bluuebunny/crossref_metadata_2025 huggingface dataset:
As2O3-poly(1H-pyrrole) nanocomposite for hydrogen generation from Red Sea water with high efficiencey
Authors: Hadia N M A , Rabia Mohamed , Alzaid Meshal , Mohamed W S , Hasaneen M F , Ezzeldien Mohammed , Shaban Mohamed , Ahmed Ashour M , Mohamed S H , Awad M A
Published: July 2023

This research focuses on the synthesis of a new composite material, As2O3-poly(1H-pyrrole) (P1HP), for the generation of hydrogen gas. The novelty lies in the utilization of eco-friendly and cost-effective seawater as the source of hydrogen gas. The study aims to develop a sustainable and efficient approach for hydrogen production using this novel composite material and seawater as the raw materials. The As2O3/P1HP nanocomposite is synthesized through the polymerization of 1H-pyrrole. The crystal structure and size of the nanocomposite are determined using XRD analysis, which indicates a lattice constant of 11.06 Å and a crystallite size of 4.03 nm via the Scherer equation. The surface topography is visualized using SEM and TEM, revealing the presence of both large agglomerate particles and very small particles with a size of approximately 21 nm. The nanocomposite exhibits excellent optical absorption behavior and a small bandgap of 1.73 eV, making it suitable for hydrogen generation using Red Sea water as an electrolyte. The hydrogen production rate is measured to be 21 μmole cm−1.h, while the current density (Jph) values with and without incidence light are −0.24 and −0.05 mA.cm−2, respectively. The Jph values increase from −0.09 to −0.15 mA.cm−2 as the incidence photon wavelengths increase from 440 to 730 nm, indicating an enhancement in the rate of hydrogen generation. The use of low-cost materials and a natural source of electrolyte make this approach a promising candidate for renewable energy production and hydrogen gas generation.
Solitons in fourth-order Schrödinger equation with parity-time-symmetric extended Rosen-Morse potentials
Authors: Zhang Jia-Rui , Zhu Fang-Yu , Li Wan-Peng , Shen Yu-Jia
Published: July 2023

We investigate the fourth-order nonlinear Schrödinger equation modulated by parity-time-symmetric extended Rosen-Morse potentials. Since the imaginary part of the potentials does not vanish asymptotically, any slight fluctuations in the field can eventually cause the nonlinear modes to become unstable. Here we obtain stable solitons by adding the constraints of coefficients, which make the imaginary part of the potentials component vanish asymptotically. Furthermore, we get other fundamental stable single-hump and double-hump solitons by numerical methods. Then we consider excitations of the soliton via adiabatical change of system parameters. The results we obtained in this work provide a way to search for stable localized modes in parity-time-symmetric extended Rosen-Morse potentials with fourth-order dispersion.
Model-independent bubble wall velocities in local thermal equilibrium
Authors: Ai Wen-Yuan , Laurent Benoit , van de Vis Jorinde
Published: July 2023

Accurately determining bubble wall velocities in first-order phase transitions is of great importance for the prediction of gravitational wave signals and the matter-antimatter asymmetry. However, it is a challenging task which typically depends on the underlying particle physics model. Recently, it has been shown that assuming local thermal equilibrium can provide a good approximation when calculating the bubble wall velocity. In this paper, we provide a model-independent determination of bubble wall velocities in local thermal equilibrium. Our results show that, under the reasonable assumption that the sound speeds in the plasma are approximately uniform, the hydrodynamics can be fully characterized by four quantities: the phase strengthαn, the ratio of the enthalpies in the broken and symmetric phases, Ψn, and the sound speeds in both phases,csandcb. We provide a code snippet that allows for a determination of the wall velocity and energy fraction in local thermal equilibrium in any model. In addition, we present a fit function for the wall velocity in the casecs=cb= 1/√(3).
Revisiting Affleck-Dine leptogenesis with light sleptons
Authors: Enomoto Kazuki , Hamaguchi Koichi , Kamada Kohei , Wada Juntaro
Published: July 2023

We revisit the Affleck-Dine leptogenesis via the L H_u flat direction with a light slepton field. Although the light slepton field is favored in low-energy SUSY phenomenologies, such as the muong- 2 anomaly and bino-slepton coannihilation, it may cause a problem in the Affleck-Dine leptogenesis: it may create an unwanted charge-breaking vacuum in the Affleck-Dine field potential so that the Affleck-Dine field is trapped during the course of leptogenesis. We investigate the conditions under which such an unwanted vacuum exists and clarify that both thermal and quantum corrections are important for the (temporal) disappearance of the charge-breaking minimum. We also confirm that if the charge-breaking vacuum disappears due to the thermal or quantum correction, the correct baryon asymmetry can be produced while avoiding the cosmological gravitino problem.
Experimental Verification of a One-dimensional Diffraction-limit Coronagraph
Authors: Itoh Satoshi , Matsuo Taro , Ota Shunsuke , Hara Kensuke , Ikeda Yuji , Kojima Reiki , Yamada Toru , Sumi Takahiro
Published: July 2023

