bluuebunny/crossref_metadata_2025 huggingface dataset:
Initiative global NILS control in source and mask optimization for process window enhancement
Authors: Xu Yiduo , Peng Fei , Song Yi , Zhao Yan
Published: February 2023

Semiconductor processing is becoming more challenging as integrated circuit dimensions shrink. An increasing number of technologies are being developed for the purpose of ensuring pattern fidelity, and source and mask optimization (SMO) method has outstanding performances. In recent times, owing to the development of the process, more attention has been paid to the process window (PW). As a crucial parameter in lithography, the normalized image log slope (NILS) is strongly correlated with the PW. However, previous methods ignored the NILS in the inverse lithography model of the SMO. They regarded the NILS as the measurement index for forward lithography. This implies that the optimization of the NILS is the result of passive rather than active control, and the final optimization effect is unpredictable. In this study, the NILS is introduced in inverse lithography. The initial NILS is controlled by adding a penalty function to ensure that it continuously increases, thus increasing the exposure latitude and enhancing the PW. For the simulation, two masks typical of a 45-nm-node are selected. The results indicate that this method can effectively enhance the PW. With guaranteed pattern fidelity, the NILS of the two mask layouts increase by 16% and 9%, and the exposure latitudes increase by 21.5% and 21.7%.
Optimizing spatio-temporal properties for an efficient source of collinear SPDC photons
Authors: Omshankar  , Kumar Ramesh , Ghosh Joyee
Published: February 2023

Here we theoretically study the spatio-temporal properties of the photons emitted from a narrowband (~ 0.18 nm) type-II spontaneous parametric down-conversion source for a collinear configuration with no/negligible walk-off in a periodically-poled potassium titanyl phosphate (ppKTP) crystal.
Thermal Management and Thermopower Waves by Anisotropic Carbon Nanomaterials
Authors: Baik Seunghyun
Published: February 2023

This talk introduces thermal management and thermoelectric energy conversion researches carried out in my group. Firstly, a recent progress about the grain structure-dependent thermal conductivity characterization of graphene, which was carried out by the optothermal Raman technique, will be discussed. We have achieved high electrical conductivity of polymer matrix composites by employing carbon nanomaterials and silver nanostructures [1-4]. This filler combination was also successful in providing high thermal conductivity (160 W/mK) in applications of polymeric thermal interface materials [5]. Secondly, the concept of thermopower waves, where chemical energy is directly converted into electricity, will be introduced [6]. The exothermic chemical reaction rate of adsorbed fuel could be controlled by anisotropic thermal property of carbon conduits [6,7]. The steep temperature gradient at the reaction front generated thermoelectric power waves [6]. Higher Seebeck coefficient materials have been actively investigated in the past to achieve greater peak voltage and specific power [8]. However, we recently employed the chemical potential gradient as a key mechanism to improve thermal to electrical conversion performance [8]. Unprecedented high maximum peak voltage (8 V) and volume-specific power (0.11 W mm−3) were demonstrated using n-type single-crystalline Bi2Te3 substrate and nitrocellulose fuel [8].
Enhanced THz Nonlinearity in Graphene and Graphene-based Materials
Authors: Rotermund Fabian
Published: February 2023

Graphene, a two-dimensional crystal of carbon atoms arranged in a hexagonal lattice, has attracted a great attention due to its outstanding mechanical, thermal and electronic properties. In addition, graphene shows a strong tunable light-matter interaction that depends on the Fermi level. For practical use of graphene in broadband nonlinear photonic applications, however, substantial increases of the light-matter interaction strength will be required while preserving the promising features of monolayers, as the interaction of light with a single atomic layer is limited due to the extremely short interaction length and low density of state, particularly for the long-wavelength region.
Large optical anisotropy in deformed rubber composites with conductive fillers revealed by terahertz polarization spectroscopy
Authors: Okano Makoto , Fujii Misako , Watanabe Shinichi
Published: February 2023

Terahertz time-domain spectroscopy (THz-TDS) is a emerging and powerful technique for investigating polymeric materials, because terahertz wave can penetrate visibly opaque polymers and the intermolecular vibration mode of polymers exists in the terahertz frequency range. Recently, a polarization sensitive (PS) THz-TDS technique has been developed and improved[1–4]. The PS THz-TDS enables us to reveal the anisotropic optical responses due to the orientation of the molecular chains and the conductive additives[5,6]. In particular, we discovered that rubber materials with conductive carbon black (CB) fillers shows strong anisotropy in the dielectric responses due to the orientation distribution of the CB aggregates, and their anisotropy is strongly modulated by the mechanical stretching[6]. In this paper, we revealed the anisotropic dielectric responses in the deformed rubber-filler composites using the effective medium approximation (EMA)[7]. Our theoretical analysis based on the EMA indicates that the large optical anisotropy in deformed rubbers is strongly linked to the internal filler network.
Solving intractable problems with coherent Ising machine
Authors: Takesue Hiroki , Inagaki Takahiro , Inaba Kensuke , Honjo Toshimori , Ikuta Takuya , Uchiyama Hiroyuki , Enbutsu Koji , Umeki Takeshi , Kasahara Ryoichi
Published: February 2023

