bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Stylosanthes guianensis supplementation on intake and nitrogen metabolism of Bos indicus cattle offered a basal diet of mixed rice straw and tropical grass
Authors: Pen Miranda , Savage Darryl B. , Nolan John V. , Seng Mom
Published: February 2013

The effect of supplementing a mixed rice straw and tropical grass diet with legume as a nitrogen (N) source on intake, digestibility, rumen ammonia and microbial protein production was evaluated in Bos indicus cattle. Four rumen-cannulated steers were used in a crossover design with two diets and two periods. The diets were T1 = 40% rice (Oryza sativa L.) straw + 60% grass (Brachiaria spp. cv. Mulato II hybrid) and T2 = 40% rice straw + 30% grass + 30% legume (Stylosanthes guianensis cv. CIAT 184) on DM basis. Supplementation with legume doubled (P < 0.01) rice straw and total N intake, and increased total DM intake by 32%. It did not affect the DM, organic matter, neutral detergent fibre and acid detergent fibre digestibility (P > 0.05) but did increase (P < 0.05) N digestibility. Faecal N and total N outputs from T2 cattle were higher (P < 0.05) than T1 cattle, but urinary N output did not differ between diets (P > 0.05). N retention in T2 cattle was improved by 83% (P < 0.05) compared with T1 cattle. Rumen ammonia concentration, microbial protein production and efficiency of microbial protein production were improved (P < 0.05) when the legume forage was included in the straw–grass diet. We conclude that when a mixed rice straw and fresh grass diet is supplemented with ~30% legume (DM basis), significant improvements in DM and N intake can be achieved.
Effect of cereal and pea monocultures and combinations and silage additives on whole-crop cereal silage nutritive and fermentation characteristics
Authors: Jacobs J. L. , Ward G. N.
Published: February 2013

The efficient production and utilisation of home-grown feed is considered one of the key factors that underpins the profitability of dairy systems in southern Australia. The use of winter forage cereals for grazing and silage provides an opportunity to achieve high dry matter yields over the winter and spring period. However, questions remain on the nutritive value of whole-crop cereal silage and its subsequent use as a production feed in livestock systems. This experiment examined the nutritive characteristics of winter wheat, triticale, forage peas and bi-crops of cereals and peas sown at different proportions, cut for silage at the soft dough growth stage of the cereals and their subsequent silage nutritive characteristics and fermentation patterns when ensiled with and without bacterial inoculant additives over 2 consecutive years. The estimated metabolisable energy (ME) (Year 1) and crude protein (CP) (Years 1 and 2) concentrations of the forage pea before and after ensiling were higher (P < 0.05) than all other forages in both years. The cereal–pea mixes had similar estimated ME values to the cereal monocultures both before harvesting and as silage, although there were significant improvements in CP concentration at the higher rates of pea inclusion. All resultant silages were well fermented as indicated by low pH, low proportions of total N as ammonia-N and high lactic acid concentrations. There were marked differences in the proportions of lactic acid and acetic acid in the pea silages between years and this is likely a result of dry matter content differences at ensiling. There was no effect of silage additives on resultant silage nutritive characteristics or fermentation parameters indicating that well fermented silage can be achieved without the additional cost of using a silage additive. This study has indicated that forage peas can be ensiled with winter cereals and produce silages that have higher CP concentrations than cereal silage but with similar fermentation parameters. Furthermore, this experiment has highlighted the potential of growing a monoculture of forage peas for ensiling with the resulting silage having higher estimated ME and CP concentrations.
A survey of free and conjugated deoxynivalenol in the 2009, 2010 and 2011 cereal crops in Australia
Authors: Tran S. T. , Smith T. K.
Published: February 2013

Free and conjugated deoxynivalenol (DON, vomitoxin) were determined in samples of cereal grain collected from the 2009, 2010 and 2011 crops in the Australian states of New South Wales, Queensland, South Australia, Victoria and Western Australia. Free DON was absent in 53–64% of analysed samples. Levels of free DON ranged from 0.10 to 7.31 µg/g. The highest levels of free DON were found in samples collected from the New South Wales 2010 crop while no samples from South Australia or Western Australia regions contained this compound. Free DON in the samples collected from the 2010 crop was significantly higher compared with those from the 2009 and the 2011 crop. Conjugated DON was detected in 61, 87 and 68% of contaminated grain samples in the 2009, 2010 and 2011 crop, respectively. Conjugated DON was found mainly in the samples collected from the 2009 crop (up to 48%) and the 2011 crop (up to 43%) but no significant difference between free DON and total DON content was observed. The current survey emphasises the frequency of non-detectable, conjugated DON in Australian cereal crops and the potential challenges in understanding the hazard posed by DON-contaminated feedstuffs.
Potential impacts of negative associative effects between concentrate supplements, pasture and conserved forage for milk production and dairy farm profit
Authors: Ho C. K. M. , Malcolm B. , Doyle P. T.
Published: February 2013

