bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using experimental human influenza infections to validate a viral dynamic model and the implications for prediction
Authors: CHEN S. C. , YOU S. H. , LIU C. Y. , CHIO C. P. , LIAO C. M. 
Published: November 2011

SUMMARYThe aim of this work was to use experimental infection data of human influenza to assess a simple viral dynamics model in epithelial cells and better understand the underlying complex factors governing the infection process. The developed study model expands on previous reports of a target cell-limited model with delayed virus production. Data from 10 published experimental infection studies of human influenza was used to validate the model. Our results elucidate, mechanistically, the associations between epithelial cells, human immune responses, and viral titres and were supported by the experimental infection data. We report that the maximum total number of free virions following infection is 103-fold higher than the initial introduced titre. Our results indicated that the infection rates of unprotected epithelial cells probably play an important role in affecting viral dynamics. By simulating an advanced model of viral dynamics and applying it to experimental infection data of human influenza, we obtained important estimates of the infection rate. This work provides epidemiologically meaningful results, meriting further efforts to understand the causes and consequences of influenza A infection.
The Goods of Human Sexuality: Ethics and Moral Theology
Authors: Wondra Ellen 
Published: November 2011

AbstractChristian ethics has always taken a complex view of the goods and purposes of human sexuality and its role in human relationships. Sexual desire and behavior have to be seen always within the overarching moral imperatives of love of God and love of neighbor. Such love entails self-giving and other-regard, and in longer-term relationships also some measure of commitment, fidelity, reciprocity or mutuality, truthfulness and generativity. Yet not all relationships with these characteristics do (or should) include sexual behavior. Nor do all sexual relationships include all these characteristics or virtues all the time. So we do better to base our moral evaluations of relationships on the exercise of these virtues than on more obvious criteria of sexual orientation or even status in the eyes of the church. At the same time, it is also possible for faithful and reasonable people to disagree faithfully and reasonably on sexual ethics, as on other things.
Historical temporal trends in overwinter and spring snowpack for the Okanagan and Similkameen River watersheds in south-central British Columbia, Canada
Authors: Rayne Sierra , Forest Kaya 
Published: November 2011

AbstractPotential historical temporal trends in the overwinter and spring snowpack were investigated for the Canadian portions of the Okanagan and Similkameen Valleys in south-central British Columbia. Significant evidence is available that the Okanagan and Similkameen River watersheds are exhibiting both spatially and temporally heterogeneous declines in snowpacks over the past several decades, but whether the causes are part of a natural cycle or result from longer term climatic changes is not clear. The variability in the magnitude, timing, and location of any significant time trends in snowpack decline also precludes efforts towards developing reliable hydrologic models that reflect a response to potential future changes in snowpack patterns for these regions of British Columbia.
Identity in research infrastructure and scientific communication: Report from the 1st IRISC workshop, Helsinki Sep 12-13, 2011
Authors: Thorisson Gudmundur , Linden Mikael , Brookes Anthony , Byrne Myles , Muilu Juha , Nyronen Tommi 
Published: November 2011

AbstractMotivation for the IRISC workshop came from the observation that identity and digital identification are increasingly important factors in modern scientific research, especially with the now near-ubiquitous use of the Internet as a global medium for dissemination and debate of scientific knowledge and data, and as a platform for scientific collaborations and large-scale e-science activities.The 1 1/2 day IRISC2011 workshop sought to explore a series of interrelated topics under two main themes: i) unambiguously identifying authors/creators & attributing their scholarly works, and ii) individual identification and access management in the context of identity federations. Specific aims of the workshop included:• Raising overall awareness of key technical and non-technical challenges, opportunities and developments.• Facilitating a dialogue, cross-pollination of ideas, collaboration and coordination between diverse – and largely unconnected – communities.• Identifying & discussing existing/emerging technologies, best practices and requirements for researcher identification.This report provides background information on key identification-related concepts & projects, describes workshop proceedings and summarizes key workshop findings.
Assessment of Economic and Environmental Cost-benefits of Developed Biorefinery Schemes
Authors: Binns Michael , Vlysidis Anestis , Theodoropoulos* Constantinos 
Published: November 2011

