bluuebunny/crossref_metadata_2025 huggingface dataset:
PEDOT:PSS stabilized paper-based piezoresistive sensor for wearable electronics
Authors: Pan Xiaoying , Zhao Cong , Sun Qingyin , Qin Chu , Wu Jiaxin , Wang Min
Published: July 2023

As a key component of electronic skins, flexible pressure sensors have attracted more and more attention because of the increasingly growing demand. Stability is a key parameter to evaluate pressure sensors, while relatively few reports have focused on it. Here, a paper-based piezoresistive sensor is developed, in which, the airlaid paper based sensing layer is modified with silver nanowires (AgNWs) and poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and sandwiched in between two convex electrodes. Due to the cross bonding of PEDOT:PSS membrane, the conductive paths of AgNWs networks are strengthened and stabilized, thus the stability of the sensor is found to be significantly improved. Besides, to regulate the compressibility by varying sensing layers, the performance of the proposed sensor can be further improved, and its practical application performances in healthcare pulse monitoring, tiny muscle motion, and voice recognition are demonstrated. The results confirm that PEDOT:PSS has the potential as stabilization media to AgNWs for paper-based flexible wearable electronics.
Effects of bendable P3CT polymers layer on the photovoltaic performance of perovskite solar cells
Authors: Chandel Anjali , Chiang Shou-En , Chang Wen-Hsin , Wu Jia-Ren , Yuan Chi-Tsu , Chang Sheng Hsiung
Published: July 2023

We report on the formation of bendable and edge-on poly[3-(4-carboxybutyl)thiophene-2,5-diyl] (P3CT) polymers thin layer used as a hole modification layer (HML) in the inverted perovskite solar cell. The aggregations of 2D layer-like P3CT polymers in dimethylformamide (DMF) solution can be formed via aromatic π–π stacking interactions and/or hydrogen-bonding interactions with the different concentration from 0.01 to 0.02 wt%, which highly influences the photovoltaic performance of the inverted perovskite solar cells. The atomic-force microscopic images and water droplet contact angle images show that the P3CT polymers modify the surface properties of the transparent conductive substrate and thereby dominating the formation of perovskite crystalline thin films, which play important roles in the highly efficient and stable perovskite solar cells. It is noted that the V
OC (J
SC) of the encapsulated solar cells values are maintained to be higher than 1.115 V (22 mA cm−2) after 104 d when an optimized π–π stacked and hydrogen-bonded P3CT polymer is used as the HML. On the other hand, the solar cell showed a high long-term stability by maintaining 85% of the initial power conversion efficiency in the ambient air for 103 d.
Mechanically induced dye-release from polyurea microcapsules in a rubbery adhesive
Authors: Koch C , Müller A , Kahlmeyer M , Riske T , Melnyk I , Dähne L , Kaden D , Baitinger M , Fery A , Böhm S
Published: July 2023

Especially in the building industry the demand for in situ monitoring concepts of adhesive joints persists. In a new approach, microcapsules filled with special dyes, are added into a rubbery adhesive. Certain stress levels within the adhesive lead to a breakage of the capsules, which release their liquid cores. This results in a detectable colour change and thus, enables non-destructive condition monitoring of the bond. Dye-filled polyurea microcapsules were produced by interfacial polymerization by varying synthesis parameters while their influence on capsule morphology and wall thickness was determined. The morphology and thermal properties of the microcapsules were characterized by scanning electron microscopy and dynamic differential calorimetry, respectively. Subsequently, the method of nanoindentation was used to study the deformation and fracture behaviour of the microcapsules. Finally, it was analysed to what extent the microcapsules break within a polymer matrix, e.g. by critical stress levels or deformations. This development is a new quality assurance method for glass façades.
Quantum-information theory of magnetic field influence on circular dots with different boundary conditions
Authors: Shafeekali H , Olendski O
Published: July 2023

Influence of the transverse uniform magnetic field B on position (subscript ρ) and momentum (γ) Shannon quantum-information entropies S

ρ,γ
Fisher informations I

ρ,γ
and informational energies O

ρ,γ
is studied theoretically for the 2D circular quantum dots (QDs) whose circumference supports homogeneous either Dirichlet or Neumann boundary condition (BC). Comparative analysis reveals similarities and differences of the influence on the properties of the structure of the surface interaction with the magnetic field. A conspicuous distinction between the two spectra are crossings at the increasing induction of the Neumann energies with the same radial quantum number n and adjacent non-positive angular indices m. At the growing B, either system undergoes Landau condensation when its characteristics turn into their uniform field counterparts. It is shown that for the Dirichlet system this transformation takes place at the smaller magnetic intensities; e.g. the Dirichlet sum

S

ρ

00

+

S

γ

00

on its approach from above to a fundamental limit

2
(
1
+
ln
π
)

is at any B smaller than the corresponding Neumann quantity what physically means that the former geometry provides more total information about the position and motion of the particle. It is pointed out that the widely accepted disequilibrium uncertainty relation

O

ρ

O

γ

≤

2
π

−
d

, with d being a dimensionality of the system, is violated by the Neumann QD in the magnetic field. Comparison with electrostatic harmonic confinement is performed; in particular, contrary to the hard-wall QDs, for this configuration the sums S

