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Race and cause specific survival with prostate cancer: influence of clinical stage, Gleason score, age and treatment.

PURPOSE: We assess the influence of race on stage stratified cause specific survival of men with prostate cancer, and Gleason score, age at diagnosis and treatment on potential racial differences in survival. MATERIALS AND METHODS: A total of 524 black and 396 white men were diagnosed with prostate cancer at a Veterans Affairs Medical Center between January 1982 and December 1992. Clinical stage was determined by retrospective review of the medical records and Gleason score of biopsy material as assigned by a single uropathologist. Of 611 patients who died the cause of death was determined by retrospective or prospective review of hospital records in 493 and by review of the death certificates in 102. In 16 cases the cause of death was indeterminate. Median potential followup was 112 months (range 60 to 182) and median period of observation was 61 months (range 1 to 182). RESULTS: Cause specific survival with stage T1b-2 cancer was lower in 231 black than in 264 white men of all ages (p = 0.02) and lower in 110 black than in 170 white men younger than in 70 years at diagnosis (p = 0.04). Gleason 7 to 10 cancer, which was associated with a less favorable cause specific survival compared to Gleason 2 to 6 cancer (p <0.0001), was more common in black than in white men with stage T1b-2 cancer of all ages (p = 0.01) and younger than 70 years at diagnosis (p = 0.04). No or unknown treatment status, which was associated with a less favorable cause specific survival compared to treatment (p = 0.05), was more common in black than in white men with stage T1b-2 cancer of all ages (p = 0.0005) but not significantly different when stratified by age. In men of all ages racial differences in cause specific survival were not significant when adjusted for age and Gleason score (p = 0.14) or age, Gleason score and treatment status (p = 0.17). In men younger than 70 years racial differences in cause specific survival were not significant when adjusted for age and Gleason score (p = 0.22). There were no significant racial differences in overall or age stratified all cause survival of men with stage T1b-2 cancer. There were no significant differences in overall or age stratified cause specific or all cause survival of 112 black and 58 white men with stage T3-4 cancer, or 181 and 74, respectively, with metastatic cancer. CONCLUSIONS: Our data indicate that local stage prostate cancer is more lethal in black than in white men and the difference is most pronounced in men younger than 70 years. The survival disadvantage of black men with local stage cancer is due in part to a propensity for development of less differentiated and more aggressive malignancies.

Age Factors↗

A microbiologist's view of factors contributing to infection.

Why some patients develop postoperative surgical wound infection and others do not remains a mystery. There are many risk factors for infection, and mathematical scoring systems are often good predictors of infection; yet, some patients with a plethora of risk factors fail to develop surgical site infections. Even patients with established abdominal infection do not automatically develop wound infection. Early experimental work, now confirmed in the clinical setting, dictates that bacteria must be in the wound to cause infection; the minimal infecting dose will depend on the environmental conditions in the wound. The presence of foreign bodies, trauma, hematoma, etc., will enhance the effect of the inoculum; therefore, surgical debridement and careful surgery are necessary to reinforce the host defenses. Some bacteria, e.g., Staphylococcus aureus and Streptococcus pyogenes, have a greater propensity to cause infection, so extensive infection-control practices are necessary to prevent or contain these pathogens. To minimize the risk of surgical site infection, individual patient risk factors must be identified and modified whenever possible. The patient should be prepared for the operation and appropriate skin antiseptics should be used on the operative site. The patient should be considered for perioperative antibiotic prophylaxis and, if appropriate, bowel preparation should be carried out. Care and attention to the theater operating environment is important, especially for cases in which airborne transmission of bacteria should be controlled, e.g., ultraclean air systems for implant surgery. In elective surgery, the source of bacteria that cause infection is either the patient's normal flora (e.g., skin or bowel), i.e., endogenous, or the surgical staff or environment, i.e., exogenous. Surgical expertise and theater discipline are essential components in the fight against surgical sepsis.

Bacterial Infections↗

Magnetocardiographic intra-QRS fragmentation analysis in the identification of patients with sustained ventricular tachycardia after myocardial infarction.

