bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlling transmembrane ion transport via photo-regulated carrier mobility
Authors: Bickerton Laura E. , Langton Matthew J.
Published: July 2022

Photo-gated anion transport is achieved by modulating the mobility of mobile carriers within a lipid bilayer membrane, using a photo-cleavable membrane anchor. This enables in situ, off–on activation of transport in vesicles.
Exploring the air stability of all-inorganic halide perovskites in the presence of photogenerated electrons by DFT and AIMD studies
Authors: Cai Ming-Quan , Busipalli Dhana Lakshmi , Xu Shi-Hong , Nachimuthu Santhanamoorthi , Jiang Jyh-Chiang
Published: July 2022

Developing ambient air and light stable perovskites could lead to significant advances in photocatalysis. Here, we report the chemical stability of CsPbX3 (X = Cl, Br, and I) perovskites upon O2 exposure in the presence of light using first-principles calculations.
Improving approximate vacuum prepared by the adiabatic quantum computation
Authors: Oshima Kazuto
Published: July 2022

According to the quantum adiabatic theorem, we can in principle obtain a true vacuum of a quantum system starting from a trivial vacuum of a simple Hamiltonian. In actual adiabatic digital quantum simulation with finite time length and non‐infinitesimal time steps, we can only obtain an approximate vacuum that is supposed to be a superposition of a true vacuum and excited states. We propose a procedure to improve the approximate vacuum.
Role of hydrocarbons and renewable energies in Iran's energy matrix focusing on bioenergy: review
Authors: Mahdavi Meisam , Schmitt Konrad , Ramos Ricardo Alan Verdú , Alhelou Hassan Haes
Published: July 2022

Iran is one of the most potent energy exporters and fastest‐growing energy consumers in the world. Its large amount of energy exported can directly impact the economy of importer countries. Iran's energy matrix mostly consists of hydrocarbons, while the remaining portion is compounded by a blend of biofuels, hydropower, wind, solar, and other renewable sources. Even though the country has an excellent potential to reach a large amount of renewable power, it is most likely that Iran will deal with a shortage in its electricity segment during the upcoming years. Besides wind and solar energy, bioenergy appears to be a good alternative for enhancing the country's energy matrix and transit Iran's energy consumption pattern from a high‐level usage of hydrocarbons to a more renewable scenario. Therefore, in the present paper, the role of Iran in global energy production is discussed, and its potential for renewable energy generation is described. The review presents a vast set of data related to environmental, infrastructural, economic, and social aspects to clarify the potential and benefits of Iran's transition to a more renewable energy matrix. The investigations revealed the country's extremely favourable conditions to use bioenergy resources as a key solution to avoiding future energy crises, besides improving quality of life. The context can help researchers, power suppliers, and energy consumers know how renewable energies, especially bioenergy, can modify the energy matrix of a country rich in hydrocarbon resources.
An innovative method to conduct temperature rise test on medium voltage switchgear assembly based on IEC standards in a power grid
Authors: Iderus Samat , Peter Geno , Ganji Vivekananda
Published: July 2022

Modern civilization is characterised by a high need for electrical energy. The importance of electricity in daily life has grown to the point that it is desirable to safeguard the power system from damage during fault situations and to ensure maximum supply continuity, which necessitates the use of switchgear. Testing of any electrical equipment indicates the extent to which the equipment is able to comply with a customer's requirements. In this paper temperature rise test on a medium voltage switchgear assembly is considered. In this research, sub‐clause 6.5.2 of IEC standard 62271‐1 is followed to conduct temperature rise test on a medium voltage switchgear assembly. The test is conducted on two modes, first following the existing method of testing and second by an innovative method of testing. The temperature rise test is conducted on a 12 kV, 50 kA, 3150 A single busbar switchgear assembly and the readings are measured, analysed and compared between the two methods. It is concluded that the temperature rise recorded following the innovative method is more accurate compared to the existing method, as an increase in the recorded temperature rise is seen in all the thermocouple locations as the heat dissipation to the ambient is reduced.
Reducing the environmental footprint of gastrointestinal endoscopy: European Society of Gastrointestinal Endoscopy (ESGE) and European Society of Gastroenterology and Endoscopy Nurses and Associates (ESGENA) Position Statement
Authors: Rodríguez de Santiago Enrique , Dinis-Ribeiro Mario , Pohl Heiko , Agrawal Deepak , Arvanitakis Marianna , Baddeley Robin , Bak Elzbieta , Bhandari Pradeep , Bretthauer Michael , Burga Patricia , Donnelly Leigh , Eickhoff Axel , Hayee Bu'Hussain , Kaminski Michal F. , Karlović Katarina , Lorenzo-Zúñiga Vicente , Pellisé Maria , Pioche Mathieu , Siau Keith , Siersema Peter D. , Stableforth William , Tham Tony C. , Triantafyllou Konstantinos , Tringali Alberto , Veitch Andrew , Voiosu Andrei M. , Webster George J. , Vienne Ariane , Beilenhoff Ulrike , Bisschops Raf , Hassan Cesare , Gralnek Ian M. , Messmann Helmut
Published: July 2022

