bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of printing parameters on 4D-printed PLA actuators
Authors: Alshebly Yousif Saad , Nafea Marwan
Published: May 2023

Controlling the printing parameters of four-dimensional (4D) printed actuators can be used to set the internal strain of the actuators. This approach can be utilised when using the fused deposition modelling method to develop 4D-printed actuators, allowing non-manual shape programming. However, there is a lack of comprehensive studies that investigate the effects of printing parameters on the actuation performance of 4D-printed actuators. In this study, the effects of four printing parameters on the bending angle of 4D-printed polylactic acid (PLA) actuators are reported. These printing parameters include the printing speed, printing temperature, ratio of passive-to-active layers, and layer height. In addition, these printing parameters are investigated while changing the height of the actuators. The results show that increasing the printing speed increases the internal strain while increasing the printing temperature, layer height, or actuator height has the opposite effect. Moreover, it is found that a ratio of passive-to-active layers of 50% maximises the strain while selecting a higher or lower ratio causes the opposite effect. Based on the results, four mathematical predictive models are developed to determine the bending angle induced in the actuators when printed based on each printing parameter. Then, a predictive model that relates all the printing parameters and actuator height to the bending angle is developed. The predictive model is based on the characterization results of 534 PLA actuators, providing an R-squared value of 0.98. Then, a finite element analysis model is developed to replicate the shape memory effect in actuators. To prove the accuracy of the proposed concept, two grippers with four and eight fingers are developed. The results show that the printing parameters can be used to control the bending angle of each finger based on the design specifications.
Monitoring of soil water content using spherical smart aggregates based on electromechanical impedance (EMI) technique
Authors: Lan Chengming , Zhuang Shuo , Han Song , Wang Jianjun , Li Weijie
Published: May 2023

Real-time monitoring of soil water content is of great significance to prevent many engineering accidents, such as landslide, water seepage of foundation dam, and reduction of foundation bearing capacity. Electromechanical impedance (EMI) technique based smart aggregates (SAs) have showed excellent monitoring capability in various engineering applications. However, there are limited reports on the application of EMI based SAs in the monitoring of the soil water content. In this paper, the EMI based spherical SAs (SSAs) were investigated in the monitoring of soil water content. Firstly, the SSAs were designed and fabricated using the monolithic concrete encapsulation method, and their stable performance in air were evaluated, and confirmed by testing and analyzing the impedance spectrum. Then, the fabricated SSAs were immersed in the water environment for 28 d to ensure the stability under the working conditions, such as the soil with high water content and the hydration process of early-age concrete. Secondly, the monitoring experiments of soil water content were carried out based on the SSAs and the traditional SAs using the EMI technique. The measured impedance signatures under different water contents in soil were quantified by three types of statistical indexes, including root mean square deviation, mean absolute percentage deviation, and correlation coefficient deviation. The experimental results show that compared with the traditional SAs, the SSAs are more sensitive and stable to monitor the soil water content. Finally, the effect of temperature on the performance of SSA based on the EMI technique were conducted experimentally. The results demonstrate that temperature has influence on the monitoring results of the SSAs based on the EMI technique.
Generalized chemical model for plasmas with application to the ionization potential depression
Authors: Davletov A E , Arkhipov Yu V , Mukhametkarimov Ye S , Yerimbetova L T , Tkachenko I M
Published: May 2023

On the basis of the generalized Poisson–Boltzmann equation derived from the Bogolyubov chain of equations for the equilibrium distribution functions in the pair correlation approximation, a general expression is proposed for the Helmholtz free energy of a system that contains any number of components and whose particles interact via arbitrary potentials. This opens up an extraordinary opportunity to simultaneously treat a whole range of physical effects including partial ionization, quantum effects of diffraction and electron degeneracy, short- and long-range interactions of charged particles with neutrals, finite size effects, etc. It is shown that all medium constituents are tied together in a single screening matrix, whose determinant and trace determine the excess contribution to the free energy. The approach developed is then applied to the problem of the ionization potential depression (IPD) leading to quite simple analytical expressions, which turn out to be useful for various practical purposes. In particular, for a single ionization from the neutral state the IPD is shown to significantly depend on the ionization degree such that it consists of the difference of charged and neutral contributions for a fully ionized plasma and turns non-zero for an almost neutral medium. On the other hand, for a multiple ionization process finite size effects of atoms and ions are demonstrated to be of great importance and accounted for in order to achieve good agreement with experimental data on the IPD under warm dense matter conditions.
Aharonov–Bohm effect with an effective complex-valued vector potential
Authors: Paiva Ismael L , Aharonov Yakir , Tollaksen Jeff , Waegell Mordecai
Published: May 2023

The interaction between a quantum charge and a dynamic source of a magnetic field is considered in the Aharonov–Bohm (AB) scenario. It is shown that, in weak interactions with a post-selection of the source, the effective vector potential is, generally, complex-valued. This leads to new experimental protocols to detect the AB phase before the source is fully encircled. While this does not necessarily change the nonlocal status of the AB effect, it brings new insights into it. Moreover, we discuss how these results might have consequences for the correspondence principle, making complex vector potentials relevant to the study of classical systems.
Zero-threshold correlated-photon laser with a single trapped atom in a bimodal cavity
Authors: Dey Anushree , Pal Arpita , Dutta Gupta Subhasish , Deb Bimalendu
Published: May 2023

