bluuebunny/crossref_metadata_2025 huggingface dataset:
Code-switching, agency, and the answer possibility space of Spanish-English bilinguals
Authors: Raymond Chase Wesley
Published: November 2023

The present study addresses the implicit monolingual bias in our understanding of polar question-answer
sequences by examining them in bilingual conversation. Drawing upon a corpus of naturally-occurring conversational data
amongst native Spanish-English bilinguals in the southwestern United States, I target and explore the ‘fit’ between polar
questions and answers in this community of practice. In this report, I focus specifically on the dimension of language
(non-)concordance between particle answers and the questions they address. Evidence is offered that speakers
produce response particles that are concordant with the language of the question as the pragmatically
unmarked answer format, whereas response particles that are non-concordant with the language of the question
(i.e., ‘code-switched’) are marked, produced agentively and for cause, routinely indexing an emergent stance that is at
variance with the terms established by the question. Some possible avenues for future comparative work on the expression of
agency in question-answer sequences are explored in the Conclusion.
Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria–ER contacts
Authors: Cardoen Ben , Vandevoorde Kurt R. , Gao Guang , Ortiz-Silva Milene , Alan Parsa , Liu William , Tiliakou Ellie , Vogl A. Wayne , Hamarneh Ghassan , Nabi Ivan R.
Published: November 2023

Identification and morphological analysis of mitochondria–ER contacts (MERCs) by fluorescent microscopy is limited by subpixel resolution interorganelle distances. Here, the membrane contact site (MCS) detection algorithm, MCS-DETECT, reconstructs subpixel resolution MERCs from 3D super-resolution image volumes. MCS-DETECT shows that elongated ribosome-studded riboMERCs, present in HT-1080 but not COS-7 cells, are morphologically distinct from smaller smooth contacts and larger contacts induced by mitochondria–ER linker expression in COS-7 cells. RiboMERC formation is associated with increased mitochondrial potential, reduced in Gp78 knockout HT-1080 cells and induced by Gp78 ubiquitin ligase activity in COS-7 and HeLa cells. Knockdown of riboMERC tether RRBP1 eliminates riboMERCs in both wild-type and Gp78 knockout HT-1080 cells. By MCS-DETECT, Gp78-dependent riboMERCs present complex tubular shapes that intercalate between and contact multiple mitochondria. MCS-DETECT of 3D whole-cell super-resolution image volumes, therefore, identifies novel dual control of tubular riboMERCs, whose formation is dependent on RRBP1 and size modulated by Gp78 E3 ubiquitin ligase activity.
Vector rogue waves and their dynamics in the nonlocal three-component Manakov system
Authors: Jiang Yongmei , Wang Xiubin
Published: November 2023

In this work, by combining the Darboux transformation and variable separation technique, we generate and discuss a semirational vector solution to the nonlocal three-component Manakov system. The semirational solution is expressed in separation-of-variables form. The semirational vector solution exhibits breathers and rogue waves on a bright-dark soliton background. Moreover, the dynamic behaviors of the semirational vector solutions are discussed with some graphics. Our results may contribute to explaining and enriching the corresponding rogue wave phenomena emerging in nonlocal wave modes.
The residual symmetry, Bäcklund transformations, CRE integrability and interaction solutions: (2+1)-dimensional Chaffee–Infante equation
Authors: Günhan Ay Nursena , Yaşar Emrullah
Published: November 2023

In this paper, we consider the (2+1)-dimensional Chaffee–Infante equation, which occurs in the fields of fluid dynamics, high-energy physics, electronic science etc. We build Bäcklund transformations and residual symmetries in nonlocal structure using the Painlevé truncated expansion approach. We use a prolonged system to localize these symmetries and establish the associated one-parameter Lie transformation group. In this transformation group, we deliver new exact solution profiles via the combination of various simple (seed and tangent hyperbolic form) exact solution structures. In this manner, we acquire an infinite amount of exact solution forms methodically. Furthermore, we demonstrate that the model may be integrated in terms of consistent Riccati expansion. Using the Maple symbolic program, we derive the exact solution forms of solitary-wave and soliton-cnoidal interaction. Through 3D and 2D illustrations, we observe the dynamic analysis of the acquired solution forms.
Theoretical Investigation of Pressure Dependent Structural and Elastic Properties of MnSi Compound
Authors: Malviya Sheetal , Jain Arvind , Dixit R. C. , Kaurav Netram
Published: November 2023

MnSi is a metallic compound that exhibits a structural phase transition as a function of pressure. At ambient conditions, MnSi has a cubic structure such as NaCl type crystal structure. However, at high pressures, it undergoes a structural phase transition to a CsCl type crystal structure. The pressure-dependent structural phase transition in MnSi has been studied using various experimental and theoretical techniques. In the present work, we have used an efficient inter-ionic potential approach to predict pressure dependent structural phase change and associated volume collapse in MnSi. Therein, the potential includes the long-range Coulomb, van der Waals (vdW) interaction, and the short-range repulsive interaction up to second neighbour ions. It has been demonstrated that the Hafemeister and Flygare approach successfully evaluates the equation of state for change in volume with respect to applied pressure. We have identified a structural phase transition from B1(NaCl) type structure to B2 (CsCl) type structure in this compound. The estimated value of phase transition pressure (Pt) is 42 GPa, which is consistent with the available reported data. The identified first order phase transformation showed a volume collapse of about 10% in the vicinity of transition. In addition, we have also investigated second order of elastic constants for MnSi compound.
Atomic Diffusion Mechanism in BF2+ Implanted and Annealed n-Fz Si junction using Analytical Approach: Comparison with 2-D TCAD Process Simulation Result
Authors: Chatterjee Puspita , Srivastava Ajay K
Published: November 2023

