bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apoptosis in the fetal testis eliminates developmentally defective germ cell clones
Authors: Nguyen Daniel H. , Laird Diana J. 
Published: April 2019

SummaryMany germ cells (GCs) are eliminated during development, long before differentiating to egg or sperm, but it is not clear why. Here, we examined how GC composition in the mouse fetal testis is altered by scheduled apoptosis during sex differentiation. Multicolored-lineage tracing revealed that apoptosis affects clonally-related GCs, suggesting that this fate decision occurs autonomously based on shared intrinsic properties. We identified extensive transcriptional heterogeneity among fetal GCs including an apoptosis-susceptible subpopulation delineated by high Trp53 and deviant differentiation. Alternatively, the GC subpopulation most likely to survive was advanced in differentiation. These results indicate that GC developmental fate is based upon discrete and cell-heritable fitnesses and imply that a dichotomy between sex-differentiation and apoptosis coordinates the removal of developmentally incompetent cells to improve gamete quality. Evidence that GC subpopulations are in different epigenetic states suggests that errors in epigenetic reprogramming form the basis of aberrant differentiation and apoptotic selection.One sentence summaryGerm cells undergo autonomous selection in the fetal testis to promote male differentiation
CNTNAP2 is targeted to endosomes by the polarity protein Par3
Authors: Gao Ruoqi , Pratt Christopher P. , Yoon Sehyoun , Martin-de-Saavedra Maria Dolores , Forrest Marc P. , Penzes Peter 
Published: April 2019

AbstractA decade of genetic studies has established Contactin-associated protein-like 2 (CNTNAP2) as a prominent susceptibility gene associated with multiple neurodevelopmental disorders. The development and characterization of Cntnap2 knockout models in multiple species have bolstered this claim by establishing clear connections with certain endophenotypes. Despite these remarkable in vivo findings, CNTNAP2’s molecular functions are relatively unexplored, highlighting the need to identify novel protein partners. Here, we characterized an interaction between CNTNAP2 and Partitioning-defective 3 (Par3) – a polarity molecule we isolated in a yeast-two hybrid screen with CNTNAP2’s C-terminus. We provide evidence that the two proteins interact via PDZ domain-mediated binding, that CNTNAP2+/Par3+ complexes are largely associated with clathrin-coated endocytic vesicles, and that Par3 causes an enlargement of these structures. Live imaging and fluorescence recovery after photobleaching (FRAP) reveals that Par3 limits the mobility of CNTNAP2 at endosomes, thus stabilizing it at that location. Finally, expression of Par3 but not Par3ΔPDZ can cluster endogenous CNTNAP2 in primary neurons. Collectively, we conclude that Par3 regulates CNTNAP2 spatial localization to endocytic compartments.
Direct migration of ambient seismic data
Authors: Girard Aaron J. , Shragge Jeffrey 
Published: April 2019

ABSTRACTUtilising ambient seismic energy naturally propagating in the Earth as an alternative approach to active body‐wave seismic investigations has been a topic of interest for a number of decades. However, because ambient surface‐wave arrivals typically are of much greater amplitude than ambient body‐wave energy, significant data signal processing and long recording times are required to mitigate this and other coherent noise sources, and to correlate sufficient reflected body‐wave energy to converge to a stable image. Even for these scenarios, identifying and validating imaged body‐wave reflection events remain challenging. In active‐source investigations, extended imaging condition gathers are used to examine velocity (in)accuracy. Herein, we develop an ambient direct migration approach that uses a novel ambient (deconvolution) extended imaging condition. We simulate synthetic ambient‐wavefield seismic data for two different models and use a field data set from Lalor Lake in Manitoba, Canada, to conduct a series of numerical experiments to demonstrate the velocity sensitivity and long‐term stationarity of ambient‐wavefield seismic data in the migration image domain. Tests with varying global velocity perturbations show a characteristic reflector moveout in deconvolution extended imaging condition gathers that can serve as a diagnostic of reflected ambient body‐wave energy. We illustrate that this imaging formalism, under idealised circumstances, gives comparable results to conventional seismic methods, which extends the use of extended imaging condition gather‐based image validation to ambient‐wavefield seismic data scenarios. We assert that this may be a valuable tool for the validation of ambient migration techniques that to date have yielded largely inconclusive results.
A hybrid optimization scheme for self‐potential measurements due to multiple sheet‐like bodies in arbitrary 2D resistivity distributions
Authors: Giannakis Iraklis , Tsourlos Panagiotis , Papazachos Costas , Vargemezis George , Giannopoulos Antonios , Papadopoulos Nikos , Tosti Fabio , Alani Amir 
Published: April 2019

