bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of mental illness on care for somatic comorbidities in France: a nation-wide hospital-based observational study
Authors: Gervaix J. , Haour G. , Michel M. , Chevreul K. 
Published: April 2018

Aims.People with a mental illness have a shorter lifespan and higher rates of somatic illnesses than the general population. They also face multiple barriers which interfere with access to healthcare. Our objective was to assess the effect of mental illness on the timeliness and optimality of access to healthcare for somatic reasons by comparing indicators reflecting the quality of prior somatic care in hospitalised patients.Methods.An observational nation-wide study was carried out using exhaustive national hospital discharge databases for the years 2009–2013. All adult inpatient stays for somatic reasons in acute care hospitals were included with the exception of obstetrics and day admissions. Admissions with coding errors were excluded. Patients with a mental illness were identified by their admissions for a psychiatric reason and/or contacts with psychiatric hospitals. The quality of prior somatic care was assessed using the number of admissions, admissions through the emergency room (ER), avoidable hospitalisations, high-severity hospitalisations, mean length of stay (LOS) and in-hospital death. Generalised linear models studied the factors associated with poor quality of primary care.Results.A total of 17 620 770 patients were included, and 6.58% had been admitted at least once for a mental illness, corresponding to 8.96% of hospital admissions. Mentally ill patients were more often hospitalised (+41% compared with non-mentally patients) and for a longer LOS (+16%). They also had more high-severity hospitalisations (+77%), were more often admitted to the ER (+113%) and had more avoidable hospitalisations (+50%). After adjusting for other covariates, regression models found that suffering from a mental illness was significantly associated with a worse state for each indicator of the quality of care except in-hospital death.Conclusion.Inadequate primary care of mentally ill patients leads to more serious conditions upon admission to hospital and avoidable hospitalisations. It is, therefore, necessary to improve primary care and prevention for those patients.
Chlorophyll to Carbon Ratio Derived From a Global Ecosystem Model With Photodamage
Authors: Álvarez E. , Thoms S. , Völker C. 
Published: April 2018

AbstractPhytoplankton harvests light by integrating chlorophyll in protein‐pigment complexes (photosystems) that are variable in number and size. In ecosystem models, the capacity of light harvesting is described as the pool of chlorophyll. Since most of the variability in phytoplankton chlorophyll content is driven by acclimation to changing nutrient and light conditions, photoacclimation is generally parameterized as a regulation of chlorophyll synthesis with changing light. However, photosystems can also be degraded, and of the few process‐based models that have been proposed in the literature for the representation of their degradation and repair, none of them have been extended to more realistic conditions offered by pelagic biogeochemical models. We proposed three potential parameterizations to treat the degradation of photosystems as a function of light intensity and included them as a source of variation in the size of the chlorophyll pool in Regulated Ecosystem Model, version 2 (REcoM2). These model versions provided chlorophyll values highly correlated with satellite chlorophyll and accurate patterns of the chlorophyll to carbon ratio at global scale. The improvement in the prediction of the ratios was remarkable in scenarios where cells are exposed to periods of low light conditions. By isolating the effects of light and nutrients on the variability of the chlorophyll to carbon ratio and the growth rate, we observed a potential reduction in photosynthetic performance under simultaneous light saturation and nutrient stress. This effect, whose strength depends on the presence of photoprotective mechanisms and the degree of nutrient limitation, allowed to assess the role of photodamage and photoprotection under stress conditions.
On Upscaling of Soil Microbial Processes and Biogeochemical Fluxes From Aggregates to Landscapes
Authors: Ebrahimi Ali , Or Dani 
Published: April 2018

