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Semiparametric analysis of two-level bivariate binary data.

In medical studies, paired binary responses are often observed for each study subject over timepoints or clusters. A primary interest is to investigate how the bivariate association and marginal univariate risks are affected by repeated measurements on each subject. To achieve this we propose a very general class of semiparametric bivariate binary models. The subject-specific effects involved in the bivariate log odds ratio and the univariate logit components are assumed to follow a nonparametric Dirichlet process (DP). We propose a hybrid method to draw model-based inferences. In the framework of the proposed hybrid method, estimation of parameters is done by implementing the Monte Carlo expectation-maximization algorithm. The proposed methodology is illustrated through a study on the effectiveness of tibolone for reducing menopausal problems experienced by Indian women. A simulation study is also conducted to evaluate the efficiency of the new methodology.

Algorithms↗

A PCR-based genetic map for human chromosome 3.

Oligonucleotide primers for 125 simple sequence repeat microsatellite-based genetic markers have been assayed by polymerase chain reaction (PCR) in the CEPH reference family panel. These microsatellites include 101 dinucleotide repeats as well as 24 new tetranucleotide repeats. The average heterozygosity of this marker set was 72.4%. Genetic data were analyzed with the genetic mapping package LINKAGE. A subset of these microsatellite markers define a set of 56 uniquely ordered loci (> 1000:1 against local inversion) that span 271 cM. Sixty-seven additional loci were tightly linked to markers on the uniquely ordered map, but could not be ordered with such high precision. These markers were positioned by CMAP into confidence intervals. One hundred thirteen of the microsatellite markers were also tested on a chromosome 3 framework somatic cell hybrid panel that divides this chromosome into 23 cytogenetically defined regions, integrating the genetic and physical maps of this chromosome. The high density, high heterozygosity, and PCR format of this genetically and physically mapped set of markers will accelerate the mapping and positional cloning of new chromosome 3 genes.

Animals↗

Whole-Genome Deep Learning Predicts Chemotherapy Response in Colorectal Cancer.

Chemotherapy response in colorectal cancer (CRC) exhibits significant heterogeneity, with current clinical predictors failing to capture complex genomic determinants of resistance. We developed a hybrid deep learning framework integrating convolutional neural networks (CNNs) and bidirectional long short-term memory (BiLSTM) networks to analyze whole-genome somatic mutations, evolutionary conservation, chromatin accessibility, and 3D genome architecture in 2,546 TCGA patients. An attention mechanism identified predictive genomic regions. The model achieved an AUC of 0.92 (95% CI: 0.89-0.94) in cross-validation and 0.88 (95% CI: 0.85-0.91) in independent validation, outperforming clinical models (&#x394;AUC = +0.18, p < 0.001). Key predictors included non-coding variants in TP53, KRAS, and PIK3CA regulatory regions. Triple-positive patients (mutations in all 3 regions) had significantly worse progression-free survival (HR = 4.7, p < 0.001). Our framework enables accurate chemotherapy response prediction and reveals novel non-coding resistance mechanisms, advancing precision oncology in CRC.

Humans↗

NMR studies of fully modified locked nucleic acid (LNA) hybrids: solution structure of an LNA:RNA hybrid and characterization of an LNA:DNA hybrid.

LNA is a bicyclic nucleic acid analogue that contains one or more 2'-O,4'-C methylene linkage(s), which effectively locks the furanose ring in a C3'-endo conformation. We report here the NMR solution structure of a nonamer LNA:RNA hybrid and a structural characterization of a nonamer LNA:DNA hybrid, where the LNA strands are composed entirely of LNA nucleotides. This is the first structural characterization of fully modified LNA oligonucleotides. The high-resolution structure reveals that the LNA:RNA hybrid adopts an almost canonical A-type duplex morphology. The helix axis is almost straight and the duplex geometry is regular. This shows that fully modified LNA oligomers can hybridize with complementary RNA and form duplexes within the Watson-Crick framework. The LNA:DNA hybrid structurally resembles an RNA:DNA hybrid as shown by determination of deoxyribose sugar puckers and analysis of NOESY NMR spectra.

