bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Hydrolase Identified by Genomic-Proteomic Analysis of Phenylurea Herbicide Mineralization by Variovorax sp. Strain SRS16
Authors: Bers Karolien , Leroy Baptiste , Breugelmans Philip , Albers Pieter , Lavigne Rob , Sørensen Sebastian R. , Aamand Jens , De Mot René , Wattiez Ruddy , Springael Dirk 
Published: October 2011

ABSTRACTThe soil bacterial isolateVariovoraxsp. strain SRS16 mineralizes the phenylurea herbicide linuron. The proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (DCA) andN,O-dimethylhydroxylamine, followed by conversion of DCA to Krebs cycle intermediates. Differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (LibA), a multicomponent chloroaniline dioxygenase, and enzymes associated with a modified chlorocatecholortho-cleavage pathway. Purified LibA is a monomeric linuron hydrolase of ∼55 kDa with aKmand aVmaxfor linuron of 5.8 μM and 0.16 nmol min−1, respectively. This novel member of the amidase signature family is unrelated to phenylurea-hydrolyzing enzymes from Gram-positive bacteria and lacks activity toward other tested phenylurea herbicides. Orthologues oflibAare present in all other tested linuron-degradingVariovoraxstrains with the exception ofVariovoraxstrains WDL1 and PBS-H4, suggesting divergent evolution of the linuron catabolic pathway in differentVariovoraxstrains. The organization of the linuron degradation genes identified in the draft SRS16 genome sequence indicates that gene patchwork assembly is at the origin of the pathway. Transcription analysis suggests that a catabolic intermediate, rather than linuron itself, acts as effector in activation of the pathway. Our study provides the first report on the genetic organization of a bacterial pathway for complete mineralization of a phenylurea herbicide and the first report on a linuron hydrolase in Gram-negative bacteria.
Butyric Acid- and Dimethyl Disulfide-Assimilating Microorganisms in a Biofilter Treating Air Emissions from a Livestock Facility
Authors: Kristiansen Anja , Lindholst Sabine , Feilberg Anders , Nielsen Per H. , Neufeld Josh D. , Nielsen Jeppe L. 
Published: October 2011

ABSTRACT

Biofiltration has proven an efficient tool for the elimination of volatile organic compounds (VOCs) and ammonia from livestock facilities, thereby reducing nuisance odors and ammonia emissions to the local environment. The active microbial communities comprising these filter biofilms have not been well characterized. In this study, a trickle biofilter treating air from a pig facility was investigated and proved efficient in removing carboxylic acids (>70% reduction), mainly attributed to the primary filter section within which reduced organic sulfur compounds were also depleted (up to 50%). The secondary filter eliminated several aromatic compounds: phenol (81%),
p
-cresol (89%), 4-ethylphenol (68%), indole (48%), and skatole (69%). The active butyric acid degrading bacterial community of an air filter sample was identified by DNA stable-isotope probing (DNA-SIP) and microautoradiography, combined with fluorescence
in situ
hybridization (MAR-FISH). The predominant 16S rRNA gene sequences from a clone library derived from “heavy” DNA from [
13
C
4
]butyric acid incubations were
Microbacterium
,
Gordonia
,
Dietzia
,
Rhodococcus
,
Propionibacterium
, and
Janibacter
, all from the
Actinobacteria. Actinobacteria
were confirmed and quantified by MAR-FISH as being the major bacterial phylum assimilating butyric acid along with several
Burkholderiales
-related
Betaproteobacteria
. The active bacterial community assimilating dimethyl disulfide (DMDS) was characterized by DNA-SIP and MAR-FISH and found to be associated with the
Actinobacteria
, along with a few representatives of
Flavobacteria
and
Sphingobacteria
. Interestingly, ammonia-oxidizing
Betaproteobacteria
were also implicated in DMDS degradation, as were fungi. Thus, multiple isotope-based methods provided complementary data, enabling high-resolution identification and quantitative assessments of odor-eliminating
Actinobacteria
-dominated populations of these biofilter environments.
Inactivation of Shiga Toxin-Producing Escherichia coli (STEC) and Degradation and Removal of Cellulose from STEC Surfaces by Using Selected Enzymatic and Chemical Treatments
Authors: Park Yoen Ju , Chen Jinru 
Published: October 2011