The aim of this study was to investigate if magnetocardiographic (MCG) analysis of cardiac micropotentials within the QRS complex can identity patients prone to ventricular arrhythmias, and to compare it to MCG time-domain, late-field analysis. The study population consisted of 136 patients with remote MI, 53 with and 83 without a history of VT. After averaging and high pass filtering of multichannel MCG signals, time-domain parameters describing the end-QRS activity and fragmentation index M and score S describing the whole QRS complex were computed. Fragmentation and time-domain parameters differed between the VT and control groups: fragmentation index M was 12 +/- 3 versus 9 +/- 2 (P <0.001), fragmentation score S was 83 +/- 42 versus 56 +/- 21 (P < 0.001), and filtered QRS duration was 144 +/- 32 versus 114 +/- 19 ms (P < 0.001) in VT and control groups, respectively. A combination of fragmentation parameters yielded 87% sensitivity and 61% specificity in VT identification. Corresponding figures for a time-domain parameter combination were 81% and 72%. Sensitivity of time-domain analysis was 88% and specificity was 75% in a subgroup with anterior MI. In multivariate analysis, fragmentation and time-domain analyses discriminated VT patients from controls independently of the extent of coronary artery disease or left ventricular dysfunction. MCG in postinfarction patients reveals pathology associated with propensity to ventricular arrhythmias inside and not only at the end of the QRS complex. MCG seems most accurate in the anterior infarct location.

Aged↗

The environment of amide groups in protein-ligand complexes: H-bonds and beyond.

A comprehensive structural analysis of interactions involving amide NH and C=O groups in protein-ligand complexes has been performed based on 3,275 published crystal structures (resolution < or =2.5 A). Most of the amide C=O and NH groups at the protein-ligand interface are highly buried within the binding site and involved in H-bonds with corresponding counter-groups. Small percentages of C=O and NH groups are solvated or embedded in hydrophobic environments. In particular, C=O groups show a higher propensity to be solvated or embedded in a hydrophobic environment than NH groups do. A small percentage of carbonyl groups is involved in weak hydrogen bonds with CH. Cases of dipolar interactions, involving carbonyl oxygen and electrophilic carbon atoms, such as amide, amidinium, guanidium groups, are also identified. A higher percentage of NH are in contact with aromatic carbons, interacting either through hydrogen bonds (preferably with the NH group pointing towards a ring carbon atom) or through stacking between amide plane and ring plane. Comprehensive studies such as the present one are thought to be important for future improvements in the molecular design area, in particular for the development of new scoring functions. [Figure: see text].

Amides↗

The comparative tea staining potential of phenolic, chlorhexidine and anti-adhesive mouthrinses.

Staining of teeth and mucous membranes is a well-known side-effect with chlorhexidine mouthrinses in which dietary chromogens play an important rôle. The purpose of this study was to determine whether a co-polymer anti-adhesive agent would prevent staining by a low concentration chlorhexidine solution. Additionally, the possibility that an essential oil/phenolic rinse product may cause staining was investigated. The rinses studied were the anti-adhesive alone and combined with 0.02% chlorhexidine and the essential oil/phenolic rinse. These were positioned against a positive control rise, 0.2% chlorhexidine, and a negative control rinse, water. The study was a single blind 5-treatment, randomised Latin square cross-over design, incorporating balance for carry-over effects. 15 volunteers participated and on Day 1 of each study period were rendered stain free by scaling and polishing of the teeth. Oral hygiene was suspended and 8 x per day subjects rinsed under supervision, firstly with the allocated formulation and then with 10 ml of warm black tea. On Day 4, tooth and tongue staining was scored by area and intensity (colour). A washout period of at least 3 1/2 days was permitted between treatment periods when oral hygiene was resumed. Before the study and during washouts, volunteers practised tongue brushing. Tooth and tongue staining was significantly increased with 0.2% chlorhexidine compared to the essential oil/phenolic rinse which in turn was significantly increased compared to the other 3 rinses. The antiadhesive/chlorhexidine rinse produced no more staining than the anti-adhesive or water rise. However, the parallel plaque regrowth study suggests this inhibition of staining resulted from the vitiation of the chlorhexidine activity by the antiadhesive. The methodology would appear a simple and quick way of assessing the propensity of mouthrinses to cause extrinsic staining.

