bluuebunny/crossref_metadata_2025_split huggingface dataset:
Top-down and bottom-up effects on zooplankton size distribution in a deep stratified lake
Authors: Braun Lisa-Marie , Brucet Sandra , Mehner Thomas 
Published: March 2021

AbstractTrophic interactions in the pelagic area of lakes and the opposing effects of fish feeding (top-down) and phytoplankton biomass (bottom-up) on zooplankton communities are central topics in limnology. We hypothesized that zooplankton size distributions should be a more sensitive approach to disentangle top-down and bottom-up effects than the commonly measured zooplankton biomass. We examined zooplankton size distributions from 148 samples collected during summer months in the upper and lower pelagic layers of a deep mesotrophic lake among 13 years of sampling. Top-down effects, namely fish size and biomass, and bottom-up effects, including water temperature and total phosphorus and chlorophyll a concentrations, were considered. To add robustness to our analyses, we expressed the zooplankton size distributions as size spectra based on log-binning, as continuous size spectra and by the size diversity, a measure that has been developed to mimic taxonomic diversity indices. Among numerous regressions tested, significant top-down or bottom-up effects could rarely been detected. Our results indicate that the overall zooplankton size distribution was not significantly affected by fish predation and lake productivity measured as total phosphorus or chlorophyll a concentration. However, we found negative correlations between fish biomass and the preferred zooplankton prey, including Bosmina longirostris, Daphnia cucullata and nauplii in the upper depth layer. However, due to their small body size, low biomass and therefore relative small contribution to the zooplankton size distribution, predation on preferred zooplankton species did not translate into a statistically significant modification of the entire size spectrum. Consequently, the size spectrum seems to be relatively robust against predation effects, but might reflect the lake-wide energy availability and transfer efficiency in the food web.
Planning for a neighborhood and city-scale green network system in Qatar: the case of MIA Park
Authors: Furlan Raffaello , Sinclair Brian R. 
Published: March 2021

AbstractIn the past decade, Doha has witnessed fast-urban growth, an increased population rate, and an over-reliance on the automobile as the main mode of urban transportation. These factors caused social and environmental problems related to (1) the loss of a compact urban pattern, (2) an increased level of air pollution (3) high traffic congestions and (4) increasing landscape fragmentation. In consideration of such concerns, The State of Qatar invested large funds into the urban landscape development of Doha, as envisioned by Qatar National Vision 2030. As a result, in the past five years various parks and/or green areas, such MIA Park, a major public green space located around the Museum of Islamic Art (MIA), were planned and developed within metropolitan Doha. The authors argue that this park is currently facing issues and challenges related to (1) accessibility to/from the neighboring districts, and (2) connectivity to/from the neighboring parks. Therefore, this research study aims at assessing the existing conditions of MIA Park, at considering the broader city context and, at recommending strategies for implementing MIA Park’s green network system. It approached the investigative challenge using a multi-pronged comprehensive methodology, that deployed focus groups, semi-structured interviews and a comprehensive network analysis based on graph theory. The findings, revealed through these hybrid research tactics, allowed the researchers to generate a framework to enhance accessibility and connectivity of MIA Park through a green network system, planned at inter-related neighborhood-scale and city-scale levels. While the research examines most notably a single case, it is advocated that the proposed framework represents not just an optional feature pertaining to the case in Doha, but a valuable reference for the sustainable master planning of future cities in the State of Qatar and across the GCC. The paper proffers numerous key contributions, including the critical exploration of manufactured landscapes in Doha Qatar and the delineation of broadly applicable environmental design strategies to improve the fabric and livability of cities.
Using Utilitarian Plants for Lemur Conservation
Authors: Konersmann Cathlin , Noromiarilanto Fanambinantsoa , Ratovonamana Yedidya R. , Brinkmann Katja , Jensen Kai , Kobbe Susanne , Köhl Michael , Kuebler Daniel , Lahann Petra , Steffens Kim J. E. , Ganzhorn Jörg U. 
Published: March 2021

