bluuebunny/crossref_metadata_2025 huggingface dataset:
Drinking Water Is Associated With Weight Loss in Overweight Dieting Women Independent of Diet and Activity
Authors: Stookey Jodi D. , Constant Florence , Popkin Barry M. , Gardner Christopher D.
Published: September 2008

Background: Data from short‐term experiments suggest that drinking water may promote weight loss by lowering total energy intake and/or altering metabolism. The long‐term effects of drinking water on change in body weight and composition are unknown, however.

Objective: This study tested for associations between absolute and relative increases in drinking water and weight loss over 12 months.

Methods and Procedures: Secondary analyses were conducted on data from the Stanford A TO Z weight loss intervention on 173 premenopausal overweight women (aged 25–50 years) who reported <1 l/day drinking water at baseline. Diet, physical activity, body weight, percent body fat (dual‐energy X‐ray absorptiometry), and waist circumference were assessed at baseline, 2, 6, and 12 months. At each time point, mean daily intakes of drinking water, noncaloric, unsweetened caloric (e.g., 100% fruit juice, milk) and sweetened caloric beverages, and food energy and nutrients were estimated using three unannounced 24‐h diet recalls. Beverage intake was expressed in absolute (g) and relative terms (% of beverages). Mixed models were used to test for effects of absolute and relative increases in drinking water on changes in weight and body composition, controlling for baseline status, diet group, and changes in other beverage intake, the amount and composition of foods consumed and physical activity.

Results: Absolute and relative increases in drinking water were associated with significant loss of body weight and fat over time, independent of covariates.

Discussion: The results suggest that drinking water may promote weight loss in overweight dieting women.
The Challenge of CT and MRI Imaging of Obese Individuals Who Present to the Emergency Department: A National Survey
Authors: Ginde Adit A. , Foianini Anthony , Renner Daniel M. , Valley Morgan , Camargo Carlos A.
Published: September 2008

The objective of this study was to estimate the availability of large weight capacity computed tomography (CT) and magnetic resonance imaging (MRI) equipment in US hospitals with emergency departments (EDs) and to evaluate animal facilities as alternate sources of imaging. We conducted a telephone survey of radiology technicians from a random sample of all the US hospitals with EDs (n = 262) and all 136 primary hospitals of academic EDs, 145 zoos, and 28 veterinary schools. We measured the prevalence of large weight capacity (>450 lb) CT and MRI, stratified by hospital characteristics. Response rates were 94–100% across samples. Nationally, 10% (95% confidence interval, 7–15) of hospitals with EDs had large weight capacity CT and 8% (95% confidence interval, 5–13) had large weight capacity MRI. In academic hospitals, access to large capacity equipment was better for CT (28%), but similar for MRI (10%) (P < 0.001 and 0.51, respectively). Few rural (5%) and critical‐access hospitals (3%) had large capacity CT. In addition, 34% of trauma centers, 23% of stroke centers, and 21% of bariatric surgery centers of excellence had large capacity CT. Only two zoos (1%) had CT scanners; both would not image human patients. Among veterinary schools, 16 (57%) had large weight capacity CT equipment, but only 4 (14%) would consider imaging human patients. Further, 23 (82%) veterinary schools reported policies that specifically prohibited imaging humans. For patients who weigh >450 lb, access to emergent CT and MRI is limited, even at academic and bariatric surgery centers. Animal facilities are not a viable alternative for diagnostic imaging of human patients.
Molecular, biochemical and functional characterizations of C1q/TNF family members: adipose-tissue-selective expression patterns, regulation by PPAR-γ agonist, cysteine-mediated oligomerizations, combinatorial associations and metabolic functions
Authors: Wong G. William , Krawczyk Sarah A. , Kitidis-Mitrokostas Claire , Revett Tracy , Gimeno Ruth , Lodish Harvey F.
Published: September 2008

The insulin-sensitizing hormone, adiponectin, belongs to the expanding C1q/TNF (tumour necrosis factor) family of proteins. We recently identified a family of adiponectin paralogues designated as CTRP (C1q/TNF-related protein) 1–7, and in the present study describe CTRP10. In the present study, we show that CTRP1, CTRP2, CTRP3, CTRP5 and CTRP7 transcripts are expressed predominantly by adipose tissue. In contrast, placenta and eye expressed the highest levels of CTRP6 and CTRP10 transcripts respectively. Expression levels of CTRP1, CTRP2, CTRP3, CTRP6 and CTRP7 transcripts are up-regulated in 8-week-old obese (ob/ob) mice relative to lean controls. Treatment of mice with a PPAR-γ (peroxisome-proliferator-activated receptor-γ) agonist, rosiglitazone, increased the expression of CTRP1 and decreased CTRP6 transcript levels. All CTRPs are secreted glycoproteins when expressed in mammalian cells. CTRP1, CTRP2, CTRP3, CTRP5 and CTRP6 circulate in the blood and are potential endocrine hormones; their serum levels vary according to the sex and genetic background of mice. Importantly, serum levels of CTRP1 and CTRP6 are increased in adiponectin-null mice. Like adiponectin, all secreted CTRP proteins form trimers as their basic structural units. CTRP3, CTRP5, CTRP6 and CTRP10 trimers are further assembled into higher-order oligomeric complexes via disulfide bonding mediated by their N-terminal cysteine residues. Besides forming homo-oligomers, CTRP1/CTRP6, CTRP2/CTRP7 and adiponectin/CTRP2 are secreted as heterotrimers, thus providing a mechanism to potentially generate functionally distinct ligands. Functional characterization of one such family member, CTRP1, showed that it specifically activates Akt and p44/42-MAPK (mitogen-activated protein kinase) signalling pathways in differentiated mouse myotubes. Moreover, injection of recombinant CTRP1 into mice significantly reduced their serum glucose levels. Thus at least CTRP1 may be considered a novel adipokine. In summary, these molecular, biochemical and functional data provide an important framework to further address the physiological functions and mechanisms of the action of this family of secreted glycoproteins in normal and disease states.
Direct heterosis for liveweight and chick mortality in ostriches
Authors: Engelbrecht A. , Cloete S. W. P. , van Wyk J. B.
Published: September 2008

