bluuebunny/crossref_metadata_2025 huggingface dataset:
A high-fidelity ensemble simulation framework for interrogating wildland-fire behaviour and benchmarking machine learning models
Authors: Wang Qing , Ihme Matthias , Gazen Cenk , Chen Yi-Fan , Anderson John
Published: November 2024

Background Wildfire research uses ensemble methods to analyse fire behaviours and assess uncertainties. Nonetheless, current research methods are either confined to simple models or complex simulations with limitations. Modern computing tools could allow for efficient, high-fidelity ensemble simulations. Aims This study proposes a high-fidelity ensemble wildfire simulation framework for studying wildfire behaviour, assessing fire risks, analysing uncertainties, and training machine learning (ML) models. Methods We present a simulation framework that integrates the Swirl-Fire large-eddy simulation tool for wildfire predictions with the Vizier optimisation platform for automated run-time management of ensemble simulations and large-scale batch processing. All simulations are executed on tensor-processing units to enhance computational efficiency. Key results A dataset of 117 simulations is created, each with 1.35 billion mesh points. The simulations are compared to existing experimental data and show good agreement in terms of fire rate of spread. Analysis is performed for fire acceleration, mean rate of spread, and fireline intensity. Conclusions Strong coupling between wind speed and slope is observed for fire-spread rate and intermittency. A critical Froude number that delineates fires from plume-dominated to wind-dominated is identified and confirmed with literature observations. Implications The ensemble simulation framework is efficient in facilitating large-scale parametric wildfire studies.
Design principles for accurate folding of DNA origami
Authors: Aksel Tural , J. Navarro Erik , Fong Nicholas , Douglas Shawn M.
Published: November 2024

We describe design principles for accurate folding of three-dimensional DNA origami. To evaluate design rules, we reduced the problem of DNA strand routing to the known problem of shortest-path finding in a weighted graph. To score candidate DNA strand routes we used a thermodynamic model that accounts for enthalpic and entropic contributions of initial binding, hybridization, and DNA loop closure. We encoded and analyzed new and previously reported design heuristics. Using design principles emerging from this analysis, we redesigned and fabricated multiple shapes and compared their folding accuracy using electrophoretic mobility analysis and electron microscopy imaging. Redesigned shapes showed 6- to 30-fold improvements in yield compared to original designs. We demonstrate accurate folding can be achieved by optimizing staple routes using our model and provide a computational framework for applying our methodology to any design.
When the discourse of strategy meets the discourse of spirituality
Authors: Pälli Pekka , Lehtinen Esa
Published: November 2024

A well-established body of research in organizational studies shows how business-oriented strategy discourse has
spread to different organizations and to society at large. Drawing insights from this research, we in this paper study how
strategy discourse intertwines with the spiritual and religious discourse in a specific case of a Finnish Church organization. The
interdiscursive analysis focuses on the Church’s formal strategy text, employees’ written reflections regarding the implementation
of the strategy, and one-on-one leadership conversations where the manager-employee dyads discussed these texts. Thus, the data
set makes a rare case of an intertextual chain of text and talk through which strategy discourse was recontextualized from the
field of strategic management to a religious realm. Our analysis specifically highlights how both the organization of textual
practices and the conversational practices — and their orchestration — contribute to the transfer and transformation, i.e.,
recontextualization of strategy discourse.
Tortuosity transformation of near-infrared diffuse reflectance spectra for the detection of enhanced and aggregate spectral changes with reference to dietary preferences of elephants
Authors: Dhanoa M.S. , López S. , Lister S.J. , Sanderson R. , Barnes R.J. , Ellis J.L. , France J.
Published: November 2024

Tortuosity, as a transformation of near-infrared spectra, is illustrated in this communication. To overcome the loss of any grouping structure, due to substrate-sample treatment or different particle size effects, a new autoregression scatter correction is described that preserves such stratification. Tortuosity applications are well established in medical, engineering and diffusion studies. Herein, tortuosity application to near-infrared diffuse reflectance spectra is presented as an additional tool for spectral change investigations.
Constructing an integrable spin–boson model with open boundary conditions
Authors: Yao Hongjia , Hao Kun
Published: November 2024

We investigate the integrability of the Rabi model, which is traditionally viewed as not Yang–Baxter-integrable despite its solvability. Building on efforts by Bogoliubov and Kulish (2013 J. Math. Sci.
192 14–30), Amico et al (2007 Nucl. Phys. B
787 283–300), and Batchelor and Zhou (2015 Phys. Rev. A
91 053808), who explored special limiting cases of the model, we develop a spin–boson interaction Hamiltonian under more general boundary conditions, particularly focusing on open boundary conditions with off-diagonal terms. Our approach maintains the direction of the spin in the z direction and also preserves the boson particle number operator a
†
a, marking a progression beyond previous efforts that have primarily explored reduced forms of the Rabi model from Yang–Baxter algebra. We also address the presence of ‘unwanted’ quadratic boson terms a
2 and a
†2, which share coefficients with the boson particle number operator. Interestingly, these terms vanish when spectral parameter u = ± θ

s
, simplifying the model to a limiting case of operator-valued twists, a scenario previously discussed by Batchelor and Zhou (2015 Phys. Rev. A
91 053808).
Angularity in Higgs boson decays via H→gg at NNLL' accuracy*
Authors: Zhu 朱 Jiawei 佳伟 , Song 宋 Yujin 昱锦 , Gao 高 Jun 俊 , Kang Daekyoung , Maji Tanmay
Published: November 2024