We demonstrate theoretically the feasibility of correlated entangled photon-pair generation with vanishing threshold in a bimodal cavity setup that uses a single V-type three level atom pumped by dual incoherent sources and driven by two coherent fields. The photon-pair is shown to be entangled only for low levels of the incoherent pumps and owes its origin solely to the coherent drives. Our results show that the dual incoherent pumping with no coherent drive can lead to amplification of the cavity fields with strong inter-mode antibunching but no entanglement. We analyse our results in terms of an interplay between coherent and incoherent processes involving cavity-dressed states. Both the inter- and intra-mode Hanbury–Brown–Twiss (HBT) functions exhibit temporal oscillations in the strong-coupling cavity QED regime. Our theoretical scheme for the generation of nonclassical and entangled photon pairs may find interesting applications in quantum metrology and quantum information science.
Room-temperature exciton-polariton and photonic lasing in GaN/InGaN core-shell microrods
Authors: Li Junchao , Chen Huanqing , Yu Guo , Lei Menglai , Li Shunkun , Hu Xiaodong
Published: May 2023

Room-temperature exciton-polariton is observed in GaN/InGaN core–shell microrods grown by metal-organic vapor phase epitaxy. We demonstrate a large Rabi splitting in the core–shell microrod structure over 265 meV. Room-temperature lasing in core–shell microrods is confirmed by power-dependent photoluminescence spectra. The lasing in the shell layer results to a modulated lasing wavelength and takes one step further to more stable polariton lasing in MQW core–shell microrods.
Defects detection in dentistry: designing a graphene multi-layered based plasmonic sensor
Authors: Tamang Jitendra Singh , Chatterjee Somenath , Dhar Rudra Sankar
Published: May 2023

Dental Restorative materials play a very important role in solving the issue of sensitivity in human teeth. Many such materials, based on their respective optical properties, are considered for various usages viz. cavity treatment, reparation of cracked or broken teeth, detection of plaque formation, etc Another way is to deal with different restorative materials for dentistry application which should be ideal and appropriate. Surface Plasmon Resonance (SPR), being an optical phenomenon, has the capability to analyze the optical properties which may be used for Bio-medical Applications also. Considering the adsorption efficiency (to bio-molecules) of Graphene material can be applied for detecting any plaque formation in the essential components of a human teeth viz. Enamel, Dentin and Cementum. Sensitivity, Figure of Merit (F.O.M.) calculations and the correlation between refractive index of different dental restorative materials and their concentration percentage have been tabulated in this manuscript. SPR curves have been obtained using MATLAB environment and Characteristic Transfer Matrix (CTM). A new theoretical approach to detect the teeth-health with harm free (without X-ray source) technique has been proposed. A new technique is considered to determine the quality (cavity formation and others) of teeth-hygiene using less health-hazard radiation. LASER beam-based SPR phenomenon is projected here to identify the tooth condition, which may be implemented for the application purpose.
Deep learning-based approach for detection of turbulence-induced distortions in free-space optical communication links
Authors: Bakır Halit , Elmabruk Kholoud
Published: May 2023

This study aims to develop a deep-learning-based approach that is able to detect turbulence-induced mode distortion in orbital angular momentum-based free-space optical communication links. The proposed and tuned deep learning-based models have been trained with a dataset that is created based on the intensity beam profiles that propagate 5 Km in four different levels of turbulent atmosphere. The random search algorithm has been adopted for conducting a hyperparameter tuning process to select the best structures for two groups of deep learning models each of which contains three different deep learning models. The proposed approach is able to not only distinguish the distorted beams but also to recognize the level of distortion. The obtained results indicate that the utilized tuned models gave 100% classification accuracy in terms of detecting distorted beams. Besides that, the proposed and tuned models obtained a very high classification accuracy reaching 97, 94.99, and 97.78% in terms of assessing the amount of distortion exposed by the transmitted beams. We believe that the obtained results will be a milestone in free-space optical communication systems that utilize orbital angular momentum.
Ge3Sb2Te6-based mid-infrared metasurfaces for polarization control and wavefront steering
Authors: Sun Chaoyan , He Canhui , Nie Ruixing , Zhang Runxuan , Song Zhengyong
Published: May 2023

Benefiting from excellent properties in wavefront control, germanium antimony telluride (GeSbTe)-based photonic devices provide new opportunities for manipulating electromagnetic wave. In this paper, Ge3Sb2Te6meta-atoms are presented to realize polarization switching for mid-infrared wave through the state transition from the crystalline Ge3Sb2Te6to the amorphous Ge3Sb2Te6. When the crystalline Ge3Sb2Te6is involved, the proposed meta-atoms with 90° phase shift achieve high-efficiency polarization conversion and 360° phase coverage. As Ge3Sb2Te6is changed to the amorphous state, phase coverage drops to only 36°, and most of the cross-polarized wave vanishes. Using these designed meta-atoms, three metasurfaces are implemented at 76.5 THz. Firstly, a gradient metasurface is constructed, and it dynamically switches between specular reflection and anomalous reflection. Next, a reflective metalens is proposed to realize switching between focusing and defocusing under different states of Ge3Sb2Te6. Lastly, a focused vortex beam is presented to reconstruct the mode of orbital angular momentum (OAM). All designs realize the switching between cross-polarization and co-polarization. Our work could have possible applications in fields such as mid-infrared switching, focusing, and wireless communication.
Effect of phthalocyanine-based charge transport layers on unleaded KSnI3 perovskite solar cell
Authors: Pindolia Grishma , Shinde Satyam M
Published: May 2023