AbstractNature and species conservation often conflict with intensive natural resource or land use. Many protected areas are too small for long-term conservation of viable vertebrate populations, especially in Madagascar, and forests are subject to exploitation for a variety of natural resources. Trying to exclude people from the use of these resources has not been successful during economic, natural, or political crises or when human population growth outruns any development effort. People need economic and other benefits, and conservation measures have to account for these needs. We compiled native and introduced tree, shrub, and herbaceous species used by both people and native vertebrates for three regions, covering the domains of the dry, transitional, and humid forest of Madagascar. We carried out semistructured interviews and group discussions in 12 different villages in each study region in November 2017. People listed 139 utilitarian plant taxa. Our literature search revealed that 72 of these plant species and 13 genera used by people, were also used by 208 different terrestrial vertebrates including 58 lemur species. Application of the Forest Landscape Restoration approach with a combination of exotic and native plant species used by both people and animals could increase the economic value of restored forest habitats for people, thus providing incentives for forest conservation. Plantations of mixed utilitarian trees and shrubs could be integrated into agricultural landscapes. Among land-living vertebrates, lemurs seem to benefit most from this approach. These measures might contribute to a successful array of biodiversity conservation in anthropogenic landscapes.
How circadian variability of the heart rate and plasma electrolytes concentration influence the cardiac electrophysiology – model-based case study
Authors: Wiśniowska Barbara , Bielecka Zofia M. , Polak Sebastian 
Published: March 2021

AbstractThe circadian rhythm of cardiac electrophysiology is dependent on many physiological and biochemical factors. Provided, that models describing the circadian patterns of cardiac activity and/or electrophysiology which have been verified to the acceptable level, modeling and simulation can give answers to many of heart chronotherapy questions. The aim of the study was to assess the performance of the circadian models implemented in Cardiac Safety Simulator v 2.2 (Certara, Sheffield, UK) (CSS), as well as investigate the influence ofcircadian rhythms on the simulation results in terms of cardiac safety. The simulations which were run in CSS accounted for inter-individual and intra-individual variability. Firstly, the diurnal variations in QT interval length in a healthy population were simulated accounting for heart rate (HR) circadian changes alone, or with concomitant diurnal variations of plasma ion concentrations. Next, tolterodine was chosen as an exemplary drug for PKPD modelling exercise to assess the role of circadian rhythmicity in the prediction of drug effects on QT interval. The results of the simulations were in line with clinical observations, what can serve as a verification of the circadian models implemented in CSS. Moreover, the results have suggested that the circadian variability of the electrolytes balance is the main factor influencing QT circadian pattern. The fluctuation of ion concentration increases the intra-subject variability of predicted drug-triggered QT corrected for HR (QTc) prolongation effect and, in case of modest drug effect on QTc interval length, allows to capture this effect.
The work-technology nexus and working-class environmentalism: Workerism versus capitalist noxiousness in Italy’s Long 1968
Authors: Feltrin Lorenzo , Sacchetto Devi 
Published: March 2021

AbstractThis article traces the trajectory of theory and praxis aroundnocivitàor noxiousness – i.e., health damage and environmental degradation – drawn by the workerist group rooted in the petrochemical complex of Porto Marghera, Venice. While Porto Maghera was an important setting for the early activism of influential theorists such as the post-workerist Antonio Negri and the autonomist feminist Mariarosa Dalla Costa, the theories produced by the workers themselves have been largely forgotten. Yet, this experience was remarkable because it involved workers employed by polluting industries denouncing in words and actions the environmental degradation caused by their companies from as early as 1968, when the workerists had a determining influence in the local factories. The Porto Marghera struggles against noxiousness contradict the widespread belief that what is today known as working-class environmentalism did not have much significance in the labour unrest of Italy’s Long 1968. The Porto Marghera group’s original contribution was based on the thesis of the inherent noxiousness of capitalist work and an antagonistic-transformative approach to capitalist technology. This led to the proposal of a counterpower able to determine “what, how, and how much to produce” on the basis of common needs encompassing the environment, pointing to the utopian prospect of struggling for a different, anti-capitalist technology, compatible with the sustainable reproduction of life on the planet.
Prediction of Spatiotemporal Evolution of Urban Traffic Emissions Based on Taxi Trajectories
Authors: Zhao Zhen-Yi , Cao Yang , Kang Yu , Xu Zhen-Yi 
Published: March 2021

