bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cost of non-coordination in urban on-demand mobility
Authors: Kondor Dániel , Bojic Iva , Resta Giovanni , Duarte Fábio , Santi Paolo , Ratti Carlo 
Published: March 2022

AbstractOver the last 10 years, ride-hailing companies (such as Uber and Grab) have proliferated in cities around the world. While generally beneficial from an economic viewpoint, having a plurality of operators that serve a given demand for point-to-point trips might induce traffic inefficiencies due to the lack of coordination between operators when serving trips. In fact, the efficiency of vehicle fleet management depends, among other things, density of the demand in the city, and in this sense having multiple operators in the market can be seen as a disadvantage. There is thus a tension between having a plurality of operators in the market, and the overall traffic efficiency. To this date, there is no systematic analysis of this trade-off, which is fundamental to design the best future urban mobility landscape. In this paper, we present the first systematic, data-driven characterization of the cost of non-coordination in urban on-demand mobility markets by proposing a simple, yet realistic, model. This model uses trip density and average traffic speed in a city as its input, and provides an accurate estimate of the additional number of vehicles that should circulate due to the lack of coordination between operators—the cost of non-coordination. We plot such cost across different cities—Singapore, New York (limited to the borough of Manhattan in this work), San Francisco, Vienna and Curitiba—and show that due to non-coordination, each additional operator in the market can increase the total number of circulating vehicles by up to 67%. Our findings could support city policy makers to make data supported decisions when regulating urban on-demand mobility markets in their cities. At the same time, our results outline the need of a more proactive government participation and the need for new, innovative solutions that would enable a better coordination of on-demand mobility operators.
Identifying optimal reference genes for gene expression studies in Eurasian spruce bark beetle, Ips typographus (Coleoptera: Curculionidae: Scolytinae)
Authors: Sellamuthu Gothandapani , Bílý Jan , Joga Mallikarjuna Reddy , Synek Jiří , Roy Amit 
Published: March 2022

AbstractEurasian spruce bark beetle (Ips typographus [L.]) causes substantial damage to spruce forests worldwide. Undoubtedly, more aggressive measures are necessary to restrict the enduring loss. Finishing genome sequencing is a landmark achievement for deploying molecular techniques (i.e., RNA interference) to manage this pest. Gene expression studies assist in understanding insect physiology and deployment of molecular approaches for pest management. RT-qPCR is a valuable technique for such studies. However, accuracy and reliability depend on suitable reference genes. With the genome sequence available and the growing requirement of molecular tools for aggressive forest pest management, it is crucial to find suitable reference genes in Ips typographus under different experimental conditions. Hence, we evaluated the stability of twelve candidate reference genes under diverse experimental conditions such as biotic (developmental, sex and tissues) and abiotic factors (i.e., temperature and juvenile hormone treatment) to identify the reference genes. Our results revealed that ribosomal protein 3a (RPS3-a) was the best reference gene across all the experimental conditions, with minor exceptions. However, the stability of the reference gene can differ based on experiments. Nevertheless, present study provides a comprehensive list of reference genes under different experimental conditions for Ips typographus and contributes to “future genomic and functional genomic research”.
Coherent surface-to-bulk vibrational coupling in the 2D topologically trivial insulator Bi2Se3 monitored by ultrafast transient absorption spectroscopy
Authors: Glinka Yuri D. , He Tingchao , Sun Xiao Wei 
Published: March 2022

