bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of three-dimensional forward modeling method for the magnetometric resistivity (MMR) method
Authors: Tada Noriko , Kido Motoyuki , Seama Nobukazu
Published: October 2024

We have developed a 3-D forward modeling method for the magnetometric resistivity (MMR) technique, specially focusing on the marine MMR method, which utilizes a vertical bipole source and seafloor receivers to measure magnetic field variations. The bipole source generates an artificial electric current between two electrodes: one on the sea surface and another on the seafloor. When computing the electric potential using the relaxation method, while conserving electric current, singularities arise at the electrode locations. To address this issue, we introduce two electrical resistivity structures to mitigate the effects of these singularities and to obtain magnetic field anomalies caused by arbitrary 3-D electrical resistivity anomalies beneath the seafloor. By determining the sign of the magnetic field anomaly, we can infer whether the electrical resistivity of the anomalous body is more conductive or more resistive compared to the surrounding oceanic crust. Furthermore, we demonstrate that increasing the number of bipole sources is more effective in exploring anomalous bodies than increasing the number of receivers.

Graphical abstract
Building paper bridges: adapting citizenship and immigration regimes to international displacement
Authors: Besserer Rayas Andrés , Finn Victoria , Freier Luisa Feline
Published: October 2024

Implementation gaps in the areas of naturalization and immigrant regularization emerge through a mismatch between the documents a residence country requires, and the documents that refugees and migrants can realistically provide. Those caught in this gap may live undocumented or risk statelessness. Residence countries can close such paperwork gaps by adapting legal interpretations and easing administrative requirements. When Colombia faced large-scale international displacement from Venezuela, state actors identified documentation-based implementation gaps in its nationality law and regularization procedures; they then took an innovative – yet not faultless – approach by adapting its citizenship and immigration regimes to accommodate displaced Venezuelans. These changes strengthened access to essential rights and increased the well-being of many. In this article, we develop the concepts of paperwork gaps and paper bridges and discuss the actors, impact, and limitations of Colombia’s policy innovations in the areas of nationality by birth, naturalization, and regularization based on research conducted from 2020 to 2023. The study advances the literature on government learning regarding policies within citizenship and immigration regimes that target internationally displaced populations.
Comprehensive analysis of a necroptosis-associated diagnostic signature for myelodysplastic syndromes based on single-cell RNA-seq and bulk RNA-seq
Authors: Zhang Huimin , Zhang Li , Liang Xiaoning , Zhang Lihong , Ma Bing , Li Yuexian , Wang Jianying , Shen Yang , Pang Yuhui , Xiong Jianjun
Published: October 2024

Background

Myelodysplastic syndromes (MDS) are heterogeneous and clonal hematological disorders. The role and mechanism of necroptosis in MDS remain poorly understood.

Methods

mRNA expression profiles and single-cell RNA-sequencing (scRNA-seq) data were sourced from the GEO database. ScRNA-seq data were processed using the “Seurat” package. After cell annotation, necroptosis-related scores (NRscores) for each cell were calculated using the “UCell” package. Differentially expressed genes (DEGs) and their associated biological functions in NRscore-related cell populations were identified. Additionally, DEGs and necroptosis-related genes (DE-NRGs) between MDS patients and healthy controls were identified. Consensus clustering was employed to classify MDS patients into distinct subclusters based on DE-NRGs. The biological functions and immune characteristics of these classifications were analyzed. Prognostic gene signatures were determined using LASSO and SVM-RFE analyses, and a nomogram was constructed based on the prognostic gene signature.

Results

A total of 12 cell types were identified in MDS and healthy controls. NRscore was found to be elevated in monocytes and common lymphoid precursors (CLPs). Enrichment analysis revealed that monocytes and CLPs with high NRscore were associated with mitochondria-related and immune-related pathways. Eleven DEGs in monocytes and CLPs between MDS patients and healthy controls were identified. Additionally, 13 DE-NRGs were identified from 951 DEGs between MDS and healthy controls. MDS patients were classified into two distinct subclusters based on these 13 DE-NRGs, revealing several immune-related processes and signaling pathways. Differences in immune subpopulations between the two subclusters were observed. A necroptosis-related diagnostic gene signature (IRF9, PLA2G4A, MLKL, BAX, JAK2, and STAT3) was identified as predictive of MDS prevalence.

