bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictions of TeV emission for a set of hard BL Lac objects
Authors: Paiano Simona , Treves Aldo , Franceschini Alberto , Falomo Renato 
Published: October 2021

ABSTRACT
We focus our analysis on 55 BL Lac objects with a hard Fermi gamma-ray spectrum, and for which a redshift or a lower limit to it has been determined by a previous study of ours. We extrapolate the spectral fits given by the 4FGL catalogue to the VHE band (&gt;0.1 TeV), which can be explored by imaging atmospheric Cherenkov telescopes. Furthermore, we take into account the absorption due to the extragalactic background light, strongly depending on the redshift. Finally, we compare our results with publicly available sensitivity curves for a selection of imaging atmospheric Cherenkov telescope arrays currently operating or under construction. From our extrapolations and simulations we find a large number of promising candidates for observation with the forthcoming Cherenkov Telescope Array observatory.
Controls for Phylogeny and Robust Analysis in Pareto Task Inference
Authors: Adler Miri , Tendler Avichai , Hausser Jean , Korem Yael , Szekely Pablo , Bossel Noa , Hart Yuval , Karin Omer , Mayo Avi , Alon Uri 
Published: October 2021

Abstract
Understanding the tradeoffs faced by organisms is a major goal of evolutionary biology. One of the main approaches for identifying these tradeoffs is Pareto task inference (ParTI). Two recent papers claim that results obtained in ParTI studies are spurious due to phylogenetic dependence (Mikami T, Iwasaki W. 2021. The flipping t-ratio test: phylogenetically informed assessment of the Pareto theory for phenotypic evolution. Methods Ecol Evol. 12(4):696–706) or hypothetical p-hacking and population-structure concerns (Sun M, Zhang J. 2021. Rampant false detection of adaptive phenotypic optimization by ParTI-based Pareto front inference. Mol Biol Evol. 38(4):1653–1664). Here, we show that these claims are baseless. We present a new method to control for phylogenetic dependence, called SibSwap, and show that published ParTI inference is robust to phylogenetic dependence. We show how researchers avoided p-hacking by testing for the robustness of preprocessing choices. We also provide new methods to control for population structure and detail the experimental tests of ParTI in systems ranging from ammonites to cancer gene expression. The methods presented here may help to improve future ParTI studies.
Complex Portal 2022: new curation frontiers
Authors: Meldal Birgit H M , Perfetto Livia , Combe Colin , Lubiana Tiago , Ferreira Cavalcante João Vitor , Bye-A-Jee Hema , Waagmeester Andra , del-Toro Noemi , Shrivastava Anjali , Barrera Elisabeth , Wong Edith , Mlecnik Bernhard , Bindea Gabriela , Panneerselvam Kalpana , Willighagen Egon , Rappsilber Juri , Porras Pablo , Hermjakob Henning , Orchard Sandra 
Published: October 2021

Abstract
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from a range of model organisms. It summarizes complex composition, topology and function along with links to a large range of domain-specific resources (i.e. wwPDB, EMDB and Reactome). Since the last update in 2019, we have produced a first draft complexome for Escherichia coli, maintained and updated that of Saccharomyces cerevisiae, added over 40 coronavirus complexes and increased the human complexome to over 1100 complexes that include approximately 200 complexes that act as targets for viral proteins or are part of the immune system. The display of protein features in ComplexViewer has been improved and the participant table is now colour-coordinated with the nodes in ComplexViewer. Community collaboration has expanded, for example by contributing to an analysis of putative transcription cofactors and providing data accessible to semantic web tools through Wikidata which is now populated with manually curated Complex Portal content through a new bot. Our data license is now CC0 to encourage data reuse. Users are encouraged to get in touch, provide us with feedback and send curation requests through the ‘Support’ link.
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis
Authors: Baltoumas Fotis A , Zafeiropoulou Sofia , Karatzas Evangelos , Paragkamian Savvas , Thanati Foteini , Iliopoulos Ioannis , Eliopoulos Aristides G , Schneider Reinhard , Jensen Lars Juhl , Pafilis Evangelos , Pavlopoulos Georgios A 
Published: October 2021

