bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical recovery of a time-dependent potential in subdiffusion
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Authors: Jin Bangti , Shin Kwancheol , Zhou Zhi
Published: December 2023

In this work we investigate an inverse problem of recovering a time-dependent potential in a semilinear subdiffusion model from an integral measurement of the solution over the domain. The model involves the Djrbashian–Caputo fractional derivative in time. Theoretically, we prove a novel conditional Lipschitz stability result, and numerically, we develop an easy-to-implement fixed point iteration for recovering the unknown coefficient. In addition, we establish rigorous error bounds on the discrete approximation. These results are obtained by crucially using smoothing properties of the solution operators and suitable choice of a weighted

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p

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norm. The efficiency and accuracy of the scheme are showcased on several numerical experiments in one- and two-dimensions.
Context-aware and local-aware fusion with transformer for medical image segmentation
Authors: Xiao Hanguang , Li Li , Liu Qiyuan , Zhang Qihang , Liu Junqi , Liu Zhi
Published: December 2023

Objective. Convolutional neural networks (CNNs) have made significant progress in medical image segmentation tasks. However, for complex segmentation tasks, CNNs lack the ability to establish long-distance relationships, resulting in poor segmentation performance. The characteristics of intra-class diversity and inter-class similarity in images increase the difficulty of segmentation. Additionally, some focus areas exhibit a scattered distribution, making segmentation even more challenging. Approach. Therefore, this work proposed a new Transformer model, FTransConv, to address the issues of inter-class similarity, intra-class diversity, and scattered distribution in medical image segmentation tasks. To achieve this, three Transformer-CNN modules were designed to extract global and local information, and a full-scale squeeze-excitation module was proposed in the decoder using the idea of full-scale connections. Main results. Without any pre-training, this work verified the effectiveness of FTransConv on three public COVID-19 CT datasets and MoNuSeg. Experiments have shown that FTransConv, which has only 26.98M parameters, outperformed other state-of-the-art models, such as Swin-Unet, TransAttUnet, UCTransNet, LeViT-UNet, TransUNet, UTNet, and SAUNet++. This model achieved the best segmentation performance with a DSC of 83.22% in COVID-19 datasets and 79.47% in MoNuSeg. Significance. This work demonstrated that our method provides a promising solution for regions with high inter-class similarity, intra-class diversity and scatter distribution in image segmentation.
An ultra-high-frequency memristor circuit model
Authors: Wang Yanji , Wang Yu , Liu Yi , Zhang Yanzhong , Yan Yu , Hu Youde , Wang Xinpeng , Zhang Hao , Xu Rongqing , Tong Yi
Published: December 2023

In the context of sixth-generation (6G) wireless communications technology, advanced radio-frequency switches are required to accommodate high-frequency terahertz range and complex modulation techniques. This paper proposes a flexible charge-controlled memristor model specifically designed for ultra-high-frequency applications. It describes in detail the derivation of the behavior model of the proposed memristor circuit. The memristor circuit model is built around four inverters, two multipliers, one integrator, one adder, and one differentiator. Through PSPICE simulation, the typical hysteresis loop of the memristor is thoroughly analyzed, demonstrating its suitability for use in wireless communication systems. The model exhibits a good typical hysteresis loop that operates over a wide frequency range from 100 kHz to 20 THz, meeting the specific requirements of terahertz applications. Compared to existing memristor designs, it operates at a much higher frequency. However, the zero crossing of the typical hysteresis loop deviates when the operating frequency exceeds 20 THz. Furthermore, the proposed memristor model can be customized in terms of set/reset voltage, operating frequency and

R

off

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R

on

, and has been verified for use in high speed switches with switching speeds of 19.5 ps. Furthermore, this research fills the gap in ultra-high-frequency memristor modeling, offering valuable insights and guidance for the utilization of memristors in the 6G technology and ultra-high frequency fields.
Research on the monitoring friction hysteresis for the bolted interface by electromechanical impedance
Authors: Sun Kepeng , Sun Qingchao , Zhang Yingzhong , Wang Yingquan , Zhao Yingjie
Published: December 2023

Friction hysteresis manifests at the bolted interface when subjected to external excitation, leading to nonlinear structural responses. But the interface evolution is rarely considered in the health monitoring. In this paper, we introduce the pioneering concept of effective mechanical impedance of the contact interface (EMICI) and formulate a coupled structural impedance model that comprehensively incorporates both tangential loading and contact impedance considerations. EMICI was deemed to encapsulate intricate information pertaining to contact nonlinearity, and the theoretical equation was derived using principles of contact mechanics. Tangential loading experiments, time domain impedance analysis and impact hammer tests were conducted to confirm the close relationship between EMICI and the structural properties. The coupled structural impedance model is proved to be effective, in which EMICI can be identified by changing the tangential force and torque. Subsequent analysis revealed that the proposed model could additionally serve in the identification of system-related parameters. The loading coefficient in the model is linearly related to the tangential force, and the calculated EMICI corresponds to the slip characteristics of the bolted interface. The introduced concept of EMICI could be considered as a metric for assessing interface properties, offering dependable insights into contact evolution, and facilitating a deeper understanding of interface dynamics.
Revisiting physical mechanism of longitudinal photonic spin splitting and Goos-Hänchen shift
Authors: Zhen Weiming , Wang Xi-Lin , Ding Jianping , Wang Hui-Tian
Published: December 2023