Conclusion

Necroptosis plays a role in MDS progression by inducing inflammation. A novel necroptotic gene signature has been developed to distinguish and diagnose MDS at early stages of the disease.
Current progress on pathogenicity-related genes in Fusarium oxysporum f. sp. cubense tropical race 4
Authors: Chen Deng , Ju Minghao , Xie Jianghui , Chen Xiao-Lin , Peng Jun
Published: October 2024

Vascular wilt, a disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), is highly destructive to bananas. Identifying genes that contribute to the fungus's virulence is crucial for understanding its pathogenesis. In this review, we provide an overview of recent research on genes involved in various aspects of Foc TR4's pathogenic process. These include signal recognition and transduction, the formation of cellular structures, regulation through microRNA and epigenetic mechanisms, effector secretion, and toxin secretion. We place a particular emphasis on discussing effectors that either facilitate virulence or serve as elicitors of host defense responses. Given the limited understanding of the molecular mechanisms underlying Foc TR4 pathogenesis, summarizing the research on these functional genes is necessary and timely. Our integrative information will facilitate research on identification of more key genes involved in the invasiveness of Foc TR4, contributing to more systemic understanding of pathogenesis of this important pathogen. These findings will, in turn, offer potential targets for the development of effective fungicides or soil disinfectants to combat this devastating disease.
The role of mobile shopping service quality in enhancing customers M-satisfaction, M-loyalty, and E-word of mouth
Authors: Hassan Heba E.
Published: October 2024

With the increasing prevalence of mobile shopping (m-shopping) apps, service quality (SQ) has been recognized as a prominent factor in distinguishing the best apps available online. As limited studies have explored how to estimate mobile SQ, this study attempts to expand our understanding of the primary dimensions that shape customer judgments of the overall mobile SQ related to m-shopping activity by validating the mobile SQ (M-S-QUAL) scale in a new cultural setting, e.g., Egypt. It also examines the interrelationships between mobile SQ and three outcome variables: mobile satisfaction (m-satisfaction), mobile loyalty (m-loyalty), and electronic word of mouth (e-WOM). The results support the validity of using the M-S-QUAL scale to assess the mobile SQ of m-shopping platforms. Moreover, the findings emphasize the role of m-shopping SQ in enhancing consumers’ m-satisfaction, thereby improving m-loyalty and increasing favorable e-WOM. The results also show that responsiveness and efficiency are the primary driving forces underlying the SQ dimensions of the investigated outcome variables.

Graphical abstract
Geostatistical inversion of frequency-domain electromagnetic data for near-surface modeling
Authors: Narciso João , Van De Vijver Ellen , Azevedo Leonardo
Published: October 2024

The detailed characterization of near-surface deposits is important for environmental and economic reasons. These shallow subsurface systems can be very complex and heterogeneous due to natural dynamics and anthropogenic interferences. Modeling techniques based exclusively on direct sampling generate limited, informed 3D models of the near surface. Geophysical methods provide valuable and additional information to model the spatial distribution of the near-surface properties for locations where direct observations are not available. From this set of methods, the frequency-domain electromagnetic induction (FDEM) method has been successfully applied to image complex near-surface deposits. Even so, predicting the spatial distribution of the relevant subsurface properties from geophysical data and the integration of direct observations is not straightforward. It requires solving a challenging geophysical inverse problem. Geostatistical modeling tools have been effectively applied to couple direct observations with geophysical data, such as seismic reflection. We develop an iterative geostatistical FDEM inversion method able to integrate the data from direct measurements of the near surface with surface loop-loop FDEM measurements to simultaneously predict the high-resolution models of electrical conductivity (EC) and magnetic susceptibility (MS) and their associated uncertainty. The iterative geostatistical inversion method is based on stochastic sequential simulation and cosimulation as model perturbation and stochastic update techniques. The iterative optimization is based on the local data misfit between observed and predicted FDEM data, weighted by the sensitivity of the acquisition equipment. Our method is first demonstrated for a synthetic landfill data set created based on real data collected at a mine tailing disposal site in Portugal and on a real data set collected at a site with archaeological features in Knowlton, UK. The results show the ability of our method to accurately predict and characterize the spatial distribution of EC and MS down to the depth of interest while reproducing the recorded FDEM data.
Quantification of the nonlinear effect in a seismic signal using Holo-Hilbert spectral analysis
Authors: Zong Zhaoyun , Wang Chaohe , Luo Chengping
Published: October 2024

Seismic signals are nonstationary and nonlinear because of excitation conditions, absorption, and the attenuation of stratum and receiving instruments. Various time-frequency analysis methods have been widely and practically applied in describing the time-varying characteristics of seismic signals. However, most methods are based on additive expansions and cannot represent the nonlinearity of signals, which is achieved by a multiplicative process. Therefore, the information provided by the time-frequency spectrum needs to be completed. The Holo-Hilbert spectral analysis (HHSA) method is introduced in this paper to show the nonlinearity of seismic signals, i.e., the modulation effect of low-frequency components on high-frequency components. HHSA contains nested empirical mode decomposition and Hilbert transforms to achieve a full informational spectrum represented by two frequency dimensions. In the Holo-Hilbert spectrum, one dimension represents the frequency-modulated frequency, which characterizes the nonstationarity of the signal, and the other dimension represents the amplitude-modulated frequency, which indicates the nonlinear effect in the signal. Synthetic and field data examples verify the feasibility of HHSA in characterizing the cross-frequency interaction of nonstationary seismic signals as a potential tool to detect reservoirs.
Improving the classification of rock samples with diffusion probabilistic machine learning
Authors: Gómez Julián Luis , Camilion Emilio
Published: October 2024

