bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tackling Data Disclosure Comparatively – Conference ‘Vectors of Data Disclosure’ in Munich, 27 and 28 June 2022
Authors: Illek Lukas 
Published: December 2022

Abstract
The disclosure of personal data and the decision by individuals to do so is ubiquitous. Which aspects influence this decision? How is disclosure regulated in different jurisdictions and how far do protective mechanisms go in favor of the ‘data subject’? These questions only scratch the surface of topics which the University of Passau research project ‘Vectors of Data Disclosure’ is addressing comparatively and with regard to Brazil, China, the European Union, Ghana, Japan, Russia, Switzerland, and the United States since January 2021. The project takes an interdisciplinary approach and aims to tackle these questions by combining cultural, legal, and business information systems perspectives. The project is led by Moritz Hennemann, Daniela Wawra, Kai von Lewinski and Thomas Widjaja. Concluding the first 18 months of the project, the project team invited international experts from different disciplines to Munich, offering a platform to discuss new insights and receive feedback on the project’s preliminary research results so far.
Effects of Morning or Evening Narrow-band Blue Light on the Compensation to Lens-induced Hyperopic Defocus in Chicks
Authors: Nickla Debora L. , Wang Xia , Rucker Frances , Chen William , Taylor Christopher 
Published: December 2022

ABSTRACT

SIGNIFICANCE
Exposure to blue light before bedtime is purported to be deleterious to various aspects of human health. In chicks, blue evening light stimulated ocular growth, suggesting a role in myopia development. To further investigate this hypothesis, we asked if brief blue light altered the compensatory responses to hyperopic defocus.

PURPOSE
Previous work showed that several hours' evening exposure to blue light stimulated ocular growth in chicks, but morning exposure was only effective at a lower illuminance. By contrast, rearing in blue light has inhibited ocular growth in untreated eyes and eyes exposed to form deprivation or defocus. We studied the effects of brief exposures to blue light on the compensation to hyperopic defocus.

METHODS
Chicks wore monocular negative lenses (−10 D) starting at age 10 days. They were subsequently exposed to blue light (460 nm) for 4 hours in the morning or evening for 8 to 9 days (“dim,” 200 lux[morning, n = 9; evening, n = 11]; “bright,” 600 lux[morning, n = 8; evening, n = 20]); controls wore lenses in white light (n = 14). Ultrasonography was done on days 1, 5, 8, and 9 for “evening” groups and days 1, 6, and 8 for “morning.” All data are reported as interocular differences (experimental minus fellow eyes). Refractions were measured on the last day.

RESULTS
For evening exposure, dim blue light enhanced the axial compensation at all times (change in axial length: day 6: 465 vs. 329 μm/9 days, analysis of variance P < .001, P = .03; day 9: 603 vs. 416 μm/9 days, analysis of variance P < .001; P < .05). Bright blue light had a transient inhibitory effect (day 5: 160 vs. 329 μm; P < .005). Refractive errors were consistent with axial growth, with dim causing more myopia than bright (−9.4 vs. −4.7 D; P < .05). Morning blue light had no significant effect.

CONCLUSIONS
We speculate that these findings reflect a complex interaction between illuminance, defocus, and time of day.
Integrated Host/Microbe Metagenomics Enables Accurate Lower Respiratory Tract Infection Diagnosis in Critically Ill Children
Authors: Mick Eran , Tsitsiklis Alexandra , Kamm Jack , Kalantar Katrina L. , Caldera Saharai , Lyden Amy , Tan Michelle , Detweiler Angela M. , Neff Norma , Osborne Christina M. , Williamson Kayla M. , Soesanto Victoria , Leroue Matthew , Maddux Aline B. , Simões Eric A. F. , Carpenter Todd C. , Wagner Brandie D. , DeRisi Joseph L. , Ambroggio Lilliam , Mourani Peter M. , Langelier Charles R. 
Published: December 2022