Ostriches from the South African Black (SAB) and Zimbabwean Blue (ZB) strains, raised to slaughter age in Oudtshoorn, South Africa, were used to investigate the possibility of improving the growth and survival of commercial ostriches through crossbreeding. Growth data from purebred and crossbred ostriches were analysed to estimate heterotic effects at different age intervals. Heterosis was significant at 1 month (P = 0.017) and 14 months of age (P = 0.03), and approached significance (P < 0.071) at 7, 8 and 13 months of age. Different growth patterns were observed between the two purebred strains, with weight at 14 months differing significantly (SAB 89.6 ± 0.9 kg v. ZB 98.3 ± 4.5 kg). The weight advantage relative to SAB birds at this stage amounted to 10% for ZB, 11% for ZB × SAB and 13% for SAB × ZB (all P < 0.05). Mortality to 30 days also showed significant heterosis (P < 0.05). ZB birds had the highest mortality rate at 0.38 ± 0.03, followed by the SAB × ZB (0.34 ± 0.03), the SAB (0.27 ± 0.01) and the ZB × SAB (0.23 ± 0.02) strains. Results indicate that crossbreeding may be utilised to improve the growth and chick survival of commercial ostriches. The breed combinations should be assessed for other productivity traits to determine the viability of a structured crossbreeding program.
Genetic relationships between water loss and shell deaths in ostrich eggs, assessed as traits of the female
Authors: Brand Z. , Cloete S. W. P. , Malecki I. A. , Brown C. R.
Published: September 2008

The ostrich industry suffers from a high rate of embryonic mortality during artificial incubation of eggs. Data from 34 285 eggs were used to derive 969 female-year records for evaporative water loss (WL), treated as a trait of the female. Heritability was significant for WL at a level of 0.40–0.41 (both after 21 and 35 days of incubation). WL at 21 and 35 days was negatively correlated on the genetic level with chick weight at hatching (–0.84 and –0.81, respectively). Shell deaths did not exhibit high levels of genetic variation (0.06), but were affected by the permanent environment of the female (0.33). Shell deaths were correlated with WL on a genetic level (–0.34 to –0.41), but the estimated genetic correlations were associated with high standard errors and are, therefore, not very robust. Further research is needed to obtain more accurate genetic relationships between traits influencing incubation.
A gross anatomical and histo-morphological study of the vagina of the emu (Dromaius novaehollandiae) and ostrich (Struthio camelus)
Authors: Madekurozwa M.-C.
Published: September 2008

The present study details anatomical features of the lining of the emu and ostrich vagina, which in birds may impede the forward movement of spermatozoa. Vaginal samples were collected for light and electron microscopy. Samples for light microscopy were fixed in Bouin’s fluid, while samples for electron microscopy were fixed in 3% glutaraldehyde. After fixation the samples were processed routinely. A series of broad annular mucosal folds bearing convoluted primary folds were present in both ratites. The lining of the vaginal folds was a combination of ciliated, non-ciliated, vesicular and mitochondrial cells. The non-ciliated and a few ciliated cells, lining the crypts, contained mucin droplets. The role of the mucus is unclear. The results of the study show a similarity in the gross anatomical and scanning electron microscope features of the vagina in the emu and ostrich. Differences in the cellular composition of the vaginal epithelium were observed at the transmission electron microscope level.
Effect of diets with different energy and protein levels on performance of grower ostriches
Authors: Glatz P. C. , Miao Z. H. , Rodda B. K. , Wyatt S. C.
Published: September 2008

Grower ostriches that are fed more expensive diets with high energy and high protein to maximise growth can exhibit health problems. Despite this there is an ‘industry view’ that birds can be grown to slaughter weight within 8 months when high energy and protein diets are used, rather than 12–14 months using conventional diets. Given this scenario it is likely that there would be lower total feed costs associated with feeding a high energy and high protein diet for only 8 months compared with feeding a traditional diet for 12–14 months. The purpose of this experiment was to conduct an on-farm trial with grower ostriches (liveweight 48.7–50.0 kg) housed in a feedlot to examine their performance when subjected to four dietary treatments fed over 4 weeks: (i) treatment 1: birds fed a commercial grower diet with 10.7 MJ/kg and 138.0 g/kg of protein; (ii) treatment 2: birds fed a low energy (10.0 MJ/kg) and low protein (126.0 g/kg) diet; (iii) treatment 3: birds fed a high energy (12.5 MJ/kg) and medium protein (136.0 g/kg) diet; and (iv) treatment 4: birds fed a high energy (12.5 MJ/kg) and high protein (143.0 g/kg) diet in a feedlot. Birds fed on the low energy and low protein diet had the highest feed intake compared with the other treatments. Birds on treatment 2 also had a significantly higher (P = 0.01) daily weight gain (277.3 g/bird) compared with treatment 1 (50.9 g), treatment 3 (49.1 g) and treatment 4 (32.0 g), respectively. The results indicate that better daily bodyweight gain is likely if ostrich growers are fed with a lower energy and lower protein diet.
L-carnitine improves egg production in black neck ostriches
Authors: Hajibabaei A. , Shivazad M. , Adabi Sh. Golzar , Lavaf A. , Eila N.
Published: September 2008

