bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vessel Density Features of Optical Coherence Tomography Angiography for Classification of Optic Neuropathies Using Machine Learning
Authors: Jalili Jalil , Nadimi Mohadeseh , Jafari Behzad , Esfandiari Amirreza , Mojarad Mohadeseh , Subramanian Prem S. , Aghsaei Fard Masoud 
Published: July 2023

Background:
To evaluate the classification performance of machine learning based on the 4 vessel density features of peripapillary optical coherence tomography angiography (OCT-A) for classifying healthy, nonarteritic anterior ischemic optic neuropathy (NAION), and optic neuritis (ON) eyes.

Methods:
Forty-five eyes of 45 NAION patients, 32 eyes of 32 ON patients, and 76 eyes of 76 healthy individuals with optic nerve head OCT-A were included. Four vessel density features of OCT-A images were developed using a threshold-based segmentation method and were integrated in 3 models of machine learning classifiers. Classification performances of support vector machine (SVM), random forest, and Gaussian Naive Bayes (GNB) models were evaluated with the area under the receiver-operating-characteristic curve (AUC) and accuracy.

Results:
We divided 121 images into a 70% training set and 30% test set. For ON-NAION classification, best results were achieved with 50% threshold, in which 3 classifiers (SVM, RF, and GNB) discriminated ON from NAION with an AUC of 1 and accuracy of 1. For ON-Normal classification, with 100% threshold, SVM and RF classifiers were able to discriminate normal from ON with AUCs of 1 and accuracies of 1. For NAION-normal classification, with 50% threshold, the SVM and RF classified the NAION from normal with AUC and accuracy of 1.

Conclusions:
ML based on the combined peripapillary vessel density features of total vessels and capillaries in the whole image and ring image could provide excellent performance for NAION and ON distinction.
Occipital Nocardia Abscess Presenting With Positive Visual Phenomenon and Quadrantanopsia
Authors: Fein Alexander S. , Kelly Sean M. , Louie Eddie , Young Matthew G. , Jain Rajan , William Christopher M. , Galetta Steven L. , Grossman Scott N. 
Published: July 2023

Abstract:
A 74-year-old man with chronic obstructive pulmonary disease, glaucoma, and Stage IIIB squamous cell lung cancer experienced several minutes of flashing lights in his right visual hemifield, followed by onset of a right visual field defect. On examination, the patient had a right homonymous hemianopsia that was most dense inferiorly by confrontation testing. Emergent CT scan of the head revealed a 2.5 × 3 cm hypodensity in the left occipital lobe, which was interpreted as an acute stroke. Continuous EEG monitoring captured left posterior quadrant seizures that were temporally correlated to the positive visual phenomena. Subsequent MRI of the brain with and without contrast revealed a conglomerate of centrally necrotic and peripherally enhancing mass lesions. On biopsy, a thick purulent material was drained and Gram stain of the sample revealed gram-positive beaded rods, which speciated to Nocardia farcinica. The patient was treated with a six-week course of intravenous meropenem and a one-year course of oral trimethroprim–sulfamethoxazole. On follow-up, the patient experienced resolution of the right visual field deficit.
Emerging Gene Therapy Technologies for Retinal Ganglion Cell Neuroprotection
Authors: Camacho David K. , Go Cammille C. , Chaqour Brahim , Shindler Kenneth S. , Ross Ahmara G. 
Published: July 2023

Abstract
Optic neuropathies encompass a breadth of diseases that ultimately result in dysfunction and/or loss of retinal ganglion cells (RGCs). Although visual impairment from optic neuropathies is common, there is a lack of effective clinical treatments. Addressing a critical need for novel interventions, preclinical studies have been generating a growing body of evidence that identify promising new drug-based and cell-based therapies. Gene therapy is another emerging therapeutic field that offers the potential of specifically and robustly increasing long-term RGC survival in optic neuropathies. Gene therapy offers additional benefits of driving improvements following a single treatment administration, and it can be designed to target a variety of pathways that may be involved in individual optic neuropathies or across multiple etiologies. This review explores the history of gene therapy, the fundamentals of its application, and the emerging development of gene therapy technology as it relates to treatment of optic neuropathies.
Inclusive dementia care for ethnically diverse families
Authors: Brijnath Bianca , Antoniades Josefine , Cavuoto Marina 
Published: July 2023

Purpose of review
With population ageing and global migration, rates of dementia are set to rapidly increase in ethnically diverse populations. This narrative review examines recent evidence on what constitutes culturally appropriate models of care.

