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PubMed2005

A theoretical study on the structures and energetics of hypothetical TiM(NCN)3 compounds of the 3d transition metals.

Quasi-ternary cyanamides and carbodiimides of general formula AB(NCN)(3) with A not equal B have neither been predicted nor synthesized. Thus, hypothetical compounds of that kind containing 3d transition metals were considered (A = Ti, B = Mn, Fe, Co, Ni, Cu) by means of density-functional calculations on 34 structural models, most of which were derived from chemically related phases. After performing structure optimizations based on the local-density approximation, the relative energetic orderings are rationalized in terms of geometrical factors such as molar volumes and polyhedral connections. Total-energy generalized-gradient calculations evidence that the most stable models are enthalpically favored with respect to the elements. Even at ambient temperatures, the ternary phases are predicted as being thermodynamically stable in terms of their Gibbs free formation energies, especially if energetically competing and low-lying binaries (TiC, TiN) can be excluded by a kinetic reaction control. The best models are characterized by low-spin magnetic transition metals found in octahedral coordination, and the TiN(6) and MN(6) polyhedra either share faces or edges.

Carbodiimides↗

PubMed2006

Synthesis and spectroscopic studies of some transition metal complexes of a novel Schiff base ligands derived from 5-phenylazo-salicyladehyde and o-amino benzoic acid.

Cu(II), Mn(II), Ni(II), and Zn(II) metal complexes with novel heterocyclic Schiff base derived from 5-phenyl azo-salicyladehyde and o-amino benzoic acid have been synthesized and characterized on the basis of elemental analyses, electronic, IR, and (1)H NMR spectra, and also by aid of scanning electron microscopy (SEM), X-ray powder diffraction, molar ratio measurements, molar conductivity measurements, and thermogravimetric analyses. It has been found that the Schiff base behaves as neutral tridentate (ONO) ligand forming chelates with 1:1 (metal:ligand) stoichiometry.

Aldehydes↗

PubMed1997

A blood center communication plan and guideline for assisting hospitals with the implementation of the new international uniform bar code-labeling standard.

BACKGROUND: Transition to the International Society of Blood Transfusion (ISBT) bar code-labeling standard known as ISBT 128 is scheduled to begin July 1, 1997. Blood centers play a pivotal role in educating and assisting hospitals with the implementation of the new standard. A communication plan and hospital guidelines to facilitate the actual transition to ISBT 128 are integral parts of a blood center's comprehensive implementation strategy. STUDY DESIGN AND METHODS: In Phase 1, the blood center identified specific target groups within the hospitals and developed educational materials for them. A survey tool was used to identify unique hospital needs. Subsequent blood center newsletters and customer service forums included ISBT 128 updates. In Phase 2, guidelines to assist hospitals with the identification of critical elements, milestones, and target dates for the transition were developed with hospital staff input. RESULTS: Survey results on the change to ISBT 128 showed that many hospitals were unfamiliar with this change and its effects on operational issues. Various forums to disseminate information about ISBT 128 are needed to provide education and assistance to diverse groups within the hospital. CONCLUSION: A partnership approach between hospitals and the regional blood center should promote a successful transition from the current bar code symbology, American Blood Commission Codabar, to ISBT 128.

Blood Banks↗

PubMed2002

Specific interaction of the nonstructural protein NS1 of minute virus of mice (MVM) with [ACCA](2) motifs in the centre of the right-end MVM DNA palindrome induces hairpin-primed viral DNA replication.

The linear single-stranded DNA genome of minute virus of mice (MVM) is replicated via a double-stranded replicative form (RF) intermediate DNA. Amplification of viral RF DNA requires the structural transition of the right-end palindrome from a linear duplex into a double-hairpin structure, which serves for the repriming of unidirectional DNA synthesis. This conformational transition was found previously to be induced by the MVM nonstructural protein NS1. Elimination of the cognate NS1-binding sites, [ACCA](2), from the central region of the right-end palindrome next to the axis of symmetry was shown to markedly reduce the efficiency of hairpin-primed DNA replication, as measured in a reconstituted in vitro replication system. Thus, [ACCA](2) sequence motifs are essential as NS1-binding elements in the context of the structural transition of the right-end MVM palindrome.