Ion implantation controls the diffusion of the dopants inside the n-Fz Si bulk of the p+n Si microstrip detector. In order to understand about the diffusion mechanism of BF2
+ molecules/dopants into the n-Fz Si bulk of Double Sided Silicon Strip Detector (back side) for the R3B Silicon Tracker, it is essential to know the precise information about the microscopic defect introduces inside the Si lattice of the detector for the next phase upgrade of the R3B experiment. The purpose of this paper is to present the atomic transport and electrical activation behavior of implanted BF2+ molecules/dopants at an energy of 80 KeV and a dose of 1015 ion/cm2 into the n-Fz Double Sided Silicon Strip Detector for the R3B Silicon Tracker after annealing at 400 °C - 1350 °C.

The result shows the amorphous-crystalline interface position and recrystallization temperature using the results revealed from the 2-D TCAD process simulation of the Si microstrip detector.
Study of Optical Properties of Non Stoichiometric Nickel Oxide
Authors: Bhataniya Lalit Kumar , Chouhan Aakanksha , Dubey Paras
Published: November 2023

In order to create non-stoichiometric nickel oxide, the precursor was thermally decomposed at various sintering temperatures up to 1100 °C. Structure of synthesis compound was characterization by X-ray diffraction method along with ritvield refinement. In UV-visible spectroscopy the band gap of the non-stoichiometric nickel oxide due to excitation of electrons can be obtained. The presence of Ni3+ ions in the oxide lattice shows charge transfer transition, with the consequent absorption in the visible region, which is mainly due to different ratio of Ni3+ and Ni2+ ions in the sample. These data were analysed, and it was discovered that by altering the decomposition temperature, the defects present in the non-stoichiometric get held up, causing neighbouring divalent nickel ions to become Ni3+ due to charge transfer process.
Synthesis of 7-Membered Heterocyclic Compounds and Their Biological Activity
Authors: Rana Rashmi , Ansari Anam
Published: November 2023

Heterocyclic compounds are an important class of organic compound. Owing to their usefulness in synthetic processes, numerous heterocyclic compounds are currently known, and this number is growing quickly. The uses of heterocyclic compounds are numerous. They are mostly used as veterinary goods, agricultural chemicals, and medications. Additionally, they are used as sanitizers, cleansers, antioxidants, corrosion inhibitors, co-polymers, and dye ingredients. The ring of a heterocyclic compound contains at least two unique components as members. On such a cyclic ring, the frequent heteroatoms are oxygen, nitrogen as well as sulphur. The most stable heterocyclic compound is a 7-membered ring over other heterocyclic compounds. Hence this article specifically reviews the synthesization of 7-membered heterocyclic compounds and their biological activity. The set of reviewed articles chosen in the current attempt is selected after the rigorous process of evaluating each aspect related to the 7-membered heterocyclic compound. This review paper will be of great interest to scientific groups working in the field of organic molecule synthesis and development.
Modeling embodied intelligence: can we capture its essence by modeling internal and external interactions?
Authors: Laschi Cecilia
Published: November 2023

In soft robotics, embodied intelligence leverages on the compliance of the physical body to let sensory-motor behaviour emerge from the interaction with the environment. Soft robot modeling often focuses on the effect of actuation on the deformable body. Can we model and describe mathematically the deformations of a soft robot body under external interaction forces? Would that capture the essence of embodied intelligence? We argue that addressing this challenge, in an interdisciplinary effort, would make embodied intelligence and soft robotics take a leap forward and transition from a trial-and-error pioneering phase to a model-informed discipline era.
A Task-to-Intelligence Mapping: When is embodied intelligence worth designing?
Authors: Carter Aja , Chen Wei-Hsi , Misra Shivangi , Sung Cynthia
Published: November 2023

While there has been much work in the space of embodied intelligence, we as a field have struggled to define what exactly embodied intelligence is and how it should be used. In this paper, we propose that there are multiple types of embodied intelligence, and that these different types of embodied intelligence are suited to different types of tasks. We introduce a method for classifying tasks according to their objective and occurrence, and we describe how existing work in embodied intelligence fits into this framework. We hope that this proposed framework will initiate a discussion to more formally think about the role that embodied intelligence plays and the value that it brings to engineering and robotics.
Heterogeneous Underwater Swarm of Robotic Fish
Authors: Iacoponi S. , Hanbaly M. , Infanti A. , Andonovski B. , Mankovskii N. , Zhilin I. , Renda F. , Stefanini C. , Masi G. De
Published: November 2023

