bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iris trauma in a highly myopic woman with one functional eye October consultation #1
Authors: Menapace Rupert 
Published: October 2020

A 58-year-old highly myopic woman had suffered a windscreen trauma to her left eye during a car accident 40 years earlier. Reportedly, iris tissue was removed in emergency surgery. Her right eye has very poor vision with only hand motion perception due to myopic maculopathy. The myopia of −12 diopters (D) in her left eye is corrected with a hard contact lens, which is well tolerated. With the contact lens and an additional spectacle correction of −1.5 D, visual acuity is 0.5 Jg1. Slitlamp biomicroscopy reveals a lacerated iris with iridodialysis extending along the superior circumference from 8:30 to 4:30 o'clock and a superior–temporal pupil coloboma. The disinserted and contracted iris tissue resides on the anterior lens surface (Figure 1). The residual pupil is slightly decentered inferiorly and still reactive to light. The lens zonular fibers are intact along the full and particularly the superior circumference. Slitlamp illumination reveals grade 2 cataract formation in nucleus center. Intraocular pressure is 12 mm Hg. The central retina shows myopic tabulation with intact macula.
During the past 6 months, the patient has been experiencing increasing shortsightedness and light sensitivity, especially outdoors, and desires cataract surgery. Given this is the only eye with reading capacity, which would be your surgical options and preferred approach to treat the cataract and remedy the traumatized iris?
Interpreting chest X-rays via CNNs that exploit disease dependencies and uncertainty labels
Authors: Pham Hieu H. , Le Tung T. , Tran Dat Q. , Ngo Dat T. , Nguyen Ha Q. 
Published: October 2020

AbstractChest radiography is one of the most common types of diagnostic radiology exams, which is critical for screening and diagnosis of many different thoracic diseases. Specialized algorithms have been developed to detect several specific pathologies such as lung nodule or lung cancer. However, accurately detecting the presence of multiple diseases from chest X-rays (CXRs) is still a challenging task. This paper presents a supervised multi-label classification framework based on deep convolutional neural networks (CNNs) for predicting the risk of 14 common thoracic diseases. We tackle this problem by training state-of-the-art CNNs that exploit dependencies among abnormality labels. We also propose to use the label smoothing technique for a better handling of uncertain samples, which occupy a significant portion of almost every CXR dataset. Our model is trained on over 200,000 CXRs of the recently released CheXpert dataset and achieves a mean area under the curve (AUC) of 0.940 in predicting 5 selected pathologies from the validation set. This is the highest AUC score yet reported to date. The proposed method is also evaluated on the independent test set of the CheXpert competition, which is composed of 500 CXR studies annotated by a panel of 5 experienced radiologists. The performance is on average better than 2.6 out of 3 other individual radiologists with a mean AUC of 0.930, which ranks first on the CheXpert leaderboard at the time of writing this paper.
Screening for early-stage Alzheimer’s disease using optimized feature sets and machine learning
Authors: Kleiman Michael J. , Barenholtz Elan , Galvin James E. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: October 2020

ABSTRACTBackgroundDetecting early-stage Alzheimer’s disease in clinical practice is difficult due to a lack of efficient and easily administered cognitive assessments that are sensitive to very mild impairment, a likely contributor to the high rate of undetected dementia.ObjectiveHere, we aim to identify groups of cognitive assessment features optimized for detecting mild impairment that can be used in routine screening. We also compare the efficacy of classifying impairment using either a two-class (impaired vs non-impaired) or three-class approach.MethodsSupervised feature selection methods generated groups of cognitive measurements targeting impairment defined at CDR 0.5 and above. Random forest classifiers then generated predictions of impairment for each group using highly stochastic cross-validation, with group outputs examined using general linear models.ResultsThe strategy of combining impairment levels for two-class classification resulted in significantly higher sensitivities and NPVs, two metrics useful in clinical screening, compared to the three-class approach. Just four neuropsychological features (delayed WAIS Logical Memory, trail-making, patient and informant memory questions), able to be administered in approximately 15 active minutes (∼30 minutes with delay), enabled classification sensitivity of 94.53% (88.43% PPV) with the addition of four more features significantly increasing sensitivity to 95.18% (88.77% PPV) when added to the model as a second classifier.ConclusionThe high detection rate paired with the minimal assessment time of the four identified features may act as an effective starting point when screening for cognitive impairment defined at CDR 0.5 and above.
Defining a master curve of abdominal aortic aneurysm growth and its potential utility of clinical management
Authors: Akkoyun Emrah , Gharahi Hamidreza , Kwon Sebastian T. , Zambrano Byron A. , Rao Akshay , Acar Aybar C. , Lee Whal , Baek Seungik 
Published: October 2020