Base Sequence↗

PubMed2004

Buffering of life histories against environmental stochasticity: accounting for a spurious correlation between the variabilities of vital rates and their contributions to fitness.

Life-history theory predicts vital rates that on average make large contributions to the annual multiplication rate of a lineage should be highly buffered against environmental variability. This prediction has been tested by looking for a negative correlation between the sensitivities (or elasticities) of the elements in a projection matrix and their variances (or coefficients of variation). Here, we show by constructing random matrices that a spurious negative correlation exists between the sensitivities and variances, and between the elasticities and coefficients of variation, of matrix elements. This spurious correlation arises in part because size transition probabilities, which are bounded by 0 and 1, have a limit to their variability that often does not apply to matrix elements representing reproduction. We advocate an alternative analysis based on the underlying vital rates (not the matrix elements) that accounts for the inherent limit to the variability of zero-to-one vital rates, corrects for sampling variation, and tests for a declining upper limit to variability as a vital rate's fitness contribution increases. Applying this analysis to demographic data from five populations of the alpine cushion plant Silene acaulis, we provide evidence of stronger buffering in the vital rates that most influence fitness.

Biological Evolution↗

PubMed2025

Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years.

Mobile genetic elements (MGEs), including plasmids, phages and genome islands, are major sources of bacterial genetic diversity. The small plasmid pT181 confers tetracycline resistance in bacterial pathogen Staphylococcus aureus via an efflux pump, TetK. pT181 was one of the earliest sequenced S. aureus plasmids, and has been isolated in both clinical and livestock-associated strains for decades, both as an independent replicon and integrated in the chromosome as part of staphylococcal cassette chromosome mec (SCCmec). Bacterial genome analysis tools and high-quality sequences with metadata are publicly available, but these resources remain underleveraged for examining historical data, especially when studying the spread of MGEs across a species and over time. Using publicly available reads and metadata, we explored the evolution of pT181 over almost seven decades of samples to identify temporal trends in sequence evolution, copy number changes, and spread across S. aureus and beyond. pT181 was prevalent across S. aureus (found in 9.5% of 83,366 genomes tested), with a conserved sequence outside of three hypervariable regions. The history of pT181 since 1954 is characterized by spread across strains, significant variation in plasmid copy number of the independent replicon, and increasing frequency of integration of the plasmid into the S. aureus chromosome. We have identified multiple chromosomal integration locations of the plasmid, including outside of the previously characterized SCCmec. We find that pT181 has been transferred across staphylococcaceae and into a Gram-negative species. The repeated integration of pT181 into the chromosome may indicate co-evolution of the plasmid and the host, potentially to facilitate increased antibiotic resistance.

Journal Article↗

PubMed2006

Complex behavior in driven unidirectionally coupled overdamped Duffing elements.

It is well known that overdamped unforced dynamical systems do not oscillate. However, well-designed coupling schemes, together with the appropriate choice of initial conditions, can induce oscillations (corresponding to transitions between the stable steady states of each nonlinear element) when a control parameter exceeds a threshold value. In recent publications [A. Bulsara, Phys. Rev. E 70, 036103 (2004); V. In, ibid. 72, 045104 (2005)], we demonstrated this behavior in a specific prototype system, a soft-potential mean-field description of the dynamics in a hysteretic "single-domain" ferromagnetic sample. These oscillations are now finding utility in the detection of very weak "target" magnetic signals, via their effect on the oscillation characteristics--e.g., the frequency and asymmetry of the oscillation wave forms. We explore the underlying dynamics of a related system, coupled bistable "standard quartic" dynamic elements; the system shows similarities to, but also significant differences from, our earlier work. dc as well as time-periodic target signals are considered; the latter are shown to induce complex oscillatory behavior in different regimes of the parameter space. In turn, this behavior can be harnessed to quantify the target signal.

Journal Article↗

PubMed1997

Spectral properties of the tubuloglomerular feedback system.