Underwater robotics is prevalent today in the field of undersea surveys. The current single-agent approach struggles to cover surveys of large areas, especially when visual analyses are required. Applications of underwater multi-robots fleets need to manage the coordination of the agents, which in turn stresses the already limited capabilities of underwater localization and communication. We propose a concept for a multilayered control architecture, which leverages visual recognition and swarm behavior to negotiate the coordination requirements of the single agent while retaining a significant level of control over the fleet of vehicles as a whole. This is obtained by including multiple control layers, paired with a heterogeneous composition of vehicles.
Task-Mediated Design: A latent space for dexterous soft robotic design
Authors: Pinskier Josh , Howard David
Published: November 2023

Soft robotics has created a paradigm shift within robotic grasping and manipulation. Rather than using complex control policies and path planning methods to undertake grasp objects, soft robots use their embodied intelligence to deform around an object and securely hold it. Yet despite major advances in the field in recent years, there remains an absence of practical methods for designing new high performing soft manipulators. In this perspective, we propose a novel task-mediated approach to soft manipulator design and discuss its application to robust and dexterous manipulation. The task-mediated approach first abstracts the manipulation task into a characteristics latent space, then designs a soft robot to minimise the distance between the actual performance and characteristic latent variables. In conjunction with state-of-the-art generative design tools and simulators, this approach can accelerate the development of bespoke and general purpose manipulators
Metaphorising and bayesian inference according to biology of cognition and enaction
Authors: Valdés-Zorrilla Amaranta , Letelier Juan-Carlos , Soto-Andrade Jorge
Published: November 2023

The most accepted paradigm of brain function sustaining mathematical thinking is the “Brain as Computer” metaphor. Since the early 1970s, however, a new viewpoint based on the Biology of Cognition, created by Humberto Maturana and Francisco Varela, has slowly positioned itself as a challenger to the computer metaphor. Here, we interpret the notion of metaphorising in mathematics in the context of Biology of Cognition. Specifically, we introduce the fundamental concept of Structural Coupling, which is the mechanism by which living systems create the “objects” populating their niche by exploiting correlations in the never-ending Perception ⟲ Action loop. Furthermore, we show that how a living system decides which action to perform is the outcome of a Bayesian Inference mechanism; therefore, randomness is fundamental to living systems and not just a consequence of the mere lack of sufficient information to compute the next action. Additionally, in Bayesian inference, the underlying conditional probability distribution P(action|perception) changes by the very execution of every Perception ⟲ Action loop, performing a biased random walk according to a Hebbian-like rule. With this rich set of concepts derived from cutting-edge biology, we show that Biology of Cognition is a good fit to understand mathematical metaphorisation.
Self-organization in Piano Playing: Why Pattern Transition?
Authors: Wang Huijiang , Iida Fumiya
Published: November 2023

Over billions of years, natural lives and organs have evolved with essential self-organized life-sustaining activities such as locomotion and respiration. Biological studies have shown that the Central Pattern Generator (CPG) is the essential mechanism for such pattern transitions. Embodied intelligence is a paradigm for investigating how humans employ the decentralized controller and embodiment of the body to interact with their environment (piano). Previously piano playing robots were hard-coded to implement mechanical contact and musical generation, resulting in clumsy non-anthropomorphic keystrokes. Instead, we revisit the piano challenge by studying the biomechanical physics of the body, the self-organization of reflexive behavior, and the neuro-muscular synergy in terms of coordinated behavioral diversity and energy minimization.
From Disembodiment to Embodiment in Artificial Intelligence and Psychology - Parallels in Thinking
Authors: Macrine Sheila L , Fugate Jennifer MB
Published: November 2023

This paper briefly traces how both Computer Science and Psychology grew-in tandem-to share similar notions of Embodied Cognition. It concludes an analysis of how the two fields are uniting in their work on Embodied Artificial Intelligence, and future challenges for the field.
How to define the correct guidelines for enhanced telepresence and task embodiment in remote palpation.
Authors: Costi Leone , Iida Fumiya
Published: November 2023

Teleoperated robots have been widely accepted in several fields of medical practice, enhancing human abilities and allowing remote operation. However, such technology has not been able yet to permeate areas such as primary care and physical examination. Such applications strongly rely on the quality of the interaction between doctor and patient, and on its multimodal nature. In order to achieve remote physical examination is thus mandatory to have a good doctor-robot interface, but what does good mean? Ultimately, the goal is for the user to achieve task embodiment, making the remote task feel like the in-person one. Several research groups have proposed a wide variety of interfaces, showcasing largely different methods of control and feedback, because of the absence of design guidelines. In this work, we argue that the ideal interface for a remote task should resemble as close as possible the experience provided by the in-person equivalent, keeping in consideration the nature of the target users. To support our claims, we analyze many remote interfaces and compare them with the respective in-person task. This analysis is not limited to the medical sector, with examples such as remote abdominal surgery, but it expands to all forms of teleoperation, up to nuclear waste handling and avionics.
Unraveling the limiting factors to electron mobility in degenerately doped SnO2 thin films
Authors: Nguyen Viet Huong , Tran Thi My Hang , T.T. Ta Huong , Vuong Kha Anh , Nguyen Hoai Hue , Nguyen Thien Thanh , Nguyen Ngoc Linh , Van Bui Hao
Published: November 2023

