magnet applications.

A nanosheet CH3COO(BiO) topotactically converted into nanocomposite of bismuth clusters and Bi2O2CO3 for highly efficient electrocatalytic reduction of CO2 to formate

Hydrogen is a promising clean energy source, and formic acid serves as a significant hydrogen storage material. The electrocatalytic reduction of carbon dioxide (ECO2RR) is a promising approach to produce fromate. However, the challenge lies in developing high-performance electrocatalysts for the conversion of CO2 to formate, due to the limited intrinsic activity, conductivity, and the low density of active sites. In this work, we have fabricated highly active and selective CH3COO(BiO) (BiOAc) nanosheets. These nanosheets undergo a transformation into Bi clusters-BiO2CO3 during electrolysis, endowing the material with superior electrocatalytic capabilities for CO2 reduction to formate, with a Faradaic selectivity of over 90 % across a wide potential window from −0.8 to −1.3 V. Additionally, this catalyst can sustain high current densities above 80 mA cm−2 at low applied potentials without compromising selectivity in a H type electron reactor. Both density functional theory (DFT) and in situ attenuated total reflection-infrared spectroscopy (in situ ATR-IR) findings indicate that the Bi3+ with reduced density facilitate the activation of CO2 to *CO2, while the charge density-enriched Bi0 atoms in Bi cluster promote the capture of HCO3– and enhance subsequent proton-coupled electron transfer reactions. Collectively, these factors significantly reduce the energy barrier for *OCHO formation on BiOAc, thereby enhancing its catalytic activity and Faradaic efficiency for the electroreduction of CO2.

Matrix-Enhanced SIMS: The Influence of Primary Ion Species and Cluster Size on Ion Yield and Ion Yield Enhancement of Lipids.

Time-of-flight secondary ion mass spectrometry is one of the most promising techniques for label-free analysis of biomolecules with nanoscale spatial resolution. However, high-resolution imaging of larger biomolecules such as phospholipids and peptides is often hampered by low yields of molecular ions. Matrix-enhanced SIMS (ME-SIMS), in which an organic matrix is added to the sample, is one promising approach to enhancing the ion yield for biomolecules. Optimizing this approach has, however, been challenging because the processes involved in increasing the ion yield in ME-SIMS are not yet fully understood. In this work, the matrix α-cyano-4-hydroxycinnamic acid (HCCA) has been combined with cluster primary ion analysis to better understand the roles of proton donation and reduced fragmentation on lipid molecule ion yield. A model system consisting of 1:100 mol ratio dipalmitoylphosphatidylcholine (DPPC) in HCCA as well as an HCCA-coated mouse brain cryosection have been studied using a range of Bi and Ar cluster ions. Although the molecular ion yield increased with an increase in cluster ion size, the enhancement of the signals from intact lipid molecules decreased with an increase in cluster ion size for both the model system and the mouse brain. Additionally, in both systems, protonated molecular ions were significantly more enhanced than sodium and potassium cationized molecules for all of the primary ions utilized. For the model system, the DPPC molecular ion yield was increased by more than an order of magnitude for all of the primary ions studied, and fragmentation of DPPC was dramatically reduced. However, on the brain sample, even though the HCCA matrix reduced DPPC fragmentation for all of the primary ions studied, the matrix coating suppressed the ion yield for some lipids when the larger cluster primary ions were employed. This indicated insufficient migration of the lipids into the matrix coating, so that dilution by the matrix overpowered the enhancement effect. This study provides strong evidence that the HCCA matrix both enhances protonation and reduces fragmentation. For imaging applications, the ability of the analytes to migrate to the surface of the matrix coating is also a critical factor for useful signal enhancement. This work demonstrates that the HCCA matrix provides a softer desorption environment when using Bi cluster ions than that obtained using the large gas cluster ions studied alone, indicating the potential for improved high spatial resolution imaging with ME-SIMS.

Xenobiotic Bi3+ Coordination by Cysteine-Rich Metallothionein-3 Reveals a Cooperatively Formed Thiolate-Sharing Bi2S5 Cluster.