A simple mathematical model was used to investigate the spectral properties of the tubuloglomerular feedback (TGF) system. A perturbation, consisting of small-amplitude broad-band forcing, was applied to simulated thick ascending limb (TAL) flow, and the resulting spectral response of the TGF pathway was assessed by computing a power spectrum from resulting TGF-regulated TAL flow. Power spectra were computed for both open- and closed-feedback-loop cases. Open-feedback-loop power spectra are consistent with a mathematical analysis that predicts a nodal pattern in TAL frequency response, with nodes corresponding to frequencies where oscillatory flow has a TAL transit time that equals the steady-state fluid transit time. Closed-feedback-loop spectra are dominated by the open-loop spectral response, provided that gamma, the magnitude of feedback gain, is less than the critical value gamma c required for emergence of a sustained TGF-mediated oscillation. For gamma exceeding gamma c, closed-loop spectra have peaks corresponding to the fundamental frequency of the TGF-mediated oscillation and its harmonics. The harmonics, expressed in a nonsinusoidal waveform for tubular flow, are introduced by nonlinear elements of the TGF pathway, notably TAL transit time and the TGF response curve. The effect of transit time on the flow waveform leads to crests that are broader than troughs and to an asymmetry in the magnitudes of increasing and decreasing slopes. For feedback gain magnitude that is sufficiently large, the TGF response curve tends to give a square waveshape to the waveform. Published waveforms and power spectra of in vivo TGF oscillations have features consistent with the predictions of this analysis.

Feedback↗

PubMed2005

A quantitative reconstruction of the amide I contour in the IR spectra of globular proteins: from structure to spectrum.

The Amide I contours of six globular proteins of varied secondary structure content along with a peptide model for collagen and pulmonary surfactant protein C have been simulated very closely by using a modified GF matrix method. The starting point for the method uses the three-dimensional structure as obtained from the Protein Data Bank. Elements of the interactions between peptide groups (e.g., transition dipole coupling) are very sensitive to tertiary structure, thus the current formalism demonstrates that the Amide I contour may be useful for a more detailed probe of 3-D conformation that goes beyond the traditional use of this band to probe the percentages of particular elements of secondary structure. For example, postulated changes to a known structure can be tested by comparing the new simulated band to the experimental band. A number of refinements to the transition dipole interaction calculation have been made. Most of the important interactions between the C=O oscillators that define the Amide I mode appear to have been identified, including through space transition dipole coupling, through valence bond and through hydrogen bond coupling. The eigenvector matrix produced by the method permits the contribution of each peptide group to the spectrum to be precisely determined. Analysis of the results shows that the often-used structure-frequency correlations are at best approximate and at worst misleading. The subbands from helices, sheets, turns, and loops are much broader and more overlapped than has been commonly assumed. Furthermore, the traditional alpha-helical marker band may be substantially distorted in short segments. Difference spectra based on isotope editing, a technique thought capable of revealing the spectral contributions of individual peptide groups, are shown to be prone to misinterpretation.

Amides↗

PubMed2000

A closer view of the conformation of the Lac repressor bound to operator.

Crystal structures of the Lac repressor, with and without isopropyithiogalactoside (IPTG), and the repressor bound to operator have provided a model for how the binding of the inducer reduces the affinity of the repressor for the operator. However, because of the low resolution of the operator-bound structure (4.8 A), the model for the allosteric transition was presented in terms of structural elements rather than in terms of side chain interactions. Here we have constructed a dimeric Lac repressor and determined its structure at 2.6 A resolution in complex with a symmetric operator and the anti-inducer orthonitrophenylfucoside (ONPF). The structure enables the induced (IPTG-bound) and repressed (operator-bound) conformations of the repressor to be compared in atomic detail. An extensive network of interactions between the DNA-binding and core domains of the repressor suggests a possible mechanism for the allosteric transition.

Allosteric Regulation↗

PubMed2003

Primary heterologous carcinosarcoma of the ureter with necrotic malignant polyps. Report of a case and review of the literature.

Carcinosarcoma is a rare and aggressive disease characterized by biphasic neoplasms with distinct mesenchymal and epithelial components. We report a case of ureteral carcinosarcoma with malignant necrotic polyps. The patient was a 58-year-old woman with painless hematuria, who was later diagnosed as having ureteral carcinosarcoma. Three long pendulous polypoid-shape tumors consisting of high-grade transitional cell carcinoma with chondrosarcomatous and osteosarcomatous elements were found. Two months after nephroureterectomy, the tumor relapsed in the bladder. Despite anterior exenteration, the patient died of local recurrence 6 months after her initial visit. To our knowledge, only 10 cases of this disease have been reported in the literature.