ABSTRACT

Some Shiga toxin-producing
Escherichia coli
(STEC) strains produce extracellular cellulose, a long polymer of glucose with β-1-4 glycosidic bonds. This study evaluated the efficacies of selected enzymatic and chemical treatments in inactivating STEC and degrading/removing the cellulose on STEC surfaces. Six cellulose-producing STEC strains were treated with cellulase (0.51 to 3.83 U/15 ml), acetic and lactic acids (2 and 4%), as well as an acidic and alkaline sanitizer (manufacturers' recommended concentrations) under appropriate conditions. Following each treatment, residual amounts of cellulose and surviving populations of STEC were determined. Treatments with acetic and lactic acids significantly (
P
< 0.05) reduced the populations of STEC, and those with lactic acid also significantly decreased the amounts of cellulose on STEC. The residual amounts of cellulose on STEC positively correlated to the surviving populations of STEC after the treatments with the organic acids (
r
= 0.64 to 0.94), and the significance of the correlations ranged from 83 to 99%. Treatments with cellulase and the sanitizers both degraded cellulose. However, treatments with cellulase had no influence on the fate of STEC, and those with the sanitizers reduced STEC cell populations to undetectable levels. Thus, the correlations between the residual amounts of cellulose and the surviving populations of STEC caused by these two treatments were not observed. The results suggest that the selected enzymatic and chemical agents degraded and removed the cellulose on STEC surfaces, and the treatments with organic acids and sanitizers also inactivated STEC cells. The amounts of cellulose produced by STEC strains appear to affect their susceptibilities to certain sanitizing treatments.
Presence of Enterohemorrhagic Escherichia coli ST678/O104:H4 in France Prior to 2011
Authors: Monecke Stefan , Mariani-Kurkdjian Patricia , Bingen Edouard , Weill François-Xavier , Balière Charlotte , Slickers Peter , Ehricht Ralf 
Published: October 2011

ABSTRACT

Two isolates of enterohemorrhagic
Escherichia coli
(EHEC) O104:H4 were isolated in France in 2004 and 2009. Both were characterized and compared to the strain which caused the German outbreak in 2011 and to other O104:H4 strains. This suggests that different O104:H4 EHEC strains were present several years prior to the 2011 outbreak.
Lack of Correlation between Virus Barosensitivity and the Presence of a Viral Envelope during Inactivation of Human Rotavirus, Vesicular Stomatitis Virus, and Avian Metapneumovirus by High-Pressure Processing
Authors: Lou Fangfei , Neetoo Hudaa , Li Junan , Chen Haiqiang , Li Jianrong 
Published: October 2011

ABSTRACT
High-pressure processing (HPP) is a nonthermal technology that has been shown to effectively inactivate a wide range of microorganisms. However, the effectiveness of HPP on inactivation of viruses is relatively less well understood. We systematically investigated the effects of intrinsic (pH) and processing (pressure, time, and temperature) parameters on the pressure inactivation of a nonenveloped virus (human rotavirus [HRV]) and two enveloped viruses (vesicular stomatitis virus [VSV] and avian metapneumovirus [aMPV]). We demonstrated that HPP can efficiently inactivate all tested viruses under optimal conditions, although the pressure susceptibilities and the roles of temperature and pH substantially varied among these viruses regardless of the presence of a viral envelope. We found that VSV was much more stable than most food-borne viruses, whereas aMPV was highly susceptible to HPP. When viruses were held for 2 min under 350 MPa at 4°C, 1.1-log, 3.9-log, and 5.0-log virus reductions were achieved for VSV, HRV, and aMPV, respectively. Both VSV and aMPV were more susceptible to HPP at higher temperature and lower pH. In contrast, HRV was more easily inactivated at higher pH, although temperature did not have a significant impact on inactivation. Furthermore, we demonstrated that the damage of virion structure by disruption of the viral envelope and/or capsid is the primary mechanism underlying HPP-induced viral inactivation. In addition, VSV glycoprotein remained antigenic although VSV was completely inactivated. Taken together, our findings suggest that HPP is a promising technology to eliminate viral contaminants in high-risk foods, water, and other fomites.
AmpH, a Bifunctional
dd
-Endopeptidase and
dd
-Carboxypeptidase of Escherichia coli
Authors: González-Leiza Silvia M. , de Pedro Miguel A. , Ayala Juan A. 
Published: October 2011