This paper presents a comprehensive theoretical study on electron mobility in highly doped polycrystalline SnO2 thin films, a widely employed material in modern devices. Our physical model incorporates phonon-electron interaction, ionised impurity, and grain boundaries as scattering mechanisms, effectively explaining the temperature and electron density-dependent variation of electron mobility in doped polycrystalline SnO2 thin films. We highlight the significant influence of trap density at grain boundaries, the self-compensation effect, and average grain size on the theoretical limit of electron mobility. At a doping level of 1019 cm−3, the limit is estimated at 100 cm2.V−1.s−1, while for 1020 cm−3, it reduces to 50 cm2.V−1.s−1. These factors are strongly influenced by deposition conditions, including temperature, precursor chemistry, and deposition atmosphere. By analysing Hall mobility with respect to carrier density, temperature, or film thickness using our model, a better understanding of the limiting mechanisms in electron mobility can be achieved. This knowledge can guide the development of appropriate experimental strategies to enhance electron mobility in highly doped polycrystalline SnO2 films for advancing the performance of SnO2-based devices across various applications.
Transient vortex dynamics and evolution of Bose metal from a 2D superconductor on MoS2
Authors: Narayanan Sreevidya , Kamalasanan Anoop , Sunny Annu Anns , Thalakulam Madhu
Published: November 2023

The true character of physical phenomena is thought to be reinforced as the system becomes disorder-free. In contrast, the two-dimensional (2D) superconductor is predicted to turn fragile and resistive away from the limit I → 0, B → 0, in the pinning-free regime. It is intriguing to note that the very vortices responsible for achieving superconductivity by pairing, condensation, and, thereby reducing the classical dissipation, render the state resistive driven by quantum fluctuations in the T → 0. While cleaner systems are being explored for technological improvements, the 2D superconductor turning resistive when influenced by weak electric and magnetic fields has profound consequences for quantum technologies. A metallic ground state in 2D is beyond the consensus of both Bosonic and Fermionic systems, and its origin and nature warrant a comprehensive theoretical understanding supplemented by in-depth experiments. A real-time observation of the influence of vortex dynamics on transport properties so far has been elusive. We explore the nature and fate of a low-viscous, clean, 2D superconducting state formed on an ionic-liquid gated few-layered MoS2 sample. The vortex-core being dissipative, the elastic depinning, intervortex interaction, and the subsequent dynamics of the vortex-lattice leave transient signatures in the transport characteristics. The temperature and magnetic field dependence of the transient nature and the noise characteristics of the magnetoresistance confirm that quantum fluctuations are solely responsible for the Bose metal state and the fragility of the superconducting state.
Room temperature control of grain orientation via directionally modulated current pulses
Authors: Rahman Md Hafijur , Oh Hajin , Waryoba Daudi , Haque Aman
Published: November 2023

Traditional approaches to control the microstructure of materials, such as annealing, require high temperature treatment for long periods of time. In this study, we present a room temperature microstructure manipulation method by using the mechanical momentum of electrical current pulses. In particular, a short burst of high-density current pulses with low duty cycle is applied to an annealed FeCrAl alloy, and the corresponding response of microstructure is captured by using Electron Backscattered Diffraction (EBSD) analysis. We show evidence of controllable changes in grain orientation at specimen temperature around 28 °C. To demonstrate such microstructural control, we apply the current pulses in two perpendicular directions and observe the corresponding grain rotation. Up to 18° of grain rotation was observed, which could be reversed by varying the electropulsing direction. Detailed analysis at the grain level reveals that electropulsing in a specific direction induces clockwise rotation from their pristine state, while subsequent cross-perpendicular electropulsing results in an anticlockwise rotation. In addition, our proposed room temperature processing yields notable grain refinement, while the average misorientation and density of low-angle grain boundaries (LAGBs) remain unaltered. The findings of this study highlight the potentials of ‘convective diffusion’ in electrical current based materials processing science towards microstructural control at room temperature.
Depth profiling analysis of the nitriding layer formed by gas nitriding of Ti13Nb13Zr alloy
Authors: Sun Xiaolei , Song Hanke , Luo Yong
Published: November 2023

The gas nitriding of Ti13Nb13Zr alloy was performed in a pure nitrogen atmosphere at 1200 °C with different holding times. The variations in the phase constituents, microstructure, and mechanical properties of the nitriding layer with depth were characterized by SEM, XRD, and nanoindentation. Depending on the phase distributions in depth, the nitriding layer could be sequentially divided into an external nitride layer mainly consisting of TiN, an internal nitride layer consisting of TiN, Ti2N and TiN0.3, and an N diffusion region consisting of TiN0.3. The mechanical properties were closely associated with the phase constituents, where the nanohardness of the internal nitride layer, internal nitride layer N diffusion region and substrate were about 17.126±0.399, 12.120±0.386, 5.627±1.080, and 3.632±0.116 GPa, respectively. In the nitriding process, the N diffusion region containing needle-like TiN0.3 precipitates formed in the initial nitriding stage, and then the precipitates were gradually converted to the external and internal nitride layers, whose thickness increased with the nitriding time. Furthermore, the influence of the alloying element redistribution on the N diffusion mechanism was discussed.
Evaluation on frictional performance of three different oil-lubricated impregnated graphite seal rings for aircraft integrated drive generators
Authors: Qi Huiying , Wang Xiao , Zhang Rui , Chen Zhangheng , Zheng Shaokan , Jiang Tao , Xu Jimin
Published: November 2023