Carcinoma, Transitional Cell↗

PubMed2000

Exploratory synthesis in the solid state. Endless wonders.

This article gives an overview of recent developments in three areas of solid state chemistry: (1) The discovery that centered and originally-adventitious interstitial elements Z are essential for the stability of M6X12-type cluster halides of group 3 and 4 metals has led to a large amount of new chemistry through tuning structures and compositions of AnM6(Z)X12Xn phases with the variables Z, x, and n. The corresponding metal-rich group 3 tellurides exhibit novel and more extensive metal aggregation, reflecting a decreased number of anions and valence electrons. (2) Many intrinsically metallic T5M3 phases with a Mn5Si3-type structure are formed by early transition metals T with main-group elements M. Each characteristically reacts with diverse elements (up to 15-20 each) to form stuffed interstitial versions T5M3Z of the same structure. The ranges of Z and some properties are described. Related reactions of hydrogen (often as an impurity) in Mn5Si3-, beta-Yb5Sb3-, and Cr5B3-type systems are extensive. Substantially all previous reports of beta-Yb5Sb3- and Cr5B3-type phases for divalent metals with pnictogen (As-Bi) and tetrel (Si-Pb) elements, respectively, have been for the hydrides, and about two-thirds do not exist without that hydrogen (or fluorine). (3) The developing chemistry of anionic polymetal cluster compounds of the main-group elements with alkali-metal cations is outlined, particularly for the triel elements In and Tl. These clusters lie to the left of what has been called the Zintl boundary, many are new hypoelectronic polyhedra, some may be centered by the same or another neighboring element, and so far all have been isolated only as neat solid state compounds in which specificity of cation-anion interactions seems important. Extended networks are also encountered.

Journal Article↗

PubMed2005

Structural transition in bidispersed electrorheological fluids.

We present results from finite element calculations on electrorheological fluids consisting of bidispersed dielectric microspheres and nanoparticles suspended in liquid, with one type much smaller than the other. The face-centered-cubic (fcc) structure of the larger microspheres is shown to be the ground state when the volume concentration of the nanoparticles is between 3-5 %. This is in contrast to the usual situation in which the body-centered-tetragonal (bct) structure is the lowest-energy state. As a function of the nanoparticles' concentration, the bct-fcc structural transition occurs when the nanoparticles' dielectric constant exceeds a threshold value, leading to the electrostatic energy curves of the two structures crossing each other.

Journal Article↗

PubMed2006

Synthesis and spectroscopic studies of mixed-ligand and polymeric dinuclear transition metal complexes with bis-acylhydrazone tetradentate ligands and 1,10-phenanthroline.

Two types of dinuclear copper(II) and nickel(II) complexes with two tetradentate N2O2 donor ligands 1,4-bis(1-anthranoylhydrazonoethyl)benzene (L1), 1,4-bis(1-salicyloylhydrazonoethyl)benzene (L2) and N,N'-bidentate heterocyclic base [1,10-phenonthroline (phen)] have been synthesized and characterized by elemental analysis, infrared spectra, UV-vis electronic absorption spectra and magnetic susceptibility measurements. The reaction of metal(II) acetates with the solution containing ligand and 1,10-phenonthroline in methanol gives mixed-ligand dinuclear metal(II) complexes with general formula [M2L(phen)2]Cl2 (L=L1 or L2), whereas, the ligands react with metal(II) acetates to form polymeric dinuclear complexes with general formula [(M2L2)n] (L=L1 or L2). In the complexes, the ligands act as dianionic tetradentate and coordination takes place in the enol tautomeric form with the enolic oxygen and azomethine nitrogen atoms while the phenolic hydroxyl and amino groups of aroylhydrazone moiety do not participate in coordination. The effect of varying pH and solvent on the absorption behavior of both ligands and complexes has been investigated.

Hydrazones↗

PubMedDate not supplied

[Study of esophageal transit with radioisotopes in the diagnosis of achalasia].

