bluuebunny/crossref_metadata_2025_split huggingface dataset:
EMDR as a treatment for long‐term depression: A feasibility study
Authors: Wood Emily , Ricketts Thomas , Parry Glenys 
Published: August 2017

ObjectiveCurrent treatments for long‐term depression – medication and psychotherapy – are effective for some but not all clients. New approaches need to be developed to complement the ones already available. This study was designed to test the feasibility of using an effective post‐traumatic stress disorder treatment for people with long‐term depression.DesignA single‐case experimental design with replications was undertaken as a feasibility study of eye movement desensitization and reprocessing (EMDR) in treating long‐term depression.MethodsThirteen people with recurrent and/or long‐term depression were recruited from primary care mental health services and given standard protocol EMDR for a maximum of 20 sessions. Levels of depression were measured before and after treatment and at follow‐up, clients also rated their mood each day.ResultsEight people engaged with the treatment; seven of these had clinically significant and statistically reliable improvement on the Hamilton Rating Scale for Depression. Daily mood ratings were highly variable both during baseline and intervention.ConclusionsEMDR is a feasible treatment for recurrent and/or long‐term depression. Research on treatment efficacy and effectiveness is now required.Practitioner points

EMDR may be an effective treatment for depression.

EMDR could be considered if first‐line approaches (CBT and counselling) have been tried and failed.

EMDR may be particularly helpful for service users with a history of trauma.
Passive recovery of small vertebrates following livestock removal in the Australian rangelands
Authors: Haby Nerissa A. , Brandle Robert 
Published: August 2017

AbstractIn arid environments, grazing by exotic herbivores, including domestic livestock, can greatly influence native, small vertebrate assemblages. Whether the removal of livestock facilitates passive recovery of these assemblages depends on habitat condition and the species present. We explore changes in small mammal and reptile species richness, abundance, and composition in a degraded chenopod shrubland dominated byAcacia victoriaessp. and openAcacia aneura(mulga) woodland destocked in 1976 and 1984, respectively. Data were obtained between 1997 and 2007, from two grazed and two ungrazed sites in each community. Species richness increased at a faster rate in ungrazed openA. aneurawoodland, but did not differ significantly between ungrazed and grazed degraded chenopod shrubland. Subsequent analyses at a finer‐scale detected disparate responses in richness and abundance for microhabitat. At this scale, a greater number of species‐specific responses were also detected, including increased abundance of generalist species and decreased abundance of species requiring low cover. These results reiterate the potential for species‐specific responses to livestock that are more apparent in particular microhabitats. Furthermore, this investigation provides evidence for the gradual passive recovery of small mammal and reptile assemblages in both communities, which is facilitated by the removal of livestock in openA. aneurawoodland in fair condition, but not degraded chenopod shrubland in poor condition.
Making restoration history: reconsidering Aldo Leopold's Arboretum dedication speeches
Authors: Greenwood David A. 
Published: August 2017

AbstractScholarship surrounding Aldo Leopold's involvement in the University of Wisconsin Arboretum in Madison, Wisconsin, has often pointed to Leopold's 1934 dedication speech as a significant historical artifact. While reflecting both Arboretum history and the development of Leopold's thought and influence, the speech may also have been the first publically articulated rationale for ecological restoration in the modern era. This scholarly personal essay describes my 50‐year relationship with both Leopold and the Arboretum, and my recent research that offers a new historical interpretation of Leopold's speech. Two versions of the speech exist; tensions between them have been discussed in at least two professional journals. What I learned from examining the archival record indicates that we really don't know for sure what Leopold said that June morning of 1934. What we can be sure of, however, is that the dedication speech usually attributed to Leopold, by such able scholars as Curt Meine and Baird Callicott, was not the one Leopold actually delivered. What many historians continue to refer to as Aldo Leopold's 1934 Arboretum dedication speech was actually written for another Wisconsin audience. As I explored this mystery, I rediscovered Leopold's passion for ecological restoration and his commitment to educate a diverse, Depression‐era public about its goals and purposes. For Leopold, restoration involved not only the expression of social and ecological values, but also public critique of the destructive social forces that make restoration necessary. Embodying social critique and ecological science, Leopold continues to model for us personal and professional roles as public ecological citizens dedicated to land.
Sowing density effects and patterns of colonization in a prairie restoration
Authors: Jaksetic Nathan , Foster Bryan L. , Bever James D. , Schwarting Julie , Alexander Helen M. 
Published: August 2017

