bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments
Authors: Danilova Olga V , Suzina Natalia E , Van De Kamp Jodie , Svenning Mette M , Bodrossy Levente , Dedysh Svetlana N 
Published: April 2016

Abstract
Although representatives with spiral-shaped cells are described for many functional groups of bacteria, this cell morphotype has never been observed among methanotrophs. Here, we show that spiral-shaped methanotrophic bacteria do exist in nature but elude isolation by conventional approaches due to the preference for growth under micro-oxic conditions. The helical cell shape may enable rapid motility of these bacteria in water-saturated, heterogeneous environments with high microbial biofilm content, therefore offering an advantage of fast cell positioning under desired high methane/low oxygen conditions. The pmoA genes encoding a subunit of particulate methane monooxygenase from these methanotrophs form a new genus-level lineage within the family Methylococcaceae, type Ib methanotrophs. Application of a pmoA-based microarray detected these bacteria in a variety of high-latitude freshwater environments including wetlands and lake sediments. As revealed by the environmental pmoA distribution analysis, type Ib methanotrophs tend to live very near the methane source, where oxygen is scarce. The former perception of type Ib methanotrophs as being typical for thermal habitats appears to be incorrect because only a minor proportion of pmoA sequences from these bacteria originated from environments with elevated temperatures.
Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps
Authors: Skennerton Connor T , Haroon Mohamed F , Briegel Ariane , Shi Jian , Jensen Grant J , Tyson Gene W , Orphan Victoria J 
Published: April 2016

Abstract
Tenericutes are a unique class of bacteria that lack a cell wall and are typically parasites or commensals of eukaryotic hosts. Environmental 16S rDNA surveys have identified a number of tenericute clades in diverse environments, introducing the possibility that these Tenericutes may represent non-host-associated, free-living microorganisms. Metagenomic sequencing of deep-sea methane seep sediments resulted in the assembly of two genomes from a Tenericutes-affiliated clade currently known as ‘NB1-n’ (SILVA taxonomy) or ‘RF3’ (Greengenes taxonomy). Metabolic reconstruction revealed that, like cultured members of the Mollicutes, these ‘NB1-n’ representatives lack a tricarboxylic acid cycle and instead use anaerobic fermentation of simple sugars for substrate level phosphorylation. Notably, the genomes also contained a number of unique metabolic features including hydrogenases and a simplified electron transport chain containing an RNF complex, cytochrome bd oxidase and complex I. On the basis of the metabolic potential predicted from the annotated genomes, we devised an anaerobic enrichment media that stimulated the growth of these Tenericutes at 10 °C, resulting in a mixed culture where these organisms represented ~60% of the total cells by targeted fluorescence in situ hybridization (FISH). Visual identification by FISH confirmed these organisms were not directly associated with Eukaryotes and electron cryomicroscopy of cells in the enrichment culture confirmed an ultrastructure consistent with the defining phenotypic property of Tenericutes, with a single membrane and no cell wall. On the basis of their unique gene content, phylogenetic placement and ultrastructure, we propose these organisms represent a novel class within the Tenericutes, and suggest the names Candidatus ‘Izimaplasma sp. HR1’ and Candidatus ‘Izimaplasma sp. HR2’ for the two genome representatives.
Reduced arginine availability and nitric oxide synthesis in cancer is related to impaired endogenous arginine synthesis
Authors: Engelen Mariëlle P.K.J. , Safar Ahmed M. , Bartter Thaddeus , Koeman Fari , Deutz Nicolaas E.P. 
Published: April 2016