Machine learning is a powerful data-driven technology for regression and classification tasks in numerous branches of science and technology. With probabilistic machine learning, we can approximate the probability density function of a given digital data set, unlocking the sampling of new and realistic data. We implement probabilistic machine learning as a statistical-based data augmentation tool to effectively improve the performance of a classifier on scarce data sets. Limited data are the norm in most practical situations, as is the case with core samples retrieved from unconventional oil and gas reservoirs. Obtaining and properly labeling rock sample images is a manual and time-consuming task. This leads to scarce data sets that make the lithologic classification of rock samples challenging. We illustrate the technology on images taken from well cores from the Argentinean Neuquén and Austral Basins, where by introducing generated samples in the training stage of a machine-learning classifier, we achieve a 5% higher accuracy with respect to the baseline obtained using the same number of samples from the original data set. We reach these results by proposing a lightweight workflow that can be run on very limited hardware. Our workflow is an alternative to classical data augmentation strategies for dealing with incomplete information, such as geometric transformations.
Grief and coping among relatives of patients who died of COVID-19 in intensive care during the height of the COVID-19 pandemic
Authors: Rodriguez-Villar Sancho , Okegbola Elijah Oluwafemi , Arevalo-Serrano Juan , Duval Yasmine , Mathew Annie , Rodriguez-Villar Carmen , Smith Kirsten V. , Kennedy Robert Charles , Prigerson Holly G.
Published: October 2024

Background

The grief of relatives of patients who died of COVID-19 in an intensive care unit (ICU) has exacted an enormous toll worldwide.

Aims

To determine the prevalence of probable prolonged grief disorder (PGD) at 12 months post-loss and beyond. We also sought to examine circumstances of the death during the COVID-19 pandemic that might pose a heightened risk of PGD, and the associations between probable PGD diagnosis, quality of life and social disconnection.

Method

We conducted an observational, cross-sectional multicentre study of the next of kin of those who died of COVID-19 between March 2020 and December 2021. Participants were recruited from ICUs in South-East London. The Prolonged Grief Disorder Scale (PG-13-R), Quality-of-Life Scale (QOLS) and Oxford Grief-Social Disconnection Scale (OG-SD) were used.

Results

A total of 73 relatives were recruited and assessed, all of them over a year after their loss. Twenty-five (34.2%; 95% CI 23.1–45.4%) relatives of patients who died in the ICU met the criteria for PGD. Those who met the criteria had significantly worse quality of life (QOLS score mean difference 26; 95% CI 17–34; P < 0.001) and endorsed greater social disconnection (OG-SD score means difference 41; 95% CI 27–54; P < 0.001).

Conclusions

The findings suggest that rates of PGD are elevated among relatives of patients who died of COVID-19 in the ICU. This, coupled with worse quality of life and greater social disconnection experienced by those meeting the criteria, suggests the need to attend to the social deprivations and social dysfunctions of this population group.
Discriminative Power of the Flow through Cell Dissolution Tester in Predicting the In Vivo Performance of Pentoxifylline SR Product under Fed and Fasting Conditions
Authors: Taha Nesrin F. , Emara Laila H.
Published: October 2024

This study explored, for the first time the role of different designs of the Flow-Through-Cell (FTC, USP IV) dissolution Tester in predicting the in-vivo performance of Pentoxifylline (PTX) sustained-release (SR) market product, under fed & fasting conditions. Release studies of Trental® SR 400 mg (Sanofi, Egypt), were carried-out in the FTC under different conditions, including: different volumes / compositions of release media, variable FTC flow patterns as well as applying open / closed loop configuration setups. Pharmacokinetic (PK) data, obtained from literature, were converted to in-vivo fraction-absorbed [FA] using Wagner-Nelson (WN) method. A 1:1 IVIVC was investigated by comparing PTX fraction-dissolved [FD] under different FTC release designs versus calculated [FA]. Predicted PK parameters were evaluated, and compared with actual data, with estimation of prediction-error (PE%). The suggested FTC design; a closed-loop setup, with turbulent-flow pattern of the dissolution medium; provided the most acceptable PTX release according to USP labeled limits (USP 27). Also, results showed that PTX release was pronouncedly increased in a finite-volume of gradient-buffer system rather than water, which guarantee complete resemblance to GIT environment. This release design presented the most predictive IVIVC model with PTX in-vivo performance under fasting / fed states, with acceptable PE% values in terms of Cmax and AUCs. A suggested FTC design is proposed as an alternative dissolution model in the official USP-monograph for PTX SR products.