AbstractObjectiveThe maximum diameter measurement of an abdominal aortic aneurysm (AAA), which depends on orthogonal and axial cross-sections or maximally inscribed spheres within the AAA, plays a significant role in the clinical decision making process. This study aims to build a large dataset of morphological parameters from longitudinal CT scans and analyze their correlations. Furthermore, this work explores the existence of a “master curve” of AAA growth, and tests which parameters serve to enhance its predictability for clinical use.Methods106 CT scan images from 25 Korean AAA patients were retrospectively obtained. We subsequently computed morphological parameters, growth rates, and pair-wise correlations, and attempted to enhance the predictability of the growth for high-risk aneurysms using non-linear curve fitting and least-square minimization.ResultsAn exponential AAA growth model was fitted to the maximum spherical diameter, as the best representative of the growth among all parameters (r-square: 0.985) and correctly predicted to 74 of 79 scans based on a 95% confidence interval. AAA volume expansion rateswere highly correlated (r=0.80) with thrombus accumulation rates.ConclusionsThe exponential growth model using spherical diameter provides useful information about progression of aneurysm size and enables AAA growth rate extrapolation during a given surveillance period.
Projected COVID-19 epidemic in the United States in the context of the effectiveness of a potential vaccine and implications for social distancing and face mask use
Authors: Shen Mingwang , Zu Jian , Fairley Christopher K. , Pagán José A. , An Li , Du Zhanwei , Guo Yuming , Rong Libin , Xiao Yanni , Zhuang Guihua , Li Yan , Zhang Lei 
Published: October 2020

ABSTRACTBackgroundMultiple candidates of COVID-19 vaccines have entered Phase III clinical trials in the United States (US). There is growing optimism that social distancing restrictions and face mask requirements could be eased with widespread vaccine adoption soon.MethodsWe developed a dynamic compartmental model of COVID-19 transmission for the four most severely affected states (New York, Texas, Florida, and California). We evaluated the vaccine effectiveness and coverage required to suppress the COVID-19 epidemic in scenarios when social contact was to return to pre-pandemic levels and face mask use was reduced. Daily and cumulative COVID-19 infection and death cases were obtained from the Johns Hopkins University Coronavirus resource center and used for model calibration.ResultsWithout a vaccine, the spread of COVID-19 could be suppressed in these states by maintaining strict social distancing measures and face mask use levels. But relaxing social distancing restrictions to the pre-pandemic level without changing the current face mask use would lead to a new COVID-19 outbreak, resulting in 0.8-4 million infections and 15,000-240,000 deaths across these four states over the next 12 months. In this scenario, introducing a vaccine would partially offset this negative impact even if the vaccine effectiveness and coverage are relatively low. However, if face mask use is reduced by 50%, a vaccine that is only 50% effective (weak vaccine) would require coverage of 55-94% to suppress the epidemic in these states. A vaccine that is 80% effective (moderate vaccine) would only require 32-57% coverage to suppress the epidemic. In contrast, if face mask usage stops completely, a weak vaccine would not suppress the epidemic, and further major outbreaks would occur. A moderate vaccine with coverage of 48-78% or a strong vaccine (100% effective) with coverage of 33-58% would be required to suppress the epidemic. Delaying vaccination rollout for 1-2 months would not substantially alter the epidemic trend if the current interventions are maintained.ConclusionsThe degree to which the US population can relax social distancing restrictions and face mask use will depend greatly on the effectiveness and coverage of a potential COVID-19 vaccine if future epidemics are to be prevented. Only a highly effective vaccine will enable the US population to return to life as it was before the pandemic.
Clinical Suspicion of COVID-19 in Nursing Home residents: symptoms and mortality risk factors
Authors: Rutten Jeanine J.S. , van Loon Anouk M. , van Kooten Janine , van Buul Laura W. , Joling Karlijn J. , Smalbrugge Martin , Hertogh Cees M.P.M. 
Published: October 2020