Climate change and the destruction of ecosystems by human activities are among the greatest challenges of the 21st century and require urgent action. Health care activities significantly contribute to the emission of greenhouse gases and waste production, with gastrointestinal (GI) endoscopy being one of the largest contributors. This Position Statement aims to raise awareness of the ecological footprint of GI endoscopy and provides guidance to reduce its environmental impact. The European Society of Gastrointestinal Endoscopy (ESGE) and the European Society of Gastroenterology and Endoscopy Nurses and Associates (ESGENA) outline suggestions and recommendations for health care providers, patients, governments, and industry. Main statements 1 GI endoscopy is a resource-intensive activity with a significant yet poorly assessed environmental impact. 2 ESGE-ESGENA recommend adopting immediate actions to reduce the environmental impact of GI endoscopy. 3 ESGE-ESGENA recommend adherence to guidelines and implementation of audit strategies on the appropriateness of GI endoscopy to avoid the environmental impact of unnecessary procedures. 4 ESGE-ESGENA recommend the embedding of reduce, reuse, and recycle programs in the GI endoscopy unit. 5 ESGE-ESGENA suggest that there is an urgent need to reassess and reduce the environmental and economic impact of single-use GI endoscopic devices. 6 ESGE-ESGENA suggest against routine use of single-use GI endoscopes. However, their use could be considered in highly selected patients on a case-by-case basis. 7 ESGE-ESGENA recommend inclusion of sustainability in the training curricula of GI endoscopy and as a quality domain. 8 ESGE-ESGENA recommend conducting high quality research to quantify and minimize the environmental impact of GI endoscopy. 9 ESGE-ESGENA recommend that GI endoscopy companies assess, disclose, and audit the environmental impact of their value chain. 10 ESGE-ESGENA recommend that GI endoscopy should become a net-zero greenhouse gas emissions practice by 2050.
Gel immersion endoscopic submucosal dissection: clinical experience with 13 cases of superficial esophageal cancer
Authors: Nakano Yuya , Tashima Tomoaki , Jinushi Ryuhei , Terada Rie , Mashimo Yumi , Kawasaki Tomonori , Uraoka Toshio , Ryozawa Shomei
Published: July 2022

Esophageal endoscopic submucosal dissection (ESD) of tumors located on the gravity side is technically challenging. Given that gel immersion ESD (GIESD) is performed by immersing lesions in gel, we hypothesized that it could be used to eliminate the disadvantage associated with submerging the gravity side. Here, we performed GIESD using VISCOCLEAR for superficial esophageal cancer on the gravity side of the esophagus, with monopolar devices. This study aimed to evaluate the short-term outcomes of GIESD for superficial esophageal cancer. Fifteen patients with 16 superficial esophageal cancers underwent GIESD by a single operator, and 13 cases were evaluated. All patients were male, and GIESD was performed in the middle (12/13, 92.3 %) and lower (1/13, 7.7 %) thoracic esophagus. The lesions were located on the left (7/13, 53.8 %), posterior (5/13, 38.5 %), and right (1/13, 7.7 %) esophageal walls. The median procedure time was 27 minutes (interquartile range [IQR], 14–68), and the median dissection speed was 20 mm2/min (IQR, 14–25.7). The median amount of gel used was 400 mL (IQR, 360–580), and no gel-related adverse events were observed. The median total dose of midazolam was 3 mg (IQR, 2–5). GIESD was completed with en bloc and R0 resections achieved in 100 % of the 13 cases. Delayed adverse events, such as bleeding or perforation, did not occur (0/13, 0 %).
Visible-Light-Initiated Oxidative Coupling of Indole and Active Methylene Compounds Using Eosin Y as a Photocatalyst
Authors: Singh Sundaram , Kushwaha Ambuj Kumar , Maury Suresh Kumar , Kumari Savita , Kamal Arsala , Singh Himanshu Kumar , Kumar Dhirendra
Published: July 2022

A novel, efficient, mild, and inexpensive photocatalytic approach has been established for the visible-light-initiated oxidative coupling of indole and active methylene compounds using atmospheric air and water as an oxidant in the presence of Eosin Y to give 3-methyleneindolin-2-ones. In this work, only one molecule of malononitrile, ethyl acetoacetate, or dimedone reacts with one molecule of indole, but, in contrast, two molecules of barbituric acid react with one molecule of indole. The essential features of this approach are metal-free reaction, high yield of the products, no side product, and use of renewable energy sources.
Brønsted Acid Catalyzed Stereospecific Dearomative Spirocyclization of Benzothiophenyl Analogues of Tertiary cis-β-Benzylstyrenes
Authors: Stokes Benjamin J. , Tohti Anargul , Lerda Victoria
Published: July 2022

3-Substituted benzothiophenyl analogues of tertiary cis-β-benzylstyrenes undergo triflic acid catalyzed dearomative spirocyclization at room temperature to afford compounds containing vicinal quaternary centers. Hydroarylation of the styrene is a competing process that occurs preferentially within substrates possessing electron-rich styrenyl alkenes, or an indole in place of the benzothiophene.
Diastereoselective Synthesis of Spiro[benzopyrrolothiazole-thioazlactone] Derivatives from Erlenmeyer Thioazlactones and Azomethine Ylides
Authors: Yavari Issa , Shirazi Hamideh , Sheikhi Sara , Taheri Zohreh
Published: July 2022

