bluuebunny/crossref_metadata_2025 huggingface dataset:
Study of bonding parameters with Al and Au wires on Pd and Ag coatings
Authors: Tomov R , Kolev G , Dobrikov G , Aleksandrova M
Published: February 2024

The process of electrical connection with gold and aluminium wires to palladium and silver electrodes is studied. Parameters of the wire bonding, such as bond force, ultrasonic power, bond time and temperature of the layers, controlled by heating the substrate are varied to explore the reliability of the bonds in terms of mechanical strength, electrical conductivity and interdiffusion of particles between the electrode and functional material at different bonding conditions. The importance of this study is due to the need of electrical connectivity at the stage of wiring and packaging of gas sensors with a novel organic nanomaterial (carbyne), requiring different types of electrodes – Ohmic or Schottky - according to the measurement principle and sensor architecture. Pd and Ag are identified as the most suitable for Ohmic and Schottky contacts, respectively, because of their favourable energy level alignment at the organic/metal interface. The chosen method for bonds testing is measurement of the pull force causing bond failure. The results show that Pd coating was bondable by Au wire, and Ag coating by Al wire, as well as Au on Pd bonds have 4 times higher strength. It is found that the bonding procedure doesn’t affect negatively on the Au/Pd/carbyne interface in terms of diffusion and redistribution of metal particles, but Al/Ag/carbyne is characterized by poor adhesion and the bonds are peeled-off. The results give new knowledge for the fabrication of advanced gas sensors and for the interaction of the carbyne with different metals, which will serve as a base for further optimization of the manufacturing technology toward their commercialization.
Optical control of coherent magneto-optical resonances in potassium
Authors: Tsvetkov S , Gateva S
Published: February 2024

The influence of Light Induced Atomic Desorption (LIAD) on the potassium D2 line magneto-optical resonances in uncoated buffer-gas optical cell is investigated. LIAD effect reduces the drawbacks of conventional heating for achieving high atomic density that is essential for many spectroscopy-based applications. Another feature of LIAD is the impact on the dwelling time of the atoms when colliding with the surface of the cell. In this work we investigate LIAD from point of view to distinguish the influence of LIAD on the atomic density from the dwelling time as well as to control and improve the parameters of magneto-optical resonances in potassium vapor. The results are interesting for development of new precise optical sensors and devices for various applications.
Characterization of the TJ-II stellarator plasma by means of reciprocating Langmuir probes
Authors: Ivanova P , Hasan E , Vasileva E , Dimitrova M , Voldiner I , McCarthy K J , Hidalgo C , Popov Tsv K
Published: February 2024

Experiments were conducted in deuterium plasma in the TJ-II stellarator by means of swept Langmuir probes mounted on reciprocating probes manipulators. The results were processed using the four-parameter fit, as well as the triple-probe and the first-derivative probe techniques. The parameters determined were the floating potential, the ion saturation current density, the electron temperature and density, and the plasma potential. The results were obtained for two plasma heating techniques – electron cyclotron resonance heating (ECRH) and neutral beam injection (NBI) heating. In the case of ECRH, employing the first-derivative probe technique resulted in finding that the electron-energy distribution function (EEDF) was not Maxwellian, but rather a bi-Maxwellian one with thermal (14-25 eV) and cold (4-5 eV) electrons. In comparison, during NBI heating we found a Maxwellian EEDF with the electron temperature being around 5 eV and slightly increasing in the confined plasma, but always remaining below 15 eV. We present a detailed analysis and discussion of the data for the plasma parameters as acquired by different techniques of using the reciprocating probe manipulator.
Mn3O4/Vulcan XC-72R composites: preparation, physicochemical characterization and electrochemical study for purification of organic contaminants
Authors: Tsacheva Ivelina , Gigova Adriana , Dimitrov Ognian , Dimitrova Mariela , Stefanov Stefan , Uzun Dzhamal
Published: February 2024

The microwave-assisted technique was applied to the preparation of composites from manganese(II) acetate and Carbon-supported (Vulcan XC-72R). Composites were prepared by chemical deposition of manganese(II) acetate nanoparticles onto Vulcan XC-72R carbon black (catalytic mass) using microwave irradiation. The new composites were physicochemically characterized by Energy-dispersive X-ray spectroscopy (EDX) with scanning electron microscopy (SEM), BET surface area, pore size distribution and X-ray diffraction (XRD). BET analysis of Mn3O4/Vulcan XC-72R composites obtained by alkali method has shown specific surface area of 1135 m2/g. Novel composites were electrochemically studied as catalysts for the remediation of organic contaminants in industrial waters. From novel catalytic mass, double-sided coated electrodes on a Nickel mesh conductor were made by pressing and heating at 250 °C. The prepared electrodes have geometric area of 2.5 cm2. The electrodes were fabricated and studied regarding the amount of catalyst and 35 % Teflonized Vulcan XC-72R. Electrochemical studies were carried out for phenol oxidation in an aqueous solution in model electrolyte: phenol solution 200 mg.L-1 and supporting electrolyte: 18 g.L-1 NaCl and 2.6 mg.L-1 Na2SO4.
Investigation of the thermal gradients formed during the process of cooling of WAAM built Al99.7 specimen
Authors: Ormanova M , Kotlarski G , Kaisheva D , Nikitin A , Ossenbrink R , Doynov N , Valkov S , Michailov V
Published: February 2024