The frictional performance of the shaft-end graphite seal rings plays a critical role in determining the maintenance-free duration of aircraft integrated drive generators, and significantly depends on the types of graphite materials used. In this study, three types of graphite materials, including epoxy resin, metal antimony and furan resin impregnated ones, were selected for evaluation using a rotating-type tribometer. The frictional test configuration involved an actual graphite seal ring sliding against the surface of a 12Cr2Ni4A disc under the lubrication of 4050 high-temperature synthetic aerospace lubricating oil, which was highly consistent with the practical operational conditions. The frictional performance of the three different impregnated graphite seal rings, including coefficient of friction, two-dimensional (2D)/three-dimensional (3D) morphologies of wear marks and wear rate of ring mass, were quantitatively analyzed and compared. The experimental results indicated that the metal antimony-impregnated graphite seal ring behaved with the smallest coefficient of friction among the three seal rings. 2D and 3D surface roughness parameters of the metal antimony impregnated graphite seal are the smallest. The wear rate of the seal ring’s mass is only approximately 22% of that of furan resin impregnated seal ring. The corresponding investigations demonstrated that the currently employed epoxy resin-impregnated graphite seal rings could be replaced by new candidates with better frictional performance to improve the service life.
Secret learning for lung cancer diagnosis—a study with homomorphic encryption, texture analysis and deep learning
Authors: Adhikary Subhrangshu , Dutta Subhayu , Dwivedi Ashutosh Dhar
Published: November 2023

Advanced lung cancer diagnoses from radiographic images include automated detection of lung cancer from CT-Scan images of the lungs. Deep learning is a popular method for decision making which can be used to classify cancerous and non-cancerous lungs from CT-Scan images. There are many experiments which show the uses of deep learning for performing such classifications but very few of them have preserved the privacy of users. Among existing methods, federated learning limits data sharing to a central server and differential privacy although increases anonymity the original data is still shared. Homomorphic encryption can resolve the limitations of both of these. Homomorphic encryption is a cryptographic technique that allows computations to be performed on encrypted data. In our experiment, we have proposed a series of textural information extraction with the implementation of homomorphic encryption of the CT-Scan images of normal, adenocarcinoma, large cell carcinoma and squamous cell carcinoma. We have further processed the encrypted data to make it classifiable and later we have classified it with deep learning. The results from the experiments have obtained a classification accuracy of 0.9347.
Efficient and selective glycerol electrolysis for the co-production of lactic acid and hydrogen with multi-component Pt/C-zeolite catalyst
Authors: Aslam Muhammad , Navlani-García Miriam , Cazorla-Amorós Diego , Luo Hui
Published: November 2023

Among various electrochemical reactions to produce fuels and chemicals, glycerol electrolysis to co-produce hydrogen and lactic acid has received great attention. However, studies have shown the benchmark Pt based catalysts are insufficient in selectively catalysing the glycerol to lactic acid transformation, resulting in a low yield of lactic acid. Here we report a study on glycerol electrolysis with anion-exchange membrane electrode assembly electrolyser. The reaction conditions including mass transport, temperature, current density and KOH concentration were optimised, among which temperature played a significant role in facilitating the reaction rate and thermodynamics. With the optimised condition a multicomponent Pt/C-zeolite electrocatalyst system (Pt/C-CBV600) was developed and tested, which is capable to increase the lactic acid selectivity to 57.3% from the 33.8% with standalone Pt/C. Although the detailed mechanism required further investigation, it is hypothesised that the CBV600 zeolite with abundant Lewis acid surface sites can effectively bind the dihydroxyacetone intermediate, and drive the reaction towards pyruvaldehyde heterogeneously, the key step to form lactic acid.
Genetics of chilling response at early growth stage in rice: a recessive gene for tolerance and importance of acclimation
Authors: Baruah Akhil Ranjan , Bannai Hiroaki , Meija Yan , Kimura Ayumi , Ueno Haruka , Koide Yohei , Kishima Yuji , Palta Jiwan , Kasuga Jun , Yamamoto Masayuki P , Onishi Kazumitsu
Published: November 2023

