bluuebunny/crossref_metadata_2025_split huggingface dataset:
Committed sea-level rise for the next century from Greenland ice sheet dynamics during the past decade
Authors: Price Stephen F. , Payne Antony J. , Howat Ian M. , Smith Benjamin E. 
Published: May 2011

We use a three-dimensional, higher-order ice flow model and a realistic initial condition to simulate dynamic perturbations to the Greenland ice sheet during the last decade and to assess their contribution to sea level by 2100. Starting from our initial condition, we apply a time series of observationally constrained dynamic perturbations at the marine termini of Greenland’s three largest outlet glaciers, Jakobshavn Isbræ, Helheim Glacier, and Kangerdlugssuaq Glacier. The initial and long-term diffusive thinning within each glacier catchment is then integrated spatially and temporally to calculate a minimum sea-level contribution of approximately 1 ± 0.4 mm from these three glaciers by 2100. Based on scaling arguments, we extend our modeling to all of Greenland and estimate a minimum dynamic sea-level contribution of approximately 6 ± 2 mm by 2100. This estimate of committed sea-level rise is a minimum because it ignores mass loss due to future changes in ice sheet dynamics or surface mass balance. Importantly, > 75% of this value is from the long-term, diffusive response of the ice sheet, suggesting that the majority of sea-level rise from Greenland dynamics during the past decade is yet to come. Assuming similar and recurring forcing in future decades and a self-similar ice dynamical response, we estimate an upper bound of 45 mm of sea-level rise from Greenland dynamics by 2100. These estimates are constrained by recent observations of dynamic mass loss in Greenland and by realistic model behavior that accounts for both the long-term cumulative mass loss and its decay following episodic boundary forcing.
Inhibition of autoprocessing of natural variants and multidrug resistant mutant precursors of HIV-1 protease by clinical inhibitors
Authors: Louis John M. , Aniana Annie , Weber Irene T. , Sayer Jane M. 
Published: May 2011

Self-cleavage at the N terminus of HIV-1 protease from the Gag-Pol precursor (autoprocessing) is crucial for stabilizing the protease dimer required for onset of mature-like catalytic activity, viral maturation, and propagation. Among nine clinical protease inhibitors (PIs), darunavir and saquinavir were the most effective in inhibiting wild-type HIV-1 group M precursor autoprocessing, with an IC50value of 1–2 μM, 3–5 orders of magnitude higher than their binding affinities to the corresponding mature protease. Accordingly, both group M and N precursor–PI complexes exhibitTms 17–21 °C lower than those of the corresponding mature protease–PI complexes suggestive of markedly reduced stabilities of the precursor dimer–PI ensembles. Autoprocessing of group N (natural variant) and three group M precursors bearing 11–20 mutations associated with multidrug resistance was either weakly responsive or fully unresponsive to inhibitors at concentrations up to a practical limit of approximately 150 μM PI. This observation parallels decreases of up to 8 × 103-fold (e.g., 5 pM to 40 nM) in the binding affinity of darunavir and saquinavir to mature multidrug resistant proteases relative to wild type, suggesting that inhibition of some of these mutant precursors will occur only in the high μM to mM range in extreme PI-resistance, which is an effect arising from coordinated multiple mutations. An extremely darunavir-resistant mutant precursor is more responsive to inhibition by saquinavir. These findings raise the questions whether clinical failure of PI therapy is related to lack of inhibition of autoprocessing and whether specific inhibitors can be designed with low-nM affinity to target autoprocessing.
Classification with correlated features: unreliability of feature ranking and solutions
Authors: Toloşi Laura , Lengauer Thomas 
Published: May 2011