AbstractSoil microbial communities respond to spatial and temporal variations in environmental conditions (e.g., saturation and ambient temperatures) as reflected in the dynamics of microbially produced greenhouse gas (GHG) fluxes (primarily CO2, N2O, and CH4) emitted from soil surfaces. Despite considerable progress in resolving key soil microbial processes, their quantification remains largely empirical with limited predictability. We report a mechanistic and analytical modeling framework for integrating local environmental effects on GHG‐producing microbial processes primarily in soil aggregates (or other hot spots) and the upscaling of these to regional GHG fluxes. The mechanistic model enables systematic evaluation of how soil structural features (e.g., aggregation and layers), spatial variability, and dynamic ambient conditions (e.g., temperature and hydration) affect soil microbial functioning. The upscaling of microbial processes from aggregates of different sizes to soil profiles and landscapes implements mechanistically derived microbial response functions with spatial information on soil type, land cover, and resource distribution. The modeling framework was evaluated using reported field data for seasonal N2O emissions from subarctic regions resulting in reasonable agreement. The proposed analytical framework offers a practical compromise balancing a simplified representation of dynamic microbial processes that respond to local conditions with an upscalable representation of soil GHG fluxes over landscapes under changing environmental conditions.
The Geological Evolution of the Aden‐Owen‐Carlsberg Triple Junction (NW Indian Ocean) Since the Late Miocene
Authors: Rodriguez Mathieu , Fournier Marc , Chamot‐Rooke Nicolas , Huchon Philippe , Delescluse Matthias 
Published: April 2018

AbstractThe Aden‐Owen‐Carlsberg triple junction is the place where Arabia, Somalia, and India meet in the Arabian Sea (NW Indian Ocean). Here we present a new seismic data set crossing a key structure of the triple junction, namely, the Beautemps‐Beaupré pull‐apart basin at the southern end of the Owen Fracture Zone. The seismic data set is tied to Ocean Drilling Program Leg 117 Sites at the top of the Owen Ridge, which provides a detailed tectono‐stratigraphic framework since the Late Miocene. We show that the triple junction configuration has been disturbed by a major kinematic change at ~8 Ma and since then experienced a series of transient structural adjustments. A major structural episode is recorded at 2.4 Ma, expressed by the opening of the Beautemps‐Beaupré Basin and the uplift of its southern flank (the Beautemps‐Beaupré Ridge). This episode is coeval with the formation of the present‐day Owen Fracture Zone and must be considered as a part of a major structural reorganization of the entire India‐Arabia plate boundary up to the Makran subduction zone. This 2.4‐Myr‐old geological episode is unrelated to any significant kinematic change, leaving questions over its driving mechanism.
Drivers of Variability in Atmospheric Evaporative Demand: Multiscale Spectral Analysis Based on Observations and Physically Based Modeling
Authors: Peng Liqing , Li Dan , Sheffield Justin 
Published: April 2018

AbstractAtmospheric evaporative demand (AED) is an important variable linking climate with the terrestrial water cycle and the biosphere. Understanding the dynamics of AED has substantial economic, ecological, and social implications. However, how AED varies at different time scales and the drivers of variability remain elusive. This study used spectral coherence analysis to analyze the relationships between observed and modeled AED and climate drivers across multiple time scales at 228 Chinese stations and explored the cross‐scale effects of climate forcings on AED. The results highlight the crucial role of vapor pressure deficit (VPD) in both energy‐limited and water‐limited regions, therefore models that do not incorporate VPD or underestimate the relative importance of VPD have relatively lower skill in predicting AED. Short‐term forcing variability has potential impacts on the long‐term AED changes through temperature and associated land‐atmosphere feedbacks. Our study implies that model predictions for AED and associated hydrologic impacts may not be valid in a changing climate when the key controls on AED and their relative importance are not appropriately represented.
Attribution of Local Temperature Response to Deforestation
Authors: Liao Weilin , Rigden Angela J. , Li Dan 
Published: April 2018