We introduce the recent progress of coherent Ising machine (CIM), which finds solutions to complex combinatorial optimization problems using a network of degenerate optical parametric oscillators (DOPO). We describe our effort to generate time-multiplexed DOPOs using long-distance fiber cavities including telecom-band phase sensitive amplifiers [1-4]. We then present our experiments where we found solutions to complex combinatorial optimization problems using a CIM with measurement-feedback scheme [5]. Finally, a future perspective of the CIM project will briefly described.
Tying Knots in a Quantum Fluid
Authors: Hall David S. , Ray Michael , Tiurev Konstantin , Ruokokoski Emmi , Gheorghe Andrei Horia , Möttönen Mikko
Published: February 2023

Knots are familiar entities that appear at a captivating nexus of art, technology, mathematics, and science. They have recently attracted significant experimental interest, in contexts ranging from knotted DNA [1] and nanostructures [2] to nontrivial vortex knots in classical fluids [3]. Within classical field theories [4], knots have been proposed as the basis of fundamental particles, as well as explaining diverse persistent phenomena such as atoms and molecules [5].
Phase separation dynamics of two-component Bose-Einstein condensates in various optical trap shapes
Authors: Shibayama Hitoshi , Torii Aki , Shibata Kosuke , Eto Yujiro , Saito Hiroki , Hirano Takuya
Published: February 2023

It is known theoretically and experimentally that multi-component Bose-Einstein condensates exhibit phase separation and form the spatial structure of spin domains [1], and expected to be a versatile source of intricate non-equilibrium pattern formation dynamics. The formation of various phase separation dynamics by varying potential shapes was theoretically predicted [2]. We investigate the dynamics of phase-separating two-component condensates in various optical trap shapes.
Electrically controllable random laser with dye-doped liquid crystals inside the capillary fiber
Authors: Lin Ja-Hon , Wu Jin-Jei , Jian Li-Hao , Tsay Shwu-Yun , Chen Yao-Hui
Published: February 2023

Owing to the intrinsic birefringence of LCs, the characteristic of random lasers (RLs) have attracted considerable attention by infilling the nematics LCs (NLCs) or polymer dispersed LCs (PDLCs), as a scattering materials, inside the glass cell, capillary tube and the hollow core fiber to produce multiple light scattering [1-3]. Unlike other scattering materials, LCs can be easily modulation through the external signals, like electric filed, magnetic field, stress, temperature and so on. Through the modulation of LCs by the temperature, the manipulation of output characteristic of RLs has been investigated previously [1-3]. In this work, the alternative characteristics from RL produced by infilling the NLC inside the single core capillary was demonstrated through the applied sinusoidal voltage and analyzed by the applied sinusoidal voltage.
Observation of Edge States in Nanoscale Topological Photonic Crystals
Authors: Miyake Hirokazu , Bank Sabyasachi , DeGottardi Wade , Waks Edo , Hafezi Mohammad
Published: February 2023

Topological photonics is a burgeoning subfield of optics, inspired by the discovery of topological insulators in condensed matter [1]. A striking feature of such materials is the existence of edge modes robust against disorder. Such modes are particularly attractive for chip-scale nanophotonic systems for telecommunications [2]. Another appeal is that directional edge states can be interfaced with quantum emitters to realize novel many-body systems such as the fractional quantum Hall state [3]. Building upon previous work [4], we present a new design for an all-dielectric nanoscale topological photonic crystal and present experimental results consistent with the existence of edge states.
Photocatalysis of layered MoS2 prepared by sonication in a mixed-solvent
Authors: Tang Jingmin , Sakamoto Masanori , Wang Yufeng , Saitow Ken-ichi
Published: February 2023

Molybdenum disulfide (MoS2) composed of layer structure attracts much attention as a semiconductor material, whose band gap energy is changed from 1.29 eV as an indirect transition to 1.85 eV as a direct one, by changing the number of layers. Here, we show the exfoliation of MoS2 using sonication in a mixed solvent (H2O and ethanol). The results of Raman spectra and atomic force microscope and transmission electron microscope images reveal that the exfoliated MoS2 is composed of a few layers. Photocatalysis of the prepared MoS2 was investigated by the degradation of a dye solution of methyl orange (MO) by irradiating light at the wavelength of 450 nm. As a result, the dye solution became colorless under the existence of the layered MoS2 as a function of irradiation time. Note that the absorption band of MO disappears at around 460 nm, whereas a new band emerges at around 240 nm. This new band is considered as a hydrazine molecule, which can be produced from the photocatalytic reaction via the decomposition of MO.
Si waveguide AWG using local rib waveguide MMI coupler structure at slab-array interface
Authors: Okayama Hideaki , Onawa Yosuke , Shimura Daisuke , Yaegashi Hiroki , Sasaki Hironori
Published: February 2023

