bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Agarolytic β-Galactosidase Acts on Agarooligosaccharides for Complete Hydrolysis of Agarose into Monomers
Authors: Lee Chan Hyoung , Kim Hee Taek , Yun Eun Ju , Lee Ah Reum , Kim Sa Rang , Kim Jae-Han , Choi In-Geol , Kim Kyoung Heon 
Published: July 2014

ABSTRACT

Marine red macroalgae have emerged to be renewable biomass for the production of chemicals and biofuels, because carbohydrates that form the major component of red macroalgae can be hydrolyzed into fermentable sugars. The main carbohydrate in red algae is agarose, and it is composed of
d
-galactose and 3,6-anhydro-
l
-galactose (AHG), which are alternately bonded by β1-4 and α1-3 linkages. In this study, a novel β-galactosidase that can act on agarooligosaccharides (AOSs) to release galactose was discovered in a marine bacterium (
Vibrio
sp. strain EJY3); the enzyme is annotated as
Vibrio
sp. EJY3 agarolytic β-galactosidase (
Vej
ABG). Unlike the
lacZ
-encoded β-galactosidase from
Escherichia coli
,
Vej
ABG does not hydrolyze common substrates like lactose and can act only on the galactose moiety at the nonreducing end of AOS. The optimum pH and temperature of
Vej
ABG on an agarotriose substrate were 7 and 35°C, respectively. Its catalytic efficiency with agarotriose was also similar to that with agaropentaose or agaroheptaose. Since agarotriose lingers as the unreacted residual oligomer in the currently available saccharification system using β-agarases and acid prehydrolysis, the agarotriose-hydrolyzing capability of this novel β-galactosidase offers an enormous advantage in the saccharification of agarose or agar in red macroalgae for its use as a biomass feedstock for fermentable sugar production.
Dead or Alive: Molecular Assessment of Microbial Viability
Authors: Cangelosi Gerard A. , Meschke John S. 
Published: July 2014

ABSTRACT
Nucleic acid-based analytical methods, ranging from species-targeted PCRs to metagenomics, have greatly expanded our understanding of microbiological diversity in natural samples. However, these methods provide only limited information on the activities and physiological states of microorganisms in samples. Even the most fundamental physiological state, viability, cannot be assessed cross-sectionally by standard DNA-targeted methods such as PCR. New PCR-based strategies, collectively called molecular viability analyses, have been developed that differentiate nucleic acids associated with viable cells from those associated with inactivated cells. In order to maximize the utility of these methods and to correctly interpret results, it is necessary to consider the physiological diversity of life and death in the microbial world. This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology.
The Contribution of Candida albicans Vacuolar ATPase Subunit V
1
B, Encoded by
VMA2
, to Stress Response, Autophagy, and Virulence Is Independent of Environmental pH
Authors: Rane Hallie S. , Bernardo Stella M. , Hayek Summer R. , Binder Jessica L. , Parra Karlett J. , Lee Samuel A. 
Published: July 2014

ABSTRACT

Candida albicans
vacuoles are central to many critical biological processes, including filamentation and
in vivo
virulence. The V-ATPase proton pump is a multisubunit complex responsible for organellar acidification and is essential for vacuolar biogenesis and function. To study the function of the V
1
B subunit of
C. albicans
V-ATPase, we constructed a tetracycline-regulatable
VMA2
mutant, tetR-
VMA2
. Inhibition of
VMA2
expression resulted in the inability to grow at alkaline pH and altered resistance to calcium, cold temperature, antifungal drugs, and growth on nonfermentable carbon sources. Furthermore, V-ATPase was unable to fully assemble at the vacuolar membrane and was impaired in proton transport and ATPase-specific activity.
VMA2
repression led to vacuolar alkalinization in addition to abnormal vacuolar morphology and biogenesis. Key virulence-related traits, including filamentation and secretion of degradative enzymes, were markedly inhibited. These results are consistent with previous studies of
C. albicans
V-ATPase; however, differential contributions of the V-ATPase V
o
and V
1
subunits to filamentation and secretion are observed. We also make the novel observation that inhibition of
C. albicans
V-ATPase results in increased susceptibility to osmotic stress. Notably, V-ATPase inhibition under conditions of nitrogen starvation results in defects in autophagy. Lastly, we show the first evidence that V-ATPase contributes to virulence in an acidic
in vivo
system by demonstrating that the tetR-
VMA2
mutant is avirulent in a
Caenorhabditis elegans
infection model. This study illustrates the fundamental requirement of V-ATPase for numerous key virulence-related traits in
C. albicans
and demonstrates that the contribution of V-ATPase to virulence is independent of host pH.
Adeno-Associated Virus Type 2 Wild-Type and Vector-Mediated Genomic Integration Profiles of Human Diploid Fibroblasts Analyzed by Third-Generation PacBio DNA Sequencing
Authors: Hüser Daniela , Gogol-Döring Andreas , Chen Wei , Heilbronn Regine 
Published: July 2014