Recent findings
Barriers to inclusive care continue to prevail, amplifying dementia disparities in ethnically diverse communities. Cultural models that can address these include ensuring health and aged care staff are culturally competent, language supports are available, and cultural practices are integrated into daily care routines. Fundamentally, systems must be reformed to ensure they meet the needs of diverse end-users. More inclusive and widespread ethno-specific services are needed, and governments need to be mindful of demographic transitions in their populations and plan accordingly to meet future demand. Digital media and new technologies offer promising new ways to deliver culturally appropriate care to ethnically diverse groups, but its full potential is yet to be realised.

Summary
Persistent dementia disparities in ethnically diverse communities can be overcome by operationalising cultural models of care, leveraging the promise of digital media, and systems redesign.
Quality testing of mifepristone and misoprostol in 11 countries
Authors: Bower Jason , Chinery Lester , Fleurent Alessandra , Gülmezoglu A. Metin , Im-Amornphong Wallada , Kilfedder Catherine , Procter Petra , Tomazzini Alessandra 
Published: July 2023

AbstractObjectivePrevious studies have demonstrated quality concerns with misoprostol. Mifepristone, however, has not been extensively assessed for quality. Between 2020 and 2021, Concept Foundation and the International Planned Parenthood Federation conducted a study to determine the quality of these medical abortion drugs in low– and middle-income countries (LMIC).MethodsCollection of batch samples of misoprostol and mifepristone was carried out by trained sampling agents in selected LMIC. Single drug packs and combipacks were sampled. A World Health Organization prequalified laboratory conducted testing method verifications and subsequent sample analysis. Tests included identification, assay, related substances, and content uniformity for misoprostol, and identification, assay, related substances, and dissolution for mifepristone.ResultsSamples were collected from Burkina Faso, Cambodia, Democratic Republic of Congo, India, Kyrgyzstan, Moldova, Nepal, Nigeria, Pakistan, Uganda and Vietnam. Sixty-four pooled batch samples were tested, consisting of 31 combipacks, 26 misoprostol-only and 7 mifepristone-only products. Overall, 54.7% of samples were non-compliant with one or more of the specifications, representing 51.6% of combipack products, 57.1% of misoprostol tablets analyzed and 23.7% of mifepristone tablets. One falsified misoprostol-only product was found.ConclusionThis study confirms that a significant problem still exists in relation to the quality of medical abortion drugs in low– and middle-income countries. For misoprostol, our findings suggest that historical concerns around primary packaging may have been largely resolved but that manufacturing processes for both finished product and active pharmaceutical ingredient need to be improved. This study also provides evidence of mifepristone quality issues.
Taxane-based Chemotherapy is Effective in Metastatic Appendiceal Adenocarcinoma
Authors: Dansby Julia , More Aditya , Zeineddine Mohammad , Yousef Abdelrahman , Bent Alisha , Dayyani Farshid , Wolff Robert , Overman Michael , Shen John Paul 
Published: July 2023

