bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community science validates climate suitability projections from ecological niche modeling
Authors: Saunders Sarah P. , Michel Nicole L. , Bateman Brooke L. , Wilsey Chad B. , Dale Kathy , LeBaron Geoffrey S. , Langham Gary M. 
Published: March 2020

AbstractClimate change poses an intensifying threat to many bird species and projections of future climate suitability provide insight into how species may shift their distributions in response. Climate suitability is characterized using ecological niche models (ENMs), which correlate species occurrence data with current environmental covariates and project future distributions using the modeled relationships together with climate predictions. Despite their widespread adoption, ENMs rely on several assumptions that are rarely validated in situ and can be highly sensitive to modeling decisions, precluding their reliability in conservation decision‐making. Using data from a novel, large‐scale community science program, we developed dynamic occupancy models to validate near‐term climate suitability projections for bluebirds and nuthatches in summer and winter. We estimated occupancy, colonization, and extinction dynamics across species’ ranges in the United States in relation to projected climate suitability in the 2020s, and used a Gibbs variable selection approach to quantify evidence of species–climate relationships. We also included a Bird Conservation Region strata‐level random effect to examine among‐strata variation in occupancy that may be attributable to land‐use and ecoregional differences. Across species and seasons, we found strong evidence that initial occupancy and colonization were positively related to 2020 climate suitability, illustrating an independent validation of projections from ENMs across a large geographic area. Random strata effects revealed that occupancy probabilities were generally higher than average in core areas and lower than average in peripheral areas of species’ ranges, and served as a first step in identifying spatial patterns of occupancy from these community science data. Our findings lend much‐needed support to the use of ENM projections for addressing questions about potential climate‐induced changes in species’ occupancy dynamics. More broadly, our work highlights the value of community scientist observations for ground‐truthing projections from statistical models and for refining our understanding of the processes shaping species’ distributions under a changing climate.
Temporal and energetic drivers of seed resource use by Clark's nutcracker, keystone seed disperser of coniferous forests
Authors: Williams Tyler J. , Tomback Diana F. , Grevstad Nels , Broms Kristin 
Published: March 2020

AbstractClark's nutcracker (Nucifraga columbiana) functions as a keystone seed disperser and ecological mobile link for many western conifers. The bird is the primary seed disperser for limber pine (Pinus flexilis), which is an important seed resource for the bird. In the Southern Rocky Mountains, annual variation in limber pine cone production and growing threats, such as exotic disease, require that nutcrackers rely on additional conifer seed resources. We investigated the utilization of limber pine, ponderosa pine (Pinus ponderosa), and Douglas‐fir (Pseudotsuga menziesii) as seed resources by nutcrackers to determine how temporal variation in seed production and maturation drives nutcracker seed resource and habitat use decisions. Working in Rocky Mountain National Park (RMNP) during three field seasons, we examined (1) cone production in limber pine, ponderosa pine, and Douglas‐fir, and seed energy availability across theRMNPlandscape; (2) timing and likelihood of nutcracker seed harvest and caching behavior for each conifer species; and (3) predictors of nutcracker visitation to the different forest stand types. Each year starting in mid‐ to late August, nutcrackers foraged on limber pine seeds. In 2014 and 2015, nutcrackers transitioned from limber pine to harvesting ponderosa pine seeds. In 2016, a year of low ponderosa pine cone production but exceptionally high Douglas‐fir cone production, they transitioned from limber pine to Douglas‐fir seeds. Cone density was a significant predictor of nutcracker counts in every negative binomial regression model in which it was used. However, the best overall model, which included interaction effects, indicated that stand type, year, and month were better predictors. We interpret these three predictors as reflecting temporal variation in patterns of cone production and maturation among the three conifers but also in habitat use by nutcrackers. In all three years of study, limber pine alone did not provide sufficient energy resources for foraging and caching, and nutcrackers used an additional conifer seed resource. With potential future limber pine losses, these other seed resources may be essential to sustain a nutcracker population. We suggest that Douglas‐fir and especially ponderosa pine will serve as increasingly important food resources as limber pine declines across the montane West.
Establishment rate of regional provenances mirrors relative share and germination rate in a climate change experiment
Authors: Madaj Anna‐Maria , Michalski Stefan G. , Durka Walter 
Published: March 2020

