bluuebunny/crossref_metadata_2025 huggingface dataset:
A three-dimensional numerical model for the motion of liquid drops by the particle finite element method
Authors: Mahrous Elaf , Valéry Roy R. , Jarauta Alex , Secanell Marc
Published: May 2022

Analysis of drop spreading and sliding on solid substrates is critical for many industrial applications, such as microfluidic devices, cooling towers, and fuel cells. A new three-dimensional model is proposed for droplet dynamics. Its numerical solution is obtained by the particle finite element method, based on an updated Lagrangian framework to accurately track the deformation of the droplet. The model hinges on boundary conditions at the solid–liquid interface to account for viscous dissipation and retention forces. These conditions are essential to obtain mesh-independent solutions and a realistic spatiotemporal evolution of the droplet deformation. Several numerical simulations are performed to assess the performance of the model for spreading and sliding drops, and results are compared to experimental data found in the literature. Good agreement is obtained with the available data. Simulations performed in two dimensions show striking discrepancies with the experimental data, thus demonstrating the need for three-dimensional simulations.
Displacement flows in eccentric annuli with a rotating inner cylinder
Authors: Jung H. , Frigaard I. A.
Published: May 2022

We experimentally study the effects of inner cylinder rotation on the displacement flow of two Newtonian fluids along a horizontal eccentric annulus, with differing viscosities and densities. With the rotation of the inner cylinder, the flow behavior changes from stratified to helical, as rotation dominates buoyancy, or directly to an azimuthally dispersive regime when rotational velocity dominates axial velocity. Flow separation is observed to occur when eccentricity is high: the displacing fluid is contained in the wide gap of the annulus, and the effective displacement is delayed. Rotation is effective in creating azimuthal flow in the narrow gap, where there is limited flow and bottom-side residual fluid may be present. In most cases, rotation improves the displacement (volumetric efficiency) by shortening the length of the axial elongation of the displacement front, and eventually, steady displacements are seen. The study is motivated by displacement flows occurring during the primary cementing of long horizontal oil and gas wells. Rotating the inner cylinder (casing) is recommended. Our results suggest that this practice increases azimuthal dispersion and can prevent a narrow mud channel from forming if the excess fluid volume is used.
Turbulent displacement flows of viscoplastic fluids in obstructed eccentric annuli: Experiments
Authors: Mitishita Rodrigo S. , Waldal Nile , Vogl Anastasia , Frigaard Ian A.
Published: May 2022

We present an experimental study of turbulent displacement flows in eccentric annuli, where the displacing fluids are water, 0.1% and 0.2% xanthan gum solutions, and the in situ fluid is a viscoplastic, 0.15% Carbopol solution. We focus on the effect of a solid obstruction on the narrow side of the annular gap, analogous to a consolidated cuttings bed in well cementing operations. For comparison we include experiments with an unobstructed test section with eccentricity e set at ∼0.5. While the displacement flow is successful without the obstruction regardless of the displacing fluid, we find that the obstruction at e∼0.5 is mostly detrimental to removal of the yield stress fluid stuck downstream of it, and a decrease in Reynolds numbers via formulation of xanthan gum solutions contribute to a less effective displacement in all situations due to the decrease in fluctuating stresses. Upstream of the obstruction, we observe complete removal of the Carbopol, likely due to enhanced vorticity effects. However, at high eccentricity values of e∼0.7, the effect of the obstruction on the displacement of Carbopol appears to be negligible, especially in the less turbulent situations with the xanthan gum solutions where the stationary Carbopol layer covers the entirety of the solid blockage, both upstream and downstream. Thus, in a highly eccentric obstructed annulus, the eccentricity remains the dominant factor to hinder the displacement.
Spatiotemporal measurement of concentration-dependent diffusion coefficient
Authors: Ahmadzadegan Adib , Zhang Jiacheng , Ardekani Arezoo M. , Vlachos Pavlos P.
Published: May 2022

We introduce a method to measure the concentration-dependent diffusion coefficient from a sequence of images of molecules diffusing from a source toward a sink. Generally, approaches measuring the diffusion coefficient, such as fluorescence recovery after photobleaching (FRAP), assume that the diffusion coefficient is constant. Hence, these methods cannot capture the concentration dependence of the diffusion coefficient if present. Other approaches measure the concentration-dependent diffusion coefficient from an instantaneous concentration profile and lose the temporal information. These methods make unrealistic assumptions, are not robust, and lead to 100% error. We introduce an image analysis framework that utilizes spatial and temporal information in a sequence of concentration images and numerically solves the general form of Fick's second law using radial basis functions (RBF) to measure the concentration-dependent diffusion coefficient. We term this approach as concentration image diffusimetry (CID). Our method makes no assumptions about the sink and source size and the diffusion dependence on concentration. CID is superior to existing methods in estimating spatiotemporal changes and concentration-dependent diffusion. CID also provides a statistical uncertainty quantification on the measurements using a bootstrapping approach, improving the reliability of the diffusion measurement. We assessed CID's performance using synthetically generated images. Our analysis suggests that CID accurately measures the diffusion coefficient with less than 2% error for most cases. We validated CID with FRAP experimental images and showed that CID agrees with established FRAP algorithms for samples with a constant diffusion coefficient. Finally, we demonstrate the application of CID to experimental datasets of a concentration gradient-driven protein diffusion into a tissue replicate. In conclusion, this work presents an image-based methodology that uses the spatial and temporal changes of concentration fields to measure the concentration-dependent diffusion coefficient.
History, archaeology and culture.
Authors: Spagnoli F. , Yavari A.
Published: May 2022

