bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-function relationship of an Urokinase Receptor-derived peptide which inhibits the Formyl Peptide Receptor type 1 activity
Authors: Minopoli Michele , Polo Andrea , Ragone Concetta , Ingangi Vincenzo , Ciliberto Gennaro , Pessi Antonello , Sarno Sabrina , Budillon Alfredo , Costantini Susan , Carriero Maria Vincenza 
Published: August 2019

AbstractThe interaction between the short 88Ser-Arg-Ser-Arg-Tyr92 sequence of the urokinase receptor (uPAR) and the formyl peptide receptor type 1 (FPR1) elicits cell migration. We generated the Ac-(D)-Tyr-(D)-Arg-Aib-(D)-Arg-NH2 (RI-3) peptide which inhibits the uPAR/FPR1 interaction, reducing migration of FPR1 expressing cells toward N-formyl-methionyl-leucyl-phenylalanine (fMLF) and Ser-Arg-Ser-Arg-Tyr (SRSRY) peptides. To understand the structural basis of the RI-3 inhibitory effects, the FPR1/fMLF, FPR1/SRSRY and FPR1/RI-3 complexes were modeled and analyzed, focusing on the binding pocket of FPR1 and the interaction between the amino acids that signal to the FPR1 C-terminal loop. We found that RI-3 shares the same binding site of fMLF and SRSRY on FPR1. However, while fMLF and SRSRY display the same agonist activation signature (i.e. the series of contacts that transmit the conformational transition throughout the complex), translating binding into signaling, RI-3 does not interact with the activation region of FPR1 and hence does not activate signaling. Indeed, fluorescein-conjugated RI-3 prevents either fMLF and SRSRY uptake on FPR1 without triggering FPR1 internalization and cell motility in the absence of any stimulus. Collectively, our data show that RI-3 is a true FPR1 antagonist and suggest a pharmacophore model useful for development of compounds that selectively inhibit the uPAR-triggered, FPR1-mediated cell migration.
Foraging activity of sperm whales (Physeter macrocephalus) off the east coast of New Zealand
Authors: Giorli Giacomo , Goetz Kimberly T. 
Published: August 2019

AbstractThe occurrence and distribution of sperm whales in New Zealand waters is mainly known from whaling records or opportunistic sightings by the public and a systematic estimation of the abundance and distribution has never been conducted. In this study, we investigated the foraging activity and occurrence of sperm whales off the Eastern coast of New Zealand using passive acoustic monitoring techniques. Three acoustic recorders were moored to the ocean floor at different locations on the east side of the North and South Island to collect passive acoustic data from June 2016 until August 2017. A total of 53,823 echolocation click trains were recorded and analyzed to understand the spatial and temporal variation of sperm whale foraging activity. No difference in the foraging activity was found between night-time and day-time periods at any of the locations. Click train detections increased toward the south, suggesting increased foraging activity near Kaikoura. At each station, sperm whale foraging activity varied by month.
atlasBREX: Automated template-derived brain extraction in animal MRI
Authors: Lohmeier Johannes , Kaneko Takaaki , Hamm Bernd , Makowski Marcus R. , Okano Hideyuki 
Published: August 2019

AbstractWe proposed a generic template-derived approach for (semi-) automated brain extraction in animal MRI studies and evaluated our implementation with different animal models (macaque, marmoset, rodent) and MRI protocols (T1, T2). While conventional MR-neuroimaging studies perform brain extraction as an initial step priming subsequent image-registration from subject to template, our proposed approach propagates an anatomical template to (whole-head) individual subjects in reverse order, which is challenging due to the surrounding extracranial tissue, greater differences in contrast pattern and larger areas with field inhomogeneity. As a novel approach, the herein introduced brain extraction algorithm derives whole-brain segmentation using rigid and non-rigid deformation based on unbiased anatomical atlas building with a priori estimates from study-cohort and an initial approximate brain extraction. We evaluated our proposed method in comparison to several other technical approaches including “Marker based watershed scalper”, “Brain-Extraction-Tool”, “3dSkullStrip”, “Primatologist-Toolbox”, “Rapid Automatic Tissue Segmentation” and “Robust automatic rodent brain extraction using 3D pulse-coupled neural networks” with manual skull-stripping as reference standard. ABX demonstrated best performance with accurate (≥92%) and consistent results throughout datasets and across species, age and MRI protocols. ABX was made available to the public with documentation, templates and sample material (https://www.github.com/jlohmeier/atlasBREX).
Cell wall integrity signaling regulates cell wall-related gene expression in Chlamydomonas reinhardtii
Authors: Cronmiller Evan , Toor Deepak , Shao Nai Chun , Kariyawasam Thamali , Wang Ming Hsiu , Lee Jae-Hyeok 
Published: August 2019