ABSTRACTBACKGROUNDLower respiratory tract infection (LRTI) is a leading cause of death in children worldwide. LRTI diagnosis is challenging since non-infectious respiratory illnesses appear clinically similar and existing microbiologic tests are often falsely negative or detect incidentally-carried microbes, resulting in antimicrobial overuse and adverse outcomes. Lower airway metagenomics has the potential to detect host and microbial signatures of LRTI. Whether it can be applied at scale and in a pediatric population to enable improved diagnosis and treatment remains unclear.METHODSWe used tracheal aspirate RNA-sequencing to profile host gene expression and respiratory microbiota in 261 children with acute respiratory failure. We developed a gene expression classifier for LRTI by training on patients with an established diagnosis of LRTI (n=117) or of non-infectious respiratory failure (n=50). We then developed a classifier that integrates the host LRTI probability, abundance of respiratory viruses, and dominance in the lung microbiome of bacteria/fungi considered pathogenic by a rules-based algorithm.RESULTSThe host classifier achieved a median AUC of 0.967 by cross-validation, driven by activation markers of T cells, alveolar macrophages and the interferon response. The integrated classifier achieved a median AUC of 0.986 and increased the confidence of patient classifications. When applied to patients with an uncertain diagnosis (n=94), the integrated classifier indicated LRTI in 52% of cases and nominated likely causal pathogens in 98% of thoseCONCLUSIONSLower airway metagenomics enables accurate LRTI diagnosis and pathogen identification in a heterogeneous cohort of critically ill children through integration of host, pathogen, and microbiome features.
Identifying secondary findings in PET/CT reports in oncological cases: A quantifying study using automated Natural Language Processing
Authors: Sekler Julia , Kämpgen Benedikt , Reinert Christian Philipp , Daul Andreas , Gückel Brigitte , Dittmann Helmut , Pfannenberg Christina , Gatidis Sergios 
Published: December 2022

AbstractBackgroundBecause of their accuracy, positron emission tomography/computed tomography (PET/CT) examinations are ideally suited for the identification of secondary findings but there are only few quantitative studies on the frequency and number of those.Most radiology reports are freehand written and thus secondary findings are not presented as structured evaluable information and the effort to manually extract them reliably is a challenge. Thus we report on the use of natural language processing (NLP) to identify secondary findings from PET/CT conclusions.Methods4,680 anonymized German PET/CT radiology conclusions of five major primary tumor entities were included in this study. Using a commercially available NLP tool, secondary findings were annotated in an automated approach. The performance of the algorithm in classifying primary diagnoses was evaluated by statistical comparison to the ground truth as recorded in the patient registry. Accuracy of automated classification of secondary findings within the written conclusions was assessed in comparison to a subset of manually evaluated conclusions.ResultsThe NLP method was evaluated twice. First, to detect the previously known principal diagnosis, with an F1 score between 0.65 and 0.95 among 5 different principal diagnoses.Second, affirmed and speculated secondary diagnoses were annotated, and the error rate of false positives and false negatives was evaluated. Overall, rates of false-positive findings (1.0%-5.8%) and misclassification (0%-1.1%) were low compared with the overall rate of annotated diagnoses. Error rates for false-negative annotations ranged from 6.1% to 24%. More often, several secondary findings were not fully captured in a conclusion. This error rate ranged from 6.8% to 45.5%.ConclusionsNLP technology can be used to analyze unstructured medical data efficiently and quickly from radiological conclusions, despite the complexity of human language. In the given use case, secondary findings were reliably found in in PET/CT conclusions from different main diagnoses.
Osmotic fragility duringin vitroerythrocyte cytotoxicity induced by aluminium chloride, lead acetate or mercuric chloride in hyposmolar sucrose media
Authors: Igbokwe Nanacha Afifi , Igbokwe Ikechukwu Onyebuchi 
Published: December 2022