ρ
+ S

γ
and the products I

ρ

I

γ
and O

ρ

O

γ
do not depend on the field. Physical interpretation is based on the different roles of the two BCs and their interplay with the field: Dirichlet (Neumann) surface is a repulsive (attractive) interface.
Transmission and Reflection properties of the incident Light via SW coherent laser field
Authors: Smait Drai Ahmed , Khalil Noor , Bashar Bashar S , Mohhamed Elaf M , Khalaf Sabreen Ali , Salman Zahraa N , Nayyef Murtadha Salam , Hadrawi Salema K
Published: July 2023

The relative phase of the applied lights has been used to explore the position dependence of the transmitted and reflected light from a defective dielectric medium. The duplicated two-level atomic system that makes up the dielectric medium interacts with a position-dependent standing wave (SW) coupling light and a weak probe laser field. We found that identical behaviors can be produced for the transmitted and reflected light in various directions due to the relative phase of the applied light. Furthermore, we understood that the transmitted and reflected spectra of the incident light become asymmetric for the asymmetric profile of the coupling light, and that these circumstances will cause the probing field to be amplified. In this instance, we found that altering the relative phase of the applied lights can modify the position of the subluminal and superluminal light.
Production and characterization of random electrode sectorization in GEM foils
Authors: Pellecchia A. , Bianco M. , De Oliveira R. , Fallavollita F. , Fiorina D. , Rosi N. , Verwilligen P.
Published: July 2023

In triple-GEM detectors, the segmentation of GEM foils in electrically independent
sectors allows reducing the probability of discharge damage to the detector and improving the
detector rate capability. However, a segmented foil presents thin dead regions in the separation
between two sectors and the segmentation pattern has to be manually aligned with the GEM hole
pattern during the foil manufacturing, a procedure potentially sensitive to errors.

We describe the production and characterization of triple-GEM detectors obtained with an
innovative GEM foil segmentation technique, the “random hole segmentation”, that allows easier
manufacturing of segmented GEM foils. The electrical stability to high voltage and the gain
uniformity of a random-hole segmented triple-GEM prototype are measured. The results of a test
beam on a prototype assembled for the Phase-2 GEM upgrade of the CMS experiment are also
presented. A high statistics efficiency measurement shows that the random hole segmentation can
limit the efficiency loss of the detector in the areas between two sectors, making it a viable
alternative to blank segmentation for the GEM foil manufacturing of large-area detector systems.
First 3D reconstruction of a blast furnace using muography
Authors: Cohu A. , Chevalier A. , Nechyporuk O. , Franzen A. , Sauerwald J. , Ianigro J-C. , Marteau J.
Published: July 2023

The blast furnace (BF) is the fundamental tool used in the
iron manufacture. Due to the difficulty of making direct
measurements of the inner state of blast furnaces, we determined the
density distribution of its internal volume in order to improve its
productivity using muography. This is an imaging technique based on
the differential absorption of a flux of incident particles, muons,
by the target under study, similar to clinical X-ray imaging. Muons
are elementary particles that have the property of passing through
dense materials, up to hundreds of meters of rocks. Their relative
absorption and deviation allows the generation of density
distribution images of an object by tracking the number of muons
received by a detector, before and after passing through a
structure. The incident direction of the detected muons is
reconstructed by means of a detector composed of 3 scintillator
panels that we moved on 3 positions around the BF. With this
technique, we obtained the first 3D image of the internal structure
of a BF using a Markov Chain Monte Carlo (MCMC) inverse problem
solving algorithm on muon flux data. We were also able to perform
density monitoring of the BF and monitor some of its operating
parameters. We distinguished the position and shape of the cohesive
zone, a key element in the productivity of a furnace, validating
this innovative measurement concept in the application to a BF and
opening the field to a series of future experiments to gain both
spatial and temporal resolution.
A review of water-energy-food-ecosystems Nexus research in the Mediterranean: evolution, gaps and applications
Authors: Lucca Enrico , El Jeitany Jerome , Castelli Giulio , Pacetti Tommaso , Bresci Elena , Nardi Fernando , Caporali Enrica
Published: July 2023

The water-energy-food-ecosystems (WEFE) Nexus has gained recognition as an innovative approach for analysing the interconnectedness of global resource systems and achieving sustainability goals. In the Mediterranean, where water scarcity, climate change, and ecosystem degradation pose significant challenges, implementing an integrated WEFE Nexus approach is crucial. We conducted a comprehensive review of scientific literature through the lenses of Nexus ‘ideas’, ‘relationship’ and ‘practices’. A total of 142 research articles were selected and characterized in terms of WEFE interlinkages being investigated, explored topics, methods and scales of analysis, and contexts of operationalization. We found that water-energy interdependences dominate WEFE Nexus research in the Mediterranean, driven by the large presence of energy-intensive water abstraction and distribution systems to meet drinking and irrigation water demands. At the same time, the expansion of the Nexus approach to additional components is only partial, mostly focusing on assessing impacts on the physical environment and climate, without capturing feedback dynamics. Geographically, Nexus research in the Mediterranean is primarily conducted in isolated case studies, with few large scale assessments developed at the entire Mediterranean scale, and with some countries not yet represented, in particular the Western Balkans. Although WEFE Nexus research in the Mediterranean is recognizing the importance of transdisciplinarity moving beyond biophysical assessments to encompass societal and governance dynamics, further research is needed on understanding the economic implications of WEFE Nexus interactions. To advance Nexus implementation in the region, sustainable technology, and natural resources management, which are key fields of WEFE Nexus research operationalization, would benefit from harmonization in their design objectives. This would enable a more comprehensive and coherent approach towards achieving water, food, and energy security while preserving the environment in the Mediterranean region.
Numerical Simulation of the Effect of Tank Shape on Sloshing Using Smoothed Particle Hydrodynamics
Authors: Utami S , Trimulyono A , Manik P
Published: July 2023