AbstractUltrafast carrier relaxation in the 2D topological insulator (TI) Bi2Se3 [gapped Dirac surface states (SS)] and how it inherits ultrafast relaxation in the 3D TI Bi2Se3 (gapless Dirac SS) remains a challenge for developing new optoelectronic devices based on these materials. Here ultrashort (~ 100 fs) pumping pulses of ~ 340 nm wavelength (~ 3.65 eV photon energy) were applied to study ultrafast electron relaxation in the 2D TI Bi2Se3 films with a thickness of 2 and 5 quintuple layers (~ 2 and ~ 5 nm, respectively) using transient absorption (TA) spectroscopy in the ultraviolet–visible spectral region (1.65–3.9 eV). The negative and positive contributions of TA spectra were attributed to absorption bleaching that mostly occurs in the bulk states and to the inverse bremsstrahlung type free carrier absorption in the gapped Dirac SS, respectively. Owing to this direct and selective access to the bulk and surface carrier dynamics, we were able to monitor coherent longitudinal optical (LO) phonon oscillations, which were successively launched in the bulk and surface states by the front of the relaxing electron population within the LO-phonon cascade emission. We have also recognized the coherent surface-to-bulk vibrational coupling that appears through the phase-dependent amplitude variations of coherent LO-phonon oscillations. This unique behavior manifests itself predominantly for the topologically trivial insulator phase of the 2D TI Bi2Se3 (2 nm thick film) in the photon energy range (~ 2.0–2.25 eV) where efficient energy exchange between the bulk and surface states occurs. We also found that the coherent surface-to-bulk vibrational coupling significantly weakens with increasing both the Bi2Se3 film thickness and pumping power.
In vitro evaluation of therapeutic antibodies against a SARS-CoV-2 Omicron B.1.1.529 isolate
Authors: Touret Franck , Baronti Cécile , Bouzidi Hawa Sophia , de Lamballerie Xavier 
Published: March 2022

AbstractThe emergence and rapid spread of the Omicron variant of SARS-CoV-2, which has more than 30 substitutions in the spike glycoprotein, compromises the efficacy of currently available vaccines and therapeutic antibodies. Using a clinical strain of the Omicron variant, we analyzed the neutralizing power of eight currently used monoclonal antibodies compared to the ancestral B.1 BavPat1 D614G strain. We observed that six of these antibodies have lost their ability to neutralize the Omicron variant. Of the antibodies still having neutralizing activity, Sotrovimab/Vir-7831 shows the smallest reduction in activity, with a factor change of 3.1. Cilgavimab/AZD1061 alone shows a reduction in efficacy of 15.8, resulting in a significant loss of activity for the Evusheld cocktail (42.6-fold reduction) in which the other antibody, Tixagevimab, does not retain significant activity against Omicron. Our results suggest that the clinical efficacy of the initially proposed doses should be rapidly evaluated and the possible need to modify doses or propose combination therapies should be considered.
The steroid hormone ecdysone regulates growth rate in response to oxygen availability
Authors: Kapali George P. , Callier Viviane , Gascoigne Samuel J. L. , Harrison Jon F. , Shingleton Alexander W. 
Published: March 2022

AbstractIn almost all animals, physiologically low oxygen (hypoxia) during development slows growth and reduces adult body size. The developmental mechanisms that determine growth under hypoxic conditions are, however, poorly understood. Here we show that the growth and body size response to moderate hypoxia (10% O2) in Drosophila melanogaster is systemically regulated via the steroid hormone ecdysone. Hypoxia increases level of circulating ecdysone and inhibition of ecdysone synthesis ameliorates the negative effect of low oxygen on growth. We also show that the effect of ecdysone on growth under hypoxia is through suppression of the insulin/IGF-signaling pathway, via increased expression of the insulin-binding protein Imp-L2. These data indicate that growth suppression in hypoxic Drosophila larvae is accomplished by a systemic endocrine mechanism that overlaps with the mechanism that slows growth at low nutrition. This suggests the existence of growth-regulatory mechanisms that respond to general environmental perturbation rather than individual environmental factors.
A tradeoff between physical encounters and consumption determines an optimal droplet size for microbial degradation of dispersed oil
Authors: Fernandez Vicente I. , Stocker Roman , Juarez Gabriel 
Published: March 2022

