bluuebunny/crossref_metadata_2025 huggingface dataset:
Pro-Ecological Exergy Tax of Electricity
Authors: Stanek Wojciech , Szargut Jan , Czarnowska Lucyna
Published: September 2016

The concept of the pro-ecological tax or support is proposed in this article. It could replace the existing subsidy mechanisms for renewable power technology or could represent the ecological taxes burdening the fabrication of consumer products based on nonrenewable resources, e.g., electricity from the conventional fossil fuel power plants. Moreover, the proposed concept for renewable power technologies could represent a new system of subsidy based on physical laws. The proposed pro-ecological tax or support is defined as proportional to the thermo-ecological cost (TEC). TEC expresses the cumulative consumption of nonrenewable exergy burdening the fabrication of the considered consumption of the product with the additional inclusion of necessity of compensating adverse environmental effects due to harmful waste products rejection. It is assumed that calculating new exergy tax or subsidy for electricity, the total cost burdening the final consumer remains the same. This principle determines the coefficient of proportionality between the cumulative consumption of nonrenewable exergy (TEC) and the value of the tax or subsidy. In the case of nonrenewable electricity generation, the TAX causes the largest price growth. The higher is the efficiency of power technology, and the lower is the TEC of fuel, the lower tax is provided. In this paper, the prices of electricity produced from renewable and nonrenewable resources are calculated, taking into account the unavoidable consumption of resources. The unavoidable exergy consumption is caused due to the power plant construction, which is distributed through the whole life cycle of the plant. Results of calculation of proposed subsidies are compared with the current Polish system for supporting renewable power technologies.
Computational Fluid Dynamics Modeling and Online Monitoring of Aerosol Jet Printing Process
Authors: Salary Roozbeh (Ross) , Lombardi Jack P. , Samie Tootooni M. , Donovan Ryan , Rao Prahalad K. , Borgesen Peter , Poliks Mark D.
Published: September 2016

The objectives of this paper in the context of aerosol jet printing (AJP)—an additive manufacturing (AM) process—are to: (1) realize in situ online monitoring of print quality in terms of line/electronic trace morphology; and (2) explain the causal aerodynamic interactions that govern line morphology based on a two-dimensional computational fluid dynamics (2D-CFD) model. To realize these objectives, an Optomec AJ-300 aerosol jet printer was instrumented with a charge coupled device (CCD) camera mounted coaxial to the nozzle (perpendicular to the platen). Experiments were conducted by varying two process parameters, namely, sheath gas flow rate (ShGFR) and carrier gas flow rate (CGFR). The morphology of the deposited lines was captured from the online CCD images. Subsequently, using a novel digital image processing method proposed in this study, six line morphology attributes were quantified. The quantified line morphology attributes are: (1) line width, (2) line density, (3) line edge quality/smoothness, (4) overspray (OS), (5) line discontinuity, and (6) internal connectivity. The experimentally observed line morphology trends as a function of ShGFR and CGFR were verified with computational fluid dynamics (CFD) simulations. The image-based line morphology quantifiers proposed in this work can be used for online detection of incipient process drifts, while the CFD model is valuable to ascertain the appropriate corrective action to bring the process back in control in case of a drift.
Improving Machined Surface Shape Prediction by Integrating Multi-Task Learning With Cutting Force Variation Modeling
Authors: Shao Chenhui , Ren Jie , Wang Hui , Jin Jionghua (Judy) , Hu S. Jack
Published: September 2016

The shapes of machined surfaces play a critical role affecting powertrain performance, and therefore, it is necessary to characterize the shapes with high resolution. State-of-the-art approaches for surface shape characterization are mostly data-driven by interpolating and extrapolating the spatial data but its precision is limited by the density of measurements. This paper explores the new opportunity of improving surface shape prediction through considering the similarity of multiple similar manufacturing processes. It is a common scenario when the process of interest lacks sufficient data whereas rich data could be available from other similar-but-not-identical processes. It is reasonable to transfer the insights gained from other relevant processes into the surface shape prediction. This paper develops an engineering-guided multitask learning (EG-MTL) surface model by fusing surface cutting physics in engineering processes and the spatial data from a number of similar-but-not-identical processes. An iterative multitask Gaussian process learning algorithm is developed to learn the model parameters. Compared with the conventional multitask learning, the proposed method has the advantages in incorporating the insights on cutting force variation during machining and is potentially able to improve the prediction performance given limited measurement data. The methodology is demonstrated based on the data from real-world machining processes in an engine plant.
Use of a Quasi-Steady Ablation Model for Design Sensitivity With Uncertainty Propagation
Authors: Anzalone R. , Barr B. W. , Upadhyay R. R. , Ezekoye O. A.
Published: September 2016

