bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficiency Through Proximity
Authors: Metson Geneviève , Aggarwal Rimjhim , Childers Daniel L. 
Published: November 2012

SummaryIn tightly coupled socioecological systems, such as cities, the interactions between socio‐economic and biophysical characteristics of an area strongly influence ecosystem function. Very often the effects of socioeconomic activities on ecosystem function are unintended, but can impact the sustainability of a city and can have irreversible effects. The food system in its entirety, from production to treatment of human waste, is one of the most important contributors to the way phosphorus (P) cycles through cities. In this article we examined the changes in P dynamics at the urban–agricultural interface of the Phoenix, Arizona, USA, metropolitan area between 1978 and 2008. We found that the contribution of cotton to harvested P decreased while the contribution of alfalfa, which is used as feed for local dairy cows, increased over the study period. This change in cropping pattern was accompanied by growth in the dairy industry and increased internal recycling of P due to dairy cow manure application to alfalfa fields and the local recycling of biosolids and treated wastewater. The proximity of urban populations with dairies and feed production and low runoff in this arid climate have facilitated this serendipitous recycling. Currently P is not strongly regulated or intentionally managed in this system, but farmers' behaviors, shaped largely by market forces and policies related to water recycling, unintentionally affect P cycling. This underscores the need to move from unintentional to deliberate and holistic management of P dynamics through collaborations between practitioners and researchers in order to enhance urban sustainability.
Compositional and Mechanical Properties of Peanuts Roasted to Equivalent Colors using Different Time/Temperature Combinations
Authors: McDaniel Kristin A. , White Brittany L. , Dean Lisa L. , Sanders Timothy H. , Davis Jack P. 
Published: November 2012

Abstract:  Peanuts in North America and Europe are primarily consumed after dry roasting. Standard industry practice is to roast peanuts to a specific surface color (Hunter L‐value) for a given application; however, equivalent surface colors can be attained using different roast temperature/time combinations, which could affect product quality. To investigate this potential, runner peanuts from a single lot were systematically roasted using 5 roast temperatures (147, 157, 167, 177, and 187 °C) and to Hunter L‐values of 53 ± 1, 48.5 ± 1, and 43 ± 1, corresponding to light, medium, and dark roasts, respectively. Moisture contents (MC) ranged from 0.41% to 1.70% after roasting. At equivalent roast temperatures, MC decreased as peanuts became darker; however, for a given color, MC decreased with decreasing roast temperature due to longer roast times required for specified color formation. Initial total tocopherol contents of expressed oils ranged from 164 to 559 μg/g oil. Peanuts roasted at lower temperatures and darker colors had higher tocopherol contents. Glucose content was roast color and temperature dependent, while fructose was only temperature dependent. Soluble protein was lower at darker roast colors, and when averaged across temperatures, was highest when samples were roasted at 187 °C. Lysine content decreased with increasing roast color but was not dependent on temperature. MC strongly correlated with several components including tocopherols (R2 = 0.67), soluble protein (R2 = 0.80), and peak force upon compression (R2 = 0.64). The variation in characteristics related to roast conditions is sufficient to suggest influences on final product shelf life and consumer acceptability.Practical Application:  Peanuts are typically dry roasted to a specified surface color for a given food application; however, it is possible to obtain equivalent colors using different temperatures. This simple observation led to the overall goal of this research which was to determine if peanuts roasted to equivalent surface colors using different temperatures are equivalent from a quality perspective. Several compositional and textural measurements important to product quality differed based on the temperature used to achieve a given roast color. Overall, this study suggests there is good potential to optimize peanut quality by simply adjusting the time/temperature profiles during roasting.
A general model of detectability using species traits
Authors: Garrard Georgia E. , McCarthy Michael A. , Williams Nicholas S. G. , Bekessy Sarah A. , Wintle Brendan A. 
Published: November 2012

Summary

Imperfect detectability is a critical source of variation that limits ecological progress and frustrates effective conservation management. Available modelling methods provide valuable detectability estimates, but these are typically species‐specific.

We present a novel application of time‐to‐detection modelling in which detectability of multiple species is a function of plant traits and observer characteristics. The model is demonstrated for plants in a temperate grassland community in south‐eastern Australia.

We demonstrate that detectability can be estimated using observer experience, species population size and likelihood of flowering. The inclusion of flower colour and species distinctiveness improves the capacity of the model to predict detection rates for new species.

