bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rib segmentation in chest x-ray images based on unsupervised domain adaptation
Authors: Zhao Jialin , Nie Ziwei , Shen Jie , He Jian , Yang Xiaoping 
Published: December 2023

Abstract
Rib segmentation in 2D chest x-ray images is a crucial and challenging task. On one hand, chest x-ray images serve as the most prevalent form of medical imaging due to their convenience, affordability, and minimal radiation exposure. However, on the other hand, these images present intricate challenges including overlapping anatomical structures, substantial noise and artifacts, inherent anatomical complexity. Currently, most methods employ deep convolutional networks for rib segmentation, necessitating an extensive quantity of accurately labeled data for effective training. Nonetheless, achieving precise pixel-level labeling in chest x-ray images presents a notable difficulty. Additionally, many methods neglect the challenge of predicting fractured results and subsequent post-processing difficulties. In contrast, CT images benefit from being able to directly label as the 3D structure and patterns of organs or tissues. In this paper, we redesign rib segmentation task for chest x-ray images and propose a concise and efficient cross-modal method based on unsupervised domain adaptation with centerline loss function to prevent result discontinuity and address rigorous post-processing. We utilize digital reconstruction radiography images and the labels generated from 3D CT images to guide rib segmentation on unlabeled 2D chest x-ray images. Remarkably, our model achieved a higher dice score on the test samples and the results are highly interpretable, without requiring any annotated rib markings on chest x-ray images. Our code and demo will be released in ‘https://github.com/jialin-zhao/RibsegBasedonUDA’.
Inward particle transport driven by biased endplate in a cylindrical magnetized plasma
Authors: GE 盖 Yue 跃 , XU 徐 Tianchao 田超 , XIAO 肖 Chijie 池阶 , GUO 郭 Zhibin 志彬 , WANG 王 Xiaogang 晓钢 , HE 何 Renchuan 任川 , YANG 杨 Xiaoyi 肖易 , ZHANG 张 Zuyu 祖煜 , YUAN 袁 Ruixin 瑞鑫 
Published: December 2023

Abstract
The inward particle transport is associated with the formation of peaked density profiles, which contributes to improve the fusion rate and the realization of steady-state discharge. The active control of inward particle transport is considered as one of the most critical issues of magnetic confinement fusion. Recently, it is realized preliminarily by adding a biased endplate in the Peking University Plasma Test (PPT) device. The results reveal that the inward particle flux increases with the bias voltage of the endplate. It is also found that the profile of radial electric field (

) shear is flattened by the increased bias voltage. Radial velocity fluctuations affect the inward particle more than density fluctuations, and the frequency of the dominant mode driving inward particle flux increases with the biased voltage applied to the endplate. The experimental results in the PPT device provide a method to actively control the inward particle flux using a biased endplate and enrich the understanding of the relationship between

shear and turbulence transport.
HER2/ERBB2 copy number analysis by targeted next-generation sequencing in breast cancer
Authors: Xia Daniel , Kuo Frank , Hughes Melissa , Lindeman Neal , Manning Danielle , Files Janet , Strauss Sarah , Kirkner Greg , Mohammed-Abreu Ayesha , Winer Eric , Tolaney Sara M , Lin Nancy U , Dillon Deborah A 
Published: December 2023

Abstract

Objectives
A combination of immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) is the current standard of care for HER2 evaluation in breast cancer. Here, we investigate the potential clinical utility of next-generation sequencing (NGS)–derived HER2/ERBB2 copy number (CN) data for predicting HER2 status as defined by American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guidelines.

Methods
In total, 294 locally recurrent and metastatic breast cancers previously tested by targeted hybrid capture–based NGS and by HER2 IHC/FISH were included. Analyses focused on the ERBB2 median log2 ratios and start-end genomic coordinates from NGS, average HER2 CN and HER2/CEP17 ratios from FISH, and the HER2 IHC scores. We also determined a more stringent log2 ratio cutoff to predict HER2-positive status with 100% specificity.

Results
Sixty-four (22%) cases were HER2 positive and 230 (78%) were HER2 negative by ASCO/CAP guidelines. The ERBB2 median log2 ratios from NGS strongly correlated with HER2 status by IHC/FISH (area under receiver operator characteristic curve = 0.951). ERBB2 log2 ratio more than 1.7 was 100% specific for HER2-positive results by IHC/FISH. Start and end genomic coordinates for regions of gain near ERBB2 by NGS also predicted HER2 status.