ABSTRACT

Genome-wide analysis of adeno-associated virus (AAV) type 2 integration in HeLa cells has shown that wild-type AAV integrates at numerous genomic sites, including AAVS1 on chromosome 19q13.42. Multiple GAGY/C repeats, resembling consensus AAV Rep-binding sites are preferred, whereas
rep
-deficient AAV vectors (rAAV) regularly show a random integration profile. This study is the first study to analyze wild-type AAV integration in diploid human fibroblasts. Applying high-throughput third-generation PacBio-based DNA sequencing, integration profiles of wild-type AAV and rAAV are compared side by side. Bioinformatic analysis reveals that both wild-type AAV and rAAV prefer open chromatin regions. Although genomic features of AAV integration largely reproduce previous findings, the pattern of integration hot spots differs from that described in HeLa cells before. DNase-Seq data for human fibroblasts and for HeLa cells reveal variant chromatin accessibility at preferred AAV integration hot spots that correlates with variant hot spot preferences. DNase-Seq patterns of these sites in human tissues, including liver, muscle, heart, brain, skin, and embryonic stem cells further underline variant chromatin accessibility. In summary, AAV integration is dependent on cell-type-specific, variant chromatin accessibility leading to random integration profiles for rAAV, whereas wild-type AAV integration sites cluster near GAGY/C repeats.

IMPORTANCE
Adeno-associated virus type 2 (AAV) is assumed to establish latency by chromosomal integration of its DNA. This is the first genome-wide analysis of wild-type AAV2 integration in diploid human cells and the first to compare wild-type to recombinant AAV vector integration side by side under identical experimental conditions. Major determinants of wild-type AAV integration represent open chromatin regions with accessible consensus AAV Rep-binding sites. The variant chromatin accessibility of different human tissues or cell types will have impact on vector targeting to be considered during gene therapy.
A methodology for a minimum data set for rare diseases to support national centers of excellence for healthcare and research
Authors: Choquet Rémy , Maaroufi Meriem , de Carrara Albane , Messiaen Claude , Luigi Emmanuel , Landais Paul 
Published: July 2014

Abstract
Background Although rare disease patients make up approximately 6–8% of all patients in Europe, it is often difficult to find the necessary expertise for diagnosis and care and the patient numbers needed for rare disease research. The second French National Plan for Rare Diseases highlighted the necessity for better care coordination and epidemiology for rare diseases. A clinical data standard for normalization and exchange of rare disease patient data was proposed. The original methodology used to build the French national minimum data set (F-MDS-RD) common to the 131 expert rare disease centers is presented.
Methods To encourage consensus at a national level for homogeneous data collection at the point of care for rare disease patients, we first identified four national expert groups. We reviewed the scientific literature for rare disease common data elements (CDEs) in order to build the first version of the F-MDS-RD. The French rare disease expert centers validated the data elements (DEs). The resulting F-MDS-RD was reviewed and approved by the National Plan Strategic Committee. It was then represented in an HL7 electronic format to maximize interoperability with electronic health records.
Results The F-MDS-RD is composed of 58 DEs in six categories: patient, family history, encounter, condition, medication, and questionnaire. It is HL7 compatible and can use various ontologies for diagnosis or sign encoding. The F-MDS-RD was aligned with other CDE initiatives for rare diseases, thus facilitating potential interconnections between rare disease registries.
Conclusions The French F-MDS-RD was defined through national consensus. It can foster better care coordination and facilitate determining rare disease patients’ eligibility for research studies, trials, or cohorts. Since other countries will need to develop their own standards for rare disease data collection, they might benefit from the methods presented here.
Predicting return to play after hamstring injuries
Authors: Moen M H , Reurink G , Weir A , Tol J L , Maas M , Goudswaard G J 
Published: July 2014