Erlenmeyer thioazlactones reacted with 3-(2-oxo-2-arylethyl)benzo[d]thiazol-3-ium bromides in the presence of Et3N in MeCN to afford 1-aryloyl-2′-(benzylthio)-2-aryl-2,3a-dihydro-1H,5′H-spiro[benzo[d]pyrrolo[2,1-b]thiazole-3,4′-thiazol]-5′-ones. Formally, this transformation can be regarded as a Huisgen reaction of the exocyclic carbon–carbon double bond of the Erlenmeyer thioazlactones and azomethine ylides generated in situ. Evidence for the structure of a product was obtained from single-crystal X-ray analyses. The important feature of this reaction is the fact it forms four stereogenic centers, one of which is quaternary, with excellent selectivity.
10.17 Benzo[b]phospholes
Authors: Aitken R. A.
Published: July 2022

This chapter is a complete revision and update of the earlier Science of Synthesis contribution from 2000 describing methods for the synthesis of benzo[b]phospholes. About half of the references cited describe newer methods reported between 2000 and 2021 and, as well as extensions to the previously described approaches, several completely new approaches are included. Among the strategies covered are reactions of metalated phenylalkyne derivatives with phosphorus halides, cyclizations of (2-alkynylphenyl)phosphorus compounds, direct reactions of phenylphosphorus compounds with alkynes, and aromatization of dihydro derivatives. In addition, the initially obtained compounds can be converted into a variety of derivatives by modification at phosphorus by oxidation, substitution, or reduction.
Spaceplate testing shows great promise for miniaturization of optical systems
Authors: Johnson-Groh Mara
Published: July 2022

The thin metamaterial optics elements could help reduce the size of cameras, microscopes, telescopes and more.
Flipping spins to enable ultralow power electronics
Authors: Lim Alane
Published: July 2022

New method to manipulate spin currents at room temperature revealed.
FPGA-based electronic system for the control and readout of superconducting quantum processors
Authors: Yang Yuchen , Shen Zhongtao , Zhu Xing , Wang Ziqi , Zhang Gengyan , Zhou Jingwei , Jiang Xun , Deng Chunqing , Liu Shubin
Published: July 2022

Electronic systems for qubit control and measurement serve as a bridge between quantum programming language and quantum information processors. With the rapid development of superconducting quantum circuit technology, synchronization in a large-scale system, low-latency execution, and low noise are required for electronic systems. Here, we present a field-programmable gate array (FPGA)-based electronic system with a distributed synchronous clock and trigger architecture. The system supports synchronous control of qubits with jitters of ∼5 ps. We implement a real-time digital signal processing system in the FPGA, enabling precise timing control, arbitrary waveform generation, in-phase and quadrature demodulation for qubit state discrimination, and the generation of real-time qubit-state-dependent trigger signals for feedback/feedforward control. The hardware and firmware low-latency design reduces the feedback/feedforward latency of the electronic system to 125 ns, significantly less than the decoherence times of the qubit. Finally, we demonstrate the functionalities and low-noise performance of this system using a fluxonium quantum processor.
The flexoelectric transition in CaCu3Ti4O12 material with colossal permittivity
Authors: Zhang Zhen , Shu Shengwen , Wang Zhiguo , Xie Zhengqiu , Wang Huizhong , Li Chunchun , Ke Shanming , Shu Longlong
Published: July 2022

Significant flexoelectricity is expected to exist in materials with colossal permittivity. Here, we systematically studied the interplay of flexoelectricity and permittivity in CaCu3Ti4O12 (CCTO) ceramic by examining the thickness and electrode dependence of the flexoelectric coefficients over a wide range of temperatures. We found that an abnormal flexoelectric transition occurs at 95 °C. Below this critical temperature, the barrier layer mechanism dominates the significant flexoelectricity in CCTO ceramic, whereas above this critical temperature, the flexoelectric response mainly originates from the contributions of semiconducting grains and insulating grain boundaries. The observed flexoelectric transition is beneficial not only for developing new materials with high flexoelectric coefficients but also for understanding the colossal permittivity mechanism in CCTO ceramics.
From charge to spin: Analogies and differences in quantum transport coefficients
Authors: Marcelli Giovanna , Monaco Domenico
Published: July 2022

We review some recent results from the mathematical theory of transport of charge and spin in gapped crystalline quantum systems. The emphasis will be on transport coefficients, such as conductivities and conductances. As for the former, those are computed as appropriate expectations of current operators in a non-equilibrium almost-stationary state (NEASS), which arises from the perturbation of an equilibrium state by an external electric field. While for charge transport the usual double-commutator Kubo formula is recovered (also beyond linear response), we obtain formulas for appropriately defined spin conductivities, which are still explicit but more involved. Certain “Kubo-like” terms in these formulas are also shown to agree with the corresponding contributions to the spin conductance. In addition to that, we employ similar techniques to show a new result, namely that even in systems with non-conserved spin, there is no generation of spin torque, that is, the spin torque operator has an expectation in the NEASS which vanishes faster than any power of the intensity of the perturbing field.
Drastic effects of an inert Pt wire on the redox behavior of the Belousov–Zhabotinsky reaction
Authors: Tang Alexander , Wang Jichang
Published: July 2022