The implementation and commercialization of perovskite solar cells (PSCs) are hindered due to the presence of toxic lead. Metal phthalocyanines (MPc) have been studied extensively as charge transport layers (CTLs) in PSCs due to their desirable properties such as thermal and chemical robustness, and low production cost. In the present work, a theoretical study of the effect of phthalocyanine-based CTLs on a non-leaded KSnI3-based PSC is carried out using SCAPS software. The defect concentration of the layers and the interfaces, doping density and thickness of the layers, shunt, and series resistance of the device is optimized. Carbon is suggested as an affordable alternative to the state of art back contact material, gold. The stability of this device with temperature is also established. The optimized solar cell showed an excellent fill factor (FF) of 86.51% with a power conversion efficiency (PCE) of 11.91% and an excellent quantum efficiency (QE) ranging from 99.42%(400 nm) to 72.02%(660 nm) in the visible region. The present study highlights the enhanced performance parameters of leadless KSnI3-based PSC with phthalocyanine-based CTLs as compared to the state-of-art CTLs, TiO2 and Spiro-OMeTAD reported in previous literature with a PCE and FF of 9.776% and 36.139% respectively.
Probing axions through tomography of anisotropic cosmic birefringence
Authors: Greco Alessandro , Bartolo Nicola , Gruppuso Alessandro
Published: May 2023

Cosmic birefringence is the in-vacuo rotation of the linear polarization plane experienced by photons of the Cosmic Microwave Background (CMB) radiation when theoretically well-motivated parity-violating extensions of Maxwell electromagnetism are considered. If the angle parametrizing such a rotation is dependent on the photon's direction, then this phenomenon is called Anisotropic Cosmic Birefringence (ACB). In this paper, we perform for the first time a tomographic treatment of the ACB, by considering photons emitted both at the recombination and reionization epoch. This allows one to extract additional and complementary information about the physical source of cosmic birefringence with respect to the isotropic case. We focus here on the case of an axion-like field χ, whose coupling with the electromagnetic sector induces such a phenomenon, by using an analytical and numerical approach (which involves a modification of theCLASScode). We find that the anisotropic component of cosmic birefringence exhibits a peculiar behavior: an increase of the axion mass implies an enhancement of the anisotropic amplitude, allowing to probe a wider range of masses with respect to the purely isotropic case. Moreover, we show that at large angular scales, the interplay between the reionization and recombination contributions to ACB is sensitive to the axion mass, so that at sufficiently low multipoles, for sufficiently light masses, the reionization contribution overtakes the recombination one, making the tomographic approach to cosmic birefringence a promising tool for investigating the properties of this axion-like field.
A fast blind source separation algorithm for decomposing ultrafast ultrasound images into spatiotemporal muscle unit kinematics
Authors: Rohlén Robin , Lundsberg Jonathan , Malesevic Nebojsa , Antfolk Christian
Published: May 2023

Objective. Ultrasound can detect individual motor unit (MU) activity during voluntary isometric contractions based on their subtle axial displacements. The detection pipeline, currently performed offline, is based on displacement velocity images and identifying the subtle axial displacements. This identification can preferably be made through a blind source separation (BSS) algorithm with the feasibility of translating the pipeline from offline to online. However, the question remains how to reduce the computational time for the BSS algorithm, which includes demixing tissue velocities from many different sources, e.g. the active MU displacements, arterial pulsations, bones, connective tissue, and noise. Approach. This study proposes a fast velocity-based BSS (velBSS) algorithm suitable for online purposes that decomposes velocity images from low-force voluntary isometric contractions into spatiotemporal components associated with single MU activities. The proposed algorithm will be compared against spatiotemporal independent component analysis (stICA), i.e. the method used in previous papers, for various subjects, ultrasound- and EMG systems, where the latter acts as MU reference recordings. Main results. We found that the computational time for velBSS was at least 20 times less than for stICA, while the twitch responses and spatial maps extracted from stICA and velBSS for the same MU reference were highly correlated (0.96 ± 0.05 and 0.81 ± 0.13). Significance. The present algorithm (velBSS) is computationally much faster than the currently available method (stICA) while maintaining the same performance. It provides a promising translation towards an online pipeline and will be important in the continued development of this research field of functional neuromuscular imaging.
Spectroscopic measurement of increases in hydrogen molecular rotational temperature with plasma-facing surface temperature and due to collisional-radiative processes in tokamaks
Authors: Yoneda N. , Shikama T. , Scotti F. , Hanada K. , Iguchi H. , Idei H. , Onchi T. , Ejiri A. , Ido T. , Kono K. , Peng Y. , Osawa Y. , Yatomi G. , Kidani A. , Kudo M. , Hiraka R. , Takeda K. , Bell R.E. , Maan A. , Boyle D.P. , Majeski R. , Soukhanovskii V.A. , Groth M. , McLean A.G. , Wilcox R.S. , Lasnier C. , Nakamura K. , Nagashima Y. , Ikezoe R. , Hasegawa M. , Kuroda K. , Higashijima A. , Nagata T. , Shimabukuro S. , Niiya I. , Sekiya I. , Hasuo M.
Published: May 2023