The field of designing artificial metalloproteins has yet to effectively tackle the incorporation of multimetal clusters, which is a key component of natural metalloproteins, such as metallothioneins (MTs) and calmodulin. MT is a physiological, essential, cysteine-rich metalloprotein that binds to a variety of metals but is only known to form metal-thiolate clusters with Cd2+, Zn2+, and Cu+. Bismuth is a xenobiotic metal and a component of metallodrugs used to treat gastric ulcers and cancer, as well as an emerging metal used in industrial practices. Electrospray ionization mass spectrometry, UV-visible spectroscopy, and extended X-ray absorption fine structure spectroscopy were used to probe the Bi3+ binding site structures in apo-MT3 (brain-located MT) at pH 7.4 and 2 and provide the complete set of binding affinities. We discovered the highly cooperative formation of a novel Bi3+ species, Bi2MT3, under physiological conditions, where each Bi3+ ion is coordinated by three cysteinyl thiolates, with one of the thiolates bridging between the two Bi3+ ions. This cluster structure was associated with a strong visible region absorption band, which was disrupted by the addition of Zn2+ and reversibly disrupted by acidification and increased temperature. This is the first reported presence of bridging cysteines for a xenobiotic metal in MT3 and the Bi2MT structure is the first Bi cluster found in a metalloprotein.

Topological biclustering ARTMAP for identifying within bicluster relationships

Biclustering is a powerful tool for exploratory data analysis in domains such as social networking, data reduction, and differential gene expression studies. Topological learning identifies connected regions that are difficult to find using other traditional clustering methods and produces a graphical representation. Therefore, to improve the quality of biclustering and module extraction, this work combines the adaptive resonance theory (ART)-based methods of biclustering ARTMAP (BARTMAP) and topological ART (TopoART), to produce TopoBARTMAP. The latter inherits the ability to detect topological associations while performing data reduction. The capabilities of TopoBARTMAP were benchmarked using 35 real world cancer datasets and contrasted with other (bi)clustering methods, where it showed a statistically significant improvement over the other assessed methods on ordered and shuffled data experiments. In experiments with 12 synthetic datasets, the method was observed to perform better at identifying constant, scale, shift, and shift scale type biclusters. The produced graphical representation was refined to represent gene bicluster associations and was assessed on the NCBI GSE89116 dataset containing expression levels of 39,326 probes sampled over 38 observations.

Influence of temperature and sputter source on Cu(In,Ga)Se2 SIMS depth profiles

The thin‐film photovoltaic technology based on Cu(In,Ga)Se2 (CIGS) has reached high conversion efficiencies exceeding 23%. The gallium gradient in the bulk and the amount of alkali metals in and between CIGS grains strongly affect the cell performance and therefore need to be accurately measured and quantified. ToF‐SIMS is well suited for this task, but the spatial resolution is strongly influenced by the measurement parameters, especially at the required micrometer and nanometer scales. Such highly resolved measurements on CIGS surfaces are challenging. For instance, small copper aggregations occur in SEM images recorded after a focused ion beam (FIB) cut and change the energy‐dispersive spectroscopy (EDS) results. SIMS systems that use an argon ion source generate Cu lamellas, which also influence the measurement. Both effects result from preferential sputtering. Cooling with liquid nitrogen can minimize this negative effect for both techniques. Recent developments in SIMS systems provide more options to avoid these effects. New sources, like the Bi liquid metal gun and cluster guns, are available. However, a systematic investigation on the effect of the ion sources on the sputter craters and the resulting measurement of CIGS absorber is necessary to choose an adequate setup. Thus, we performed a comparison of four different ion sources (argon ion gun, oxygen gun, cesium metal gun, and oxygen cluster gun) and measured CIGS depth profiles at three temperatures [−120°C, −50°C, and room temperature (RT)]. We investigate the influence of these conditions not only on the resulting SIMS depth profile and quantification but also on the morphology of the sputter crater.