The intrinsic connection between the transverse photonic spin Hall effect (PSHE) and the Imbert–Fedorov shift has been well characterized. However, physical insights into the longitudinal photonic spin splitting associated with the Goos-Hänchen (GH) shift remain elusive. This paper aims to expand the theory of the PSHE generation mechanism from the transverse to the longitudinal case by examining the reflection of each spin component from an arbitrarily linearly polarized incident Gaussian beam on the air-dielectric interface. Unlike the transverse case, both spin-maintained and spin-flipped modes exhibit non-zero longitudinal displacements, with the latter being affected by the second-order expansion term of the Fresnel reflection coefficient with respect to the in-plane wave-vector component. Meanwhile, the polarization angle plays a crucial role in determining the longitudinal PSHE since each reflected total spin component is a coherent superposition of these two corresponding modes. Remarkably, the imaginary part of the relative permittivity of the dielectric significantly affects the symmetry of the longitudinal PSHE. Furthermore, the GH shift results from a superposition of individual spin states’ longitudinal displacements, taking into account their energy weights. By incorporating the corresponding extrinsic orbital angular momentum, we explore the generation mechanism of the symmetric/asymmetric longitudinal PSHE. The unified physical framework elucidating the longitudinal photonic spin splitting and GH shift provides a comprehensive understanding of the fundamental origin of the PSHE and beam shifts, paving the way for potential applications in spin-controlled nanophotonics.
Wave field structure and power coupling features of blue-core helicon plasma driven by various antenna geometries and frequencies
Authors: Wang 王 Chao 超 , Liu 刘 Jia 佳 , Chang 苌 Lei 磊 , Lu 卢 Ling-Feng 凌峰 , Zhang 张 Shi-Jie 世杰 , Zhou 周 Fan-Tao 帆涛
Published: December 2023

This paper deals with wave propagation and power coupling in blue-core helicon plasma driven by various antennas and frequencies. It is found that compared to non-blue-core mode, for blue-core mode, the wave can propagate in the core region, and it decays sharply outside the core. The power absorption is lower and steeper in radius for blue-core mode. Regarding the effects of antenna geometry for blue-core mode, it shows that half helix antenna yields the strongest wave field and power absorption, while loop antenna yields the lowest. Moreover, near axis, for antennas with m = +1, the wave field increases with axial distance. In the core region, the wave number approaches to a saturation value at much lower frequency for non-blue-core mode compared to blue-core mode. The total loading resistance is much lower for blue-core mode. These findings are valuable to understanding the physics of blue-core helicon discharge and optimizing the experimental performance of blue-core helicon plasma sources for applications such as space propulsion and material treatment.
Theoretical investigation of electron-impact ionization of W8+ ion
Authors: Zhang 张 Shiping 世平 , Zhang 张 Fangjun 芳军 , Zhang 张 Denghong 登红 , Ding 丁 Xiaobin 晓彬 , Jiang 蒋 Jun 军 , Xie 颉 Luyou 录有 , Ma 马 Yulong 玉龙 , Li 李 Maijuan 麦娟 , Sikorski Marek , Dong 董 Chenzhong 晨钟
Published: December 2023

The electron-impact single ionization cross section for W8+ ion has been calculated using flexible atomic code, employing the level-to-level distorted-wave approximation. This calculations takes into account contributions form both direct ionization (DI) and excitation autoionization (EA). However, the theoretical predictions, based solely on the ground state, tends to underestimate the experimental values. This discrepancy can be mitigated by incorporation contributions from excited states. We extended the theoretical analysis, including the contributions from the long-lived metastable states with lifetimes exceeding 1.5 × 10−5 s. We employed two statistical models to predict the fraction of ground state ions in the parent ion beam. Assuming a 79% fraction of parent ions in ground configuration, the experiment measurements align with the predictions. Furthermore we derived the theoretical cross-section for the ground state as correlated plasma rate coefficients, and compared it with existing data. Despite the uncertainty in our calculations, our results are still acceptable.
Study of the efficiency of radio frequency assisted heat pump drying of shrimp
Authors: Van Kien Pham , Thanh Tan Nguyen , Huu Son Le , Nguyen Nhanh Van , Nguyen Ngoc Xuan , Nguyen Hay
Published: December 2023

