bluuebunny/crossref_metadata_2025 huggingface dataset:
Revisiting AGN as the source of IceCube's diffuse neutrino flux
Authors: Smith Daniel , Hooper Dan , Vieregg Abigail
Published: March 2021

The origin of the astrophysical neutrino flux reported by
the IceCube Collaboration remains an open question. In this study,
we use three years of publicly available IceCube data to search for
evidence of neutrino emission from the blazars and non-blazar Active
Galactic Nuclei (AGN) contained the Fermi 4LAC catalog. We find no
evidence that these sources produce high-energy neutrinos, and
conclude that blazars can produce no more than 15% of IceCube's
observed flux. The constraint we derive on the contribution from
non-blazar AGN, which are less luminous and more numerous than
blazars, is significantly less restrictive, and it remains possible
that this class of sources could produce the entirety of the diffuse
neutrino flux observed by IceCube. With our non-blazar AGN
constraints approaching IceCube's reported astrophysical neutrino
flux, we anticipate that it will become possible to definitively
test such scenarios as IceCube accumulates and releases more data,
and as gamma-ray catalogs of AGN become increasingly complete. We
also comment on starburst and other starforming galaxies, and
conclude that these sources could contribute substantially to the
signal observed by IceCube, in particular at the lowest detected
energies.
Layer-specific parameters of intracortical microstimulation of the somatosensory cortex
Authors: Urdaneta Morgan E , Kunigk Nicolas G , Delgado Francisco , Fried Shelley I , Otto Kevin J
Published: March 2021

Objective. Intracortical microstimulation of the primary somatosensory cortex (S1) has shown great progress in restoring touch sensations to patients with paralysis. Stimulation parameters such as amplitude, phase duration, and frequency can influence the quality of the evoked percept as well as the amount of charge necessary to elicit a response. Previous studies in V1 and auditory cortices have shown that the behavioral responses to stimulation amplitude and phase duration change across cortical depth. However, this depth-dependent response has yet to be investigated in S1. Similarly, to our knowledge, the response to microstimulation frequency across cortical depth remains unexplored. Approach. To assess these questions, we implanted rats in S1 with a microelectrode with electrode-sites spanning all layers of the cortex. A conditioned avoidance behavioral paradigm was used to measure detection thresholds and responses to phase duration and frequency across cortical depth. Main results. Analogous to other cortical areas, the sensitivity to charge and strength–duration chronaxies in S1 varied across cortical layers. Likewise, the sensitivity to microstimulation frequency was layer dependent. Significance. These findings suggest that cortical depth can play an important role in the fine-tuning of stimulation parameters and in the design of intracortical neuroprostheses for clinical applications.
Theoretical and experimental studies of molecular (atomic) exchange at the installation for measuring and analyzing the residual gas medium UID-2
Authors: Bushin S A , Nesterov S B
Published: March 2021

The paper presents the results of studies of mass transfer in the measuring circuit of the UID-2 installation (installation of pressure measurement and analysis of the residual gas medium in the electro-vacuum devices), which consists of two parallel vacuum paths, in the volumes of which are placed a total pressure transducer and a monopolar mass spectrometric sensor, limited by pairs of inlet and outlet diaphragms. Using the Monte-Carlo method, estimates of the average density of the distribution of the number of molecules within specified intervals of the number of collisions of the latter with surfaces of characteristic dimensions of these volumes are obtained.The experimental results obtained within the accuracy of the experiment are consistent with the calculated data on the protective properties of diaphragms that prevent the negative influence of the heated cathode of the gauge transducer on the gas composition of the analytical sample during the quantitative and qualitative analysis of the residual gas medium in the electro-vacuum devices based on the implementation of the destructive method.
Investigation of the quantum efficiency degradation over time for InGaAs photocathodes in hybrid devices for near infrared spectral range
Authors: Egorenkov A A , Zubkov V I
Published: March 2021

The structure and operating principle of InGaAs photocathode in near-IR hybrid photo device are considered. The mechanisms leading to the degradation of the quantum efficiency of the photocathode are being studied. The rate of the quantum efficiency degradation of the photocathode is measured for three hybrid devices. The methods to reduce the degradation of the photocathode sensitivity are suggested.
Field ion microscopy of radiation damage on an atomically clean surface of materials
Authors: Ivchenko V A
Published: March 2021

The defects induced by neutrons (E >0.1 MeV) and Ar+ beams (E = 30 KeV) on the atomically pure surface and in the near-surface volume of platinum were studied using field ion microscopy. Experimental results of radiation defect formation in surface layers of materials initiated by neutron bombardment (Pt, E > 0.1 MeV) and ion implantation (in Cu3Au: E = 40 keV, F = 1020 ion/m2, j = 10∼3 A/cm2) are considered. Quantitative estimates of the size, shape, and volume fraction of atomic displacement cascades formed during various types of irradiation in these materials are obtained. It is shown that the average size of radiation clusters after irradiation of platinum with a fast neutron fluence of 6.7« 1022 m−2 (E > 0.1 MeV) is about 3.2 nm. The experimentally established average size of a radiation cluster (disordered zone) in an alloy after ion bombardment is 4 • 4 • 1,5 nm.
Peculiarities of ripening and spinodal decomposition of self-organizing fractal systems
Authors: Pronin I A , Yakushova N D , Averin I A , Karmanov A A , Moshnikov V A
Published: March 2021