We performed an experimental verification of a coronagraph. As a result, we confirmed that, at the focal region where the planetary point spread function exists, the coronagraph system mitigates the raw contrast of a star-planet system by at least 1 × 10−5 even for the 1-λ/D star-planet separation. In addition, the verified coronagraph keeps the shapes of the off-axis point spread functions when the setup has the source angular separation of 1λ/D. The low-order wave front error and the non-zero extinction ratio of the linear polarizer may affect the currently confirmed contrast. The sharpness of the off-axis point spread function generated by the sub-λ/D separated sources is promising for the fiber-based observation of exoplanets. The coupling efficiency with a single mode fiber exceeds 50% when the angular separation is greater than 3–4×10−1
λ/D. For sub-λ/D separated sources, the peak positions (obtained with Gaussian fitting) of the output point spread functions are different from the angular positions of sources; the peak position moved from about 0.8λ/D to 1.0λ/D as the angular separation of the light source varies from 0.1λ/D to 1.0λ/D. The off-axis throughput including the fiber-coupling efficiency (with respect to no focal plane mask) is about 40% for 1-λ/D separated sources and 10% for 0.5-λ/D separated ones (excluding the factor of the ratio of pupil aperture width and Lyot stop width), where we assumed a linear-polarized-light injection. In addition, because this coronagraph can remove point sources on a line in the sky, it has another promising application for high-contrast imaging of exoplanets in binary systems.
Comparison of the detection efficiency of the four elpasolite scintillators
Authors: Chen Wei , Cao Jinjia , Zhang Biao , Zhang Yulong , Zheng Xiaochang , Gong Xueyu
Published: July 2023

Elpasolite scintillator is a new inorganic scintillator with
excellent performance, which can be used for neutron and γ
dual mode measurement. The model of elpasolite scintillator detector
was established by Geant4 program based on Monte Carlo method, and
the detection efficiency of four kinds of elpasolite scintillator
was compared, including Cs2LiYCl6 (CLYC),
Cs2LiLaCl6 (CLLC), Cs2LiYBr6 (CLYB), and
Cs2LiLaBr6 (CLLB). The effects on the detection efficiency
of scintillators are studied in four aspects: different section
shape, crystal size, γ/neutron energy, and distance between
radiation source and detector. The results indicate that the
detection efficiencies of CLYB and CLLB are better than those of
CLYC and CLLC, and the detection efficiencies of CLYC and CLLC are
better than those of CLYB and CLLB when the scintillators take the
same cross section parameters. The simulation results also show that
CLYC and CLLC crystals are more suitable for thermal neutron
measurement, while CLYB and CLLB are suitable for slow neutron
detection. This study has certain reference value for designing and
practical application of elpasolite scintillator detector.
Sensitivity analysis of SPH parameters for long-distance water wave propagation
Authors: Trimulyono A , Abror I , Yudo H , Purwanto D B
Published: July 2023

The hydrodynamics field continues to be interested in one of the classic free surface flow problems, the propagation of water waves. In this paper, long-distance water wave propagation is investigated using smoothed particle hydrodynamics (SPH). One of the mesh-free, Lagrangian particle approaches is SPH. The study’s goal is to derive a set of parameters appropriate for water wave propagation in a large wave tank. A 24.6 m wave gauge was placed in front of the piston wavemaker, which was used to replicate regular waves. Several SPH parameters are subjected to the sensitive analysis. In this investigation, DualSPHysics version 5.0, an open-source SPH solver, was employed. The findings demonstrated that a parameter with a substantial impact on the accuracy of wave profile is double-precision, particle distance, and coefficient of artificial viscosity.
A Study of the Resistance Components of Planing Hull Using Interceptors
Authors: Samuel S. , Yulianti Serliana , Manik Parlindungan
Published: July 2023

The extreme motions created a negative effect on planing hull. Otherwise, interceptors enable the improvement of hydrodynamic characteristics of the highspeed craft. The total drag of the ship can be divided into two components: pressure and shear forces. This project specifically aims to predict the drag component based on CFD simulation with and without an interceptor based on resistance components. The volume of fluid is used in a compound with a RANS solver to determine drag and trim in calm water conditions. SIMPLE algorithm using overset mesh and DFBI was modeled free in heave and pitch to simulate the rigid body motion as a response to shear and pressure drag exerted by the fluid. A grid independence study has been used to predict uncertainties using time-step and grid spacing. Additionally, to guarantee to proceed with the simulation, ITTC recommendations had been followed. The benchmark study was undertaken as an experimental comparison by Park et al. In general, ship performance was controlled by pressure force in the displacement phase and planing phase, the shear and pressure forces are balanced. The interceptor can decrease the pressure force by 5% in the hump region and planing phase.
Hydraulic Stability of Concrete Armour Unit: A 2D Physical Model Study
Authors: Utami W , Armono H D , Wahyudi  , Sutanto M H
Published: July 2023