We present improved predictions of a class of event-shape distributions called angularity for a contribution from an effective operator

in Higgs hadronic decay that suffers from large perturbative uncertainties. In the framework of the soft-collinear effective theory, logarithmic terms of the distribution are resummed at NNLL' accuracy, for which a two-loop constant of gluon-jet function for angularity is independently determined using a fit to the fixed-order distribution at the NLO corresponding to

relative to the Born rate. Our determination has reasonable agreement with the value in a recently released thesis. In the fit, we use an asymptotic form with a fractional power conjectured from recoil corrections at one-loop order, and it improves the accuracy of determining positive values of the angularity parameter a. The resummed distribution is matched to the NLO fixed-order results to make our predictions valid at all angularity values. We also discuss the first and subtracted moments of angularity as a function of a that enable the extraction of information on leading and subleading nonperturbative corrections associated with gluons.
On the rationale for recent updates to the SI Brochure concerning angles and quantities with the unit one
Authors: Brown Richard J C , Stock Michael
Published: November 2024

This paper documents the recent evolution of the International System of Units (SI) Brochure, the official document describing the SI, the only globally agreed system of units. In particular, the changes implemented in the most recent version of the 9th edition of the SI Brochure, version 3.01, published in August 2024 are described, along with the rationale for these updates. It is explained that these updates originated from work done by the International Committee for Weights and Measures’ Consultative Committee for Units and have concentrated on the treatment of angle and quantities with the unit one. The aim of the changes in these specific areas has been to provide clarification, harmonise language, improve understanding, acknowledge nuance and reflect new consensus in the understanding of these quantities and their application. By outlining the process and rationale behind these updates, it is hoped that users of the SI Brochure are provided with improved transparency and a better understanding of the ongoing development of this essential document.
Atomic frequency standards, physical constants, and metrology
Authors: Vanier Jacques
Published: November 2024

The paper describes the physics behind the change that has taken place recently of the nature of the International System of Units, commonly called SI. This change took place in 2019 in the definition of the units forming the basis of the System: those base units, some of them defined originally by means of laws and artefacts, are now all defined in terms of physical constants. An important aspect of this fundamental change is the role played by the base unit, the second, associated with frequency and time measurements. Its definition in terms of the ground state hyperfine frequency of the 133Cs atom plays now a central role entering into the definition of all base units, except the mol. The paper shows how this is done and consequently shows the importance of the developments of atomic frequency standards for obtaining the greatest precision and accuracy in the field of metrology.
Development of a molecular Hg2 clock to investigate fundamental physics
Authors: Witkowski M. , Linek A. , Zawada M. , Ciuryło R.
Published: November 2024

We describe the development of an experimental system based on ultra-cold Hg atoms. We will use it to explore search possibilities for new interactions beyond the Standard Model. For this proposal, we will use two-color photoassociation and molecular clock transitions, and we will test the linearity of King’s plot with clock transitions in ultra-cold mercury.
Atomic Clock Ensemble in Space
Authors: Cacciapuoti L. , Busso A. , Jansen R. , Pataraia S. , Peignier T. , Weinberg S. , Crescence P. , Helm A. , Kehrer J. , Koller S. , Lachaud R. , Niedermaier T. , Esnault F.-X. , Massonnet D. , Goujon D. , Pittet J. , Perri A. , Wang Q. , Liu S. , Schaefer W. , Schwall T. , Prochazka I. , Schlicht A. , Schreiber U. , Laurent P. , Lilley M. , Wolf P. , Salomon C.
Published: November 2024

The Atomic Clock Ensemble in Space (ACES) mission is developing high performance clocks and links for space to test Einstein’s theory of general relativity. From the International Space Station, the ACES payload will distribute a clock signal with fractional frequency stability and accuracy of 1 × 10−16 establishing a worldwide network to compare clocks in space and on the ground. ACES will provide an absolute measurement of Einstein’s gravitational redshift, it will search for time variations of fundamental constants, contribute to test topological dark matter models, and perform Standard Model Extension tests. Moreover, the ground clocks connected to the ACES network will be compared over different continents and used to measure geopotential differences at the clock locations.

After solving some technical problems, the ACES flight model is now approaching its completion. System tests involving the laser-cooled Cs clock PHARAO, the active H-maser SHM and the on-board frequency comparator FCDP have measured the performance of the clock signal delivered by ACES. The ACES microwave link MWL is currently under test. The single-photon avalanche detector of the optical link ELT has been tested and will now be integrated in the ACES payload.