BackgroundPrevious studies on the prognostic value of clinical and MRI parameters for the time to return to play (TTRTP) in acute hamstring injuries showed only limited to moderate evidence for the various investigated parameters. Some studies had multiple methodological limitations, including retrospective designs and the use of univariate analysis only. The aim of this study was to assess the prognostic value of clinical and MRI parameters for TTRTP using multivariate analysis.Methods28 clinical and MRI parameters were prospectively investigated for an association with TTRTP in 80 non-professional athletes with MRI positive hamstring injuries undergoing a standardised rehabilitation programme. The association between possible prognostic parameters and TTRTP was assessed with a multivariate linear regression model. Parameters that had a p value <0.2 on univariate testing were included in this model.Results74 athletes were available for analysis. A total of nine variables met the criteria for the multivariate analysis: intensity of sports, level of sports, self-predicted TTRTP by the athlete, length of discomfort on palpation, deficit in passive straight leg raise, pain score on isometric knee flexion, isometric knee flexion strength deficit and distance of the proximal pole of the MRI hyperintensity to the tuber ischiadicum. Of these, only self-predicted TTRTP by the athlete and a passive straight leg raise deficit remained significantly associated with TTRTP after stepwise logistic regression.ConclusionsThe clinical parameters self-predicted TTRTP and passive straight leg raise deficit are independently associated with the TTRTP. MRI parameters in grade 1 and 2 hamstring injuries, as described in the literature, are not associated with TTRTP. For clinical practice, prognosis of the TTRTP in these injuries should better be based on clinical parameters.
Prevalence of birefringent crystals in cardiac and prostatic tissues, an observational study
Authors: Park Jane J , Roudier Martine P , Soman Divya , Mokadam Nahush A , Simkin Peter A 
Published: July 2014

IntroductionThe prevalence of urate crystals in residual tissue samples from coronary arteries, aortic valves and prostate glands was assessed.MethodsAlcohol-fixed coronary arteries from 55 explanted hearts, alcohol-fixed aortic valves collected from 75 valve replacement surgeries and 40 frozen, unfixed prostate specimens resected during cancer surgery were examined for birefringent crystals with polarising microscopy.ResultsIn the 55 explanted hearts, 6 (10.9%) contained a coronary artery with birefringent crystals. One of the 75 aortic valves (1.4%) contained negatively and positively birefringent crystals. Nineteen of the 40 (47.5%) prostates contained birefringent crystals.ConclusionsWe found that a remarkable percentage of coronary arteries and prostate specimens contained birefringent crystals. Crystal presence is an obvious prerequisite for possible crystal induced-inflammation in these tissues, just as similar crystals elicit a gouty inflammatory cascade in synovial joints. Further studies are necessary to determine whether urate crystals may play this role in these tissues and, if so, to establish whether urate-lowering therapy may be beneficial in prostatitis and coronary disease.
‘It sounds like a great idea but…’: a qualitative study of GPs’ attitudes towards the development of a national diabetes register
Authors: Mc Hugh Sheena M , O'Mullane Monica , Perry Ivan J , Bradley Colin 
Published: July 2014

