bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental study on the wave-induced fluid resonance and suppression scheme in the narrow gap of two floating rectangular structures
Authors: Wang Xin-yu , Liu Yong , Meringolo Domenico D. , Lu Lin
Published: December 2023

An experimental study on the wave-induced gap resonance and resonant suppression scheme for two floating rectangular structures (TFRSs) is systematically presented. The instantaneous velocity fields for the present problem are measured using an enhanced underwater particle image velocimetry measurement system. Detailed experimental results have been presented to study the influences of the wave and structural parameters on the gap resonant characteristics. The resonant wave height and wave frequency were sensitive to the variation of the gap width but not very sensitive to the variation of the surface roughness on the rounded corner of TFRSs. The nonlinear effects of harmonic components on resonant free surface elevation are estimated. To analyze the vortex structures, different vortex identification methods in literature are analyzed and their merits and demerits are summarized based on a comparative analysis of the measured velocity data. The Ω-criterion vortex identification approach is then selected to evaluate the vortex intensity and capture the main vortex cores. Thanks to the adopted technique, the subsequent separation of the two quasi-symmetric vortex structures is considered to be a significant contribution to energy dissipation. The vortex shedding and dissipation modes of different TFRSs are very similar and exhibit slight variations in resonant responses. A formula of the modified Reynolds number for the gap resonance problem of TFRSs is proposed. The non-dimensional vortex strengths are nonlinearly dependent on the newly modified Reynolds number and linearly dependent on the Keulegan–Carpenter (KC) number. Finally, an optimal suppression scheme for the gap resonance problem of TFRSs is suggested.
Divergent interfacial thermal transport in MoS2/Si heterostructure over optical phonon modes
Authors: Li Dongsheng , Huang Xiaona , Liu Zeyu , Liu Wenxiang , Xu Shen , Yue Yanan
Published: December 2023

Thermal transport within nanostructures is highly confined by interfaces, and non-trivial physics can emerge at boundaries. Theoretical studies have shown that different phonon modes can exhibit varying thermal resistances at interfaces. Experimental observation of these variations, however, is lacking. Using the steady-state Raman thermometry, the E2g1 and A1g vibrational modes of MoS2 were utilized to characterize the thermal transport properties across the MoS2/Si interface. Our results revealed distinct temperature rises associated with different modes, indicating various mode contributions in the interfacial thermal conductance. Combining experimental and numerical simulations, the out-of-plane mode in MoS2 was found to contribute less to the interfacial transport, by 21.5%, attributed to the less variational mode mismatch of the in-plane phonon, compared to the in-plane mode. Furthermore, our results confirmed a 26.9% higher thermal conductivity from the out-of-plane mode than the in-plane one.
Weibel-like instability in magnetohydrodynamics
Authors: Davies J. R.
Published: December 2023

In magnetohydrodynamics (MHD), a density perturbation perpendicular to an electron temperature gradient generates a magnetic field around itself that acts to increase the perturbation, which can lead to instability. An MHD dispersion relation is obtained for perturbations perpendicular to a fixed electron temperature gradient with an initial in-plane magnetic field, including resistivity, viscosity, and the electrothermal coefficient. Instability occurs for sufficiently small electron temperature-gradient scale lengths determined by the ion collisionless skin depth. Both viscosity and resistivity are required to prevent growth at arbitrarily small spatial scales and to give a physical result for the fastest growing mode. The perpendicular electrothermal coefficient is only significant for a narrow range of low electron Hall parameters, causing a modest reduction in magnetic field growth and modifying the criteria for instability in the presence of viscosity. If the definition of the Weibel instability [E. S. Weibel, Phys. Rev. Lett. 2, 83 (1959)] is extended to include all instabilities due to anisotropy in the electron velocity distribution, then this is a Weibel-like instability because an electron temperature gradient implies an anisotropic electron velocity distribution. The implications for the formation of filaments in laser-produced plasmas and for the verification of MHD codes are considered.
Intrinsic carrier mobility limits in the transparent bipolar semiconductor CuInO2
Authors: Yao Xiaoping , Zhu Ziye , Zhao Shu , Li Wenbin
Published: December 2023

The delafossite semiconductor CuInO2 has shown great potential in transparent electronics for its bipolar dopability. However, little is known about the limiting factors about its carrier mobility, which impedes its further development. Applying abinitio Boltzmann transport formalism, here we calculate the intrinsic, phonon-limited carrier mobility of CuInO2 and study its carrier–phonon coupling mechanisms. The calculated room-temperature electron and hole mobilities along the in-plane direction are μe=97.6 cm2V−1s−1 and μh=1.4 cm2V−1s−1, respectively. We find that the electron mobility is limited by the combination of acoustic phonons and polar longitudinal optical (LO) phonons, while the hole mobility is mainly limited by carrier–acoustic phonon scattering. We further show that the electron effective mass and bandgap of CuInO2 can be tuned through strain engineering for improved carrier transport properties. Our work uncovers the underlying factors that govern the intrinsic carrier mobility of the transparent bipolar semiconductor CuInO2 and sheds light on the design and exploration of bipolar conducting transparent conductive oxides (TCOs) based on delafossite semiconductors.
Somatic mutations of MLL4/COMPASS induce cytoplasmic localization providing molecular insight into cancer prognosis and treatment
Authors: Zhao Zibo , Aoi Yuki , Philips Cassandra N. , Meghani Khyati A. , Gold Sarah R. , Yu Yanni , John Luke St , Qian Jun , Zeidner Jacob M. , Meeks Joshua J. , Shilatifard Ali
Published: December 2023

