BAPCP: A comprehensive and user-friendly web tool for identifying biomarkers from protein microarray technologies.

BACKGROUND AND OBJECTIVE: Proteome microarrays are one of the popular high-throughput screening methods for large-scale investigation of protein interactions in cells. These interactions can be measured on protein chips when coupled with fluorescence-labeled probes, helping indicate potential biomarkers or discover drugs. Several computational tools were developed to help analyze the protein chip results. However, existing tools fail to provide a user-friendly interface for biologists and present only one or two data analysis methods suitable for limited experimental designs, restricting the use cases. METHODS: In order to facilitate the biomarker examination using protein chips, we implemented a user-friendly and comprehensive web tool called BAPCP (Biomarker Analysis tool for Protein Chip Platforms) in this research to deal with diverse chip data distributions. RESULTS: BAPCP is well integrated with standard chip result files and includes 7 data normalization methods and 7 custom-designed quality control/differential analysis filters for biomarker extraction among experiment groups. Moreover, it can handle cost-efficient chip designs that repeat several blocks/samples within one single slide. Using experiments of the human coronavirus (HCoV) protein microarray and the E. coli proteome chip that helps study the immune response of Kawasaki disease as examples, we demonstrated that BAPCP can accelerate the time-consuming week-long manual biomarker identification process to merely 3 min. CONCLUSIONS: The developed BAPCP tool provides substantial analysis support for protein interaction studies and conforms to the necessity of expanding computer usage and exchanging information in bioscience and medicine. The web service of BAPCP is available at https://cosbi.ee.ncku.edu.tw/BAPCP/.

KDmarkers: A biomarker database for investigating epigenetic methylation and gene expression levels in Kawasaki disease.

Kawasaki disease (KD) is a form of acute systemic vasculitis that primarily affects children and has become the most common cause of acquired heart disease. While the etiopathogenesis of KD remains unknown, the diagnostic criteria of KD have been well established. Nevertheless, the diagnosis of KD is currently based on subjective clinical symptoms, and no molecular biomarker is yet available. We have previously performed and combined methylation array (Illumina HumanMethylation450 BeadChip) and transcriptome array (Affymetrix GeneChip Human Transcriptome Array 2.0) to identify genes that are differentially methylated/expressed in KD patients compared with control subjects. We have found that decreased methylation levels combined with elevated gene expression can indicate genes (e.g., toll-like receptors and CD177) involved in the disease mechanisms of KD. In this study, we constructed a database called KDmarkers to allow researchers to access these valuable potential KD biomarkers identified via methylation array and transcriptome array. KDmarkers provides three search modes. First, users can search genes differentially methylated and/or differentially expressed in KD patients compared with control subjects. Second, users can check the KD patient groups in which a given gene is differentially methylated and/or differentially expressed. Third, users can explore the DNA methylation levels and gene expression levels in all samples (KD patients and controls) for a particular gene of interest. We further demonstrated that the results in KDmarkers are strongly associated with KD immune responses. All analysis results can be downloaded for downstream experimental designs. KDmarkers is available online at https://cosbi.ee.ncku.edu.tw/KDmarkers/.

Self-assembled lanthanide-based helixes: synthetic control of the helical handedness by chirality of the ligand.

The control of the self-assembly of lanthanide helical chain and their helical handedness have been investigated for the first time. Δ- and Λ-form lanthanide chain complexes were obtained by introducing thiazolidine ligands that were synthesised from L- and D-cysteine, respectively, and shared the same formula: [Ln2(L)3(H2O)5]∞·3H2O (Ln: Sm and Eu) (L: 2-(2-hydroxy-3,5-dinitrophenyl)thiazolidine-4-carboxylic acid). The crystallographic, circular dichroism, and luminescence properties of these novel lanthanide chain complexes were studied.

Cancer DEIso: An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers.