We have reported a low loss Si wire arrayed waveguide grating (AWG) using parabolic rib waveguide taper [1] to realize 100GHz-class channel spacing. We proposed recently a more simple structure using multi-mode interference coupler with minimum terrace area [2] for loss reduction. In this report we demonstrate an experimental results showing lower loss obtained by foundry dependent improved fabrication process for the latter device.
Observation of Optical Bistability in Oppositely Directed Coupler
Authors: Nithyanandan K.
Published: February 2023

Nonlinear directional couplers (NDCs) find wide interest in optical communication system because of its potential application in signal processing including optical switching and logic operation. In couplers, if any one of the channel of NDCs is replaced with negative index material (NIM), then the coupler is called as oppositely directed coupler (ODC) because of the opposite direction of input and output fields. The electromagnetic wave entering in one channel of the coupler leave through other channel in opposite direction. Optical bistability (OB) is a nonlinear phenomenon observed in optical systems such that, the system possesses two output intensities for the same input intensity. The importance of optical bistability arises due to its potential application for the development of devices such as optical switches, memories, and amplifiers. The primary requirements of OB are the intensity dependent refractive index and optical feedback mechanism. A two core directional coupler with channels made of nonlinear and homogeneous materials is not bistable. However, ODC shows the phenomenon of OB and admit gap solitons due to effective feedback mechanism in NIM channel arising as a result of opposite directionality of phase velocity and energy flow.
Transmission-type active amplitude modulator with indium tin oxides
Authors: Lee Yohan , Kim Sun-Je , Lee Byoungho
Published: February 2023

Recent studies have focused on the demonstration of active nano-devices whose optical properties can be controlled electrically for applications. Studies using electro-optical materials, such as graphene, phase change materials, and transparent conducting oxides have been reported [1-3]. In particular, indium tin oxides (ITOs) have attracted a lot of attention owing to outstanding electro-optical characteristics, where the refractive index change reaches unity if biased in near-infrared range. However, the thickness of charge accumulation layer of which the refractive index changes is about only 1 nm when electric field is applied on ITO. In addition, owing to the structural limitation for applying the voltage, so far, only research on reflection-type with metal layers has been reported.
Highly efficient, modal phase-matched second harmonic generation in a double-layered thin film lithium niobate waveguide
Authors: Du Haoyang , Zhang Xiuquan , Wang Lei , Chen Feng
Published: February 2023

In this contribution, we numerically investigate second harmonic generation in double-layered lithium niobate on the insulator platform by means of the modal phase matching. The modal dispersion of the ridge waveguides at the C waveband of optical fiber communication is calculated numerically and analyzed. Modal phase matching can be achieved by changing the geometric dimensions of the ridge waveguide. The phase-matching wavelength and conversion efficiencies versus the geometric dimensions in the modal phase-matching process are investigated. We also analyze the thermal-tuning ability of the present modal phase matching scheme. Our results show that highly efficient second harmonic generation can be realized by the modal phase matching in the double-layered thin film lithium niobate ridge waveguide.
Strong light–matter interactions of exciton in bulk WS2 and a toroidal dipole resonance
Authors: You Shaojun , Zhang Ying , Fan Menghui , Luo Shengyun , Zhou Chaobiao
Published: February 2023

Exciton-polaritonic states are generated by strong interactions between
photons and excitons in nanocavities. Bulk transition metal
dichalcogenides (TMDCs) host excitons with a large binding energy at
room temperature, and thus are regarded as an ideal platform for
realizing exciton-polaritons. In this work, we investigate the strong
coupling properties between high-Q toroidal dipole
(TD) resonance and bulk WS2 excitons in a hybrid
metasurface, consisting of Si3N4 nanodisk arrays
with embedded WS2. Multipole decomposition and near-field
distribution confirm that Si3N4 nanodisk arrays
support strong TD resonance. The TD resonance wavelength is easily
tuned to overlap with the bulk WS2 exciton wavelength, and
strong coupling is observed when the bulk WS2 is integrated
with the hollow nanodisk and the oscillator strength of the
WS2 material is adjusted to be greater than 0.6. The Rabi
splitting of the hybrid device is up to 65 meV. In addition,
strong coupling is confirmed by the anticrossing of fluorescence
enhancement in the hybrid
Si3N4–WS2 metastructure. Our
findings are expected to be of importance for both fundamental
research in TMDC-based light–matter interactions and practical
applications in the design of high-performance exciton-polariton
devices.
One-dimensional grating coupler on lithium-niobate-on-insulator for high-efficiency and polarization-independent coupling
Authors: Chen Bin , Ruan Ziliang , Chen Kaixuan , Liu Liu
Published: February 2023