AbstractErythrocyte death by eryptosis or erythronecrosis may induce erythrocyte shrinking or swelling with increase in osmotic resistance or fragility as indication of cytotoxicity. We investigated heterogeneous cytotoxic outcomes during in vitro exposure of goat erythrocytes to aluminium chloride, lead acetate or mercuric chloride using erythrocyte osmotic fragility (EOF) testing. The metallic salt solution (MSS) was added to 4.0 μL of high (100 mosmol/L) and low (250 mosmol/L) hyposmolar sucrose media at 0.3 or 0.4 mosmol/L concentration during testing of the osmotic fragility of 5.0 μL of blood from 10 goats. Hemolysis induced in the media (with and without MSS) was estimated in the supernatant with spectrophotometer at 540 nm. Osmotic stabilization or destabilization was calculated with probability for each test. Inducible osmotic resistance (IOR) was the ratio of mean stabilization to destabilization in both high and low hyposmolar media. Each MSS induced both osmotic resistance (stabilization) and fragility (destabilization) in varied media concentrations, with greater likelihood (P) of stabilization (0.93) or destabilization (0.77) in high or low media hyposmolarity, respectively. The EOF outcomes of the goats diverged within the group. High IOR induced by mercuric chloride (2.90) and low IOR by lead acetate (0.07) and aluminium chloride (0.04) reflected high stabilizing and destabilizing outcomes, respectively. In conclusion, MSS induced dual EOF outcomes (stabilization or destabilization) on the fragility domain, suggesting occurrence of both eryptosis (as stabilization) and erythronecrosis (as destabilization) at low exposure level, whereby biphasic, nonmonotonic or hormetic response to MSS toxic action might exist.
Neuron-astrocyte metabolic coupling facilitates spinal plasticity and maintenance of persistent pain
Authors: Marty-Lombardi Sebastián , Lu Shiying , Ambroziak Wojciech , Wende Hagen , Schrenk-Siemens Katrin , DePaoli-Roach Anna A. , Hagenston Anna M. , Tappe-Theodor Anke , Simonetti Manuela , Kuner Rohini , Fleming Thomas , Siemens Jan 
Published: December 2022

AbstractLong-lasting pain stimuli can trigger maladaptive changes in the spinal cord, reminiscent of plasticity associated with memory formation. Metabolic coupling between astrocytes and neurons has been implicated in neuronal plasticity and memory formation in the CNS, but neither its involvement in pathological pain nor in spinal plasticity has been tested. Here, we report a novel form of neuroglia signaling involving spinal astrocytic glycogen dynamics triggered by persistent noxious stimulation via upregulation of the metabolic signaling molecule PTG exclusively in spinal astrocytes. PTG drove glycogen build-up in astrocytes, and blunting glycogen accumulation and turnover byPtggene deletion reduced pain-related behaviors and promoted faster recovery by shortening pain maintenance. Furthermore, mechanistic analyses revealed that glycogen dynamics is a critically required process for maintenance of pain by facilitating neuronal plasticity in spinal lamina 1 neurons. Finally, metabolic analysis indicated that glycolysis and lactate transfer between astrocytes and neurons fuels spinal neuron hyperexcitability.Spinal glycogen-metabolic cascades therefore hold therapeutic potential to alleviate pathological pain.
High resolution cryo-EM structures of two potently SARS-CoV-2 neutralizing monoclonal antibodies of same donor origin that vary in neutralizing Omicron variants
Authors: Rencilin Clayton Fernando , Ansari Mohammad Yousuf , Chatterjee Arnab , Deshpande Suprit , Mukherjee Sohini , Singh Randhir , Jayatheertha Sowrabha , Reddy Poorvi M. , Das Payel , Hingankar Nitin , Rathore Deepak , Varadarajan Raghavan , Bhattacharya Jayanta , Dutta Somnath 
Published: December 2022