Graphical Abstract
Proposed Quality Metrics for Congenital Cardiac Anesthesia: A Scoping Review
Authors: Brown Morgan L. , Dorste Anna , Adams Phillip S. , Caplan Lisa A. , Gleich Stephen J. , Hernandez Jennifer L. , Riegger Lori Q. ,   For the Quality and Safety Committee of the Congenital Cardiac Anesthesia Society
Published: October 2024

Congenital cardiac anesthesiologists practice in a unique environment with high risk for morbidity and mortality. Quality metrics can be used to focus clinical initiatives on evidence-based care and provide a target for local quality improvement measures. However, there has been no comprehensive review on appropriate quality metrics for congenital cardiac anesthesia to date. Members of the Quality and Safety Committee for the Congenital Cardiac Anesthesia Society proposed 31 possible candidate topics for metrics. Using a scoping review strategy, 3649 abstracts were reviewed with 30 articles meeting final criteria. Of these, 5 candidate metrics were unanimously proposed for local collection and national benchmarking efforts: use of a structured handover in the intensive care unit, use of an infection prevention bundle, use of blood conservation strategies, early extubation of cardiopulmonary bypass cases, and cardiac arrest under the care of a cardiac anesthesiologist. Many metrics were excluded due to a lack of primary data and perceived complexity beyond the scope of cardiac anesthesia practice. There is a need to develop more primary data including linking process measures with outcomes, developing risk-stratification for our patients, and collecting national data for benchmarking purposes.
Survival of a Perverse Nation
Authors: Shirinian Tamar R.
Published: October 2024

In Survival of a Perverse Nation, Tamar R. Shirinian traces two widespread rhetorics of perversion—sexual and moral—in postsocialist Armenia, showing how they are tied to anxieties about the nation’s survival. In her fieldwork with Armenians, Shirinian found that right-wing nationalists’ focus on sexual perversion centers the figure of the homosexual, while questions of moral perversion surround oligarchs and other members of the political economic elite. While the homosexual is seen as non- or improperly reproductive, the oligarch’s moral deviations from the caring and paternalistic expectations associated with national leadership also endanger Armenia’s survival. Shirinian shows how both figures threaten the nation’s proper social reproduction, a source of great anxiety for a nation whose primary point of identity is surviving genocide. In the existential threat posed by these forms of perversion Shirinian finds paths where nonsurvival might mean the creation of futures that are queerer and more just. Detailing how the language of perversion offers trenchant critiques of capitalism as a perversion of life, Shirinian presents a new queer theory of political economy.
Illuminating cellular architecture and dynamics with fluorescence polarization microscopy
Authors: Dean William F. , Mattheyses Alexa L.
Published: October 2024

Ever since Robert Hooke's 17th century discovery of the cell using a humble compound microscope, light–matter interactions have continuously redefined our understanding of cell biology. Fluorescence microscopy has been particularly transformative and remains an indispensable tool for many cell biologists. The subcellular localization of biomolecules is now routinely visualized simply by manipulating the wavelength of light. Fluorescence polarization microscopy (FPM) extends these capabilities by exploiting another optical property – polarization – allowing researchers to measure not only the location of molecules, but also their organization or alignment within larger cellular structures. With only minor modifications to an existing fluorescence microscope, FPM can reveal the nanoscale architecture, orientational dynamics, conformational changes and interactions of fluorescently labeled molecules in their native cellular environments. Importantly, FPM excels at imaging systems that are challenging to study through traditional structural approaches, such as membranes, membrane proteins, cytoskeletal networks and large macromolecular complexes. In this Review, we discuss key discoveries enabled by FPM, compare and contrast the most common optical setups for FPM, and provide a theoretical and practical framework for researchers to apply this technique to their own research questions.
Railway security checks at the border: between intrusive security technologies and fundamental traveller rights
Authors: Kubrak Kacper , Havârneanu Grigore M.
Published: October 2024

European railway borders are facing a particular exposure to security threats and need a delicate balance between securitization and free movement, especially amid globalisation, the current geopolitical landscape and increased migrant flows. For example, the war in Ukraine illustrated the challenges experienced at the Eastern EU borders by the refugee migration surge in early 2022. This exploratory focuses on the European border security control process from the rail border perspective. It encompasses a descriptive synthesis of the lessons learned from the UIC Refugee Task Force as well as insights from the ongoing EU-funded Horizon Europe project ODYSSEUS (Unobtrusive Technologies for Secure and Seamless Border Crossing for Travel Facilitation). Project ODYSSEUS aims to support the security and integrity of the European space, reduce illegal movements of people and goods across EU borders, facilitate travelling for citizens all while protecting fundamental rights of travellers. The project will test a combination of multi-behavioural and General Data Protection Regulation (GDPR) compliant biometric user identity verification tools, allowing, when possible, citizens to cross EU border without any interruption or queue. Further, novel luggage and baggage checks will allow citizens’ vehicles and cargos to be remotely checked at land borders to speed up the border check processes in a secure and reliable manner. The project will run three pilot tests at road, rail and water borders. In this paper, we analyse the implementation of project’s technologies in the rail border crossing pilot test and discuss the implications for the actors involved in the process of railway border crossing (e.g., border authorities, railway operators and railway travellers).
How physical activity opportunities seized by adolescents differ between Europe and the Pacific Islands: the example of France and New Caledonia
Authors: Derigny Thibaut , Urvoy Marie-Jeanne , Wattelez Guillaume , Leroux Pierre-Yves , Zongo Paul , Schnitzler Christophe , Galy Olivier , Potdevin Francois
Published: October 2024