We demonstrate the application of the general model to plants in a temperate grassland community, but this modelling method may be extended to other communities or taxa for which time‐to‐detection models are appropriate.

Detectability is influenced by traits of the species and the observer. General models can be used to derive detectability estimates where repeat survey data, point counts or mark‐recapture data are not available. As these data are almost always absent for species of conservation concern, general models such as ours will be useful for informing minimum survey requirements for monitoring and impact assessment, without the delays and costs associated with data collection.
Factors affecting the (in)accuracy of mammalian mesocarnivore scat identification in South‐western Europe
Authors: Monterroso P. , Castro D. , Silva T. L. , Ferreras P. , Godinho R. , Alves P. C. 
Published: November 2012

AbstractResearch on terrestrial carnivore ecology frequently relies on scat identification and analysis. However, species assignment is commonly based on scat morphology. Potential errors in scat identification are rarely accounted for and might contribute to substantial bias of the final results. Using molecular methods, we evaluate the accuracy of species identification based on morphological characteristics of mammalian mesocarnivore scats collected in two areas in the Iberian Peninsula. Our results revealed that error rates in species assignment of scats based on morphology were highly variable, ranging from 14%, for putative red fox Vulpes vulpes samples, to 88%, for putative wildcats Felis silvestris. The developed models revealed that putative species, season, study area and target species abundance are among the factors involved in identification accuracy. However, the low variability explained suggests that unaccounted factors also had significant effects on accuracy rates. The error rates in scat species assignment constitute a potential source of bias in ecological studies, with serious consequences for the management of threatened species, as unrealistic estimates of status and distribution are prone to occur. Our results suggest that scat identification accuracy rates are circumstance‐specific and therefore should not be transferred or extrapolated. We suggest that scat‐based studies should implement measures (molecular or others) that allow researchers to determine their own circumstance‐specific error rates in scat identification, which should be incorporated in subsequent analyses, ensuring reliable ecological inferences.
PomZ, a ParA‐like protein, regulates Z‐ring formation and cell division in Myxococcus xanthus
Authors: Treuner‐Lange Anke , Aguiluz Kryssia , van der Does Chris , Gómez‐Santos Nuria , Harms Andrea , Schumacher Dominik , Lenz Peter , Hoppert Michael , Kahnt Jörg , Muñoz‐Dorado José , Søgaard‐Andersen Lotte 
Published: November 2012

SummaryAccurate positioning of the division site is essential to generate appropriately sized daughter cells with the correct chromosome number. In bacteria, division generally depends on assembly of the tubulin homologue FtsZ into the Z‐ring at the division site. Here, we show that lack of the ParA‐like protein PomZ in Myxococcus xanthus resulted in division defects with the formation of chromosome‐free minicells and filamentous cells. Lack of PomZ also caused reduced formation of Z‐rings and incorrect positioning of the few Z‐rings formed. PomZ localization is cell cycle regulated, and PomZ accumulates at the division site at midcell after chromosome segregation but prior to FtsZ as well as in the absence of FtsZ. FtsZ displayed cooperative GTP hydrolysis in vitro but did not form detectable filaments in vitro. PomZ interacted with FtsZ in M. xanthus cell extracts. These data show that PomZ is important for Z‐ring formation and is a spatial regulator of Z‐ring formation and cell division. The cell cycle‐dependent localization of PomZ at midcell provides a mechanism for coupling cell cycle progression and Z‐ring formation. Moreover, the data suggest that PomZ is part of a system that recruits FtsZ to midcell, thereby, restricting Z‐ring formation to this position.
FadD3 is an acyl‐CoA synthetase that initiates catabolism of cholesterol rings C and D in actinobacteria
Authors: Casabon Israël , Crowe Adam M. , Liu Jie , Eltis Lindsay D. 
Published: November 2012