Anti-Infective Agents, Local↗

Cardiac and clinical phenotype in Barth syndrome.

OBJECTIVE: Barth syndrome, an X-linked disorder that is characterized by cardiomyopathy, neutropenia, skeletal myopathy, and growth delay, is caused by mutations in the taffazin gene at Xq28 that result in cardiolipin deficiency and abnormal mitochondria. The clinical phenotype in Barth syndrome has not been characterized systematically, and the condition may be underrecognized. We sought to evaluate extent of cardioskeletal myopathy, potential for arrhythmia, delays in growth, and biochemical correlates of disease severity in patients with this disorder. METHODS: We conducted an observational, cross-sectional study of the largest cohort of patients with Barth syndrome to date (n = 34; age range: 1.2-22.6 years). Evaluation included echocardiography, electrocardiography (standard and signal-averaged), microvolt T wave alternans analysis, biochemical and hematologic laboratory analyses, and physical therapy evaluation of skeletal myopathy. RESULTS: Family history was positive for confirmed or suspected Barth syndrome in 63%. Ninety percent of patients had a clinical history of cardiomyopathy (mean age at diagnosis of cardiomyopathy: 5.5 months; at genetic confirmation of Barth syndrome: 4.6 years). Echocardiography revealed a mean ejection fraction of 50% +/- 10%, mean fractional shortening of 28% +/- 5%, and mean left ventricular end-diastolic volume z score of 1.9 +/- 1.8. Left ventricular morphology demonstrated increased trabeculations or true noncompaction in 53%. Of 16 patients who were evaluated at > or = 11 years of age, 7 (43%) had documented ventricular arrhythmia. Growth deficiency was present (mean weight percentile: 15%; mean height percentile: 8%). Laboratory analysis revealed low total white blood cell count (absolute count: < 4000 cells per microL) in 25% of those who were not on granulocyte colony-stimulating factor. Hypocholesterolemia was present in 24%, decreased low-density lipoprotein cholesterol in 56%, low prealbumin in 79%, and mildly elevated creatine kinase in 15%. CONCLUSIONS: Our cohort demonstrated clinical variability, but most had cardiomyopathy and diminished growth velocity, with a propensity toward neutropenia and low cholesterol. There was increased incidence of ventricular arrhythmia, predominantly in adolescents and young adults. Barth syndrome should be considered when boys present with cardiomyopathy, especially when associated with increased left ventricular trabeculations, neutropenia, skeletal muscle weakness, or family history indicating an X-linked pattern of inheritance.

Acyltransferases↗

Bcl-2 expression is correlated with a low apoptotic index and associated with progesterone receptor immunoreactivity in endometrial carcinomas.

A total of 103 endometrial carcinomas (endometrioid type), as well as 15 samples of normal (atrophic or proliferative phase) and 26 of hyperplastic endometrium, were immunohistochemically investigated for expression of Bcl-2, and oestrogen and progesterone receptors (ER and PR), and the results compared with findings for apoptosis and cell proliferation. Carcinoma cases were subdivided into tubular and solid components on the basis of tumour growth patterns. Immunopositivity for Bcl-2, ER, and PR in tubular components was significantly higher than in the solid category, being negatively associated with histological grading. Immunoreactivity scores revealed that Bcl-2 in the tubular group was positively correlated with PR but not ER, while its expression in normal and hyperplastic endometrium was closely linked with both. Apoptotic and mitotic indices (AI and MI) were both significantly lower in tubular than in solid areas. In the tubular areas, AI, values were significantly lower in the subgroup with a high level of Bcl-2 expression than in either low-level or negative groups. These results indicate that Bcl-2 expression may play a central role in the inhibition of apoptosis in endometrial carcinoma, in particular those cases with tubular components, possibly being associated with PR rather than ER. Changes in the propensity for apoptosis may be related to alterations of tumour growth pattern and of features of differentiation.