Spatially resolved rotational temperature of ground state hydrogen molecules desorbed from plasma-facing surface was measured in QUEST, LTX-β, and DIII-D tokamaks, and the increases of the rotational temperature with the surface temperature and due to collisional-radiative processes in the plasmas were evaluated. The increase due to collisional-radiative processes was calculated by solving rate equations considering electron and proton collisional excitation and deexcitation and spontaneous emission. The calculation results suggest a high sensitivity for the rotational temperature to electron and proton densities, but a negligible sensitivity to the electron, proton, and surface temperatures. In the three tokamaks with different plasma parameters and plasma-facing surface materials, the spatial profile of the rotational temperature was estimated using Fulcher-α emission lines (600–608 nm). In QUEST, the spatial profile of the rotational temperature was estimated from spatially resolved spectra. In the other tokamaks, the rotational temperature was evaluated assuming a single point emission with a location determined from the Fulcher-α emission profile as measured with a filtered camera. In metal-walled devices QUEST and LTX-β, the rotational temperature increased with the surface temperature, and the calculated collisional-radiative increase is consistent with measured increase assuming that the rotational temperature at the surface is approximately 500–600 K higher than the surface temperature. In DIII-D with carbon walls, a larger collisional-radiative increase than the other tokamaks was observed because of the higher density leading to a large difference from the calculated increase compared to the other smaller tokamaks. Measurement of the Fulcher-α emission profile with higher spatial resolution in DIII-D may reduce the difference and reveal the effect of the surface temperature on the rotational temperature. These results show the increases in the rotational temperature with the surface temperature and due to the collisional-radiative processes.
Quantum optics with Rydberg superatoms
Authors: Kumlin Jan , Braun Christoph , Tresp Christoph , Stiesdal Nina , Hofferberth Sebastian , Paris-Mandoki Asaf
Published: May 2023

Quantum optics based on highly excited atoms, also known as Rydberg atoms, has cemented itself as a powerful platform for the manipulation of light at the few-photon level. The Rydberg blockade, resulting from the strong interaction between individual Rydberg atoms, can turn a large ensemble of atoms into a system which collectively resembles a single two-level emitter, a so-called Rydberg superatom. The coupling of this artificial emitter to a driving photonic mode is collectively enhanced by Rydberg interactions, enabling strong coherent coupling at the few-photon level in free-space. The exquisite level of control achievable through this has already demonstrated its utility in applications of quantum computing and information processing. Here, we review the derivation of the collective coupling between a Rydberg superatom and a single light mode and discuss the similarity of this free-space setup to waveguide quantum electrodynamics systems of quantum emitters coupled to photonic waveguides. We also briefly review applications of Rydberg superatoms to quantum optics such as single-photon generation and single-photon subtraction.
Seems fishy: environmental DNA impacts on sketa22 quality control in salmonidae dominated waterbodies using qPCR and ddPCR
Authors: Hart John J , Tardani Renee A , Ruetz Carl R , Rediske Richard R
Published: May 2023

Globally, water resources used for recreation and drinking water are threatened by fecal pollution. These pollutants can cause gastrointestinal illness and environmental degradation. Additionally, most sources of fecal pollution are non-point sources stemming from multiple species. Identifying these sources is vital to categorizing the exposure risk from contact and improving remediation efforts. A common technique to provide species-specific information for fecal source identification is microbial source tracking (MST). MST quantifies DNA of host or host-associated microorganisms through polymerase chain reaction (PCR) technologies such as quantitative PCR (qPCR) or droplet digital PCR (ddPCR). MST techniques have been implemented globally and are used for routine monitoring. In the United States (US), the US Environmental Protection Agency has provided several approved standard PCR methods for MST and other recreational water quality applications. These methods have specified quality controls including sample processing controls (SPC) and assessments for sample inhibition. A standard SPC used in EPA methods involves spiking samples with salmon testes DNA (nominally originating from Chum Salmon, Oncorhynchus keta and quantifying them using Sketa22, a genus specific TaqManTM assay). This quality control (QC) behaves similarly to the microbial species being monitored. MST testing in Fall 2022 indicated elevated Sketa22 recoveries and re-analysis of samples indicated the detection of external Salmonidae DNA on both qPCR and ddPCR platforms. Our research was designed to identify the cause of this interference. Results indicate that the primer probe set may react with wild Salmonidae DNA. Analyzing the Sketa22 sequence using BLAST indicated matches with many species of Salmonidae present in the sampled stream system. Consequently, further research is required to identify the effectiveness of Sketa22 as a QC when native and migratory Salmonidae are present. General recommendations are provided to account for excess ambient Salmonidae DNA.
Recent progress in optoelectronic memristors for neuromorphic and in-memory computation
Authors: Pereira Maria Elias , Martins Rodrigo , Fortunato Elvira , Barquinha Pedro , Kiazadeh Asal
Published: May 2023