Qualitative and quantitative patterns for the synthesis of nanostructured films by the sol-gel technology method, established on the basis of theoretical models and experiments, are presented. The effect of annealing temperature, types of solvents and substrates on the morphostructure of the film surface is shown. A technique for the synthesis of films for sensitive elements of gas sensors and vacuum sensors based on orthosilicic acid has been developed.
Phase state features of non-equilibrium thermodynamic polymer-solvent systems
Authors: Pronin I A , Yakushova N D , Averin I A , Karmanov A A , Moshnikov V A
Published: March 2021

A boundary between the regions of labile and metastable phases of non-equilibrium thermodynamic polymer-solvent systems is determined as applied to the synthesis products of the sol-gel technology. Models that qualitatively and quantitatively predict properties and morphology of nanostructured composites, obtained on the basis of the analyzed systems, have been developed. The simulation results were verified using experimental data of atomic force microscopy.
Reducing the number of craters on quartz glass surface suffering high-velocity impacts of microparticles by application of SiAlN and TaN protective films
Authors: Sergeev V P , Kalashnikov M P , Sergeev O V , Voronov A V , Neyfeld V V , Paraev Yu N
Published: March 2021

On the quartz glass specimens, visually transparent single-layer SiAlN and two-layer SiAlN/TaN films were applied to compare their protective properties against shock impact of high-velocity (5-8 km/s) iron microparticles. The tests performed using a two-stage light-gas gun have shown that the most effective coatings are two-layer films. The structure, optical and mechanical properties of the films were determined.
Wear resistance of adaptive arc-PVD Ti-Al-Mo-Ni-N coatings under impact loading and hydroabrasive wear
Authors: Sergevnin V S , Blinkov I V , Volkhonskii A O , Smirnov N I
Published: March 2021

The behavior of Ti-Al-Mo-Ni-N coatings obtained by arc-PVD deposition under conditions of impact loading and hydroabrasive wear is studied. Nanostructured coatings samples with a thickness of 4 µm with a modulation period of 30 nm and hardness of 45 GPa were obtained. Under impact loading, the coating performs a protective function up to 105 loading cycles of 250 N without opening the substrate, and during hydroabrasive tests, after 3 hours of exposure to a flow at a speed of 8.5 m/s, there is a spot wear on the coating surface, opening minor segments oft the substrate area. It is shown that the introduction of Ni into the Ti-Al-Mo-N system leads to the appearance of coating failure by brittle mechanism with delamination and opening of the substrate under significant loads in the case of impact and hydroabrasive wear.
Multifunctional high-vacuum plant for cryovacuum systems in aerospace applications
Authors: Sokolov A N , Rozanov L N , Schedrincky M Z , Bebyakov V M , Sukharev K N , Sinkova V A , Koldyba A I
Published: March 2021

The article describes a design and main features of a multifunctional high-vacuum plant. This installation provides high-vacuum pumping of cryovacuum systems for space applications during a long time with 100 liter volume, leak detection with 5-1013 m3Pa/s minimum registered helium flow and monitoring of the mass spectrum within 1…100 AMU range.
Improving the quality of nanofilms produced by magnetron sputtering
Authors: Tupik V A , Potapov A A , Margolin V I , Kostrin D K
Published: March 2021

Technological and structural aspects of the synthesis of nanoscale films by magnetron sputtering methods and ways for improving their uniformity and structural perfection are considered. Experimental results demonstrate that the proposed technological solution makes it possible to obtain high-quality coatings with almost complete absence of the droplet component.
Differential mapping spiking neural network for sensor-based robot control
Authors: Zahra Omar , Tolu Silvia , Navarro-Alarcon David
Published: March 2021

In this work, a spiking neural network (SNN) is proposed for approximating differential sensorimotor maps of robotic systems. The computed model is used as a local Jacobian-like projection that relates changes in sensor space to changes in motor space. The SNN consists of an input (sensory) layer and an output (motor) layer connected through plastic synapses, with inter-inhibitory connections at the output layer. Spiking neurons are modeled as Izhikevich neurons with a synaptic learning rule based on spike timing-dependent plasticity. Feedback data from proprioceptive and exteroceptive sensors are encoded and fed into the input layer through a motor babbling process. A guideline for tuning the network parameters is proposed and applied along with the particle swarm optimization technique. Our proposed control architecture takes advantage of biologically plausible tools of an SNN to achieve the target reaching task while minimizing deviations from the desired path, and consequently minimizing the execution time. Thanks to the chosen architecture and optimization of the parameters, the number of neurons and the amount of data required for training are considerably low. The SNN is capable of handling noisy sensor readings to guide the robot movements in real-time. Experimental results are presented to validate the control methodology with a vision-guided robot.
The water use of heating pathways to 2050: analysis of national and urban energy scenarios
Authors: Kaandorp C , van de Giesen N , Abraham E
Published: March 2021

