bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping global zoonotic niche and interregional transmission risk of monkeypox: a retrospective observational study
Authors: Sun Yan-Qun , Chen Jin-Jin , Liu Mei-Chen , Zhang Yuan-Yuan , Wang Tao , Che Tian-Le , Li Ting-Ting , Liu Yan-Ning , Teng Ai-Ying , Wu Bing-Zheng , Hong Xue-Geng , Xu Qiang , Lv Chen-Long , Jiang Bao-Gui , Liu Wei , Fang Li-Qun 
Published: August 2023

Abstract
Background
Outbreaks of monkeypox have been ongoing in non-endemic countries since May 2022. A thorough assessment of its global zoonotic niche and potential transmission risk is lacking.

Methods
We established an integrated database on global monkeypox virus (MPXV) occurrence during 1958 − 2022. Phylogenetic analysis was performed to examine the evolution of MPXV and effective reproductive number (Rt) was estimated over time to examine the dynamic of MPXV transmissibility. The potential ecological drivers of zoonotic transmission and inter-regional transmission risks of MPXV were examined.

Results
As of 24 July 2022, a total of 49 432 human patients with MPXV infections have been reported in 78 countries. Based on 525 whole genome sequences, two main clades of MPXV were formed, of which Congo Basin clade has a higher transmissibility than West African clade before the 2022-monkeypox, estimated by the overall Rt (0.81 vs. 0.56), and the latter significantly increased in the recent decade. Rt of 2022-monkeypox varied from 1.14 to 4.24 among the 15 continuously epidemic countries outside Africa, with the top three as Peru (4.24, 95% CI: 2.89–6.71), Brazil (3.45, 95% CI: 1.62–7.00) and the United States (2.44, 95% CI: 1.62–3.60). The zoonotic niche of MPXV was associated with the distributions of Graphiurus lorraineus and Graphiurus crassicaudatus, the richness of Rodentia, and four ecoclimatic indicators. Besides endemic areas in Africa, more areas of South America, the Caribbean States, and Southeast and South Asia are ecologically suitable for the occurrence of MPXV once the virus has invaded. Most of Western Europe has a high-imported risk of monkeypox from Western Africa, whereas France and the United Kingdom have a potential imported risk of Congo Basin clade MPXV from Central Africa. Eleven of the top 15 countries with a high risk of MPXV importation from the main countries of 2022-monkeypox outbreaks are located at Europe with the highest risk in Italy, Ireland and Poland.

Conclusions
The suitable ecological niche for MPXV is not limited to Africa, and the transmissibility of MPXV was significantly increased during the 2022-monkeypox outbreaks. The imported risk is higher in Europe, both from endemic areas and currently epidemic countries. Future surveillance and targeted intervention programs are needed in its high-risk areas informed by updated prediction.
Effectiveness of bladder filling control during online MR-guided adaptive radiotherapy for rectal cancer
Authors: Feng Xi , Tang Bin , Yao Xinghong , Liu Min , Liao Xiongfei , Yuan Ke , Peng Qian , Orlandini Lucia Clara 
Published: August 2023

Abstract
Background
Magnetic resonance-guided adaptive radiotherapy (MRgART) treatment sessions at MR-Linac are time-consuming and changes in organs at risk volumes can impact the treatment dosimetry. This study aims to evaluate the feasibility to control bladder filling during the rectum MRgART online session and its effectiveness on plan dosimetry.

Methods
A total of 109 online adaptive sessions of 24 rectum cancer patients treated at Unity 1.5 T MR-Linac with a short course radiotherapy (25 Gy, 5 Gy × 5) for whom the adaptive plan was optimized and recalculated online based on the daily magnetic resonance imaging (MRI) were analysed. Patients were fitted with a bladder catheter to control bladder filling; the bladder is emptied and then partially filled with a known amount of saline at the beginning and end of the online session. A first MRI ($${\mathrm{MRI}}_{\mathrm{i}}$$

MRI
i

) acquired at the beginning of the session was used for plan adaptation and the second ($${\mathrm{MRI}}_{\mathrm{f}}$$

MRI
f

) was acquired while approving the adapted plan and rigidly registered with the first to ensure the appropriateness of the isodoses on the ongoing delivery treatment. For each fraction, the time interval between the two MRIs and potential bladder changes were assessed with independent metrics, and the impact on the plan dosimetry was evaluated by comparing target and organs at risk dose volume histogram cut-off points of the plan adapted on $${\mathrm{MRI}}_{\mathrm{i}}$$

MRI
i

and recalculated on $${\mathrm{MRI}}_{\mathrm{f}}$$

MRI
f

.

Results
Median bladder volume variations, DSC, and HD of 8.17%, 0.922, and 2.92 mm were registered within a median time of 38 min between $${\mathrm{MRI}}_{\mathrm{i}}$$

MRI
i

and $${\mathrm{MRI}}_{\mathrm{f}}$$

MRI
f

; dosimetric differences < 0.65% were registered for target coverage, and < 0.5% for bladder, small bowel and femoral heads constraints, with a p value > 0.05.

