bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of
Methylosinus
sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field
Authors: Bao Zhihua , Shinoda Ryo , Minamisawa Kiwamu 
Published: September 2016

ABSTRACT

N
2
-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of
Methylosinus
sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input.
Chair-based fidgeting and energy expenditure
Authors: Koepp Gabriel A , Moore Graham K , Levine James A 
Published: September 2016

IntroductionSedentariness is associated with chronic health conditions, impaired cognitive function and obesity. Work contributes significantly to sedentariness because many work tasks necessitate sitting. Few sustained solutions exist to reverse workplace sedentariness. Here, we evaluated a chair and an under-table device that were designed to promote fidgeting while seated. Our hypothesis was that an under-table leg-fidget bar and/or a fidget-promoting chair significantly increased energy expenditure. We compared these devices with chair-based exercise and walking.Materials and methodsWe measured energy expenditure and heart rate in 16 people while they sat and worked using a standard chair, an under-desk device that encourages leg fidgeting and a fidget-promoting chair. We compared outcomes with chair-based exercise and walking.ResultsEnergy expenditure increased significantly while using either an under-table leg-fidget bar or a fidget-promoting chair, when compared to the standard office chair (standard chair, 76±31 kcal/hour; leg-fidget bar, 98±42 kcal/hour (p<0.001); fidget chair, 89±40 kcal/hour (p=0.03)). However, heart rate did not increase significantly in either case. Bouts of exercise performed while seated provided energetic and heart rate equivalency to walking at 2 mph.ConclusionsChairs and devices that promote fidgeting can increase energy expenditure by ∼20–30% but not increase heart rate. Dynamic sitting may be among a lexicon of options to help people move more while at work.
Stent retrieval thrombectomy in acute stoke is facilitated by the concurrent use of intracranial aspiration catheters
Authors: Jindal Gaurav , Serulle Yafell , Miller Timothy , Le Elizabeth , Wozniak Marcella , Phipps Michael , Iyoha Moronke , Gupta Vikash , Shivashankar Ravi , Gandhi Dheeraj 
Published: September 2016

BackgroundNew device technology has changed the techniques used for revascularization of emergent large vessel occlusion in acute stroke. We report technical results using stent retrievers (SRs) for thrombectomy alone versus SRs used in conjunction with a new group of devices, intracranial aspiration catheters (IACs). Our aim is to demonstrate differences in procedural time and thrombectomy attempts between these two groups.MethodsA retrospective evaluation was performed of a prospectively maintained database of 97 patients treated at a single institution for anterior circulation stroke with SRs. Patients were divided into two groups, a combination group defined as the SR/IAC group and the SR alone group defined as the SR group.ResultsPatients in the SR/IAC group had a mean age of 66 years vs 59 years in the SR group (p=0.008). Mean presenting National Institutes of Health Stroke Scale (NIHSS) scores in the SR/IAC and control groups were 18.7 and 18.2, respectively (p=0.50). Recanalization rates (Thrombolysis In Cerebral Infarction (TICI) 2b or 3) in the SR/IAC and SR groups were 85% (58/68) and 90% (26/29), respectively (p=0.41). Mean time from groin arteriotomy to recanalization was 50±3.6 min (range 19–136) in the SR/IAC group (n=59) and 61±6.6 min (range 28–140) in the SR group (n=27) (p=0.049). The total number of thrombectomy attempts in the SR/IAC and SR groups were 1.9±0.1 (range 1–4) and 2.5±0.6 (range 1–6), respectively (p=0.009). Post-procedural subarachnoid hemorrhage was seen in 15% (10/68) and 10% (3/29) of cases in the SR/IAC and SR groups, respectively (p=0.41).ConclusionWhen using SRs for intracranial stroke thrombectomy, the concurrent use of IACs is associated with a decrease in procedural time and thrombectomy attempts compared with use of SRs alone.
Association of Ovarian Tumor β2-Adrenergic Receptor Status with Ovarian Cancer Risk Factors and Survival
Authors: Huang Tianyi , Tworoger Shelley S. , Hecht Jonathan L. , Rice Megan S. , Sood Anil K. , Kubzansky Laura D. , Poole Elizabeth M. 
Published: September 2016