Sustainable energy systems can only be achieved when reducing both carbon emissions and water use for energy generation. Although the water use for electricity generation has been well studied, integrated assessments of the water use by low-carbon heat systems are lacking. In this paper we present an analysis of the water use of scenarios for heat and electricity production for the year 2050 for the Netherlands and its capital, Amsterdam. The analysis shows that (i) the water withdrawal for heating can increase up to the same order of magnitude as the current water withdrawal of thermoelectric plants due to the use of aquifer thermal energy storage, (ii) the virtual water use for heating can become higher than the operational water consumption for heating, and (iii) the water use for electricity production becomes a relevant indicator for the virtual water use for heat generation because of the increase of power-to-heat applications.
Does formalizing artisanal gold mining mitigate environmental impacts? Deforestation evidence from the Peruvian Amazon
Authors: Álvarez-Berríos Nora , L’Roe Jessica , Naughton-Treves Lisa
Published: March 2021

A global surge in ‘artisanal’, smallscale mining (ASM) threatens biodiverse tropical forests and exposes residents to dangerous levels of mercury. In response, governments and development agencies are investing millions (USD) on ASM formalization; registering concessions and demarcating extraction zones to promote regulatory adherence and direct mining away from ecologically sensitive areas. The environmental outcomes of these initiatives are seldom systematically assessed. We examine patterns of mining-related deforestation associated with formalization efforts in a gold-rich region of the Peruvian Amazon. We track changes from 2001 to 2014 when agencies: (a) issued 1701 provisional titles and (b) tried to restrict mining to a >5000 km2 ‘corridor’. We use fixed-effect regression models and matching methods to control for gold price, geology, and accessibility. Mining increased dramatically during this period, clearing ∼40 000 ha of forest. After the mining corridor was declared and enforcement increased, new mining sites were opened more frequently within titled areas and inside the corridor than elsewhere. However, mining also increased in protected area buffer zones and native communities, and the proportion of mining area occurring outside the corridor grew, concentrated in a few hotspots. Interviews (n = 47) revealed that the hoped-for regulatory adherence failed to materialize because miners who were issued provisional titles started operations without complying with attendant environmental rules. Overlapping land claims for agriculture and forest extraction proved a major obstacle for obtaining full legal rights to mine. Miners resented the slow, costly formalization process but many sought titles to bolster territorial claims, avoid policing, obtain credit and recruit paying ‘guest’ miners who generally ignored regulations. We find that responses to formalization varied with changing context and while formalization may curb mining in some circumstances, it may exacerbate it in others. Without adequate enforcement, interagency coordination, and attention to competing land claims, formalizing ASM may accelerate ecological destruction.
Critical inundation level for methane emissions from wetlands
Authors: Calabrese Salvatore , Garcia Alicia , Wilmoth Jared L , Zhang Xinning , Porporato Amilcare
Published: March 2021

Global methane (CH4) emissions have reached approximately 600 Tg per year, 20%–40% of which are from wetlands. Of the primary factors affecting these emissions, the water table level is among the most uncertain. Here we conduct a global meta-analysis of chamber and flux-tower observations of CH4 emissions and employ a novel mechanistic model to show that wetlands have maximum emissions at a critical level of inundation and discuss its origin. This maximum arises from an interplay between methanogenesis, methanotrophy, and transport, whose rates vary differently with the inundation level. The specific location of the critical water level above the soil surface may differ depending on wetland characteristics, for example temperature or the presence of macrophytes with aerenchyma. However, data suggest that globally a water level of about 50 cm is the most favorable to CH4 emissions. Keeping the water level away from this critical value could reduce methane emissions in human-made wetlands, which comprise at least one fifth of the global wetland area.
MONITORING AND DIAGNOSTICS OF FOREST CONDITION USING SOUND SENSORS AND ARTIFICIAL INTELLIGENCE TECHNOLOGIES
Authors: Bogomolov Alexander
Published: March 2021

The article examines the state of the planet’s forests based on statistics and threats to their existence, which are proposed to be diagnosed based on sound signals emitted by the forest, recorded using special sensors and recognized using artificial intelligence. References are given to studies of the reaction of plants to stressful situations, technologies for recording plant sounds and forest sounds. The results of forest assessment are proposed to be presented in visual form on the interactive forest map. Linking the forest sound field with the interactive map will facilitate early diagnosis of possible forest diseases and prevent the spread of epidemics, as well as the use of interactive maps of the planet’s forests in simulation models of global development will clarify the limits of civilization growth and move these limits to a later date.
Antivirus architecture: links between epidemic thought and images
Authors: Kadhim Ibrahim Jawad , Mohsin Abbas Na’im
Published: March 2021