In this work modelling and optimisation studies for the evaluation and improvement of several biorefinery schemes were performed. Economic and environmental objectives were considered with the aim to find configurations that maximise profits while minimising the environmental impact. Biorefineries were modelled using a commercial simulator (Aspen Plus) combined with calculations in MatLab. Optimisation studies (including multi-objective optimisation) were carried out using both stochastic (simulated annealing) and deterministic (sequential-quadratic-programming based) approaches. The results show that for a number of schemes improved profits can be found including biodiesel and biogas production in addition to supercritical CO2 extraction from wheat straws. An oil-to-methanol ratio of around 1:13 to 1:14 was found to be optimal for the biodiesel-producing transesterification reaction. The optimum conditions for the biogas case involved recycling most of the digestate, which leads to a high productivity of biogas. Supercritical CO2 extraction was found to be most profitable at around 36,000 tons per year capacity.
Multi-objective optimisation was also performed in order to find how the optimal profits change when different constraints are placed on the emissions from each process. For the biodiesel cases these constraints reduced the profits by up to €10 per ton of feed. For biogas production reducing the emissions meant using more of the digestate as fertiliser. For supercritical CO2 extraction reducing emissions requires reducing the yearly capacity, which in turn reduces the profits by €63 per ton.
Comparisons of the different schemes are performed using calculations of profits and emissions ‘per ton of feed’ in order to give a fair comparison of biorefinery processes operating at different scales. These comparisons showed that the most profitable schemes were those with the lowest capacity. These lower capacity schemes could be very profitable if they can be scaled up and if there is sufficient feedstock available. Comparison of the emissions for these cases showed that the most profitable schemes also have the highest emissions. This is because these cases involve either high-energy usage (usually with larger quantities of electricity) or combustion.
Tensor–vector–scalar-modified gravity: from small scale to cosmology
Authors: Bekenstein Jacob D. 
Published: November 2011

The impressive success of the standard cosmological model has suggested to many that its ingredients are all that one needs to explain galaxies and their systems. I summarize a number of known problems with this programme. They might signal the failure of standard gravity theory on galaxy scales. The requisite hints as to the alternative gravity theory may lie with the modified Newtonian dynamics (MOND) paradigm, which has proved to be an effective summary of galaxy phenomenology. A simple nonlinear modified gravity theory does justice to MOND at the non-relativistic level, but cannot be consistently promoted to relativistic status. The obstacles were first side-stepped with the formulation of tensor–vector–scalar theory (T
e
V
e
S), a covariant-modified gravity theory. I review its structure, its MOND and Newtonian limits, and its performance in the face of galaxy phenomenology. I also summarize features of T
e
V
e
S cosmology and describe the confrontation with data from strong and weak gravitational lensing.
Double‐blind placebo‐controlled evaluation of the PROMETA™ protocol for methamphetamine dependence
Authors: Ling Walter , Shoptaw Steven , Hillhouse Maureen , Bholat Michelle A. , Charuvastra Charles , Heinzerling Keith , Chim David , Annon Jeffrey , Dowling Patrick T. , Doraimani Geetha 
Published: November 2011

ABSTRACTAims  To evaluate the efficacy and safety of the PROMETA™ Protocol for treating methamphetamine dependence.Design  A double‐blind, placebo‐controlled 108‐day study with random assignment to one of two study conditions: active medication with flumazenil (2 mg infusions on days 1, 2, 3, 22, 23), gabapentin (1200 mg to day 40) and hydroxazine (50 mg to day 10) versus placebo medication (with active hydroxazine only).Setting  Three substance abuse treatment clinics: two in‐patient, one out‐patient.Participants  Treatment‐seeking, methamphetamine‐dependent adults (n = 120).Measurements  Primary outcome was percentage of urine samples testing negative for methamphetamine during the trial.Findings  No statistically significant between‐group differences were detected in urine drug test results, craving, treatment retention or adverse events.Conclusions  The PROMETA protocol, consisting of flumazenil, gabapentin and hydroxyzine, appears to be no more effective than placebo in reducing methamphetamine use, retaining patients in treatment or reducing methamphetamine craving.
Analysis of very elderly (≥80 years) non‐hodgkin lymphoma: impact of functional status and co‐morbidities on outcome
Authors: Nabhan Chadi , Smith Sonali M. , Helenowski Irene , Ramsdale Erika , Parsons Benjamin , Karmali Reem , Feliciano Josephine , Hanson Britt , Smith Scott , McKoy June , Larsen Annette , Hantel Andrew , Gregory Stephanie , Evens Andrew M. 
Published: November 2011

