Radiotherapy dose and survival outcomes in human papillomavirus positive oropharyngeal cancer.

OBJECTIVE: To evaluate the effect of definitive radiotherapy dose on survival in patients with human papillomavirus positive oropharyngeal carcinoma. METHODS: Human papillomavirus positive oropharyngeal carcinoma patients staged T1-3 and N0-2c, who received definitive radiotherapy (fraction sizes of 180 cGy to less than 220 cGy), were identified from the National Cancer Database 2010-2014 and stratified by radiation dose (50 Gy to less than 66 Gy, or 66 Gy or more). RESULTS: A total of 2173 patients were included, of whom 124 (6 per cent) received a radiation dose of 50 Gy to less than 66 Gy. With a median follow up of 33.8 months, patients had a 3-year overall survival rate of 88.6 per cent (95 per cent confidence interval = 87.1-90.1 per cent). On multivariate Cox analysis, a radiotherapy dose of 50 Gy to less than 66 Gy (hazard ratio = 0.95, 95 per cent confidence interval = 0.52-1.74, p = 0.86) was not a predictor of increased mortality risk. CONCLUSION: Human papillomavirus positive oropharyngeal carcinoma patients had excellent outcomes with definitive radiotherapy doses of 50 Gy to less than 66 Gy. These results further support patients enrolling into clinical trials for radiation dose de-escalation.

Aircraft soot from conventional fuels and biofuels during ground idle and climb-out conditions: Electron microscopy and X-ray micro-spectroscopy.

Aircraft soot has a significant impact on global and local air pollution and is of particular concern for the population working at airports and living nearby. The morphology and chemistry of soot are related to its reactivity and depend mainly on engine operating conditions and fuel-type. We investigated the morphology (by transmission electron microscopy) and chemistry (by X-ray micro-spectroscopy) of soot from the exhaust of a CFM 56-7B26 turbofan engine, currently the most common engine in aviation fleet, operated in the test cell of SR Technics, Zurich airport. Standard kerosene (Jet A-1) and a biofuel blend (Jet A-1 with 32% HEFA) were used at ground idle and climb-out engine thrust, as these conditions highly influence air quality at airport areas. The results indicate that soot reactivity decreases from ground idle to climb-out conditions for both fuel types. Nearly one third of the primary soot particles generated by the blended fuel at climb-out engine thrust bear an outer amorphous shell implying higher reactivity. This characteristic referring to soot reactivity needs to be taken into account when evaluating the advantage of HEFA blending at high engine thrust. The soot type that is most prone to react with its surrounding is generated by Jet A-1 fuel at ground idle. Biofuel blending slightly lowers soot reactivity at ground idle but does the opposite at climb-out conditions. As far as soot reactivity is concerned, biofuels can prove beneficial for airports where ground idle is a common situation; the benefit of biofuels for climb-out conditions is uncertain.

Decoupling the role of stress and corrosion in the intergranular cracking of noble-metal alloys.

Intergranular stress-corrosion cracking (IGSCC) is a form of environmentally induced crack propagation causing premature failure of elemental metals and alloys. It is believed to require the simultaneous presence of tensile stress and corrosion; however, the exact nature of this synergy has eluded experimental identification. For noble metal alloys such as Ag-Au, IGSCC is a consequence of dealloying corrosion, forming a nanoporous gold layer that is believed to have the ability to transmit cracks into grain boundaries in un-dealloyed parent phase via a pure mechanical process. Here using atomic-scale techniques and statistical characterizations for this alloy system, we show that the separate roles of stress and anodic dissolution can be decoupled and that the apparent synergy exists owing to rapid time-dependent morphology changes at the dealloyed layer/parent phase interface. We discuss the applicability of our findings to the IGSCC of important engineering Fe- and Ni-based alloys in critical applications.

A method for site-specific and cryogenic specimen fabrication of liquid/solid interfaces for atom probe tomography.