Cancer genome sequencing consortiums have recently catalogued an abundance of somatic mutations, across a wide range of human cancers, in the chromatin-modifying enzymes that regulate gene expression. Defining the molecular mechanisms underlying the potentially oncogenic functions of these epigenetic mutations could serve as the basis for precision medicine approaches to cancer therapy. MLL4 encoded by theKMT2Dgene highly mutated in a large number of human cancers, is a key histone lysine monomethyltransferase within the Complex of Proteins Associated with Set1 (COMPASS) family that regulates gene expression through enhancer function, potentially functioning as a tumor suppressor. We report that theKMT2Dmutations which cause MLL4 protein truncation also alter MLL4’s subcellular localization, resulting in loss-of-function in the nucleus and gain-of-function in the cytoplasm. We demonstrate that isogenic correction ofKMT2Dtruncation mutation rescues the aberrant localization phenotype and restores multiple regulatory functions of MLL4, including COMPASS integrity/stabilization, histone H3K4 mono-methylation, enhancer activation, and therefore transcriptional regulation. Moreover, isogenic correction diminishes the sensitivity ofKMT2D-mutated cancer cells to targeted metabolic inhibition. Using immunohistochemistry, we identified that cytoplasmic MLL4 is unique to the tissue of bladder cancer patients withKMT2Dtruncation mutations. Using a preclinical carcinogen model of bladder cancer in mouse, we demonstrate that truncated cytoplasmic MLL4 predicts response to targeted metabolic inhibition therapy for bladder cancer and could be developed as a biomarker forKMT2D-mutated cancers. We also highlight the broader potential for prognosis, patient stratification and treatment decision-making based onKMT2Dmutation status in MLL4 truncation-relevant diseases, including human cancers and Kabuki Syndrome.
Divergent bleaching and recovery trajectories in reef-building corals following a decade of successive marine heatwaves
Authors: Brown Kristen T. , Lenz Elizabeth A. , Glass Benjamin H. , Kruse Elisa , McClintock Rayna , Drury Crawford , Nelson Craig E. , Putnam Hollie M. , Barott Katie L.
Published: December 2023

Increasingly frequent marine heatwaves are devastating coral reefs. Corals that survive these extreme events must rapidly recover if they are to withstand subsequent events, and long-term survival in the face of rising ocean temperatures may hinge on recovery capacity and acclimatory gains in heat tolerance over an individual’s lifespan. To better understand coral recovery trajectories in the face of successive marine heatwaves, we monitored the responses of bleaching-susceptible and bleaching-resistant individuals of two dominant coral species in Hawai’i,
Montipora capitata
and
Porites compressa
, over a decade that included three marine heatwaves. Bleaching-susceptible colonies of
P. compressa
exhibited beneficial acclimatization to heat stress (i.e., less bleaching) following repeat heatwaves, becoming indistinguishable from bleaching-resistant conspecifics during the third heatwave. In contrast, bleaching-susceptible
M. capitata
repeatedly bleached during all successive heatwaves and exhibited seasonal bleaching and substantial mortality for up to 3 y following the third heatwave. Encouragingly, bleaching-resistant individuals of both species remained pigmented across the entire time series; however, pigmentation did not necessarily indicate physiological resilience. Specifically,
M. capitata
displayed incremental yet only partial recovery of symbiont density and tissue biomass across both bleaching phenotypes up to 35 mo following the third heatwave as well as considerable partial mortality. Conversely,
P. compressa
appeared to recover across most physiological metrics within 2 y and experienced little to no mortality. Ultimately, these results indicate that even some visually robust, bleaching-resistant corals can carry the cost of recurring heatwaves over multiple years, leading to divergent recovery trajectories that may erode coral reef resilience in the Anthropocene.
The tension between English-medium instruction and Vietnamese-medium instruction in higher education
Authors: Tang Hoa K. , Nguyen Khanh H. , Luong Nguyen H. N.
Published: December 2023

In Vietnam, English-medium instruction (EMI) has been implemented in parallel with Vietnamese-medium instruction
(VMI) in higher education, partly to help remedy its shortcomings. However, only economically advantaged students can access EMI,
which suggests EMI graduates may accrue discrepant advantages compared to VMI graduates. Research has, nonetheless, not explored the effects on these
stakeholders. Hence, to partially address the gap, this study explores EMI in information technology (IT). Using the theoretical concepts
of parity, distribution, and self-amplifying loop, this study draws on eight in-depth semi-structured interviews with EMI and VMI
graduates. Thematic analysis of the data reveals disparities in advantages ensuing from EMI and VMI including English skills and
Anglo-American acculturation, access to English-speaking jobs at different rates, and divergent professional opportunities. These
disparities are accounted for by the disciplinary paradigm of IT and the unevenly distributed resources between EMI and VMI and
are then enlarged by self-amplifying loops. In this process, EMI in IT constitutes a double accelerator and therefore enables EMI
graduates to gain the foregoing advantages by a larger margin and VMI graduates to do so but at a slower rate. The study
recommends addressing this widening gap through the formation and implementation of VMI- and EMI-related policies at all
levels.
Responses from Businesses in Rural Communities Recovering from the 2011 Tohoku Disasters during the 2020 Tokyo Olympics
Authors: Nguyen David N. , Cordoba Gabriel Fuentes
Published: December 2023