AbstractObjectivesTo describe symptomatology, mortality and risk factors for mortality in a large group of Dutch nursing home (NH) residents with clinically-suspected COVID-19 who were tested with a Reverse Transcription Polymerase Chain Reaction (RT-PCR) test.DesignProspective cohort study.Setting and participantsResidents of Dutch NHs with clinically-suspected COVID-19 and who received RT-PCR test.MethodsWe collected data of NH residents with clinically-suspected COVID-19, via electronic health records between March 18th and May 13th, 2020. Registration was performed on diagnostic status (confirmed (COVID-19+)/ruled out (COVID-19-)) and symptomatology (typical and atypical symptoms). Information on mortality and risk factors for mortality were extracted from usual care data.ResultsIn our sample of residents with clinically-suspected COVID-19 (N=4007), COVID-19 was confirmed in 1538 residents (38%). Although, symptomatology overlapped between residents with COVID-19+ and COVID-19-, those with COVID-19+ were three times more likely to die within 30 days (hazard ratio (HR), 3·1; 95% CI, 2·7 to 3·6). Within this group, mortality was higher for men than for women (HR, 1·8; 95%, 1·5-2·2) and we observed a higher mortality for residents with dementia, reduced kidney function, and Parkinson’s Disease, even when corrected for age, gender, and comorbidities.Conclusions and implicationsAbout 40% of the residents with clinically-suspected COVID-19 actually had COVID-19, based on the RT-PCR test. Despite an overlap in symptomatology, mortality rate was three times higher for residents with COVID-19+. This emphasizes the importance of using low-threshold testing in NH residents which is an essential prerequisite to using limited personal protective equipment and isolation measures efficiently.
The Risk of Indoor Sports and Culture Events for the Transmission of COVID-19 (Restart-19)
Authors: Moritz Stefan , Gottschick Cornelia , Horn Johannes , Popp Mario , Langer Susan , Klee Bianca , Purschke Oliver , Gekle Michael , Ihling Angelika , Mikolajczyk Rafael 
Published: October 2020

AbstractNearly all mass gathering events (MGEs) worldwide have been banned since the outbreak of SARS-CoV-2 as they are supposed to pose a considerable risk for transmission of COVID-19. We investigated transmission risk of SARS-CoV-2 by droplets and aerosols during an experimental indoor MGE (using N95 masks and contact tracing devices) and conducted a simulation study to estimate the resulting burden of disease under conditions of controlled epidemics. The number of exposed contacts was <10 for scenarios with hygiene concept and good ventilation, but substantially higher otherwise. Of subsequent cases, 0%-23% were attributable to MGEs. Overall, the expected additional effect of indoor MGEs on burden of infections is low if hygiene concepts are applied and adequate ventilation exists.One Sentence SummarySeated indoor events, when conducted under hygiene precautions and with adequate ventilation, have small effects on the spread of COVID-19.
Rapid Support for Older Adults during the initial stages of the COVID-19 Pandemic: Results from a Geriatric Psychiatry helpline
Authors: Wahl Anna-Sophia , Benson Gloria S. , Hausner Lucrezia , Schmitt Sandra , Knoll Annika , Bondy Adriana Feretti , Hefter Dimitri , Frölich Lutz 
Published: October 2020

AbstractBackgroundThe COVID-19 pandemic and governmental lockdown measures disproportionally impacts older adults. This study presents the results from a psychiatric helpline for older adults in Mannheim, Germany, during the lockdown, set up to provide information and psychosocial support measures. We aim to elucidate the needs of older adults, their reported changes and the psychological impact during the initial stages of the health crisis.Methods55 older adults called the psychiatric helpline between April and June 2020. Information on demographics, previous diagnosis of psychiatric and somatic diseases as well as changes in daily life due to the pandemic was collected anonymously. Current mental health status was assessed using the depression HAMD-7 and the anxiety HAM-A scales.ResultsMost callers were women, older adults (M = 74.69 years), single and retired. 69% of callers reported new or an increase in psychiatric symptoms, with anxiety and depressive symptoms being the most common ones. Age was significantly negatively correlated to higher levels of anxiety and depression symptoms. Individuals with a previous diagnosis of a psychiatric disease reported significantly higher levels of depressive and anxiety symptoms than those without a diagnosis.ConclusionIn older adults, the perceived psychological impact of the COVID-19 crisis appears to ameliorate with age. Individuals with a history of psychiatric disease are most vulnerable to negative mental health outcomes. Rapid response in the form of a geriatric helpline are useful initiatives to support the needs and the psychological well-being of older adults during a health crisis.
Cognitive screening instruments for dementia: comparing metrics of test limitation
Authors: Larner Andrew J 
Published: October 2020

