bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences
Authors: Balech Bachir , Sandionigi Anna , Marzano Marinella , Pesole Graziano , Santamaria Monica 
Published: January 2022

Abstract
Nucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventual integration. To adequately address data integration process, many aspects should be markedly considered starting from DNA sequence curation followed by taxonomy alignment with solid reference backbone and metadata harmonization according to universal standards. Here, we present MetaCOXI, an integrated collection of curated metazoan COXI DNA sequences with their associated harmonized taxonomy and metadata. This collection was built on the two most extensive available data resources, namely the European Nucleotide Archive (ENA) and the Barcode of Life Data System (BOLD). The current release contains more than 5.6 million entries (39.1% unique to BOLD, 3.6% unique to ENA, and 57.2% shared between both), their related taxonomic classification based on NCBI reference taxonomy, and their available main metadata relevant to environmental DNA studies, such as geographical coordinates, sampling country and host species. MetaCOXI is available in standard universal formats (‘fasta’ for sequences & ‘tsv’ for taxonomy and metadata), which can be easily incorporated in standard or specific DNA barcoding and/or metabarcoding data analysis pipelines.
Database URL: https://github.com/bachob5/MetaCOXI
Safety and efficacy of different P2Y12 inhibitors in patients with acute coronary syndromes stratified by the PRAISE risk score: a multicentre study
Authors: Patti Giuseppe , D'Ascenzo Fabrizio , De Filippo Ovidio , Bruno Francesco , Leonardi Sergio , Chieffo Alaide , Iannaccone Mario , Liebetrau Christoph , Manzano-Fernández Sergio , Gallone Guglielmo , Omedè Pierluigi , Cerrato Enrico , Kinnaird Tim , Conrotto Federico , Piroli Francesco , Henriques Jose Paulo Simao , Wańha Wojciech , Elia Edoardo , Dominguez-Rodriguez Alberto , Raposeiras-Roubin Sergio , Abu-Assi Emad , De Ferrari Gaetano Maria ,   PRAISE Study Group
Published: January 2022

Abstract

Aims
To establish the safety and efficacy of different dual antiplatelet therapy (DAPT) combinations in patients with acute coronary syndrome (ACS) according to their baseline ischaemic and bleeding risk estimated with a machine learning derived model [machine learning-based prediction of adverse events following an acute coronary syndrome (PRAISE) score].

Methods and results
Incidences of death, re-acute myocardial infarction (re-AMI), and Bleeding Academic Research Consortium 3–5 bleeding with aspirin plus different P2Y12 inhibitors (clopidogrel or potent P2Y12 inhibitors: ticagrelor or prasugrel) were appraised among patients of the PRAISE data set grouped in four subcohorts: low-to-moderate ischaemic and bleeding risk; low-to-moderate ischaemic risk and high bleeding risk; high ischaemic risk and low-to-moderate bleeding risk; and high ischaemic and bleeding risk. Hazard ratios (HRs) for the outcome measures were derived with inverse probability of treatment weighting adjustment. Among patients with low-to-moderate bleeding risk, clopidogrel was associated with higher rates of re-AMI in those at low-to-moderate ischaemic risk [HR 1.69, 95% confidence interval (CI) 1.16–2.51; P = 0.006] and increased risk of death (HR 3.2, 1.45–4.21; P = 0.003) and re-AMI (HR 2.23, 1.45–3.41; P &lt; 0.001) in those at high ischaemic risk compared with prasugrel or ticagrelor, without a difference in the risk of major bleeding. Among patients with high bleeding risk, clopidogrel showed comparable risk of death, re-AMI, and major bleeding vs. potent P2Y12 inhibitors, regardless of the baseline ischaemic risk.