A site-specific, cryogenic, focused ion beam (FIB) method is presented for the preparation of atom probe tomography (APT) specimens from a frozen liquid/solid interface. As a practical example, the interface between water and a corroded boroaluminosilicate glass has been characterized by APT for the first time. The water/glass interface is preserved throughout specimen preparation by plunge freezing the corroding glass particles with the corrosion solution into slush nitrogen. Site-specific specimen preparation is enabled through a new approach to extract and mount a small volume of material using a cryogenically cooled FIB stage and micromanipulator. The prepared APT specimens are subsequently transferred from the FIB to APT under cryogenic and high-vacuum conditions using a novel FIB/APT transfer shuttle and home-built environmental transfer hub attached to the APT system. Particular focus is given to the technical methods for specimen fabrication under cryogenic conditions. Persistent challenges are discussed in addition to future opportunities for this new specimen preparation method.

[Magneto-encephalographic (MEG) brain recordings during traumatic memory recall in women with post-traumatic stress disorder: A pilot study]. / Enregistrement magnéto-encéphalographique (MEG) de réminiscences du trauma chez des femmes souffrant de stress post-traumatique : une étude pilote.

AIM OF THE STUDY: The experiment studied the effects of a short duration exposure to traumatic memories using magneto-encephalography (MEG). PATIENTS: Nine right-handed DSM-4 PTSD patients were recruited from a unit for anxiety disorders and an organisation supporting victims of violence. In order to have a homogeneous sample, we included only women who suffered from civilian PTSD. Exclusion criteria were co-morbid major medical illness, metallic dental prostheses that would interfere in the magnetic measurement, and current drug treatment. All participants were free from neurological disease and had normal hearing. They signed a written informed consent form. An ethics committee accepted the study. METHOD: A tape-recorded voice administered a script-driven imagery. The patients had to imagine, successively, a neutral image, a traumatic memory and rest, while MEG measured brain activities across delta, theta, alpha and beta bands. Each condition lasted three minutes. Heart rate (HR), anxiety and the vividness of mental images were recorded at the end of each phase. MEG power analysis was carried out with Statistical Parametric Mapping (SPM) 8. The signals were averaged for each of the three conditions of threeminutes duration. The dependent variable was a subtracted value: (trauma - rest) - (neutral - rest). The significance threshold was set at P<0.01. RESULTS: Anxiety and HR significantly increased during the trauma condition and returned to the neutral level during rest. The vividness of the mental imagery remained stable across the three conditions. The left-brain demonstrated a statistically significant power decrease in the secondary visual cortex (BA 18-19) in the delta band, the insula (BA13) in the beta band, the insula (BA13), premotor cortex (BA 6), Broca area (BA 44), and BA 43, in the alpha band. DISCUSSION: The symptom provocation protocol was successful in eliciting subjective anxiety and HR response in relation to traumatic memories. Our MEG results are in keeping with previous neuro-imagery studies showing decreased activities in the insula and Broca area during PTSD symptom provocation. However, we did not replicate the activation in the amygdala and the cingulate and prefrontal cortex found in some studies. Moreover, the within-group design, the small sample, and the inclusion of only female patients with milder dissociative symptoms limit our conclusions. The MEG protocol we used may also explain some partial discrepancies with previous MEG studies. However, our aim was to provoke a specific autobiographic recall of a traumatic event unfolding several sequential mental images along three minutes as in exposure therapy for PTSD. CONCLUSION: Despite its limitations, this pilot study is the first to provide MEG data during trauma recall. It suggests that recalling a specific traumatic event along three minutes results in hypo-activations of the brain regions regulating language and emotions. This paves the way to recording whole sessions of specific therapies for PTSD, with MEG using the millisecond resolution. MEG might be of interest to study the suppression of traumatic memories and their activation and habituation through prolonged graduated exposure in imagination across several sessions. MEG could also be used to study the effects of medication on PTSD symptoms. A controlled replication in a larger sample including male and female patients with various traumatic experiences is needed.

Thermal stability of MnBi magnetic materials.

MnBi has attracted much attention in recent years due to its potential as a rare-earth-free permanent magnet material. It is unique because its coercivity increases with increasing temperature, which makes it a good hard phase material for exchange coupling nanocomposite magnets. MnBi phase is difficult to obtain, partly because the reaction between Mn and Bi is peritectic, and partly because Mn reacts readily with oxygen. MnO formation is irreversible and harmful to magnet performance. In this paper, we report our efforts toward developing MnBi permanent magnets. To date, high purity MnBi (>90%) can be routinely produced in large quantities. The produced powder exhibits 74.6 emu g(-1) saturation magnetization at room temperature with 9 T applied field. After proper alignment, the maximum energy product (BH)max of the powder reached 11.9 MGOe, and that of the sintered bulk magnet reached 7.8 MGOe at room temperature. A comprehensive study of thermal stability shows that MnBi powder is stable up to 473 K in air.