DNA↗

Atmospheric mercury deposition to Lake Michigan during the Lake Michigan Mass Balance Study.

Wet and dry mercury (Hg) deposition were calculated to Lake Michigan using a hybrid receptor modeling framework. The model utilized mercury monitoring data collected during the Lake Michigan Mass Balance Study and the Atmospheric Exchange Over Lakes and Oceans Studytogether with high-resolution over-water meteorological date provided by the National Oceanic and Atmospheric Administration (July, 1994-October, 1995). Atmospheric deposition was determined to be the primary pathway for mercury inputto Lake Michigan, contributing approximately 84% of the estimated 1403 kg total annual input (atmospheric deposition + tributary input). Wet (10.6 microg m(-2)) and dry deposition (9.7 microg m(-2)) contributed almost equally to the annual atmospheric Hg deposition of 20.3 microg m(-2) (1173 kg). Re-emission of dissolved gaseous Hg from the lake was also significant (7.8 microg m(-2)), reducing the net atmospheric deposition to 12.5 microg m(-2) (720 kg). A strong urban influence was observed in the over-water mercury deposition estimates in the southern portion of the lake. The Chicago/Gary urban area was estimated to contribute approximately 20% (127 kg) of the annual atmospheric mercury deposition to Lake Michigan. The magnitude of local anthropogenic mercury sources in the Chicago/Gary urban area suggests that emission reductions could significantly reduce atmospheric mercury deposition into Lake Michigan.

Air Movements↗

NMR heteronuclear correlation between quadrupolar nuclei in solids.

We show for the first time that it is possible to acquire high-resolution heteronuclear NMR correlation experiments in solid state between second-order-broadened half integer quadrupolar nuclei (i.e., 27Al and 17O) using the scalar J-coupling. The sensitivity of the experiment is dramatically improved at high fields (gain proportional to the fourth power of the principal field) with a combination of signal enhancement techniques. This turns a challenging experiment into a real tool. We apply this experiment to characterize a calcium aluminate glass in which we prove the presence of tricluster mu3 oxygen sites and describe the signature of their directly bonded aluminum sites. Applications involve a large range of possible pairs of quadrupolar nuclei in different materials, such as glasses, porous or mesoporous framework materials, zeolites, hybrid organic-inorganic, and bioinvolved materials.

Crystallization↗

Six-fold coordinated carbon dioxide VI.

Under standard conditions, carbon dioxide (CO2) is a simple molecular gas and an important atmospheric constituent, whereas silicon dioxide (SiO2) is a covalent solid, and one of the fundamental minerals of the planet. The remarkable dissimilarity between these two group IV oxides is diminished at higher pressures and temperatures as CO2 transforms to a series of solid phases, from simple molecular to a fully covalent extended-solid V, structurally analogous to SiO2 tridymite. Here, we present the discovery of an extended-solid phase of CO2: a six-fold coordinated stishovite-like phase VI, obtained by isothermal compression of associated CO2-II (refs 1,2) above 50 GPa at 530-650 K. Together with the previously reported CO2-V (refs 3-5) and a-carbonia, this extended phase indicates a fundamental similarity between CO2 (a prototypical molecular solid) and SiO2 (one of Earth's fundamental building blocks). We present a phase diagram with a limited stability domain for molecular CO2-I, and suggest that the conversion to extended-network solids above 40-50 GPa occurs via intermediate phases II (refs 1,2), III (refs 7,8) and IV (refs 9,10). The crystal structure of phase VI suggests strong disorder along the c axis in stishovite-like P42/mnm, with carbon atoms manifesting an average six-fold coordination within the framework of sp3 hybridization.

Journal Article↗

The effective application of contingency theory in health settings: problems and recommended solutions.

Contingency theory as a managerial perspective is conceptually elegant, but it may cause a number of unforeseen problems when applied in real work settings. Health care administrators can avoid many of these problems by using a hybrid contingency theory framework that blends the manager's own perceptions and experience with established contingency models.

Health Facility Administrators↗

Toward a systems- and control-oriented agent framework.