Apoptosis↗

Preferential denervation of the adductor muscles of the equine larynx. I: Muscle pathology.

The laryngeal muscles of 18 horses were examined histologically. The neurogenic changes found in each muscle were scored by four reviewers and the results evaluated statistically. Fifteen of these horses had endoscopic evidence of abnormal laryngeal function, three of which were defined as having adductor paralysis. Measurement of muscle fibre area in two horses with idiopathic laryngeal hemiplegia (ILH) was performed. In the quantitative study of neurogenic change, the adductor muscles were more significantly affected than the abductor muscle. This was also true in the clinical cases of ILH where measurement of muscle fibre area demonstrated that the lateral cricoarytenoid (adductor) muscles showed a wider range of pathological changes than the dorsal cricoarytenoid muscle (abductor). Those horses with the most severe muscle pathology also had the most abnormal endoscopic findings. The propensity for denervation of the adductor muscles should provide clues as to the pathogenesis and natural history of horses with sub-clinical laryngeal disease and ILH.

Analysis of Variance↗

Quetiapine or haloperidol as monotherapy for bipolar mania--a 12-week, double-blind, randomised, parallel-group, placebo-controlled trial.

METHODS: Patients (n=302) with bipolar I disorder (manic episode) were randomised to 12 weeks' double-blind treatment with quetiapine (flexibly dosed up to 800 mg/day), placebo, or haloperidol (up to 8 mg/day). The primary efficacy outcome variable was change from baseline to Day 21 in Young Mania Rating Scale (YMRS) score. RESULTS: YMRS score improved with quetiapine at Day 21 (-12.29 versus -8.32 for placebo; P<0.01). The difference in favor of quetiapine increased by Day 84 (-17.52 versus -9.48; P<0.001). Haloperidol also showed an advantage over placebo at Days 21 and 84 (P<0.001). There was no significant difference in efficacy measures between quetiapine and haloperidol groups at any assessment except Day 21. The only common adverse event with quetiapine was somnolence (12.7%). Extrapyramidal symptoms (EPS), including akathisia, occurred at 59.6% with haloperidol, 12.7% with quetiapine, 15.8% with placebo. Most quetiapine responders (84%) received a dose of 400-800 mg/day. CONCLUSIONS: Quetiapine was effective and well tolerated. The efficacy and tolerability profile of haloperidol (including its propensity for EPS) supported study validity.

Adult↗

Catastrophic thinking and heightened perception of pain in others.

Past research has shown that pain catastrophizing contributes to heightened pain experience. The hypothesis advanced in this study was that individuals who score high on measures of pain catastrophizing would also perceive more intense pain in others. The study also examined the role of pain behaviour as a determinant of the relation between catastrophizing and estimates of others' pain. To test the hypothesis, 60 undergraduates were asked to view videotapes of individuals taking part in a cold pressor procedure. Each individual in the videotapes was shown three times over the course of a 1min immersion such that the same individual was observed experiencing different levels of pain. Correlational analyses revealed a significant positive correlation between levels of pain catastrophizing and inferred pain intensity, r=.31, p<.01. Follow-up analyses indicated that catastrophizing was associated with a heightened propensity to rely on pain behaviour as a basis for drawing inferences about others' pain experience. Catastrophizing was associated with more accurate pain inferences on only one of three indices of inferential accuracy. The pattern of findings suggests that increasing reliance on pain behaviour as a means of inferring others' pain will not necessarily yield more accurate estimates. Discussion addresses the processes that might underlie the propensity to attend more to others' pain behaviour, and the clinical and interpersonal consequences of perceiving more pain in others.

Adult↗

Logistic versus additive EuroSCORE. A comparative assessment of the two models in an independent population sample.