This research investigated responses of the Belousov–Zhabotinsky (BZ) reaction to the presence of a chemically inert Pt wire in solution. Experiments showed that connecting the Pt wire to a neutral ground caused a spontaneous drastic shift in the redox potential and might even induce complex behavior. Characterizations using an unstirred ferriin solution demonstrated the formation of a red colored propagating front at the grounded Pt wire, suggesting the reduction of ferriin to ferroin. Measurements with different combinations of electrodes in both stirred and reaction-diffusion media further confirmed the reduction of BZ metal catalysts at the Pt wire and the accompanying oxidation reaction at the reference electrode. The observed drastic change in redox potential and oscillation waveform can be understood based on the passive reduction reaction at the indicator electrode that is connected to the reference electrode through a potential meter. The obtained influence can be further manipulated by adding a resistor between the Pt wire and the neutral ground, making this convenient perturbation method attractive for the study of redox chemical reaction dynamics.
The evolution of synaptic and cognitive capacity: Insights from the nervous system transcriptome ofAplysia
Authors: Orvis Joshua , Albertin Caroline B. , Shrestha Pragya , Chen Shuangshuang , Zheng Melanie , Rodriguez Cheyenne J. , Tallon Luke J. , Mahurkar Anup , Zimin Aleksey V. , Kim Michelle , Liu Kelvin , Kandel Eric R. , Fraser Claire M. , Sossin Wayne , Abrams Thomas W.
Published: July 2022

The gastropod molluskAplysiais an important model for cellular and molecular neurobiological studies, particularly for investigations of molecular mechanisms of learning and memory. We developed an optimized assembly pipeline to generate an improvedAplysianervous system transcriptome. This improved transcriptome enabled us to explore the evolution of cognitive capacity at the molecular level. Were there evolutionary expansions of neuronal genes between this relatively simple gastropodAplysia(20,000 neurons) andOctopus(500 million neurons), the invertebrate with the most elaborate neuronal circuitry and greatest behavioral complexity? Are the tremendous advances in cognitive power in vertebrates explained by expansion of the synaptic proteome that resulted from multiple rounds of whole genome duplication in this clade? Overall, the complement of genes linked to neuronal function is similar betweenOctopusandAplysia.As expected, a number of synaptic scaffold proteins have more isoforms in humans than inAplysiaorOctopus. However, several scaffold families present in mollusks and other protostomes are absent in vertebrates, including the Fifes, Lev10s, SOLs, and a NETO family. Thus, whereas vertebrates have more scaffold isoforms from select families, invertebrates have additional scaffold protein families not found in vertebrates. This analysis provides insights into the evolution of the synaptic proteome. Both synaptic proteins and synaptic plasticity evolved gradually, yet the last deuterostome-protostome common ancestor already possessed an elaborate suite of genes associated with synaptic function, and critical for synaptic plasticity.
Development of an improved inhibitor of Lats kinases to promote regeneration of mammalian organs
Authors: Kastan Nathaniel R. , Oak Sanyukta , Liang Rui , Baxt Leigh , Myers Robert W. , Ginn John , Liverton Nigel , Huggins David J. , Pichardo John , Paul Matthew , Carroll Thomas S. , Nagiel Aaron , Gnedeva Ksenia , Hudspeth A. J.
Published: July 2022

The Hippo signaling pathway acts as a brake on regeneration in many tissues. This cascade of kinases culminates in the phosphorylation of the transcriptional cofactors Yap and Taz, whose concentration in the nucleus consequently remains low. Various types of cellular signals can reduce phosphorylation, however, resulting in the accumulation of Yap and Taz in the nucleus and subsequently in mitosis. We earlier identified a small molecule, TRULI, that blocks the final kinases in the pathway, Lats1 and Lats2, and thus elicits proliferation of several cell types that are ordinarily postmitotic and aids regeneration in mammals. In the present study, we present the results of chemical modification of the original compound and demonstrate that a derivative, TDI-011536, is an effective blocker of Lats kinases in vitro at nanomolar concentrations. The compound fosters extensive proliferation in retinal organoids derived from human induced pluripotent stem cells. Intraperitoneal administration of the substance to mice suppresses Yap phosphorylation for several hours and induces transcriptional activation of Yap target genes in the heart, liver, and skin. Moreover, the compound initiates the proliferation of cardiomyocytes in adult mice following cardiac cryolesions. After further chemical refinement, related compounds might prove useful in protective and regenerative therapies.
Multichannel single center method
Authors: Novikovskiy Nikolay M , Artemyev Anton N , Rezvan Dmitrii V , Lagutin Boris M , Demekhin Philipp V
Published: July 2022

A multichannel single center (MCSC) method for the theoretical description of the electron continuum spectrum in molecules is reported. The method includes coupling between different continuum channels via electron correlations and describes, thereby, photoelectron continuum in the Tamm–Dancoff (configuration interaction singles) approximation. Basic equations of the non-iterative one-channel single center (SC) method and their extension to the MCSC method are presented, and an efficient scheme for their numerical solution is outlined. The method is tested on known illustrative examples of the Ar 3s-, HCl 4σ- and N2 1σ-photoionization processes, where inter-channel coupling plays a very important role. Unlike our previous SC studies, the present MCSC method can be reliably applied to photoionization of outer and valence molecular orbitals, where inter-channel correlations in the continuum might be relevant.
Sea urchin-like CoNi2S4 materials derived from nickel hexamyanocobaltate for high-performance asymmetric hybrid supercapacitor
Authors: Wu Shang , Xu Xin , Yan Xiangtao , Zhao Huanlei , Liu Chaoyang , Wang Yanbin , Su Qiong , Yin Fenping , Yang Quanlu
Published: July 2022