Examinations of oxidation and sulfidation of grain boundaries in alloy 600 exposed to simulated pressurized water reactor primary water.

High-resolution characterizations of intergranular attack in alloy 600 (Ni-17Cr-9Fe) exposed to 325°C simulated pressurized water reactor primary water have been conducted using a combination of scanning electron microscopy, NanoSIMS, analytical transmission electron microscopy, and atom probe tomography. The intergranular attack exhibited a two-stage microstructure that consisted of continuous corrosion/oxidation to a depth of ~200 nm from the surface followed by discrete Cr-rich sulfides to a further depth of ~500 nm. The continuous oxidation region contained primarily nanocrystalline MO-structure oxide particles and ended at Ni-rich, Cr-depleted grain boundaries with spaced CrS precipitates. Three-dimensional characterization of the sulfidized region using site-specific atom probe tomography revealed extraordinary grain boundary composition changes, including total depletion of Cr across a several nm wide dealloyed zone as a result of grain boundary migration.

Caprylic acid reduces Salmonella Enteritidis populations in various segments of digestive tract and internal organs of 3- and 6-week-old broiler chickens, therapeutically.

We investigated the efficacy of feed supplemented with caprylic acid (CA), a natural, 8-carbon fatty acid for reducing Salmonella enterica serovar Enteritidis colonization in commercial broiler chickens. In separate 3- and 6-wk trials, 1-d-old straight-run broiler chicks (n = 70 birds/trial) were assigned to a control group (challenged with Salmonella Enteritidis, no CA) and 2 replicates of 0.7 and 1% CA (n = 14 birds/group). Water and feed were provided ad libitum. On d 1, birds were tested for any inherent Salmonella (n = 2 birds/group). For the 3-wk trial, on d 5, birds were challenged with 8 log(10) cfu of Salmonella Enteritidis of a 4-strain mixture by crop gavage, and after 5 d postchallenge, birds (n = 2 birds/group) were euthanized to ensure Salmonella Enteritidis colonization. Caprylic acid was supplemented the last 5 d before tissue collection (n = 10 birds/group). For the 6-wk trial, on d 25, birds were challenged and confirmed for Salmonella Enteritidis colonization. The birds (n = 10 birds/group) were euthanized for tissue samples after CA supplementation for the last 5 d. Caprylic acid at 0.7 or 1% decreased Salmonella Enteritidis populations in cecum, small intestine, cloaca, liver, and spleen in both 3- and 6-wk trials. Body weight of birds did not differ between the groups (P ≥ 0.05). Further, to elucidate a potential antibacterial mechanism of action of CA, we investigated if CA could reduce Salmonella Enteritidis invasion of an avian epithelial cell line and expression of invasion genes hilA and hilD. The cell invasion study revealed that CA reduced invasive abilities of all Salmonella Enteritidis strains by ~80% (P < 0.05). Gene expression studies indicated that CA downregulated (P < 0.001) Salmonella invasion genes hilA and hilD. These results suggest that supplementation of CA through feed could reduce Salmonella Enteritidis colonization in broiler chicken and potentially reduces the pathogen's ability to invade intestinal epithelial cells by downregulating key invasion genes, hilA and hilD.

A new in vivo model for luteolysis using systemic pulsatile infusions of PGF(2α).