SummaryData on outcome, prognostic factors, and treatment for very elderly non‐Hodgkin lymphomas (NHL) is sparse. We conducted a multicentre retrospective analysis of NHL patients ≥80 years (at diagnosis) treated between 1999 and 2009. Detailed characteristics were obtained including geriatric syndromes, activities of daily living (ADLs), and co‐morbidities using the Cumulative Illness Rating Scale‐Geriatrics (CIRS‐G). We identified 303 patients: 170 aggressive NHL (84% B cell/16% T cell) and 133 indolent NHL (82% B cell/18% T cell). Median age was 84 years (80–95). A geriatric syndrome was present in 26% of patients, 18% had ≥1 grade 4 CIRS‐G, and 14% had loss of ADLs. At 49‐month median follow‐up, 4‐year progression‐free (PFS) and overall survival (OS) for aggressive NHLs were 31% and 44% respectively (stage I/II: PFS 53% and OS 66%; stage III/IV: PFS 20% and OS 32%; P < 0·0001 and 0·0002, respectively). Four‐year PFS and OS for indolent NHL were 44% and 66% respectively, regardless of stage. Multivariate regression analysis identified two key factors that predicted inferior PFS and OS for both NHL groups: lack of CR and loss of ADLs. Prospective studies for very elderly NHL that incorporate geriatric tools, especially ADLs, are warranted.
Parental phase status affects the cold hardiness of progeny eggs in locusts
Authors: Wang Hongsheng , Ma Zongyuan , Cui Feng , Wang Xianhui , Guo Wei , Lin Zhe , Yang Pengcheng , Kang Le 
Published: November 2011

Summary1. The capacity to adapt to low temperature is critical for the persistence of insect populations in heterogeneous environments. Locusts show remarkable phenotypic plasticity, termed ‘phase change’, in response to local population density.2. In this study, the hypothesis that population density, as a social factor, affects the cold hardiness of progeny is validated in the migratory locust, Locusta migratoria, which shows remarkable density‐dependent phase changes between gregarious and solitarious phases.3. We demonstrated that eggs of gregarious and solitarious migratory locusts significantly differ not only in size and weight, but also in cold hardiness. Eggs of solitarious locusts are more resistant to cold stress compared with those of gregarious locusts, with longer 50% lethal time at different low temperatures and under different acclimation treatments of cooling rates or cold exposure time, lower upper limit of chill injury zone, and lower sum of injurious temperature resulting from temperature–time regression. The lowest cooling rate (0·05 °C min−1) yields the highest survival of cold for eggs.4. A custom‐made microarray covering 9154 unigenes of the migratory locust demonstrated quite different gene expression profiles in the two phases in response to normal or low temperature. Under cold stress, the gregarious‐phase eggs have higher transcriptional levels of heat‐shock proteins, DOPA decarboxylases and tyrosine hydroxylase, whereas the solitarious‐phase eggs exhibit stimulated lipid metabolism and carboxylic acid transport.5. Hybridization between the two phases showed that the cold hardiness of eggs from the hybrid with solitarious females is significantly higher than that of the hybrid with gregarious females, and the cold hardiness of eggs from each reciprocal hybrid is close to their maternal origins. These results indicate that the cold hardiness of progeny is affected by the parental phase status.
The foraging tightrope between predation risk and plant toxins: a matter of concentration
Authors: McArthur Clare , Orlando Paul , Banks Peter B. , Brown Joel S. 
Published: November 2011