Coastal structures designed to protect against erosion caused by wave action, storm surge, and currents are called revetment. The revetment armour layer design is the critical component of the stability of the structure. Structural failure could occur due to a faulty armour unit’s weight design. The stability test of the BPPT Lock primary layer unit for revetment will be conducted in this study. This study employs an experimental approach to evaluate revetment models in the laboratory using three different structural slope configurations and BPPT Lock primary layer units. It was shown that structure with a 1: 1.15 slope has the least stability, while a structure with a slope of 1: 2 is the most stable for the various wave heights identified in the test. The damage was found in the run-up and run-down areas. A 16 cm wave height in the 1: 1.15 structure’s slope results in 8.99% damage, while at the slope of 1: 1.5 and 1: 2, the damage occurs at 5.42% and 2.56%, respectively.
Conducting Vessel Data Imputation Method Selection Based on Dataset Characteristics
Authors: Fatyanosa Tirana Noor , Firdausanti Neni Alya , Soto Luis Francisco Japa , Santos Israel Mendonça dos , Prayoga Putu Hangga Nan , Aritsugi Masayoshi
Published: July 2023

Time series datasets collected from marine sensors inevitably undergo missing data problems. This cause unreliable sensor data to assist the decision-making process. Many methods are offered to impute missing values. However, selecting the best imputation method is not a trivial task, as it usually requires domain expertise and several trial-and-error iterations. Furthermore, when imputations are carried out in a careless way, it generates a high error factor that can lead stakeholders to wrong assumptions. This paper provides a systematic approach that is able to extract characteristics of underlying data and, based on it, recommends the less error-prone imputation method. We evaluate our proposed method using nine real-world vessel datasets. In total, we generated 3859 data samples consisting of 17 inputs and 1 target feature. Experimental results show that the proposed approach is capable of obtaining a weighted F1-Score of 92.6%. Additionally, when compared with the application of careless selected imputation methods, our work is able to gain up to 86% on the average imputation score, with the worst case gain being of 5%. We empirically demonstrate that the proposed approach is efficient when selecting the best imputation methods.
Comparative Study of Tubular Joint Design Formulas According to API RP 2A WSD 21st Edition and 22nd Edition
Authors: Primastuti R A , Prastianto R W , Alfian D , Susanto I , Fadlianto P , Syalsabila F
Published: July 2023

The strength of the jacket substructure on a fixed offshore platform is dictated by the strength of the tubular connecting the jacket leg and the braces. The accuracy of the static strength calculation of the tubular joint is very important to ensure the integrity of the structure during its operation. Therefore, as a Recommended Practice, API RP 2A WSD always regularly was updated based on the results of the latest research to obtain more accurate results in the analysis of the tubular joint. This paper discusses the difference between simple tubular joint design calculation based on API RP 2A WSD 21st Edition and API RP 2A WSD 22nd Edition. This study will show simple joint design calculation for joint types of K, T, and X. The results will be compared to the modelling results for validation. Furthermore, this paper will study variables affecting the difference in the calculation of the result between these two versions and which factors the API considers in changing the formula. This analysis results certainly show the difference in the formula between these two editions of the API, and the comparison with the finite element analysis demonstrates good results.
Fleet Ownership Model for Mineral Export Products Concerning Indonesia’s Downstream Mineral Policy: A Case Study of Copper Ore Exports
Authors: Achmadi T , Lazuardi S D , Buana IGNS , Mustakim A , Rahmawati R S
Published: July 2023

Indonesia’s copper ore has a contribution of 3% in the world’s copper ore needs and has rank of the 5th largest export of mining materials after briquette, kerosene, coal, and crude oil. According to Mineral and Coal Mining Law Number 4 of 2009 that raw materials of mining products have been prohibited to be exported including copper ore due to increasing the value of mineral export products. Thus, it would affect to the current copper ore shipment, which should firstly be processed by smelter to be work-in-process products, namely cathodes. In order to comply with the downstream policy, this study aimed to select the optimum vessel used for delivering copper ores to smelter as well as to define the minimum unit cost for transporting cathodes from smelter to importing countries. The method of non-linear programming was used to produce the minimum unit cost of transport for these three scenarios of fleet ownership model: (1) charter vessel, (2) new shipbuilding vessel, (3) second-hand vessel. The results obtained that the selected domestic ship was a new shipbuilding scenario with the type of bulk carrier, transporting copper ores from site to smelter. Meanwhile, the selected export ship was a voyage charter scenario with the type of general cargo vessel, delivering cathodes from smelter to importing countries.
Evaluation of Energy Efficiency Existing Ship Index (EEXI) on Container Ship in Indonesian Shipping
Authors: Wiliyan Ricco , Made Ariana I , Widhi Dhimas
Published: July 2023