Sloshing is the violent motion of a resonant fluid in a moving tank. When the fluid moves and interacts with the tank, the dynamic pressure from such an interaction can cause large deformations of the tank walls and structure. In this study, a 3D numerical simulation was carried out with five variations of the LNG ship tank model: prismatic, rectangular, tube, spherical, and the new model with a filling ratio of 25%. Forced oscillation motion in a roll with f = 1.04 Hz and amplitude of movement 8.66°. Smoothed Particle Hydrodynamics is a Lagrangian meshless (non-grid) method known as mesh-free computational fluid dynamics. This method is very appropriate for the sloshing phenomenon because the sloshing phenomenon is closely related to free surface motion. Advanced visualization was performed using Blender version 2.92, and the sloshing simulation visualization is more realistic and attractive than conventional SPH post-processing. The results of this study indicate that different tank shapes influence reducing the dynamic pressure value. It is found that an effective tank shape is a tube tank and a new model tank with a reduced dynamic pressure value of 9% and 11%.
Structural design evaluation for Underwater Remotely Operated Vehicle (ROV), case study: Madura Straits
Authors: Syahab H , Ariesta R C , Misbah M N , Zubaydi A , Sujiatanti S H , Putra W H A , Setyawan D
Published: July 2023

Using Remotely Operated Vehicles (ROV) is very important, especially in underwater investigations. The Madura Strait, located between the Java islands and Madura, is used as an industrial area, especially for oil and gas sources. Therefore, the ROV structure must be designed in such a way that it can withstand the hydrostatic loads it receives during operations in the deep sea. The study was conducted to determine the ROV’s ability to withstand hydrostatic loads using materials such as steel, aluminium, and HDPE. The pre-designed ROV is converted and modeled in 3D. The model formed and detailed as the basic form of the ROV is imported to the Finite Element Analysis tools to obtain the value of the stress and deformation of the ROV. Therefore, the load is adjusted to the hydrostatic pressure, with the seawater depth up to 200 m. The study structural design evaluation is able used as a reference for selecting materials used in the ROV.
Hydrodynamic Derivatives of a Ferry Ship Maneuvering in Deep and Shallow Water with Computational Fluid Dynamic Method
Authors: Muhammad A.H. , Paroka D. , Rahman S. , Nikmatullah M.I. , Sudirman L.
Published: July 2023

The mathematical model and hydrodynamic derivatives can be developed in the simulation program to investigate a ship’s maneuvering performance using numerical simulation. This research describes a study to investigate the hydrodynamic derivatives of maneuvering a ferry ship in shallow and deep water. Using virtual drift and rotating arm model simulated, the hydrodynamic derivatives for a ferry ship’s surging, swaying, and yawing motions were obtained through Computational Fluid Dynamics (CFD). The hydrodynamic derivatives of the ferry ship were analyzed from the model test data using the least-square method. This study investigated three conditions of the ferry ship with various water depth conditions. The simulation result indicated that the ferry ship’s water depth affected its maneuvering performance.
Comparative study of spread and vertical mooring configuration in floating collar net cage under irregular waves and current
Authors: Murdjito  , Athallah A G , Prasetywan I , Djatmiko E B
Published: July 2023

Offshore aquaculture is one of the national strategic programs of the Ministry of Fishery and Ocean Affairs of Indonesia to increase national fish cultivation capacity. One solution is using a simple flexible floating collar net which is suitable for small to medium cage volume. In designing such floating net, its mooring line configuration is vital to maintain fixed position of structural part of the cage volume. The purpose of this study is to compare design aspect of two types of mooring systems, i.e., spread and vertical configuration, by investigating selected parameters: mooring line tension, collar offset, and volume reduction. The mooring configuration and floating collar net cage are analysed through a numerical model based on Morison-force equations, under environmental condition adopted from Kangean field East Java. Load cases from collinearly in-line and between-line directions under extreme waves and current condition are checked against relevant safety factor. The dynamics analysis using the time domain simulation is based on 900 seconds cut-off according to its maximum wave elevation profile to generate the hydrodynamics forces to the mooring systems.
RANS CFD Model for Global Performance Evaluation of Floating Vessel in Extreme Head Waves
Authors: Ardhiansyah F , Prastianto R W , Djatmiko E B , Murdjito
Published: July 2023