The study focused on the efficiency of radio frequency (RF) assisted heat pump (HP) drying of shrimp. The experimental drying was conducted with input drying parameters as the drying-air temperature of 45°C, the drying-air velocity of 2.0 m/s, and RF power of 0, 0.5 and 1.0 kW, in which, HP only drying was corresponding to RF power of 0 kW. In the study, the effect of RF power on drying rate, color change, and protein content of dried shrimp were considered. When RF power increased, the drying rate and protein retention of dried shrimp increased significantly. At RF power of 1.0 kW, the drying time was 260 minutes, that reduced about 19% and 38% as compared to RF power of 0.5 and 0 kW. The protein content of shrimp after drying was 62.06%, 66.02% and 69.87% corresponding to the drying modes at RF power of 0, 0.5 and 1.0 kW. Besides, in RF assisted HP drying, the shrimp samples after drying got better color, appearance, and taste than those of HP only drying. At RF power of 1.0 kW, the dried shrimp got the best redness and lightness color, followed by the drying modes at RF power of 0.5 and 0 kW. In both RF assisted HP drying and HP only drying, the dried shrimp surface was not cracked, and the dried products obtained the good taste and the level of redness and lightness required.
Effectiveness of vessel monitoring systems in managing and monitoring fishing vessels in Ca Mau province, Vietnam
Authors: Phuong To Van , Hang Duong Thanh
Published: December 2023

Since October 2017, Vietnam’s fisheries have made efforts to address the European Commission (EC)’s yellow card warning. One key factor in removing the yellow card warning was implementing a fishing vessel monitoring system (VMS) to manage and monitor fishing vessels at sea and prevent them from violating foreign waters. However, there has been limited research evaluating the effectiveness of VMS in Vietnam. To address this gap, this study focused on evaluating the use of VMS in Ca Mau province, one of the country’s dominant fisheries. The study collected primary and secondary data from 94 surveyed fishermen who were captains and owners of Ca Mau fishing vessels equipped with VMS between December 2021 and April 2022. The findings showed that 99.5% of fishing vessels were equipped with VMS, with the ZuniVN-01 equipment being the most commonly selected (39.7%), followed by Viettel S-tracking (24.2%), and BA-SAT-01 (23.5%). However, these VMS failures occurred frequently, with the most significant being disconnection for more than ten days between the VMS onboard and the local control center. Despite these failures, 96.8% of respondents believed that VMS was effective, particularly for emergency rescue functions (73.4%). The automatic transmission of the vessel’s location via GPS every two or three hours received the highest rating (78.7%) from respondents. Additionally, most fishers (68.5%) believed that the core requirements of VMS were appropriate. Based on the study’s results, practical recommendations were proposed to stakeholders to improve the effectiveness of VMS.
Diversity of marine macro molluscan bivalves and gastropods in the intertidal areas of Barangay Paniman, Caramoan, Camarines Sur, Philippines
Authors: Caril AN , Vergara RL , Santos RRC , Estandarte MLA , Bernabe J , Aggabao MJ , Bantigue PC , Guinto A , Saguil NA
Published: December 2023

There have been very few studies on mollusk diversity in remote areas of the Philippines. The coastal areas of Caramoan, Camarines Sur, are ideal for studying marine molluscs because they have been discovered to be abundant, diverse, and essential to the locals’ livelihood. However, due to the remoteness of the mentioned area, this lack of information remains scientifically lacking. Thus, this study aimed to determine the diversity of marine macro-molluscan bivalves and gastropods in the intertidal areas of Barangay Paniman, Caramoan, Camarines Sur, Philippines. Purposive sampling and transect methods assessed the species composition, abundance, and occurrence of marine macro bivalves and gastropods. The Shannon-Wiener index was used to determine the area’s diversity. A total of 557 individual molluscs were sampled and classified, obtaining 43 species of bivalves from 32 genera and 18 families and 47 species of gastropods from 34 genera and 20 families. The family Veneridae had the highest among the bivalves, and the family Strombidae had the highest species richness among the gastropods. This study provided baseline information on the status of marine macro molluscan bivalves and gastropods in the intertidal area of Barangay Paniman, Caramoan, Camarines Sur, Philippines. As a result, this will provide solid empirical evidence for conservation and sustainability plans.
Assessing the impact of irradiation-induced defects on the hardening of reactor pressure vessel materials for sustainable development of nuclear energy
Authors: Ba-Vu-Chinh Nguyen , Kenta Murakami , Tom Phongsakorn Prak , Liang Chen , Tatsuya Suzuki
Published: December 2023

