bluuebunny/crossref_metadata_2025_split huggingface dataset:
The benefits of ensemble prediction for forecasting an extreme event: The Queensland Floods of February 2019
Authors: Hawcroft Matt , Lavender Sally , Copsey Dan , Milton Sean , Rodríguez José , Tennant Warren , Webster Stuart , Cowan Tim 
Published: May 2021

AbstractFrom late January to early February 2019, a quasi-stationary monsoon depression situated over northeast Australia caused devastating floods. During the first week of February, when the event had its greatest impact in northwest Queensland, record-breaking precipitation accumulations were observed in several locations, accompanied by strong winds, substantial cold maximum temperature anomalies and related wind chill. In spite of the extreme nature of the event, the monthly rainfall outlook for February issued by Australia’s Bureau of Meteorology on 31st January provided no indication of the event. In this study, we evaluate the dynamics of the event and assess how predictable it was across a suite of ensemble model forecasts using the UK Met Office numerical weather prediction (NWP) system, focussing on a one week lead time. In doing so, we demonstrate the skill of the NWP system in predicting the possibility of such an extreme event occurring. We further evaluate the benefits derived from running the ensemble prediction system at higher resolution than used operationally at the Met Office and with a fully coupled dynamical ocean. We show that the primary forecast errors are generated locally, with key sources of these errors including atmosphere-ocean coupling and a known bias associated with the behaviour of the convection scheme around the coast. We note that a relatively low resolution ensemble approach requires limited computing resource, yet has the capacity in this event to provide useful information to decision makers with over aweek’s notice, beyond the duration of many operational deterministic forecasts.
Winter Surface Air Temperature Prediction over Japan Using Artificial Neural Networks
Authors: Ratnam J. V. , Nonaka Masami , Behera Swadhin K. 
Published: May 2021

AbstractThe machine learning technique, namely artificial neural networks (ANN), is used to predict the surface air temperature (SAT) anomalies over Japan in the winter months of December, January, and February for the period 1949/50–2019/20. The predictions are made for the four regions Hokkaido, North, Central, and West of Japan. The inputs to the ANN model are derived from the anomaly correlation coefficients among the SAT anomalies over the regions of Japan and the global SAT and sea surface temperature anomalies. The results are validated using anomaly correlation coefficient (ACC) skill scores with the observation. It is found that the ANN predictions over Hokkaido have higher ACC skill scores compared to the ACC scores over the other three regions. The ANN-predicted SAT anomalies are compared with that of ensemble mean of eight of the North American Multimodel Ensemble (NMME) models besides comparing them with the persistent anomalies. The ANN predictions over all the four regions have higher ACC skill scores compared to the NMME model skill scores in the common period of 1982/83–2018/19. The ANN-predicted SAT anomalies also have higher hit rate and lower false alarm rate compared to the NMME-predicted SAT anomalies. All these indicate that the ANN model is a promising tool for predicting the winter SAT anomalies over Japan.
Severity of Sleep Apnea and COVID‐19 Illness
Authors: Kravitz Meryl B. , Yakubova Elizabeth , Yu Nick , Park Steven Y. 
Published: May 2021