AbstractAppendiceal cancer is a rare, orphan disease with no therapies currently approved by the FDA for its treatment. Given the limited data regarding drug efficacy, these tumors have historically been treated with chemotherapy designed for colon cancer. However, an overwhelming body of molecular data has demonstrated that appendiceal adenocarcinoma is a distinct entity with key molecular differences from colon cancer, notably rareAPCmutation. Recognizing that APC loss-of-function is thought to contribute to taxane resistance, and that taxanes are effective in the treatment of other gastrointestinal tumors including gastric, esophageal, and small bowel adenocarcinoma, we completed a single-center retrospective study to assess efficacy. In a cohort of 13 patients with metastatic appendiceal adenocarcinoma, treated with taxane chemotherapy the median overall survival was 8.3 months. Of 10 evaluable patients we observed 3 responses, 4 patients with stable disease, and 3 with progression (30% response rate, 70% disease control rate). The results of this study showing activity of taxane-based chemotherapy in appendiceal adenocarcinoma support further clinical investigation of taxane therapy in this orphan disease.
Low and Borderline Ankle Brachial Index is Associated with Intracranial Aneurysms – A Retrospective Cohort Study
Authors: Laukka Dan , Kangas Essi , Kuusela Aino , Hirvonen Jussi , Rissanen Tiia , Rahi Melissa , Kivelev Juri , Rantasalo Ville , Rinne Jaakko , Hakovirta Harri 
Published: July 2023

AbstractBackground and AimsA low ankle-brachial index (ABI) is associated with a higher risk of cardiovascular diseases, stroke, and systemic inflammation. Intracranial aneurysms (IAs) share similar risk factors with other cardiovascular diseases. However, the association between low ABI and IAs lacks sufficient investigation.MethodsThis retrospective study reviewed 2751 patients who had ABI measurements at a tertiary hospital from January 2011 to December 2013. Patients with available cerebrovascular imaging or a diagnosis of ruptured IA were included in the study (n=776) to examine the association between ABI and saccular IAs. The patients were classified into four groups: low ABI (≤0.9, n=464), borderline ABI (0.91-0.99; n=47), high ABI (>1.4, n=57), and normal ABI (1.00-1.40; n=208).ResultsThe prevalence of IAs was 20.3% (18.1% unruptured IAs) in the low ABI group, 14.9% (12.8% unruptured IAs) in the borderline ABI group, 7.0 % (5.3% unruptured IAs) in the high ABI group, and 2.4% (1.9% unruptured IAs) in the normal ABI group (p<0.001). Sex- and age-adjusted multinomial regression, including clinically relevant variables, revealed that low ABI (odds ratio [OR], 11.33; 95% confidence interval [CI], 4.08-31.51;p<0.001) and borderline ABI (0.91-0.99) (OR, 7.13; 95% CI, 1.91-26.63;p=0.004) were the only variables significantly associated with unruptured IAs.ConclusionsThe prevalence of unruptured IAs was 9-fold higher in the low ABI group and nearly 7-fold higher in the borderline ABI group when compared to the normal ABI group. ABI measurements could be clinically relevant for identifying individuals at higher risk of IAs and may help guide screening and preventive strategies.
Acidic nanoparticles restore lysosomal acidification and rescue metabolic dysfunction in pancreatic β-cells under lipotoxic condition
Authors: Lo Chih Hung , O’Connor Lance M. , Loi Gavin Wen Zhao , Saipuljumri Eka Norfaishanty , Indajang Jonathan , Lopes Kaitlynn M. , Shirihai Orian S. , Grinstaff Mark W. , Zeng Jialiu 
Published: July 2023

AbstractType 2 diabetes (T2D), a prevalent metabolic disorder lacking effective treatments, is associated with lysosomal acidification dysfunction as well as autophagic and mitochondrial impairments. Here, we report a series of biodegradable poly(butylene tetrafluorosuccinate-co-succinate) (PBFSU) polyesters, comprising an 1,4-butanediol linker and varying ratios of tetrafluorosuccinic acid (TFSA) and succinic acid as components, to engineer new lysosome acidifying nanoparticles (NPs). Notably, TFSA NPs, which composed entirely of TFSA, exhibit the strongest degradation capability and superior acidifying property. We further reveal significant downregulation of lysosomal vacuolar (H+)-ATPase (V-ATPase) subunits, which are responsible for maintaining lysosomal acidification, in human T2D pancreatic islets and INS-1 β-cells under lipotoxic condition. Treatment of TFSA NPs counteracts lipotoxicity in INS-1 β-cells by restoring lysosomal acidification, autophagic function, and mitochondrial activity, along with promoting glucose-stimulated insulin secretion. Administration of TFSA NPs to high-fat diet T2D mice improves glucose clearance and reduces insulin resistance. These findings highlight the therapeutic potential of lysosome acidifying TFSA NPs for T2D.Graphical Table of Contents
Predictions and errors are distinctly represented across V1 layers
Authors: Thomas Emily R , Haarsma Joost , Nicholson Jessica , Yon Daniel , Kok Peter , Press Clare 
Published: July 2023