AbstractAn intact cell wall is critical for cellular interactions with the environment and protecting the cell from environmental challenges. Signaling mechanisms are necessary to monitor cell wall integrity and to regulate cell wall production and remodeling during growth and division cycles. The green alga, Chlamydomonas, has a proteinaceous cell wall of defined structure that is readily removed by gametolysin (g-lysin), a metalloprotease released during sexual mating. Naked cells treated with g-lysin induce the mRNA accumulation of >100 cell wall-related genes within an hour, offering a system to study signaling and regulatory mechanisms for de novo cell wall assembly. Combining quantitative RT-PCR and luciferase reporter assays to probe transcript accumulation and promoter activity, we revealed that up to 500-fold upregulation of cell wall-related genes was driven at least partly by transcriptional activation upon g-lysin treatment. To investigate how naked cells trigger this rapid transcriptional activation, we tested whether osmotic stress and cell wall integrity are involved in this process. Under a constant hypotonic condition, comparable levels of cell wall-gene activation were observed by g-lysin treatment. In contrast, cells in an iso- or hypertonic condition showed up to 80% reduction in the g-lysin-induced gene activation, suggesting that osmotic stress is required for full-scale responses to g-lysin treatment. To test whether mechanical perturbation of cell walls is involved, we isolated and examined a new set of cell wall mutants with defective or little cell walls. All cell wall mutants examined showed a constitutive upregulation of cell wall-related genes at a level that is only achieved by treatment with g-lysin in wild-type cells. Our study suggests a cell wall integrity monitoring mechanism that senses both osmotic stress and mechanical defects of cell walls and regulates cell wall-gene expression in Chlamydomonas, which may relate to cell wall integrity signaling mechanisms in other organisms.
Exhaustion of CD4+ T-cells mediated by the Kynurenine Pathway in Melanoma
Authors: Rad Pour Soudabeh , Morikawa Hiromasa , Kiani Narsis A. , Yang Muyi , Azimi Alireza , Shafi Gowhar , Shang Mingmei , Baumgartner Roland , Ketelhuth Daniel F. J. , Kamleh Muhammad Anas , Wheelock Craig E. , Lundqvist Andreas , Hansson Johan , Tegnér Jesper 
Published: August 2019

AbstractKynurenine pathway (KP) activation by the enzymatic activity of indoleamine 2,3-dioxygenase1 (IDO1) and kynurenine (KYN) production represents an attractive target for reducing tumour progression and improving anti-tumour immunity in multiple cancers. However, immunomodulatory properties of other KP metabolites such as 3-hydroxy kynurenine (3-HK) and kynurenic acid (KYNA) are poorly understood. The association of the kynurenine metabolic pathway with T-cell status in the tumour microenvironment were characterized, using gene expression data of 368 cutaneous skin melanoma (SKCM) patients from the TCGA cohort. Based on the identified correlations, we characterized the production of KYN, 3-HK, and KYNA in vitro using melanoma-derived cell lines and primary CD4+ CD25− T-cells. Activation of the CD4+ T-cells produced IFNγ, which yielded increased levels of KYN and KYNA. Concurrently, kynurenine 3-monooxygenase (KMO) expression and proliferation of CD4+ T-cells were reduced, whereas exhaustion markers such as PD-L1, AHR, FOXP3, and CTLA4 were increased. Additionally, an analysis of the correlation network reconstructed using TCGA-SKCM emphasized KMO and KYNU with high variability among BRAF wild-type compared with V600E, which underscored their role in distinct CD4+ T-cell behavior in tumour immunity. Our results suggest that, in addition to IDO1, there is an alternative immune regulatory mechanism associated with the lower KMO expression and the higher KYNA production, which contributes to dysfunctional effector CD4+ T-cell response.
Variation of spatiotemporal parameters in school children carrying different backpack loads: a cross sectional study
Authors: Paez-Moguer Joaquin , Montes-Alguacil Jesus , Garcia-Paya Irene , Medina-Alcantara Miguel , Evans Angela Margaret , Gijon-Nogueron Gabriel 
Published: August 2019