Background France (FR) and New Caledonia (NC) are both French territories, one in Western Europe, the other as part of the Pacific Island Countries and Territories (PICTs). Despite schooling in similar educational systems, FR and NC adolescents develop distinct relationships with physical activity, which is influenced by the geographical-cultural and symbolic structures of their respective societies. This study explored the distribution of physical activity according to geographical culture and opportunity-temporal dimensions. Methods Participants were randomly selected, with individual (boys vs. girls), spatial (rural vs. urban), and geographical (FR vs. NC) stratifications. Accelerometers GT3X (ActiGraphTM, Pensacola FL, USA) and daily logbooks were used to measure the physical activity intensity and opportunities during the week. Results A total of 156 participants were included in this study. A significant effect was found in moderate to vigorous physical activity (MVPA) intensity with the geographical-cultural dimension; participants living in FR were more likely to engage in MVPA, especially in five opportunities: school, supervised leisure, home, school breaks, and transport. For both FR and NC adolescents, physical education lessons had the highest MVPA. Conclusion This study showed that MVPA differed in the same national educational system according to geographical culture. Physical education lessons could catch the challenge of an “opportunity education” (opportunities are defined as temporal invitations to engage in PA) by opening the door to two particular opportunities: supervised leisure and active transport.
Feasibility of a nurse-led, mHealth-assisted, and team-based collaborative care model for heart failure care in India: Findings from a multi-stakeholder qualitative study
Authors: Thomas Sunu C. , Neenumol Kandagathuparambil , Chacko Susanna , Prinu Jose , Pillai Meera R. , Pisharody Sunil , Chozhakkat Somanathan , Vijay MS Jyothi , Iliyas A. Mohamed , Harikrishnan Sivadasanpillai , Ganapathi Sanjay , Jeemon Panniyammakal
Published: October 2024

Background Heart failure (HF) management is often challenging due to poor adherence to GDMT and self-care. Continuous monitoring of patients by a dedicated care manager may enhance adherence to self-care and treatment and prevent hospitalisations. For the adoption and acceptance of a collaborative care model (CCM) for HF management in Indian settings, understanding the perspectives of all stakeholders regarding its various components and feasibility is needed. Therefore, we aimed to obtain perceptions of potential challenges to care and suggestions on multiple components of the proposed CCM in managing HF and its feasibility. Methods In-depth interviews were done among HF patients, caregivers, nurses, and cardiologists from private, co-operative, and public sector tertiary care hospital settings that cater to HF patients in Kerala, India. An in-depth interview guide was used to elicit the data. Data were analysed using Python QualCoder version 2.2. We used a framework method for the analysis of data. Results A total of 22 in-depth interviews were conducted. We found that the existing care for HF in many settings was inadequate for continuous engagement with the patients. Non-adherence to treatment and other self-care measures, was noted as a major challenge to HF care. Healthcare providers and patients felt nurses were better at leading collaborative care. However, various barriers, including technical and technological, and the apprehensions of nurses in leading the CCM were identified. The stakeholders also identified the mHealth-assisted CCM as a potential tool to save money. The stakeholders also appreciated the role of nurses in creating confidence in patients. Conclusions A nurse-led, mHealth-assisted, and team-based collaborative care was recognised as an excellent step to improve patient adherence. Effective implementation of it could reduce hospitalisations and improve patients' ability to manage their HF symptoms.
The genome sequence of a soldier beetle, Cantharis flavilabris Fallén, 1807
Authors: Barclay Maxwell V. L. ,   Natural History Museum Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,   Wellcome Sanger Institute Scientific Operations: Sequencing Operations,   Wellcome Sanger Institute Tree of Life Core Informatics team,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: October 2024

We present a genome assembly from an individual female Cantharis flavilabris (soldier beetle; Arthropoda; Insecta; Coleoptera; Cantharidae). The genome sequence is 348.3 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,711 protein coding genes.
Taxonomy Identifiers (TaxId) for Biodiversity Genomics: a guide to getting TaxId for submission of data to public databases
Authors: Blaxter Mark , Pauperio Joana , Schoch Conrad , Howe Kerstin
Published: October 2024

