bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrochemical treatment of chemical oxygen demand in produced water using flow‐by porous graphite electrode
Authors: Abdel‐Salam Omar E. , Abou Taleb Enas M. , Afify Ahmed A. 
Published: February 2018

AbstractProduced water is the largest wastewater stream generated in the oil and gas industries. In this study, experiments were carried out using a bench‐scale electrochemical cell using flow‐by porous graphite electrode, for oxidation of organic matter in produced water which was collected from natural gas processing field (real sample). The effect of anodic current density and influent feed flow rate on chemical oxygen demand (COD) removal efficiency, and energy consumption were investigated. The maximum removal efficiency of 66.52% was obtained for a flow rate of 50 mL/min, current density of 1.41 mA/cm2 and pH of 7.3 for an influent COD of 2845 mg O2/L. The energy consumption at these conditions was 2.12 kWh/kgCOD.
Effects of run‐of‐the‐river hydropower plants on the surface water quality in the Solakli stream watershed, Northeastern Turkey
Authors: Koralay Necla , Kara Omer , Kezik Ugur 
Published: February 2018

AbstractIn recent years, Turkey has turned its attention to alternative energy sources rather than fossil fuels. The Eastern Black Sea Region of Turkey has steep mountains with hilly topography and has large potential in terms of energy production with run‐of‐the‐river hydropower plants (RHPPs). In this study, the effects of two RHPPs on some water quality parameters were examined in the Solaklı stream watershed. This research was conducted over the course of 12 months (January–December 2014). In total, 12 sampling points were selected and various water quality parameters, such as temperature, pH, dissolved oxygen, total suspended solids, electrical conductivity, total dissolved solid, chloride and salinity, were monitered at each point. Statistically, significant changes occured in water quality parameters such as total suspended solids, pH and temperature. In particular, total suspended solids ranged from 10 to 440 mg/L.These results suggest that the RHPP negatively effect water quality and quantity in the main stream in both the operational and constructional phases.
Mouse and Human Monoclonal Antibodies Protect against Infection by Multiple Genotypes of Japanese Encephalitis Virus
Authors: Fernandez Estefania , Kose Nurgun , Edeling Melissa A. , Adhikari Jagat , Sapparapu Gopal , Lazarte Susana M. , Nelson Christopher A. , Govero Jennifer , Gross Michael L. , Fremont Daved H. , Crowe James E. , Diamond Michael S. 
Published: February 2018

ABSTRACTJapanese encephalitis virus (JEV) remains a leading cause of viral encephalitis worldwide. Although JEV-specific antibodies have been described, an assessment of their ability to neutralize multiple genotypes of JEV has been limited. Here, we describe the development of a panel of mouse and human neutralizing monoclonal antibodies (MAbs) that inhibit infection in cell culture of four different JEV genotypes tested. Mechanism-of-action studies showed that many of these MAbs inhibited infection at a postattachment step, including blockade of virus fusion. Mapping studies using site-directed mutagenesis and hydrogen-deuterium exchange with mass spectrometry revealed that the lateral ridge on domain III of the envelope protein was a primary recognition epitope for our panel of strongly neutralizing MAbs. Therapeutic studies in mice demonstrated protection against lethality caused by genotype I and III strains when MAbs were administered as a single dose even 5 days after infection. This information may inform the development of vaccines and therapeutic antibodies as emerging strains and genotypic shifts become more prevalent.IMPORTANCEAlthough Japanese encephalitis virus (JEV) is a vaccine-preventable cause of viral encephalitis, the inactivated and live attenuated platforms available are derived from strains belonging to a single genotype (GIII) due to its historical prevalence in areas of JEV epidemics. Related to this, studies with vaccines and antibodies have focused on assessing thein vitroandin vivoprotective responses to homologous or heterologous GIII strains. An epidemiological shift in JEV genotype distribution warrants the induction of broadly neutralizing antibody responses that inhibit infection of multiple JEV genotypes. Here, we generated a panel of mouse and human neutralizing monoclonal antibodies and evaluated their inhibitory activity, epitope location, and capacity for protection against multiple JEV genotypes in mice.
Widespread Distribution and Functional Specificity of the Copper Importer CcoA: Distinct Cu Uptake Routes for Bacterial Cytochrome
c
Oxidases
Authors: Khalfaoui-Hassani Bahia , Wu Hongjiang , Blaby-Haas Crysten E. , Zhang Yang , Sandri Federica , Verissimo Andreia F. , Koch Hans-Georg , Daldal Fevzi 
Published: February 2018