A case study and whole-farm modelling approach was used to examine the potential impacts of negative associative effects on milk production and economic performance of two dairy farms in northern Victoria. The two case studies differed in herd and farm size, calving pattern, forages grown and use of labour, but both had production systems based on grazed pasture, grain fed in the dairy at milking and conserved hay fed out in the paddock. The feeding system of each farm was altered by implementing a partial mixed ration (PMR), where cows grazed once a day and received supplements in a well formulated mix once a day. Negative associative effects between feeds were included in the biophysical modelling by deriving a relationship from published studies between declining neutral detergent fibre digestibility and increasing grain intake. Before applying a PMR system, both farms were profitable and earning competitive rates of return after tax, with mean real internal rate of return higher than 5%, and positive mean annual operating profit and mean net present value, at a discount rate of 5%. Feeding a PMR enabled both farms to increase profitability and internal rate of return, particularly if milk production was increased as well, but only when associative effects were less than those in the feeding system based on grain fed in the dairy and hay in the paddock. Increased profitability was also associated with higher standard deviation in annual operating profit, internal rate of return and net present value, in other words risk increased under the PMR feeding system, as the businesses would be more vulnerable to fluctuating supplementary feed prices.
The oral administration of meat and bone meal-derived protein fractions improved the performance of young broiler chicks
Authors: Muir W. I. , Lynch G. W. , Williamson P. , Cowieson A. J.
Published: February 2013

A study was designed to assess the impact of water-soluble proteins and peptides extracted from meat and bone meal (MBM) on broiler chick performance, following their oral delivery during the early post-hatch period. Proteinaceous material was fractionated by size exclusion filtration into weight ranges of <3 kDa (Fraction 1; 0.5 mg protein/mL), 3–100 kDa (Fraction 2; 0.5 mg protein/mL) and >100 kDa (Fraction 3; 0.8 mg protein/mL), which formed the three protein fraction treatments. A total of 1 mL of each of the respective preparations was delivered orally via gavage over 4 days (0.25 µL each day) to Cobb broiler hatchlings. Three control groups: control–unhandled, control–phosphate-buffered saline and control–handled were also included. Chicks were grown to 30 days of age. Feed intake, chick weight gain and feed conversion ratio were determined from day old through to 29 days of age. On Days 10, 16, 23 and 30, the weight of the breast and the small intestine was determined from 10 birds/treatment. For all parameters measured there was no interaction between experimental week and protein fraction treatment. Chicks receiving Fraction 2 had a statistically significant increase in feed intake and weight gain (P = 0.012) compared with the control–unhandled chicks. Chicks receiving Fraction 2 also demonstrated a numerically higher final bodyweight. Mass spectrometric analysis of all three fractions revealed that they each contained a wide array of proteinacious material. The results of this study suggests the likelihood that protein or protein-derived fragment components within the 3–100 kDa molecular weight range of MBM can generate improvements in broiler chick production, and thus promote the need for further research to identify the specific protein(s) responsible for the observed positive growth effects.
Genetic polymorphism at the CSN1S1 gene in Girgentana dairy goat breed
Authors: Mastrangelo S. , Sardina M. T. , Tolone M. , Portolano B.
Published: February 2013

The aim of this work was to evaluate the variability of the αs1-casein locus in the endangered Girgentana dairy goat breed in order to define genetic improvement and a conservation program for this breed. The study was performed on 200 dairy goats by means of different PCR protocols. The most frequent alleles were A (0.590) and F (0.290) followed by B (0.065) and N (0.047). CSN1S1 E allele was identified with a very low frequency (0.008). The most common genotype was AF (0.365) followed by AA (0.340). The high frequency of the strong genotypes is associated with the production of milk with high fat and protein content and with optimal technological properties. In Girgentana goat breed, the CSN1S1 genotype information could be utilised in selection strategies for milk protein content and milk yield, in order to select genetic lines for the production of ‘drinking milk’ using weak and null genotypes, and for niche products using strong genotypes.
Chemical composition of cover plants and its effect on maize yield in no-tillage systems in the Brazilian savanna
Authors: de Carvalho A. M. , Coelho M. C. , Dantas R. A. , Fonseca O. P. , Júnior R. Guimarães , Figueiredo C. C.
Published: February 2013