Low-temperature adaptation in rice is mediated by the ability of a genotype to tolerate chilling temperatures. A genetic locus on chromosome 11 was analysed for chilling tolerance at the plumule stage in rice. The tolerant allele of A58, a japonica landrace in Japan, was inherited as a recessive gene (ctp-1A58), whereas the susceptible alleles from wild rice (Ctp-1W107) and modern variety (Ctp-1HY) were the dominant genes. Another recessive tolerant allele (ctp-1Silewah) was found in a tropical japonica variety (Silewah). Fine-mapping revealed that a candidate gene for the ctp-1 locus encoded a protein similar to the nucleotide-binding domain and leucine-rich repeat (NLR) protein, in which frameshift mutation by a 73 bp-deletion might confer chilling tolerance in ctp-1A58. Analysis of near-isogenic lines demonstrated that ctp-1A58 imparted tolerance effects only at severe chilling temperatures of 0.5 °C and 2 °C, both at plumule and seedling stages. Chilling acclimation treatments at a wide range of temperatures (8 °C–16 °C) for 72 h concealed the susceptible phenotype of Ctp-1W107 and Ctp-1HY. Furthermore, short-term acclimation treatment of 12 h at 8 °C was enough to be fully acclimated. These results suggest that the NLR gene induces a susceptible response upon exposure to severe chilling stress, however, another interacting gene(s) for acclimation response could suppress the maladaptive phenotype caused by the Ctp-1 allele. This study provides new insights for the adaptation and breeding of rice in a low-temperature environment.
DOSE-L1000: unveiling the intricate landscape of compound-induced transcriptional changes
Authors: Wang Junmin , Novick Steven
Published: November 2023

Motivation

The LINCS L1000 project has collected gene expression profiles for thousands of compounds across a wide array of concentrations, cell lines, and time points. However, conventional analysis methods often fall short in capturing the rich information encapsulated within the L1000 transcriptional dose–response data.

Results

We present DOSE-L1000, a database that unravels the potency and efficacy of compound-gene pairs and the intricate landscape of compound-induced transcriptional changes. Our study uses the fitting of over 140 million generalized additive models and robust linear models, spanning the complete spectrum of compounds and landmark genes within the LINCS L1000 database. This systematic approach provides quantitative insights into differential gene expression and the potency and efficacy of compound-gene pairs across diverse cellular contexts. Through examples, we showcase the application of DOSE-L1000 in tasks such as cell line and compound comparisons, along with clustering analyses and predictions of drug–target interactions. DOSE-L1000 fosters applications in drug discovery, accelerating the transition to omics-driven drug development.

Availability and implementation

DOSE-L1000 is publicly available at https://doi.org/10.5281/zenodo.8286375.
Skin cell-derived extracellular vesicles: a promising therapeutic strategy for cutaneous injury
Authors: Wang Min , Wu Peipei , Huang Jin , Liu Wenhui , Qian Hui , Sun Yaoxiang , Shi Hui
Published: November 2023

Wound healing refers to the healing process that occurs after the skin and other tissues are separated or damaged by internal or external forces. It is a complex combination of tissue regeneration, granulation tissue hyperplasia, and scar formation, and shows the synergistic effects of these processes. After skin damage, the environment around the wound and the cells at site of the damage respond immediately, and a range of cytokines and growth factors are released. In cutaneous injury, extracellular vesicle (EV) signaling plays a vital role in the healing process via paracrine and endocrine mechanisms. EVs are natural intercellular and inter-organ communication tools that carry various bioactive substances for message exchange. Stem cells and stem cell EVs facilitate tissue repair, showing promising potential in regenerative medicine. Nevertheless, EVs derived from specific skin tissue cells, such as epidermal cells, fibroblasts, vascular endothelial cells and inflammatory cells, also play important roles in cutaneous tissue repair. Here, we describe the characteristics of wound healing, concentrating on the production and functions of EVs derived from specific skin cells, and provide new ideas for wound therapy using EVs.
The GNAR-edge model: a network autoregressive model for networks with time-varying edge weights
Authors: Mantziou Anastasia , Cucuringu Mihai , Meirinhos Victor , Reinert Gesine
Published: November 2023

In economic and financial applications, there is often the need for analysing multivariate time series, comprising of time series for a range of quantities. In some applications, such complex systems can be associated with some underlying network describing pairwise relationships among the quantities. Accounting for the underlying network structure for the analysis of this type of multivariate time series is required for assessing estimation error and can be particularly informative for forecasting. Our work is motivated by a dataset consisting of time series of industry-to-industry transactions. In this example, pairwise relationships between Standard Industrial Classification (SIC) codes can be represented using a network, with SIC codes as nodes and pairwise transactions between SIC codes as edges, while the observed time series of the amounts of the transactions for each pair of SIC codes can be regarded as time-varying weights on the edges. Inspired by Knight et al. (2020, J. Stat. Softw., 96, 1–36), we introduce the GNAR-edge model which allows modelling of multiple time series utilizing the network structure, assuming that each edge weight depends not only on its past values, but also on past values of its neighbouring edges, for a range of neighbourhood stages. The method is validated through simulations. Results from the implementation of the GNAR-edge model on the real industry-to-industry data show good fitting and predictive performance of the model. The predictive performance is improved when sparsifying the network using a lead–lag analysis and thresholding edges according to a lead–lag score.
A case report of constrictive pericarditis following COVID-19 vaccination
Authors: Bain Eric , Guglin Maya
Published: November 2023

Background

COVID-19 infection and the COVID-19 vaccines have been associated with rare cases of pericarditis. We present a case of constrictive pericarditis (CP) following the vaccine.

