bluuebunny/crossref_metadata_2025_split huggingface dataset:
RECOVERY OF ENDOTHELIOPATHY AT 24 HOURS IN AN ESTABLISHED MOUSE MODEL OF HEMORRHAGIC SHOCK AND TRAUMA
Authors: Barry Mark , Trivedi Alpa , Vivona Lindsay R. , Chui Jenna , Pathipati Praneeti , Miyazawa Byron , Pati Shibani 
Published: October 2022

ABSTRACT

Introduction
The endotheliopathy of trauma develops early after injury and consists of increased vascular permeability, inflammation, and dysfunctional coagulation. Persistence of these abnormalities ultimately leads to multi-organ failure. We hypothesized that extending an established 3-hour acute mouse model of hemorrhagic shock and trauma (HS/T) to a 24-hour survival model would allow for evaluation of persistent endotheliopathy and organ injury after HS/T.

Methods
Adult male C57BL/6 J mice underwent laparotomy, femoral artery cannulation, and blood withdrawal to induce HS to a mean arterial pressure of 35 mmHg for 90 minutes. Mice were resuscitated with either lactated Ringer’s (LR) or fresh frozen plasma (FFP). Vascular permeability in the lung and gut were assessed by measuring extravasation of a fluorescent dextran dye. Lungs were evaluated for histopathologic injury, and immunofluorescent staining was used to evaluate intercellular junction integrity. Pulmonary inflammatory gene expression was evaluated using NanoString (Seattle, WA). All endpoints were evaluated at both 3 and 24 hours after initiation of shock.

Results
LR- and FFP-treated mice had an equal mortality rate of 17% in the 24-hour model. LR-treated mice demonstrated increased vascular permeability in the lung and gut at 3 hours compared to sham mice (lung p < .01; gut p < .001), which was mitigated by FFP treatment (lung p < .05; gut p < .001). Twenty-four hours after shock, however, there were no differences in vascular permeability between groups. Similarly, although at 3 hours the lungs of LR-treated mice demonstrated significant histopathologic injury, loss of tight and adherens junctions, and a pro-inflammatory gene expression profile at 3 hours, these endpoints in LR mice were similar to sham mice by 24 hours.

Conclusions
In an established mouse model of HS/T, endotheliopathy and lung injury are evident at 3 hours but recover by 24 hours. Larger animal models allowing for more severe injury coupled with supportive care are likely necessary to evaluate endotheliopathy and organ injury outside of the acute period.
Should Aquaporin-4 Antibody Test Be Performed in all Patients With Isolated Optic Neuritis?
Authors: Siantar Rosalynn G. , Ibrahim Farah N.I. , Htoon Hla M. , Tow Sharon L.C. , Goh Kong Yong , Loo Jing Liang , Lim Su Ann , Milea Dan , Tien Melissa C.H. , Chen Zhiyong , Yeo Tianrong , Chai Josiah Y.H. , Singhal Shweta , Chin Chee Fang , Tan Kevin 
Published: October 2022

Background:
Optic neuritis (ON) may be the initial manifestation of neuromyelitis optica spectrum disorder (NMOSD). Aquaporin-4 antibody (AQP4 Ab) is used to diagnose NMOSD. This has implications on prognosis and is important for optimal management. We aim to evaluate if clinical features can distinguish AQP4 Ab seropositive and seronegative ON patients.

Methods:
We reviewed patients with first episode of isolated ON from Tan Tock Seng Hospital and Singapore National Eye Centre who tested for AQP4 Ab from 2008 to 2017. Demographic and clinical data were compared between seropositive and seronegative patients.

Results:
Among 106 patients (120 eyes) with first episode of isolated ON, 23 (26 eyes; 22%) were AQP4 Ab positive and 83 (94 eyes; 78%) were AQP4 Ab negative. At presentation, AQP4 Ab positive patients had older mean onset age (47.9 ± 13.6 vs 36.8 ± 12.6 years, P < 0.001), worse nadir VA (OR 1.714; 95% CI, 1.36 to 2.16; P < 0.001), less optic disc swelling (OR 5.04; 95% CI, 1.682 to 15.073; p = 0.004), and higher proportions of concomitant anti-Ro antibody (17% vs 4%, p = 0.038) and anti-La antibody (17% vs 1%, p = 0.008). More AQP4 Ab positive patients received steroid-sparing immunosuppressants (74% vs 19%, p < 0.001) and plasma exchange (13% vs 0%, p = 0.009). AQP4 Ab positive patients had worse mean logMAR VA (visual acuity) at 12 months (0.70 ± 0.3 vs 0.29 ± 0.5, p = 0.051) and 36 months (0.37±0.4 vs 0.14 ± 0.2, p = 0.048) follow-up.