The operational longevity of a nuclear power plant, specifically of the light water reactor type, hinges on the assessment of component degradation, with a particular focus on the reactor pressure vessel (RPV) materials. Among the most prevalent defects responsible for irradiation-induced hardening in RPV materials are point defects (PDs) and dislocation loops (DLs). However, their respective contributions to the overall hardening of RPV materials have not been clearly determined. To address this issue, this study was conducted using iron alloys with equivalent Mn and Ni content to those used in nuclear RPV in Japan. The study employed transmission electron microscopy (TEM), atom probe tomography (APT), and nanoindentation to assess the roles of PDs and DLs in contributing to the hardening behaviour of RPV materials. The results indicated that both solute clusters (SCs), which are formed by the aggregation of PDs, and DLs play equally important roles in the hardening behaviour of RPV materials. However, an in-depth analysis of three-dimensional images using the APT method revealed that there may have been errors in evaluating SCs and DLs, leading to double counting when assessing the impact of irradiation-induced defects on the hardening behaviour of RPV materials. These findings highlight the need for improved accuracy in evaluating these defects to better understand the behaviour of RPV materials under irradiation.
Environmental pollution along the coast of Binh Thuan province, caused by the discharge of wastewater into the main river basins from the mainland
Authors: Huynh P , Tran T M H , Huynh T N H
Published: December 2023

Socio-economic activities of Binh Thuan province are associated with rivers flowing through districts, towns, and cities in this province. Along with the strong socio-economic development, seven river basins have to receive a large amount of wastewater from industrial parks, livestock farms and urban areas as well, these are the main sources that lead to coastal water pollution. For the purpose of both economic growth and environmental protection in coastal areas, the study used survey methods to collect data on socio-economic activities and waste discharge activities from the mainland. In addition, the study also conducted statistical processing of monitoring data and predictive analytics for forecasting water quality. The results have shown that environmental pollution in the coastal area of Binh Thuan province originates from the discharge of wastewater from the mainland. Furthermore, this study contributed to proposing solutions being able to prevent and protect the coastal environment effectively.
Evaluate and propose solutions for sustainable development of water resources in coastal areas of Binh Thuan province, Vietnam
Authors: Huynh P , Le C T , Nguyen L N T , Tran T M H
Published: December 2023

Binh Thuan province has a coastline of about 192 km, the coastline connecting with the surrounding space to create the coastal ecosystem. This is an important area for the socio-economic development of Binh Thuan province. However, in the process of development, some existing problems have been revealed, limiting the manifestation of unsustainability, especially the use of water resources. Research results show that, at present, Binh Thuan province has 188 mining and mineral processing enterprises, which not only consume a lot of water but also pollute the environment and exhaust water resources of Binh Thuan province. In order to reduce water shortage in Binh Thuan province, it is necessary to have specific and strict solutions to improve water efficiency. On the basis of monitoring data and the help of Seawat model, the study has determined coastal water reserves of Binh Thuan province, thereby determining the amount of water to be safely exploited. These data have been integrated with the RCP4.5 scenario and forecast for the years 2030, 2060 and 2090. From there, we propose some solutions to overcome water shortage, serving sustainable development. coastal water resources of Binh Thuan province.
Developing and solving the mathematical model of transient heat and mass transfer in the freeze-drying of Cordyceps militaris
Authors: Nguyen Van-Phuc , Nguyen Nguyen-An , Nguyen Huu-Nghia
Published: December 2023

This study developed a mathematical model of the transient mass and heat transfer of Cordyceps militaris during lyophilization. This mathematical model was solved using a program coded in MATLAB to simulate the relationship between product temperature and sublimation rate over time. The parameters of the drying mode were set in the simulation as follows: heating plate temperature from 273.2 to 303.2 K, the absolute pressure of the drying chamber is from 30 Pa to 60 Pa. The fruiting body of cordyceps analyzed in the study is considered a cylindrical shape with a radius of 1.5 mm and length of 60 mm, which was arranged in 1 layer on a tray with dimensions of 200x300x20 mm. Research shows that the sublimation rate increases when the heating plate temperature increases. Besides, the decrease in sublimation chamber pressure will lead to rapid increases in drying speed. This result can also be used to build software to set the technological mode for the cordyceps drying process by sublimation.
Are Political “Attacks” on the Judiciary Ever Justifiable? The Relationship Between Unfair Criticism and Public Accountability
Authors: Stephenson Scott
Published: December 2023