Biodiversity genomics critically depends on correct taxonomic identification of the sample from which data are derived. Tracking of that taxonomic information through systems that archive data and report on genome sequencing efforts. For submission of data to the International Nucleotide Sequence Database Collaboration (INSDC) databases (DNA DataBank of Japan [DDBJ], European Nucleotide Archive [ENA] and National Center for Biotechnology Information [NCBI]), samples and data derived from them must be assigned a species-level NCBI Taxonomy taxonomic identifier (TaxId, sometimes referred to as taxId or txid). We thus need to be able to identify the TaxId for a target species efficiently. Because the NCBI Taxonomy does not include all known species and cannot preemptively represent unknown taxa, we also need an efficient process for generating new TaxIds for species not yet listed. This document provides workflows for different kinds of TaxId acquisition scenarios and was created to guide users in these processes. Although developed for European projects such as Darwin Tree of Life and the European Reference Genome Atlas, the workflows are universally applicable and describe the use of ENA in resolving taxonomic issues. Too Long: Didn't Read (TL;DR): Use the ENA REST API programmatically to retrieve TaxIds for target species and confirm that sequence data can be submitted to those TaxIds. Use the NCBI Web interface to NCBI Taxonomy to identify potential homotypic synonyms. Request a new TaxId from ENA for a species not yet in NCBI Taxonomy, and for species-like entries for which the full Linnaean binomen is not determined (see https://ena-docs.readthedocs.io/en/latest/faq/taxonomy_requests.html#creating-taxon-requests). Discuss directly with the NCBI Taxonomy curators or the curators at ENA and NCBI whenever you think there is an opportunity to improve their database.
The genome sequence of fat-hen, Chenopodium album L.
Authors: Mian Sahr , Christenhusz Maarten J. M. ,   Royal Botanic Gardens Kew Genome Acquisition Lab,   Plant Genome Sizing collective,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,   Wellcome Sanger Institute Scientific Operations: Sequencing Operations,   Wellcome Sanger Institute Tree of Life Core Informatics team,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: October 2024

We present a genome assembly from an individual Chenopodium album (fat-hen; Streptophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence has a total length of 1,593.80 megabases. Most of the assembly (99.61%) is scaffolded into 27 chromosomal pseudomolecules suggesting the individual is an allohexaploid (2n = 6x = 54). The mitochondrial and plastid genome assemblies have lengths of 312.95 kilobases and 152.06 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 50,077 protein-coding genes.
SAHELI: Study and Action on Hysterectomy: Evidence on women’s health through the life course in India. Protocol for a mixed-methods study
Authors: Desai Sapna , Govil Dipti , Nambiar Devaki , Sinha Hemali Heidi , Roy Archana , Vora Kranti , Lakshmi Josyula K , Kumari Archana , Mishra Gita D , Bhatla Neerja
Published: October 2024

Hysterectomy, removal of the uterus, is a commonly performed surgery for gynaecological morbidities. Emerging evidence indicates that hysterectomy performed before age 45 (early hysterectomy), is associated with considerable risks to women’s health. While most evidence on hysterectomy is from high-income settings, national surveys from India report high prevalence of early hysterectomy in specific regions, as well as higher prevalence amongst women in rural areas and with less education. The median age at hysterectomy in India is close to ten years before the onset of natural menopause. India has recently introduced national guidelines to address early hysterectomy, but large evidence gaps on the causes and consequences remain – which in turn limits the potential effectiveness of interventions at the clinical, health system and community level. Methods SAHELI is a Team Science study that will examine: (i) individual, social and health system determinants of early hysterectomy; (ii) women’s treatment pathways to hysterectomy and for gynaecological morbidity in general; and (iii) the consequences of undergoing hysterectomy on women’s physical, mental, economic and social well-being across the life course. This mixed-methods study includes population surveys amongst women in ages 25–49 in three high-prevalence states; qualitative health systems research to trace treatment journeys with women, health care providers and other stakeholders; evidence syntheses; and knowledge translation activities to ensure findings inform co-produced strategies and interventions. The study is grounded in a feminist epidemiology approach, aiming to examine individual and structural causes of vulnerability and prioritising the views of women, particularly in knowledge translation. Conclusions SAHELI, implemented by an all-women, multi-disciplinary team, is the first study in India to examine the causes and consequences of hysterectomy in a life course approach. We aim to influence interventions, policy and future research on women’s health, particularly access to quality gynaecological care and comprehensive health services through the life course.
The genome sequence of the White-spotted Pug moth, Eupithecia tripunctaria Herrich-Schäffer, 1852
Authors: Boyes Douglas , McCulloch James , Crowley Liam M. ,   University of Oxford and Wytham Woods Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,   Wellcome Sanger Institute Scientific Operations: Sequencing Operations,   Wellcome Sanger Institute Tree of Life Core Informatics team,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: October 2024