The 2011 Great East Japan Earthquake (GEJE) significantly impacted the Tohoku Region in north-eastern Japan, leading to a large number of human casualties and environmental devastation. It exacerbated pre-existing economic and demographic decline. Tourism development was promoted as part of economic recovery and revitalization efforts. With Japan securing the winning bid for the 2020 Tokyo Olympics, it was hoped that having some of the Olympic activities hosted in Tohoku would contribute to recovery efforts. This case study examines the perspectives of businesses in areas located near the Olympic venues in Tohoku, on what kind of effects the Olympics had on their operations.

Information

© The Authors 2023
Seven-shaped beam design for improving the sensitivity of two-dimensional MEMS sensors
Authors: Zhou Nanyan , Liu Wu , Cui Feng , Zhang Xinwei , Lv Leyang
Published: December 2023

The spring constant of the connecting beam is one of the most crucial factors that affect the detection sensitivity of MEMS sensors. Existing researches reduce the spring constant by changing the parameters or number of connecting beams. In this paper, we propose a seven-shaped beam structure to modify the spring constant of MEMS sensors. The acute angle between the two segments of seven-shaped structure lowers spring constant. Compared with the crab-leg beam, it can bring a maximum sensitivity gain of 1.29 times through different angle designs. At the same time, compared with those combined beams, seven-shaped combined beams can bring a maximum sensitivity gain of 1.6 times. The two-dimensional MEMS sensor with seven-shaped beam has been designed and fabricated. According to the experimental results, the sensor reached a detection sensitivity of 25 fF/g. The relative error of the differential capacitance change between the measurement result and the simulation result is only 8.6%.
Genuine Bell locality and its maximal violation in quantum networks
Authors: Hsu Li-Yi
Published: December 2023

In K-locality networks, local hidden variables emitted from classical sources are distributed among limited observers. We explore genuine Bell locality in classical networks, where, regarding all local hidden variables as classical objects that can be perfectly cloned and spread throughout the networks, any observer can access all local hidden variables plus shared randomness. In the proposed linear and nonlinear Bell-type inequalities, there are more correlators to reveal genuine Bell locality than those in the K-locality inequalities, and their upper bounds can be specified using the probability normalization of the predetermined probability distribution. On the other hand, the no-cloning theorem limits the broadcast of quantum correlations in quantum networks. To explore genuine Bell nonlocality, the stabilizing operators play an important role in designing the segmented Bell operators and assigning the incompatible measurements for the spatially separated observers. We prove the maximal violations of the proposed Bell-type inequalities tailored for the given qubit distributions in quantum networks.
Nested multibar cladding elements in negative curvature fibers for CO laser guidance
Authors: Khan Asfandyar , Ordu Mustafa
Published: December 2023

A numerical study on the multi-bar nested cladding design of chalcogenide glass-based negative curvature hollow-core fiber was carried out to achieve a low-loss light guidance in the mid-infrared spectrum centered at 5.4 μm. Fiber design parameters were systematically optimized, and the effect of the nested bars on the confinement and total loss performance of a five-tubular cladding structure was investigated. An ultra-low transmission loss of 0.112 dB km−1 at 5.4 μm was achieved with As2Se3 triple-bar negative curvature fiber while maintaining low bending sensitivity. The design is also suitable for high transmission performance with alternative infrared glasses and can be potentially used for low-loss light guidance in a wide mid-infrared spectrum.
The manufacture and magnetic field tuning of a merged four-row APPLE-Knot undulator at HEPS
Authors: Huang Y.S. , Li X.Y. , Li Y.H. , Lu H.H. , Yang Y.W. , Chen W. , Li Z.Q. , Zhao S.T. , Sun Y.J. , Zhang L. , Sun S.C. , Gong K.Y.
Published: December 2023

A merged four-row APPLE-Knot undulator has been manufactured
at the High Energy Photon Source(HEPS) and the magnetic field
tunning has been completed. Inclined magnetization magnetic blocks
are used in this undulator in large scale, new skills are used in
magnetic blocks' manufacturing and assembling. Magnet field tunning
is conducted by combination of various methods and resulted in a
satisfactory photon performance. The practical mechanical
deformation of aluminum girder has been measured and compared with
theoretical calculation, results indicate a significant discrepancy
between these two data, the reasons causing this discrepancy have
also been analyzed. The merged four-row APPLE-Knot undulator at HEPS
holds significant reference value for its uniqueness and
specificity.
Comment on ‘CO2 fertilization effect may balance climate change impacts on oil palm cultivation’
Authors: Monteith Paterson Robert Russell
Published: December 2023