ABSTRACT

In
Escherichia coli
, low-molecular-mass penicillin-binding proteins (LMM PBPs) are important for correct cell morphogenesis. These enzymes display
dd
-carboxypeptidase and/or
dd
-endopeptidase activities associated with maturation and remodeling of peptidoglycan (PG). AmpH has been classified as an AmpH-type class C LMM PBP, a group closely related to AmpC β-lactamases. AmpH has been associated with PG recycling, although its enzymatic activity remained uncharacterized until now. Construction and purification of His-tagged AmpH from
E. coli
permitted a detailed study of its enzymatic properties. The N-terminal export signal of AmpH is processed, but the protein remains membrane associated. The PBP nature of AmpH was demonstrated by its ability to bind the β-lactams Bocillin FL (a fluorescent penicillin) and cefmetazole.
In vitro
assays with AmpH and specific muropeptides demonstrated that AmpH is a bifunctional
dd
–endopeptidase and
dd
-carboxypeptidase. Indeed, the enzyme cleaved the cross-linked dimers tetrapentapeptide (D45) and tetratetrapeptide (D44) with efficiencies (
k
cat
/

K
m

) of 1,200 M
−1
s
−1
and 670 M
−1
s
−1
, respectively, and removed the terminal
d
-alanine from muropeptides with a C-terminal
d
-Ala-
d
-Ala dipeptide. Both
dd
-peptidase activities were inhibited by 40 μM cefmetazole. AmpH also displayed a weak β-lactamase activity for nitrocefin of 1.4 × 10
−3
nmol/μg protein/min, 1/1,000 the rate obtained for AmpC under the same conditions. AmpH was also active on purified sacculi, exhibiting the bifunctional character that was seen with pure muropeptides. The wide substrate spectrum of the
dd
-peptidase activities associated with AmpH supports a role for this protein in PG remodeling or recycling.
Clinical Utility of Electrodermal Activity at Acupuncture Points: A Narrative Review
Authors: Colbert Agatha P , Spaulding Keith P , Ahn Andrew C , Cutro Janet A 
Published: October 2011

Objectives To provide an in-depth analysis of seven well-reported studies that examined electrodermal activity (EDA) at acupuncture points with regard to three commonly held tenets of acupuncture: (1) EDA at pathology-related acupuncture points is distinguishable from non-pathology-related acupuncture points; (2) EDA at acupuncture points can assist in diagnosing and monitoring therapeutic progress; and (3) EDA at acupuncture points is able to identify substances that are either therapeutically beneficial or toxic to an individual. Methods Seven of 29 studies that scored >50% on their quality of reporting 54 essential technical and clinical details of EDA testing in human patients were identified from a previous literature review. Fourteen categories of data were extracted from these seven studies for further discussion. Results Two studies compared EDA at pathology-related auricular acupuncture points to non-pathology-related sites. Two studies correlated EDA measurements at sites other than auricular acupuncture points with the presence of specific medical conditions. The final three studies assessed changes in EDA at acupuncture points on the fingers and toes when different substances were placed in the electrical circuit with the patient. Conclusions This review highlights the heterogeneity of approaches to EDA assessments and the discrepancies between common clinical practice and the scientific evidence to support that practice. It also provides pilot data that suggest EDA testing at auricular acupuncture points may distinguish pathology-related acupuncture points from non-pathology-related points; decreased skin conductance correlates with tiredness or low energy; and EDA testing at the Jing-Well acupuncture points, on the tips of the fingers and toes, may assist in monitoring effectiveness of acupuncture treatment. The evidence does not support the use of VEGA testing for allergic status.
CT angiography spot sign predicts in-hospital mortality in patients with secondary intracerebral hemorrhage
Authors: Delgado Almandoz Josser E , Kelly Hillary R , Schaefer Pamela W , Brouwers H Bart , Yoo Albert J , Stone Michael J , Goldstein Joshua N , Rosand Jonathan , Lev Michael H , Gonzalez R Gilberto , Romero Javier M 
Published: October 2011