AbstractWhile vaccines have by large been found to effective against the evolving SARS-CoV-2 variants, the profound and rapid effectivity of monoclonal antibodies (mAbs) in significantly reducing hospitalization to severe disease outcomes have also been demonstrated. In the present study, by high resolution cryo-electron microscopy (cryo-EM), we examined the structural insights of two trimeric spike (S) protein bound mAbs isolated from an Indian convalescent individual infected with ancestral SARS-CoV-2 which we recently reported to potently neutralize SARS-CoV-2 from its ancestral form through highly virulent Delta form however different in their ability to neutralize Omicron variants. Our findings showed binding and conformational heterogeneities of both the mAbs (THSC20.HVTR04 and THSC20.HVTR26) bound to S trimer in its apo and hACE-2 bound forms. Additionally, cryo-EM resolved structure assisted modeling highlighted key residues associated with the ability of these two mAbs to neutralize Omicron variants. Our findings highlighted key interacting features modulating antigen-antibody interacting that can further aid in structure guided antibody engineering to enhance their breadth and potency.HighlightsTwo potent human mAbs obtained from a single donor differ binding to Omicron spikesPattern of binding and conformation of these mAbs bound to full length spike differsAntibody binding alters the conformational states of S trimer in its apo and hACE-2 bound forms.Cryo-EM structure guided modeling highlighted correlates of interacting residues associated with resistance and sensitivity of BA.1, BA.2, BA.4/BA.5 resistance and sensitivity against these mAbs.
The PRALINE database: Protein and Rna humAn singLe nucleotIde variaNts in condEnsates
Authors: Vandelli Andrea , Segura Magdalena Arnal , Monti Michele , Fiorentino Jonathan , Broglia Laura , Colantoni Alessio , de Groot Natalia Sanchez , Burgas Marc Torrent , Armaos Alexandros , Tartaglia Gian Gaetano 
Published: December 2022

ABSTRACTSummaryBiological condensates are membraneless organelles with different material properties. Proteins and RNAs are the main components, but most of their interactions are still unknown. Here we introduce PRALINE, a database for the interrogation of proteins and RNAs contained in stress-granules, processing bodies, and other assemblies including droplets and amyloids. PRALINE provides information about the predicted and experimentally validated protein-protein, protein-RNA and RNA-RNA interactions. For proteins, it reports the liquid-liquid phase separation and liquid-solid phase separation propensities. For RNAs, it provides information on predicted secondary structure content. PRALINE shows detailed information on human single-nucleotide variants, their clinical significance and presence in protein and RNA binding sites, and how they can affect condensates’ physical properties.AvailabilityPRALINE is freely accessible on the web athttp://alvinlee.bio.uniroma1.it/praline.Supplementary informationGeneral information is athttp://alvinlee.bio.uniroma1.it/praline/about, where we provide a detailed description of the datasets and the tools employed in the database. Data provided in PRALINE are available athttp://alvinlee.bio.uniroma1.it/praline/downloads. The tutorial is athttp://alvinlee.bio.uniroma1.it/praline/tutorial.
Scope+: An open source generalizable architecture for single-cell atlases at sample and cell levels
Authors: Yin Danqing , Cao Yue , Chen Junyi , Mak Candice L.Y. , Yu Ken H.O. , Lin Yingxin , Zhang Jiaxuan , Li Jia , Ho Joshua W. K. , Yang Jean Y.H. 
Published: December 2022

AbstractWith the recent advancement in single-cell technologies and the increased availability of integrative tools, challenges arise in easy and fast access to large collections of cell atlas. Existing cell atlas portals rarely are open sourced and adaptable, and do not support meta-analysis at cell level. Here, we present an open source, highly optimised and scalable architecture, named Scope+, to allow quick access, meta-analysis and cell-level selection of the atlas data. We applied this architecture to our well-curated 5 million Covid-19 blood and immune cells, as a portal, Covidscope (https://covidsc.d24h.hk/). We achieved efficient access to atlas-scale data via three strategies, such as server-side rendering, novel database optimization strategies and an innovative architectural design. Scope+ serves as an open source architecture for researchers to build on with their own atlas, and demonstrated its capability in the Covidscope portal for an effective meta-analysis to atlas data at cellular resolution for reproducible research.
Evaluating the impact of minimum unit pricing for alcohol on road traffic accidents in Scotland: a controlled interrupted time series study
Authors: Manca Francesco , Parab Rakshita , Mackay Daniel , Fitzgerald Niamh , Lewsey Jim 
Published: December 2022

