bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating a sustainability index for nutrients in a short rotation energy cropping system
Authors: Sochacki Stanley J. , Harper Richard J. , Smettem Keith R. J. , Dell Bernard , Wu Hongwei 
Published: August 2012

AbstractIn dryland environments 3–5 year rotations of tree crops and agriculture represent a major potential bioenergy feedstock and a means to restore landscape hydrologic balances and phytoremediate sites, while maintaining food production. In soils with low natural fertility, the long‐term viability of these systems will be critically affected by site nutrient status and subsequent cycling of nutrients. A nutrient assimilation index (NAI) was developed to allow comparison of species and tree component nutrient assimilation and to optimize nutrient management, by quantifying different strategies to manage site nutrients. Biomass, nutrient export and nutrient use efficiency were assessed for three short rotation tree crop species. Nutrient exports following harvest at 3 years of high density (4000 trees ha−1) were consistently higher in Pinus radiata, with values of 85 kg ha−1 of N, 11kg ha−1 of P, and 62 kg ha−1 of K, than Eucalyptus globulus and Eucalyptus occidentalis. Component NAI was generally in the order of leaf<twig<bark<root<stem‐wood for N, P, K, S, Ca, and Mg. The NAI ranged from 0.06 Mg kg−1 for N in leaves of P. radiata to 4.7 Mg kg−1 for P in stem‐wood of E. occidentalis, indicating higher sustainability of wood biomass compared with leaf biomass. The leaves for each species contained between 40 and 60% of the total nutrient contents while comprising around 25–30% of the total biomass. These nutrient exports via biomass removal are similar to those that follow 3 years of wheat production in the same region, indicating there is no additional drawdown of nutrient reserves during the tree cropping phase of the rotation.
The Limits of Feedforward Vision: Recurrent Processing Promotes Robust Object Recognition when Objects Are Degraded
Authors: Wyatte Dean , Curran Tim , O'Reilly Randall 
Published: August 2012

Abstract
Everyday vision requires robustness to a myriad of environmental factors that degrade stimuli. Foreground clutter can occlude objects of interest, and complex lighting and shadows can decrease the contrast of items. How does the brain recognize visual objects despite these low-quality inputs? On the basis of predictions from a model of object recognition that contains excitatory feedback, we hypothesized that recurrent processing would promote robust recognition when objects were degraded by strengthening bottom–up signals that were weakened because of occlusion and contrast reduction. To test this hypothesis, we used backward masking to interrupt the processing of partially occluded and contrast reduced images during a categorization experiment. As predicted by the model, we found significant interactions between the mask and occlusion and the mask and contrast, such that the recognition of heavily degraded stimuli was differentially impaired by masking. The model provided a close fit of these results in an isomorphic version of the experiment with identical stimuli. The model also provided an intuitive explanation of the interactions between the mask and degradations, indicating that masking interfered specifically with the extensive recurrent processing necessary to amplify and resolve highly degraded inputs, whereas less degraded inputs did not require much amplification and could be rapidly resolved, making them less susceptible to masking. Together, the results of the experiment and the accompanying model simulations illustrate the limits of feedforward vision and suggest that object recognition is better characterized as a highly interactive, dynamic process that depends on the coordination of multiple brain areas.
FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry
Authors: Lun Aaron TL , Wong Jason WH , Downard Kevin M 
Published: August 2012

Abstract

Background
Influenza is one of the oldest and deadliest infectious diseases known to man. Reassorted strains of the virus pose the greatest risk to both human and animal health and have been associated with all pandemics of the past century, with the possible exception of the 1918 pandemic, resulting in tens of millions of deaths. We have developed and tested new computer algorithms, FluShuffle and FluResort, which enable reassorted viruses to be identified by the most rapid and direct means possible. These algorithms enable reassorted influenza, and other, viruses to be rapidly identified to allow prevention strategies and treatments to be more efficiently implemented.

