Phase-field lattice kinetic scheme for the numerical simulation of dendritic growth

A phase-field lattice kinetic model is presented for the numerical simulation of the dendritic growth of a pure crystal in the presence of thermal transport. A finite-difference scheme for the phase field is combined with an explicit lattice kinetic scheme for the temperature field. The resulting scheme is advanced in time with an adaptive time-marching procedure which permits us to achieve long simulation times with larger time steps than explicit finite-difference and previous kinetic methods. The method is demonstrated for the case of dendritic growth of a single crystal over a wide range of Stefan and capillarity numbers.

Risk of silicosis in cohorts of Chinese tin and tungsten miners and pottery workers (II): Workplace-specific silica particle surface composition

BACKGROUND

It is hypothesized that surface occlusion by alumino-silicate affects the toxic activity of silica particles in respirable dust. In conjunction with an epidemiological investigation of silicosis disease risk in Chinese tin and tungsten mine and pottery workplaces, we analyzed respirable silica dusts using a multiple-voltage scanning electron microscopy-energy dispersive X-ray spectroscopy (MVSEM-EDS).

METHODS

Forty-seven samples of respirable sized dust were collected on filters from 13 worksites and were analyzed by MVSEM-EDS using high (20 keV) and low (5 keV) electron beam accelerating voltages. Changes in the silicon-to-aluminum X-ray line intensity ratio between the two voltages are compared particle-by-particle with the 90th percentile value of the same measurements for a ground glass homogeneous control sample. This provides an index that distinguishes a silica particle that is homogeneously aluminum-contaminated from a clay-coated silica particle.

RESULTS

The average sample percentages of respirable-sized silica particles alumino-silicate occlusion were: 45% for potteries, 18% for tin mines, and 13% for tungsten mines. The difference between the pottery and the metal mine worksites accounted for one third of an overall chi-square statistic for differences in change in measured silicon fraction between the samples.

CONCLUSION

The companion epidemiological study found lower silicosis risk per unit cumulative respirable silica dust exposure for pottery workers compared to metal miners. Using these surface analysis results resolves differences in risk when exposure is normalized to cumulative respirable surface-available silica dust.

Comparative analyses of multi-species sequences from targeted genomic regions

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.

Randomized clinical trial of ganciclovir vs acyclovir for prevention of cytomegalovirus antigenemia after allogeneic transplantation

Cytomegalovirus (CMV) disease remains a major cause of morbidity following allogeneic stem cell transplantation (SCT). In a prospective randomized trial, we tested prophylactic therapy with ganciclovir or acyclovir for patients at high risk of disease. Ninety-one CMV seropositive recipients of related (n = 53) and unrelated (n = 38) donor transplants were enrolled. All patients received intravenous (i.v.) ganciclovir 5 mg/kg every 12 h days -7 to -2, followed by acyclovir 10 mg/kg i.v. every 8 h from day -1 until neutrophil engraftment. Patients were then randomly assigned to either ganciclovir (n = 45) or acyclovir (n = 46) until day 100 post transplant. Any degree of antigenemia was treated with ganciclovir 5 mg/kg i.v. twice a day for 2 weeks, followed by 5 mg/kg i.v. each weekday for 6 weeks. At day 100, the cumulative incidence of antigenemia was 31% (95% CI 17-45%) for ganciclovir and 41% (95% CI 26-56%) (P = 0.22) for acyclovir prophylaxis, respectively. The assigned prophylaxis cohort did not predict for CMV antigenemia. The cumulative incidence of CMV disease at 12 months was 13% (95% CI 3-23%) and 17% (95% CI 6-28%) (P = 0.59) for the ganciclovir- and acyclovir-treated groups, respectively. An absolute neutrophil count (ANC) <or=1500 x 10(6)/l at randomization (P < 0.01) and grade II-IV acute graft-versus-host-disease (P = 0.01), but not the assigned prophylaxis cohort (P = 0.62), were independent risk factors for CMV disease. The incidence of fungal infections and renal insufficiency was similar across treatment groups; however, bacterial infections and secondary neutropenia occurred more frequently in the ganciclovir group. With our study powered to detect a 60% reduction in antigenemia with ganciclovir prophylaxis, we did not find a statistically significant difference between ganciclovir and acyclovir when used as part of an overall strategy for prevention of CMV antigenemia and disease in SCT, although fewer side-effects occurred with acyclovir treatment.