ABSTRACT

Cytochrome
c
oxidases are members of the heme-copper oxidase superfamily. These enzymes have different subunits, cofactors, and primary electron acceptors, yet they all contain identical heme-copper (Cu
B
) binuclear centers within their catalytic subunits. The uptake and delivery pathways of the Cu
B
atom incorporated into this active site, where oxygen is reduced to water, are not well understood. Our previous work with the facultative phototrophic bacterium
Rhodobacter capsulatus
indicated that the copper atom needed for the Cu
B
site of
cbb
3
-type cytochrome
c
oxidase (
cbb
3
-Cox) is imported to the cytoplasm by a major facilitator superfamily-type transporter, CcoA. In this study, a comparative genomic analysis of CcoA orthologs in alphaproteobacterial genomes showed that CcoA is widespread among organisms and frequently co-occurs with cytochrome
c
oxidases. To define the specificity of CcoA activity, we investigated its function in
Rhodobacter sphaeroides
, a close relative of
R. capsulatus
that contains both
cbb
3
- and
aa
3
-Cox. Phenotypic, genetic, and biochemical characterization of mutants lacking CcoA showed that in its absence, or even in the presence of its bypass suppressors, only the production of
cbb
3
-Cox and not that of
aa
3
-Cox was affected. We therefore concluded that CcoA is dedicated solely to
cbb
3
-Cox biogenesis, establishing that distinct copper uptake systems provide the Cu
B
atoms to the catalytic sites of these two similar cytochrome
c
oxidases. These findings illustrate the large variety of strategies that organisms employ to ensure homeostasis and fine control of copper trafficking and delivery to the target cuproproteins under different physiological conditions.

IMPORTANCE
The
cbb
3
- and
aa
3
-type cytochrome
c
oxidases belong to the widespread heme-copper oxidase superfamily. They are membrane-integral cuproproteins that catalyze oxygen reduction to water under hypoxic and normoxic growth conditions. These enzymes diverge in terms of subunit and cofactor composition, yet they all share a conserved heme-copper binuclear site within their catalytic subunit. In this study, we show that the copper atoms of the catalytic center of two similar cytochrome
c
oxidases from this superfamily are provided by different copper uptake systems during their biogenesis. This finding illustrates different strategies by which organisms fine-tune the trafficking of copper, which is an essential but toxic micronutrient.
Mmf1p Couples Amino Acid Metabolism to Mitochondrial DNA Maintenance in
Saccharomyces cerevisiae
Authors: Ernst Dustin C. , Downs Diana M. 
Published: February 2018

ABSTRACT

A variety of metabolic deficiencies and human diseases arise from the disruption of mitochondrial enzymes and/or loss of mitochondrial DNA. Mounting evidence shows that eukaryotes have conserved enzymes that prevent the accumulation of reactive metabolites that cause stress inside the mitochondrion. 2-Aminoacrylate is a reactive enamine generated by pyridoxal 5′-phosphate-dependent α,β-eliminases as an obligatory intermediate in the breakdown of serine. In prokaryotes, members of the broadly conserved RidA family (PF14588) prevent metabolic stress by deaminating 2-aminoacrylate to pyruvate. Here, we demonstrate that unmanaged 2-aminoacrylate accumulation in
Saccharomyces cerevisiae
mitochondria causes transient metabolic stress and the irreversible loss of mitochondrial DNA. The RidA family protein Mmf1p deaminates 2-aminoacrylate, preempting metabolic stress and loss of the mitochondrial genome. Disruption of the mitochondrial pyridoxal 5′-phosphate-dependent serine dehydratases (Ilv1p and Cha1p) prevents 2-aminoacrylate formation, avoiding stress in the absence of Mmf1p. Furthermore, chelation of iron in the growth medium improves maintenance of the mitochondrial genome in yeast challenged with 2-aminoacrylate, suggesting that 2-aminoacrylate-dependent loss of mitochondrial DNA is influenced by disruption of iron homeostasis. Taken together, the data indicate that Mmf1p indirectly contributes to mitochondrial DNA maintenance by preventing 2-aminoacrylate stress derived from mitochondrial amino acid metabolism.

