bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters
Authors: Kim Lavane , Pagaling Eulyn , Zuo Yi Y. , Yan Tao 
Published: October 2013

ABSTRACT

The impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,
Burkholderiales
and
Rhodocyclales
of the
Betaproteobacteria
class were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.
Novel Characteristics of Succinate Coenzyme A (Succinate-CoA) Ligases: Conversion of Malate to Malyl-CoA and CoA-Thioester Formation of Succinate Analogues
In Vitro
Authors: Nolte Johannes Christoph , Schürmann Marc , Schepers Catherine-Louise , Vogel Elvira , Wübbeler Jan Hendrik , Steinbüchel Alexander 
Published: October 2013

ABSTRACT

Three succinate coenzyme A (succinate-CoA) ligases (SucCD) from
Escherichia coli
,
Advenella mimigardefordensis
DPN7
T
, and
Alcanivorax borkumensis
SK2 were characterized regarding their substrate specificity concerning succinate analogues. Previous studies had suggested that SucCD enzymes might be promiscuous toward succinate analogues, such as itaconate and 3-sulfinopropionate (3SP). The latter is an intermediate of the degradation pathway of 3,3′-dithiodipropionate (DTDP), a precursor for the biotechnical production of polythioesters (PTEs) in bacteria. The
sucCD
genes were expressed in
E. coli
BL21(DE3)/pLysS. The SucCD enzymes of
E. coli
and
A. mimigardefordensis
DPN7
T
were purified in the native state using stepwise purification protocols, while SucCD from
A. borkumensis
SK2 was equipped with a C-terminal hexahistidine tag at the SucD subunit. Besides the preference for the physiological substrates succinate, itaconate, ATP, and CoA, high enzyme activity was additionally determined for both enantiomeric forms of malate, amounting to 10 to 21% of the activity with succinate.

K
m

values ranged from 2.5 to 3.6 mM for
l
-malate and from 3.6 to 4.2 mM for
d
-malate for the SucCD enzymes investigated in this study. As
l
-malate-CoA ligase is present in the serine cycle for assimilation of C
1
compounds in methylotrophs, structural comparison of these two enzymes as members of the same subsubclass suggested a strong resemblance of SucCD to
l
-malate-CoA ligase and gave rise to the speculation that malate-CoA ligases and succinate-CoA ligases have the same evolutionary origin. Although enzyme activities were very low for the additional substrates investigated, liquid chromatography/electrospray ionization-mass spectrometry analyses proved the ability of SucCD enzymes to form CoA-thioesters of adipate, glutarate, and fumarate. Since all SucCD enzymes were able to activate 3SP to 3SP-CoA, we consequently demonstrated that the activation of 3SP is not a unique characteristic of the SucCD from
A. mimigardefordensis
DPN7
T
. The essential role of
sucCD
in the activation of 3SP
in vivo
was proved by genetic complementation.
Nonclinical and Clinical Enterococcus faecium Strains, but Not Enterococcus faecalis Strains, Have Distinct Structural and Functional Genomic Features
Authors: Kim Eun Bae , Marco Maria L. 
Published: October 2013

ABSTRACT

Certain strains of
Enterococcus faecium
and
Enterococcus faecalis
contribute beneficially to animal health and food production, while others are associated with nosocomial infections. To determine whether there are structural and functional genomic features that are distinct between nonclinical (NC) and clinical (CL) strains of those species, we analyzed the genomes of 31
E. faecium
and 38
E. faecalis
strains. Hierarchical clustering of 7,017 orthologs found in the
E. faecium
pangenome revealed that NC strains clustered into two clades and are distinct from CL strains. NC
E. faecium
genomes are significantly smaller than CL genomes, and this difference was partly explained by significantly fewer mobile genetic elements (ME), virulence factors (VF), and antibiotic resistance (AR) genes.
E. faecium
ortholog comparisons identified 68 and 153 genes that are enriched for NC and CL strains, respectively. Proximity analysis showed that CL-enriched loci, and not NC-enriched loci, are more frequently colocalized on the genome with ME. In CL genomes, AR genes are also colocalized with ME, and VF are more frequently associated with CL-enriched loci. Genes in 23 functional groups are also differentially enriched between NC and CL
E. faecium
genomes. In contrast, differences were not observed between NC and CL
E. faecalis
genomes despite their having larger genomes than
E. faecium
. Our findings show that unlike
E. faecalis
, NC and CL
E. faecium
strains are equipped with distinct structural and functional genomic features indicative of adaptation to different environments.
Characterization of Two Mitochondrial Flavin Adenine Dinucleotide-Dependent Glycerol-3-Phosphate Dehydrogenases in Trypanosoma brucei
Authors: Škodová Ingrid , Verner Zdeněk , Bringaud Fréderic , Fabian Peter , Lukeš Julius , Horváth Anton 
Published: October 2013