Abstract
Motivation: Classification and feature selection of genomics or transcriptomics data is often hampered by the large number of features as compared with the small number of samples available. Moreover, features represented by probes that either have similar molecular functions (gene expression analysis) or genomic locations (DNA copy number analysis) are highly correlated. Classical model selection methods such as penalized logistic regression or random forest become unstable in the presence of high feature correlations. Sophisticated penalties such as group Lasso or fused Lasso can force the models to assign similar weights to correlated features and thus improve model stability and interpretability. In this article, we show that the measures of feature relevance corresponding to the above-mentioned methods are biased such that the weights of the features belonging to groups of correlated features decrease as the sizes of the groups increase, which leads to incorrect model interpretation and misleading feature ranking.
Results: With simulation experiments, we demonstrate that Lasso logistic regression, fused support vector machine, group Lasso and random forest models suffer from correlation bias. Using simulations, we show that two related methods for group selection based on feature clustering can be used for correcting the correlation bias. These techniques also improve the stability and the accuracy of the baseline models. We apply all methods investigated to a breast cancer and a bladder cancer arrayCGH dataset and in order to identify copy number aberrations predictive of tumor phenotype.
Availability: R code can be found at: http://www.mpi-inf.mpg.de/~laura/Clustering.r.
Contact: laura.tolosi@mpi-inf.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Developing and evaluating harvest control rules with different biological reference points for the American lobster (Homarus americanus) fishery in the Gulf of Maine
Authors: Zhang Yuying , Chen Yong , Wilson Carl 
Published: May 2011

Abstract
Zhang, Y., Chen, Y., and Wilson, C. 2011. Developing and evaluating harvest control rules with different biological reference points for the American lobster (Homarus americanus) fishery in the Gulf of Maine. – ICES Journal of Marine Science, 68: 1511–1524. The American lobster (Homarus americanus) supports one of the most valuable commercial fisheries in the United States. Controversy exists, however, in terms of the biological reference point (BRP) used in assessing lobster stock status, and there is no fully established or evaluated harvest control rule (HCR). A sex-specific, size-dependent operating model is developed to evaluate the performance of two HCRs, discrete and continuous, which adjust annual fishing mortality discretely and linearly, respectively, based on the status of the fishery. For each HCR, different BRPs are considered along with management duration, recruitment dynamics, and natural mortality. HCRs with a suitable set of BRPs can drive the fishery from an undesirable status to an optimal status. The continuous HCR tends to perform better than the discrete one. The Ftarget of 0.31 year−1 showed the best performance in the long term by balancing the needs of the fishing industry and conservation bodies. However, this was not the case in the short term. An Ntarget of 49.6 million would allow the American lobster to be maintained at its current stock level, with high recruitment and stable natural mortality. The study provides a framework for a systematic evaluation of management regulations for the American lobster.
Modality-specific Somatosensory Changes in a Human Surrogate Model of Postoperative Pain
Authors: Fißmer Ina , Klein Thomas , Magerl Walter , Treede Rolf-Detlef , Zahn Peter K. , Pogatzki-Zahn Esther M. 
Published: May 2011

Background
Postoperative pain remains a challenging problem in part because the underlying mechanisms are still not well understood. There is a compelling need for translational studies in human models of postoperative pain to bridge the gap between animal models und human clinical studies.

Methods
Somatosensory changes using Quantitative Sensory Testing for up to 72 h after an experimental 4-mm incision were characterized in 20 male volunteers.

Results
During incision, perceived pain was 29 on a 100-point numeric rating scale and declined rapidly over the next 60 min. After incision, thresholds at the site of incision were lowered to painful heat (primary heat hyperalgesia; P < 0.01, effect size: 0.68) but not to painful cold (P > 0.05, effect size: 0.00). Remote to the incision, mechanical pain thresholds were lowered, pain ratings were increased, and an area of hyperalgesia occurred (P < 0.05, effect size: 0.56; P < 0.01, effect size: 0.70; P < 0.01, respectively; secondary mechanical hyperalgesia). All signs of heat and mechanical hyperalgesia declined until full resolution at 27-72 h after incision. Increased mechanical pain ratings remote to the incision (r = 0.47; P < 0.01) but not the area of hyperalgesia (r = 0.28) or heat hyperalgesia (r = 0.12) correlated with incision-induced pain.

Conclusions
Ongoing activity of nociceptors underlying nonevoked pain after incision in humans may not be explained by sensitization of nociceptors to heat but triggers the increased painfulness of mechanical stimuli in the area of secondary hyperalgesia. However, the spatial expansion of hyperalgesia seems to rely on at least partly different mechanisms. These findings may contribute to the understanding of pain and hyperalgesia after surgery.
Effect of Formula Composition on the Development of Infant Gut Microbiota
Authors: Hascoët Jean‐Michel , Hubert Claire , Rochat Florence , Legagneur Henryse , Gaga Simona , Emady‐Azar Shahram , Steenhout Philippe G 
Published: May 2011