This chapter discusses: (1) the etymology of the fig; (2) the domestication, dispersal and archaeological evidence of the fig; (3) fig in ancient Egypt; (4) the fig in Neolithic Levant and East Mediterranean; (5) figs in Greece and West Mediterranean in the Iron Age; (6) the fig in Roman culture; and (7) the fig tree in the Holy Books.
Taxonomy, botany and physiology.
Authors: Gaaliche B. , Narzary D. , Ben Mimoun M. , Sarkhosh A.
Published: May 2022

This chapter focuses on the botany and physiology of the horticulturally important fig (Ficus carica) species. Through understanding of its reproductive complexity and developmental biology, complete genome sequencing could place the fig as a model plant in horticulture and evolutionary biology. And, in Mediterranean regions and Western Asia, where both cultivated and semiwild figs are found, a systematic germplasm collection of the traditional fig cultivars and wild relatives is imperative for proper germplasm management and conservation.
World fig cultivars.
Authors: Aljane F. , Neily M. H. , Rodrigues M. G. F. , Mazri C. , Stournaras V. , Kokaj T. , Yavari A. , Ferguson L. , Sarkhosh Ali
Published: May 2022

This chapter provides information on the various fig types, i.e. caprifig fig (Ficus carica var. sylvestris), common-type figs (F. carica var. hortensis), Smyrna-type figs (F. carica var. smyrna) and San Pedro-type figs (F. carica var. intermedia), their various cultivars and the countries where these cultivars are commonly cultivated. Notes on the adaptability to multiple microclimates, production methods, marketing and uses of these cultivars are also presented.
Irrigation and water requirements.
Authors: Abdolahipour M. , Kamgar-Haghighi A. A. , Sepaskhah A. R. , Davatgar N. , Dalir N.
Published: May 2022

This chapter reviews the water requirements and irrigation strategies of rainfed fig trees. The supplemental irrigation of rainfed orchards and its effect on growth and yield, selection of irrigation method, and fertigation are discussed.
Arthropod pests of fig and their management.
Authors: Singh S. , Li Z. , Zhang Y. , Grieshop M. J. , Giliomee J. , Cocuzza G. E. Massimino , Sandhu R. K.
Published: May 2022

This chapter provides an overview of the most important arthropod pests of fig, taking into consideration their destructiveness, distribution and regularity of occurrence, and discusses their main management approaches. Some of these arthropod pests include Phycodes radiata, Serrodes partita, Carpophilus hemipterus, Hypoborus ficus, Homotoma ficus, Bactrocera dorsalis, Frankliniella occidentalis and Tetranychus urticae, among others.
Laser properties of active media based on ZnSe doped with Fe and In from spray pyrolysis deposited films
Authors: Gavrishchuk E M , Savin D V , Tomilova T S , Ikonnikov V B , Kurashkin S V , Rodin S A , Kononov I G , Podlesnykh S V , Firsov K N
Published: May 2022

A technique was presented for obtaining laser media based on polycrystalline zinc selenide doped with iron from spray pyrolysis deposited films in the solid-phase diffusion process. The effect of the ligature film composition and the high-temperature treatment conditions on the lasing characteristics of Fe:(In):ZnSe active elements was investigated. Lasing with an energy of 100 mJ at a differential absorbed energy efficiency of 42% was obtained on 20 mm disk Fe:ZnSe element pumped by a pulsed electric-discharge HF laser.
Bound states in the continuum in metal–dielectric photonic crystal with a birefringent defect
Authors: Tang Hongzhen , Hu Peng , Cui Da-Jian , Xiang Hong , Han Dezhuan
Published: May 2022

By using the difference of the band structure for the TE and TM waves in the metal–dielectric photonic crystals beyond the light cone and the birefringence of the anisotropic crystal, a one-dimensional photonic system is constructed to realize the bound states in the continuum (BICs). In addition to the BICs arising from the polarization incompatibility, the Friedrich–Wintgen BICs are also achieved when the leaking TM wave is eliminated due to the destructive interference of its ordinary and extraordinary wave components in the anisotropic crystal. A modified scheme favorable for practical application is also proposed. This scheme for BICs may help to suppress the radiation loss in the metal–dielectric photonic crystal systems.
Epilepsy dynamics of an astrocyte-neuron model with ammonia intoxication
Authors: Yuan Zhixuan , Du Mengmeng , Yu Yangyang , Wu Ying
Published: May 2022

Experimental records in the cerebral cortex indicate that ammonia injection can lead to seizures. Considering that astrocytes play a vital role in mediating the uptake and absorption of ammonium ions in the extracellular space of the cortical circuit, we constructed a new astrocyte neuron coupling model, which is composed of a neuron and its astrocytes connected through the extracellular space, taking into account of the influence of extracellular ammonium ions. The numerical results verified the previous experimental observation that obtained epileptic firing modes of neurons and postsynaptic GABA reversal potential depolarization triggered by ammonia injection. In addition, we also determined the concentration–response relationship between the ammonium ion concentration and the time of entering epilepsy and predicted the threshold of the ammonium ion concentration for the onset of epilepsy.
Low-voltage soft robots based on carbon nanotube/polymer electrothermal composites
Authors: Wang Qi , Yong Ying-Qiong , Bai Zhi-Ming
Published: May 2022