Neuromorphic computing has been gaining momentum for the past decades and has been appointed as the replacer of the outworn technology in conventional computing systems. Artificial neural networks (ANNs) can be composed by memristor crossbars in hardware and perform in-memory computing and storage, in a power, cost and area efficient way. In optoelectronic memristors (OEMs), resistive switching (RS) can be controlled by both optical and electronic signals. Using light as synaptic weigh modulator provides a high-speed non-destructive method, not dependent on electrical wires, that solves crosstalk issues. In particular, in artificial visual systems, OEMs can act as the artificial retina and combine optical sensing and high-level image processing. Therefore, several efforts have been made by the scientific community into developing OEMs that can meet the demands of each specific application. In this review, the recent advances in inorganic OEMs are summarized and discussed. The engineering of the device structure provides the means to manipulate RS performance and, thus, a comprehensive analysis is performed regarding the already proposed memristor materials structure and their specific characteristics. Moreover, their potential applications in logic gates, ANNs and, in more detail, on artificial visual systems are also assessed, taking into account the figures of merit described so far.
Impacts of droughts and floods on agricultural productivity in New Zealand as measured from space
Authors: Blanc Elodie , Noy Ilan
Published: May 2023

We estimate the impact of precipitation extremes on the productivity of agricultural land parcels in New Zealand using satellite data. This type of post-disaster damage assessment aims to allow for the quantification of disaster damage when an on-the-ground assessment of damage is too costly or too difficult to conduct. It can also serve as a retroactive data collection tool for disaster loss databases where data collection did not happen at the time. We use satellite-derived observations of terrestrial vegetation (the enhanced vegetation index (EVI)) over the growing season, with data at the land parcel level identifying five land use types (annual and perennial crops, and three types of pasture), and with precipitation records, which we use to identify both excessively dry (drought) and excessively wet (flood) episodes. Using regression analyses, we examine whether these precipitation extremes had an observable impact on agricultural productivity. We find statistically significant declines in agricultural productivity that are associated with both droughts and floods. The average impact of these events is usually less than 1%, but the impacts are quite heterogeneous across years and across regions, with some parcels experiencing a much more significant decline in the EVI. We also identify several impact patterns related to the varying drought and flood vulnerability of the analysed land use types.
Activation of the toll-like receptor 2 signaling pathway by GAPDH from bacterial strain RD055328
Authors: Kurata Atsushi , Takeuchi Shimpei , Fujiwara Ryo , Tamura Kento , Imai Tomoya , Yamasaki-Yashiki Shino , Onuma Hiroki , Fukuta Yasuhisa , Shirasaka Norifumi , Uegaki Koichi
Published: May 2023

We characterized the membrane vesicle fraction (RD-MV fraction) from bacterial strain RD055328, which is related to members of the genus Companilactobacillus and Lactiplantibacillus plantarum. RD-MVs and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were detected in the RD-MV fraction. Immunoglobulin A (IgA) was produced by Peyer's patch cells following the addition of the RD-MV fraction. In the presence of the RD-MV fraction, RAW264 cells produced the pro-inflammatory cytokine IL-6. Recombinant GAPDH probably induced the production of IL-6 by RAW264 cells via superficial toll-like receptor 2 (TLR2) recognition. A confocal laser scanning microscopy image analysis indicated that RD-MVs and GAPDH were taken up by RAW264 cells. GAPDH wrapped around RAW264 cells. We suggest that GAPDH from strain RD055328 enhanced the production of IgA by acquired immune cells via the production of IL-6 by innate immune cells through TLR2 signal transduction.
(E)-7-phenyl-2-heptene-4,6-diyn-1-ol fromBidens pilosaas a repellent against isopods
Authors: Ishida Masashi , Yamaji Yuika , Isoda Wakana , Abe Haruki , Sato Masashi , Kariya Keisuke , Ishihara Atsushi , Tebayashi Shin-ichi , Sato Shu-ushi
Published: May 2023

The development of repellents as alternatives to insecticides has expanded in recent years. However, their use in isopod pest control is limited. To develop an isopod repellent, a plant extract library from wild plants native to the Kochi Prefecture was screened for repellent activity against pillbugs, and 82 samples (87%) exhibited repellent activity. Among them, (E)-7-phenyl-2-heptene-4,6-diyn-1-ol was isolated and identified as a repellent from the root of Bidens pilosa. It had a half-maximal effective concentration of 0.20 µm, with a strong repellency. A study of the structure–activity relationship to (E)-7-phenyl-2-heptene-4,6-diyn-1-ol revealed that the presence of a hydroxyl group and an aromatic at both ends of the length of the seven-carbon chain is important for the expression of repellency. These results can potentially lead to a new repellent of phenylalkyl alcohol.
Aggression and spatial positioning of kin and non-kin fish in social groups
Authors: Bose Aneesh P H , Dabernig-Heinz Johanna , Oberkofler Jan , Koch Lukas , Grimm Jacqueline , Sefc Kristina M , Jordan Alex
Published: May 2023