The use of cover plants is an important agricultural practice in no-tillage systems. Soil cover and nutrient recycling depend on the dynamics of plant residue decomposition. The objective of this study was to evaluate the effect of the chemical composition and decomposition rates of cover plants on maize yield in no-tillage systems in the savannah, central Brazil. Levels of hemicellulose, cellulose, and lignin, along with decomposition rates of the following plant species were determined at flowering and maturation: Urochloa ruziziensis, Cajanus cajan, Canavalia brasiliensis, Crotalaria juncea, Mucuna aterrima, Pennisetum glaucum, Raphanus sativus, Sorghum bicolor, and Triticum aestivum. Spontaneous vegetation growth in the fallow was used as a control. The highest dry matter yields were obtained from Sorghum bicolor, followed by P. glaucum, when harvested at maturation. Canavalia brasiliensis and U. ruziziensis, the species with lowest lignin levels, presented faster decomposition and lower half-life values compared with the residues of C. cajan and S. bicolor. Cover plants with the lowest lignin concentrations, and thus the fastest residue decomposition rates, such as C. brasiliensis, U. ruziziensis, and P. glaucum, resulted in higher maize yields. Urochloa ruziziensis and C. brasiliensis contributed to nutrient recycling due to their faster decomposition, while C. cajan aids in the formation of soil cover due to slower decomposition of its residues.
Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program
Authors: Guo Xin , Bernard Allister , Orlando David A. , Haase Steven B. , Hartemink Alexander J.
Published: February 2013

Due to cell-to-cell variability and asymmetric cell division, cells in a synchronized population lose synchrony over time. As a result, time-series measurements from synchronized cell populations do not reflect the underlying dynamics of cell-cycle processes. Here, we present a branching process deconvolution algorithm that learns a more accurate view of dynamic cell-cycle processes, free from the convolution effects associated with imperfect cell synchronization. Through wavelet-basis regularization, our method sharpens signal without sharpening noise and can remarkably increase both the dynamic range and the temporal resolution of time-series data. Although applicable to any such data, we demonstrate the utility of our method by applying it to a recent cell-cycle transcription time course in the eukaryote
Saccharomyces cerevisiae
. Our method more sensitively detects cell-cycle–regulated transcription and reveals subtle timing differences that are masked in the original population measurements. Our algorithm also explicitly learns distinct transcription programs for mother and daughter cells, enabling us to identify 82 genes transcribed almost entirely in early G1 in a daughter-specific manner.
Coexistence of ribbon and helical fibrils originating from hIAPP
20–29
revealed by quantitative nanomechanical atomic force microscopy
Authors: Zhang Shuai , Andreasen Maria , Nielsen Jakob T. , Liu Lei , Nielsen Erik H. , Song Jie , Ji Gang , Sun Fei , Skrydstrup Troels , Besenbacher Flemming , Nielsen Niels C. , Otzen Daniel E. , Dong Mingdong
Published: February 2013

Uncontrolled misfolding of proteins leading to the formation of amyloid deposits is associated with more than 40 types of diseases, such as neurodegenerative diseases and type-2 diabetes. These irreversible amyloid fibrils typically assemble in distinct stages. Transitions among the various intermediate stages are the subject of many studies but are not yet fully elucidated. Here, we combine high-resolution atomic force microscopy and quantitative nanomechanical mapping to determine the self-assembled structures of the decapeptide hIAPP
20–29
, which is considered to be the fibrillating core fragment of the human islet amyloid polypeptide (hIAPP) involved in type-2 diabetes. We successfully follow the evolution of hIAPP
20–29
nanostructures over time, calculate the average thickening speed of small ribbon-like structures, and provide evidence of the coexistence of ribbon and helical fibrils, highlighting a key step within the self-assembly model. In addition, the mutations of individual side chains of wide-type hIAPP
20–29
shift this balance and destabilize the helical fibrils sufficiently relative to the twisted ribbons to lead to their complete elimination. We combine atomic force microscopy structures, mechanical properties, and solid-state NMR structural information to build a molecular model containing β sheets in cross-β motifs as the basis of self-assembled amyloids.
BMP4-mediated brown fat-like changes in white adipose tissue alter glucose and energy homeostasis
Authors: Qian Shu-Wen , Tang Yan , Li Xi , Liu Yuan , Zhang You-You , Huang Hai-Yan , Xue Rui-Dan , Yu Hao-Yong , Guo Liang , Gao Hui-Di , Liu Yan , Sun Xia , Li Yi-Ming , Jia Wei-Ping , Tang Qi-Qun
Published: February 2013

Expression of bone morphogenetic protein 4 (BMP4) in adipocytes of white adipose tissue (WAT) produces “white adipocytes” with characteristics of brown fat and leads to a reduction of adiposity and its metabolic complications. Although BMP4 is known to induce commitment of pluripotent stem cells to the adipocyte lineage by producing cells that possess the characteristics of preadipocytes, its effects on the mature white adipocyte phenotype and function were unknown. Forced expression of a BMP4 transgene in white adipocytes of mice gives rise to reduced WAT mass and white adipocyte size along with an increased number of a white adipocyte cell types with brown adipocyte characteristics comparable to those of beige or brite adipocytes. These changes correlate closely with increased energy expenditure, improved insulin sensitivity, and protection against diet-induced obesity and diabetes. Conversely, BMP4-deficient mice exhibit enlarged white adipocyte morphology and impaired insulin sensitivity. We identify peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC1α) as the target of BMP signaling required for these brown fat-like changes in WAT. This effect of BMP4 on WAT appears to extend to human adipose tissue, because the level of expression of BMP4 in WAT correlates inversely with body mass index. These findings provide a genetic and metabolic basis for BMP4’s role in altering insulin sensitivity by affecting WAT development.
Hematopoietic stem cell and progenitor cell mechanisms in myelodysplastic syndromes
Authors: Pang Wendy W. , Pluvinage John V. , Price Elizabeth A. , Sridhar Kunju , Arber Daniel A. , Greenberg Peter L. , Schrier Stanley L. , Park Christopher Y. , Weissman Irving L.
Published: February 2013

