bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Machine Learning to Model Wetland Inundation Patterns Across a Large Semiarid Floodplain
Authors: Shaeri Karimi Sara , Saintilan Neil , Wen Li , Valavi Roozbeh 
Published: October 2019

AbstractInundation is a primary driver of floodplain ecology. Understanding temporal and spatial variability of inundation patterns is critical for optimum resource management, particularly in striking an appropriate balance between environmental water application and extractive use. Nevertheless, quantifying inundation at the fine resolution required of ecological modeling is an immense challenge in these environments. In this study, Random Forest, a machine learning technique, was implemented to predict the inundation pattern in a section of the Darling River Floodplain, Australia, at a spatial scale of 30 m and daily temporal resolution. The model achieved very good performance with an average accuracy of 0.915 based on the area under the receiver operating characteristic curve over 10 runs of the model in testing data sets. Six variables explained 70% of the total contribution to inundation occurrence, with the most influential being landscape shape (local deviation from global mean elevation), elevation‐weighted distance to the river, the magnitude of river flow (10‐ and 30‐day accumulated river discharge), local rainfall, and soil moisture. This approach is applicable to other floodplains across the world where understanding of fine‐scale inundation pattern is for operational ecological management and scenario testing.
Membrane-bound TNF mediates microtubule-targeting chemotherapeutics-induced cancer cytolysis via juxtacrine inter-cancer-cell death signaling
Authors: Zhang Jing , Yang Yu , Zhou Shen’ao , He Xueyan , Cao Xuan , Wu Chenlu , Hu Hong , Qin Jie , Wei Gang , Wang Huayi , Liu Suling , Sun Liming 
Published: October 2019

AbstractMicrotubule-targeting agents (MTAs) are a class of most widely used chemotherapeutics and their mechanism of action has long been assumed to be mitotic arrest of rapidly dividing tumor cells. In contrast to such notion, here we show—in many cancer cell types—MTAs function by triggering membrane TNF (memTNF)-mediated cancer-cell-to-cancer-cell killing, which differs greatly from other non-MTA cell-cycle-arresting agents. The killing is through programmed cell death (PCD), either in way of necroptosis when RIP3 kinase is expressed, or of apoptosis in its absence. Mechanistically, MTAs induce memTNF transcription via the JNK-cJun signaling pathway. With respect to chemotherapy regimens, our results establish that memTNF-mediated killing is significantly augmented by IAP antagonists (Smac mimetics) in a broad spectrum of cancer types, and with their effects most prominently manifested in patient-derived xenograft (PDX) models in which cell–cell contacts are highly reminiscent of human tumors. Therefore, our finding indicates that memTNF can serve as a marker for patient responsiveness, and Smac mimetics will be effective adjuvants for MTA chemotherapeutics. The present study reframes our fundamental biochemical understanding of how MTAs take advantage of the natural tight contact of tumor cells and utilize memTNF-mediated death signaling to induce the entire tumor regression.
Structural consequences of arrested foveal development in preterms with persisting signs of immaturity
Authors: Sjöstrand Johan , Popović Zoran 
Published: October 2019

Abstract

Purpose
To evaluate the impact of structural changes in a limited sample of adult preterms with foveal immaturity from optical coherence tomography (OCT) B-scan images and to estimate layer displacement and changes in areal and volume magnification within the inner fovea.

Subjects and methods
Layer thickness was measured in conventional and directional OCT scans from eight preterms with different degrees of foveal immaturity (24–33 weeks of gestation, 22–33 years of age) and five controls (20–33 years of age). We obtained reflectivity profiles of the outer plexiform layer (OPL) and manual segmentation data of the inner nuclear layer (INL) and the combined ganglion cell layer (GCL) and inner plexiform layer (IPL) at specified eccentricities from 300 to 900 µm. Displacement of cumulative thickness curves of preterms compared with that of the controls was used to estimate retardation of layer displacement. Changes in areal magnification and layer thickness were used to construct a structural model of redistribution within the fovea of preterms.

Results
Retardation of centrifugal layer displacement of OPL and all inner retinal layers (IRL) was marked in both preterm groups with foveal immaturity, whereas retardation was marginal in the preterm group without clinical signs of immaturity. Retarded displacement within the IRL and OPL had a major impact on available space within the central fovea.