CO2 has been one of the biggest contributors of Green House Effect, crippling the ozone of our own earth over the years. Ships, as the biggest transportation mode in the world, estimated to produce 1,046 millioin tonnes of CO2 approximately 3,3% from the total of CO2 emission across the globe. International Maritime Organization, through Marine Pollution (Annex VI) convention, has set a goal to reach carbon intensity reduction by 40% on 2030 and 100% by 2100. Furthermore, by 2023, a similar but novel regulation would be forced entry for those more than 400 GT existing ships which called “Energy Efficiency for Existing Ship” (EEXI). NKClass stated, about 6050 ships would be further regulated and 80% of NKClass Container vessel would need to be “Technically” adjusted in order to comply with the regulation and CO2 reducing program. “EPL” is one of the ways to achieve it. In this study, one of Indonesian Container Vessel would be analysed in the face of EEXI. With the calculation being done, a good understanding on how ship owner and other stakeholders must do, in order to comply with CO2 reduction programme while maintaining the best performance and business process as it can, might be more cleared.
Verification and validation of ITTC benchmark ship CFD performance towards development of CFD and EFD combined methods
Authors: Sunarsih  , Nanda M. I. , Purnamasari D. , Baidowi A. , Syarif I. S.
Published: July 2023

CFD applications in ship hydrodynamics have been remarkably exploited in the past decades. However, the supremacy of experimental tests, known as EFD, are irreplaceable even against the urgency of less laborious and low-cost hydrodynamic prediction methods. Recently, ITTC has introduced and worked out on CFD and EFD combined methods to benefit the best combination of CFD and EFD for the predictions of ship hydrodynamics. This study explores CFD performance towards development of CFD and EFD combined methods by employing ITTC benchmark ships. The ships were modeled and tested in various operating conditions where results were examined against EFD values from previous studies. Accuracy of the simulation results yielded as high as 97.03% indicates that the presented approach is rigor as a basis of CFD and EFD combined methods for sustainable fluid dynamic analysis.
Economic Recovery of Coastal Communities Post COVID-19 Through Marine Ecotourism Management in Wongsorejo, Banyuwangi (case study: Grand Watudodol Beach)
Authors: Zubaidah A F , Pratikto W A , Zikra M
Published: July 2023

Banyuwangi is known for its abundant natural, coastal, and marine resources potential. The existence of tourism potential in each region as well as tourism sector development policies make Banyuwangi a global region in the tourism sector. The tourism sector is the leading sector of economic growth in Banyuwangi to contribute to a source of national income. For the national maritime industry, Banyuwangi marine tourism has the opportunity to be developed in a sustainable manner. One of them is the coastal district of Wongsorejo Banyuwangi which has many marine tourism destinations along its coastline. However, COVID-19 pandemic since 2020 until now continues to reduce the economic conditions on the Wongsorejo coastal. So, using Fault Tree Analysis method, a study of the reasons behind the decreasing economic conditions in the marine ecotourism management industry was conducted. The findings revealed a total of 6 factors. The primary issues identified are the poor quality of human resources and the lack of innovation in utilizing the potential of marine ecotourism in a sustainable. The solution is ecotourism management, which involves community and stakeholder empowerment, mapping the potential of marine ecotourism and its protected areas, implementing integrated tourism destination programs to promote equity, and providing training.
The analysis of delay factors on the construction of submerged turret production buoy structure
Authors: Silvianita  , Sidiq R B , Utomo C
Published: July 2023

In every project implementation, not everything is according to plan, many factors are causing project delays. This paper identifies the common factors contributing to project delays. The above problems occurred in the construction of the Submerged Turret Production Buoy structure which was carried out by PT. XYZ with height 28937 mm. In this study, an analysis of the factors causing project delay was carried out using a Fault Tree Analysis method. From the calculations obtained that the main factor contributing to project delay is a problematic client with a probability of 0.048812, the second factor is poor planning and management with a probability of 0.218186, the third factor is problematic contractors with a probability of 0.037472. The probability of project delay in the Submerged Turret Production Buoy structure is 0.304470. Knowing these factors will help to degrade the project delay in the future.
Risk assessment on offshore pipes
Authors: Silvianita  , Agustina C , Hadiwidodo Y S , Suntoyo  , Dhanistha W L
Published: July 2023

Pipelines are the most frequently failed parts of oil production installations. Therefore, the safety of underwater gas pipelines became a very concerned focus in this study. This study aims to assess the risk of the pipeline due to changes in the new ABC Port shipping line that have the potential to pose a risk of pipeline damage. This study conducted a risk assessment on pipes at PT. XYZ due to anchor dropping, anchor dragging, and sinking ships. Based on the risk assessment that has been carried out on all risks, it is found that the level of risk is in an acceptable area and in the ALARP zone (As Low as reasonably Practicable Risk). Based on the results of the analysis using Ansys structural software, the maximum value of equivalent stress that occurs in the pipe due to dropped anchor can be received is no more than 0.9 of the SMYS (Specified Minimum Yield Stress) value of 4.05E+08 Pa.
A reasoning of economic complexity based on simulated general equilibrium international trade model
*
Authors: Hu Yumin , Fan Zhongchen , Yifu Lin Justin , Xu Mingzhi (Jimmy)
Published: July 2023

