bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fast approach to determine excitation eigenfrequencies for TD-EIT and FD-EIT
Authors: Li Yang , Wang Nan , Fan Li-Feng , Wang Yong-Qian , Zhao Peng-Fei , Huang Lan , Wang Zhong-Yi 
Published: July 2023

Abstract
Electrical impedance tomography can reconstruct the complex conductivity distribution by injecting a current or voltage at a specific frequency into the target domain. The complex conductivity spectroscopy of numerous biological tissues is frequency-dependent. A suitable excitation frequency is vital to high-quality imaging over a wide frequency range. This paper investigates the relationship between the parameters of the biological tissue impedance model and the impedance spectroscopy. A frequency selection method based on the impedance spectroscopy is proposed, in which the impedance spectroscopy on a specific electrode at the domain boundary to be measured is first scanned. In TD-EIT, the difference between the target’s impedance spectroscopy and the null field is calculated, and the frequency corresponding to its extreme value is used as the excitation signal for TD-EIT. The excitation frequency in FD-EIT is the frequency corresponding to the extreme point in the target impedance spectroscopy, and we have also used this method to image the interior of the maize ear. This study provides a quick and efficient method for determining the excitation frequency for EIT, allowing researchers to find the best excitation frequency for high-quality imaging during actual measurements.
ZnO nanoparticles-copper metal-organic framework composite on 3D porous nickel foam: a novel electrochemical sensing platform to detect serotonin in blood serum
Authors: Mukundan Gopika , Ganapathy Nagarajan , Badhulika Sushmee 
Published: July 2023

Abstract
Herein, we report a simple non-enzymatic electrochemical sensor for the detection of serotonin (5-HT) in blood serum using ZnO oxide nanoparticles-copper metal-organic framework (MOF) composite on 3D porous nickel foam, namely, ZnO-Cu MOF/NF. The x-ray diffraction analysis reveals the crystalline nature of synthesized Cu MOF and Wurtzite structure of ZnO nanoparticles, whereas SEM characterization confirms the high surface area of the composite nanostructures. Differential pulse voltammetry analysis under optimal conditions yields a wide linear detection range of 1 ng ml−1 to 1 mg ml−1 to 5-HT concentrations and a LOD (signal to noise ratio = 3.3) of 0.49 ng ml−1, which is well below the lowest physiological concentration of 5-HT. The sensitivity of the fabricated sensor is found to be 0.0606 mA ng−1 ml−1.cm2, and it exhibited remarkable selectivity towards serotonin in the presence of various interferants, including dopamine and AA, which coexist in the real biological matrix. Further, successful determination of 5-HT is achieved in the simulated blood serum sample with a good recovery percentage from ∼102.5% to ∼99.25%. The synergistic combination of the excellent electrocatalytic properties and surface area of the constituent nanomaterials proves the overall efficacy of this novel platform and shows immense potential to be used in developing versatile electrochemical sensors.
The role of imaging in the selection of patients for HFpEF therapy
Authors: Baron Tomasz , Gerovasileiou Spyridon , Flachskampf Frank A 
Published: July 2023

Abstract
Heart failure with preserved ejection fraction (HFpEF) traditionally has been characterized as a form of heart failure without therapeutic options, in particular with a lack of response to the established therapies of heart failure with reduced ejection fraction (HFrEF). However, this is no longer true. Besides physical exercise, risk factor modification, aldosterone blocking agents, and sodium-glucose cotransporter 2 inhibitors, specific therapies are emerging for specific HFpEF etiologies, such as hypertrophic cardiomyopathy or cardiac amyloidosis. This development justifies increased efforts to arrive at specific diagnoses within the umbrella of HFpEF. Cardiac imaging plays by far the largest role in this effort and is discussed in the following review.
Unusual case report of malignant pheochromocytoma presenting with STEMI
Authors: Demir Muhammed , Özbek Mehmet , Güzel Tuncay , Aktan Adem 
Published: July 2023

Abstract

Background
Pheochromocytomas (PHEOs) are a group of tumours that leads to multiple symptoms and can induce hypercoagulability and promote thrombosis. Pheochromocytomas may also present without elevated serum and urinary markers. We aimed to provide tips and tricks for the diagnostic and therapeutic management of an unusual case of PHEOs.