Precise modification of poly(aryl ether ketone sulfone) proton exchange membranes with positively charged bismuth oxide clusters for high proton conduction performance

AbstractIn the field of proton exchange membranes (PEMs), it is still a great challenge to explore new Nafion alternatives, maintaining the high proton conductivity and lowering the cost of practical application. In this work, a series of low sulfonated poly(aryl ether ketone sulfone) (SPAEKS) membranes hybridized by [Bi6O5(OH)3]2(NO3)10·6H2O (H6Bi12O16) have been successfully fabricated. When the doping amount of H6Bi12O16 reaches 5 wt%, the DS15‐Bi12‐5 showing the best proton conductive ability and mechanical properties. The proton conductivity can achieve 72.8 mS·cm−1 at 80°C and the tensile strength can reach 43.57 MPa. Confirmed by experimental data and activation energy (Ea) calculations, the existence of Bi cluster makes more hydrogen bonds, providing additional proton hopping sites and offers more proton transport vehicles, leading to a high proton conduction performance. This work proved that polyoxometalates (POMs) can replace the role of sulfonate groups in SPAEKS to a certain extent and work out the defects of high sulfonation, making a remarkable contribution to the practical application of low sulfonated SPAEKS.

Theoretical and experimental study of the microstructure of a metallic melt in an In50Bi50 alloy based on the Wulff cluster model

In this paper, the Wulff cluster model which has been proved to successfully describe the melt structure of pure metals, homogenous alloys and eutectic alloys has been extended to an alloy with intermetallic compounds (In50Bi50). According to the cohesive energy and the solid-state XRD patterns, the most possible types of clusters in the melt are Bi and InBi. At relatively high temperatures, the superimposed XRD (simulated) patterns of Bi and InBi clusters are in good agreement with the experimental HTXRD patterns in terms of the position and intensity of the peaks. With the decrease of temperature, there is an obvious deviation in the simulated XRD value at the second peak caused by the nucleation process of Bi clusters, which would be modified by adding simulated XRD patterns of the Bi bulk. The proportion of the superimposed Bi bulk XRD pattern increases with the decrease of temperature suggesting that the nucleation process of the Bi cluster begins at 160 °C.

Molecular speciation analysis of oxidized metal surfaces by TOF SIMS

Molecular speciation by Time of Flight Secondary Ion Mass Spectrometry (TOF SIMS) was applied to oxidized bismuth, lead, tin, and tellurium. In their pure elemental form, they are basic constituent elements of both topological insulators and topological crystalline insulators, which are very hot topics in the last decade.The range of specific ions masses used to evaluate the valence of investigated oxides has been significantly expanded towards high-mass clusters MexOy (2 ≤ x ≤ 5). The significant enhancement in the secondary high-mass ion yield by using the Bi cluster ion source reflects the valence of primary ion clusters used in molecular speciation of inorganic species. The results show that chemical composition of clusters differs in three 2, 3, and 4 oxidation states studied. This implies that each oxidation state possesses its own set of the high-mass clusters extracted from oxidized metal surfaces during measurement.Such an approach allows for the first time to perform a semi-quantitatively molecular speciation of oxides exploiting the empirical Plog's model. It describes the secondary ion yield as a function of the metal valency in the oxide. We found that the estimated lattice valence state G0 is close to the valence state of the metal in stable oxides.

Effect of cocrystallization due to bile acid on molecular‐ion sensitivity of biological phospholipids in Bi cluster time‐of‐flight secondary ion mass spectrometry measurements

Bi cluster time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) is a useful method for evaluating organic surfaces. However, its ability to detect large molecules is limited. One of the problems is that the sensitivities of macromolecules are lower than those of small molecules because larger molecules tend to exhibit lower ionization efficiencies and/or higher probabilities of fragmentation. Matrix‐enhanced (ME)‐SIMS is a sensitivity enhancement technique for intact molecular ions. The crystal structure of a mixed substance composed of an analyte and a matrix is known to affect the sensitivity of the analysis target. In this study, the effect of cocrystallization, which occurs due to the presence of bile acid, on the molecular‐ion sensitivity was investigated using Bi cluster TOF‐SIMS. Biological phospholipids and bile acids, which exhibit surfactant behaviors, were selected as the evaluated molecules and additives, respectively. The mass spectra indicated that the secondary‐ion yields of phospholipids with bile acid were substantially greater than those of the pristine lipid. Specifically, samples with an analyte/bile acid ratio of 1:100 achieved approximately 60–100‐fold sensitivity enhancement of [M + H]+ and [2M + H]+ molecular ions than the sensitivity achieved with the pristine samples. In the evaluation of molecular distribution, higher signal counts of intact ions were obtained from the cocrystallization area, although less‐fragmented ions were emitted from these regions. Consequently, the results indicate that the cocrystallization due to the presence of bile acid provides an effective crystal structure for facilitating emission of larger molecules.

IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES USING BI-CLUSTERING

Inorder to identify the biologically relevant gene module and also which are the genes responsible for causing a disease,we use Biclustering technique which is also a useful co-clustering technique.In this paper, we present a exceptional method to state specific gene modules and also functionally related gene modules which are the reason for disease causing ,by applying a genetic algorithm to genetic data which is in the form of microarray data. To detect these differentially expressed gene modules, the anticipated method finds biclusters in which genes are overexpressed or under expressed, and also which are differentially-expressed in the samples of genetic data. Inorder to get the differentially expressed we perform three steps in which we use K means alogorithm for clustering and Cheng and Chruch algorithm for biclustering. As to overcome the drawbacks in clustering we use Biclustering technique which reduce redundancy in the data.The ensuing gene modules uncover preferable exhibitions over near techniques in the GO (Gene Ontology) term enhancement test and an analyzed association between gene modules and infection.

Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.)

Bitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.

A Survey on Deep learning Models for Disease Detection and Diagnosis in Agriculture Field

This paper shows a brief thought of a percentage of the broadly utilized data mining systems over agri-business information sets. It is a contemporary system to discover the arrangement over the customary and traditional technique. It is a new concept as for data mining in the field of farming. Data mining is a procedure of separating/comparing the important information from the extensive database by utilizing diverse tools and methods. Different Data Mining techniques are in use, such as K-Means, K-Nearest Neighbor(KNN), Artificial Neural Networks(ANN) and Support Vector Machines(SVM) for very recent applications of Data Mining techniques in agriculture field. Bi clustering is a technique that can also utilized in agriculture mining. Data mining in agriculture is an emerging research field. It is our opinion that efficient techniques can be developed and tailored for solving complex agricultural problems using data mining. At the end of this study we provide suggestions for future research directions in agriculture-related fields

Effects of polymer crystallization on the molecular sensitivity in TOF-SIMS measurements using Bi1+ and Bi32+ ions

Bi cluster ions are among the most utilized primary sources for time-of-flight secondary ion mass spectrometry (TOF-SIMS). Although Bi clusters have advantages over larger clusters, such as C60+ and Arn+, TOF-SIMS is less sensitive for macromolecules when Bi clusters are used as primary ions. Matrix-enhanced SIMS is a more sensitive technique for large molecules, because the matrix limits fragmentation. The matrix is thought to reduce molecular crystallinity and cohesiveness, which facilitate the extraction of large molecules from the sample surface. In this study, the authors investigate the effects of polyethylene glycol structure on the molecular sensitivity of TOF-SIMS using different primary Bi ion species. The results indicate that amorphous PEG enables the detection of larger molecules than crystalline PEG by TOF-SIMS when either Bi1+ or Bi32+ ions are used for irradiation. This suggests that the structures of organic molecules affect the propagation of kinetic energy from the primary ions. This phenomenon reduces damage to polymer chains and enhances the sensitivity of TOF-SIMS for intact molecular ions.

Effect of thermal annealing on the optical and structural properties of (311)B and (001) GaAsBi/GaAs single quantum wells grown by MBE

The effect of Furnace Annealing (FA) and Rapid Thermal annealing (RTA) on the structural and optical properties of GaAs1 − xBix/GaAs single quantum wells grown on (001) and (311)B substrates by molecular beam epitaxy was investigated. The structural properties were investigated by high-resolution x-ray diffraction (HR-XRD) and Transmission Electron Microscopy. The Bi concentration profiles were determined by simulating the HR-XRD 2θ−ω scans using dynamical scattering theory to estimate the Bi content, lattice coherence, and quality of the interfaces. The Bi composition was found to be similar for both samples grown on (001) and (311)B GaAs substrates. However, the simulations indicate that the Bi composition is not only limited in the GaAsBi quantum well (QW) layer but also extends out of the GaAsBi QW toward the GaAs barrier. Photoluminescence (PL) measurements were performed as a function of temperature and laser power for samples with a nominal Bi composition of 3%. PL spectra showed that (001) and (311)B samples have different peak energies at 1.23 eV and 1.26 eV, respectively, at 10 K. After RTA at 300 °C for 2 min, the PL intensity of (311)B and (001) samples was enhanced by factors of ∼2.5 and 1.75, respectively. However, for the (001) and (311)B FA samples, an enhancement of the PL intensity by a factor of only 1.5 times could be achieved. The enhancement of PL intensity in annealed samples was interpreted in terms of PL activation energies, with a reduction in the alloy disorder and an increase in the Bi cluster.