Scoring pairwise genomic sequence alignments

The parameters by which alignments are scored can strongly affect sensitivity and specificity of alignment procedures. While appropriate parameter choices are well understood for protein alignments, much less is known for genomic DNA sequences. We describe a straightforward approach to scoring nucleotide substitutions in genomic sequence alignments, especially human-mouse comparisons. Scores are obtained from relative frequencies of aligned nucleotides observed in alignments of non-coding, non-repetitive genomic regions, and can be theoretically motivated through substitution models. Additional accuracy can be attained by down-weighting alignments characterized by low compositional complexity. We also describe an evaluation protocol that is relevant when alignments are intended to identify all and only the orthologous positions. One particular scoring matrix, called HOXD70, has proven to be generally effective for human-mouse comparisons, and has been used by the PipMaker server since July, 2000. We discuss but leave open the problem of effectively scoring regions of strongly biased nucleotide composition, such as low G + C content.

Heat shock protein expression in cerebral vessels after subarachnoid hemorrhage

OBJECTIVE

The mechanisms of cerebral vasospasm after subarachnoid hemorrhage (SAH) remain controversial. Recent data have implicated two small heat shock proteins (HSPs), namely HSP20 and HSP27, in the regulation of vascular tone. Increases in the phosphorylation of HSP20 are associated with vasorelaxation, and increases in the phosphorylation of HSP27 are associated with impaired vasorelaxation. Therefore, we hypothesized that alterations in the expression and/or phosphorylation of these two small HSPs might play a role in cerebral vasospasm after SAH.

METHODS

A rat model of endovascular perforation was used to induce SAH. Middle cerebral arteries were harvested from control animals, sham-treated animals, and animals with SAH, 48 hours after SAH induction. Dose-response curves for endothelium-independent (sodium nitroprusside, 10(-8) to 10(-4) mol/L) and endothelium-dependent (bradykinin, 10(-10) to 10(-5) mol/L) relaxing agents were recorded ex vivo. Physiological responses were correlated with the expression and phosphorylation of HSP20 and HSP27 by using one- and two-dimensional immunoblots.

RESULTS

There was impaired endothelium-independent and endothelium-dependent relaxation in cerebral vessels after SAH. These changes were associated with decreased expression of both total and phosphorylated HSP20 and increases in the amount of phosphorylated HSP27.

CONCLUSION

In this model, impaired relaxation of cerebral vessels after SAH was associated with increases in the amount of phosphorylated HSP27 and decreases in the expression and phosphorylation of HSP20. These data are consistent with alterations in the expression and phosphorylation of these small HSPs in other models of vasospasm.

Discovery of the first non-peptide antagonist of the motilin receptor

A first-in-class non-peptide antagonist of the motilin receptor was identified through electronic screening of our corporate database against a 3D pharmacophore. The pharmacophore was developed from the motilin 22 residue endogenous peptide using NMR structural data, principles of peptide folding, and peptide structure activity relationships. The NMR data supported helical content within the peptide, and both the hydrophobic staple and N-capping box motifs were identified in the motilin sequence. The conformational features of these motifs were imposed on the peptide structure, providing a constrained conformer as a starting point for database searching. A trisubstituted cyclopentene lead was identified directly from the electronic search. Compounds in this series inhibit the binding of 125I-motilin to human antral smooth muscle membrane and antagonize motilin-induced intracellular calcium mobilization in cells expressing the human motilin receptor. A potent compound developed through optimization, RWJ 68023, is active in binding and cell-based functional assays and is also effective in inhibiting motilin-induced contractility in segments of rabbit duodenum. This orally active compound is currently undergoing clinical evaluation for the treatment of gastrointestinal disorders associated with altered motility.

Association between divergence and interspersed repeats in mammalian noncoding genomic DNA

The amount of noncoding genomic DNA sequence that aligns between human and mouse varies substantially in different regions of their genomes, and the amount of repetitive DNA also varies. In this report, we show that divergence in noncoding nonrepetitive DNA is strongly correlated with the amount of repetitive DNA in a region. We investigated aligned DNA in four large genomic regions with finished human sequence and almost or completely finished mouse sequence. These regions, totaling 5.89 Mb of DNA, are on different chromosomes and vary in their base composition. An analysis based on sliding windows of 10 kb shows that the fraction of aligned noncoding nonrepetitive DNA and the fraction of repetitive DNA are negatively correlated, both at the level of an entire region and locally within it. This conclusion is strongly supported by a randomization study, in which repetitive elements are removed and randomly relocated along the sequences. Thus, regions of noncoding genomic DNA that accumulated fewer point mutations since the primate-rodent divergence also suffered fewer retrotransposition events. These results indicate that some regions of the genome are more "flexible" over the time scale of mammalian evolution, being able to accommodate many point mutations and insertions, whereas other regions are more "rigid" and accumulate fewer changes. Stronger conservation is generally interpreted as indicating more extensive or more important function. The evidence presented here of correlated variation in the rates of different evolutionary processes across noncoding DNA must be considered in assessing such conservation for evidence of selection.

