bluuebunny/crossref_metadata_2025_split huggingface dataset:
iDynoMiCS: next‐generation individual‐based modelling of biofilms
Authors: Lardon Laurent A. , Merkey Brian V. , Martins Sónia , Dötsch Andreas , Picioreanu Cristian , Kreft Jan‐Ulrich , Smets Barth F. 
Published: March 2011

SummaryIndividual‐based modelling of biofilms accounts for the fact that individual organisms of the same species may well be in a different physiological state as a result of environmental gradients, lag times in responding to change, or noise in gene expression, which we have become increasingly aware of with the advent of single‐cell microbiology. But progress in developing and using individual‐based modelling has been hampered by different groups writing their own code and the lack of an available standard model. We therefore set out to merge most features of previous models and incorporate various improvements in order to provide a common basis for further developments. Four improvements stand out: the biofilm pressure field allows for shrinking or consolidating biofilms; the continuous‐in‐time extracellular polymeric substances excretion leads to more realistic fluid behaviour of the extracellular matrix, avoiding artefacts; the stochastic chemostat mode allows comparison of spatially uniform and heterogeneous systems; and the separation of growth kinetics from the individual cell allows condition‐dependent switching of metabolism. As an illustration of the model's use, we used the latter feature to study how environmentally fluctuating oxygen availability affects the diversity and composition of a community of denitrifying bacteria that induce the denitrification pathway under anoxic or low oxygen conditions. We tested the hypothesis that the existence of these diverse strategies of denitrification can be explained solely by assuming that faster response incurs higher costs. We found that if the ability to switch metabolic pathways quickly incurs no costs the fastest responder is always the best. However, if there is a trade‐off where faster switching incurs higher costs, then there is a strategy with optimal response time for any frequency of environmental fluctuations, suggesting that different types of denitrifying strategies win in different environments. In a single environment, biodiversity of denitrifiers is higher in biofilms than chemostats, higher with than without costs and higher at intermediate frequency of change. The highly modular nature of the new computational model made this case study straightforward to implement, and reflects the sort of novel studies that can easily be executed with the new model.
Diversity of extremophilic purple phototrophic bacteria in Soap Lake, a Central Washington (USA) Soda Lake
Authors: Asao Marie , Pinkart Holly C. , Madigan Michael T. 
Published: March 2011

SummaryCulture‐based and culture‐independent methods were used to explore the diversity of phototrophic purple bacteria in Soap Lake, a small meromictic soda lake in the western USA. Among soda lakes, Soap Lake is unusual because it consists of distinct upper and lower water bodies of vastly different salinities, and its deep waters contain up to 175 mM sulfide. From Soap Lake water new alkaliphilic purple sulfur bacteria of the families Chromatiaceae and Ectothiorhodospiraceae were cultured, and one purple non‐sulfur bacterium was isolated. Comparative sequence analysis of pufM, a gene that encodes a key photosynthetic reaction centre protein universally found in purple bacteria, was used to measure the diversity of purple bacteria in Soap Lake. Denaturing gradient gel electrophoresis and subsequent phylogenetic analyses of pufMs amplified from Soap Lake water revealed that a significant diversity of purple bacteria inhabit this soda lake. Although close relatives of several of the pufM phylotypes obtained from cultured species could also be detected in Soap Lake water, several other more divergent pufM phylotypes were also detected. It is possible that Soap Lake purple bacteria are major contributors of organic matter into the ecosystem of this lake, especially in its extensive anoxic and sulfidic deep waters.
The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms
Authors: Silva‐Rocha Rafael , Tamames Javier , dos Santos Vitor Martins , de Lorenzo Víctor 
Published: March 2011

SummaryThe regulatory and metabolic networks that rule biodegradation of pollutants by environmental bacteria are wired to the rest of the cellular physiology through both transcriptional factors and intermediary signal molecules. In this review, we examine some formalisms for describing catalytic/regulatory circuits of this sort and advocate the adoption of Boolean logic for combining transcriptional and enzymatic occurrences in the same biological system. As an example, we show how known regulatory and metabolic actions that bring about biodegradation of m‐xylene by Pseudomonas putida mt‐2 can be represented as clusters of binary operations and then reconstructed as a digital network. Despite the many simplifications, Boolean tools still capture the gross behaviour of the system even in the absence of kinetic constants determined experimentally. On this basis, we argue that still with a limited volume of data binary formalisms allow us to penetrate the raison d'être of extant regulatory and metabolic architectures.
Comparison of intraoperative outcomes using the new and old generation da Vinci® robot for robot‐assisted laparoscopic prostatectomy
Authors: Shah Ketul , Abaza Ronney 
Published: March 2011