A metal-based one-dimensional grating coupler on an x-cut lithium-niobate-on-insulator wafer structure for a polarization-independent fiber interface is designed and demonstrated. By using a metal-based plasmonic mode, the diffractive angle for the two polarized modes in the lithium niobate ridge waveguide can be tuned to be the same. The polarization dependence of the grating coupler therefore can be effectively reduced. The fabricated device exhibits −3.56-dB and −4.08-dB peak coupling losses per coupler at 1573 nm for the TE and TM modes, respectively. The polarization-dependent losses are less than 0.69 dB in a 44-nm wavelength range. The demonstrated grating coupler can serve as a polarization-independent optical fiber interface on lithium-niobate-on-insulator and facilitate on-chip polarization diversity applications.
Recent advances in liquid metal photonics: technologies and applications [Invited]
Authors: Liu Peter Q. , Miao Xianglong , Datta Shreyan
Published: February 2023

Near-room-temperature liquid metals offer unique and crucial advantages over solid metals for a broad range of applications that require soft, stretchable, and/or reconfigurable structures and devices. In particular, gallium-based liquid metals are the most suitable for a wide range of applications, not only owing to their low melting points but also thanks to their low toxicity and negligible vapor pressure. In addition, gallium-based liquid metals exhibit attractive optical properties, which make them highly suitable for a variety of photonics applications. This review summarizes the material properties of gallium-based liquid metals, highlights several effective techniques for fabricating liquid-metal-based structures and devices, and then focuses on the various photonics applications of these liquid metals in different spectral regions, following with a discussion on the challenges and opportunities for future research in this relatively nascent field.
100 W, Tunable In-band Pumped Thulium Fiber Amplifier
Authors: Richardson Martin , Cook Justin , Sincore Alex , Vail Nicholas , Krämer Ria G. , Goebel Thorsten A. , Roumayah Patrick , Bryan Joshua , Bodnar Nathan , Nolte Stefan
Published: February 2023

We detail the design and performance of a high efficiency in-band pumped thulium fiber amplifier operating at the 100 W level. Using a novel pumping architecture based on three incoherently combined thulium fiber oscillators at 1904 nm and a seed laser tunable from 1970-1990 nm, efficient amplification is demonstrated in a high dopant concentration 25/65/250 μm thulium fiber. Here we use the 65 μm pedestal surrounding the core as a pump cladding to increase the cladding to core overlap and improve the overall pump absorption. Up to 89% slope efficiency is obtained with ~100 W output power at 1990 nm. These results indicate that in-band pumping is a viable route to circumvent the thermal limitations associated with 793 nm diode pumping and provide a pathway for development of multi-kW laser sources in the 2 μm spectral window.
Regrowth-free AlGaInAs MQW polarization controller integrated with a sidewall grating DFB laser
Authors: Sun Xiao , Liang Song , Cheng Weiqing , Ye Shengwei , Sun Yiming , Huang Yongguang , Zhang Ruikang , Xiong Jichuan , Liu Xuefeng , Marsh John H. , Hou Lianping
Published: February 2023

Polarization control is at the heart of high-capacity data optical communication systems, such as polarization-division multiplexers and Stokes vector modulation transmitters. Despite passive polarization control being mature, the realization of monolithically integrated polarization controllers and single longitudinal mode light sources, such as distributed-feedback (DFB) lasers, is of importance. In this research, we report an AlGaInAs multiple-quantum-well photonic integrated circuit device which can control the state of polarization of the output light source, consisting of a polarization mode converter (PMC), a differential phase shifter (DPS), and a sidewall grating DFB laser. We demonstrate an asymmetrical stepped-height ridge waveguide PMC to realize TE to TM polarization conversion and a symmetrical straight waveguide DPS to enable polarization rotation from approximately counterclockwise circular polarization to linear polarization. Based on the identical epitaxial layer scheme, all the PMC, DPS, and DFB lasers can be integrated monolithically using only a single step of metalorganic vapor-phase epitaxy and two steps of III-V material dry etching. For the DFB-PMC device, a high TE to TM polarization conversion efficiency (98.4%) over a wide range of DFB injection currents is reported at 1555 nm wavelength. For the DFB-PMC-DPS device, a nearly 60° rotation of the Stokes vector on the Poincaré sphere was obtained with a range of bias voltage from 0 to −3.0  V at a laser drive current of 170 mA.
Applications for wavelength division multiplexers based on topological photonic crystals
Authors: Ruan Yuhang , Qian Xinyue , Wang Hai-Xiao , Hu Zheng-Da , Yang Yuting , Wang Jicheng , Shen Xiaopeng , Wang Yixiang
Published: February 2023

Topological edge states have an important role in optical modulation with potential applications in wavelength division multiplexers (WDMs). In this paper, 2D photonic crystals (PCs) with different rotation angles are combined to generate topological edge states. We reveal the relationship between the edge states and the rotation parameters of PCs, and further propose a WDM to realize the application of adjustable beams. Our findings successfully reveal the channel selectivity for optical transmission and provide a flexible way to promote the development of topological photonic devices.
Low temperature sensitivity on-chip Fourier-transform spectrometer based on dual-layer Si3N4 spiral waveguides
Authors: Lu Liangjun , Zhang Hongyi , Li Xin , Chen Jianping , Zhou Linjie
Published: February 2023