Conclusions
A marked retardation of displacement was demonstrated for all IRL within the immature fovea of preterms with decreased areal and volume magnification and reduced space available for synaptic communication coupled to the degree of immaturity.
Minute-scale persistence of a GPCR conformation state triggered by non-cognate G protein interactions primes signaling
Authors: Gupte Tejas M. , Ritt Michael , Dysthe Matthew , Malik Rabia U. , Sivaramakrishnan Sivaraj 
Published: October 2019

AbstractDespite the crowded nature of the cellular milieu, ligand–GPCR–G protein interactions are traditionally viewed as spatially and temporally isolated events. In contrast, recent reports suggest the spatial and temporal coupling of receptor–effector interactions, with the potential to diversify downstream responses. In this study, we combine protein engineering of GPCR–G protein interactions with affinity sequestration and photo-manipulation of the crucial Gα C terminus, to demonstrate the temporal coupling of cognate and non-cognate G protein interactions through priming of the GPCR conformation. We find that interactions of the Gαs and Gαq C termini with the β2-adrenergic receptor (β2-AR), targeted at the G-protein-binding site, enhance Gs activation and cyclic AMP levels. β2-AR–Gα C termini interactions alter receptor conformation, which persists for ~90 s following Gα C terminus dissociation. Non-cognate G-protein expression levels impact cognate signaling in cells. Our study demonstrates temporal allostery in GPCRs, with implications for the modulation of downstream responses through the canonical G-protein-binding interface.
Pan-cancer whole-genome analyses of metastatic solid tumours
Authors: Priestley Peter , Baber Jonathan , Lolkema Martijn P. , Steeghs Neeltje , de Bruijn Ewart , Shale Charles , Duyvesteyn Korneel , Haidari Susan , van Hoeck Arne , Onstenk Wendy , Roepman Paul , Voda Mircea , Bloemendal Haiko J. , Tjan-Heijnen Vivianne C. G. , van Herpen Carla M. L. , Labots Mariette , Witteveen Petronella O. , Smit Egbert F. , Sleijfer Stefan , Voest Emile E. , Cuppen Edwin 
Published: October 2019

AbstractMetastatic cancer is a major cause of death and is associated with poor treatment efficacy. A better understanding of the characteristics of late-stage cancer is required to help adapt personalized treatments, reduce overtreatment and improve outcomes. Here we describe the largest, to our knowledge, pan-cancer study of metastatic solid tumour genomes, including whole-genome sequencing data for 2,520 pairs of tumour and normal tissue, analysed at median depths of 106× and 38×, respectively, and surveying more than 70 million somatic variants. The characteristic mutations of metastatic lesions varied widely, with mutations that reflect those of the primary tumour types, and with high rates of whole-genome duplication events (56%). Individual metastatic lesions were relatively homogeneous, with the vast majority (96%) of driver mutations being clonal and up to 80% of tumour-suppressor genes being inactivated bi-allelically by different mutational mechanisms. Although metastatic tumour genomes showed similar mutational landscape and driver genes to primary tumours, we find characteristics that could contribute to responsiveness to therapy or resistance in individual patients. We implement an approach for the review of clinically relevant associations and their potential for actionability. For 62% of patients, we identify genetic variants that may be used to stratify patients towards therapies that either have been approved or are in clinical trials. This demonstrates the importance of comprehensive genomic tumour profiling for precision medicine in cancer.
Understanding PDE4's function in Alzheimer's disease; a target for novel therapeutic approaches
Authors: Tibbo Amy J. , Tejeda Gonzalo S. , Baillie George S. 
Published: October 2019