Conclusions
Copy number data from our NGS panel strongly correlate with HER2 status. Using a stringent cutoff, ERBB2 log2 ratio accurately predicts HER2 positivity with high specificity. The NGS CN assessment may have utility in determining HER2 status in certain clinical settings.
Do We Need New Electrocardiographic Criteria for Left Ventricular Hypertrophy? The Case of the Peguero–Lo Presti Criterion. A Narrative Review
Authors: Faggiano Andrea , Gherbesi Elisa , Tadic Marijana , Carugo Stefano , Grassi Guido , Cuspidi Cesare 
Published: December 2023

Abstract
The cardiovascular risk associated with left ventricular hypertrophy (LVH) in the community and, particularly, in the hypertensive fraction of the general population, represents the rationale for its timely and accurate identification in order to implement adequate preventive strategies. Although electrocardiography (ECG) is the first-line and most economical method of diagnosing LVH its accuracy is largely suboptimal. Over the last 70 years, dozens of different ECG criteria, mostly based on measurements of QRS voltages, have been proposed. In this long journey, a few years ago Peguero et al. developed a novel ECG voltage criterion, currently recognized as Peguero–Lo Presti (PLP) suggesting that it has greater sensitivity than traditional ECG-LVH criteria. Considering that in the last 5 years numerous studies have investigated the diagnostic value of this new index, this review aimed to summarize the data published so far on this topic focusing both on the accuracy in identifying the presence of LVH compared with imaging techniques such as echocardiography (ECHO) and magnetic resonance imaging (MRI) and the value in predicting hard outcomes. The evidence in favor of the greater diagnostic accuracy of the PLP criterion in detecting LVH, phenotyped by ECHO or MRI, and in the stratification of hard outcomes compared with traditional ECG criteria does not appear to be sufficiently proven. Given that the diagnosis of LVH by all ECG criteria (including the PLP) exclusively based on the QRS amplitude is largely imprecise, the development of new multiparametric ECG criteria based on artificial intelligence could represent a real improvement in the diagnostic capacity of the ECG.
MBDBMetrics: an online metrics tool to measure the impact of biological data resources
Authors: Insana Giuseppe , Ignatchenko Alex , Martin Maria , Bateman Alex ,   UniProt Consortium, Bateman Alex , Martin Maria-Jesus , Orchard Sandra , Magrane Michele , Ahmad Shadab , Bowler-Barnett Emily H , Bye-A-Jee Hema , Denny Paul , Dogan Tunca , Ebenezer ThankGod , Fan Jun , da Costa Gonzales Leonardo Jose , Hussein Abdulrahman , Ignatchenko Alexandr , Insana Giuseppe , Ishtiaq Rizwan , Joshi Vishal , Jyothi Dushyanth , Kandasaamy Swaathi , Lock Antonia , Luciani Aurelien , Luo Jie , Lussi Yvonne , Raposo Pedro , Rice Daniel L , Saidi Rabie , Santos Rafael , Speretta Elena , Stephenson James , Totoo Prabhat , Tyagi Nidhi , Vasudev Preethi , Warner Kate , Zaru Rossana , Wijerathne Supun , Ibrahim Khawaja Talal , Kim Minjoon , Marin Juan , Bridge Alan J , Aimo Lucila , Argoud-Puy Ghislaine , Auchincloss Andrea H , Axelsen Kristian B , Bansal Parit , Baratin Delphine , Batista Neto Teresa M , Bolleman Jerven T , Boutet Emmanuel , Breuza Lionel , Gil Blanca Cabrera , Casals-Casas Cristina , Coudert Elisabeth , Cuche Beatrice , de Castro Edouard , Estreicher Anne , Famiglietti Maria L , Feuermann Marc , Gasteiger Elisabeth , Gehant Sebastien , Gos Arnaud , Gruaz Nadine , Hulo Chantal , Hyka-Nouspikel Nevila , Jungo Florence , Kerhornou Arnaud , Mercier Philippe Le , Lieber-herr Damien , Masson Patrick , Morgat Anne , Pedruzzi Ivo , Pilbout Sandrine , Pourcel Lucille , Poux Sylvain , Pozzato Monica , Pruess Manuela , Redaschi Nicole , Rivoire Catherine , Sigrist Christian J A , Sundaram Shya-mala , Sveshnikova Anastasia , Wu Cathy H , Arighi Cecilia N , Chen Chuming , Chen Yongxing , Huang Hongzhan , Laiho Kati , Leh-vaslaiho Minna , McGarvey Peter , Natale Darren A , Ross Karen , Vinayaka C R , Wang Yuqi , Zhang Jian 
Published: December 2023