Nowadays, soft robots have become a research hot spot due to high degree of freedom, adaptability to the environment and safer interaction with humans. The carbon nanotube (CNT)/polydimethylsiloxane (PDMS) electrothermal composites have attracted wide attention in the field of flexible actuations due to large deformation at low voltages. Here, the preparation process of CNT/PDMS composites was designed and optimized, and electrothermal actuators (ETAs) were fabricated by cutting the CNT/PDMS composite films into a “U” shape and coating conductive adhesive. The deformation performance of the ETAs with different thicknesses at different voltages was studied. At a low voltage of about 7 V, the ETA has a deformation rate of up to 93%. Finally, two kinds of electrothermal soft robots (ETSRs) with four-legged and three-legged structures were fabricated, and their inchworm-like motion characteristics were studied. The ETSR2 has the best motion performance due to the moderate thickness and three-legged electrode structure.
Liquid-liquid phase transition in confined liquid titanium
Authors: Zhang Di , Duan Yunrui , Zheng Peiru , Ma Yingjie , Qian Junping , Li Zhichao , Huang Jian , Jiang Yanyan , Li Hui
Published: May 2022

We report the layering and liquid–liquid phase transition of liquid titanium confined between two parallel panel walls. Abnormal changes in the volume and the potential energy confirm the existence of the liquid–liquid phase transition of the liquid titanium. The typical feature of the liquid–liquid phase transition is layering, which is induced by the slit size, pressure and temperature. We highlight the fact that the slit size and pressure will determine the number of layers. In addition, with the change in the slit size, the density of the confined liquid expresses a fluctuating law. The phase diagram of the layering transition is drawn to clearly understand the layering. This study provides insights into the liquid–liquid phase transition of liquid metal in a confined space.
Single-interface bioelectronic medicines—concept, clinical applications and preclinical data
Authors: Sevcencu Cristian
Published: May 2022

Presently, large groups of patients with various diseases are either intolerant, or irresponsive to drug therapies and also intractable by surgery. For several diseases, one option which is available for such patients is the implantable neurostimulation therapy. However, lacking closed-loop control and selective stimulation capabilities, the present neurostimulation therapies are not optimal and are therefore used as only ‘third’ therapeutic options when a disease cannot be treated by drugs or surgery. Addressing those limitations, a next generation class of closed-loop controlled and selective neurostimulators generically named bioelectronic medicines seems within reach. A sub-class of such devices is meant to monitor and treat impaired functions by intercepting, analyzing and modulating neural signals involved in the regulation of such functions using just one neural interface for those purposes. The primary objective of this review is to provide a first broad perspective on this type of single-interface devices for bioelectronic therapies. For this purpose, the concept, clinical applications and preclinical studies for further developments with such devices are here analyzed in a narrative manner.
Quantum unitary evolution interspersed with repeated non-unitary interactions at random times: the method of stochastic Liouville equation, and two examples of interactions in the context of a tight-binding chain
Authors: Das Debraj , Dattagupta Sushanta , Gupta Shamik
Published: May 2022

In the context of unitary evolution of a generic quantum system interrupted at random times with non-unitary evolution due to interactions with either the external environment or a measuring apparatus, we adduce a general theoretical framework to obtain the average density operator of the system at any time during the dynamical evolution. The average is with respect to the classical randomness associated with the random time intervals between successive interactions, which we consider to be independent and identically-distributed random variables. The formalism is very general in that it applies to any quantum system, to any form of non-unitary interaction, and to any probability distribution for the random times. We provide two explicit applications of the formalism in the context of the so-called tight-binding model relevant in various contexts in solid-state physics, e.g. in modelling nano wires. Considering the case of one dimension, the corresponding tight-binding chain models the motion of a charged particle between the sites of a lattice, wherein the particle is for most times localized on the sites, owing to spontaneous quantum fluctuations tunnels between the nearest-neighbour sites. We consider two representative forms of interactions, one that implements a stochastic reset of quantum dynamics in which the density operator is at random times reset to its initial form, and one in which projective measurements are performed on the system at random times. In the former case, we demonstrate with our exact results how the particle is localized on the sites at long times, leading to a time-independent mean-squared displacement (MSD) of the particle about its initial location. This stands in stark contrast to the behavior in the absence of interactions, when the particle has an unbounded growth of the MSD in time, with no signatures of localization. In the case of projective measurements at random times, we show that repeated projection to the initial state of the particle results in an effective suppression of the temporal decay in the probability of the particle to be found on the initial state. The amount of suppression is comparable to the one in conventional Zeno effect scenarios, but which it does not require us to perform measurements at exactly regular intervals that are hallmarks of such scenarios.
Weakly Aligned Molecules: From Molecular Detectors to Room-Temperature Tunable Masers
Authors: Roy Colin , Branković Zorica , Rostovtsev Yuri
Published: May 2022