This work presents a preliminary experiment used to determine the possibility of developing a thermal model used to predict the thermal gradients formed during the process of wire and arc additive manufacturing (WAAM). For this purpose, an Al99.7 specimen was built using gas metal arc welding (GMAW) in the cold arc pulse mode. The temperature of both the substrate and each consecutive layer was measured using thermocouples and infrared thermometers and the experimental data was used for the calibration of the developed thermal model. The obtained results can be used for the further development of the thermal model.
Data mining techniques for quality improvement of electron beam welding process
Authors: Kolev G , Asenova-Robinzonova A , Koleva L , Koleva E
Published: February 2024

Besides the fulfilment of the technological requirements for the geometry of the obtained welded joints by electron beam welding, there is a necessity to avoid the conditions, which more probably will lead to defect appearance. It is assumed that the appearance of defects is more probable under some regime conditions. For the modelling of the dependence of bivariate quality characteristics (such as the defect appearance) on the process parameters two different modelling approaches are applied and compared – logistic regression and neural networks. The implemented model-based approaches are compared and applied for the prediction of the defect appearance, depending on the variation of the electron beam process parameters.
Colorful image reconstruction from neuromorphic event cameras with biologically inspired deep color fusion neural networks
Authors: Cohen-Duwek Hadar , Tsur Elishai Ezra
Published: February 2024

Neuromorphic event-based cameras communicate transients in luminance instead of frames, providing visual information with a fine temporal resolution, high dynamic range and high signal-to-noise ratio. Enriching event data with color information allows for the reconstruction of colorful frame-like intensity maps, supporting improved performance and visually appealing results in various computer vision tasks. In this work, we simulated a biologically inspired color fusion system featuring a three-stage convolutional neural network for reconstructing color intensity maps from event data and sparse color cues. While current approaches for color fusion use full RGB frames in high resolution, our design uses event data and low-spatial and tonal-resolution quantized color cues, providing a high-performing small model for efficient colorful image reconstruction. The proposed model outperforms existing coloring schemes in terms of SSIM, LPIPS, PSNR, and CIEDE2000 metrics. We demonstrate that auxiliary limited color information can be used in conjunction with event data to successfully reconstruct both color and intensity frames, paving the way for more efficient hardware designs.
Agrivoltaic system design tools for managing trade-offs between energy production, crop productivity and water consumption
Authors: Warmann Emily , Jenerette G Darrel , Barron-Gafford Greg A
Published: February 2024

Agrivoltaic systems that locate crop production and photovoltaic energy generation on the same land have the potential to aid the transition to renewable energy by reducing the competition between food, habitat, and energy needs for land while reducing irrigation requirements. Experimental efforts to date have not adequately developed an understanding of the interaction among local climate, array design and crop selection sufficient to manage trade-offs in system design. This study simulates the energy production, crop productivity and water consumption impacts of agrivoltaic array design choices in arid and semi-arid environments in the Southwestern region of the United States. Using the Penman–Monteith evapotranspiration model, we predict agrivoltaics can reduce crop water consumption by 30%–40% of the array coverage level, depending on local climate. A crop model simulating productivity based on both light level and temperature identifies afternoon shading provided by agrivoltaic arrays as potentially beneficial for shade tolerant plants in hot, dry settings. At the locations considered, several designs and crop combinations exceed land equivalence ratio values of 2, indicating a doubling of the output per acre for the land resource. These results highlight key design axes for agrivoltaic systems and point to a decision support tool for their development.
Sea surface temperature driven modulation of decadal co-variability in mean and extreme precipitation
Authors: Adamu Mustapha , McGregor Shayne , Gallant Ailie J E
Published: February 2024

This study investigates the role that sea surface temperature (SST) variability plays in modulating the relationship between decadal-scale mean precipitation and monthly-scale extreme precipitation using the Australian Community Climate and Earth System Simulator Earth System model (ACCESS ESM1.5) climate model. The model large ensemble successfully reproduces the observed strong co-variability between monthly mean rainfall and wet extreme rainfall, defined as monthly rainfall totals above the 95th percentile. Removing SST variability in the ACCESS ESM1.5 model significantly weakens the co-variability between mean and wet extremes over most of the globe, showing that SSTs play a key role in modulating this co-variability. The study identifies Pacific and Atlantic SST patterns as the main drivers of the decadal scale co-variability in mean and extreme wet precipitation. On the other hand, observations and model results show that co-variability between mean and dry extremes is generally weaker than for wet extremes, with highly regional signals. Model experiments also show that SST variability plays a weaker role in modulating the co-variability between the mean precipitation and dry extremes as compared to wet extremes. These results suggest that stochastic atmospheric variability plays a stronger role in generating dry precipitation extremes compared SST forcing.
The impacts of shipping emissions on lightning: roles of aerosol-radiation-interactions and aerosol-cloud-interactions
Authors: Sun Ruize , Lu Xiao , Gao Meng , Du Yu , Lin Haipeng , Wright Chris , He Cheng , Yin Ke
Published: February 2024