AbstractImmiscible hydrocarbons occur in the ocean water column as droplets of varying diameters. Although microbial oil degradation is a central process in the remediation of hydrocarbon pollution in marine environments, the relationship between droplet size distribution and oil degradation rates by bacteria remains unclear, with a conflicting history of laboratory studies. Despite this knowledge gap, the use of chemical dispersants in oil spill response and mitigation is based on the rationale that increasing the surface-area-to-volume ratio of droplets will enhance net bacterial biodegradation rates. We demonstrate that this intuitive argument does not apply to most natural marine environments, where the abundance of oil droplets is much lower than in laboratory experiments and droplet-bacteria encounters are the limiting factor. We present a mechanistic encounter-consumption model to predict the characteristic time for oil degradation by marine bacteria as a function of the initial oil concentration, the distribution of droplet sizes, and the initial abundance of oil-degrading bacteria. We find that the tradeoff between the encounter time and the consumption time leads to an optimal droplet size larger than the average size generated by the application of dispersants. Reducing droplet size below this optimum can increase the persistence of oil droplets in the environment from weeks to years. The new perspective granted by this biophysical model of biodegradation that explicitly accounts for oil–microbe encounters changes our understanding of biodegradation particularly in the deep ocean, where droplets are often small and oil concentrations low, and explains degradation rate discrepancies between laboratory and field studies.
Potential limitations of diagnostic standard codes to distinguish polycythemia vera and secondary erythrocytosis
Authors: Barrios-Ruiz Alanna , Davila-Gonzalez Daniel , Fountain Eric , Cheng Lee , Verstovsek Srdan , Rojas-Hernandez Cristhiam M. 
Published: March 2022

AbstractRed cell overproduction is seen in polycythemia vera (PV), a bone marrow myeloproliferative neoplasm characterized by trilinear cell proliferation (WBC, platelets), as well as in secondary erythrocytosis (SE), a group of heterogeneous disorders characterized by elevated EPO gene transcription. We aimed to verify the concordance of the International Classification of Diseases (ICD) code-based diagnosis of “polycythemia” or “erythrocytosis” with the true clinical diagnosis of these conditions. We retrospectively reviewed the electronic medical records (January 1, 2005, to December 31, 2016) of adult patients with ICD codes of polycythemia and/or erythrocytosis who had testing done for the presence of the JAK2V617F mutation. We verified the accuracy of the ICD code-based diagnoses by meticulous chart review and established whether these patients fulfilled the criteria by the evaluating physician for PV or SE and according to the World Health Organization 2016 diagnostic guidelines. The reliability of ICD coding was calculated using Cohen's kappa. We identified and chart reviewed a total of 578 patient records. Remarkably, 11% of the patients had concurrent diagnosis codes for PV and SE and were unable to be classified appropriately without individual chart review. The ICD code-based diagnostic system led to misidentification in an important fraction of cases. This represents a problem for the detection of PV or SE cases by ICD-based registries and their derived studies. Research based exclusively on ICD codes could have a potential impact on patient care and public health, and limitations must be weighed when research findings are conveyed.
Incidence and risk of advanced age-related macular degeneration in eyes with drusenoid pigment epithelial detachment
Authors: Shijo Taiyo , Sakurada Yoichi , Tanaka Koji , Miki Akiko , Sugiyama Atsushi , Onoe Hajime , Chubachi Aya , Kikushima Wataru , Wakatsuki Yu , Yoneyama Seigo , Mori Ryusaburo , Kashiwagi Kenji 
Published: March 2022