Sensitivity analysis and design calculations are often best performed using low-order models. This work details work done on adding complementary pieces to a low-order, quasi-steady-state ablation model to facilitate uncertainty propagation. The quasi-steady-state ablation model is a one-dimensional, quasi-steady-state, algebraic ablation model that uses finite-rate surface chemistry and equilibrium pyrolysis-gas-production submodels to predict surface recession rate. The material response model is coupled to a film-transfer boundary layer model to enable the computation of heat and mass transfer from an ablating surface. For comparison to arcjet data, a simple shock heated gas model is coupled. A coupled model consisting of submodels for the shock heated gases, film heat and mass transfer, and material response is exercised against recession rate data for surface and in-depth ablators. Comparisons are made between the quasi-steady-state ablation model and the unsteady ablation code, Chaleur, as well as to other computations for a graphite ablator in arcjet facilities. The simple models are found to compare reasonably well to both the experimental results and the other calculations. Uncertainty propagation using a moment based method is presented. The results of this study are discussed, and conclusions about the utility of the method as well as the properties of the ablation code are drawn.
Predicting the Sabine absorption coefficients of fibrous absorbers for various air backing conditions with a frequency-dependent diffuseness correction
Authors: Jeong Cheol-Ho
Published: September 2016

Fibrous absorbers can be installed with various air backing conditions to fulfil a given low frequency acoustic requirement. Since absorber manufacturers cannot provide the absorption coefficients for all possible mounting conditions, acousticians have difficulties knowing the absorption characteristics of their own configurations. This study aims to predict the absorption coefficient for various mounting conditions from a single measurement of an arbitrary mounting condition by extracting the air flow resistivity of the test specimen and the frequency-dependent effect of the chamber on the measured absorption coefficients. With two homogeneous fibrous absorbers, the predicted absorption coefficients agree well with the measurements.
Pattern recognition with “materials that compute”
Authors: Fang Yan , Yashin Victor V. , Levitan Steven P. , Balazs Anna C.
Published: September 2016

We design a self-powered materials system that transduces chemical, mechanical, and electrical energy to perform computation.
A C9ORF72/SMCR8-containing complex regulates ULK1 and plays a dual role in autophagy
Authors: Yang Mei , Liang Chen , Swaminathan Kunchithapadam , Herrlinger Stephanie , Lai Fan , Shiekhattar Ramin , Chen Jian-Fu
Published: September 2016

A dual role of the C9ORF72/SMCR8-containing complex in autophagy initiation and autophagic flux.
Quasi-ballistic carbon nanotube array transistors with current density exceeding Si and GaAs
Authors: Brady Gerald J. , Way Austin J. , Safron Nathaniel S. , Evensen Harold T. , Gopalan Padma , Arnold Michael S.
Published: September 2016

Nearly ballistic carbon nanotube array transistors are realized with current densities outmatching conventional semiconductors.
Nanogeochronology of discordant zircon measured by atom probe microscopy of Pb-enriched dislocation loops
Authors: Peterman Emily M. , Reddy Steven M. , Saxey David W. , Snoeyenbos David R. , Rickard William D. A. , Fougerouse Denis , Kylander-Clark Andrew R. C.
Published: September 2016

Atom probe yields geologically meaningful ages from nanoscale Pb-enriched dislocation loops in discordant zircon.
Cinnamon Oil Inhibits Shiga Toxin Type 2 Phage Induction and Shiga Toxin Type 2 Production in Escherichia coli O157:H7
Authors: Sheng Lina , Rasco Barbara , Zhu Mei-Jun
Published: September 2016

This study evaluated the inhibitory effect of cinnamon oil against
Escherichia coli
O157:H7 Shiga toxin (Stx) production and further explored the underlying mechanisms. The MIC and minimum bactericidal concentration (MBC) of cinnamon oil against
E. coli
O157:H7 were 0.025% and 0.05% (vol/vol), respectively. Cinnamon oil significantly reduced Stx2 production and the
stx
2
mRNA expression that is associated with diminished Vero cell cytotoxicity. Consistently, induction of the Stx-converting phage where the
stx
2
gene is located, along with the total number of phages, decreased proportionally to cinnamon oil concentration. In line with decreased Stx2 phage induction, cinnamon oil at 0.75× and 1.0× MIC eliminated RecA, a key mediator of SOS response, polynucleotide phosphorylase (PNPase), and poly(A) polymerase (PAP I), which positively regulate Stx-converting phages, contributing to reduced Stx-converting phage induction and Stx production. Furthermore, cinnamon oil at 0.75× and 1.0× MIC strongly inhibited the
qseBC
and
luxS
expression associated with decreased AI-2 production, a universal quorum sensing signaling molecule. However, the expression of oxidative stress response genes
oxyR
,
soxR
, and
rpoS
was increased in response to cinnamon oil at 0.25× or 0.5× MIC, which may contribute to stunted bacterial growth and reduced Stx2 phage induction and Stx2 production due to the inhibitory effect of OxyR on prophage activation. Collectively, cinnamon oil inhibits Stx2 production and Stx2 phage induction in
E. coli
O157:H7 in multiple ways.