Long-term (2005–2021) observations from the World Wide Lightning Location Network reveal significantly larger flash counts over heavily trafficked shipping lanes in the northeastern Indian Ocean compared to nearby regions. Here, we use the online coupled meteorology-chemistry model WRF-Chem to examine the impact of aerosols from shipping emissions on lightning activity over one of the world’s busiest shipping lanes (5–7° N, 82–92° E). We conduct three case simulations in January 2013, 2015, and 2018 when frequent lightning activities were recorded. The WRF-Chem model with lightning parameterized based on convective cloud-top height captures the temporal evolution of lightning activities but overestimates the magnitude of lightning counts. We find that all three cases consistently show enhanced lightning flash counts due to shipping-induced aerosols by 6.2%–22.3%, accompanied by increased cloud droplet number, cloud water concentration, radar reflectivity, and cloud-top height. Sensitivity simulations show that aerosol-cloud-interactions from shipping aerosols consistently enhance the strength of convection and lightning frequency in all three cases, by increasing cloud condensation nuclei and cloud droplet numbers, delaying precipitation of cloud water, allowing the lift and accumulation of water vapor, increasing release of latent heat, and finally invigorating convections. In comparison, aerosol-radiation-interactions show inconsistent contributions to convection and lightning, which enhance lightning frequency in the 2013 and 2015 cases but decrease lightning frequency in the 2018 case. This inconsistency may be attributed to differences in the number and vertical structure of shipping aerosols and cloud droplet in the three cases. Our study thus approves the certain but complicated anthropogenic impacts on lightning activities through shipping-induced aerosols, which has important implications for understanding future trends in lightning and its impact on atmospheric chemistry and climate.
Magnetic and electronic properties of anisotropic magnetite nanoparticles
Authors: Mitra Arijit , Mohapatra Jeotikanta , Aslam M
Published: February 2024

Magnetic materials at the nanometer scale can demonstrate highly tunable properties as a result of their reduced dimensionality. While significant advancements have been made in the production of magnetic oxide nanoparticles over the past decades, maintaining the magnetic and electronic phase stabilities in the nanoscale regime continues to pose a critical challenge. Finite-size effects modify or even eliminate the strongly correlated magnetic and electronic properties through strain effects, altering density and intrinsic electronic correlations. In this review, we examine the influence of nanoparticle size, shape, and composition on magnetic and tunneling magnetoresistance (TMR) properties, using magnetite (Fe3O4) as an example. The magnetic and TMR properties of Fe3O4 nanoparticles are strongly related to their size, shape, and synthesis process. Remarkably, faceted nanoparticles exhibit bulk-like magnetic and TMR properties even at ultra-small size-scale. Moreover, it is crucial to comprehend that TMR can be tailored or enhanced through chemical and/or structural modifications, enabling the creation of ‘artificially engineered’ magnetic materials for innovative spintronic applications.
The influence of NaOH concentration on the strength and microstructure of ceramic binders prepared from coal gangue through geopolymerization
Authors: Zhu Boheng , Yu Ruien , Shang Jinyu , Xi Xuanye , Liu Yao , Zhu Xijing
Published: February 2024

The efficient utilization of coal gangue plays an indispensable role in reducing environmental pressure, improving resource utilization efficiency and promoting green development. As a kind of solid waste rich in silicon and aluminium, coal gangue can be used to prepare ceramic materials. Therefore, a new ceramic preparation process was proposed in this study to prepare ceramic binders for grinding wheels by geopolymerization. The SiO2-B2O3-Al2O3-RO-R2O ceramic binder, a green and low-cost material, was successfully prepared using this method. The effect of the concentration of NaOH on the mechanical properties and microstructure of the ceramic binder was also studied. The strength and microstructure of different ceramic binders were characterized by XRD, TG-DTG, SEM-EDS and FT-IR. The results show that the bending strength of the geopolymer ceramic binder increases proportionately with the increase of NaOH concentration. When the concentration of sodium hydroxide is 15 M, the bending strength reaches 19 MPa. N-A-S-H gel and zeolite formed in the geopolymerization reaction and the pores formed in the sintering process have a significant effect on the bending strength of the ceramic binder. This technology can significantly stimulate the chemical activity of coal gangue and provide innovative ideas for efficient utilization of coal gangue.
Phase composition, surface chemistry and electrochemical studies of electrodeposited AlMnFeCuNi high entropy alloy composite coatings incorporated with carbon nanotubes
Authors: Mohan Mansha , Pandel Upender , Kumar Krishna
Published: February 2024