AbstractTo investigate the incidence and risk of advanced age-related macular degeneration (AMD), including geographic atrophy (GA) and macular neovascularization (MNV), in eyes with drusenoid pigment epithelial detachment (PED). Eighty-five eyes with drusenoid PED from 85 patients (77.2 ± 7.0 years, male/female: 44/41) were included in this study. Patients were followed up every 1–3 months via spectral-domain optical coherence tomography (SD-OCT) and color fundus photography. If exudation was observed on SD-OCT, fluorescein and indocyanine green angiography were performed to confirm the MNV subtype accordingly. The maximum follow-up period was 60 months. During the study period, GA developed in 8 eyes while MNV also developed in 8 eyes. The Kaplan–Meier estimator revealed that the cumulative incidence for 60 months was 17.9% and 12.2% for GA and MNV, respectively. In eyes developing MNV, retinal angiomatous proliferation was the most common. Cox regression analysis revealed that baseline PED width was the only factor associated with advanced AMD. (p = 0.0026, Cox regression analysis). The 5-year cumulative incidence of advanced AMD, including GA and MNV, was approximately 30% in eyes with drusenoid PED among the Japanese elderly. A larger baseline PED width was the only risk factor for advanced AMD.
Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)
Authors: Sun Shao’e , Xiao Ning , Sha Zhongli 
Published: March 2022

AbstractThe deep sea (> 200 m) is considered as the largest and most remote biome, which characterized by low temperatures, low oxygen level, scarce food, constant darkness, and high hydrostatic pressure. The sea stars (class Asteroidea) are ecologically important and diverse echinoderms in all of the world’s oceans, occurring from the intertidal to the abyssal zone (to about 6000 m). To date, the phylogeny of the sea stars and the relationships of deep-sea and shallow water groups have not yet been fully resolved. Here, we recovered five mitochondrial genomes of deep-sea asteroids. The A+T content of the mtDNA in deep-sea asteroids were significantly higher than that of the shallow-water groups. The gene orders of the five new mitogenomes were identical to that of other asteroids. The phylogenetic analysis showed that the orders Valvatida, Paxillosida, Forcipulatida are paraphyletic. Velatida was the sister order of all the others and then the cladeValvatida-Spinulosida-Paxillosida-Notomyotida versus Forcipulatida-Brisingida. Deep-sea asteroids were nested in different lineages, instead of a well-supported clade. The tropical Western Pacific was suggested as the original area of asteroids, and the temperate water was initially colonized with asteroids by the migration events from the tropical and cold water. The time-calibrated phylogeny showed that Asteroidea originated during Devonian-Carboniferous boundary and the major lineages of Asteroidea originated during Permian–Triassic boundary. The divergence between the deep-sea and shallow-water asteroids coincided approximately with the Triassic-Jurassic extinction. Total 29 positively selected sites were detected in fifteen mitochondrial genes of five deep-sea lineages, implying a link between deep-sea adaption and mitochondrial molecular biology in asteroids.
Synthetic exposure with a CMOS camera for multiple exposure speckle imaging of blood flow
Authors: Chammas M. , Pain F. 
Published: March 2022

AbstractSpeckle contrast imaging is an established technique to obtain relative blood flow maps over wide fields of view. A major improvement of the method relies on the acquisition of raw speckle images at different exposure times but requires simultaneous modulation of a laser pulse in duration and intensity and precise synchronization with a camera. This complex instrumentation has limited the use of multiple exposure speckle imaging. We evaluate here the use of a CMOS camera for a simplified approach based on synthetic exposure images created from the sum of successive frames acquired at a 1 ms exposure time. Both methods have been applied to evaluate controlled flows in micro-channels. The contribution of noises to the speckle contrast have been quantified and compared. Dark, readout and shot noise contributions to the total contrast remain constant for modulated exposure, while all these contributions decrease with increasing exposure time for synthetic exposure. The relative contribution of noises to speckle contrast depends on the level of illumination and the exposure time. Guidelines for flow measurements and limitations of the use of a CMOS camera with a limited frame rate for synthetic exposure acquisition scheme are discussed. The synthetic exposure method is simple to implement and should facilitate the translation of multiple exposure speckle imaging to clinical set-ups.
Decreased brain network global efficiency after attachment memories retrieval in individuals with unresolved/disorganized attachment-related state of mind
Authors: Massullo Chiara , Imperatori Claudio , De Vico Fallani Fabrizio , Ardito Rita B. , Adenzato Mauro , Palmiero Luigia , Carbone Giuseppe Alessio , Farina Benedetto 
Published: March 2022