Case summary
Thirty-four-year-old woman with the unremarkable medical history presented with epigastric pain and dyspnoea. Electrocardiogram showed ST-segment elevation in the inferior limb leads. She underwent an emergency coronary angiogram, which showed a high thrombus burden in the distal right coronary artery. A subsequent echocardiogram demonstrated a 31 × 33 mm right atrial mass adhering to the inferior vena cava and abdominal computed tomography (CT) scan revealed a 113 × 85 mm necrotic mass in the left adrenal bed, with tumour thrombus extending proximally to the confluence of hepatic veins immediately inferior to the right atrium and distally to iliac vein bifurcation. Blood parameters, thrombophilia panel, vanillylmandelic acid, 5 hydroxy indole acetic acid, and homovanillic acid levels were normal. Tissue sampling confirmed the diagnosis of PHEOs. The surgical procedure was not planned due to the presence of metastatic foci on imaging, including positron emission tomography (PET)–CT. Anticoagulation with rivaroxaban and treatment with 177Lu-DOTATATE-based peptide receptor radionuclide therapy (PRRT) was initiated.

Discussion
The coexistence of arterial and venous thrombosis is extremely rare in patients with PHEOs. Multidisciplinary approaches are required for the care of such patients. Catecholamines likely contributed to the development of thrombosis in our patient. Early recognition of PHEOs is the key point to ameliorate clinical outcomes.
One-week Impella CP support for papillary muscle rupture as a bridge to surgery: a case report
Authors: Kawanami Shodai , Egami Yasuyuki , Nishino Masami , Tanouchi Jun 
Published: July 2023

AbstractBackgroundPapillary muscle rupture (PMR) is a catastrophic complication of acute myocardial infarction. However, the best timing and modality of circulatory support for surgery are unknown.Case SummaryA 75-year-old man presented to the emergency room in our hospital for worsening shortness of breath accompanied by chest pain. Transthoracic echocardiograph showed severe mitral regurgitation (MR) with a flail posterior mitral valve leaflet, and coronary angiography demonstrated distal right coronary artery occlusion. We diagnosed as cardiogenic shock due to subacute myocardial infarction and ischaemic PMR. An Impella CP (Abiomed, Danvers, MA, USA) was introduced to improve haemodynamics. Despite the grade of MR was still severe, the mean blood pressure and pulmonary artery pressure improved 4 h after an Impella CP support. At day 8, the patient underwent elective mitral valve replacement with single coronary artery bypass grafting.DiscussionPMR is a rare but lethal complication of acute myocardial infarction. Expeditious surgical treatment offers the optimal chance of survival, but the post-operative mortality or morbidity is very high. Therefore, preoperative stabilization can be closely correlated with outcomes in these patients. It was reported that directly unloading the left ventricle by an Impella decreased wall stress, external work, and myocardial oxygen consumption. Therefore, an Impella can be the most suitable mechanical circulatory support for PMR. In conclusion, Impella CP alone can become one of the suitable bridges to surgery in the patients with PMR.
Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome
Authors: Wagner C Isabel , Kopp Martina E L , Thorburn James , Jones Catherine S , Hoarau Galice , Noble Leslie R 
Published: July 2023

Abstract
Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish's genome, of which 31,979 are functionally annotated.
Deep neural networks with knockoff features identify nonlinear causal relations and estimate effect sizes in complex biological systems
Authors: Fan Zhenjiang , Kernan Kate F , Sriram Aditya , Benos Panayiotis V , Canna Scott W , Carcillo Joseph A , Kim Soyeon , Park Hyun Jung 
Published: July 2023

Abstract

Background
Learning the causal structure helps identify risk factors, disease mechanisms, and candidate therapeutics for complex diseases. However, although complex biological systems are characterized by nonlinear associations, existing bioinformatic methods of causal inference cannot identify the nonlinear relationships and estimate their effect size.

