bluuebunny/crossref_metadata_2025_split huggingface dataset:
scDOT: enhancing single-cell RNA-Seq data annotation and uncovering novel cell types through multi-reference integration
Authors: Xiong Yi-Xuan , Zhang Xiao-Fei 
Published: March 2024

Abstract
The proliferation of single-cell RNA-seq data has greatly enhanced our ability to comprehend the intricate nature of diverse tissues. However, accurately annotating cell types in such data, especially when handling multiple reference datasets and identifying novel cell types, remains a significant challenge. To address these issues, we introduce Single Cell annotation based on Distance metric learning and Optimal Transport (scDOT), an innovative cell-type annotation method adept at integrating multiple reference datasets and uncovering previously unseen cell types. scDOT introduces two key innovations. First, by incorporating distance metric learning and optimal transport, it presents a novel optimization framework. This framework effectively learns the predictive power of each reference dataset for new query data and simultaneously establishes a probabilistic mapping between cells in the query data and reference-defined cell types. Secondly, scDOT develops an interpretable scoring system based on the acquired probabilistic mapping, enabling the precise identification of previously unseen cell types within the data. To rigorously assess scDOT’s capabilities, we systematically evaluate its performance using two diverse collections of benchmark datasets encompassing various tissues, sequencing technologies and diverse cell types. Our experimental results consistently affirm the superior performance of scDOT in cell-type annotation and the identification of previously unseen cell types. These advancements provide researchers with a potent tool for precise cell-type annotation, ultimately enriching our understanding of complex biological tissues.
Artificial intelligence in medicine: mitigating risks and maximizing benefits via quality assurance, quality control, and acceptance testing
Authors: Mahmood Usman , Shukla-Dave Amita , Chan Heang-Ping , Drukker Karen , Samala Ravi K , Chen Quan , Vergara Daniel , Greenspan Hayit , Petrick Nicholas , Sahiner Berkman , Huo Zhimin , Summers Ronald M , Cha Kenny H , Tourassi Georgia , Deserno Thomas M , Grizzard Kevin T , Näppi Janne J , Yoshida Hiroyuki , Regge Daniele , Mazurchuk Richard , Suzuki Kenji , Morra Lia , Huisman Henkjan , Armato Samuel G , Hadjiiski Lubomir 
Published: March 2024

Abstract
The adoption of artificial intelligence (AI) tools in medicine poses challenges to existing clinical workflows. This commentary discusses the necessity of context-specific quality assurance (QA), emphasizing the need for robust QA measures with quality control (QC) procedures that encompass (1) acceptance testing (AT) before clinical use, (2) continuous QC monitoring, and (3) adequate user training. The discussion also covers essential components of AT and QA, illustrated with real-world examples. We also highlight what we see as the shared responsibility of manufacturers or vendors, regulators, healthcare systems, medical physicists, and clinicians to enact appropriate testing and oversight to ensure a safe and equitable transformation of medicine through AI.
Nosocomial Infections in Adults Receiving Extracorporeal Membrane Oxygenation: A Review for Infectious Diseases Clinicians
Authors: Marcus Joseph E , Shah Aditya , Peek Giles J , MacLaren Graeme 
Published: March 2024

AbstractOver the past 10 years, there has been a rapid expansion in the use of extracorporeal membrane oxygenation (ECMO) in the care of patients with refractory cardiac or respiratory failure. Infectious diseases clinicians must reconcile conflicting evidence from limited studies as they develop practices at their own institutions, which has resulted in considerably different practices globally. This review describes infection control and prevention as well as antimicrobial prophylaxis strategies in this population. Data on diagnostics and treatment for patients receiving ECMO with a focus on diagnostic and antimicrobial stewardship is then examined. This review summarizes gaps in the current ECMO literature and proposes future needs, including developing clear definitions for infections and encouraging transparent reporting of practices at individual facilities in future clinical trials.
BotGSL: Twitter Bot Detection with Graph Structure Learning
Authors: Wei Chuancheng , Liang Gang , Yan Kexiang 
Published: March 2024