OBJECTIVE: Validation of EuroSCORE outside the boundaries of the original database has been limited to the additive model and has occasionally shown inconsistencies. Therefore we sought to validate the logistic model and assess its predictive performance compared to the additive approach. METHODS: Twenty-four hundred and twenty-six consecutive patients were prospectively assigned individual expected risks of dying calculated by the logistic and the additive EuroSCORE algorithms. Discriminating ability of the two models was tested by Receiver Operating Characteristic (ROC) curves. Calibration was assessed by the Hosmer-Lemeshow (H-T) test and further explored by additional cross-tabulations. A percent difference among the estimates was calculated and plotted across score groups. The series was then sorted by date of operation and split in halves to separately explore the potential effect of variation of performance. RESULTS: Observed mortality (5.6%) was not significantly different from the additive (5.3%) and the logistic estimates (6.9%). Both models satisfactorily discriminated outcomes (ROC areas of 0.80 and 0.79 for the logistic and the additive model, respectively). The H-T test showed that calibration was good for the logistic model (P=0.12) but turned out being inadequate for the additive model (P<0.0001). Further cross-tabulations confirmed a good correlation among observed and predicted death rates by the logistic model across all groups. The additive model, on the other hand, revealed a propensity to over-predict in medium-risk categories and under-predict in the very high-risk cases. Direct comparison of additive vs logistic estimates showed a similar behaviour demonstrating it as an intrinsic property of the additive approach. The split-file analysis revealed a significantly improved outcome for patients treated in the second half of the series though the predictive performance of the two models was unaltered. CONCLUSIONS: Logistic EuroSCORE reliably predicted outcomes in our series despite the higher risk profile compared to the reference EuroSCORE sample and the observed variation in clinical performance during the study period. The additive model was less precise, exhibiting a predictive distortion which should be accounted for, particularly when employing it at the individual patient level.

Aged↗

Promoter trapping reveals significant differences in integration site selection between MLV and HIV vectors in primary hematopoietic cells.

Recent reports have indicated that human immunodeficiency virus (HIV) and murine leukemia virus (MLV) vectors preferentially integrate into active genes. Here, we used a novel approach based on genetic trapping to rapidly score several thousand integration sites and found that MLV vectors trapped cellular promoters more efficiently than HIV vectors. Remarkably, 1 in 5 MLV integrations trapped an active promoter in different cell lines and primary hematopoietic cells. Such frequency was even higher in growth-stimulated lymphocytes. We show that the different behavior of MLV and HIV vectors was dependent on a different integration pattern within transcribed genes. Whereas MLV-based traps showed a strong bias for promoter-proximal integration leading to efficient reporter expression, HIV-based traps integrated throughout transcriptional units and were limited for expression by the distance from the promoter and the reading frame of the targeted gene. Our results indicate a strong propensity of MLV to establish transcriptional interactions with cellular promoters, a behavior that may have evolved to enhance proviral expression and may increase the insertional mutagenesis risk. Promoter trapping efficiency provides a convenient readout to assess transcriptional interactions between the vector and its flanking genes at the integration site and to compare integration site selection among different cell types and in different growth conditions.

Cell Line↗

Differences in locomotor response to an inescapable novel environment predict sensitivity to aversive effects of amphetamine.

Differences in locomotor response to an inescapable novel environment have previously been shown to predict sensitivity to amphetamine reward, where high responders (HR), compared to low responders (LR), showed greater initial sensitivity to amphetamine self-administration. The present experiments sought to extend these findings and assessed the relationship between locomotor response to an inescapable novel environment and conditioned taste aversion (CTA) with amphetamine and lithium chloride (LiCl). Male Sprague-Dawley rats were tested for their locomotor response to an inescapable novel environment and divided into high (HR) or low (LR) responders, based on whether their locomotor scores were above or below the median activity level of the subject sample. After several days, the animals were tested in a CTA procedure and conditioned with either amphetamine or lithium chloride. Compared to HR rats, LR rats showed greater sensitivity to amphetamine CTA at the doses tested. In contrast, the results with LiCl showed no relationship between locomotor response to an inescapable novel environment and CTA. Taken together, the present results suggest that LR, compared to HR, rats show less sensitivity to the rewarding effects of amphetamine because they are more sensitive to aversive effects of amphetamine, as reflected in CTA. In contrast, HR rats display less sensitivity to aversive effects of amphetamine, which may explain their greater propensity to self-administer amphetamine.