The ACES mission concept, its scientific objectives, and the recent test results are discussed here together with the major milestones that will lead us to the ACES launch.
Low-noise optical frequency divider for precision measurement
Authors: Jiang Yanyi , Shi Haosen , Yao Yuan , Yu Hongfu , Ma Longsheng
Published: November 2024

We describe the development of an accurate optical frequency divider based on a Ti:Sapphire optical frequency comb. The division instability and uncertainty of the optical frequency divider are demonstrated to be 10−18 at 1 s averaging time and 3 × 10−22, respectively. The ability of coherence transfer is also demonstrated by resolving a hertz-level-linewidth spectroscopy.
Progress on Optical Clock Technology for Operational Timescales
Authors: Peil S. , Tobias W. , Whalen J. , Hemingway B. , Akin T. G.
Published: November 2024

While optical clock technology has advanced rapidly in recent years, incorporating the technology into operational timescales has progressed more slowly. The highest accuracy frequency standards for groundbreaking measurements do not easily translate to critical timing where continuous, uninterrupted operation over many months and years is required. For example, intermittent steering of a hydrogen maser with an optical standard fails to harness all of the dramatic improvements possible with optical technology. Here we present progress on development and integration of optical-clock technology for operational timescales. An optical oscillator steered to an atomic fountain comprises a hybrid clock with optical-level stability at short times and a reliable long-term reference, and obviates the need for a steered maser. Atomic-beam optical clocks are being developed to support 24/7 operations at a level that improves upon the performance of the U.S. Naval Observatory’s rubidium fountains. An optical-lattice is being developed as a gold-standard frequency reference, complementing the role of the atomic beam clocks.
171Yb+ ion optical clock at NPL: advances in automation and assessment of the trap-induced ac Zeeman shift in an endcap trap geometry
Authors: Curtis E. A. , Tofful A. , Parsons A. O. , Robertson B. I. , Godun R. M.
Published: November 2024

Ensuring robust operation of optical clock systems requires increasingly complex automation of experimental protocols. This includes real-time monitoring of system output for data validation and for high accuracy assessment of systematic frequency shifts. We report here on recent advances in the control system of the 171 Yb+ ion optical clock at NPL (National Physical Laboratory, UK) and describe how this has led to improvements in systematic shift metrology and reduced the overall uncertainty budget for the optical clock. Additionally we present an assessment of the rf trap drive-induced ac Zeeman effect for our experimental system. These system advances enable us to provide improved contributions to the international efforts in the redefinition of the SI second and other applications such as tests of fundamental physics.
Development of commercial fountain clocks in NIM
Authors: Liu Kun , Zheng Fasong , Chen Weiliang , Yacong Xiao , Dai Shaoyang , Fang Fang
Published: November 2024

A new Rb fountain clock has been built in NIM aiming to operate semi-continuously and achieve an excellent long-term instability for time keeping. A double metal microwave cavity with a thermal expansion self-compensating mechanism is used for Ramsey interrogation to reduce the sensitivity to ambient temperature fluctuations and increase the operating temperature range. With an optimized design, the thermal coefficient of the resonance frequency has been reduced to less than 10 kHz/°C. This represents an improvement of more than an order of magnitude compared to a copper cavity. The optical system with two independent frequency stabilized lasers with automatic re-locking system is located on a 400×600 mm optical breadboard with special designed optical mounts to ensure stable output light powers, which ensure to resume operating without any realignment of optical system after transportation. The clock has been operated for more than a year without any failure. A long-term instability of 3.7×10−16 was achieved compared with NIM5 Cs fountain clock. By implementing feedback of the frequency difference to the Voltage Controlled Crystal Oscillator within a servo-loop, the fountain clock can generate a standard frequency output, the instability of which can enter 10−16 order at 40000 seconds.
Ultrastable lasers: investigations of crystalline mirrors and closed cycle cooling at 124 K
Authors: Ma C Y , Yu J , Legero T , Herbers S , Nicolodi D , Kempkes M , Riehle F , Kedar D , Robinson J M , Ye J , Sterr U
Published: November 2024

We have investigated crystalline AlGaAs/GaAs optical coatings with three ultra-stable cavities operating at 4 K, 16 K, 124 K and 297 K. The response of the cavities’ resonance frequencies to variations in optical power indicates non-thermal effects beyond the photo-thermo-optic effect observed in dielectric coatings. These effects are strongly dependent on the intensity of the intracavity light at 1.5 μm. When the rear side of the mirrors is illuminated with external light, we observe a prominent photo-modified birefringence for photon energies above the GaAs bandgap, which points to a possible mechanism relating our observations to the semiconductor properties of the coatings. Separately, we also present a low maintenance evolution of our 124 K silicon cavity system where the liquid nitrogen based cooling system is replaced with closed cycle cooling from a pulse-tube cryo-cooler.
Limitations of Electric Drive and Local Control Systems in Asymmetric Rolling of Fine-Grained Steels
Authors: Pesin A.M. , Kornilov G.P. , Bochkarev A.A. , Pustovoytov D.O.
Published: November 2024

Rolling with different circumferential speeds of work rolls, each of which is driven by two independent motors, is the most suitable way to implement asymmetric rolling technology. The paper studies the limiting capabilities of an induction motor electric drive of an asymmetric rolling mill. It has been investigated that during asymmetric rolling in the torque limitation zone, the drive roll speed significantly decreases relative to the specified speed. This is due to the limitation of the current consumed by the work roll motor rotating at a higher speed. This phenomenon significantly limits the real range of the asymmetry factor at large thickness reductions. An improved control system for the work roll electric drive for the speed asymmetry mode has been developed. Such a system can be used, among other things, on multi-stand asymmetric rolling mills. Using low-carbon steel as an example, a study was carried out on the relationship between the actual asymmetry factor and the grain refinement capabilities during asymmetric hot rolling. Fine-grained microstructure with an average grain size of 1.45 μm (grain size number G=15.57 according to ASTM E1382) was obtained. It is expected that increase of the actual asymmetry factor above 1.6 in asymmetric hot rolling has the potential to further refine the average grain size in the processed steels to 1 μm or even lower.
Influence of Wear on Surface Crack Growth of PPS Thrust Bearing in Water Lubrication under 2300 N at 1200 rpm
Authors: Kajiwara Shuhei , Machino Sasuga , Kida Katsuyuki
Published: November 2024