AlMnFeCuNi high entropy alloy (HEA) coatings were electrodeposited onto mild steel substrate with and without incorporation of carbon nano tubes (CNT). This paper focused on the morphology, hardness, wear and corrosion behaviour for as deposited HEA and HEA-CNT coatings. Both the coatings constituted simple solid solution with face-centered cubic (FCC) structure. The addition of carbon nano tubes in the HEA coatings as revealed by scanning electron microscopy showed more smaller granules and compact morphology with least coating thickness value (5 ± 0.35 μm). Enhanced Anti-wear performance results in higher hardness and lower coefficient of friction. The presence of CNTs resulted improvised corrosion resistant properties in 3.5% NaCl corrosive media. The formation of more protective oxides such as Alox
+3, Mnox
+2 and Feox
+3 on passive oxide layer in HEA-CNT coatings acted as a barrier, protected it from corrosion.
Two distinct declining trend of autumn Arctic sea ice concentration before and after 2002
Authors: Li Yijiao , Jiang Zhina , Yao Yao , Ding Minghu , Zhang Lei
Published: February 2024

This study investigates the Arctic sea ice concentration trend during 1979–2021 and explores why the autumn Arctic sea ice loss is accelerated after 2002 and its trend declining center shifts from the Chukchi Sea to the Barents-Kara-Laptev Seas. Attribution analysis reveals that the enhanced summer sea ice concentration negative trend in large part explains the autumn sea ice concentration accelerating reduction, whereas it is the trend center shift of increased downward longwave radiation that accounts for mostly of the autumn sea ice concentration decline center shift. Further analysis suggests the downward longwave radiation trend is closely related to large-scale atmospheric circulation changes. A tendency towards a dipole structure with an anticyclonic circulation over Greenland and the Arctic Ocean and a cyclonic circulation over Barents-Kara Seas enhances (suppresses) the downward longwave radiation over Western (Eastern) Arctic by warming and moistening (cooling and drying) the lower troposphere during 1979–2001. In comparison, a tendency towards a stronger Ural anticyclone combined with positive phase of the North Atlantic Oscillation pattern significantly promotes the increase of downward longwave radiation over Barents-Kara-Laptev Seas during 2002–2021. Our results set new insights into the Arctic sea ice variability and deepen our understanding of the climate change.
The spatiotemporal changes and trade-off synergistic effects of ecosystem services in the Jianghan Plain of China under different scenarios
Authors: Ren Wei , Zhang Xuesong , Peng Hongjie
Published: February 2024

Disturbance from human activities has intensified the evolution of ecosystem structure in the Jianghan Plain of China, leading to intensified conflicts between ecosystem services. It is essential to clarify the trade-off synergies between ecosystem services in the Jianghan Plain of China to better coordinate the economic and social development and ecological protection of the region. Based on historical data and scenario predictions using the GeoSOS-FLUS model, the InVEST model was applied to five key ecosystem services: Carbon storage, crop production, habitat quality, soil conservation and water yield from 2000 to 2020. Spearman correlation analysis was used to explore the trade-off synergies between different ecosystem services in space and time. The results showed that arable land and water land areas are the most important land types in the Jianghan Plain of China. From 2000 to 2020, the increase in build-up land and water land areas was accompanied by a decrease in arable land, forest land and unused land, and an increase in forest land. The natural development scenario in 2035 continues this trend except forest land reduction, while the ecological protection scenario reverses this trend. From 2000 to 2020, crop production, water yield, and soil conservation increased in the Jianghan Plain of China, while carbon storage and habitat quality declined significantly, showing a spatial distribution pattern of higher in the northwest and lower in the southeast. The comprehensive ecosystem services simulated in 2035 showed a downward trend compared with 2020, and the ecological protection scenario has the smallest decrease. There is an overall synergistic relationship between the five ecosystem services in the Jianghan Plain of China, and the strongest synergistic relationship is between soil conservation and water yield. The spatiotemporal relationship between the ecosystems in the Jianghan Plain of China is dynamic and requires sustainable management. Thus, it is necessary to rationally utilize land resources and enhance the ecological functions of the area to minimize trade-offs based on scientific land and spatial planning to maximize synergy.
Research on the impact of public environmental participation on foreign direct investment: evidence from China
Authors: Xu Yihua , Du Zizhe , Kong Lingqian , Xu Kai
Published: February 2024

Since the reform and opening up, the scale of foreign direct investment (FDI) inflows into China has been continuously expanding, but the imperfect environmental governance mechanism has led to increasingly severe environmental problems in China. This paper studies the impact and mechanism of public environmental participation (PEP) on FDI. The results show that PEP has a significant negative impact on the FDI inflow of enterprises. Hindrance effect of PEP on enterprise FDI is more obvious in economically developed eastern regions, coastal cities and first-tier cities. PEP has a greater impact on FDI in high-tech industries. The economic growth target has a restraining effect on China’s environmental protection, weakening public supervision of FDI. The constraint of economic growth targets increases the pressure to develop the economy, and weakens the inhibitory effect of PEP on corporate FDI. This study provides important empirical evidence for improving China’s environmental governance system and high-quality utilization of foreign investment.
Bibliometric analysis of traffic-related air pollution: using CiteSpace to explore the knowledge structure and trends
Authors: Lin Haochuan
Published: February 2024