IMPORTANCE
This study reports the inhibitory effect of cinnamon oil on Shiga toxin 2 phage induction and Shiga toxin 2 production. Subinhibitory concentrations (concentrations below the MIC) of cinnamon oil reduced Stx2 production,
stx
2
mRNA expression, and cytotoxicity on Vero cells. Subinhibitory concentrations of cinnamon oil also dramatically reduced both the Stx2 phage and total phage induction in
E. coli
O157:H7, which may be due to the suppression of RNA polyadenylation enzyme PNPase at 0.25× to 1.0× MIC and the downregulation of bacterial SOS response key regulator RecA and RNA polyadenylation enzyme PAP I at 0.75× or 1.0× MIC. Cinnamon oil at higher levels (0.75× and 1.0× MIC) eliminated quorum sensing and oxidative stress. Therefore, cinnamon oil has potential applications as a therapeutic to control
E. coli
O157:H7 infection through inhibition of bacterial growth and virulence factors.
Lack of Overt Genome Reduction in the Bryostatin-Producing Bryozoan Symbiont “Candidatus Endobugula sertula”
Authors: Miller Ian J. , Vanee Niti , Fong Stephen S. , Lim-Fong Grace E. , Kwan Jason C.
Published: September 2016

The uncultured bacterial symbiont “
Candidatus
Endobugula sertula” is known to produce cytotoxic compounds called bryostatins, which protect the larvae of its host,
Bugula neritina
. The symbiont has never been successfully cultured, and it was thought that its genome might be significantly reduced. Here, we took a shotgun metagenomics and metatranscriptomics approach to assemble and characterize the genome of “
Ca
. Endobugula sertula.” We found that it had specific metabolic deficiencies in the biosynthesis of certain amino acids but few other signs of genome degradation, such as small size, abundant pseudogenes, and low coding density. We also identified homologs to genes associated with insect pathogenesis in other gammaproteobacteria, and these genes may be involved in host-symbiont interactions and vertical transmission. Metatranscriptomics revealed that these genes were highly expressed in a reproductive host, along with
bry
genes for the biosynthesis of bryostatins. We identified two new putative
bry
genes fragmented from the main
bry
operon, accounting for previously missing enzymatic functions in the pathway. We also determined that a gene previously assigned to the pathway,
bryS
, is not expressed in reproductive tissue, suggesting that it is not involved in the production of bryostatins. Our findings suggest that “
Ca
. Endobugula sertula” may be able to live outside the host if its metabolic deficiencies are alleviated by medium components, which is consistent with recent findings that it may be possible for “
Ca
. Endobugula sertula” to be transmitted horizontally.

IMPORTANCE
The bryostatins are potent protein kinase C activators that have been evaluated in clinical trials for a number of indications, including cancer and Alzheimer's disease. There is, therefore, considerable interest in securing a renewable supply of these compounds, which is currently only possible through aquaculture of
Bugula neritina
and total chemical synthesis. However, these approaches are labor-intensive and low-yielding and thus preclude the use of bryostatins as a viable therapeutic agent. Our genome assembly and transcriptome analysis for “
Ca
. Endobugula sertula” shed light on the metabolism of this symbiont, potentially aiding isolation and culturing efforts. Our identification of additional
bry
genes may also facilitate efforts to express the complete pathway heterologously.
Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food
Authors: Miranda Robyn C. , Schaffner Donald W.
Published: September 2016

Bacterial cross-contamination from surfaces to food can contribute to foodborne disease. The cross-contamination rate of
Enterobacter aerogenes
on household surfaces was evaluated by using scenarios that differed by surface type, food type, contact time (<1, 5, 30, and 300 s), and inoculum matrix (tryptic soy broth or peptone buffer). The surfaces used were stainless steel, tile, wood, and carpet. The food types were watermelon, bread, bread with butter, and gummy candy. Surfaces (25 cm
2
) were spot inoculated with 1 ml of inoculum and allowed to dry for 5 h, yielding an approximate concentration of 10
7
CFU/surface. Foods (with a 16-cm
2
contact area) were dropped onto the surfaces from a height of 12.5 cm and left to rest as appropriate. Posttransfer, surfaces and foods were placed in sterile filter bags and homogenized or massaged, diluted, and plated on tryptic soy agar. The transfer rate was quantified as the log percent transfer from the surface to the food. Contact time, food, and surface type all had highly significant effects (
P
< 0.000001) on the log percent transfer of bacteria. The inoculum matrix (tryptic soy broth or peptone buffer) also had a significant effect on transfer (
P
= 0.013), and most interaction terms were significant. More bacteria transferred to watermelon (∼0.2 to 97%) than to any other food, while the least bacteria transferred to gummy candy (∼0.1 to 62%). Transfer of bacteria to bread (∼0.02 to 94%) was similar to transfer of bacteria to bread with butter (∼0.02 to 82%), and these transfer rates under a given set of conditions were more variable than with watermelon and gummy candy.

