bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying human presence in a heterogeneous urban landscape
Authors: Corsini Michela , Marrot Pascal , Szulkin Marta 
Published: July 2019

AbstractHumans are a keystone species in urban ecosystems. Although the impact of human activities is increasingly reported in behavioral and evolutionary ecology, little is known about the effects of physical human presence per se. Of particular relevance is the extent to which human presence (sometimes referred to as human disturbance), is repeatable across the urban mosaic over time. We quantified human presence at fixed locations—here in a 15-m radius of great tit nestboxes—within six urban and suburban study sites. While overall human presence did not differ between urban sites, it was significantly higher than in the suburban village. Moreover, considerable variance between fixed locations was observed within each site. We reported overall high repeatability of human presence for all sites (0.57 < R < 0.88, mean: 0.76, median: 0.77). We further simulated datasets of human presence made of an increasing number of counts, and demonstrated that 10 counts of human presence (each 30 s long) made at each fixed location can generate a highly reliable indicator of human presence (R ≥ 0.6) for any urban site. We thus confirm that human presence is repeatable across the urban mosaic, thereby offering consistent cues to urban wildlife of human presence or absence in space and time. Importantly, our approach of human presence quantification allows for an effort-efficient approach to understand the effects of physical human presence at designated temporal timeframes, thereby allowing to reliably test the effects of human presence on the behavior and ecology of urban wildlife.
Optimized adaptive enrichment designs for three-arm trials: learning which subpopulations benefit from different treatments
Authors: Steingrimsson Jon Arni , Betz Joshua , Qian Tianchen , Rosenblum Michael 
Published: July 2019

Summary
We consider the problem of designing a confirmatory randomized trial for comparing two treatments versus a common control in two disjoint subpopulations. The subpopulations could be defined in terms of a biomarker or disease severity measured at baseline. The goal is to determine which treatments benefit which subpopulations. We develop a new class of adaptive enrichment designs tailored to solving this problem. Adaptive enrichment designs involve a preplanned rule for modifying enrollment based on accruing data in an ongoing trial. At the interim analysis after each stage, for each subpopulation, the preplanned rule may decide to stop enrollment or to stop randomizing participants to one or more study arms. The motivation for this adaptive feature is that interim data may indicate that a subpopulation, such as those with lower disease severity at baseline, is unlikely to benefit from a particular treatment while uncertainty remains for the other treatment and/or subpopulation. We optimize these adaptive designs to have the minimum expected sample size under power and Type I error constraints. We compare the performance of the optimized adaptive design versus an optimized nonadaptive (single stage) design. Our approach is demonstrated in simulation studies that mimic features of a completed trial of a medical device for treating heart failure. The optimized adaptive design has $25\%$ smaller expected sample size compared to the optimized nonadaptive design; however, the cost is that the optimized adaptive design has $8\%$ greater maximum sample size. Open-source software that implements the trial design optimization is provided, allowing users to investigate the tradeoffs in using the proposed adaptive versus standard designs.
The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication
Authors: Defoort Jonas , Van de Peer Yves , Carretero-Paulet Lorenzo 
Published: July 2019

Abstract
Gene duplicates, generated either through whole genome duplication (WGD) or small-scale duplication (SSD), are prominent in angiosperms and are believed to play an important role in adaptation and in generating evolutionary novelty. Previous studies reported contrasting evolutionary and functional dynamics of duplicate genes depending on the mechanism of origin, a behaviour that is hypothesized to stem from constraints to maintain the relative dosage balance between the genes concerned and their interaction context. However, the mechanisms ultimately influencing loss and retention of gene duplicates over evolutionary time are not yet fully elucidated. Here, by using a robust classification of gene duplicates in Arabidopsis thaliana, Solanum lycopersicum and Zea mays, large RNAseq expression compendia and an extensive protein-protein interaction (PPI) network from Arabidopsis, we investigated the impact of PPIs on the differential evolutionary and functional fate of WGD and SSD duplicates. In all three species, retained WGD duplicates show stronger constraints to diverge at the sequence and expression level than SSD ones, a pattern that is also observed for shared PPI partners between Arabidopsis duplicates. PPIs are preferentially distributed among WGD duplicates and specific functional categories. Furthermore, duplicates with PPIs tend to be under stronger constraints to evolve than their counterparts without PPIs regardless of their mechanism of origin. Our results support dosage balance constraint as a specific property of genes involved in biological interactions, including physical PPIs, and suggest that additional factors may be differently influencing the evolution of genes following duplication, depending on the species, time and mechanism of origin.
Dynamic rupture and earthquake sequence simulations using the wave equation in second-order form
Authors: Duru Kenneth , Allison Kali L , Rivet Maxime , Dunham Eric M 
Published: July 2019