Abstract

Motivation
There now exist thousands of molecular biology databases covering every aspect of biological data. This database infrastructure takes significant effort and funding to develop and maintain. The creators of these databases need to make strong justifications to funders to prove their impact or importance. There are many publication metrics and tools available such as Google Scholar to measure citation impact or AltMetrics covering multiple measures including social media coverage.

Results
In this article, we describe a series of novel impact metrics that have been applied initially to the UniProt database, and now made available via a Google Colab to enable any molecular biology resource to gain several additional metrics. These metrics, powered by freely available APIs from Europe PubMedCentral and SureCHEMBL cover mentions of the resource in full text articles, including which section of the paper the mention occurs in, grant acknowledgements and mentions in patent applications. This tool, that we call MBDBMetrics, is a useful adjunct to existing tools.

Availability and implementation
The MBDBMetrics tool is available at the following locations: https://colab.research.google.com/drive/1aEmSQR9DGQIZmHAIuQV9mLv7Mw9Ppkin and https://github.com/g-insana/MBDBMetrics.
Alcohol reduces choosiness and relaxes mate preferences in female Drosophila simulans
Authors: Archer C Ruth , Alper Cleo , Mack Laura , Weedon Melanie , Sharma Manmohan D , Sutter Andreas , Hosken David J 
Published: December 2023

Abstract
Alcohol can alter sexual behaviour. However, our understanding of alcohol’s effects on sexual interactions is limited because males are usually the focus of nonhuman studies. Alcohol could in theory alter female mate-choice and, in turn, affect sexual selection, a major mechanism of evolution. Here we tested whether alcohol exposure affected female mate-preference, choosiness, and copulation duration in the fly Drosophila simulans, while simultaneously testing for genetic variation in these effects. We found that alcohol exposure did not affect copulation duration, but did weaken mate-preference, as females copulated with a broader range of males after exposure, and it tended to reduce female choosiness as females mated more quickly. Although female genotype significantly affected copulation duration and choosiness, the effects of alcohol appeared to be reasonably consistent across genotypes, but this depended on the analysis employed. Nonetheless, alcohol reduced female choosiness and weakened mate-preference, and may therefore reduce the strength of sexual selection. Testing whether these changes impact female fitness is now required.
Cortical resting motor threshold difference in asleep-awake craniotomy for motor eloquent gliomas: WHO grading influences motor pathway excitability
Authors: Pescador Ana M , Lavrador José P , Baamonde Alba D , Soumpasis Christos , Ghimire Prajwal , Mosquera José D S , Fiandeiro Carlos , Jones Holly , Gosavi Smita , Lejarde Arjel , Lawson Emily , Murace Sian , Gullan Richard , Ashkan Keyoumars , Bhangoo Ranjeev , Vergani Francesco 
Published: December 2023

Abstract
Developing neurophysiological tools to predict WHO tumor grade can empower the treating teams for a better surgical decision-making process. A total of 38 patients with supratentorial diffuse gliomas underwent an asleep-awake-sedated craniotomies for tumor removal with intraoperative neuromonitoring. The resting motor threshold was calculated for different train stimulation paradigms during awake and asleep phases. Receiver operating characteristic analysis and Bayesian regression models were performed to analyze the prediction of tumor grading based on the resting motor threshold differences. Significant positive spearman correlations were observed between resting motor threshold excitability difference and WHO tumor grade for train stimulation paradigms of 5 (R = 0.54, P = 0.00063), 4 (R = 0.49, P = 0.002), 3 (R = 0.51, P = 0.001), and 2 pulses (R = 0.54, P = 0.0007). Kruskal–Wallis analysis of the median revealed a positive significant difference between the median of excitability difference and WHO tumor grade in all paradigms. Receiver operating characteristic analysis showed 3 mA difference as the best predictor of high-grade glioma across different patterns of motor pathway stimulation. Bayesian regression found that an excitability difference above 3 mA would indicate a 75.8% probability of a glioma being high grade. Our results suggest that cortical motor excitability difference between the asleep and awake phases in glioma surgery could correlate with tumor grade.
Myocardial protection in cardiac surgery—hindsight from the 2020s
Authors: Mukharyamov Murat , Schneider Ulrich , Kirov Hristo , Caldonazo Tulio , Doenst Torsten 
Published: December 2023