On-chip Fourier-transform spectrometers (FTSs) based on Mach–Zehnder interferometer (MZI) arrays suffer from severe central wavelength and fringe contrast variation due to fabrication errors. Even though a calibration matrix can be employed to correctly retrieve the input spectra, environmental temperature variation greatly degrades the retrieving performance. In this paper, we devise a dual-layer Si3N4 waveguide interferometer to reduce the temperature sensitivity. The beating of the even and odd supermodes in the dual-layer waveguide generates periodic intensity fluctuations in the spectrum. Since these two modes have similar modal profiles, their thermal sensitivity and propagation loss are relatively balanced, leading to a low temperature sensitivity and a high interference extinction ratio. We designed and fabricated a passive FTS based on a 32-channel dual-layer Si3N4 waveguide array. Experimental results show that the temperature sensitivity is reduced to 10 pm/°C, which is almost half that of single-layer Si3N4 MZI-based FTSs. With this chip, we accurately reconstructed various types of optical spectra, including single and two sparse laser lines, and broadband optical spectra. Our method can fit a wide wavelength range, which is a promising technology to improve the practical applications of on-chip FTSs.
Transcellular chaperone signaling is an intercellular stress-response distinct from the HSF-1–mediated heat shock response
Authors: Miles Jay , Townend Sarah , Milonaitytė Dovilė , Smith William , Hodge Francesca , Westhead David R. , van Oosten-Hawle Patricija
Published: February 2023

Organismal proteostasis is maintained by intercellular signaling processes including cell nonautonomous stress responses such as transcellular chaperone signaling (TCS). When TCS is activated upon tissue-specific knockdown of hsp-90 in the Caenorhabditis elegans intestine, heat-inducible hsp-70 is induced in muscle cells at the permissive temperature resulting in increased heat stress resistance and lifespan extension. However, our understanding of the molecular mechanism and signaling factors mediating transcellular activation of hsp-70 expression from one tissue to another is still in its infancy. Here, we conducted a combinatorial approach using transcriptome RNA-Seq profiling and a forward genetic mutagenesis screen to elucidate how stress signaling from the intestine to the muscle is regulated. We find that the TCS-mediated “gut-to-muscle” induction of hsp-70 expression is suppressed by HSF-1 and instead relies on transcellular-X-cross-tissue (txt) genes. We identify a key role for the PDZ-domain guanylate cyclase txt-1 and the homeobox transcription factor ceh-58 as signaling hubs in the stress receiving muscle cells to initiate hsp-70 expression and facilitate TCS-mediated heat stress resistance and lifespan extension. Our results provide a new view on cell-nonautonomous regulation of “inter-tissue” stress responses in an organism that highlight a key role for the gut. Our data suggest that the HSF-1–mediated heat shock response is switched off upon TCS activation, in favor of an intercellular stress-signaling route to safeguard survival.
AI reveals insights into link between CD33 and cognitive impairment in Alzheimer’s Disease
Authors: Raschka Tamara , Sood Meemansa , Schultz Bruce , Altay Aybuge , Ebeling Christian , Fröhlich Holger
Published: February 2023

Modeling biological mechanisms is a key for disease understanding and drug-target identification. However, formulating quantitative models in the field of Alzheimer’s Disease is challenged by a lack of detailed knowledge of relevant biochemical processes. Additionally, fitting differential equation systems usually requires time resolved data and the possibility to perform intervention experiments, which is difficult in neurological disorders. This work addresses these challenges by employing the recently published Variational Autoencoder Modular Bayesian Networks (VAMBN) method, which we here trained on combined clinical and patient level gene expression data while incorporating a disease focused knowledge graph. Our approach, called iVAMBN, resulted in a quantitative model that allowed us to simulate a down-expression of the putative drug target CD33, including potential impact on cognitive impairment and brain pathophysiology. Experimental validation demonstrated a high overlap of molecular mechanism predicted to be altered by CD33 perturbation with cell line data. Altogether, our modeling approach may help to select promising drug targets.
An overview of bioinformatics courses delivered at the academic level in Italy: Reflections and recommendations from BITS
Authors: Marangoni Roberto , Bevilacqua Vitoantonio , Cannataro Mario , Mele Bruno Hay , Mauri Giancarlo , Marabotti Anna ,   on behalf of the BITS Training&Teaching group
Published: February 2023

In Italian universities, bioinformatics courses are increasingly being incorporated into different study paths. However, the content of bioinformatics courses is usually selected by the professor teaching the course, in the absence of national guidelines that identify the minimum indispensable knowledge in bioinformatics that undergraduate students from different scientific fields should achieve. The Training&Teaching group of the Bioinformatics Italian Society (BITS) proposed to university professors a survey aimed at portraying the current situation of bioinformatics courses within undergraduate curricula in Italy (i.e., bioinformatics courses activated within both bachelor’s and master’s degrees). Furthermore, the Training&Teaching group took a cue from the survey outcomes to develop recommendations for the design and the inclusion of bioinformatics courses in academic curricula. Here, we present the outcomes of the survey, as well as the BITS recommendations, with the hope that they may support BITS members in identifying learning outcomes and selecting content for their bioinformatics courses. As we share our effort with the broader international community involved in teaching bioinformatics at academic level, we seek feedback and thoughts on our proposal and hope to start a fruitful debate on the topic, including how to better fulfill the real bioinformatics knowledge needs of the research and the labor market at both the national and international level.
Synaptic self-organization of spatio-temporal pattern selectivity
Authors: Dehghani-Habibabadi Mohammad , Pawelzik Klaus
Published: February 2023