Extreme waves acting on the floating vessel would cause serious physical behavior and could cause a catastrophic incident. Such phenomena should be put of high interest during the designing step of the floating vessel. The numerical CFD (Computational Fluid Dynamics) viscous fluid approach along with the recent development of computer hardware gives us advantages to simulate a huge number of scenarios in the very early design phase. The current study will explain the CFD method to investigate the global performance of stationer floating vessel Fn = 0 on its motion and green water occurrence due to extreme waves λ/L = 2.0. Based on the simulation results, the CFD model can handle well the green water on deck phenomenon during extreme head waves. The water on deck affected vessel pitch motion amplitude not symmetric under regular waves i.e. 8 degrees by stern and 6 degrees by bow. Similar results were also found in heave motion amplitude by the maximum +4 centimeter and minimum -12 centimeter. Those asymmetric results of heave & pitch motion amplitude under regular waves indicate the contribution of green water to the vessel motion. In addition, green water on deck only affects the motion amplitude but not the motion frequency.
Reassessment of Minimum Facilities Wellhead Platform due to Installation of Extension Compressors against Earthquake Loads
Authors: Bukhari M H , Prastianto R W , Syalsabila F
Published: July 2023

For increasing the production capacity of existing oil and gas wells, adding, or modifying the equipment with more sophisticated process equipment is necessary. One effort is by the addition of compressors such as on a minimum wellhead platform facility, which are installed on the top side of the platform. In addition to increasing the weight of the topside, which must be supported by the jacket, this installation makes the platform become more sensitive to seismic loads. This paper discusses the reassessment of the platform to determine the structural integrity due to the installation of the extension compressor to earthquake loads based on the API code RP 2A-WSD 22nd 2014 and RP 2SIM. Seismic analysis methods performed in this study include super element analysis, eigenvalue analysis, dynamic response analysis, earthquake analysis, post analysis, and single pile analysis. According to the code and company specifications, the analysis shows promising results in terms of the unity check, natural period, and displacement check, so the structural integrity is still acceptable for further operation.
Setting exciter to obtain output synchronous generator to be used in wind energy conversion system
Authors: Hadi B D , Musyafa A
Published: July 2023

Indonesia has well natural resource potential, one of which is the wind energy potential which can be utilized for electricity needs. However, the utilization of wind energy in Indonesia is still lacking. Therefore, it is necessary to have a system for utilizing wind energy with the aim of obtaining large electrical energy, one of which is the Wind Power Plant (PLTB) system. Synchronous generators have two important parts, namely the main generator (Alternator) and the exciter (Main Exciter). This exciter has a role as a trigger for the initial electricity generation to supply electricity to the main generator coil. The amount of electricity delivered to the main generator depends on the value of the magnetic flux in the generator exciter. The value of this magnetic flux depends on the amount of DC electric current flowing from the DC-DC Converter or Buck Converter. Therefore, a controller is needed to adjust the amount of electricity that enters the exciter. From the research that has been done, the optimal power at the rotational speed of the generator when the frequency is 50 Hz is 200.36 Watts with a generator voltage of 142.1 Volts and a duty cycle at 81.38%.
LiDAR DEM and HEC-RAS On-Grid Rainfall Hydrograph Model for Irrigation System
Authors: Ontowirjo B , Fathurrahman I , Ramadhan M V , Zahriani A , Zahra M , Wahyudi H
Published: July 2023

The capacity of the Saddang River Irrigation Canal will be increased by 30% to accommodate long-term irrigation discharge needs. Analysis of the hydraulic model of the irrigation and discharge channels is examined in this study. High resolution LiDAR Digital Elevation and HEC-RAS Model are used to estimate the flow depth and velocities in the event of rain with extreme intensity. HEC-RAS Model solves the 2-D depth-averaged St.Venant equations that are mainly used for river simulation. The HEC-RAS model uses on-grid precipitation hydrograph and flexible meshes that may contain arbitrarily quadrilateral and triangular cells. A hybrid mesh may achieve the best compromise between solution accuracy and computing demand. The HEC-RAS model solved variables include water surface elevation, water depth, depth averaged velocity, Froude number, and bed shear stress. The optimization of the model is useful for improving the drainage modulus, lining channel, drain time period and the performance of the irrigation and drainage channels.
Three-dimensional simulations of fluid flows in oscillating lid-driven cavities using lattice Boltzmann method
Authors: Bhopalam Sthavishtha R , Perumal D Arumuga , Yadav Ajay Kumar
Published: July 2023

We utilize the lattice Boltzmann method to conduct three-dimensional simulations of incompressible flows in oscillating cubic lid-driven cavities. Our investigation focuses on examining the impact of Reynolds number and oscillating frequency on the flow field. Notably, we observe that the flow field can be adequately approximated as two-dimensional within the low and intermediate Reynolds number range, but this approximation is no longer valid for high Reynolds numbers. Additionally, we find that high Reynolds numbers correspond to transient flow fields, while low and moderate Reynolds numbers exhibit quasi-steady periodic flow fields. Our study holds significant relevance for industrial processing applications, where the Reynolds numbers and oscillating frequencies can be optimized to achieve a desired flow field.
Electronic dispersion, correlations and stacking in the photoexcited state of 1T-TaS2
Authors: Dong Jingwei , Shin Dongbin , Pastor Ernest , Ritschel Tobias , Cario Laurent , Chen Zhesheng , Qi Weiyan , Grasset Romain , Marsi Marino , Taleb-Ibrahimi Amina , Park Noejung , Rubio Angel , Perfetti Luca , Papalazarou Evangelos
Published: July 2023