Conclusion:
Other than older onset age and retrobulbar optic neuritis, clinical features are non-discriminatory for NMOSD. We propose a low threshold for AQP4 Ab serology testing in inflammatory ON patients, particularly in high NMOSD prevalence populations, to minimize diagnostic and treatment delays.
A Consensus Statement on the Terminology for Automated Visual Field Abnormalities
Authors: Kruger Joshua M. , Almer Zina , Almog Yehoshua , Aloni Eyal , Bachar-Zipori Anat , Bialer Omer , Ben-Bassat Mizrachi Iris , Horowitz Josepha , Huna-Baron Ruth , Ivanir Yair , Jabaly-Habib Haneen , Klein Ainat , Krasnitz Irena , Leiba Hana , Maharshak Idit , Marcus Mira , Ostashinsky Michal , Paul Michael , Rappoport Daniel , Stiebel-Kalish Hadas , Rath Eitan Z. , Tam Guy , Walter Eyal , Johnson Chris A. 
Published: October 2022

Background:
A multitude of terms have been used to describe automated visual field abnormalities. To date, there is no universally accepted system of definitions or guidelines. Variability among clinicians creates the risk of miscommunication and the compromise of patient care. The purposes of this study were to 1) assess the degree of consistency among a group of neuro-ophthalmologists in the description of visual field abnormalities and 2) to create a consensus statement with standardized terminology and definitions.

Methods:
In phase one of the study, all neuro-ophthalmologists in Israel were asked to complete a survey in which they described the abnormalities in 10 selected automated visual field tests. In phase 2 of the study, the authors created a national consensus statement on the terminology and definitions for visual field abnormalities using a modified Delphi method. In phase 3, the neuro-ophthalmologists were asked to repeat the initial survey of the 10 visual fields using the consensus statement to formulate their answers.

Results:
Twenty-six neuro-ophthalmologists participated in the initial survey. On average, there were 7.5 unique descriptions for each of the visual fields (SD 3.17), a description of only the location in 24.6% (SD 0.19), and an undecided response in 6.15% (SD 4.13). Twenty-two neuro-ophthalmologists participated in the creation of a consensus statement which included 24 types of abnormalities with specific definitions. Twenty-three neuro-ophthalmologists repeated the survey using the consensus statement. On average, in the repeated survey, there were 5.9 unique descriptions for each of the visual fields (SD 1.79), a description of only the location in 0.004% (SD 0.01), and an undecided response in 3.07% (SD 2.11%). Relative to the first survey, there was a significant improvement in the use of specific and decisive terminology.

Conclusions:
The study confirmed a great degree of variability in the use of terminology to describe automated visual field abnormalities. The creation of a consensus statement was associated with improved use of specific terminology. Future efforts may be warranted to further standardize terminology and definitions.
Comparison of a New Head Mount Virtual Reality Perimeter (C3 Field Analyzer) With Automated Field Analyzer in Neuro-Ophthalmic Disorders
Authors: Odayappan Annamalai , Sivakumar Priya , Kotawala Sandal , Raman Ramalakshmi , Nachiappan Sivagami , Pachiyappan Arulmozhivarman , Venkatesh Rengaraj 
Published: October 2022

Background:
Automated perimetry in neurologically disabled patients is a challenge. We have devised a patient-friendly virtual reality perimeter, the C3 field analyzer (CFA). We aim to assess the utility of this as a visual field-testing device in neuro-ophthalmic patients for screening and monitoring.

Methods:
Neuro-ophthalmic patients and controls were selected to participate in the study between September and December 2018. They randomly underwent either the CFA or automated field analyzer (HFA) first followed by the other in an undilated state. The CFA results were compared with the HFA, and the correlation of the pattern of the field defect was assessed by an independent masked physician.