AbstractThe purpose of this study was to analyze spatiotemporal parameters of gait in children using varyingly loaded Backpacks(BP). This cross-sectional study examined 231 schoolchildren (118 boys, 113 girls) aged six to 12 years, carrying a traditional BP to manipulate loading (Crossing Backpack Children Arpenaz 7 Litres, Junior Red Quechua). Load was added to the BPs in increments of 5%, 10%, 15% and 20% of the child’s body weight. Spatio-temporal parameters were measured with the OptoGait system. Significant differences were observed in single support (p < 0.001), and double support (p < 0.001). No statistically significant differences were observed in step length (p = 0.959) between the five loading conditions. Similarly, no statistically significant differences were found in the contact phase (p = 0.208), although significant changes were seen between baseline, 15% of body weight (p < 0.005), and 20% of body weight (p < 0.005). The effect sizes from the ANOVA in the single support was low (0.015), and double support was moderate (0.02). Increased weight in BPs reduced both children’s balance and single support, increased double support, but did not change step length. The children increase double support with heavier loads to help their balance. The spatio-temporal changes were most evident with BP loads between 15–20% of body weight. Affective responses, including the perception of heaviness or difficulty in carrying the schoolbags need to be included in further and prospective investigations.
Prolongation of The Activation Time in Ischemic Myocardium is Associated with J-wave Generation in ECG and Ventricular Fibrillation
Authors: Azarov Jan E. , Ovechkin Alexey O. , Vaykshnorayte Marina A. , Demidova Marina M. , Platonov Pyotr G. 
Published: August 2019

AbstractJ-wave pattern has been recognized as an arrhythmic risk marker, particularly in myocardial infarction patients. Mechanisms underlying J-wave development in ischemia remain unknown. In myocardial infarction model, we evaluated activation time delay as a prerequisite of J-wave appearance and predictor of ventricular fibrillation. Body surface ECGs and myocardial unipolar electrograms were recorded in 14 anesthetized pigs. 48 intramural leads were positioned across ventricular free walls and interventricular septum. Myocardial ischemia was induced by ligation of the left anterior descending coronary artery and the recordings were done during 40-minute coronary occlusion. The local activation times were determined as instants of dV/dt minimum during QRS complex in unipolar electrograms. During occlusion, ventricular local activation time prolonged in the middle portion of the left ventricular free wall, and basal and middle portions of septum, while J-waves appeared in precordial leads in 11 animals. In logistic regression and ROC curve analyses, activation time delay at a given time-point was associated with J-wave development, and a longer activation time was associated with ventricular fibrillation appearance. In experimental coronary occlusion, activation delay in ischemic myocardium was associated with generation of the J waves in the body surface ECG and predicted ventricular fibrillation.
Hybrid methods combining atmospheric reanalysis data and a parametric typhoon model to hindcast storm surges in Tokyo Bay
Authors: Liu Fei , Sasaki Jun 
Published: August 2019

AbstractReanalysis data and a parametric typhoon model formula are often used to prepare wind and pressure fields for storm surge hindcasting. However, their optimum selection and usage have not been well established. To enhance the accuracy of wind and pressure fields, two hybrid methods were proposed by applying a parametric typhoon model of Mitsuta–Fujii’s formula, which is determined from the typhoon center to a certain radius of Rb, and then switching to the reanalysis data of ERA-Interim in the outer region through the interpolated transition bandwidth of Wb. In hybrid model I, Rb and Wb were fixed because the time-varying radius of the maximum wind speed was determined by the typhoon formula. In hybrid model II, these parameters were determined to minimize the mean difference between the reanalysis data and the fields obtained by typhoon formula in the transition band at each time step of the typhoon track. The hindcasting of eight significant typhoon events approaching Tokyo Bay was performed. This validated the proposed methods in comparison with the observed storm surge anomalies. Both models performed satisfactorily. Hybrid model II was found to be superior in terms of the balance of accuracy and preparation cost.
Humans, but not their dogs, displace pumas from their kills: An experimental approach
Authors: Suraci Justin P. , Smith Justine A. , Clinchy Michael , Zanette Liana Y. , Wilmers Christopher C. 
Published: August 2019