IMPORTANCE
The popular notion of the “five-second rule” is that food dropped on the floor and left there for <5 s is “safe” because bacteria need time to transfer. The rule has been explored by a single study in the published literature and on at least two television shows. Results from two academic laboratories have been shared through press releases but remain unpublished. We explored this topic by using four different surfaces (stainless steel, ceramic tile, wood, and carpet), four different foods (watermelon, bread, bread with butter, and gummy candy), four different contact times (<1, 5, 30, and 300 s), and two bacterial preparation methods. Although we found that longer contact times result in more transfer, we also found that other factors, including the nature of the food and the surface, are of equal or greater importance. Some transfer takes place “instantaneously,” at times of <1 s, disproving the five-second rule.
Transposon Mutagenesis Identifies Genes Critical for Growth of Pseudomonas nitroreducens TX1 on Octylphenol Polyethoxylates
Authors: Nguyen Tuan Ngoc , Yeh Chen-Wei , Tsai Po-Chun , Lee Kyoung , Huang Shir-Ly
Published: September 2016

Pseudomonas nitroreducens
TX1 is of special interest because of its ability to utilize 0.05% to 20% octylphenol polyethoxylates (OPEO

n

) as a sole source of carbon. In this study, a library containing 30,000 Tn
5
-insertion mutants of the wild-type strain TX1 was constructed and screened for OPEO

n

utilization, and 93 mutants were found to be unable to grow on OPEO

n

. In total, 42 separate disrupted genes were identified, and the proteins encoded by the genes were then classified into various categories, namely, information storage and processing (14.3%), cellular processes and signaling (28.6%), metabolism (35.7%), and unknown proteins (21.4%). The individual deletion of genes encoding isocitrate lyase (
aceA
), malate synthase (
aceB
), and glycolate dehydrogenase (
glcE
) was carried out, and the requirement for
aceA
and
aceB
but not
glcE
confirmed the role of the glyoxylate cycle in OPEO

n

degradation. Furthermore, acetaldehyde dehydrogenase and acetyl-coenzyme A (acetyl-CoA) synthetase activity levels were 13.2- and 2.1-fold higher in TX1 cells grown on OPEO

n

than in TX1 cells grown on succinate, respectively. Growth of the various mutants on different carbon sources was tested, and based on these findings, a mechanism involving exoscission to liberate acetaldehyde from the end of the OPEO

n

chain during degradation is proposed for the breakdown of OPEO

n

.

IMPORTANCE
Octylphenol polyethoxylates belong to the alkylphenol polyethoxylate (APEO

n

) nonionic surfactant family. Evidence based on the analysis of intermediate metabolites suggested that the primary biodegradation of APEO

n

can be achieved by two possible pathways for the stepwise removal of the C
2
ethoxylate units from the end of the chain. However, direct evidence for these hypotheses is still lacking. In this study, we described the use of transposon mutagenesis to identify genes critical to the catabolism of OPEO

n

by
P. nitroreducens
TX1. The exoscission of the ethoxylate chain leading to the liberation of acetaldehyde is proposed. Isocitrate lyase and malate synthase in glyoxylate cycle are required in the catabolism of ethoxylated surfactants. Our findings also provide many gene candidates that may help elucidate the mechanisms in stress responses to ethoxylated surfactants by bacteria.
Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils
Authors: Pold Grace , Billings Andrew F. , Blanchard Jeff L. , Burkhardt Daniel B. , Frey Serita D. , Melillo Jerry M. , Schnabel Julia , van Diepen Linda T. A. , DeAngelis Kristen M.
Published: September 2016

As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated withActinobacteriain all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.

IMPORTANCEThe massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.
Glycosulfatase-Encoding Gene Cluster in Bifidobacterium breve UCC2003
Authors: Egan Muireann , Jiang Hao , O'Connell Motherway Mary , Oscarson Stefan , van Sinderen Douwe
Published: September 2016

Bifidobacteria constitute a specific group of commensal bacteria typically found in the gastrointestinal tract (GIT) of humans and other mammals.
Bifidobacterium breve
strains are numerically prevalent among the gut microbiota of many healthy breastfed infants. In the present study, we investigated glycosulfatase activity in a bacterial isolate from a nursling stool sample,
B. breve
UCC2003. Two putative sulfatases were identified on the genome of
B. breve
UCC2003. The sulfated monosaccharide
N
-acetylglucosamine-6-sulfate (GlcNAc-6-S) was shown to support the growth of
B. breve
UCC2003, while
N
-acetylglucosamine-3-sulfate,
N
-acetylgalactosamine-3-sulfate, and
N
-acetylgalactosamine-6-sulfate did not support appreciable growth. By using a combination of transcriptomic and functional genomic approaches, a gene cluster designated
ats2
was shown to be specifically required for GlcNAc-6-S metabolism. Transcription of the
ats2
cluster is regulated by a repressor open reading frame kinase (ROK) family transcriptional repressor. This study represents the first description of glycosulfatase activity within the
Bifidobacterium
genus.