Local architecture has succeeded in treating general issues related to human life and interests within various areas, including the social, economic, and environmental; however, it has been unable to address a global viral epidemic as a variable affecting human needs, thus necessitating diagnosis of defects and the development of alternative solutions, working with the idea of the overlap between thought and images in the systems of both the local architecture and the intelligent architecture, and the research problem thus emerged as “the necessity to develop the concept of an antivirus architecture with a local character and to examine its impact on improving reality during an epidemic crisis based on creating a locally intelligent architecture”. The aim of the research was thus to develop a theoretical model represented in an antivirus architecture with a local character that defines its components and mechanisms within the apparent system and carries within itself ideas that interact with both spatial and time dimensions in light of the current epidemic crisis. The research method included applying several procedures based on developing the theoretical framework and selecting samples for practical application, allowing the presentation of the most important conclusions that clarified the possibility of extracting specific components of the apparent system of that theoretical model.
Climate change impacts on potential water savings through household rainwater tanks in Adelaide (Australia)
Authors: Paudel U , Imteaz M A
Published: March 2021

This paper presents impacts of climate change on future water savings through rainwater tanks for the city of Adelaide in South Australia. Four rainfall stations within Adelaide metropolitan were selected for the current study. The projected rainfall data was generated by the Australian government applying Statistical Downscaling Modelling (SDSM) technique using observed data for the period of 1986-2005. Projected data was downloaded from the Australian government’s climate portal for three future years (2040, 2065 and 2090) and for two climate change scenarios. Projected daily rainfall data was applied to an earlier developed daily water balance model, eTank, which was widely used for the analysis of rainwater tank outcomes. Analyses were conducted for a single demand of rainwater (300 L/day) for two roof sizes (150 m2 and 300 m2) and two tank volumes (5 kL and 10 kL). It is found that potential future water savings for all the selected future years for the three selected stations are expected to reduce; considering all the variables, ranges of potential reductions for “Adelaide Airport” is 1%∼53%, for “Kent Town” is 4%∼29% and for “Happy Valley Reservoir” is 1%∼27%. For the fourth station, Edinburgh Royal Australian Air Force (RAAF), water savings are expected to increase under all the scenarios with a roof size of 150 m2. Whereas, with a roof size of 300 m2, for the same station water savings are expected to decrease under all the scenarios. The maximum potential increase in water savings is expected to be 16% (with a roof of 150 m2), while the maximum potential decrease in water savings is expected to be 23% (with a roof of 300 m2).
Transformation of asymmetric Schell-model beams with a wavefront-folding interferometer
Authors: Tang Miaomiao , Feng Xinxin , Liu Siyu , Li Hehe , Li Xinzhong
Published: March 2021

We consider a class of random light beams, which are generated by inserting an asymmetric Schell-model beam into a wavefront-folding interferometer. Typical propagation behavior of such optical beams modulated by several legitimate complex coherence states has been investigated. In certain cases, these beams exhibit novel rotationally symmetric intensity patterns with rectangular or lattice-like lobes, and the pattern and location of each lobe can be controlled by adjusting the source coherence parameters. Besides, beam characteristics can be flexibly modulated by varying the phase delay between the two paths of the interferometer. Our results may be applied in free-space optical communication.
Functional polyaspartic acid fibers hydrogel membrane with enhanced mechanical performance prepared by coaxial electrospinning
Authors: Li Sijie , Zhang Caidan , Yu Qiaozhen , Jia Lin
Published: March 2021

Coaxial electrospinning is a practical technique to combine the advantages of different materials. In this work, polyaspartic acid (PASP) fibers hydrogel membrane (FHM) was enhanced by thermoplastic polyurethane (TPU) via coaxial electrospinning. Firstly, polysuccinimide (PSI) served as the intermediate of PASP was employed for coaxial electrospining with TPU. TPU/PSI core-shell fiber possessed cracked shell on core, uniform core-shell structure, dumbbell-shape and beaded-on-string morphology according to parameters adjustment. Then TPU/PASP-FHM was produced by the crosslinking and hydrolysis treatment of TPU/PSI fibers membrane. TPU with excellent mechanical properties improved the tensile strength of TPU/PASP-FHM. Owing to the Cu2+ absorption capability of PASP hydrogel shell, TPU/PASP-FHM was successfully used to detect 1 mg L−1 Cu2+ with color change from white to blue, which was able to be observed by naked-eye. Moreover, TPU/PASP-FHM after Cu2+ detection returned to its original color with acid elution, and it was able to be used repeatedly for Cu2+ detection.
Olympus: a benchmarking framework for noisy optimization and experiment planning
Authors: Häse Florian , Aldeghi Matteo , Hickman Riley J , Roch Loïc M , Christensen Melodie , Liles Elena , Hein Jason E , Aspuru-Guzik Alán
Published: March 2021

Research challenges encountered across science, engineering, and economics can frequently be formulated as optimization tasks. In chemistry and materials science, recent growth in laboratory digitization and automation has sparked interest in optimization-guided autonomous discovery and closed-loop experimentation. Experiment planning strategies based on off-the-shelf optimization algorithms can be employed in fully autonomous research platforms to achieve desired experimentation goals with the minimum number of trials. However, the experiment planning strategy that is most suitable to a scientific discovery task is a priori unknown while rigorous comparisons of different strategies are highly time and resource demanding. As optimization algorithms are typically benchmarked on low-dimensional synthetic functions, it is unclear how their performance would translate to noisy, higher-dimensional experimental tasks encountered in chemistry and materials science. We introduce Olympus, a software package that provides a consistent and easy-to-use framework for benchmarking optimization algorithms against realistic experiments emulated via probabilistic deep-learning models. Olympus includes a collection of experimentally derived benchmark sets from chemistry and materials science and a suite of experiment planning strategies that can be easily accessed via a user-friendly Python interface. Furthermore, Olympus facilitates the integration, testing, and sharing of custom algorithms and user-defined datasets. In brief, Olympus mitigates the barriers associated with benchmarking optimization algorithms on realistic experimental scenarios, promoting data sharing and the creation of a standard framework for evaluating the performance of experiment planning strategies.
The Wentzel-Kramers-Brillouin approximation for light scattering by horizontally oriented prismatic particles
Authors: Tari E M , Bahaoui A , Lamsoudi R , Khouilid M , Ibnchaikh M
Published: March 2021

