bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of Nitrilotriacetate-Degrading Aminobacter aminovorans KCTC 2477
T
Authors: Lee Sang-Heon , Choe Hanna , Nasir Arshan , Park Doo-Sang , Kim Kyung Mo 
Published: December 2016

ABSTRACT

Aminobacter aminovorans
is a Gram-negative, pleomorphic rod-shaped, flagellated, and obligately aerobic bacterium that was isolated from soil. Here, we report the complete genome sequence of
A. aminovorans
KCTC 2477
T
, which degrades nitrilotriacetate-metal complexes and iminodiacetate, a metabolic intermediate of nitrilotriacetate.
Draft Genome Sequence of the Anaerobic Ammonium-Oxidizing Bacterium “
Candidatus
Brocadia sp. 40”
Authors: Ali Muhammad , Haroon Mohamed Fauzi , Narita Yuko , Zhang Lei , Rangel Shaw Dario , Okabe Satoshi , Saikaly Pascal E. 
Published: December 2016

ABSTRACT

The anaerobic ammonium-oxidizing (anammox) bacterium “
Candidatus
Brocadia sp. 40” demonstrated the fastest growth rate compared to others in this taxon. Here, we report the 2.93-Mb draft genome sequence of this bacterium, which has 2,565 gene-coding regions, 41 tRNAs, and a single
rrn
operon.
Nearly Complete Genome Sequences of Two
Mimivirus
Strains Isolated from a Japanese Freshwater Pond and River Mouth
Authors: Takemura Masaharu , Mikami Tatsuya , Murono Shingo 
Published: December 2016

ABSTRACT

Members of the
Mimiviridae
family are large DNA viruses that infect
Acanthamoeba
cells. Here, we report the genome sequences of two new
Mimiviridae
family members, isolated from water samples from Shirakoma Pond and the mouth of the Arakawa River in Japan, with nearly complete genome sizes of 1,182,849 and 1,182,801 bp, respectively.
A new attraction-detachment model for explaining flow sliding in clay-rich tephras
Authors: Kluger Max O. , Moon Vicki G. , Kreiter Stefan , Lowe David J. , Churchman G.J. , Hepp Daniel A. , Seibel David , Jorat M. Ehsan , Mörz Tobias 
Published: December 2016

Abstract
Altered pyroclastic (tephra) deposits are highly susceptible to landsliding, leading to fatalities and property damage every year. Halloysite, a low-activity clay mineral, is commonly associated with landslide-prone layers within altered tephra successions, especially in deposits with high sensitivity, which describes the post-failure strength loss. However, the precise role of halloysite in the development of sensitivity, and thus in sudden and unpredictable landsliding, is unknown. Here we show that an abundance of mushroom cap–shaped (MCS) spheroidal halloysite governs the development of sensitivity, and hence proneness to landsliding, in altered rhyolitic tephras, North Island, New Zealand. We found that a highly sensitive layer, which was involved in a flow slide, has a remarkably high content of aggregated MCS spheroids with substantial openings on one side. We suggest that short-range electrostatic and van der Waals interactions enabled the MCS spheroids to form interconnected aggregates by attraction between the edges of numerous paired silanol and aluminol sheets that are exposed in the openings and the convex silanol faces on the exterior surfaces of adjacent MCS spheroids. If these weak attractions are overcome during slope failure, multiple, weakly attracted MCS spheroids can be separated from one another, and the prevailing repulsion between exterior MCS surfaces results in a low remolded shear strength, a high sensitivity, and a high propensity for flow sliding. The evidence indicates that the attraction-detachment model explains the high sensitivity and contributes to an improved understanding of the mechanisms of flow sliding in sensitive, altered tephras rich in spheroidal halloysite.
The dynamics of gold in regolith change with differing environmental conditions over time
Authors: Anand Ravi , Lintern Mel , Hough Rob , Noble Ryan , Verrall Mike , Salama Walid , Balkau Jens , Radford Nigel 
Published: December 2016