AbstractA cost‐effective approach in plant restorations could be to increase sowing density for species known to be challenging to establish, while reducing sowing density for species that easily colonize on their own. Sowing need not occur evenly across the site for rapidly dispersing species. We explored these issues using a prairie restoration experiment on a high‐school campus with three treatments: plots sown only to grasses (G plots), to grasses and forbs (GF1), and to grasses and forbs with forbs sown at twice the density (GF2). In year 2, GF1 and GF2 plots had higher diversity than G plots, as expected, but GF2 treatments did not have twice the sown forb cover. However, high forb sowing density increased forb richness, probably by reducing stochastic factors in establishment. Cover of nonsown species was highest in G plots and lowest in GF2 plots, suggesting suppressive effects of native forbs on weedy species. Colonization of G plots by two sown forbs (Coreopsis tinctoria and Rudbeckia hirta) was apparent after 2.5 years, providing evidence that these species are self‐sustaining. Colonization was greater in edges than in the central areas of G plots. Through construction of establishment kernels, we infer that the mean establishment distance was shorter for R. hirta (6.7 m) compared to C. tinctoria (21.1 m). Our results lead us to advocate for restoration practices that consider not only seed sowing but also subsequent dispersal of sown species. Furthermore, we conclude that restoration research is particularly amenable for outdoor education and university‐high school collaborations.
Clustering in Small Area Estimation with Area Level Linear Mixed Models
Authors: Torkashvand Elaheh , Jafari Jozani Mohammad , Torabi Mahmoud 
Published: August 2017

Summary
Finding reliable estimates of parameters of subpopulations (areas) in small area estimation is an important problem especially when there are few or no samples in some areas. Clustering small areas on the basis of the Euclidean distance between their corresponding covariates is proposed to obtain smaller mean-squared prediction error (MSPE) for the predicted values of area means by using area level linear mixed models. We first propose a statistical test to investigate the homogeneity of variance components between clusters. Then, we obtain the empirical best linear unbiased predictor of small area means by taking into account the difference between variance components in different clusters. We study the performance of our proposed test as well as the effect of the clustering on the MSPE of small area means by using simulation studies. We also obtain a second-order approximation to the MSPE of small area means and derive a second-order unbiased estimator of the MSPE. The results show that the MSPE of small area means can be improved when the variance components are different. The improvement in the MSPE is significant when the difference between variance components is considerable. Finally, the methodology proposed is applied to a real data set.
Differences in Temperature and Water Chemistry Shape Distinct Diversity Patterns in Thermophilic Microbial Communities
Authors: Chiriac Cecilia M. , Szekeres Edina , Rudi Knut , Baricz Andreea , Hegedus Adriana , Dragoş Nicolae , Coman Cristian 
Published: August 2017