Abstract‘Predictive processing’ frameworks of cortical functioning propose that neural populations in different cortical layers serve distinct roles in representing the world. There are distinct testable theories within this framework that we examined with a 7T fMRI study, where we contrasted responses in primary visual cortex (V1) to expected (75% likely) and unexpected (25%) Gabor orientations. Multivariate decoding analyses revealed an interaction between expectation and layer, such that expected events could be decoded with comparable accuracy across layers, while unexpected events could only be decoded in superficial laminae. These results are in line with predictive processing accounts where expected virtual input is injected into deep layers, while superficial layers process the ‘error’ with respect to expected signals. While this account of cortical processing has been popular for decades, such distinctions have not previously been demonstrated in the human sensory brain. We discuss how both prediction and error processes may operate together to shape our unitary perceptual experiences.
Natural transformation specific DprA coordinate DNA double strand break repair pathways in heavily irradiatedD. radiodurans
Authors: Sharma Dhirendra Kumar , Soni Ishu , Misra Hari S. , Rajpurohit Yogendra Singh 
Published: July 2023

AbstractDeinococcus radioduransexhibits remarkable survival under extreme conditions, including ionizing radiation, desiccation, and various DNA-damaging agents. It employs unique repair mechanisms, such as single-strand annealing (SSA) and extended synthesis-dependent strand annealing (ESDSA), to efficiently restore damaged DNA fragments. In this study, we investigate the regulatory role of the NT-specific protein DprA in DNA repair pathways following acute gamma radiation exposure. Our findings demonstrate that the absence of DprA leads to rapid repair of gamma radiation-induced DNA double-strand breaks (DSBs), with diminished involvement of the ESDSA pathway. Furthermore, our data suggest that the SSA pathway becomes the primary mechanism for DNA DSB repair in the absence of DprA. Overall, our results highlight the regulatory function of DprA in modulating the choice between SSA and ESDSA pathways for DNA repair in the radiation-resistant bacteriumD. radioduransx.
Orthogonal analysis of mitochondrial function in Parkinson’s disease patients
Authors: Barnhoorn Sander , Milanese Chiara , Li Tracy , Dons Lieke , Ghazvini Mehrnaz , Farina Stefania , Sproviero Daisy , Gomez Cesar Payan , Mastroberardino Pier G. 
Published: July 2023

AbstractThe etiopathology of Parkinson’s disease has been associated with mitochondrial defects at genetic, laboratory, epidemiological, and clinical level. These converging lines of evidence suggest that mitochondrial defects are systemic and causative factors in the pathophysiology of PD, rather than being mere correlates. Understanding mitochondrial biology in PD at granular level is therefore crucial from both basic science and translational perspectives.In a recent study, we investigated mitochondrial alterations in fibroblasts obtained from PD patients assessing mitochondrial function in relation to clinical measures. Our findings demonstrated that the magnitude of mitochondrial alterations parallels disease severity. In this study, we extend these investigations to blood cells and dopamine neurons derived from induced pluripotent stem cells reprogrammed from PD patients. To overcome the inherent metabolic heterogeneity of blood cells, we focused our analyses on metabolically homogeneous, accessible, and expandable erythroblasts. Our results confirm the presence of mitochondrial anomalies in erythroblasts and induced dopamine neurons. Consistent with our previous findings in fibroblasts, we observed that mitochondrial alterations are reversible, as evidenced by enhanced mitochondrial respiration when PD erythroblasts were cultured in a galactose medium that restricts glycolysis. This observation indicates that suppression of mitochondrial respiration may constitute a protective, adaptive response in PD pathogenesis. Notably, this effect was not observed in induced dopamine neurons, suggesting their distinct bioenergetic behavior.In summary, we provide additional evidence for the involvement of mitochondria in the disease process by demonstrating mitochondrial abnormalities in additional cell types relevant to PD. These findings contribute to our understanding of PD pathophysiology and may have implications for the development of novel biomarkers and therapeutic strategies.
DNAGPT: A Generalized Pre-trained Tool for Multiple DNA Sequence Analysis Tasks
Authors: Zhang Daoan , Zhang Weitong , Zhao Yu , Zhang Jianguo , He Bing , Qin Chenchen , Yao Jianhua 
Published: July 2023