Abstract
Significant Au discoveries are becoming less common because the remaining prospective, underexplored areas are obscured by transported cover. At Moolart Well (Western Australia), secondary Au deposits hosted in transported pisolitic ferricrete and saprolite are overlain by younger transported cover. Here, we show how Au has been, and is being, dispersed and concentrated in these deposits and the overlying younger transported cover and biota during the evolution of the landscape. We identified coarse (&gt;400 µm), Ag-rich, primary, angular Au accumulated residually along with some precipitated, Ag-poor (&lt;0.5% Ag) secondary Au in saprolite. Gold enrichment in the pisolitic ferricrete is mostly secondary nanometer- to micron-sized spheres, chains, triangles, and wires in precipitates of organic carbon (C), goethite, kaolinite, and amorphous Si within cortices, cracks, and cavities in pisoliths. Spectacular secondary Au as clumps and larger clusters, not previously reported in ferricrete, occurs in organic C-rich zones of the cortices and cavities of pisoliths, implying a role for organic matter in their formation. To our knowledge, the organic C–Au relationship in pisolitic ferricrete described in this study has not been documented previously. We propose that minor Au was recycled from the pisolitic ferricrete formed during humid conditions (Miocene) into an overlying silicified subsoil that was formed in an arid climate of the mid-Miocene to the present. The presence of Au in vegetation (Acacia aneura) and termite mounds indicates active dispersion.
Economic valuation of the impact of a large surgical charity using the value of lost welfare approach
Authors: Corlew Daniel Scott , Alkire Blake C , Poenaru Dan , Meara John G , Shrime Mark G 
Published: December 2016

BackgroundThe assessment of the economic burden of surgical disease is integral to determining allocation of resources for health globally. We estimate the economic gain realised over an 11-year period resulting from a vertical surgical programme addressing cleft lip (CL) and cleft palate (CP).MethodsThe database from a large non-governmental organisation (Smile Train) over an 11-year period was analysed. Incidence-based disability-adjusted life years (DALYs) averted through the programme were calculated, discounted 3%, using disability weights from the Global Burden of Disease (GBD) study and an effectiveness factor for each surgical intervention. The effectiveness factor allowed for the lack of 100% resolution of the disability from the operation. We used the value of lost welfare approach, based on the concept of the value of a statistical life (VSL), to assess the economic gain associated with each operation. Using income elasticities (IEs) tailored to the income level of each country, a country-specific VSL was calculated and the VSL-year (VSLY) was determined. The VSLY is the economic value of a DALY, and the DALYs averted were converted to economic gain per patient and aggregated to give a total value and an average per patient. Sensitivity analyses were performed based on the variations of IE applied for each country.ResultsEach CL operation averted 2.2 DALYs on average and each CP operation 3.3. Total averted DALYs were 1 325 678 (CP 686 577 and CL 639 102). The economic benefit from the programme was between US$7.9 and US$20.7 billion. Per patient, the average benefit was between US$16 133 and US$42 351. Expense per DALY averted was estimated to be $149.ConclusionsAddressing basic surgical needs in developing countries provides a massive economic boost through improved health. Expansion of surgical capacity in the developing world is of significant economic and health value and should be a priority in global health efforts.
Development of a critical appraisal tool to assess the quality of cross-sectional studies (AXIS)
Authors: Downes Martin J , Brennan Marnie L , Williams Hywel C , Dean Rachel S 
Published: December 2016

ObjectivesThe aim of this study was to develop a critical appraisal (CA) tool that addressed study design and reporting quality as well as the risk of bias in cross-sectional studies (CSSs). In addition, the aim was to produce a help document to guide the non-expert user through the tool.DesignAn initial scoping review of the published literature and key epidemiological texts was undertaken prior to the formation of a Delphi panel to establish key components for a CA tool for CSSs. A consensus of 80% was required from the Delphi panel for any component to be included in the final tool.ResultsAn initial list of 39 components was identified through examination of existing resources. An international Delphi panel of 18 medical and veterinary experts was established. After 3 rounds of the Delphi process, the Appraisal tool for Cross-Sectional Studies (AXIS tool) was developed by consensus and consisted of 20 components. A detailed explanatory document was also developed with the tool, giving expanded explanation of each question and providing simple interpretations and examples of the epidemiological concepts being examined in each question to aid non-expert users.ConclusionsCA of the literature is a vital step in evidence synthesis and therefore evidence-based decision-making in a number of different disciplines. The AXIS tool is therefore unique and was developed in a way that it can be used across disciplines to aid the inclusion of CSSs in systematic reviews, guidelines and clinical decision-making.
Meaning of living with severe chronic obstructive lung disease: a qualitative study
Authors: Marx Gabriella , Nasse Maximilian , Stanze Henrikje , Boakye Sonja Owusu , Nauck Friedemann , Schneider Nils 
Published: December 2016