Myelodysplastic syndromes (MDS) are a group of disorders characterized by variable cytopenias and ineffective hematopoiesis. Hematopoietic stem cells (HSCs) and myeloid progenitors in MDS have not been extensively characterized. We transplanted purified human HSCs from MDS samples into immunodeficient mice and show that HSCs are the disease-initiating cells in MDS. We identify a recurrent loss of granulocyte-macrophage progenitors (GMPs) in the bone marrow of low risk MDS patients that can distinguish low risk MDS from clinical mimics, thus providing a simple diagnostic tool. The loss of GMPs is likely due to increased apoptosis and increased phagocytosis, the latter due to the up-regulation of cell surface calreticulin, a prophagocytic marker. Blocking calreticulin on low risk MDS myeloid progenitors rescues them from phagocytosis in vitro. However, in the high-risk refractory anemia with excess blasts (RAEB) stages of MDS, the GMP population is increased in frequency compared with normal, and myeloid progenitors evade phagocytosis due to up-regulation of CD47, an antiphagocytic marker. Blocking CD47 leads to the selective phagocytosis of this population. We propose that MDS HSCs compete with normal HSCs in the patients by increasing their frequency at the expense of normal hematopoiesis, that the loss of MDS myeloid progenitors by programmed cell death and programmed cell removal are, in part, responsible for the cytopenias, and that up-regulation of the “don’t eat me” signal CD47 on MDS myeloid progenitors is an important transition step leading from low risk MDS to high risk MDS and, possibly, to acute myeloid leukemia.
The dimensional structure of people's fears, threats, and concerns and their relationship with right‐wing authoritarianism and social dominance orientation
Authors: Shaffer Barbara , Duckitt John
Published: February 2013

Most theories addressing the topic have proposed that threat and fear underlie right‐wing authoritarianism (RWA), and many empirical findings have been consistent with this proposition. Important questions, however, remain unanswered, such as whether RWA is associated with fear and threat in general or only specific kinds of fear and threat. Theories of RWA generate markedly different predictions on this issue, particularly with respect to social or personal fears, and whether the association would also hold for the closely related construct of social dominance orientation (SDO). We investigated the issue by asking 463 undergraduate students to rate their feelings of fear, concern, and anxiety to a comprehensive 93‐item list of potential fears and threats, which were formulated as either personal or social. Exploratory factors analysis identified five distinct fear–threat factors: Harm to Self, Child, or Country; Personal and Relationship Failures; Environmental and Economic Fears; Political and Personal Uncertainties; and Threats to Ingroup. All the fear–threat factors were correlated with RWA, with the strongest correlations being for Threats to Ingroup, and with stronger effects for social than for personal fears. None of the fear factors correlated with SDO. These relationships were not affected by controlling for Social Desirability or Emotional Stability (EMS). When the intercorrelations between fear factors and EMS were controlled using ridge regression, only Threats to Ingroup predicted RWA. Structural equation modeling indicated good fit for a model in which low levels of EMS had a significant path to Threats to Ingroup, which in turn had a significant path to RWA, and EMS having a significant though weak indirect (fully mediated) inverse effect on RWA. Implications of these findings for theories of authoritarianism and future research are discussed.
Authoritarianism and fear responses to pictures: The role of social differences
Authors: Butler J. Corey
Published: February 2013

Authoritarianism can be defined as the covariation of authoritarian submission, authoritarian aggression, and conventionalism (Altemeyer, 1981). All three of these tendencies involve adherence to specific standards of behavior: standards that could be exposed to threat and disruption. This study is an investigation of the self‐reported fear of authoritarians in response to threats. A sample of 126 university students was exposed to a series of pictures of potentially threatening people and situations. In general, participants with high scores on authoritarianism were more fearful than participants with low scores. This result was found for both social threats (i.e., social differences, social disorder) and personal threats (i.e., animals, dangerous situations). The strongest association between authoritarianism and fear involved cases of social differences, defined as elements of a person's appearance or behavior that involve diversity or deviance from common social norms. Regression analyses also indicated that variation in authoritarianism could be best predicted by fear of social differences. Thus, these data suggest that authoritarians are relatively sensitive to threat, and particularly to threats involving the “outsider” who does not fit authoritarian standards of uniformity and order. The data are also consistent with recent research and theory that right‐wing ideology is at least partly motivated by threat and fear.
When threat to society becomes a threat to oneself: Implications for right‐wing attitudes and ethnic prejudice
Authors: Onraet Emma , Van Hiel Alain
Published: February 2013