Reduced plasma arginine (ARG) concentrations are found in various types of cancer. ARG and its product nitric oxide (NO) are important mediators in the immune function and the defense against tumour cells. It remains unclear whether the diminished systemic ARG availability in cancer is related to insufficient endogenous ARG synthesis, negatively affecting NO synthesis, and whether a dietary amino acid mixture is able to restore this. In 13 patients with advanced non-small cell lung cancer (NSCLC) and 11 healthy controls, whole body ARG and CIT (citrulline) rates of appearance were measured by stable isotope methodology before and after intake of a mixture of amino acids as present in whey protein. The conversions of CIT to ARG (indicator of de novo ARG synthesis) and ARG to CIT (marker of NO synthesis), and ARG clearance (reflecting ARG disposal capacity) were calculated. Plasma isotopic enrichments and amino acid concentrations were measured by LC–MS/MS. Conversions of CIT to ARG and ARG to CIT (P&lt;0.05), and CIT rate of appearance (P=0.07) were lower in NSCLC. ARG rate of appearance and clearance were comparable suggesting no enhanced systemic ARG production and disposal capacity in NSCLC. After intake of the mixture, ARG rate of appearance and concentration increased (P&lt;0.001), and ARG to CIT conversion was restored in NSCLC. In conclusion, an impaired endogenous ARG synthesis plays a role in the reduced systemic ARG availability and NO synthesis in advanced NSCLC. Nutritional approaches may restore systemic ARG availability and NO synthesis in cancer, but the clinical implication remains unclear.
Comparison of Outcomes following Mitral Valve Repair versus Replacement for Chronic Ischemic Mitral Regurgitation: A Meta-Analysis
Authors: Yun-dan Deng , Wen-jing Du , Xi-jun Xiao 
Published: April 2016

Background The selection of mitral valve surgery, including mitral valve repair and mitral valve replacement, is still an important dilemma for patients with chronic ischemic mitral regurgitation. We carry out a meta-analysis to evaluate the effectiveness and safety of mitral valve repair versus replacement for ischemic mitral regurgitation.
Methods We searched PubMed, Embase, the Cochrane Library, and Web of Science to identify studies from their inception to July 2015. A meta-analysis was performed using RevMan 5.3 software (Cochrane Collaboration, Oxford, United Kingdom). A random-effect model was used and sensitivity analysis was performed on studies reporting on operation after 2000, high-quality studies, and those studies reporting on more than 150 patients.
Result A total of 2,324 patients were identified from 10 retrospective studies. Mitral valve repair was associated with a trend toward lower operative mortality (odds ratio [OR] = 0.45; 95% confidence interval [CI]: 0.31–0.65; p < 0.0001) and higher recurrence of mitral regurgitation (OR = 5.89; 95% CI: 3.34–10.39; p < 0.00001). Five-year survival rate was similar between the two groups (OR = 1.20; 95% CI: 0.88–1.65; p = 0.25). No differences in reoperation, the incidence of acute renal failure and acute respiratory failure, the length of ICU stay, and the length of hospital stay were found.
Conclusion Mitral valve repair was associated with lower operative mortality but a higher recurrence of mitral regurgitation compared with mitral valve replacement. Owing to the limited quantity and quality of the included studies, this conclusion still needs to be further confirmed by conducting more high-quality, multicenter randomized controlled trials with large sample size.
Psychopathy and internalism
Authors: Kumar Victor 
Published: April 2016

AbstractDo psychopaths make moral judgments but lack motivation? Or are psychopaths’ judgments are not genuinely moral? Both sides of this debate seem to assume either externalist or internalist criteria for the presence of moral judgment. However, if moral judgment is a natural kind, we can arrive at a theory-neutral criterion for moral judgment. A leading naturalistic criterion suggests that psychopaths have an impaired capacity for moral judgment; the capacity is neither fully present nor fully absent. Psychopaths are therefore not counterexamples to internalism. Nonetheless, internalism is empirically problematic because it is unable to explain psychopaths’ moral deficits.
Clenbuterol changes phosphorylated FOXO1 localization and decreases protein degradation in the sartorius muscle of neonatal chicks
Authors: Shimamoto Saki , Ijiri Daichi , Nakashima Kazuki , Kawaguchi Mana , Ishimaru Yoshitaka , Furukawa Airi , Ohtsuka Akira 
Published: April 2016