IMPORTANCE
Bifidobacteria are saccharolytic organisms naturally found in the digestive tract of mammals and insects.
Bifidobacterium breve
strains utilize a variety of plant- and host-derived carbohydrates that allow them to be present as prominent members of the infant gut microbiota as well as being present in the gastrointestinal tract of adults. In this study, we introduce a previously unexplored area of carbohydrate metabolism in bifidobacteria, namely, the metabolism of sulfated carbohydrates.
B. breve
UCC2003 was shown to metabolize
N
-acetylglucosamine-6-sulfate (GlcNAc-6-S) through one of two sulfatase-encoding gene clusters identified on its genome. GlcNAc-6-S can be found in terminal or branched positions of mucin oligosaccharides, the glycoprotein component of the mucous layer that covers the digestive tract. The results of this study provide further evidence of the ability of this species to utilize mucin-derived sugars, a trait which may provide a competitive advantage in both the infant gut and adult gut.
CYP101J2, CYP101J3, and CYP101J4, 1,8-Cineole-Hydroxylating Cytochrome P450 Monooxygenases from Sphingobium yanoikuyae Strain B2
Authors: Unterweger Birgit , Bulach Dieter M. , Scoble Judith , Midgley David J. , Greenfield Paul , Lyras Dena , Johanesen Priscilla , Dumsday Geoffrey J.
Published: September 2016

We report the isolation and characterization of three new cytochrome P450 monooxygenases: CYP101J2, CYP101J3, and CYP101J4. These P450s were derived from
Sphingobium yanoikuyae
B2, a strain that was isolated from activated sludge based on its ability to fully mineralize 1,8-cineole. Genome sequencing of this strain in combination with purification of native 1,8-cineole-binding proteins enabled identification of 1,8-cineole-binding P450s. The P450 enzymes were cloned, heterologously expressed (N-terminally His
6
tagged) in
Escherichia coli
BL21(DE3), purified, and spectroscopically characterized. Recombinant whole-cell biotransformation in
E. coli
demonstrated that all three P450s hydroxylate 1,8-cineole using electron transport partners from
E. coli
to yield a product putatively identified as (1
S
)-2α-hydroxy-1,8-cineole or (1
R
)-6α-hydroxy-1,8-cineole. The new P450s belong to the CYP101 family and share 47% and 44% identity with other 1,8-cineole-hydroxylating members found in
Novosphingobium aromaticivorans
and
Pseudomonas putida
. Compared to P450
cin
(CYP176A1), a 1,8-cineole-hydroxylating P450 from
Citrobacter braakii
, these enzymes share less than 30% amino acid sequence identity and hydroxylate 1,8-cineole in a different orientation. Expansion of the enzyme toolbox for modification of 1,8-cineole creates a starting point for use of hydroxylated derivatives in a range of industrial applications.

IMPORTANCE
CYP101J2, CYP101J3, and CYP101J4 are cytochrome P450 monooxygenases from
S. yanoikuyae
B2 that hydroxylate the monoterpenoid 1,8-cineole. These enzymes not only play an important role in microbial degradation of this plant-based chemical but also provide an interesting route to synthesize oxygenated 1,8-cineole derivatives for applications as natural flavor and fragrance precursors or incorporation into polymers. The P450 cytochromes also provide an interesting basis from which to compare other enzymes with a similar function and expand the CYP101 family. This could eventually provide enough bacterial parental enzymes with similar amino acid sequences to enable
in vitro
evolution via DNA shuffling.
Cleavage of Rubber by the Latex Clearing Protein (Lcp) of Streptomyces sp. Strain K30: Molecular Insights
Authors: Röther Wolf , Austen Stefanie , Birke Jakob , Jendrossek Dieter
Published: September 2016

Gram-positive rubber degraders such as
Streptomyces
sp. strain K30 cleave rubber [poly(
cis
-1,4-isoprene)] to low-molecular-mass oligoisoprenoid products with terminal keto and aldehyde groups by the secretion of a latex clearing protein (Lcp) designated rubber oxygenase. Lcp
K30
is a heme
b
cytochrome and has a domain of unknown function (DUF2236) that is characteristic of orthologous Lcps. Proteins with a DUF2236 domain are characterized by three highly conserved residues (R164, T168, and H198 in Lcp
K30
). Exchange of R164 or T168 by alanine and characterization of the purified Lcp
K30
muteins revealed that both were stable and contained a heme group (red color) but were inactive. This finding identifies both residues as key residues for the cleavage reaction. The purified H198A mutein was also inactive and stable but was colorless due to the absence of heme. We constructed and characterized alanine muteins of four additional histidine residues moderately conserved in 495 Lcp
K30
homologous sequences (H203A, H232A, H259A, H266A). All muteins revealed wild-type properties, excluding any importance for activity and/or heme coordination. Since Lcp
K30
has only eight histidines and the three remaining residues (H103, H184, and H296) were not conserved (<11%), H198 presumably is the only essential histidine, indicating its putative function as a heme ligand. The second axial position of the heme is likely occupied by a not yet identified molecule. Mutational analysis of three strictly conserved arginine residues (R195, R202, R328) showed that R195A and R202A muteins were colorless and instable, suggesting that these residues are important for the protein stability.