SUMMARYWe present a numerical method for simulating both single-event dynamic ruptures and earthquake sequences with full inertial effects in antiplane shear with rate-and-state fault friction. We use the second-order form of the wave equation, expressed in terms of displacements, discretized with high-order-accurate finite difference operators in space. Advantages of this method over other methods include reduced computational memory usage and reduced spurious high frequency oscillations. Our method handles complex geometries, such as non-planar fault interfaces and free surface topography. Boundary conditions are imposed weakly using penalties. We prove time stability by constructing discrete energy estimates. We present numerical experiments demonstrating the stability and convergence of the method, and showcasing applications of the method, including the transition in rupture style from crack-like ruptures to slip pulses for strongly rate-weakening friction and the simulation of earthquake sequences in a viscoelastic solid with a fully dynamic coseismic phase.
GAG positioning on IL-1RI; A mechanism regulated by dual effect of glycosylation
Authors: Azimzadeh Irani Maryam , Ejtehadi Mohammad Reza 
Published: July 2019

AbstractIL-1RI is the signaling receptor for the IL-1 family of cytokines that are involved in establishment of the innate and acquired immune systems. Glycosylated extracellular (EC) domain of the IL-1RI binds to agonist such as IL-1β or antagonist ligands and the accessory protein to form the functional signaling complex. Dynamics and ligand binding of the IL-1RI is influenced by presence of the glycosaminoglycans (GAGs) of the EC matrix. Here a combination of molecular dockings and molecular dynamics simulations of the unglycosylated, partially N-glycosylated and fully N-glycosylated IL-1RI EC domain in the apo, GAG-bound and IL-1β-bound states were carried out to explain the co-occurring dynamical effect of receptor’s glycosylation and GAGs. It was shown that the IL-1RI adopts two types of “extended” and “locked” conformations in its dynamical pattern, and glycosylation maintains the receptor in the latter form. Maintaining the receptor in the locked conformation disfavors IL-1β binding by burying its two binding site on the IL-1RI EC domain. Glycosylation disfavors GAG binding to the extended IL-1RI EC domain by sterically limiting the GAGs degrees of freedom in targeting its binding site, while it favors GAG binding to the locked IL-1RI by favorable packing interactions.
Infaunal community responses to ancient clam gardens
Authors: Cox Kieran D , Gerwing Travis G , Macdonald Tara , Hessing-Lewis Margot , Millard-Martin Ben , Command Rylan J , Juanes Francis , Dudas Sarah E 
Published: July 2019

AbstractAquatic ecosystems have been managed for millennia. Indigenous communities in North America pioneered numerous marine resource management strategies to ensure food security and support thriving economies, which have been active throughout the Northwest Coast of North America for over 14 000 years. Developed to increase shellfish productivity, clam gardens have been active for millennia. The diverse infaunal communities within these ecosystems can act as indicators of habitat alterations and provide an opportunity to study ecological community responses to seascapes shaped by millennia-old resource management structures. To determine how community structure differs between clam gardens and unmodified areas, we assessed infaunal diversity and density between intertidal mudflats, sandflats, and clam gardens. Differences in community composition were found among site types, with certain taxa, including culturally important species increasing within clam gardens. Per cent similarity analyses indicated that infaunal communities were more dissimilar among, than within site types. Furthermore, regression trees indicated that increases in diversity and density were closely correlated with the amount of shell and gravel within each habitat, which are associated with clam garden function and management practices. Species-specific and environmental responses to clam gardens indicate that human modifications in nearshore habitats created novel and distinct types of soft sediment communities.
(R)-Ketamine Induces a Greater Increase in Prefrontal 5-HT Release Than (S)-Ketamine and Ketamine Metabolites via an AMPA Receptor-Independent Mechanism
Authors: Ago Yukio , Tanabe Wataru , Higuchi Momoko , Tsukada Shinji , Tanaka Tatsunori , Yamaguchi Takumi , Igarashi Hisato , Yokoyama Rei , Seiriki Kaoru , Kasai Atsushi , Nakazawa Takanobu , Nakagawa Shinsaku , Hashimoto Kenji , Hashimoto Hitoshi 
Published: July 2019