AbstractPre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genome generation tasks demonstrates DNAGPT’s superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.
Tutorial: guidelines for manual cell type annotation of single-cell multi-omics datasets using interactive software
Authors: Kim Yang-Joon , Tarashansky Alexander , Liang Karen , Urisko Meg , Dorman Leah , Borja Michael , Neff Norma , Pisco Angela Oliveira , Granados Alejandro 
Published: July 2023

AbstractAssigning cell identity to clusters of single cells is an essential step towards extracting biological insights from many genomics datasets. Although annotation workflows for datasets built with asinglemodality are well established, limitations exist in annotating cell types in datasets withmultiplemodalities due to the need for a framework to exploit them jointly. While, in principle, different modalities could convey complementary information about cell identity, it is unclear to what extent they can be combined to improve the accuracy and resolution of cell type annotations.Here, we present a conceptual framework to examine and jointly interrogate distinct modalities to identify cell types. We integrated our framework into a series of vignettes, using immune cells as a well-studied example, and demonstrate cell type annotation workflows ranging from using single-cell RNA-seq datasets alone, to using multiple modalities such as single-cell Multiome (RNA and chromatin accessibility), CITE-seq (RNA and surface proteins). In some cases, one or other single modality is superior to the other for identification of specific cell types, in others combining the two modalities improves resolution and the ability to identify finer subpopulations. Finally, we use interactive software from CZ CELLxGENE community tools to visualize and integrate histological and spatial transcriptomic data.
Platelet hyperactivity in patients of vascular dementia
Authors: Dev Priya , Ekhlak Mohammad , Yadav Ashish , Dash Debabrata , Pathak Abhishek 
Published: July 2023

AbstractBackgroundPlatelet-monocyte (PMA) and platelet-neutrophil aggregations (PNA) are critical in causing acute inflammatory reactions favoring vascular dysfunction. However, the precise pathophysiological link between Platelet-leukocyte aggregates and Vascular Dementia (VaD) remains undetermined. Our study aimed to investigate whether platelet hyperresponsiveness is independently associated with a predictor of VaD.MethodsPlatelet from 19 VaD patients and 18 age-matched healthy controls were subjected to different investigations.ResultPMA, PNA, P-selectin externalization, and intracellular free Ca+2([Ca+2i]) flux were evaluated either in whole blood or in platelet-rich plasma. The result revealed that PMA, PNA, P-selectin, and [Ca+2]iwere found to be significantly outnumbered in the VaD group (4.1, 2.8, 2.7, and 2.5 times higher) compared to the control group with p-value <0.001, <0.001, <0.001, and 0.001 at 95% CI = 31.164 to 54.855, 8.653 to 22.793, 35.064 to 94.369 and 8747.015 to 28829.618 respectively.ConclusionPatients with Vascular Dementia have increased platelet leucocyte interaction, and PMA has the most significant prediction of vascular dementia than in subjects of healthy control. Thus, platelets in VaD patients switch to a ‘hyperactive’ phenotype.
WITHDRAWN: Comparative Analysis of Four Scoring Systems (APACHE II, CURB-65, Pneumonia Severity Index [PSI], and CHA2DS2-VASc) for Predicting New-Onset Cardiovascular Events, Including Atrial Fibrillation, in Critically Ill Patients with Pneumonia
Authors: Lin Yi-Tsung , Wang Tzu-Lin 
Published: July 2023

Withdrawal StatementThis manuscript has been withdrawn by the authors as it was submitted and made public without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author (Yi-Tsung Linytlin8@vghtpe.gov.tw).