In this research, we propose a simple approximation technique based on the decomposition of particles and on the Wentzel-Kramers-Brillouin approximation (WKB). The latter allows us to express analytically the expression of the form factor of a particle of a regular prismatic ice crystal shape. Our focus will be on studying the light scattering by horizontally oriented prismatic particles which rotate about their principal axes. To illustrate our formalism, a few numerical examples will be analyzed.
Severe brachial plexopathy secondary to shingles (herpes zoster)
Authors: McFeely Aoife , Doyle Rachael , O’Riordan Sean , Connolly Sean , O’Dwyer Clodagh
Published: March 2021

Varicella zoster reactivation (“shingles” or “herpes zoster”) usually presents as a self-limiting, unilateral, dermatomal vesicular rash in older adults. We present the case of a 73 year-old woman with unilateral brachial plexopathy, an unusual but debilitating complication of shingles. Despite treatment with intravenous acyclovir and immunoglobulin she had a marked residual motor paresis that required an upper limb rehabilitation program after discharge.
Retroperitoneal Dedifferentiated Liposarcoma
Authors: Dehner Carina A , Hagemann Ian S , Chrisinger John S A
Published: March 2021

Objectives

We aimed to test the hypothesis that in retroperitoneal dedifferentiated liposarcoma (DDLS) the presence of the dedifferentiated (DD) component at the resection margin is associated with adverse outcome.

Methods

We retrospectively searched the archive for primary resections of retroperitoneal DDLS performed at our institution between 1990 and 2017. Slides were rereviewed for diagnosis, Fédération Nationale des Centres de Lutte Contre le Cancer grade, myogenic differentiation, and the presence of the well-differentiated (WD) or DD component at the resection margin. The medical records were reviewed for patient age, sex, tumor size, tumor focality, adjuvant/neoadjuvant therapy, local recurrence, distant metastases, local recurrence-free survival (LRFS), overall survival (OS), and follow-up duration.

Results

The presence of the DD component at the resection margin was associated with worse LRFS compared with cases without the DD component at the margin (P = .002). However, OS was not significantly affected (P = .11).

Conclusions

LRFS is significantly shorter in cases with the DD component at the margin compared with cases without DD tumor at the margin, while there is no association with OS. We recommend reporting the presence or absence of DD tumor at the margin in retroperitoneal DDLS, as it adds meaningful prognostic information.
Associations of Binge Drinking With the Risks of Ischemic Heart Disease and Stroke: A Study of Pooled Norwegian Health Surveys
Authors: Degerud Eirik , Høiseth Gudrun , Mørland Jørg , Ariansen Inger , Graff-Iversen Sidsel , Ystrom Eivind , Zuccolo Luisa , Tell Grethe S , Næss Øyvind
Published: March 2021

Norwegian health survey data (1987–2003) were analyzed to determine if binge drinking increases the risk of incident major events from ischemic heart disease (IHD) and stroke. Among current drinkers reporting average alcohol intakes of 2.00–59.99 g/day (n = 44,476), frequent binge drinking (≥5 units at least once per month) was not associated with a greater risk of IHD (adjusted hazard ratio (HR) = 0.91, 95% confidence interval (CI): 0.76, 1.09) or stroke (adjusted HR = 0.98, 95% CI: 0.81, 1.19), in comparison with participants who reported that they never or only infrequently (less than once per month) had episodes of binge drinking. Participants with an average alcohol intake of 2.00–59.99 g/day had a lower risk of IHD in comparison with participants with very low intakes (<2.00 g/day), both among frequent binge drinkers (adjusted HR = 0.67, 95% CI: 0.56, 0.80) and among never/infrequent binge drinkers (adjusted HR = 0.75, 95% CI: 0.67, 0.84). The findings suggest that frequent binge drinking, independent of average alcohol intake, does not increase the risk of incident IHD or stroke events. However, the findings should be interpreted in light of the limitations of the study design.
Synthesis of a plasmenylethanolamine
Authors: Maeda Satoshi , Mohri Tomoyo , Inoue Tsubasa , Asano Yoshio , Otoki Yurika , Enomoto Masaru , Nakagawa Kiyotaka , Kuwahara Shigefumi , Ogura Yusuke
Published: March 2021