AbstractTwitter bot detection is an important and meaningful task. Existing methods can be bypassed by the latest bots that disguise themselves as genuine users and evade detection by mimicking them. These methods also fail to leverage the clustering tendencies of users, which is the most important feature for detecting bots at the community level. Moreover, they neglect the implicit relations between users that contain crucial clues for detection. Furthermore, the user relation graphs, which are essential for graph-based methods, may be unreliable due to noise and incompleteness in datasets. To address these issues, a bot detection framework with graph structure learning is proposed. The framework constructs a heterogeneous graph with users and their relations, extracts multiple features to characterise user intent and establishes a feature similarity graph using metric learning. Implicit relations are discovered to derive an implicit relation graph. Additionally, a semantic relation graph is generated by aggregating relation semantics among users. The graphs are then fused and embedded into a Graph Transformer for training with partially known user labels. The framework demonstrated a 91.92% average detection accuracy on three real-world benchmark, outperforming state-of-the-art methods, while also showcasing the effectiveness and necessity of each module.
Deep Learning-Based Cyberbullying Detection in Kurdish Language
Authors: Badawi Soran 
Published: March 2024

Abstract
Cyberbullying is a significant concern in this digital age due to its harmful effects on individuals and society. Sadly, social media platforms have only exacerbated the problem, making it imperative to find effective ways to identify and prevent offensive content. While previous research has extensively focused on English and explored machine learning techniques to tackle this issue. To address this gap, this paper introduces a new hybrid deep learning model called Gray Wolf Algorithm-convolutional neural network (GWA-CNN), explicitly designed to detect cyberbullying in the Kurdish language on Twitter. The proposed model combines the CNN framework with an optimised GWA version to improve CNN’s parameters and reduce training time. We evaluated GWA-CNN thoroughly utilizing the first-ever manually annotated Kurdish dataset of 30k tweets that have been meticulously curated and divided into three categories, namely sexism, racism and neutral expressions, and compared its performance to those of state-of-the-art algorithms such as Naïve Bayes, K-Nearest Neighbors, Recurrent Neural Networks, Gated Recurrent Units and attention-based transformer. The experimental results demonstrate that GWA-CNN exhibited superior performance in all scenarios, outperforming other approaches in detecting cyberbullying on Twitter.
Functional characterization of HNF4A gene variants identify promoter and cell line specific transactivation effects
Authors: Kaci Alba , Solheim Marie Holm , Silgjerd Trine , Hjaltadottir Jorunn , Hornnes Lorentze Hope , Molnes Janne , Madsen Andre , Sjøholt Gry , Bellanné-Chantelot Christine , Caswell Richard , Sagen Jørn V , Njølstad Pål R , Aukrust Ingvild , Bjørkhaug Lise 
Published: March 2024

Abstract
Hepatocyte nuclear factor-4 alpha (HNF-4A) regulates genes with roles in glucose metabolism and β-cell development. Although pathogenic HNF4A variants are commonly associated with maturity-onset diabetes of the young (MODY1; HNF4A-MODY), rare phenotypes also include hyperinsulinemic hypoglycemia, renal Fanconi syndrome and liver disease. While the association of rare functionally damaging HNF1A variants with HNF1A-MODY and type 2 diabetes is well established owing to robust functional assays, the impact of HNF4A variants on HNF-4A transactivation in tissues including the liver and kidney is less known, due to lack of similar assays. Our aim was to investigate the functional effects of seven HNF4A variants, located in the HNF-4A DNA binding domain and associated with different clinical phenotypes, by various functional assays and cell lines (transactivation, DNA binding, protein expression, nuclear localization) and in silico protein structure analyses. Variants R85W, S87N and R89W demonstrated reduced DNA binding to the consensus HNF-4A binding elements in the HNF1A promoter (35, 13 and 9%, respectively) and the G6PC promoter (R85W ~10%). While reduced transactivation on the G6PC promoter in HepG2 cells was shown for S87N (33%), R89W (65%) and R136W (35%), increased transactivation by R85W and R85Q was confirmed using several combinations of target promoters and cell lines. R89W showed reduced nuclear levels. In silico analyses supported variant induced structural impact. Our study indicates that cell line specific functional investigations are important to better understand HNF4A-MODY genotype–phenotype correlations, as our data supports ACMG/AMP interpretations of loss-of-function variants and propose assay-specific HNF4A control variants for future functional investigations.
Sweden, NATO and the gendered silencing of feminist foreign policy
Authors: Wright Katharine A M , Rosamond Annika Bergman 
Published: March 2024

