bluuebunny/crossref_metadata_2025 huggingface dataset:
Multilevel correlates of household anthropometric typologies in Colombian mothers and their infants
Authors: Parra D. C. , Gomez L. F. , Iannotti L. , Haire-Joshu D. , Sebert Kuhlmann A. K. , Brownson R. C.
Published: April 2018

Background.

The aim of this study was to establish the association of maternal, family, and contextual correlates of anthropometric typologies at the household level in Colombia using 2005 Demographic Health Survey (DHS/ENDS) data.

Methods.

Household-level information from mothers 18–49 years old and their children <5 years old was included. Stunting and overweight were assessed for each child. Mothers were classified according to their body mass index. Four anthropometric typologies at the household level were constructed: normal, underweight, overweight, and dual burden. Four three-level [households (n = 8598) nested within municipalities (n = 226), nested within states (n = 32)] hierarchical polytomous logistic models were developed. Household log-odds of belonging to one of the four anthropometric categories, holding ‘normal’ as the reference group, were obtained.

Results.

This study found that anthropometric typologies were associated with maternal and family characteristics of maternal age, parity, maternal education, and wealth index. Higher municipal living conditions index was associated with a lower likelihood of underweight typology and a higher likelihood of overweight typology. Higher population density was associated with a lower likelihood of overweight typology.

Conclusion.

Distal and proximal determinants of the various anthropometric typologies at the household level should be taken into account when framing policies and designing interventions to reduce malnutrition in Colombia.
A three-dimensional Dirichlet-to-Neumann operator for water waves over topography
Authors: Andrade D. , Nachbin A.
Published: April 2018

Surface water waves are considered propagating over highly variable non-smooth topographies. For this three-dimensional problem a Dirichlet-to-Neumann (DtN) operator is constructed reducing the numerical modelling and evolution to the two-dimensional free surface. The corresponding discrete Fourier integral operator is defined through a matrix decomposition. The topographic component of the decomposition requires special care, and a Galerkin method is provided accordingly. One-dimensional numerical simulations, along the free surface, validate the DtN formulation in the presence of a large-amplitude rapidly varying topography. An alternative conformal-mapping-based method is used for benchmarking. A two-dimensional simulation in the presence of a Luneburg lens (a particular submerged mound) illustrates the accurate performance of the three-dimensional DtN operator.
Dynamics of detonations with a constant mean flow divergence
Authors: Radulescu Matei I. , Borzou Bijan
Published: April 2018

An exponential horn geometry is introduced in order to establish cellular detonations with a constant mean lateral mass divergence, propagating at quasi-steady speeds below the Chapman–Jouguet value. The experiments were conducted in $2\text{C}_{2}\text{H}_{2}+5\text{O}_{2}+21\text{Ar}$ and $\text{C}_{3}\text{H}_{8}+5\text{O}_{2}$. Numerical simulations were also performed for weakly unstable cellular detonations to test the validity of the exponential horn geometry. The experiments and simulations demonstrated that such quasi-steady state detonations can be realized, hence permitting us to obtain the relations between the detonation speed and mean lateral flow divergence for cellular detonations in an unambiguous manner. The experimentally obtained speed ($D$) dependencies on divergence ($K$) were compared with the predictions for steady detonations with lateral flow divergence obtained with the real thermo-chemical data of the mixtures. For the $2\text{C}_{2}\text{H}_{2}+5\text{O}_{2}+21\text{Ar}$ system, reasonable agreement was found between the experiments and steady wave prediction, particularly for the critical divergence leading to failure. Observations of the reaction zone structure in these detonations indicated that all the gas reacted very close to the front, as the transverse waves were reactive. The experiments obtained in the much more unstable detonations in $\text{C}_{3}\text{H}_{8}+5\text{O}_{2}$ showed significant differences between the experimentally derived $D(K)$ curve and the prediction of steady wave propagation. The latter was found to significantly under-predict the detonability of cellular detonations. The transverse waves in this mixture were found to be non-reactive, hence permitting the shedding of non-reacted pockets, which burn via turbulent flames on their surface. It is believed that the large differences between experiment and the inviscid model in this class of cellular structures is due to the importance of diffusive processes in the burn-out of the non-reacted pockets. The empirical tuning of a global one-step chemical model to describe the macro-scale kinetics in cellular detonations revealed that the effective activation energy was lower by 14 % in $2\text{C}_{2}\text{H}_{2}+5\text{O}_{2}+21\text{Ar}$ and 54 % in the more unstable $\text{C}_{3}\text{H}_{8}+5\text{O}_{2}$ system. This confirms previous observations that diffusive processes in highly unstable detonations are responsible for reducing the thermal ignition character of the gases processed by the detonation front.
New and Mesozoic-relict mollusks from Paleocene wood-fall communities in Urahoro Town, eastern Hokkaido, northern Japan
Authors: Amano Kazutaka , Jenkins Robert G. , Kurita Hiroshi
Published: April 2018