ObjectiveThe aim of this study was to investigate the attitudes of general practitioners (GPs) to the development of a national diabetes register as a way of improving the quality of care.DesignQualitative study using semistructured interviews.SettingGeneral practice, Ireland.ParticipantsPurposive sample of 29 GPs and two practice nurses. Participants’ practices varied by (a) location (rural/urban), (b) size (single-handed/group practice) and (c) extent of computerisation.MethodsThe semistructured topic guide focused on experiences of change in the health system at a local and national level and attitudes towards the development of a national diabetes register. Analysis was conducted using the Framework approach.ResultsParticipants were sceptical about the development of a national diabetes register. The main advantage was ‘knowing the numbers’ for epidemiological and policy purposes. However, participants questioned the benefits for their practice and patients. There were concerns that it would drain resources from other priorities and distract from patient management. These attitudes were strongly influenced by previous experience of change in the health system. Participants felt that remuneration would be necessary to ensure full engagement, reflecting wider frustrations with payment structures for general practice. There was a sense of wariness towards health service administration which was not specific to diabetes care but which coloured some participants’ attitudes towards a national register. In contrast, participants referred to positive experiences of change at a local level, facilitated by a ‘practice ethos’ and professional leadership.ConclusionsThis study highlights the growing sense of scepticism and inertia towards change within the health system. This inertia stems from previous experience and the competing demands of maintaining versus improving care in a system with dwindling resources.
The WHO surgical safety checklist: survey of patients’ views
Authors: Russ Stephanie Jane , Rout Shantanu , Caris Jochem , Moorthy Krishna , Mayer Erik , Darzi Ara , Sevdalis Nick , Vincent Charles 
Published: July 2014

BackgroundEvidence suggests that full implementation of the WHO surgical safety checklist across NHS operating theatres is still proving a challenge for many surgical teams. The aim of the current study was to assess patients’ views of the checklist, which have yet to be considered and could inform its appropriate use, and influence clinical buy-in.MethodPostoperative patients were sampled from surgical wards at two large London teaching hospitals. Patients were shown two professionally produced videos, one demonstrating use of the WHO surgical safety checklist, and one demonstrating the equivalent periods of their operation before its introduction. Patients’ views of the checklist, its use in practice, and their involvement in safety improvement more generally were captured using a bespoke 19-item questionnaire.Results141 patients participated. Patients were positive towards the checklist, strongly agreeing that it would impact positively on their safety and on surgical team performance. Those worried about coming to harm in hospital were particularly supportive. Views were divided regarding hearing discussions around blood loss/airway before their procedure, supporting appropriate modifications to the tool. Patients did not feel they had a strong role to play in safety improvement more broadly.ConclusionsIt is feasible and instructive to capture patients’ views of the delivery of safety improvements like the checklist. We have demonstrated strong support for the checklist in a sample of surgical patients, presenting a challenge to those resistant to its use.
Interaction of arc magmas with subvolcanic hydrothermal systems: insights from compositions and metasomatic textures of olivine crystals in fresh basalts of Daisen and Mengameyama, Western Honshu, Japan
Authors: Zellmer Georg F. , Hwang Shyh-Lung , Sakamoto Naoya , Iizuka Yoshiyuki , Harada Sakiko , Kimura Jun-Ichi , Tamura Yoshihiko , Yurimoto Hisayoshi 
Published: July 2014

Abstract

Pleistocene basalts from Daisen and Mengameyama in the SW Japan volcanic arc of western Honshu are characterized by an abundance of olivine crystals with Fe-rich rims. At Daisen, these have previously been interpreted to have formed from their host melt by equilibrium crystal fractionation and by disequilibrium fractionation during supercooling. Here we use combined electron probe microanalysis, isotopography, transmission electron microscopy and selected area electron diffraction to show that crystal rims are significantly enriched in aluminium (up to
c.
1 wt%) and hydrogen (up to
c.
10 000 ppm) hosted in oriented low-density amorphous domains. These domains are interpreted to have formed by melting of deuteric and/or post-deuteric metasomatic alteration minerals upon uptake of older olivine crystals into fresh, initially aphyric host melts up to a few hours prior to eruption. It is argued that uptake of variably altered crystals into initially aphyric or sparsely phyric melts may be a common process at subduction zones, and can account for typical disequilibrium textures displayed by arc magmas erupted in SW Japan and elsewhere. Analyses of the altered crystal cargo in arc volcanic rocks therefore provides an important tool for understanding subvolcanic hydrothermal systems and the interaction of ascending melts with such systems.