Abstract
Background: The β2-adrenergic signaling pathway mediates the effects of chronic stress on ovarian cancer progression in mouse models. The relevance of this pathway to human ovarian cancer remains unknown.
Methods: We assessed tumor expression of β2-adrenergic receptor (ADRB2) using tissue microarrays in 237 ovarian cancer cases from the Nurses' Health Studies (NHS/NHSII). Competing risks Cox regression was used to evaluate whether associations of reproductive, hormonal, and psychosocial factors with ovarian cancer risk differed by ADRB2. We also examined the association between tumor ADRB2 expression and ovarian cancer survival.
Results: Forty-five (19%) cases were positive for ADRB2 staining. High levels of anxiety symptoms were positively associated with ADRB2-positive tumors (HR, 2.59; 95% confidence interval [CI], 1.15–5.84) but not with ADRB2-negative tumors (HR, 1.16; 95% CI, 0.81–1.66; Pheterogeneity = 0.07). We observed similar results for depression. No associations were observed for job strain, caregiving stress, or widowhood for either positive or negative ADRB2 status. Lifetime ovulatory years were more strongly associated with ADRB2-positive tumors (HR per 5 years, 1.60; 95% CI, 1.15–2.21) compared with ADRB2-negative tumors (HR, 1.11; 95% CI, 0.96–1.27; Pheterogeneity = 0.04). Significant heterogeneity by ADRB2 was also observed for parity (Pheterogeneity = 0.01), oral contraceptive use (Pheterogeneity = 0.03), and age at menopause (Pheterogeneity = 0.04). Tumor expression of ADRB2 was not associated with ovarian cancer mortality (HR, 1.05; 95% CI, 0.69–1.59).
Conclusions: Several stress- and ovulation-related factors were differentially associated with ovarian tumors responsive to β2-adrenergic signaling.
Impact: Replication in larger studies is warranted to confirm the role of β2-adrenergic signaling in ovarian cancer etiology. Cancer Epidemiol Biomarkers Prev; 25(12); 1587–94. ©2016 AACR.
Necrotic Cell Sensor Clec4e Promotes a Proatherogenic Macrophage Phenotype Through Activation of the Unfolded Protein Response
Authors: Clément Marc , Basatemur Gemma , Masters Leanne , Baker Lauren , Bruneval Patrick , Iwawaki Takao , Kneilling Manfred , Yamasaki Sho , Goodall Jane , Mallat Ziad 
Published: September 2016

Background:

Atherosclerotic lesion expansion is characterized by the development of a lipid-rich necrotic core known to be associated with the occurrence of complications. Abnormal lipid handling, inflammation, and alteration of cell survival or proliferation contribute to necrotic core formation, but the molecular mechanisms involved in this process are not properly understood. C-type lectin receptor 4e (Clec4e) recognizes the cord factor of Mycobacterium
tuberculosis
but also senses molecular patterns released by necrotic cells and drives inflammation.

Methods:

We hypothesized that activation of Clec4e signaling by necrosis is causally involved in atherogenesis. We addressed the impact of Clec4e activation on macrophage functions in vitro and on the development of atherosclerosis using low-density lipoprotein receptor–deficient (
Ldlr

−/−

) mice in vivo.

Results:

We show that Clec4e is expressed within human and mouse atherosclerotic lesions and is activated by necrotic lesion extracts. Clec4e signaling in macrophages inhibits cholesterol efflux and induces a Syk-mediated endoplasmic reticulum stress response, leading to the induction of proinflammatory mediators and growth factors.
Chop
and
Ire1a
deficiencies significantly limit Clec4e-dependent effects, whereas
Atf3
deficiency aggravates Clec4e-mediated inflammation and alteration of cholesterol efflux. Repopulation of
Ldlr

−/−

mice with
Clec4e

−/−

bone marrow reduces lipid accumulation, endoplasmic reticulum stress, and macrophage inflammation and proliferation within the developing arterial lesions and significantly limits atherosclerosis.

Conclusions:
Our results identify a nonredundant role for Clec4e in coordinating major biological pathways involved in atherosclerosis and suggest that it may play similar roles in other chronic inflammatory diseases.
Stroke Treatment Academic Industry Roundtable
Authors: Jovin Tudor G. , Albers Gregory W. , Liebeskind David S. ,   for the STAIR IX Consortium
Published: September 2016

Background and Purpose—
The STAIR (Stroke Treatment Academic Industry Roundtable) meeting aims to advance acute stroke therapy development through collaboration between academia, industry, and regulatory institutions. In pursuit of this goal and building on recently available level I evidence of benefit from endovascular therapy (ET) in large vessel occlusion stroke, STAIR IX consensus recommendations were developed that outline priorities for future research in ET.