ObjectiveTo characterize the relationship between severity of sleep apnea and coronavirus disease 2019 (COVID‐19) hospitalization and severe illness.Study DesignRetrospective cohort study.SettingMontefiore Health System in the Bronx, New York.MethodsThe data set consisted of adult patients with an active diagnosis of obstructive sleep apnea in the past 2 years and a positive severe acute respiratory syndrome coronavirus 2 quantitative polymerase chain reaction test at our institution between March 16, 2020, and May 26, 2020. Sleep apnea severity and continuous positive airway pressure compliance data were abstracted from the electronic medical record. The International Classification of Diseases, 10th Revision was used to classify comorbidities.ResultsA total of 461 patients with sleep apnea tested positive for COVID‐19, of whom 149 were excluded for missing data in the electronic medical record. Patients with moderate and severe sleep apnea had higher rates of COVID‐19 hospitalization compared to those with mild sleep apnea (P =. 003). This association was reduced when accounting for confounders, most notably the Charlson Comorbidity Index, a measure of comorbid illness burden. Moderate and severe sleep apnea were associated with increased Charlson Comorbidity Indices, compared to mild sleep apnea (P =. 01). Sleep apnea severity was not associated with a composite outcome of mechanical ventilation, intensive care unit admission, and death.ConclusionSleep apnea severity was associated with the Charlson Comorbidity Index and may be a risk factor for COVID‐19 hospitalization. We found no evidence that sleep apnea severity among hospitalized patients was associated with a composite outcome of mechanical ventilation, intensive care unit admission, and death.
Long term safety, tolerability, and efficacy of intracutaneous zolmitriptan (M207) in the acute treatment of migraine
Authors: Nahas Stephanie J. , Hindiyeh Nada , Friedman Deborah I. , Elbuluk Nada , Kellerman Donald J. , Foreman Pamela K. , Schmidt Peter 
Published: May 2021

Abstract
Objective
To determine the long-term safety and tolerability profile of M207 in the acute treatment of migraine.

Background
M207 is an investigational microneedle-based system for intracutaneous delivery of zolmitriptan for the treatment of migraine attacks. Following on the positive results of a Phase 2/3 placebo-controlled efficacy study (ZOTRIP), this study was designed to evaluate the safety of this novel product during repeated use for the treatment of migraine attacks.

Methods
In this 6–12 month open-label, multicenter observational study, participants used an eDiary to record headache symptoms and adverse events at specified intervals up to 48 h following treatment of a qualifying attack with M207 3.8 mg (intracutaneous zolmitriptan). Participants underwent clinical evaluations at specified intervals up to 12 months.

Results
Among 335 participants who treated ≥1 migraine attack, 257 completed 6 months and 127 completed 1 year of treatment. The most common reason for withdrawal from the study was a low frequency of reported attacks post randomization. Overall, 5963 migraine attacks were treated. Most participants (96%) experienced at least 1 adverse event, the vast majority of which concerned the application site, and > 95% of which were mild. Fifteen participants (4%) withdrew due to adverse events; 4 withdrew due to 7 application site reactions, 6 of which were mild.
Participants achieved pain freedom in 2477/5617 (44%) of attacks, most bothersome symptom freedom in 3315/5330 (62%) of attacks, and pain relief 2 h post-dose in 4552/5617 (81%) of attacks. Sustained pain freedom 2–24 h was seen in 1761/4698 (38%) of attacks, and 2–48 h in 1534/4429 (35%) of attacks.

Conclusions
The majority of participants experienced cutaneous adverse reactions such as application site erythema, swelling, and bleeding, and most reactions were scored as mild. These results are consistent with what was observed in the single migraine attack treatment ZOTRIP trial indicating that M207 is well tolerated in the setting of longer-term repeated use. Efficacy findings were also similar to those in the ZOTRIP trial.

Trial registration
Clinicaltrials.gov on September 13, 2017 (NCT03282227).
Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers
Authors: Delli Ponti Riccardo , Mutwil Marek 
Published: May 2021

Abstract
Background
With more than 300 million potentially infected people every year, and with the expanded habitat of mosquitoes due to climate change, Dengue virus (DENV) cannot be considered anymore only a tropical disease. The RNA secondary structure is a functional characteristic of RNA viruses, and together with the accumulated high-throughput sequencing data could provide general insights towards understanding virus biology. Here, we profiled the RNA secondary structure of > 7000 complete viral genomes from 11 different species focusing on viral hemorrhagic fevers, including DENV serotypes, EBOV, and YFV.