ABSTRACT

Glycerol-3-phosphate dehydrogenases (G3PDHs) constitute a shuttle that serves for regeneration of NAD
+
reduced during glycolysis. This NAD-dependent enzyme is employed in glycolysis and produces glycerol-3-phosphate from dihydroxyacetone phosphate, while its flavin adenine dinucleotide (FAD)-dependent homologue catalyzes a reverse reaction coupled to the respiratory chain.
Trypanosoma brucei
possesses two FAD-dependent G3PDHs. While one of them (mitochondrial G3PDH [mtG3PDH]) has been attributed to the mitochondrion and seems to be directly involved in G3PDH shuttle reactions, the function of the other enzyme (putative G3PDH [putG3PDH]) remains unknown. In this work, we used RNA interference and protein overexpression and tagging to shed light on the relative contributions of both FAD-G3PDHs to overall cellular metabolism. Our results indicate that mtG3PDH is essential for the bloodstream stage of
T. brucei
, while in the procyclic stage the enzyme is dispensable. Expressed putG3PDH-V5 was localized to the mitochondrion, and the data obtained by digitonin permeabilization, Western blot analysis, and immunofluorescence indicate that putG3PDH is located within the mitochondrion.
Binding and Transcriptional Regulation by 14-3-3 (Bmh) Proteins Requires Residues Outside of the Canonical Motif
Authors: Parua Pabitra K. , Young Elton T. 
Published: October 2013

ABSTRACT

Evolutionarily conserved 14-3-3 proteins have important functions as dimers in numerous cellular signaling processes, including regulation of transcription. Yeast 14-3-3 proteins, known as Bmh, inhibit a post-DNA binding step in transcription activation by Adr1, a glucose-regulated transcription factor, by binding to its regulatory domain, residues 226 to 240. The domain was originally defined by regulatory mutations,
ADR1

c

alleles that alter activator-dependent gene expression. Here, we report that
ADR1

c

alleles and other mutations in the regulatory domain impair Bmh binding and abolish Bmh-dependent regulation both directly and indirectly. The indirect effect is caused by mutations that inhibit phosphorylation of Ser230 and thus inhibit Bmh binding, which requires phosphorylated Ser230. However, several mutations inhibit Bmh binding without inhibiting phosphorylation and thus define residues that provide important interaction sites between Adr1 and Bmh. Our proposed model of the Adr1 regulatory domain bound to Bmh suggests that residues Ser238 and Tyr239 could provide cross-dimer contacts to stabilize the complex and that this might explain the failure of a dimerization-deficient Bmh mutant to bind Adr1 and to inhibit its activity. A bioinformatics analysis of Bmh-interacting proteins suggests that residues outside the canonical 14-3-3 motif might be a general property of Bmh target proteins and might help explain the ability of 14-3-3 to distinguish target and nontarget proteins. Bmh binding to the Adr1 regulatory domain, and its failure to bind when mutations are present, explains at a molecular level the transcriptional phenotype of
ADR1

c

mutants.
Problems Caused by Heterogeneity in Meta-Analysis: A Case Study of Acupuncture Trials
Authors: Prady Stephanie L , Burch Jane , Crouch Simon , MacPherson Hugh 
Published: October 2013