Although traffic-related air pollution (TRAP) has been a long-standing problem, few bibliometric- and visual analysis-based literature reviews have been performed. In light of this issue, future research plans and directions in the field of TRAP must be determined. Therefore, this study performed a bibliometric analysis of the TRAP publishing trends, including the countries, institutional collaborations, author collaborations, keywords, and hotspots. The information visualization software CiteSpace was used to analyze the relevant literature collected from the Web of Science (WoS) from 2003 to 2022. The main findings of this study included the following: (1) the main keywords in TRAP research are particulate matter, exposure, health, nitrogen dioxide, and mortality; (2) current research is focused on the impacts of TRAP on humans; and (3) potential hotspots for future TRAP research are source apportionment, asthma, heart rate variability, and mobile monitoring. This article aims to develop a better understanding of current research trends in TRAP and provide directions for future research.
The End of the Augustinian Atemporality around the Turn of the First Millennium
Authors: Gabriele Matthew
Published: February 2024

In tenth- and eleventh-century Europe, time began to become unstuck. Although this has been called a fallow period in the history of biblical exegesis, we can actually see how exegesis overwhelmed our subjects. For authors such as Odo of Cluny and Rodulfus Glaber, among others, everything around them seemed pregnant with meaning. As such, history-writing itself began to become a form of exegesis—a way of interpreting God’s plan. More importantly, the hermeneutics of the cloister were pushed outwards from the cloister and the aristocracy was called to enact events in sacred history. It seemed like a new age of prophecy had begun.
Use, failure, and non-compliance of respiratory personal protective equipment and risk of upper respiratory tract infections—A longitudinal repeated measurement study during the COVID-19 pandemic among healthcare workers in Denmark
Authors: Biering Karin , Kinnerup Martin , Cramer Christine , Dalbøge Annett , Toft Würtz Else , Lund Würtz Anne Mette , Kolstad Henrik Albert , Schlünssen Vivi , Meulengracht Flachs Esben , Nielsen Kent J
Published: February 2024

Introduction

Upper respiratory tract infections (URTI) are common and a common cause of sick-leave for healthcare workers, and furthermore pose a threat especially for patients susceptible to other diseases. Sufficient use of respiratory protective equipment (RPE) may protect both the workers and the patients. The COVID-19 pandemic provided a unique opportunity to study the association between use of RPE and URTI in a real-life setting. The aim of this study was to examine if failure of RPE or non-compliance with RPE guidelines increases the risk of non-COVID-19 URTI symptoms among healthcare workers.

Methods

In a longitudinal cohort study, we collected self-reported data daily on work tasks, use of RPE, and URTI symptoms among healthcare workers with patient contact in 2 Danish Regions in 2 time periods during the COVID-19 pandemic. The association between failure of RPE or non-compliance with RPE guidelines and URTI symptoms was analyzed separately by generalized linear models. Persons tested positive for severe acute respiratory syndrome coronavirus 2 were censored from the analyses. The 2 waves of data collection were analyzed separately, as there were differences in recommendations of RPE during the 2 waves.

Results

We found that for healthcare workers performing work tasks with a risk of transmission of viruses or bacteria, failure of RPE was associated with an increased risk of URTI symptoms, RR: 1.65[0.53–5.14] in wave 1 and RR: 1.30[0.56–3.03] in wave 2. Also non-compliance with RPE guidelines was associated with an increased risk of URTI symptoms compared to the use of RPE in wave 1, RR: 1.28[0.87–1.87] and wave 2, RR: 1.39[1.01–1.91]. Stratifying on high- versus low-risk tasks showed that the risk related to failure and non-compliance was primarily associated with high-risk tasks, although not statistically significant.

Discussion

The study was conducted during the COVID-19 pandemic and thus may be affected by other preventive measures in society. However, this gave the opportunity to study the use of RPE in a real-life setting, also in departments that did not previously use RPE. The circumstances in the 2 time periods of data collection differed and were analyzed separately and thus the sample size was limited and affected the precision of the estimates.

Conclusion

Failures of RPE and non-compliance with RPE guidelines may increase the risk of URTI, compared to those who reported use of RPE as recommended. The implications of these findings are that the use of RPE to prevent URTI could be considered, especially while performing high-risk tasks where other prevention strategies are not achievable.
A compressive seeding algorithm in conjunction with reordering-based compression
Authors: Ji Fahu , Zhou Qian , Ruan Jue , Zhu Zexuan , Liu Xianming
Published: February 2024

Motivation

Seeding is a rate-limiting stage in sequence alignment for next-generation sequencing reads. The existing optimization algorithms typically utilize hardware and machine-learning techniques to accelerate seeding. However, an efficient solution provided by professional next-generation sequencing compressors has been largely overlooked by far. In addition to achieving remarkable compression ratios by reordering reads, these compressors provide valuable insights for downstream alignment that reveal the repetitive computations accounting for more than 50% of seeding procedure in commonly used short read aligner BWA-MEM at typical sequencing coverage. Nevertheless, the exploited redundancy information is not fully realized or utilized.

Results

In this study, we present a compressive seeding algorithm, named CompSeed, to fill the gap. CompSeed, in collaboration with the existing reordering-based compression tools, finishes the BWA-MEM seeding process in about half the time by caching all intermediate seeding results in compact trie structures to directly answer repetitive inquiries that frequently cause random memory accesses. Furthermore, CompSeed demonstrates better performance as sequencing coverage increases, as it focuses solely on the small informative portion of sequencing reads after compression. The innovative strategy highlights the promising potential of integrating sequence compression and alignment to tackle the ever-growing volume of sequencing data.