AbstractClimate change and land‐use changes are among the major threats to biodiversity as they alter global and local environmental conditions in unprecedented dimensions. Therefore, the investigation of the ability of species and communities to cope with rapidly changing environments as well as the comprehensive understanding of possible evolutionary adaptation processes is urgently needed for their sustainable management and the maintenance of associated ecosystem processes. Here, seminatural grasslands receive special attention, because they are among the most species‐rich ecosystems in Central Europe, which are threatened by global change and land‐use intensification already since the beginning of the twentieth century. Hence, understanding their potential to respond to rapidly changing environments is important for future management. Here, the Global Change Experimental Facility (GCEF) is an opportunity to investigate the role of microevolution in response to climate change. Two of the land‐use regimes in the GCEF are seminatural, extensively used species‐rich meadow and pasture grasslands established by sowing common, native, and regionally typical grassland species in 2014. In view of ecological restoration, for each species a seed mixture of up to seven source populations was sown aiming to establish high levels of intraspecific variation from the regional gene pool. Here, we present the first evaluation of genetic and trait variation of source populations and of their establishment in the GCEF two years after sowing for six grassland species. Using AFLP markers, we assessed genetic variation of source populations and tested whether the source gene pools have established in the experiment. Additionally, we investigated phenotypic variation of source populations and performed PST‐FST comparisons to test whether trait differentiation is adaptive. Our study revealed that genetic and phenotypic differentiation of source populations is widespread in the grassland species studied, even on small geographic scales. The GCEF populations are highly diverse due to the mixture of the different, often genetically and phenotypically differentiated source populations. They represent a genetically diverse source for both selection among existing and evolution of new genotypes. Thus, the GCEF can be used as experiment to study evolutionary processes in response to the climate change and land‐use scenarios.
TIM‐3 and CEACAM1 do not interact incisand intrans
Authors: De Sousa Linhares Annika , Kellner Florian , Jutz Sabrina , Zlabinger Gerhard J. , Gabius Hans‐Joachim , Huppa Johannes B. , Leitner Judith , Steinberger Peter 
Published: March 2020

AbstractTIM‐3 has been considered as a target in cancer immunotherapy. In T cells, inhibitory as well as activating functions have been ascribed to this molecule. Its role may therefore depend on the state of T cells and on the presence of interaction partners capable to perform functional pairing. Carcinoembryonic antigen‐related cell adhesion molecule (CEACAM1) has been proposed to bind TIM‐3 and to regulate its function. Using a T cell reporter platform we confirmed CEACAM1‐mediated inhibition, but CEACAM1 did not functionally engage TIM‐3. TIM‐3 and CEACAM1 coexpression was limited to a small subset of activated T cells. Moreover, results obtained in extensive binding studies were not in support of an interaction between TIM‐3 and CEACAM1. Cytoplasmic sequences derived from TIM‐3 induced inhibitory signaling in our human T cell reporter system.Our results indicate that TIM‐3 functions are independent of CEACAM1 and that this receptor has the capability to promote inhibitory signaling pathways in human T cells.
Malaria exposure drives both cognate and bystander human B cells to adopt an atypical phenotype
Authors: Aye Racheal , Sutton Henry J. , Nduati Eunice W. , Kai Oscar , Mwacharo Jedida , Musyoki Jennifer , Otieno Edward , Wambua Juliana , Bejon Philip , Cockburn Ian A. , Ndungu Francis M. 
Published: March 2020

AbstractAtypical memory B cells (aMBCs) are found in elevated numbers in individuals exposed to malaria. A key question is whether malaria induces aMBCs as a result of exposure to Ag, or non‐Ag‐specific mechanisms. We identified Plasmodium and bystander tetanus toxoid (TT) specific B cells in individuals from areas of previous and persistent exposure to malaria using tetramers. Malaria‐specific B cells were more likely to be aMBCs than TT‐specific B cells. However, TT‐specific B cells from individuals with continuous exposure to malaria were more likely to be aMBCs than TT‐specific B cells in individuals from areas where transmission has ceased. Finally, sequences of BCRs specific for a blood stage malaria‐Ag were more highly mutated than sequences from TT‐specific BCRs and under strong negative selection, indicative of ongoing antigenic pressure. Our data suggest both persistent Ag exposure and the inflammatory environment shape the B‐cell response to malaria and bystander Ags.
Psychological and pain profiles in persons with patellofemoral pain as the primary symptom
Authors: Maclachlan Liam R. , Collins Natalie J. , Hodges Paul W. , Vicenzino Bill 
Published: March 2020