Abstract
Sweden was the first state to adopt a Feminist Foreign Policy (FFP) in 2014, drawing on its state feminist tradition and support for the United Nations' Women, Peace and Security (WPS) agenda. Yet following the full-scale Russian invasion of Ukraine in February 2022 and Sweden's move to seek NATO membership—abandoning its policy of non-alignment—a gendered silence on FFP pervaded. Significantly, this therefore predated the official abandonment of FFP following the election of a new government in October 2022. NATO membership was viewed as incompatible with FFP. Yet, NATO has long sought to project itself as a gender-just actor, including through engagement with the WPS agenda culminating in its inclusion in the 2022 Strategic Concept. Further, Sweden—as a NATO partner—had been a stalwart of the alliance's work on WPS. This article contributes to understanding the role of gendered silences in shaping strategic narratives, in this case concerning Sweden's NATO membership bid. It provides insight for policy-makers and diplomats on the impact gendered silence can have on the wider efficacy of FFP and WPS, even during processes such as NATO enlargement which might otherwise be viewed as ‘gender neutral’, particularly when imbued with urgency.
How peacekeeping has reshaped Latin America
Authors: Jenne Nicole 
Published: March 2024

Abstract
The United Nations Stabilization Mission in Haiti (MINUSTAH, 2004–2017) was an unprecedented effort of Latin American peacekeeping. Nine countries contributed the majority of troops to the mission in which regional governments sought to handle a security crisis in their neighbourhood rather than leaving the lead to western countries. However, when the mission came to an end after thirteen years, peacekeeping faded from the regional and national security agendas, with the exception of Uruguay. How and why did MINUSTAH impact the region's current hesitation to engage in peace operations? To answer this question, the article draws on assemblage theory and uses data from policy documents, academic literature and previous research on peacekeeping in Latin America. I argue that contrary to what Latin America's current, limited peacekeeping engagement suggests, MINUSTAH produced significant changes in the region's political landscape. While these could have paved the way to greater involvement in peace operations, however, parallel developments shaped Latin American security policies and military planning at the expense of the region's future participation in UN peacekeeping. The article adds to existing scholarship by probing the conditions that drive the temporality of assemblages and provides a new perspective on Latin American peacekeeping.
Arbuscular mycorrhizae status of host plant affects offspring’s phenotype and transcriptome expression in a low-phosphorus environment
Authors: Liu Shijun , Xu Jing , Huang Hong , Tang Jianjun , Chen Xin 
Published: March 2024