Five species of bivalves and two species of gastropods are described from late Selandian to earliest Thanetian wood-fall communities from the Katsuhira Formation in Urahoro Town, eastern Hokkaido, northern Japan. Three bivalves and two gastropods are new to science:Thyasira(Thyasira)oliveriAmano and Jenkins, new species,Astarte(Astarte)paleocenicaAmano and Jenkins, new species,Poromya katsuhiraensisAmano and Jenkins, new species,Neverita majimaiAmano and Jenkins, new species, andBiplica paleocenicaAmano and Jenkins, new species.Poromya katsuhiraensisn. sp. andNeverita majimain. sp. are the earliest records of their genus.Astarte paleocenican. sp. is the last species before the genus disappeared from the northern Pacific region during the Eocene, only to reappear with the opening of the Bering Strait during the latest Miocene. Moreover, two bivalve species and one gastropod genus are Cretaceous relict forms:Propeamussium yubarense(Yabe and Nagao, 1928),Myrtea ezoensis(Nagao, 1938), andBiplicaPopenoe, 1957. These species and other relict protobranch bivalves had wide geographical ranges in the deep sea during the Cretaceous, which helped them to survive the end-Cretaceous mass extinction. The chemosynthesis-based speciesBathyacmaea? sp.,Myrtea ezoensis, andThyasira oliverin. sp. were recovered, but small bathymodioline mussels have not been found. This confirms that the small deep-sea mussels did not appear in the wood-fall communities at least by the earliest Thanetian.

UUID:http://zoobank.org/125bd4ab-b172-43d9-80b9-57b75a805150
A redescription and phylogenetic analysis based on new material of the fossil newtsTaricha oligocenicaVan Frank, 1955 andTaricha lindoeiNaylor, 1979 (Amphibia, Salamandridae) from the Oligocene of Oregon
Authors: Jacisin John J. , Hopkins Samantha S.B.
Published: April 2018

Complete body fossils of salamanders are relatively rare, but provide critical information on the evolutionary roots of extant urodele clades. We describe new specimens of the fossil salamandridsTaricha oligocenicaVan Frank, 1955, andTaricha lindoeiNaylor, 1979, from the Oligocene Mehama and John Day formations of Oregon that illustrate aspects of skeletal morphology previously unseen in these taxa, and contribute to our understanding of population-level variation. Morphological analysis of these specimens supports the classification ofT.oligocenicaandT.lindoeias two different species, distinct from extantTaricha. Parsimony-based, heuristic analysis of phylogeny using 108 morphological characters for 40 taxa yields different results from a phylogenetic analysis that excludes four taxa known only via vertebrae. Our smaller analysis generally agrees with molecular phylogenies of the family Salamandridae, but with poorer resolution for molgin newts, especially betweenTarichaandNotophthalmus. The analysis including all taxa produced polytomies mostly related to complications from several fossil taxa. The presence or absence of dorsally expanded, sculptured neural spine tables on trunk vertebrae, an important character in past descriptions of fossil salamandrids, appears to be either homoplastic within the Salamandridae, or requires an expansion of characters or character states.Taricha oligocenicaandT. lindoeiare separate species of an at least 33 million-year-old clade, but their relationships with each other and extant North American salamandrids remain unclear with current levels of morphological data. Salamandrid research requires additional morphological data, particularly for the vertebrae and ribs, to better resolve salamandrid evolutionary history through morphological characters.
A late Quaternary paleoenvironmental record in sand dunes of the northern Atacama Desert, Chile
Authors: Finstad Kari M. , Pfeiffer Marco , McNicol Gavin , Tuite Michael , Williford Kenneth , Amundson Ronald
Published: April 2018