Abstract
Extracting and processing information from documents is of great importance as lots of experimental results and findings are stored in local files. Therefore, extracting and analyzing biomedical terms from such files in an automated way is absolutely necessary. In this article, we present OnTheFly2.0, a web application for extracting biomedical entities from individual files such as plain texts, office documents, PDF files or images. OnTheFly2.0 can generate informative summaries in popup windows containing knowledge related to the identified terms along with links to various databases. It uses the EXTRACT tagging service to perform named entity recognition (NER) for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and gene ontology terms. Multiple files can be analyzed, whereas identified terms such as proteins or genes can be explored through functional enrichment analysis or be associated with diseases and PubMed entries. Finally, protein–protein and protein–chemical networks can be generated with the use of STRING and STITCH services. To demonstrate its capacity for knowledge discovery, we interrogated published meta-analyses of clinical biomarkers of severe COVID-19 and uncovered inflammatory and senescence pathways that impact disease pathogenesis. OnTheFly2.0 currently supports 197 species and is available at http://bib.fleming.gr:3838/OnTheFly/ and http://onthefly.pavlopouloslab.info.
Implicit–explicit gradient of nondual awareness or consciousness as such
Authors: Josipovic Zoran 
Published: October 2021

AbstractConsciousness is multi-dimensional but is most often portrayed with a two-dimensional (2D) map that has global levels or states on one axis and phenomenal contents on the other. On this map, awareness is conflated either with general alertness or with phenomenal content. This contributes to ongoing difficulties in the scientific understanding of consciousness. Previously, I have proposed that consciousness as such or nondual awareness—a basic non-conceptual, non-propositional awareness in itself free of subject-object fragmentation—is a unique kind that cannot be adequately specified by this 2D map of states and contents. Here, I propose an implicit–explicit gradient of nondual awareness to be added as the z-axis to the existing 2D map of consciousness. This gradient informs about the degree to which nondual awareness is manifest in any experience, independent of the specifics of global state or local content. Alternatively, within the multi-dimensional state space model of consciousness, nondual awareness can be specified by several vectors, each representing one of its properties. In the first part, I outline nondual awareness or consciousness as such in terms of its phenomenal description, its function and its neural correlates. In the second part, I explore the implicit–explicit gradient of nondual awareness and how including it as an additional axis clarifies certain features of everyday dualistic experiences and is especially relevant for understanding the unitary and nondual experiences accessed via different contemplative methods, mind-altering substances or spontaneously.
O022 Long-term cardiovascular risk in obstructive sleep apnoea: a sleep clinic cohort study
Authors: Shenoy B , Singh B , Cadby G , McQuillan B , Hung J , Rea S , Walsh J , Eastwood P , Hillman D , Mukherjee S , Palmer L , McArdle N 
Published: October 2021

Abstract
The relationship between obstructive sleep apnoea (OSA) and the development of long-term cardiovascular disease (CVD) is incompletely understood. We therefore investigated the impact of OSA severity, assessed by polysomnographic (PSG) metrics, on the development of long-term CVD in a sleep clinic cohort.
Participants in the Western Australian Sleep Health Study, who attended a sleep clinic at a tertiary hospital between 2006 and 2010, were linked to state health administrative data from 1969 to 2016. Cox regression was used to investigate associations between standard PSG metrics of OSA severity (including the apnoea-hypopnoea index [AHI], time with oxygen saturation &lt;90% [T90], and arousal index) and a CVD composite outcome (hospitalisation due to coronary heart disease, heart failure, stroke, or atrial fibrillation), controlling for baseline CVD risk factors such as age, sex, and body mass index (BMI).
A total of 4067 participants were included: mean (SD) age of 50.6 (14.0) years, with 60.8% men. The mean BMI was 32.7 (7.7) kg/m². Over a median follow-up of 7.3 years, 584 (14.4%) participants developed the composite CVD outcome. Following adjustment for risk factors, independent predictors of incident CVD were an AHI ≥30 events/hour (hazard ratio [HR], 1.21; 95% CI, 1.02–1.45), log (T90 + 1) (HR, 1.16; 95% CI, 1.03–1.31), and the periodic limb movements of sleep index (PLMSI) (HR, 1.01; 95% CI, 1.00–1.01).
We demonstrated independent effects of AHI, hypoxaemia, and PLMSI on incident CVD in this large sleep clinic cohort, suggesting multi-faceted aspects of disrupted sleep influence cardiovascular risk in OSA.
O030 Changes in sleep-wake patterns, circadian timing, and mood in Australian teens during the COVID-19 pandemic
Authors: Stone J , Phillips A , Wiley J , Chachos E , Hand A , Lu S , Carskadon M , Klerman E , Lockley S , Bei B , Rajaratnam S 
Published: October 2021

