bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-level genome assembly and characterization of the Calophaca sinica genome
Authors: Cao Jianting , Zhu Hui , Gao Yingqi , Hu Yue , Li Xuejiao , Shi Jianwei , Chen Luqin , Kang Hao , Ru Dafu , Ren Baoqing , Liu Bingbing 
Published: April 2024

Abstract
Calophaca sinica is a rare plant endemic to northern China which belongs to the Fabaceae family and possesses rich nutritional value. To support the preservation of the genetic resources of this plant, we have successfully generated a high-quality genome of C. sinica (1.06 Gb). Notably, transposable elements (TEs) constituted ~73% of the genome, with long terminal repeat retrotransposons (LTR-RTs) dominating this group of elements (~54% of the genome). The average intron length of the C. sinica genome was noticeably longer than what has been observed for closely related species. The expansion of LTR-RTs and elongated introns emerged had the largest influence on the enlarged genome size of C. sinica in comparison to other Fabaceae species. The proliferation of TEs could be explained by certain modes of gene duplication, namely, whole genome duplication (WGD) and dispersed duplication (DSD). Gene family expansion, which was found to enhance genes associated with metabolism, genetic maintenance, and environmental stress resistance, was a result of transposed duplicated genes (TRD) and WGD. The presented genomic analysis sheds light on the genetic architecture of C. sinica, as well as provides a starting point for future evolutionary biology, ecology, and functional genomics studies centred around C. sinica and closely related species.
The plasma proteome is linked with left ventricular and left atrial function parameters in patients with chronic heart failure
Authors: Abou Kamar S , Andrzejczyk K , Petersen T B , Chin J F , Aga Y S , de Bakker M , Akkerhuis K M , Geleijnse M , Brugts J J , Sorop O , de Boer R A , Rizopoulos D , Asselbergs F W , Boersma E , den Ruijter H , van Dalen B M , Kardys I 
Published: April 2024

Abstract

Aims
Examining the systemic biological processes in the heterogeneous syndrome of heart failure with reduced ejection fraction (HFrEF), as reflected by circulating proteins, in relation to echocardiographic characteristics, may provide insights into heart failure pathophysiology. We investigated the link of 4210 repeatedly measured circulating proteins with repeatedly measured echocardiographic parameters as well as with elevated left atrial pressure (LAP), in patients with HFrEF, to provide insights into underlying mechanisms.

Methods and results
In 173 patients with HFrEF, we performed 6-monthly echocardiography and trimonthly blood sampling during a median follow-up of 2.7 (inter-quartile range: 2.5–2.8) years. We investigated circulating proteins in relation to echocardiographic parameters of left ventricular [left ventricular ejection fraction (LVEF), global longitudinal strain (GLS)] and left atrial function [left atrial reservoir strain (LASr)] and elevated LAP (E/eʹ ratio &gt;15) and used gene enrichment analyses to identify underlying pathophysiological processes. We found 723, 249, 792, and 427 repeatedly measured proteins, with significant associations with LVEF, GLS, LASr, and E/eʹ ratio, respectively. Proteins associated with LASr reflected pathophysiological mechanisms mostly related to the extracellular matrix. Proteins associated with GLS reflected cardiovascular biological processes and diseases, whereas those associated with LVEF reflected processes involved in the sympathetic nervous system. Moreover, 49 proteins were associated with elevated LAP; after correction for LVEF, three proteins remained: cystatin-D, fibulin-5, and HSP40.

Conclusion
Circulating proteins show varying associations with different echocardiographic parameters in patients with HFrEF. These findings suggest that pathways involved in atrial and ventricular dysfunction, as reflected by the plasma proteome, are distinct.
Global burden of cardiovascular disease attributable to smoking, 1990–2019: an analysis of the 2019 Global Burden of Disease Study
Authors: Khan Minhas Abdul Mannan , Sedhom Ramy , Jean Estelle D , Shapiro Michael D , Panza Julio A , Alam Mahboob , Virani Salim S , Ballantyne Christie M , Abramov Dmitry 
Published: April 2024

Abstract

Aims
This study aims to investigate the trends in the global cardiovascular disease (CVD) burden attributable to smoking from 1990 to 2019.