Supplementary material:

Olivine mineral chemistry data from two typical Daisen basalts and one typical Mengameyama basalt, and a figure showing the locations of all focussed ion beam (FIB) sections studied here, are available at
http://www.geolsoc.org.uk/SUP18760
.
Synthesis and Crystal Structure of 1-Methyl-3-(2-pyridyl)imidazolium Hexafluorophosphate
Authors: Kandasamy Elango 
Published: July 2014

Compound 1-Methyl-3-(2-pyridyl)imidazolium hexafluorophosphate was crystallized in monoclinic system with space group P21/c and unit cell parameters a=7.3740(8) Å, b=15.5931(16) Å, c=10.4787(11) Å, β= 105.3102°, and  ν=1162.12Å3. The obtained solid state structure of 1-Methyl-3-(2-pyridyl)imidazolium hexafluorophosphate shows CH⋯F type weak interactions and was analyzed.
Optimal Effector Functions in Human Natural Killer Cells Rely upon Autocrine Bone Morphogenetic Protein Signaling
Authors: Robson Neil C. , Hidalgo Laura , McAlpine Tristan , Wei Heng , Martínez Víctor G. , Entrena Ana , Melen Gustavo J. , MacDonald Andrew S. , Phythian-Adams Alexander , Sacedón Rosa , Maraskovsky Eugene , Cebon Jonathan , Ramírez Manuel , Vicente Angeles , Varas Alberto 
Published: July 2014

AbstractNatural killer (NK) cells are critical for innate tumor immunity due to their specialized ability to recognize and kill neoplastically transformed cells. However, NK cells require a specific set of cytokine-mediated signals to achieve optimal effector function. Th1-associated cytokines promote effector functions that are inhibited by the prototypic Th2 cytokine IL4 and the TGFβ superfamily members TGFβ1 and activin-A. Interestingly, the largest subgroup of the TGFβ superfamily are the bone morphogenetic proteins (BMP), but the effects of BMP signaling on NK cell effector functions have not been evaluated. Here, we demonstrate that blood-circulating NK cells express type I and II BMP receptors, BMP-2 and BMP-6 ligands, and phosphorylated isoforms of Smad-1/-5/-8, which mediate BMP family member signaling. In opposition to the inhibitory effects of TGFβ1 or activin-A, autocrine BMP signaling was supportive to NK cell function. Mechanistic investigations in cytokine and TLR-L–activated NK cells revealed that BMP signaling optimized IFNγ and global cytokine and chemokine production, phenotypic activation and proliferation, and autologous dendritic cell activation and target cytotoxicity. Collectively, our findings identify a novel auto-activatory pathway that is essential for optimal NK cell effector function, one that might be therapeutically manipulated to help eradicate tumors. Cancer Res; 74(18); 5019–31. ©2014 AACR.
Novel Drug Candidates for the Treatment of Metastatic Colorectal Cancer through Global Inverse Gene-Expression Profiling
Authors: van Noort Vera , Schölch Sebastian , Iskar Murat , Zeller Georg , Ostertag Kristina , Schweitzer Christine , Werner Kristin , Weitz Jürgen , Koch Moritz , Bork Peer 
Published: July 2014

Abstract
Drug-induced gene-expression profiles that invert disease profiles have recently been illustrated to be a starting point for drug repositioning. In this study, we validate this approach and focus on prediction of novel drugs for colorectal cancer, for which there is a pressing need to find novel antimetastatic compounds. We computationally predicted three novel and still unknown compounds against colorectal cancer: citalopram (an antidepressant), troglitazone (an antidiabetic), and enilconazole (a fungicide). We verified the compounds by in vitro assays of clonogenic survival, proliferation, and migration and in a subcutaneous mouse model. We found evidence that the mode of action of these compounds may be through inhibition of TGFβ signaling. Furthermore, one compound, citalopram, reduced tumor size as well as the number of circulating tumor cells and metastases in an orthotopic mouse model of colorectal cancer. This study proposes citalopram as a potential therapeutic option for patients with colorectal cancer, illustrating the potential of systems pharmacology. Cancer Res; 74(20); 5690–9. ©2014 AACR.