Study Type – Therapy (case series)Level of Evidence 4OBJECTIVE
To review and compare intraoperative outcomes for robotic prostatectomy procedures performed on two generations of the da Vinci robotic surgery platform.
MATERIAL AND METHODS
We reviewed 100 consecutive robotic prostatectomy cases and compared intraoperative outcomes for procedures randomly performed on either the da Vinci S robot or first‐generation standard robot.
Baseline demographic data and intra‐operative variables potentially impacting outcomes were reviewed and compared between the two groups.
RESULTS
Mean total operative time was 191 min using the standard da Vinci robot (range 132–266) versus 169 min with S robot (range 98–230), representing a mean difference of 22 min (P = 0.002).
This difference was statistically significant despite no difference in mean patient BMI of 30.6 (range 19–51) for standard versus 29.3 (range 21–37) for S (P = 0.31), no difference in mean prostate size of 54.6 g (range 26–101) for standard versus 57.3 g (range 32–151) for S (P = 0.55), and no difference in frequency of nerve‐sparing (P = 0.99).
There was also no difference in the portions of procedues performed by residents, which in some cases was none and some the entire procedure, but the standard was more often used for the surgeon’s first case of the day (P = 0.006).
There was no difference in blood loss (P = 0.08), positive margins (P = 0.87), or mean number of lymph nodes removed (10.7 vs 10.6).
CONCLUSIONS
Both generations of da Vinci robotic technology are equally effective for PALP, but the S robot appears to allow shorter procedure times.
Further such evaluations are necessary to guide institutions and public policy decision‐makers on investments in newer generations of robotic technology as incremental advances continue.
‘The Changelessness of God’ as Kierkegaard's Final Theodicy: God and the Gift of Suffering
Authors: MARTENS PAUL , MILLAY TOM 
Published: March 2011

AbstractIn the midst of his final ‘attack on Christendom’, Kierkegaard published a short discourse devoted to James 1:17–21 entitled ‘The Changelessness of God’. Aside from providing a pleasant rhetorical anomaly at this juncture in his corpus, Kierkegaard's final discourse also introduces another surprise: a defense of the God who sits silently by and watches true Christianity disappear from Denmark. Kierkegaard's defense of God also accounts for Christian suffering – Christ's, the apostles' and perhaps his own – and it does so by creating a sharp division of reality between temporality and eternity, a division that echoes through from the earliest discourses on the same biblical passage. This article contextualizes ‘The Changelessness of God’ by tracing these developments and then continues to press the logic of Kierkegaard's construal of the relationship between temporality and eternity which ultimately leads to a rather problematic description of suffering as a necessary good and perfect gift from God.
Moral Taint: On the Transfer of the Implications of Moral Culpability
Authors: ØVERLAND GERHARD 
Published: March 2011

abstractSuppose two people are about to drown. We are in a position to save only one, so the other will have to die. One of the two has just culpably killed an innocent person, but has no intention of killing anybody else and there is no reason to expect that he will. Everything else being equal, should we give them an equal chance of being saved by flipping a coin? In this paper I argue that we should not. I argue that the implications of a person's moral culpability for (recent or prospective) harm to a particular victim should transfer to other conflict situations in which the wrongdoer might find him or herself. This requires establishing the extent to which a person's contributing to harming another person — and his moral culpability for that harm — impinges on our decision making in situations where it is possible only to assist either the wrongdoer or some other person that is not his victim.
Population recovery of black rhinoceros in north‐west Namibia following poaching
Authors: Brodie J. F. , Muntifering J. , Hearn M. , Loutit B. , Loutit R. , Brell B. , Uri‐Khob S. , Leader‐Williams N. , du Preez P. 
Published: March 2011

AbstractCurtailing overharvest, whether illegal or legal, is often a critical conservation objective. Yet even if overexploitation can be stopped, subsequent rates of population recovery can be highly variable due to Allee effects, alterations to age and sex structure and disruptions of animal social systems. Moreover, understanding the influence of density dependence can be difficult but important for long‐term management. Here, we investigate the dynamics of black rhinoceros Diceros bicornis in the Kunene region of Namibia as they recover from illegal hunting. We use multi‐strata mark–recapture models to examine survival and stage‐transition rates from 1992 to 2005. Survivorship estimates ranged from 0.793 for calves to 0.910 for adult males and 0.944 for adult females. The annual reproductive rate in adult females was estimated at 0.315. Model selection showed that these vital rates were time invariant, suggesting that Allee effects and transient dynamics did not have an important effect upon population dynamics, even in the early stages of recovery. Relative population density increased significantly from 1992 to 2005 once illegal hunting had ceased in Kunene. However, the best‐fit models did not include relative density in the estimation of survival or stage‐transition rates. We then used the vital rates generated from our mark–recapture analysis to build matrix projection models that assessed overall population dynamics. The female‐only model gave a population growth rate estimate of λ=1.011. Two‐sex models suggest that the growth rate of the population could range from 0.990 to 1.012. The relatively slow growth rate of this population, even without hunting or density dependence, could stem from the low productivity of the region. Adult females had the highest reproductive value and their survival had the highest elasticity among vital rates. Translocating adult females would lead to the fastest initial population growth rate in founder populations but would have the most impact on the source population.
Myopia, posture and the visual environment
Authors: Neil Charman W 
Published: March 2011