Methods and results
Global Burden of Disease Study 2019 was used to analyse the burden of CVD attributable to smoking (i.e. ischaemic heart disease, peripheral artery disease, stroke, atrial fibrillation and flutter, and aortic aneurysm). Age-standardized mortality rates (ASMRs) per 100 000 and age-standardized disability-adjusted life year rates (ASDRs) per 100 000, as well as an estimated annual percentage change (EAPC) in ASMR and ASDR, were determined by age, sex, year, socio-demographic index (SDI), regions, and countries or territories. The global ASMR of smoking-attributed CVD decreased from 57.16/100 000 [95% uncertainty interval (UI) 54.46–59.97] in 1990 to 33.03/100 000 (95% UI 30.43–35.51) in 2019 [EAPC −0.42 (95% UI −0.47 to −0.38)]. Similarly, the ASDR of smoking-attributed CVD decreased between 1990 and 2019. All CVD subcategories showed a decline in death burden between 1990 and 2019. The burden of smoking-attributed CVD was higher in men than in women. Significant geographic and regional variations existed such that Eastern Europe had the highest ASMR and Andean Latin America had the lowest ASMR in 2019. In 2019, the ASMR of smoking-attributed CVD was lowest in high SDI regions.

Conclusion
Smoking-attributed CVD morbidity and mortality are declining globally, but significant variation persists, indicating a need for targeted interventions to reduce smoking-related CVD burden.
Longer and better lives for patients with atrial fibrillation: the 9th AFNET/EHRA consensus conference
Authors: Linz Dominik , Andrade Jason G , Arbelo Elena , Boriani Giuseppe , Breithardt Guenter , Camm A John , Caso Valeria , Nielsen Jens Cosedis , De Melis Mirko , De Potter Tom , Dichtl Wolfgang , Diederichsen Søren Zoega , Dobrev Dobromir , Doll Nicolas , Duncker David , Dworatzek Elke , Eckardt Lars , Eisert Christoph , Fabritz Larissa , Farkowski Michal , Filgueiras-Rama David , Goette Andreas , Guasch Eduard , Hack Guido , Hatem Stéphane , Haeusler Karl Georg , Healey Jeff S , Heidbuechel Hein , Hijazi Ziad , Hofmeister Lucas H , Hove-Madsen Leif , Huebner Thomas , Kääb Stefan , Kotecha Dipak , Malaczynska-Rajpold Katarzyna , Merino José Luis , Metzner Andreas , Mont Lluís , Ng Ghulam Andre , Oeff Michael , Parwani Abdul Shokor , Puererfellner Helmut , Ravens Ursula , Rienstra Michiel , Sanders Prashanthan , Scherr Daniel , Schnabel Renate , Schotten Ulrich , Sohns Christian , Steinbeck Gerhard , Steven Daniel , Toennis Tobias , Tzeis Stylianos , van Gelder Isabelle C , van Leerdam Roderick H , Vernooy Kevin , Wadhwa Manish , Wakili Reza , Willems Stephan , Witt Henning , Zeemering Stef , Kirchhof Paulus 
Published: April 2024

Abstract

Aims
Recent trial data demonstrate beneficial effects of active rhythm management in patients with atrial fibrillation (AF) and support the concept that a low arrhythmia burden is associated with a low risk of AF-related complications. The aim of this document is to summarize the key outcomes of the 9th AFNET/EHRA Consensus Conference of the Atrial Fibrillation NETwork (AFNET) and the European Heart Rhythm Association (EHRA).

Methods and results
Eighty-three international experts met in Münster for 2 days in September 2023. Key findings are as follows: (i) Active rhythm management should be part of the default initial treatment for all suitable patients with AF. (ii) Patients with device-detected AF have a low burden of AF and a low risk of stroke. Anticoagulation prevents some strokes and also increases major but non-lethal bleeding. (iii) More research is needed to improve stroke risk prediction in patients with AF, especially in those with a low AF burden. Biomolecules, genetics, and imaging can support this. (iv) The presence of AF should trigger systematic workup and comprehensive treatment of concomitant cardiovascular conditions. (v) Machine learning algorithms have been used to improve detection or likely development of AF. Cooperation between clinicians and data scientists is needed to leverage the potential of data science applications for patients with AF.