A paper modeling future CO2 fertilization of oil palm (OP) resulting in higher palm oil yields is a significant advance. However, climate and disease effects on OP are discussed herein inferring that CO2 fertilization will not occur significantly. It is important that logical assessments of future climate effects on the palm oil industry occur.
Hot or cold temperature disproportionately impacts U.S. energy burdens
Authors: Yu Ying , Kittner Noah
Published: December 2023

The lack of affordable, reliable, and resilient energy services remains a challenge for many U.S. households. Few studies have investigated how temperature makes already vulnerable Black, low-income, and less-educated households more likely to experience energy poverty. We construct a unique 8-year historical panel dataset to unpack the relationship between temperatures and energy burdens, paying specific attention to additional burdens among the most vulnerable groups. We find that hot and cold temperatures have further exacerbated the disproportionate impact on energy burdens across regions and multiple vulnerable groups. Extremely low-income groups are ∼6 times more adversely affected by temperatures than high-income groups. Temperatures also put other already marginalized groups, such as those less-educated/unemployed/living in energy-inefficient old houses, at higher risk of falling into an energy poverty trap. Considering temperatures are the dominant feature differentiating households in their ability to meet basic electricity needs, we recommend more equitable and inclusive electrification strategies and compensation mechanisms for affected communities to improve energy equity.
Technological methods for pavement block repairs in road bridges
Authors: Bogdanova Evgenia
Published: December 2023

Pavement block is a part of bridge a bridge superstructure. During the service life damage accumulates and there is need to repair. The aim of the article is to discuss the types of pavement blocks and to present the results of a study on the most common design solutions for realisation of the repair works. Factors influencing the choice of construction technology are systematized. Information about novelty formwork solutions and types of equipment for working at heights in Bulgaria is provided. A particular example of a bridge structure is presented and a conclusion is drawn regarding the preferred method of work in our country.
About effect of dynamic loading caused by concrete pump on bending moments, anchor forces and deformations in single level anchored retaining wall
Authors: Markov Iliyan , Radlov Kalin
Published: December 2023

This paper explore effect of dynamic loading caused by concrete pump on bending moments, anchor forces and deformations in single level anchored retaining wall. Dynamic loading is obtained by using a special developed dynamic mathematical model of truck-mounted concrete pump, by means of which are calculated the maximal dynamic loadings (acceleration and forces), which are transferred from concrete pump to the soil, and from there accordingly – from soil to the retaining wall under consideration. After that is performed a detailed finite element analysis of the retaining wall, by using software product Plaxis 3D, during which are analyzed the variation of bending moments, anchor forces and deformations in single level anchored retaining wall and after dynamic loading applying. There is also a numerical example considered, for which are calculated the maximal dynamic loadings, which are transferred from concrete pump to the soil, and from ground supports to the retaining wall. An amplification factor (dynamic factor) due to dynamic effects is calculated, by which is necessary to be multiplied the static loadings caused by concrete pump on soil. In the conclusion is made a qualitative assessment of the dynamic influence of concrete pump on the soil and the retaining wall section and ground anchor.
Analysis of a two pile frame for a horizontal force
Authors: Markov Iliyan
Published: December 2023

The article analyzes a pile frame composed of two bored piles with a diameter of 40 cm. The frame is subjected to a horizontal force. Calculations in three different method are conducted – subgrade reaction approach, 2D plaxis and 3D plaxis, after which a comparison was made between the results of the individual methods. The aim is to see under what conditions a subgrade reaction method is suitable for use without moving away from sure side. Results were also obtained for the distribution of the value of the spring constant by depth, as well as values for the ratio between the resistance of the second and first pile. A proposal has been made for obtaining a p-curve that can be applied to any of the linear approximation methods.
Application of artificial intelligence in road network inventory and network-wide road safety assessment
Authors: Katsarov I , Penkov S
Published: December 2023

This research paper examines the application of artificial intelligence (AI) in road network inventory and network-wide road safety assessment. An overview of current research related to this field is presented and various aspects of the use of AI in road infrastructure and safety assessment are analysed. In today’s world, where the road network continues to develop and grow, the use of AI can offer significant advantages in the inventory and assessment of road infrastructure and safety. AI can be used to process large volumes of data collected from various sources such as geographic data, photos, documentation and more. One of the main aspects that the article looks at is the use of AI to automatically process data and create a digital inventory of the road network. AI systems can analyse geographic data and photos to identify and classify roads, road signs, markings, and other elements of road infrastructure. This can facilitate engineers and competent authorities in the process of road inventory and maintenance. Another important aspect discussed in the paper is the use of AI for the general assessment of road safety. AI models can analyse road infrastructure inventory data, as well as traffic data, crashes, and other factors, to provide a comprehensive assessment of road network safety. This allows the competent authorities to identify vulnerable places, carry out preventive measures and plan appropriate interventions aimed at improving road safety. In conclusion, the paper highlights the possibilities and advantages of using artificial intelligence in road network inventory and network-wide road safety assessment. Such an approach can contribute to more efficient management of road infrastructure and improvement of road safety.
3D Printed customized diabetic foot insoles with architecture designed lattice structures – a case study
Authors: Kumar Ravi , Sarangi Saroj Kumar
Published: December 2023