Summary

Myocardial protection and specifically cardioplegia have been extensively investigated in the beginnings of cardiac surgery. After cardiopulmonary bypass had become routine, more and more cardiac operations were possible, requiring reliable and reproducible protection for times of blood flow interruptions to the most energy-demanding organ of the body. The concepts of hypothermia and cardioplegia evolved as tools to extend cardiac ischaemia tolerance to a degree considered safe for the required operation. A plethora of different solutions and delivery techniques were developed achieving remarkable outcomes with cross-clamp times of up to 120 min and more. With the beginning of the new millennium, interest in myocardial protection research declined and, as a consequence, conventional cardiac surgery is currently performed using myocardial protection strategies that have not changed in decades. However, the context, in which cardiac surgery is currently performed, has changed during this time. Patients are now older and suffer from more comorbidities and, thus, other organs move more and more into the centre of risk assessment. Yet, systemic effects of cardioplegic solutions have never been in the focus of attention. They say hindsight is always 20–20. We therefore review the biochemical principles of ischaemia, reperfusion and cardioplegic extension of ischaemia tolerance and address the concepts of myocardial protection with ‘hindsight from the 2020s’. In light of rising patient risk profiles, minimizing surgical trauma and improving perioperative morbidity management becomes key today. For cardioplegia, this means accounting not only for cardiac, but also for systemic effects of cardioplegic solutions.
Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize
Authors: Yang Zhikai , Zhao Tianjing , Cheng Hao , Yang Jinliang 
Published: December 2023

Abstract
Root-associated microbiomes in the rhizosphere (rhizobiomes) are increasingly known to play an important role in nutrient acquisition, stress tolerance, and disease resistance of plants. However, it remains largely unclear to what extent these rhizobiomes contribute to trait variation for different genotypes and if their inclusion in the genomic selection protocol can enhance prediction accuracy. To address these questions, we developed a microbiome-enabled genomic selection method that incorporated host SNPs and amplicon sequence variants from plant rhizobiomes in a maize diversity panel under high and low nitrogen (N) field conditions. Our cross-validation results showed that the microbiome-enabled genomic selection model significantly outperformed the conventional genomic selection model for nearly all time-series traits related to plant growth and N responses, with an average relative improvement of 3.7%. The improvement was more pronounced under low N conditions (8.4–40.2% of relative improvement), consistent with the view that some beneficial microbes can enhance N nutrient uptake, particularly in low N fields. However, our study could not definitively rule out the possibility that the observed improvement is partially due to the amplicon sequence variants being influenced by microenvironments. Using a high-dimensional mediation analysis method, our study has also identified microbial mediators that establish a link between plant genotype and phenotype. Some of the detected mediator microbes were previously reported to promote plant growth. The enhanced prediction accuracy of the microbiome-enabled genomic selection models, demonstrated in a single environment, serves as a proof-of-concept for the potential application of microbiome-enabled plant breeding for sustainable agriculture.
A pair of RNA binding proteins inhibit ion transporter expression to maintain lifespan
Authors: Napier-Jameson Rebekah , Marx Olivia , Norris Adam 
Published: December 2023