The investigations employed in the diagnosis of oesophageal achalasia have been assessed critically. Although electromanometry contributes most to diagnosis and pinpoints with absolute precision the physiopathological elements that characterise the disease, radioisotopic study of oesophageal transit is an important diagnostic aid. More readily than any other, this technique permits morphofunctional evaluation in selected patients; it also represents the most physiological investigation and the best tolerated and, second only to manometry, the most reliable. Oesophagography with baritate meal and oesophagoscopy also play a diagnostic role in oesophageal achalasia. The former makes it possible to document the cardial stop and the presence or otherwise of mega-oesophagus, the second excludes the presence of organic dysphagias and also has a therapeutic use because cycles of dilatation of the oesophago-cardial junction can be carried out.

Esophageal Achalasia↗

PubMed2006

The inherent structure landscape of a protein.

Using the Gō model of a real protein, we explore the landscape of its metastable structures. First, we show how the inherent structure energy density can be obtained from the probability density determined by sampling molecular dynamics trajectories and quenching. The analysis of the inherent structure landscape can characterize the folding transition. Then we show how thermodynamics of the inherent states can be established to study the equilibrium properties of proteins. Our work brings some elements into the current discussion about the protein dynamical transition. The study uses a simplified model to illustrate the ideas, but, as the inherent structure landscape is much simpler than the free energy surface of the protein, it appears to be accessible for an all-atom model of a small protein, at the expense of much longer calculations.

Protein Conformation↗

PubMed1988

Cell-cycle regulation of a human histone H2b gene is mediated by the H2b subtype-specific consensus element.

Mammalian histone gene transcription is increased approximately fivefold during the transition from the G1 phase to the S phase of the cell cycle. In this study, we present a detailed in vivo analysis of the human histone H2b promoter, which establishes that transcriptional regulation of this gene is mediated by a subtype-specific consensus element containing the core octanucleotide ATTTGCAT. Our results demonstrate that the activity of this sequence is specific for S phase. Comparative analysis of different replication variant mammalian histone gene promoters and our knowledge of the transcription factors interacting with the human histone H2b and H4 promoters allow us to conclude that coordinate regulation of histone gene transcription in higher eukaryotes is mediated by distinct factors. We propose a simple model for transcriptional regulation of mammalian histone gene expression, which incorporates both the distinct features of the individual histone gene promoters and the apparent functional equivalence of the specific sequence elements regulating transcription of each histone gene subtype.

Aphidicolin↗

PubMed2005

Structural and thermal characterization of ternary complexes of piroxicam and alanine with transition metals: uranyl binary and ternary complexes of piroxicam. Spectroscopic characterization and properties of metal complexes.

Ternary Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and UO2(II) complexes with piroxicam (Pir) drug (H2L1) and dl-alanine (Ala) (HL2) and also the binary UO2(II) complex with Pir were studied. The structures of the complexes were elucidated using elemental, IR, molar conductance, magnetic moment, diffused reflectance and thermal analyses. The UO2(II) binary complex was isolated in 1:2 ratio with the formula [UO2(H2L)2](NO3)2. The ternary complexes were isolated in 1:1:1 (M:H2L1:L2) ratios. The solid complexes were isolated in the general formulae [M(H2L)(L2)(Cl)n(H2O)m].yH2O (M=Fe(III) (n=2, m=0, y=1), Co(II) (n=1, m=1, y=2) and Ni(II) (n=1, m=1, y=0)); [M(H2L)(L2)](X)z.yH2O (M=Cu(II) (X=AcO, z=1, y=0), Zn(II) (X=AcO, z=1, y=3) and UO2(II) (X=NO3, z=1, y=2)). Pir behaves as a neutral bidentate ligand coordinated to the metal ions via the pyridine-N and carbonyl-O groups, while Ala behaves as a uninegatively bidentate ligand coordinated to the metal ions via the deprotonated carboxylate-O and amino-N. The magnetic and reflectance spectral data show that the complexes have octahedral geometry except Cu(II) and Zn(II) complexes have tetrahedral structures. The thermal decomposition of the complexes was discussed in relation to structure, and the thermodynamic parameters of the decomposition stages were evaluated.

Alanine↗