Many factors determine the fatigue life of mechanical components for transmission of rotational motion. In particular, since engineering polymer components exhibit complex tribological behaviours, a variety of studies are needed. For this reason, a large number of studies have been published on polymer components under rolling and sliding contacts. However, researches on the subject have been done for specific conditions. In addition, it is still unclear whether the finding can be applied to bearing based on industrial standards. For ball bearing based on the industrial standards, several studies suggest that the fatigue life of polymer bearings under water was caused by flaking with surface cracks. On the other hand, these studies did not discuss the initiation and propagation of the surface crack under the effect of wear. Therefore, fatigue tests under rolling contact were performed in this study to investigate the surface crack behaviour on the groove surface of PPS thrust bearing based on industrial standards.
Numerical modelling of gas flow in a random packed bed with a helical flow deflector
Authors: Marek Maciej
Published: November 2024

Random packed beds are often employed in chemical reactors as a means to increase the contact surface between reactants or a catalyst. The present work proposes a helical flow deflector placed within the bed and numerical simulations are performed to analyse the influence of the deflector on the tortuosity of the flow paths in the reactor and the pressure drop. The geometry of the packed bed is obtained in a separate numerical simulation with sequential deposition of ring-like equilateral particles. The flow equations are solved on a structured grid and the immersed boundary method accounts for the complex geometry of the random packing and the cylindrical walls of the reactor. The increase of the tortuosity leads to increase of the pressure drop along the reactor and the relation between them is studied as a function of the rise per revolution of the helical surface.
East–West asymmetry in intensity, duration, frequency of heatwaves over Northern India
Authors: Dalal Ganaraj , Chaudhary Shushobhit , Dutta Riya , Karmakar Subhankar , Koppa Akash , Hari Vittal
Published: November 2024

Anthropogenic global warming has led to widespread increase in the heatwave intensity, duration, and frequency (HIDF) of events across the globe. Although the three characteristics of heatwaves are closely interconnected, they are often studied separately, especially over the Indian subcontinent. Here, we assess the HIDF over India during the period 1961–2023, and show that there exists a systematic East–West asymmetry in their characteristics over northern India. Specifically, we show that a substantial increase (decrease) in HIDF exists over major cities in the western (eastern) parts of North India. For example, Ahmedabad (a city in the western part) shows a 67.5% increase in the likelihood of four-day heatwaves in the recent decades (1991–2023) compared to the reference period 1961–1990. On the other hand, in the city of Patna (in the eastern part), we notice a 78% decrease in the likelihood of four-day heatwaves in the recent decades. Furthermore, we show that the East–West asymmetry in the HIDF is caused by a major climatic mode, i.e. the Atlantic Niño. Overall, our study provides a first insight into the contrasting characteristics of heatwaves over Northern India and their potential drivers. Such information is vital for the design of regionally appropriate adaptation strategies across India.
Does artificial intelligence bias perceptions of environmental challenges?
Authors: van der Ven Hamish , Corry Diego , Elnur Rawie , Provost Viola Jasmine , Syukron Muh , Tappauf Niklas
Published: November 2024

Artificial intelligence (AI) is reshaping how humans obtain information about environmental challenges. Yet the outputs of AI chatbots contain biases that affect how humans view these challenges. Here, we use qualitative and quantitative content analysis to identify bias in AI chatbot characterizations of the issues, causes, consequences, and solutions to environmental challenges. By manually coding an original dataset of 1512 chatbot responses across multiple environmental challenges and chatbots, we identify a number of overlapping areas of bias. Most notably, chatbots are prone to proposing incremental solutions to environmental challenges that draw heavily on past experience and avoid more radical changes to existing economic, social, and political systems. We also find that chatbots are reluctant to assign accountability to investors and avoid associating environmental challenges with broader social justice issues. These findings present new dimensions of bias in AI and auger towards a more critical treatment of AI’s hidden environmental impacts.
A q-version of the relation between the hypercube, the Krawtchouk chain and Dicke states
Authors: Bernard Pierre-Antoine , Poliquin Etienne , Vinet Luc
Published: November 2024

It is shown how the spin chain based on dual q-Krawtchouk polynomials is connected to a weighted hypercube through the use of q-Dicke states. The representation theoretic underpinnings based on the quantum algebra

U
q

(

su

(
2
)
)

are emphasized.
Designing quantum circuits for decoding binary linear codes
Authors: Yoo Hyungkee , Choi Whan-Hyuk , Lee Yoonjin
Published: November 2024