ABSTRACTSelf‐potential is a passive geophysical method that can be applied in a straightforward manner with minimum requirements in the field. Nonetheless, interpretation of self‐potential data is particularly challenging due to the inherited non‐uniqueness present in all potential methods. Incorporating information regarding the target of interest can facilitate interpretation and increase the reliability of the final output. In the current paper, a novel method for detecting multiple sheet‐like targets is presented. A numerical framework is initially described that simulates sheet‐like bodies in an arbitrary 2D resistivity distribution. A scattered field formulation based on finite differences is employed that allows the edges of the sheet to be independent of the grid geometry. A novel analytical solution for two‐layered models is derived and subsequently used to validate the accuracy of the proposed numerical scheme. Lastly, a hybrid optimization is proposed that couples linear least‐squares with particle‐swarm optimization in order to effectively locate the edges of multiple sheet‐like bodies. Through numerical and real data, it is proven that the hybrid optimization overcomes local minimal that occurs in complex resistivity distributions and converges substantially faster compared to traditional particle‐swarm optimization.
Top‐down effects of repatriating bald eagles hinder jointly recovering competitors
Authors: Cruz Jennyffer , Windels Steve K. , Thogmartin Wayne E. , Crimmins Shawn M. , Grim Leland H. , Larson James H. , Zuckerberg Benjamin 
Published: April 2019

AbstractThe recovery of piscivorous birds around the world is touted as one of the great conservation successes of the 21st century, but for some species, this success was short‐lived. Bald eagles, ospreys and great blue herons began repatriating Voyageurs National Park, USA, in the mid‐20th century. However, after 1990, only eagles continued their recovery, while osprey and heron recovery failed for unknown reasons.We aimed to evaluate whether top‐down effects of bald eagles and bottom‐up effects of inclement weather, habitat quality and fish resources contributed to the failed recovery of ospreys and herons in a protected area.We quantified the relative influence of top‐down and bottom‐up factors on nest colonization, persistence (i.e., nest reuse) and success for ospreys, and occurrence and size of heronries using 26 years (1986–2012) of spatially explicit monitoring data coupled with multi‐response hierarchical models and Bayesian variable selection approaches.Bald eagles were previously shown to recover faster due to intensive nest protection and management. Increased numbers of eagles were associated with a reduction in the numbers of osprey nests, their nesting success and heronry size, while higher local densities of nesting eagles deterred heronries nearby. We found little evidence of bottom‐up limitations on the failed recovery of herons and ospreys.We present a conservation conundrum: bald eagles are top predators and a flagship species of conservation that have benefited from intensive protection, but this likely hindered the recovery of ospreys and herons. Returning top predators, or rewilding, is widely promoted as a conservation strategy for top‐down ecosystem recovery, but managing top predators in isolation of jointly recovering species can halt or reverse ecosystem recovery. Previous studies warn of the potential consequences of ignoring biotic interactions amongst recovering species, but we go further by quantifying how these interactions contributed to failed recoveries via impacts on the nesting demography of jointly recovering species. Multi‐species management is paramount to realizing the ecosystem benefits of top predator recovery.
Native forage mediates influence of irrigated agriculture on migratory behaviour of elk
Authors: Barker Kristin J. , Mitchell Michael S. , Proffitt Kelly M. 
Published: April 2019

Abstract

Ungulates migrate to maximize nutritional intake when forage varies seasonally. Populations of ungulates often include both migratory and non‐migratory individuals, but the mechanisms driving individual differences in migratory behaviour are not well‐understood.