Results
The FluShuffle and FluResort algorithms were tested with both experimental and simulated mass spectra of whole virus digests. FluShuffle considers different combinations of viral protein identities that match the mass spectral data using a Gibbs sampling algorithm employing a mixed protein Markov chain Monte Carlo (MCMC) method. FluResort utilizes those identities to calculate the weighted distance of each across two or more different phylogenetic trees constructed through viral protein sequence alignments. Each weighted mean distance value is normalized by conversion to a Z-score to establish a reassorted strain.

Conclusions
The new FluShuffle and FluResort algorithms can correctly identify the origins of influenza viral proteins and the number of reassortment events required to produce the strains from the high resolution mass spectral data of whole virus proteolytic digestions. This has been demonstrated in the case of constructed vaccine strains as well as common human seasonal strains of the virus. The algorithms significantly improve the capability of the proteotyping approach to identify reassorted viruses that pose the greatest pandemic risk.
Evolution of the Rdr1 TNL-cluster in roses and other Rosaceous species
Authors: Terefe-Ayana Diro , Kaufmann Helgard , Linde Marcus , Debener Thomas 
Published: August 2012

Abstract

Background
The resistance of plants to pathogens relies on two lines of defense: a basal defense response and a pathogen-specific system, in which resistance (R) genes induce defense reactions after detection of pathogen-associated molecular patterns (PAMPS). In the specific system, a so-called arms race has developed in which the emergence of new races of a pathogen leads to the diversification of plant resistance genes to counteract the pathogens’ effect. The mechanism of resistance gene diversification has been elucidated well for short-lived annual species, but data are mostly lacking for long-lived perennial and clonally propagated plants, such as roses. We analyzed the rose black spot resistance gene, Rdr1, in five members of the Rosaceae: Rosa multiflora, Rosa rugosa, Fragaria vesca (strawberry), Malus x domestica (apple) and Prunus persica (peach), and we present the deduced possible mechanism of R-gene diversification.

Results
We sequenced a 340.4-kb region from R. rugosa orthologous to the Rdr1 locus in R. multiflora. Apart from some deletions and rearrangements, the two loci display a high degree of synteny. Additionally, less pronounced synteny is found with an orthologous locus in strawberry but is absent in peach and apple, where genes from the Rdr1 locus are distributed on two different chromosomes. An analysis of 20 TIR-NBS-LRR (TNL) genes obtained from R. rugosa and R. multiflora revealed illegitimate recombination, gene conversion, unequal crossing over, indels, point mutations and transposable elements as mechanisms of diversification.
A phylogenetic analysis of 53 complete TNL genes from the five Rosaceae species revealed that with the exception of some genes from apple and peach, most of the genes occur in species-specific clusters, indicating that recent TNL gene diversification began prior to the split of Rosa from Fragaria in the Rosoideae and peach from apple in the Spiraeoideae and continued after the split in individual species. Sequence similarity of up to 99% is obtained between two R. multiflora TNL paralogs, indicating a very recent duplication.

Conclusions
The mechanisms by which TNL genes from perennial Rosaceae diversify are mainly similar to those from annual plant species. However, most TNL genes appear to be of recent origin, likely due to recent duplications, supporting the hypothesis that TNL genes in woody perennials are generally younger than those from annuals. This recent origin might facilitate the development of new resistance specificities, compensating for longer generation times in woody perennials.
Heart Disease and Left Ventricular Rotation – A Systematic Review and Quantitative Summary
Authors: Phillips Aaron A , Cote Anita T , Bredin Shannon SD , Warburton Darren ER 
Published: August 2012

Abstract

Background
Left ventricular (LV) rotation is increasingly examined in those with heart disease. The available evidence measuring LV rotation in those with heart diseases has not been systematically reviewed.

Methods
To review systematically the evidence measuring LV rotational changes in various heart diseases compared to healthy controls, literature searches were conducted for appropriate articles using several electronic databases (e.g., MEDLINE, EMBASE). All randomized-controlled trials, prospective cohort and case–controlled studies that assessed LV rotation in relation to various heart conditions were included. Three independent reviewers evaluated each investigation’s quality using validated scales. Results were tabulated and levels of evidence assigned.