In the coding theory, it is one of the most important research problems to find an efficient algorithm for the decoding process. A quantum computer is an innovative computing device that performs calculations using the principles of quantum mechanics. In this paper, we find a decoding algorithm for binary linear codes using quantum circuits; this is the first time that quantum circuits are used as a main tool for decoding binary linear codes. Our decoding algorithm is mainly based on Grover’s search algorithm. In detail, we study the process of implementing the exhaustive search using quantum circuits for decoding binary linear codes. For our purpose, we design a modified Grover’s algorithm (algorithm 1) using three tools: the matrix multiplier, the Hamming weight counter, and the state indicator. We present algorithm 2, which is a quantum decoding algorithm for binary linear codes. We illustrate algorithm 1 using the [7, 4, 3] Hamming code, and algorithm 2 is implemented by IBM Quantum Composer.
Exploring the wear mechanism of surface hardfacing Stellite 6 alloy on the cast iron over the wide temperature range
Authors: Luo Changzeng , Li Zhijie , Zeng Xiaoxiao , Ma Xiaoyue , Qu Shengguan , Sun Pengfei
Published: November 2024

Cast iron is widely used as a heat-resistant material in the automotive industry, but it increasingly struggles to meet the demands of high-temperature friction applications. This study employs surface hardfacing with Stellite 6 alloy to improve the wear resistance of cast iron. By conducting sliding friction tests at various temperatures, we systematically investigate the friction behavior of both cast iron and hardfacing specimens over a broad temperature range. The results reveal that hardfacing-treated specimens exhibit exceptional wear resistance. At ambient temperatures, the hardfacing specimen shows a 65.5% reduction in wear loss compared to the cast iron specimen. This reduction increases to 83.8% at temperatures up to 600 °C. At room temperature, the wear mechanisms of cast iron include abrasive wear and fatigue wear. At medium temperatures, abrasive wear is the primary mechanism of cast iron. At high temperatures, the wear mechanisms of cast iron consist of abrasive wear, oxidative wear, and adhesive wear. In contrast, the wear mechanisms of the hardfacing specimens differ: at room and medium temperatures, abrasive wear is the predominant mechanism, while at high temperatures, the main mechanisms are abrasive wear and adhesive wear. The superior mechanical properties and enhanced resistance to high-temperature oxidation of the hardfacing specimens are the primary factors contributing to their improved friction performance across the temperature spectrum.
The problematic
Authors: Davies Wendy
Published: November 2024

This introduction sets the scene in time, place, and cultural contexts. After indicating the basic geography of the region and summarizing its political trends and ecclesiastical structures, it goes on to survey early medieval writing about gardens and garden practice in western Europe and in al-Andalus, with attention to the place of gardening in Visigothic monastic thinking and its biblical origins. It ends by posing the main questions that set the agenda for the book: Was gardening practised? What was grown? Who were the gardeners? Did they garden for a market? Did practice reflect the idealized descriptions of gardens in literature?
Dissecting AlphaFold2’s capabilities with limited sequence information
Authors: Gut Jannik Adrian , Lemmin Thomas
Published: November 2024

Protein structure prediction aims to infer a protein’s three-dimensional (3D) structure from its amino acid sequence. Protein structure is pivotal for elucidating protein functions, interactions, and driving biotechnological innovation. The deep learning model AlphaFold2, has revolutionized this field by leveraging phylogenetic information from multiple sequence alignments (MSAs) to achieve remarkable accuracy in protein structure prediction. However, a key question remains: how well does AlphaFold2 understand protein structures? This study investigates AlphaFold2’s capabilities when relying primarily on high-quality template structures, without the additional information provided by MSAs. By designing experiments that probe local and global structural understanding, we aimed to dissect its dependence on specific features and its ability to handle missing information. Our findings revealed AlphaFold2’s reliance on sterically valid Cβ for correctly interpreting structural templates. Additionally, we observed its remarkable ability to recover 3D structures from certain perturbations and the negligible impact of the previous structure in recycling. Collectively, these results support the hypothesis that AlphaFold2 has learned an accurate biophysical energy function. However, this function seems most effective for local interactions. Our work advances understanding of how deep learning models predict protein structures and provides guidance for researchers aiming to overcome limitations in these models.

Availability and implementation

Data and implementation are available at https://github.com/ibmm-unibe-ch/template-analysis.
The association of hidradenitis suppurativa with cigarette smoking and cannabis use: a cross-sectional study in the All of Us Research Program
Authors: Chen Gloria F , Shipman William D , Hodelin Christine , Hsia Henry C , Cohen Jeffrey M , Eisenstein Anna
Published: November 2024

We sought to examine the association between hidradenitis suppurativa, and cigarette smoking and cannabis use with a cross-sectional study using All of Us, a National Institutes of Health research programme that focuses on traditionally underrepresented populations in research. Using electronic health record and survey data, we found that the odds of cigarette smoking and cannabis use are increased by 75% and 54%, respectively, in patients with hidradenitis suppurativa.
Zoonotic and other veterinary chlamydiae – an update, the role of the plasmid and plasmid-mediated transformation
Authors: Marti Hanna , Shima Kensuke , Boutin Sebastien , Rupp Jan , Clarke Ian N , Laroucau Karine , Borel Nicole
Published: November 2024