This paper develops a systems- and control-oriented intelligent agent framework called the hybrid intelligent control agent (HICA), as well as its composition into specific kinds of multiagent systems. HICA is essentially developed around a hybrid control system core so that knowledge-based planning and coordination can be integrated with verified hybrid control primitives to achieve the coordinated control of multiple multimode dynamical systems. The scheme is applied to the control of teams of unmanned air and ground vehicles engaged in a pursuit-evasion war game. Results are demonstrated in simulation.

Algorithms↗

Cutting edges: deconstructive inquiry and the mission of the border ethnographer.

Research is an activity nursing 'cannot not want'. Such an imperative compels me to sketch out some theoretical borders of a hybrid postmodern methodological framework that I have called 'border' ethnography. It is a methodology suspended between a still authoritative modernity and an as yet only partially legitimate postmodernity. At one level this position is somewhat uncomfortably in a post-methodological terrain. The text that issues from such a tension-laden research space is, I argue, intensely autobiographical, inescapably ethnographic and inherently deconstructive. Ethno(autobio) graphy is a method 'on the run'; it destabilizes while it authorizes, it represents while it misrepresents, and it threatens to disintegrate as it comes into view. But, most importantly, it is the creature of a praxis-oriented endeavour not only to better understand a culture, but to actively intervene in its (re) production.

Anthropology, Cultural↗

V(H) gene family utilization in different B-cell lymphoma subgroups.

V(H) gene family specific polymerase chain reaction (PCR) amplification was performed in 87 B-cell lymphoma samples from 4 different subgroups. No apparent restriction in the VH gene usage was found in follicular lymphomas, lymphoplasmacytoid lymphomas or large B-cell lymphomas, whereas a biased VH1 utilization was shown in patients with chronic lymphocytic leukemia. Eleven of 18 chronic lymphocytic leukemia cases utilized the VH1 gene family, and nucleotide sequencing of the VH1 gene rearrangements revealed that a majority utilized the DP10 (51p1) germline gene, which has been reported to be strongly associated with autoimmune disease. No VH5 or VH6 rearrangements were amplified in the chronic lymphocytic leukemia subgroup, 2 gene families which previously have been found to be over-represented in these patients. In a high proportion (40%) of large B-cell lymphomas, VH gene family-specific PCR failed to amplify any rearrangement. Using primers hybridizing to the framework regions 2 and 3 and Southern blot analysis of the immunoglobulin heavy chain locus, clonal rearrangements were displayed in two-thirds of these PCR negative cases. However, the rearrangement status could not be elucidated in 5 of 35 patients with large B-cell lymphoma.

DNA Primers↗

Steroidal conjugates and their pharmacological applications.

Nature continues to be the main source of inspiration for synthetic chemists in their quest to make novel conjugates, which can have different physical, biological and medicinal properties. Nature makes these conjugates from mixed biosynthesis and some of these chimeras are found to exhibit unusual biological properties. During the past two decades design of such entities has been receiving increasing attention. Among the hybrid natural products, hybrids of steroid frameworks have attracted great attention due to the significant biological properties and numerous therapeutic effects of steroids. The developments made over the past few years in the isolation, design and synthesis of steroidal conjugates and their pharmacological applications are discussed in this review.

Amino Acids↗

Gene transfer directly demonstrates a role for TCR V alpha elements in superantigen recognition.

Recent structure-function studies of ours and others indicating that regions of the TCR other than V beta are involved in the TCR-superantigen (SAg)-MHC class II trimolecular interaction were correlative; thus, while the conclusions were persuasive, they were not unequivocal. The transfection experiments described in this report show that 1) responsiveness to staphylococcal enterotoxin B in V beta6 T cells was transferred by a V alpha4- but not by V alpha8- and V alpha10-containing alpha-chain cDNA constructs, 2) responsiveness was not transferred by a chimeric alpha-chain construct containing the N and J regions from a responsive T hybrid clone and the V alpha10 V alpha region from a nonresponsive clone, and 3) responsiveness was transferred by a chimeric alpha-chain construct in which most of the V alpha region (from the N terminus to the C-terminal end of the complementarity-determining region 2) was derived from the V alpha4 alpha-chain of a responsive T hybrid and the rest (framework 3, N, and J) from the V alpha8 alpha-chain of a nonresponsive T hybrid. Thus, these data provide the first direct evidence for a specific SAg response facilitating activity in a defined V alpha segment and map this activity N-terminal of framework region 3. Furthermore, the diversity in the alpha- and beta-chain junctional regions of a panel of staphylococcal enterotoxin B-responsive V beta6 T hybrid clones excludes a stringent corequirement for a particular junctional region for the V alpha4 segment to mediate its facilitating activity. Finally, a model postulating a universal role for V alpha elements in TCR recognition of SAg is presented.