We present a genome assembly from an individual female Eupithecia tripunctaria (the White-spotted Pug moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 494.80 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.51 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,799 protein-coding genes.
The genome sequence of the corn cockle, Agrostemma githago L., 1753 (Caryophyllaceae)
Authors: Mian Sahr , Leitch Ilia J. ,   Royal Botanic Gardens Kew Genome Acquisition Lab,   Plant Genome Sizing collective,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,   Wellcome Sanger Institute Scientific Operations: Sequencing Operations,   Wellcome Sanger Institute Tree of Life Core Informatics team,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: October 2024

We present a genome assembly from an individual Agrostemma githago (the corn cockle; Tracheophyta; Magnoliopsida; Caryophyllales; Caryophyllaceae). The genome sequence has a total length of 1,735.0 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules suggesting the individual is a tetraploid (2n = 4x = 48). The organelle genomes have been assembled, and the length of the mitochondrial genome is 262.91 and the plastid genome 151.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 38,816 protein-coding genes.
The genome sequence of the Golden-tabbed robberfly, Eutolmus rufibarbis (Meigen, 1820)
Authors: Nash Will J. , Halstead Andrew ,   Natural History Museum Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,   Wellcome Sanger Institute Scientific Operations: Sequencing Operations,   Wellcome Sanger Institute Tree of Life Core Informatics team,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: October 2024

We present a genome assembly from an individual female Golden-tabbed robberfly, Eutolmus rufibarbis (Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 285.90 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.22 kilobases in length.
The genome sequence of a tachinid fly, Dexiosoma caninum (Fabricius, 1781)
Authors: Sivell Olga , Mitchell Ryan , Raper Chris ,   Natural History Museum Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,   Wellcome Sanger Institute Scientific Operations: Sequencing Operations,   Wellcome Sanger Institute Tree of Life Core Informatics team,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: October 2024

We present a genome assembly from a female tachinid fly Dexiosoma caninum (Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence has a total length of 517.10 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.7 kilobases in length.
Current perspectives on the pharmacological treatment of advanced
hepatocellular carcinoma: a narrative review
Authors: Yoo Hye-Jin , Yoo Jeong-Ju , Kim Sang Gyune , Kim Young Seok
Published: October 2024

Hepatocellular carcinoma (HCC) remains a critical health concern in Korea,
ranking as the second leading cause of cancer mortality and imposing substantial
economic burdens, particularly among the working-age population. This review
examines recent advancements in treating advanced HCC, referencing the updated
2022 HCC guidelines and the Barcelona Clinical Liver Cancer system.
Historically, first-line systemic therapies included sorafenib and lenvatinib,
with regorafenib, cabozantinib, or ramucirumab serving as second-line options.
Since 2020, immune checkpoint inhibitors have shown superior overall survival
than sorafenib, leading to the adoption of combination therapies such as
atezolizumab with bevacizumab and durvalumab with tremelimumab as first-line
treatments. The IMbrave150 study demonstrated that
atezolizumab–bevacizumab significantly extended median overall survival
and progression-free survival, with the longest survival reported in any phase 3
trial for advanced HCC. Similarly, the HIMALAYA study indicated that durvalumab
combined with tremelimumab significantly improved survival rates. Second-line
therapies now include regorafenib, cabozantinib, ramucirumab, nivolumab with
ipilimumab, and pembrolizumab, each offering benefits for specific patient
populations. Nonetheless, these therapies are associated with side effects that
require careful management. Traditional targeted therapies can lead to
hypertension, cardiovascular events, and hand-foot skin reactions, whereas
immune checkpoint inhibitors may cause immune-related adverse events affecting
the skin, gastrointestinal tract, and endocrine system. Clinicians must be
well-versed in these treatments and their potential side effects to provide
optimal patient care. The emergence of combination therapies targeting complex
biological pathways signifies a new paradigm in HCC treatment, emphasizing the
importance of continuous education and vigilant monitoring to optimize patient
outcomes.
Pathogenesis and management of metabolic dysfunction-associated
steatohepatitis-related hepatocellular carcinoma: a narrative
review
Authors: Lee Han Ah
Published: October 2024