The obligate intracellular bacterial genus Chlamydia harbours species with zoonotic potential, particularly C. psittaci, causative agent of psittacosis, and C. abortus, which may lead to miscarriage in pregnant women. The impact of other bird chlamydiae such as C. avium, C. gallinaceae, and C. buteonis, or reptilian species such as C. crocodili, amongst others, on human health is unclear. The chlamydial native plasmid, a suspected virulence factor, is present in all currently described 14 Chlamydia species except for some plasmid-free strains. The plasmid is also the primary tool to study chlamydial genetics, a still developing field that has mostly focused on C. trachomatis. Only recently, genetic transformation of C. felis, C. pecorum, C. pneumoniae, C. psittaci, and C. suis has succeeded, but existing methods have yet to be refined. In this review article, we will provide an update on the recent developments concerning the zoonotic potential of chlamydiae. Furthermore, we present an overview about the current state of knowledge regarding the chlamydial plasmid in terms of prevalence and significance as a virulence factor. Finally, we give insights into the progress of developing genetic tools for chlamydial species other than C. trachomatis with a special focus on zoonotic and veterinary chlamydiae.
Long-term effects of group selection, single-tree selection, and clearcutting on individual-tree and stand volume growth in northern hardwoods of the Great Lakes region
Authors: Halpin Corey R , Lorimer Craig G , Burton Julia I , Webster Christopher R , Palik Brian J
Published: November 2024

Group selection and small patch cutting are widely viewed as more aesthetically acceptable alternatives to clearcutting for regenerating tree species of low shade tolerance, and they may enhance resilience in the face of climate change. However, little evidence is available on how production rates compare with those of other silvicultural systems. We used CANOPY, a spatially explicit, individual-tree model, to investigate the link between individual-tree growth and net volume growth at the stand level under alternative silvicultural systems in northern hardwood forests. The model predicted peak growing space efficiency (volume increment per unit of crown projection area) in the pole or mature stage under all silvicultural systems and a decline for larger and older trees. Trees in uneven-aged stands were generally less efficient, slower growing at a given size, and harvested at more advanced ages compared to even-aged stands. Nevertheless, there was little predicted difference in net growth between single-tree selection, group selection, and thinned even-aged stands. However, stands managed by small patch cutting (800–2000-m2 openings) without thinning, as well as unthinned even-aged stands, had substantially lower net growth and higher mortality rates. The paradox that lower efficiency of trees in uneven-aged stands did not result in lower net growth at the stand level was not explainable by improved efficiency of mature trees due to adjacent canopy gaps or by low harvest volumes of smaller, less efficient trees. Rather, production in even-aged stands was lower than expected due to the slow recovery of merchantable growing stock following clearcutting, which negated the higher productivity of even-aged stands during the mature phase. A secondary factor was the asymptotic trend of production rates beyond an opening size of 200 m2, so that larger openings under group selection or clearcutting did not stimulate higher production levels.
TIdeS: A Comprehensive Framework for Accurate Open Reading Frame Identification and Classification in Eukaryotic Transcriptomes
Authors: Maurer-Alcalá Xyrus X , Kim Eunsoo
Published: November 2024

Studying fundamental aspects of eukaryotic biology through genetic information can face numerous challenges, including contamination and intricate biotic interactions, which are particularly pronounced when working with uncultured eukaryotes. However, existing tools for predicting open reading frames (ORFs) from transcriptomes are limited in these scenarios. Here we introduce Transcript Identification and Selection (TIdeS), a framework designed to address these nontrivial challenges associated with current ‘omics approaches. Using transcriptomes from 32 taxa, representing the breadth of eukaryotic diversity, TIdeS outperforms most conventional ORF-prediction methods (i.e. TransDecoder), identifying a greater proportion of complete and in-frame ORFs. Additionally, TIdeS accurately classifies ORFs using minimal input data, even in the presence of “heavy contamination”. This built-in flexibility extends to previously unexplored biological interactions, offering a robust single-stop solution for precise ORF predictions and subsequent decontamination. Beyond applications in phylogenomic-based studies, TIdeS provides a robust means to explore biotic interactions in eukaryotes (e.g. host–symbiont, prey–predator) and for reproducible dataset curation from transcriptomes and genomes.
Comparative evaluation of eravacycline susceptibility testing methods in 587 clinical carbapenem-resistant Acinetobacter baumannii isolates: broth microdilution, MIC test strip and disc diffusion
Authors: Liu Qihui , Li Shirong , Wang Xuan , Lin Yijing , Jiang Haoqin , Li Ning
Published: November 2024

Objectives

The study aimed to evaluate the accuracy of different methods for determining carbapenem-resistant Acinetobacter baumannii (CRAB) susceptibility to eravacycline.

Methods

We collected 587 CRAB strains from Huashan Hospital affiliated to Fudan University between 2019 and 2023. The broth microdilution (BMD) method served as the reference standard. The susceptibility results were evaluated using the clinical breakpoints established by the Chinese Committee on Antimicrobial Susceptibility Testing (ChinaCAST) (susceptible MIC,  ≤ 1 mg/L; inhibition zone diameter,  ≥ 15 mm). The study compared the reliability of the MIC test strip (MTS) and disc diffusion (DD) methods in detecting CRAB susceptibility to eravacycline.