AbstractBackgroundPatellofemoral pain (PFP) is defined biomechanically, but is characterized by features that fit poorly within nociceptive pain. Mechanisms associated with central sensitization may explain why, for some, symptoms appear nociplastic. This study compares psychological and somatosensory characteristics between those with persistent PFP and controls.MethodsA total of 150 adults with PFP were compared to 61 controls. All participants completed a survey evaluating participant characteristics, PFP‐related constructs and psychological factors: anxiety, depression, pain catastrophizing, kinesiophobia, pain self‐efficacy. Participants also attended a session of somatosensory testing, which included knee and elbow thermal and mechanical detection and pain thresholds, conditioned pain modulation (CPM), and temporal summation of pain (TSP). Differences were evaluated using analysis of covariance (sex as covariate). Multivariate backward stepwise linear regression examined how psychological and somatosensory variables relate to PFP (knee injury and osteoarthritis outcome score‐patellofemoral [KOOS‐PF]).ResultsThe PFP group had multimodal reduced pain thresholds at the knee and elbow (standardized mean difference [SMD], p: 0.86–1.2, <.001), reduced mechanical detection at the elbow (0.43, .01) and higher TSP (0.41, .01). CPM was not different. Psychological features demonstrated small effects (0.47–0.59, 0.01–0.04). The PFP group had a 55% (95% CI: 0.47–0.62) risk of kinesiophobia and an 11% (0.06–0.15) reduced pain self‐efficacy risk. Kinesiophobia, knee pressure pain threshold, pain self‐efficacy and pain catastrophizing explained 40% of KOOS‐PF variance (p = <.001).ConclusionsWidespread hyperalgesia and evidence of symptom amplification may reflect nociplastic pain. Clinicians should be aware that kinesiophobia and the nociplastic pain may characterize the condition.Significance(a) Individuals with PFP have widespread reduced pain thresholds to pressure and thermal stimuli. (b) Mechanically induced pain is likely amplified in those with PFP. (c) Pain‐related fear is highly prevalent and helps explain PFP‐related disability.
Interpretation biases and visual attention in the processing of ambiguous information in chronic pain
Authors: Chan Frederick H. F. , Suen Hin , Hsiao Janet H. , Chan Antoni B. , Barry Tom J. 
Published: March 2020

AbstractBackgroundTheories propose that interpretation biases and attentional biases might account for the maintenance of chronic pain symptoms, but the interactions between these two forms of biases in the context of chronic pain are understudied.MethodsTo fill this gap, 63 participants (40 females) with and without chronic pain completed an interpretation bias task that measures participants’ interpretation styles in ambiguous scenarios and a novel eye‐tracking task where participants freely viewed neutral faces that were given ambiguous pain/health‐related labels (i.e. ‘doctor’, ‘patient’ and ‘healthy people’). Eye movements were analysed with the Hidden Markov Models (EMHMM) approach, a machine‐learning data‐driven method that clusters people's eye movements into different strategy subgroups.ResultsAdults with chronic pain endorsed more negative interpretations for scenarios related to immediate bodily injury and long‐term illness than healthy controls, but they did not differ significantly in terms of their eye movements on ambiguous faces. Across groups, people who interpreted illness‐related scenarios in a more negative way also focused more on the nose region and less on the eye region when looking at patients’ and healthy people's faces and, to a lesser extent, doctors’ faces. This association between interpretive and attentional processing was particularly apparent in participants with chronic pain.ConclusionsIn summary, the present study provided evidence for the interplay between multiple forms of cognitive biases. Future studies should investigate whether this interaction might influence subsequent functioning in people with chronic pain.
Experimental Estimation of 44 Pharmaceutical Polar Organic Chemical Integrative Sampler Sampling Rates in an Artificial River under Various Flow Conditions
Authors: Guibal R. , Lissalde S. , Guibaud G. 
Published: March 2020