Background and objectiveThe presence of active contrast extravasation during CT angiography, the spot sign, is a potent predictor of in-hospital mortality in patients with primary intracerebral hemorrhage (ICH). However, its predictive value in patients with ICH due to a vascular abnormality, secondary ICH (SICH), is unknown. The aim of this study was to determine the clinical and radiological predictors of a spot sign and in-hospital mortality in patients with SICH.MethodsTwo experienced readers independently reviewed CT angiograms performed on 215 consecutive patients presenting to the emergency department with SICH over a 10-year period to assess the presence of spot signs according to strict radiological criteria. Differences in reader interpretation were resolved by consensus. Medical records were reviewed for baseline clinical characteristics and in-hospital mortality. Univariate and multivariate logistic regression analyses were performed to determine the clinical and radiological predictors of a spot sign and in-hospital mortality in patients with SICH.ResultsSpot signs were identified in 31 of 215 patients with SICH (14.4%), four of which were delayed spot signs (12.9%). Spot signs were most common in patients with arteriovenous fistulas (42%), Moyamoya (40%), elevated admission blood glucose (23%) and large intraventricular hemorrhage volumes (29%). Spot signs were most predictive of in-hospital mortality in patients with aneurysms of the anterior cerebral artery (100%) and anterior communicating artery (75%). In univariate analysis, the presence of a spot sign significantly increased the risk of in-hospital mortality in patients with SICH (38.7%, OR 2.2, 95% CI 1.0 to 4.9, p=0.0497). However, in multivariate logistic regression analysis the admission Glasgow Coma Scale was the only independent predictor of in-hospital mortality in patients with SICH (OR 2.8, 95% CI 1.6 to 5.1, p=0.0004).ConclusionThe spot sign identifies patients with SICH at increased risk of in-hospital mortality. However, the admission Glasgow Coma Scale was the only independent predictor of in-hospital mortality in this cohort of patients with SICH.
Conserved valproic-acid-induced lipid droplet formation in Dictyostelium and human hepatocytes identifies structurally active compounds
Authors: Elphick Lucy M. , Pawolleck Nadine , Guschina Irina A. , Chaieb Leila , Eikel Daniel , Nau Heinz , Harwood John L. , Plant Nick J. , Williams Robin S. B. 
Published: October 2011

SUMMARY
Lipid droplet formation and subsequent steatosis (the abnormal retention of lipids within a cell) has been reported to contribute to hepatotoxicity and is an adverse effect of many pharmacological agents including the antiepileptic drug valproic acid (VPA). In this study, we have developed a simple model system (Dictyostelium discoideum) to investigate the effects of VPA and related compounds in lipid droplet formation. In mammalian hepatocytes, VPA increases lipid droplet accumulation over a 24-hour period, giving rise to liver cell damage, and we show a similar effect in Dictyostelium following 30 minutes of VPA treatment. Using 3H-labelled polyunsaturated (arachidonic) or saturated (palmitic) fatty acids, we shown that VPA treatment of Dictyostelium gives rise to an increased accumulation of both types of fatty acids in phosphatidylcholine, phosphatidylethanolamine and non-polar lipids in this time period, with a similar trend observed in human hepatocytes (Huh7 cells) labelled with [3H]arachidonic acid. In addition, pharmacological inhibition of β-oxidation in Dictyostelium phenocopies fatty acid accumulation, in agreement with data reported in mammalian systems. Using Dictyostelium, we then screened a range of VPA-related compounds to identify those with high and low lipid-accumulation potential, and validated these activities for effects on lipid droplet formation by using human hepatocytes. Structure-activity relationships for these VPA-related compounds suggest that lipid accumulation is independent of VPA-catalysed teratogenicity and inositol depletion. These results suggest that Dictyostelium could provide both a novel model system for the analysis of lipid droplet formation in human hepatocytes and a rapid method for identifying VPA-related compounds that show liver toxicology.
Chasing a Moving Target: Exploitation and Exploration in Dynamic Environments
Authors: Posen Hart E. , Levinthal Daniel A. 
Published: October 2011