Availability and implementation

CompSeed is available at https://github.com/i-xiaohu/CompSeed.
Inferring HIV transmission patterns from viral deep-sequence data via latent typed point processes
Authors: Bu Fan , Kagaayi Joseph , Grabowski Mary Kate , Ratmann Oliver , Xu Jason
Published: February 2024

Viral deep-sequencing data play a crucial role toward understanding disease transmission network flows, providing higher resolution compared to standard Sanger sequencing. To more fully utilize these rich data and account for the uncertainties in outcomes from phylogenetic analyses, we propose a spatial Poisson process model to uncover human immunodeficiency virus (HIV) transmission flow patterns at the population level. We represent pairings of individuals with viral sequence data as typed points, with coordinates representing covariates such as gender and age and point types representing the unobserved transmission statuses (linkage and direction). Points are associated with observed scores on the strength of evidence for each transmission status that are obtained through standard deep-sequence phylogenetic analysis. Our method is able to jointly infer the latent transmission statuses for all pairings and the transmission flow surface on the source-recipient covariate space. In contrast to existing methods, our framework does not require preclassification of the transmission statuses of data points, and instead learns them probabilistically through a fully Bayesian inference scheme. By directly modeling continuous spatial processes with smooth densities, our method enjoys significant computational advantages compared to previous methods that rely on discretization of the covariate space. We demonstrate that our framework can capture age structures in HIV transmission at high resolution, bringing valuable insights in a case study on viral deep-sequencing data from Southern Uganda.
A flexible framework for spatial capture-recapture with unknown identities
Authors: van Dam-Bates Paul , Papathomas Michail , Stevenson Ben C , Fewster Rachel M , Turek Daniel , Stewart Frances E C , Borchers David L
Published: February 2024

Camera traps or acoustic recorders are often used to sample wildlife populations. When animals can be individually identified, these data can be used with spatial capture-recapture (SCR) methods to assess populations. However, obtaining animal identities is often labor-intensive and not always possible for all detected animals. To address this problem, we formulate SCR, including acoustic SCR, as a marked Poisson process, comprising a single counting process for the detections of all animals and a mark distribution for what is observed (eg, animal identity, detector location). The counting process applies equally when it is animals appearing in front of camera traps and when vocalizations are captured by microphones, although the definition of a mark changes. When animals cannot be uniquely identified, the observed marks arise from a mixture of mark distributions defined by the animal activity centers and additional characteristics. Our method generalizes existing latent identity SCR models and provides an integrated framework that includes acoustic SCR. We apply our method to estimate density from a camera trap study of fisher (Pekania pennanti) and an acoustic survey of Cape Peninsula moss frog (Arthroleptella lightfooti). We also test it through simulation. We find latent identity SCR with additional marks such as sex or time of arrival to be a reliable method for estimating animal density.
Leaf micromorphology in Rosaceae tribe Spiraeeae (subfamily Amygdaloideae) and its systematic and ecological implications
Authors: Song Jun-Ho , Oak Min-Kyeong , Hong Suk-Pyo
Published: February 2024

We conducted a comparative micromorphological study on the leaves of all nine genera of the Rosaceae tribe Spiraeeae, including the monotypic Korean genus Pentactina. Spiraeeae possess amphistomatic and hypostomatic leaves. Leaf epidermal characteristics varied with the morphology of stomatal complexes, epidermal cells, trichomes, and epicuticular waxes. Specific leaf epidermal features may be systematically relevant for identifying lower taxonomic levels, genera, and/or species. For example, papillate epidermal cell types were consistently observed in Spiraea sect. Calospira. Hirtellous trichomes are diagnostic characteristics of the genera Holodiscus and Kelseya among this tribe. Short-stalked capitate glandular and crispate villous trichomes were only observed in Holodiscus microphyllus and Spiraea douglasii, respectively. We also confirmed that leaf epidermal characteristics strongly support the independent taxonomic position of the Korean endemic Pentactina and the transfer from Physocarpus to Spiraea of Physocarpus insularis. Moreover, we identified xeromorphic features in the studied taxa and inferred their ecological functions, such as water repellence and anti-transpirant activities. This study presents new perspectives for future research on character evolution and xeromorphic adaptation on the basis of leaf epidermal characteristics.
Spatiotemporal Trends in Group A Streptococcal Pharyngitis in the United States
Authors: Kline Madeleine C , Kissler Stephen M , Whittles Lilith K , Barnett Michael L , Grad Yonatan H
Published: February 2024

Background

Group A Streptococcus (GAS) causes an estimated 5.2 million outpatient visits for pharyngitis annually in the United States, with incidence peaking in winter, but the annual spatiotemporal pattern of GAS pharyngitis across the United States is poorly characterized.

Methods

We used outpatient claims data from individuals with private medical insurance between 2010 and 2018 to quantify GAS pharyngitis visit rates across U.S. census regions, subregions, and states. We evaluated seasonal and age-based patterns of geographic spread and the association between school start dates and the summertime upward inflection in GAS visits.