Results:
In total, 59 eyes of 33 neuro-ophthalmic patients (cases) and another 95 normal individuals (controls) were enrolled. CFA was found to have greater proportion of reliable fields (81.4%) than HFA (59.3%) (P = 0.009). There were less false negatives (P < 0.001) and more false positives in CFA (P < 0.001) among neuro-ophthalmic patients compared with controls. Among neuro-ophthalmology patients, the number of fixation losses was greater with CFA (P < 0.001), whereas false negatives were greater in HFA (P < 0.001). On assessing the pattern of the field defects, we found that there was almost 70% correlation of CFA with HFA. Moreover, in classical neurological fields such as hemianopia, the correlation was 87.5%.

Conclusions:
The CFA seems to correlate well with HFA in classic neurological fields such as hemianopias and may serve as an alternative in patients unable to perform a standard automated perimetry. Further developments are currently underway to incorporate threshold testing.
Estimating the neural spike train from an unfused tetanic signal of low threshold motor units using convolutive blind source separation
Authors: Rohlén Robin , Lundsberg Jonathan , Antfolk Christian 
Published: October 2022

AbstractThe central nervous system initiates voluntary force production by providing excitatory inputs to spinal motor neurons, each connected to a set of muscle fibres to form a motor unit. Motor units have been imaged and analysed using ultrafast ultrasound based on the separation of ultrasound images. Although this method has great potential to identify regions and trains of motor unit twitches (unfused tetanus) evoked by the spike trains, it currently has a limited motor unit identification rate. One potential explanation is that the current method neglects the temporal information in the separation process of ultrasound images, and including it could lead to significant improvement. Here, we take the first step by asking if it is possible to estimate the spike train of an unfused tetanic signal from simulated and experimental signals using convolutive blind source separation. This finding will provide a direction for ultrasound-based method improvement. In this study, we found that the estimated spike trains highly agreed with the simulated and reference spike trains. This result implies that the convolutive blind source separation of an unfused tetanic signal can be used to estimate its spike train. Although extending this approach to ultrasound images is promising, the translation remains to be investigated in future studies where spatial information is inevitable as a discriminating factor between different motor units.
A meta-analysis of neural systems underlying delay discounting: implications for transdiagnostic research
Authors: Souther Min Kang , Boateng Bema , Kable Joseph W. 
Published: October 2022

ABSTRACTDelay discounting is a promising paradigm for transdiagnostic research because both excessive and insufficient tendency to discount future rewards have been reported across diagnoses. Because delay discounting involves multiple neurocognitive functions, researchers have used many strategies to characterize brain activity during delay discounting. However, which of these analytic approaches yield truly robust and replicable findings remains unclear. To this end, we conducted a meta-analysis of 78 fMRI studies of delay discounting, testing which statistical contrasts yield reliable effects across studies. Despite being a widely used analytic approach, comparing impulsive and patient choices did not yield reliable effects across studies. Instead, subjective value reliably engaged the valuation network across studies. We also found that task versus baseline and choice difficulty contrasts reliably engaged regions in the frontoparietal and salience networks. We strongly recommend that future neuroimaging studies of delay discounting use these analytic approaches shown to reliably identify specific networks. In addition, we provide all cluster maps from our meta-analysis for use asa prioriregions of interest for future experiments.
An e-cigarette aerosol generation, animal exposure and toxicants quantification system to characterizein vivonicotine kinetics in arterial and venous blood
Authors: Zhang Jushan , Xue Mo , Pan Rong , Zhu Yujie , Zhang Zhongyang , Cheng Haoxiang , Björkegren Johan L M , Chen Jia , Shi Zhiqiang , Hao Ke 
Published: October 2022