Transcript isoforms regulated by alternative splicing can substantially impact carcinogenesis, leading to a need to obtain clues for both gene differential expression and malfunctions of isoform distributions in cancer studies. The Cancer Genome Atlas (TCGA) project was launched in 2008 to collect cancer-related genome mutation raw data from the population. While many repositories tried to add insights into the raw data in TCGA, no existing database provides both comprehensive gene-level and isoform-level cancer stage marker investigation and survival analysis. We constructed Cancer DEIso to facilitate in-depth analyses for both gene-level and isoform-level human cancer studies. Patient RNA-seq data, sample sheets, patient clinical data, and human genome datasets were collected and processed in Cancer DEIso. And four functions to search differentially expressed genes/isoforms between cancer stages were implemented: (i) Search potential gene/isoform markers for a specified cancer type and its two stages; (ii) Search potentially induced cancer types and stages for a gene/isoform; (iii) Expression survival analysis on a given gene/isoform for some cancer; (iv) Gene/isoform stage expression comparison visualization. As an example, we demonstrate that Cancer DEIso can indicate potential colorectal cancer isoform diagnostic markers that are not easily detected when only gene-level expressions are considered. Cancer DEIso is available at http://cosbi4.ee.ncku.edu.tw/DEIso/.

The TVGH-NYCU Thal-Classifier: Development of a Machine-Learning Classifier for Differentiating Thalassemia and Non-Thalassemia Patients.

Thalassemia and iron deficiency are the most common etiologies for microcytic anemia and there are indices discriminating both from common laboratory simple automatic counters. In this study a new classifier for discriminating thalassemia and non-thalassemia microcytic anemia was generated via combination of exciting indices with machine-learning techniques. A total of 350 Taiwanese adult patients whose anemia diagnosis, complete blood cell counts, and hemoglobin gene profiles were retrospectively reviewed. Thirteen prior established indices were applied to current cohort and the sensitivity, specificity, positive and negative predictive values were calculated. A support vector machine (SVM) with Monte-Carlo cross-validation procedure was adopted to generate the classifier. The performance of our classifier was compared with original indices by calculating the average classification error rate and area under the curve (AUC) for the sampled datasets. The performance of this SVM model showed average AUC of 0.76 and average error rate of 0.26, which surpassed all other indices. In conclusion, we developed a convenient tool for primary-care physicians when deferential diagnosis contains thalassemia for the Taiwanese adult population. This approach needs to be validated in other studies or bigger database.

Risk factor analysis of fragility fractures in rheumatoid arthritis: A 3-year longitudinal, real-world, observational, cohort study.

OBJECTIVES: To explore the risk factors for fragility fractures in rheumatoid arthritis (RA) patients using a 3-year longitudinal, observational cohort study. METHODS: This RA registry study included consecutive RA patients in the outpatient clinic of Chang Gung Memorial Hospital since September 1, 2014. The demographics, clinical characteristics, lifestyle, evidence of previous fracture, risk factors according to the Fracture Risk Assessment Tool (FRAX®), and the FRAX score of each participant were recorded. The participants were categorized into the new incident fracture (group A) and no incident fracture (group B) groups based on evidence or absence of new incident fractures and propensity score matching (age and gender, 1:2). RESULTS: Overall, 477 participants completed the 3-year observation period. After matching, 103 and 206 participants were allocated to groups A and B, respectively. The non-adjusted model revealed, presented as hazard ratio (HR) (95% confidence interval [CI]), that the presence of co-morbidity (1.80 [1.17-2.78], p = 0.008), Health Assessment Questionnaire Disability Index (1.35 [1.07-1.69], p = 0.010), lower baseline hip bone mineral density (0.11 [0.02-0.48], p = 0.004), longer disease duration (1.02 [1.00-1.04], p = 0.026), higher FRAX score of major fracture (1.03 [1.02-1.04], p<0.001) or hip fracture (1.03 [1.02-1.04], p<0.001), and previous fracture history (2.65 [1.79-3.94], p<0.001) were associated with new incident fracture. After adjustment, it was disclosed that a previous fracture is an independent risk factor for fragility fractures in RA patients (2.17 [1.20-3.90], p = 0.010). CONCLUSIONS: In addition to aging and disease-related factors, previous fracture history is the most important risk factor for fragility fractures in RA patients.