Objectives To illustrate the pitfalls of using meta-analysis to combine estimates of effect in trials that are highly varied and have a high potential for bias. Methods We used a random-effects meta-analysis to pool the results of 51 sham-controlled acupuncture trials of chronic pain published in English before 2008 and explored the heterogeneity using meta-regression. We repeated the process on a subset of these trials that used a visually credible non-penetrating sham device as control (N = 12). Results In both analyses there were high levels of heterogeneity and many studies were at risk from potential bias. The heterogeneity was not explained by meta-regression. Conclusions Trials of interventions that have high potential for bias, such as many in the acupuncture literature, do not meet the assumptions of the statistical procedure that underlie random-effects meta-analysis. Even in the absence of bias, heterogeneity in meta-analyses is not accounted for by the CIs around the pooled estimate.
Multicomponent intervention to reduce daily sedentary time: a randomised controlled trial
Authors: Carr Lucas J , Karvinen Kristina , Peavler Mallory , Smith Rebecca , Cangelosi Kayla 
Published: October 2013

ObjectivesTo test the efficacy of a multicomponent technology intervention for reducing daily sedentary time and improving cardiometabolic disease risk among sedentary, overweight university employees.DesignBlinded, randomised controlled trial.SettingA large south-eastern university in the USA.Participants49 middle-aged, primarily female, sedentary and overweight adults working in sedentary jobs enrolled in the study. A total of 40 participants completed the study.InterventionsParticipants were randomised to either: (1) an intervention group (N=23; 47.6+9.9 years; 94.1% female; 33.2+4.5 kg/m2); (2) or wait-list control group (N=17; 42.6+8.9 years; 86.9% female; 31.7+4.9 kg/m2). The intervention group received a theory-based, internet-delivered programme, a portable pedal machine at work and a pedometer for 12 weeks. The wait-list control group maintained their behaviours for 12 weeks.Outcome measuresPrimary (sedentary and physical activity behaviour measured objectively through StepWatch) and secondary (heart rate, blood pressure, height, weight, waist circumference, per cent body fat, cardiorespiratory fitness, fasting lipids) outcomes were measured at baseline and postintervention (12 weeks). Exploratory outcomes including intervention compliance and process evaluation measures were also assessed postintervention.ResultsCompared to controls, the intervention group reduced daily sedentary time (mean change (95%CI): −58.7 min/day (−118.4 to 0.99; p<0.01)) after adjusting for baseline values and monitor wear time. Intervention participants logged on to the website 71.3% of all intervention days, used the pedal machine 37.7% of all working intervention days and pedalled an average of 31.1 min/day.ConclusionsThese findings suggest that the intervention was engaging and resulted in reductions in daily sedentary time among full-time sedentary employees. These findings hold public health significance due to the growing number of sedentary jobs and the potential of these technologies in large-scale worksite programmes.Trial RegistrationClinicalTrials.gov #NCT01371084.
Continuation rates of oral hormonal contraceptives in a cohort of first-time users: a population-based registry study, Sweden 2005–2010
Authors: Josefsson Ann , Wiréhn Ann-Britt , Lindberg Malou , Foldemo Anniqa , Brynhildsen Jan 
Published: October 2013