Conclusion
Among ACS patients with non-high risk of bleeding, the use of potent P2Y12 inhibitors is associated with a lower risk of death and recurrent ischaemic events, without bleeding excess. Patients deemed at high bleeding risk may instead be safely addressed to a less intensive DAPT strategy with clopidogrel.
Incidence and 1-year outcome of periprocedural myocardial infarction following cardiac surgery: are the Universal Definition and Society for Cardiovascular Angiography and Intervention criteria fit for purpose?
Authors: Hinton Jonathan , Augustine Maclyn , Gabara Lavinia , Mariathas Mark , Allan Rick , Borca Florina , Nicholas Zoe , Ikwuobe John , Gillett Neil , Kwok Chun Shing , Cook Paul , Grocott Michael P W , Mamas Mamas , Curzen Nick 
Published: January 2022

Abstract

OBJECTIVES
The diagnosis and clinical implications of periprocedural myocardial infarction (PPMI) following coronary artery bypass grafting (CABG) are contentious, especially the importance of PPMI in the interpretation of trial data.

METHODS
Consecutive patients admitted to a cardiothoracic critical care unit over a 6-month period following open cardiac surgery had high-sensitivity cardiac troponin I assay performed on admission and every day for 48 h, regardless of whether there was a request by the supervising clinical team. Patients were categorized as PPMI using both the Universal Definition of Myocardial Infarction (UDMI) and Society of Cardiovascular Angiography and Interventions (SCAI) criteria. Multivariable Cox regression analysis was performed to assess whether any relationships between PPMI diagnoses and 1-year mortality were independent.

RESULTS
There were 2 groups of consecutive patients: (i) after CABG (n = 245) and (ii) after non-CABG surgery (n = 243). Of the CABG patients, 20.4% met criteria for UDMI PPMI and 87.6% for SCAI PPMI. The diagnosis of UDMI PPMI was independently associated with 1-year mortality on multivariable Cox regression analysis [hazard ratio 4.16 (95% confidence interval 1.28–13.49)]. Of 243 patients who had non-CABG cardiac surgery, 11.4% met criteria for UDMI PPMI and 85.2% for SCAI PPMI but neither were associated with 1-year mortality.

CONCLUSIONS
The incidence of SCAI PPMI in a real-world cohort of cardiac surgery patients is so high as to be of limited clinical value. In contrast, a diagnosis of UDMI PPMI post-CABG is independently associated with 1-year mortality, so may have clinical (and research) utility.
The benefits and challenges of established peer support programmes for patients, informal caregivers, and healthcare providers
Authors: Joo Jin Hui , Bone Lee , Forte Joan , Kirley Erin , Lynch Thomas , Aboumatar Hanan 
Published: January 2022

AbstractPurposePeer support programmes that provide services for various health conditions have been in existence for many years; however, there is little study of their benefits and challenges. Our goal was to explore how existing peer support programmes help patients with a variety of health conditions, the challenges that these programmes meet, and how they are addressed.MethodsWe partnered with 7 peer support programmes operating in healthcare and community settings and conducted 43 semi-structured interviews with key informants. Audiorecordings were transcribed and qualitative analysis was conducted using grounded theory methods.ResultsPeer support programmes offer informational and psychosocial support, reduce social isolation, and connect patients and caregivers to others with similar health issues. These programmes provide a supportive community of persons who have personal experience with the same health condition and who can provide practical information about self-care and guidance in navigating the health system. Peer support is viewed as different from and complementary to professional healthcare services. Existing programmes experience challenges such as matching of peer supporter and peer recipient and maintaining relationship boundaries. They have gained experience in addressing some of these challenges.ConclusionsPeer support programmes can help persons and caregivers manage health conditions but also face challenges that need to be addressed through organizational processes. Peer support programmes have relevance for improving healthcare systems, especially given the increased focus on becoming more patient-centred. Further study of peer programmes and their relevance to improving individuals’ well-being is warranted.
Trends in the conduct and reporting of clinical prediction model development and validation: a systematic review
Authors: Yang Cynthia , Kors Jan A , Ioannou Solomon , John Luis H , Markus Aniek F , Rekkas Alexandros , de Ridder Maria A J , Seinen Tom M , Williams Ross D , Rijnbeek Peter R 
Published: January 2022

Abstract

Objectives
This systematic review aims to provide further insights into the conduct and reporting of clinical prediction model development and validation over time. We focus on assessing the reporting of information necessary to enable external validation by other investigators.

Materials and Methods
We searched Embase, Medline, Web-of-Science, Cochrane Library, and Google Scholar to identify studies that developed 1 or more multivariable prognostic prediction models using electronic health record (EHR) data published in the period 2009–2019.