Here we perform angle and time-resolved photoelectron spectroscopy on the commensurate charge density wave (CDW) phase of 1T-TaS2. Data with different probe pulse polarization are employed to map the dispersion of electronic states below and above the chemical potential. Upon photoexcitation, the fluctuations of CDW order erase the band dispersion and squeeze the electronic states near to the chemical potential. This transient phase sets within half a period of the coherent lattice motion and is favored by strong electronic correlations. The experimental results are compared to density-functional theory calculations with a self-consistent evaluation of the Coulomb repulsion. Our simulations indicate that the screening of Coulomb repulsion depends on the stacking order of the TaS2 layers. The entanglement of such degrees of freedom suggest that both the structural order and electronic repulsion are locally modified by the photoinduced CDW fluctuations.
An environmentally friendly and high current efficiency acid mist inhibitor for zinc electrowinning
Authors: Ji Qi , Chen Bu-Ming , Gao Chao , Pan Ming-Xi , Huang Hui , Guo Zhong-Cheng , He Ya-Peng
Published: July 2023

Acid mist inhibitor is an effective additive for suppressing the generation of acid mist during electrowinning process. However, the traditional acid mist inhibitor has a low current efficiency, leading to high energy consumption. Thus, novel acid mist inhibitors are crucial for the development of the electrowinning industry. In this paper, three new acid mist inhibitors (Famigo® FS-101, Famigo® FS-301, and Famigo® FS-401) are used in zinc electrowinning process, while the mechanism of action in suppressing the generation of acid mist is characterized by the volume of bubble attached on the cathode surface and surface tension. The impacts of the concentration of the acid mist inhibitors on the bath voltage, current efficiency, power consumption, and electrochemical properties, as well as the enhancement mechanism on the current efficiency, are studied. The obtained results demonstrate that an adequate concentration of Famigo®FS-101, Famigo®FS-301, and Famigo®FS-401 allows to increase the cathode current efficiency and decrease the energy consumption, from 3219 kWh t−1 in zinc electrolyzer to 2948 kWh t−1, 3090 kWh t−1, and 2884 kWh t−1 using a concentration of 5 mg l−1 of Famigo®FS-101, Famigo®FS-301, and Famigo®FS-401, respectively. The proposed inhibitors have high acid mist inhibition efficiency and current efficiency in the zinc electrowinning process. Furthermore, if engineered, they may contribute to the development of the electroposition industry.
Intelligent real-time prediction of multi-region thrust of EPB shield machine based on SSA-LSTM
Authors: Zhang Wenshuai , Liu Xuanyu , Zhang Lingyu , Wang Yudong
Published: July 2023

During the tunneling process of shield machine, the accurate determination of tunneling parameters is the guarantee of safe operation of shield machine. Through the real-time construction data analysis and mining of shield machine, the tunneling parameters at the next moment are obtained in real-time. Based on this, this paper proposes an intelligent real-time prediction method for multi-region thrust of EPB shield machine based on Sparrow Search algorithm-Long and Short-term Memory (SSA-LSTM). By correlation analysis of the construction big data, the data features with a great correlation of shield machine thrust are obtained. And it is used as the input of LSTM prediction model to explore the nonlinear relationship between inputs and output. SSA is used to optimize LSTM prediction model to establish a more accurate nonlinear relationship, and then the multi-region thrust of shield machine at the next moment is accurately obtained. The simulation results show that SSA-LSTM model can accurately predict the thrust of each region of shield machine at the next moment, and the prediction performance is better than other models. The method provides a reference basis for shield machine to implement accurate thrust regulation and provides a guarantee for effective control of Earth pressure balance (EPB) in sealed cabin to ensure construction safety, which has engineering application value.
Network-augmented compartmental models to track asymptomatic disease spread
Authors: Dabke Devavrat Vivek , Karntikoon Kritkorn , Aluru Chaitanya , Singh Mona , Chazelle Bernard
Published: July 2023

A major challenge in understanding the spread of certain newly emerging viruses is the presence of asymptomatic cases. Their prevalence is hard to measure in the absence of testing tools, and yet the information is critical for tracking disease spread and shaping public health policies. Here, we introduce a framework that combines classic compartmental models with travel networks and we use it to estimate asymptomatic rates. Our platform, traSIR (“tracer”), is an augmented susceptible-infectious-recovered (SIR) model that incorporates multiple locations and the flow of people between them; it has a compartment model for each location and estimates of commuting traffic between compartments. TraSIR models both asymptomatic and symptomatic infections, as well as the dampening effect symptomatic infections have on traffic between locations. We derive analytical formulae to express the asymptomatic rate as a function of other key model parameters. Next, we use simulations to show that empirical data fitting yields excellent agreement with actual asymptomatic rates using only information about the number of symptomatic infections over time and compartments. Finally, we apply our model to COVID-19 data consisting of reported daily infections in the New York metropolitan area and estimate asymptomatic rates of COVID-19 to be ∼34%, which is within the 30–40% interval derived from widespread testing. Overall, our work demonstrates that traSIR is a powerful approach to express viral propagation dynamics over geographical networks and estimate key parameters relevant to virus transmission.