A new in vivo model for studying luteolysis was developed in sheep to provide a convenient method for collecting corpora lutea for molecular, biochemical, and histological analysis during a procedure that mimics natural luteolysis. It was found that the infusion of prostaglandin F(2α) (PGF(2α)) at 20 µg/min/h into the systemic circulation during the mid luteal phase of the cycle allowed sufficient PGF(2α) to escape across the lungs and thus mimic the transient 40% decline in the concentration of progesterone in peripheral plasma seen at the onset of natural luteolysis in sheep. Additional 1h-long systemic infusions of PGF(2α), given at physiological intervals, indicated that two infusions were not sufficient to induce luteolysis. However, an early onset of luteolysis and estrus was induced in one out of three sheep with three infusions, two out of three sheep with four infusions, and three out of three sheep with five infusions. Reducing the duration of each systemic infusion of PGF(2α) from 1h to 30 min failed to induce luteolysis and estrus even after six systemic infusions indicating that, not only are the amplitude and frequency of PGF(2α) pulses essential for luteolysis, but the actual duration of each pulse is also critical. We conclude that a minimum of five systemic pulses of PGF(2α), given in an appropriate amount and at a physiological frequency and duration, are required to mimic luteolysis consistently in all sheep. The five pulse regimen thus provides a new accurate in vivo model for studying molecular mechanisms of luteolysis.

Evidence for a potential role of neuropeptide Y in ovine corpus luteum function.

Neuropeptide Y (NPY) is a neurohormone that is typically associated with food intake, but it has also been reported to affect the production of progesterone from luteal tissue in vitro. However, NPY has not been previously immunolocalized in the ovine ovary or in the corpus luteum (CL) of any species, and the effects of this neurohormone on luteal function in vivo are not known. Thus, we performed fluorescent immunohistochemistry (IHC) to localize NPY in the ovine ovary and used avidin-biotin immunocytochemistry (ICC) to further define the intracellular localization within follicles and the CL. We then infused NPY directly into the arterial supply of the autotransplanted ovaries of sheep to determine the in vivo effect of exogenous NPY on ovarian blood flow and on the luteal secretion rate of progesterone and oxytocin. Immunohistochemistry revealed that the NPY antigen was localized to cells within the follicles and CL, in the nerve fibers of the ovarian stroma, and in the vessels of the ovarian hilus. In the follicle, the NPY antigen was localized to nerves and vessels within the theca interna layer, and strong staining was observed in the granulosal cells of antral follicles. In the CL, NPY was localized in large luteal cells and in the vascular pericytes and/or endothelial cells of blood vessels, found dispersed throughout the gland and within the luteal capsule. In vivo incremental infusions of NPY at 1, 10, 100, and 1,000 ng/min, each for a 30-min period, into the arterial supply of the transplanted ovary of sheep bearing a CL 11 d of age increased (P< or =0.05) ovarian blood flow. The intra-arterial infusions of NPY also increased (P< or =0.05) in a dose-dependent manner the secretion rate of oxytocin, which was positively correlated (P< or =0.05) with the observed increase in ovarian blood flow. The infusions of NPY had a minimal effect on the secretion rate of progesterone, and similar intra-arterial infusions of NPY into sheep with ovarian transplants bearing a CL over 30 d of age had no significant effect on ovarian blood flow or on the secretion rate of progesterone. These results suggest that NPY acts on the luteal vascular system and the large luteal cells to rapidly stimulate blood flow and the secretion of oxytocin, respectively, which collectively implies a putative role for NPY during the process of luteolysis when increasing amounts of oxytocin are secreted from the ovine CL in response to uterine pulses of prostaglandin F2alpha.

Independent protein-profiling studies show a decrease in apolipoprotein A1 levels in schizophrenia CSF, brain and peripheral tissues.

Although some insights into the etiology of schizophrenia have been gained, an understanding of the illness at the molecular level remains elusive. Recent advances in proteomic profiling offer great promise for the discovery of markers underlying pathophysiology of diseases. In the present study, we employed two high-throughput proteomic techniques together with traditional methods to investigate cerebrospinal fluid (CSF), brain and peripheral tissues (liver, red blood cells and serum) of schizophrenia patients in an attempt to identify peripheral/surrogate disease markers. The cohorts used to investigate each tissue were largely independent, although some CSF and serum samples were collected from the same patient. To address the major confounding factor of antipsychotic drug treatment, we also included a large cohort of first-onset drug-naive patients. Apolipoprotein A1 (apoA1) showed a significant decrease in expression in schizophrenia patients compared to controls in all five tissues examined. Specifically, using SELDI-TOF mass spectrometry, apoA1 was found decreased in CSF from schizophrenia patients (-35%, P=0.00001) and, using 2D-DIGE, apoA1 was also found downregulated in liver (-30%, P=0.02) and RBCs (-60%, P=0.003). Furthermore, we found a significant reduction of apoA1 in sera of first-onset drug-naive schizophrenia patients using enzyme-linked immunosorbent assay (-18%, P=0.00008) and in two investigations of post-mortem brain tissue using western blot analysis (-35%, P=0.05; -51%, P=0.05). These results show that apoA1 is consistently downregulated in the central nervous system as well as peripheral tissues of schizophrenia patients and may be linked to the underlying disease mechanism.