Abstract
Phosphodiesterases (PDEs) have long been considered as targets for the treatment of Alzheimer's disease (AD) and a substantial body of evidence suggests that one sub-family from the super-family of PDEs, namely PDE4D, has particular significance in this context. This review discusses the role of PDE4 in the orchestration of cAMP response element binding signaling in AD and outlines the benefits of targeting PDE4D specifically. We examine the limited available literature that suggests PDE4 expression does not change in AD brains together with reports that show PDE4 inhibition as an effective treatment in this age-related neurodegenerative disease. Actually, aging induces changes in PDE4 expression/activity in an isoform and brain-region specific manner that proposes a similar complexity in AD brains. Therefore, a more detailed account of AD-related alterations in cellular/tissue location and the activation status of PDE4 is required before novel therapies can be developed to target cAMP signaling in this disease.
Influence of Altered Auditory Feedback on Oral–Nasal Balance in Speakers of Brazilian Portuguese
Authors: de Boer Gillian , Marino Viviane , Berti Larissa , Fabron Eliana , Spazzapan Evelyn Alves , Bressmann Tim 
Published: October 2019

Purpose
This study explored the role of auditory feedback in the regulation of oral–nasal balance in speakers of Brazilian Portuguese.

Method
Twenty typical speakers of Brazilian Portuguese (10 male, 10 female) wore a Nasometer headset and headphones while continuously repeating stimuli with oral and nasal sounds. Oral–nasal balance was quantified with nasalance scores. The signals from 2 additional oral and nasal microphones were played back to the participants through the headphones. The relative loudness of the nasal channel in the mix was gradually changed, so that the speakers heard themselves as more or less nasal.

Results

A repeated-measures analysis of variance of the mean nasalance scores of the stimuli at baseline, minimum, and maximum nasal feedback conditions demonstrated significant effects of nasal feedback condition (
p
< .0001) and stimuli (
p
< .0001). Post hoc analyses demonstrated that the mean nasalance scores were lowest for the maximum nasal feedback condition. The scores of the minimum nasal feedback condition were significantly higher than 2 of 3 baseline feedback conditions. The speaking amplitude of the participants did not change between the nasal feedback conditions.

Conclusions
Increased nasal signal level feedback led to a compensatory adjustment in the opposite direction, confirming that oral–nasal balance is regulated by auditory feedback. However, reduced nasal signal level feedback resulted in a compensatory response that was lower in magnitude. This suggests that, even in Brazilian Portuguese, a language with phonetic and phonological vowel nasalization, decreased nasality was not perceived as critically as increased nasality by the speakers.
Massive and old quiescent galaxies at high redshift
Authors: Girelli Giacomo , Bolzonella Micol , Cimatti Andrea 
Published: October 2019

Aims. Questions of how massive quiescent galaxies rapidly assembled and how abundant they are at high redshift are increasingly important in the study of galaxy formation. Looking at these systems can shed light on the processes of galaxy mass assembly and quenching of the star formation at early epochs. In order to address these questions, we aim to identify and characterize massive quiescent galaxies from z ∼ 2.5 out to the highest redshifts at which these systems can be found. The final purpose is to compare the results with the predictions of state-of-the-art semi-analytical models of galaxy formation and evolution.
Methods. We defined observer-frame color–color diagrams to optimally select quiescent galaxies at z >  2.5 and applied them to the COSMOS2015 catalog. We refined the spectral energy distribution (SED) fitting analysis for the selected candidates to confirm their quiescent nature, then derived their number density, mass density, and stellar mass functions. Finally, we compared the results with previous observations and some current semi-analytic models.
Results. We selected candidates for quiescent galaxies in the redshift range 2.5 ≲ z ≲ 4.5 from the COSMOS2015 catalog by means of two color–color diagrams. The additional SED fitting analysis allowed us to select 128 galaxies, consistent with being massive (log(M*/M⊙)≥10.6), old (ages ≳0.5 Gyr), and quiescent (log(sSFR [yr−1]) ≤ −10.5) objects at high redshift (2.5 <  z <  4.5). Their number and mass densities are in fair agreement with previous observations and, if confirmed, show a discrepancy with current semi-analytical models of galaxy formation and evolution, that underpredict the number of massive quiescent systems up to a factor of ∼12 at 2.5 ≤ z <  3.0 and ∼10 at z ∼ 4.0. The evolution of the stellar mass functions (SMFs) of these systems is similar to previous estimates and indicates a disagreement with models, particularly with regard to the shape of the SMF.
Conclusions. The present results add further evidence to the possibility that massive and quiescent galaxies can exist out to at least z ∼ 4. If future spectroscopic observations carried out with, for example, the James Webb Space Telecope (JWST), confirm the substantial presence of such a population, further work on modeling the stellar mass assembly, as well as supermassive black hole accretion and feedback processes at early cosmic epochs, is needed to understand how these systems formed, evolved, and quenched their star formation.
Lyman continuum escape fraction and mean free path of hydrogen ionizing photons for brightz∼ 4 QSOs from SDSS DR14
Authors: Romano M. , Grazian A. , Giallongo E. , Cristiani S. , Fontanot F. , Boutsia K. , Fiore F. , Menci N. 
Published: October 2019