Methods—
Three key directions for advancing the field were identified: (1) development of systems of care for ET in large vessel occlusion stroke, (2) development of therapeutic approaches adjunctive to ET, and (3) exploring clinical benefit of ET in patient population insufficiently studied in recent trials. Methodological issues such as optimal trial design and outcome measures have also been addressed.

Results—
Development of systems of care strategies should be geared both toward ensuring broad access to ET for eligible patients and toward shortening time to reperfusion to the minimum possible. Adjunctive therapy development includes neuroprotective approaches, adjuvant microcirculatory/collateral enhancing strategies, and periprocedural management. Future research priorities seeking to expand the eligible patient population are to determine benefit of ET in patients presenting beyond conventional time windows, in patients with large baseline ischemic core lesions, and in other important subgroups.

Conclusions—
Research priorities in ET for large vessel occlusion stroke are to improve systems of care, investigate effective adjuvant therapies, and explore whether patient eligibility could be expanded.
Investigating Exchange Processes over Complex Topography: The Innsbruck Box (i-Box)
Authors: Rotach Mathias W. , Stiperski Ivana , Fuhrer Oliver , Goger Brigitta , Gohm Alexander , Obleitner Friedrich , Rau Gabriele , Sfyri Eleni , Vergeiner Johannes 
Published: September 2016

Abstract
The flow and turbulence structure in the atmospheric boundary layer over complex mountainous terrain determines Earth–atmosphere interaction, that is, the exchange of energy, mass, and momentum between the surface over such terrain and the free atmosphere. Numerical models for weather and climate, even when operated at high or very high grid resolution, are known to be deficient, leading to inaccurate local forecasts (weather) or scenarios (climate). The nature and reasons for these deficiencies, however, are difficult to assess because systematic and long-term combined observational/modeling studies in mountainous terrain are missing. The Innsbruck Box (i-Box) project aims at filling in this gap through a network of long-term turbulence sites in truly complex terrain, complemented by similarly continuous (surface based) remote sensing and numerical modeling at high to highest [i.e., large-eddy simulation (LES)] resolution. This contribution details the i-Box approach, the experimental design, and available data, as well as the numerical modeling strategy. The first scientific highlights are presented to illustrate the potential of the i-Box data pool and possible future directions.
Estimating the Continental Response to Global Warming Using Pattern-Scaled Sea Surface Temperatures and Sea Ice
Authors: Bichet Adeline , Kushner Paul J. , Mudryk Lawrence 
Published: September 2016

Abstract
Better constraining the continental climate response to anthropogenic forcing is essential to improve climate projections. In this study, pattern scaling is used to extract, from observations, the patterned response of sea surface temperature (SST) and sea ice concentration (SICE) to anthropogenically dominated long-term global warming. The SST response pattern includes a warming of the tropical Indian Ocean, the high northern latitudes, and the western boundary currents. The SICE pattern shows seasonal variations of the main locations of sea ice loss. These SST–SICE response patterns are used to drive an ensemble of an atmospheric general circulation model, the National Center for Atmospheric Research (NCAR) Community Atmosphere Model, version 5 (CAM5), over the period 1980–2010 along with a standard AMIP ensemble using observed SST—SICE. The simulations enable attribution of a variety of observed trends of continental climate to global warming. On the one hand, the warming trends observed in all seasons across the entire Northern Hemisphere extratropics result from global warming, as does the snow loss observed over the northern midlatitudes and northwestern Eurasia. On the other hand, 1980–2010 precipitation trends observed in winter over North America and in summer over Africa result from the recent decreasing phase of the Pacific decadal oscillation and the recent increasing phase of the Atlantic multidecadal oscillation, respectively, which are not part of the global warming signal. The method holds promise for near-term decadal climate prediction but as currently framed cannot distinguish regional signals associated with oceanic internal variability from aerosol forcing and other sources of short-term forcing.
Changes in Sea Salt Emissions Enhance ENSO Variability
Authors: Yang Yang , Russell Lynn M. , Lou Sijia , Lamjiri Maryam A. , Liu Ying , Singh Balwinder , Ghan Steven J. 
Published: September 2016