Conclusions
Patients with AF and a low arrhythmia burden have a lower risk of stroke and other cardiovascular events than those with a high arrhythmia burden. Combining active rhythm control, anticoagulation, rate control, and therapy of concomitant cardiovascular conditions can improve the lives of patients with AF.
Whole-genome assembly of a hybrid Trypanosoma cruzi strain assembled with Nanopore sequencing alone
Authors: Hakim Jill M C , Gutierrez Guarnizo Sneider A , Málaga Machaca Edith , Gilman Robert H , Mugnier Monica R 
Published: April 2024

Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, which causes 10,000 deaths per year. Despite the high mortality associated with Chagas, relatively few parasite genomes have been assembled to date, with genome assemblies unavailable even for some commonly used laboratory strains. This is at least partially due to T. cruzi's highly complex and highly repetitive genome, which defies investigation using traditional short-read sequencing methods. In this study, we have generated a high-quality whole-genome assembly of the hybrid Tulahuen strain, a commercially available type VI strain, using long-read Nanopore sequencing without short-read scaffolding. The assembled genome contains 25% repeat regions, 17% variable multigene family members, and 27% transposable elements (TEs) and is of comparable quality with T. cruzi genome assemblies that utilized both long- and short-read data. Notably, we find that regions with TEs are significantly enriched for multicopy surface proteins, and that surface proteins are, on average, closer to TEs than to other coding regions. This finding suggests that mobile genetic elements such as transposons may drive recombination within surface protein gene families. This work demonstrates the feasibility of Nanopore sequencing to resolve complex regions of T. cruzi genomes, and with these resolved regions, provides support for a possible mechanism for genomic diversification.
An analysis of Nepal’s Draft Mental Health Acts 2006–2017: competing values and power
Authors: Stephens Jane , Simkhada Padam , van Teijlingen Edwin , Porter John , Eaton Julian 
Published: April 2024

Abstract
This qualitative study maps the process of drafting and consulting on Nepal’s mental health legislation from 2006 to 2017. A total of 14 people were interviewed and interviews were analysed thematically. These themes were subsequently interpreted in light of Shiffman and Smith’s policy analysis framework, as the process was found to be at the agenda-setting stage. Two groups of actors were identified with different views on appropriate policy content and how the policy process should be conducted. The first group included psychiatrists who initiated and controlled the drafting process and who did not consider people with psychosocial disabilities to be equal partners. The psychiatrists viewed forced detention and treatment as upholding people’s right to health and lobbied the Ministry of Health and Population (MoHP) to pass the draft acts to parliament. The second included the rights-based civil society actors and lawyers who saw the right to equality before the law as of utmost priority, opposed forced detention and treatment, and actively blocked the draft acts at the MoHP. There is no clear legal definition of mental health and illness in Nepal, legal and mental capacity are not differentiated, and people with mental and behavioural conditions are assumed to lack capacity. The analysis indicates that there were few favourable conditions to support the progression of this policy into law. It is unclear whether the drafters or blockers will prevail in the future, but we predict that professionals will continue to have more input into content than service users due to national policy dynamics.
Health impact and cost-effectiveness of expanding routine immunization coverage in India through Intensified Mission Indradhanush
Authors: Clarke-Deelder Emma , Suharlim Christian , Chatterjee Susmita , Portnoy Allison , Brenzel Logan , Ray Arindam , Cohen Jessica L , Menzies Nicolas A , Resch Stephen C 
Published: April 2024

Abstract
Many children do not receive a full schedule of childhood vaccines, yet there is limited evidence on the cost-effectiveness of strategies for improving vaccination coverage. Evidence is even scarcer on the cost-effectiveness of strategies for reaching ‘zero-dose children’, who have not received any routine vaccines. We evaluated the cost-effectiveness of periodic intensification of routine immunization (PIRI), a widely applied strategy for increasing vaccination coverage. We focused on Intensified Mission Indradhanush (IMI), a large-scale PIRI intervention implemented in India in 2017–2018. In 40 sampled districts, we measured the incremental economic cost of IMI using primary data, and used controlled interrupted time-series regression to estimate the incremental vaccination doses delivered. We estimated deaths and disability-adjusted life years (DALYs) averted using the Lives Saved Tool and reported cost-effectiveness from immunization programme and societal perspectives. We found that, in sampled districts, IMI had an estimated incremental cost of 2021US$13.7 (95% uncertainty interval: 10.6 to 17.4) million from an immunization programme perspective and increased vaccine delivery by an estimated 2.2 (−0.5 to 4.8) million doses over a 12-month period, averting an estimated 1413 (−350 to 3129) deaths. The incremental cost from a programme perspective was $6.21 per dose ($2.80 to dominated), $82.99 per zero-dose child reached ($39.85 to dominated), $327.63 ($147.65 to dominated) per DALY averted, $360.72 ($162.56 to dominated) per life-year saved and $9701.35 ($4372.01 to dominated) per under-5 death averted. At a cost-effectiveness threshold of 1× per-capita GDP per DALY averted, IMI was estimated to be cost-effective with 90% probability. This evidence suggests IMI was both impactful and cost-effective for improving vaccination coverage, though there is a high degree of uncertainty in the results. As vaccination programmes expand coverage, unit costs may increase due to the higher costs of reaching currently unvaccinated children.
Ultrashort echo time MRI detects significantly lower collagen but higher pore water in the tibial cortex of female patients with osteopenia and osteoporosis
Authors: Jerban Saeed , Ma Yajun , Wei Zhao , Shen Meghan , Ibrahim Zubaid , Jang Hyungseok , Lu Pengzhe , Chang Douglas G , Woods Gina , Chung Christine B , Chang Eric Y , Du Jiang 
Published: April 2024