Results
To overcome these limitations, we developed the first computational method that explicitly learns nonlinear causal relations and estimates the effect size using a deep neural network approach coupled with the knockoff framework, named causal directed acyclic graphs using deep learning variable selection (DAG-deepVASE). Using simulation data of diverse scenarios and identifying known and novel causal relations in molecular and clinical data of various diseases, we demonstrated that DAG-deepVASE consistently outperforms existing methods in identifying true and known causal relations. In the analyses, we also illustrate how identifying nonlinear causal relations and estimating their effect size help understand the complex disease pathobiology, which is not possible using other methods.

Conclusions
With these advantages, the application of DAG-deepVASE can help identify driver genes and therapeutic agents in biomedical studies and clinical trials.
Training Infrastructure as a Service
Authors: Rasche Helena , Hyde Cameron , Davis John , Gladman Simon , Coraor Nate , Bretaudeau Anthony , Cuccuru Gianmauro , Bacon Wendi , Serrano-Solano Beatriz , Hillman-Jackson Jennifer , Hiltemann Saskia , Zhou Miaomiao , Grüning Björn , Stubbs Andrew 
Published: July 2023

Abstract

Background
Hands-on training, whether in bioinformatics or other domains, often requires significant technical resources and knowledge to set up and run. Instructors must have access to powerful compute infrastructure that can support resource-intensive jobs running efficiently. Often this is achieved using a private server where there is no contention for the queue. However, this places a significant prerequisite knowledge or labor barrier for instructors, who must spend time coordinating deployment and management of compute resources. Furthermore, with the increase of virtual and hybrid teaching, where learners are located in separate physical locations, it is difficult to track student progress as efficiently as during in-person courses.

Findings
Originally developed by Galaxy Europe and the Gallantries project, together with the Galaxy community, we have created Training Infrastructure-as-a-Service (TIaaS), aimed at providing user-friendly training infrastructure to the global training community. TIaaS provides dedicated training resources for Galaxy-based courses and events. Event organizers register their course, after which trainees are transparently placed in a private queue on the compute infrastructure, which ensures jobs complete quickly, even when the main queue is experiencing high wait times. A built-in dashboard allows instructors to monitor student progress.

Conclusions
TIaaS provides a significant improvement for instructors and learners, as well as infrastructure administrators. The instructor dashboard makes remote events not only possible but also easy. Students experience continuity of learning, as all training happens on Galaxy, which they can continue to use after the event. In the past 60 months, 504 training events with over 24,000 learners have used this infrastructure for Galaxy training.
Beyond demonstrations: implementing a primary care hybrid payment model in Medicare
Authors: Berenson Robert A , Shartzer Adele , Pham Hoangmai H 
Published: July 2023

Abstract
The National Academies of Sciences, Engineering, and Medicine's (NASEM’s) 2021 report on primary care called for a hybrid payment approach—a mix of fee-for-service and population-based payment—with performance accountability to strike the proper balance for desired practice transformation and to support primary care's important and expanding role. The NASEM report also proposed substantial increases to primary care payment and reforms to the Medicare Physician Fee Schedule. This paper addresses pragmatic ways to implement these recommendations, describing and proposing solutions to the main implementation challenges. The urgent need for primary care payment reform calls for adopting a hybrid model within the Medicare fee schedule rather than engaging in another round of demonstrations, despite legal and practical obstacles to adoption. The paper explores reasons for adopting a roughly 50:50 blend of fee-for-service and population-based payment and addresses other design features, presenting reasons why spending accountability should rely on utilization measures under primary care control rather than performance on total cost of care, and proposes a fresh approach to quality, emphasizing that quality measures should be parsimonious, focused on important outcomes with demonstrated quality improvement.
South Korea's role conceptions and the liberal international order
Authors: Ryu Yongwook 
Published: July 2023