Results
A total of 1,782 studies were found through the systematic literature search. Upon review of the articles, 47 were included. The articles were separated into those investigating changes in LV rotation in participants with: aortic stenosis, myocardial infarction, hypertrophic cardiomyopathy, dilated cardiomyopathy, non-compaction, restrictive cardiomyopathy/ constrictive pericarditis, heart failure, diastolic dysfunction, heart transplant, implanted pacemaker, coronary artery disease and cardiovascular disease risk factors. Evidence showing changes in LV rotation due to various types of heart disease was supported by evidence with limited to moderate methodological quality.

Conclusions
Despite a relatively low quality and volume of evidence, the literature consistently shows that heart disease leads to marked changes in LV rotation, while rotational systolic-diastolic coupling is preserved. No prognostic information exists on the potential value of rotational measures of LV function. The literature suggests that measures of LV rotation may aid in diagnosing subclinical aortic stenosis and diastolic dysfunction.
Double-blind, placebo-controlled first in human study to investigate an oral vaccine aimed to elicit an immune reaction against the VEGF-Receptor 2 in patients with stage IV and locally advanced pancreatic cancer
Authors: Niethammer Andreas G , Lubenau Heinz , Mikus Gerd , Knebel Philipp , Hohmann Nicolas , Leowardi Christine , Beckhove Philipp , Akhisaroglu Mustafa , Ge Yingzi , Springer Marco , Grenacher Lars , Buchler Markus W , Koch Moritz , Weitz Jürgen , Haefeli Walter E , Schmitz-Winnenthal Friedrich H 
Published: August 2012

Abstract

Background
The investigational oral DNA vaccine VXM01 targets the vascular endothelial growth factor receptor 2 (VEGFR-2) and uses Salmonella typhi Ty21a as a vector. The immune reaction elicited by VXM01 is expected to disrupt the tumor neovasculature and, consequently, inhibit tumor growth. VXM01 potentially combines the advantages of anti-angiogenic therapy and active immunotherapy.

Methods/Design
This phase I trial examines the safety, tolerability, and immunological and clinical responses to VXM01. The randomized, placebo-controlled, double blind dose-escalation study includes up to 45 patients with locally advanced and stage IV pancreatic cancer. The patients will receive four doses of VXM01 or placebo in addition to gemcitabine as standard of care. Doses from 106 cfu up to 1010 cfu of VXM01 will be evaluated in the study. An independent data safety monitoring board (DSMB) will be involved in the dose-escalation decisions. In addition to safety as primary endpoint, the VXM01-specific immune reaction, as well as clinical response parameters will be evaluated.

Discussion
The results of this study shall provide the first data regarding the safety and immunogenicity of the oral anti-VEGFR-2 vaccine VXM01 in cancer patients. They will also define the recommended dose for phase II and provide the basis for further clinical evaluation, which may also include additional cancer indications.

Trial registration
EudraCT No.: 2011-000222-29, NCT01486329, ISRCTN68809279
Sex differences in response to maximal exercise stress test in trained adolescents
Authors: Fomin Åsa , Ahlstrand Mattias , Schill Helena Gyllenhammar , Lund Lars H , Ståhlberg Marcus , Manouras Aristomenis , Gabrielsen Anders 
Published: August 2012

Abstract

Background
Sex comparisons between girls and boys in response to exercise in trained adolescents are missing and we investigated similarities and differences as a basis for clinical interpretation and guidance.

Methods
A total of 24 adolescent females and 27 adolescent males aged 13–19 years underwent a maximal bicycle exercise stress test with measurement of cardiovascular variables, cardiac output, lung volumes, metabolic factors/lactate concentrations and breath-by-breath monitoring of ventilation, and determination of peak VO2.

Results
Maximum heart rate was similar in females (191 ± 9 bpm) and males (194 ± 7 bpm), cardiac index at maximum exercise was lower in females (7.0 ± 1.0 l/min/m2) than in males (8.3 ± 1.4 l/min/m2, P < 0.05). Metabolic responses and RQ at maximum exercise were similar (females: 1.04 ± 0.06 vs. males: 1.05 ± 0.05). Peak VO2 was lower in females (2.37 ± 0.34 l/min) than in males (3.38 ± 0.49 l/min, P < 0.05). When peak VO2 was normalized to leg muscle mass sex differences disappeared (females: 161 ± 21 ml/min/kg vs. males: 170 ± 23 ml/min/kg). The increase in cardiac index during exercise is the key factor responsible for the greater peak VO2 in adolescent boys compared to girls.