The important functions of L-carnitine are fostering the oxidation of long-chain fatty acids by mitochondria and stimulating protein-sparing action by increasing energy derived from lipids. The present study was conducted to investigate dietary effects of L-carnitine on egg production of breeder ostriches. Ninety black neck ostrich breeder birds (60 females and 30 males) were examined randomly (completely randomised design) within three treatments and five replicates for 7 months in breeding season. A basal diet was formulated and used for the control group (L1), while two levels of L-carnitine, 250 mg/kg and 500 mg/kg, were included in the basal diet for treatments L2 and L3, respectively. The egg production percentage, egg weight and defective eggshell percentage were measured. The supplementary diet with 500 mg/kg L-carnitine increased (P < 0.01) the egg production percentage. Means (±s.e.) of egg production percentage for L1, L2 and L3 were 9.68, 12.95 and 17.13% (±1.08), respectively. L-carnitine had no effect on the egg weight and the defective eggshell percentage. The results suggest that basal diet supplemented with 500 mg/kg L-carnitine can increase the egg production percentage of ostriches.
Comparison of the antioxidant properties of emu oil with other avian oils
Authors: Bennett Darin C. , Code William E. , Godin David V. , Cheng Kimberly M.
Published: September 2008

The antioxidant properties of emu oil were compared with oils derived from the fat of other avian species. We first examined their free radical scavenging activity against the 2,2-diphenyl-1-picryl hydracyl radical. The concentration of emu oil in the test solution that caused 50% neutralisation (IC50) was variable (24.5 ± 5.9 mg/mL, range 5.3–55.4 mg/mL), but similar to values obtained for other ratites (10.7 ± 5.9 mg/mL). In contrast, the IC50 values for duck and chicken oil were much higher (118.0 ± 8.1 mg/mL). The variability in the radical scavenging activity of emu oil preparations may reflect variations in the diets of the birds, the processing protocol and/or the storage age of the oil. We also evaluated some of the ratite oils for their inhibitory capacity on human erythrocyte membrane oxidation, by measuring the reduction of the thiobarbituric acid-reactive substance (TBAR) production. Emu oil had a greater effect in decreasing TBAR production than either the ostrich or rhea oil, suggesting that it offers more protection than the other ratite oils against oxidative damage. In conclusion, we demonstrated that emu oil has both antioxidant properties in vitro and a protective role against oxidative damage in a model biological membrane system. The antioxidant or radical scavenging properties of emu oil appear to be due to minor constituents in the non-triglyceride fraction of the oil, while its high ratio of unsaturated to saturated fatty acids (UFA : SFA) offers protection against oxidative damage.
Husbandry of ratites and potential welfare issues: a review
Authors: Glatz P. C. , Miao Z. H.
Published: September 2008

Since the mid-1980s, there has been worldwide farming of ratites, particularly with ostriches, emus and rheas for feathers, meat, skin and oil. Most of these ratites are produced commercially outside their native habitat. This has raised concerns about welfare, particularly whether birds are provided the five freedoms: food and water; shelter; health care; alleviation of pain and suffering; and the freedom of movement. This paper reviews the factors that influence bird welfare before hatch with breeder, egg and hatchery management and after hatch with brooding and rearing systems, stocking density, handling, transport, disease and slaughter. Assessment of bird welfare in each of the production sectors in the industry is based on how well the five freedoms are being met. The review identifies egg handling practices and hatchery hygiene that can have a major impact on the subsequent health of hatched chicks. In addition, feeding of appropriate diets, reducing stocking density and improving housing can improve bird health and freedom of movement. When the husbandry practice of toe trimming is not practiced according to the best practice method, chronic pain may result and impair walking ability of birds. Stress and injuries to birds can be reduced when birds are handled correctly on farm and in the lairage and are transported using appropriate vehicles. Farmers, transporters and abattoir staff can have a major impact on maintaining bird welfare if best practice farming systems and husbandry practices are implemented.
Simulation models used for determining food intake and growth of ostriches: an overview
Authors: Gous R. M. , Brand T. S.
Published: September 2008

A formal method for determining the amino acid requirements of ostriches, from which a feeding strategy may be developed, requires characterisation of the growth potential of the body and feather proteins of these birds. Allometric equations may then be used to predict the growth of the physical parts of the ostrich, from which the optimal harvest time can be determined. Reasonable estimates of the parameters describing body and feather growth are now available. These values, together with the amino acid composition of the ostrich carcasses obtained at various stages of growth, make it possible to calculate the daily amino acid requirements of an ostrich growing at its potential. Subsequently, when given a description of the feed being offered, the desired food intake can be determined. The constraining effects of feed bulk and high temperatures are not yet well defined, but voluntary food intake in these birds when fed intensively under normal environmental conditions can now be predicted with the use of simulation models, from which it is possible to design a feeding strategy that will optimise performance.
Value adding and processing of ratite meat: a review
Authors: Hoffman L. C.
Published: September 2008