Results

The MICs required to inhibit 50% and 90% of CRAB growth were as follows: BMD, 0.5/1 mg/L; MTS, 0.38/0.75 mg/L. According to the ChinaCAST breakpoints, the BMD method demonstrated a 98.13% (576/587) susceptibility rate, whereas the MTS and DD methods showed susceptibility rates of 97.96% (575/587) and 97.61% (573/587), respectively. The essential agreement rate between the MTS and BMD methods was 94.55%. Categorical agreement (CA) rates for the MTS and DD methods were 99.83% and 99.49%, respectively. The major error (ME) rate for MTS was 0.17%, with no very major errors (VMEs) observed. For the DD method, the ME rate was 0.51%, also with no VMEs.

Conclusion

The MTS and DD methods demonstrated strong consistency with the BMD reference method, with CA, ME and VME rates meeting methodological evaluation criteria. Both MTS and DD methods are reliable alternatives for assessing the antibacterial activity of eravacycline in clinical microbiology laboratories.
Expanding the ICC’s Jurisdiction Over the Crime of Aggression
Authors: McDougall Carrie
Published: November 2024

The Global Institute for the Prevention of Aggression (GIPA) recently prepared model amendments to the International Criminal Court (ICC) Statute, aimed at aligning the ICC’s jurisdiction over the crime of aggression with its jurisdiction over genocide, crimes against humanity and war crimes. GIPA also prepared a draft resolution under which the recommended amendments could be adopted, and a brief explanatory memorandum to assist States Parties in their consideration of these texts. In consultation with other members of GIPA’s Council of Advisers, I was the primary author of these documents. This article details the reasons for the shape of the recommended amendments and key resolution provisions. Through an explanation of the interpretive debate surrounding the provision governing the exercise of the ICC’s jurisdiction over crimes of aggression involving States Parties, the article demonstrates that the simple deletion of offending limitations on the ICC’s jurisdiction, or parts thereof, would be unwise, because such an approach could inadvertently result in a further narrowing of the Court’s jurisdiction. The article also explains the technical issues and policy imperatives that lie behind the choice of the provision to govern the amendments’ entry into force, and why it is prudent to set out the effect of the proposed amendment for both states that have already ratified the 2010 aggression amendments, and states yet to ratify those amendments, or the ICC Statute.
Assessment of antibiotic utilization and prescribing quality in a teaching hospital in Iraq
Authors: Abdullah Marwan I , Essa Narmin S , Aladul Mohammed I , Taki Abdulrahman M , Taki Ismael M
Published: November 2024

Objectives

This study aimed to assess the prevalence of antibiotic use, quantify antibiotic consumption, and evaluate the quality of prescribing.

Methods

This was a point prevalence study conducted at a teaching hospital in Mosul, Iraq. The antibiotics prescribing data were retrieved from the medical records of admitted patients between January and February 2023. The trends of utilization of prescribed antibiotics were expressed in defined daily doses per 100 bed days (DDD/100 BD).

Key findings

The records of 546 patients were checked. Antibiotics were prescribed for 88.46% of admitted patients. The main mode of antibiotic therapy in gynecology and obstetrics (97.59%) and surgical (86.84%) wards was surgical prophylaxis and 54% of these patients received antibiotics for more than 24 hours. The overall antibiotic consumption in the hospital was 135.09 DDD/100 BD. The highest consumption was in the gynecology and obstetrics ward (242.17 DDD/100 BD). Ceftriaxone (73.65 DDD/100 BD) and metronidazole (41.76 DDD/100 BD) were the most frequently prescribed antibiotics for the admitted patients. The internal medicine ward had the highest percentage (94.22%) of Watch-class antibiotic use, while the gynecology and obstetrics ward had the highest percentage (64.53%) of Access-class antibiotic use.

Conclusions

This study highlighted the high prevalence of antibiotic use, particularly ceftriaxone. Furthermore, the study highlighted the lack of adherence to both national and international guidelines. Urgent action should be undertaken to implement antimicrobial stewardship programs.
Evidence-based approach for the generation of a multivariate logistic regression model that predicts instrument failure
Authors: Cleveland Stephan L , Carman Carol A , Vyas Niti , Salazar Jose H , Rojo Juan U
Published: November 2024

Objective

Identification of instrument failure (IF) represents a point to improve the quality of services provided by medical laboratories. Here, a logistic regression model was created to define the relationship between instrument downtime and laboratory quality management systems.

Methods

Interval-level quality control (QC) and categorical quality assurance data from 3 identical chemistry analyzers was utilized to generate a logistic regression model able to predict IF. A case-control approach and the forward stepwise likelihood-ratio method was used to develop the logistic regression model. The model was tested using a case-control dataset and again using the complete sample.

Results

A total of 650 downtime events were identified. A total of 22,880 QC data points, 187 calibrations, 24 proficiency testing events, and 107 maintenance records were analyzed. The regression model was able to correctly predict 59.2% of no instrument downtime events and 69.2% of instrument downtime events using the case-control data. Using the entire data set, the sensitivity of the model was 69.2% and the specificity was 58.2%.