Summary1. Plants defend and predators attack, provoking the foraging dilemma faced by herbivores and frugivores of how to eat enough without being eaten. High toxin concentration in leaves and fruits inhibits consumption, while predation risk reduces feeding opportunities, as prey forage to avoid encountering predators. Thus, both factors vary and define the quality of the landscape. How foraging animals directly quantify, compare and respond to these two costs has rarely been tested.2. We show that free‐ranging bushbabies – small, frugivorous primates – change their behaviour and use of artificial food patches based on the interplay between toxin concentration in food and patch safety. Using a titration experiment, we demonstrate that bushbabies quantify the relative costs of toxin and fear. We pinpoint where these costs are equivalent and show that animals seek food patches with the lower net cost.3. We conclude that the ecological effectiveness of plant toxins as defence against consumers needs to be considered in the context of a landscape of fear – and the relative impact of anti‐predator tactics and plant defence is strongly shaped by the concentration of these defences.4. A corollary is that plants may benefit from fear as a substitute for their own chemical defence, adding a new dimension to the concept of indirect plant defence. Whether, from the plant’s perspective, the benefits derived from fear can be considered evolutionarily adaptive rather than simply ecologically serendipitous remains to be tested.
Methyl chloride isotopic signatures from Irish forest soils and a comparison between abiotic and biogenic methyl halide soil fluxes
Authors: Redeker Kelly R. , Kalin Robert M. 
Published: November 2011

AbstractForest soils demonstrate in a microcosm the difficulties that are faced in quantifying methyl halide budgets. Carbon isotopic analyses have been proposed as a potential tool to address these concerns and in this study we have measured significant enrichment of the methyl chloride 13C/12C isotopic ratio (from −40.2 ± 0.8‰ to −33.4 ± 7.4‰) after 9 min chamber emplacement on local Irish forest soils. This enrichment occurred independent of direction of methyl chloride fluxes. Measurements from soil cores in a flow‐through system (FTS) are comparable with chamber‐based isotopic measurements and indicate that methyl chloride produced abiotically from organic soil horizons has an isotopic 13C signature of −53 ± 49‰, significantly less depleted than previously reported. Average net methyl chloride, methyl bromide and methyl iodide fluxes from soils (77.8 ± 2.1, 1.25 ± 3.63 and 0.35 ± 2.00 μg MeX m−2 day−1, respectively) are in line with previously reported values; however, a better understanding of spatial and temporal variability is needed for budget quantification. Methyl halide fluxes from FTS soil cores demonstrate that, on a per gram basis, most consumption occurs through biologically driven processes in the O horizon, with progressively smaller contributions in deeper horizons. Sporadic biogenic production was observed in shallow soil horizons only. Abiotic production was at most one‐tenth the net biological reaction rate in the O horizon and did not appear to be significantly different from zero in lower horizons. Modelled emissions based upon observed and reported rates for production, consumption and diffusion within the soil atmosphere system are unable to replicate all observed isotopic signatures from chamber fluxes.
Mixed competition–predation: potential vs. realized interactions
Authors: Persson Lennart , De Roos André M. 
Published: November 2011

Summary1. Life‐history omnivory or size‐induced mixed competition–predation systems have under many conditions theoretically been shown to be fragile, whereas at the same time existing empirical data suggest such systems to be common in nature.2. In a whole lake experiment covering 17 years, we analysed the effects of the introduction of the intraguild prey roach (Rutilus rutilus) on the population size and individual performance of the intraguild predator perch (Perca fluviatilis) and on resource levels in two low productivity systems.3. A strong long‐term effect of roach on the zooplankton resource but not on the macroinvertebrate resource was present. Competitive effects of roach on perch were observed in one of the lakes the first years after the introduction, but at the end of the study no competitive effect of roach on either size class of perch was observed in any of the two lakes. In contrast, a positive predatory effect reflected in improved growth rates of older perch was present.4. The lack of a support for a competitive effect of roach on small perch raises the question of the importance of mixed competition–predation interactions in life‐history omnivorous systems and the problem of comparing descriptive data on feeding relationships with theoretical predictions based on interaction modules.
Swarming motility and the control of master regulators of flagellar biosynthesis
Authors: Patrick Joyce E. , Kearns Daniel B. 
Published: November 2011