Common risk factors seen in secondary carpal tunnel surgery.

BACKGROUND: We hypothesized that there are several common risk factors associated with secondary carpal tunnel releases. Therefore, we chose to investigate these common factors by analyzing the charts of those patients requiring a second carpal tunnel release (CTR) procedure. METHODS: A retrospective chart review was performed, and patients were identified by searching hospital medical record databases using the Common Procedural Terminology. RESULTS: Between January 1, 2000, and March 31, 2004, 2357 patients had a primary CTR, and 48 of them were found to have had a secondary CTR (of these 48, 9 had diabetes mellitus, 11 had hypertension, and 6 had gastrointestinal-related illnesses). Seven percent of those who had an open release primarily required a second CTR, while only 0.2% of those who had an endoscopic release primarily required a second CTR. CONCLUSION: A greater number of secondary CTR procedures were required for those patients with symptoms of carpal tunnel syndrome in the group that had an open release primarily versus those that had an endoscopic release primarily. Diabetes mellitus and hypertension may also contribute to the need for secondary surgery.

[Sonographie von pleura und lunge]. / Ultrasonography of Pleura and Lung.

The value of ultrasound examination of the pleura and lungs remains highly underestimated to this day. While the ventilated lungs and the osseous skeleton of the thorax represent potent obstacles for ultrasound, a multitude of pathological processes of the chest wall, pleura, and lungs results in altered tissue composition, providing markedly increased access and visibility for sonographic examination. These conditions support the sonographic diagnosis of pleural and pulmonary disorders. However, the main value of pleura and lung ultrasonography is not the primary diagnosis of chest lesions but the follow up, differential diagnosis, detection of complications, such as abscesses and post embolic lung infarction, and guidance of diagnostic and therapeutic interventions in patients with pathological pleural and pulmonary findings. Punctures and drainages of fluids, e. g., haematothorax, empyema, chylothorax as well as biopsies of solid lesions can safely be performed under ultrasound-guidance. It is of special importance that pleura and lung ultrasonography, as a non-invasive method, can be repeated without discomfort or radiation exposure for the patient and is therefore valuable in the follow-up of pathological findings. Adequate interpretation of sonographic pleura and lung findings has to consider the patient's history, physical examination, chest X-ray and other results obtained by complementary imaging technologies (e. g. thoracic computed tomography).

Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences.

When protein sequences divergently evolve under functional constraints, some individual amino acid replacements that reverse the charge (e.g. Lys to Asp) may be compensated by a replacement at a second position that reverses the charge in the opposite direction (e.g. Glu to Arg). When these side-chains are near in space (proximal), such double replacements might be driven by natural selection, if either is selectively disadvantageous, but both together restore fully the ability of the protein to contribute to fitness (are together "neutral"). Accordingly, many have sought to identify pairs of positions in a protein sequence that suffer compensatory replacements, often as a way to identify positions near in space in the folded structure. A "charge compensatory signal" might manifest itself in two ways. First, proximal charge compensatory replacements may occur more frequently than predicted from the product of the probabilities of individual positions suffering charge reversing replacements independently. Conversely, charge compensatory pairs of changes may be observed to occur more frequently in proximal pairs of sites than in the average pair. Normally, charge compensatory covariation is detected by comparing the sequences of extant proteins at the "leaves" of phylogenetic trees. We show here that the charge compensatory signal is more evident when it is sought by examining individual branches in the tree between reconstructed ancestral sequences at nodes in the tree. Here, we find that the signal is especially strong when the positions pairs are in a single secondary structural unit (e.g. alpha helix or beta strand) that brings the side-chains suffering charge compensatory covariation near in space, and may be useful in secondary structure prediction. Also, "node-node" and "node-leaf" compensatory covariation may be useful to identify the better of two equally parsimonious trees, in a way that is independent of the mathematical formalism used to construct the tree itself. Further, compensatory covariation may provide a signal that indicates whether an episode of sequence evolution contains more or less divergence in functional behavior. Compensatory covariation analysis on reconstructed evolutionary trees may become a valuable tool to analyze genome sequences, and use these analyses to extract biomedically useful information from proteome databases.