ABSTRACT

This report describes the biodiversity and ecology of microbial mats developed in thermal gradients (20 to 65°C) in the surroundings of three drillings (Chiraleu [CH], Ciocaia [CI], and Mihai Bravu [MB]) tapping a hyperthermal aquifer in Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physicochemical factors were explored. Additionally, the cDNA data were used for
in silico
functionality predictions, bringing new insights into the functional potential and dynamics of these communities. The results showed that each hot spring determined the formation of distinct microbial communities. In the CH mats (40 to 53°C), the abundance of
Cyanobacteria
decreased with temperature, opposite to those of
Chloroflexi
and
Proteobacteria
.
Ectothiorhodospira
,
Oscillatoria
, and methanogenic archaea dominated the CI communities (20 to 65°C), while the MB microbial mats (53 to 65°C) were mainly composed of
Chloroflexi
,
Hydrogenophilus
,
Thermi
, and
Aquificae
. Alpha-diversity was negatively correlated with the increase in water temperature, while beta-diversity was shaped in each hot spring by the unique combination of physicochemical parameters, regardless of the type of nucleic acid analyzed (DNA versus cDNA). The rank correlation analysis revealed a unique model that associated environmental data with community composition, consisting in the combined effect of Na
+
, K
+
, HCO
3
−
, and PO
4
3−
concentrations, together with temperature and electrical conductivity. These factors seem to determine the grouping of samples according to location, rather than with the similarities in thermal regimes, showing that other parameters beside temperature are significant drivers of biodiversity.

IMPORTANCE
Hot spring microbial mats represent a remarkable manifestation of life on Earth and have been intensively studied for decades. Moreover, as hot spring areas are isolated and have a limited exchange of organisms, nutrients, and energy with the surrounding environments, hot spring microbial communities can be used in model studies to elucidate the colonizing potential within extreme settings. Thus, they are of great importance in evolutionary biology, microbial ecology, and exobiology. In spite of all the efforts that have been made, the current understanding of the influence of temperature and water chemistry on the microbial community composition, diversity, and abundance in microbial mats is limited. In this study, the composition and diversity of microbial communities developed in thermal gradients in the vicinity of three hot springs from Romania were investigated, each having particular physicochemical characteristics. Our results expose new factors that could determine the formation of these ecosystems, expanding the current knowledge in this regard.
Coordinated Regulation of the EII
Man
and
fruRKI
Operons of Streptococcus mutans by Global and Fructose-Specific Pathways
Authors: Zeng Lin , Chakraborty Brinta , Farivar Tanaz , Burne Robert A. 
Published: August 2017

ABSTRACT

The glucose/mannose-phosphotransferase system (PTS) permease EII
Man
encoded by
manLMN
in the dental caries pathogen
Streptococcus mutans
has a dominant influence on sugar-specific, CcpA-independent catabolite repression (CR). Mutations in
manL
affect energy metabolism and virulence-associated traits, including biofilm formation, acid tolerance, and competence. Using promoter::reporter fusions, expression of the
manLMN
and the
fruRKI
operons, encoding a transcriptional regulator, a fructose-1-phosphate kinase and a fructose-PTS permease EII
Fru
, respectively, was monitored in response to carbohydrate source and in mutants lacking CcpA, FruR, and components of EII
Man
. Expression of genes for EII
Man
and EII
Fru
was directly regulated by CcpA and CR, as evinced by
in vivo
and
in vitro
methods. Unexpectedly, not only was the
fruRKI
operon negatively regulated by FruR, but also so was
manLMN
. Carbohydrate transport by EII
Man
had a negative influence on expression of
manLMN
but not
fruRKI
. In agreement with the proposed role of FruR in regulating these PTS operons, loss of
fruR
or
fruK
substantially altered growth on a number of carbohydrates, including fructose. RNA deep sequencing revealed profound changes in gene regulation caused by deletion of
fruK
or
fruR
. Collectively, these findings demonstrate intimate interconnection of the regulation of two major PTS permeases in
S. mutans
and reveal novel and important contributions of fructose metabolism to global regulation of gene expression.