This study proposes a 3D printed, custom insole using an architectural lattice structure infill targeting diabetic patients at risk of foot ulcers. An analysis of five lattice configurations: Fluorite, Kelvin, Octet, Isotruss unit cells, and Truncated Octahedron was conducted to identify the most effective insole infill for plantar pressure and weight redistribution. The Kelvin lattice demonstrated minimal stiffness, suggesting its superiority in balancing plantar pressure and weight. Such lattice-structured insoles offer enhanced foot support and cushioning, crucial for ulcer-prone individuals. This research innovatively employs architectural lattice structures in designing insoles for diabetic patients, offering an insightful comparison of lattice designs for optimized foot care.
Modeling organic negative-transconductance transistors for circuit simulation
Authors: Joshi Saurabh Suredra , Yoo Hocheon , Kim Chang-Hyun
Published: December 2023

Organic negative-transconductance (NTC) transistors are emerging as a new versatile element of flexible and printed electronics. However, there is no standard model of these transistors available in circuit simulators. This paper introduces the first current–voltage model for organic NTC transistors. The model reflects unique structural features of a state-of-the-art NTC transistor platform, incorporating a p-type, an n-type, and a back-conduction channel into a single heterojunction architecture. The details of modeling approach and development are systematically illustrated. Then, the model is firmly validated by experimental data from a high-performance device. Finally, controllability over the abruptness of inter-regime transitions is emphasized as a key advantage of the model for the accuracy of fitting results. This compact, closed-form, and analytical model covering all regimes of operation bridges the gap between device- and circuit-level perspective of organic NTC transistors, promoting their integration into practical electronics technologies.
Comment on ‘From counterportation to local wormholes’
Authors: Dressel Justin , Reznik Gregory , Vaidman Lev
Published: December 2023

Hatim Salih discovered a method for transferring a quantum state with no particles present in the transmission channel, which he named counterportation. Recently (Salih 2023 Quantum Sci. Technol.
8 025016), he presented a feasible procedure for its implementation. The modification of the protocol by Aharonov and Vaidman, adopted by Salih, justifies the claim that no photons were present in the transmission channel during counterportation. We argue, however, that there is an error in this paper. The analysis of a simplified protocol, which questions the validity of the two-state vector formalism description of the photon presence in the communication channel, is incorrect.
Nontraditional energy-assisted mechanical machining of difficult-to-cut materials and components in aerospace community: a comparative analysis
Authors: Zhao Guolong , Zhao Biao , Ding Wenfeng , Xin Lianjia , Nian Zhiwen , Peng Jianhao , He Ning , Xu Jiuhua
Published: December 2023

The aerospace community widely uses difficult-to-cut materials, such as titanium alloys, high-temperature alloys, metal/ceramic/polymer matrix composites, hard and brittle materials, and geometrically complex components, such as thin-walled structures, microchannels, and complex surfaces. Mechanical machining is the main material removal process for the vast majority of aerospace components. However, many problems exist, including severe and rapid tool wear, low machining efficiency, and poor surface integrity. Nontraditional energy-assisted mechanical machining is a hybrid process that uses nontraditional energies (vibration, laser, electricity, etc) to improve the machinability of local materials and decrease the burden of mechanical machining. This provides a feasible and promising method to improve the material removal rate and surface quality, reduce process forces, and prolong tool life. However, systematic reviews of this technology are lacking with respect to the current research status and development direction. This paper reviews the recent progress in the nontraditional energy-assisted mechanical machining of difficult-to-cut materials and components in the aerospace community. In addition, this paper focuses on the processing principles, material responses under nontraditional energy, resultant forces and temperatures, material removal mechanisms, and applications of these processes, including vibration-, laser-, electric-, magnetic-, chemical-, advanced coolant-, and hybrid nontraditional energy-assisted mechanical machining. Finally, a comprehensive summary of the principles, advantages, and limitations of each hybrid process is provided, and future perspectives on forward design, device development, and sustainability of nontraditional energy-assisted mechanical machining processes are discussed.
On the Montgomery–Vaughan weighted generalization of Hilbert’s inequality
Authors: Yangjit Wijit
Published: December 2023

This paper concerns the problem of determining the optimal constant in the Montgomery–Vaughan weighted generalization of Hilbert’s inequality. We consider an approach pursued by previous authors via a parametric family of inequalities. We obtain upper and lower bounds for the constants in inequalities in this family. A lower bound indicates that the method in its current form cannot achieve any value below

3.19497
3.19497

, so cannot achieve the conjectured constant

π
\pi

. The problem of determining the optimal constant remains open.
The Abolition of the Right to Trial by Jury in Civil Cases in England
Authors: Bullock Charles S
Published: December 2023

Prior to 1854, jury trial was the exclusive mode of resolving cases involving disputed facts at common law. By 1935, the civil jury trial had been virtually eliminated in all but a few obscure types of tort action. This article consists of a detailed examination, based primarily on legislative sources and contemporary legal periodicals, of how the right to trial by jury in civil cases was abolished. The first concrete step towards jury abolition occurred in 1854, when litigants in high court cases were empowered to waive their right to jury trial in favour of trial by judge alone. Thereafter, a series of legislative acts and judicial rules incrementally transferred the power to choose the mode of trial in particular types of cases from litigants to trial judges, who routinely chose trial by judge alone.
Model-based evaluation of spatiotemporal data reduction methods with unknown ground truth through optimal visualization and interpretability metrics
Authors: Atitey Komlan , Motsinger-Reif Alison A , Anchang Benedict
Published: December 2023