AbstractCognitive screening instruments (CSIs) for dementia and mild cognitive impairment are usually characterised in terms of measures of discrimination such as sensitivity, specificity, and likelihood ratios. However, CSIs also have limitations. Several metrics exist which may be used to denote test limitations but they are seldom examined. Data from several pragmatic test accuracy studies of CSIs were interrogated to calculate various measures of limitation, namely: misclassification rate; net harm to net benefit ratio; and the likelihood to be diagnosed or misdiagnosed. Intra- and inter-test performance for measures of discrimination and limitation were compared. The study found that some tests with very high sensitivity but low specificity for dementia fared poorly on measures of limitation, with high misclassification rates, low net harm to net benefit ratios, and low likelihoods to be diagnosed or misdiagnosed; some had likelihoods favouring misdiagnosis over diagnosis. Tests with a better balance of sensitivity and specificity fared better on measures of limitation. When choosing which CSIs to administer, measures of test limitation should be considered as well as measures of test discrimination. Although high test sensitivity may be desirable to avoid false negatives, false positives also have a cost. Identification of tests having high misclassification rate, low net harm to net benefit ratio, and low likelihood to be diagnosed or misdiagnosed, may have implications for their use in clinical practice.
Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain
Authors: Newton JC , Li GY , Naik MT , Fawzi NL , Sedivy JM , Jogl G 
Published: October 2020

AbstractLong Interspersed Nuclear Element-1 (LINE-1 or L1) is a retrotransposable element that autonomously replicates in the human genome, resulting in DNA damage and genomic instability. Activation of L1 in senescent cells triggers a type I interferon response and age-associated inflammation. Two open reading frames encode an ORF1 protein functioning as mRNA chaperone and an ORF2 protein providing catalytic activities necessary for retrotransposition. No function has been identified for the conserved, disordered N-terminal region of ORF1. Using microscopy and NMR spectroscopy, we demonstrate that ORF1 forms liquid droplets in vitro in a salt-dependent manner and that interactions between its N-terminal region and coiled-coil domain are necessary for phase separation. Mutations disrupting blocks of charged residues within the N-terminus impair phase separation while some mutations within the coiled-coil domain enhance phase separation. Demixing of the L1 particle from the cytosol may provide a mechanism to protect the L1 transcript from degradation.Statement of significanceOver half of the human genome is comprised of repetitive sequences. The Long Interspersed Nuclear Element-1 (L1) is an autonomous mobile DNA element that can alter its genomic location, resulting in genomic instability and DNA damage. L1 encodes two proteins that are required for this function: the ORF1 RNA chaperone and the enzymatic ORF2. Here, we demonstrate that ORF1 forms liquid-liquid phase separated states in vitro, which is mediated by electrostatic interactions between the conserved, disordered N-terminus and coiled-coil domain. This work provides a framework to explore how L1 phase separation may enhance the ability of the retrotransposable element to colonize the genome by preventing degradation of the L1 transcript and evasion of host immune responses.
MiSebastes: An eDNA metabarcoding primer set for rockfishes (genusSebastes)
Authors: Min Markus A. , Barber Paul H. , Gold Zachary 
Published: October 2020