Animals↗

Multiple myeloma clones are derived from a cell late in B lymphoid development.

We have previously demonstrated that the immunoglobulin (Ig) heavy chain variable region (VH) sequences expressed by the malignant clone in multiple myeloma (MM) contain a high degree of somatic mutation without clonal diversity. This sequence can be used to identify all members of the malignant clone in this B cell malignancy. We sequenced the variable regions expressed by patients with MM and generated primers from the complementarity determining region (CDR) sequences specific for each patient's tumor. Using these primers, we performed PCR amplification on highly purified subpopulations of cells separated by expression of CD10, CD34 and CD38. The results of these experiments demonstrate: 1) there is a small fraction of CD10-expressing tumor cells in MM patients, 2) CD34-bearing malignant cells do not exist in MM, and 3) although the vast amount of tumor is in the CD38-expressing cells, a small amount of tumor is in the CD38-negative population. We also used these primers to determine whether pre-class switch (i.e., Cmu-expressing lymphocytes) clonal cells exist in these patients. After PCR amplification with CDR1 and Cmu primers, colony hybridization was performed using both framework 3 (FR3) and CDR3 probes. Out of > 200 FR3-hybridizing colonies, < or = 5 colonies also hybridized with the CDR3 probe. Colonies which hybridized with both these probes were sequenced, and none of these sequences matched even closely the CDR3 expressed by the malignant clone. These results make the existence of a pre-class switch malignant cell unlikely in MM. Overall, these results suggest that the malignant clone in MM derives from a cell late in B lymphocyte development.

ADP-ribosyl Cyclase↗

Nanocluster with one missing core atom: a three-dimensional hybrid superlattice built from dual-sized supertetrahedral clusters.

In addition to having size-dependent properties, nanoclusters also behave like large pseudo-atoms and serve as building blocks for the construction of superlattices with properties that differ from either individual clusters or the bulk. While colloidal nanoparticles usually self-assemble into close-packed lattices, supertetrahedral clusters that are regular fragments of the zinc blende-type lattice can form covalent lattices with large pore size and high pore volume. Unfortunately, the size of the known supertetrahedral cluster is still small, and only a few types are currently known. In addition, their superlattices invariably consist of clusters of identical size. Here we report an open framework sulfide (denoted as UCR-15) that extends the cluster size from 20 metal ions in a T4 supertetrahedron to 34 metal ions in a novel T5 supertetrahedron with a missing core atom, [In34S54]6-. T5 clusters are joined by smaller T3 clusters (i.e., [In10S18]6-) to form an extended superlattice. UCR-15 is the first example of a covalent open framework built from supertetrahedral clusters of different sizes, thus revealing new possibilities in the construction of crystalline nanoporous semiconducting superlattices. It is proposed here that the formation of the dual-sized T3 and T5 hybrid framework is related to the host-guest charge density matching.

Journal Article↗

Hybrid molecular-continuum fluid models: implementation within a general coupling framework.

Over the past three years we have been developing a new approach for the modelling and simulation of complex fluids. This approach is based on a multiscale hybrid scheme, in which two or more contiguous subdomains are dynamically coupled together. One subdomain is described by molecular dynamics while the other is described by continuum fluid dynamics; such coupled models are of considerable importance for the study of fluid dynamics problems in which only a restricted aspect requires a fully molecular representation. Our model is representative of the generic set of coupled models whose algorithmic structure presents interesting opportunities for deployment on a range of architectures including computational grids. Here we describe the implementation of our HybridMD code within a coupling framework that facilitates flexible deployment on such architectures.