Heterocyclic-Additive-Activated Dinuclear Dysprosium Electrocatalysts for Heterogeneous Water Oxidation.

Heterogeneous catalysis based on air-stable lanthanide complexes is relatively rare, especially for electrochemical water oxidation and reduction. Therefore, it is highly desired to investigate the synergy caused by cocatalysts on the lanthanide complex family for heterogeneous catalysis because of their structural diversity, air/moisture insensitivity, and easy preparation under an air atmosphere. Two mononuclear and three dinuclear dysprosium complexes containing a series of Schiff-base ligands have been demonstrated as robust electrocatalysts for triggering heterogeneous water oxidation in alkaline solution, in which the complex [Dy2(hmb)2(OAc)4]·MeCN(3) was revealed to have the best activity toward heterogeneous water oxidation among all five complexes in the present study. The molecular activation of dysprosium complexes has also been investigated with a series of N-containing heterocyclic additives [i.e., 4-(dimethylamino)pyridine (DMAP), bis(triphenylphosphine)iminium chloride ([PPN]Cl), indole, and quinoline]. In particular, the corresponding overpotential was effectively enhanced by 211 mV (at a current density of 10 mA cm-2) with the assistance of DMAP. On the basis of electrochemical and ex situ/in situ spectroscopic investigations, the best catalyst, DMAP-complex 3 on a carbon paper electrode, was confirmed with well-maintained molecular identity during heterogeneous water oxidation free of forming any dysprosium oxide and/or undesired products.

Mononuclear and trinuclear DyIII SMMs with Schiff-base ligands modified by nitro-groups: first triangular complex with a N-N pathway.

Using two Schiff-base ligands containing an electron-withdrawing group (NO2), we obtained two mononuclear and two trinuclear complexes with the general formula [Dy(hni)(NO3)(DMF)2]·DMF (1·DMF), [Dy(hni)2(H2O)2]·NO3·EtOH (2·NO3·EtOH), [Dy3(hnc)3(DMF)6] (3) and [Gd3(hnc)3(DMF)6] (4) (H-hni: 2-(hydroxyl-3-methoxy-5-nitrophenyl)methylene(isonictino)hydrazine and H3-hnc: 1,5-bis(2-hydroxy-3-methoxy-5-nitrobenzylidene)carbonohydrazide). Four complexes were confirmed by infrared spectroscopy and single-crystal X-ray diffraction. The crystal structure of complex 3 reveals that the modified Schiff-base ligand provides two different tridentate coordination pockets (ONN and ONO) to encapsulate DyIII with a unique N-N pathway. The magnetic properties of all four complexes have been investigated using dc and ac susceptibility measurements. The frequency-dependent ac susceptibility is indicative of single-molecule magnetic behavior without and/or with an optimum dc field with a relaxation barrier Ueff = 34 K (400 Oe), 19 K (0 Oe) and 80 K (0 Oe) for complexes 1, 2 and 3, respectively.

A Dinuclear Dysprosium Complex as an Air-Stable and Recyclable Catalyst: Applications in the Deacetylation of Carbohydrate, Aliphatic, and Aromatic Molecules.

Two dinuclear DyIII complexes, [Dy2 (hmb)2 (OTf)2 (H2 O)4 ]⋅HOTf⋅2 THF (A⋅HOTf⋅2 THF) and [Dy2 (hmi)3 (H2 O)2 ]⋅2 HOTf (B⋅2 HOTf), have been synthesized by the reaction of Dy(OTf)3 and the Schiff-base ligands H2 hmb (N'-(2-hydroxy-3-methoxybenzylidene)benzohydrazide) or H2 hmi ((2-hydroxy-3-methoxyphenyl)methylene isonicotinohydrazine). Disarmed glycosyl trichloroacetimidates can be activated by complex A in the synthesis of 1,2-trans-glycosides with primary and secondary acceptors. This method offers an efficient route to selectively deacetylated monosaccharides and disaccharides in high yields and a green catalyst that can be easily recycled and reused.

Influence of Energy Barriers in Triangular Dysprosium Single-Molecule Magnets through Different Substitutions on a Nitrophenolate-Type Coligand.

