An Exploratory Study of the Inputs for Ensemble Clustering Technique as a Subset Selection Problem

Ensemble and Consensus Clustering address the problem of unifying multiple clustering results into a single output to best reflect the agreement of input methods. They can be used to obtain more stable and robust clustering results in comparison with a single clustering approach. In this study, we propose a novel subset selection method that looks at controlling the number of clustering inputs and datasets in an efficient way. The authors propose a number of manual selection and heuristic search techniques to perform the selection. Our investi‐ gation and experiments demonstrate very promising results. Using these techni‐ ques can ensure better selection methods and datasets for Ensemble and Consensus Clustering and thus more efficient clustering results

Status-dependent selection in the dimorphic beetle Onthophagus taurus.

The occurrence of alternative reproductive phenotypes is widespread in most animal taxa. The majority of known examples best fit the notion of alternative tactics within a conditional strategy where the fitness pay-offs depend on an individual's competitive ability or status. Individuals are proposed as "choosing" the tactic that maximizes their fitness, given their status relative to others in the population. Theoretically, status-dependent selection should determine when an animal should switch between alternative tactics. While a number of studies have demonstrated unequal fitness pay-offs associated with alternative tactics, none, to our knowledge, have examined the fitness functions necessary for predicting when individuals should switch between tactics. Here, we use a dimorphic male beetle in order to provide the first empirically derived fitness function across alternative reproductive phenotypes. Our data provide empirical support for a game-theoretic conditional strategy that has evolved under status-dependent selection

Development of Highly Sensitive Anti-Mouse HER2 Monoclonal Antibodies for Flow Cytometry

Overexpression of human epidermal growth factor receptor 2 (HER2) in breast cancer is an important target of monoclonal antibody (mAb) therapy such as trastuzumab. Due to the development of trastuzumab–deruxtecan, an antibody-drug conjugate, the targetable HER2-positive breast cancer patients have been expanded. To evaluate the developing modalities using anti-HER2 mAbs, reliable preclinical mouse models are required. Therefore, sensitive mAbs against mouse HER2 (mHER2) should be established. This study developed anti-mHER2 mAbs using the Cell-Based Immunization and Screening (CBIS) method. The established anti-mHER2 mAbs, H2Mab-300 (rat IgG2b, kappa) and H2Mab-304 (rat IgG1, kappa), reacted with mHER2-overexpressed Chinese hamster ovary-K1 (CHO/mHER2) and endogenously mHER2-expressed cell line, NMuMG (a mouse mammary gland epithelial cell) via flow cytometry. Furthermore, these mAbs never recognized mHER2-knockout NMuMG cells. The kinetic analysis using flow cytometry indicated that the dissociation constant (KD) values of H2Mab-300 and H2Mab-304 for CHO/mHER2 were 1.2 × 10−9 M and 1.7 × 10−9 M, respectively. The KD values of H2Mab-300 and H2Mab-304 for NMuMG were 4.9 × 10−10 M and 9.0 × 10−10 M, respectively. These results indicated that H2Mab-300 and H2Mab-304 could apply to the detection of mHER2 using flow cytometry and may be useful to obtain the proof of concept in preclinical studies

Development of a Novel Anti-CD44 Variant 8 Monoclonal Antibody C₄₄Mab-94 against Gastric Carcinomas

Gastric cancer (GC) is the third leading cause of cancer-related deaths worldwide. GC with peritoneal metastasis exhibits a poor prognosis due to the lack of effective therapy. A comprehensive analysis of malignant ascites identified the genomic alterations and significant amplifications of cancer driver genes, including CD44. CD44 and its splicing variants are overexpressed in tumors, and play crucial roles in the acquisition of invasiveness, stemness, and resistance to treatments. Therefore, the development of CD44-targeted monoclonal antibodies (mAbs) is important for GC diagnosis and therapy. In this study, we immunized mice with CD44v3–10-overexpressed PANC-1 cells and established several dozens of clones that produce anti-CD44v3–10 mAbs. One of the clones (C44Mab-94; IgG1, kappa) recognized the variant-8-encoded region and peptide, indicating that C44Mab-94 is a specific mAb for CD44v8. Furthermore, C44Mab-94 could recognize CHO/CD44v3–10 cells, oral squamous cell carcinoma cell line (HSC-3), or GC cell lines (MKN45 and NUGC-4) in flow cytometric analyses. C44Mab-94 could detect the exogenous CD44v3–10 and endogenous CD44v8 in western blotting and stained the formalin-fixed paraffin-embedded gastric cancer cells. These results indicate that C44Mab-94 is useful for detecting CD44v8 in a variety of experimental methods and is expected to become usefully applied to GC diagnosis and therapy