In this work, a mild chemical precipitation method and simple hydrothermal treatment of the nickel hexamyanocobaltate precursor strategy are developed to prepare a sea urchin-like CoNi2S4 compound with remarkable specific capacity and excellent cycling stability. The prepared CoNi2S4 has an outstanding specific capacity of 149.1 mA h g−1 at 1 A g−1 and an initial capacity of 83.1% after 3000 cycles at 10 A g−1. Moreover, the porous carbon nanospheres (PCNs) with exhibit cycling stability (94.7% of initial specific capacity after 10 000 cycles at 10 A g−1) are selected as negative electrode to match CoNi2S4 positive electrode for assembly of CoNi2S4//PCNs asymmetric supercapacitor (ASC). Satisfactorily, the as-assembled CoNi2S4//PCNs ASC exhibits an impressive energy density of 41.6 Wh kg−1 at 797 W kg−1, as well as the suitable capacity retention of 82.8% after 10 000 cycles. The superior properties of the device demonstrated that the as-prepared material is potential energy storage material.
Pairwise and higher-order measures of brain-heart interactions in children with temporal lobe epilepsy
Authors: Pernice Riccardo , Faes Luca , Feucht Martha , Benninger Franz , Mangione Stefano , Schiecke Karin
Published: July 2022

Objective. While it is well-known that epilepsy has a clear impact on the activity of both the central nervous system (CNS) and the autonomic nervous system (ANS), its role on the complex interplay between CNS and ANS has not been fully elucidated yet. In this work, pairwise and higher-order predictability measures based on the concepts of Granger Causality (GC) and partial information decomposition (PID) were applied on time series of electroencephalographic (EEG) brain wave amplitude and heart rate variability (HRV) in order to investigate directed brain-heart interactions associated with the occurrence of focal epilepsy. Approach. HRV and the envelopes of δ and α EEG activity recorded from ipsilateral (ipsi-EEG) and contralateral (contra-EEG) scalp regions were analyzed in 18 children suffering from temporal lobe epilepsy monitored during pre-ictal, ictal and post-ictal periods. After linear parametric model identification, we compared pairwise GC measures computed between HRV and a single EEG component with PID measures quantifying the unique, redundant and synergistic information transferred from ipsi-EEG and contra-EEG to HRV. Main results. The analysis of GC revealed a dominance of the information transfer from EEG to HRV and negligible transfer from HRV to EEG, suggesting that CNS activities drive the ANS modulation of the heart rhythm, but did not evidence clear differences between δ and α rhythms, ipsi-EEG and contra-EEG, or pre- and post-ictal periods. On the contrary, PID revealed that epileptic seizures induce a reorganization of the interactions from brain to heart, as the unique predictability of HRV originated from the ipsi-EEG for the δ waves and from the contra-EEG for the α waves in the pre-ictal phase, while these patterns were reversed after the seizure. Significance. These results highlight the importance of considering higher-order interactions elicited by PID for the study of the neuro-autonomic effects of focal epilepsy, and may have neurophysiological and clinical implications.
Automated optimization of multilevel models of collective behaviour: application to mixed society of animals and robots
Authors: Cazenille Leo , Bredeche Nicolas , Halloy José
Published: July 2022

Animal societies exhibit complex dynamics that require multi-level descriptions. They are difficult to model, as they encompass information at different levels of description, such as individual physiology, individual behaviour, group behaviour and features of the environment. The collective behaviour of a group of animals can be modelled as a dynamical system. Typically, models of behaviour are either macroscopic (differential equations of population dynamics) or microscopic (such as Markov chains, explicitly specifying the spatio-temporal state of each individual). These two kind of models offer distinct and complementary descriptions of the observed behaviour. Macroscopic models offer mean field description of the collective dynamics, where collective choices are considered as the stable steady states of a nonlinear system governed by control parameters leading to bifurcation diagrams. Microscopic models can be used to perform computer simulations or as building blocks for robot controllers, at the individual level, of the observed spatial behaviour of animals. Here, we present a methodology to translate a macroscopic model into different microscopic models. We automatically calibrate the microscopic models so that the resulting simulated collective dynamics fit the solutions of the reference macroscopic model for a set of parameter values corresponding to a bifurcation diagram leading to multiple steady states. We apply evolutionary algorithms to simultaneously optimize the parameters of the models at different levels of description. This methodology is applied, in simulation, to an experimentally validated shelter-selection problem solved by gregarious insects and robots. Our framework can be used for multi-level modelling of collective behaviour in animals and robots.
Wide-range characteristics of beam perveance and saddle point potential of LIPS-200 ion thruster
Authors: ZHANG Xueer , ZHANG Tianping , LI Detian , CHEN Juanjuan , JIA Yanhui
Published: July 2022

Both the long-life and multi-mode versions of LIPS-200 ion thruster are under investigation in LIP (Lanzhou Institute of Physics). To confirm the feasible ranges of the beam current and accel (abbreviation for accelaration) grid potential to apply to the thruster, the wide-range beam perveance (the state of beam focus) and saddle point potential (the lowest potential along beamlet centerline) characteristics of LIPS-200 are studied with a test-verified PIC-MCC (Particle in Cell-Monte Carlo Collisions) model. These characteristics are investigated with both the initial and the eroded states of the accel grid aperture diameter. The results show that the feasible ranges of these parameters with respect to perveance/crossover (overfocused) limit extend as the operating time accumulates, while the feasible range of accel grid potential narrows due to a reduced EBSF (electron backstreaming failure) margin. The feasible ranges determined by the initial condition are: (i) the beam current up to 0.981 A, and (ii) the accel grid potential up to −85 V. A 23% enlargement of the aperture diameter would bring up to 48 V of EBSF margin loss.
Recent developments and perspectives of advanced high-strength medium Mn steel: from material design to failure mechanisms
Authors: Huang Chengpeng , Hu Chen , Liu Yuxuan , Liang Zhiyuan , Huang Mingxin
Published: July 2022