Ratite meat is usually sold as fresh meat (steaks), with trimmings being processed into products such as burger patties and sausages. Most of the steaks are vacuum packed and exported. With the outbreak of Avian influenza, all fresh meat exports were halted from South Africa. However, if the meat has been exposed to an internal core temperature of 70°C, it may then be exported under the Meat Products Directive (EEC 2004) because it is assumed safe for human consumption; this placed an urgency in developing value-added meat products. These products are sold as vacuum packed and cooked ostrich steaks. Salt infusion is frequently used to improve water retention of these sous vide products. Other products that have been developed are functional foods, such as emu snack sticks (higher creatine levels) for athletes. The quality and composition of other more traditional meat products such as sausages, patties, salami and pâté have also been determined and are discussed. A strong emphasis has been to develop products that will enhance the healthy perception of ratite meat amongst consumers. These include the development of low-salt bacon, hams with lower levels of phosphates and polonies with olive oil replacing pork fat. The quality attributes of these products are also discussed as are future trends in the processing trade.
Can emu oil ameliorate inflammatory disorders affecting the gastrointestinal system?
Authors: Howarth Gordon S. , Lindsay Ruth J. , Butler Ross N. , Geier Mark S.
Published: September 2008

Emu oil possesses significant anti-inflammatory properties in vivo, primarily when applied topically. However, to date, the evidence supporting its therapeutic application has been largely anecdotal, and significant batch-to-batch variations in potency have been reported. Nevertheless, the anti-inflammatory properties of emu oil suggest therapeutic promise for the adjunctive treatment of a range of disparate gastrointestinal diseases and disorders characterised by inflammatory processes. These include the idiopathic condition inflammatory bowel disease, chemotherapy-induced mucositis, non-steroidal anti-inflammatory drug enteropathy and the various infective enteritides (i.e. fungal, bacterial and viral gastroenteritis). Although rigorous scientific investigations are in their infancy, the evidence for emu oil efficacy in extra-intestinal disorders, supported by limited in vivo investigations of other naturally sourced oils, identifies emu oil as a possible adjunct to conventional treatment approaches for inflammatory disorders affecting the gastrointestinal system.
Intestinal development and nutrient utilisation in the ostrich: a brief review
Authors: Iji P. A.
Published: September 2008

The ostrich industry is plagued by a high level of neonatal mortality among chicks that are under 3 months of age. Although ostrich chicks hatch with a gastrointestinal tract that is more than 10% of their liveweight, there appear to be deficiencies in structural and functional development of the intestinal mucosa (and possibly pancreatic function) that do not support adequate digestive function. There is also insufficient knowledge of the nutritional requirements of the ostrich, which results in the provision of diets that may not be suitable, particularly for the hatchlings. Recent evidence suggests that ostrich chicks under the age of 10 weeks have poor ability to digest fibre. Further evaluations have revealed generally low activities of amylase, trypsin and lipase in ostrich chicks within the first 10 weeks of life. It is not certain if digestive function can be improved by supplementation with microbial enzymes, which are routinely used by the poultry industry. There is still a paucity of data on the digestive physiology of the ostrich and areas of intervention through applied nutrition are still vague. This paper reviews existing knowledge of the digestive physiology of the ostrich and examines the potential of interventions that could reduce neonatal mortality in the species.
Thermoregulation in ratites: a review
Authors: Maloney Shane K.
Published: September 2008

Laboratory and free-ranging studies on the emu, ostrich and kiwi show ratites to be competent homeotherms. While body temperature and basal metabolic rate are lower in ratites than other birds, all of the thermoregulatory adaptations present in other birds are well established in ratites. The thermoneutral zone has been established for the emu and kiwi, and extends to 10°C. Below that zone, homeothermy is achieved via the efficient use of insulation and elevated metabolic heat production. In the heat, emus and ostriches increase respiratory evaporative water loss and use some cutaneous water loss. Respiratory alkalosis is avoided by reducing tidal volume. In severe heat, tidal volume increases, but the emu becomes hypoxic and hypocapnic, probably by altering blood flow to the parabronchi, resulting in ventilation/perfusion inhomogeneities. Ostriches are capable of uncoupling brain temperature from arterial blood temperature, a phenomenon termed selective brain cooling. This mechanism may modulate evaporative effector responses by manipulating hypothalamic temperature, as in mammals. The implications of thermal physiology for ratite production systems include elevated metabolic costs for homeothermy at low ambient temperature. However, the emu and ostrich are well adapted to high environmental temperatures.
Ostrich farming and environmental management tools: an overview
Authors: Rodrigues G. S. , Buschinelli C. C. de A. , Muniz L. R.
Published: September 2008

There is an increasing demand in the ostrich farming sector for management tools that are capable of motivating, preparing and guiding producers to meet the requirements of ‘environmentally conscious’ consumers. Many methodological options are currently available to conduct sustainability assessments and to ensure the best environmental management of rural activities. One option, the ‘System for weighed environmental impact assessment of rural activities’ (APOIA-NovoRural), has recently been validated for ostrich farming, as a tool for checking the contributions of the activity to local sustainable development. Case studies have favoured the understanding of the main environmental impacts and provided valuable recommendations regarding natural resources management and landscape ecology improvements in ostrich farming systems. Most importantly, the criteria and indicators constructed in this environmental management tool may be used for defining general ‘Terms of Reference’ for sustainable ostrich farming.
Direct and indirect roles for Nodal signaling in two axis conversions during asymmetric morphogenesis of the zebrafish heart
Authors: Baker Kari , Holtzman Nathalia G. , Burdine Rebecca D.
Published: September 2008