We have developed and demonstrated a new mechanism of manipulation of population in molecular rotational levels in a weakly aligned molecules. The mechanism is based on an adiabatically changing electric field interacting with the molecules with dipole moments. Treating molecules as simple rotators, we have described their behavior using the density matrix taking into account the relaxation processes. We have considered the interaction of the weakly aligned molecules with a microwave field in a high finesse cavity. We have found that, on one hand, the population inversion can be reached in the ensemble of the weakly aligned molecules to be used for the maser operation at room temperature. On the another hand, we have found that the enhancement of the absorption can reach the theoretical limit and be used for gas sensing with high sensitivity and selectivity. Such sensors can efficiently analyze the multi-gas mixtures and be used for a huge range of applications – stretching from technology, sciences, control of environment, biology and medicine.
A general locomotion control framework for multi-legged locomotors
Authors: Chong Baxi , O Aydin Yasemin , Rieser Jennifer M , Sartoretti Guillaume , Wang Tianyu , Whitman Julian , Kaba Abdul , Aydin Enes , McFarland Ciera , Diaz Cruz Kelimar , Rankin Jeffery W , Michel Krijn B , Nicieza Alfredo , Hutchinson John R , Choset Howie , Goldman Daniel I
Published: May 2022

Serially connected robots are promising candidates for performing tasks in confined spaces such as search and rescue in large-scale disasters. Such robots are typically limbless, and we hypothesize that the addition of limbs could improve mobility. However, a challenge in designing and controlling such devices lies in the coordination of high-dimensional redundant modules in a way that improves mobility. Here we develop a general framework to discover templates to control serially connected multi-legged robots. Specifically, we combine two approaches to build a general shape control scheme which can provide baseline patterns of self-deformation (‘gaits’) for effective locomotion in diverse robot morphologies. First, we take inspiration from a dimensionality reduction and a biological gait classification scheme to generate cyclic patterns of body deformation and foot lifting/lowering, which facilitate the generation of arbitrary substrate contact patterns. Second, we extend geometric mechanics, which was originally introduced to study swimming at low Reynolds numbers, to frictional environments, allowing the identification of optimal body–leg coordination in this common terradynamic regime. Our scheme allows the development of effective gaits on flat terrain with diverse numbers of limbs (4, 6, 16, and even 0 limbs) and backbone actuation. By properly coordinating body undulation and leg placement, our framework combines the advantages of both limbless robots (modularity and narrow profile) and legged robots (mobility). Our framework can provide general control schemes for rapid deployment of general multi-legged robots, paving the way toward machines that can traverse complex environments. In addition, we show that our framework can also offer insights into body–leg coordination in living systems, such as salamanders and centipedes, from a biomechanical perspective.
Phosphorene—an emerging two-dimensional material: recent advances in synthesis, functionalization, and applications
Authors: Chaudhary Vivek , Neugebauer P , Mounkachi O , Lahbabi S , El Fatimy A
Published: May 2022

Two-dimensional (2D) materials are the focal point of intensive research efforts due to their unique properties and ability to reveal fascinating new phenomena. As an analog to graphene, phosphorene is a monolayer of black phosphorus crystals. Phosphorene obtained a special place among the family of 2D semiconducting materials because of its fascinating features such as high optical absorption, high carrier mobility, and several other attractive features having an exceptional interest in electronic and optoelectronic applications. The anisotropic orthorhombic crystal structure of phosphorene provides remarkable mechanical, electronic, optical, and transport properties. This review summarizes phosphorene’s chemical and physical properties and highlights the recent progress made in the synthesis. The application of phosphorene-based devices in high-speed electronics and optoelectronics has been surveyed. Also, sufficient emphasis has been given to emerging biomedical applications. Finally, phosphorene’s remaining challenges and potential applications are outlined.
The influence of laser etching biomimicking configuration on the strength of metal-plastic connection
Authors: Liu Fengde , Xu Xiaoni , Liu Jiaming , Fan Haiqi , Huang Genzhe , Zhang Hong
Published: May 2022

This study uses a laser to etch biomimicking locking patterns on the surface of 304 stainless steel to strengthen the connection between metal-plastic products. Under heat and pressure from the device, the plastic melts into the pattern and coalesces it, while the burrs formed from the etching process lock the joint of the metal-plastic. Three biomimicking configurations, honeycomb, leaf vein, and dragonfly head-and-neck hair interlocking, are studied. As shear strength determines the connection strength, we simulate the tensile-shearing process of stainless steel and plastic connectors of the three biomimicking configurations on ABAQUS, and predict the effects of the configurations on their connection strength. Experiments show that the plastic and metal are effectively connected at a heating temperature of 400 °C and a pressure of 70 kN. When the burr rate is 7.66% and the coverage rate is 29.4 ± 0.5%, the three biomimicking connectors break at the plastic base material, and the dragonfly head-and-neck hair interlocking configuration can withstand a shear force of 942 ± 9.23 N.
Cleaning of nitrogen-containing carbon contamination by atmospheric pressure plasma jet
Authors: YANG Li , WANG Sishu , WU Andong , CHEN Bo , CHEN Jianjun , WANG Hongbin , CHEN Shuwei , WEI Jianjun , ZHANG Kun , YE Zongbiao , GOU Fujun
Published: May 2022