Conclusion
The use of a bladder filling control procedure can help ensure the dosimetric accuracy of the online adapted treatment delivered.
Physiological effects of awake prone position in acute hypoxemic respiratory failure
Authors: Grieco Domenico Luca , Delle Cese Luca , Menga Luca S. , Rosà Tommaso , Michi Teresa , Lombardi Gianmarco , Cesarano Melania , Giammatteo Valentina , Bello Giuseppe , Carelli Simone , Cutuli Salvatore L. , Sandroni Claudio , De Pascale Gennaro , Pesenti Antonio , Maggiore Salvatore M. , Antonelli Massimo 
Published: August 2023

Abstract
Background
The effects of awake prone position on the breathing pattern of hypoxemic patients need to be better understood. We conducted a crossover trial to assess the physiological effects of awake prone position in patients with acute hypoxemic respiratory failure.

Methods
Fifteen patients with acute hypoxemic respiratory failure and PaO2/FiO2 < 200 mmHg underwent high-flow nasal oxygen for 1 h in supine position and 2 h in prone position, followed by a final 1-h supine phase. At the end of each study phase, the following parameters were measured: arterial blood gases, inspiratory effort (ΔPES), transpulmonary driving pressure (ΔPL), respiratory rate and esophageal pressure simplified pressure–time product per minute (sPTPES) by esophageal manometry, tidal volume (VT), end-expiratory lung impedance (EELI), lung compliance, airway resistance, time constant, dynamic strain (VT/EELI) and pendelluft extent through electrical impedance tomography.

Results
Compared to supine position, prone position increased PaO2/FiO2 (median [Interquartile range] 104 mmHg [76–129] vs. 74 [69–93], p < 0.001), reduced respiratory rate (24 breaths/min [22–26] vs. 27 [26–30], p = 0.05) and increased ΔPES (12 cmH2O [11–13] vs. 9 [8–12], p = 0.04) with similar sPTPES (131 [75–154] cmH2O s min−1 vs. 105 [81–129], p > 0.99) and ΔPL (9 [7–11] cmH2O vs. 8 [5–9], p = 0.17). Airway resistance and time constant were higher in prone vs. supine position (9 cmH2O s arbitrary units−3 [4–11] vs. 6 [4–9], p = 0.05; 0.53 s [0.32–61] vs. 0.40 [0.37–0.44], p = 0.03). Prone position increased EELI (3887 arbitrary units [3414–8547] vs. 1456 [959–2420], p = 0.002) and promoted VT distribution towards dorsal lung regions without affecting VT size and lung compliance: this generated lower dynamic strain (0.21 [0.16–0.24] vs. 0.38 [0.30–0.49], p = 0.004). The magnitude of pendelluft phenomenon was not different between study phases (55% [7–57] of VT in prone vs. 31% [14–55] in supine position, p > 0.99).

Conclusions
Prone position improves oxygenation, increases EELI and promotes VT distribution towards dependent lung regions without affecting VT size, ΔPL, lung compliance and pendelluft magnitude. Prone position reduces respiratory rate and increases ΔPES because of positional increases in airway resistance and prolonged expiratory time. Because high ΔPES is the main mechanistic determinant of self-inflicted lung injury, caution may be needed in using awake prone position in patients exhibiting intense ΔPES.
Clinical trail registeration: The study was registered on clinicaltrials.gov (NCT03095300) on March 29, 2017.
Statistical analysis plan for a randomized controlled trial examining pedometer-based walking intervention in patients with heart failure with reduced ejection fraction: the WATCHFUL trial
Authors: Vetrovsky Tomas , Siranec Michal , Frybova Tereza , Gant Iulian , Semerad Miroslav , Miklikova Marie , Bunc Vaclav , Vesely Jiri , Stastny Jiri , Griva Martin , Precek Jan , Pelouch Radek , Parenica Jiri , Jarkovsky Jiri , Belohlavek Jan 
Published: August 2023

Abstract
Background
Physical activity is an effective management strategy for heart failure with reduced ejection fraction, but patients’ compliance is challenging. Walking is a suitable form of physical activity due to its convenience and sustainability, and it can potentially improve functional capacity in heart failure patients.

Objectives
The WATCHFUL trial aims to determine whether a pedometer-based walking intervention combined with face-to-face sessions and regular telephone contact improves functional capacity in heart failure patients.

Methods
The WATCHFUL trial is a 6-month multicenter, parallel-group, randomized, controlled, superiority trial with a 6-month follow-up. A total of 202 patients were recruited for the trial. The primary analysis will evaluate the change in distance walked during the 6-min walk test from baseline to 6 months based on the intention-to-treat population; the analysis will be performed using a linear mixed-effect model adjusted for baseline values. Missing data will be imputed using multiple imputations, and the impact of missing data will be assessed using a sensitivity analysis. Adverse events are monitored and recorded throughout the trial period.

Discussion
The trial has been designed as a pragmatic trial with a scalable intervention that could be easily translated into routine clinical care. The trial has been affected by the COVID-19 pandemic, which slowed patients’ recruitment and impacted their physical activity patterns.

Conclusions
The present publication provides details of the planned statistical analyses for the WATCHFUL trial to reduce the risks of reporting bias and erroneous data-driven results.