The Nodal signaling pathway plays a conserved role in determining left-sided identity in vertebrates with this early left-right (L/R) patterning influencing the asymmetric development and placement of visceral organs. We have studied the role of Nodal signaling in asymmetric cardiac morphogenesis in zebrafish and describe two distinct rotations occurring within the heart. The first is driven by an asymmetric migration of myocardial cells during cardiac jogging, resulting in the conversion of the L/R axis to the dorsal-ventral (D/V) axis of the linear heart. This first rotation is directly influenced by the laterality of asymmetric gene expression. The second rotation occurs before cardiac looping and positions the original left cells exposed to Nodal signaling back to the left of the wild-type (WT) heart by 48 hours postfertilization (hpf). The direction of this second rotation is determined by the laterality of cardiac jogging and is not directly influenced by asymmetric gene expression. Finally, we have identified a role for Nodal signaling in biasing the location of the inner ventricular and outer atrial curvature formations. These results suggest that Nodal signaling directs asymmetric cardiac morphogenesis through establishing and subsequently reinforcing laterality information over the course of cardiac development.
A microRNA signature for a BMP2-induced osteoblast lineage commitment program
Authors: Li Zhaoyong , Hassan Mohammad Q. , Volinia Stefano , van Wijnen Andre J. , Stein Janet L. , Croce Carlo M. , Lian Jane B. , Stein Gary S.
Published: September 2008

Bone morphogenetic proteins (BMPs) are potent morphogens that activate transcriptional programs for lineage determination. How BMP induction of a phenotype is coordinated with microRNAs (miRNAs) that inhibit biological pathways to control cell differentiation, remains unknown. Here, we show by profiling miRNAs during BMP2 induced osteogenesis of C2C12 mesenchymal cells, that 22 of 25 miRNAs which significantly changed in response to BMP2 are down-regulated. These miRNAs are each predicted to target components of multiple osteogenic pathways. We characterize two representative miRNAs and show that miR-133 directly targets Runx2, an early BMP response gene essential for bone formation, and miR-135 targets Smad5, a key transducer of the BMP2 osteogenic signal, controlled through their 3′UTR sequences. Both miRNAs functionally inhibit differentiation of osteoprogenitors by attenuating Runx2 and Smad5 pathways that synergistically contribute to bone formation. Although miR-133 is known to promote MEF-2-dependent myogenesis, we have identified a second complementary function to inhibit Runx2-mediated osteogenesis. Our key finding is that BMP2 controls bone cell determination by inducing miRNAs that target muscle genes but mainly by down-regulating multiple miRNAs that constitute an osteogenic program, thereby releasing from inhibition pathway components required for cell lineage commitment. Thus, our studies establish a mechanism for BMP morphogens to selectively induce a tissue-specific phenotype and suppress alternative lineages.
A helix scaffold for the assembly of active protein kinases
Authors: Kornev Alexandr P. , Taylor Susan S. , Ten Eyck Lynn F.
Published: September 2008

Structures of set of serine-threonine and tyrosine kinases were investigated by the recently developed bioinformatics tool Local Spatial Patterns (LSP) alignment. We report a set of conserved motifs comprised mostly of hydrophobic residues. These residues are scattered throughout the protein sequence and thus were not previously detected by traditional methods. These motifs traverse the conserved protein kinase core and play integrating and regulatory roles. They are anchored to the F-helix, which acts as an organizing “hub” providing precise positioning of the key catalytic and regulatory elements. Consideration of these discovered structures helps to explain previously inexplicable results.
Derivation and Validation of a Clinical Prediction Score for Isolation of Inpatients With Suspected Pulmonary Tuberculosis
Authors: Rakoczy Kara S. , Cohen Stuart H. , Nguyen Hien H.
Published: September 2008

Background.

The use of a clinical prediction score to improve the practice of instituting airborne-transmission precautions in patients with suspected tuberculosis holds promise for increasing appropriate isolation and decreasing unnecessary isolation. The objective of this study was to derive and validate a clinical prediction score for patients with suspected tuberculosis.

Methods.

We used a case—control study design to evaluate differences between patients with a diagnosis of tuberculosis and those placed under airborne precautions who had negative culture results. We developed risk scores based on a multivariable analysis of independently significant factors associated with tuberculosis. Subsequently, we evaluated the sensitivity and specificity of the score in a separate (validation) cohort of patients.

Results.

Within our population, we found 4 clinical factors associated with tuberculosis: chronic symptoms (odds ratio [OR], 10.2 [95% confidence interval {CI}, 2.95-35.4]), upper lobe disease on chest radiograph (OR, 5.27 [95% CI, 1.6-17.23]), foreign-born status (OR, 7.01 [95% CI, 2.1-23.8]), and immunocompromised state other than human immunodeficiency virus infection (OR, 8.14 [95% CI, 2.08-31.8]). Shortness of breath (OR, 0.13 [95% CI, 0.04-0.45]) was found to be associated with non-tuberculosis diagnoses and considered a negative predictor in the model. Using a cut-off point to maximize sensitivity, we applied the prediction rule to the validation cohort, resulting in a sensitivity of 97% and a specificity of 42%.