AbstractTwo 150-yr preindustrial simulations with and without interactive sea salt emissions from the Community Earth System Model (CESM) are performed to quantify the interactions between sea salt emissions and El Niño–Southern Oscillation (ENSO). Variations in sea salt emissions over the tropical Pacific Ocean are affected by changing wind speed associated with ENSO variability. ENSO-induced interannual variations in sea salt emissions result in decreasing (increasing) aerosol optical depth (AOD) by 0.03 over the equatorial central-eastern (western) Pacific Ocean during El Niño events compared to those during La Niña events. These changes in AOD further increase (decrease) radiative fluxes into the atmosphere by +0.2 (−0.4) W m−2 over the tropical eastern (western) Pacific. Thereby, sea surface temperature increases (decreases) by 0.2–0.4 K over the tropical eastern (western) Pacific Ocean during El Niño compared to La Niña events and enhances ENSO variability by 10%. The increase in ENSO amplitude is a result of systematic heating (cooling) during the warm (cold) phase of ENSO in the eastern Pacific. Interannual variations in sea salt emissions then produce the anomalous ascent (subsidence) over the equatorial eastern (western) Pacific between El Niño and La Niña events, which is a result of heating anomalies. Owing to variations in sea salt emissions, the convective precipitation is enhanced by 0.6–1.2 mm day−1 over the tropical central-eastern Pacific Ocean and weakened by 0.9–1.5 mm day−1 over the Maritime Continent during El Niño compared to La Niña events, enhancing the precipitation variability over the tropical Pacific.
Analyzing the Adaptive Mesh Refinement (AMR) Characteristics of a High-Order 2D Cubed-Sphere Shallow-Water Model
Authors: Ferguson Jared O. , Jablonowski Christiane , Johansen Hans , McCorquodale Peter , Colella Phillip , Ullrich Paul A. 
Published: September 2016

AbstractAdaptive mesh refinement (AMR) is a technique that has been featured only sporadically in atmospheric science literature. This paper aims to demonstrate the utility of AMR for simulating atmospheric flows. Several test cases are implemented in a 2D shallow-water model on the sphere using the Chombo-AMR dynamical core. This high-order finite-volume model implements adaptive refinement in both space and time on a cubed-sphere grid using a mapped-multiblock mesh technique. The tests consist of the passive advection of a tracer around moving vortices, a steady-state geostrophic flow, an unsteady solid-body rotation, a gravity wave impinging on a mountain, and the interaction of binary vortices. Both static and dynamic refinements are analyzed to determine the strengths and weaknesses of AMR in both complex flows with small-scale features and large-scale smooth flows. The different test cases required different AMR criteria, such as vorticity or height-gradient based thresholds, in order to achieve the best accuracy for cost. The simulations show that the model can accurately resolve key local features without requiring global high-resolution grids. The adaptive grids are able to track features of interest reliably without inducing noise or visible distortions at the coarse–fine interfaces. Furthermore, the AMR grids keep any degradations of the large-scale smooth flows to a minimum.
Multidrug-resistant tuberculosis treatment failure detection depends on monitoring interval and microbiological method
Authors: Mitnick Carole D. , White Richard A. , Lu Chunling , Rodriguez Carly A. , Bayona Jaime , Becerra Mercedes C. , Burgos Marcos , Centis Rosella , Cohen Theodore , Cox Helen , D'Ambrosio Lia , Danilovitz Manfred , Falzon Dennis , Gelmanova Irina Y. , Gler Maria T. , Grinsdale Jennifer A. , Holtz Timothy H. , Keshavjee Salmaan , Leimane Vaira , Menzies Dick , Migliori Giovanni Battista , Milstein Meredith B. , Mishustin Sergey P. , Pagano Marcello , Quelapio Maria I. , Shean Karen , Shin Sonya S. , Tolman Arielle W. , van der Walt Martha L. , Van Deun Armand , Viiklepp Piret 
Published: September 2016