This paper reports a previously unidentified paleoenvironmental record found in sand dunes of the Atacama Desert, Chile. Long-term aeolian deflation by prevailing onshore winds has resulted in the deposition of sand on the irregular surface of a Miocene-aged anhydrite outcrop. Two deposits ~25 km apart, along the prevailing wind trajectory, were hand excavated then analyzed for vertical (and temporal) changes in physical and chemical composition. Radiocarbon ages of organic matter embedded within the deposits show that rapid accumulation of sediment began at the last glacial maximum and slowed considerably after the Pacific Ocean attained its present post-glacial level. Over this time period, grain sizes are seen to increase while accumulation rates simultaneously decrease, suggesting greater wind speeds and/or a change or decrease in sediment supply. Changes in δ34S values of sulfate in the sediment beginning ~10 ka indicate an increase in marine sources. Similarly, δ2H values from palmitic acid show a steady increase at ~10 ka, likely resulting from aridification of the region during the Holocene. Due to the extreme aridity in the region, these sand dunes retain a well-preserved chemical record that reflects changes in elevation and coastal proximity after the last glacial maximum.
Radiocarbon Dating and Intercomparison of Some Early Historical Radiocarbon Samples
Authors: Jull A J T , Pearson C L , Taylor R E , Southon J R , Santos G M , Kohl C P , Hajdas I , Molnar M , Baisan C , Lange T E , Cruz R , Janovics R , Major I
Published: April 2018

We performed a new series of measurements on samples that were part of early measurements on radiocarbon (14C) dating made in 1948–1949. Our results show generally good agreement to the data published in 1949–1951, despite vast changes in technology, with only two exceptions where there was a discrepancy in the original studies. Our new measurements give calibrated ages that overlap with the known ages. We dated several samples at four different laboratories, and so we were also able to make a small intercomparison at the same time. In addition, new measurements on samples from other Egyptian materials used by Libby and co-workers were made at UC Irvine. Samples of tree rings used in the original studies (from Broken Flute Cave and Centennial Stump) were obtained from the University of Arizona Laboratory of Tree-Ring Research archive and remeasured. New data were compared to the original studies and other records.
The evolution of human trafficking messaging in the United States and its effect on public opinion
Authors: Bonilla Tabitha , Mo Cecilia Hyunjung
Published: April 2018

Despite a near unanimous agreement that human trafficking is a morally reprehensible practice, there is confusion around what qualifies as human trafficking in the United States. Adopting a mixed-method strategy, we examine how human trafficking is defined by the public; how contemporary (mis)understanding of human trafficking developed; and the public opinion consequence of this (mis)understanding. The definition of human trafficking has evolved over time to become nearly synonymous with slavery; however, we demonstrate that media and anti-trafficking organisations have been focussing their attention on the sexual exploitation of foreign women. We show that general public opinion reflects this skewed attention; the average citizen equates human trafficking with the smuggling of women for sexual slavery. Using a survey experiment, we find that shining light on other facets of human trafficking – the fact that human trafficking is a security problem and a domestic issue – can increase public response to the issue.
Understanding the link between exposure to violence and aggression in justice-involved adolescents
Authors: Wall Myers Tina D. , Salcedo Abigail , Frick Paul J. , Ray James V. , Thornton Laura C. , Steinberg Laurence , Cauffman Elizabeth
Published: April 2018

The current study advanced research on the link between community violence exposure and aggression by comparing the effects of violence exposure on different functions of aggression and by testing four potential (i.e., callous–unemotional traits, consideration of others, impulse control, and anxiety) mediators of this relationship. Analyses were conducted in an ethnically/racially diverse sample of 1,216 male first-time juvenile offenders (M = 15.30 years, SD = 1.29). Our results indicated that violence exposure had direct effects on both proactive and reactive aggression 18 months later. The predictive link of violence exposure to proactive aggression was no longer significant after controlling for proactive aggression at baseline and the overlap with reactive aggression. In contrast, violence exposure predicted later reactive aggression even after controlling for baseline reactive aggression and the overlap with proactive aggression. Mediation analyses of the association between violence exposure and reactive aggression indicated indirect effects through all potential mediators, but the strongest indirect effect was through impulse control. The findings help to advance knowledge on the consequences of community violence exposure on justice-involved youth.
Appropriate Use Criteria for paediatric echocardiography in an outpatient practice: a validation study
Authors: Cartoski Mark J. , Kiley Meghan , Spevak Philip J.
Published: April 2018

Background

Although transthoracic echocardiography is the dominant imaging modality in CHD, optimal utilisation is unclear. We assessed whether adherence to the paediatric Appropriate Use Criteria for outpatient transthoracic echocardiography could reduce inappropriate use without missing significant cardiac disease.

Methods

Using the Appropriate Use Criteria, we determined the indication and appropriateness rating for each initial echocardiogram performed at our institution during calendar year 2014 (N=1383). Chart review documented ordering provider training, patient demographics, and study result, classified as normal, abnormal, or abnormal motivating treatment within a 2-year follow-up period. We tested whether provider training level or patient age correlated with echocardiographic findings or appropriateness rating.