Abstract
To investigate the intracellular signaling mechanisms by which clenbuterol reduces muscle protein degradation, we examined the phosphorylation level and intracellular localization of FOXO1 in the sartorius muscle of neonatal chicks. One-day-old chicks were given a single intraperitoneal injection of clenbuterol (0.1 mg/kg body weight). Three hours after injection, AKT protein was phosphorylated in the sartorius muscle by clenbuterol injection. Coincidentally, clenbuterol increased cytosolic level of phosphorylated FOXO1 protein, while it decreased nuclear level of FOXO1 protein in the sartorius muscle. Furthermore, clenbuterol decreased the expression of mRNAs for muscle-specific ubiquitin ligases (atrogin-1/MAFbx and MuRF1) in the sartorius muscle accompanied by decreased plasma 3-methylhistidine concentration, an index of muscle protein degradation, at 3 h after injection. These results suggested that, in the sartorius muscle of the chicks, clenbuterol changed the intracellular localization of phosphorylated FOXO1, and consequently decreased protein degradation via suppressing the expression of genes encoding muscle-specific ubiquitin ligases.
MGEScan: a Galaxy-based system for identifying retrotransposons in genomes
Authors: Lee Hyungro , Lee Minsu , Mohammed Ismail Wazim , Rho Mina , Fox Geoffrey C. , Oh Sangyoon , Tang Haixu 
Published: April 2016

Abstract
Summary: MGEScan-long terminal repeat (LTR) and MGEScan-non-LTR are successfully used programs for identifying LTRs and non-LTR retrotransposons in eukaryotic genome sequences. However, these programs are not supported by easy-to-use interfaces nor well suited for data visualization in general data formats. Here, we present MGEScan, a user-friendly system that combines these two programs with a Galaxy workflow system accelerated with MPI and Python threading on compute clusters. MGEScan and Galaxy empower researchers to identify transposable elements in a graphical user interface with ready-to-use workflows. MGEScan also visualizes the custom annotation tracks for mobile genetic elements in public genome browsers. A maximum speed-up of 3.26× is attained for execution time using concurrent processing and MPI on four virtual cores. MGEScan provides four operational modes: as a command line tool, as a Galaxy Toolshed, on a Galaxy-based web server, and on a virtual cluster on the Amazon cloud.
Availability and implementation: MGEScan tutorials and source code are available at http://mgescan.readthedocs.org/
Contact: hatang@indiana.edu or syoh@ajou.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Immune checkpoint inhibition in ovarian cancer
Authors: Hamanishi Junzo , Mandai Masaki , Konishi Ikuo 
Published: April 2016

AbstractRecent studies have shown that tumor cells acquire escape mechanisms to evade host immunity in the tumor microenvironment. Two key immune checkpoint pathways mediated by immunosuppressive co-signaling, the first via programmed cell death 1 (PD-1) and PD-1 ligand 1 (PD-1/PD-L1) and the second via CTLA-4 and B7 (CTLA-4/B7), have been previously described. Several clinical trials have revealed an outstanding anti-tumor efficacy of immune checkpoint inhibitors (anti-CTLA-4 antibody, anti-PD-1 antibody and/or anti-PD-L1 antibody) in patients with various types of solid malignancies, including non-small cell lung cancer, melanoma, renal cell cancer and ovarian cancer. In this review, we examine pre-clinical studies that described the local immune status and immune checkpoint signals in ovarian cancer, highlight recent clinical trials that evaluated immune checkpoint inhibitors against ovarian cancer and discuss the clinical issues regarding immune checkpoint inhibitors.
Retrospective Study of Cryptococcal Meningitis With Elevated Minimum Inhibitory Concentration to Fluconazole in Immunocompromised Patients
Authors: Nasri Hashem , Kabbani Sarah , Bou Alwan Melhim , Wang Yun F. , Rebolledo Paulina A. , Kraft Colleen S. , Nguyen Minh L. , Anderson Albert M. , Rouphael Nadine 
Published: April 2016

Abstract
Background.  Mortality for cryptococcal meningitis remains significant, in spite of available treatment. Resistance to first-line maintenance therapy, particularly fluconazole, has been reported.
Methods.  A retrospective chart review was performed on immunocompromised patients with cryptococcal meningitis, who had susceptibility testing performed between January 2001 and December 2011, at 3 hospitals in Atlanta, Georgia.
Results.  A total of 35 immunocompromised patients with cryptococcal meningitis were identified, 13 (37.1%) of whom had an elevated minimum inhibitory concentration (MIC) to fluconazole (MIC ≥16 µg/mL). Eighty percent of patients were males with African American predominance, the median age was 37 years, and 80% of the patients were human immunodeficiency virus (HIV) positive. Subsequent recurrence of cryptococcal meningitis was more likely in HIV patients compared with solid organ transplant patients (P = .0366). Overall, there was a statistically significant increase in an elevated MIC to fluconazole in patients who had a history of prior azole use (odds ratio, 10.12; 95% confidence interval, 2.04–50.16). Patients with an elevated MIC to fluconazole and those with a high cerebrospinal fluid cryptococcal antigen load (≥1:512) were more likely to have central nervous system complications (P = .0358 and P = .023, respectively). Although no association was observed between an elevated MIC to fluconazole and mortality, those who received voriconazole or high-dose fluconazole (≥800 mg) for maintenance therapy were more likely to survive (P = .0288).
Conclusions.  Additional studies are required to further investigate the morbidity and mortality associated with an elevated MIC to fluconazole in cryptococcal meningitis, to determine when it is appropriate to perform susceptibility testing, and to evaluate its cost effectiveness.
Accurate measurement of the effects of all amino-acid mutations to influenza hemagglutinin
Authors: Doud Michael B. , Bloom Jesse D. 
Published: April 2016