Spiking model neurons can be set up to respond selectively to specific spatio-temporal spike patterns by optimization of their input weights. It is unknown, however, if existing synaptic plasticity mechanisms can achieve this temporal mode of neuronal coding and computation. Here it is shown that changes of synaptic efficacies which tend to balance excitatory and inhibitory synaptic inputs can make neurons sensitive to particular input spike patterns. Simulations demonstrate that a combination of Hebbian mechanisms, hetero-synaptic plasticity and synaptic scaling is sufficient for self-organizing sensitivity for spatio-temporal spike patterns that repeat in the input. In networks inclusion of hetero-synaptic plasticity that depends on the pre-synaptic neurons leads to specialization and faithful representation of pattern sequences by a group of target neurons. Pattern detection is robust against a range of distortions and noise. The proposed combination of Hebbian mechanisms, hetero-synaptic plasticity and synaptic scaling is found to protect the memories for specific patterns from being overwritten by ongoing learning during extended periods when the patterns are not present. This suggests a novel explanation for the long term robustness of memory traces despite ongoing activity with substantial synaptic plasticity. Taken together, our results promote the plausibility of precise temporal coding in the brain.
Copy number footprints of platinum-based anticancer therapies
Authors: Gonzalez Santiago , Lopez-Bigas Nuria , Gonzalez-Perez Abel
Published: February 2023

Recently, distinct mutational footprints observed in metastatic tumors, secondary malignancies and normal human tissues have been demonstrated to be caused by the exposure to several chemotherapeutic drugs. These characteristic mutations originate from specific lesions caused by these chemicals to the DNA of exposed cells. However, it is unknown whether the exposure to these chemotherapies leads to a specific footprint of larger chromosomal aberrations. Here, we address this question exploiting whole genome sequencing data of metastatic tumors obtained from patients exposed to different chemotherapeutic drugs. As a result, we discovered a specific copy number footprint across tumors from patients previously exposed to platinum-based therapies. This footprint is characterized by a significant increase in the number of chromosomal fragments of copy number 1–4 and size smaller than 10 Mb in exposed tumors with respect to their unexposed counterparts (median 14–387% greater across tumor types). The number of chromosomal fragments characteristic of the platinum-associated CN footprint increases significantly with the activity of the well known platinum-related footprint of single nucleotide variants across exposed tumors.
Attitudes, preference and personality in relation to behavioral intention of autonomous vehicle use: An SEM analysis
Authors: Ding Ling , Yang Xu
Published: February 2023

Autonomous vehicles (AVs) are entering the market, which will have a great impact on future decision making on mode choice in transportation systems. The aim of this study is to explore the determinants which influence travelers’ intentions to use AVs based on structural equation modelling (SEM). 310 valid sets of data from an online survey were collected to analyze factors which influence travelers’ intentions. Data analyses were conducted using IBM SPSS Statistics 23 and AMOS 23. The results showed that personality and preferences in relation to AVs are the main potential factors that cause travelers’ AVs use. Attitudes to modal services also affect intentions to use AVs. Personality has a significant positive effect on both attitude and preferences. The results provide exploratory empirical support for all hypotheses. The research results will help understand travelers’ choice motivation from psychological and service perspectives, and provide support for governments and enterprises to improve the management and services of autonomous vehicles.
Strengthening health system’s capacity for linkage to HIV care for adolescent girls and young women and adolescent boys and young men in South Africa (SheS’Cap-Linkage): Protocol for a mixed methods study in KwaZulu-Natal, South Africa
Authors: Nicol Edward , Basera Wisdom , Lombard Carl , Jonas Kim , Ramraj Trisha , Govindasamy Darshini , Hlongwa Mbuzeleni , McClinton-Appollis Tracy , Mehlomakulu Vuyelwa , Naqvi Nuha , Bedford Jason , Drummond Jennifer , Cheyip Mireille , Dladla Sibongile , Pass Desiree , Funani Noluntu , Mathews Cathy
Published: February 2023

Introduction

Adolescent girls and young women (AGYW) aged 15–24 years and adolescent boys and young men (ABYM) aged 15–34 years represent one of the populations at highest risk for HIV-infection in South Africa. The National Department of Health adopted the universal test and treat (UTT) strategy in 2016, resulting in increases in same-day antiretroviral therapy initiations and linkage to care. Monitoring progress towards attainment of South Africa’s 95-95-95 targets amongst AGYW and ABYM relies on high quality data to identify and address gaps in linkage to care. The aim of this study is to describe the current approaches for engaging AGYW and ABYM in the treatment continuum to generate knowledge that can guide efforts to improve linkage to, and retention in, HIV care among these populations in KwaZulu-Natal, South Africa.