Animals↗

Helix propensities of short peptides: molecular dynamics versus bioinformatics.

Knowledge-based potential functions for protein structure prediction assume that the frequency of occurrence of a given structure or a contact in the protein database is a measure of its free energy. Here, we put this assumption to test by comparing the results obtained from sequence-structure cluster analysis with those obtained from long all-atom molecular dynamics simulations. Sixty-four eight-residue peptide sequences with varying degrees of similarity to the canonical sequence pattern for amphipathic helix were drawn from known protein structures, regardless of whether they were helical in the protein. Each was simulated using AMBER6.0 for at least 10 ns using explicit waters. The total simulation time was 1176 ns. The resulting trajectories were tested for reproducibility, and the helical content was measured. Natural peptides whose sequences matched the amphipathic helix motif with greater than 50% confidence were significantly more likely to form helix during the course of the simulation than peptides with lower confidence scores. The sequence pattern derived from the simulation data closely resembles the motif pattern derived from the database cluster analysis. The difficulties encountered in sampling conformational space and sequence space simultaneously are discussed.

Amino Acid Motifs↗

Partial REM-sleep deprivation increases the dream-like quality of mentation from REM sleep and sleep onset.

STUDY OBJECTIVES: Sleep onset (SO) is cognitively and physiologically similar to rapid eye movement (REM) sleep, supporting the notion that REM sleep-related processes are 'covertly' active at this time. The objective was to determine if SO mentation is sensitive to REM sleep deprivation. DESIGN: Two-group cross-sectional design; sleep recordings for 3 nights. SETTING: Standard sleep laboratory with 24-channel polysomnography recording. PARTICIPANTS: Fourteen female, 13 male healthy volunteers (18-41 yrs, mean=24.8 +/- 6.07). INTERVENTIONS: On Night 2, half were and half were not partially REM sleep-deprived (REMD), recalled REM mentation, and rated it for dream-like quality (DLQ), sleepiness, and sensory attributes. On Night 3, all were awakened from SO substages 4 and 5 for mentation reports and further ratings. REMD measures were derived from scored sleep tracings. MEASUREMENTS AND RESULTS: REMD produced increases in DLQ for both REM and SO reports (P < .05); DLQ scores were higher for REM than for SO mentation (P < .001). Covarying sleepiness preserved the (REMD) effect but abolished the REM/SO difference. Whereas 2 sensory attributes (presence of self, visual intensity) tended to distinguish the REM-mentation reports of REMD and control subjects, only 1, self-movement, distinguished their SO mentation reports (P < .06). Multiple regression revealed that increased DLQ of both REM and SO mentation was associated with increased sleepiness and decreased REM sleep time on Night 2. CONCLUSIONS: SO mentation responds to REMD much like REM mentation does, a finding consistent with other work supporting the notion of covert REM-sleep processes at SO. DLQ may be mediated by both increases in REM-sleep propensity and a circadian process indexed by sleepiness ratings.

Adolescent↗

Periodic limb movements and sleepiness in obstructive sleep apnea patients.

BACKGROUND AND PURPOSE: The aim of this study was to assess the possibility that periodic limb movements during sleep (PLMS) could play an additive role in the sleepiness associated with obstructive sleep apnea syndrome (OSAS) before treatment, or could account for residual sleepiness in successfully CPAP-treated patients. PATIENTS AND METHODS: In order to test this hypothesis, we compared objective sleepiness, assessed by the Multiple Sleep Latency Test (MSLT) and subjective sleep propensity, assessed by the Epworth Sleepiness Scale (ESS), in a clinical series of 57 patients consecutively diagnosed with OSAS (apnea/hypopnea index, 53.3+/-26.15), before and after 1 year of treatment with CPAP. RESULTS: Twenty-two patients (38.5%) had significant PLMS (at least 5 PLMS/h of sleep; mean 52.9+/-53.9) in absence of apneas (with CPAP). The two groups (with and without PLMS) were similar in gender distribution, BMI, apnea/hypopnea index or CPAP level. Patients with PLMS were older than those without PLMS. Sleepiness measurements following OSAS diagnosis and after 1 year of CPAP treatment were similar in patients PLMS compared to those without significant PLMS. There was no correlation in the PLMS patient group between the PLM index, Epworth Sleepiness Scale score and mean latency in the MSLT. CONCLUSION: In this study we did not find a link between PLMS and increased objective or self-evaluated sleepiness in OSAS patients, before or after treatment with CPAP.