Group-living animals are faced with the challenge of sharing space and local resources amongst group members who may be either relatives or non-relatives. Individuals may reduce the inclusive fitness costs they incur from competing with relatives by either reducing their levels of aggression toward kin, or by maintaining physical separation between kin. In this field study, we used the group-living cichlid Neolamprologus multifasciatus to examine whether within-group aggression is reduced among group members that are kin, and whether kin occupy different regions of their group’s territory to reduce kin competition over space and local resources. We determined the kinship relationships among cohabiting adults via microsatellite genotyping and then combined these with spatial and behavioral analyses of groups in the wild. We found that aggressive contests between group members declined in frequency with spatial separation between their shelters. Female kin did not engage in aggressive contests with one another, whereas non-kin females did, despite the fact these females lived at similar distances from one another on their groups’ territories. Contests within male–male and male–female dyads did not clearly correlate with kinship. Non-kin male-male and male–female dyads lived at more variable distances from one another on their territories than their corresponding kin dyads. Together, our study indicates that contests among group members can be mediated by relatedness in a sex-dependent manner. We also suggest that spatial relationships can play an important role in determining the extent to which group members compete with one another.
Efficient short read mapping to a pangenome that is represented by a graph of ED strings
Authors: Büchler Thomas , Olbrich Jannik , Ohlebusch Enno
Published: May 2023

Motivation

A pangenome represents many diverse genome sequences of the same species. In order to cope with small variations as well as structural variations, recent research focused on the development of graph-based models of pangenomes. Mapping is the process of finding the original location of a DNA read in a reference sequence, typically a genome. Using a pangenome instead of a (linear) reference genome can, e.g. reduce mapping bias, the tendency to incorrectly map sequences that differ from the reference genome. Mapping reads to a graph, however, is more complex and needs more resources than mapping to a reference genome. Reducing the complexity of the graph by encoding simple variations like SNPs in a simple way can accelerate read mapping and reduce the memory requirements at the same time.

Results

We introduce graphs based on elastic-degenerate strings (ED strings, EDS) and the linearized form of these EDS graphs as a new representation for pangenomes. In this representation, small variations are encoded directly in the sequence. Structural variations are encoded in a graph structure. This reduces the size of the representation in comparison to sequence graphs. In the linearized form, mapping techniques that are known from ordinary strings can be applied with appropriate adjustments. Since most variations are expressed directly in the sequence, the mapping process rarely has to take edges of the EDS graph into account. We developed a prototypical software tool GED-MAP that uses this representation together with a minimizer index to map short reads to the pangenome. Our experiments show that the new method works on a whole human genome scale, taking structural variants properly into account. The advantage of GED-MAP, compared with other pangenomic short read mappers, is that the new representation allows for a simple indexing method. This makes GED-MAP fast and memory efficient.

Availability and implementation

Sources are available at: https://github.com/thomas-buechler-ulm/gedmap.
Timing of rectal cancer surgery after short-course radiotherapy: national database study
Authors: Verweij Maaike E , Franzen Jolien , van Grevenstein Wilhelmina M U , Verkooijen Helena M , Intven Martijn P W
Published: May 2023

Background

Previous randomized trials found that a prolonged interval between short-course radiotherapy (SCRT, 25 Gy in 5 fractions) and surgery for rectal cancer (4–8 weeks, SCRT-delay) results in a lower postoperative complication rate and a higher pCR rate than SCRT and surgery within a week (SCRT-direct surgery). This study sought to confirm these results in a Dutch national database.

Methods

Patients with intermediate-risk rectal cancer (T3(mesorectal fascia (MRF)–) N0 M0 and T1–3(MRF–) N1 M0) treated with either SCRT-delay (4–12 weeks) or SCRT-direct surgery in 2018–2021 were selected from a Dutch national colorectal cancer database. Confounders were adjusted for using inverse probability of treatment weighting (IPTW). The primary endpoint was the 90-day postoperative complication rate. Secondary endpoints included the pCR rate. Endpoints were compared using log-binomial and Poisson regression.

Results

Some 664 patients were included in the SCRT-direct surgery and 238 in the SCRT-delay group. After IPTW, the 90-day postoperative complication rate was comparable after SCRT-direct surgery and SCRT-delay (40.1 versus 42.3 per cent; risk ratio (RR) 1.1, 95 per cent c.i. 0.9 to 1.3). A pCR occurred more often after SCRT-delay than SCRT-direct surgery (10.7 versus 0.4 per cent; RR 39, 11 to 139).