ABSTRACTObjectives:Breast‐feeding induces a gut microbiota rich in bifidobacteria, whereas formula‐fed babies have a more diverse colonization. This ecosystem contributes to the development of the immune response and the lower incidence of diarrhea and allergy in breast‐fed infants. This randomized double‐blind controlled trial aimed to evaluate the bifidogenic effect of a mainly whey protein study formula low in phosphate and protein, allowing a composition closer to that of human milk.Patients and Methods:One hundred ninety healthy infants exclusively received study formula with or without Bifidobacterium longum (BL999), or a control formula for up to 4 months. Breast‐fed infants served as a reference population. Stool samples collected at 2 months of age were analyzed for bacterial counts (log colony‐forming unit [CFU]/g).Results:Bifidobacteria counts were significantly higher in infants receiving the study formula alone (10.0[0.8], P < 0.0001, median [interquartile range]) or with BL999 (9.8[1.4], P < 0.01) than control (9.2[3.5]), and were similar to breast‐fed infants (10.1[0.4], P > 0.05). The difference between the 2 study groups was 0.16 log CFU/g (90% confidence interval [CI] [0–0.4]), within the predefined equivalence margin. Microbiota profile, as a percentage of total bacteria counts, showed about 50% Bifidobacteria, 8% Enterobacteria, and <10% Clostridia in study formulae and breast‐fed infants versus 22%, 13%, and 19% in controls, respectively. There were no significant differences in growth measurements, digestive tolerance, and adverse events between groups.Conclusions:This study showed that infant formula closer resembling human milk was more bifidogenic than the control formula and led to a microbiota profile similar to that for breast‐fed infants.
Role of Eosinophils in Inflammatory Bowel and Gastrointestinal Diseases
Authors: Woodruff Samantha A , Masterson Joanne C , Fillon Sophie , Robinson Zachary D , Furuta Glenn T 
Published: May 2011

ABSTRACTInflammatory bowel diseases (IBD) are characterized by the invasion of leukocytes into the intestinal mucosa. However, a mixed inflammatory picture is observed that includes neutrophils, lymphocytes, monocytes, and eosinophils. To this day, the role of eosinophils in health and in disease remains unclear. Investigations into their function stem primarily from allergic diseases, asthma, and parasitic infections. This makes it even more difficult to discern a role for the fascinating eosinophil in IBDs because, unlike the lung or the skin, eosinophils reside in normal intestinal mucosa and increase in disease states; consequently, an intricate system must regulate their migration and numbers. These granulocytes are equipped with the machinery to participate in gastrointestinal (GI) inflammation and in the susceptible microenvironment, they may initiate or perpetuate an inflammatory response. A significant body of literature characterizes eosinophils present in the GI microenvironment where they have the potential to interact with other resident cells, thus promoting intestinal remodeling, mucus production, epithelial barrier, cytokine production, angiogenesis, and neuropeptide release. A number of lines of evidence support both potential beneficial and deleterious roles of eosinophils in the gut. Although studies from the gut and other mucosal organs suggest eosinophils affect mucosal GI inflammation, definitive roles for eosinophils in IBDs await discovery.
Role of Dietary Factors and Food Habits in the Development of Childhood Obesity: A Commentary by the ESPGHAN Committee on Nutrition
Authors: Agostoni Carlo , Braegger Christian , Decsi Tamas , Kolacek Sanja , Koletzko Berthold , Mihatsch Walter , Moreno Luis A , Puntis John , Shamir Raanan , Szajewska Hania , Turck Dominique , van Goudoever Johannes ,   ESPGHAN Committee on Nutrition
Published: May 2011

ABSTRACTThis Comment by the Committee on Nutrition of the European Society for Paediatric Gastroenterology, Hepatology, and Nutrition aims to provide a summary of the role of nutrition‐related factors on obesity prevention in children ages 2 to 18 years. This Comment emphasizes that dietary interventions should be incorporated into a multidisciplinary strategy for obesity prevention. No single nutrient has been unequivocally associated with the development of obesity. Methodological limitations in study design and the complex nature of obesity must be taken into account when interpreting the association with reported dietary factors. Energy intake should be individually determined, taking into account energy expenditure and growth. Preferential intake of slowly absorbed carbohydrates and limiting the ingestion of rapidly absorbed carbohydrates and simple sugars should be promoted. No specific recommendations for macronutrient intakes to prevent obesity can be made. Plant foods can be used as the main food contributors to a well‐balanced diet with adequate monitoring of nutrient intake. Plain water should be promoted as the main source of fluids for children instead of sugar‐sweetened beverages. Children should eat at least 4 meals, including breakfast, every day. Regular family meals should be encouraged. Regular consumption of fast food with large portion sizes and high energy density should be avoided. Healthy food options should be promoted for snacking. Food portion sizes should be appropriate for age and body size. Nutrition and lifestyle education aimed at the prevention of obesity should be included in the routine care of children by health care professionals.
ARGONAUTE2 Mediates RNA-Silencing Antiviral Defenses againstPotato virus Xin Arabidopsis
Authors: Jaubert Marianne , Bhattacharjee Saikat , Mello Alexandre F.S. , Perry Keith L. , Moffett Peter 
Published: May 2011