Advanced high-strength steels are key structural materials for the development of next-generation energy-efficient and environmentally friendly vehicles. Medium Mn steel, as one of the latest generation advanced high-strength steels, has attracted tremendous attentions over the past decade due to its excellent mechanical properties. Here, the state-of-the-art developments of medium Mn steel are systematically reviewed with focus on the following crucial aspects: (a) the alloy design strategies; (b) the thermomechanical processing routes for the optimizations of microstructure and mechanical properties; (c) the fracture mechanisms and toughening strategies; (d) the hydrogen embrittlement mechanisms and improvement strategies.
Solid-state Z-scheme assisted hydrated tungsten trioxide/ZnIn2S4 photocatalyst for efficient photocatalytic H2 production
Authors: Ye Lin , Peng Xinxin , Wen Zhenhai , Huang Haitao
Published: July 2022

Efficient water splitting for H2 evolution over semiconductor photocatalysts is highly attractive in the field of clean energy. It is of great significance to construct heterojunctions, among which the direct Z-scheme nanocomposite photocatalyst provides effective separation of photo-generated carriers to boost the photocatalytic performance. Herein, Z-scheme hydrated tungsten trioxide/ZnIn2S4 is fabricated via an in-situ hydrothermal method where ZnIn2S4 nanosheets are grown on WO3⋅xH2O. The close contact between WO3⋅0.5H2O and WO3⋅0.33H2O as well as ZnIn2S4 improve the charge carrier separation and migration in the photocatalyst, where the strong reducing electrons in the conduction band of ZnIn2S4 and the strong oxidizing holes in the valence band of WO3⋅0.33H2O are retained, leading to enhanced photocatalytic hydrogen production. The obtained WO3⋅xH2O/ZnIn2S4 shows an excellent H2 production rate of 7200 μmol g−1 h−1, which is 11 times higher than pure ZnIn2S4. To the best of our knowledge, this value is higher than most of the WO3-based noble metal-free semiconductor photocatalysts. The improved stability and activity are attributed to the formation of the Z-scheme heterojunction, which can markedly accelerate the interfacial charge separation for surface reaction. This work offers a promising strategy towards the design of an efficient Z-scheme photocatalyst to suppress electron–hole recombination and optimize redox potential.
Rhytidoplasty Through Minimal Incisions (Rhythmic)
Authors: Castillo-Campos Porfirio
Published: July 2022

Background

In the present report, an innovative alternative approach for rhytidoplasty is described. Rhytidoplasty Through Minimal Incisions (Rhythmic) is an effective, efficient, safe, and reproducible alternative procedure for facial rejuvenation. It has several advantages over traditional procedures.

Objective

The main objective of this report is to describe the surgical technique of Rhythmic.

Methods

The surgical technique for the foreheadplasty requires only a transverse ~7-mm incision ~1 cm behind the hairline at the midline. The upper and lower blepharoplasty are made with incisions of ~3 mm, and no suture is needed. Liposuction of the neck can also be performed, and the face-lift can be achieved through preauricular incisions.

Results

Here, we summarize the results obtained in 741 patients subjected to rhytidoplasty through minimal incisions. The follow-up of these patients extended up to 20 years. This technique drastically reduced the length of scars; the eyebrows elevated 8-13 mm, and in some cases, the tip of the nose was also elevated ~7 mm. It minimized or eliminated the vertical frown lines and the horizontal furrows in the forehead. The use of this technique allowed an excellent definition of the cervicofacial angle in the patients.

Conclusions

In conclusion, rhytidoplasty through minimal incisions drastically reduced the length of scars, bleeding, surgical time, avoided the use of drains, reduced costs, and shorted the convalescent period. It also offered the patients a natural appearance with minor complications.

Level of Evidence: 2
BubbleGun: enumerating bubbles and superbubbles in genome graphs
Authors: Dabbaghie Fawaz , Ebler Jana , Marschall Tobias
Published: July 2022

Motivation

With the fast development of sequencing technology, accurate de novo genome assembly is now possible even for larger genomes. Graph-based representations of genomes arise both as part of the assembly process, but also in the context of pangenomes representing a population. In both cases, polymorphic loci lead to bubble structures in such graphs. Detecting bubbles is hence an important task when working with genomic variants in the context of genome graphs.

Results

Here, we present a fast general-purpose tool, called BubbleGun, for detecting bubbles and superbubbles in genome graphs. Furthermore, BubbleGun detects and outputs runs of linearly connected bubbles and superbubbles, which we call bubble chains. We showcase its utility on de Bruijn graphs and compare our results to vg’s snarl detection. We show that BubbleGun is considerably faster than vg especially in bigger graphs, where it reports all bubbles in less than 30 min on a human sample de Bruijn graph of around 2 million nodes.