Case summary

A 19-year-old healthy male started having progressive abdominal pain, emesis, dyspnoea, and pleuritic chest pain 2 weeks after the second dose of Pfizer vaccine. Computed tomography angiography chest revealed bilateral pleural effusions and pericardial thickening with effusion. Cardiac catheterization showed ventricular interdependence. Cardiac magnetic resonance (CMR) showed septal bounce and left ventricular tethering suggestive of CP. A total pericardiectomy was performed with significant symptom improvement. Pathology showed chronic fibrosis without amyloid, iron deposits, or opportunistic infections. Patient had Epstein–Barr Virus (EBV) viraemia 825 IU/mL and histoplasmosis complement-fixation positive with negative serum and urine antigen. Hypercoagulable panel and infectious workup were otherwise negative. The patient had resolution of cardiac symptoms at 3 months of follow-up.

Discussion

The patient developed progressive symptoms within 2 weeks of his second Pfizer vaccine. Echocardiogram and CMR had classic signs of CP, and pericardial pathology confirmed fibrotic pericardium. The patient had no prior surgery, thoracic radiation, or bacterial infection. Epstein–Barr Virus viraemia was thought to be reactionary, and histoplasmosis complement likely represented chronic exposure. The timing of symptoms and negative multidisciplinary workup raises the suspicion for COVID vaccine–induced CP. The COVID vaccines benefits far exceed the risks, but complications still can occur. Practitioners should have a high index of suspicion to allow prompt diagnosis of CP.
Implant, assessment, and management of conduction system pacing
Authors: Vernooy Kevin , Keene Daniel , Huang Weijian , Vijayaraman Pugazhendhi
Published: November 2023

His bundle pacing and left bundle branch pacing, together referred to as conduction system pacing, have (re)gained considerable interest over the past years as it has the potential to preserve and/or restore a more physiological ventricular activation when compared with right ventricular pacing and may serve as an alternative for cardiac resynchronization therapy. This review manuscript dives deeper into the implantation techniques and the relevant anatomy of the conduction system for both pacing strategies. Furthermore, the manuscript elaborates on better understanding of conduction system capture with its various capture patterns, its potential complications as well as appropriate follow-up care. Finally, the limitations and its impact on clinical care for both His bundle pacing and left bundle branch pacing are being discussed.
Frontiers in conduction system pacing: treatment of long PR in patients with heart failure
Authors: Kaza Nandita , Keene Daniel , Vijayaraman Pugazhendhi , Whinnett Zachary
Published: November 2023

Patients with heart failure who have a prolonged PR interval are at a greater risk of adverse clinical outcomes than those with a normal PR interval. Potential mechanisms of harm relating to prolonged PR intervals include reduced ventricular filling and also the potential progression to a higher degree heart block. There has, however, been relatively little work specifically focusing on isolated PR prolongation as a therapeutic target. Secondary analyses of trials of biventricular pacing in heart failure have suggested that PR prolongation is both a prognostic marker and a promising treatment target. However, while biventricular pacing offers an improved activation pattern, it is nonetheless less physiological than native conduction in patients with a narrow QRS duration, and thus, may not be the ideal option for achieving therapeutic shortening of atrioventricular delay. Conduction system pacing aims to preserve physiological ventricular activation and may therefore be the ideal method for ventricular pacing in patients with isolated PR prolongation. Acute haemodynamic experiments and the recently reported His-optimized pacing evaluated for heart failure (HOPE HF) Randomised Controlled Trial demonstrates the potential benefits of physiological ventricular pacing on patient symptoms and left ventricular function in patients with heart failure.
Promoter insertion leads to polyembryony in mango — a case of convergent evolution with citrus
Authors: Yadav Chandra Bhan , Rozen Ada , Eshed Ravit , Ish-Shalom Mazal , Faigenboim Adi , Dillon Natalie , Bally Ian , Webb Matthew , Kuhn David , Ophir Ron , Cohen Yuval , Sherman Amir
Published: November 2023

Sexual reproduction in plants is the main pathway for creating new genetic combinations in modern agriculture. In heterozygous plants, after the identification of a plant with desired traits, vegetative propagation (cloning) is the primary path to create genetically uniform plants. Another natural plant mechanism that creates genetically uniform plants (clones) is apomixis. In fruit crops like citrus and mango, sporophytic apomixis results in polyembryony, where seeds contain multiple embryos, one of which is sexually originated and the others are vegetative clones of the parent mother tree. Utilizing the mango genome and genetic analysis of a diverse germplasm collection, we identified MiRWP as the gene that causes polyembryony in mango. There is a strong correlation between a specific insertion in the gene’s promoter region and altered expression in flowers and developing fruitlets, inducing multiple embryos. The MiRWP gene is an ortholog of CitRWP that causes polyembryony in citrus. Based on the data, we speculate that promoter insertion events, which occurred independently in citrus and mango, induced nucellar embryogenesis. The results suggest convergent evolution of polyembryony in the two species. Further work is required to demonstrate the utility of these genes (mango and citrus) in other biological systems as a tool for the clonal production of other crops.
Physiological and molecular bases of the boron deficiency response in tomatoes
Authors: Li Junjun , Fan Huihui , Song Qianqian , Jing Lili , Yu Hao , Li Ruishan , Zhang Ping , Liu Fei , Li Weimin , Sun Liangliang , Xu Jin
Published: November 2023