Results

The South had the most visits per person (yearly average, 39.11 visits per 1000 people; 95% confidence interval, 36.21–42.01) and the West had the fewest (yearly average, 17.63 visits per 1000 people; 95% confidence interval, 16.76–18.49). Visits increased earliest in the South and in school-age children. Differences in visits between the South and other regions were most pronounced in the late summer through early winter. Visits peaked earliest in central southern states, in December to January, and latest on the coasts, in March. The onset of the rise in GAS pharyngitis visits correlated with, but preceded, average school start times.

Conclusions

The burden and timing of GAS pharyngitis varied across the continental United States, with the South experiencing the highest overall rates and earliest onset and peak in outpatient visits. Understanding the drivers of these regional differences in GAS pharyngitis will help in identifying and targeting prevention measures.
Pattern Models: A Dynamic Epistemic Logic For Distributed Systems
Authors: Castañeda Armando , van Ditmarsch Hans , Rosenblueth David A , Velázquez Diego A
Published: February 2024

We introduce pattern models, a dynamic epistemic logic for analyzing distributed systems. First, we present a version of pattern models where the full-information protocol, widely studied in distributed computability, is static in the product definition of pattern models. Next, we parametrize such a logic so as to add the capability to model dynamics of arbitrary deterministic protocols. We thus give a systematic construction of pattern models for a large variety of distributed-computing models called dynamic-network models. Using pattern models, the epistemic dynamics of a proper subclass of dynamic-network models called oblivious can be described using a static pattern model, hence using constant space. For this case, we present a sufficient unsolvability condition for the consensus task that can be easily verified analyzing the structure of the initial epistemic model and the pattern model for a given oblivious dynamic-network model.
Relation among hypertriglyceridaemia, cardiometabolic disease, and hereditary factors—design and rationale of the Stockholm hyperTRIglyceridaemia REGister study
Authors: Andersson Daniel P , Littmann Karin , Kindborg Gustav , Eklund Daniel , Sejersen Kristina , Yan Jane , Eriksson Hogling Daniel , Parini Paolo , Brinck Jonas
Published: February 2024

Aims

Hypertriglyceridaemia (hTG) is associated with atherosclerotic cardiovascular disease, pancreatitis, and non-alcoholic fatty liver disease (NAFLD) in large population-based studies. The understanding of the impact of hereditary hTG and cardiometabolic disease status on the development of hTG and its associated cardiometabolic outcomes is more limited. We aimed to establish a multigenerational cohort to enable studies of the relationship between hTG, cardiometabolic disease and hereditary factors.

Methods and results

The population-based observational Stockholm hyperTRIglyceridaemia REGister (STRIREG) study includes 1 460 184 index individuals who have measured plasma triglycerides in the clinical routine in Region Stockholm, Sweden, between 1 January 2000 and 31 December 2021. The laboratory measurements also included basic haematology, blood lipid panel, liver function tests, and HbA1c. Using the Swedish Multi-Generation register, 2 147 635 parents and siblings to the indexes were identified to form the complete study cohort. Laboratory data from participants were combined with data from several national registers that provided information on the cause of death, medical diagnoses, dispensed medicines, and socioeconomic factors including country of birth, education level, and marital status.

Conclusion

The multi-generational longitudinal STRIREG cohort provides a unique opportunity to investigate different aspects of hTG as well as heredity for other metabolic diseases. Important outcome measures include mortality, cardiovascular mortality, major cardiovascular events, development of incident diabetes, and NAFLD. The STRIREG study will provide a deeper understanding of the impact of hereditary factors and associated cardiometabolic complications.
Risk and incidence of cardiovascular disease associated with polycystic ovary syndrome
Authors: Wan Zhengwei , Zhao Jianhui , Ye Yongju , Sun Zhaochen , Li Kangning , Chen Yan , Fang Yuan , Zhang Yixuan , Lin Jiali , Sun Ping , Zhang Tingting , Shuai Ping , Li Dongyu , Li Pan , Zheng Huimin , Li Xue , Liu Yuping
Published: February 2024

Aims

We aimed to evaluate the risk of cardiovascular disease (CVD) in women with polycystic ovary syndrome (PCOS) and estimate the global incidence of PCOS-associated CVD.

Methods and results

We conducted a meta-analysis across five databases to evaluate the risk of CVD among women with PCOS. The global incidence of PCOS-associated CVD was calculated by a population attributable fraction modelling using the pooled risk ratio (RR), PCOS prevalence, CVD incidence number, and age-standardized rate (ASIR), from the Global Burden of Diseases 2019. An estimated annual percentage change (EAPC) was used to assess the temporal trend of PCOS-associated CVD. The risk of CVD was significantly increased in women with PCOS for an all-age group (pooled RR 1.51, 95% confidence interval 1.36–1.69) and 10- to 54-year-olds (1.37, 1.17–1.59). Globally, from 1990 to 2019, the PCOS-associated CVD cases in women across the all-age group has raised from 102 530 to 235 560. The most affected regions were East Asia and the Pacific (108 430, 66 090–166 150) in 2019. South Asia has the highest increase trend of PCOS-associated CVD ASIRs (EAPC 2.61%, 2.49–2.73). The annual increase in ASIR in PCOS–CVD incidence for the 10–54 age group (EAPC 0.49%, 0.41–0.56) is faster than that of the all-age group (0.34, 0.27–0.42). The middle- or low-middle sociodemographic index countries experienced higher increase trend of CVD due to PCOS in the past 30 years.