Availability and implementation

BubbleGun is available and documented as a Python3 package at https://github.com/fawaz-dabbaghieh/bubble_gun under MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images
Authors: Wang Yanan , Hu Changyuan , Kwok Terry , Bain Christopher A , Xue Xiangyang , Gasser Robin B , Webb Geoffrey I , Boussioutas Alex , Shen Xian , Daly Roger J , Song Jiangning
Published: July 2022

Motivation

The molecular subtyping of gastric cancer (adenocarcinoma) into four main subtypes based on integrated multiomics profiles, as proposed by The Cancer Genome Atlas (TCGA) initiative, represents an effective strategy for patient stratification. However, this approach requires the use of multiple technological platforms, and is quite expensive and time-consuming to perform. A computational approach that uses histopathological image data to infer molecular subtypes could be a practical, cost- and time-efficient complementary tool for prognostic and clinical management purposes.

Results

Here, we propose a deep learning ensemble approach (called DEMoS) capable of predicting the four recognized molecular subtypes of gastric cancer directly from histopathological images. DEMoS achieved tile-level area under the receiver-operating characteristic curve (AUROC) values of 0.785, 0.668, 0.762 and 0.811 for the prediction of these four subtypes of gastric cancer [i.e. (i) Epstein–Barr (EBV)-infected, (ii) microsatellite instability (MSI), (iii) genomically stable (GS) and (iv) chromosomally unstable tumors (CIN)] using an independent test dataset, respectively. At the patient-level, it achieved AUROC values of 0.897, 0.764, 0.890 and 0.898, respectively. Thus, these four subtypes are well-predicted by DEMoS. Benchmarking experiments further suggest that DEMoS is able to achieve an improved classification performance for image-based subtyping and prevent model overfitting. This study highlights the feasibility of using a deep learning ensemble-based method to rapidly and reliably subtype gastric cancer (adenocarcinoma) solely using features from histopathological images.

Availability and implementation

All whole slide images used in this study was collected from the TCGA database. This study builds upon our previously published HEAL framework, with related documentation and tutorials available at http://heal.erc.monash.edu.au. The source code and related models are freely accessible at https://github.com/Docurdt/DEMoS.git.

Supplementary information

Supplementary data are available at Bioinformatics online.
SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins
Authors: Özsarı Gökhan , Rifaioglu Ahmet Sureyya , Atakan Ahmet , Doğan Tunca , Martin Maria Jesus , Çetin Atalay Rengül , Atalay Volkan
Published: July 2022

Accurate prediction of the subcellular locations (SLs) of proteins is a critical topic in protein science. In this study, we present SLPred, an ensemble-based multi-view and multi-label protein subcellular localization prediction tool. For a query protein sequence, SLPred provides predictions for nine main SLs using independent machine-learning models trained for each location. We used UniProtKB/Swiss-Prot human protein entries and their curated SL annotations as our source data. We connected all disjoint terms in the UniProt SL hierarchy based on the corresponding term relationships in the cellular component category of Gene Ontology and constructed a training dataset that is both reliable and large scale using the re-organized hierarchy. We tested SLPred on multiple benchmarking datasets including our-in house sets and compared its performance against six state-of-the-art methods. Results indicated that SLPred outperforms other tools in the majority of cases.

Availability and implementation

SLPred is available both as an open-access and user-friendly web-server (https://slpred.kansil.org) and a stand-alone tool (https://github.com/kansil/SLPred). All datasets used in this study are also available at https://slpred.kansil.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design
Authors: Panei F P , Torchet R , Ménager H , Gkeka P , Bonomi M
Published: July 2022

Motivation

RNA molecules are implicated in numerous fundamental biological processes and many human pathologies, such as cancer, neurodegenerative disorders, muscular diseases and bacterial infections. Modulating the mode of action of disease-implicated RNA molecules can lead to the discovery of new therapeutical agents and even address pathologies linked to ‘undruggable’ protein targets. This modulation can be achieved by direct targeting of RNA with small molecules. As of today, only a few RNA-targeting small molecules are used clinically. One of the main obstacles that have hampered the development of a rational drug design protocol to target RNA with small molecules is the lack of a comprehensive understanding of the molecular mechanisms at the basis of RNA-small molecule (RNA-SM) recognition.

Results

Here, we present Harnessing RIBOnucleic acid—Small molecule Structures (HARIBOSS), a curated collection of RNA-SM structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and cryo-electron microscopy. HARIBOSS facilitates the exploration of drug-like compounds known to bind RNA, the analysis of ligands and pockets properties and ultimately the development of in silico strategies to identify RNA-targeting small molecules.

Availability and implementation

HARIBOSS can be explored via a web interface available at http://hariboss.pasteur.cloud.

Supplementary information

Supplementary data are available at Bioinformatics online.
Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy
Authors: Tao Huanyu , Zhao Xuejun , Zhang Keqiong , Lin Peicong , Huang Sheng-You
Published: July 2022

Motivation

Cyclization is a common strategy to enhance the therapeutic potential of peptides. Many cyclic peptide drugs have been approved for clinical use, in which the disulfide-driven cyclic peptide is one of the most prevalent categories. Molecular docking is a powerful computational method to predict the binding modes of molecules. For protein-cyclic peptide docking, a big challenge is considering the flexibility of peptides with conformers constrained by cyclization.