IMPORTANCE
Deleterious reactive metabolites are produced as a consequence of many intracellular biochemical transformations. Importantly, reactive metabolites that appear short-lived
in vitro
have the potential to persist within intracellular environments, leading to pervasive cell damage and diminished fitness. To overcome metabolite damage, organisms utilize enzymatic reactive-metabolite defense systems to rid the cell of deleterious metabolites. In this report, we describe the importance of the RidA/YER057c/UK114 enamine/imine deaminase family in preventing 2-aminoacrylate stress in yeast.
Saccharomyces cerevisiae
lacking the enamine/imine deaminase Mmf1p was shown to experience pleiotropic growth defects and fails to maintain its mitochondrial genome. Our results provide the first line of evidence that uncontrolled 2-aminoacrylate stress derived from mitochondrial serine metabolism can negatively impact mitochondrial DNA maintenance in eukaryotes.
Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB
Authors: Filippova Ekaterina V. , Zemaitaitis Bozena , Aung Theint , Wolfe Alan J. , Anderson Wayne F. 
Published: February 2018

ABSTRACT

RcsB is a highly conserved transcription regulator of the Rcs phosphorelay system, a complex two-component signal transduction system (N. Majdalani and S. Gottesman, Annu Rev Microbiol 59:379–405, 2005; A. J. Wolfe, Curr Opin Microbiol 13:204–209, 2010,
https://doi.org/10.1016/j.mib.2010.01.002
; D. J. Clarke, Future Microbiol 5:1173–1184, 2010,
https://doi.org/10.2217/fmb.10.83
). RcsB plays an important role in virulence and pathogenicity in human hosts by regulating biofilm formation. RcsB can regulate transcription alone or together with its auxiliary transcription regulators by forming heterodimers. This complexity allows RcsB to regulate transcription of more than 600 bacterial genes in response to different stresses (D. Wang et al., Mol Plant Microbe Interact 25:6–17, 2012,
https://doi.org/10.1094/MPMI-08-11-0207
). Despite increasing knowledge of RcsB importance, molecular mechanisms that drive the ability of RcsB to control transcription of a large number of genes remain unclear. Here, we present crystal structures of unphosphorylated RcsB in complex with the consensus DNA-binding sequence of 22-mer (DNA22) and 18-mer (DNA18) of the
flhDC
operon from
Escherichia coli
determined at 3.15- and 3.37-Å resolution, respectively. The results of our structural analysis combined with the results of
in vitro
binding assays provide valuable insights to the protein regulatory mechanism, demonstrate how RcsB recognizes target DNA sequences, and reveal a unique oligomeric state that allows RcsB to form homo- and heterodimers. This information will help us understand the complex mechanisms of transcriptional regulation by RcsB in bacteria.

IMPORTANCE
RcsB is a well-studied two-component response regulator of the Rcs phosphorelay system, conserved within the family
Enterobacteriaceae
, which includes many pathogens. It is a global regulator, controlling more than 5% of bacterial genes associated with capsule biosynthesis, flagellar biogenesis, cell wall biosynthesis, antibiotic resistance, biofilm formation, and virulence in pathogens. Knowledge of RcsB structure represents a unique opportunity to explore mechanisms that regulate the Rcs phosphorelay system and its role in the family
Enterobacteriaceae
.
Tracking Electron Uptake from a Cathode into
Shewanella
Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors
Authors: Rowe Annette R. , Rajeev Pournami , Jain Abhiney , Pirbadian Sahand , Okamoto Akihiro , Gralnick Jeffrey A. , El-Naggar Mohamed Y. , Nealson Kenneth H. 
Published: February 2018

ABSTRACT

While typically investigated as a microorganism capable of extracellular electron transfer to minerals or anodes,
Shewanella oneidensis
MR-1 can also facilitate electron flow from a cathode to terminal electron acceptors, such as fumarate or oxygen, thereby providing a model system for a process that has significant environmental and technological implications. This work demonstrates that cathodic electrons enter the electron transport chain of
S. oneidensis
when oxygen is used as the terminal electron acceptor. The effect of electron transport chain inhibitors suggested that a proton gradient is generated during cathode oxidation, consistent with the higher cellular ATP levels measured in cathode-respiring cells than in controls. Cathode oxidation also correlated with an increase in the cellular redox (NADH/FMNH
2
) pool determined with a bioluminescence assay, a proton uncoupler, and a mutant of proton-pumping NADH oxidase complex I. This work suggested that the generation of NADH/FMNH
2
under cathodic conditions was linked to reverse electron flow mediated by complex I. A decrease in cathodic electron uptake was observed in various mutant strains, including those lacking the extracellular electron transfer components necessary for anodic-current generation. While no cell growth was observed under these conditions, here we show that cathode oxidation is linked to cellular energy acquisition, resulting in a quantifiable reduction in the cellular decay rate. This work highlights a potential mechanism for cell survival and/or persistence on cathodes, which might extend to environments where growth and division are severely limited.