Abstract
During the COVID-19 pandemic, schools rapidly transitioned from in-person to remote learning. We examined sleep- and mood-related changes in early adolescents, before and after this transition to assess the impact of in-person vs. remote learning. Sleep-wake timing was measured using wrist-actigraphy and sleep diaries over 1–2 weeks in Year 7 students (age M±SD =12.79±0.42 years) during in-person learning (n=28) and remote learning (n=58; n=27 were studied in both conditions). Circadian timing was measured under a single condition in each individual using salivary melatonin (Dim Light Melatonin Onset; DLMO). Online surveys assessed mood (PROMIS Pediatric Anxiety and Depressive Symptoms) and sleepiness (Epworth Sleepiness Scale – Child and Adolescent) in each condition. During remote vs. in-person learning: (i) on school days, students went to sleep 26 min later and woke 49 min later, resulting in 22 min longer sleep duration (all p&lt;0.0001); (ii) DLMO time did not differ significantly between conditions, although participants woke at a later relative circadian phase (43 minutes, p=0.03) during remote learning; (iii) participants reported significantly lower sleepiness (p=0.048) and lower anxiety symptoms (p=0.006). Depressive symptoms did not differ between conditions. Changes in mood symptoms were not mediated by changes in sleep timing. Although remote learning had the same school start times as in-person learning, removing morning commutes likely enabled adolescents to sleep longer, wake later, and to wake at a later circadian phase. These results indicate that remote learning, or later school start times, may extend sleep duration and improve some subjective symptoms in adolescents.
P044 Primary care management of chronic insomnia by general practitioners: an Australian perspective
Authors: Grivell N , Haycock J , Redman A , Saini B , Vakulin A , Lack L , Lovato N , Sweetman A , Zwar N , Stocks N , Franks O , Mukherjee S , Adams R , McEvoy R , Hoon E 
Published: October 2021

Abstract

Introduction
Chronic insomnia is a common sleep disorder, with an estimated 15% of Australian adults reporting symptoms of insomnia. Australian general practitioner (GP) guidelines recommend cognitive behavioural therapy for insomnia (CBTi) as first-line treatment for insomnia however research suggests that GPs instead rely heavily on sleep hygiene and pharmacotherapy. GPs commonly provide treatment for insomnia; however, little is known about the experiences of Australian GPs and their interest when managing patients with insomnia. This study was conducted to explore the perspectives of GPs towards insomnia management and to identify factors that could influence the implementation of new models of insomnia care within general practice.

Methods
A pragmatic, inductive qualitative study. Purposive sampling was used to recruit 28 Australian GPs varying in age, experience, and distance from specialist sleep services. Semi-structured interviews were conducted, and data were analysed using thematic analysis.

Results
Three themes were identified: 1) Responsibility for insomnia care; 2) Complexities in managing insomnia; and 3) Navigating treatment pathways. Whilst GPs accepted insomnia care as part of their role, they often found it difficult to provide evidence-based care within the time and funding limitations of general practice. Co-morbidity of mental health conditions and insomnia, and long-term use of benzodiazepines presented challenges for GPs. GPs’ knowledge and experience of CBTi and access to specialised referral pathways for insomnia was limited.

Discussion
Insomnia presents complexities for GPs. Education about insomnia treatments, funding that enables recommended treatment, and pathways to specialist services would support insomnia management within general practice.
P050 Familiar locations and new locations: sleep’s role in the consolidation of spatial navigation information using a novel virtual Morris water maze task in older adults with mild cognitive impairment
Authors: Haroutonian C , Johnston I , Ricciardiello A , Lam A , Grunstein R , D’Rozario A , Naismith S 
Published: October 2021

Abstract

Introduction
The ability to navigate oneself in space is one of the first functional impairments in Alzheimer’s disease (AD). A 3D-computerised spatial navigation (SN) task was designed to delineate, for the first time in a sleep-dependent memory paradigm, egocentric and allocentric SN, the latter identified as one cognitive biomarker of AD. We examined group differences in SN memory and associations with sleep macroarchitecture.