Results
We identified 422 studies that developed a total of 579 clinical prediction models using EHR data. We observed a steep increase over the years in the number of developed models. The percentage of models externally validated in the same paper remained at around 10%. Throughout 2009–2019, for both the target population and the outcome definitions, code lists were provided for less than 20% of the models. For about half of the models that were developed using regression analysis, the final model was not completely presented.

Discussion
Overall, we observed limited improvement over time in the conduct and reporting of clinical prediction model development and validation. In particular, the prediction problem definition was often not clearly reported, and the final model was often not completely presented.

Conclusion
Improvement in the reporting of information necessary to enable external validation by other investigators is still urgently needed to increase clinical adoption of developed models.
Spinosyns Delivered in Sugar Meals to Aedes aegypti and Aedes albopictus (Diptera: Culicidae): Acute Toxicity and Subacute Effects on Survival, Fecundity, and Fertility
Authors: Alomar Abdullah A , Alto Barry W , Walker Edward D 
Published: January 2022

Abstract
Sugar is an essential source of nutrition for adult mosquitoes to acquire energy. Toxic sugar bait (TSB) provides a promising method for mosquito control by incorporating toxins into artificial sources of sugar (i.e., toxic baits) presented to wild populations. Spinosyns comprise a family of bacterial secondary metabolites with a unique mode of action against the insect nervous system, an appealing environmental safety profile, and potential for incorporation into sugar baits. This research evaluated acute and subacute effects of spinosad (spinosyns A and D) and spinetoram (spinosyns J and L) in sugar meals on survival, fecundity, and fertility of Aedes aegypti and Aedes albopictus. Acute toxicity of spinosyns doubled from 24 to 48 h of assessment, revealing a relatively slow and cumulative action of the formulated spinosyns. Median lethal concentrations at 48 h were lower for spinetoram than for spinosad, lower for Ae. albopictus than Ae. aegypti, and lower for males than females. When exposed to subacute LC50 concentrations of spinosad and spinetoram for 24 h, survival of males and females of both species was diminished compared with controls, fecundity of females was increased, but fertility as measured by hatch rate of eggs was decreased. The formulations may have increased the nutritive value of the sugar meals thereby boosting fecundity, while toxifying embryos, reducing fertility. The inclusion of subacute effects of spinosyns allows assessment of the broader consequences of TSB for adult mosquito control.
Racial Disparities in Medication Adherence Barriers: Pediatric Epilepsy as an Exemplar
Authors: Gutierrez-Colina Ana M , Wetter Sara E , Mara Constance A , Guilfoyle Shanna , Modi Avani C 
Published: January 2022

Abstract

Objective
To evaluate how racial disparities in medication adherence barriers relate to key clinical outcomes (i.e., seizure control and adherence) in pediatric epilepsy and to identify the most critical barriers in determining health outcomes in Black youth and White youth.

Methods
This observational study included a sample of youth aged 2–17 years with epilepsy obtained by combining data from four different studies. A total of 226 caregivers and 43 adolescents reported on adherence barriers. An electronic monitor was used to measure adherence to the primary antiepileptic drug. Racial disparities in individual barriers were examined. The relative importance of different types of barriers in determining clinical outcomes was evaluated in both Black and White youth.

Results
Adherence barriers, including running out of medications, access to pharmacies, competing demands, and difficulty swallowing, disproportionally affected Black children with epilepsy compared to White children. System- and community-level barriers emerged as the most important in determining seizure outcomes among Black youth. Both system- and individual-level barriers, on the other hand, were important for adherence outcomes.