Citation information:Charman WN. Myopia, posture and the visual environment.Ophthalmic Physiol Opt2011,31, 494–501. doi: 10.1111/j.1475‐1313.2011.00825.xAbstractEvidence for a possible role for the peripheral retina in the control of refractive development is discussed, together with Howland’s suggestion (Paper presented at the 13th International Myopia Conference, Tubingen, Germany, July 26–29, 2010) that signals to generate appropriate growth might be derived from ocular oblique astigmatism. The dependence of this, or similar peripheral mechanisms, on exposure to a uniform field of near‐zero dioptric vergence is emphasized: this is required to ensure a consistent relationship between the astigmatic image fields and the retina. This condition is satisfied by typical outdoor environments. In contrast, indoor environments are likely to be unfavourable to peripherally‐based emmetropization, since dioptric stimuli may vary widely across the visual field. This is particularly the case when short working distances or markedly asymmetric head postures with respect to the visual task are adopted.
Television, computer and portable display device use by people with central vision impairment
Authors: Woods Russell L , Satgunam PremNandhini 
Published: March 2011

Citation information: Woods RL & Satgunam P. Television, computer and portable display device use by people with central vision impairment. Ophthalmic Physiol Opt 2011, 31, 258–274. doi: 10.1111/j.1475‐1313.2011.00833.xAbstractPurpose:  To survey the viewing experience (e.g. hours watched, difficulty) and viewing metrics (e.g. distance viewed, display size) for television (TV), computers and portable visual display devices for normally‐sighted (NS) and visually impaired participants. This information may guide visual rehabilitation.Methods:  Survey was administered either in person or in a telephone interview on 223 participants of whom 104 had low vision (LV, worse than 6/18, age 22–90 years, 54 males), and 94 were NS (visual acuity 6/9 or better, age 20–86 years, 50 males). Depending on their situation, NS participants answered up to 38 questions and LV participants answered up to a further 10 questions.Results:  Many LV participants reported at least ‘some’ difficulty watching TV (71/103), reported at least ‘often’ having difficulty with computer displays (40/76) and extreme difficulty watching videos on handheld devices (11/16). The average daily TV viewing was slightly, but not significantly, higher for the LV participants (3.6 h) than the NS (3.0 h). Only 18% of LV participants used visual aids (all optical) to watch TV. Most LV participants obtained effective magnification from a reduced viewing distance for both TV and computer display. Younger LV participants also used a larger display when compared to older LV participants to obtain increased magnification. About half of the TV viewing time occurred in the absence of a companion for both the LV and the NS participants. The mean number of TVs at home reported by LV participants (2.2) was slightly but not significantly (p = 0.09) higher than NS participants (2.0). LV participants were equally likely to have a computer but were significantly (p = 0.004) less likely to access the internet (73/104) compared to NS participants (82/94). Most LV participants expressed an interest in image enhancing technology for TV viewing (67/104) and for computer use (50/74), if they used a computer.Conclusions:  In this study, both NS and LV participants had comparable video viewing habits. Most LV participants in our sample reported difficulty watching TV, and indicated an interest in assistive technology, such as image enhancement. As our participants reported that at least half their video viewing hours are spent alone and that there is usually more than one TV per household, this suggests that there are opportunities to use image enhancement on the TVs of LV viewers without interfering with the viewing experience of NS viewers.
Changes in Vertisol properties as affected by organic amendments application rates
Authors: Ghosh S. , Lockwood P. , Daniel H. , Hulugalle N. , King K. , Kristiansen P. 
Published: March 2011

AbstractThere is considerable global interest in using recycled organic materials because of perceived benefits to soil health and environment. However, information on the effects of organic waste products and their optimal application rates on the quality of heavy clay soils such as Vertisols is sparse. An incubation experiment was therefore conducted using five organic amendments at various rates to identify their optimal application rates, which could improve the quality of the Vertisol. Cotton gin trash, cattle manure, biosolids (dry weight basis 7.5–120 t/ha), chicken manure (dry weight basis 2.25–36 t/ha) and a liquefied vermicast (60–960 L/ha, volumetric basis) changed the soil chemical, physical and microbiological properties compared with a control where no amendments were applied, viz. higher light fraction of organic matter, nutrient content (N and P) and soil microbial activity. Higher application of chicken manure resulted in an increase in dry‐sieved mean weight diameter. Increasing rates of cattle manure increased exchangeable Na concentration and ESP. Although vermicast itself did not contribute a significant amount of N into the soil, when applied at higher rates (60–960 L/ha), its application resulted in increased concentration of NO3‐N in soil by amounts ranging from 43 to 429%. Optimal application rates for cattle manure and cotton gin trash were 30 t/ha, whereas for biosolids and chicken manure, the optimum rate was 60–18 t/ha, respectively.
Near‐surface macropore flow and saturated hydraulic conductivity in drained and restored blanket peatlands
Authors: Wallage Z. E. , Holden J. 
Published: March 2011