IMPORTANCE
The majority of our knowledge of the physiology of extracellular electron transfer derives from studies of electrons moving to the exterior of the cell. The physiological mechanisms and/or consequences of the reverse processes are largely uncharacterized. This report demonstrates that when coupled to oxygen reduction, electrode oxidation can result in cellular energy acquisition. This respiratory process has potentially important implications for how microorganisms persist in energy-limited environments, such as reduced sediments under changing redox conditions. From an applied perspective, this work has important implications for microbially catalyzed processes on electrodes, particularly with regard to understanding models of cellular conversion of electrons from cathodes to microbially synthesized products.
SecurAstaP trial: securement with SecurAcath versus StatLock for peripherally inserted central catheters, a randomised open trial
Authors: Goossens Godelieve Alice , Grumiaux Niel , Janssens Christel , Jérôme Martine , Fieuws Steffen , Moons Philip , Stas Marguerite , Maleux Geert 
Published: February 2018

ObjectivesTo assess the effect on needed nursing time for dressing change.Design, setting, participantsA parallel-group, open-label, randomised controlled trial in patients who are in need for a peripherally inserted central catheter insertion in one teaching hospital in Belgium. The follow-up lasted 180 days or until catheter removal, whatever came first. A computer generated table was used to allocate devices. Randomised patients were 105 adults (StatLock, n=53; SecurAcath, n=52) and primary analysis was based on all patients (n=92) with time measurements (StatLock, n=43; SecurAcath, n=49).InterventionsStatLock which has to be changed weekly versus SecurAcath which could remain in place for the complete catheter dwell time.Main outcome measureNeeded time for the dressing change at each dressing change (SecurAcath) or at each dressing change combined with the change of the securement device (StatLock).ResultsMedian time needed for dressing change was 7.3 min (95% CI 6.4 min to 8.3 min) in the StatLock group and in the SecurAcath group 4.3 min (95% CI 3.8 min to 4.9 min) (P<0.0001). The time in the SecurAcath group was reduced with 41% (95% CI 29% to 51%). Incidence rates of migration, dislodgement and catheter-related bloodstream infection were comparable across groups. Pain scores were higher with SecurAcath than with StatLock at insertion (P=0.02) and at removal (P<0.001) and comparable during dressing change (P=0.38) and during dwell time (P=0.995). User-friendliness was scored at insertion and removal. All statements regarding the user-friendliness were scored significantly higher for StatLock than for SecurAcath (P<0.05). Only for the statement regarding the recommending routine use of the device, which was asked at removal, no difference was found between the two devices (P=0.32).ConclusionUse of SecurAcath saves time during dressing change compared with StatLock. Training on correct placement and removal of SecurAcath is critical to minimise pain.Trial registration numberNCT02311127; Pre-results.
IRAK1 Augments Cancer Stemness and Drug Resistance via the AP-1/AKR1B10 Signaling Cascade in Hepatocellular Carcinoma
Authors: Cheng Bowie Y. , Lau Eunice Y. , Leung Hoi-Wing , Leung Carmen Oi-Ning , Ho Nicole P. , Gurung Shilpa , Cheng Lily K. , Lin Chi Ho , Lo Regina Cheuk-Lam , Ma Stephanie , Ng Irene Oi-Lin , Lee Terence K. 
Published: February 2018

Abstract
Frequent relapse and drug resistance in patients with hepatocellular carcinoma (HCC) can be attributed to the existence of tumor-initiating cells (TIC) within the tumor bulk. Therefore, targeting liver TICs may improve the prognosis of these patients. From transcriptome sequencing of 16 pairs of clinical HCC samples, we report that interleukin-1 receptor-associated kinase 1 (IRAK1) in the TLR/IRAK pathway is significantly upregulated in HCC. IRAK1 overexpression in HCC was further confirmed at the mRNA and protein levels and correlated with advanced tumor stages and poor patient survival. Interestingly, IRAK4, an upstream regulator of IRAK1, was also consistently upregulated. IRAK1 regulated liver TIC properties, including self-renewal, tumorigenicity, and liver TIC marker expression. IRAK1 inhibition sensitized HCC cells to doxorubicin and sorafenib treatment in vitro via suppression of the apoptotic cascade. Pharmacological inhibition of IRAK1 with a specific IRAK1/4 kinase inhibitor consistently suppressed liver TIC populations. We identified aldo-keto reductase family 1 member 10 (AKR1B10) as a novel downstream target of IRAK1, which was found to be overexpressed in HCC and significantly correlated with IRAK1 expression. Knockdown of AKR1B10 negated IRAK1-induced TIC functions via modulation of the AP-1 complex. Inhibition of IRAK1/4 inhibitor in combination with sorafenib synergistically suppressed tumor growth in an HCC xenograft model. In conclusion, targeting the IRAK4/IRAK1/AP-1/AKR1B10 signaling pathway may be a potential therapeutic strategy against HCC.
Significance: IRAK4/IRAK1/AP-1/AKR1B10 signaling pathway regulates cancer stemness and drug resistance and may be a novel therapeutic target in HCC. Cancer Res; 78(9); 2332–42. ©2018 AACR.
Phase I Study of LY2940680, a Smo Antagonist, in Patients with Advanced Cancer Including Treatment-Naïve and Previously Treated Basal Cell Carcinoma
Authors: Bendell Johanna , Andre Valerie , Ho Alan , Kudchadkar Ragini , Migden Michael , Infante Jeffrey , Tiu Ramon V. , Pitou Celine , Tucker Trevor , Brail Les , Von Hoff Daniel 
Published: February 2018