The relationships between threat on one hand and right‐wing attitudes and ethnic prejudice on the other were investigated in a heterogeneous sample (N = 588). Specifically, we considered the perception of economic and terroristic threats in terms of their consequences at the societal and personal levels. Previous studies revealed that societal consequences of threat, rather than personal consequences, are related to right‐wing attitudes. However, the present results challenge these findings. More specifically, three important results emerged. First, items probing the distinct threat levels loaded on separate dimensions for economic and terroristic threat, validating the distinction between societal and personal threat consequences. Second, consistent with previous research, this study revealed that perceived societal consequences of threat yield strong and robust relationships with all target variables. However, personal consequences of threat were also associated with higher levels of right‐wing authoritarianism (RWA), social dominance orientation (SDO), and ethnic prejudice in particular. Third, societal and personal consequences of threat interacted in explaining the target variables. More specifically, feeling personally threatened by terrorism was only related to higher levels of RWA in the presence of low levels of threat to society, whereas experiencing personal economic threat was only related to higher levels of SDO and ethnic prejudice when high societal economic threat was experienced. In sum, although the perception of societal consequences of threat plays a prominent role in explaining right‐wing attitudes and ethnic prejudice, the perception of being personally affected by threat is also associated with higher levels of RWA and SDO, and especially ethnic prejudice.
SuperIDR: A Tool for Fish Identification and Information Retrieval
Authors: Murthy Uma , Fox Edward A , Chen Yinlin , Hallerman Eric M , Orth Donald J , S Torres Ricardo , Li Lin Tzy , Kozievitch Nádia P , Andrade Felipe SP , Falcao Tiago RC , Ramos Evandro
Published: February 2013

Students, fisheries professionals, and the general public may value computer-facilitated assistance for fish identification and access to ecological and life history information. We developed SuperIDR, a software package supporting such applications, by utilizing the search and data retrieval capabilities of digital libraries, as well as key features of tablet PCs. We demonstrated SuperIDR utilizing a database with information on 207 freshwater fishes of Virginia. A user may annotate fish images and identify fishes by using a dichotomous key; searching for key words, similar images, subimages, or annotations on images; or combinations of these approaches. Students using the software demonstrated enhanced ability to correctly identify specimens. Their comments led to improvements, including the addition of new features. The PC-based system for identifying freshwater fishes of Virginia may be downloaded and modified. SuperIDR is a prototype for PC-based species identification applications—the system architecture and the open-source software that we developed are applicable to other fish faunas and to a broader range of species identification tasks.

RESUMEN

estudiantes, profesionales de las pesquerías y público en general pudieran valorar la asistencia computarizada que facilite la identificación de peces y acceso a información sobre su ecología e historia de vida. Se desarrolla SuperIDR, un paquete computacional que contiene tales aplicaciones, basado en la búsqueda y capacidades de recuperación de datos de las bibliotecas digitales, así como también una plataforma para tabletas digitales. Se demuestra que SuperIDR utiliza una base de datos con información de 207 peces de agua dulce de Virginia. El usuario puede ingresar imágenes de peces e identificarlos mediante una clave dicotómica; además el programa busca palabras clave, imágenes similares, sub-imágenes o anotaciones hechas sobre las imágenes; así como también combinaciones entre estos enfoques. Los estudiantes que utilizan el paquete demostraron aumentar su habilidad para identificar correctamente los especímenes. Sus comentarios permitieron hacer mejorías, que incluyen la adición de nuevas características. El sistema computarizado para la identificación de peces de agua dulce presentes en Virginia puede obtenerse en línea y modificarse. SuperIDR es un prototipo basado en computadoras personales para aplicaciones de identificación de especies—la arquitectura y programas abiertos que se desarrollaron, son aplicables a otras faunas de peces y a un rango más amplio de tareas de identificación de especies.
A sharp lower bound for the scalar curvature of certain steady gradient Ricci solitons
Authors: Fernández-López Manuel , García-Río Eduardo
Published: February 2013

We give a sharp lower bound for the scalar curvature of a steady gradient Ricci soliton in terms of the hyperbolic secant of the distance from a fixed point under the assumption that

2

|

R
c

|

2

≤

R
2

2|Rc|^2\leq R^2

, a condition that is satisfied by any steady gradient Ricci soliton with nonnegative sectional curvature.
On the regularity of the 2+1 dimensional equivariant Skyrme model
Authors: Geba Dan-Andrei , da Silva Daniel
Published: February 2013

One of the most interesting open problems concerning the Skyrme model of nuclear physics is the regularity of its solutions. In this article, we study2+12+1dimensional equivariant Skyrme maps, for which we prove, using the method of multipliers, that the energy does not concentrate. This is one of the important steps towards a global regularity theory.
Fast thermodynamically constrained flux variability analysis
Authors: Müller Arne C. , Bockmayr Alexander
Published: February 2013

Motivation: Flux variability analysis (FVA) is an important tool to further analyse the results obtained by flux balance analysis (FBA) on genome-scale metabolic networks. For many constraint-based models, FVA identifies unboundedness of the optimal flux space. This reveals that optimal flux solutions with net flux through internal biochemical loops are feasible, which violates the second law of thermodynamics. Such unbounded fluxes may be eliminated by extending FVA with thermodynamic constraints.