Results
In our work we demonstrated that the secondary structure and presence of protein-binding domains in the genomes can be used as intrinsic signature to further classify the viruses. With our predictive approach, we achieved high prediction scores of the secondary structure (AUC up to 0.85 with experimental data), and computed consensus secondary structure profiles using hundreds of in silico models. We observed that viruses show different structural patterns, where e.g., DENV-2 and Ebola virus tend to be less structured than the other viruses. Furthermore, we observed virus-specific correlations between secondary structure and the number of interaction sites with human proteins, reaching a correlation of 0.89 in the case of Zika virus. We also identified that helicases-encoding regions are more structured in several flaviviruses, while the regions encoding for the contact proteins exhibit virus-specific clusters in terms of RNA structure and potential protein-RNA interactions. We also used structural data to study the geographical distribution of DENV, finding a significant difference between DENV-3 from Asia and South-America, where the structure is also driving the clustering more than sequence identity, which could imply different evolutionary routes of this subtype.

Conclusions
Our massive computational analysis provided novel results regarding the secondary structure and the interaction with human proteins, not only for DENV serotypes, but also for other flaviviruses and viral hemorrhagic fevers-associated viruses. We showed how the RNA secondary structure can be used to categorise viruses, and even to further classify them based on the interaction with proteins. We envision that these approaches can be used to further classify and characterise these complex viruses.
ddRAD sequencing: an emerging technology added to the biosecurity toolbox for tracing the origin of brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae)
Authors: Yan Juncong , Vétek Gábor , Pal Chandan , Zhang Jinping , Gmati Rania , Fan Qing-Hai , Gunawardana Disna N. , Burne Allan , Anderson Diane , Balan Rebijith Kayattukandy , George Sherly , Farkas Péter , Li Dongmei 
Published: May 2021

AbstractBackgroundBrown marmorated stink bug (BMSB),Halyomorpha halys(Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. BMSB is a polyphagous insect pest and causes significant economic losses to agriculture worldwide. Knowledge on the genetic diversity among BMSB populations is scarce but is essential to understand the patterns of colonization and invasion history of local populations. Efforts have been made to assess the genetic diversity of BMSB using partial mitochondrial DNA sequences but genetic divergence on mitochondria is not high enough to precisely accurately identify and distinguish various BMSB populations. Therefore, in this study, we applied a ddRAD (double digest restriction-site associated DNA) sequencing approach to ascertain the genetic diversity of BMSB populations collected from 12 countries (2 native and 10 invaded) across four continents with the ultimate aim to trace the origin of BMSBs intercepted during border inspections and post-border surveillance.ResultA total of 1775 high confidence single nucleotide polymorphisms (SNPs) were identified from ddRAD sequencing data collected from 389 adult BMSB individuals. Principal component analysis (PCA) of the identified SNPs indicated the existence of two main distinct genetic clusters representing individuals sampled from regions where BMSB is native to, China and Japan, respectively, and one broad cluster comprised individuals sampled from countries which have been invaded by BMSB. The population genetic structure analysis further discriminated the genetic diversity among the BMSB populations at a higher resolution and distinguished them into five potential genetic clusters.ConclusionThe study revealed hidden genetic diversity among the studied BMSB populations across the continents. The BMSB populations from Japan were genetically distant from the other studied populations. Similarly, the BMSB populations from China were also genetically differentiated from the Japanese and other populations. Further genetic structure analysis revealed the presence of at least three genetic clusters of BMSB in the invaded countries, possibly originating via multiple invasions. Furthermore, this study has produced novel set of SNP markers to enhance the knowledge of genetic diversity among BMSB populations and demonstrates the potential to trace the origin of BMSB individuals for future invasion events.
Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data
Authors: Smolander Johannes , Khan Sofia , Singaravelu Kalaimathy , Kauko Leni , Lund Riikka J. , Laiho Asta , Elo Laura L. 
Published: May 2021

Abstract
Background
Detection of copy number variations (CNVs) from high-throughput next-generation whole-genome sequencing (WGS) data has become a widely used research method during the recent years. However, only a little is known about the applicability of the developed algorithms to ultra-low-coverage (0.0005–0.8×) data that is used in various research and clinical applications, such as digital karyotyping and single-cell CNV detection.