Abstract
Purpose: The purpose of this study was to determine a recommended phase II dose and schedule of LY2940680 (taladegib) for safe administration to patients with locally advanced/metastatic cancer.
Experimental Design: This was a phase I, multicenter, open-label study of oral LY2940680. The maximum tolerable dose (MTD) was determined using a 3+3 design, the dose was confirmed, and then treatment-naïve and previously hedgehog (Hh)-inhibitor–treated patients with basal cell carcinoma (BCC) were enrolled.
Results: Eighty-four patients were treated (dose escalation, n = 25; dose confirmation, n = 19; and BCC dose expansion, n = 40). Common treatment-emergent adverse events were dysgeusia [41 (48.8%)], fatigue [40 (47.6%)], nausea [38 (45.2%)], and muscle spasms [34 (40.5%)]. Four patients experienced events (3 were grade 3; 1 was grade 2) that were considered dose-limiting toxicities (DLT). The MTD was determined to be 400 mg because of DLTs and dose reductions. Pharmacokinetic analyses showed no clear relationship between exposure and toxicity. Analysis of Gli1 mRNA from skin biopsies from unaffected areas suggested that all doses were biologically active [inhibition median of 92.3% (80.9% to 95.7%)]. All clinical responses (per RECIST 1.1) were in patients with BCC (n = 47); the overall and estimated response rate was 46.8% (95% confidence interval, 32.1%–61.9%). Responses were observed in patients previously treated with Hh therapy (11/31) and in Hh treatment–naïve (11/16) patients.
Conclusions: LY2940680 treatment resulted in an acceptable safety profile in patients with advanced/metastatic cancer. Clinical responses were observed in patients with locally advanced/metastatic BCC who were previously treated with Hh therapy and in Hh treatment–naïve patients. Clin Cancer Res; 24(9); 2082–91. ©2018 AACR.
<b>Records of new larval host plants of some common butterflies of Bangladesh</b>
Authors: Shihan Tahsinur Rahman 
Published: February 2018

This paper presents the record of Clausena heptaphylla (Roxburgh) Wright & Arn. (Rutaceae) as a new larval host plant for Papilio polytes Linnaeus, 1758 and Papilio demoleus Linnaeus, 1758 (Papilionidae). Ravenia spectabilis Engl. (Rutaceae) for Papilio demoleus Linnaeus, 1758 (Papilionidae). Hemigraphis hirta (Vahl) T. Anders. (Acanthaceae) is the new recorded host for Junonia almana (Linnaeus, 1758) and Junonia lemonis (Linnaeus, 1758) (Nymphalidae) from Chuadanga, Bangladesh.
<b>Vascular plant assemblage of cliffs in northern Western Ghats, India</b>
Authors: Datar Mandar N. , Watve Aparna V. 
Published: February 2018

Vertical rocky cliffs, which consist of various types of rock, are widespread all over the world. India’s northern Western Ghats consisting of basaltic rocks form probably the largest cliff ecosystem globally, however, almost no studies are available concerning their floristic richness. In an attempt to understand the vascular plant assemblage of this habitat, cliffs of the northern Western Ghats were surveyed for their microhabitats, species diversity, distribution of endemics, occurrence of particular adaptive traits and potential threats. A total of 102 species of vascular plants were documented from the cliff habitats of which 55 are endemic. Flowering of the species on cliffs is triggered by the advent of the south-west monsoon and peak flowering is seen between August and October. Of the total species, 27 grow exclusively on cliffs. Owing to habitat specificity, cliffs show a greater number of narrow endemic and threatened species when compared with other habitats like deciduous, evergreen and semi-evergreen forests, which are widespread in the northern Western Ghats. Unfortunately, this habitat faces threats in the form of landslides, periodic burning and habitat loss due to road-widening.