Results

We found that 83.9% of echocardiograms were normal and that 66.7% had an appropriate indication. Nearly all abnormal results and all results motivating treatment were in appropriate studies, giving an odds ratio of 2.73 for an abnormal result if an appropriate indication was present (95% confidence interval 1.92–3.89, p<0.001). None of the remaining initial abnormal results with less than appropriate indications became significant, resulting in treatment over 2 years. Results suggest a potential reduction in imaging volume of as much as 33% with application of the criteria. Cardiologists ordered nearly all studies resulting in treatment but also more echocardiograms with less appropriate indications. Most examinations were in older patients; however, most abnormal results were in patients younger than 1 year.

Conclusions

The Appropriate Use Criteria can be used to safely reduce echocardiography volume while still detecting significant heart disease.
Canadian adaptation of the Newest Vital Sign©, a health literacy assessment tool
Authors: Mansfield Elizabeth D , Wahba Rana , Gillis Doris E , Weiss Barry D , L’Abbé Mary
Published: April 2018

Objective

The Newest Vital Sign© (NVS) was developed in the USA to measure patient health literacy in clinical settings. We adapted the NVS for use in Canada, in English and French, and created a computerized version. Our objective was to evaluate the reliability of the Canadian NVS as a self-administered computerized tool.

Design

We used a randomized crossover design with a washout period of 3–4 weeks to compare health literacy scores obtained using the computerized version with scores obtained using the standard interviewer-administered NVS. ANOVA models and McNemar’s tests assessed differences in outcomes assessed with each version of the NVS and order effects of the testing.

Setting

Participants were recruited from multicultural catchment areas in Ontario and Nova Scotia.

Subjects

English- and French-speaking adults aged 18 years or older.

Results

A total of 180 (81 %) of the 222 adults (112 English/110 French) initially recruited completed both the interviewer-NVS and computer-NVS. Scores for those who completed both assessments ranged from 0 to 6 with a mean of 3·63 (sd 2·11) for the computerized NVS and 3·41 (sd 2·21) for the interview-administered NVS. Few (n 18; seven English, eleven French) participants’ health literacy assessments differed between the two versions.

Conclusions

Overall, the computerized Canadian NVS performed as well as the interviewer-administered version for assessing health literacy levels of English- and French-speaking participants. This Canadian adaptation of the NVS provides Canadian researchers and public health practitioners with an easily administered health literacy assessment tool that can be used to address the needs of Canadians across health literacy levels and ultimately improve health outcomes.
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.
Extended Twin Study of Alcohol Use in Virginia and Australia
Authors: Verhulst Brad , Neale Michael C. , Eaves Lindon J. , Medland Sarah E. , Heath Andrew C. , Martin Nicholas G. , Maes Hermine H.
Published: April 2018

Drinking alcohol is a normal behavior in many societies, and prior studies have demonstrated it has both genetic and environmental sources of variation. Using two very large samples of twins and their first-degree relatives (Australia ≈ 20,000 individuals from 8,019 families; Virginia ≈ 23,000 from 6,042 families), we examine whether there are differences: (1) in the genetic and environmental factors that influence four interrelated drinking behaviors (quantity, frequency, age of initiation, and number of drinks in the last week), (2) between the twin-only design and the extended twin design, and (3) the Australian and Virginia samples. We find that while drinking behaviors are interrelated, there are substantial differences in the genetic and environmental architectures across phenotypes. Specifically, drinking quantity, frequency, and number of drinks in the past week have large broad genetic variance components, and smaller but significant environmental variance components, while age of onset is driven exclusively by environmental factors. Further, the twin-only design and the extended twin design come to similar conclusions regarding broad-sense heritability and environmental transmission, but the extended twin models provide a more nuanced perspective. Finally, we find a high level of similarity between the Australian and Virginian samples, especially for the genetic factors. The observed differences, when present, tend to be at the environmental level. Implications for the extended twin model and future directions are discussed.
Chlorophyll to Carbon Ratio Derived From a Global Ecosystem Model With Photodamage
Authors: Álvarez E. , Thoms S. , Völker C.
Published: April 2018

Phytoplankton 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

Soil 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

The 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

Atmospheric 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.
How Paleofire Research Can Better Inform Ecosystem Management
Authors: Lestienne Marion , Aleman Julie , Colombaroli Daniele
Published: April 2018

Global Paleofire Working Group 2: Paleofire Knowledge for Current and Future Ecosystem Management; Saint-Hippolyte, Quebec, Canada, 10–14 October 2017
New NASA Administrator Sworn In
Authors: Showstack Randy
Published: April 2018