SummaryThe cholesterol catabolic pathway occurs in most mycolic acid‐containing actinobacteria, such as Rhodococcus jostii RHA1, and is critical for Mycobacterium tuberculosis (Mtb) during infection. FadD3 is one of four predicted acyl‐CoA synthetases potentially involved in cholesterol catabolism. A ΔfadD3 mutant of RHA1 grew on cholesterol to half the yield of wild‐type and accumulated 3aα‐H‐4α(3′‐propanoate)‐7aβ‐methylhexahydro‐1,5‐indanedione (HIP), consistent with the catabolism of half the steroid molecule. This phenotype was rescued by fadD3 of Mtb. Moreover, RHA1 but not ΔfadD3 grew on HIP. Purified FadD3Mtb catalysed the ATP‐dependent CoA thioesterification of HIP and its hydroxylated analogues, 5α‐OH HIP and 1β‐OH HIP. The apparent specificity constant (kcat/Km) of FadD3Mtb for HIP was 7.3 ± 0.3 × 105 M−1 s−1, 165 times higher than for 5α‐OH HIP, while the apparent Km for CoASH was 110 ± 10 μM. In contrast to enzymes involved in the catabolism of rings A and B, FadD3Mtb did not detectably transform a metabolite with a partially degraded C17 side‐chain. Overall, these results indicate that FadD3 is a HIP‐CoA synthetase that initiates catabolism of steroid rings C and D after side‐chain degradation is complete. These findings are consistent with the actinobacterial kstR2 regulon encoding ring C/D degradation enzymes.
Evolutionarily conserved differences in pallial and thalamic short‐term synaptic plasticity in striatum
Authors: Ericsson Jesper , Stephenson‐Jones Marcus , Kardamakis Andreas , Robertson Brita , Silberberg Gilad , Grillner Sten 
Published: November 2012

Key points
Recent studies have shown that the striatum and the basal ganglia are to a remarkable degree conserved throughout the vertebrate phylum.
As the basic organization of the neural machinery for action selection is present in the lamprey, it is essential to understand how the striatum is activated.
In this study we characterize the pharmacology and synaptic dynamics from the lateral pallium (LPal; cortex) and thalamus (Th), the main excitatory input to the striatum.
We show that, as in mammals, the LPal and Th provide glutamatergic excitation to the striatum, but with completely opposite short‐term synaptic plasticity due to differences in presynaptic properties.
These synaptic differences are also characteristic of the mammalian striatum, suggesting that these are fundamental components of the vertebrate mechanisms for action selection.
Abstract  The striatum of the basal ganglia is conserved throughout the vertebrate phylum. Tracing studies in lamprey have shown that its afferent inputs are organized in a manner similar to that of mammals. The main inputs arise from the thalamus (Th) and lateral pallium (LPal; the homologue of cortex) that represents the two principal excitatory glutamatergic inputs in mammals. The aim here was to characterize the pharmacology and synaptic dynamics of afferent fibres from the LPal and Th onto identified striatal neurons to understand the processing taking place in the lamprey striatum. We used whole‐cell current‐clamp recordings in acute slices of striatum with preserved fibres from the Th and LPal, as well as tract tracing and immunohistochemistry. We show that the Th and LPal produce monosynaptic excitatory glutamatergic input through NMDA and AMPA receptors. The synaptic input from the LPal displayed short‐term facilitation, unlike the Th input that instead displayed strong short‐term synaptic depression. There was also an activity‐dependent recruitment of intrastriatal oligosynaptic inhibition from both inputs. These results indicate that the two principal inputs undergo different activity‐dependent short‐term synaptic plasticity in the lamprey striatum. The difference observed between Th and LPal (cortical) input is also observed in mammals, suggesting a conserved trait throughout vertebrate evolution.
Dampened dopamine‐mediated neuromodulation in prefrontal cortex of fragile X mice
Authors: Paul Kush , Venkitaramani Deepa V. , Cox Charles L. 
Published: November 2012