Abstract
Despite South Korea's general support of the liberal international order (LIO), its actions often deviate from or weaken the practices and values of the LIO. Applying role theory, the article argues that this apparent contradiction in South Korea's foreign policy arises from a situation of role conflict due to its multiple and conflicting role conceptions. Following an analysis of leaders’ speeches and official policy statements, the article contends that it is the interpretation of the past, not just the past per se, that matters for role conception and contestation. For South Korea, the experience and differing interpretations of the Korean War have simultaneously produced both LIO-supporting role conceptions (‘responsible international citizen’, ‘middle power’ and ‘global pivotal state’) and LIO-deviating or weakening roles (‘US ally’, ‘balancer’ and ‘independent nation’), thereby causing role conflict and inconsistency in the country's foreign policy behavior. The latter roles push Seoul either toward a more realist, alliance-based form of order or causes it to focus more exclusively on the Korean peninsula order, which emphasizes independence and inter-Korean unity. Based on these insights, the article suggests that it is imperative to minimize domestic dissensus on the interpretation of critical historical events, in order to avoid potential role conflict and to promote consistency in foreign policy.
Strongman politics and China's foreign policy actors: maritime assertiveness under Xi Jinping
Authors: Miura Kacie 
Published: July 2023

Abstract
Since Xi Jinping's ascension to power, China's foreign policy behaviour—including in the maritime domain—has become increasingly assertive. While a number of systemic, domestic and individual-level factors have contributed to China's more muscular approach, adequately understanding the dramatic intensification of its assertiveness under Xi requires a careful examination of the foreign policy implications of his strongman rule. This article contributes to such studies by examining how Xi's efforts to consolidate power, particularly through nationalistic appeals and an anti-corruption campaign, have mobilized China's foreign policy actors. I argue that the political environment that Xi has fostered shapes the career incentives of individual actors, motivating them to demonstrate their loyalty through displays of assertiveness. Drawing on a case-study of China's maritime actors, with a focus on their behaviour in the South China Sea, I show how Xi's consolidation of power has elevated the stakes of zealously showcasing support for his call to ‘resolutely safeguard’ China's sovereignty claims. I find that Xi's emphasis on demonstrations of loyalty often comes at the cost of other interests, such as reassuring potential rivals, suggesting that the current political environment risks pushing foreign policy in an even more assertive direction than perhaps intended.
Mean disease alleviation between surgery and continuous positive airway pressure in matched adults with obstructive sleep apnea
Authors: Every James D , Mackay Stuart G , Sideris Anders W , Do Timothy Q , Jones Andrew , Weaver Edward M 
Published: July 2023

Abstract

Study Objectives
Polysomnography parameters measure treatment efficacy for obstructive sleep apnea (OSA), such as reduction in apnea–hypopnea index (AHI). However, for continuous positive airway pressure (CPAP) therapy, polysomnography measures do not factor in adherence and thus do not measure effectiveness. Mean disease alleviation (MDA) corrects polysomnography measures for CPAP adherence and was used to compare treatment effectiveness between CPAP and multilevel upper airway surgery.

Methods
This retrospective cohort study consisted of a consecutive sample of 331 patients with OSA managed with multilevel airway surgery as second-line treatment (N = 97) or CPAP (N = 234). Therapeutic effectiveness (MDA as % change or as corrected change in AHI) was calculated as the product of therapeutic efficacy (% or absolute change in AHI) and adherence (% time on CPAP of average nightly sleep). Cardinality and propensity score matching was utilized to manage confounding variables.

Results
Surgery patients achieved greater MDA % than CPAP users (67 ± 30% vs. 60 ± 28%, p = 0.04, difference 7 ± 3%, 95% confidence interval 4% to 14%) in an unmatched comparison, despite a lower therapeutic efficacy seen with surgery. Cardinality matching demonstrated comparable MDA % in surgery (64%) and CPAP (57%) groups (p = 0.14, difference 8 ± 5%, 95% confidence interval −18% to 3%). MDA measured as corrected change in AHI showed similar results.