We quantified associations between hypothesized drivers of partial migration and the likelihood of migration for individual ungulates that experienced a range of environmental conditions and anthropogenic influences.

We evaluated the effects of forage variation, conspecific density, and human land uses on migratory behaviour of 308 adult female elk in 16 herds across western Montana.

We found irrigated agriculture on an individual's winter range reduced migratory behaviour, but individuals were more likely to migrate away from irrigated agricultural areas if better forage was available elsewhere or if they experienced high conspecific density on their winter range. When the forage available during the summer growing season varied predictably between years, elk were more likely to migrate regardless of whether they had access to irrigated agriculture.

Our study shows that predictable availability of beneficial native forage can encourage migration even for ungulates with irrigated agriculture on their winter range. Perturbations that can affect the forage available to ungulates include wildfires, timber harvest, livestock grazing and changing weather patterns. If these or other disturbances negatively affect forage on summer ranges of migrants, or if they cause forage to vary unpredictably across space and time, our results suggest migratory behaviour may decline as a result.
Plant functional trait shifts explain concurrent changes in the structure and function of grassland soil microbial communities
Authors: Boeddinghaus Runa S. , Marhan Sven , Berner Doreen , Boch Steffen , Fischer Markus , Hölzel Norbert , Kattge Jens , Klaus Valentin H. , Kleinebecker Till , Oelmann Yvonne , Prati Daniel , Schäfer Deborah , Schöning Ingo , Schrumpf Marion , Sorkau Elisabeth , Kandeler Ellen , Manning Peter 
Published: April 2019

Abstract

Land‐use intensification drives changes in microbial communities and the soil functions they regulate, but the mechanisms underlying these changes are poorly understood as land use can affect soil communities both directly (e.g. via changes in soil fertility) and indirectly (e.g. via changes in plant inputs).

The speed of microbial responses is also poorly understood. For instance, whether it is long‐term legacies or short‐term changes in land‐use intensity that drive changes in microbial communities.

To address these topics, we measured multiple microbial functions, bacterial and fungal biomass and abiotic soil properties at two time intervals 3 years apart. This was performed in 150 grassland sites differing greatly in management intensity across three German regions.

Observed changes in microbial soil properties were related to both long‐term means and short‐term changes in: abiotic soil properties, land‐use intensity, community abundance‐weighted means of plant functional traits and plant biomass properties in regression and structural equation models. Plant traits, particularly leaf phosphorus, and soil pH were the best predictors of change in soil microbial function, as well as fungal and bacterial biomass, while land‐use intensity showed weaker effects.

Indirect legacy effects, in which microbial change was explained by the effects of long‐term land‐use intensity on plant traits, were important, thus indicating a time lag between plant community and microbial change. Whenever the effects of short‐term changes in land‐use intensity were present, they acted directly on soil microorganisms.

Synthesis. The results provide new evidence that soil communities and their functioning respond to short‐term changes in land‐use intensity, but that both rapid and longer time‐scale responses to changes in plant functional traits are at least of equal importance. This suggests that management which shapes plant communities may be an effective means of managing soil communities and the functions and services they provide.
Trait identity and functional diversity co‐drive response of ecosystem productivity to nitrogen enrichment
Authors: Zhang Dianye , Peng Yunfeng , Li Fei , Yang Guibiao , Wang Jun , Yu Jianchun , Zhou Guoying , Yang Yuanhe 
Published: April 2019

Abstract

Exploring the mechanisms underlying the change in ecosystem productivity under anthropogenic nitrogen (N) inputs is of fundamental ecological interest. It has been proposed that functional traits, environmental factors and species richness are central drivers linking ecosystem productivity with environmental change. However, few studies have considered the joint effects of functional traits, environmental factors and species richness on ecosystem productivity under increasing N inputs.