Bridenstine says bipartisanship “is important in space.” Many Democrats, however, worry that he will be too partisan.
Attribution of Local Temperature Response to Deforestation
Authors: Liao Weilin , Rigden Angela J. , Li Dan
Published: April 2018

Land 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

Excessive 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

The 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

The 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

Many 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

Microfluidic 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

We 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

Preclinical 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

The 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.
Dehydration prompts increased activity and blood feeding by mosquitoes
Authors: Hagan Richard W. , Didion Elise M. , Rosselot Andrew E. , Holmes Christopher J. , Siler Samantha C. , Rosendale Andrew J. , Hendershot Jacob M. , Elliot Kiaira S. B. , Jennings Emily C. , Nine Gabriela A. , Perez Paula L. , Rizlallah Alexandre E. , Watanabe Miki , Romick-Rosendale Lindsey E. , Xiao Yanyu , Rasgon Jason L. , Benoit Joshua B.
Published: April 2018

Current insights into the mosquito dehydration response rely on studies that examine specific responses but ultimately fail to provide an encompassing view of mosquito biology. Here, we examined underlying changes in the biology of mosquitoes associated with dehydration. Specifically, we show that dehydration increases blood feeding in the northern house mosquito, Culex pipiens, which was the result of both higher activity and a greater tendency to land on a host. Similar observations were noted for Aedes aegypti and Anopheles quadrimaculatus. RNA-seq and metabolome analyses in C. pipiens following dehydration revealed that factors associated with carbohydrate metabolism are altered, specifically the breakdown of trehalose. Suppression of trehalose breakdown in C. pipiens by RNA interference reduced phenotypes associated with lower hydration levels. Lastly, mesocosm studies for C. pipiens confirmed that dehydrated mosquitoes were more likely to host feed under ecologically relevant conditions. Disease modeling indicates dehydration bouts will likely enhance viral transmission. This dehydration-induced increase in blood feeding is therefore likely to occur regularly and intensify during periods when availability of water is low.
Effective in vivo treatment of acute lung injury with helical, amphipathic peptoid mimics of pulmonary surfactant proteins
Authors: Czyzewski Ann M. , McCaig Lynda M. , Dohm Michelle T. , Broering Lauren A. , Yao Li-Juan , Brown Nathan J. , Didwania Maruti K. , Lin Jennifer S. , Lewis Jim F. , Veldhuizen Ruud , Barron Annelise E.
Published: April 2018

Acute lung injury (ALI) leads to progressive loss of breathing capacity and hypoxemia, as well as pulmonary surfactant dysfunction. ALI’s pathogenesis and management are complex, and it is a significant cause of morbidity and mortality worldwide. Exogenous surfactant therapy, even for research purposes, is impractical for adults because of the high cost of current surfactant preparations. Priorin vitrowork has shown that poly-N-substituted glycines (peptoids), in a biomimetic lipid mixture, emulate key biophysical activities of lung surfactant proteins B and C at the air-water interface. Here we report goodin vivoefficacy of a peptoid-based surfactant, compared with extracted animal surfactant and a synthetic lipid formulation, in a rat model of lavage-induced ALI. Adult rats were subjected to whole-lung lavage followed by administration of surfactant formulations and monitoring of outcomes. Treatment with a surfactant protein C mimic formulation improved blood oxygenation, blood pH, shunt fraction, and peak inspiratory pressure to a greater degree than surfactant protein B mimic or combined formulations. All peptoid-enhanced treatment groups showed improved outcomes compared to synthetic lipids alone, and some formulations improved outcomes to a similar extent as animal-derived surfactant. Robust biophysical mimics of natural surfactant proteins may enable new medical research in ALI treatment.
Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
Authors: Stroehlein Andreas J. , Young Neil D. , Gasser Robin B.
Published: April 2018

Despite the substantial amount of genomic and transcriptomic data available for a wide range of eukaryotic organisms, most genomes are still in a draft state and can have inaccurate gene predictions. To gain a sound understanding of the biology of an organism, it is crucial that inferred protein sequences are accurately identified and annotated. However, this can be challenging to achieve, particularly for organisms such as parasitic worms (helminths), as most gene prediction approaches do not account for substantial phylogenetic divergence from model organisms, such as Caenorhabditis elegans and Drosophila melanogaster, whose genomes are well-curated. In this paper, we describe a bioinformatic strategy for the curation of gene families and subsequent annotation of encoded proteins. This strategy relies on pairwise gene curation between at least two closely related species using genomic and transcriptomic data sets, and is built on recent work on kinase complements of parasitic worms. Here, we discuss salient technical aspects of this strategy and its implications for the curation of protein families more generally.