AbstractLand use and land cover change such as deforestation can directly induce changes in land surface temperature (LST). Using observational data from four paired eddy covariance sites, we attribute changes in LST induced by deforestation to changes in radiation, aerodynamic resistance, the Bowen ratio or surface resistance, and heat storage using two different methods: the intrinsic biophysical mechanism (IBM) method and the two‐resistance mechanism method. The two models are first optimized to reduce the root‐mean‐square error of the simulated daily LST change by using daily‐averaged inputs and a weighted average approach for computing the sensitivities. Both methods indicate that the daytime warming effect of deforestation is mostly induced by changes in aerodynamic resistance as the surface becomes smoother after deforestation, and the nighttime cooling effect of deforestation is controlled by changes in aerodynamic resistance, surface resistance, radiation, and heat storage. Both methods also indicate that changes in atmospheric temperature have a large impact on LST and need to be included in the LST attribution. However, there are significant differences between the two methods. The IBM method tends to overestimate the contribution of aerodynamic resistance due to the assumption that aerodynamic resistance and the Bowen ratio are independent. Additionally, the IBM method underestimates the contributions of radiation and heat storage during the daytime but overestimates them at night. By highlighting the similarity and dissimilarity between the two methods, this study suggests that acceptable agreement between observed and modeled LST change is the prerequisite for attribution but does not guarantee correct attribution.
Adherence to a Mediterranean diet and long-term changes in weight and waist circumference in the EPIC-Italy cohort
Authors: Agnoli Claudia , Sieri Sabina , Ricceri Fulvio , Giraudo Maria Teresa , Masala Giovanna , Assedi Melania , Panico Salvatore , Mattiello Amalia , Tumino Rosario , Giurdanella Maria Concetta , Krogh Vittorio 
Published: April 2018

AbstractExcessive calorie intake and physical inactivity are considered key determinants of the rapid worldwide increase in obesity prevalence, however the relationship between diet and weight gain is complex. We investigated associations between adherence to a Mediterranean diet and long-term changes in weight and waist circumference in volunteers recruited to the Italian section of the prospective European Prospective Investigation into Cancer and Nutrition (EPIC). We investigated 32,119 cohort members who provided anthropometric measures at recruitment and updated information on recall a mean of 12 years later. Adherence to a Mediterranean diet was assessed using the Italian Mediterranean Index (score range 0–11). Associations between index score and weight and waist changes were assessed by multivariate linear regression models. Risks of developing overweight/obesity and abdominal obesity were investigated by multivariate logistic models. Increasing Italian Mediterranean Index score (indicating better adherence) was associated with lower 5-year weight change in volunteers of normal weight at baseline (β −0.12, 95% CI −0.16 to −0.08 for 1 tertile increase in score), but not in those overweight/obese at baseline (P interaction between Index score and BMI 0.0001). High adherence was also associated with reduced risk of becoming overweight/obese (OR 0.91, 95% CI 0.84–0.99 third vs. first tertile); smaller 5-year change in waist circumference (β −0.09, 95% CI −0.14 to −0.03 for 1 tertile increase in score); and lower risk of abdominal obesity (OR 0.91, 95% CI 0.84–0.99 third vs. first tertile). Adherence to a traditional Italian Mediterranean diet may help prevent weight gain and abdominal obesity.
Repression of let-7a cluster prevents adhesion of colorectal cancer cells by enforcing a mesenchymal phenotype in presence of liver inflammation
Authors: Cheng Lipeng , Geng Li , Dai Binghua , Zheng Tao , Fu Jun , Qiao Liang , Cai Wenchang , Wang Yue , Yang Jiamei 
Published: April 2018

AbstractThe liver is the most common site of metastasis in patients with colorectal cancer, and colorectal cancer liver metastasis (CRLM) is associated with poor rates of survival. However, CRLM occurs infrequently in livers exhibiting signs of hepatitis or cirrhosis, suggesting a role for inflammation in attenuating CRLM. The molecular mechanisms driving this phenomenon remain unclear. The aim of this study was to confirm the mechanism by which liver inflammation inhibits CRLM. We used BALB/c animal models of inflammatory liver diseases to confirm that liver inflammation inhibits CRLM, and then elucidated the molecular mechanisms governing that process. Out data showed that liver inflammation induces IFN-γ expression, which then downregulates expression of the let-7a cluster through IRF-1 in colorectal cancer cells. Finally, we showed that modulation of let-7a expression regulated the epithelial–mesenchymal transition in colorectal cancer cell lines, and inhibited their capacity to metastasize in vivo. Cumulatively, we clarified the critical role played by the IFN-γ/IRF-1/let-7a cluster/EMT pathway in regulating the spread of circulating colorectal cancer cells to the liver, and highlighted the critical role that the hepatitis microenvironment plays in modulating that process.
Validating the concept of mutational signatures with isogenic cell models
Authors: Zou Xueqing , Owusu Michel , Harris Rebecca , Jackson Stephen P. , Loizou Joanna I. , Nik-Zainal Serena 
Published: April 2018