AbstractDomestic dogs are the most abundant large carnivore on the planet, and their ubiquity has led to concern regarding the impacts of dogs as predators of and competitors with native wildlife. If native large carnivores perceive dogs as threatening, impacts could extend to the community level by altering interactions between large carnivores and their prey. Dog impacts may be further exacerbated if these human-associated predators are also perceived as indicators of risk from humans. However, observational approaches used to date have led to ambiguity regarding the effects of dog presence on wildlife. We experimentally quantified dog impacts on the behavior of a native large carnivore, presenting playbacks of dog vocalizations to pumas in central California. We show that the perceived presence of dogs has minimal impacts on puma behavior at their kill sites, and is no more likely to affect total feeding time at kills than non-threatening controls. We previously demonstrated that pumas exhibit strong responses to human cues, and here show that perceived risk from human presence far exceeds that from dogs. Our results suggest that protected areas management policies that restrict dogs but permit human access may in some cases be of limited value for large carnivores.
RhoBTB1 interacts with ROCKs and inhibits invasion
Authors: Haga Raquel B. , Garg Ritu , Collu Francesca , Borda D'Agua Bárbara , Menéndez Sofia T. , Colomba Audrey , Fraternali Franca , Ridley Anne J. 
Published: August 2019

Abstract
RhoBTB1 is an atypical Rho GTPase with two BTB domains in addition to its Rho domain. Although most Rho GTPases regulate actin cytoskeletal dynamics, RhoBTB1 is not known to affect cell shape or motility. We report that RhoBTB1 depletion increases prostate cancer cell invasion and induces elongation in Matrigel, a phenotype similar to that induced by depletion of ROCK1 and ROCK2. We demonstrate that RhoBTB1 associates with ROCK1 and ROCK2 and its association with ROCK1 is via its Rho domain. The Rho domain binds to the coiled-coil region of ROCK1 close to its kinase domain. We identify two amino acids within the Rho domain that alter RhoBTB1 association with ROCK1. RhoBTB1 is a substrate for ROCK1, and mutation of putative phosphorylation sites reduces its association with Cullin3, a scaffold for ubiquitin ligases. We propose that RhoBTB1 suppresses cancer cell invasion through interacting with ROCKs, which in turn regulate its association with Cullin3. Via Cullin3, RhoBTB1 has the potential to affect protein degradation.
Relationship Between Working Memory and Speech-in-Noise Recognition in Young and Older Adult Listeners With Age-Appropriate Hearing
Authors: Vermeire Katrien , Knoop Allart , De Sloovere Marleen , Bosch Peggy , van den Noort Maurits 
Published: August 2019

Purpose
The purpose of this study was to investigate the relationship between working memory (WM) capacity and speech recognition in noise in both a group of young adults and a group of older adults.

Method
Thirty-three older adults with a mean age of 71.0 (range: 60.4–82.7) years and 27 young adults with a mean age of 21.7 (range: 19.1–25.0) years participated in the study. All participants had age-appropriate hearing and no history of central nervous system dysfunction. WM capacity was measured using the van den Noort version of the Reading Span Test, and recognition of sentences in the presence of a stationary speech-shaped noise was measured as the speech reception threshold for 50% correct identification by using the Leuven Intelligibility Sentence Test.

Results

The older adults had significantly worse WM capacity scores,
t
(58) = 8.266,
p
< .001, and significantly more difficulty understanding sentences in noise than the younger adults,
t
(58) = −6.068,
p
< .001. In the group of older adults, a correlation was found (
r
= −.488,
n
= 33,
p
= .004) between the results of the WM capacity test (Reading Span Test) and the results of the speech-recognition-in-noise test (Leuven Intelligibility Sentence Test), meaning that the higher the WM performance was, the better was the speech recognition in noise. This correlation cannot be found in young normal-hearing listeners.