Political “attacks” on the judiciary are a well-known threat to constitutional democracy. Criticism of the judiciary by politicians is often said to constitute one form of attack when it is unfair in the sense that it is not relevant to the judiciary’s constitutional role and/or not respectful. Unfair criticism is frequently claimed to be unacceptable on the basis that it threatens judicial independence and impartiality and, therefore, the rule of law. The Article critically interrogates this claim, arguing that unfair criticism can have value as a form of public accountability of the judiciary. It can hold the judiciary to account for aspects of its decision making that should be subject to scrutiny and that other accountability mechanisms, such as the appeals procedure and the lawmaking process, do not. In particular, it is apt to hold the judiciary to account for the diffuse societal effects, values, and principles of its decision making. As a result, the justifiability of unfair criticism is contestable and context specific because it involves taking into consideration both its potential value and its potential threat. The Article evaluates the subject by drawing on the experiences with unfair criticism of the judiciary by members of the executive and legislature in Australia and the United Kingdom.
How to score the impact of treatment on cutaneous neurofibromas in clinical trials
Authors: Ortonne Nicolas
Published: December 2023

Most patients with neurofibromatosis 1 (NF1) develop a variable number of cutaneous neurofibromas (cNFs) which have a major impact on patients’ quality of life0. A major problem is how to score the response to therapy in clinical practice and trials. A measurement instrument recognized by all experts in the field is required to be able to judge the efficacy of treatments and the benefits perceived by the patients. Fertitta and colleagues propose a system for assessing cNFs severity and impact with a list of items validated by a consensus of experts and patients.This qualitative approach has the advantage of integrating multiple parameters of interest, based in part on a “patient-centric” approach.
Vitamin D did not reduce multiple sclerosis disease activity after a clinically isolated syndrome
Authors: Butzkueven Helmut , Ponsonby Anne-Louise , Stein Mark S , Lucas Robyn M , Mason Deborah , Broadley Simon , Kilpatrick Trevor , Lechner-Scott Jeannette , Barnett Michael , Carroll William , Mitchell Peter , Hardy Todd A , Macdonell Richard , McCombe Pamela , Lee Andrew , Kalincik Tomas , van der Walt Anneke , Lynch Chris , Abernethy David , Willoughby Ernest , Barkhof Frederik , MacManus David , Clarke Michael , Andrew Julie , Morahan Julia , Zhu Chao , Dear Keith , Taylor Bruce V ,   the PREVANZ Investigators, Gebski Val , Kimber Thomas , Barber Alan , Wraight Paul , Sampangi Sandeep , Ali Rashida , Miller David , Krupp Lauren , Churilov Leonid , Ching Michael , Hodkinson Susanne , Butler Ernie , Shaw Cameron , Fraser Claire , Mottershead John
Published: December 2023

Low serum levels of 25-hydroxyvitamin D [25(OH)D] and low sunlight exposure are known risk factors for the development of multiple sclerosis. Add-on vitamin D supplementation trials in established multiple sclerosis have been inconclusive. The effects of vitamin D supplementation to prevent multiple sclerosis is unknown.

We aimed to test the hypothesis that oral vitamin D3 supplementation in high-risk clinically isolated syndrome (abnormal MRI, at least three T2 brain and/or spinal cord lesions), delays time to conversion to definite multiple sclerosis, that the therapeutic effect is dose-dependent, and that all doses are safe and well tolerated.

We conducted a double-blind trial in Australia and New Zealand. Eligible participants were randomized 1:1:1:1 to placebo, 1000, 5000 or 10 000 international units (IU) of oral vitamin D3 daily within each study centre (n = 23) and followed for up to 48 weeks. Between 2013 and 2021, we enrolled 204 participants. Brain MRI scans were performed at baseline, 24 and 48 weeks.

The main study outcome was conversion to clinically definite multiple sclerosis based on the 2010 McDonald criteria defined as either a clinical relapse or new brain MRI T2 lesion development.

We included 199 cases in the intention-to-treat analysis based on assigned dose. Of these, 116 converted to multiple sclerosis by 48 weeks (58%). Compared to placebo, the hazard ratios (95% confidence interval) for conversion were 1000 IU 0.87 (0.50, 1.50); 5000 IU 1.37 (0.82, 2.29); and 10 000 IU 1.28 (0.76, 2.14). In an adjusted model including age, sex, latitude, study centre and baseline symptom number, clinically isolated syndrome onset site, presence of infratentorial lesions and use of steroids, the hazard ratios (versus placebo) were 1000 IU 0.80 (0.45, 1.44); 5000 IU 1.36 (0.78, 2.38); and 10 000 IU 1.07 (0.62, 1.85). Vitamin D3 supplementation was safe and well tolerated.