Methods and analysis

This is a mixed methods study, which will be conducted in uMgungundlovu district of KwaZulu-Natal, over a 24-month period, in 22 purposively selected HIV testing and treatment service delivery points (SDPs). For the quantitative component, a sample of 1100 AGYW aged 15–24 years and ABYM aged 15–35 years old will be recruited into the study, in addition to 231 healthcare providers (HCPs) involved in the implementation of the UTT program. The qualitative component will include 30 participating patients who were successfully linked to care, 30 who were not, and 30 who have never tested for HIV. Key informant interviews will also be conducted with 24 HCPs. Logistic regression will be used to model the primary outcomes on SDP types, while a time to event analysis will be conducted using a Cox regression model and adjusting the standard errors of the hazard ratio for the clustering of participants within SDPs. For qualitative data, a general inductive approach of analysis will be used.

Dissemination

Findings from the study will be communicated to the study population and results will be presented to stakeholders and at appropriate local and international conferences. Outputs will also include a policy brief, peer reviewed journal articles and research capacity building through research degrees.
A study about management of drugs for leprosy patients under medical monitoring: A solution based on AHP-Electre decision-making methods
Authors: Falcão Igor W. S. , Souza Daniel S. , Cardoso Diego L. , Costa Fernando A. R. , Leite Karla T. F. , de M. Harold D. , Salgado Claudio G. , da Silva Moisés B. , Barreto Josafá G. , da Costa Patricia F. , Santos Adriano M. dos , Conde Guilherme A. B. , Seruffo Marcos C. da R.
Published: February 2023

Leprosy, also known as Hansen’s, is one of the listed neglected tropical diseases as a major health problem global. Treatment is one of the main alternatives, however, the scarcity of medication and its poor distribution are important factors that have driven the spread of the disease, leading to irreversible and multi-resistant complications. This paper uses a distribution methodology to optimize medication administration, taking into account the most relevant attributes for the epidemiological profile of patients and the deficit in treatment via Polychemotherapy. Multi-criteria Decision Methods were applied based on AHP-Electre model in a database with information from patients in the state of Para between 2015 and 2020. The results pointed out that 84% of individuals did not receive any treatment and, among these, the method obtained a gain in the distribution of 68% in patients with positive diagnosis for leprosy.
Numerical solution of magnetohydrodynamics effects on a generalised power law fluid model of blood flow through a bifurcated artery with an overlapping shaped stenosis
Authors: Zain Norliza Mohd , Ismail Zuhaila
Published: February 2023

This paper presents a numerical analysis of blood flow in a diseased vessel within the presence of an external magnetic field. The blood flow was considered to be incompressible and fully developed, in that the non-Newtonian nature of the fluid was characterised as a generalised power law model for shear-thinning, Newtonian, and shear-thickening fluids. The impact of a transverse directed external magnetic field on blood flow through a stenosed bifurcated artery was investigated. The arterial geometry was considered as a bifurcated channel with overlapping shaped stenosis. The problem was treated mathematically using the Galerkin Least-Squares (GLS) method. The implementation of this numerical method managed to overcome the numerical instability faced by the classical Galerkin technique when adopted to a highly viscous flow. The benefit of GLS in circumventing the Ladyzhenskaya-Babuška-Brezzi (LBB) condition was utilized by evaluating both the velocity and pressure components at corner nodes of a unstructured triangular element. The non-linearity that emerged from the convective terms was then treated using the Newton-Raphson method, while the numerical integrals were computed using a Gaussian quadrature rule with six quadrature points. The findings obtained from this study were then compared with available results from the literature as well as Comsol multiphysics software to verify the accuracy and validity of the numerical algorithms. It was found that the application of magnetic field was able to overcome flow reversal by 39% for a shear-thinning fluid, 26% for a Newtonian fluid, and 27% for a shear-thickening fluid. The negative pressure and steep wall shear stress which occurs at the extremities of an overlapping stenosis throat were diminished by rise in magnetic intensity. This prevented thrombosis occurrence and produced a uniform calm flow.
Reinforcement learning approach to control an inverted pendulum: A general framework for educational purposes
Authors: Israilov Sardor , Fu Li , Sánchez-Rodríguez Jesús , Fusco Franco , Allibert Guillaume , Raufaste Christophe , Argentina Médéric
Published: February 2023