Optimizing and benchmarking data reduction methods for dynamic or spatial visualization and interpretation (DSVI) face challenges due to many factors, including data complexity, lack of ground truth, time-dependent metrics, dimensionality bias and different visual mappings of the same data. Current studies often focus on independent static visualization or interpretability metrics that require ground truth. To overcome this limitation, we propose the MIBCOVIS framework, a comprehensive and interpretable benchmarking and computational approach. MIBCOVIS enhances the visualization and interpretability of high-dimensional data without relying on ground truth by integrating five robust metrics, including a novel time-ordered Markov-based structural metric, into a semi-supervised hierarchical Bayesian model. The framework assesses method accuracy and considers interaction effects among metric features. We apply MIBCOVIS using linear and nonlinear dimensionality reduction methods to evaluate optimal DSVI for four distinct dynamic and spatial biological processes captured by three single-cell data modalities: CyTOF, scRNA-seq and CODEX. These data vary in complexity based on feature dimensionality, unknown cell types and dynamic or spatial differences. Unlike traditional single-summary score approaches, MIBCOVIS compares accuracy distributions across methods. Our findings underscore the joint evaluation of visualization and interpretability, rather than relying on separate metrics. We reveal that prioritizing average performance can obscure method feature performance. Additionally, we explore the impact of data complexity on visualization and interpretability. Specifically, we provide optimal parameters and features and recommend methods, like the optimized variational contractive autoencoder, for targeted DSVI for various data complexities. MIBCOVIS shows promise for evaluating dynamic single-cell atlases and spatiotemporal data reduction models.
Cofea: correlation-based feature selection for single-cell chromatin accessibility data
Authors: Li Keyi , Chen Xiaoyang , Song Shuang , Hou Lin , Chen Shengquan , Jiang Rui
Published: December 2023

Single-cell chromatin accessibility sequencing (scCAS) technologies have enabled characterizing the epigenomic heterogeneity of individual cells. However, the identification of features of scCAS data that are relevant to underlying biological processes remains a significant gap. Here, we introduce a novel method Cofea, to fill this gap. Through comprehensive experiments on 5 simulated and 54 real datasets, Cofea demonstrates its superiority in capturing cellular heterogeneity and facilitating downstream analysis. Applying this method to identification of cell type-specific peaks and candidate enhancers, as well as pathway enrichment analysis and partitioned heritability analysis, we illustrate the potential of Cofea to uncover functional biological process.
The panzootic potential of SARS-CoV-2
Authors: Mabry Makenzie E , Fanelli Angela , Mavian Carla , Lorusso Alessio , Manes Costanza , Soltis Pamela S , Capua Ilaria
Published: December 2023

Each year, SARS-CoV-2 is infecting an increasingly unprecedented number of species. In the present article, we combine mammalian phylogeny with the genetic characteristics of isolates found in mammals to elaborate on the host-range potential of SARS-CoV-2. Infections in nonhuman mammals mirror those of contemporary viral strains circulating in humans, although, in certain species, extensive viral circulation has led to unique genetic signatures. As in other recent studies, we found that the conservation of the ACE2 receptor cannot be considered the sole major determinant of susceptibility. However, we are able to identify major clades and families as candidates for increased surveillance. On the basis of our findings, we argue that the use of the term panzootic could be a more appropriate term than pandemic to describe the ongoing scenario. This term better captures the magnitude of the SARS-CoV-2 host range and would hopefully inspire inclusive policy actions, including systematic screenings, that could better support the management of this worldwide event.
Assessing and managing the mental health of people with vitiligo: a UK-wide consultation exercise
Authors: Barlow Richard , Ahmed Alia , Fellows Jodie , Goulding Jon , Handley Kelly , Schneider Alex , Thompson Andrew , Valente Marie , Waters Cerith , Eleftheriadou Viktoria
Published: December 2023

Significant variation exists in the assessment and management of people with vitiligo and psychological distress. This consultation exercise suggests an unmet need for an online, centralized intervention for people with vitiligo and moderate-to-severe psychological distress. Further actions should be taken to raise awareness of sources of support to clinicians around pathways available to mental health services.
Furuncular myiasis caused by Dermatobia hominis: entodermoscopic findings
Authors: Aguilar-Calderón Patrizia E , Garza-García Leslie M , Brussolo-Marroquín Elizabeth , Cuellar-Barboza Adrian , Ocampo-Candiani Jorge , Fernández Lucía T
Published: December 2023

A 27-year-old male traveller returning from the Amazon forest came to our dermatology consultation with a furuncle-like nodule in the temporal region. During examination we observed an erythematous nodule with a central opening. We describe the entodermoscopic characteristics of Dermatobia hominis.
The clinical differentiation of blood culture-positive and -negative sepsis in burn patients: a retrospective cohort study
Authors: Yoon Jaechul , Kym Dohern , Hur Jun , Park Jongsoo , Kim Myongjin , Cho Yong Suk , Chun Wook , Yoon Dogeon
Published: December 2023

Background

Sepsis is a potentially life-threatening condition that occurs when the body’s response to infection leads to widespread inflammation and tissue damage. Negative cultures can make it difficult for clinicians to make a diagnosis and may raise questions about the validity of the definition of sepsis. In addition, the clinical distinctions between burn patients with blood culture-positive and -negative sepsis are also poorly understood. Therefore, this study aimed to examine the clinical differences between blood culture-positive and -negative sepsis in burn patients in order to improve the understanding of the pathophysiology and epidemiology of sepsis in this population.