Conclusions
Differences in peak VO2 in adolescent boys and girls disappear when peak VO2 is normalized to estimated leg muscle mass and therefore provide a tool to conduct individual and intersex comparisons of fitness when evaluating adolescent athletes in aerobic sports.
Prevalence and determinants of complementary and alternative medicine use among infertile patients in Lebanon: a cross sectional study
Authors: Ghazeeri Ghina S , Awwad Johnny T , Alameddine Mohamad , Younes Zeina MH , Naja Farah 
Published: August 2012

Abstract

Background
Complementary and alternative medicine (CAM) is widely used for the treatment of infertility. While the Middle East and North Africa region has been shown to house one of the fastest growing markets of CAM products in the world, research describing the use of CAM therapies among Middle-Eastern infertile patients is minimal. The aim of this study is to examine the prevalence, characteristics and determinants of CAM use among infertile patients in Lebanon.

Methods
A cross sectional survey design was used to carry out face-to-face interviews with 213 consecutive patients attending the Assisted Reproductive Unit at a major academic medical center in Beirut. The questionnaire comprised three sections: socio-demographic and lifestyle characteristics, infertility-related aspects and information on CAM use. The main outcome measure was the use of CAM modalities for infertility treatment. Determinants of CAM use were assessed through the logistic regression method.

Results
Overall, 41% of interviewed patients reported using a CAM modality at least once for their infertility. There was a differential by gender in the most commonly used CAM therapies; where males mostly used functional foods (e.g. honey & nuts) (82.9%) while females mostly relied on spiritual healing/prayer (56.5%). Factors associated with CAM use were higher household income (OR: 0.305, 95% CI: 0.132–0.703) and sex, with females using less CAM than males (OR: 0.12, 95% CI: 0.051–0.278). The older patients were diagnosed with infertility, the lower the odds of CAM use (p for trend <0.05). Almost half of the participants (48%) were advised on CAM use by their friends, and only 13% reported CAM use to their physician.

Conclusions
The considerably high use of CAM modalities among Lebanese infertile patients, added to a poor CAM use disclosure to physicians, underscore the need to integrate CAM into the education and training of health professionals, as well as enhance infertile patients' awareness on safe use of CAM products.
RETRACTED ARTICLE: The proto-oncogene c-src is involved in primordial follicle activation through the PI3K, PKC and MAPK signaling pathways
Authors: Du Xiao-Yu , Huang Jian , Xu Liang-Quan , Tang Dan-Feng , Wu Lei , Zhang Li-Xia , Pan Xiao-Ling , Chen Wei-Yun , Zheng Li-Ping , Zheng Yue-Hui 
Published: August 2012

Abstract
Background
C-src is an evolutionarily conserved proto-oncogene that regulates cell proliferation, differentiation and apoptosis. In our previous studies, we have reported that another proto-oncogene, c-erbB2, plays an important role in primordial follicle activation and development. We also found that c-src was expressed in mammalian ovaries, but its functions in primordial follicle activation remain unclear. The objective of this study is to investigate the role and mechanism of c-src during the growth of primordial follicles.

Methods
Ovaries from 2-day-old rats were cultured in vitro for 8 days. Three c-src-targeting and one negative control siRNA were designed and used in the present study. PCR, Western blotting and primordial follicle development were assessed for the silencing efficiency of the lentivirus c-src siRNA and its effect on primordial follicle onset. The expression of c-src mRNA and protein in primordial follicle growth were examined using the PCR method and immunohistochemical staining. Furthermore, the MAPK inhibitor PD98059, the PKC inhibitor Calphostin and the PI3K inhibitor LY294002 were used to explore the possible signaling pathways of c-src in primordial folliculogenesis.