Result
Here, the performance of six popular read-depth based CNV detection algorithms (BIC-seq2, Canvas, CNVnator, FREEC, HMMcopy, and QDNAseq) was studied using ultra-low-coverage WGS data. Real-world array- and karyotyping kit-based validation were used as a benchmark in the evaluation. Additionally, ultra-low-coverage WGS data was simulated to investigate the ability of the algorithms to identify CNVs in the sex chromosomes and the theoretical minimum coverage at which these tools can accurately function. Our results suggest that while all the methods were able to detect large CNVs, many methods were susceptible to producing false positives when smaller CNVs (< 2 Mbp) were detected. There was also significant variability in their ability to identify CNVs in the sex chromosomes. Overall, BIC-seq2 was found to be the best method in terms of statistical performance. However, its significant drawback was by far the slowest runtime among the methods (> 3 h) compared with FREEC (~ 3 min), which we considered the second-best method.

Conclusions
Our comparative analysis demonstrates that CNV detection from ultra-low-coverage WGS data can be a highly accurate method for the detection of large copy number variations when their length is in millions of base pairs. These findings facilitate applications that utilize ultra-low-coverage CNV detection.
LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome
Authors: Vangelisti Alberto , Simoni Samuel , Usai Gabriele , Ventimiglia Maria , Natali Lucia , Cavallini Andrea , Mascagni Flavia , Giordani Tommaso 
Published: May 2021

AbstractBackgroundLong Terminal Repeat retrotransposons (LTR-REs) are repetitive DNA sequences that constitute a large part of the genome. The improvement of sequencing technologies and sequence assembling strategies has achieved genome sequences with much greater reliability than those of the past, especially in relation to repetitive DNA sequences.ResultsIn this study, we analysed the genome ofFicus caricaL., obtained using third generation sequencing technologies and recently released, to characterise the complete complement of full-length LTR-REs to study their dynamics during fig genome evolution. A total of 1867 full-length elements were identified.Those belonging to theGypsysuperfamily were the most abundant; among these, theChromovirus/Tekaylineage was the most represented. For theCopiasuperfamily,Alewas the most abundant lineage. Measuring the estimated insertion time of each element showed that, on average,IvanaandChromovirus/Tekaywere the youngest lineages ofCopiaandGypsysuperfamilies, respectively. Most elements were inactive in transcription, both constitutively and in leaves of plants exposed to an abiotic stress, except for some elements, mostly belonging to theCopia/Alelineage. A relationship between the inactivity of an element and inactivity of genes lying in close proximity to it was established.ConclusionsThe data reported in this study provide one of the first sets of information on the genomic dynamics related to LTR-REs in a plant species with highly reliable genome sequence. Fig LTR-REs are highly heterogeneous in abundance and estimated insertion time, and only a few elements are transcriptionally active. In general, the data suggested a direct relationship between estimated insertion time and abundance of an element and an inverse relationship between insertion time (or abundance) and transcription, at least forCopiaLTR-REs.
Reorganisation of GP surgeries during the COVID-19 outbreak: analysis of guidelines from 15 countries
Authors: Tsopra Rosy , Frappe Paul , Streit Sven , Neves Ana Luisa , Honkoop Persijn J. , Espinosa-Gonzalez Ana Belen , Geroğlu Berk , Jahr Tobias , Lingner Heidrun , Nessler Katarzyna , Pesolillo Gabriella , Sivertsen Øyvind Stople , Thulesius Hans , Zoitanu Raluca , Burgun Anita , Kinouani Shérazade 
Published: May 2021

Abstract
Background
General practitioners (GPs) play a key role in managing the COVID-19 outbreak. However, they may encounter difficulties adapting their practices to the pandemic. We provide here an analysis of guidelines for the reorganisation of GP surgeries during the beginning of the pandemic from 15 countries.