Inhibition of CMP-sialic acid transport into Golgi vesicles by nucleoside monophosphates

We examined the interactions of nucleotides with the CMP-sialic acid transporter in order to better understand which features play a role in binding and to investigate the relationship between binding and subsequent transport. With respect to the sugar, the transporter requires a complete ribose ring for tight binding, and the 2'-ara hydrogen makes an important contact. The enzyme exhibits little specificity with respect to the 2'- and 3'-hydroxyls, as it tolerated substitutions ranging from fluorine to an azido group. In the base, the C4 amine and C2 carbonyl groups make important contacts, while the N3 nitrogen does not. However, adding a methyl group to N3 dramatically reduced binding, indicating that mass at this position sterically hinders binding. Adding a group at C5 had either no effect or slightly enhanced binding. To determine if the transporter recognizes these CMP analogues as substrates, we assayed them for their ability to trans stimulate CMP-sialic acid import. These data suggest that the enzyme transports a wide variety of NMPs, and the rate of transport is inversely proportional to the K(I) of the analogue. The importance of our findings for understanding the specificities of the different nucleotide-sugar tranlocators and the design of novel glycosylation inhibitors are discussed.

Complete genome sequence of Salmonella enterica serovar Typhimurium LT2

Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of non-typhoid salmonellosis is increasing worldwide, causing millions of infections and many deaths in the human population each year. Here we sequenced the 4,857-kilobase (kb) chromosome and 94-kb virulence plasmid of S. typhimurium strain LT2. The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria, sample sequencing of both S. enterica serovar Paratyphi A (S. paratyphi A) and Klebsiella pneumoniae, and hybridization of three unsequenced genomes to a microarray of S. typhimurium LT2 genes. Lateral transfer of genes is frequent, with 11% of the S. typhimurium LT2 genes missing from S. enterica serovar Typhi (S. typhi), and 29% missing from Escherichia coli K12. The 352 gene homologues of S. typhimurium LT2 confined to subspecies I of S. enterica-containing most mammalian and bird pathogens-are useful for studies of epidemiology, host specificity and pathogenesis. Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets.

Promising strategies help employers integrate pharmacy and medical programs--and reap cost, quality advantages

Providing quality pharmacy benefits while managing costs is an escalating challenge for employers. Easy solutions such as higher copays and standard three-tier systems will not provide effective, long-lasting results that include improved clinical outcomes. Employers must concentrate on educating employees on the real cost and value of their pharmacy benefits and they must also take an integrated view of medical and pharmacy benefits.

Early-phase adaptations of traditional-speed vs. superslow resistance training on strength and aerobic capacity in sedentary individuals

We performed a randomized exercise training study to assess the effects of traditional Nautilus-style (TR) or superslow (SS) strength training on muscular strength, body composition, aerobic capacity, and cardiovascular endurance. Subjects were 14 healthy, sedentary women, 19-45 years of age (mean +/- SD age, 32.7 +/- 8.9 years), randomized to either the SS or TR training protocols and trained 3 times per week for 10 weeks. Measurements were taken both before and after training, which included a maximal incremental exercise test on a cycle ergometer, body composition, and 1 repetition maximum (1RM) tests on 8 Nautilus machines. Both groups increased their strength significantly on all 8 exercises, whereas the TR group increased significantly more than the SS group on bench press (34% vs. 11%), torso arm (anterior lateral pull-down) (27% vs. 12%), leg press (33% vs. 7%), leg extension (56% vs. 24%), and leg curl (40% vs. 15%). Thus, the TR group's improvement in total exercise weight lifted was significantly greater than that of the SS group after testing (39% vs. 15%). Exercise duration on the cycle ergometer and work rate significantly improved for both groups, but there was no group-by-training interaction. No significant differences were found for body composition or additional aerobic variables measured. Both strength training protocols produced a significant improvement in strength during a 10-week training period, but the TR protocol produced better gains in the absence of changes in percentage of body fat, body mass index, lean body mass, and body weight. In addition, strength training alone did not improve Vo2max, yet short-term endurance increased.

Bacteremia, central catheters, and neonates: when to pull the line

OBJECTIVES

Physicians who treat neonates who become bacteremic while dependent on central venous catheters face a serious and common dilemma. We sought 1) to evaluate the relationship between central venous catheter removal and outcome in bacteremic neonates, 2) to determine species of bacteria that are associated with an increased risk of infectious complications if the central catheter is not removed promptly, and 3) to provide evidence-based recommendations for central catheter management.