Conclusion

A logistic regression model can predict instrument downtime nearly 70% of the time. This study acts as a proof of concept using a limited data set collected by the chemistry laboratory.
Isolation of Lactiplantibacillus plantarum for treatment of Salmonella infection in mice
Authors: Zhang Silu , Liu Tian , Zhou Xiaoli , Wang Jun , Zhang Tengxun , Xiao Guoxun , Huang Song , Rao Chitong , Teng Xin
Published: November 2024

Salmonella infections, often acquired through contaminated food or water, pose significant health risks, particularly amid rising antibiotic resistance and the adverse effects of conventional treatments on gut microbiota. This study isolated the probiotic Lactiplantibacillus plantarum GOLDGUT-LP618 from healthy human fecal samples, demonstrating its potential against Salmonella enterica. Lactiplantibacillus plantarum LP618 produced high levels of short-chain fatty acids (SCFAs) and exhibited robust inhibition of Salmonella in vitro. The strain showed resilience in gastric and bile environments, effectively curbing Salmonella growth. Post-infection treatment with L. plantarum LP618 significantly alleviated diarrhea, improved body weight, and moderated inflammatory responses. Histological analysis indicated restoration of intestinal structure, suggesting protection against mucosal damage. These results highlight L. plantarum LP618 as a promising probiotic candidate, offering a safe and effective alternative to antibiotics for managing Salmonella infections and promoting recovery in affected individuals.
Lower Extremity Musculoskeletal Injuries in United States Active Duty Service Members: Prevalence/Incidence, Health Care Utilization, and Cost Analysis Spanning Fiscal Years 2016–2021
Authors: Isaacson Brad , Hando Ben , Pav Veronika , Wagner Linzie , Colahan Courtney , Pasquina Paul , Yuan Xiaoning
Published: November 2024

Introduction

Lower Extremity musculoskeletal injuries (LE MSKIs) represent a significant portion of overuse injuries in active duty service members (ADSMs). However, variations in study methods and research gaps related to LE MSKIs have prevented Department of Defense (DoD) leaders from assessing the burden of these conditions. The purpose of this study was to report the incidence, prevalence, and types of LE MSKIs sustained by ADSMs across four branches of service and describe associated health care utilization and private sector costs.

Materials and Methods

This was a retrospective, longitudinal population study, including ADSMs from the Air Force, Army, Marine Corps, and Navy. Prevalence and incidence rates for LE MSKIs, associated health care utilization, and costs were obtained by querying electronic health records (EHR) from military treatment facilities (MTFs), private sector care (PC) claims, and theater medical data from the Military Health System Data Repository (MDR) from October 1, 2015 to September 30, 2021 (FY16–21). Utilization associated with LE MSKIs in both the direct care (DC) and PC settings was classified into mutually exclusive outpatient encounter categories and acute inpatient stays. PC costs related to LE MSKIs were captured for each year.

Results

In FY21, LE MSKIs occurred in 25.3% of ADSMs (n = 378,615). A higher proportion of females sustained an LE MSKI (33.3%), compared to males (23.7%). From FY16–21, the Army had the highest annual prevalence of LE MSKIs (30.9–35.5%), followed by the Air Force (23.8–31.0%), Marine Corps (23.4–27.0%), and Navy (17.2–19.8%). Incidence rate patterns were similar, with the Army sustaining LE MSKIs at 320 to 377 injuries per 1,000 person-years, followed by the Air Force (241–318), Marines (255–288), and Navy (173–203). Overuse/non-specific MSKIs of the knee were the most common injury type and body region affected, respectively. There were 10,675,543 DC and 1,875,307 PC outpatient encounters from FY16–21 with a primary or secondary diagnosis of LE MSKI. The Air Force was most reliant on PC, with 21.5 to 36.8% of LE MSKI-related encounters occurring outside MTFs during FY16–21. Over $99 million was paid by TRICARE on LE MSKI in FY21 alone with Same Day Surgeries accounting for almost half ($48 million) of this total.

Conclusions

Among U.S. ADSMs, LE MSKIs remain highly prevalent and costly. We observed disparities across the Services in the prevalence and incidence of LE MSKIs, and their respective reliance on the private sector for management of these conditions. Findings from this work may support military leaders and MSKI researchers who seek to reduce the impact of LE MSKIs on the readiness and overall health of the U.S. Military.
The moon-forming impact as a constraint for the inner Solar system’s formation
Authors: Fang Tong , Bi Rongxi , Zhang Hui , Zhou You , Reinhardt Christian , Deng Hongping
Published: November 2024

The Solar system planets are benchmarks for the planet formation theory. Yet two paradigms coexist for the four terrestrial planets: the prolonged collisional growth among planetesimals lasting $\gt 100$ million years (Myr) and the fast formation via planetesimals accreting pebbles within 10 Myr. Despite their dramatic difference, we can hardly tell which theory is more relevant to the true history of the terrestrial planets’ formation. Here, we show that the Moon’s origin puts stringent constraints on the pebble accretion scenario, rendering it less favourable. In the pebble accretion model, the one-off giant impact between proto-Earth and Theia rarely (probability $\lt $ 1‰) occurs at the right timing and configuration for the Moon formation. Even if a potential impact happens by chance, giant impact simulations reveal perfect mixing between proto-Earth and Theia, leaving no room for the observed primordial Earth mantle heterogeneity and the compositional difference, though small, between Earth and the Moon. Thus, the Earth–Moon system along other terrestrial planets should preferably form from chaotic collisional growth in the inner Solar system.