Results: We present a new algorithm for efficient flux variability (and flux balance) analysis with thermodynamic constraints, suitable for analysing genome-scale metabolic networks. We first show that FBA with thermodynamic constraints is NP-hard. Then we derive a theoretical tractability result, which can be applied to metabolic networks in practice. We use this result to develop a new constraint programming algorithm Fast-tFVA for fast FVA with thermodynamic constraints (tFVA). Computational comparisons with previous methods demonstrate the efficiency of the new method. For tFVA, a speed-up of factor 30–300 is achieved. In an analysis of genome-scale metabolic networks in the BioModels database, we found that in 485 of 716 networks, additional irreversible or fixed reactions could be detected.

Availability and implementation:  Fast-tFVA is written in C++ and published under GPL. It uses the open source software SCIP and libSBML. There also exists a Matlab interface for easy integration into Matlab. Fast-tFVA is available from page.mi.fu-berlin.de/arnem/fast-tfva.html.

Contact:  arne.mueller@fu-berlin.de; Alexander.Bockmayr@fu-berlin.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effect of atrioventricular optimization on circulating N‐terminal pro brain natriuretic peptide following cardiac resynchronization therapy
Authors: Shanmugam Nesan , Campos Ana Garcia , Prada‐Delgado Oscar , Bizrah Mukhtar , Valencia Oswaldo , Jones Sue , Collinson Paul , Anderson Lisa
Published: February 2013

Aims

Following CRT, atrioventricular (AV) optimization is not routinely practised. To evaluate its clinical utility, we examined the effect of AV delay optimization on the prognostic biomarker NT‐proBNP.

Methods and results

We prospectively studied 72 patients (mean age 73 ± 12.5 years, 70.8% male, 55.6% ischaemic) undergoing iterative AV optimization. Patients were divided into those whose nominal setting appeared ideal and not changed (Group 1, n = 22) and those whose AV delay was optimized (Group 2, n = 50). All patients underwent NT‐proBNP assessment prior to CRT, and pre‐ and a median 5 days post‐optimization. Compared with Group 1, NT‐proBNP fell significantly in Group 2 patients (median 474 pg/mL) following optimization (P = 0.00001). A significant change in filling pattern (defined as a change in AV delay >50 ms) was required in 30% of patients, and it was this subgroup that derived the greater reduction in NT‐proBNP levels [–1407 pg/mL, interquartile range (IQR) –3042 to –346 pg/mL] compared with those requiring <50 ms AV delay change (–125 pg/mL, IQR –1038 to 6 pg/mL), P = 0.0011. The benefit of AV optimization was principally observed in reverse remodelling non‐responders (median –2167 pg/mL, IQR –3042 to –305 pg/mL) and in patients with a pseudonormal or restrictive filling pattern (median –1407 pg/mL, IQR –2809 to –342 pg/mL), compared with those with more benign diastolic filling (median – 264 pg/mL, IQR –1038 to –21 pg/mL), P = 0.033.

Conclusions

In one‐third of patients, major filling pattern changes are achieved with AV optimization, associated with subsequent rapid falls in NT‐proBNP. The greater the AV delay change, the larger the NT‐proBNP fall, and non‐responders and those with restrictive or pseudonormal filling despite CRT are most likely to benefit.
Plasma microRNAs serve as biomarkers of therapeutic efficacy and disease progression in hypertension‐induced heart failure
Authors: Dickinson Brent A. , Semus Hillary M. , Montgomery Rusty L. , Stack Christianna , Latimer Paul A. , Lewton Steven M. , Lynch Joshua M. , Hullinger Thomas G. , Seto Anita G. , van Rooij Eva
Published: February 2013

Aims

Recent studies have shown that microRNAs (miRNAs), besides being potent regulators of gene expression, can additionally serve as circulating biomarkers of disease. The aim of this study is to determine if plasma miRNAs can be used as indicators of disease progression or therapeutic efficacy in hypertension‐induced heart disease.

Methods and results

In order to define circulating miRNAs that change during hypertension‐induced heart failure and that respond to therapeutic treatment, we performed miRNA arrays on plasma RNA from hypertensive rats that show signs of heart failure. Array analysis indicated that approximately one‐third of the miRNAs on the array are detectable in plasma. Quantitative real‐time polymerase chain reaction (PCR) analysis for a selected panel of miRNAs indicated that circulating levels of miR‐16, miR‐20b, miR‐93, miR‐106b, miR‐223, and miR‐423‐5p were significantly increased in response to hypertension‐induced heart failure, while this effect was blunted in response to treatment with antimiR‐208a as well as an ACE inhibitor. Moreover, treatment with antimiR‐208a resulted in a dramatic increase in one miRNA, miR‐19b. A time course study indicated that several of these miRNA changes track with disease progression.