AbstractThe main aim of the study was to examine how brain network metrics change after retrieval of attachment memories in individuals with unresolved/disorganized (U/D) attachment-related state of mind and those with organized/resolved (O/R) state of mind. We focused on three main network metrics associated with integration and segregation: global (Eglob) efficiency for the first function, local (Eloc) efficiency and modularity for the second. We also examined assortativity and centrality metrics. Electroencephalography (EEG) recordings were performed before and after the Adult Attachment Interview (AAI) in a sample of 50 individuals previously assessed for parenting quality. Functional connectivity matrices were constructed by means of the exact Low-Resolution Electromagnetic Tomography (eLORETA) software and then imported into MATLAB to compute brain network metrics. Compared to individuals with O/R attachment-related state of mind, those with U/D show a significant decrease in beta Eglob after AAI. No statistically significant difference among groups emerged in Eloc and modularity metrics after AAI, neither in assortativity nor in betweenness centrality. These results may help to better understand the neurophysiological patterns underlying the disintegrative effects of retrieving traumatic attachment memories in individuals with disorganized state of mind in relation to attachment.
A coordinate-based co-localization index to quantify and visualize spatial associations in single-molecule localization microscopy
Authors: Willems Jelmer , MacGillavry Harold D. 
Published: March 2022

AbstractVisualizing the subcellular distribution of proteins and determining whether specific proteins co-localize is one of the main strategies in determining the organization and potential interactions of protein complexes in biological samples. The development of super-resolution microscopy techniques such as single-molecule localization microscopy (SMLM) has tremendously increased the ability to resolve protein distribution at nanometer resolution. As super-resolution imaging techniques are becoming instrumental in revealing novel biological insights, new quantitative approaches that exploit the unique nature of SMLM datasets are required. Here, we present a new, local density-based algorithm to quantify co-localization in dual-color SMLM datasets. We show that this method is broadly applicable and only requires molecular coordinates and their localization precision as inputs. Using simulated point patterns, we show that this method robustly measures the co-localization in dual-color SMLM datasets, independent of localization density, but with high sensitivity towards local enrichments. We further validated our method using SMLM imaging of the microtubule network in epithelial cells and used it to study the spatial association between proteins at neuronal synapses. Together, we present a simple and easy-to-use, but powerful method to analyze the spatial association of molecules in dual-color SMLM datasets.
Targeting lung cancer cells with MUC1 aptamer-functionalized PLA-PEG nanocarriers
Authors: Shahrad Shima , Rajabi Mohammad , Javadi Hamidreza , Karimi Zarchi Ali Akbar , Darvishi Mohammad Hasan 
Published: March 2022

AbstractMUC1 aptamer-functionalized PLA-PEG nanocarriers at various w/w ratios (polymer to doxorubicin weight ratio) were prepared by a double emulsion method. Physiochemical properties, encapsulation efficiency (EE), loading content (LC) and in vitro release kinetics of DOX were assessed. Furthermore, cytotoxicity and antitumor activity of prepared PLA-PEG-Apt/DOX NPs at w/w ratio 10:1 were evaluated by MTT assay and flow cytometry against MUC1-overexpressing A-549 cell line. Targeted nanocarriers (PLA-PEG-Apt/DOX NPs at w/w ratio 10:1) induced higher apoptosis rate (36.3 ± 3.44%) for 24 h in MUC1 positive A-549 cancer cells in compare to non-targeted form (PLA-PEG/DOX NPs at w/w ratio 10:1, 11.37 ± 1.65%) and free DOX (4.35 ± 0.81%). In other word, the percentage of cell death in A-549 lung cancer cells treated with PLA-PEG-Apt/DOX NPs at w/w ratio 10:1 is 3.19 and 8.34 fold higher than in non-targeted form and Free DOX treated cancer cells, respectively. Therefore, PLA-PEG-Apt/DOX NPs might be considered a promising drug delivery system for targeted drug delivery towards MUC1-overexpressing tumors cells.