BiGAnts: network-constrained biclustering of patients and multi-omics data

BiGAnts: network-constrained biclustering of patients and multi-omics data

Impact of a small change in growth temperature on the tail states of GaAsBi

The influence of growth temperature (Tsub) on the tail states of GaAs1−xBix (0 ≦ x ≦ 0.05) was studied via its sub-bandgap absorption and photoluminescence (PL) characteristics. The Urbach energy (E0) was estimated from the spectral response of the photocurrent of pin GaAs1−xBix photodiodes grown at a low Tsub of 360 °C and a high Tsub of 380 °C. The E0 of GaAs1−xBix is greater than that of GaAs. Once Bi atoms are incorporated, the tail states are formed probably due to Bi atom clustering. The E0 of the GaAs1−xBix sample at Tsub = 380 °C was smaller than the E0 of the sample grown at Tsub = 360 °C; therefore, the formation of the tail states was suppressed by a small increase in the Tsub of 20 °C. At a Tsub of 380 °C, the E0 decreases as the GaBi molar fraction increases. The increase in the Bi flux upon an increase in the GaBi molar fraction may enhance the surfactant effect of the Bi atoms, resulting in an enhancement in the migration of adsorbed atoms at Tsub = 380 °C and a reduction in the tail states. The full-width at half-maximum of the PL peak and the characteristic energy of the temperature dependence of the PL peak energy confirmed the same Tsub tendency of the tail states. The small increase in the Tsub of 20 °C suppressed the inhomogeneous incorporation of Bi atoms into GaAs1−xBix, such as an atomic-scale Bi clustering and the formation of tail states.

Direct observation of oxygen-vacancy formation and structural changes in Bi2WO6 nanoflakes induced by electron irradiation.

The prominent role of oxygen vacancies in the photocatalytic performance of bismuth tungsten oxides is well recognized, while the underlying formation mechanisms remain poorly understood. Here, we use the transmission electron microscopy to investigate the formation of oxygen vacancies and the structural evolution of Bi2WO6 under in situ electron irradiation. Our experimental results reveal that under 200 keV electron irradiation, the breaking of relatively weak Bi–O bonds leads to the formation of oxygen vacancies in Bi2WO6. With prolonged electron irradiation, the reduced Bi cations tend to form Bi clusters on the nanoflake surfaces, and the oxygen atoms are released from the nanoflakes, while the W–O networks reconstruct to form WO3. A possible mechanism that accounts for the observed processes of Bi cluster formation and oxygen release under energetic electron irradiation is also discussed.

Atomistic tight binding study of quantum confined Stark effect in GaBixAs1−x/GaAs quantum wells

Recently, there has been tremendous research interest in novel bismide semiconductor materials (such as GaBixAs1−x) for wavelength-engineered, low-loss optoelectronic devices. We report a study of the quantum confined Stark effect (QCSE) computed for GaBixAs1−x/GaAs quantum well (QW) structures based on large-scale atomistic tight-binding calculations. A comprehensive investigation of the QCSE as a function of the applied electric field orientations and the QW Bi fractions reveals unconventional character of the Stark shift at low Bi compositions (). This atypical QCSE is attributed to a strong confinement of the ground-state hole wave functions due to the presence of Bi clusters. At technologically-relevant large Bi fractions (10%), the impact of Bi clustering on the electronic structure is found to be weak, leading to a quadratic Stark shift of the ground-state transition wavelength, similar to previously observed in other conventional III–V materials. Our results provide useful insights for the understanding of the electric field dependence of the electronic and optical properties of GaBixAs1−x/GaAs QWs, and will be important for the design of devices in the optoelectronics and spintronics areas of research.