ObjectiveTo investigate if continuation rates in first-time users of oral hormonal contraceptives differed between different formulations and to measure if the rates were related to the prescribing categories, that is, physicians and midwives.DesignA longitudinal national population-based registry study.SettingThe Swedish prescribed drug register.ParticipantsAll women born between 1977 and 1994 defined as first-time users of hormonal contraceptives from 2007 to 2009 (n=226 211).Main outcome measuresA tendency to switch the type of hormonal contraceptive within 6 months use and repeated dispensation identical to the first were estimated as percentages and relative risks (RRs). Physicians’ and midwives’ prescription patterns concerning the women's continuation rates of oral hormonal contraceptive type.ResultsIn Sweden, there were 782 375 women born between 1977 and 1994 at the time of the study. Of these, 226 211 women were identified as first-time users of hormonal contraceptives. Ethinylestradiol+levonorgestrel, desogestrel-only and ethinylestradiol+drospirenone were the hormonal contraceptives most commonly dispensed to first-time users at rates of 43.3%, 24.4% and 11.1%, respectively. The overall rate of switching contraceptive types in the first 6 months was 11.3%, which was highest for desogestrel-only (14.3%) and lowest for ethinylestradiol+drospirenone (6.6%). The switching rate for all three products was highest in the 16-year to 19-year age group. Having a repeated dispensation identical to the initial dispensation was highest for users of ethinylestradiol either combined with levonorgestrel or drospirenone, 81.4% and 81.2%, respectively, whereas this rate for the initial desogestrel-only users was 71.5%. The RR of switching of contraceptive type within the first 6 months was 1.35 (95% CI 1.32 to 1.39) for desogestrel-only and 0.63 (0.59 to 0.66) for ethinylestradiol+drospirenone compared with ethinylestradiol+levonorgestrel as the reference category. There were no differences in the women's continuation rates depending on the prescriber categories.ConclusionsDesogestrel-only users conferred the highest switcher rate to another hormonal contraceptive within a 6-month period. Users of ethinylestradiol+levonorgestrel were more prone to switch to another product within 6 months than women using ethinylestradiol+drospirenone. These findings may be of clinical importance when tailoring hormonal contraceptives on an individual basis.
Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for identification of clinically significant bacteria that are difficult to identify in clinical laboratories
Authors: Lau Susanna K P , Tang Bone S F , Teng Jade L L , Chan Tsz-Ming , Curreem Shirly O T , Fan Rachel Y Y , Ng Ricky H Y , Chan Jasper F W , Yuen Kwok-Yung , Woo Patrick C Y 
Published: October 2013

AimsAlthough the revolutionary matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been evaluated for identification of various groups of bacteria, its application in bacteria that are ‘difficult-to-identify’ by phenotypic tests has been less well studied. We aim to evaluate the usefulness of MALDI-TOF MS for identification of ‘difficult-to-identify’ bacterial isolates.MethodsWe evaluated the performance of the Bruker MALDI-TOF MS system for a collection of 67 diverse clinically important bacterial isolates that were less commonly encountered, possessed ambiguous biochemical profiles or belonged to newly discovered species. The results were compared with 16S rRNA gene sequencing as a reference method for species identification.ResultsUsing 16S rRNA gene sequencing as the reference method, 30 (45%) isolates were identified correctly to species level (score ≥2.0), 20 (30%) were only identified to genus level (score ≥1.7), four (6%) were misidentified (incorrect species with score ≥2.0 or incorrect genus with score ≥1.7) and 13 (19%) showed ‘no identification’ (score <1.7). Aerobic Gram-positive bacteria showed the highest percentage of correct species identification, followed by aerobic Gram-negative, anaerobic Gram-positive and anaerobic Gram-negative bacteria. Sixteen isolates identified to genus level actually showed the correct species but with scores below the threshold for species identification. Most isolates which showed ‘no identification’ were due to the absence of the corresponding species in the Bruker database.ConclusionsExpansion of commercial databases to include reference spectra of less commonly encountered and newly discovered species and to increase available spectra for each species is required to improve the accuracy of MALDI-TOF MS for identifying ‘difficult-to-identify’ bacteria.
Evaluation of MR safety for a new liquid embolic device
Authors: Audet-Griffin Annabelle J , Pakbaz Sean , Shellock Frank G 
Published: October 2013