The effect of the directions of the anisotropy axes on the energy barriers of single-molecule magnets (SMMs) was investigated. By introducing nitrophenolate (NP)-type coligands with different substitutions, the energy barrier was significantly changed. The structural and magnetic properties of three novel SMMs based on trinuclear {Dy3O5} phenoxo- and methoxyl-bridged triangular motifs were explored. All complexes share the formula [Dy3(Hhmb)4(µ3-OMe)2(OMe)(NP)][Dy3(Hhmb)4(µ3-OMe)2(NP)]·solvent·3Cl, where Hhmb = (2-hydroxy-3-methoxyphenyl)methylene(benzoicotino)hydrazine, secondary ligand NP = 2-nitrophenol (2-NP, complex 1), 2,4-dinitrophenol (2,4-DNP, complex 2), and 2,4,6-trinitrophenol (2,4,6-TNP, complex 3), and solvent = 2MeOH·2Et2O (1) and 4MeOH (2 and 3). Magnetic measurements for 1 and 2 revealed observable slow magnetic relaxation behavior with anisotropic energy barriers of 12.18 and 4.96 K, respectively, for SMMs and only the tail of the peaks in the out-of-phase susceptibility, χ″, was observed in complex 3. Comparing a series of NP coligands, we could easily study the correlation between the directions of the anisotropic axes and magnetic properties for this trinuclear SMM system.

[Ln16] complexes (Ln = GdIII, DyIII): molecular analogues of natural minerals such as hydrotalcite.

Two new hexadecanuclear lanthanide complexes employing the 1,5-bis(salicylidene)carbohydrazide (H2bsc) ligand are reported herein. These polynuclear aggregates crystallize in the R3[combining macron] space group, which is unprecedented in a family of lanthanide complexes with such high nuclearity. Magnetic susceptibility measurements reveal weak intramolecular interactions between the magnetic centres, and in the case of compound 2 (DyIII), single-molecule magnet properties are observed.

A propeller-shaped µ4-carbonate hexanuclear dysprosium complex with a high energetic barrier to magnetisation relaxation.

A Dy6 complex composed of two Dy3 triangular units, [Dy6(µ3-OH)(CO3)3(bsc)3(MeOH)14(H2O)](Cl)5·(H2O)·(MeOH)2 (1), was isolated and found to exhibit slow relaxation of the magnetisation under zero applied dc field, resulting in a high energetic barrier to relaxation.

Effect of the Mn Oxidation State on Single-Molecule-Magnet Properties: Mn(III) vs Mn(IV) in Biologically Inspired DyMn3O4 Cubanes.

Inspired by the ferromagnetic coupling in the cubane model CaMn(IV)3O4 of the oxygen-evolving complex of photosystem II, 3d-4f mixed-metal DyMn3O4 clusters were prepared for investigation of the magnetic properties. For comparison, YMn(IV)3O4 and YMn(IV)2Mn(III)O4 clusters were investigated as well and showed ferromagnetic interactions, like the calcium analogue. DyMn(IV)3O4 displays single-molecule-magnet properties, while the one-electron-reduced species (DyMn(IV)2Mn(III)O4) does not, despite the presence of a Mn(III) center with higher spin and single-ion anisotropy.

Slight synthetic changes eliciting different topologies: synthesis, structure and magnetic properties of novel dinuclear and nonanuclear dysprosium complexes.

Using the Schiff-base ligand 1,5-bis(2-hydroxy-3-methoxybenzylidene)carbonohydrazide (H2hmc), dinuclear and nonanuclear compounds, [Dy2(Hhmc)2(NO3)4]·THF·MeCN (1) and [Dy9(µ3-O)4(µ-OH)6(hmc)4(NO3)4(DMF)4](OH)·H2O·THF·DMF (2) are generated through the addition of different bases, respectively. Single-crystal X-ray diffraction analysis revealed a unique Dy9 core structure of complex 2, and the magnetic properties of both compounds are fully studied.