ObjectivesTo explore what it means for patients to live with chronic obstructive pulmonary disease (COPD) as an incurable and constantly progressing disease.DesignQualitative longitudinal study using narrative and semistructured interviews. This paper presents findings of the initial interviews. Analysis using grounded theory.SettingLung care clinics and community care in Lower Saxony, Germany.Participants17 patients with advanced-stage COPD (Global Initiative for Chronic Obstructive Lung Disease (GOLD) III/IV).FindingsAnalysis shows that these patients have difficulties accepting their life situation and feel at the mercy of the disease, which could be identified as a core-experienced phenomenon. Over a long period of time, patients have only a vague feeling of being ill, caused by uncertain knowledge, slow progress and doubtful attribution of clinical symptoms of the disease (causal conditions). As an action strategy, patients try to maintain daily routines for as long as possible after diagnosis. Both effective standard and rescue medication, which helps to reduce breathlessness and other symptoms, and the feeling of being faced with one's own responsibility (intervening conditions) support this strategy, whereby patients' own responsibility is too painful to acknowledge. As a consequence, patients try to deny the threat to life for a long period of time. Frequently, they need to experience facing their own limits, often in the form of an acute crisis, to realise their health situation. The experience of the illness is contextualised by a continuous increase in limited mobility and social isolation.ConclusionIn order to help patients to improve disease awareness, to accept their life situation and to improve their reduced quality of life, patients may benefit from the early integration of palliative care (PC), considering its multiprofessional patient-centred and team-centred approach. Psychological support and volunteer work, which are relevant aspects of PC, should be appropriate to address psychosocial needs. More research is needed to evaluate how patients could benefit from early PC.
Older patient considering treatment for advanced renal disease: protocol for a scoping review of the information available for shared decision-making
Authors: Raj Rajesh , Ahuja Kiran D K , Frandsen Mai , Jose Matthew 
Published: December 2016

IntroductionOlder adults constitute the largest group of patients on dialysis in most parts of the world. Management of advanced renal disease in the older adult is complex; treatment outcomes and prognosis can be markedly different from younger patients. Clinical teams caring for such patients are often called on to provide information regarding prognosis and outcomes with treatment—particularly, the comparison between having dialysis treatment versus not having dialysis. These discussions can be difficult for clinicians because they have to contend with incomplete or nascent data regarding prognosis and outcomes in this age group. We aim to summarise the currently available information regarding the prognosis and outcomes of advanced renal disease in the older adult by means of a scoping review of the literature. This article discusses our protocol.MethodsThis scoping review will be undertaken in accordance with the Joanna Briggs Institute's methodology for scoping reviews. A directed search will look for relevant articles in English (within electronic databases and the grey literature), written between 2000 and 2016, which have studied older patients with advanced renal disease (estimated glomerular filtration rate <30 mL/min/1.73 m2). After screening by two independent reviewers, selected articles will be analysed using a data charting tool. Reporting will include descriptions, analysis of themes using qualitative software and display of information using charts.Ethics and disseminationThis scoping review will analyse previously collected data, and so does not require ethical approval. Results will be disseminated through academic journals, conferences and seminars. We anticipate that our summary of the currently available knowledge regarding the older adult with advanced renal disease will be a repository of information for clinicians in the field. We expect to identify areas of study that are suited to systematic reviews. Our findings can also be expected to influence guidelines and clinical practice recommendations in the future.
Molecular Pathways: The Necrosome—A Target for Cancer Therapy
Authors: Seifert Lena , Miller George 
Published: December 2016