Methods
A network of GPs collaborated together in a three-step process: (i) identification of key recommendations of GP surgery reorganisation, according to WHO, CDC and health professional resources from health care facilities; (ii) collection of key recommendations included in the guidelines published in 15 countries; (iii) analysis, comparison and synthesis of the results.

Results
Recommendations for the reorganisation of GP surgeries of four types were identified: (i) reorganisation of GP consultations (cancelation of non-urgent consultations, follow-up via e-consultations), (ii) reorganisation of GP surgeries (area partitioning, visual alerts and signs, strict hygiene measures), (iii) reorganisation of medical examinations by GPs (equipment, hygiene, partial clinical examinations, patient education), (iv) reorganisation of GP staff (equipment, management, meetings, collaboration with the local community).

Conclusions
We provide here an analysis of guidelines for the reorganisation of GP surgeries during the beginning of the COVID-19 outbreak from 15 countries. These guidelines focus principally on clinical care, with less attention paid to staff management, and the area of epidemiological surveillance and research is largely neglected. The differences of guidelines between countries and the difficulty to apply them in routine care, highlight the need of advanced research in primary care. Thereby, primary care would be able to provide recommendations adapted to the real-world settings and with stronger evidence, which is especially necessary during pandemics.
Ambient bright light treatment improved proxy-rated sleep but not sleep measured by actigraphy in nursing home patients with dementia: a placebo-controlled randomised trial
Authors: Hjetland Gunnhild J. , Kolberg Eirin , Pallesen Ståle , Thun Eirunn , Nordhus Inger Hilde , Bjorvatn Bjørn , Flo-Groeneboom Elisabeth 
Published: May 2021

Abstract
Background
Up to 70% of nursing home patients with dementia suffer from sleep problems. Light is the main zeitgeber to the circadian system and thus has a fundamental impact on sleep-wake behaviour. Low indoor light levels in nursing homes have been reported, and in combination with age-related reductions in light sensitivity, insufficient light exposure is likely to contribute to sleep problems in this population. Increasing daytime light exposure using bright light treatment (BLT) may represent a feasible non-pharmacological treatment for sleep problems in nursing home patients with dementia.

Methods
The present study reports on sleep outcomes, which are the primary outcomes of the DEM.LIGHT trial (Therapy Light Rooms for Nursing Home Patients with Dementia– Designing Diurnal Conditions for Improved Sleep, Mood and Behavioural Problems), a 24-week cluster-randomised placebo-controlled trial including 8 nursing home units and 69 resident patients. The intervention comprised ambient light of 1000 lx and 6000 K from 10:00 to 15:00, with gradually increasing and decreasing light levels prior to and following this interval, using ceiling mounted light-fixtures and light emitting diode technology. The placebo condition had continuous standard light levels (150–300 lx, ~ 3000 K). Sleep was assessed at baseline and follow-up at week 8, 16, and 24, using the proxy-rated Sleep Disorder Inventory (SDI) and actigraphy (Actiwatch II, Philips Respironics). Mixed linear models were used to evaluate intervention effects, adjusting for relevant covariates such as age, gender, number of drugs, severity of dementia, eye disease, and estimated light exposure.

Results
Sleep as measured by the SDI was significantly improved in the intervention group compared to the control group from baseline to week 16 (B = − 0.06, 95% CI -0.11 - -0.01, p < .05) and from baseline to week 24 (B = − 0.05, 95% CI -0.10 - -0.01, p < .05). There was no effect according to the SDI at week 8 and no significant effects in terms of actigraphically measured sleep.

Conclusions
Proxy-rated sleep improved among nursing home patients with dementia following 16 and 24 weeks of BLT. These improvements were not corroborated by actigraphy recordings.

Trial registration
ClinicalTrials.gov Identifier: NCT03357328. Registered 29 November 2017 – Retrospectively registered.