Key points
Activation of D1 receptors produces an initial suppression followed by facilitation of evoked inhibitory postsynaptic currents (IPSCs) in layer II pyramidal neurons of mouse prefrontal cortex.
In Fmr1 knockout (KO) mice, the D1‐mediated facilitation of evoked IPSCs is absent whereas the initial suppression is unaltered.
Downstream mechanisms of the D1‐mediated facilitation (i.e. cAMP‐dependent facilitation) persists in Fmr1 KO neurons; however, there is a decrease in D1 receptor protein in the Fmr1 KO tissues.
These results indicate the dopamine‐dependent modulation of inhibition is dampened in Fmr1 KO animals, which could produce a relative hyperexcitability of neural circuitry within decision‐making regions of the prefrontal cortex in fragile X syndrome.
Abstract  Fragile X syndrome (FXS) is the most common form of inheritable mental retardation caused by transcriptional silencing of the Fmr1 gene resulting in the absence of fragile X mental retardation protein (FMRP). The role of this protein in neurons is complex and its absence gives rise to diverse alterations in neuronal function leading to neurological disorders including mental retardation, hyperactivity, cognitive impairment, obsessive‐compulsive behaviour, seizure activity and autism. FMRP regulates mRNA translation at dendritic spines where synapses are formed, and thus the lack of FMRP can lead to disruptions in synaptic transmission and plasticity. Many of these neurological deficits in FXS probably involve the prefrontal cortex, and in this study, we have focused on modulatory actions of dopamine in the medial prefrontal cortex. Our data indicate that dopamine produces a long‐lasting enhancement of evoked inhibitory postsynaptic currents (IPSCs) mediated by D1‐type receptors seen in wild‐type mice; however, such enhancement is absent in the Fmr1 knock‐out (Fmr1 KO) mice. The facilitation of IPSCs produced by direct cAMP stimulation was unaffected in Fmr1 KO, but D1 receptor levels were reduced in these animals. Our results show significant disruption of dopaminergic modulation of synaptic transmission in the Fmr1 KO mice and this alteration in inhibitory activity may provide insight into potential targets for the rescue of deficits associated with FXS.
Vancomycin Treatment's Association with Delayed Intestinal Tissue Injury, Clostridial Overgrowth, and Recurrence of Clostridium difficile Infection in Mice
Authors: Warren Cirle A. , van Opstal Edward J. , Riggins Mary S. , Li Yuesheng , Moore John H. , Kolling Glynis L. , Guerrant Richard L. , Hoffman Paul S. 
Published: November 2012

ABSTRACT

Antibiotic treatment, including vancomycin, for
Clostridium difficile
infection (CDI) has been associated with recurrence of disease in up to 25% of infected persons. This study investigated the effects of vancomycin on the clinical outcomes, intestinal histopathology, and anaerobic community during and after treatment in a murine model of CDI. C57BL/6 mice were challenged with
C. difficile
strain VPI 10463 after pretreatment with an antibiotic cocktail. Twenty-four hours after infection, mice were treated daily with vancomycin, nitazoxanide, fidaxomicin, or metronidazaole for 5 days. Mice were monitored for either 6 or 12 days postinfection. Clinical, diarrhea, and histopathology scores were measured. Cecal contents or stool samples were assayed for clostridial or
Bacteroides
DNA and
C. difficile
toxins A and B. Vancomycin treatment of infected mice was associated with improved clinical, diarrhea, and histopathology scores and survival during treatment. However, after discontinuation of the drug, clinical scores and histopathology were worse in treated mice than in untreated infected controls. At the end of the study, 62% of the vancomycin-treated mice succumbed to recurrence, with an overall mortality rate equivalent to that of the untreated infected control group. Fidaxomicin-treated mice had outcomes similar to those of vancomycin-treated mice.
C. difficile
predominated over
Bacteroides
in cecal contents of vancomycin-treated mice, similar to findings for untreated infected mice. Decreasing the duration of vancomycin treatment from 5 days to 1 day decreased recurrence and deaths. In conclusion, vancomycin improved clinical scores and histopathology acutely but was associated with poor outcome posttreatment in
C. difficile
-infected mice. Decreasing vancomycin exposure may decrease relapse and improve survival in CDI.
A Rationally Engineered Anti-HIV Peptide Fusion Inhibitor with Greatly Reduced Immunogenicity
Authors: Brauer Frances , Schmidt Kerstin , Zahn Roland C. , Richter Cornelia , Radeke Heinfried H. , Schmitz Jörn E. , von Laer Dorothee , Egerer Lisa 
Published: November 2012