AbstractThe diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they evolved towards malignancy. Correlations between mutational signatures and environmental exposures, enzymatic activities and genetic defects have been described, but human cancers are not ideal experimental systems—the exposures to different mutational processes in a patient’s lifetime are uncontrolled and any relationships observed can only be described as an association. Here, we demonstrate the proof-of-principle that it is possible to recreate cancer mutational signatures in vitro using CRISPR-Cas9-based gene-editing experiments in an isogenic human-cell system. We provide experimental and algorithmic methods to discover mutational signatures generated under highly experimentally-controlled conditions. Our in vitro findings strikingly recapitulate in vivo observations of cancer data, fundamentally validating the concept of (particularly) endogenously-arising mutational signatures.
The AFF-1 exoplasmic fusogen is required for endocytic scission and seamless tube elongation
Authors: Soulavie Fabien , Hall David H. , Sundaram Meera V. 
Published: April 2018

AbstractMany membranes must merge during cellular trafficking, but fusion and fission events initiating at exoplasmic (non-cytosolic) membrane surfaces are not well understood. Here we show that the C. elegans cell–cell fusogen anchor-cell fusion failure 1 (AFF-1) is required for membrane trafficking events during development of a seamless unicellular tube. EGF-Ras-ERK signaling upregulates AFF-1 expression in the excretory duct tube to promote tube auto-fusion and subsequent lumen elongation. AFF-1 is required for scission of basal endocytic compartments and for apically directed exocytosis to extend the apical membrane. Lumen elongation also requires the transcytosis factor Rab11, but occurs independently of dynamin and clathrin. These results support a transcytosis model of seamless tube lumen growth and show that cell–cell fusogens also can play roles in intracellular membrane trafficking events.
Magnetic nanochain integrated microfluidic biochips
Authors: Xiong Qirong , Lim Chun Yee , Ren Jinghua , Zhou Jiajing , Pu Kanyi , Chan-Park Mary B. , Mao Hui , Lam Yee Cheong , Duan Hongwei 
Published: April 2018

AbstractMicrofluidic biochips hold great potential for liquid analysis in biomedical research and clinical diagnosis. However, the lack of integrated on-chip liquid mixing, bioseparation and signal transduction presents a major challenge in achieving rapid, ultrasensitive bioanalysis in simple microfluidic configurations. Here we report magnetic nanochain integrated microfluidic chip built upon the synergistic functions of the nanochains as nanoscale stir bars for rapid liquid mixing and as capturing agents for specific bioseparation. The use of magnetic nanochains enables a simple planar design of the microchip consisting of flat channels free of common built-in components, such as liquid mixers and surface-anchored sensing elements. The microfluidic assay, using surface-enhanced Raman scattering nanoprobes for signal transduction, allows for streamlined parallel analysis of multiple specimens with greatly improved assay kinetics and delivers ultrasensitive identification and quantification of a panel of cancer protein biomarkers and bacterial species in 1 μl of body fluids within 8 min.
Starting geometry creation and design method for freeform optics
Authors: Bauer Aaron , Schiesser Eric M. , Rolland Jannick P. 
Published: April 2018