Abstract
Although the effects of arbuscular mycorrhizal fungi (AMF) on host plants have been well documented, whether the effects of AMF on parental generations affect offspring performance is not fully clear. We conducted a common garden experiment to determine whether AMF status of host plants (Medicago truncatula) affects phenotype and transcriptome expression of their offspring. Seeds from four type parental treatments (low-phosphorus (P) soil without AMF, low-P soil with AMF, high-P soil without AMF and high-P soil with AMF) were grown under low-P (LPS) and normal-P soil (OHS) conditions. The flowering pattern of LP offspring was similar to their parents, such that plants with AMF flowered earlier than those without AMF under OHS condition but were opposite under LPS condition. The transcriptome differential analysis showed that some differential transcripts (45 for parental plants growing under low-P condition and 3 for parental plants growing under high-P condition) expression patterns between offspring were comparable, and that only affected by parental AMF status regardless of the P environment that offspring was grown. Others (146 for parental plants growing under low-P condition and 2 for parental plants growing under high-P condition), however, were affected both by the parental AMF status and the offspring P environment. In addition, the number of differential transcripts between offspring whose parental plants grew under high-P condition was far less than under low-P condition. These results indicate that AMF may not only affect the current generation of host plants but also affect the offspring especially when their parents have experienced a stressful environment.
Estimating the size of undeclared work from partially misclassified survey data via the Expectation–Maximization algorithm
Authors: Arezzo Maria Felice , Guagnano Giuseppina , Vitale Domenico 
Published: March 2024

Abstract
Undeclared work (UW) is pervasive in economies. This explains the interest of public authorities in knowing its size and drivers. Unfortunately, this is a very complex task because several issues often arise in the collected data, due to the sensitivity of the topic. In sample surveys, one major problem is misclassification. Without appropriate adjustments, inference would provide biased estimates, the reason being the concealing of undeclared status. In order to overcome such problem, we developed a methodology based on a Expectation–Maximization algorithm that accounts for misclassification due to dishonest answering. Through the proposed approach, we are able to estimate the prevalence of UW and its determinants. The reliability of the methodology is validated through an extensive simulation study. An application to the Special Eurobarometer survey no. 402 on UW is provided.
Illuminating stomatal responses to red light: establishing the role of Ci-dependent versus -independent mechanisms in control of stomatal behaviour
Authors: Taylor Georgia , Walter Julia , Kromdijk Johannes 
Published: March 2024

Abstract
The stomatal response to red light appears to link stomatal conductance (gs) with photosynthetic rates. Initially, it was suggested that changes in intercellular CO2 concentration (Ci) provide the main cue via a Ci-dependent response. However, evidence for Ci-independent mechanisms suggests an additional, more direct relationship with photosynthesis. While both Ci-dependent and -independent mechanisms clearly function in stomatal red light responses, little is known regarding their relative contribution. The present study aimed to quantify the relative magnitude of Ci-dependent and -independent mechanisms on the stomatal red light response, to characterize their interplay and to assess the putative link between plastoquinone redox state and Ci-independent stomatal responses. Red light response curves measured at a range of Ci values for wild-type Arabidopsis (Col-0) and the CO2 hyposensitive mutant ca1ca4 allowed deconvolution of Ci-dependent and -independent pathways. Surprisingly, we observed that both mechanisms contribute equally to stomatal red light responses, but Ci-independent stomatal opening is suppressed at high Ci. The present data are also consistent with the involvement of the plastoquinone redox state in coordinating the Ci-independent component. Overall, it seems that while Ci-independent mechanisms are distinct from responses to Ci, interplay between these two pathways is important to facilitate effective coordination between gs and photosynthesis.
FLOWERING LOCUS T-mediated thermal signalling regulates age-dependent inflorescence development in Arabidopsis thaliana
Authors: González-Suárez Pablo , Walker Catriona H , Lock Thomas , Bennett Tom 
Published: March 2024

Abstract
Many plants show strong heteroblastic changes in the shape and size of organs as they transition from juvenile to reproductive age. Most attention has been focused on heteroblastic development in leaves, but we wanted to understand heteroblastic changes in reproductive organ size. We therefore studied the progression of reproductive development in the model plant Arabidopsis thaliana, and found strong reductions in the size of flowers, fruit, seed, and internodes during development. These did not arise from correlative inhibition by older fruits, or from changes in inflorescence meristem size, but seemed to stem from changes in the size of floral organ primordia themselves. We hypothesized that environmental conditions might influence this heteroblastic pattern and found that the ambient temperature during organ initiation strongly influences organ size. We show that this temperature-dependent heteroblasty is dependent on FLOWERING LOCUS T (FT)-mediated signal integration, adding to the repertoire of developmental processes regulated by this pathway. Our results demonstrate that rising global temperatures will not affect just fertility, as is widely described, but also the size and seed number of fruits produced. However, we also show that such effects are not hard-wired, and that selective breeding for FT expression during reproductive development could mitigate such effects.
Integrating multi-modal imaging in radiation treatments for glioblastoma
Authors: Breen William G , Aryal Madhava P , Cao Yue , Kim Michelle M 
Published: March 2024