Methods

This study had a retrospective design, and the participants were adults aged ≥18 years. Patients diagnosed with sepsis were divided into two groups based on their blood culture results within 1 week of sepsis diagnosis.

Results

We enrolled 1643 patients admitted to our institution’s burn intensive care unit between January 2010 and December 2021. pH, platelet count, bicarbonate and haematocrit were significant in both the positive and negative groups. However, lymphocyte, red cell distribution width and blood urea nitrogen were significant only in the positive group, whereas lactate dehydrogenase was significant only in the negative group. Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumonia are common gram-negative bacterial species, and Staphylococcus aureus and Staphylococcus epidermidis are common gram-positive bacterial species seen in burn patients with positive blood cultures. Carbapenem resistance was found to be associated with an unfavourable prognosis in gram-negative bacteria, with the exception of P. aeruginosa.

Conclusions

pH, platelet count, bicarbonate and haematocrit were routine biomarkers that demonstrated statistical significance in both groups. Lactate dehydrogenase was significant in the blood-negative group, while red cell distribution width, blood urea nitrogen and lymphocyte count were significant in the positive group. Furthermore, the most common causes of sepsis are gram-negative bacteria, including A. baumannii, K. pneumoniae and P. aeruginosa. Additionally, resistance to carbapenems is associated with unfavourable outcomes.
Clinical Trial Design in Ulcerative Colitis: Interpreting Evolving Endpoints Based on Post Hoc Analyses of the Vedolizumab Phase 3 Trials GEMINI 1 and VISIBLE 1
Authors: Sandborn William J , Sands Bruce E , Uddin Sharif , Qasim Khan Rana M , Sagar Mukherjee Richa
Published: December 2023

Background

The 12-point total Mayo score including a Physician’s Global Assessment (PGA) of disease activity has been used to assess outcomes in clinical trials for ulcerative colitis (UC). In 2016, the US Food and Drug Administration (FDA) issued guidance advising the removal of the PGA in future trials. We examined how endpoints in UC trials have evolved and conducted a post hoc analysis of the GEMINI 1 and VISIBLE 1 trials to understand how the use of a 9-point modified Mayo score, excluding PGA, compares with the total Mayo score.

Methods

Endpoint definitions of clinical remission in phase 3 trials were extracted from published literature and ClinicalTrials.gov. The difference (%Δ) between the proportions of patients in GEMINI 1 and VISIBLE 1 achieving clinical remission with vedolizumab versus placebo at week 52 was measured according to 4 endpoint definitions.

Results

Trials completed up to the end of 2019 used the total Mayo score to assess clinical remission. Most trials that were completed or estimated to be completed by June 2020 or later used modified Mayo scores. Post hoc analysis revealed decreasing endpoint stringency was associated with increasing %Δ values. The modified Mayo score definition most like the definition recommended by the FDA produced %Δ values like those reported using the total Mayo score in GEMINI 1 and VISIBLE 1.

Conclusions

Endpoint definitions for UC clinical trials have evolved following FDA guidance. The efficacy of vedolizumab, measured using modified Mayo scoring, was comparable to values reported using the total Mayo score.
Prolonged adrenal insufficiency following discontinuation of osilodrostat treatment for intense hypercortisolism
Authors: Ferriere Amandine , Salenave Sylvie , Puerto Marie , Young Jacques , Tabarin Antoine
Published: December 2023

The cases of 3 patients with Cushing's disease who developed long-term adrenal insufficiency after discontinuation of prolonged osilodrostat therapy were recently described for the first time. We report 2 additional cases of persistent prolonged adrenal insufficiency after discontinuation of osilodrostat treatment for intense hypercortisolism due to Cushing's disease and ectopic ACTH syndrome. In addition, we show for that adrenal insufficiency in these patients was associated with low/normal 11-deoxycortisol concentrations despite high plasma ACTH concentrations. These results suggest that CYP11B1 is not the only target of osilodrostat and that, in vivo, osilodrostat has other prolonged and strong inhibitory effect on adrenal steroidogenesis upstream of CYP11B1. Knowledge of this remnant effect is important for the care of patients with Cushing's syndrome treated with osilodrostat. Further studies are needed to clarify the frequency and the mechanisms of this remnant effect.
Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family
Authors: Wang Jing , Xu Qing , Chen Min , Chen Yang , Wang Chunde , Chen Nansheng
Published: December 2023