Conclusion.

The tuberculosis prediction rule derived from our patient population could improve utilization of airborne precautions. Clinical prediction rules continue to show their utility for improvement in isolation practices in different demographic areas.
Beryllium flux distribution and layer deposition in the ITER divertor
Authors: Schmid K.
Published: September 2008

The deposition of Be eroded from the main chamber wall on the W surfaces in the ITER divertor could result in the formation of Be rich Be/W mixed layers with a low melting temperature compared with pure W. To predict whether or not these layers form the Be flux distribution in the ITER divertor is required. This paper presents the results of a combination of plasma transport with erosion/deposition simulations that allow one to calculate both the Be flux distribution and the Be layer deposition in the ITER divertor. This model includes the Be source due to Be erosion in the main chamber and the deposition, re-erosion and re-deposition of Be in the ITER divertor. The calculations show that the fraction of Be in the incident particle flux in the divertor ranges from ≈10−3 to ≈5% with a pronounced inner–outer divertor asymmetry. The flux fractions in the inner divertor are on average ten times higher than in the outer divertor. Thick Be layers only form at the inner strike point and the dome baffles. The highest Be layer growth rate is found to be 1.0 nm s−1. Despite the Be deposition the formation of Be rich Be/W mixed layers is not to be expected in ITER. The expected surface temperature at these locations during steady-state operation is too low as to result in Be diffusion into W and thus Be/W mixed layers cannot form. The paper also discusses the influence of off normal events such as ELMs or VDEs on the formation of Be/W mixed layers.
Light impurity transport at an internal transport barrier in Alcator C-Mod
Authors: Rowan William L. , Bespamyatnov Igor O. , Fiore C.L.
Published: September 2008

Density profiles for a light impurity, boron, are reported for internal transport barrier (ITB) discharges in Alcator C-Mod. During the ITB, the light impurity gradient steepens because the impurity pinch increases relative to diffusion. The ITB-induced impurity profile steepening is at approximately the same major radius as that for the main-ion profile. Neoclassical transport does not describe the light impurity profiles but transport is closer to neoclassical in the ITB region. In previous work on C-Mod, profiles of seeded heavy impurities (introduced by puffing) peaked during the ITB, but a marked difference between transport of heavy and light impurities has been reported for other tokamaks. With the addition of light impurity profiles described here, the ITB on C-Mod is shown to share additional profile traits with the ITB on other tokamaks. This confirms that the macroscopic features of the C-Mod ITB are similar to those on other devices although it leaves open the details of the onset of the ITB.
Cyclin G2 Is Degraded through the Ubiquitin-Proteasome Pathway and Mediates the Antiproliferative Effect of Activin Receptor-like Kinase 7
Authors: Xu Guoxiong , Bernaudo Stefanie , Fu Guodong , Lee Daniel Y. , Yang Burton B. , Peng Chun
Published: September 2008

We have previously reported that Nodal, a member of the TGF-β superfamily, acts through activin receptor-like kinase 7 (ALK7) to inhibit ovarian cancer cell proliferation. To determine the mechanism underlying their effects, a cell cycle gene array was performed and cyclin G2 mRNA was found to be strongly up-regulated by Nodal and ALK7. To study the function and regulation of cyclin G2 in ovarian cancer cells, expression constructs were generated. We found that cyclin G2 protein level decreased rapidly after transfection, and this decrease was prevented by 26S proteasome inhibitors. Immunoprecipitation and pull-down studies showed that ubiquitin, Skp1, and Skp2 formed complexes with cyclin G2. Knockdown of Skp2 by siRNA increased, whereas overexpression of Skp2 decreased cyclin G2 levels. Nodal and ALK7 decreased the expression of Skp1 and Skp2 and increased cyclin G2 levels. Overexpression of cyclin G2 inhibited cell proliferation whereas cyclin G2-siRNA reduced the antiproliferative effect of Nodal and ALK7. Taken together, these findings provide strong evidence that cyclin G2 is degraded by the ubiquitin–proteasome pathway and that Skp2 plays a role in regulating cyclin G2 levels. Furthermore, our results also demonstrate that the antiproliferative effect of Nodal/ALK7 on ovarian cancer cells is in part mediated by cyclin G2.
Activation of TORC1 Transcriptional Coactivator through MEKK1-induced Phosphorylation
Authors: Siu Yeung-Tung , Ching Yick-Pang , Jin Dong-Yan
Published: September 2008

CREB is a prototypic bZIP transcription factor and a master regulator of glucose metabolism, synaptic plasticity, cell growth, apoptosis, and tumorigenesis. Transducers of regulated CREB activity (TORCs) are essential transcriptional coactivators of CREB and an important point of regulation on which various signals converge. In this study, we report on the activation of TORC1 through MEKK1-mediated phosphorylation. MEKK1 potently activated TORC1, and this activation was independent of downstream effectors MEK1/MEK2, ERK2, JNK, p38, protein kinase A, and calcineurin. MEKK1 induced phosphorylation of TORC1 both in vivo and in vitro. Expression of the catalytic domain of MEKK1 alone in cultured mammalian cells sufficiently caused phosphorylation and subsequent activation of TORC1. MEKK1 physically interacted with TORC1 and stimulated its nuclear translocation. An activation domain responsive to MEKK1 stimulation was mapped to amino acids 431–650 of TORC1. As a physiological activator of CREB, interleukin 1α triggered MEKK1-dependent phosphorylation of TORC1 and its consequent recruitment to the cAMP response elements in the interleukin 8 promoter. Taken together, our findings suggest a new mechanism for regulated activation of TORC1 transcriptional coactivator and CREB signaling.
F-Seq: a feature density estimator for high-throughput sequence tags
Authors: Boyle Alan P. , Guinney Justin , Crawford Gregory E. , Furey Terrence S.
Published: September 2008