By simulating a multi-country general equilibrium international trade model, we investigate how the economic complexity index (ECI) and fitness index (FI) are related directly to economic fundamentals with a clear basis in theory. The model is based on Eaton and Kortum (2002 Econometrica
70 1741–79) and combines factor endowment (Heckscher-Ohlin) and technological (Ricardian) reasons for specialization, which further determines economic complexity across countries. First, we find that FI performs better than ECI in explaining the real-world specialization pattern, where successful countries not only produce complex products due to the comparative advantage but also tend to produce a wide range of possible products due to the absolute advantage. Second, we highlight that the predictive power of various economic complexity measures for income is crucially sensitive to other factors that shift marginal cost from its efficient level in manufacturing sectors. The essence of such an issue lies in the assumption that the revealed comparative advantage (RCA) correctly reflects a country’s real capability of specialization across different goods. However, there would exist a gap between the core idea of learning the national complexity from RCA and the fact that the revealed specialization pattern in data may not necessarily suggest a country’s actual capability in the presence of distortions, the latter of which is ubiquitous across developing countries.
Vestigial sciences
Authors: Gordin Michael D.
Published: July 2023

“Vestigial sciences” are those doctrines that were once considered to be legitimate science, but have since fallen out of the mainstream, whether because they came to be considered empirically inadequate, theoretically misguided, or simply no longer relevant. If someone continues to advocate for such ideas after they have been rejected, that individual is frequently deemed a pseudoscientist. Most of the theories today considered pseudosciences have this vestigial quality. Two in particular, that were quite prominent in sixteenth- and seventeenth-century Europe, are examined here: astrology and alchemy. Astrology was at one point highly respectable and supported by states; alchemy, by contrast, always had elements of secrecy and disreputability, but was still a candidate for legitimate knowledge. The process of “fringing out,” by which such theories lose their currency, is discussed as a general phenomenon.
Mind over matter
Authors: Gordin Michael D.
Published: July 2023

The notion that our minds are capable of manipulating matter directly, or perceiving by means of more than the commonly accepted five senses, has been a durable staple of a number of fringe theories. This chapter traces a lineage of such doctrines, exhibiting continuities of practices, personnel, and doctrines: mesmerism (a form of animal magnetism) in eighteenth-century France; spiritualism (communication with departed souls) in nineteenth-century Europe; and extra-sensory perception (clairvoyance and telepathy) research in the twentieth-century United States. Each of these doctrines is not just connected to each other, but the efforts of mainstream scientists to “debunk” them have added important elements to today’s repertoire of experimental practices: the placebo sham, randomized controls, and statistical analysis.
The Russian questions
Authors: Gordin Michael D.
Published: July 2023

This chapter explores two questions about the phenomenon of pseudoscience: Who is to blame for it, and what can be done about it? Each of these questions has sparked a variety of answers. Some blame has gone to corporations that have funded research designed to muddy the waters of the scientific consensus, a practice sometimes called “denialism,” most commonly associated with the tobacco and fossil fuel industries. Others blame failures of scientific literacy. The conclusion states that some degree of fringe science is inevitable, given the structure of our knowledge system, but also that not all of these doctrines are equally damaging to public health or the environment. Careful analysis can focus the scientific community’s efforts to responding to the more pressing epistemic crises.
Genes as markers
Authors: Slack Jonathan
Published: July 2023

‘Genes as markers’ shows that most genetic variation does not affect gene function or activity, but it is still of enormous interest. Notably it enables the identification of individual people, useful in forensics in the form of DNA fingerprinting, the establishment of paternity, and other information about family relationships. Recently it has become possible to deduce something of the appearance of an individual from a DNA sample. The study of genetic markers also provides some evidence about the migration of human populations in historic and prehistoric times. In particular the mitochondrial DNA provides information about the female line of descent and the Y chromosome about the male line of descent. The study of ancient DNA, from archaeological specimens, has added greatly to this understanding. Genetic variation between populations has enabled biologists to examine the thorny issue of human racial differences and establish the degree to which there is any biological basis for perceived race. Kits are now widely used by people wanting to discover more about their own ancestry.
The West Riding Lunatic Asylum Medical Reports: the precursor of Brain?
Authors: Larner Andrew J
Published: July 2023

First published in 1878, Brain: A Journal of Neurology is generally considered to be the world’s first neuroscientific journal. However, this claim might be challenged since the West Riding Lunatic Asylum Medical Reports, another journal with significant neuroscientific content, was published between 1871 and 1876. Some have suggested this journal was the precursor of Brain, since it shared similar subject matter as well as editorial and authorial contributors, including James Crichton-Browne, David Ferrier and John Hughlings Jackson.

To address this question, this article examines the origins, aims, structure and contents of, and some of the contributors and contributions to, the West Riding Lunatic Asylum Medical Reports and compares these elements to the first six volumes of Brain (1878–9 to 1883–4). Although the two journals did overlap in terms of some shared neuroscientific interests, Brain evidently had a broader scope and a more international authorship.