AbstractWith the rapid increase of the amount of vehicles in urban areas, the pollution of vehicle emissions is becoming more and more serious. Precise prediction of the spatiotemporal evolution of urban traffic emissions plays a great role in urban planning and policy making. Most existing methods usually focus on estimating vehicle emissions at historical or current moments which cannot well meet the demands of future planning. Recent work has started to pay attention to the evolution of vehicle emissions at future moments using multiple attributes related to emissions, however, they are not effective and efficient enough in the combination and utilization of different inputs. To address this issue, we propose a joint framework to predict the future evolution of vehicle emissions based on the GPS trajectories of taxis with a multi-channel spatiotemporal network and the motor vehicle emission simulator (MOVES) model. Specifically, we first estimate the spatial distribution matrices with GPS trajectories through map-matching algorithms. These matrices can reflect the attributes related to the traffic status of road networks such as volume, speed and acceleration. Then, our multi-channel spatiotemporal network is used to efficiently combine three key attributes (volume, speed and acceleration) through the feature sharing mechanism and generate a precise prediction of them in the future period. Finally, we adopt an MOVES model to estimate vehicle emissions by integrating several traffic factors including the predicted traffic states, road networks and the statistical information of urban vehicles. We evaluate our model on the Xi’an taxi GPS trajectories dataset. Experiments show that our proposed network can effectively predict the temporal evolution of vehicle emissions.
Suicide and the agent–host–environment triad: leveraging surveillance sources to inform prevention
Authors: Keyes Katherine M. , Kandula Sasikiran , Olfson Mark , Gould Madelyn S. , Martínez-Alés Gonzalo , Rutherford Caroline , Shaman Jeffrey 
Published: March 2021

AbstractSuicide in the US has increased in the last decade, across virtually every age and demographic group. Parallel increases have occurred in non-fatal self-harm as well. Research on suicide across the world has consistently demonstrated that suicide shares many properties with a communicable disease, including person-to-person transmission and point-source outbreaks. This essay illustrates the communicable nature of suicide through analogy to basic infectious disease principles, including evidence for transmission and vulnerability through the agent–host–environment triad. We describe how mathematical modeling, a suite of epidemiological methods, which the COVID-19 pandemic has brought into renewed focus, can and should be applied to suicide in order to understand the dynamics of transmission and to forecast emerging risk areas. We describe how new and innovative sources of data, including social media and search engine data, can be used to augment traditional suicide surveillance, as well as the opportunities and challenges for modeling suicide as a communicable disease process in an effort to guide clinical and public health suicide prevention efforts.
Reducing the risk of collision between ships in a close-quarters situation by simulating collision avoidance actions
Authors: Mohovic Djani , Mohovic Robert , Suljic Marko , Njegovan Marko 
Published: March 2021

Abstract‘Close-quarters situation’ is a term used in the International Regulations for Preventing Collisions at Sea. As the term is not precisely defined, this paper analyses the interpretations and definitions of the term by various authors or courts, based on judicial processes and judgments. In the end, the authors suggest their own definition of the term ‘close-quarters situation’. Knowing the minimum distance from another ship and the time to the closest point of approach at which collision may still be avoided by one's own manoeuvre is information that every ship's officer needs to know. In accordance with the proposed definition of the term ‘close-quarters situation’, minimum distances between ships and time to the closest point of approach in which the ship can still take action to avoid a collision by its own manoeuvring are determined by means of simulations on a navigational simulator. A total of 168 simulations were performed with three fine-form vessel sizes and three full-form vessel sizes. Due to the extensive amount of data, the paper presents the results for one vessel only.
Aurora-A kinase oncogenic signaling mediates TGF-β-induced triple-negative breast cancer plasticity and chemoresistance
Authors: Jalalirad Mohammad , Haddad Tufia C. , Salisbury Jeffrey L. , Radisky Derek , Zhang Minzhi , Schroeder Mark , Tuma Ann , Leof Eduard , Carter Jodi M. , Degnim Amy C. , Boughey Judy C. , Sarkaria Jann , Yu Jia , Wang Liewei , Liu Minetta C. , Zammataro Luca , Malatino Lorenzo , Galanis Evanthia , Ingle James N. , Goetz Matthew P. , D’Assoro Antonino B. 
Published: March 2021