Summary: Tag sequencing using high-throughput sequencing technologies are now regularly employed to identify specific sequence features, such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). To intuitively summarize and display individual sequence data as an accurate and interpretable signal, we developed F-Seq, a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

Availability: The software is written in the Java language and is available on all major computing platforms for download at http://www.genome.duke.edu/labs/furey/software/fseq.

Contact:  terry.furey@duke.edu
The expression of secondary sexual characteristics in recruit- and repeat-spawning farmed and wild Atlantic cod (Gadus morhua)
Authors: Skjæraasen Jon Egil , Meager Justin J. , Karlsen Ørjan
Published: September 2008

Skjæraasen, J. E., Meager, J. J., and Karlsen, Ø. 2008. The expression of secondary sexual characteristics in recruit- and repeat-spawning farmed and wild Atlantic cod (Gadus morhua). – ICES Journal of Marine Science, 65: 1710–1716. We examined the expression of the two known secondary sexual characteristics of Atlantic cod, the pelvic fin and the drumming muscle, in farmed and wild cod stemming from the same population. Farmed and wild males had longer pelvic fins and larger drumming muscles than females, but wild cod had longer fins than farmed cod. The size of the drumming muscle of males was similar among wild and farmed cod, but farmed females had smaller muscles than their wild counterparts. Repeat-spawning wild males tended to invest less in drumming-muscle mass and more in pelvic-fin growth than recruit-spawning fish, whereas the reverse was true for farmed males. Males use pelvic fins to embrace females during ventral mounts, a key mating behaviour, and display them to other males during agonistic interactions. The drumming muscle is used by males to produce sound during courtship and aggressive displays, whereas females only use sound outside the spawning season, for agonistic and defensive behaviours that are unlikely to be as important in the farming environment. The results are discussed in the context of the reproductive success of farmed escapees in the wild.
Enrichment of Phosphoproteins and Phosphopeptide Derivatization Identify Universal Stress Proteins in Elicitor-Treated Arabidopsis
Authors: Lenman Marit , Sörensson Carolin , Andreasson Erik
Published: September 2008

Protein phosphorylation is a key biological process that regulates reactions involved in plant-microbe interactions. The phosphorylated form of a protein often represents only a small fraction of the total population and can be problematic to analyze in a mass spectrometer. We demonstrate how a titanium dioxide (TiO2) resin can be employed for the enrichment of phosphoproteins, as well as a method to derivatize TiO2-purified phosphopeptides to facilitate determination of the exact site of phosphorylation. The use of these methods was exemplified by the identification of two plant proteins that were shown to be phosphorylated after the elicitation of Arabidopsis cells with Phytophthora infestans zoospores and xylanase. Both of the proteins that were identified, At5g54430.1 and At4g27320.1, were found to contain a universal stress protein domain with conserved residues for ATP binding.
Signaling Pathways That Regulate the Enhanced Disease Resistance of Arabidopsis “Defense, No Death” Mutants
Authors: Genger Ruth K. , Jurkowski Grace I. , McDowell John M. , Lu Hua , Jung Ho Won , Greenberg Jean T. , Bent Andrew F.
Published: September 2008

Arabidopsis dnd1 and dnd2 mutants lack cyclic nucleotide-gated ion channel proteins and carry out avirulence or resistance gene–mediated defense with a greatly reduced hypersensitive response (HR). They also exhibit elevated broad-spectrum disease resistance and constitutively elevated salicylic acid (SA) levels. We examined the contributions of NPR1, SID2 (EDS16), NDR1, and EIN2 to dnd phenotypes. Mutations that affect SA accumulation or signaling (sid2, npr1, and ndr1) abolished the enhanced resistance of dnd mutants against Pseudomonas syringae pv. tomato and Hyaloperonospora parasitica but not Botrytis cinerea. When SA-associated pathways were disrupted, the constitutive activation of NPR1-dependent and NPR1-independent and SA-dependent pathways was redirected toward PDF1.2-associated pathways. This PDF1.2 overexpression was downregulated after infection by P. syringae. Disruption of ethylene signaling abolished the enhanced resistance to B. cinerea but not P. syringae or H. parasitica. However, loss of NPR1, SID2, NDR1, or EIN2 did not detectably alter the reduced HR in dnd mutants. The susceptibility of dnd ein2 plants to B. cinerea despite their reduced-HR phenotype suggests that cell death repression is not the primary cause of dnd resistance to necrotrophic pathogens. The partial restoration of resistance to B. cinerea in dnd1 npr1 ein2 triple mutants indicated that this resistance is not entirely EIN2 dependent. The above findings indicate that the broad-spectrum resistance of dnd mutants occurs due to activation or sensitization of multiple defense pathways, yet none of the investigated pathways are required for the reduced-HR phenotype.
Elevated Ozone Alters Soybean-Virus Interaction
Authors: Bilgin Damla D. , Aldea Mihai , O'Neill Bridget F. , Benitez Marisol , Li Min , Clough Steven J. , DeLucia Evan H.
Published: September 2008