Abstract
The present study pertains to a polar organic chemical integrative sampler (POCIS) laboratory calibration to estimate the sampling rates for 44 pharmaceuticals featuring a wide range of polarity (–0.6 &lt; octanol/water partition coefficient [log KOW] &lt; 5.4). The calibration was performed at 16.0 ± 1.5 °C for 4 water flow velocities (0, 2–3, 6–7, and 20 cm/s) in both a tank (for calibration at 0 cm/s) and a laboratory-scale artificial river filled with 200 and 500 L of tap water spiked with 0.3 µg/L of each compound, respectively. Twelve new sampling rates and 26 sampling rates already available in the literature were determined, whereas the sampling rates for 6 pharmaceuticals could not be determined due to nonlinearity or poor accumulation in POCIS. An increase in the sampling rate value with flow velocity was observed, which is consistent with a decrease in the effective thickness of the water boundary layer at the POCIS membrane surface. Environ Toxicol Chem 2020;39:1186–1195. © 2020 SETAC
Interaction of a deformable solid with two‐phase flows: An Eulerian‐based numerical model for fluid‐structure interaction using the level contour reconstruction method
Authors: Shin Seungwon , Chergui Jalel , Juric Damir 
Published: March 2020

SummaryWe describe the formulation of a method for fluid‐structure interaction involving the coupling of moving and/or flexible solid structures with multiphase flows in the framework of the Level Contour Reconstruction Method. We present an Eulerian‐based numerical procedure for tracking the motion and interaction of a liquid‐gas interface with a fluid‐solid interface in the Lagrangian frame together with the evaluation of the fluid transport equations coupled to those for the solid transport, namely the left Cauchy‐Green strain tensor field, in the Eulerian frame. To prevent excessive dissipation due to the convective nature of the solid transport equation, a simple incompressibility constraint for the strain field is enforced. A single grid structure is used for both the fluid and solid phases which allows for a simple and natural coupling of the fluid and solid dynamics. Several benchmark tests are performed to show the accuracy of the numerical method and which demonstrate accurate results compared to several of those in the existing literature. In particular we show that surface tension effects including contact line dynamics on the deforming solid phase can be properly simulated. The three‐phase interaction of a droplet impacting on a flexible cantilever is investigated in detail. The simulations follow the detailed motion of the droplet impact (and subsequent deformation, breakup, and fall trajectory) along with the motion of the deformable solid cantilever due to its own weight as well as due to the force of the droplet impact.
Motion, deformation, and coalescence of ferrofluid droplets subjected to a uniform magnetic field
Authors: Khan Adnan , Niu Xiao‐Dong , Li You , Wen Ming‐Fu , Li De‐Cai , Yamaguchi Hiroshi 
Published: March 2020

AbstractIn this article, we present the motion, deformation, and coalescence of ferrofluid droplets suspended in a nonmagnetic fluid, subjected to a uniform magnetic field in both vertical and horizontal directions. A coupling between the simplified multiphase lattice Boltzmann method and the self‐correcting scheme is constructed to numerically solve the two‐dimensional flow field and the magnetostatics equations, respectively. The Cahn‐Hilliard equation is employed to seize the diffuse interface between magnetic and nonmagnetic fluids. In order to validate the model, deformation of a ferrofluid droplet suspended in nonmagnetic fluid is simulated as a test case and the results are compared with numerical and experimental results. Furthermore, a detailed analysis on the behavior of falling ferrofluid droplets and the coalescence between a pair of ferrofluid droplets under the effect of different magnetic fields and different droplets configurations are also presented in this article. The results provide significant insight and a better understanding of these phenomena. It is found that for higher values of magnetic bond number and susceptibility, the droplet deformation is significant and the falling process is faster while a reverse behavior is observed for higher values of Eötvös number. Moreover, the magnetic energy density exhibits an interesting behavior in the vicinity of the droplets. It is concentrated between the droplets with a nonuniform distribution when the droplets are close to each other.
Plant‐Based and Animal‐Based Low‐Carbohydrate Diets and Risk of Hepatocellular Carcinoma Among US Men and Women
Authors: Liu Yue , Yang Wanshui , VoPham Trang , Ma Yanan , Simon Tracey G. , Gao Xiang , Chan Andrew T. , Meyerhardt Jeffrey A. , Giovannucci Edward L. , Zhang Xuehong 
Published: March 2020

Background and Aims
Little is known about the role of low‐carbohydrate diets (LCDs) in the development of hepatocellular carcinoma (HCC). We prospectively evaluated the associations between plant‐based and animal‐based LCDs and risk of HCC in the Nurses’ Health Study (NHS) and the Health Professionals Follow‐up Study (HPFS).