A concise synthesis of a plasmenylethanolamine (PlsEtn-[16:0/18:1 n-9]), known as antioxidative phospholipids commonly found in cell membranes, has been achieved from an optically active known diol through 8 steps. The key transformations for the synthesis of PlsEtn-[16:0/18:1 n-9] are (1) regio- and Z-selective vinyl ether formation via the alkylation of a lithioalkoxy allyl intermediate with an alkyl iodide, and (2) a one-pot phosphite esterification–oxidation sequence to construct the ethanolamine phosphonate moiety in the presence of the vinyl ether functionality. The piperidine salt of synthetic PlsEtn-[16:0/18:1 n-9] was desalinated through reversed-phase high-performance liquid chromatography purification.
Integration and interplay of machine learning and bioinformatics approach to identify genetic interaction related to ovarian cancer chemoresistance
Authors: Chen Kexin , Xu Haoming , Lei Yiming , Lio Pietro , Li Yuan , Guo Hongyan , Ali Moni Mohammad
Published: March 2021

Although chemotherapy is the first-line treatment for ovarian cancer (OCa) patients, chemoresistance (CR) decreases their progression-free survival. This paper investigates the genetic interaction (GI) related to OCa-CR. To decrease the complexity of establishing gene networks, individual signature genes related to OCa-CR are identified using a gradient boosting decision tree algorithm. Additionally, the genetic interaction coefficient (GIC) is proposed to measure the correlation of two signature genes quantitatively and explain their joint influence on OCa-CR. Gene pair that possesses high GIC is identified as signature pair. A total of 24 signature gene pairs are selected that include 10 individual signature genes and the influence of signature gene pairs on OCa-CR is explored. Finally, a signature gene pair-based prediction of OCa-CR is identified. The area under curve (AUC) is a widely used performance measure for machine learning prediction. The AUC of signature gene pair reaches 0.9658, whereas the AUC of individual signature gene-based prediction is 0.6823 only. The identified signature gene pairs not only build an efficient GI network of OCa-CR but also provide an interesting way for OCa-CR prediction. This improvement shows that our proposed method is a useful tool to investigate GI related to OCa-CR.
Network-based modeling of herb combinations in traditional Chinese medicine
Authors: Wang Yinyin , Yang Hongbin , Chen Linxiao , Jafari Mohieddin , Tang Jing
Published: March 2021

Traditional Chinese medicine (TCM) has been practiced for thousands of years for treating human diseases. In comparison to modern medicine, one of the advantages of TCM is the principle of herb compatibility, known as TCM formulae. A TCM formula usually consists of multiple herbs to achieve the maximum treatment effects, where their interactions are believed to elicit the therapeutic effects. Despite being a fundamental component of TCM, the rationale of combining specific herb combinations remains unclear. In this study, we proposed a network-based method to quantify the interactions in herb pairs. We constructed a protein–protein interaction network for a given herb pair by retrieving the associated ingredients and protein targets, and determined multiple network-based distances including the closest, shortest, center, kernel, and separation, both at the ingredient and at the target levels. We found that the frequently used herb pairs tend to have shorter distances compared to random herb pairs, suggesting that a therapeutic herb pair is more likely to affect neighboring proteins in the human interactome. Furthermore, we found that the center distance determined at the ingredient level improves the discrimination of top-frequent herb pairs from random herb pairs, suggesting the rationale of considering the topologically important ingredients for inferring the mechanisms of action of TCM. Taken together, we have provided a network pharmacology framework to quantify the degree of herb interactions, which shall help explore the space of herb combinations more effectively to identify the synergistic compound interactions based on network topology.
FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations
Authors: Rausch Atilio O , Freiberger Maria I , Leonetti Cesar O , Luna Diego M , Radusky Leandro G , Wolynes Peter G , Ferreiro Diego U , Parra R Gonzalo
Published: March 2021

Once folded, natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they are highly frustrated. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein–protein interactions, small ligand recognition, catalytic sites and allostery. Here, we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and molecular dynamics (MD) trajectories, allowing straightforward integration of local frustration analysis into pipelines for protein structural analysis.

Availability and implementation

https://github.com/proteinphysiologylab/frustratometeR.

Supplementary information

Supplementary data are available at Bioinformatics online.
Igf3: a novel player in fish reproduction
Authors: Li Jianzhen , Liu Zhiquan , Kang Tao , Li Minghui , Wang Deshou , Cheng Christopher H K
Published: March 2021

As in other vertebrates, fish reproduction is tightly controlled by gonadotropin signaling. One of the most perplexing aspects of gonadotropin action on germ cell biology is the restricted expression of gonadotropin receptors in somatic cells of the gonads. Therefore, the identification of factors conveying the action of gonadotropins on germ cells is particularly important for understanding the mechanism of reproduction. Insulin-like growth factors (Igfs) are recognized as key factors in regulating reproduction by triggering a series of physiological processes in vertebrates. Recently, a novel member of Igfs called Igf3 has been identified in teleost. Different from the conventional Igf1 and Igf2 that are ubiquitously expressed in a majority of tissues, Igf3 is solely or highly expressed in the fish gonads. The role of Igf3 in mediating the action of gonadotropin through Igf type 1 receptor on several aspects of oogenesis and spermatogenesis have been demonstrated in several fish species. In this review, we will summarize existing data on Igf3. This new information obtained from Igf3 provides insight into elucidating the molecular mechanism of fish reproduction, and also highlights the importance of Igf system in mediating the action of gonadotropin signaling on animal reproduction.
Anatomical and cellular heterogeneity in the mouse oviduct—its potential roles in reproduction and preimplantation development
Authors: Harwalkar Keerthana , Ford Matthew J , Teng Katie , Yamanaka Nobuko , Yang Brenna , Burtscher Ingo , Lickert Heiko , Yamanaka Yojiro
Published: March 2021