AbstractTriple-negative breast cancer (TNBCs) account for 15–20% of all breast cancers and represent the most aggressive subtype of this malignancy. Early tumor relapse and progression are linked to the enrichment of a sub-fraction of cancer cells, termed breast tumor-initiating cells (BTICs), that undergo epithelial to mesenchymal transition (EMT) and typically exhibit a basal-like CD44high/CD24low and/or ALDH1high phenotype with critical cancer stem-like features such as high self-renewal capacity and intrinsic (de novo) resistance to standard of care chemotherapy. One of the major mechanisms responsible for the intrinsic drug resistance of BTICs is their high ALDH1 activity leading to inhibition of chemotherapy-induced apoptosis. In this study, we demonstrated that aurora-A kinase (AURKA) is required to mediate TGF-β-induced expression of the SNAI1 gene, enrichment of ALDH1high BTICs, self-renewal capacity, and chemoresistance in TNBC experimental models. Significantly, the combination of docetaxel (DTX) with dual TGF-β and AURKA pharmacologic targeting impaired tumor relapse and the emergence of distant metastasis. We also showed in unique chemoresistant TNBC cells isolated from patient-derived TNBC brain metastasis that dual TGF-β and AURKA pharmacologic targeting reversed cancer plasticity and enhanced the sensitivity of TNBC cells to DTX-based-chemotherapy. Taken together, these findings reveal for the first time the critical role of AURKA oncogenic signaling in mediating TGF-β-induced TNBC plasticity, chemoresistance, and tumor progression.
Inverse design of photonic meta-structure for beam collimation in on-chip sensing
Authors: Singh Robin , Nie Yuqi , Gao Mingye , Agarwal Anuradha Murthy , Anthony Brian W. 
Published: March 2021

AbstractDesigned or patterned structured surfaces, metasurfaces, enable the miniaturization of complex arrangements of optical elements on a plane. Most of the existing literature focuses on miniaturizing the optical detection; little attention is directed to on-chip optical excitation. In this work, we design a metasurface to create a planar integrated photonic source beam collimator for use in on-chip optofluidic sensing applications. We use an iterative inverse design approach in order to optimize the metasurface to achieve a target performance using gradient descent method. We then fabricate beam collimators and experimentally compare performance characteristics with conventional uniform binary grating-based photonic beam diffractors. The optimal design enhances the illumination power by a factor of 5. The reinforced beam is more uniform with 3 dB beam spot increased almost ~ 3 times for the same device footprint area. The design approach will be useful in on-chip applications of fluorescence imaging, Raman, and IR spectroscopy and will enable better multiplexing of light sources for high throughput biosensing.
Conservation of the glycogen metabolism pathway underlines a pivotal function of storage polysaccharides in Chlamydiae
Authors: Colpaert Matthieu , Kadouche Derifa , Ducatez Mathieu , Pillonel Trestan , Kebbi-Beghdadi Carole , Cenci Ugo , Huang Binquan , Chabi Malika , Maes Emmanuel , Coddeville Bernadette , Couderc Loïc , Touzet Hélène , Bray Fabrice , Tirtiaux Catherine , Ball Steven , Greub Gilbert , Colleoni Christophe 
Published: March 2021

AbstractThe order Chlamydiales includes obligate intracellular pathogens capable of infecting mammals, fishes and amoeba. Unlike other intracellular bacteria for which intracellular adaptation led to the loss of glycogen metabolism pathway, all chlamydial families maintained the nucleotide-sugar dependent glycogen metabolism pathway i.e. the GlgC-pathway with the notable exception of both Criblamydiaceae and Waddliaceae families. Through detailed genome analysis and biochemical investigations, we have shown that genome rearrangement events have resulted in a defective GlgC-pathway and more importantly we have evidenced a distinct trehalose-dependent GlgE-pathway in both Criblamydiaceae and Waddliaceae families. Altogether, this study strongly indicates that the glycogen metabolism is retained in all Chlamydiales without exception, highlighting the pivotal function of storage polysaccharides, which has been underestimated to date. We propose that glycogen degradation is a mandatory process for fueling essential metabolic pathways that ensure the survival and virulence of extracellular forms i.e. elementary bodies of Chlamydiales.
Structure of membrane diacylglycerol kinase in lipid bilayers
Authors: Li Jianping , Shen Yang , Chen Yanke , Zhang Zhengfeng , Ma Shaojie , Wan Qianfen , Tong Qiong , Glaubitz Clemens , Liu Maili , Yang Jun 
Published: March 2021