AbstractThe increasing e-cigarette use worldwide presents an urgent need to characterize their nicotine delivery property, brain stimulation and potential long-term health effects. We constructed an end-to-end system enabling combustible-cigarette (c-cigarette) and e-cigarette aerosol generation, animal exposure, and effect assessment. The system consists of (1) a 10-channel aerosol generator resembling human smoking/vaping scenarios, (2) nose-only and whole-body exposure chambers suitable for long- or short-duration studies, (3) a lab protocol for animal exposure and collecting arterial and venous blood <1 minute after the exposure, and (4) chromatograph and mass spectrometry to quantify nicotine concentrations in aerosol and biospecimens. We applied the system in a proof-of-principle study characterizingin vivonicotine delivery after e-cigarette aerosol inhalation. Groups of Sprague-Dawley rats were exposed to e-cigarette aerosols for 1, 2 and 4 minutes, respectively. Arterial and venous blood samples were collected immediately after the exposure. We also directly compared nose-only and whole-body exposure approaches. After nose-only e-cigarette aerosol exposure, the nicotine concentration in arterial blood was substantially higher (11.32 ng/mL in average) than in veins. Similar arterio-venous concentration difference was observed in whole-body exposure experiments. In summary, we described a complete system ideal for e- and c-cigarettein vivonicotine kinetics and long-term health research. Our findings highlight arterial blood as the suitable bio-specimen for e-cigarette nicotine delivery studies.HighlightWe constructed a combustible- and e-cigarette aerosol generation - exposure - effect assessment system resembling real world human smoking/vaping scenarios.Proof-of-principle study characterizedin vivonicotine delivery from e-cigarette aerosol to arterial and venous blood at high temporal resolution.After exposure, the nicotine concentration was substantially higher (11.32 ng/mL) in arterial blood than in veins.Our results suggest arterial blood as the suitable bio-specimen to study nicotine delivery and brain stimulation.
Knowledge Mapping of Alternative Splicing of Cancer From 2012 to 2021: A Bibliometric Analysis
Authors: Tian Bo , Bian Yan , Bian De-Jian , Gao Ye , Zhang Xun , Zhou Si-Wei , Zhang Yan-Hui , Pang Ya-Nan , Li Zhao-Shen , Wang Luo-Wei 
Published: October 2022

ABSTRACTBackgroundAs a processing method of RNA precursors, alternative splicing plays a critical role in normal cell physiological activities. Aberrant alternative splicing events are associated with cancer development and are promising targets for cancer treatment. However, no detailed and unbiased study describes the current state of alternative splicing of cancer research. This study aims to conduct a bibliometric analysis of alternative splicing of cancer research in the last decade to measure and recognize the current state and trends.MethodsWeb of Science Core Collection was used to acquire the articles. Utilizing three bibliometric tools (CiteSpace, VOSviewer, R-bibliometrix), we were able to measure and recognize the influence and collaboration data of individual articles, journals, and co-citations. Analysis of co-occurrence and bursts information helped us identify the trending research areas related to alternative splicing of cancer.ResultsFrom 2012 to 2021, the total number of papers on alternative splicing of cancer published in 766 academic journals was 3,507, authored by 20,406 researchers in 405 institutions from 80 countries/regions. Research involving alternative splicing of cancer genes was primarily conducted in the United States and China, with the United States retaining the prime status; simultaneously, the Chinese Academy of Sciences, Fudan University and National Cancer Institute were the institutions with strong research capabilities. Scorilas Andreas is the scholar with the most publications, while the most co-citations were generated by Wang, Eric T. Plos One published the most papers on alternative splicing of cancer, while J biol chem was the most co-cited academic journal in this field. Furthermore, these publications covered a wide range of areas, but were still primarily focused on the fields of molecular, biology, and immunology. The results of keyword co-occurrence analysis can be divided into three types: molecular (P53, CD44, Androgen receptor, SRSF3, ESRP1), pathological process (apoptosis, EMT, metastasis, angiogenesis, proliferation), and disease (breast cancer, colorectal cancer, prostate cancer, hepatocellular carcinoma, gastric cancer).ConclusionResearch on alternative splicing of cancer has been a hot topic over the past decade, increasing in intensity each year. Current alternative splicing of cancer studies focused on hallmarks of alternative splicing in cancer, and alternative splicing signatures including diagnostic and therapeutic targets. Among them, the current trends are splicing factors regulating epithelial-mesenchymal transition and other hallmarks, aberrant splicing events in tumors, and further mechanisms. These might give researchers interested in this field a forward-looking perspective and inform further research.
Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity
Authors: Sun Yuliangzi , Shim Woo Jun , Shen Sophie , Sinniah Enakshi , Pham Duy , Su Zezhuo , Mizikovsky Dalia , White Melanie D. , Ho Joshua W.K. , Nguyen Quan , Bodén Mikael , Palpant Nathan J. 
Published: October 2022