Context.One of the main challenges in observational cosmology is related to the redshift evolution of the average hydrogen (HI) ionization in the Universe, as evidenced by the changing in ionization level of the intergalactic medium (IGM) through cosmic time. Starting from the first cosmic reionization, the rapid evolution of the IGM physical properties in particular poses severe constraints for the identification of the sources responsible for maintaining its high level of ionization up to lower redshifts.Aims.In order to probe the ionization level of the IGM and the ionization capabilities of bright quasi-stellar objects (QSOs) atz = 4, we selected a sample of 2508 QSOs drawn from the Sloan Digital Sky Survey (SDSS, DR14) in the redshift interval 3.6 ≤ z ≤ 4.6 and absolute magnitude range −29.0 ≲ M1450 ≲ −26.0. Particularly, we focus on the estimate of the escape fraction of HI-ionizing photons and their mean free path (MFP), which are fundamental for characterizing the surrounding IGM.Methods.Starting from UV/optical rest-frame spectra of the whole QSO sample from the SDSS survey, we estimated the escape fraction and free path individually for each of the QSOs. We calculated the Lyman continuum (LyC) escape fraction as the flux ratio blueward (∼900 Å rest frame) and redward (∼930 Å rest frame) of the Lyman limit. We then obtained the probability distribution function (PDF) of the individual free paths of the QSOs in the sample and studied its evolution in luminosity and redshift, comparing our results with those in literature.Results.We find a lower limit to the mean LyC escape fraction of 0.49, in agreement with the values obtained for both brighter and fainter sources at the same redshift. We show that the free paths of ionizing photons are characterized by a skewed distribution function that peaks at low values, with an average of ∼49 − 59 proper Mpc atz ∼ 4, after possible associated absorbers (AAs) were excluded. This value is higher than the one obtained at the same redshift by many authors in the literature using different techniques. Moreover, the PDF of free path gives information that is complementary to the MFP derived through the stacking technique. Finally, we also find that the redshift evolution of this parameter might be milder than previously thought.Conclusions.Our new determination of the MFP atz ∼ 4 implies that previous estimates of the HI photoionization rate ΓHIavailable in the literature should be corrected by a factor of 1.2−1.7. These results have important implications when they are extrapolated at the epoch of reionization.
Reconstructing solar magnetic fields from historical observations
Authors: Virtanen I. O. I. , Virtanen I. I. , Pevtsov A. A. , Mursula K. 
Published: October 2019

Context. The axial dipole moments of emerging active regions control the evolution of the axial dipole moment of the whole photospheric magnetic field and the strength of polar fields. Hale’s and Joy’s laws of polarity and tilt orientation affect the sign of the axial dipole moment of an active region. If both laws are valid (or both violated), the sign of the axial moment is normal. However, for some active regions, only one of the two laws is violated, and the signs of these axial dipole moments are the opposite of normal. Those opposite-sign active regions can have a significant effect, for example, on the development of polar fields.
Aims. Our aim is to determine the axial dipole moments of active regions identified from magnetographic observations and study how the axial dipole moments of normal and opposite signs are distributed in time and latitude in solar cycles 21−24.
Methods. We identified active regions in the synoptic maps of the photospheric magnetic field measured at the National Solar Observatory (NSO) Kitt Peak (KP) observatory, the Synoptic Optical Long term Investigations of the Sun (SOLIS) vector spectromagnetograph (VSM), and the Helioseismic and Magnetic Imager (HMI) aboard the Solar Dynamics Observatory (SDO), and determined their axial dipole moments.
Results. We find that, typically, some 30% of active regions have opposite-sign axial moments in every cycle, often making more than 20% of the total axial dipole moment. Most opposite-signed moments are small, but occasional large moments, which can affect the evolution of polar fields on their own, are observed. Active regions with such a large opposite-sign moment may include only a moderate amount of total magnetic flux. We find that in cycles 21−23 the northern hemisphere activates first and shows emergence of magnetic flux over a wider latitude range, while the southern hemisphere activates later, and emergence is concentrated to lower latitudes. Cycle 24 differs from cycles 21−23 in many ways. Cycle 24 is the only cycle where the northern butterfly wing includes more active regions than the southern wing, and where axial dipole moment of normal sign emerges on average later than opposite-signed axial dipole moment. The total axial dipole moment and even the average axial moment of active regions is smaller in cycle 24 than in previous cycles.
L'Analyse du Cycle de Vie pour réduire l'impact environnemental de la viticulture biologique
Authors: Renaud-Gentié C. , Dieu V. , Thiollet-Scholtus M. , van der Werf H.M.G. , Perrin A. , Mérot A. 
Published: October 2019