Atmospheric pressure plasma jet (APPJ) was used to clean nitrogen-containing carbon films (C–N) fabricated by plasma-assisted chemical vapor deposition method employing the plasma surface interaction linear device at Sichuan University (SCU-PSI). The properties of the contaminated films on the surface of pristine and He-plasma pre-irradiated tungsten matrix, such as morphology, crystalline structure, element composition and chemical structure were characterized by scanning electron microscopy, grazing incidence x-ray diffraction and x-ray photoelectron spectroscopy. The experimental results revealed that the removal of C–N film with a thickness of tens of microns can be realized through APPJ cleaning regardless of the morphology of the substrates. Similar removal rates of 16.82 and 13.78 μm min−1 were obtained for C–N films deposited on a smooth pristine W surface and rough fuzz-covered W surface, respectively. This is a remarkable improvement in comparison to the traditional cleaning method. However, slight surface oxidation was found after APPJ cleaning, but the degree of oxidation was acceptable with an oxidation depth increase of only 3.15 nm. Optical emission spectroscopy analysis and mass spectrometry analysis showed that C–N contamination was mainly removed through chemical reaction with reactive oxygen species during APPJ treatment using air as the working gas. These results make APPJ cleaning a potentially effective method for the rapid removal of C–N films from the wall surfaces of fusion devices.
KLFDAPC: a supervised machine learning approach for spatial genetic structure analysis
Authors: Qin Xinghu , Chiang Charleston W K , Gaggiotti Oscar E
Published: May 2022

Geographic patterns of human genetic variation provide important insights into human evolution and disease. A commonly used tool to detect and describe them is principal component analysis (PCA) or the supervised linear discriminant analysis of principal components (DAPC). However, genetic features produced from both approaches could fail to correctly characterize population structure for complex scenarios involving admixture. In this study, we introduce Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC), a supervised non-linear approach for inferring individual geographic genetic structure that could rectify the limitations of these approaches by preserving the multimodal space of samples. We tested the power of KLFDAPC to infer population structure and to predict individual geographic origin using neural networks. Simulation results showed that KLFDAPC has higher discriminatory power than PCA and DAPC. The application of our method to empirical European and East Asian genome-wide genetic datasets indicated that the first two reduced features of KLFDAPC correctly recapitulated the geography of individuals and significantly improved the accuracy of predicting individual geographic origin when compared to PCA and DAPC. Therefore, KLFDAPC can be useful for geographic ancestry inference, design of genome scans and correction for spatial stratification in GWAS that link genes to adaptation or disease susceptibility.
DeepSCP: utilizing deep learning to boost single-cell proteome coverage
Authors: Wang Bing , Wang Yue , Chen Yu , Gao Mengmeng , Ren Jie , Guo Yueshuai , Situ Chenghao , Qi Yaling , Zhu Hui , Li Yan , Guo Xuejiang
Published: May 2022

Multiplexed single-cell proteomes (SCPs) quantification by mass spectrometry greatly improves the SCP coverage. However, it still suffers from a low number of protein identifications and there is much room to boost proteins identification by computational methods. In this study, we present a novel framework DeepSCP, utilizing deep learning to boost SCP coverage. DeepSCP constructs a series of features of peptide-spectrum matches (PSMs) by predicting the retention time based on the multiple SCP sample sets and fragment ion intensities based on deep learning, and predicts PSM labels with an optimized-ensemble learning model. Evaluation of DeepSCP on public and in-house SCP datasets showed superior performances compared with other state-of-the-art methods. DeepSCP identified more confident peptides and proteins by controlling q-value at 0.01 using target–decoy competition method. As a convenient and low-cost computing framework, DeepSCP will help boost single-cell proteome identification and facilitate the future development and application of single-cell proteomics.
Gilda: biomedical entity text normalization with machine-learned disambiguation as a service
Authors: Gyori Benjamin M , Hoyt Charles Tapley , Steppi Albert
Published: May 2022

Gilda is a software tool and web service that implements a scored string matching algorithm for names and synonyms across entries in biomedical ontologies covering genes, proteins (and their families and complexes), small molecules, biological processes and diseases. Gilda integrates machine-learned disambiguation models to choose between ambiguous strings given relevant surrounding text as context, and supports species-prioritization in case of ambiguity.

Availability and implementation

The Gilda web service is available at http://grounding.indra.bio with source code, documentation and tutorials available via https://github.com/indralab/gilda.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies
Authors: Segura Joan , Rose Yana , Bittrich Sebastian , Burley Stephen K , Duarte Jose M
Published: May 2022

Motivation

Mapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level.

Results

We present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies.

Availability and implementation

https://github.com/rcsb/rcsb-saguaro-3d.

Supplementary information

Supplementary data are available at Bioinformatics online.
Nezzle: an interactive and programmable visualization of biological networks in Python
Authors: Lee Daewon
Published: May 2022

High-quality visualization of biological networks often requires both manual curation for proper alignment and programming to map external data to the graphical components. Nezzle is a network visualization software written in Python, which provides programmable and interactive interfaces for facilitating both manual and automatic curation of the graphical components of networks to create high-quality figures.

Availability and implementation

Nezzle is an open-source project under MIT license and is available from https://github.com/dwgoon/nezzle.