Metabolic dysfunction-associated steatohepatitis (MASH) is increasingly
recognized as a leading cause of hepatocellular carcinoma (HCC), the
third-leading cause of cancer mortality worldwide, driven by the global obesity
epidemic. Projected to become the primary cause of HCC by 2030, MASH-HCC
presents unique clinical challenges. This review examines its clinical
management, including surveillance strategies and treatment advances, and
discusses prospects to overcome existing challenges. MASH-HCC accounts for
10%–20% of HCC cases, particularly in Western countries, with a rising
incidence due to obesity. Risk factors include cirrhosis, diabetes, obesity,
alcohol, smoking, genetic polymorphisms (e.g., PNPLA3), and microbiome
alterations. The pathogenesis involves fibrosis, immune dysfunction (e.g.,
T-cell impairment), and molecular changes. Prevention focuses on lifestyle
modifications. Surveillance in patients with MASH cirrhosis is crucial but is
hindered by poor ultrasound sensitivity in obese patients, necessitating
alternative methods. Treatment mirrors that of other HCC types, but
comorbidities and potentially reduced efficacy of immunotherapy necessitate
tailored approaches. MASH is becoming the leading cause of HCC, necessitating
lifestyle interventions for prevention. Improved surveillance and early
detection are critical but challenging due to obesity-related factors.
Treatments align with those for other HCC types, but comorbidities and potential
differences in immunotherapy efficacy due to T-cell dysfunction require careful
consideration. Key needs include identifying molecular drivers in non-cirrhotic
metabolic dysfunction-associated steatotic liver disease, developing preventive
therapies, refining surveillance methods, and tailoring treatments. Trials
should specifically report MASH-HCC outcomes to enable personalized therapies.
Further research is needed to understand T-cell dysfunction, optimize
immunotherapies, and identify predictive biomarkers.
Large Language Model in Creative Work: The Role of Collaboration Modality and User Expertise
Authors: Chen Zenan , Chan Jason
Published: October 2024

Since the launch of ChatGPT in December 2022, large language models (LLMs) have been rapidly adopted by businesses to assist users in a wide range of open-ended tasks, including creative work. Although the versatility of LLM has unlocked new ways of human-artificial intelligence collaboration, it remains uncertain how LLMs should be used to enhance business outcomes. To examine the effects of human-LLM collaboration on business outcomes, we conducted an experiment where we tasked expert and nonexpert users to write an ad copy with and without the assistance of LLMs. Here, we investigate and compare two ways of working with LLMs: (1) using LLMs as “ghostwriters,” which assume the main role of the content generation task, and (2) using LLMs as “sounding boards” to provide feedback on human-created content. We measure the quality of the ads using the number of clicks generated by the created ads on major social media platforms. Our results show that different collaboration modalities can result in very different outcomes for different user types. Using LLMs as sounding boards enhances the quality of the resultant ad copies for nonexperts. However, using LLMs as ghostwriters did not provide significant benefits and is, in fact, detrimental to expert users. We rely on textual analyses to understand the mechanisms, and we learned that using LLMs as ghostwriters produces an anchoring effect, which leads to lower-quality ads. On the other hand, using LLMs as sounding boards helped nonexperts achieve ad content with low semantic divergence to content produced by experts, thereby closing the gap between the two types of users.

This paper was accepted by D. J. Wu, information systems.

Supplemental Material: The online appendix and data files are available at https://doi.org/10.1287/mnsc.2023.03014 .
A Structural Model for Maternal Adaptation and Family Stress in Families with Mentally Handicapped Children
Authors: Koh Hyo Jung , Kwon Young Sook , Kim Chung-Nam , Park Young Sook , Park Jeong Sook , Park Chung Ja , Shin Yeong Hee , Lee Kyung Hee
Published: October 2024

In comparison with the long and continuous history of research in the general area of stress and coping, theoretical and clinical interest in family stresses, hardships, and adaptation is a recent phenomenon.Today family behavior in response to predictable and unpredictable life events has gained respect as an important area of theory building, research, and intervention.To understand the phenomena of family behavior, comprehensive theoretical frame work is needed which gives a background to us.For the purpose that, this study was designed to develop and generalize a structural model for family stress and adaptation in families with handicapped children.A hypothetical model was constructed on the basis of the family stress theory developed by McCubbin etc. The model included 6 theoretical concepts and 12 paths. For the purpose of model testing, empirical data were collected from June to December, 1993. The subjects of the study constituted 82 mothers of chidren in three special schools in Taegu.An SPSS PC+ and PC-LISREL 7. 13 computer programs were used for descriptive and covariance structure analysis.The results of the study were as follows.1) The results of covariance structure analysis indicated :The hypothetical model showed itself a good fit to the empirical data 64(df=5, P=0.343), Goodness of Fit Index=0.994, Adjusted Goodness of Fit Index=0.969, Root Mean Square Residual=0.035].2) The results of Hypothesis testing indicated (1) Social Support(yii=.336, T=2.052) and Family Functioning (y 12=. 697, T=4.163) had direct effects on Situational Definition.(2) Social Support(p3=-.229, T=4.453) and Situatioal Defiition(y21 =-.263, T=-2.070) had direct effects on the effect of the handicapped child on the family.(3) Family Functioning(y32=.411, T=3.591) had direct effects on Family Adaptation.(4) The Family Stress(바2=-.301，T=2.59) had direct effects on Family Adaptation. The model was supported by the empirical data. Thus it was suggested that the model could be adequately applied to family nursing care with families with handicapped.