Abstract
Ultrashort echo time (UTE) MRI can quantify the major proton pool densities in cortical bone, including total (TWPD), bound (BWPD), and pore water (PWPD) proton densities, as well as the macromolecular proton density (MMPD), associated with the collagen content, which is calculated using macromolecular fraction (MMF) from UTE magnetization transfer (UTE-MT) modeling. This study aimed to investigate the differences in water and collagen contents in tibial cortical bone, between female osteopenia (OPe) patients, osteoporosis (OPo) patients, and young participants (Young). Being postmenopausal and above 55 yr old were the inclusion criteria for OPe and OPo groups. The tibial shaft of 14 OPe (72.5 ± 6.8 yr old), 31 OPo (72.0 ± 6.4 yr old), and 31 young subjects (28.0 ± 6.1 yr old) were scanned using a knee coil on a clinical 3T scanner. Basic UTE, inversion recovery UTE, and UTE-MT sequences were performed. Investigated biomarkers were compared between groups using Kruskal–Wallis test. Spearman’s correlation coefficients were calculated between the TH DXA T-score and UTE-MRI results. MMF, BWPD, and MMPD were significantly lower in OPo patients than in the young group, whereas T1, TWPD, and PWPD were significantly higher in OPo patients. The largest OPo/Young average percentage differences were found in MMF (41.9%), PWPD (103.5%), and MMPD (64.0%). PWPD was significantly higher (50.7%), while BWPD was significantly lower (16.4%) in OPe than the Young group on average. MMF was found to be significantly lower (27%) in OPo patients compared with OPe group. T1, MMF, TWPD, PWPD, and MMPD values significantly correlated with the TH DXA T-scores (provided by the patients and only available for OPe and OPo patients). DXA T-score showed the highest correlations with PWPD (R = 0.55) and MMF (R = 0.56) values. TWPD, PWPD, and MMF estimated using the UTE-MRI sequences were recommended to evaluate individuals with OPe and OPo.
Protection of natural infection against reinfection with SARS-CoV-2 JN.1 variant
Authors: Chemaitelly Hiam , Coyle Peter , Ben Kacem Mohamed Ali , Ayoub Houssein H , Tang Patrick , Hasan Mohammad R , Yassine Hadi M , Al Thani Asmaa A , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar H , Latif Ali N , Shaik Riyazuddin M , Abdul-Rahim Hanan F , Nasrallah Gheyath K , Al-Kuwari Mohamed Ghaith , Butt Adeel A , Al-Romaihi Hamad E , Al-Thani Mohamed H , Al-Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J 
Published: April 2024

Overall effectiveness of infection in preventing reinfection with SARS-CoV-2 JN.1 variant was estimated at 1.8% (95% CI: −9.3to 12.6%), and demonstrated rapid decline over time since the previous infection, decreasing from 82.4% (95% CI: 40.9 to 94.7%) within 3 to less than 6 months, to a negligible level after one year.
A simple method to measure νmax for asteroseismology: application to 16 000 oscillating Kepler red giants
Authors: Sreenivas K R , Bedding Timothy R , Li (李亚光) Yaguang , Huber Daniel , Crawford Courtney L , Stello Dennis , Yu Jie 
Published: April 2024