AbstractInfluenza genes evolve mostly via point mutations, and so knowing the effect of every amino-acid mutation provides information about evolutionary paths available to the virus. We previously used high-throughput mutagenesis and deep sequencing to estimate the effects of all mutations to an H1 influenza hemagglutinin on viral replication in cell culture (Thyagarajan and Bloom, 2014); however, these measurements suffered from sub-stantial noise. Here we describe advances that greatly improve the accuracy and reproducibility of our measurements. The largest improvements come from using a helper virus to reduce bottlenecks when generating viruses from plasmids. Our measurements confirm that antigenic sites on the globular head of hemagglutinin are highly tolerant of mutations. However, other regions – including stalk epitopes targeted by broadly neutralizing antibodies – have a limited capacity to evolve. The ability to accurately measure the effects of all influenza mutations should enhance efforts to understand and predict viral evolution.
Crystal structures of (Z)-5-[2-(benzo[b]thiophen-2-yl)-1-(3,5-dimethoxyphenyl)ethenyl]-1H-tetrazole and (Z)-5-[2-(benzo[b]thiophen-3-yl)-1-(3,4,5-trimethoxyphenyl)ethenyl]-1H-tetrazole
Authors: Penthala Narsimha Reddy , Yadlapalli Jaishankar K. B. , Parkin Sean , Crooks Peter A. 
Published: April 2016

(Z)-5-[2-(Benzo[b]thiophen-2-yl)-1-(3,5-dimethoxyphenyl)ethenyl]-1H-tetrazole methanol monosolvate, C19H16N4O2S·CH3OH, (I), was prepared by the reaction of (Z)-3-(benzo[b]thiophen-2-yl)-2-(3,5-dimethoxyphenyl)acrylonitrile with tributyltin azideviaa [3 + 2]cycloaddition azide condensation reaction. The structurally related compound (Z)-5-[2-(benzo[b]thiophen-3-yl)-1-(3,4,5-trimethoxyphenyl)ethenyl]-1H-tetrazole, C20H18N4O3S, (II), was prepared by the reaction of (Z)-3-(benzo[b]thiophen-3-yl)-2-(3,4,5-trimethoxyphenyl)acrylonitrile with tributyltin azide. Crystals of (I) have two molecules in the asymmetric unit (Z′ = 2), whereas crystals of (II) haveZ′ = 1. The benzothiophene rings in (I) and (II) are almost planar, with r.m.s deviations from the mean plane of 0.0084 and 0.0037 Å in (I) and 0.0084 Å in (II). The tetrazole rings of (I) and (II) make dihedral angles with the mean planes of the benzothiophene rings of 88.81 (13) and 88.92 (13)° in (I), and 60.94 (6)° in (II). The dimethoxyphenyl and trimethoxyphenyl rings make dihedral angles with the benzothiophene rings of 23.91 (8) and 24.99 (8)° in (I) and 84.47 (3)° in (II). In both structures, molecules are linked into hydrogen-bonded chains. In (I), these chains involve both tetrazole and methanol, and are parallel to thebaxis. In (II), molecules are linked into chains parallel to theaaxis by N—H...N hydrogen bonds between adjacent tetrazole rings.
Reverse innovation antecedents
Authors: Borini Felipe Mendes , Costa Sidney , Oliveira Junior Moacir de Miranda 
Published: April 2016

Purpose
– The purpose of this paper is to determine the antecedents of reverse innovation.