Direct Synthesis of Palladium Nanocrystals in Aqueous Solution with Systematic Shape Evolution.

Palladium octahedra, truncated octahedra, cuboctahedra, truncated cubes, and nanocubes with sizes of tens of nanometers have been synthesized in an aqueous mixture of H2PdCl4 solution, cetyltrimethylammonium chloride (CTAC) surfactant, KBr solution, dilute KI solution, and ascorbic acid solution at 35 °C for 30 min. By tuning the amount of dilute KBr solution introduced, particle shape control can be achieved. Adjusting the volumes of the Pd precursor and KBr solutions added, smaller and larger Pd nanocrystals were obtained with excellent shape control. Extensive structural and optical characterization of these nanocrystals has been performed. Two absorption bands in the ultraviolet region can be discerned for these Pd nanocrystals. Concave Pd cubes can also be prepared. Pd cubes were found to grow at a faster rate than that for the formation of octahedra. The concentrations of KBr and KI in the solution are so low that spectral shifts were not detected upon their addition to the solution. The Pd nanocrystals can readily be used for various applications after simple removal of surfactant.

Investigations of the effect of the non-manganese metal in heterometallic-oxido cluster models of the oxygen evolving complex of photosystem II: lanthanides as substitutes for calcium.

We report the syntheses and electrochemical properties of nine new clusters ([LLnMn(IV)3O4(OAc)3(DMF)n](+) (Ln = La(3+), Ce(3+), Nd(3+), Eu(3+), Gd(3+), Tb(3+), Dy(3+), Yb(3+), and Lu(3+), n = 2 or 3)) supported by a ligand (L(3-)) based on a 1,3,5-triarylbenzene motif appended with alkoxide and pyridine donors. All complexes were obtained by metal substitution of Ca(2+) with lanthanides upon treatment of previously reported LMn3CaO4(OAc)3(THF) with Ln(OTf)3. Structural characterization confirmed that the clusters contain the [LnMn3O4] cubane motif. The effect of the redox-inactive centers on the electronic properties of the Mn3O4 cores was investigated by cyclic voltammetry. A linear correlation between the redox potential of the cluster and the ionic radii or pKa of the lanthanide metal ion was observed. Chemical reduction of the LMn(IV)3GdO4(OAc)3(DMF)2 cluster with decamethylferrocene, resulted in the formation of LGdMn(IV)2Mn(III)O4(OAc)3(DMF)2, a rare example of mixed-valence [MMn3O4] cubane. The lanthanide-coordinated ligands can be substituted with other donors, including water, the biological substrate.

Toward models for the full oxygen-evolving complex of photosystem II by ligand coordination to lower the symmetry of the Mn3CaO4 cubane: demonstration that electronic effects facilitate binding of a fifth metal.

Synthetic model compounds have been targeted to benchmark and better understand the electronic structure, geometry, spectroscopy, and reactivity of the oxygen-evolving complex (OEC) of photosystem II, a low-symmetry Mn4CaOn cluster. Herein, low-symmetry Mn(IV)3GdO4 and Mn(IV)3CaO4 cubanes are synthesized in a rational, stepwise fashion through desymmetrization by ligand substitution, causing significant cubane distortions. As a result of increased electron richness and desymmetrization, a specific µ3-oxo moiety of the Mn3CaO4 unit becomes more basic allowing for selective protonation. Coordination of a fifth metal ion, Ag(+), to the same site gives a Mn3CaAgO4 cluster that models the topology of the OEC by displaying both a cubane motif and a "dangler" transition metal. The present synthetic strategy provides a rational roadmap for accessing more accurate models of the biological catalyst.

Facet-dependent optical properties of polyhedral Au-Cu2O core-shell nanocrystals.