IMPORTANCE
The ability of
Streptococcus mutans
and other streptococcal pathogens to survive and cause human diseases is directly dependent upon their capacity to metabolize a variety of carbohydrates, including glucose and fructose. Our research reveals that metabolism of fructose has broad influences on the regulation of utilization of glucose and other sugars, and mutants with changes in certain genes involved in fructose metabolism display profoundly different abilities to grow and express virulence-related traits. Mutants lacking the FruR regulator or a particular phosphofructokinase, FruK, display changes in expression of a large number of genes encoding transcriptional regulators, enzymes required for energy metabolism, biofilm development, biosynthetic and degradative processes, and tolerance of a spectrum of environmental stressors. Since fructose is a major component of the modern human diet, the results have substantial significance in the context of oral health and the development of dental caries.
Transcriptional Regulator PhlH Modulates 2,4-Diacetylphloroglucinol Biosynthesis in Response to the Biosynthetic Intermediate and End Product
Authors: Yan Xu , Yang Rui , Zhao Rui-Xue , Han Jian-Ting , Jia Wen-Juan , Li Di-Yin , Wang Yong , Zhang Nannan , Wu Yi , Zhang Li-Qun , He Yong-Xing 
Published: August 2017

ABSTRACT

Certain strains of biocontrol bacterium
Pseudomonas fluorescens
produce the secondary metabolite 2,4-diacetylphloroglucinol (2,4-DAPG) to antagonize soilborne phytopathogens in the rhizosphere. The gene cluster responsible for the biosynthesis of 2,4-DAPG is named
phlACBDEFGH
and it is still unclear how the pathway-specific regulator
phlH
within this gene cluster regulates the metabolism of 2,4-DAPG. Here, we found that PhlH in
Pseudomonas fluorescens
strain 2P24 represses the expression of the
phlG
gene encoding the 2,4-DAPG hydrolase by binding to a sequence motif overlapping with the −35 site recognized by σ
70
factors. Through biochemical screening of PhlH ligands we identified the end product 2,4-DAPG and its biosynthetic intermediate monoacetylphloroglucinol (MAPG), which can act as signaling molecules to modulate the binding of PhlH to the target sequence and activate the expression of
phlG
. Comparison of 2,4-DAPG production between the Δ
phlH
, Δ
phlG
, and Δ
phlHG
mutants confirmed that
phlH
and
phlG
impose negative feedback regulation over 2,4-DAPG biosynthesis. It was further demonstrated that the 2,4-DAPG degradation catalyzed by PhlG plays an insignificant role in 2,4-DAPG tolerance but contributes to bacterial growth advantages under carbon/nitrogen starvation conditions. Taken together, our data suggest that by monitoring and down-tuning
in situ
levels of 2,4-DAPG, the
phlHG
genes could dynamically modulate the metabolic loads attributed to 2,4-DAPG production and potentially contribute to rhizosphere adaptation.

IMPORTANCE
2,4-DAPG, which is synthesized by biocontrol pseudomonad bacteria, is a broad-spectrum antibiotic against bacteria, fungi, oomycetes, and nematodes and plays an important role in suppressing soilborne plant pathogens. Although most of the genes in the 2,4-DAPG biosynthetic gene cluster (
phl
) have been characterized, it is still not clear how the pathway-specific regulator
phlH
is involved in 2,4-DAPG metabolism. This work revealed the role of PhlH in modulating 2,4-DAPG levels by controlling the expression of 2,4-DAPG hydrolase PhlG in response to 2,4-DAPG and MAPG. Since 2,4-DAPG biosynthesis imposes a metabolic burden on biocontrol pseudomonads, it is expected that the fine regulation of
phlG
by PhlH offers a way to dynamically modulate the metabolic loads attributed to 2,4-DAPG production.
Crystal Structure of TetR Family Repressor AlkX from Dietzia sp. Strain DQ12-45-1b Implicated in Biodegradation of
n
-Alkanes
Authors: Liang Jie-Liang , Gao Yuan , He Zheng , Nie Yong , Wang Meng , JiangYang Jing-Hong , Zhang Xuejun C. , Shu Wen-Sheng , Wu Xiao-Lei 
Published: August 2017