SummarySwarming motility is the movement of bacteria over a solid surface powered by rotating flagella. The expression of flagellar biosynthesis genes is governed by species‐specific master regulator transcription factors. Mutations that reduce or enhance master regulator activity have a commensurate effect on swarming motility. Here we review what is known about the proteins that modulate swarming motility and appear to act upstream of the master flagellar regulators in diverse swarming bacteria. We hypothesize that environmental control of the master regulators is important to the swarming phenotype perhaps at the level of controlling flagellar number.
In Arabidopsis, the spatial and dynamic organization of the endoplasmic reticulum and Golgi apparatus is influenced by the integrity of the C‐terminal domain of RHD3, a non‐essential GTPase
Authors: Stefano Giovanni , Renna Luciana , Moss Tyler , McNew James A. , Brandizzi Federica 
Published: November 2011

SummaryThe mechanisms underlying the organization and dynamics of plant endomembranes are largely unknown. Arabidopsis RHD3, a distant member of the dynamin superfamily, has recently been implicated in plant ER morphology and Golgi movement through analyses of dominant‐negative mutants of the putative GTPase domain in a heterologous system. Whether RHD3 is indispensable for ER architecture and what role regions other than the putative GTPase domain play in RHD3 function are unanswered questions. Here we characterized an EMS mutant, gom8, with disrupted Golgi movement and positioning and compromised ER shape and dynamics. gom8 mapped to a missense mutation in the RHD3 hairpin loop domain, causing accumulation of the mutant protein into large structures, a markedly different distribution compared with wild‐type RHD3 over the ER network. Despite the GOM8 distribution, tubules fused in the peripheral ER of the gom8 mutant. These data imply that integrity of the hairpin region is important for the subcellular distribution of RHD3, and that reduced availability of RHD3 over the ER can cause ER morphology defects, but does not prevent peripheral fusion between tubules. This was confirmed by evidence that gom8 was phenocopied in an RHD3 null background. Furthermore, we established that the region encompassing the RHD3 hairpin domain and the C‐terminal cytosolic domain is necessary for RHD3 function. We conclude that RHD3 is important in ER morphology, but is dispensable for peripheral ER tubulation in an endogenous context, and that its activity relies on the C‐terminal region in addition to the GTPase domain.
Hippocampal α7 nicotinic acetylcholine receptor levels in patients with schizophrenia, bipolar disorder, or major depressive disorder
Authors: Thomsen Morten S , Weyn Annelies , Mikkelsen Jens D 
Published: November 2011

Thomsen MS, Weyn A, Mikkelsen JD. Hippocampal α7 nicotinic acetylcholine receptor levels in patients with schizophrenia, bipolar disorder, or major depressive disorder. Bipolar Disord 2011: 13: 701–707. © 2011 The Authors. Journal compilation © 2011 John Wiley & Sons A/S.Background:  The α7 nicotinic acetylcholine receptor (nAChR) is involved in cognitive function and synaptic plasticity. Consequently, changes in α7 nAChR function have been implicated in a variety of mental disorders, especially schizophrenia. However, there is little knowledge regarding the levels of the α7 nAChR in patients with bipolar disorder.Methods:  We performed [125I]‐bungarotoxin autoradiography to selectively visualize and measure α7 nAChRs on postmortem sections of the temporal lobe from patients with schizophrenia, bipolar disorder, or major depressive disorder, as well as control subjects. Radioligand binding was determined in the dentate gyrus, CA3, and CA1 subfields of the hippocampus and the perirhinal cortex.Results:  Bungarotoxin binding was significantly increased in the CA1 and perirhinal cortex of patients with bipolar disorder compared to control subjects, whereas in patients with schizophrenia or major depressive disorder the level of binding did not significantly differ from control subjects in any region measured.Conclusions:  These data are consistent with the reported genetic associations linking the α7 nAChR to the pathology of bipolar disorder, and may suggest a dysfunction of α7 nAChR‐dependent signalling in bipolar disorder. We could not reproduce the previously reported decrease in hippocampal bungarotoxin binding in schizophrenia.