Reproductive characteristics of cloned heifers derived from adult somatic cells.

This study examined the onset of puberty, follicular dynamics, reproductive hormone profiles, and ability to maintain pregnancy in cloned heifers produced by somatic cell nuclear transfer. Four adult somatic cell-cloned heifers, derived from a 13-yr-old Holstein cow, were compared to 4 individual age- and weight-matched heifers produced by artificial insemination (AI). From 7 to 9 mo of age, jugular venous blood samples were collected twice weekly, and from 10 to 11 or 12 mo of age, blood sampling was carried out every other day. After the heifers reached puberty (defined as the first of 3 consecutive blood samples with peripheral plasma progesterone concentrations of >1 ng/ml), ultrasound examination of ovaries and jugular plasma sample collection were carried out daily for 1 estrous cycle. Cloned heifers reached puberty later than controls (mean +/- SEM, 314.7 +/- 9.6 vs. 272 +/- 4.4 days and 336.7 +/- 13 vs. 302.8 +/- 4.5 kg for clones and controls, respectively; P < 0.05). However, cloned and control heifers were not different in estrous cycle length, ovulatory follicle diameter, number of follicular waves, or profiles of hormonal changes (LH, FSH, estradiol, and progesterone). Three of the 4 clones and all 4 control heifers became pregnant after AI. These results demonstrate that clones from an aged adult have normal reproductive development.

The adaptive evolution database (TAED).

BACKGROUND: The Master Catalog is a collection of evolutionary families, including multiple sequence alignments, phylogenetic trees and reconstructed ancestral sequences, for all protein-sequence modules encoded by genes in GenBank. It can therefore support large-scale genomic surveys, of which we present here The Adaptive Evolution Database (TAED). In TAED, potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotide substitution rates (KA/KS values) on branches of an evolutionary tree between nodes representing reconstructed ancestral sequences. RESULTS: Evolutionary trees and reconstructed ancestral sequences were extracted from the Master Catalog for every subtree containing proteins from the Chordata only or the Embryophyta only. Branches with high KA/KS values were identified. These represent candidate episodes in the history of the protein family when the protein may have undergone positive selection, where the mutant form conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. An unexpectedly large number of families (between 10% and 20% of those families examined) were found to have at least one branch with high KA/KS values above arbitrarily chosen cut-offs (1 and 0.6). Most of these survived a robustness test and were collected into TAED. CONCLUSIONS: TAED is a raw resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study. It can be expanded to include other evolutionary information (for example changes in gene regulation or splicing) placed in a phylogenetic perspective.

Bedside multimarker testing for risk stratification in chest pain units: The chest pain evaluation by creatine kinase-MB, myoglobin, and troponin I (CHECKMATE) study.

BACKGROUND: Earlier, rapid evaluation in chest pain units may make patient care more efficient. A multimarker strategy (MMS) testing for several markers of myocardial necrosis with different time-to-positivity profiles also may offer clinical advantages. METHODS AND RESULTS: We prospectively compared bedside quantitative multimarker testing versus local laboratory results (LL) in 1005 patients in 6 chest pain units. Myoglobin, creatine kinase-MB, and troponin I were measured at 0, 3, 6, 9 to 12, and 16 to 24 hours after admission. Two MMS were defined: MMS-1 (all 3 markers) and MMS-2 (creatine kinase-MB and troponin I only). The primary assessment was to relate marker status with 30-day death or infarction. More patients were positive by 24 hours with MMS than with LL (MMS-1, 23.9%; MMS-2, 18.8%; LL, 8.8%; P=0.001, all comparisons), and they became positive sooner with MMS-1 (2.5 hours, P=0.023 versus LL) versus MMS-2 (2.8 hours, P=0.026 versus LL) or LL (3.4 hours). The relation between baseline MMS status and 30-day death or infarction was stronger (MMS-1: positive, 18.8% event rate versus negative, 3.0%, P=0.001; MMS-2: 21.9% versus 3.2%, P=0.001) than that for LL (13.6% versus 5.5%, P=0.038). MMS-1 discriminated 30-day death better (positive, 2.0% versus negative, 0.0%, P=0.007) than MMS-2 (positive, 1.8% versus negative, 0.2%; P=0.055) or LL (positive, 0.0% versus negative, 0.5%; P=1.000). CONCLUSIONS: Rapid multimarker analysis identifies positive patients earlier and provides better risk stratification for mortality than a local laboratory-based, single-marker approach.