Approach and Results
Dietary intake was assessed every 4 years using validated food frequency questionnaires. Cox proportional hazards regression models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs). HRs are shown for a 1‐standard deviation (SD) increment with variables modeled as continuous. During 3,664,769 person‐years of follow‐up, there were 156 incident HCC cases. Although there were no associations between overall or animal‐based LCD score and risk of HCC, plant‐based LCD score was inversely associated with HCC risk (HR, 0.83; 95% CI, 0.70‐0.98; P
trend = 0.03). Carbohydrate intake, especially from refined grains (HR, 1.18; 95% CI, 1.00‐1.39; P
trend = 0.04), was positively, while plant fat (HR, 0.78; 95% CI, 0.65‐0.95; P
trend = 0.01) was inversely associated with HCC risk. Substituting 5% of energy from plant fat and protein for carbohydrate (HR, 0.74; 95% CI, 0.58‐0.93; P
trend = 0.01) or refined grains (HR, 0.70; 95% CI, 0.55‐0.90; Ptrend
= 0.006) was associated with lower HCC risk. In conclusion, a plant‐based LCD and dietary restriction of carbohydrate from refined grains were associated with a lower risk of HCC. Substituting plant fat and protein for carbohydrate, particularly refined grains, may decrease HCC incidence.

Conclusions
Our findings support a potential benefit in emphasizing plant sources of fat and protein in the diet for HCC primary prevention; additional studies that carefully consider hepatitis B and C virus infections and chronic liver diseases are needed to confirm our findings.
Regional Differences in Human Biliary Tissues and Corresponding In Vitro–Derived Organoids
Authors: Rimland Casey A. , Tilson Samantha G. , Morell Carola M. , Tomaz Rute A. , Lu Wei‐Yu , Adams Simone E. , Georgakopoulos Nikitas , Otaizo‐Carrasquero Francisco , Myers Timothy G. , Ferdinand John R. , Gieseck Richard L. , Sampaziotis Fotios , Tysoe Olivia C. , Ross Alexander , Kraiczy Judith M. , Wesley Brandon , Muraro Daniele , Zilbauer Matthias , Oniscu Gabriel C. , Hannan Nicholas R.F. , Forbes Stuart J. , Saeb‐Parsy Kourosh , Wynn Thomas A. , Vallier Ludovic 
Published: March 2020

Background and Aims
Organoids provide a powerful system to study epithelia in vitro. Recently, this approach was applied successfully to the biliary tree, a series of ductular tissues responsible for the drainage of bile and pancreatic secretions. More precisely, organoids have been derived from ductal tissue located outside (extrahepatic bile ducts; EHBDs) or inside the liver (intrahepatic bile ducts; IHBDs). These organoids share many characteristics, including expression of cholangiocyte markers such as keratin (KRT) 19. However, the relationship between these organoids and their tissues of origin, and to each other, is largely unknown.

Approach and Results
Organoids were derived from human gallbladder, common bile duct, pancreatic duct, and IHBDs using culture conditions promoting WNT signaling. The resulting IHBD and EHBD organoids expressed stem/progenitor markers leucine‐rich repeat–containing G‐protein‐coupled receptor 5/prominin 1 and ductal markers KRT19/KRT7. However, RNA sequencing revealed that organoids conserve only a limited number of regional‐specific markers corresponding to their location of origin. Of particular interest, down‐regulation of biliary markers and up‐regulation of cell‐cycle genes were observed in organoids. IHBD and EHBD organoids diverged in their response to WNT signaling, and only IHBDs were able to express a low level of hepatocyte markers under differentiation conditions.

Conclusions
Taken together, our results demonstrate that differences exist not only between extrahepatic biliary organoids and their tissue of origin, but also between IHBD and EHBD organoids. This information may help to understand the tissue specificity of cholangiopathies and also to identify targets for therapeutic development.