Contexte : La viticulture est très exigeante en intrants. La viticulture biologique est souvent considérée comme un système durable, mais elle a des impacts environnementaux. L'analyse du cycle de vie (ACV) permet de discriminer les itinéraires viticoles. Objectif : Notre article présente et discute l'intérêt de l'ACV pour évaluer, comparer et améliorer les itinéraires viticoles biologiques par une comparaison (i) des inventaires des pratiques, (ii) des inventaires du cycle de vie (ICV) et (iii) des ACV. Matériel et méthodes : Huit cas ont été étudiés dans trois régions viticoles françaises et deux années. L'ICV et l'ACV ont été calculés, cinq impacts ont été sélectionnés par corrélations (changement climatique, eutrophisation de l'eau douce, écotoxicité terrestre, acidification terrestre, eutrophisation marine). Résultats et discussion : des différences importantes entre les cas pour les pratiques et les quantités d'intrants ont été observées et l'étude des impacts sur le changement climatique a révélé la hiérarchie d'importance des opérations notamment mécaniques et un classement différent pour des impacts au kg de raisin et à l'ha de vigne. Les défis de l'ACV sont de mieux prendre en compte le soufre et le cuivre ; enrichir les bases de données sur les engrais organiques ; et construire des indicateurs de biodiversité. Conclusion : L'ACV est meilleure que les inventaires des pratiques pour évaluer la viticulture biologique. Mots-clés : évaluation environnementale, viticulture durable, conduite de la vigne, cuivre, carburant, fertilisation.
Astringency estimation of wines maturing in different types of containers
Authors: Basalekou M. , Pappas C. , Tarantilis P. , Kyraleou M. , Cotea V. , Kallithraka S. 
Published: October 2019

Astringency is a parameter of great importance for wine quality. During wine maturation in wooden barrels it can be enhanced by tannins extracted by the wood. However, their concentration is not directly correlated with astringency. Mean Degree of Polymerization (mDP) is often employed to characterize the structural characteristics of tannins in wines, providing also information on their proanthocyanidin content. The prodelphinidin content (%P), as well as the percentage of epigallocatechin (EGC) in extension and terminal units, have been negatively linked with astringency. Since the intensity of astringency is a decisive factor for the quality of a barrel-aged wine in this experiment, the structural characteristics of wine proanthocyanidins were determined in four different Greek wines, two white (Vilana and Dafni) and two red (Kotsifali and Mandilari). All wines matured for nine months in different types of containers (stainless steel tanks and barrels made of different woods). The prodelphinidin (terminal or extension) content was determined by means of phloroglucinolysis, followed by HPLC-UV-MS analysis, while astringency was assessed by a panel of trained tasters. Multivariate analysis showed that only white wines that matured in Acacia barrels contained high %P values independently of the variety used and were characterized as less astringent by the panel. Moreover, the determination of %extension and terminal EGC units revealed that the tannins of the wines maturing in Acacia barrels, contain higher amounts of EGC as terminal units. These findings could be used by winemakers in order to select the appropriate type of barrel according to the type of wine.
Keywords: Astringency, proanthocyanidin, tannin, barrel