We did not demonstrate reduction in multiple sclerosis disease activity by vitamin D3 supplementation after a high-risk clinically isolated syndrome.
Granulomatous rosacea: a clue to the diagnosis of STAT1 gain of function in a child with immunodeficiency
Authors: Buján Bonino Cecilia , Moreiras Arias Noelia , López-Pardo Rico María , López Franco Montserrat , Loidi Lourdes , Suárez Peñaranda José Manuel , Vázquez Osorio Igor
Published: December 2023

Recurrent granulomatous rosacea in a paediatric patient prompted an investigation that unveiled a rare gain-of-function mutation in the STAT1 gene. This case highlights the clinical diversity associated with STAT1 mutations and underscores the importance of considering genetic factors in unexplained immunodeficiency and skin conditions, offering valuable insights for diagnosis and treatment.
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences
Authors: Deng Cecilia H , Naithani Sushma , Kumari Sunita , Cobo-Simón Irene , Quezada-Rodríguez Elsa H , Skrabisova Maria , Gladman Nick , Correll Melanie J , Sikiru Akeem Babatunde , Afuwape Olusola O , Marrano Annarita , Rebollo Ines , Zhang Wentao , Jung Sook
Published: December 2023

Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021–22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals.

Database URL: https://www.agbiodata.org.
Sign language delays in deaf 3- to 5-year-olds with deaf parents
Authors: Morere Donna A , Allen Thomas E , Jaeger Maura , Winthrop Dana
Published: December 2023

Research has demonstrated that deaf children of deaf signing parents (DOD) are afforded developmental advantages. This can be misconstrued as indicating that no DOD children exhibit early language delays (ELDs) because of their early access to a visual language. Little research has studied this presumption. In this study, we examine 174 ratings of DOD 3- to 5-year-old children, for whom signing in the home was indicated, using archival data from the online database of the Visual Communication and Sign Language Checklist. Our goals were to (1) examine the incidence of ELDs in a cohort of DOD children; (2) compare alternative scaling strategies for identifying ELD children; (3) explore patterns among behavioral ratings with a view toward developing a greater understanding of the types of language behaviors that may lie at the root of language delays; and (4) suggest recommendations for parents and professionals working with language-delayed DOD children. The results indicated that a significant number of ratings suggested ELDs, with a subset significantly delayed. These children likely require further evaluation. Among the less delayed group, ASL skills, rather than communication or cognition, were seen as the major concern, suggesting that even DOD children may require support developing linguistically accurate ASL. Overall, these findings support the need for early and ongoing evaluation of visual language skills in young DOD children.
Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication
Authors: Dallaire Xavier , Bouchard Raphael , Hénault Philippe , Ulmo-Diaz Gabriela , Normandeau Eric , Mérot Claire , Bernatchez Louis , Moore Jean-Sébastien
Published: December 2023

Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise FST values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths.
Safety and feasibility study of uniportal video-assisted thoracoscopic pulmonary wedge resection without postoperative chest tube drainage: a retrospective propensity score-matched study
Authors: Yang Qingjie , Lv Shenghua , Li Qingtian , Lan Linhui , Sun Xiaoyan , Feng Xinhai , Han Kaibao
Published: December 2023

OBJECTIVES

The aim of this study was to assess the impact of postoperative chest tube drainage (CTD) on safety and postoperative recovery by comparing patients with pulmonary nodule undergoing uniportal video-assisted thoracoscopic pulmonary wedge resection with and without postoperative CTD.

METHODS

We retrospectively analysed the data of patients who underwent video-assisted thoracoscopic pulmonary wedge resection for pulmonary nodule at our hospital between 2018 and 2022. In cases where a 12-Fr chest tube was used following the procedure, the tube was not usually removed until the day after surgery. Therefore, the eligible patients were categorized into the drainage tube or the no-drainage tube group according to the use of postoperative CTD. Propensity score matching at a ratio of 1:1 was performed using clinicopathologic and demographic variables. The highest postoperative pain score, postoperative complication rate, postoperative length of stay and hospitalization costs were compared between the 2 groups.

RESULTS

A total of 275 eligible patients, including 150 and 125 patients in the drainage tube and no-drainage tube groups, respectively, were included in the study. After propensity score matching, there were 102 patients in each group. The postoperative complication rate during hospitalization and at 1 week and 1 month after discharge were not significantly different between the 2 groups (P > 0.05 for all). The highest postoperative pain score was significantly lower in the no-drainage tube group than in the drainage tube group [2.02 (standard deviation: 0.81) days vs 2.31 (standard deviation: 0.76) days, P = 0.008]. The postoperative length of stay was significantly shorter in the no-drainage tube group than in the drainage tube group {3.00 [interquartile ranges (IQRs): 2.00–4.00] days vs 2.00 (IQRs: 1.00–3.00) days, P < 0.001}. Similarly, the total hospitalization costs were significantly lower in the no-drainage tube group than in the drainage tube group [33283.74 (IQRs: 27098.61–46718.56) yuan vs 26598.67 (IQRs: 22965.14–29933.67) yuan, P < 0.001].