IMPORTANCE
Large amounts of rubber waste materials have been permanently released into the environment for more than a century, yet accumulation of rubber particles released, e.g., by abrasion of tires along highways has not been observed. This is indicative of the ubiquitous presence and activity of rubber-degrading microorganisms. Despite increasing research activities on rubber biodegradation during the last 2 decades, the knowledge of the enzymatic cleavage mechanism of rubber by latex clearing protein (Lcp) still is limited. In particular, the catalytic cleavage mechanism and the amino acids of Lcp proteins (Lcps) that are involved have not yet been identified for any Lcp. In this study, we investigated the importance of 10 amino acid residues of Lcp from
Streptomyces
sp. K30 (Lcp
K30
) by mutagenesis, mutein purification, and biochemical characterization. We identified several essential residues, one of which most likely represents an axial heme ligand in Lcp of
Streptomyces
sp. K30.
Essential Genes forIn VitroGrowth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing
Authors: Rosconi Federico , de Vries Stefan P. W. , Baig Abiyad , Fabiano Elena , Grant Andrew J.
Published: September 2016

The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil.Herbaspirillum seropedicaestrain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions ofH. seropedicaewith its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination ofin vivohigh-densitymarinerTn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) inH. seropedicaeSmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth ofH. seropedicaeSmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential inH. seropedicaeSmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of theH. seropedicaeendophytic lifestyle.

IMPORTANCEA focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyteHerbaspirillum seropedicaeSmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms ofH. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria.
Onsite midwife-led birth units (OMBUs) for care around the time of childbirth: a systematic review
Authors: Long Qian , Allanson Emma R , Pontre Jennifer , Tunçalp Özge , Hofmeyr George Justus , Gülmezoglu Ahmet Metin
Published: September 2016

Introduction

To ensure timely access to comprehensive emergency obstetric care in low- and middle-income countries, a number of interventions have been employed. This systematic review assesses the effects of onsite midwife-led birth units (OMBUs) embedded within hospitals which provide comprehensive emergency obstetric and newborn care.

Methods

Both interventional and observational studies that compared OMBUs with standard medical-led obstetric care were eligible for inclusion. Cochrane Central Register of Controlled Trials, PubMed/Medline, EMBASE, CINAHL, Science Citation and Social Sciences Citation Index, Global Health Library and one Chinese database were searched. Meta-analysis was conducted to synthesise data from randomised controlled trials (RCTs). Findings of observational studies were summarised by forest plots with brief narratives.

Results

Three RCTs, one controlled before-and-after study and six cohort studies were included. There were no or very few maternal and perinatal deaths in either OMBUs or standard obstetric units, with no significant differences between the two. Women giving birth in OMBUs were less likely to use epidural analgesia (risk ratio (RR) 0.67, 95% CI 0.55 to 0.82; three trials, n=2431). The UK national cohort study and two other cohorts in China and Nepal found less oxytocin augmentation, more spontaneous vaginal deliveries, fewer caesarean sections and fewer episiotomies performed in OMBUs than in standard obstetric units. These differences were not statistically significant in RCTs and the remaining cohorts. One study investigated satisfaction with midwife-led birth care among women and midwives, with positive findings in both groups favouring OMBUs. In addition, two studies found that the total cost of birth was lower in OMBUs than in standard obstetric units.

Conclusions

OMBUs could be an alternative model for providing safe and cost-effective childbirth care, which may be particularly important in low- and middle-income countries to meet the growing demand for facility-based birth for low-risk women and improve efficiency of health systems.
Is self-monitoring of blood glucose effective in improving glycaemic control in type 2 diabetes without insulin treatment: a meta-analysis of randomised controlled trials
Authors: Zhu Hongmei , Zhu Yanan , Leung Siu-wai
Published: September 2016

Objective

The present study aimed to verify the effectiveness of self-monitoring of blood glucose (SMBG) in patients with non-insulin-treated type 2 diabetes (T2D).

Methods

A comprehensive literature search was conducted in PubMed, Cochrane Library, Web of Science, ScienceDirect and ClinicalTrials.gov from their respective inception dates to 26 October 2015. Eligible randomised controlled trials (RCTs) were included according to prespecified criteria. The quality of the included RCTs was evaluated according to the Cochranerisk ofbiastool, and the evidence quality of meta-analyses was assessed by the Grading of Recommendation, Assessment, Development, and Evaluation (GRADE) criteria. A meta-analysis of primary and secondary outcome measures was performed. Sensitivity and subgroup analyses were carried out to evaluate the robustness and heterogeneity of the findings. Begg's and Egger's tests were used to quantify publication biases.

Results

A total of 15 RCTs, comprising 3383 patients with non-insulin-treated T2D, met the inclusion criteria. The SMBG intervention improved glycated haemoglobin (HbA1c) (mean difference −0.33; 95% CI −0.45 to −0.22; p=3.0730e−8; n=18), body mass index (BMI; −0.65; −1.18 to −0.12; p=0.0164; n=9) and total cholesterol (TC; −0.12; −0.20 to −0.04; p=0.0034; n=8) more effectively than the control in overall effect. The sensitivity analysis revealed little difference in overall effect, indicating the robustness of the results. SMBG moderated HbA1c levels better than the control in all subgroup analyses. Most of the RCTs had high risk of bias in blinding, while the overall quality of evidence for HbA1c was moderate according to the GRADE criteria. Publication bias was moderate for BMI.