AbstractThe impacts of blanket peatland management on water tables, near‐surface macropore flow and saturated hydraulic conductivity were investigated using automated dipwells and mini‐disc tension infiltrometers. Three neighbouring hillslopes which were undisturbed, drained and restored by drain blocking were studied. Mean water table depths at the undisturbed sites were slightly shallower than at the restored site and water tables at both sites were significantly shallower relative to the drained treatment. Through time, however, the water table at the restored treatment behaved in a markedly different way to that at the undisturbed site. Water tables reached the peat surface for only 2% of the time for the drained and restored treatments compared to 18% for the undisturbed treatment. The proportion of runoff flowing through macropores in the near‐surface layers of the peat was found to be large (≥60%) across all three treatments, yet functional macroporosity was found to be significantly greater in the undisturbed peat relative to the two other treatments. Meanwhile, saturated hydraulic conductivity was found to be significantly higher at the restored treatment relative to the two other treatments, with mean conductivities ca. 1.5 times greater, suggesting a form of heightened soil–water interaction. Combined, the results indicate that although restoration by ditch blocking may result in a relatively successful water table recovery, there may not be the full reinstatement of peatland hydrological processes.
Hepatitis C virus infection in USA: an estimate of true prevalence
Authors: Chak Eric , Talal Andrew H. , Sherman Kenneth E. , Schiff Eugene R. , Saab Sammy 
Published: March 2011

AbstractThe recent National Health and Nutrition Examination Survey (NHANES) sampled only the civilian, non‐institutionalized population of USA and may have underestimated the prevalence of hepatitis C virus (HCV) in this country. We searched the database MEDLINE, the Bureau of Justice Statistics, Center for Medicare and Medicaid and individual states Department of Corrections for all epidemiological studies regarding the prevalence of HCV in populations not sampled by the NHANES survey namely the incarcerated, homeless, nursing home residents, hospitalized and those on active military duty. Because of their relatively low frequency in the NHANES sample, we also expanded our search to include healthcare workers and long‐term dialysis patients. Although included in the NHANES sample, we also performed searches on drug users (injection and non‐injection) and veterans to confirm the findings of the NHANES study. Based on the prevalence of studies identified meeting our inclusion criteria, our most conservative estimates state that there at least 142 761 homeless persons, 372 754 incarcerated persons and 6805 persons on active military duty unaccounted for in the NHANES survey. While the NHANES estimates of drug users (both injection and non‐injection) appear to be reasonable, the survey seems to have underestimated the number of HCV‐positive veterans. Our most conservative estimates suggest that there are at least 5.2 million persons living with HCV in USA today, approximately 1.9 million of whom were unaccounted for in the NHANES survey.
An Alternative, Sensitive Method to Detect Helicobacter pylori DNA in Feces
Authors: Horemans Tessa , Deschacht Maartje , Clais Sofie , Van Camp John , de Rijk Pim , Holvoet Jan , Van Assche Tim , Maes Louis , Cos Paul 
Published: March 2011

AbstractBackground:  Despite the high sensitivity and specificity of PCR, detection of Helicobacter pylori DNA in feces is still challenging. Fecal samples contain inhibitory molecules that can prevent amplification of the target DNA. Even by using specific DNA extraction kits for stools, monitoring of infection by analyzing stool samples remains problematic and endorses the need for improved diagnostic methods.Materials and Methods:  The newly proposed method uses selective hybridization of target DNA with biotin‐labeled probes, followed by DNA isolation with streptavidin‐coated magnetic beads. After three washing steps, the purified DNA can be amplified immediately using conventional or quantitative PCR. In order to test this technique on biological samples, Mongolian gerbils were infected with H. pylori ATCC 43504 and fecal samples were analyzed on days 1, 4, and 10 post infection.Results:  A detection limit of one bacterial cell per 100 mg stool sample was established, but only after removal of the magnetic beads from the target DNA by heating. This resulted in a 10‐fold increase of sensitivity compared to a commercially available stool DNA extraction kit. Analysis of fecal samples from infected gerbils demonstrated the presence of H. pylori DNA on each time point, while the uninfected animal remained negative.Conclusions:  The proposed technique allows detection of very low quantities of H. pylori DNA in biological samples. In laboratory animal models, detailed monitoring of infection and complete clearance of infection can be demonstrated thanks to the low detection limit.