BackgroundAs an alternative to conventional treatments, a new liquid embolic device (Neucrylate) may be used to treat aneurysms or arteriovenous malformation (AVMs). Because this device contains metal for opacification, an investigation was performed to evaluate MRI issues for this liquid embolic device.MethodsThe liquid embolic device was evaluated for magnetic field interactions (translational attraction and torque) at 3 T, MRI-related heating at 1.5 T/64 MHz and 3 T/128 MHz and artifacts at 3 T using standardized techniques. In each case, MRI-related heating was assessed with the liquid embolic device in a gelled saline-filled phantom and MRI was performed using relatively high levels of radiofrequency energy. Artifacts were characterized using T1-weighted spin echo and gradient echo pulse sequences. Additionally, conductivity (ie, electrical resistance) measurements were recorded.ResultsThe liquid embolic device exhibited no magnetic field interactions. Heating was at the same level as background temperature rises (ie, the temperatures recorded without the liquid embolic device present in the phantom) under 1.5 T/64 MHz (highest temperature change 1.4°C) and 3 T/128 MHz (highest temperature change 1.8°C) MRI conditions. Artifacts were small in relation to the size and shape of the liquid embolic device. The device was found to pose no risks with regard to the conductivity of the material.ConclusionsThese findings demonstrate that it is acceptable for a patient with this new liquid embolic device to undergo MRI at ≤3 T. Notably, the associated artifacts are unlikely to create issues for diagnostic MRI examinations.
Chapter 13 Eruptive, volcano-tectonic and magmatic history of the Stromboli volcano (north-eastern Aeolian archipelago)
Authors: Francalanci L. , Lucchi F. , Keller J. , De Astis G. , Tranne C. A. 
Published: October 2013

Abstract

Stromboli is famous for its persistent volcanic activity consisting of periodic discrete explosions alternating with lava effusion and more violent explosions. This paper presents a detailed reconstruction of the geological history of Stromboli and description of the characteristics and distribution of the volcanic units and structural features. Six main growth stages (Eruptive Epochs 1–6), in addition to the
c.
200 ka activity of Strombolicchio, are recognized between
c.
85 ka and the present day, displaying a magma composition ranging from calc-alkaline to potassic series which usually varies with changing Eruptive Epochs. The Epochs are subdivided into sequences of eruptions and characterized by dominant central-vent summit activity with episodic phases of flank activity along fissures and eccentric vents. The activity was repeatedly interrupted by erosional and destructive phases driven by recurrent vertical caldera-type (cc1–5) and sector (and flank) collapses (sc1–7) and generally associated with significant quiescences. The different serial character of the Stromboli rocks is associated with largely variable trace element contents and isotope ratios. These petrochemical characteristics together with our new stratigraphy indicate that magmas, generated in a heterogeneous mantle wedge, underwent complex differentiation processes during their ascent. Magmas are characterized by polybaric evolution residing in small magma reservoirs that are alternatively tapped by the different collapses.

DVD:

The 10 000 scale geological map of Stromboli is included on the DVD in the printed book and can also be accessed online at
http://www.geolsoc.org.uk/Memoir37-electronic
. Also included is a full geochemical dataset for Stromboli.
Molecular Profiling of Tumor Cells in Cerebrospinal Fluid and Matched Primary Tumors from Metastatic Breast Cancer Patients with Leptomeningeal Carcinomatosis
Authors: Magbanua Mark Jesus M. , Melisko Michelle , Roy Ritu , Sosa Eduardo V. , Hauranieh Louai , Kablanian Andrea , Eisenbud Lauren E. , Ryazantsev Artem , Au Alfred , Scott Janet H. , Park John W. 
Published: October 2013

AbstractAlthough leptomeningeal carcinomatosis is a well-established clinical syndrome, virtually nothing is known about the tumor cells responsible for this particularly aggressive metastatic process. To isolate cerebrospinal fluid–derived tumor cells (CSFTC) from 15 patients with metastatic breast cancer diagnosed with leptomeningeal carcinomatosis, CSF samples were subjected to a two-step method involving immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS), a technique previously used for isolating circulating tumor cells (CTC) from blood. CSFTCs were subjected to genome-wide copy number analysis by array comparative genomic hybridization. Genomic profiling was successfully performed for 13 of 15 patients (87%). Copy number analysis in CSFTCs revealed genomic alterations commonly observed in primary breast cancer and CTCs, indicating their malignant origin. Interestingly, 12 (92%) harbored high-level gains on the 8q24 locus, which includes the MYC oncogene. Comparison of CSFTCs against corresponding archival primary tumors in six patients revealed clonal relationships with some divergence. Good concordance among serial samples attested to the reproducibility of the assay. Our approach for isolation and molecular analysis of CSFTCs yielded new insights into the molecular nature of these cells. Further genomic and functional analyses may help elucidate mechanisms by which tumor cells metastasize to the central nervous system. Cancer Res; 73(23); 7134–43. ©2013 AACR.