Abstract
Necroptosis is a caspase-8–independent cell death that requires coactivation of receptor-interacting protein 1 (RIP1) and receptor-interacting protein 3 (RIP3) kinases. The necrosome is a complex consisting of RIP1, RIP3, and Fas-associated protein with death domain leading to activation of the pseudokinase mixed lineage kinase like followed by a rapid plasma membrane rupture and inflammatory response through the release of damage-associated molecular patterns and cytokines. The necrosome has been shown to be relevant in multiple tumor types, including pancreatic adenocarcinoma, melanoma, and several hematologic malignancies. Preclinical data suggest that targeting this complex can have differential impact on tumor progression and that the effect of necroptosis on oncogenesis is cell-type and context dependent. The emerging data suggest that targeting the necrosome may lead to immunogenic reprogramming in the tumor microenvironment in multiple tumors and that combining therapies targeting the necrosome with either conventional chemotherapy or immunotherapy may have beneficial effects. Thus, understanding the interplay of necroptotic cell death, transformed cells, and the immune system may enable the development of novel therapeutic approaches. Clin Cancer Res; 23(5); 1132–6. ©2016 AACR.
Local Vascular Gene Therapy With Apolipoprotein A-I to Promote Regression of Atherosclerosis
Authors: Wacker Bradley K. , Dronadula Nagadhara , Zhang Jingwan , Dichek David A. 
Published: December 2016

Objective—
Gene therapy, delivered directly to the blood vessel wall, could potentially prevent atherosclerotic lesion growth and promote atherosclerosis regression. Previously, we reported that a helper-dependent adenoviral (HDAd) vector expressing apolipoprotein A-I (apoA-I) in carotid endothelium of fat-fed rabbits reduced early (4 weeks) atherosclerotic lesion growth. Here, we tested whether the same HDAd—delivered to the existing carotid atherosclerotic lesions—could promote regression.

Approach and Results—

Rabbits (n=26) were fed a high-fat diet for 7 months, then treated with bilateral carotid gene transfer. One carotid was infused with an HDAd expressing apoA-I (HDAdApoAI) and the other with a control nonexpressing HDAd (HDAdNull). The side with HDAdApoAI was randomized. Rabbits were then switched to regular chow, lowering their plasma cholesterols by over 70%. ApoA-I mRNA and protein were detected in HDAdApoAI-transduced arteries. After 7 weeks of gene therapy, compared with HDAdNull-treated arteries in the same rabbits, HDAdApoAI-treated arteries had significantly less vascular cell adhesion molecule-1 expression (28%;
P
=0.04) along with modest but statistically insignificant trends toward decreased intimal lesion volume, lipid and macrophage content, and intercellular adhesion molecule-1 expression (9%–21%;
P
=0.1–0.4). Post hoc subgroup analysis of rabbits with small-to-moderate–sized lesions (n=20) showed that HDAdApoAI caused large reductions in lesion volume, lipid content, intercellular adhesion molecule-1, and vascular cell adhesion molecule-1 expression (30%–50%;
P
≤0.04 for all). Macrophage content was reduced by 30% (
P
=0.06). There was a significant interaction (
P
=0.02) between lesion size and treatment efficacy.

Conclusions—
Even when administered on a background of aggressive lowering of plasma cholesterol, local HDAdApoAI vascular gene therapy may promote rapid regression of small-to-moderate–sized atherosclerotic lesions.
Telomerase Reverse Transcriptase Deficiency Prevents Neointima Formation Through Chromatin Silencing of E2F1 Target Genes
Authors: Endorf Elizabeth B. , Qing Hua , Aono Jun , Terami Naoto , Doyon Geneviève , Hyzny Eric , Jones Karrie L. , Findeisen Hannes M. , Bruemmer Dennis 
Published: December 2016

Objective—
Aberrant proliferation of smooth muscle cells (SMC) in response to injury induces pathological vascular remodeling during atherosclerosis and neointima formation. Telomerase is rate limiting for tissue renewal and cell replication; however, the physiological role of telomerase in vascular diseases remains to be determined. The goal of the present study was to determine whether telomerase reverse transcriptase (TERT) affects proliferative vascular remodeling and to define the molecular mechanism by which TERT supports SMC proliferation.