The oviduct/fallopian tube is a tube-like structure that extends from the uterus to the ovary. It is an essential reproductive organ that provides an environment for internal fertilization and preimplantation development. However, our knowledge of its regional and cellular heterogeneity is still limited. Here, we examined the anatomical complexity of mouse oviducts using modern imaging techniques and fluorescence reporter lines. We found that there are consistent coiling patterns and turning points in the coiled mouse oviduct that serve as reliable landmarks for luminal morphological regionalities. We also found previously unrecognized anatomical structures in the isthmus and uterotubal junction, which likely play roles in reproduction. Furthermore, we demarcated the ampulla–isthmus junction as a distinct region. Taken together, the oviduct mucosal epithelium has highly diverse structures with distinct epithelial cell populations, reflecting its complex functions in reproduction.
GABAergic cortical network physiology in frontotemporal lobar degeneration
Authors: Adams Natalie E , Hughes Laura E , Rouse Matthew A , Phillips Holly N , Shaw Alexander D , Murley Alexander G , Cope Thomas E , Bevan-Jones W Richard , Passamonti Luca , Street Duncan , Holland Negin , Nesbitt David , Friston Karl , Rowe James B
Published: March 2021

The clinical syndromes caused by frontotemporal lobar degeneration are heterogeneous, including the behavioural variant frontotemporal dementia (bvFTD) and progressive supranuclear palsy. Although pathologically distinct, they share many behavioural, cognitive and physiological features, which may in part arise from common deficits of major neurotransmitters such as γ-aminobutyric acid (GABA). Here, we quantify the GABAergic impairment and its restoration with dynamic causal modelling of a double-blind placebo-controlled crossover pharmaco-magnetoencephalography study. We analysed 17 patients with bvFTD, 15 patients with progressive supranuclear palsy, and 20 healthy age- and gender-matched controls. In addition to neuropsychological assessment and structural MRI, participants undertook two magnetoencephalography sessions using a roving auditory oddball paradigm: once on placebo and once on 10 mg of the oral GABA reuptake inhibitor tiagabine. A subgroup underwent ultrahigh-field magnetic resonance spectroscopy measurement of GABA concentration, which was reduced among patients. We identified deficits in frontotemporal processing using conductance-based biophysical models of local and global neuronal networks. The clinical relevance of this physiological deficit is indicated by the correlation between top-down connectivity from frontal to temporal cortex and clinical measures of cognitive and behavioural change. A critical validation of the biophysical modelling approach was evidence from parametric empirical Bayes analysis that GABA levels in patients, measured by spectroscopy, were related to posterior estimates of patients’ GABAergic synaptic connectivity. Further evidence for the role of GABA in frontotemporal lobar degeneration came from confirmation that the effects of tiagabine on local circuits depended not only on participant group, but also on individual baseline GABA levels. Specifically, the phasic inhibition of deep cortico-cortical pyramidal neurons following tiagabine, but not placebo, was a function of GABA concentration. The study provides proof-of-concept for the potential of dynamic causal modelling to elucidate mechanisms of human neurodegenerative disease, and explains the variation in response to candidate therapies among patients. The laminar- and neurotransmitter-specific features of the modelling framework, can be used to study other treatment approaches and disorders. In the context of frontotemporal lobar degeneration, we suggest that neurophysiological restoration in selected patients, by targeting neurotransmitter deficits, could be used to bridge between clinical and preclinical models of disease, and inform the personalized selection of drugs and stratification of patients for future clinical trials.
The role of noradrenaline in cognition and cognitive disorders
Authors: Holland Negin , Robbins Trevor W , Rowe James B
Published: March 2021

Many aspects of cognition and behaviour are regulated by noradrenergic projections to the forebrain originating from the locus coeruleus, acting through alpha and beta adrenoreceptors. Loss of these projections is common in neurodegenerative diseases and contributes to their cognitive and behavioural deficits. We review the evidence for a noradrenergic modulation of cognition in its contribution to Alzheimer’s disease, Parkinson’s disease and other cognitive disorders. We discuss the advances in human imaging and computational methods that quantify the locus coeruleus and its function in humans, and highlight the potential for new noradrenergic treatment strategies.
Conventional generation emulation for power grids with a high penetration of wind power
Authors: El-Azab Rasha , Wazeer Eslam M , Daowd Mohamed , Abdel Ghany A M
Published: March 2021