Conclusions
This study shows deleterious effects of age on both WM capacity and speech recognition in noise. Interestingly, only in the group of older adults was a significant relation found between WM capacity and speech recognition in noise. The current results caution against the assumption that WM necessarily supports speech-in-noise identification independently of the age and hearing status of the listener.
Test–Retest Reproducibility of Response Duration in Tinnitus Patients With Positive Residual Inhibition
Authors: Deklerck Ann N. , Degeest Sofie , Dhooge Ingeborg J. M. , Keppler Hannah 
Published: August 2019

PurposeFunctional imaging is often used to try to elucidate the pathophysiological mechanism of tinnitus. Residual inhibition, the temporary suppression of tinnitus after application of a masking noise, could be an interesting technique to modulate tinnitus perception in functional imaging paradigms. The purposes of this study were to primarily assess reproducibility of the (partial) positive residual inhibition response duration in patients with tinnitus and to explore its utility in experimental designs.MethodPatients with tinnitus exhibiting a (partial) positive residual inhibition response or tinnitus reduction after a 1-min white noise presentation were selected from a broad consulting tinnitus population. In 27 patients, this response was tested 4 times: twice during initial testing and twice during a retest of the psychoacoustic tinnitus measures, 4–8 weeks after initial consultation. In 17 patients with stable residual inhibition responses, reproducibility of response duration, the duration of tinnitus reduction up to pretesting state, was analyzed.ResultsInitial testing showed a residual inhibition duration of 29.5 s on average. Test–retest reproducibility of response duration was shown to be reliable with an ICC(3, 4) of .871 (95% CI [0.733, 0.948]) and a standard error of measurement of 6.64 s.ConclusionsThis study indicates the good test–retest reproducibility of residual inhibition duration in our subset of 17 patients with stable (partial) positive residual inhibition. Residual inhibition is, therefore, a technique that can potentially be used for temporary tinnitus manipulation in experimental paradigms to unravel tinnitus pathophysiology.
Design of a compact ultra‐wideband MIMO antenna
Authors: Youcheng Wang , Yanjiao Yang , Qingxi Chi , Hucheng Pei 
Published: August 2019

A compact ultra‐wideband (UWB) multiple‐input multiple‐output (MIMO) antenna is presented. The MIMO antenna consists of four monopoles which are printed on FR4 substrate, whose impedance bandwidth is from 2 to 12 GHz, and the isolation of two adjacent antennas is less than−20 dB in mostly frequency band. The current distribution of the antenna is discussed by simulation, and the radiation characteristics of the antenna are improved by increasing the parasitic radiation patch and digging holes in the radiation patch. Four monopoles are placed with polarisation orthogonality, and the adjacent units are separated by slot to cut off the coupling current on the floor, thus effectively improving the isolation of the antenna.
Time-dependent galactic winds
Authors: Dorfi E. A. , Steiner D. , Ragossnig F. , Breitschwerdt D. 
Published: August 2019

Context. Cosmic rays (CRs) are transported out of the galaxy by diffusion and advection due to streaming along magnetic field lines and resonant scattering off self-excited magnetohydrodynamic (MHD) waves. Thus momentum is transferred to the plasma via the frozen-in waves as a mediator assisting the thermal pressure in driving a galactic wind.
Aims. Galactic CRs (GCRs) are accelerated by shock waves generated in supernova remnants (SNRs), and they propagate from the disc into the halo. Therefore CR acceleration in the halo strongly depends on the inner disc boundary conditions.
Methods. We performed hydrodynamical simulations of galactic winds in flux tube geometry appropriate for disc galaxies, describing the CR diffusive-advective transport in a hydrodynamical fashion (by taking appropriate moments of the Fokker-Planck equation) along with the energy exchange with self-generated MHD waves.
Results. Our time-dependent CR hydrodynamic simulations confirm that the evolution of galactic winds with feedback depends on the structure of the galactic halo. In case of a wind-structured halo, the wind breaks down after the last super nova (SN) has exploded.
Conclusions. The mechanism described here offers a natural and elegant solution to explain the power-law distribution of CRs between the “knee” and the “ankle”. The transition will be naturally smooth, because the Galactic CRs accelerated at SN shocks will be “post-accelerated” by shocks generated at the inner boundary and travelling through the halo.