Design/methodology/approach
– Data were collected through an online survey administered using telephone assistance and sent to the 1,000 largest (in terms of revenue) foreign subsidiaries in Brazil. The responding companies numbered 167. For the data analysis, the authors chose the statistical technique of structural equation modeling.

Findings
– The paper shows that reverse innovation is related to headquarters’ support, autonomy, and integration. Specifically, the authors consider the power of strategic integration between headquarters and subsidiaries as one of the important antecedents of reverse innovation.

Practical implications
– Integration has an important role to reverse innovation. In order to stimulate integration, the executive of a subsidiary can make such efforts as invest in the mechanism of the relationship and exchange knowledge with headquarters. For example, it is recommended to encourage travel to the headquarters to more accurately align perceptions of parent and subsidiary executives and to utilize expatriates from headquarters to provide knowledge to subsidiaries about the main processes of the company and to promote subsidiary innovations.

Originality/value
– Literature contains some articles discussing and relating some cases of reverse innovation. However, this paper shows the organizational structure necessary for reverse innovation.
Is collective efficiency in subsistence clusters a growth strategy? The case of the wood industry in Oberá, Argentina
Authors: F-Jardon Carlos M. , Pagani Regina Negri 
Published: April 2016

Purpose
– Small and medium enterprises (SMEs), which main objective is to satisfy the basic needs of the entrepreneur, when geographically concentrated make up subsistence clusters. The purpose of this paper is to analyze collective efficiency in subsistence clusters as growth strategy and how is the process through which the relational capital and territorial proximity altogether improve performance of firms.

Design/methodology/approach
– The research uses partial least squares techniques applied to a sample of 113 SMEs of wood industry in Oberá, Argentina.

Findings
– SMEs in subsistence clusters can use relational capital and territory as resources to generate competitive advantages. These competitive advantages foster performance. In consequence, collective efficiency appears as growth strategy in subsistence SMEs.

Research limitations/implications
– Data are cross-sectional and in a conjuncture of economy expansion, future research should monitor the sample of firms using panel data to assess the development of relations. Sample is in a particular region and sector and generalizations should be done carefully.

Practical implications
– SMEs probably should integrate and share industrial and business structures to develop systemic competitive advantages with a collective character. SMEs should leverage their spatial interaction to build trust and establish networks of cooperation that will be the source of their collective efficiency. These collaboration networks should base in the local knowledge.

Social implications
– Subsistence SMEs have strong impact on the most disadvantaged areas in developing countries. Growth strategies to professionalize these SMEs will have a major impact on the endogenous development of those territories.

Originality/value
– The research provides a mechanism through which collective efficiency leads to better performance for subsistence SMEs.
Towards a calculative model of supply chain enabling IT implementation
Authors: Power Damien , Gruner Richard L. 
Published: April 2016

Purpose
Research provides inconsistent findings regarding motivations for the implementation of information technology (IT) in the supply chain. Two main theoretical perspectives emerge from the literature. The first predicts a logical progressive implementation of technology over time. The second views situational factors as moderating progressive implementation over time. We propose a third, calculative IT implementation model and empirically assess the validity of these diverging models.

Design/methodology/approach
We took a qualitative, theory-testing approach. Cross-sectional surveys conducted in 2001 and 2011 – yielding responses from 62 matching firms – showed dynamic IT implementation patterns over time and allowed the selection of nine case studies for comparison.

Findings
Results provide substantial support for a calculative model alongside the situational and progressive perspectives. This model addresses three problematic assumptions that underpin the progressive and situational perspectives: (1) that IT implementation will follow logical stages, (2) that implementation of these technologies represents a rational choice, and (3) that managers implement these technologies to improve the performance of entire supply chains.

Research limitations/implications
The empirical investigations were limited to Australian manufacturers. Further studies should extend the generalisability of the findings and study the phenomenon in different contexts.

Practical implications
The study enhances practitioners’ understanding of the difficulties and complexities of IT implementation decisions among supply chain partners. Such an understanding may motivate managers to pursue IT adoption that goes beyond addressing locally focused performance metrics.

Originality/value
Our findings make a significant theoretical and practical contribution and provide the basis for isolating and operationalising the calculative model for further empirical testing.