Integrating large-scale wind plants with the electricity grids has many challenges for grid operators. Besides the variability and uncertainty of wind power, coordinating between different technologies of generation in the same grid can be considered the main problem, specifically for short-term frequency stability. Therefore, a large penetration of wind power generation in modern power grids has a risky influence on the power-system frequency. Wind-generation plants have contradictory behaviour compared to classic thermal plants, especially in active generated power-shortage events due to the variable nature of wind power. Existing experience in wind plants keeps part of the available wind power unloaded, using what are known as deloading techniques. Different deloading techniques are usually applied to emulate the thermal-plant-governor function and confirm a proper spinning reserve for any active-power shortages. These techniques decrease the generated power from wind plants continuously from maximum point tracking ones. Consequently, the practical capacity, annual generated energy and economical income of wind plants are reduced. In addition, grid-protection and control sub-schemes are set and designed according to the well-known conventional responses of thermal plants, which increase the need for thermal-plant-behaviour emulation. In this paper, instead of the usual deloading methods, a supercapacitors scheme is proposed with wind turbines to emulate the response of conventional power plants. The study discusses the technical and economic benefits of the proposed addition of supercapacitors in the wind-plant-planning phase. Restricted frequency grid-code indices are selected to evaluate studied behaviours. Simulation results of the IEEE four-generation two-area system determines the effectiveness of suggested schemes technically. The System Advisor Model (SAM) program estimates the economic benefits of a typical US study case compared with the existing wind-deloading technique.
New aspects of endocrine control of atrial fibrillation and possibilities for clinical translation
Authors: Aguilar Martin , Rose Robert A , Takawale Abhijit , Nattel Stanley , Reilly Svetlana
Published: March 2021

Hormones are potent endo-, para-, and autocrine endogenous regulators of the function of multiple organs, including the heart. Endocrine dysfunction promotes a number of cardiovascular diseases, including atrial fibrillation (AF). While the heart is a target for endocrine regulation, it is also an active endocrine organ itself, secreting a number of important bioactive hormones that convey significant endocrine effects, but also through para-/autocrine actions, actively participate in cardiac self-regulation. The hormones regulating heart-function work in concert to support myocardial performance. AF is a serious clinical problem associated with increased morbidity and mortality, mainly due to stroke and heart failure. Current therapies for AF remain inadequate. AF is characterized by altered atrial function and structure, including electrical and profibrotic remodelling in the atria and ventricles, which facilitates AF progression and hampers its treatment. Although features of this remodelling are well-established and its mechanisms are partly understood, important pathways pertinent to AF arrhythmogenesis are still unidentified. The discovery of these missing pathways has the potential to lead to therapeutic breakthroughs. Endocrine dysfunction is well-recognized to lead to AF. In this review, we discuss endocrine and cardiocrine signalling systems that directly, or as a consequence of an underlying cardiac pathology, contribute to AF pathogenesis. More specifically, we consider the roles of products from the hypothalamic-pituitary axis, the adrenal glands, adipose tissue, the renin–angiotensin system, atrial cardiomyocytes, and the thyroid gland in controlling atrial electrical and structural properties. The influence of endocrine/paracrine dysfunction on AF risk and mechanisms is evaluated and discussed. We focus on the most recent findings and reflect on the potential of translating them into clinical application.
Quantifying the mortality impact of the 1935 old-age assistance
Authors: Galofré-Vilà Gregori , McKee Martin , Stuckler David
Published: March 2021

In 1935, the United States introduced the old-age assistance (OAA) program, a means-tested program to help the elderly poor. The OAA improved retirement conditions and aimed to enable older persons to live independently. We use the transition from early elderly plans to OAA and the large differences in payments and eligibility across states to show that OAA reduced mortality by between 30 and 39 percent among those older than 65 years. This finding, based on an event study design, is robust to a range of specifications, a range of fixed effects, placebo tests, and a border-pair policy discontinuity design using county-level data. The largest mortality reductions came from drops in communicable and infectious diseases, such as influenza and nephritis, and mostly affected white citizens.
The association between screen time and reported depressive symptoms among adolescents in Sweden
Authors: Ma Li , Evans Brittany , Kleppang Annette Lovheim , Hagquist Curt
Published: March 2021

Background

How screen use is associated with adolescents’ mental health has been widely debated in public media during the last decade, but there is still lack of information about if and how the associations vary between types of electronic media.

Objective

This study aimed to examine how time spent on types of screen use (social media, gaming alone, gaming in groups and watching TV) was associated with depressive symptoms among adolescents in Sweden, and whether gender moderated these associations.

Methods

We analysed data from the Swedish section of the Children of Immigrants: Longitudinal Survey in Four European Countries. The final sample consisted of 3556 eighth grade adolescents in 2011 (51% girls). We used logistic regression analysis to estimate the odds ratio of feeling depressed often versus less often/not at all using time spent on different types of screen use as predictor variables. Additionally, we tested interaction effects between gender and the predictor variables.

Results

Our results showed that spending more than 2 hours on social media was associated with higher odds of feeling depressed often compared with spending 2 hours or less. Not watching TV was associated with higher odds of feeling depressed often compared with watching TV. These patterns did not differ across genders. Gaming alone and gaming in groups were not associated with depressive symptoms.

Conclusions

Our findings suggest that more frequent social media use and not watching TV were associated with a higher level of depressive symptoms.