Supplementary information

Supplementary data are available at Bioinformatics online.
Prognostication of responsive neurostimulation system responsiveness using presurgical magnetoencephalography
Authors: Joshi Rasesh B. , Zaveri Hitten P.
Published: May 2022

This scientific commentary refers to ‘Network connectivity predicts effectiveness of responsive neurostimulation in focal epilepsy’, by Fan et al. (https://doi.org/10.1093/braincomms/fcac104)
Strategies for improving adipose-derived stem cells for tissue regeneration
Authors: Yuan Xin , Li Li , Liu Haofan , Luo Jing , Zhao Yongchao , Pan Cheng , Zhang Xue , Chen Yuwen , Gou Maling
Published: May 2022

Adipose-derived stem cells (ADSCs) have promising applications in tissue regeneration. Currently, there are only a few ADSC products that have been approved for clinical use. The clinical application of ADSCs still faces many challenges. Here, we review emerging strategies to improve the therapeutic efficacy of ADSCs in tissue regeneration. First, a great quantity of cells is often needed for the stem cell therapies, which requires the advanced cell expansion technologies. In addition cell-derived products are also required for the development of ‘cell-free’ therapies to overcome the drawbacks of cell-based therapies. Second, it is necessary to strengthen the regenerative functions of ADSCs, including viability, differentiation and paracrine ability, for the tissue repair and regeneration required for different physiological and pathophysiological conditions. Third, poor delivery efficiency also restricts the therapeutic effect of ADSCs. Effective methods to improve cell delivery include alleviating harsh microenvironments, enhancing targeting ability and prolonging cell retention. Moreover, we also point out some critical issues about the sources, effectiveness and safety of ADSCs. With these advanced strategies to improve the therapeutic efficacy of ADSCs, ADSC-based treatment holds great promise for clinical applications in tissue regeneration.
Two stages of speech envelope tracking in human auditory cortex modulated by speech intelligibility
Authors: Xu Na , Zhao Baotian , Luo Lu , Zhang Kai , Shao Xiaoqiu , Luan Guoming , Wang Qian , Hu Wenhan , Wang Qun
Published: May 2022

The envelope is essential for speech perception. Recent studies have shown that cortical activity can track the acoustic envelope. However, whether the tracking strength reflects the extent of speech intelligibility processing remains controversial. Here, using stereo-electroencephalogram technology, we directly recorded the activity in human auditory cortex while subjects listened to either natural or noise-vocoded speech. These 2 stimuli have approximately identical envelopes, but the noise-vocoded speech does not have speech intelligibility. According to the tracking lags, we revealed 2 stages of envelope tracking: an early high-γ (60–140 Hz) power stage that preferred the noise-vocoded speech and a late θ (4–8 Hz) phase stage that preferred the natural speech. Furthermore, the decoding performance of high-γ power was better in primary auditory cortex than in nonprimary auditory cortex, consistent with its short tracking delay, while θ phase showed better decoding performance in right auditory cortex. In addition, high-γ responses with sustained temporal profiles in nonprimary auditory cortex were dominant in both envelope tracking and decoding. In sum, we suggested a functional dissociation between high-γ power and θ phase: the former reflects fast and automatic processing of brief acoustic features, while the latter correlates to slow build-up processing facilitated by speech intelligibility.
Mortality prediction of retinal vessel diameters and function in a long-term follow-up of haemodialysis patients
Authors: Günthner Roman , Streese Lukas , Angermann Susanne , Lorenz Georg , Braunisch Matthias C , Matschkal Julia , Hausinger Renate , Stadler David , Haller Bernhard , Heemann Uwe , Kotliar Konstantin , Hanssen Henner , Schmaderer Christoph
Published: May 2022

Aim

Retinal vessel diameters are candidate biomarkers of mortality prediction in large population-based studies. We aimed to investigate the predictive value of retinal vessel diameters and flicker-induced retinal arteriolar and venular dilation on all-cause mortality in long-term follow-up of haemodialysis patients.

Methods and results

Retinal vessel diameters as well as maximum arteriolar (aMax) and venular dilation (vMax) were investigated in 275 and 214 haemodialysis patients, respectively. Patients were observed in a long-term follow-up for a median period of 73 months. About 36% (76/214) and 41% (113/275) of patients died. Arteriolar and venular diameters were 175 ± 19 and 208 ± 20 µm, respectively. Median aMax and vMax were 1.6 (0.3–3.3) and 3.2 (2.0–5.1)%. Patients within the lowest tertile of vMax showed lower 5-year survival rates compared with the highest tertile (50.6 vs. 82.1%) and also exhibited a higher incidence of infection-related deaths (21.7 vs. 4.0%). Univariate hazard ratio (HR) per standard deviation increase of vMax for all-cause mortality was 0.69 (0.54–0.88) and was even more pronounced for infection-related mortality [HR 0.53 (0.33–0.83)]. Regarding all-cause mortality, multivariate adjustment for eight non-retinal mortality predictors including interleukin-6 did not attenuate the HR relevantly [0.73 (0.54–0.98)]. Arteriolar and venular diameters did not predict all-cause nor cardiovascular and infection-related mortality.