Availability and implementation

No public repository.
Generating interacting protein sequences using domain-to-domain translation
Authors: Meynard-Piganeau Barthelemy , Fabbri Caterina , Weigt Martin , Pagnani Andrea , Feinauer Christoph
Published: July 2023

Motivation

Being able to artificially design novel proteins of desired function is pivotal in many biological and biomedical applications. Generative statistical modeling has recently emerged as a new paradigm for designing amino acid sequences, including in particular models and embedding methods borrowed from natural language processing (NLP). However, most approaches target single proteins or protein domains, and do not take into account any functional specificity or interaction with the context. To extend beyond current computational strategies, we develop a method for generating protein domain sequences intended to interact with another protein domain. Using data from natural multidomain proteins, we cast the problem as a translation problem from a given interactor domain to the new domain to be generated, i.e. we generate artificial partner sequences conditional on an input sequence. We also show in an example that the same procedure can be applied to interactions between distinct proteins.

Results

Evaluating our model’s quality using diverse metrics, in part related to distinct biological questions, we show that our method outperforms state-of-the-art shallow autoregressive strategies. We also explore the possibility of fine-tuning pretrained large language models for the same task and of using Alphafold 2 for assessing the quality of sampled sequences.

Availability and implementation

Data and code on https://github.com/barthelemymp/Domain2DomainProteinTranslation.
Lesser kestrels of the same colony do not overwinter together
Authors: García-Macía Jorge , Chaouni Munir , Morollón Sara , Bustamante Javier , López-Ricaurte Lina , Martínez-Dalmau Juan , Rodríguez-Moreno Beatriz , Urios Vicente
Published: July 2023

Migratory connectivity describes the linkage between breeding and nonbreeding sites, having major ecological implications in birds: 1 season influence the success of an individual or a population in the following season. Most studies on migratory connectivity have used large-scale approaches, often considering regional populations, but fine-scale studies are also necessary to understand colony connectivity. The lesser kestrel Falco naumanni, an insectivorous migratory raptor which form colonies during the breeding period, was considered to have strong connectivity based on regional populations. However, no small-scale studies on migratory connectivity have been conducted. Therefore, we GPS (Global Positioning System)-tracked 40 adult lesser kestrels from 15 different Spanish breeding colonies, estimating the overlap index between home ranges and the distance between their centroids. It was found that lesser kestrels from the same breeding colony placed their nonbreeding areas at 347 ± 281 km (mean ± standard deviation) away from each other (range = 23–990), and their home ranges overlapped by 38.4 ± 23.6%. No differences between intra-colony and inter-colony metrics were found, which suggests that lesser kestrels from the same breeding cluster do not overwinter together, but they spread out and mixed independently of the colony belonging throughout the nonbreeding range of the species. Ultimately, this study highlights the importance of performing connectivity studies using fine-scale approaches.
Inflammatory myofibroblastic tumors: recent progress and future of targeted therapy
Authors: Nakano Kenji
Published: July 2023

An inflammatory myofibroblastic tumor is a rare component of bone and soft-tissue sarcomas that has distinct pathological features as a lymphoplasmacytic inflammatory infiltrate. As is the case for other non-small round cell sarcomas, surgical resection remains the standard treatment strategy for inflammatory myofibroblastic tumors, but recurrence is possible. Concerning systemic therapy, the available data for conventional chemotherapy (such as those of doxorubicin-based regimens) are limited, and case reports of anti-inflammatory inflammatory myofibroblastic tumor treatments describe some degree of symptom relief and efficacy against tumor progression. However, as more information about cancer genomics accumulates, the potential for molecularly targeted therapies for inflammatory myofibroblastic tumors has become more promising. Approximately half of inflammatory myofibroblastic tumors harbor anaplastic lymphoma kinase (ALK) fusion genes, and the other half could have potentially targetable fusion genes or mutations such as ROS1, NTRK and RET; case reports demonstrating the clinical efficacy of treatments targeted to inflammatory myofibroblastic tumor have been published, as have several prospective clinical trials. Few drugs are approved for the treatment of inflammatory myofibroblastic tumor, and most of them were approved for tumor-agnostic indications. Drugs that could be used for pediatric indications and dosing in inflammatory myofibroblastic tumor have also not been established. To provide effective targeted therapy for rare diseases such as inflammatory myofibroblastic tumor, it is necessary to obtain clinical evidence by designing and performing clinical trials and to find a path toward regulatory approval.
Evictionism, Libertarianism, and Duties of the Fetus
Authors: Dominiak Łukasz , Wysocki Igor
Published: July 2023

In “Evictionism and Libertarianism,” published in this journal, Walter Block defends the view that, although the fetus is a human being with all the rights to its body, it may nonetheless be evicted from the woman’s body as a trespasser, provided the pregnancy is unwanted. We argue that this view is untenable: the statement that the unwanted fetus is a trespasser does not follow from the premises that the fetus uninvitedly resides in the woman’s body and that the woman is a full self-owner. For this statement to follow, one more statement would have to be true; namely, the woman would have to hold her self-ownership rights specifically against the fetus, and for this to be the case, the fetus would have to have a correlative duty to the woman to abstain from interfering with her body. This statement, however, is false.
Consistent and fast inference in compartmental models of epidemics using Poisson Approximate Likelihoods
Authors: Whitehouse Michael , Whiteley Nick , Rimella Lorenzo
Published: July 2023