AbstractMethods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-seq) data are essential for biological interpretation of cell processes. Here we present TRIAGE-Cluster which uses genome-wide epigenetic data from diverse bio-samples to identify genes demarcating cell diversity in scRNA-seq data. TRIAGE-Cluster integrates patterns of repressive chromatin deposited across diverse cell types with weighted density estimation to determine cell type clusters in a 2D UMAP space. We then present TRIAGE-ParseR, a machine learning method that evaluates gene expression rank lists to define gene groups governing the identity and function of cell types. We demonstrate the utility of this two-step approach using atlases ofin vivoandin vitrocell diversification and organogenesis. We also provide a web accessible dashboard for analysis and download of data and software. Collectively, genome-wide epigenetic repression provides a versatile strategy to define cell diversity and study gene regulation of scRNA-seq data.
Deduplication Improves Cost-Efficiency and Yields ofDe novoAssembly and Binning of Shot-Gun Metagenomes in Microbiome Research
Authors: Zhang Zhiguo , Zhang Lu , Zhao Ze , Wang Hui , Ju Feng 
Published: October 2022

AbstractMetagenomics has in the last decade greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads mainly raised from the preparation of metagenomic DNA sequencing library and their impacts on metagenomic assembly and binning have never brought to the attention. Here, we explicitly investigated the effects of duplicate reads on metagenomic assembly and binning, based on analyses of four groups of representative metagenomes with distinct microbiome complexity. Our results showed that deduplication considerably increased the binning yields (by 3.5% to 80%) for most of the metagenomic datasets examined thanks to improved contig length and coverage profiling of metagenome-assembled contigs. Specifically, 411 versus 397, 331 versus 317, 104 versus 88 and 9 versus 5 metagenome-assembled genomes (MAGs) were recovered from MEGAHIT assemblies of bioreactor sludge, surface water, lake sediment, and forest soil metagenomes, respectively. Noticeably, deduplication reduced the computational costs of metagenomic assembly including elapsed time (by 9.0% to 29.9%) and maximum memory requirement (by 4.3% to 37.1%). Collectively, it is recommended to remove duplicate reads in metagenomic data before assembly and binning analyses, particularly for complex environmental samples, such as forest soils examined in this study.ImportanceDuplicated reads are usually considered as technical artefacts. Their presence in metagenomes would theoretically not only introduce bias in the quantitative analysis, but also result in mistakes in coverage profile, leading to negative effects or even failures on metagenomic assembly and binning, as the widely used metagenome assemblers and binners all need coverage information for graph partitioning and assembly binning, respectively. However, this issue was seldomly noticed and its impacts on the downstream key bioinformatic procedures (e.g., assembly and binning) still remained unclear. In this study, we comprehensively evaluated for the first time the impacts of duplicate reads on de novo assembly and binning of real metagenomic datasets by comparing assembly quality, binning yields and the requirements of computational resources with and without the removal of duplicate reads. It was revealed that deduplication considerably increased the binning yields and significantly reduced the computational costs including elapsed time and maximum memory requirement. The results provide empirical reference for more cost-efficient metagenomic analyses in microbiome research.
Arctic humpback whales respond to nutritional opportunities before migration
Authors: Kettemer Lisa Elena , Ramm Theresia , Broms Fredrik , Biuw Martin , Blanchet Marie-Anne , Bourgeon Sophie , Dubourg Paul , Ellendersen Anna C. J. , Horaud Mathilde , Kershaw Joanna , Miller Patrick J. O. , Øien Nils , Pallin Logan J. , Rikardsen Audun H. 
Published: October 2022

AbstractRapid climate change in Arctic and Subarctic ecosystems is altering the spatio-temporal dynamics and abundance of resources. Whether highly mobile predators can respond and match their movements to changed resource peaks remains largely unclear. In the last decade, humpback whales (Megaptera novaeangliae) established a new foraging site in fjords of northern Norway during the winter, outside of their presumed foraging season. We used photographic matching to show that whales first sighted during fall in the Barents Sea foraged in northern Norway from late October to February, staying for up to three months and showing high inter-annual return rates (up to 82%). The number of identified whales increased steadily from 2010 to 2016. Genetic sexing and hormone profiling in both areas suggest higher proportions of pregnancy and a female bias in Norwegian waters. This indicates that the new site may be particularly important for pregnant females, likely to improve body condition before migration. Our results suggest that baleen whales can respond to nutritional opportunities along their migration pathways, in some cases by extending their feeding season. This supports the idea that migrating marine mammals can access novel prey resources as part of their response to environmental changes.