Nevertheless, this analysis suggests that, through the agency of Crichton-Browne, Ferrier and Hughlings Jackson, it is appropriate to regard the West Riding Lunatic Asylum Medical Reports as not only the antecedent but also the precursor of Brain.
Glucocorticoid withdrawal syndrome following surgical remission of endogenous hypercortisolism: a longitudinal observational study
Authors: Zhang Catherine D , Li Dingfeng , Singh Sumitabh , Suresh Malavika , Thangamuthu Karthik , Nathani Rohit , Achenbach Sara J , Atkinson Elizabeth J , Van Gompel Jamie J , Young William F , Bancos Irina
Published: July 2023

Objective

Glucocorticoid withdrawal syndrome (GWS) is a scarcely studied phenomenon that complicates the recovery following surgical remission of hypercortisolism. We aimed to characterize the presence and trajectory of glucocorticoid withdrawal symptoms in the postoperative period and to determine presurgical predictors of GWS severity.

Design

Longitudinal observational study.

Methods

Glucocorticoid withdrawal symptoms were prospectively evaluated weekly for the first 12 weeks following surgical remission of hypercortisolism. Quality of life (CushingQoL and Short-Form-36) and muscle function (hand grip strength and sit-to-stand test) were assessed at the baseline and at 12 weeks after surgery.

Results

Prevalent symptoms were myalgias and arthralgias (50%), fatigue (45%), weakness (34%), sleep disturbance (29%), and mood changes (19%). Most symptoms persisted, while myalgias, arthralgias, and weakness worsened during weeks 5-12 postoperatively. At 12 weeks after surgery, normative hand grip strength was weaker than at baseline (mean Z-score delta −0.37, P = .009), while normative sit-to-stand test performance improved (mean Z-score delta 0.50, P = .013). Short-Form-36 Physical Component Summary score worsened (mean delta −2.6, P = .015), but CushingQoL score improved (mean delta 7.8, P < .001) at 12 weeks compared to baseline. Cushing syndrome (CS) clinical severity was predictive of postoperative GWS symptomology.

Conclusion

Glucocorticoid withdrawal symptoms are prevalent and persistent following surgical remission of hypercortisolism with baseline CS clinical severity predictive of postoperative GWS symptom burden. Differential changes observed in muscle function and quality of life in the early postoperative period may reflect the competing influences of GWS and recovery from hypercortisolism.
Selection on weapon allometry in the wild
Authors: Emberts Zachary , Somjee Ummat , Wiens John J
Published: July 2023

Allometry is the scaling relationship between a trait and body size. This relationship can often explain considerable morphological variation within and among species. Nevertheless, much remains unknown about the factors that underlie allometric patterns. For example, when different allometric relationships are observed amongst closely related species, these differences are regularly considered to be products of selection. However, directional selection on allometry (particularly the slope) has rarely been tested and observed in natural populations. Here, we investigate selection on the scaling relationship between weapon size and body size (i.e., weapon allometry) in a wild population of giant mesquite bugs, Pachylis neocalifornicus (previously Thasus neocalifornicus). Males in this species use their weapons (enlarged femurs) to compete with one another over access to resources and females. We found that large males with relatively large weapons successfully secured access to mates. However, we also found that small males with relatively small weapons could access mates as well. These two patterns together can increase the allometric slope of the sexually selected weapon, suggesting a straightforward process by which the allometric slope can evolve.
The Philippines and the liberal rules-based international order
Authors: Misalucha-Willoughby Charmaine
Published: July 2023

How do small powers choose the version of an international order to subscribe to? What factors are at play when a state subscribes to the rules-based order or decides to abandon those commitments and shift to an alternative version of order? The argument put forth in this article is that this choice is a function of domestic dynamics and the expected foreign policy gains of the sitting leader. In questioning the automaticity of a small power's choice, the article makes two important contributions. At the conceptual level, it supports the idea that orders persist because of the mutually constitutive actions of great and small powers. It lends credence to the claim of intersubjectivity in international relations and emphasizes that agency is anchored in relations between states. At the policy level, the article finds that while the Philippines seems to automatically subscribe to the United States-led order, pockets of resistance are a function of a colonial past that lingers to this day, which became fertile ground for the country's pivot to China during the Duterte administration. The article closes by highlighting that alliances risk their cohesion and effectiveness without coordinated maintenance, so policy lessons on alliance management are necessary to improve collective security arrangements.
Unpacking Thailand's conceptions of and position within the liberal international order
Authors: na Thalang Chanintira
Published: July 2023