Conclusions

SMBG improved HbA1c levels in the short term (≤6-month follow-up) and long term (≥12-month follow-up) in patients with T2D who were not using insulin.

Trial registration number

CRD42015019099.
Barriers and facilitators to patient and public engagement and recruitment to digital health interventions: protocol of a systematic review of qualitative studies
Authors: O'Connor Siobhan , Hanlon Peter , O'Donnell Catherine A , Garcia Sonia , Glanville Julie , Mair Frances S
Published: September 2016

Introduction

Patients and the public are beginning to use digital health tools to assist in managing chronic illness, support independent living and self-care, and remain connected to health and care providers. However, engaging with and enrolling in digital health interventions, such as telehealth systems, mobile health applications, patient portals and personal health records, in order to use them varies considerably. Many factors affect people's ability to engage with and sign up to digital health platforms.

Objectives

The primary aim is to identify the barriers and facilitators patients and the public experience to engagement and recruitment to digital health interventions. The secondary aim is to identify engagement and enrolment strategies, leading if possible to a taxonomy of such approaches, and a conceptual framework of digital health engagement and recruitment processes.

Methods

A systematic review of qualitative studies will be conducted by searching six databases: MEDLINE, CINAHL, PubMed, EMBASE, Scopus and the ACM Digital Library for papers published between 2000 and 2015. Titles and abstracts along with full-text papers will be screened by two independent reviewers against predetermined inclusion and exclusion criteria. A data extraction form will be used to provide details of the included studies. Quality assessment will be conducted using the Consolidated Criteria for Reporting Qualitative Research checklist. Any disagreements will be resolved through discussion with an independent third reviewer. Analysis will be guided by framework synthesis and informed by normalization process theory and burden of treatment theory, to aid conceptualisation of digital health engagement and recruitment processes.

Discussion

This systematic review of qualitative studies will explore factors affecting engagement and enrolment in digital health interventions. It will advance our understanding of readiness for digital health by examining the complex factors that affect patients’ and the public's ability to take part.

Trial registration number

CRD42015029846.
Cross-sectional study on the relationship between the level of serum cystatin C and blood pressure reverse dipping in hypertensive patients
Authors: Han Jin , Gao Ya , Guo Qi , Su Dan , Yan Bin , Peng Liyuan , Du Yuxing , Li Ke , Wang Gang
Published: September 2016

Objective

To investigate the relationship between the level of serum cystatin C (s-CC) and reverse-dipper blood pressure (BP) pattern.

Design

Cross-sectional study.

Setting

Single centre.

Participants

A total of 718 hypertensive patients were eventually recruited from cardiac clinics between 2012 and 2014 in the Second Affiliated Hospital, Xi'an Jiaotong University. They were diagnosed as essential hypertension according to their casual office records of systolic blood pressure (SBP) and/or diastolic blood pressure (DBP). Patients were excluded if they were <18 or >90 years old, under antihypertensive treatment, night workers, suffering from acute stroke or myocardial infarction within the past 6 months, diagnosed as secondary hypertension, sleep apnoea or other sleep disorders, renal failure, cardiac failure, chronic obstructive pulmonary disease, women during pregnancy or intolerant to the ambulatory BP monitoring (ABPM).

Measurement

The selected patients were evaluated with 24 hours ABPM. Peripheral venous blood samples were collected to evaluate the s-CC levels by ELISA.

Methods

The distribution of hypertensive patients with different levels of s-CC among each circadian BP pattern group was analysed using analysis of variance. Multinomial logistic regression analysis was applied to explore the relationship between the relevant variables and ABPM results.

Results

S-CC level in reverse-dipper group (1.19±0.53 mg/L) was increased significantly when compared with dipper group (1.06±0.36 mg/L) (p=0.021). In addition, after multinomial logistic regression analysis, s-CC (OR 1.717; 95% CI 1.033 to 2.854; p=0.037) and diabetes (OR 2.313; 95% CI 1.401 to 3.821; p=0.01) were significantly different between the reverse-dipper group and dipper group. On the other hand, the decline rate of nocturnal SBP (r=−0.117; p=0.002) and DBP (r=−0.089; p=0.018) was negatively correlated with the s-CC level.

Conclusions

The s-CC level was significantly higher in the reverse-dipper group than the dipper group and that s-CC was associated with the reverse-dipper pattern of BP examined with 24 hour ABPM.
Substance-related and addictive disorders among adults with intellectual and developmental disabilities (IDD): an Ontario population cohort study
Authors: Lin Elizabeth , Balogh Robert , McGarry Caitlin , Selick Avra , Dobranowski Kristin , Wilton Andrew S , Lunsky Yona
Published: September 2016

Objectives

Describe the prevalence of substance-related and addictive disorders (SRAD) in adults with intellectual and developmental disabilities (IDD) and compare the sociodemographic and clinical characteristics of adults with IDD and SRAD to those with IDD or SRAD only.