AbstractDiacylglycerol kinase (DgkA) is a small integral membrane protein, responsible for the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. Its structures reported in previous studies, determined in detergent micelles by solution NMR and in monoolein cubic phase by X-ray crystallography, differ significantly. These differences point to the need to validate these detergent-based structures in phospholipid bilayers. Here, we present a well-defined homo-trimeric structure of DgkA in phospholipid bilayers determined by magic angle spinning solid-state NMR (ssNMR) spectroscopy, using an approach combining intra-, inter-molecular paramagnetic relaxation enhancement (PRE)-derived distance restraints and CS-Rosetta calculations. The DgkA structure determined in lipid bilayers is different from the solution NMR structure. In addition, although ssNMR structure of DgkA shows a global folding similar to that determined by X-ray, these two structures differ in monomeric symmetry and dynamics. A comparative analysis of DgkA structures determined in three different detergent/lipid environments provides a meaningful demonstration of the influence of membrane mimetic environments on the structure and dynamics of membrane proteins.
APOL1 variant alleles associate with reduced risk for opportunistic infections in HIV infection
Authors: An Ping , Sezgin Efe , Kirk Gregory D. , Duggal Priya , Binns-Roemer Elizabeth , Nelson George , Limou Sophie , Van Natta Mark L. , Jabs Douglas A. , Estrella Michelle , Kopp Jeffrey B. , Winkler Cheryl A. 
Published: March 2021

AbstractApolipoprotein L1 (APOL1), an innate immune factor against African trypanosoma brucei, inhibits HIV-1 in vitro. The impact of APOL1 G1-G2 variants on HIV-1-associated opportunistic infections (OIs) is unknown. Here, we report findings from a metaanalysis of four HIV/AIDS prospective cohorts (ALIVE, LSOCA, MACS, and WIHS) including 2066 African American participants. Using a global test combining all four cohorts, carriage of two APOL1 variant alleles is associated with a 50% reduction in odds of OI (combined OR 0.50, 95% CI 0.33-0.76). Subgroup analysis of OI etiological categories (viral, parasitic, fungal and Mycobacterial) suggests the possibility of specific protection from fungal infections (OR 0.54. 95% CI 0.32-0.93; PBonferroni corrected = 0.08). We observe an association of APOL1 variant alleles with host protection against OI in HIV-positive individuals. The study suggests a broader role of APOL1 variant alleles in innate immunity in vivo.
Circadian regulation of night feeding and daytime detoxification in a formidable Asian pest Spodoptera litura
Authors: Zhang Jiwei , Li Shenglong , Li Wanshun , Chen Zhiwei , Guo Huizhen , Liu Jianqiu , Xu Yajing , Xiao Yingdan , Zhang Liying , Arunkumar Kallare P. , Smagghe Guy , Xia Qingyou , Goldsmith Marian R. , Takeda Makio , Mita Kazuei 
Published: March 2021

AbstractVoracious feeding, trans-continental migration and insecticide resistance make Spodoptera litura among the most difficult Asian agricultural pests to control. Larvae exhibit strong circadian behavior, feeding actively at night and hiding in soil during daytime. The daily pattern of larval metabolism was reversed, with higher transcription levels of genes for digestion (amylase, protease, lipase) and detoxification (CYP450s, GSTs, COEs) in daytime than at night. To investigate the control of these processes, we annotated nine essential clock genes and analyzed their transcription patterns, followed by functional analysis of their coupling using siRNA knockdown of interlocked negative feedback system core and repressor genes (SlituClk, SlituBmal1 and SlituCwo). Based on phase relationships and overexpression in cultured cells the controlling mechanism seems to involve direct coupling of the circadian processes to E-boxes in responding promoters. Additional manipulations involving exposure to the neonicotinoid imidacloprid suggested that insecticide application must be based on chronotoxicological considerations for optimal effectiveness.