Based on statements made by political and military elites and government officials, the article explores how Thailand selectively supports and capitalizes on certain elements of the contemporary world order, namely United States-led security cooperation and economic liberalism, while half-heartedly embracing the ideals of liberal democracy. Although this never caused problems with the West during the Cold War, matters began to change in the 1990s against the backdrop of systemic-level shifts. While these developments have caused sporadic tensions with the West and effectively brought Thailand closer to China, Thailand has pragmatically sought ways to maintain its autonomy from both the United States and China. Based on Thailand's experience, this article reveals how smaller states pursue a variety of strategies to enhance their agency despite their lack of material capabilities. In turn, the discussion exemplifies how smaller states are not always determined by systemic level factors but possess the ability to prioritize and actualize regime security and national ideals while navigating the evolving international and regional orders.
A highly contiguous reference genome for the Steller’s jay (Cyanocitta stelleri)
Authors: Benham Phred M , Cicero Carla , DeRaad Devon A , McCormack John E , Wayne Robert K , Escalona Merly , Beraut Eric , Marimuthu Mohan P A , Nguyen Oanh , Nachman Michael W , Bowie Rauri C K
Published: July 2023

The Steller’s jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller’s jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.
Single-cell clonal tracing of glandular and circulating T cells identifies a population of CD9+ CD8+ T cells in primary Sjogren's syndrome
Authors: Chang Ling , Zheng Zihan , Xiao Fan , Zhou Yingbo , Zhong Bing , Ni Qingshan , Qian Can , Chen Chengshun , Che Tiantian , Zhou Yiwen , Zhao Zihua , Zou Qinghua , Li Jingyi , Lu Liwei , Zou Liyun , Wu Yuzhang
Published: July 2023

Primary Sjogren's syndrome (pSS) is a complex chronic autoimmune disease in which local tissue damage in exocrine glands is combined with broader systemic involvement across the body in tissues including the skin. These combined manifestations negatively impact patient health and quality of life. While studies have previously reported differences in immune cell composition in the peripheral blood of pSS patients relative to healthy control subjects, a detailed immune cell landscape of the damaged exocrine glands of these patients remains lacking. Through single-cell transcriptomics and repertoire sequencing of immune cells in paired peripheral blood samples and salivary gland biopsies, we present here a preliminary picture of adaptive immune response in pSS. We characterize a number of points of divergence between circulating and glandular immune responses that have been hitherto underappreciated, and identify a novel population of CD8+ CD9+ cells with tissue-residential properties that are highly enriched in the salivary glands of pSS patients. Through comparative analyses with other sequencing data, we also observe a potential connection between these cells and the tissue-resident memory cells found in cutaneous vasculitis lesions. Together, these results indicate a potential role for CD8+ CD9+ cells in mediating glandular and systemic effects associated with pSS and other autoimmune disorders.
Effect of treatment interruptions on overall survival in patients with triple-negative breast cancer
Authors: Chow Ronald , Hasan Shaakir , Choi J Isabelle , Fox Jana , Chhabra Arpit M , Marshall Deborah C , Bakst Richard L , Simone Charles B
Published: July 2023

Introduction

Currently, there are no data regarding the impact of treatment interruptions during radiotherapy for breast cancer. In this study, we examine the correlation between treatment interruptions during radiotherapy and outcomes in triple-negative breast cancer patients.

Methods

A total of 35 845 patients with triple-negative breast cancer treated between 2010 and 2014 were identified and analyzed from the National Cancer Database. The number of interrupted radiotherapy treatment days was calculated as the difference between the total elapsed days from the start to end of radiation treatment (both initial treatment and boost treatment, when boost was administered) and the total number of expected treatment days, defined as the number of expected treatment days with an addition of 2 weekend days for every multiple of 5 treatment days. Binomial multivariate regression analysis was used to detect correlates of treatment interruptions, and propensity-score matched multivariable Cox proportional hazard models were used to evaluate the association between treatment interruption and overall survival (OS).

Results

When modeled as a continuous variable, longer treatment duration was associated with poorer OS (hazard ratio [HR] = 1.023, 95% confidence interval [CI] = 1.015 to 1.031). In reference to 0-1 days of interruption, patients with 2-5 interrupted days (HR = 1.069, 95% CI = 1.002 to 1.140 interrupted days), 6-10 interrupted days (HR = 1.239, 95% CI = 1.140 to 1.348 interrupted days), and 11-15 interrupted days (HR = 1.265, 95% CI = 1.126 to 1.431 interrupted days) experienced increasing likelihood of mortality.

Conclusion

In the first study of its kind, we report a correlation between treatment interruptions during adjuvant radiotherapy in triple-negative breast cancer and OS.
Hierarchical confusion matrix for classification performance evaluation
Authors: Riehl Kevin , Neunteufel Michael , Hemberg Martin
Published: July 2023

This study proposes the novel concept of hierarchical confusion matrix, opening the door for popular confusion-matrix-based (flat) evaluation measures from binary classification problems, while considering the peculiarities of hierarchical classification problems. The concept is developed to a generalised form and proven its applicability to all types of hierarchical classification problems including directed acyclic graphs, multi-path labelling, and non-mandatory leaf-node prediction. Finally, measures based on the novel confusion matrix are used for three real-world hierarchical classification applications and compared to established evaluation measures. The results, the conformity with important attributes of hierarchical classification schemes and its broad applicability justify its recommendation.
Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses
Authors: Lucaci Alexander G , Zehr Jordan D , Enard David , Thornton Joseph W , Kosakovsky Pond Sergei L
Published: July 2023