We established a N‐manipulation experiment in a Tibetan alpine steppe in 2013. Using structural equation models, we assessed the effects of N‐induced changes in environmental factors, species richness and trait metrics (mean, variance, skewness and kurtosis of trait distribution) on gross ecosystem productivity as well as three resource use efficiencies (water, light and phosphorus (P) use efficiencies), based on measurements during the peak growing season in 2016.

We found that both light and P use efficiencies decreased under N enrichment, largely due to the N‐induced decline in functional diversity of leaf P concentration. However, both gross ecosystem productivity and water use efficiency exhibited initial increases and subsequent slight decreases with N addition. These nonlinear patterns were closely associated with both the increased morphological trait (i.e. mean of leaf area) and decreased diversity of leaf P concentration.

Synthesis. Our results illustrate how N‐induced changes in functional traits may have dual effects on ecosystem productivity: the stimulating effects of the dominant trait identity via increasing canopy light interception versus the inhibiting effect of decreasing trait diversity via declining resource use efficiencies. Our results highlight the importance of including functional traits in land surface models to improve predictions of the response of ecosystem function to N inputs.
Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon‐degrading bacterium Alcanivorax borkumensis SK2T
Authors: Gregson Benjamin H. , Metodieva Gergana , Metodiev Metodi V. , McKew Boyd A. 
Published: April 2019

SummaryAlcanivorax borkumensis SK2T is an important obligate hydrocarbonoclastic bacterium (OHCB) that can dominate microbial communities following marine oil spills. It possesses the ability to degrade branched alkanes which provides it a competitive advantage over many other marine alkane degraders that can only degrade linear alkanes. We used LC–MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on linear (n‐C14) or branched (pristane) alkanes. During growth on n‐C14, A. borkumensis expressed a complete pathway for the terminal oxidation of n‐alkanes to their corresponding acyl‐CoA derivatives including AlkB and AlmA, two CYP153 cytochrome P450s, an alcohol dehydrogenase and an aldehyde dehydrogenase. In contrast, during growth on pristane, an alternative alkane degradation pathway was expressed including a different cytochrome P450, an alcohol oxidase and an alcohol dehydrogenase. A. borkumensis also expressed a different set of enzymes for β‐oxidation of the resultant fatty acids depending on the growth substrate utilized. This study significantly enhances our understanding of the fundamental physiology of A. borkumensis SK2T by identifying the key enzymes expressed and involved in terminal oxidation of both linear and branched alkanes. It has also highlights the differential expression of sets of β‐oxidation proteins to overcome steric hinderance from branched substrates.
Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed
Authors: Molina Lázaro , Rosa Ruggero La , Nogales Juan , Rojo Fernando 
Published: April 2019

SummaryPseudomonas putida is a soil bacterium with a versatile and robust metabolism. When confronted with mixtures of carbon sources, it prioritizes the utilization of the preferred compounds, optimizing metabolism and growth. This response is particularly strong when growing in a complex medium such as LB. This work examines the changes occurring in P. putida KT2440 metabolic fluxes, while it grows exponentially in LB medium and sequentially consumes the compounds available. Integrating the uptake rates for each compound at three different moments during the exponential growth with the changes observed in the proteome, and with the metabolic fluxes predicted by the iJN1411 metabolic model for this strain, allowed the metabolic rearrangements that occurred to be determined. The results indicate that the bacterium changes significantly the configuration of its metabolism during the early, mid and late exponential phases of growth. Sugars served as an energy source during the early phase and later as energy and carbon source. The configuration of the tricarboxylic acids cycle varied during growth, providing no energy in the early phase, and turning to a reductive mode in the mid phase and to an oxidative mode later on. This work highlights the dynamism and flexibility of P. putida metabolism.
Understanding Heterogeneous Consumer Preferences in Chinese Milk Markets: A Latent Class Approach
Authors: Wu Xiang , Hu Bin , Xiong Jie 
Published: April 2019