AbstractEnvironmental DNA (eDNA) is a promising biomonitoring tool for marine ecosystems, but its effectiveness for North Pacific coastal fishes is limited by the inability of existing barcoding primers to differentiate among rockfishes in the genusSebastes.Comprised of 110 commercially and ecologically important species, this recent radiation is exceptionally speciose, and exhibits high sequence similarity among species at standard barcoding loci. Here, we report newSebastes-specific metabarcoding primers that target mitochondrialcytochrome B.Amongst the 110Sebastesspecies, 85 unique barcodes (of which 62 are species-specific) were identified in our amplicon region based on available reference sequences. The majority of the remaining barcodes are shared by only two species. Importantly, MiSebastes yield unique barcodes for 28 of 44 commercially harvested species in California, a dramatic improvement compared to the widely employed MiFish12Sprimers which only recover one of 44. Tests of these primers in an aquarium mesocosm containing 16 rockfish species confirms the utility of these new primers for eDNA metabarcoding, providing an important biomonitoring tool for these key coastal marine fishes.
Synergism of TNF-α and IFN-γ triggers inflammatory cell death, tissue damage, and mortality in SARS-CoV-2 infection and cytokine shock syndromes
Authors: Karki Rajendra , Sharma Bhesh Raj , Tuladhar Shraddha , Williams Evan Peter , Zalduondo Lillian , Samir Parimal , Zheng Min , Sundaram Balamurugan , Banoth Balaji , Malireddi R. K. Subbarao , Schreiner Patrick , Neale Geoffrey , Vogel Peter , Webby Richard , Jonsson Colleen Beth , Kanneganti Thirumala-Devi 
Published: October 2020

SUMMARYThe COVID-19 pandemic has caused significant morbidity and mortality. Currently, there is a critical shortage of proven treatment options and an urgent need to understand the pathogenesis of multi-organ failure and lung damage. Cytokine storm is associated with severe inflammation and organ damage during COVID-19. However, a detailed molecular pathway defining this cytokine storm is lacking, and gaining mechanistic understanding of how SARS-CoV-2 elicits a hyperactive inflammatory response is critical to develop effective therapeutics. Of the multiple inflammatory cytokines produced by innate immune cells during SARS-CoV-2 infection, we found that the combined production of TNF-α and IFN-γ specifically induced inflammatory cell death, PANoptosis, characterized by gasdermin-mediated pyroptosis, caspase-8-mediated apoptosis, and MLKL-mediated necroptosis. Deletion of pyroptosis, apoptosis, or necroptosis mediators individually was not sufficient to protect against cell death. However, cells deficient in both RIPK3 and caspase-8 or RIPK3 and FADD were resistant to this cell death. Mechanistically, the JAK/STAT1/IRF1 axis activated by TNF-α and IFN-γ co-treatment induced iNOS for the production of nitric oxide. Pharmacological and genetic deletion of this pathway inhibited pyroptosis, apoptosis, and necroptosis in macrophages. Moreover, inhibition of PANoptosis protected mice from TNF-α and IFN-γ-induced lethal cytokine shock that mirrors the pathological symptoms of COVID-19. In vivo neutralization of both TNF-α and IFN-γ in multiple disease models associated with cytokine storm showed that this treatment provided substantial protection against not only SARS-CoV-2 infection, but also sepsis, hemophagocytic lymphohistiocytosis, and cytokine shock models, demonstrating the broad physiological relevance of this mechanism. Collectively, our findings suggest that blocking the cytokine-mediated inflammatory cell death signaling pathway identified here may benefit patients with COVID-19 or other cytokine storm-driven syndromes by limiting inflammation and tissue damage. The findings also provide a molecular and mechanistic description for the term cytokine storm. Additionally, these results open new avenues for the treatment of other infectious and autoinflammatory diseases and cancers where TNF-α and IFN-γ synergism play key pathological roles.
Environmental DNA degradation simulation from water temperature and DNA fragment length: A meta-analysis approach
Authors: Saito Tatsuya , Doi Hideyuki 
Published: October 2020

AbstractEnvironmental DNA (eDNA) analysis can detect aquatic organisms, including rare and endangered species, in a variety of habitats. The degradation of eDNA concentration is important to investigate their distribution and has also been experimentally evaluated. It is important to integrate these data to synthesize eDNA degradation in various environments. We collected the eDNA degradation rates and related factors, especially water temperature and fragment lengths of the measured DNA from 28 studies. Our results suggest that water temperature and fragment length are significantly related to the eDNA degradation rate. From the 95% quantile model simulation, we predicted the maximum eDNA degradation rate in various combinations of water temperature and fragment length. Predicting eDNA degradation could be important for evaluating species distribution and inducing innovation of eDNA methods, especially for rare and endangered species with lower DNA concentrations.