AbstractRNA-silencing mechanisms control many aspects of gene regulation including the detection and degradation of viral RNA through the action of, among others, Dicer-like and Argonaute (AGO) proteins. However, the extent to which RNA silencing restricts virus host range has been difficult to separate from other factors that can affect virus-plant compatibility. Here we show that Potato virus X (PVX) can infect Arabidopsis (Arabidopsis thaliana), which is normally a nonhost for PVX, if coinfected with a second virus, Pepper ringspot virus. Here we show that the pepper ringspot virus 12K protein functions as a suppressor of silencing that appears to enable PVX to infect Arabidopsis. We also show that PVX is able to infect Arabidopsis Dicer-like mutants, indicating that RNA silencing is responsible for Arabidopsis nonhost resistance to PVX. Furthermore, we find that restriction of PVX on Arabidopsis also depends on AGO2, suggesting that this AGO protein has evolved to specialize in antiviral defenses.
Analysis of the subcellular localisation of lipoxygenase in legume and actinorhizal nodules
Authors: Demchenko K. , Zdyb A. , Feussner I. , Pawlowski K. 
Published: May 2011

AbstractPlant lipoxygenases (LOXs; EC 1.13.11.12) catalyse the oxygenation of polyunsaturated fatty acids, linoleic (18:2) and α‐linolenic acid (18:3(n‐3)) and are involved in processes such as stress responses and development. Depending on the regio‐specificity of a LOX, the incorporation of molecular oxygen leads to formation of 9‐ or 13‐fatty acid hydroperoxides, which are used by LOX itself as well as by members of at least six different enzyme families to form a series of biologically active molecules, collectively called oxylipins. The best characterised oxylipins are the jasmonates: jasmonic acid (JA) and its isoleucine conjugate that are signalling compounds in vegetative and propagative plant development. In several types of nitrogen‐fixing root nodules, LOX expression and/or activity is induced during nodule development. Allene oxide cyclase (AOC), a committed enzyme of the JA biosynthetic pathway, has been shown to localise to plastids of nodules of one legume and two actinorhizal plants, Medicago truncatula, Datisca glomerata and Casuarina glauca, respectively. Using an antibody that recognises several types of LOX interspecifically, LOX protein levels were compared in roots and nodules of these plants, showing no significant differences and no obvious nodule‐specific isoforms. A comparison of the cell‐specific localisation of LOXs and AOC led to the conclusion that (i) only cytosolic LOXs were detected although it is generally assumed that the (13S)‐hydroperoxy α‐linolenic acid for JA biosynthesis is produced in the plastids, and (ii) in cells of the nodule vascular tissue that contain AOC, no LOX protein could be detected.
Effects of dietary inclusion of Rhus coriaria on internal milieu of rabbits
Authors: Capcarova M. , Slamecka J. , Abbas K. , Kolesarova A. , Kalafova A. , Valent M. , Filipejova T. , Chrastinova L. , Ondruska L. , Massanyi P. 
Published: May 2011

SummaryThe aim of the present work was to investigate the effect of Rhus coriaria L. inclusion to the diet on some biochemical, haematological parameters and the level of antioxidant status of male rabbits. Adult rabbits were divided into five groups: one control (C) and four experimental groups. Experimental animals received sumac per os in feed in various doses (0.50%, 0.75%, 1.00% and 1.50%) for 90 days. Significant increase in PDWc (platelet distribution width) in E3 group when compared with control group was recorded. Sumac administration resulted in decreased cholesterol levels in all experimental groups vs. control group. Significantly lower level of cholesterol was found in E4 group with highest dose of sumac (1.50%). Higher values of total antioxidant status (TAS) and albumins were observed in all experimental groups in comparison with control group. A significant increase in TAS was detected in group E1 and E4. Concentrations of albumins were significantly higher in groups E3 and E4 vs. control group. Sumac administration had no significant effect on bilirubin content. In conclusion, these results show a positive effect of sumac consumption on antioxidant status and cholesterol level in adult male rabbits.
Management of perianal abscess with hainosankyuto in neonates and young infants
Authors: Kawahara Hisayoshi , Nakai Hiroshi , Yoneda Akihiro , Kubota Akio 
Published: May 2011