We fabricated Au-Cu2O core-shell octahedra, cuboctahedra, and nanocubes having sizes of 90-220 nm using 50 nm octahedral cores. The smaller particle sizes minimize the strong light scattering features from the Cu2O shells and enable the surface plasmon resonance (SPR) absorption band of the gold cores to be clearly identified. Beyond a lower shell thickness limit, the SPR band positions of the gold cores are independent of the shell thickness, but are strongly dependent on the exposed particle surfaces. The plasmonic band red-shifts from Au-Cu2O octahedra to cuboctahedra and nanocubes, and differs by as much as 26 nm between the octahedra and the nanocubes. The same facet-dependent optical effects were observed using larger octahedral gold cores and cubic gold cores. In contrast, simulation spectra show progressively red-shifted SPR band positions with increasing shell thickness. The Cu2O shells are also found to exhibit facet-dependent optical behavior. These nanocrystals can respond to changes in the solvent environment such as solvents with different refractive indices, indicating that the plasmonic field of the gold cores can extend beyond the particle surfaces despite the presence of thick shells. Plane-selective spectral responses to low concentrations of surfactants were also recorded.

Nickel(I) monomers and dimers with cyclopentadienyl and indenyl ligands.

The reaction of (µ-Cl)2Ni2(NHC)2 (NHC = 1,3-bis(2,6-diisopropylphenyl)-1,3-dihydro-2H-imidazol-2-ylidene (IPr) or 1,3-bis(2,6-diisopropylphenyl)imidazolidin-2-ylidene (SIPr)) with either one equivalent of sodium cyclopentadienyl (NaCp) or lithium indenyl (LiInd) results in the formation of diamagnetic NHC supported Ni(I) dimers of the form (µ-Cp)(µ-Cl)Ni2(NHC)2 (NHC = IPr (1 a) or SIPr (1 b); Cp = C5H5) or (µ-Ind)(µ-Cl)Ni2(NHC)2 (NHC = IPr (2 a) or SIPr (2 b); Ind = C7H9), which contain bridging Cp and indenyl ligands. The corresponding reaction between two equivalents of NaCp or LiInd and (µ-Cl)2Ni2(NHC)2 (NHC = IPr or SIPr) generates unusual 17 valence electron Ni(I) monomers of the form (η(5)-Cp)Ni(NHC) (NHC = IPr (3 a) or SIPr (3 b)) or (η(5)-Ind)Ni(NHC) (NHC = IPr (4 a) or SIPr (4 b)), which have nonlinear geometries. A combination of DFT calculations and NBO analysis suggests that the Ni(I) monomers are more strongly stabilized by the Cp ligand than by the indenyl ligand, which is consistent with experimental results. These calculations also show that the monomers have a lone unpaired-single-electron in their valence shell, which is the reason for the nonlinear structures. At room temperature the Cp bridged dimer (µ-Cp)(µ-Cl)Ni2(NHC)2 undergoes homolytic cleavage of the Ni-Ni bond and is in equilibrium with (η(5)-Cp)Ni(NHC) and (µ-Cl)2Ni2(NHC)2. There is no evidence that this equilibrium occurs for (µ-Ind)(µ-Cl)Ni2(NHC)2. DFT calculations suggest that a thermally accessible triplet state facilitates the homolytic dissociation of the Cp bridged dimers, whereas for bridging indenyl species this excited triplet state is significantly higher in energy. In stoichiometric reactions, the Ni(I) monomers (η(5)-Cp)Ni(NHC) or (η(5)-Ind)Ni(NHC) undergo both oxidative and reductive processes with mild reagents. Furthermore, they are rare examples of active Ni(I) precatalysts for the Suzuki-Miyaura reaction. Complexes 1 a, 2 b, 3 a, 4 a and 4 b have been characterized by X-ray crystallography.

Speckle reduction in laser imaging applications using rotating magneto-optical disk.

Effective methods for speckle reduction are essential in improving the image quality of laser imaging applications. Accordingly, the present study proposes a novel technique for reducing the speckle contrast in laser imaging applications by means of the magneto-optic Kerr effect induced by a rotating magneto-optical (MO) disk. The performance of the proposed method is evaluated experimentally using a laboratory-built prototype model. The experimental results show that the rotating MO disk can reduce the speckle contrast of the captured image by 60% of the previous value. As a result, the proposed method yields an effective improvement in image quality. Overall, the proposed method provides a promising solution for improving the performance of a wide range of laser imaging applications.