Abstract
Regulation of lifespan by transcription factors has been well established. More recently, a role for RNA binding proteins (RBPs) in regulating lifespan has also emerged. In both cases, a major challenge is to determine which regulatory targets are functionally responsible for the observed lifespan phenotype. We recently identified a pair of neuronal RBPs, exc-7/ELAVL and mbl-1/Muscleblind, which in Caenorhabditis elegans display synthetic (nonadditive) lifespan defects: single mutants do not affect lifespan, but exc-7; mbl-1 double mutants have strongly reduced lifespan. Such a strong synthetic phenotype represented an opportunity to use transcriptomics to search for potential causative targets that are synthetically regulated. Focus on such genes would allow us to narrow our target search by ignoring the hundreds of genes altered only in single mutants, and provide a shortlist of synthetically regulated candidate targets that might be responsible for the double mutant phenotype. We identified a small handful of genes synthetically dysregulated in double mutants and systematically tested each candidate gene for functional contribution to the exc-7; mbl-1 lifespan phenotype. We identified 1 such gene, the ion transporter nhx-6, which is highly upregulated in double mutants. Overexpression of nhx-6 causes reduced lifespan, and deletion of nhx-6 in an exc-7; mbl-1 background partially restores both lifespan and healthspan. Together, these results reveal that a pair of RBPs mediate lifespan in part by inhibiting expression of an ion transporter, and provide a template for how synthetic phenotypes (including lifespan) can be dissected at the transcriptomic level to reveal potential causative genes.
Lifetime risk of maternal near miss morbidity: a novel indicator of maternal health
Authors: Gazeley Ursula , Polizzi Antonino , Romero-Prieto Julio E , Aburto José Manuel , Reniers Georges , Filippi Veronique 
Published: December 2023

Abstract

Background
The lifetime risk of maternal death quantifies the probability that a 15-year-old girl will die of a maternal cause in her reproductive lifetime. Its intuitive appeal means it is a widely used summary measure for advocacy and international comparisons of maternal health. However, relative to mortality, women are at an even higher risk of experiencing life-threatening maternal morbidity called ‘maternal near miss’ (MNM) events—complications so severe that women almost die. As maternal mortality continues to decline, health indicators that include information on both fatal and non-fatal maternal outcomes are required.

Methods
We propose a novel measure—the lifetime risk of MNM—to estimate the cumulative risk that a 15-year-old girl will experience a MNM in her reproductive lifetime, accounting for mortality between the ages 15 and 49 years. We apply the method to the case of Namibia (2019) using estimates of fertility and survival from the United Nations World Population Prospects along with nationally representative data on the MNM ratio.

Results
We estimate a lifetime risk of MNM in Namibia in 2019 of between 1 in 40 and 1 in 35 when age-disaggregated MNM data are used, and 1 in 38 when a summary estimate for ages 15–49 years is used. This compares to a lifetime risk of maternal death of 1 in 142 and yields a lifetime risk of severe maternal outcome (MNM or death) of 1 in 30.

Conclusions
The lifetime risk of MNM is an urgently needed indicator of maternal morbidity because existing measures (the MNM ratio or rate) do not capture the cumulative risk over the reproductive life course, accounting for fertility and mortality levels.
Optimization of artificial membrane feeding system for lone star ticks, Amblyomma americanum (Acari: Ixodidae), and experimental infection with Rickettsia amblyommatis (Rickettsiales: Rickettsiaceae)
Authors: Rochlin Ilia , Chu Dennis , Gmelin Matthew , Le Justin , Furie Martha B , Thanassi David G , Kim Hwan Keun 
Published: December 2023

Abstract
With the introduction of siliconized artificial membranes, various artificial feeding systems (AFS) for hard ticks (Ixodidae) have been developed over the last decades. Most AFS utilize similar core components but employ diverse approaches, materials, and experimental conditions. Published work describes different combinations of the core components without experimental optimizations for the artificial feeding of different tick species. Amblyomma americanum L., (Acari: Ixodidae) (lone star tick) is a known vector and reservoir for diverse tick-borne pathogens, such as Rickettsia amblyommatis and Ehrlichia chaffeensis. Ongoing environmental changes have supported the expansion of A. americanum into new habitats, contributing to increased tick-borne diseases in endemic areas. However, a significant knowledge gap exists in understanding the underlying mechanisms involved in A. americanum interactions with tick-borne pathogens. Here, we performed a systematic analysis and developed an optimized AFS for nymphal lone star ticks. Our results demonstrate that Goldbeater’s membranes, rabbit hair, hair extract, and adult lone star ticks significantly improved the attachment rate of nymphal ticks, whereas tick frass and frass extract did not. With the optimized conditions, we achieved an attachment rate of 46 ± 3% and a success rate of 100% (i.e., one or more attached ticks) in each feeding experiment for nymphal lone star ticks. When fed on sheep blood spiked with R. amblyommatis, both nymphal and adult lone star ticks acquired and maintained R. amblyommatis, demonstrating the feasibility of studying A. americanum–pathogen interactions using AFS. Our study can serve as a roadmap to optimize and improve AFS for other medically relevant tick species.