Abstract

Background
Although recent studies provide insight into the molecular mechanisms of the effects of ketamine, the antidepressant mechanism of ketamine enantiomers and their metabolites is not fully understood. In view of the involvement of mechanisms other than the N-methyl-D-aspartate receptor in ketamine’s action, we investigated the effects of (R)-ketamine, (S)-ketamine, (R)-norketamine [(R)-NK], (S)-NK, (2R,6R)-hydroxynorketamine [(2R,6R)-HNK], and (2S,6S)-HNK on monoaminergic neurotransmission in the prefrontal cortex of mice.

Methods
The extracellular monoamine levels in the prefrontal cortex were measured by in vivo microdialysis.

Results
(R)-Ketamine and (S)-ketamine acutely increased serotonin release in a dose-dependent manner, and the effect of (R)-ketamine was greater than that of (S)-ketamine. In contrast, (S)-ketamine caused a robust increase in dopamine release compared with (R)-ketamine. Both ketamine enantiomers increased noradrenaline release, but these effects did not differ. (2R,6R)-HNK caused a slight but significant increase in serotonin and noradrenaline but not dopamine release. (S)-NK increased dopamine and noradrenaline but not serotonin release. Differential effects between (R)-ketamine and (S)-ketamine were also observed in a lipopolysaccharide-induced model of depression. An α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptor antagonist, 2,3-dioxo-6-nitro-1,2,3,4- tetrahydrobenzo[f]quinoxaline-7-sulfonamide (NBQX), attenuated (S)-ketamine-induced, but not (R)-ketamine-induced serotonin release, whereas NBQX blocked dopamine release induced by both enantiomers. Local application of (R)-ketamine into the prefrontal cortex caused a greater increase in prefrontal serotonin release than that of (S)-ketamine.

Conclusions
(R)-Ketamine strongly activates the prefrontal serotonergic system through an AMPA receptor-independent mechanism. (S)-Ketamine-induced serotonin and dopamine release was AMPA receptor-dependent. These findings provide a neurochemical basis for the underlying pharmacological differences between ketamine enantiomers and their metabolites.
The Mutual Singularity of Harmonic Measure and Hausdorff Measure of Codimension Smaller than One
Authors: Tolsa Xavier 
Published: July 2019

Abstract
Let $\Omega \subset{\mathbb{R}}^{n+1}$ be open and let $E\subset \partial \Omega $ with $0&lt;{\mathcal{H}}^s(E)&lt;\infty $, for some $s\in (n,n+1)$, satisfy a local capacity density condition. In this paper it is shown that the harmonic measure cannot be mutually absolutely continuous with the Hausdorff measure ${\mathcal{H}}^s$ on $E$. This answers a question of Azzam and Mourgoglou, who had proved the same result under the additional assumption that $\Omega $ is a uniform domain.
In Vivo Validation of Peptidoglycan Recycling as a Target to Disable AmpC-Mediated Resistance and Reduce Virulence Enhancing the Cell-Wall–Targeting Immunity
Authors: Torrens Gabriel , Sánchez-Diener Irina , Jordana-Lluch Elena , Barceló Isabel María , Zamorano Laura , Juan Carlos , Oliver Antonio 
Published: July 2019

Abstract

Background
Searching for new strategies to defeat Pseudomonas aeruginosa is of paramount importance. Previous works in vitro showed that peptidoglycan recycling blockade disables AmpC-dependent resistance and enhances susceptibility against cell-wall–targeting immunity. Our objective was to validate these findings in murine models.
This study shows for the first time in different murine models of infection that blocking the peptidoglycan recycling in Pseudomonas aeruginosa causes an important virulence impairment and disables AmpC-mediated resistance, being hence validated as a promising therapeutic target.