ABSTRACTPeptides derived from the C-terminal heptad repeat 2 (HR2) region of the HIV-1 gp41 envelope glycoprotein, so-called C peptides, are very efficient HIV-1 fusion inhibitors. We previously developed innovative gene therapeutic approaches aiming at the directin vivoproduction of C peptides from genetically modified host cells and found that T cells expressing membrane-anchored or secreted C peptides are protected from HIV-1 infection. However, an unwanted immune response against such antiviral peptides may significantly impair clinical efficacy and pose safety risks to patients. To overcome this problem, we engineered a novel C peptide, V2o, with greatly reduced immunogenicity and excellent antiviral activity. V2o is based on the chimeric C peptide C46-EHO, which is derived from the HR2 regions of HIV-2EHOand HIV-1HxB2and has broad anti-HIV and anti-simian immunodeficiency virus activity. Antibody and major histocompatibility complex class I epitopes within the C46-EHO peptide sequence were identified byin silicoandin vitroanalyses. Using rational design, we removed these epitopes by amino acid substitutions and thus minimized antigenicity and immunogenicity considerably. At the same time, the antiviral activity of the deimmunized peptide V2o was preserved or even enhanced compared to that of the parental C46-EHO peptide. Thus, V2o is an ideal candidate, especially for those novel therapeutic approaches for HIV infection that involve directin vivoproduction of antiviral C peptides.
Effects of Obesity and Sex on Antimicrobial Pharmacokinetics and Acute Kidney Injury: Validation of a Preclinical Model
Authors: Pai Manjunath P. , Chen Wen Zhen , Garba Adinoyi , Cui Huadong , Zaffo Barbara , El-Fawal Hassan A. N. , Mousa Shaker A. 
Published: November 2012

ABSTRACTObese patients may be at a greater risk for acute kidney injury (AKI) with the use of certain antimicrobial agents that are dosed by weight. Current preclinical models of AKI utilize the male rat within a narrow weight range that limits extrapolation of the generated results. We evaluated the pharmacokinetics and AKI potential of gentamicin in 14-week-old diet-induced obesity-prone (n= 40) and obesity-resistant (n= 40) rats of both sexes. Single daily doses of gentamicin (12.5, 18.75, or 25 mg/kg of body weight) or saline (control) were administered intraperitoneally for 14 doses. Blood samples were collected after doses 1, 7, and 14, assayed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and analyzed using a nonparametric population pharmacokinetic approach for gentamicin. Urine was collected after doses 1, 3, and 5 and assayed for kidney injury molecule 1 (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) and normalized to creatinine (Cr) values. Histology was performed on all animals, and the degree of proximal tubular injury was graded. The mean (minimum, maximum) weight of the rats was 330 (136, 580) g. NGAL/Cr predicted AKI better than did KIM-1/Cr and was detectable in male rats after dose 1 and in obesity-prone female rats after dose 5. Proximal tubular injury by histology was significantly higher in male than in female rats. A significant relationship between the gentamicin area under the curve from zero to 24 hours (AUC0–24) estimates and the maximum NGAL/Cr ratio was observed. This preclinical model has the potential to aid with dose extrapolation for body size and improve assessment of the toxicology potential of antimicrobials in development.
Population Pharmacokinetics of Fusidic Acid: Rationale for Front-Loaded Dosing Regimens Due to Autoinhibition of Clearance
Authors: Bulitta Jürgen B. , Okusanya Olanrewaju O. , Forrest Alan , Bhavnani Sujata M. , Clark Kay , Still J. Gordon , Fernandes Prabhavathi , Ambrose Paul G. 
Published: November 2012

ABSTRACT

The objectives of this analysis were to develop a population pharmacokinetic (PK) model to describe the absorption and disposition of fusidic acid after single and multiple doses and to determine the effect of food on the rate and extent of bioavailability. Plasma PK data from three phase 1 studies (
n
= 75;
n
= 14 with and without food) in which healthy subjects received sodium fusidate (500 to 2,200 mg) as single or multiple oral doses every 8 h (q8h) or q12h for up to 7 days were modeled using S-ADAPT (MCPEM algorithm). Accumulation of fusidic acid after multiple doses was more than that predicted based on single-dose data. The PK of fusidic acid was best described using a time-dependent mixed-order absorption process, two disposition compartments, and a turnover process to describe the autoinhibition of clearance. The mean total clearance (% coefficient of variation) was 1.28 liters/h (33%) and the maximum extent of autoinhibition was 71.0%, with a 50% inhibitory concentration (IC
50
) of 46.3 mg/liter (36%). Food decreased the extent of bioavailability by 18%. As a result of the autoinhibition of clearance, steady state can be achieved earlier with dosing regimens that contain higher doses (after 8 days for 750 mg q12h and 1 day for 1,500 mg q12h on day 1 followed by 600 mg q12h versus 3 weeks for 500 mg q12h). Given that large initial doses autoinhibit the clearance of fusidic acid, this characteristic provides a basis for the administration of front-loaded dosing regimens of sodium fusidate which would allow for effective concentrations to be achieved early in therapy.