Results
The results showed that Src protein was distributed in the ooplasmic membrane and the granulosa cell membrane in the primordial follicles, and c-src expression level increased with the growth of primordial follicle. The c-src -targeting lentivirus siRNAs had a silencing effect on c-src mRNA and protein expression. Eight days after transfection of rat ovaries with c-src siRNA, the GFP fluorescence in frozen ovarian sections was clearly discernible under a fluorescence microscope, and its relative expression level was 5-fold higher than that in the control group. Furthermore, the c-src-targeting lentivirus siRNAs lowered its relative expression level 1.96 times. We also found that the development of cultured primordial follicles was completely arrested after c-src siRNA knockdown of c-src expression. Furthermore, our studies demonstrated that folliculogenesis onset was inhibited by Calphostin, PD98059 or LY294002 treatment,but none of them down-regulated c-src expression. In contrast, the expression levels of p-PKC, p-ERK1/2 and p-PI3K in the follicles were clearly decreased by c-src siRNA transfection. Correspondingly, both Calphostin and LY294002 treatment resulted in a decrease in the p-PKC level in follicles, but no change was observed in the PD98059 group. Finally, LY294002 treatment decreased the p-PI3K expression level in the follicles, but no changes were observed in the PD98059 and Calphostin groups.

Conclusions
C-src plays an important role in regulating primordial follicle activation and growth via the PI3K-PKC- ERK1/2 pathway.
Neurog1 and Neurog2 coordinately regulate development of the olfactory system
Authors: Shaker Tarek , Dennis Daniel , Kurrasch Deborah M , Schuurmans Carol 
Published: August 2012

Abstract

Background
Proneural genes encode basic helix–loop–helix transcription factors that specify distinct neuronal identities in different regions of the nervous system. In the embryonic telencephalon, the proneural genes Neurog1 and Neurog2 specify a dorsal regional identity and glutamatergic projection neuron phenotype in the presumptive neocortex, but their roles in cell fate specification in the olfactory bulb, which is also partly derived from dorsal telencephalic progenitors, have yet to be assessed. Given that olfactory bulb development is guided by interactions with the olfactory epithelium in the periphery, where proneural genes are also expressed, we investigated the roles of Neurog1 and Neurog2 in the coordinated development of these two olfactory structures.

Results

Neurog1/2 are co-expressed in olfactory bulb progenitors, while only Neurog1 is widely expressed in progenitors for olfactory sensory neurons in the olfactory epithelium. Strikingly, only a remnant of an olfactory bulb forms in Neurog1
−/−
;Neurog2
−/− double mutants, while this structure is smaller but distinguishable in Neurog1
−/− single mutants and morphologically normal in Neurog2

−/−
single mutants. At the cellular level, fewer glutamatergic mitral and juxtaglomerular cells differentiate in Neurog1
−/−
;Neurog2
−/− double-mutant olfactory bulbs. Instead, ectopic olfactory bulb interneurons are derived from dorsal telencephalic lineages in Neurog1
−/−
;Neurog2
−/− double mutants and to a lesser extent in Neurog2

−/−
single mutants. Conversely, cell fate specification is normal in Neurog1

−/−
olfactory bulbs, but aberrant patterns of cell proliferation and neuronal migration are observed in Neurog1

−/−
single and Neurog1
−/−
;Neurog2
−/− double mutants, probably contributing to their altered morphologies. Finally, in Neurog1

−/−
and Neurog1
−/−
;Neurog2
−/− embryos, olfactory sensory neurons in the epithelium, which normally project to the olfactory bulb to guide its morphogenesis, fail to innervate the olfactory bulb.

Conclusions
We have identified a cell autonomous role for Neurog1/ 2 in specifying the glutamatergic identity of olfactory bulb neurons. Furthermore, Neurog1 (and not Neurog2) is required to guide olfactory sensory neuron innervation of the olfactory bulb, the loss of which results in defects in olfactory bulb proliferation and tissue morphogenesis. We thus conclude that Neurog1/2 together coordinate development of the olfactory system, which depends on tissue interactions between the olfactory bulb and epithelium.