Addressing the challenge of scaling-up epidemiological inference to complex and heterogeneous models, we introduce Poisson approximate likelihood (PAL) methods. In contrast to the popular ordinary differential equation (ODE) approach to compartmental modelling, in which a large population limit is used to motivate a deterministic model, PALs are derived from approximate filtering equations for finite-population, stochastic compartmental models, and the large population limit drives consistency of maximum PAL estimators. Our theoretical results appear to be the first likelihood-based parameter estimation consistency results which apply to a broad class of partially observed stochastic compartmental models and address the large population limit. PALs are simple to implement, involving only elementary arithmetic operations and no tuning parameters, and fast to evaluate, requiring no simulation from the model and having computational cost independent of population size. Through examples we demonstrate how PALs can be used to: fit an age-structured model of influenza, taking advantage of automatic differentiation in Stan; compare over-dispersion mechanisms in a model of rotavirus by embedding PALs within sequential Monte Carlo; and evaluate the role of unit-specific parameters in a meta-population model of measles.
Genomic basis of multiphase evolution driving divergent selection of zinc-finger homeodomain genes
Authors: Jang Min-Jeong , Hong Woo-Jong , Park Young-Soo , Jung Ki-Hong , Kim Seungill
Published: July 2023

Gene families divergently evolve and become adapted as different genes with specific structures and functions in living organisms. We performed comprehensive structural and functional analyses of Zinc-finger homeodomain genes (ZF-HDs), including Mini zinc-finger genes (MIFs) and Zinc-finger with homeodomain genes (ZHDs), displaying competitive functions each other. Intensive annotation updates for 90 plant genomes verified that most MIFs (MIF-Is) exhibited distinct motif compositions from ZHDs, although some MIFs (MIF-Zs) contained ZHD-specific motifs. Phylogenetic analyses suggested that MIF-Zs and ZHDs originated from the same ancestral gene, whereas MIF-Is emerged from a distinct progenitor. We used a gene-editing system to identify a novel function of MIF-Is in rice: regulating the surface material patterns in anthers and pollen through transcriptional regulation by interacting ZHDs. Kingdom-wide investigations determined that (i) ancestral MIFs diverged into MIF-Is and MIF-Zs in the last universal common ancestor, (ii) integration of HD into the C-terminal of MIF-Zs created ZHDs after emergence of green plants and (iii) MIF-Is and ZHDs subsequently expanded independently into specific plant lineages, with additional formation of MIF-Zs from ZHDs. Our comprehensive analysis provides genomic evidence for multiphase evolution driving divergent selection of ZF-HDs.
CasDinG is a 5′-3′ dsDNA and RNA/DNA helicase with three accessory domains essential for type IV CRISPR immunity
Authors: Domgaard Hannah , Cahoon Christian , Armbrust Matthew J , Redman Olivine , Jolley Alivia , Thomas Aaron , Jackson Ryan N
Published: July 2023

CRISPR-associated DinG protein (CasDinG) is essential to type IV-A CRISPR function. Here, we demonstrate that CasDinG from Pseudomonas aeruginosa strain 83 is an ATP-dependent 5′-3′ DNA translocase that unwinds double-stranded (ds)DNA and RNA/DNA hybrids. The crystal structure of CasDinG reveals a superfamily 2 helicase core of two RecA-like domains with three accessory domains (N-terminal, arch, and vestigial FeS). To examine the in vivo function of these domains, we identified the preferred PAM sequence for the type IV-A system (5′-GNAWN-3′ on the 5′-side of the target) with a plasmid library and performed plasmid clearance assays with domain deletion mutants. Plasmid clearance assays demonstrated that all three domains are essential for type IV-A immunity. Protein expression and biochemical assays suggested the vFeS domain is needed for protein stability and the arch for helicase activity. However, deletion of the N-terminal domain did not impair ATPase, ssDNA binding, or helicase activities, indicating a role distinct from canonical helicase activities that structure prediction tools suggest involves interaction with dsDNA. This work demonstrates CasDinG helicase activity is essential for type IV-A CRISPR immunity as well as the yet undetermined activity of the CasDinG N-terminal domain.
G-quadruplexes in the evolution of hepatitis B virus
Authors: Brázda Václav , Dobrovolná Michaela , Bohálová Natália , Mergny Jean-Louis
Published: July 2023

Hepatitis B virus (HBV) is one of the most dangerous human pathogenic viruses found in all corners of the world. Recent sequencing of ancient HBV viruses revealed that these viruses have accompanied humanity for several millenia. As G-quadruplexes are considered to be potential therapeutic targets in virology, we examined G-quadruplex-forming sequences (PQS) in modern and ancient HBV genomes. Our analyses showed the presence of PQS in all 232 tested HBV genomes, with a total number of 1258 motifs and an average frequency of 1.69 PQS per kbp. Notably, the PQS with the highest G4Hunter score in the reference genome is the most highly conserved. Interestingly, the density of PQS motifs is lower in ancient HBV genomes than in their modern counterparts (1.5 and 1.9/kb, respectively). This modern frequency of 1.90 is very close to the PQS frequency of the human genome (1.93) using identical parameters. This indicates that the PQS content in HBV increased over time to become closer to the PQS frequency in the human genome. No statistically significant differences were found between PQS densities in HBV lineages found in different continents. These results, which constitute the first paleogenomics analysis of G4 propensity, are in agreement with our hypothesis that, for viruses causing chronic infections, their PQS frequencies tend to converge evolutionarily with those of their hosts, as a kind of ‘genetic camouflage’ to both hijack host cell transcriptional regulatory systems and to avoid recognition as foreign material.
Integration of gene expression and DNA methylation data across different experiments
Authors: Itai Yonatan , Rappoport Nimrod , Shamir Ron
Published: July 2023