CONCLUSIONS

Omission of postoperative CTD was safe and feasible in patients with pulmonary nodule undergoing wedge resection. The no-postoperative-drainage policy can substantially shorten the length of hospital stay and reduce the postoperative pain and hospitalization costs without increasing the risk of postoperative complications.
Nirmatrelvir/ritonavir for COVID-19: an overview of systematic reviews
Authors: Cruciani Mario , Pati Ilaria , Masiello Francesca , Pupella Simonetta , De Angelis Vincenzo
Published: December 2023

Objectives

A reappraisal of the validity of the conclusions of systematic reviews (SRs) related to nirmatrelvir/ritonavir for the treatment of COVID-19.

Methods

An overview of SRs (umbrella review). The methodological quality of the SRs was assessed using the AMSTAR 2 checklist; quality of the evidence from the trials included in each SR was appraised following the GRADE approach.

Results

Sixteen SRs with meta-analysis published between 2020 and 2023 were included in this overview. The SRs reported data from 108 overlapping reports, based on 43 individual primary studies [3 randomized clinical trials (RCTs), 40 non-RCTs]. In outpatient settings the use of nirmatrelvir/ritonavir reduced overall mortality, hospital admission and progression of disease compared with controls (from moderate to low certainty of evidence); nirmatrelvir/ritonavir reduced mortality, hospital admission and progression of disease in both immunized and non-immunized patients. No differences in the occurrence of any adverse events between groups were observed in the large majority of SRs; serious adverse events, including adverse events requiring discontinuation of treatment, were reported with lower prevalence in nirmatrelvir recipients compared with controls (from low to moderate certainty of evidence).

Conclusions

There is low to moderate certainty of evidence from SRs that nirmatrelvir/ritonavir reduces mortality, clinical progression and hospitalization rate in COVID-19 patients compared with controls, without increasing the occurrence of overall and serious adverse events. Based on the overall methodological assessment, on average we can have high confidence in the quality of results generated by the SRs.
Combined purebred and crossbred genetic evaluation of Columbia, Suffolk, and crossbred lamb birth and weaning weights: systematic effects and heterogeneous variances
Authors: Vargas Jurado Napoleón , Notter David R , Taylor Joshua B , Brown Daniel J , Mousel Michelle R , Lewis Ronald M
Published: December 2023

Despite the benefits of crossbreeding on animal performance, genetic evaluation of sheep in the U.S. does not directly incorporate records from crossbred lambs. Crossbred animals may be raised in different environments as compared to purebreds. Systemic factors such as age of dam and birth and rearing type may, therefore, affect purebred and crossbred performance differently. Furthermore, crossbred performance may benefit from heterozygosity, and genetic and environmental variances may be heterogeneous in different breeds and their crosses. Such issues must be accounted for in a combined (purebred and crossbred) genetic evaluation. The objectives of this study were to i) determine the effect of dam age and birth type on birth weight, and dam age and birth-rearing type on weaning weight, in purebred and crossbred lambs, ii) test for heterogeneous genetic and environmental variances in those weights, and iii) assess the impact of including weights on crossbred progeny on sire estimated breeding values (EBV). Performance records were available on purebred Columbia and Suffolk lambs. Crossbred information was available on lambs sired by Suffolk, Columbia or Texel rams mated to Columbia, Suffolk, or crossbred ewes. A multiple-trait animal model was fitted in which weights from Columbia, Suffolk, or crossbred lambs were considered different traits. At birth, there were 4,160, 2,356, and 5,273 Columbia, Suffolk, and crossbred records, respectively, with means (SD) of 5.14 (1.04), 5.32 (1.14), and 5.43 (1.23) kg, respectively. At weaning, on average at 122 (12) d, there were 2,557, 980, and 3,876 Columbia, Suffolk, and crossbred records, respectively, with corresponding means of 39.8 (7.2), 40.3 (7.9), and 39.6 (8.0) kg. Dam age had a large positive effect on birth and weaning weight in pure and crossbred lambs. At birth, however, the predicted effect was larger in crossbred and Suffolk lambs. While an increase in a number of lambs born and reared had a strong and negative influence on birth and weaning weight, the size of the effect did not differ across-breed types. Environmental variances were similar at birth and weaning, but additive variances differed among breed types for both weights. Combining purebred and crossbred information in the evaluation not only improved predictions of genetic merit in purebred sires but also allowed for direct comparisons of sires of different breeds. Breeders thus can benefit from an additional tool for making selection decisions.
The use of R in forestry research
Authors: Lai Jiangshan , Zhu Weijie , Cui Dongfang , Fan Dayong , Mao Lingfeng
Published: December 2023