AbstractWe describe a method for designing freeform optics based on the aberration theory of freeform surfaces that guides the development of a taxonomy of starting-point geometries with an emphasis on manufacturability. An unconventional approach to the optimization of these starting designs wherein the rotationally invariant 3rd-order aberrations are left uncorrected prior to unobscuring the system is shown to be effective. The optimal starting-point geometry is created for an F/3, 200 mm aperture-class three-mirror imager and is fully optimized using a novel step-by-step method over a 4 × 4 degree field-of-view to exemplify the design method. We then optimize an alternative starting-point geometry that is common in the literature but was quantified here as a sub-optimal candidate for optimization with freeform surfaces. A comparison of the optimized geometries shows the performance of the optimal geometry is at least 16× better, which underscores the importance of the geometry when designing freeform optics.
Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients with metastatic triple-negative breast cancer
Authors: Stover Daniel G. , Gil Del Alcazar Carlos R. , Brock Jane , Guo Hao , Overmoyer Beth , Balko Justin , Xu Qiong , Bardia Aditya , Tolaney Sara M. , Gelman Rebecca , Lloyd Maxwell , Wang Yu , Xu Yaomin , Michor Franziska , Wang Vivian , Winer Eric P. , Polyak Kornelia , Lin Nancy U. 
Published: April 2018

AbstractPreclinical data support a role for the IL-6/JAK2/STAT3 signaling pathway in breast cancer. Ruxolitinib is an orally bioavailable receptor tyrosine inhibitor targeting JAK1 and JAK2. We evaluated the safety and efficacy of ruxolitinib in patients with metastatic breast cancer. This was a non-randomized phase II study enrolling patients with refractory, metastatic triple-negative breast cancer. The primary endpoint was objective response by RECIST 1.1. The study was designed to enroll patients whose archival tumor tissue was pSTAT3-positive (T-score >5) by central immunohistochemistry. pSTAT3 staining was available from 171 of 217 consented patients and pSTAT3 T-score was positive in 67/171 (39.2%) tumors, suggesting that JAK–STAT activation is frequent. Twenty-three patients including one patient with inflammatory breast cancer were enrolled. Ruxolitinib was well-tolerated with infrequent grade 3 or higher toxicities with fatigue as the most common toxicity. Among 21 patients who received at least one dose of protocol therapy, no objective responses were observed and the study was closed to further accrual. Pharmacodynamic analyses of baseline vs. cycle 2 biopsies suggest on-target activity, including a significant decrease in the proportion of pSTAT3+ cells in three patients with paired biopsies and downregulation of JAK–STAT target genes and signatures via transcriptional analyses of 11 total baseline and four metastatic biopsies. Immuno-FISH analyses demonstrate intratumoral heterogeneity of pSTAT3 and JAK2 amplification. Ruxolitinib, as a single agent, did not meet the primary efficacy endpoint in this refractory patient population despite evidence of on-target activity.
In-patient outcomes of Hematopoietic Stem Cell Transplantation in Patients with Immune Mediated Inflammatory Diseases: A Nationwide Study
Authors: Mehta Kathan , Jaiswal Palashkumar , Briggs Farren , Faubion William A. , Tabibian James H. , Cominelli Fabio , Dave Maneesh 
Published: April 2018

AbstractThe impact of underlying immune-mediated inflammatory diseases (IMID) in patients undergoing hematopoietic stem cell transplant (HSCT) is unclear. Hematopoietic cell transplantation co-morbidity index (HCT-CI) is gaining acceptance as a reliable clinical method to score pre-transplant co-morbidities. Higher HCT-CI from a co-morbid IMID implies higher NRM. However, HCT-CI integrates many IMIDs with different pathogenesis and treatment together which may lead to spurious results. We performed a cross-sectional study using Nationwide Inpatient Sample dataset from 1998 to 2011 to compare the outcomes of HSCT in patients with different co-morbid IMIDs with patients without any co-morbid IMIDs. In both our multivariate and stringent matched-pair analysis, ulcerative colitis (UC) was associated with increased mortality while rheumatoid arthritis and psoriasis were associated with lower mortality as compared to no IMID group. Furthermore, in allogeneic HSCT subgroup, UC was associated with higher mortality and psoriasis was associated with lower mortality. In conclusion, we found that depending on the type of HSCT, each IMID has a different impact on outcomes of HSCT. Furthermore, UC patients had increased mortality if they had primary sclerosing cholangitis and had a higher risk of opportunistic infections like tuberculosis and cytomegalovirus suggesting the need for increased vigilance in this cohort.