Integrative analysis of multi-omic datasets has proven to be extremely valuable in cancer research and precision medicine. However, obtaining multimodal data from the same samples is often difficult. Integrating multiple datasets of different omics remains a challenge, with only a few available algorithms developed to solve it. Here, we present INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples. To enable integration, INTEND learns a predictive model between the two omics by training on multi-omic data measured on the same set of samples. In comprehensive testing on 11 TCGA (The Cancer Genome Atlas) cancer datasets spanning 4329 patients, INTEND achieves significantly superior results compared with four state-of-the-art integration algorithms. We also demonstrate INTEND’s ability to uncover connections between DNA methylation and the regulation of gene expression in the joint analysis of two lung adenocarcinoma single-omic datasets from different sources. INTEND’s data-driven approach makes it a valuable multi-omic data integration tool. The code for INTEND is available at https://github.com/Shamir-Lab/INTEND.
School inspections and headteachers’ mental health
Authors: Sen Dil , Nicholson Paul J
Published: July 2023

Media attention has highlighted the risk of suicides among headteachers whose schools were downgraded by school inspectors. The authors emphasize the wider problem of mental ill-health among teachers. They argue that more should be done to protect and promote teachers’ mental health—starting with job-specific stress risk assessments. They also argue for a comprehensive review to understand and address the broad factors that place teachers and headteachers at increased risk of mental ill-health.
Fulminant Hepatic Failure as the Initial Presentation of Hodgkin Lymphoma in 4 Patients With Human Immunodeficiency Virus
Authors: Cook Mary , Williams Matthew , Law Jennie Y , Riedel David J
Published: July 2023

In the era of antiretroviral therapy (ART), Hodgkin Lymphoma (HL) is a common non-AIDS-defining cancer with increasing incidence in people with human immunodeficiency virus (PWH). Through review of these cases, we identify clinical patterns such as declining CD4 count despite ART, hyperbilirubinemia and recurrent fever, which preceded diagnosis. Identifying these important signs and symptoms may lead to earlier diagnosis and initiation of therapy. Fulminant hepatic failure limits the ability to give standard of care chemotherapy, likely jeopardizing outcomes in this patient population. Alternative bridging therapies should be considered until hepatic function improves.
Unexpected Loa loa Finding in an Asymptomatic Patient From The Gambia: A Case Report
Authors: Treviño Begoña , Zarzuela Francesc , Oliveira-Souto Inés , Maturana Carles Rubio , Serre-Delcor Núria , Aznar Maria L , Pou Diana , Goterris Lidia , Salvador Fernando , Bosch-Nicolau Pau , Rubio José M , Ruiz Edurne , Molina Israel , Sulleiro Elena
Published: July 2023

A 17-year-old asymptomatic male from The Gambia presented for a routine health examination after migration to Spain. Laboratory diagnosis confirmed the presence of Loa loa microfilariae. This unusual finding emphasizes the importance of screening in newly arrived migrants and the need of an extended anamnesis including migratory route and previous travels.
A single amino acid substitution in MdLAZY1A dominantly impairs shoot gravitropism in Malus
Authors: Dougherty Laura , Borejsza-Wysocka Ewa , Miaule Alexandre , Wang Ping , Zheng Desen , Jansen Michael , Brown Susan , Piñeros Miguel , Dardick Christopher , Xu Kenong
Published: July 2023

Plant architecture is 1 of the most important factors that determines crop yield potential and productivity. In apple (Malus domestica), genetic improvement of tree architecture has been challenging due to a long juvenile phase and growth as complex trees composed of a distinct scion and a rootstock. To better understand the genetic control of apple tree architecture, the dominant weeping growth phenotype was investigated. We report the identification of MdLAZY1A (MD13G1122400) as the genetic determinant underpinning the Weeping (W) locus that largely controls weeping growth in Malus. MdLAZY1A is 1 of the 4 paralogs in apple that are most closely related to AtLAZY1 involved in gravitropism in Arabidopsis (Arabidopsis thaliana). The weeping allele (MdLAZY1A-W) contains a single nucleotide mutation c.584T>C that leads to a leucine to proline (L195P) substitution within a predicted transmembrane domain that colocalizes with Region III, 1 of the 5 conserved regions in LAZY1-like proteins. Subcellular localization revealed that MdLAZY1A localizes to the plasma membrane and nucleus in plant cells. Overexpressing the weeping allele in apple cultivar Royal Gala (RG) with standard growth habit impaired its gravitropic response and altered the growth to weeping-like. Suppressing the standard allele (MdLAZY1A-S) by RNA interference (RNAi) in RG similarly changed the branch growth direction to downward. Overall, the L195P mutation in MdLAZY1A is genetically causal for weeping growth, underscoring not only the crucial roles of residue L195 and Region III in MdLAZY1A-mediated gravitropic response but also a potential DNA base editing target for tree architecture improvement in Malus and other crops.