Conclusions

Circulating levels of miRNAs are responsive to therapeutic interventions and change during the progression of hypertension‐induced heart disease.
The relation of evidence-based medicine and tacit knowledge in clinical judgement
Authors: Thornton Tim
Published: February 2013

The presence of evidence-based medicine in psychiatry

Hume’s challenge to induction

Responses to Hume

Hume’s own response

Mill’s methods

The consequences of Hume’s problem and Mill’s methods for RCTs and EBM

The role of individual judgement in induction

A Wittgensteinian response to Hume’s challenge to induction

Conclusions
Free will and responsibility
Authors: Callender John S.
Published: February 2013

This resource explores the evolution of morality and the roles of reason and emotion in the making of moral judgments. It describes scientific research on volitional behaviour, moral decision-making, and criminality, discussing what this might mean for our practices of blame and punishment, and applying this knowledge to clinical conditions.
Emergencies
Authors: Bloom Stuart , Webster George , Marks Daniel
Published: February 2013

Acute abdominal pain is a common casualty presentation (‘the acute
abdomen’) and a reason for patients to require review on the ward. The
duration of pain that defines it as acute is ill-defined, but would
usually be no more than a few days. With a huge range of GI and non-GI
causes of abdominal pain (...
Understanding data, information, and knowledge
Authors: Tennison Barry
Published: February 2013

The aim of this chapter is to help the public health practitioner to appreciate the subtleties of the varied forms of information about the health of a population and related matters, develop a toolkit for thinking about the complexity of information and its uses, and orientate themselves positively towards the decisions and actions needed, applying wisely and with good judgement the information and knowledge available. The classification (taxonomy) of types of information given in this chapter should help the public health practitioner toassess the relevance, timeliness, accuracy, and completeness of available information, decide which types of information are most appropriate for a particular public health task, and make optimal use of information that is not ideal, and assess the effects of its departure from perfection.
Engaging communities in participatory research and action
Authors: Minkler Meredith , Chang Charlotte
Published: February 2013

After reading this chapter you will be able to define participatory research and its core principles, describe how engaging communities in participatory research and action can add value to research, while building community capacity and helping achieve action to promote community health, identify some of the challenges that arise in such work and how they may be addressed, and describe a case study that started with an important issue in the community and demonstrates core principles of CBPR, challenges faced in such work, and subsequent community action for change.
Translating evidence to policy
Authors: Smith Lauren , An Jane , Kawachi Ichiro
Published: February 2013

As a result of reading this chapter you will be more able to identify the challenges that arise in translating research findings to public policy, understand the frequently cited barriers to evidence-based public health policy making from the perspective of legislators, and take steps to bridge the gap between evidence and policy formation.
Controlling expenditures
Authors: Rice Thomas , Lang Iain
Published: February 2013

This chapter will help you understand why controlling health care expenditures is key to achieving other public health goals, the primary reasons for rising expenditures, how rising expenditures have been addressed at national and sub-national levels, and ways in which controlling expenditures can fit into your professional role.
Using guidance and frameworks
Authors: Minhas Rubin , Feder Gene , Griffiths Chris
Published: February 2013

After reading this chapter you should be better able to understand, appreciate, and identify issues where guidance and frameworks could help, identify existing and relevant guidelines, assess their validity, adapt them to local circumstances, and support clinicians in their integration into practice.
Evaluating health care technologies
Authors: Milne Ruairidh , Stevens Andrew
Published: February 2013

Reading this chapter will help you to explain what Health Technology Assessment (HTA) is, understand the importance of HTA to public health, make the best use of HTA, and know the basics of how to do HTA.
Evaluating health care systems
Authors: McKee Martin , Khoshaba Bernadette , Karanikolos Marina
Published: February 2013

This chapter aims to help the reader understand the importance of defining the boundaries of a health system in a given country, explain the functions of a health system and how these relate to one another, describe the goals of a health system and how to evaluate progress towards them, be aware of the major contemporary initiatives to assess health system performance internationally, and recognize the limitations, including the scope for abuse, of health systems comparisons.
Working with the media
Authors: Maryon-Davis Alan
Published: February 2013

This chapter addresses the basics of working with the print and broadcast media. After reading this chapter you should be able to develop a strategy for working with the media, both as an individual practitioner and as a representative of your team or organization, review and strengthen your strategy, if you already have one in place, undertake simple media tasks, such as writing a press release or being interviewed by a journalist, with more confidence.
Knowledge transfer
Authors: Ward Jeanette , Grimshaw Jeremy , Eccles Martin
Published: February 2013