Conclusion

Women with PCOS have a significantly increased risk of CVD. Efficient measures to enhance its prevention and treatment are important for regions with a high PCOS-associated CVD burden, especially premature CVD in women under 55 years.
High-throughput genetic manipulation of multicellular organisms using a machine-vision guided embryonic microinjection robot
Authors: Alegria Andrew D , Joshi Amey S , Mendana Jorge Blanco , Khosla Kanav , Smith Kieran T , Auch Benjamin , Donovan Margaret , Bischof John , Gohl Daryl M , Kodandaramaiah Suhasa B
Published: February 2024

Microinjection is a technique used for transgenesis, mutagenesis, cell labeling, cryopreservation, and in vitro fertilization in multiple single and multicellular organisms. Microinjection requires specialized skills and involves rate-limiting and labor-intensive preparatory steps. Here, we constructed a machine-vision guided generalized robot that fully automates the process of microinjection in fruit fly (Drosophila melanogaster) and zebrafish (Danio rerio) embryos. The robot uses machine learning models trained to detect embryos in images of agar plates and identify specific anatomical locations within each embryo in 3D space using dual view microscopes. The robot then serially performs a microinjection in each detected embryo. We constructed and used three such robots to automatically microinject tens of thousands of Drosophila and zebrafish embryos. We systematically optimized robotic microinjection for each species and performed routine transgenesis with proficiency comparable to highly skilled human practitioners while achieving up to 4× increases in microinjection throughput in Drosophila. The robot was utilized to microinject pools of over 20,000 uniquely barcoded plasmids into 1,713 embryos in 2 days to rapidly generate more than 400 unique transgenic Drosophila lines. This experiment enabled a novel measurement of the number of independent germline integration events per successfully injected embryo. Finally, we showed that robotic microinjection of cryoprotective agents in zebrafish embryos significantly improves vitrification rates and survival of cryopreserved embryos post-thaw as compared to manual microinjection. We anticipate that the robot can be used to carry out microinjection for genome-wide manipulation and cryopreservation at scale in a wide range of organisms.
Characteristics of and Variation in Suicide Mortality Related to Retirement During the Great Recession: Perspectives From the National Violent Death Reporting System
Authors: Ananthasubramaniam Aparna , Jurgens David , Kahsay Eskira , Mezuk Briana
Published: February 2024

Background and Objectives

Suicide rates typically increase during recessions. However, few studies have explored how recessions affect risk among older adults nearing retirement. This study used a large suicide mortality registry to characterize and quantify suicide related to retirement during the Great Recession (GR).

Research Design and Methods

Data come from the National Violent Death Reporting System (NVDRS, 2004–2017; N = 53,298 suicide deaths age ≥50). We analyzed the text narratives (i.e., descriptions of the most salient circumstances to each suicide) of these decedents using natural language processing (NLP) to identify cases that were “retirement-related” (RR, e.g., anticipating, being unable to, or recently retiring). We used time-series analysis to quantify variation in RR over the GR, and compared these trends to retirees (i.e., decedents whose occupation was “retired”) and all decedents aged ≥50. We used content and network analysis to characterize themes represented in the narratives.

Results

There were 878 RR cases (1.6% of suicides aged ≥50) identified by the NLP model; only 52% of these cases were among retirees. RR cases were younger (62 vs 75 years) and more educated (41.5% vs 24.5% college degree) than retirees. The rate of RR suicide was positively associated with indicators of the GR (e.g., short-term unemployment R2 = 0.70, p = .024), but economic indicators were not correlated with the suicide rate among retirees or older adults in general. Economic issues were more central to the narratives of RR cases during the GR compared to other periods.

Discussion and Implications

Recessions shape suicide risk related to retirement transitions.
Passive sustainability strategies in traditional Gaziantep residences: a critical report on historical development
Authors: Anaç Merve , Cuce Pinar Mert , Cuce Erdem
Published: February 2024

In recent years, the increase in the need for energy and the rapid depletion of energy resources have revealed that energy control in buildings is of vital importance. This situation requires energy efficiency not only in new buildings but also in existing building stocks. For this reason, passive strategic measures affecting thermal comfort and energy efficiency in historical buildings built in Gaziantep in the late 18th and early 19th centuries have been evaluated in this study. First, the cultural, technological and natural images of the region that are effective in the development of these strategies were identified. The reflection of these images on architectural design and the parameters affecting energy use as a result were revealed. In order to examine the effect of passive strategy measures in the spaces, a field study was carried out on a selected Gaziantep traditional residential building. For the field study, measurements were taken from the selected building and the street every hour during the day. These measurements have been made under the following conditions: sunny inside the courtyard, sunny outside the courtyard, shade inside the courtyard and shade outside the courtyard. Afterwards, all measurements have been compared. As a result, it is concluded that the courtyard systems that form the cultural, technological and natural image of the region have a great effect on thermal comfort.