Approach and Results—
We first demonstrate high levels of TERT expression in replicating SMC of atherosclerotic and neointimal lesions. Using a model of guidewire-induced arterial injury, we demonstrate decreased neointima formation in TERT-deficient mice. Studies in SMC isolated from TERT-deficient and TERT overexpressing mice with normal telomere length established that TERT is necessary and sufficient for cell proliferation. TERT deficiency did not induce a senescent phenotype but resulted in G1 arrest albeit hyperphosphorylation of the retinoblastoma protein. This proliferative arrest was associated with stable silencing of the E2F1-dependent S-phase gene expression program and not reversed by ectopic overexpression of E2F1. Finally, chromatin immunoprecipitation and accessibility assays revealed that TERT is recruited to E2F1 target sites and promotes chromatin accessibility for E2F1 by facilitating the acquisition of permissive histone modifications.

Conclusions—
These data indicate a previously unrecognized role for TERT in neointima formation through epigenetic regulation of proliferative gene expression in SMC.
Impact of Long-Term Observation on the Sampling Characteristics of TRMM PR Precipitation
Authors: Hirose Masafumi , Takayabu Yukari N. , Hamada Atsushi , Shige Shoichi , Yamamoto Munehisa K. 
Published: December 2016

AbstractObservations of the Tropical Rainfall Measuring Mission Precipitation Radar (TRMM PR) over 16 yr yielded hundreds of large precipitation systems (≥100 km) for each 0.1° grid over major rainy regions. More than 90% of the rainfall was attributed to large systems over certain midlatitude regions such as La Plata basin and the East China Sea. The accumulation of high-impact snapshots reduced the significant spatial fluctuation of the rain fraction arising from large systems and allowed the obtaining of sharp images of the geographic rainfall pattern. Widespread systems were undetected over low-rainfall areas such as regions off Peru. Conversely, infrequent large systems brought a significant percentage of rainfall over semiarid tropics such as the Sahel. This demonstrated an increased need for regional sampling of extreme phenomena. Differences in data collected over a period of 16 yr were used to examine sampling adequacy. The results indicated that more than 10% of the 0.1°-scale sampling error accounted for half of the TRMM domain even for a 10-yr data accumulation period. Rainfall at the 0.1° scale was negatively biased in the first few years for over more than half of the areas because of a lack of high-impact samples. The areal fraction of the 0.1°-scale climatology with a 50% accuracy exceeded 95% in the ninth year and in the fifth year for those areas with rainfall >2 mm day−1. A monotonic increase in the degree of similarity of finescale rainfall to the best estimate with an accuracy of 10% illustrated the need for further sampling.
Bayesian Retrievals of Vertically Resolved Cloud Particle Size Distribution Properties
Authors: Posselt Derek J. , Kessler James , Mace Gerald G. 
Published: December 2016

AbstractRetrievals of liquid cloud properties from remote sensing observations by necessity assume sufficient information is contained in the measurements, and in the prior knowledge of the cloudy state, to uniquely determine a solution. Bayesian algorithms produce a retrieval that consists of the joint probability distribution function (PDF) of cloud properties given the measurements and prior knowledge. The Bayesian posterior PDF provides the maximum likelihood estimate, the information content in specific measurements, the effect of observation and forward model uncertainties, and quantitative error estimates. It also provides a test of whether, and in which contexts, a set of observations is able to provide a unique solution. In this work, a Bayesian Markov chain Monte Carlo (MCMC) algorithm is used to sample the joint posterior PDF for retrieved cloud properties in shallow liquid clouds over the remote Southern Ocean. Combined active and passive observations from spaceborne W-band cloud radar and visible and near-infrared reflectance are used to retrieve the parameters of a gamma particle size distribution (PSD) for cloud droplets and drizzle. Combined active and passive measurements are able to distinguish between clouds with and without precipitation; however, unique retrieval of PSD properties requires specification of a scene-appropriate prior estimate. While much of the uncertainty in an unconstrained retrieval can be mitigated by use of information from 94-GHz passive brightness temperature measurements, simply increasing measurement accuracy does not render a unique solution. The results demonstrate the robustness of a Bayesian retrieval methodology and highlight the importance of an appropriately scene-consistent prior constraint in underdetermined remote sensing retrievals.