Effective research transfer will ensure patients and populations benefit from evidence-based best practice. While there is an increasing rigor with which to approach research transfer in health care settings, greater demand among those responsible for research transfer for a more scientifically sound knowledge base will accelerate development of the discipline. There is greater recognition that research transfer requires sophisticated, theoretically informed and phased designs. Practitioners who seek to transfer evidence into practice must work with these epistemological deficits as best they can. Reading this chapter will help you to identify and respond to situations that require research transfer, apply a systematic approach to research transfer, learning from the work of others and planning locally in context, and contribute to a growing body of evidence about research transfer itself.
Mayo Clinic Preventive Medicine and Public Health Board Review
Authors: Varkey, MD, MPH, MHPE Prathibha
Published: February 2013

This online resource provides a concise review of preventive medicine and public health topics that are relevant to any practitioner in preventive medicine, occupational medicine, internal medicine, or aerospace medicine needing a comprehensive review of the topics in preventive medicine and public health. It will also serve as an ideal review before preventive medicine board examinations for candidates taking them for the first time and those taking them for recertification.
Immunization
Authors: Swanton Claudia L. , Timm Barbara J. , Roeber Rice Heidi K.
Published: February 2013

The use of vaccines can be traced back to China and India before 200 BC. Vaccination, now considered one of the most effective public health interventions, became common practice in the 1940s with the introduction of vaccines for diphtheria and tetanus. Since that time, many infectious diseases have been well controlled through vaccination. This chapter focuses on live and attenuated bacterial and viral vaccines and those that are composed of toxoids. Hepatitis B, pneumococcal disease, and influenza are the most common vaccine-preventable diseases in adults. Rates of childhood vaccination remain suboptimal. Ideally, vaccination begins before infants are dismissed home after birth. Targeted awareness campaigns can be used to educate providers and the public about the importance of immunization.
Secondary Prevention 1: Cancers and Principles of Screening
Authors: Millman Martha P. , Limburg Paul J.
Published: February 2013

Screening tests are used to differentiate between persons with and without the condition of interest in a defined population. Screening strategies, or mass screening, is applied relatively indiscriminately to a population. Cancer is the second-leading overall cause of death in the United States; however, it is the leading cause of death for those under 85. Cancer risk is associated with environmental risk factors. Racial disparities in cancer incidence and death persist in the United States; level of education also appears to affect cancer survival. The United States Preventive Services Task Force has established evidence-based guidelines for screening, counseling, and chemoprevention.
Occupational Medicine
Authors: Orford Robert R. , Rehman Hamid
Published: February 2013

Occupational medicine is the medical specialty devoted to 1) prevention and management of occupational injury, illness, and disability, and 2) promotion of health and productivity of workers, their families, and communities. Historically, occupational medicine was termed industrial medicine when heavy industry (eg, lumbering, automobile manufacturing, mining, railroads, steel manufacturing) employed physicians to provide acute medical and surgical care for workers. However, by 1945, medical programs had spread to business organizations that predominantly were staffed with clerical and service employees (eg, banks, insurance companies, mercantile establishments). The broader designation of occupational medicine then came into common use. Occupational medicine was recognized as a specialty by the American Board of Preventive Medicine in 1955.
Aerospace Medicine
Authors: Steinkraus Lawrence , Stepanek Jan
Published: February 2013

Aerospace medicine focuses on the clinical care, research, and operational support of the health, safety, and performance of crewmembers and passengers of air and space vehicles, together with the support personnel who assist operation of such vehicles. Understanding of the 5 basic gas laws aids understanding of aeromedically significant effects, specifically hypoxia, volume changes at higher altitudes, and decompression illness. Signs and symptoms of decompression illness may include pain in and around joints. More serious is the affliction of heart and lungs or neurologic problems. Physiologic stressors of commercial flight can include decreased partial pressure of oxygen, vibration, noise, humidity, expansion of trapped gases, and thermal stress. Aeromedical transportation of patients with more serious medical conditions requires appropriate equipment, staffing, and coordination of logistical issues. There are 15 specific conditions that disqualify aviators under FAA rules. The primary purpose of aircraft mishap investigations is to prevent future accidents, injuries, and fatalities. Accidents are investigated with multidisciplinary teams, including physicians, following standardized investigation guidelines.
AGP: A Multimethods Web Server for Alignment-Free Genome Phylogeny
Authors: Cheng Jinkui , Cao Fuliang , Liu Zhihua
Published: February 2013

Phylogenetic analysis based on alignment method meets huge challenges when dealing with whole-genome sequences, for example, recombination, shuffling, and rearrangement of sequences. Thus, various alignment-free methods for phylogeny construction have been proposed. However, most of these methods have not been implemented as tools or web servers. Researchers cannot use these methods easily with their data sets. To facilitate the usage of various alignment-free methods, we implemented most of the popular alignment-free methods and constructed a user-friendly web server for alignment-free genome phylogeny (AGP). AGP integrated the phylogenetic tree construction, visualization, and comparison functions together. Both AGP and all source code of the methods are available at http://www.herbbol.org:8000/agp (last accessed February 26, 2013). AGP will facilitate research in the field of whole-genome phylogeny and comparison.