Computer Simulation↗

Syntheses, structures, and magnetic properties of inorganic-organic hybrid cobalt(II) phosphites containing bifunctional ligands.

Seven new cobalt(II) phosphites, [Co(HPO(3))(C(14)H(14)N(4))(H(2)O)(2)].2H(2)O (1), [Co(HPO(3))(C(22)H(18)N(4))].H(2)O (2), [Co(2)(HPO(3))(2)(C(22)H(18)N(4))(2)H(2)O].H(2)O (3), [Co(2)(HPO(3))(2)(C(12)H(10)N(4))(1.5)H(2)O].1.5H(2)O (4), [Co(HPO(3))(C(14)H(14)N(4))(0.5)].H(2)O (5), [Co(HPO(3))(C(18)H(16)N(4))(0.5)] (6), and [Co(HPO(3))(C(18)H(16)N(4))(0.5)] (7) were synthesized in the presence of 1,2-bis(imidazol-1-ylmethyl)benzene (L1), 1,4-bis(benzimidazol-1-ylmethyl)benzene (L2), 1,3-bis(benzimidazol-1-ylmethyl)benzene (L3), 1,4-bis(1-imidazolyl)benzene (L4), 1,4-bis(imidazol-1-ylmethyl)benzene (L5), 1,4-bis(imidazol-1-ylmethyl)naphthalene (L6), and 1,5-bis(imidazol-1-ylmethyl)naphthalene (L7), respectively, and their structures were determined by X-ray crystallography. Compound 1 is a molecular compound in which two cobalt(II) ions are held together by double mu-O linkages. The inorganic framework of compounds 2 and 3 are composed of vertex-shared CoO(2)N(2)/CoO(3)N(2) and HPO(3) polyhedra that form four rings; these are further linked by an organic ligand to generate 2D sheets. Compounds 4 and 5 both have 1D inorganic structures, with the bifunctional ligands connected to each side of the ladder by coordination bonds to give 2D hybrid sheets. A 3D organically pillared hybrid framework is observed in 6 and 7. In 6, the stacking of the interlayer pillars gives rise to a small hydrophobic channel that extends through the entire structure parallel to the sheets. The temperature-dependent magnetic susceptibility measurements of these compounds show weak interactions between the metal centers, mediated through the mu-O and/or O-P-O linkages.

Journal Article↗

Beyond parental lines: multi-omics analyses reveal epigenetic and transcriptional mechanisms underlying heterosis in Oryza sativa &#xd7; Oryza rufipogon hybrids.

Heterosis, or hybrid vigor, refers to the superior phenotypes of a hybrid compared with their parents and is widely exploited in agriculture. Interspecific hybrids within the Oryza genus demonstrate significant potential for the systematic improvement of rice varieties. Nevertheless, the mechanistic basis underlying heterosis in interspecific Oryza hybrids remains poorly understood. Here, we systematically performed phenotypic characterization, whole-genome bisulfite sequencing, RNA sequencing, and small RNA profiling using Oryza sativa L. ssp. japonica cv. Nipponbare (NIP), Oryza rufipogon Griff. acc. CWR, and their resulting F1 hybrid (named as NC). NIP and CWR showed distinct phenotypic and molecular differences. The interspecific hybrid, NC, exhibited significant yield heterosis. In the hybrid, most epigenetic and transcriptional features displayed additive inheritance patterns relative to parental lines. Analysis revealed that domestication-selected genes maintained relatively low DNA methylation coupled with high expression levels in both hybrid and parental lines. Additionally, we identified that non-additive miRNAs were potentially involved in regulating fertility, cell growth, and cell division processes in the hybrid. A significant negative correlation was observed between DNA methylation level and gene expression. Functional enrichment analysis revealed that hybrid-MPV DEGs were significantly associated with flowering time regulation, carbohydrate metabolism, photosynthesis, protein phosphorylation, seed development, and defense responses. Through weighted gene co-expression network analysis, we identified 102 functional gene modules, six of which were significantly associated with yield-related heterosis. Collectively, our results provide a multi-omics framework for understanding interspecific hybridization between elite cultivars and wild rice relatives, highlighting CWR as an untapped genetic reservoir for rice improvement.

Oryza↗