AbstractBackground:  Perianal abscess (PA) is a common condition acquired in infancy, yet its treatment method remains controversial. We reviewed the outcome of neonates and young infants with PA who were treated with the traditional Japanese medicine, hainosankyuto (TJ‐122).Methods:  Fifteen male infants with PA under the age of 3 months were reviewed. The median age of infants at disease onset was 33 days (range, 18–88 days) and the median bodyweight was 4.1 kg (range, 2.5–6.4 kg). TJ‐122 was administered at a dose of 0.20 g/kg/day (n= 13) or 0.25 g/kg/day (n= 2) orally in two or three divided doses before meals. Antibiotics were not used in any of the patients.Results:  Of the 15 patients, 14 were cured and had no recurrence, with a median TJ‐122 administration of 28 days (range, 14–117 days). Eight patients were cured within 28 days (53%) and 12 were cured within 60 days (80%). One patient, who was later diagnosed with growth hormone deficiency, showed incomplete healing of PA with intermittent pus discharge and recurrence. The patient was cured by 1 year of age following repeated administration of TJ‐122 and juzentaihoto (TJ‐48).Conclusion:  Medical management with TJ‐122 was effective in most neonates and young infants with PA. It appears prudent to manage these patients with hainosankyuto before resorting to surgical intervention.
The bionic eye: a review
Authors: Ong Jong Min , da Cruz Lyndon 
Published: May 2011

AbstractVisual prostheses including artificial retinal devices are a novel and revolutionary approach to the treatment of profound visual loss. The development of the field of visual prosthesis began with cortical prosthetic devices but since then, a variety of devices which target different sites along the visual pathway have been developed with the retinal prosthesis being the most advanced. We present a review of the history of these devices, an update on the current state of play and future prospects of this field.
Severe vernal keratoconjunctivitis requiring trabeculectomy with mitomycin C for corticosteroid‐induced glaucoma
Authors: Ang Marcus , Ho Ching‐Lin , Tan Donald , Chan Cordelia 
Published: May 2011

AbstractBackground:  To describe clinical features of severe vernal keratoconjunctivitis with steroid response in Asian children and risk factors for glaucoma filtration surgery.Design:  Retrospective non‐controlled, comparative case series.Participants:  Patients with severe vernal keratoconjunctivitis seen at a single centre over 6 years.Methods:  Clinical features, symptoms and treatment modalities were recorded for patients (i) diagnosed with severe VKC (clinical grade ≥3); (ii) had >2 recordings of increased intraocular pressures of >21 mmHg; (iii) and a minimum follow‐up period of 1 year post‐presentation.Main Outcome Measure:  Corticosteroid‐induced glaucoma requiring trabeculectomy with mitomycin‐C.Results:  Six patients (eight eyes) of 36 patients required trabeculectomy/mitomycin‐C. All were male. Mean age of disease onset was 9.3 ± 4.5 years for a mean duration of 6.08 ± 3.5 years. Mean intraocular pressures increase from baseline was 29.0 ± 8.2 mmHg and all required >2 anti‐glaucoma medications. The main risk factor for trabeculectomy was a greater increase in intraocular pressures from baseline (odds ratio 1.3; 95% confidence interval, 1.0–1.5; P = 0.011), which was independent of potential confounders such as type and duration of corticosteroid use. Comparing eyes pre‐ and post‐trabeculectomy, all improved in clinical severity of vernal keratoconjunctivitis (mean clinical grade improvement 2.1; 95% confidence interval, 1.3–3.0; P < 0.001) and reduced dependence on topical corticosteroids for mean duration of 22.5 ± 15.3 months.Conclusion:  In our study, patients with a ‘greater steroid response’, that is, higher increase in intraocular pressures from baseline are associated with a 30% higher risk toftrabeculectomy.