ABSTRACT
The importance of νmax (the frequency of maximum oscillation power) for asteroseismology has been demonstrated widely in the previous decade, especially for red giants. With the large amount of photometric data from CoRoT (Convection, Rotation, and planetary Transits), Kepler, and Transiting Exoplanet Survey Satellite, several automated algorithms to retrieve νmax values have been introduced. Most of these algorithms correct the granulation background in the power spectrum by fitting a model and subtracting it before measuring νmax. We have developed a method that does not require fitting to the granulation background. Instead, we simply divide the power spectrum by a function of the form $\rm \nu ^{-2}$, to remove the slope due to granulation background, and then smooth to measure νmax. This method is fast and simple and avoids degeneracies associated with fitting. The method is able to measure oscillations in 99.9 per cent of previously studied Kepler red giants, with a systematic offset of 1.5 per cent in νmax values that we are able to calibrate. On comparing the seismic radii from this work with Gaia, we see similar trends to those observed in previous studies. Additionally, our values of width of the power envelope can clearly identify the dipole mode suppressed stars as a distinct population, hence as a way to detect them. We also applied our method to stars with low νmax (0.19–18.35 µHz) and found that it works well to correctly identify the oscillations.
Primordial intermediate and supermassive black hole formation during the electron–positron annihilation epoch
Authors: Sobrinho J L G , Augusto P 
Published: April 2024

ABSTRACT
Some of the Intermediate Mass Black Hole candidates observed at the centre of galaxies or in globular clusters and some of the Supermassive Black Holes seen at the centre of many galaxies might be of primordial origin. Indeed, Primordial Black Holes (PBHs) of such mass could have formed when the Universe was ∼1–103 s old, due to the collapse of density fluctuations. In particular, when the Universe was ∼1 s in age, Electron–Positron Annihilation (EPA) took place. We explore the formation of intermediate mass and supermassive PBHs, taking into account the effect of the EPA when the fluctuations have a running tilt power-law spectrum: when these cross the 10−0.5–103.0 s Universe horizon they could produce 5 × 103–5 × 108 M⊙ PBHs with a density as high as ∼1010/Gpc3. On average, this implies a population of about one thousand PBHs in the Local Group of Galaxies, with the nearest one at about 250 kpc, just under half the distance to the Andromeda galaxy (M31).
Oryzomys texensis (Rodentia: Cricetidae)
Authors: Rose Robert K 
Published: April 2024

Abstract
Oryzomys texensis Allen, 1894, the Texas Marsh Rice Rat, is a yellowish gray-brown oryzomyine rodent with whitish feet and venter, black eyes, small hairy ears, short vibrissae, and a tail about one-half of total length. It was elevated to species status based on the results of an extensive molecular genetics analysis of the O. palustris complex. The poorly defined eastern boundary of O. texensis includes Mississippi, Arkansas, southern Missouri, and southern Illinois, with populations extending westward to southeastern Kansas, eastern Oklahoma, eastern and coastal Texas, into northeastern Tamaulipas, Mexico. Present in tidal marshes and other habitats near water, O. texensis is omnivorous, with some populations being highly carnivorous.
Redox Regulation by Priming Agents Toward a Sustainable Agriculture
Authors: Tripathi Durgesh Kumar , Bhat Javaid Akhter , Antoniou Chrystalla , Kandhol Nidhi , Singh Vijay Pratap , Fernie Alisdair R , Fotopoulos Vasileios 
Published: April 2024

Abstract
Plants are sessile organisms that are often subjected to a multitude of environmental stresses, with the occurrence of these events being further intensified by global climate change. Crop species therefore require specific adaptations to tolerate climatic variability for sustainable food production. Plant stress results in excess accumulation of reactive oxygen species leading to oxidative stress and loss of cellular redox balance in the plant cells. Moreover, enhancement of cellular oxidation as well as oxidative signals has been recently recognized as crucial players in plant growth regulation under stress conditions. Multiple roles of redox regulation in crop production have been well documented, and major emphasis has focused on key redox-regulated proteins and non-protein molecules, such as NAD(P)H, glutathione, peroxiredoxins, glutaredoxins, ascorbate, thioredoxins and reduced ferredoxin. These have been widely implicated in the regulation of (epi)genetic factors modulating growth and health of crop plants, with an agricultural context. In this regard, priming with the employment of chemical and biological agents has emerged as a fascinating approach to improve plant tolerance against various abiotic and biotic stressors. Priming in plants is a physiological process, where prior exposure to specific stressors induces a state of heightened alertness, enabling a more rapid and effective defense response upon subsequent encounters with similar challenges. Priming is reported to play a crucial role in the modulation of cellular redox homeostasis, maximizing crop productivity under stress conditions and thus achieving yield security. By taking this into consideration, the present review is an up-to-date critical evaluation of promising plant priming technologies and their role in the regulation of redox components toward enhanced plant adaptations to extreme unfavorable environmental conditions. The challenges and opportunities of plant priming are discussed, with an aim of encouraging future research in this field toward effective application of priming in stress management in crops including horticultural species.