Conclusions
System- and community-level barriers, as opposed to individual-level barriers, are more highly endorsed by Black families compared to White families. These barriers are also the most critical in driving seizure outcomes among Black youth. There is a critical need to shift from a primary focus on individual-level barriers to an approach that deliberately targets larger systemic barriers to reduce the existing adherence and health disparities that affect Black children with pediatric conditions.
A highly mutually inclined compact warm-Jupiter system KOI-984?
Authors: Sun L , Ioannidis P , Gu S , Schmitt J H M M , Wang X , Kouwenhoven M B N , Perdelwitz V , Flammini Dotti F , Czesla S 
Published: January 2022

ABSTRACT
The discovery of a population of close-orbiting giant planets (≤ 1 au) has raised a number of questions about their origins and dynamical histories. These issues have still not been fully resolved, despite over 20 years of exoplanet detections and a large number of discovered exoplanets. In particular, it is unclear whether warm Jupiters (WJs) form in situ, or whether they migrate from further outside and are even currently migrating to form hot Jupiters. Here, we report the possible discovery and characterization of the planets in a highly mutually inclined (Imut ≃ 45°) compact two-planet system (KOI-984), in which the newly discovered warm Jupiter KOI-984c is on a 21.5-d moderately eccentric (e ≃ 0.4) orbit, in addition to a previously known 4.3-d planet candidate KOI-984b. Meanwhile, the orbital configuration of a moderately inclined (Imut ≃ 15°) low-mass (mc ≃ 24M⊕; Pb ≃ 8.6 d) perturbing planet near the 1:2 mean-motion resonance with KOI-984b could also well reproduce the observed transit-timing variations and transit-duration variations of KOI-984b. Such an eccentric WJ with a close-in sibling would pose a challenge to the proposed formation and migration mechanisms of WJs if the first scenario is supported with more evidence in the near future; this system with several other well measured inclined WJ systems (e.g. Kepler-419 and Kepler-108) may provide additional clues to the origin and dynamical histories of WJs.
A Suzaku sample of unabsorbed narrow-line and broad-line Seyfert 1 galaxies – II. Iron emission and absorption
Authors: Waddell S G H , Gallo L C 
Published: January 2022

ABSTRACTA sample of 22 narrow-line type 1 Seyfert (NLS1) and 47 broad-line type 1 Seyfert (BLS1) galaxies observed with Suzaku is used to examine the Fe K-band properties of each group. Three different models are used to examine the presence of: narrow neutral Fe K α line at $6.4{\rm \, keV}$ and ionized Fe xxv and Fe xxvi emission lines (model A); a broad emission feature at around $6{-}7{\rm \, keV}$ (model B); and an absorption edge at ${\sim}7.1{\rm \, keV}$ (model C). In all three models, the neutral Fe K α line is weaker (lower luminosity and equivalent width) in NLS1s than in BLS1s. Model (B) also finds a more significant broad component (larger equivalent width) in NLS1s than in BLS1s. The feature does not appear to be an artifact of steeper spectra in NLS1s, but rather an intrinsic property of these sources. From model (C), the optical depth of the absorption edge appears comparable between the two samples. When comparing the absorption with the emission line properties, NLS1s seem to exhibit a lower ratio of emission-to-absorption of iron than BLS1s, and have a lower value than expected based on the fluorescence yield. The observed differences may arise from different torus geometries (e.g. larger opening angle in NLS1s), and/or additional sources of Fe K emission and absorption in NLS1s beyond pure fluorescence (e.g. originating in the disc and broad-line region).
Optical line spectra of tidal disruption events from reprocessing in optically thick outflows
Authors: Parkinson Edward J , Knigge Christian , Matthews James H , Long Knox S , Higginbottom Nick , Sim Stuart A , Mangham Samuel W 
Published: January 2022

ABSTRACT
A significant number of tidal disruption events (TDEs) radiate primarily at optical and ultraviolet (UV) wavelengths, with only weak soft X-ray components. One model for this optical excess proposes that thermal X-ray emission from a compact accretion disc is reprocessed to longer wavelengths by an optically thick envelope. Here, we explore this reprocessing scenario in the context of an optically thick accretion disc wind. Using state-of-the-art Monte Carlo radiative transfer and ionization software, we produce synthetic UV and optical spectra for wind and disc-hosting TDEs. Our models are inspired by observations, spanning a realistic range of accretion rates and wind kinematics. We find that such outflows can efficiently reprocess the disc emission and produce the broad Balmer and helium recombination features commonly seen in TDEs and exhibit asymmetric red wings. Moreover, the characteristic colour temperature of the reprocessed spectral energy distribution (SED) is much lower than that of the accretion disc. We show explicitly how changes in black hole mass, accretion rate, and wind properties affect the observed broad-band SED and line spectrum. In general, slower, denser winds tend to reprocess more radiation and produce stronger Balmer emission. Most of the outflows we consider are too highly ionized to produce UV absorption features, but this is sensitive to the input SED. For example, truncating the inner disc at just ≃4RISCO lowers the wind ionization state sufficiently to produce UV absorption features for sightlines looking into the wind.
Dynamic RNA Fitness Landscapes of a Group I Ribozyme during Changes to the Experimental Environment
Authors: Peri Gianluca , Gibard Clémentine , Shults Nicholas H , Crossin Kent , Hayden Eric J 
Published: January 2022