ABSTRACT

n
-Alkanes are ubiquitous in nature and are widely used by microorganisms as carbon sources. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of
n
-alkanes, which plays important roles in natural alkane attenuation and is used in industrial and environmental applications. The alkane oxidation operon,
alkW1-alkX
, in the alkane-degrading strain
Dietzia
sp. strain DQ12-45-1b is negatively autoregulated by the TetR family repressor AlkX via a product positive feedback mechanism. To predict the gene regulation mechanism, we determined the 3.1-Å crystal structure of an AlkX homodimer in a non-DNA-bound state. The structure showed traceable long electron density deep inside a hydrophobic cavity of each monomer along the long axis of the helix bundle, and further gas chromatography-mass spectrometry analysis of AlkX revealed that it contained the
Escherichia coli
-derived long-chain fatty acid molecules as a ligand. Moreover, an unusual structural feature of AlkX is an extra helix, α6′, forming a lid-like structure with α6 covering the inducer-binding pocket and occupying the space between the two symmetrical DNA-binding motifs in one dimer, indicating a distinct conformational transition mode in modulating DNA binding. Sequence alignment of AlkX homologs from
Dietzia
strains showed that the residues involved in DNA and inducer binding are highly conserved, suggesting that the regulation mechanisms of
n
-alkane hydroxylation are possibly a common characteristic of
Dietzia
strains.

IMPORTANCE
With
n
-alkanes being ubiquitous in nature, many bacteria from terrestrial and aquatic environments have evolved
n
-alkane oxidation functions. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of
n
-alkanes, which plays important roles in natural alkane attenuation and petroleum-contaminating environment bioremediation. The gene regulation of the most common alkane hydroxylase, AlkB, has been studied widely in Gram-negative bacteria but has been less explored in Gram-positive bacteria. Our previous study showed that the TetR family regulator (TFR) AlkX negatively autoregulated the alkane oxidation operon,
alkW1-alkX
, in the Gram-positive strain
Dietzia
sp. strain DQ12-45-1b. Although TFRs are one of the most common transcriptional regulator families in bacteria, the TFR involved in
n
-alkane metabolism has been reported only recently. In this study, we determined the crystal structure of AlkX, which implies a distinct DNA/ligand binding mode. Our results shed light upon the regulation mechanism of the common alkane degradation process in nature.
Heterologous Production of the Photosynthetic Reaction Center and Light Harvesting 1 Complexes of the Thermophile Thermochromatium tepidum in the Mesophile Rhodobacter sphaeroides and Thermal Stability of a Hybrid Core Complex
Authors: Jun D. , Huang V. , Beatty J. T. 
Published: August 2017

ABSTRACT

The photosynthetic complexes of the thermophile
Thermochromatium tepidum
are of considerable interest in biohybrid solar cell applications because of the ability of thermophilic proteins to tolerate elevated temperatures. Synthetic operons encoding reaction center (RC) and light harvesting 1 (LH1) pigment-protein complexes of
T. tepidum
were expressed in the mesophile
Rhodobacter sphaeroides
. The
T. tepidum
RC (TRC) was assembled and was found to be functional with the addition of menadione to populate the Q
A
pocket. The production of
T. tepidum
LH1 (TLH1) was increased by selection of a phototrophy-capable mutant after UV irradiation mutagenesis, which yielded a hybrid RC-TLH1 core complex consisting of the
R. sphaeroides
RC and
T. tepidum
TLH1, confirmed by the absorbance peak of TLH1 at 915 nm. Affinity chromatography partial purification and subsequent sucrose gradient analysis of the hybrid RC-TLH1 core complex indicated that this core complex assembled as a monomer. Furthermore, the RC-TLH1 hybrid core complex was more tolerant of a temperature of 70°C than the
R. sphaeroides
RC-LH1 core complexes in both the dimeric and monomeric forms; after 1 h, the hybrid complex retained 58% of the initial starting value, compared to values of 11% and 53% for the
R. sphaeroides
RC-LH1 dimer and monomer forms, respectively.

IMPORTANCE
This work is important because it is a new approach to bioengineering of photosynthesis proteins for potential use in biophotovoltaic solar energy capture. The work establishes a proof of principle for future biohybrid solar cell applications.