Body Mass Index↗

The effect of feeding ractopamine (Paylean) on muscle quality and sensory characteristics in three diverse genetic lines of swine.

The present experiment utilized Berkshire (n = 76), Duroc (n = 81), and high-lean commercial crossbred (n = 75) barrows and gilts with an initial BW of approximately 85.1 kg. Pigs were fed a standard commercial diet (17.6% CP, 1.02% lysine) supplemented with ractopamine hydrochloride at a level of 0 or 10 ppm for 28 d. The experiment was conducted in a randomized complete block design, with animals blocked within genetic line according to litter, gender, and weight, for a total of four blocks per genetic line for each treatment. Pigs were harvested at a commercial abattoir and chilled for 24 h at 1 to 4 degrees C. At 24 h postmortem, wetness and firmness scores and ultimate muscle pH were measured in the center of the longissimus muscle (LM) at the 10th to 11th rib interface. Visual and instrumental color and marbling score were measured at 48 h postmortem on a fresh cut LM surface. Percentage of chemically extracted intramuscular fat (IMF) was measured, and a trained sensory panel evaluated cooked LM chops for juiciness, tenderness, and chewiness. Cooking loss (%) and instrumental measurement of tenderness also were measured on cooked LM chops. Ractopamine treatment increased ADG (P < 0.01) and LM area (P < 0.05), but had no effect (P > 0.05) on LM quality, sensory attributes, or instrumental measures of palatability. Berkshire LM received higher tenderness and juiciness (P < 0.05) scores and had lower cooking losses (P < 0.05) and instrumental tenderness (P < 0.05) than LM from the Duroc and high-lean lines. Loins from barrows were firmer (P < 0.05), had lower drip loss percentages (P < 0.05), and received greater tenderness scores (P < 0.05) than the LM from gilts. Genetic line x treatment and gender x treatment interactions were detected for IMF. The LM of Berkshire pigs fed ractopamine had lower (P < 0.05) IMF than Berkshires fed the control diet, with no interaction in the other lines. Purebred barrows (Berkshire and Duroc) had greater (P < 0.001 and P < 0.05, respectively) IMF than their respective purebred gilts, with no gender difference in IMF in the high-lean line. Results from the present study indicate that feeding ractopamine does not affect most muscle quality and palatability characteristics. However, the genetic line x treatment interaction for loin IMF suggests that feeding ractopamine might reduce IMF within the loin muscle of genetic lines that have a propensity to produce greater levels of IMF.

Adipose Tissue↗

An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.

MOTIVATION: Large-scale sequence data require methods for the automated annotation of protein domains. Many of the predictive methods are based either on a Position Specific Scoring Matrix (PSSM) of fixed length or on a window-less Hidden Markov Model (HMM). The performance of the two approaches is tested for Coiled-Coil Domains (CCDs). The prediction of CCDs is used frequently, and its optimization seems worthwhile. RESULTS: We have conceived MARCOIL, an HMM for the recognition of proteins with a CCD on a genomic scale. A cross-validated study suggests that MARCOIL improves predictions compared to the traditional PSSM algorithm, especially for some protein families and for short CCDs. The study was designed to reveal differences inherent in the two methods. Potential confounding factors such as differences in the dimension of parameter space and in the parameter values were avoided by using the same amino acid propensities and by keeping the transition probabilities of the HMM constant during cross-validation. AVAILABILTY: The prediction program and the databases are available at http://www.wehi.edu.au/bioweb/Mauro/Marcoil

Algorithms↗