Boron is an essential microelement for plant growth. Tomato is one of the most cultivated fruits and vegetables in the world, and boron deficiency severely inhibits its yield and quality. However, the mechanism of tomato in response to boron deficiency remains largely unclear. Here, we investigated the physiological and molecular bases of the boron deficiency response in hydroponically grown tomato seedlings. Boron deficiency repressed the expression of genes associated with nitrogen metabolism, while it induced the expression of genes related to the pentose phosphate pathway, thereby altering carbon flow to provide energy for plants to cope with stress. Boron deficiency increased the accumulation of copper, manganese and iron, thereby maintaining chlorophyll content and photosynthetic efficiency at the early stage of stress. In addition, boron deficiency downregulated the expression of genes involved in cell wall organization and reduced the contents of pectin and cellulose in roots, ultimately retarding root growth. Furthermore, boron deficiency markedly altered phytohormone levels and signaling pathways in roots. The contents of jasmonic acid, jasmonoy1-L-isoleucine, trans-zeatin riboside, abscisic acid, salicylic acid, and SA glucoside were decreased; in contrast, the contents of isopentenyladenine riboside and ethylene precursor 1-aminocyclopropane-1-carboxylic acid were increased in the roots of boron-deficient tomato plants. These results collectively indicate that tomato roots reprogram carbon/nitrogen metabolism, alter cell wall components and modulate phytohormone pathways to survive boron deficiency. This study provides a theoretical basis for further elucidating the adaptive mechanism of tomato in response to boron deficiency.
The Spirit of the Convention and the Letter of the Colony: Refugees Defining States in a British Overseas Territory
Authors: Demetriou Olga
Published: November 2023

Whereas asylum policy is predicated on the assumption that states define refugees, this paper examines how refugees define states. Through the legal case of refugees stranded on a British military base in Cyprus since 1998, I show how refugees and the states that grant them or deny them protection become co-constitutive. The processes involved in judicial activism delineate the modalities through which sovereign governance and refugee agencies operate. I argue that modalities of sovereignty (colonialism, exceptionalism, and diplomacy) interact with modalities of agency (protest, vulnerability, and endurance) to redefine issues of refugee protection, state sovereignty, and externalization of migration management. The case shows the risks that denial of protection entails for states and not just refugees. Methodologically, I propose that a nuanced, ground-level understanding of the role of law in activism allows us a clearer view to these imbrications of sovereign governance and agency, and thus to the ambivalent and multivalent aspects of activism.
109 Animal Behavior Analysis Using Unsupervised Machine Learning Techniques
Authors: Liu Jiefei , Bailey Derek W , Cao Huiping , Son Tran Cao , Tobin Colin T
Published: November 2023

With recent technological advances, Global Positioning Systems (GPS) and other tracking sensors can collect large amounts of data and transfer information to the cloud and then to producers to remotely monitor livestock health and well-being. Currently, supervised machine learning, such as random forest and linear or quadratic discriminant analysis techniques are used to develop algorithms to identify changes in animal behavior that may be associated with well-being concerns. Supervised machine learning requires behavior observation of monitored animals and may hinder normal expression. However, recording behavioral observations is time consuming and expensive. Our goal was to design a new unsupervised machine learning framework to identify animal behavior without the utilization of human observations. The framework contains two steps. The first step is to segment the tracking data of the animal using time series segmentation, and the second step is to group the segments into clusters where each cluster represents one type of behavior. To validate the applicability of our proposed framework, we utilize GPS tracking data collected at 2-minute intervals from eight cows from May 28 to June 22, 2018, in a 1096 ha rangeland pasture near Prescott, Arizona. After extensive experiments, our framework can partition the movement of the cow using the speed, direction, and distance of the cow from water. These segments were grouped into meaningful behavior clusters using clustering analysis. Speed was the most successful feature for clustering into behaviors. Results are similar to approaches based only on expert knowledge, that rely on speed for classification. Our study demonstrated that we can directly use unlabeled data to group animal behaviors from GPS tracking data. The proposed unsupervised two-step framework allows the analysis of cattle tracking data without direct human observation of behaviors. It is applicable for analyzing the immense amount of data that can be obtained from real-time tracking and sensor devices.
44 Developing New Traits Using Precision Breeding Tools
Authors: Sonstegard Tad S
Published: November 2023

Genome editing in the genetic stocks of food animals has tremendous potential as a tool for genetic improvement best suited to introduce traits not readily available for intensive selection in commercial breeding populations, especially those affecting disease resistance and adaptation to climate. To date, gene-editing has been used to alter prolactin receptor and produce heat-tolerant, registered Angus for commercial production of semen and embryos that rapidly improves efficient quality beef production in the tropics. More recently, genome alterations based on rationale design have been tested to demonstrate host resistance to porcine reproductive and respiratory syndrome virus and bovine viral diarrhea virus in swine and cattle, respectively. This presentation will highlight the results of these new traits to breed healthier commercial animals that will eventually change global market dynamics of livestock production.