Conclusions

Long-term follow-up of patients on haemodialysis demonstrated the potential of retinal venular dilation capacity for mortality prediction, which was most pronounced for infection-related mortality. In the same cohort, retinal arteriolar and venular diameters showed no predictive value for hard endpoints. Retinal venular dilation but not arteriolar and venular diameters is a valuable diagnostic biomarker for risk prediction in patients with end-stage renal disease and should be considered for monitoring of critically ill patients.
Daily ambulatory remote monitoring system for drug escalation in chronic heart failure with reduced ejection fraction: pilot phase of DAVID-HF study
Authors: Wong Chun Ka , Un Ka Chun , Zhou Mi , Cheng Yangyang , Lau Yuk Ming , Shea Puigi Catherine , Lui Hin Wai , Zuo Ming Liang , Yin Li Xue , Chan Esther W , Wong Ian C K , Sin Simon Wai Ching , Yeung Pauline Pui Ning , Chen Hao , Wibowo Sandi , Wei Tong Li Nikki , Lee Sze Ming , Chow Augustine , Tong Raymond Cheuk Fung , Hai Jojo , Tam Frankie Chor Cheung , Siu Chung Wah
Published: May 2022

Aims

Underutilization of guideline-directed heart failure with reduced ejection fraction (HFrEF) medications contributes to poor outcomes.

Methods and results

A pilot study to evaluate the safety and efficacy of a home-based remote monitoring system for HFrEF management was performed. The system included wearable armband monitors paired with the smartphone application. An HFrEF medication titration algorithm was used to adjust medication daily. The primary endpoint was HFrEF medication utilization at 120 days. Twenty patients (60.5 ± 8.2 years, men: 85%) with HFrEF were recruited. All received angiotensin-converting enzyme inhibitor (ACEI)/angiotensin receptor blocker (ARB)/angiotensin receptor-neprilysin inhibitor (ARNI) at recruitment; 45% received ≥50% maximal targeted dose (MTD) with % MTD of 44.4 ± 31.7%. At baseline, 90 and 70% received beta-adrenergic blocker and mineralocorticoid receptor antagonist (MRA), 35% received ≥50% MTD beta-adrenergic blocker with % MTD of 34.1 ± 29.6%, and 25% received ≥50% MTD MRA with % MTD of 25.0 ± 19.9%. At 120 days, 70% received ≥50% MTD ACEI/ARB/ARNI (P = 0.110) with % MTD increased to 64.4 ± 33.5% (P = 0.060). The proportion receiving ≥50% MTD ARNI increased from 15 to 55% (P = 0.089) with % MTD ARNI increased from 20.6 ± 30.9 to 53.1 ± 39.5% (P = 0.006*). More patients received ≥50% MTD MRA (65 vs. 25%, P = 0.011*) with % MTD MRA increased from 25.0 ± 19.9 to 46.2 ± 28.8% (P = 0.009*). Ninety-five per cent of patients had reduced NT-proBNP with the percentage reduction of 26.7 ± 19.7%.

Conclusion

Heart failure with reduced ejection fraction medication escalation with remote monitoring appeared feasible.
Reduction and discharge of SARS-CoV-2 RNA in Chicago-area water reclamation plants
Authors: Owen Christopher , Wright-Foulkes Dorothy , Alvarez Prisila , Delgado Haidy , Durance Eva C , Wells George F , Poretsky Rachel , Shrestha Abhilasha
Published: May 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is commonly excreted in the feces and urine of infected individuals and is, therefore, detected in wastewaters where infection is present in the surrounding population. Water reclamation plants (WRPs) that treat these wastewaters commonly discharge treated effluents into the surrounding environment, yet little is known about the removal or persistence of SARS-CoV-2 RNA through wastewater treatment systems and potential for eventual release into the environment. We collected 361 24-hour composite influent and effluent samples from seven WRPs in the Greater Chicago Area in Illinois. Samples were collected over a period of 21 weeks for three large WRPs (with design max flows of 1.89-2.32 billion gallons per day and serving a combined population of 4.62 million people) and 11 weeks for four smaller WRPs (with design max flows of 96.3-186 million gallons per day and serving a combined population of >0.5 million people). A total of two of the larger WRPs implemented seasonal disinfection (using UV light or chlorination/dechlorination) for 8 weeks of this sampling period. SARS-CoV-2 RNA was quantified in the influent and effluent samples by reverse-transcription quantitative PCR (RT-qPCR) of the N1 and N2 targets of the nucleocapsid (N) gene. Although SARS-CoV-2 RNA was regularly detected in influent and effluent from all WRPs, viral RNA concentrations in the effluent samples were considerably lower, with mean effluent: influent gene copy concentration ratios ranging from 1:160 to 1:2.95 between WRPs. Samples collected while disinfection was active vs. inactive did not show any significant difference in the portion of RNA persisting through the treatment process (P > .05).
Rapid detection of fluoroquinolone residues in aquatic products based on a gold-labeled microwell immunochromatographic assay
Authors: Xiao Jiaxu , Yang Hongfei , Qin Liangni , Liang Jixiang , Li Long , Fan Xiaohui , Peng Dapeng
Published: May 2022

Objectives

Fluoroquinolones (FQs) are widely used in aquaculture, and their residues have caused many problems threatening human health. Here, this study aims to develop a colloidal gold immunochromatographic strip based on gold-labeled microwells to screen the residues of FQs on site.