METHOD

A retrospective cohort study of all neonates who had central venous access and developed bacteremia between July 1, 1995, and July 31, 1999, was conducted in the Duke University neonatal intensive care unit.

RESULTS

The outcome for patients in whom the central catheter was not removed within 24 hours of organism identification was significantly worse (odds ratio = 9.8) than it was for those whose catheters were removed promptly. For patients who were infected with Staphylococcus aureus or with nonenteric Gram-negative rods, delayed removal of the central catheter was associated with complicated bacteremia. Catheter sterilization was attempted in 27 neonates who were infected with enteric Gram-negative rods; only 10 of these infants retained their catheters without infection-related complications. Infants who had 4 consecutive blood cultures that were positive for coagulase-negative staphylococcus (CoNS) were at significantly increased risk for end-organ damage and death, compared with infants who had 3 or fewer positive blood culture for CoNS (odds ratio = 29.58).

CONCLUSIONS

Bacteremic infants experienced fewer infection-related complications when the central catheter was removed promptly. One positive blood culture for S aureus or a Gram-negative rod warrants central line removal in a neonate. Clinicians who are faced with a neonate who has 1 positive culture for CoNS may attempt medical management without central catheter removal, but documentation of subsequent negative blood cultures is crucial. Once a neonate has 3 positive blood cultures for CoNS, the central catheter should be removed.central line, neonate, bacteremia, bacteria, umbilical catheter, Broviac, percutaneous.

Sequence conservation at human and mouse orthologous common fragile regions, FRA3B/FHIT and Fra14A2/Fhit

It has been suggested that delayed DNA replication underlies fragility at common human fragile sites, but specific sequences responsible for expression of these inducible fragile sites have not been identified. One approach to identify such cis-acting sequences within the large nonexonic regions of fragile sites would be to identify conserved functional elements within orthologous fragile sites by interspecies sequence comparison. This study describes a comparison of orthologous fragile regions, the human FRA3B/FHIT and the murine Fra14A2/Fhit locus. We sequenced over 600 kbp of the mouse Fra14A2, covering the region orthologous to the fragile epicenter of FRA3B, and determined the Fhit deletion break points in a mouse kidney cancer cell line (RENCA). The murine Fra14A2 locus, like the human FRA3B, was characterized by a high AT content. Alignment of the two sequences showed that this fragile region was stable in evolution despite its susceptibility to mitotic recombination on inhibition of DNA replication. There were also several unusual highly conserved regions (HCRs). The positions of predicted matrix attachment regions (MARs), possibly related to replication origins, were not conserved. Of known fragile region landmarks, five cancer cell break points, one viral integration site, and one aphidicolin break cluster were located within or near HCRs. Thus, comparison of orthologous fragile regions has identified highly conserved sequences with possible functional roles in maintenance of fragility.

Comparison of genomic DNA sequences: solved and unsolved problems

MOTIVATION

The DNA sequences of entire genomes are being determined at a rapid rate. Whereas initial genome sequencing efforts were for organisms chosen to be widely spaced in the tree of life, there is a growing emphasis on projects to sequence a species that is sufficiently similar to an already-sequenced species to allow direct comparison of those two DNA sequences. This and other changes in genome sequencing strategies have created a strong need for new methods to compare genomic sequences.

RESULTS

We sketch the current state of software for comparing genomic DNA sequences and outline research directions that we believe are likely to result in important advances in practice.

Sequences flanking hypersensitive sites of the beta-globin locus control region are required for synergistic enhancement

The major distal regulatory sequence for the beta-globin gene locus, the locus control region (LCR), is composed of multiple hypersensitive sites (HSs). Different models for LCR function postulate that the HSs act either independently or synergistically. To test these possibilities, we have constructed a series of expression cassettes in which the gene encoding the enhanced green fluorescent protein (EGFP) is under the control of DNA fragments containing single and multiple HSs of the LCR. LCR DNA fragments containing only the minimal region needed for position-independent expression (HS cores) or containing cores plus flanking sequences (HS units) were compared to ascertain whether conserved sequences between the HS cores contributed to enhancement. Expression of these constructs was measured after targeted integration into three defined loci in murine erythroleukemia cells using recombinase-mediated cassette exchange. At all three marked loci, synergistic enhancement of expression was observed in cassettes containing a combination of HS2, HS3, and HS4 units. In contrast, HS2, HS3, and HS4 cores (without flanking sequences) give an activity equivalent to the sum of the activities of the individual HS cores. These data suggest a model in which an HS core plus flanking regions, bound by specific proteins, forms a structure needed for interaction with other HS units to confer strong enhancement by the LCR. The three targeted integration sites differ substantially in their permissivity for expression, but even the largest LCR construct tested could not overcome these position effects to confer equal expression at all three sites.