Methods
Wildtype PAO1, recycling-defective AmpG and NagZ mutants, an AmpC hyperproducer dacB mutant, and their combinations were used to cause systemic/respiratory infections in mice. Their survival, bacterial burden, inflammation level, and effectiveness of ceftazidime or subtherapeutic colistin to treat the infections were assessed.

Results
Inactivation of AmpG or NagZ significantly attenuated the virulence in terms of mice mortality, bacterial load, and inflammation. When inactivating these genes in the dacB-defective background, the β-lactam resistance phenotype was abolished, disabling the emergence of ceftazidime-resistant mutants, and restoring ceftazidime for treatment. Subtherapeutic colistin was shown to efficiently clear the infection caused by the recycling-defective strains, likely due to the combined effect with the mice cell-wall– targeting immunity.

Conclusions
This study brings us one step closer to new therapies intended to disable P. aeruginosa AmpC-mediated resistance and dampen its virulence, and strongly support the interest in developing efficient AmpG and/or NagZ inhibitors.
Biotic Potential and Life Tables of Chrysodeixis includens (Lepidoptera: Noctuidae), Rachiplusia nu, and Trichoplusia ni on Soybean and Forage Turnip
Authors: Specht Alexandre , Sosa-Gómez Daniel Ricardo , Roque-Specht Vânia Ferreira , Valduga Eduardo , Gonzatti Felipe , Schuh Sabrina Maurer , Carneiro Eduardo 
Published: July 2019

AbstractLoopers such as Chrysodeixis includens (Walker), Rachiplusia nu (Guenée), and Trichoplusia ni (Hübner) are important defoliators in soybean, sunflower, and crucifer crops, respectively, in countries of the Americas. The biotic potential of these polyphagous species of Plusiinae was comparatively examined considering crop rotation and succession scenarios in which crucifer crops are cultivated during or after Brazilian winter. All the species developed and reproduced on soybean (BRS 133 Embrapa) and forage turnip (Cati AL 1000, Wolf Seeds do Brasil). The development of C. includens was similar on both host plants. The survival of R. nu was lower on forage turnip than on soybean. In contrast, T. ni performance (survival, fecundity, pupal weight) was better on forage turnip than on soybean. This suggests that in crop rotation and succession scenarios of soybean after brassicacea, C. includens is likely to have a higher number of generations per year and could be potentially more harmful.
Multicenter study of primary systemic therapy with docetaxel, cyclophosphamide and trastuzumab for HER2-positive operable breast cancer: the JBCRG-10 study
Authors: Ueno Takayuki , Masuda Norikazu , Sato Nobuaki , Ohtani Shoichiro , Yamamura Jun , Matsunami Nobuki , Kashiwaba Masahiro , Takano Toshimi , Takahashi Masato , Kaneko Koji , Ohno Shinji , Morita Satoshi , Toi Masakazu 
Published: July 2019

Abstract

Background
The original aim of this study was to evaluate the treatment sequence and anthracycline requirement in docetaxel, cyclophosphamide and trastuzumab therapy. After one death in the anthracycline-containing arm, the protocol was amended to terminate the randomization. The single-docetaxel, cyclophosphamide and trastuzumab arm was continued to examine the efficacy and safety of the anthracycline-free regimen.

Methods
Women with human epidermal growth factor receptor-2-positive, operable and primary breast cancer were randomized to receive 5-fluorouracil, epirubicin and cyclophosphamide (four cycles) followed by docetaxel, cyclophosphamide and trastuzumab (four cycles), or docetaxel, cyclophosphamide and trastuzumab followed by 5-fluorouracil, epirubicin and cyclophosphamide, or docetaxel, cyclophosphamide and trastuzumab (six cycles). After the protocol amendment, patients were allocated to the docetaxel, cyclophosphamide and trastuzumab arm alone. The primary endpoint was a pathological complete response.