Methods
Older adults with mild cognitive impairment (MCI, n=32) and controls (n=25) underwent overnight polysomnography and completed the SN task before and after sleep. Participants learnt the location of a target over 5 trials (familiar location; egocentric-dependent), then were instructed to find the target from a novel start location (allocentric-dependent). Memory % retention (MR) from both start locations were calculated by the XY coordinate of marked location to correct location of the target, pre- and post-sleep. Navigational strategies were coded using self-reported description of how participants’ found the target. Associations between MR with REM and SWS % duration, and AHI in REM and NREM were examined using Spearman’s correlations.

Results
Repeated-measures ANOVA showed Controls MR improved overnight whereas MCI performed worse (F=7.46, p=.009), with greatest differences on familiar start location MR (p=.02). Strategy as a covariate revealed a location by strategy interaction (p=01). Novel location MR was associated with REM%, rho=.448, (p=.02) in Controls, and REM-AHI, rho=.400 (p=.02) in MCI.

Conclusion
Behavioural and self-reported results suggest disrupted SN strategies relative to environment in MCI. Future studies should examine SN in association with sleep-wake neurophysiology and neuronal integrity.
P110 The association between sleep spindles and cognitive function in middle-aged and older men: A community-based study
Authors: Parker J , Melaku Y , D’Rozario A , Wittert G , Martin S , Catcheside P , Lechat B , Teare A , Appleton S , Adams R , Vakulin A 
Published: October 2021

Abstract

Introduction
The association between sleep spindles and cognitive function and the potential confounding influence of obstructive sleep apnea (OSA) remains uncertain. This study examined cross-sectional associations between sleep spindle metrics and cognitive function outcomes in community-dwelling men.

Methods
Men, Androgen, Inflammation, Lifestyle, Environment, and Stress (MAILES) study participants (n=477) underwent home-based polysomnography between 2010–2011 and completed the inspection time task, trail-making test A (TMT-A) and B (TMT-B), and Fuld object memory evaluation. Frontal spindle metrics derived from sleep electroencephalography included occurrence (total no. of sleep spindle events) and slow (11–13 Hz) and fast (13–16 Hz) spindle density (no./min) during N2 and N3 sleep.

Results
Men with OSA (any OSA and severe OSA) had significantly impaired sleep spindles (reduced occurrence and densities). In the complete study sample, higher spindle occurrence during N2 sleep was independently associated with faster inspection time (B= -0.44, 95% CI [-0.87, -0.02], p=0.041), whereas higher fast spindle density during N3 sleep was independently associated with worse TMT-B performance (B=20.7, 95% CI [0.55, 40.9], p=0.044). Furthermore, in men with severe OSA (apnea-hypopnea index ≥30/h), higher slow spindle density during N2 sleep was independently associated with worse TMT-A and TMT-B performance, whereas only higher spindle occurrence during N2 sleep was independently associated with worse TMT-A performance (all p&lt;0.05).

Discussion
Specific spindle metrics during N2 and N3 sleep are independently associated with cognitive function in an unselected population of men and men with undiagnosed severe OSA. The utility of sleep spindles for predicting cognitive dysfunction and decline requires further investigation.
P114 The effect of light interventions on sleep macro- and micro-architecture in sleep and circadian rhythm disorders: A scoping review
Authors: Pun T , Phillips C , Marshall N , Comas M , Hoyos C , D’Rozario A , Bartlett D , Davis W , Hu W , Naismith S , Cain S , Postnova S , Grunstein R , Gordon C 
Published: October 2021

Abstract

Introduction
Light interventions have been used to treat sleep and circadian rhythm disorders. However, there are limited studies on the effect of light on electroencephalographic (EEG) activity during sleep. Therefore, we aimed to provide an overview of research using light intervention on sleep macro- and micro-architecture.

Methods
We searched for randomised controlled trials that used light interventions and examined the effect on sleep measured using EEG in MEDLINE, PubMed, CINAHL, CENTRAL and PsycINFO databases. We included studies that examined the light intervention on sleep EEG in participants with a sleep or circadian rhythm disorder.

Results
Four studies met the inclusion criteria in patients with insomnia only. These studies reported only sleep macro-architecture outcomes with three studies showing no effect of the timing or intensity of light intervention on total sleep time, wake after sleep onset, sleep efficiency and sleep stage duration. Only one study reported a significantly higher sleep efficiency after night-time light intervention (&gt;4,000 lx, 21:00-23:00 h) compared with afternoon light intervention (&gt;4,000 lx, 15:00-17:00 h). However, none of these studies reported sleep micro-architecture (power spectral analysis).