Machine learning is often cited as a new paradigm in control theory, but is also often viewed as empirical and less intuitive for students than classical model-based methods. This is particularly the case for reinforcement learning, an approach that does not require any mathematical model to drive a system inside an unknown environment. This lack of intuition can be an obstacle to design experiments and implement this approach. Reversely there is a need to gain experience and intuition from experiments. In this article, we propose a general framework to reproduce successful experiments and simulations based on the inverted pendulum, a classic problem often used as a benchmark to evaluate control strategies. Two algorithms (basic Q-Learning and Deep Q-Networks (DQN)) are introduced, both in experiments and in simulation with a virtual environment, to give a comprehensive understanding of the approach and discuss its implementation on real systems. In experiments, we show that learning over a few hours is enough to control the pendulum with high accuracy. Simulations provide insights about the effect of each physical parameter and tests the feasibility and robustness of the approach.
Distribution and densities of fish larvae species with contrasting life histories as a function of oceanographic variables in the deep-water region of the southern Gulf of Mexico
Authors: Gonzalo Daudén-Bengoa , Jiménez-Rosenberg Sylvia Patricia Adelheid , Echeverri-García Laura del Pilar , Fernández-Álamo María Ana , Ordóñez-López Uriel , Herzka Sharon Z.
Published: February 2023

We describe the larval occurrence and density of six fish species with contrasting life histories and examine their relationships with oceanographic variables during two seasons in the deep-water region (> 1000 m) of the southern Gulf of Mexico based on 12 cruises (2011–2018). Given thatCaranx crysosadults are neritic, larval presence close to the continental shelf indicates offshore cross-shelf transport to oceanic waters, which likely leads to mortality. Generalized additive models indicated thatC.crysosdensity was not related with oceanographic variables, whileAuxisspp. (with neritic and oceanic adults) was related to wind speed, sea surface temperature, sea surface height, and surface chlorophyll a. The mesopelagicBenthosema suborbitale,Notolychnus valdiviaeandBregmaceros atlanticuswere more abundant and broadly distributed, and higher density was found in conditions indicative of higher nutrient availability and productivity, suggesting greater feeding success and survival. The distribution of the epi- and mesopelagicCubiceps pauciradiatusextended through the southern Gulf of Mexico, and was related to wind speed, sea surface temperature, stratification and chlorophyll a. Our results suggest that the density of the neritic species in oceanic waters could be mediated by regional cross-shelf transport, while for oceanic species is linked with productivity.
Detection and measurement of butterfly eyespot and spot patterns using convolutional neural networks
Authors: Cunha Carolina , Narotamo Hemaxi , Monteiro Antónia , Silveira Margarida
Published: February 2023

Butterflies are increasingly becoming model insects where basic questions surrounding the diversity of their color patterns are being investigated. Some of these color patterns consist of simple spots and eyespots. To accelerate the pace of research surrounding these discrete and circular pattern elements we trained distinct convolutional neural networks (CNNs) for detection and measurement of butterfly spots and eyespots on digital images of butterfly wings. We compared the automatically detected and segmented spot/eyespot areas with those manually annotated. These methods were able to identify and distinguish marginal eyespots from spots, as well as distinguish these patterns from less symmetrical patches of color. In addition, the measurements of an eyespot’s central area and surrounding rings were comparable with the manual measurements. These CNNs offer improvements of eyespot/spot detection and measurements relative to previous methods because it is not necessary to mathematically define the feature of interest. All that is needed is to point out the images that have those features to train the CNN.
Variable post-release mortality in common shark species captured in Texas shore-based recreational fisheries
Authors: Binstock Addie L. , Richards Travis M. , Wells R. J. David , Drymon J. Marcus , Gibson-Banks Kesley , Streich Matthew K. , Stunz Gregory W. , White Connor F. , Whitney Nicholas M. , Mohan John A.
Published: February 2023

The practice of catch and release fishing is common among anglers but has been shown to cause unintended mortalities in some species. Current post-release mortality estimates used in coastal shark stock assessments are typically derived from boat-based shark fisheries, which differ from shore-based operations that expose sharks to potentially more stressful environmental and handling conditions. Recreational post-release mortality rates in shore-based fisheries must be quantified to improve stock assessment models and to create guidelines that protect species from overexploitation. Here, we partnered with experienced anglers acting as citizen scientists to deploy pop-up satellite archival transmitting tags (PSAT, n = 22) and acceleration data loggers (ADLs, n = 22). on four commonly caught sharks including the blacktip shark (Carcharhinus limbatus, n = 11), bull shark (Carcharhinus leucas, n = 14), tiger shark (Galeocerdo cuvier, n = 6), and great hammerheads (Sphyrna mokarran, n = 2). Mortality occurred within minutes to hours post-release. If evidence of mortality occurred after normal diving behavior had been re-established for 10 days, then the mortality was considered natural and not related to the catch-and-release process. Post-release mortality estimates ranged from 0% for bull and tiger sharks to 45.5% for blacktip sharks. Of the two great hammerheads, one died within 30 minutes post-release while the other exhibited mortality characteristics 14 days after release. Moribund blacktip sharks experienced on average 3.4–4.9°C warmer water compared with survivors. Recovery periods were estimated for survivors of each species and were highly variable, differing based on duration of tag deployment. High variability in responses to capture and release between species demonstrates the need for species-specific assessments of post-release mortality in shore-based recreational fisheries.