EMab-300 Detects Mouse Epidermal Growth Factor Receptor-Expressing Cancer Cell Lines in Flow Cytometry

Epidermal Growth Factor Receptor (EGFR) overexpression or its mutation mediates the sustaining proliferative signaling, which is an important hallmark of cancer. Human EGFR-targeting monoclonal antibody (mAb) therapy such as cetuximab has been approved for clinical use in patients with colorectal cancers and head and neck squamous cell carcinomas. A reliable preclinical mouse model is essential to further develop the mAb therapy against EGFR. Therefore, sensitive mAbs against mouse EGFR (mEGFR) should be established. In this study, we developed a specific and sensitive mAb for mEGFR using the Cell-Based Immunization and Screening (CBIS) method. The established anti-mEGFR mAb, EMab-300 (rat IgG1, kappa), reacted with mEGFR-overexpressed Chinese hamster ovary-K1 (CHO/mEGFR) and endogenously mEGFR-expressed cell lines, including NMuMG (a mouse mammary gland epithelial cell) and Lewis lung carcinoma cells, using flow cytometry. The kinetic analysis using flow cytometry indicated that the KD of EMab-300 for CHO/mEGFR and NMuMG was 4.3 × 10−8 M and 1.9 × 10−8 M, respectively. These results indicated that EMab-300 applies to the detection of mEGFR using flow cytometry and may be useful to obtain the proof of concept in preclinical studies

Transformation of Coiled α‑Helices into <i>Cross</i>-β-Sheets Superstructure

The fibrous silk produced by bees, wasps, ants, or hornets is known to form a four-strand α-helical coiled coil superstructure. We have succeeded in showing the formation of this coiled coil structure not only in natural fibers, but also in artificial films made of regenerated silk of the hornet <i>Vespa simillima xanthoptera</i> using wide- and small-angle X-ray scatterings and polarized Fourier transform infrared spectroscopy. On the basis of time-resolved simultaneous synchrotron X-ray scattering observations for in situ monitoring of the structural changes in regenerated silk material during tensile deformation, we have shown that the application of tensile force under appropriate conditions induces a transition from the coiled α-helices to a <i>cross</i>-β-sheet superstructure. The four-stranded tertiary superstructure remains unchanged during this process. It has also been shown that the amorphous protein chains in the regenerated silk material are transformed into conventional β-sheet arrangements with varying orientation

Local structures of isovalent and heterovalent dilute impurities in Si crystal probed by fluorescence x-ray absorption fine structure

Local structures of dilute isovalent and heterovalent impurity atoms in Si crystal (Si:X, X=Ga, Ge, As) have been studied by fluorescence x-ray absorption fine structure. The distortion of local lattice around the impurity atoms was evaluated from the Si-X bond length determined by extended x-ray absorption fine structure. The results demonstrate that the local lattice deformation is strongly dependent on the electronic configuration of impurity atoms, i.e., we find an anomalous expansion (0.09±0.01Å) along the [111] direction for donor (As) atoms but much smaller magnitude (0.03±0.01Å) for isovalent (Ge) atoms and acceptor (Ga) atoms. The results suggest that the local lattice distortions are strongly affected by the Coulomb interactions between the localized charge, which piles up to screen the ion core and the bond charge, and the ion-core repulsion. Absence of anomaly in case of negatively charged Ga atoms suggests that the former mechanism is a dominant factor for anomalous lattice expansion