The field of forestry research has greatly benefited from the integration of computational tools and statistical methods in recent years. Among these tools, the programming language R has emerged as a powerful and versatile platform for forestry research, ranging from data analysis, modeling to visualization. However, the key trends in general reported R use and patterns in forestry research remain unknown. We analyzed R and R package usage frequencies for 14 800 research articles published in eight top forestry journals across a span of 10 years, from 2013 to 2022. Among these articles, a notable number of 6790 (accounting for 45.7%) explicitly utilized R as their primary tool for data analysis. The adoption of R exhibited a linear growth trend, rising from 28.3% in 2013 to 60.9% in 2022. The top five used packages reported were vegan, lme4, nlme, MuMIn, and ggplot2. Diverse journals have their unique areas of emphasis, resulting in disparities in the frequency of R package application among journals. The average number of R packages used per article also showed an increasing trend over time. The study underscores the recognition that R, with its powerful data statistical and visualization capabilities, plays a pivotal role in enabling researchers to conduct thorough analyses and acquire comprehensive insights into various aspects of forestry science.
Identifying dietary consumption patterns from survey data: a Bayesian nonparametric latent class model
Authors: Stephenson Briana J K , Wu Stephanie M , Dominici Francesca
Published: December 2023

Dietary assessments provide the snapshots of population-based dietary habits. Questions remain about how generalisable those snapshots are in national survey data, where certain subgroups are sampled disproportionately. We propose a Bayesian overfitted latent class model to derive dietary patterns, accounting for survey design and sampling variability. Compared to standard approaches, our model showed improved identifiability of the true population pattern and prevalence in simulation. We focus application of this model to identify the intake patterns of adults living at or below the 130% poverty income level. Five dietary patterns were identified and characterised by reproducible code/data made available to encourage further research.
Into the Hills: Challenges of Writing Postemancipation Agency in the Caribbean
Authors: Eller Anne
Published: December 2023

As Caribbean postemancipation scholarship has deepened so richly in recent decades, writers have been able to shake major distortions such as the progressive teleologies of freedom that lurk as the very scaffolding of congratulatory imperial records. The full dynamism of repression directed at postslavery generations still demands attention, as does the difficult task of reconstructing communities’ and individuals’ responses to these serious restraints, efforts that sometimes yielded nothing. Especially given archival difficulties, Johnson’s exhortation to seek everyday understandings and actions, ineffable registers like love and fear, and internal community politics, including discord, continue to present high aims for scholars seeking to conceive and describe agency in such an archivally and politically difficult era.
Effects of onset of phase transition on binary neutron star mergers
Authors: Haque Shamim , Mallick Ritam , Thakur Shashikesh K
Published: December 2023

Quantum Chromodynamics predicts phase transition from hadronic matter to quark matter at high density, which is highly probable in astrophysical systems like binary neutron star mergers. To explore the critical density where such phase transition can occur, we performed numerical relativity simulations of binary neutron star mergers with various masses (equal and unequal binaries). We aim to understand the effect of the onset of phase transition on the merger dynamics and gravitational wave spectra. We generated a set of equations of states by agnostically changing the onset of phase transition, having the hadronic matter part and quark matter part fixed. This particular arrangement of the equation of states explores the scenario of mergers where mixed phases of matter are achieved before or during the merger. Under these circumstances, if the matter properties with hadronic and quark degrees differ significantly, it is reflected in the stability of the final merger product for the intermediate mass binary. We performed a case study on mixed species merger, where one of the binary companions is hybrid star. If quark matter appears at low densities, we observe significant change in post-merger gravitational wave analysis in terms of higher peak frequencies and post-merger frequencies in power spectral density. We report indications expressed as spikes in phase difference plots at merger time for mixed mergers. We found that the expression of phase transition in post-merger gravitational wave signals is more significant for unequal mass binary than for equal mass binary having the same total baryonic mass.
Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses
Authors: Flores Samuel Coulbourn , Malý Michal , Hrebík Dominik , Plevka Pavel , Černý Jiří
Published: December 2023

The revolution in cryo-electron microscopy has resulted in unprecedented power to resolve large macromolecular complexes including viruses. Many methods exist to explain density corresponding to proteins and thus entire protein capsids have been solved at the all-atom level. However methods for nucleic acids lag behind, and no all-atom viral double-stranded DNA genomes have been published at all. We here present a method which exploits the spiral winding patterns of DNA in icosahedral capsids. The method quickly generates shells of DNA wound in user-specified, idealized spherical or cylindrical spirals. For transition regions, the method allows guided semiflexible fitting. For the kuravirus SU10, our method explains most of the density in a semiautomated fashion. The results suggest rules for DNA turns in the end caps under which two discrete parameters determine the capsid inner diameter. We suggest that other kuraviruses viruses may follow the same winding scheme, producing a discrete rather than continuous spectrum of capsid inner diameters. Our software may be used to explain the published density maps of other double-stranded DNA viruses and uncover their genome packaging principles.