Conclusion
Overall, there was limited evidence about the effect of light intervention on EEG sleep measures and studies were confined to insomnia patients only. This review could not find any data on sleep EEG spectral power related to light interventions. Research needs to be conducted into the effect of lighting interventions in clinical populations on sleep macro- and micro-architecture to better understand the effect on objective sleep timing and quality.
P119 CPAP and adverse cardiovascular events in OSA: Are participants of randomized trials representative of sleep clinic patients?
Authors: Reynor A , McArdle N , Shenoy B , Dhaliwal S , Rea S , Walsh J , Eastwood P , Maddison K , Hillman D , Ling I , Keenan B , Maislin G , Magalang U , Pack A , Mazzotti D , Lee R , Singh B 
Published: October 2021

Abstract

Introduction
Randomized controlled trials (RCTs) have shown no reduction in adverse cardiovascular (CV) events in patients randomized to continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea (OSA). This study examined whether randomized study populations were representative of OSA patients attending a sleep clinic.

Methods
Sleep clinic patients were 3,965 consecutive adults diagnosed with OSA by in-laboratory polysomnography from 2006–2010 at a tertiary hospital sleep clinic. Characteristics of these sleep clinic OSA patients were compared with participants of 5 well-known RCTs examining the effect of CPAP on adverse CV events in OSA. We determined the percentage of patients with severe (apnea hypopnea index, [AHI]≥30/h) or any OSA (AHI≥5/h) who met the selection criteria of each RCT, as well as identified those criteria that excluded the most patients.

Results
Compared to RCT participants, sleep clinic OSA patients were younger, sleepier, more likely to be female and less likely to have established CV disease. The percentage of patients with severe or any OSA who met the RCT selection criteria ranged from 1.2% to 20.2% and 0.8% to 21.1%, respectively. The selection criteria that excluded most patients were pre-existing CV disease, symptoms of excessive sleepiness, nocturnal hypoxemia and co-morbidities.

Discussion
A minority of sleep clinic patients diagnosed with OSA meet the selection criteria of RCTs of CPAP on adverse CV events in OSA. OSA populations in RCTs differ considerably from typical sleep clinic OSA patients. This suggests that the findings of RCTs may not be generalisable to most sleep clinic OSA patients.
P133 Backward Rotating Shifts are Associated with Real-Time Drowsiness During Daytime Drives in Heavy Vehicle Drivers
Authors: Shekari Soleimanloo S , Sletten T , Clark A , Cori J , Wolkow A , Beatty C , Shiferaw B , Barnes M , Tucker A , Anderson C , Rajaratnam S , Howard M 
Published: October 2021

Abstract

Purpose
While 10–20% of heavy vehicle crashes (HVDs) are drowsiness-related, the contributions of subsequent shifts to chronic drowsiness in HVDs is largely unknown. Eye-blink parameters indicate driver drowsiness reliably. This study examined the association of consecutive shifts and real-time drowsiness in HVDs.

Methods
Habitual sleep-wake of HVDs (all males, aged 49.5 ± 8 years) was monitored objectively (Philips Actiwatch, N=15) for 5 weeks (5.75± 1.4 hours). Johns Drowsiness Score (JDS, a composite eye-blink parameter in one-min intervals) was monitored for 4 weeks in HVDs (N=14) using an infrared oculography (Optalert, Melbourne, Australia) device. We assessed the association of drowsiness events (JDS equal or larger than 2.6) with consecutive shift types via mixed linear regression models.

Results
Eigth consecutive shifts increased drowsiness by 1.06 times compared to 2 shifts (8.37 events/h vs 6.77 events/h, P= 0.03). Consecutive shift sequences included afternoons (9%), mornings (29%), nights (5%), mixed rotating shifts (28%), forward-rotating shifts (11%) and backward-rotating shifts (12%). Drowsiness event rates were 1.23 times greater during night consecutive shifts relative to afternoon shifts (8.37 events/h vs 6.67 events/h, P= 0.03). Backward-rotating shifts (morning-night-evening- afternoon) elevated daytime drowsiness between 10 am and 3 pm by 1.55 times (10.01 events/h vs 6.47 events/h, P= 0.016).

Conclusions
Regardless of the number of consecutive shifts, sequential night shifts increase real-time drowsiness in HVDs, with backward rotating shifts resulting in higher rates of drowsiness events during daytime. The interaction of schedule features should inform the work scheduling of HVDs to reduce the risk of drowsiness.