AbstractWe examine heterogeneous consumer preferences in Chinese milk markets. Using a discrete choice experiment, we examine how the brand, quality certification, traceability label and price influence consumers' milk choices. We identify four consumer segments using a latent class model: price conscious (9.8%), balanced thinking (19.8%), health conscious (57.5%), and environment conscious (12.9%) consumers. These four segments have distinct preferences: price conscious consumers prefer green certification; balanced thinking consumers have the highest willingness to pay for traceability labels; health conscious consumers have strong brand awareness; and environment conscious consumers prefer organic certification and traceability labels and use price as a quality signal. Such diversity of consumer preference can be explained by four psychological factors: price consciousness, food safety concerns, health consciousness and environmental concerns.
Visual analog scale rating change cut‐offs for detection of improvement in nausea severity
Authors: Meek Robert , Graudins Andis 
Published: April 2019

AbstractObjectiveTo determine accuracy and best cut‐point of measured and percentage visual analog scale (VAS) change for detection of symptom improvement.MethodsA pooled analysis of three previously published studies was conducted. All patients had baseline and 30 min VAS ratings linked to described symptom change. A receiver operating characteristic curve analysis was performed.ResultsArea under the curve for detecting symptom improvement was 0.86 (95% CI 0.83–0.90) and 0.87 (95% CI 0.84–0.90) for measured and percentage VAS change. Best cut‐points were −8 mm and −20%.ConclusionAccuracy of VAS change for detection of symptom improvement is good to excellent. Use of this outcome measure in future ED antiemetic trials is supported.
Effect of Blood Pump Flow and Arteriovenous Fistula Blood Flow on the Blood Pressure and Cardiac Function in Patients Undergoing Maintenance Hemodialysis
Authors: Tang Chun‐Yuan , Zhu Chun‐Ping , Wang Rao‐Ping , Ye Xiao‐Qing , Chen Xiao‐Fan , Feng Wan‐Na , Li Ping 
Published: April 2019

AbstractThe effect of blood pump flow rate on the cardiac functions of hemodialysis patients with arteriovenous fistula (AVF) is largely unknown. This study aimed to investigate if blood pump flow rate (Qb) and AVF access flow rate (Qa) can affect the cardiac function of Chinese hemodialysis patients. A total of 72 patients undergoing AVF hemodialysis were included from March 2010 to June 2014 and dichotomized into the high‐ and low‐flow groups using the medians of Qb (220 mL/min) and Qa (1000 mL/min) as the cutoffs. The cardiac function parameters were measured by ultrasound dilution technique within the first (t + 30) and the last (t − 30) 30 min of dialysis. At t + 30, Qb‐high group had significantly higher systolic blood pressure (SBP) and mean arterial pressure (MAP) than Qb‐low group. At t − 30, Qb‐high group had higher SBP, diastolic blood pressure (DBP), and MAP than Qb‐low group. Qa‐high group had higher SBP, MAP, cardiac output (CO), cardiac index (CI), central blood volume (CBV), and lower peripheral resistance than Qa‐low group. Multiple linear regression showed that at t − 30, Qb was positively correlated with SBP and MAP. Qa was positively correlated with CO, CI, CBV, and PR but negatively correlated with heart rate. Although Qb > 220 mL/min and Qa >1000 mL/min would elevate some parameters, the means of SBP, DBP, MAP remain within the normal range, indicating that appropriate increase in blood pump flow rate has little effect on the cardiac function of hemodialysis patients.
A ‘Most Interesting Subject for the Investigation of the Philosopher’: Conjectural History in John Barrow's Travels in China
Authors: Choi Ja Yun 
Published: April 2019

AbstractThis article re‐examines John Barrow's Travels in China (1804), an account of the Macartney embassy seen as having contributed to the emergence of Britain's derogatory attitude to China. By drawing connections between his cross‐cultural comparisons and conjectural history, it demonstrates how Barrow employs China's cultural differences not only to sophisticate stadial theory but also to present a complex view of Chinese civilisation that does not lend itself to an evaluative judgement of superiority. Through a comparison of Barrow's travelogue and other contemporary writings, it aims to show that British opinion on China continued to fluctuate in the early nineteenth century.