The Pacific geoduck Panopea generosa (class Bivalvia, order Adapedonta, family Hiatellidae, genus Panopea) is the largest known burrowing bivalve with considerable commercial value. Pacific geoduck and other geoduck clams play important roles in maintaining ecosystem health for their filter feeding habit and coupling pelagic and benthic processes. Here, we report a high-quality chromosome-level genome assembly of P. generosa to characterize its phylogeny and molecular mechanisms of its life strategies. The assembled P. generosa genome consists of 19 chromosomes with a size of 1.47 Gb, a contig N50 length of 1.6 Mb, and a scaffold N50 length of 73.8 Mb. The BUSCO test of the genome assembly showed 93.0% completeness. Constructed chromosome synteny revealed many occurrences of inter- and intrachromosomal rearrangements between P. generosa and Sinonovacula constricta. Of the 35,034 predicted protein-coding genes, 30,700 (87.6%) could be functionally annotated in public databases, indicating the high quality of genome annotation. Comparison of gene copy numbers of gene families among P. generosa and 11 selected species identified 507 rapidly expanded P. generosa gene families that are functionally enriched in immune and gonad development and may be involved in its complex survival strategies. In particular, genes carrying the copine domains underwent additional duplications in P. generosa, which might be important for neuronal development and immune response. The availability of a fully annotated chromosome-level genome provides a valuable dataset for genetic breeding of P. generosa.
The effect of heterogeneous contact impedances on complex resistivity measurements
Authors: Zimmermann E , Huisman J A
Published: December 2023

Spectral induced polarization (SIP) and electrical impedance tomography (EIT) are advanced approaches for structural characterisation of soils and rocks based on measurements of the frequency-dependent complex electrical resistivity. Accurate SIP and EIT measurements require the reduction of electrode effects, which have often been attributed to the polarization of metal electrodes in the current pathway. In this study, we demonstrate an alternative electrode effect that influences the accuracy of complex impedance measurements. This alternative electrode effect is caused by a heterogeneous distribution of the contact impedance, which can occur due to ageing or corrosion of the electrode. First, theoretical considerations are given to explain how this electrode effect influences the accuracy of complex impedance measurements. Next, we demonstrate using SIP and EIT measurements that this alternative mechanism better explains the observed electrode effects than previous explanations based only on the presence of metal. The SIP measurements were made on a water-filled container with a metal sphere between two non-polarizing electrodes, which showed that the mere presence of metal in the current pathway only leads to small electrode effects that are typically well below 1 mrad even for small electrode spacings. When the same metal sphere was used as a potential electrode, the observed electrode effect was about 2.5 times larger and varied with rotation. These changes can be explained by a heterogeneous contact impedance resulting in a varying electrode voltage. The EIT measurements were performed with a cylindrical sample holder filled with water. They are used to illustrate how the presented theoretical considerations can be used to investigate the magnitude of the electrode effects for different electrode configurations. We conclude that electrode effects are important to consider for laboratory SIP and EIT measurements and field measurement with closely spaced electrodes.
Neisseria gonorrhoeae antimicrobial susceptibility trends in Bangkok, Thailand, 2015–21: Enhanced Gonococcal Antimicrobial Surveillance Programme (EGASP)
Authors: Kittiyaowamarn Rossaphorn , Girdthep Natnaree , Cherdtrakulkiat Thitima , Sangprasert Pongsathorn , Tongtoyai Jaray , Weston Emily , Borisov Andrey , Dunne Eileen F , Chinhiran Kittipoom , Woodring Joseph , Ngarmjiratam Nattapon , Masciotra Silvina , Frankson Rebekah , Sirivongrangson Pachara , Unemo Magnus , Wi Teodora
Published: December 2023

Objectives

Rising antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global public health concern. Many ceftriaxone-resistant cases have been linked to Asia. In the WHO/CDC global Enhanced Gonococcal Antimicrobial Surveillance Programme (EGASP), we conducted AMR surveillance at two clinical sites in Bangkok, Thailand, 2015–21.

Methods

Urethral discharge samples, from males with urethral discharge and/or dysuria, were Gram-stained and cultured. ETEST was performed to determine AMR. EGASP MIC alert values, CLSI and EUCAST breakpoints were used.

Results

In 2015–21, gonococcal isolates were cultured from 1928 cases; most (64.1%) were males reporting having sex with females. The sensitivity and specificity of Gram-stained microscopy compared with culture for detection of gonococci were 97.5% and 96.6%, respectively. From 2015 to 2021, the azithromycin MIC90 increased from 0.125 to 1 mg/L, and the MIC90 of ceftriaxone and cefixime increased from 0.008 and ≤0.016 mg/L to 0.032 and 0.064 mg/L, respectively. Eight EGASP MIC alert values (in seven isolates) were identified. Five alert values were for cefixime (all resistant according to EUCAST breakpoints) and three for azithromycin (all resistant according to EUCAST breakpoints). The average annual resistance to ciprofloxacin during 2015–21 was 92%.

Conclusions

A continuous high susceptibility to ceftriaxone, Thailand’s first-line gonorrhoea treatment, was found. However, the increasing MICs of ceftriaxone, cefixime and azithromycin are a substantial threat, especially considering these are the last remaining options for the treatment of gonorrhoea. To monitor AMR, continuous and quality-assured gonococcal AMR surveillance such as the Thai WHO/CDC EGASP, ideally including WGS, is imperative globally.