Materials and methods

The Protein A Magarose Beads affinity chromatography method was adopted to purify the ascites against FQs. By using a strategy of heterologous coating antigen, different coating antigens are applied to detect FQs. The gold-labeled microwell immunochromatographic assay was used to improve the sensitivity of the test strip by the advanced reaction of antigen and antibody.

Results

The antibodies were verified to be of high purity up to 99%, and the titer reached 1:1 024 000. The combination (enoxacin-OVA and the antibody) detected the 4 banned FQs (pefloxacin, PEF; norfloxacin, NOR; lomefloxacin, LOM; ofloxacin, OFL) with the 50% inhibiting concentration (IC50) values ranging from 1.3 to 2.1 ng/mL and cross-reactions ranging from 67.3% to 106.1%. The analysis of spiked crucian carp, silver carp, grass carp, and shrimp samples showed that the limit of detection for PEF, NOR, LOM, and OFL was 4 μg/kg. A comparative study with liquid chromatography tandem mass spectrometry (LC-MS/MS) demonstrated that the assay provided an effective screening tool for the rapid detection of FQs residues.

Conclusions

The results indicated that the test strip can realize full coverage recognition of the 4 banned FQs and has good accuracy, specificity, reproducibility, and stability; therefore, they are more suitable for rapid detection of FQs in aquatic products.
Elevated preoperative CA125 is associated with poor survival in patients with metastatic colorectal cancer undergoing primary tumor resection: a retrospective cohort study
Authors: Huang Jun-Hua , Liu Hua-Shan , Hu Tuo , Zhang Zong-Jin , He Xiao-Wen , Mo Tai-Wei , Wen Xiao-Feng , Lan Ping , Lian Lei , Wu Xian-Rui
Published: May 2022

Background

The impact of the preoperative carbohydrate antigen 125 (CA125) level on the survival of metastatic colorectal cancer (CRC) patients undergoing primary tumor resection (PTR) remains uncertain. The aim of this study was to assess the prognostic value in overall survival (OS) and cancer-specific survival (CSS) between patients with and without an elevated preoperative CA125 level.

Methods

All metastatic CRC patients receiving PTR between 2007 and 2017 at the Sixth Affiliated Hospital of Sun Yat-sen University (Guangzhou, China) were retrospectively included. OS and CSS rates were compared between patients with and without elevated preoperative CA125 levels.

Results

Among 326 patients examined, 46 (14.1%) exhibited elevated preoperative CA125 levels and the remaining 280 (85.9%) had normal preoperative CA125 levels. Patients with elevated preoperative CA125 levels had lower body mass index, lower preoperative albumin level, lower proportion of preoperative chemotherapy, higher carcinoembryonic antigen and carbohydrate antigen 19–9 (CA19–9) levels, poorer differentiation, and more malignant histopathological type than patients with normal preoperative CA125 levels. In addition, patients with elevated preoperative CA125 levels exhibited more advanced pathological T and N stages, more peritoneal metastasis, and more vessel invasion than patients with normal preoperative CA125 levels. Moreover, the primary tumor was more likely to be located at the colon rather than at the rectum in patients with elevated CA125 levels. Both OS and CSS rates in patients with elevated preoperative CA125 levels were significantly lower than those in patients with normal preoperative CA125 levels. Multivariate Cox regression analysis revealed that an elevated preoperative CA125 level was significantly associated with poor prognosis in metastatic CRC patients undergoing PTR. The hazard ratio (HR) in OS was 2.36 (95% confidence interval [CI], 1.67–3.33, P < 0.001) and the HR in CSS was 2.50 (95% CI, 1.77–3.55, P < 0.001). The survival analysis stratified by peritoneal metastasis also demonstrated that patients with elevated preoperative CA125 levels had lower OS and CSS rates regardless of peritoneal metastasis.

Conclusion

Based on an analysis of metastatic CRC patients undergoing PTR, an elevated preoperative CA125 level was associated with poor prognosis, which should be taken into consideration in clinical practice.
Potential Regulators of the Senescence-Associated Secretory Phenotype During Senescence and Aging
Authors: Han Xiaojuan , Lei Qing , Xie Jiamei , Liu Huanhuan , Li Jing , Zhang Xiaohua , Zhang Tianying , Gou Xingchun
Published: May 2022

Senescent cells express and secrete a variety of extracellular modulators that include cytokines, chemokines, proteases, growth factors, and some enzymes associated with extracellular matrix remodeling, defined as the senescence-associated secretory phenotype (SASP). SASP reinforces senescent cell cycle arrest, stimulates and recruits immune cells for immune-mediated clearance of potentially tumorigenic cells, limits or induces fibrosis, and promotes wound healing and tissue regeneration. On the other hand, SASP mediates chronic inflammation leading to the destruction of tissue structure and function and stimulating the growth and survival of tumor cells. SASP is highly heterogeneous and the role of SASP depends on the context. The regulation of SASP occurs at multiple levels including chromatin remodeling, transcription, mRNA translation, intracellular trafficking, and secretion. Several SASP modulators have already been identified setting the stage for future research on their clinical applications. In this review, we summarize in detail the potential signaling pathways that trigger and regulate SASP production during aging and senescence.