Inference and interpretation of evolutionary processes, in particular of the types and targets of natural selection affecting coding sequences, are critically influenced by the assumptions built into statistical models and tests. If certain aspects of the substitution process (even when they are not of direct interest) are presumed absent or are modeled with too crude of a simplification, estimates of key model parameters can become biased, often systematically, and lead to poor statistical performance. Previous work established that failing to accommodate multinucleotide (or multihit, MH) substitutions strongly biases dN/dS-based inference towards false-positive inferences of diversifying episodic selection, as does failing to model variation in the rate of synonymous substitution (SRV) among sites. Here, we develop an integrated analytical framework and software tools to simultaneously incorporate these sources of evolutionary complexity into selection analyses. We found that both MH and SRV are ubiquitous in empirical alignments, and incorporating them has a strong effect on whether or not positive selection is detected (1.4-fold reduction) and on the distributions of inferred evolutionary rates. With simulation studies, we show that this effect is not attributable to reduced statistical power caused by using a more complex model. After a detailed examination of 21 benchmark alignments and a new high-resolution analysis showing which parts of the alignment provide support for positive selection, we show that MH substitutions occurring along shorter branches in the tree explain a significant fraction of discrepant results in selection detection. Our results add to the growing body of literature which examines decades-old modeling assumptions (including MH) and finds them to be problematic for comparative genomic data analysis. Because multinucleotide substitutions have a significant impact on natural selection detection even at the level of an entire gene, we recommend that selection analyses of this type consider their inclusion as a matter of routine. To facilitate this procedure, we developed, implemented, and benchmarked a simple and well-performing model testing selection detection framework able to screen an alignment for positive selection with two biologically important confounding processes: site-to-site synonymous rate variation, and multinucleotide instantaneous substitutions.
Stepwise Evolution of E. coli C and ΦX174 Reveals Unexpected Lipopolysaccharide (LPS) Diversity
Authors: Romeyer Dherbey Jordan , Parab Lavisha , Gallie Jenna , Bertels Frederic
Published: July 2023

Phage therapy is a promising method for the treatment of multidrug-resistant bacterial infections. However, its long-term efficacy depends on understanding the evolutionary effects of the treatment. Current knowledge of such evolutionary effects is lacking, even in well-studied systems. We used the bacterium Escherichia coli C and its bacteriophage ΦX174, which infects cells using host lipopolysaccharide (LPS) molecules. We first generated 31 bacterial mutants resistant to ΦX174 infection. Based on the genes disrupted by these mutations, we predicted that these E. coli C mutants collectively produce eight unique LPS structures. We then developed a series of evolution experiments to select for ΦX174 mutants capable of infecting the resistant strains. During phage adaptation, we distinguished two types of phage resistance: one that was easily overcome by ΦX174 with few mutational steps (“easy” resistance) and one that was more difficult to overcome (“hard” resistance). We found that increasing the diversity of the host and phage populations could accelerate the adaptation of phage ΦX174 to overcome the hard resistance phenotype. From these experiments, we isolated 16 ΦX174 mutants that, together, can infect all 31 initially resistant E. coli C mutants. Upon determining the infectivity profiles of these 16 evolved phages, we uncovered 14 distinct profiles. Given that only eight profiles are anticipated if the LPS predictions are correct, our findings highlight that the current understanding of LPS biology is insufficient to accurately forecast the evolutionary outcomes of bacterial populations infected by phage.
ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development
Authors: Graham-Paquin Adda-Lee , Saini Deepak , Sirois Jacinthe , Hossain Ishtiaque , Katz Megan S , Zhuang Qinwei Kim-Wee , Kwon Sin Young , Yamanaka Yojiro , Bourque Guillaume , Bouchard Maxime , Pastor William A
Published: July 2023

ZMYM2 is a transcriptional repressor whose role in development is largely unexplored. We found that Zmym2−/− mice show embryonic lethality by E10.5. Molecular characterization of Zmym2−/− embryos revealed two distinct defects. First, they fail to undergo DNA methylation and silencing of germline gene promoters, resulting in widespread upregulation of germline genes. Second, they fail to methylate and silence the evolutionarily youngest and most active LINE element subclasses in mice. Zmym2−/− embryos show ubiquitous overexpression of LINE-1 protein as well as aberrant expression of transposon-gene fusion transcripts. ZMYM2 homes to sites of PRC1.6 and TRIM28 complex binding, mediating repression of germline genes and transposons respectively. In the absence of ZMYM2, hypermethylation of histone 3 lysine 4 occurs at target sites, creating a chromatin landscape unfavourable for establishment of DNA methylation. ZMYM2−/− human embryonic stem cells also show aberrant upregulation and demethylation of young LINE elements, indicating a conserved role in repression of active transposons. ZMYM2 is thus an important new factor in DNA methylation patterning in early embryonic development.