Abstract
Advances in diagnostic and treatment technology along with rapid developments in translational research may now allow the realization of precision radiotherapy. Integration of biologically informed multimodality imaging to address the spatial and temporal heterogeneity underlying treatment resistance in glioblastoma is now possible for patient care, with evidence of safety and potential benefit. Beyond their diagnostic utility, several candidate imaging biomarkers have emerged in recent early-phase clinical trials of biologically based radiotherapy, and their definitive assessment in multicenter prospective trials is already in development. In this review, the rationale for clinical implementation of candidate advanced magnetic resonance imaging and positron emission tomography imaging biomarkers to guide personalized radiotherapy, the current landscape, and future directions for integrating imaging biomarkers into radiotherapy for glioblastoma are summarized. Moving forward, response-adaptive radiotherapy using biologically informed imaging biomarkers to address emerging treatment resistance in rational combination with novel systemic therapies may ultimately permit improvements in glioblastoma outcomes and true individualization of patient care.
Establishing the relationship between wildfire smoke and performance metrics on finished beef cattle in Western Rangelands
Authors: Macias Franco Arturo , Elins Moreira da Silva Aghata , Holton Graham , Brody Tio , Alves Fonseca Mozart 
Published: March 2024

Abstract
Identifying causal relationships is complicated. Researchers usually overlook causality behind relationships which can generate misleading associations. Herein, we carefully examine the parametric relationship and causality between wildfire smoke exposure and animal performance and behavior metrics over a period of 2 yr in Reno, Nevada. The animals in the 2020 smoke season were grain-finished (n = 12) and grass-finished (n = 12), whereas the animals during the 2021 season were fed under the same diet but finished with either a hormonal implant (n = 9), or without (n = 9). The dataset included daily records of feed intake (FI), body weight (BW), water intake (WI), average daily gain (ADG), and WI behavior (time spent drinking [TSD]; water intake events [WIE]; no-WIE [NWIE]). Variable tree length Bayesian additive regression trees (BART) were utilized to investigate the relationships between air quality index (AQI), particulate matter 2.5 μm (PM2.5) and 10 μm (PM10), NO2, SO2, Ozone, and CO levels in the air (sensors &lt; 1.6 km from animals) with the animal data. Additionally, linear mixed models with a 7-d lag were used to evaluate parametric relationships among the same variables. All statistical analyses were performed on R Statistical Software (R Core Team 2023). Under the linear mixed model with a 7-d lag, significant positive and negative associations were found for all parameters examined (P &lt; 0.05). Negative associations were found between FI, WI, ADG, BW, WIE, NWIE, TSD, and PM2.5 (P &lt; 0.05) for at least one animal group. Positive linear associations between wildfire smoke parameters and the metrics evaluated were more variable and dependent on year, treatment, and smoke parameters. When examining the credible intervals and the variable importance in the BART, relationships were more difficult to identify. However, some associations were found for Ozone, AQI, NO2, CO, and PM10 (P &lt; 0.05). Overall, our results carefully examine the relationship between smoke parameters and cattle performance and present interesting pathways previously unexplored that could guide early culling/finishing of animals to avoid economic losses associated with performance decrease in response to wildfire smoke exposure. Though interesting associations are found under linear mixed models, causality is difficult to establish, which highlights the need for controlled exposure experiments.