Increasing concentrations of ozone (O3) in the troposphere affect many organisms and their interactions with each other. To analyze the changes in a plant–pathogen interaction, soybean plants were infected with Soybean mosaic virus (SMV) while they were fumigated with O3. In otherwise natural field conditions, elevated O3treatment slowed systemic infection and disease development by inducing a nonspecific resistance against SMV for a period of 3 weeks. During this period, the negative effect of virus infection on light-saturated carbon assimilation rate was prevented by elevated O3exposure. To identify the molecular basis of a soybean nonspecific defense response, high-throughput gene expression analysis was performed in a controlled environment. Transcripts of fungal, bacterial, and viral defense-related genes, including PR-1, PR-5, PR-10, and EDS1, as well as genes of the flavonoid biosynthesis pathways (and concentrations of their end products, quercetin and kaempherol derivatives) increased in response to elevated O3. The drastic changes in soybean basal defense response under altered atmospheric conditions suggest that one of the elements of global change may alter the ecological consequences and, eventually, coevolutionary relationship of plant–pathogen interactions in the future.
HRT-Mediated Hypersensitive Response and Resistance to Turnip crinkle virus in Arabidopsis Does Not Require the Function of TIP, the Presumed Guardee Protein
Authors: Jeong Rae-Dong , Chandra-Shekara A. C. , Kachroo Aardra , Klessig Daniel F. , Kachroo Pradeep
Published: September 2008

The Arabidopsis resistance protein HRT recognizes the Turnip crinkle virus (TCV) coat protein (CP) to induce a hypersensitive response (HR) in the resistant ecotype Di-17. The CP also interacts with a nuclear-targeted NAC family of host transcription factors, designated TIP (TCV-interacting protein). Because binding of CP to TIP prevents nuclear localization of TIP, it has been proposed that TIP serves as a guardee for HRT. Here, we have tested the requirement for TIP in HRT-mediated HR and resistance by analyzing plants carrying knockout mutation in the TIP gene. Our results show that loss of TIP does not alter HR or resistance to TCV. Furthermore, the mutation in TIP neither impaired the salicylic acid–mediated induction of HRT expression nor the enhanced resistance conferred by overexpression of HRT. Strikingly, the mutation in TIP resulted in increased replication of TCV and Cucumber mosaic virus, suggesting that TIP may play a role in basal resistance but is not required for HRT-mediated signaling.
The Yeast Signal Sequence Trap Identifies Secreted Proteins of the Hemibiotrophic Corn PathogenColletotrichum graminicola
Authors: Krijger Jorrit-Jan , Horbach Ralf , Behr Michael , Schweizer Patrick , Deising Holger B. , Wirsel Stefan G. R.
Published: September 2008

The hemibiotroph Colletotrichum graminicola is the causal agent of stem rot and leaf anthracnose on Zea mays. Following penetration of epidermal cells, the fungus enters a short biotrophic phase, followed by a destructive necrotrophic phase of pathogenesis. During both phases, secreted fungal proteins are supposed to determine progress and success of the infection. To identify genes encoding such proteins, we constructed a yeast signal sequence trap (YSST) cDNA-library from RNA extracted from mycelium grown in vitro on corn cell walls and leaf extract. Of the 103 identified unigenes, 50 showed significant similarities to genes with a reported function, 25 sequences were similar to genes without a known function, and 28 sequences showed no similarity to entries in the databases. Macroarray hybridization and quantitative reverse-transcriptase polymerase chain reaction confirmed that most genes identified by the YSST screen are expressed in planta. Other than some genes that were constantly expressed, a larger set showed peaks of transcript abundances at specific phases of pathogenesis. Another set exhibited biphasic expression with peaks at the biotrophic and necrotrophic phase. Transcript analyses of in vitro-grown cultures revealed that several of the genes identified by the YSST screen were induced by the addition of corn leaf components, indicating that host-derived factors may have mimicked the host milieu.
Investigation of Downstream Signals of the Soybean Autoregulation of Nodulation Receptor Kinase GmNARK
Authors: Kinkema Mark , Gresshoff Peter M.
Published: September 2008

The Glycine max nodule autoregulation receptor kinase (GmNARK) plays a central role in the systemic signal transduction pathway controlling nodulation in soybean. We used transcriptional profiling to identify potential downstream signals of this receptor kinase. These studies revealed that GmNARK-mediated signaling controls the expression of genes involved in the jasmonic acid (JA) pathway. Genes encoding the key enzymes controlling JA biosynthesis as well as JA-response genes were regulated systemically but not locally by root inoculation with Bradyrhizobium japonicum. This systemic regulation was abolished in Gmnark mutant plants, indicating that their expression was specifically controlled by signaling events associated with this receptor kinase. Foliar application of a JA biosynthesis inhibitor significantly reduced nodulation specifically in supernodulating mutant plants. These results indicate that the receptor-mediated regulation of JA signaling plays an important role in the AON signal transduction pathway. A second class of genes was identified that were controlled by GmNARK in a rhizobia-independent manner. These candidates provide insight on additional, nonsymbiotic signaling pathways that are likely regulated by GmNARK, such as those involved in root growth and defense. The discovery of downstream components of the GmNARK receptor kinase advances our understanding of the systemic control of nodule development and its association with other signaling networks.