Design

Population-based cohort study (the Health Care Access Research and Development Disabilities (H-CARDD) cohort).

Setting

All legal residents of Ontario, Canada.

Participants

66 484 adults, aged 18–64, with IDD identified through linked provincial health and disability income benefits administrative data from fiscal year 2009. 96 589 adults, aged 18–64, with SRAD but without IDD drawn from the provincial health administrative data.

Main outcome measures

Sociodemographic (age group, sex, neighbourhood income quintile, rurality) and clinical (psychiatric and chronic disease diagnoses, morbidity) characteristics.

Results

The prevalence of SRAD among adults with IDD was 6.4%, considerably higher than many previous reports and also higher than found for adults without IDD in Ontario (3.5%). Among those with both IDD and SRAD, the rate of psychiatric comorbidity was 78.8%, and the proportion with high or very high overall morbidity was 59.5%. The most common psychiatric comorbidities were anxiety disorders (67.6%), followed by affective (44.6%), psychotic (35.8%) and personality disorders (23.5%). These adults also tended to be younger and more likely to live in the poorest neighbourhoods compared with adults with IDD but no SRAD and adults with SRAD but no IDD.

Conclusions

SRAD is a significant concern for adults with IDD. It is associated with high rates of psychiatric and other comorbidities, indicating that care coordination and system navigation may be important concerns. Attention should be paid to increasing the recognition of SRAD among individuals with IDD by both healthcare and social service providers and to improving staff skills in successfully engaging those with both IDD and SRAD.
Exploring experiences of cancer care in Wales: a thematic analysis of free-text responses to the 2013 Wales Cancer Patient Experience Survey (WCPES)
Authors: Bracher Michael , Corner Dame Jessica , Wagland Richard
Published: September 2016

Objectives

To provide the first systematic analysis of a national (Wales) sample of free-text comments from patients with cancer, to determine emerging themes and insights regarding experiences of cancer care in Wales.

Design

Thematic analysis of free-text data from a population-based survey.

Setting and participants

Adult patients with a confirmed cancer diagnosis treated within a 3-month period during 2012 in the 7 health boards and 1 trust providing cancer care in Wales.

Main outcome measures

Free-text categorised by theme, coded as positive or negative, with ratios. Overarching themes are identified incorporating comment categories.

Methods

4672 respondents (of n=7352 survey respondents) provided free-text comments. Data were coded using a multistage approach: (1) coding of comments into general categories (eg, nursing, surgery, etc), (2) coding of subcategories within main categories (eg, nursing care, nursing communication, etc), (3) cross-sectional analysis to identify themes cutting across categories, (4) mapping of categories/subcategories to corresponding closed questions in the Wales Cancer Patient Experience Survey (WCPES) data for comparison.

Results

Most free-text respondents (82%, n 3818) provided positive comments about their cancer care, with 49% (n=2313) giving a negative comment (ratio 0.6:1, negative-to-positive). 3172 respondents (67.9% of free-text respondents) provided a comment mapping to 1 of 4 overarching themes: communication (n=1673, 35.8% free-text respondents, a ratio of 1.0:1); waiting during the treatment and/or post-treatment phase (n=923, 19.8%, ratio 1.5:1); staffing and resource levels (n=671, 14.4% ratio 5.3:1); speed and quality of diagnostic care (n=374, 8.0%, ratio 1.5:1). Within these areas, constituent subthemes are discussed.

Conclusions

This study presents specific areas of concern for patients with cancer, and reveals a number of themes present across the cancer journey. While the majority of comments were positive, analysis reveals concerns shared by significant numbers of respondents. Timely communication can help to manage these anxieties, even where delays or difficulties in treatment may be encountered.
Noise-induced hearing loss in a longitudinal study of Norwegian railway workers
Authors: Lie Arve , Skogstad Marit , Johnsen Torstein Seip , Engdahl Bo , Tambs Kristian
Published: September 2016

Objective

The aim of this study was to analyse longitudinal data to assess the risk of noise-induced hearing loss (NIHL) in Norwegian railway workers.

Design

Longitudinal.

Setting

A major Norwegian railway company.

Methods

We examined data from the first and last audiograms for the period 1991–2014, from 9640 railway workers with varying occupational noise exposure and with an average observation period of 10 years. The course of hearing acuity in seven groups of railway workers (train drivers, conductors, bus drivers, traffic controllers, train maintenance workers, track maintenance workers and others) were compared with each other and with ISO standards (ISO 1999).

Results

The change in hearing threshold during the observation period was 2–3 dB in the 0.5–4 kHz range and 6–7 dB in the 3–6 kHz range adjusted for age and sex, for all occupational groups, which is slightly less than expected (8 dB) according to ISO 1999.

Conclusions

The risk of NIHL in Norwegian railway workers during the period 1991–2014 has been negligible.