Conclusion

There was no difference in surgical complication rates between SCRT-delay and SCRT-direct, but SCRT-delay was associated with more patients having a pCR.
Computational studies on glycosaminoglycan recognition of sialyl transferases
Authors: Sankaranarayanan Nehru Viji , Sistla Srinivas , Nagarajan Balaji , Chittum John E , Lau Joseph T Y , Desai Umesh R
Published: May 2023

Despite decades of research, glycosaminoglycans (GAGs) have not been known to interact with sialyl transferases (STs). Using our in-house combinatorial virtual library screening (CVLS) technology, we studied seven human isoforms, including ST6GAL1, ST6GAL2, ST3GAL1, ST3GAL3, ST3GAL4, ST3GAL5, and ST3GAL6, and predicted that GAGs, especially heparan sulfate (HS), are likely to differentially bind to STs. Exhaustive CVLS and molecular dynamics studies suggested that the common hexasaccharide sequence of HS preferentially recognized ST6GAL1 in a site overlapping the binding site of the donor substrate CMP-Sia. Interestingly, CVLS did not ascribe any special role for the rare 3-O-sulfate modification of HS in ST6GAL1 recognition. The computational predictions were tested using spectrofluorimetric studies, which confirmed preferential recognition of HS over other GAGs. A classic chain length-dependent binding of GAGs to ST6GAL1 was observed with polymeric HS displaying a tight affinity of ~65 nM. Biophysical studies also confirmed a direct competition between CMP-Sia and an HS oligosaccharide and CS polysaccharide for binding to ST6GAL1. Overall, our novel observation that GAGs bind to ST6GAL1 with high affinity and compete with the donor substrate is likely to be important because modulation of sialylation of glycan substrates on cells has considerable physiological/pathological consequences. Our work also brings forth the possibility of developing GAG-based chemical probes of ST6GAL1.
Serious Infections in Offspring Exposed in Utero to Vedolizumab
Authors: Gorodensky Jonah H , Bernatsky Sasha , Afif Waqqas , St-Pierre Yvan , Filion Kristian B , Vinet Évelyne
Published: May 2023

Lay Summary

Controlling IBD during pregnancy is important for maternal and fetal outcomes. We created a cohort of children born to mothers with IBD, comparing the risk of infections in those exposed to vedolizumab vs unexposed. We detected no increased risk.
Whole-body perfusion improves intraoperative transfusions in neonatal aortic arch surgery
Authors: Sandoval Boburg Rodrigo , Berger Rafal , Mustafi Migdat , Faust Charlotte , Magunia Harry , Neunhoeffer Felix , Hofbeck Michael , Rosenberger Peter , Schlensak Christian
Published: May 2023

OBJECTIVES

Whole-body perfusion is the combination of lower body perfusion and antegrade cerebral perfusion. This perfusion technique is used in some centres when performing aortic arch reconstruction surgery in neonates and infants. Several studies have shown intra- and postoperative benefits of this technique. However, no studies have analysed the impact it may have on the transfusion of blood products and coagulation factors.

METHODS

We retrospectively analysed 65 consecutive neonates and infants who underwent aortic arch reconstruction surgery from January 2014 to July 2020. Patients operated from 2014 to 2017 underwent surgery with antegrade cerebral perfusion; in patients who underwent surgery from 2017 to 2020 a whole-body perfusion strategy was used. Demographic, intra- and postoperative parameters were compared as well as intraoperative blood product and coagulation factor transfusions, chest-tube output in the first 24 h and postoperative bleeding complications.

RESULTS

Both groups required intraoperative transfusion of red blood cells, fresh frozen plasma, and platelets, as well as substitution of coagulation factors. The amount of transfused volumes of red blood cells, fresh frozen plasma and platelets (P-values 0.01, <0.01 and <0.01) and intraoperative transfusions of fibrinogen and von Willebrand factor were significantly lower in the whole-body perfusion group (P-value 0.04 and <0.01).

CONCLUSIONS

A whole-body perfusion strategy may lead to fewer intraoperative blood product and coagulation factor transfusions when compared to antegrade cerebral perfusion alone in neonates and infants undergoing complex aortic arch reconstruction surgery.
Occult Hepatitis B Virus Infection and Liver Fibrosis in Chinese Patients
Authors: Tang Xi , Yang Liu , Zhang Panli , Wang Cong , Luo Shengxue , Liu Bochao , Fu Yongshui , Candotti Daniel , Allain Jean-Pierre , Zhang Ling , Li Chengyao , Li Tingting
Published: May 2023

Background

The impact of hepatitis B surface antigen (HBsAg)–negative/hepatitis B virus (HBV) DNA–positive occult HBV infection (OBI) on the severity of liver fibrosis remains unclear.

Methods

A total of 1772 patients negative for HBsAg but positive for antibody to hepatitis B core antigen (HBcAg), stratified by the presence or absence of OBI, were selected for long-term carriage leading to elevation of ≥2 of 4 liver fibrosis indexes—hyaluronic acid (HA), laminin, type III procollagen peptide (PCIII), and type IV collagen (CIV)—at testing in a Chinese hospital. Patients were tested for serum viral load, HBV markers, and histopathological changes in liver biopsy specimens.