Debate persists about monitoring method (culture or smear) and interval (monthly or less frequently) during treatment for multidrug-resistant tuberculosis (MDR-TB). We analysed existing data and estimated the effect of monitoring strategies on timing of failure detection.We identified studies reporting microbiological response to MDR-TB treatment and solicited individual patient data from authors. Frailty survival models were used to estimate pooled relative risk of failure detection in the last 12 months of treatment; hazard of failure using monthly culture was the reference.Data were obtained for 5410 patients across 12 observational studies. During the last 12 months of treatment, failure detection occurred in a median of 3 months by monthly culture; failure detection was delayed by 2, 7, and 9 months relying on bimonthly culture, monthly smear and bimonthly smear, respectively. Risk (95% CI) of failure detection delay resulting from monthly smear relative to culture is 0.38 (0.34–0.42) for all patients and 0.33 (0.25–0.42) for HIV-co-infected patients.Failure detection is delayed by reducing the sensitivity and frequency of the monitoring method. Monthly monitoring of sputum cultures from patients receiving MDR-TB treatment is recommended. Expanded laboratory capacity is needed for high-quality culture, and for smear microscopy and rapid molecular tests.
Impact of sleep disordered breathing on behaviour among elementary school-aged children: a cross-sectional analysis of a large community-based sample
Authors: Smith Dale L. , Gozal David , Hunter Scott J. , Philby Mona F. , Kaylegian Jaeson , Kheirandish-Gozal Leila 
Published: September 2016

Sleep disordered breathing (SDB) in children has been associated with inattention, impulsivity and hyperactivity, but the associations between SDB severity and the type and severity of behavioural disruption are unclear.1022 children aged 5–7 years old prospectively underwent sleep studies and behavioural assessments through completion of standardised instruments. Participants were subdivided into four categorical groups based on the apnoea–hypopnoea index (AHI; measured per hour of total sleep time (hTST)),i.e.Group 1: nonsnoring and AHI <1 hTST–1; Group 2: habitual snoring and AHI <1 hTST–1; Group 3: habitual snoring and AHI 1–5 hTST–1; and Group 4: habitual snoring and AHI >5 hTST–1, followed by comparisons of behavioural functioning across the groups.All 10 behavioural variables differed significantly between Group 1 and all other groups.Post hoccomparisons indicated that Group 2 was the most impaired for most behavioural measures. Furthermore, differences between Group 2 and more severe sleep pathology conditions were rarely significant.This large community-based paediatric cohort confirms earlier findings highlighting a significant impact of SDB on behavioural regulation, with the greatest impact being already apparent among habitually snoring children. Thus, a likely low asymptote exists regarding SDB behavioural impact, such that further increases in severity do not measurably increase parent-rated difficulties with behavioural regulation relative to controls. Our findings do support the need for considering early intervention, particularly among those children manifesting a behavioural impact of SDB.
Peripheral blood myeloid-derived suppressor cells reflect disease status in idiopathic pulmonary fibrosis
Authors: Fernandez Isis E. , Greiffo Flavia R. , Frankenberger Marion , Bandres Julia , Heinzelmann Katharina , Neurohr Claus , Hatz Rudolf , Hartl Dominik , Behr Jürgen , Eickelberg Oliver 
Published: September 2016

Idiopathic pulmonary fibrosis (IPF) is a fibroproliferative disease with irreversible lung function loss and poor survival. Myeloid-derived suppressor cells (MDSC) are associated with poor prognosis in cancer, facilitating immune evasion. The abundance and function of MDSC in IPF is currently unknown.Fluorescence-activated cell sorting was performed in 170 patients (IPF: n=69; non-IPF interstitial lung disease (ILD): n=56; chronic obstructive pulmonary disease (COPD): n=23; healthy controls: n=22) to quantify blood MDSC and lymphocyte subtypes. MDSC abundance was correlated with lung function, MDSC localisation was performed by immunofluorescence. Peripheral blood mononuclear cell (PBMC) mRNA levels were analysed by qRT-PCR.We detected increased MDSC in IPF and non-IPF ILD compared with controls (30.99±15.61%versus18.96±8.17%, p≤0.01). Circulating MDSC inversely correlated with maximum vital capacity (r= −0.48, p≤0.0001) in IPF, but not in COPD or non-IPF ILD. MDSC suppressed autologous T-cells. The mRNA levels of co-stimulatory T-cell signals were significantly downregulated in IPF PBMC. Importantly, CD33+CD11b+cells, suggestive of MDSC, were detected in fibrotic niches of IPF lungs.We identified increased MDSC in IPF and non-IPF ILD, suggesting that elevated MDSC may cause a blunted immune response. MDSC inversely correlate with lung function only in IPF, identifying them as potent biomarkers for disease progression. Controlling expansion and accumulation of MDSC, or blocking their T-cell suppression, represents a promising therapy in IPF.