Results
In total, 103 patients were enrolled between September 2009 and September 2011: 21, 22 and 24 patients in the 5-fluorouracil, epirubicin and cyclophosphamide followed by docetaxel, cyclophosphamide and trastuzumab; docetaxel, cyclophosphamide and trastuzumab followed by 5-fluorouracil, epirubicin and cyclophosphamide and docetaxel, cyclophosphamide and trastuzumab arms, respectively, and 36 patients in the docetaxel, cyclophosphamide and trastuzumab arm after the protocol amendment. In total, 60 patients were allocated to the docetaxel, cyclophosphamide and trastuzumab arm, in which the pathological complete response rate was 45.8%, and disease-free survival at 3 years was 96.6%. Patients with stage I or IIA in the docetaxel, cyclophosphamide and trastuzumab arm showed good disease-free survival (100% at 3 years). The comparison of efficacy among the three arms was statistically underpowered. Left ventricular ejection fraction decreased significantly after 5-fluorouracil, epirubicin and cyclophosphamide followed by docetaxel–docetaxel, cyclophosphamide and trastuzumab (P = 0.017), but not after docetaxel, cyclophosphamide and trastuzumab followed by 5-fluorouracil, epirubicin and cyclophosphamide or docetaxel, cyclophosphamide and trastuzumab.

Conclusions
The pathological complete response rate for docetaxel, cyclophosphamide and trastuzumab was similar to previous reports of anthracycline-containing regimens. Docetaxel, cyclophosphamide and trastuzumab might be an option for primary systemic therapy in human epidermal growth factor receptor-2-positive early breast cancer. A larger confirmatory study is necessary.
Flooding and Arboviral Disease: Predicting Ross River Virus Disease Outbreaks Across Inland Regions of South-Eastern Australia
Authors: Tall Julie A , Gatton Michelle L 
Published: July 2019

AbstractFlood frequency is expected to increase across the globe with climate change. Understanding the relationship between flooding and arboviral disease can reduce disease risk and associated costs. South-eastern Australia is dominated by the flood-prone Murray-Darling River system where the incidence of Australia’s most common arboviral disease, Ross River virus (RRV), is high. This study aimed to determine the relationship between riverine flooding and RRV disease outbreaks in inland south-eastern Australia, specifically New South Wales (NSW). Each study month from 1991 to 2013, for each of 37 local government areas (LGAs) was assigned ‘outbreak/non-outbreak’ status based on long-term trimmed-average age-standardized RRV notification rates and ‘flood/non-flood’ status based on riverine overflow. LGAs were grouped into eight climate zones with the relationship between flood and RRV outbreak modeled using generalized estimating equations. Modeling adjusted for rainfall in the previous 1–3 mo. Spring–summer flooding increased the odds of summer RRV outbreaks in three climate zones before and after adjusting for rainfall 1, 2, and 3 mo prior to the outbreak. Flooding at any time of the year was not predictive of RRV outbreaks in the remaining five climate zones. Predicting RRV disease outbreaks with flood events can assist with more targeted mosquito spraying programs, thereby reducing disease transmission and mosquito resistance.
Assessment of abdominal organ motion using cine magnetic resonance imaging in different gastric motilities: a comparison between fasting and postprandial states
Authors: Nonaka Hotaka , Onishi Hiroshi , Watanabe Makoto , Nam Vu Hong 
Published: July 2019

Abstract
This study assessed abdominal organ motion induced by gastroduodenal motilities in volunteers during fasting and postprandial states, using cine magnetic resonance imaging (cine-MRI). Thirty-five volunteers underwent cine-MRI while holding their breath in the fasting and postprandial states. Gastric motility was quantified by the amplitude and velocity of antral peristaltic waves. Duodenal motility was evaluated as the change of duodenal diameter. Abdominal organ motion was measured in the liver, pancreas and kidneys. Motion was quantified by calculating maximal organ displacement in the left–right, antero–posterior and caudal–cranial directions. Median antral amplitude and velocity in the fasting and postprandial states were 7.7 and 15.1 mm (P &lt; 0.01), and 1.3 and 2.5 mm/s (P &lt; 0.01), respectively. Duodenal motility did not change. Median displacement for all organs ranged from 0.9 to 2.9 mm in the fasting state and from 1.0 to 2.9 mm in the postprandial state. Significant increases in abdominal organ displacement in the postprandial state were observed in the right lobe of the liver, pancreatic head and both kidneys. Differences in the median displacement of these organs between the two states were all &lt;1 mm. Although the motion of several abdominal organs increased in the postprandial state, the difference between the two states was quite small. Thus, our study suggests that treatment planning and irradiation need not include strict management of gastric conditions, nor the addition of excess margins to compensate for differences in the intra-fractional abdominal organ motion under different gastric motilities in the fasting and postprandial states.