Results

OBI was identified in 148 patients with liver fibrosis (8.4%), who had significantly higher levels of HA, laminin, PCIII, and CIV than 1624 fibrotic patients without OBI (P < .05). In 36 patients with OBI who underwent liver biopsy, significant correlations were observed between OBI viral load and serum HA levels (P = .01), PCIII levels (P = .01), and pathological histological activity index (HAI) scores (P < .001), respectively; HAI scores and PCIII levels (P = .04); HBcAg immunohistochemical scores and HA levels (P < .001); and HBcAg immunohistochemical scores and PCIII levels (P = .03). Positive fluorescent in situ hybridization results were significantly more frequent in patients with OBIs (80.6% vs 37.5% in those without OBIs). Among patients with OBIs, HBcAg was detected in the liver tissue in 52.8% and HBsAg in 5.6%.

Conclusions

OBI status appears to be associated with liver fibrosis severity.
A Highly Attenuated Panfilovirus VesiculoVax Vaccine Rapidly Protects Nonhuman Primates Against Marburg Virus and 3 Species of Ebola Virus
Authors: Woolsey Courtney , Borisevich Viktoriya , Agans Krystle N , O’Toole Rachel , Fenton Karla A , Harrison Mack B , Prasad Abhishek N , Deer Daniel J , Gerardi Cheryl , Morrison Nneka , Cross Robert W , Eldridge John H , Matassov Demetrius , Geisbert Thomas W
Published: May 2023

Background

The family Filoviridae consists of several virus members known to cause significant mortality and disease in humans. Among these, Ebola virus (EBOV), Marburg virus (MARV), Sudan virus (SUDV), and Bundibugyo virus (BDBV) are considered the deadliest. The vaccine, Ervebo, was shown to rapidly protect humans against Ebola disease, but is indicated only for EBOV infections with limited cross-protection against other filoviruses. Whether multivalent formulations of similar recombinant vesicular stomatitis virus (rVSV)–based vaccines could likewise confer rapid protection is unclear.

Methods

Here, we tested the ability of an attenuated, quadrivalent panfilovirus VesiculoVax vaccine (rVSV-Filo) to elicit fast-acting protection against MARV, EBOV, SUDV, and BDBV. Groups of cynomolgus monkeys were vaccinated 7 days before exposure to each of the 4 viral pathogens. All subjects (100%) immunized 1 week earlier survived MARV, SUDV, and BDBV challenge; 80% survived EBOV challenge. Survival correlated with lower viral load, higher glycoprotein-specific immunoglobulin G titers, and the expression of B-cell–, cytotoxic cell–, and antigen presentation–associated transcripts.

Conclusions

These results demonstrate multivalent VesiculoVax vaccines are suitable for filovirus outbreak management. The highly attenuated nature of the rVSV-Filo vaccine may be preferable to the Ervebo “delta G” platform, which induced adverse events in a subset of recipients.
Size And Locomotor Ecology Have Differing Effects on the External and Internal Morphologies of Squirrel (Rodentia: Sciuridae) Limb Bones
Authors: Rickman J , Burtner A E , Linden T J , Santana S E , Law C J
Published: May 2023

Synopsis

Mammals exhibit a diverse range of limb morphologies that are associated with different locomotor ecologies and structural mechanics. Much remains to be investigated, however, about the combined effects of locomotor modes and scaling on the external shape and structural properties of limb bones. Here, we used squirrels (Sciuridae) as a model clade to examine the effects of locomotor mode and scaling on the external shape and structure of the two major limb bones, the humerus and femur. We quantified humeral and femoral morphologies using 3D geometric morphometrics and bone structure analyses on a sample of 76 squirrel species across their four major ecotypes. We then used phylogenetic generalized linear models to test how locomotor ecology, size, and their interaction influenced morphological traits. We found that size and locomotor mode exhibit different relationships with the external shape and structure of the limb bones, and that these relationships differ between the humerus and femur. External shapes of the humerus and, to a lesser extent, the femur are best explained by locomotor ecology rather than by size, whereas structures of both bones are best explained by interactions between locomotor ecology and scaling. Interestingly, the statistical relationships between limb morphologies and ecotype were lost when accounting for phylogenetic relationships among species under Brownian motion. That assuming Brownian motion confounded these relationships is not surprising considering squirrel ecotypes are phylogenetically clustered; our results suggest that humeral and femoral variation partitioned early between clades and their ecomorphologies were maintained to the present. Overall, our results show how mechanical constraints, locomotor ecology, and evolutionary history may enact different pressures on the shape and structure of limb bones in mammals.
A Step-by-Step Guide to Writing a Scientific Review Article
Authors: Bahl Manisha
Published: May 2023

Scientific review articles are comprehensive, focused reviews of the scientific literature written by subject matter experts. The task of writing a scientific review article can seem overwhelming; however, it can be managed by using an organized approach and devoting sufficient time to the process. The process involves selecting a topic about which the authors are knowledgeable and enthusiastic, conducting a literature search and critical analysis of the literature, and writing the article, which is composed of an abstract, introduction, body, and conclusion, with accompanying tables and figures. This article, which focuses on the narrative or traditional literature review, is intended to serve as a guide with practical steps for new writers. Tips for success are also discussed, including selecting a focused topic, maintaining objectivity and balance while writing, avoiding tedious data presentation in a laundry list format, moving from descriptions of the literature to critical analysis, avoiding simplistic conclusions, and budgeting time for the overall process.