The Adaptive Evolution Database (TAED).

BACKGROUND: Developing an understanding of the molecular basis for the divergence of species lies at the heart of biology. The Adaptive Evolution Database (TAED) serves as a starting point to link events that occur at the same time in the evolutionary history (tree of life) of species, based upon coding sequence evolution analyzed with the Master Catalog. The Master Catalog is a collection of evolutionary models, including multiple sequence alignments, phylogenetic trees, and reconstructed ancestral sequences, for all independently evolving protein sequence modules encoded by genes in GenBank [1]. RESULTS: We have estimated from these models the ratio of nonsynonymous to synonymous nucleotide substitution (Ka/Ks), for each branch in their respective evolutionary trees of every subtree containing only chordata or only embryophyta proteins. Branches with high Ka/Ks values represent candidate episodes in the history of the family where the protein may have undergone positive selection, a phenomenon in molecular evolution where the mutant form of a gene must have conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. We have found that an unexpectedly large number of families (between 10 and 20% of those families examined) have at least one branch with a notably high Ka/Ks value (putative adaptive evolution). As a resource for biologists wishing to understand the interaction between protein sequences and the Darwinian processes that shape these sequences, we have collected these into The Adaptive Evolution Database (TAED). CONCLUSIONS: Placed in a phylogenetic perspective, candidate genes that are undergoing evolution at the same time in the same lineage can be viewed together. This framework based upon coding sequence evolution can be readily expanded to include other types of evolution. In its present form, TAED provides a resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study.

Synthesis and biophysical analysis of transmembrane domains of a Saccharomyces cerevisiae G protein-coupled receptor.

The Ste2p receptor for alpha-factor, a tridecapeptide mating pheromone of the yeast Saccharomyces cerevisiae, belongs to the G protein-coupled family of receptors. In this paper we report on the synthesis of peptides corresponding to five of the seven transmembrane domains (M1-M5) and two homologues of the sixth transmembrane domain corresponding to the wild-type sequence and a mutant sequence found in a constitutively active receptor. The secondary structures of all new transmembrane peptides and previously synthesized peptides corresponding to domains 6 and 7 were assessed using a detailed CD analysis in trifluoroethanol, trifluoroethanol-water mixtures, sodium dodecyl sulfate micelles, and dimyristoyl phosphatidyl choline bilayers. Tryptophan fluorescence quenching experiments were used to assess the penetration of the membrane peptides into lipid bilayers. All peptides were predominantly (40-80%) helical in trifluoroethanol and most trifluoroethanol-water mixtures. In contrast, two of the peptides M3-35 (KKKNIIQVLLVASIETSLVFQIKVIFTGDNFKKKG) and M6-31 (KQFDSFHILLINleSAQSLLVPSIIFILAYSLK) formed stable beta-sheet structures in both sodium dodecyl sulfate micelles and DMPC bilayers. Polyacrylamide gel electrophoresis showed that these two peptides formed high molecular aggregates in the presence of SDS whereas all other peptides moved as monomeric species. The peptide (KKKFDSFHILLIMSAQSLLVLSIIFILAYSLKKKS) corresponding to the sequence in the constitutive mutant was predominantly helical under a variety of conditions, whereas the homologous wild-type sequence (KKKFDSFHILLIMSAQSLLVPSIIFILAYSLKKKS) retained a tendency to form beta-structures. These results demonstrate a connection between a conformational shift in secondary structure, as detected by biophysical techniques, and receptor function. The aggregation of particular transmembrane domains may also reflect a tendency for intermolecular interactions that occur in the membrane environment facilitating formation of receptor dimers or multimers.