AbstractBackgroundOn 1stMay 2018, Scotland implemented Minimum Unit Pricing (MUP) of £0.50 per unit of alcohol to lower alcohol consumption and related harms, and reduce health inequalities. We assessed the impact of MUP on road traffic accidents (RTAs) after 20 months of implementation.MethodsA controlled interrupted time series design was used to evaluate the impact of MUP on RTAs (total, fatal, night-time) in Scotland and any effect modification across socio-economic deprivation groups. RTAs in England and Wales (E&W) were used as a control group. Covariates of severe weather events, bank holidays, seasonal and underlying trends were included.ResultsIn Scotland, MUP implementation was associated with a 7.2% (95% CI: 0.9%,13.7% P=0.03) increase in the total number of RTAs. For the corresponding period in E&W, there was a 0.9% increase (95% CI: -2.3%,3.2% P=0.75). It is implausible that MUP caused this increase in RTAs, with the most likely explanation of these results being that unmeasured time-varying confounding affected Scotland and E&W differently. There was no evidence of differential impacts of MUP by level of socio-economic deprivation.ConclusionThe introduction of MUP in Scotland was not associated with a lower level of RTAs.
Spatial organization of the mouse retina at single cell resolution
Authors: Choi Jongsu , Li Jin , Ferdous Salma , Liang Qingnan , Moffitt Jeffrey R. , Chen Rui 
Published: December 2022

SummaryThe visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. We performed spatial transcriptomic profiling of over 100,000 cells from the mouse retina, uncovering the spatial distribution of all major retina cell types with over 100 cell subtypes. Our data revealed that the retina is organized in a laminar structure at the major cell type and subgroup level, both of which has strong correlation with the birth order of the cell. In contrast, overall random dispersion of cells within sub-laminar layers indicates that retinal mosaics are driven by dendritic field patterning rather than neuron soma placement. Through the integration of single cell transcriptomic and spatial data, we have generated the first comprehensive spatial single cell reference atlas of the mouse retina, a resource to the community and an essential step toward gaining a comprehensive understanding of the mechanism of retinal function.Graphical Abstract
Robust Online Multiband Drift Estimation in Electrophysiology Data
Authors: Windolf Charlie , Paulk Angelique C. , Kfir Yoav , Trautmann Eric , Garcia Samuel , Meszéna Domokos , Muñoz William , Hardstone Richard , Caprara Irene , Jamali Mohsen , Boussard Julien , Williams Ziv M. , Cash Sydney S. , Paninski Liam , Varol Erdem 
Published: December 2022

ABSTRACTHigh-density electrophysiology probes have opened new possibilities for systems neuroscience in human and non-human animals, but probe motion (or drift) while recording poses a challenge for downstream analyses, particularly in human recordings. Here, we improve on the state of the art for tracking this drift with an algorithm termedDREDge(DecentralizedRegistration ofElectrophysiologyData) with four major contributions. First, we extend previous decentralized methods to exploitmultibandinformation, leveraging the local field potential (LFP), in addition to spikes detected from the action potentials (AP). Second, we show that the LFP-based approach enables registration atsub-secondtemporal resolution. Third, we introduce an efficientonlinemotion tracking algorithm, allowing the method to scale up to longer and higher spatial resolution recordings, which could facilitate real-time applications. Finally, we improve therobustnessof the approach by accounting for the nonstationarities that occur in real data and by automating parameter selection. Together, these advances enable fully automated scalable registration of challenging datasets from both humans and mice.
Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants
Authors: Li Min , Passos Dario Oliveira , Shan Zelin , Smith Steven J. , Sun Qinfang , Biswas Avik , Choudhuri Indrani , Strutzenberg Timothy S. , Haldane Allan , Deng Nanjie , Li Zhaoyang , Zhao Xue Zhi , Burke Terrence R. , Levy Ronald M. , Hughes Stephen H. , Craigie Robert , Lyumkis Dmitry 
Published: December 2022

ABSTRACTHIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug resistant HIV-1 intasomes bound toDTGor4d, with better than 3 Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms ofDTGresistance involving E138K+G140A/S+Q148H/K/R and show why4dmaintains potency better thanDTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.