A common justification for organizational change is that the circumstances in which the organization finds itself have changed, thereby eroding the value of utilizing existing knowledge. On the surface, the claim that organizations should adapt by generating new knowledge seems obvious and compelling. However, this standard wisdom overlooks the possibility that the reward to generating new knowledge may itself be eroded if change is an ongoing property of the environment. This observation in turn suggests that environmental change is not a self-evident call for strategies of greater exploration. Indeed, under some conditions the appropriate response to environmental change is a renewed focus on exploiting existing knowledge and opportunities. We develop a computational model based on the canonical multiarmed bandit formulation of exploration and exploitation. We endeavor to understand the mechanisms by which environmental change acts to make purposeful efforts at organizational adaptation less (or more) valuable. This paper was accepted by Jesper Sørensen, organizations.
Density Forecasting of Intraday Call Center Arrivals Using Models Based on Exponential Smoothing
Authors: Taylor James W. 
Published: October 2011

A key input to the call center staffing process is a forecast for the number of calls arriving. Density forecasts of arrival rates are needed for analytical call center models, which assume Poisson arrivals with a stochastic arrival rate. Density forecasts of call volumes can be used in simulation models and are also important for the analysis of outsourcing contracts. A forecasting method, which has previously shown strong potential, is Holt–Winters exponential smoothing adapted for modeling the intraday and intraweek cycles in intraday data. To enable density forecasting of the arrival volume and rate, we develop a Poisson count model, with gamma distributed arrival rate, which captures the essential features of this exponential smoothing method. The apparent stationary level in our data leads us to develop versions of the new model for series with stationary levels. We evaluate forecast accuracy up to two weeks ahead using data from three organizations. We find that the stationary level models improve prediction beyond approximately two days ahead, and that these models perform well in comparison with sophisticated benchmarks. This is confirmed by the results of a call center simulation model, which demonstrates the use of arrival rate density forecasting to support staffing decisions. This paper was accepted by Yossi Aviv, operations management.
Measuring diversity: the importance of species similarity
Authors: Leinster Tom , Cobbold Christina A. 
Published: October 2011

Realistic measures of biodiversity should reflect not only the relative abundances of species, but also the differences between them. We present a natural family of diversity measures taking both factors into account. This is not just another addition to the already long list of diversity indices. Instead, a single formula subsumes many of the most popular indices, including Shannon's, Simpson's, species richness, and Rao's quadratic entropy. These popular indices can then be used and understood in a unified way, and the relationships between them are made plain. The new measures are, moreover, effective numbers, so that percentage changes and ratio comparisons of diversity value are meaningful.We advocate the use of diversity profiles, which provide a faithful graphical representation of the shape of a community; they show how the perceived diversity changes as the emphasis shifts from rare to common species. Communities can usefully be compared by comparing their diversity profiles. We show by example that this is a far more subtle method than any relying on a single statistic.Some ecologists view diversity indices with suspicion, questioning whether they are biologically meaningful. By dropping the naive assumption that distinct species have nothing in common, working with effective numbers, and using diversity profiles, we arrive at a system of diversity measurement that should lay much of this suspicion to rest.
Natural Disasters and Vulnerability: Evidence from the 1997 Forest Fires in Indonesia
Authors: Wong Po. Yin , Brown Philip H. 
Published: October 2011

Abstract
Few studies have attempted to investigate the link between poverty and vulnerability with respect to natural disasters. By applying a utility model to panel data from Indonesia that brackets a major forest fire, this paper estimates and analyzes households’ vulnerability in both total consumption and food consumption. We find that households with a high degree of exposure to smoke from the fires were more vulnerable in total consumption than households with lower exposure, but that they were no more vulnerable in food consumption.
Compositions of n as alternating sequences of weakly increasing and strictly decreasing partitions
Authors: Blecher Aubrey , Brennan Charlotte , Mansour Toufik 
Published: October 2011

Abstract
Compositions and partitions of positive integers are often studied in separate frameworks where partitions are given by q-series generating functions and compositions exhibiting specific patterns are designated by generating functions for these patterns. Here, we view compositions as alternating sequences of weakly increasing and strictly decreasing partitions (i.e. alternating blocks). We obtain generating functions for the number of such partitions in terms of the size of the composition, the number of parts and the total number of “valleys” and “peaks”. From this, we find the total number of “peaks” and “valleys” in the composition of n which have the mentioned pattern. We also obtain the generating function for compositions which split into just two partition blocks. Finally, we obtain the two generating functions for compositions of n that start either with a weakly increasing partition or a strictly decreasing partition.