Abstract
Fitness landscapes of protein and RNA molecules can be studied experimentally using high-throughput techniques to measure the functional effects of numerous combinations of mutations. The rugged topography of these molecular fitness landscapes is important for understanding and predicting natural and experimental evolution. Mutational effects are also dependent upon environmental conditions, but the effects of environmental changes on fitness landscapes remains poorly understood. Here, we investigate the changes to the fitness landscape of a catalytic RNA molecule while changing a single environmental variable that is critical for RNA structure and function. Using high-throughput sequencing of in vitro selections, we mapped a fitness landscape of the Azoarcus group I ribozyme under eight different concentrations of magnesium ions (1–48 mM MgCl2). The data revealed the magnesium dependence of 16,384 mutational neighbors, and from this, we investigated the magnesium induced changes to the topography of the fitness landscape. The results showed that increasing magnesium concentration improved the relative fitness of sequences at higher mutational distances while also reducing the ruggedness of the mutational trajectories on the landscape. As a result, as magnesium concentration was increased, simulated populations evolved toward higher fitness faster. Curve-fitting of the magnesium dependence of individual ribozymes demonstrated that deep sequencing of in vitro reactions can be used to evaluate the structural stability of thousands of sequences in parallel. Overall, the results highlight how environmental changes that stabilize structures can also alter the ruggedness of fitness landscapes and alter evolutionary processes.
Control of backbone chemistry and chirality boost oligonucleotide splice switching activity
Authors: Kandasamy Pachamuthu , McClorey Graham , Shimizu Mamoru , Kothari Nayantara , Alam Rowshon , Iwamoto Naoki , Kumarasamy Jayakanthan , Bommineni Gopal R , Bezigian Adam , Chivatakarn Onanong , Butler David C D , Byrne Michael , Chwalenia Katarzyna , Davies Kay E , Desai Jigar , Shelke Juili Dilip , Durbin Ann F , Ellerington Ruth , Edwards Ben , Godfrey Jack , Hoss Andrew , Liu Fangjun , Longo Kenneth , Lu Genliang , Marappan Subramanian , Oieni Jacopo , Paik Ik-Hyeon , Estabrook Erin Purcell , Shivalila Chikdu , Tischbein Maeve , Kawamoto Tomomi , Rinaldi Carlo , Rajão-Saraiva Joana , Tripathi Snehlata , Yang Hailin , Yin Yuan , Zhao Xiansi , Zhou Cong , Zhang Jason , Apponi Luciano , Wood Matthew J A , Vargeese Chandra 
Published: January 2022

AbstractAlthough recent regulatory approval of splice-switching oligonucleotides (SSOs) for the treatment of neuromuscular disease such as Duchenne muscular dystrophy has been an advance for the splice-switching field, current SSO chemistries have shown limited clinical benefit due to poor pharmacology. To overcome limitations of existing technologies, we engineered chimeric stereopure oligonucleotides with phosphorothioate (PS) and phosphoryl guanidine-containing (PN) backbones. We demonstrate that these chimeric stereopure oligonucleotides have markedly improved pharmacology and efficacy compared with PS-modified oligonucleotides, preventing premature death and improving median survival from 49 days to at least 280 days in a dystrophic mouse model with an aggressive phenotype. These data demonstrate that chemical optimization alone can profoundly impact oligonucleotide pharmacology and highlight the potential for continued innovation around the oligonucleotide backbone. More specifically, we conclude that chimeric stereopure oligonucleotides are a promising splice-switching modality with potential for the treatment of neuromuscular and other genetic diseases impacting difficult to reach tissues such as the skeletal muscle and heart.