Conclusions
In adult patients with OSA, multilevel upper airway surgery and CPAP provide comparable therapeutic effectiveness on polysomnography. For patients with inadequate CPAP use, surgery should be considered.
Short-Term Clinical Response and Changes in the Fecal Microbiota and Metabolite Levels in Patients with Crohn’s Disease After Stem Cell Infusions
Authors: Yang Fan , Zheng Xiaofang , Liang Weicheng , Ni Beibei , Lu Jianxi , Liu Qiuli , Xu Ruixuan , He Yizhan , Yee Waye Mary Miu , Zhang Qi , Chen Yufeng , Zou Xiaoguang , Chen Wenjie 
Published: July 2023

Abstract
Recent studies have shown a close relationship between the gut microbiota and Crohn’s disease (CD). This study aimed to determine whether mesenchymal stem cell (MSC) treatment alters the gut microbiota and fecal metabolite pathways and to establish the relationship between the gut microbiota and fecal metabolites. Patients with refractory CD were enrolled and received 8 intravenous infusions of MSCs at a dose of 1.0 × 106 cells/kg. The MSC efficacy and safety were evaluated. Fecal samples were collected, and their microbiomes were analyzed by 16S rDNA sequencing. The fecal metabolites at baseline and after 4 and 8 MSC infusions were identified by liquid chromatography-mass spectrometry (LC--MS). A bioinformatics analysis was conducted using the sequencing data. No serious adverse effects were observed. The clinical symptoms and signs of patients with CD were substantially relieved after 8 MSC infusions, as revealed by changes in weight, the CD activity index (CDAI) score, C-reactive protein (CRP) level, and erythrocyte sedimentation rate (ESR). Endoscopic improvement was observed in 2 patients. A comparison of the gut microbiome after 8 MSC treatments with that at baseline showed that the genus Cetobacterium was significantly enriched. Linoleic acid was depleted after 8 MSC treatments. A possible link between the altered Cetobacterium abundance and linoleic acid metabolite levels was observed in patients with CD who received MSCs. This study enabled an understanding of both the gut microbiota response and bacterial metabolites to obtain more information about host-gut microbiota metabolic interactions in the short-term response to MSC treatment.
Transplantation of hESCs-Derived Neural Progenitor Cells Alleviates Secondary Damage of Thalamus After Focal Cerebral Infarction in Rats
Authors: Li Kongping , Peng Linhui , Xing Qi , Zuo Xialin , Huang Wenhao , Zhan Lixuan , Li Heying , Sun Weiwen , Zhong Xiaofen , Zhu Tieshi , Pan Guangjin , Xu En 
Published: July 2023

Abstract
Human embryonic stem cells-derived neural progenitor cells (hESCs-NPCs) transplantation holds great potential to treat stroke. We previously reported that delayed secondary degeneration occurs in the ventroposterior nucleus (VPN) of ipsilateral thalamus after distal branch of middle cerebral artery occlusion (dMCAO) in adult male Sprague-Dawley (SD) rats. In this study, we investigate whether hESCs-NPCs would benefit the neural recovery of the secondary damage in the VPN after focal cerebral infarction. Permanent dMCAO was performed with electrocoagulation. Rats were randomized into Sham, dMCAO groups with or without hESCs-NPCs treatment. HESCs-NPCs were engrafted into the peri-infarct regions of rats at 48 h after dMCAO. The transplanted hESCs-NPCs survive and partially differentiate into mature neurons after dMCAO. Notably, hESCs-NPCs transplantation attenuated secondary damage of ipsilateral VPN and improved neurological functions of rats after dMCAO. Moreover, hESCs-NPCs transplantation significantly enhanced the expression of BDNF and TrkB and their interaction in ipsilateral VPN after dMCAO, which was reversed by the knockdown of TrkB. Transplantated hESCs-NPCs reconstituted thalamocortical connection and promoted the formation of synapses in ipsilateral VPN post-dMCAO. These results suggest that hESCs-NPCs transplantation attenuates secondary damage of ipsilateral thalamus after cortical infarction, possibly through activating BDNF/TrkB pathway, enhancing thalamocortical projection, and promoting synaptic formation. It provides a promising therapeutic strategy for secondary degeneration in the ipsilateral thalamus post-dMCAO.