Results

Integrating our efficient peptide 3D conformation sampling algorithm MODPEP2.0 and knowledge-based scoring function ITScorePP, we have proposed an extended version of our hierarchical peptide docking algorithm, named HPEPDOCK2.0, to predict the binding modes of the peptide cyclized through a disulfide against a protein. Our HPEPDOCK2.0 approach was extensively evaluated on diverse test sets and compared with the state-of-the-art cyclic peptide docking program AutoDock CrankPep (ADCP). On a benchmark dataset of 18 cyclic peptide-protein complexes, HPEPDOCK2.0 obtained a native contact fraction of above 0.5 for 61% of the cases when the top prediction was considered, compared with 39% for ADCP. On a larger test set of 25 cyclic peptide-protein complexes, HPEPDOCK2.0 yielded a success rate of 44% for the top prediction, compared with 20% for ADCP. In addition, HPEPDOCK2.0 was also validated on two other test sets of 10 and 11 complexes with apo and predicted receptor structures, respectively. HPEPDOCK2.0 is computationally efficient and the average running time for docking a cyclic peptide is about 34 min on a single CPU core, compared with 496 min for ADCP. HPEPDOCK2.0 will facilitate the study of the interaction between cyclic peptides and proteins and the development of therapeutic cyclic peptide drugs.

Availability and implementation

http://huanglab.phys.hust.edu.cn/hpepdock/.

Supplementary information

Supplementary data are available at Bioinformatics online.
GenBank as a source to monitor and analyze Host-Microbiome data
Authors: Ramanan Vivek , Mechery Shanti , Sarkar Indra Neil
Published: July 2022

Motivation

Microbiome datasets are often constrained by sequencing limitations. GenBank is the largest collection of publicly available DNA sequences, which is maintained by the National Center of Biotechnology Information (NCBI). The metadata of GenBank records are a largely understudied resource and may be uniquely leveraged to access the sum of prior studies focused on microbiome composition. Here, we developed a computational pipeline to analyze GenBank metadata, containing data on hosts, microorganisms and their place of origin. This work provides the first opportunity to leverage the totality of GenBank to shed light on compositional data practices that shape how microbiome datasets are formed as well as examine host–microbiome relationships.

Results

The collected dataset contains multiple kingdoms of microorganisms, consisting of bacteria, viruses, archaea, protozoa, fungi, and invertebrate parasites, and hosts of multiple taxonomical classes, including mammals, birds and fish. A human data subset of this dataset provides insights to gaps in current microbiome data collection, which is biased towards clinically relevant pathogens. Clustering and phylogenic analysis reveals the potential to use these data to model host taxonomy and evolution, revealing groupings formed by host diet, environment and coevolution.

Availability and implementation

GenBank Host-Microbiome Pipeline is available at https://github.com/bcbi/genbank_holobiome. The GenBank loader is available at https://github.com/bcbi/genbank_loader.

Supplementary information

Supplementary data are available at Bioinformatics online.
In Search of Social justice-informed Services: A Research Agenda for the Study of Resistance to Neo-managerialism
Authors: Timor-Shlevin Shachar , Hermans Koen , Roose Rudi
Published: July 2022

One of the main characteristics of social work is the fundamental tension between the profession’s conservative and critical rationales. In the last three decades, this tension has informed the development of critical resistance to the deprofessionalisation effects of neo-managerial rationality, which establishes cost reduction and fiscal accountability as the basis for professional practice. However, the theoretical conceptualisation of such critical resistance is caught between minor and major operations, both of which are considered insufficient. Addressing this gap, this article builds on the theoretical framework of radical incrementalism to develop a research agenda for the future study of resistance processes, which we conceptualise as operating in the middle range of a power exertion scale, between minor and major forms of operation. We portray the operation of resistance in the middle range of such a power exertion scale and offer a research agenda that includes relevant research directions and methodological considerations. In this way, the article suggests new ways of understanding, conceptualising and operating resistance to enable further development of the social justice-informed professionalisation of social work.
Fear conditioning as a pathogenic mechanism in the postural tachycardia syndrome
Authors: Norcliffe-Kaufmann Lucy , Palma Jose-Alberto , Martinez Jose , Camargo Celeste , Kaufmann Horacio
Published: July 2022

Despite its increasing recognition and extensive research, there is no unifying hypothesis on the pathophysiology of the postural tachycardia syndrome. In this cross-sectional study, we examined the role of fear conditioning and its association with tachycardia and cerebral hypoperfusion on standing in 28 patients with postural tachycardia syndrome (31 ± 12 years old, 25 females) and 21 matched controls. We found that patients had higher somatic vigilance (P = 0.0167) and more anxiety (P < 0.0001). They also had a more pronounced anticipatory tachycardia right before assuming the upright position in a tilt-table test (P = 0.015), a physiological indicator of fear conditioning to orthostasis. While standing, patients had faster heart rate (P < 0.001), higher plasma catecholamine levels (P = 0.020), lower end-tidal CO2 (P = 0.005) and reduced middle cerebral artery blood flow velocity (P = 0.002). Multi-linear logistic regression modelling showed that both epinephrine secretion and excessive somatic vigilance predicted the magnitude of the tachycardia and the hyperventilation. These findings suggest that the postural tachycardia syndrome is a functional disorder in which standing may acquire a frightful quality, so that even when experienced alone it may elicit a fearful conditioned response. Heightened somatic anxiety is associated with and may predispose to a fear-conditioned hyperadrenergic state when standing. Our results have therapeutic implications.