Trial registration
ClinicalTrials.gov (identifier: NCT03041610, registered: 3/2/2017).
Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation
Authors: Yan Tongtong , Wang Kexin , Feng Kexin , Gao Xiangchen , Jin Yinghong , Wu Hongping , Zhang Wenfei , Wei Li 
Published: August 2023

Abstract
Background
Genomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized.

Results
Accordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the ‘fatty acid metabolism’, ‘response to stress’, ‘carbon fixation’ and ‘photosynthesis’ functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression.

Conclusions
Overall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.
Invasive hematophagous arthropods and associated diseases in a changing world
Authors: Cuthbert Ross N. , Darriet Frédéric , Chabrerie Olivier , Lenoir Jonathan , Courchamp Franck , Claeys Cecilia , Robert Vincent , Jourdain Frédéric , Ulmer Romain , Diagne Christophe , Ayala Diego , Simard Frédéric , Morand Serge , Renault David 
Published: August 2023

AbstractBiological invasions have increased significantly with the tremendous growth of international trade and transport. Hematophagous arthropods can be vectors of infectious and potentially lethal pathogens and parasites, thus constituting a growing threat to humans—especially when associated with biological invasions. Today, several major vector-borne diseases, currently described as emerging or re-emerging, are expanding in a world dominated by climate change, land-use change and intensive transportation of humans and goods. In this review, we retrace the historical trajectory of these invasions to better understand their ecological, physiological and genetic drivers and their impacts on ecosystems and human health. We also discuss arthropod management strategies to mitigate future risks by harnessing ecology, public health, economics and social-ethnological considerations. Trade and transport of goods and materials, including vertebrate introductions and worn tires, have historically been important introduction pathways for the most prominent invasive hematophagous arthropods, but sources and pathways are likely to diversify with future globalization. Burgeoning urbanization, climate change and the urban heat island effect are likely to interact to favor invasive hematophagous arthropods and the diseases they can vector. To mitigate future invasions of hematophagous arthropods and novel disease outbreaks, stronger preventative monitoring and transboundary surveillance measures are urgently required. Proactive approaches, such as the use of monitoring and increased engagement in citizen science, would reduce epidemiological and ecological risks and could save millions of lives and billions of dollars spent on arthropod control and disease management. Last, our capacities to manage invasive hematophagous arthropods in a sustainable way for worldwide ecosystems can be improved by promoting interactions among experts of the health sector, stakeholders in environmental issues and policymakers (e.g. the One Health approach) while considering wider social perceptions.
Graphical abstract
Validating opioid use disorder diagnoses in administrative data: a commentary on existing evidence and future directions
Authors: Scherrer Jeffrey F. , Sullivan Mark D. , LaRochelle Marc R. , Grucza Richard 
Published: August 2023

Abstract
Background
A valid opioid use disorder (OUD) identification algorithm for use in administrative medical record data would enhance investigators’ ability to study consequences of OUD, OUD treatment seeking and treatment outcomes.

Main body
Existing studies indicate ICD-9 and ICD-10 codes for opioid abuse and dependence do not accurately measure OUD. However, critical appraisal of existing literature suggests alternative validation methods would improve the validity of OUD identification algorithms in administrative data. Chart abstraction may not be sufficient to validate OUD, and primary data collection via structured diagnostic interviews might be an ideal gold standard.

Conclusion and commentary
Generating valid OUD identification algorithms is critical for OUD research and quality measurement in real world health care settings.
Safety and efficacy of enterprise stenting for symptomatic atherosclerotic severe posterior circulation stenosis
Authors: Zhou Zhi-Long , Li Tian-Xiao , Zhu Liang-Fu , Wu Li-Heng , Guan Min , Ma Zhen-Kai , Liu Yang-Hui , Qin Jin , Gao Bu-Lang 
Published: August 2023

Abstract
Purpose
To investigate the safety and efficacy of Enterprise stent angioplasty and risk factors for the prognoses in treating symptomatic severe posterior circulation atherosclerotic stenosis (SSPCAS).

Materials and methods
Patients with SSPCAS who were treated with the Enterprise stent angioplasty were retrospectively enrolled. The clinical data, peri-procedural complications, postoperative residual stenosis, in-stent restenosis and recurrent stroke at follow-up were analyzed.

Results
262 patients with 275 stenotic lesions treated with the Enterprise stent angioplasty were enrolled. The stenosis degree was reduced from 86.3 ± 6.2% before to 19.3 ± 5.4% after stenting. Complications occurred in 14 (5.3%) patients. Clinical follow-up was performed in 245 (93.51%) patients for 16.5 ± 7.3 months. During 1 year follow-up, 7 patients (2.9%) had recurrent symptoms, including 4 patients with stenting in the intracranial vertebral artery and 3 in the basilar artery. Imaging follow-up was conducted in 223 (85.11%) patients. In-stent restenosis was present in 35 patients (15.7%), with the restenosis rate of 26.4% (n = 23) in the intracranial vertebral artery, which was significantly (P < 0.001) greater than in the basilar artery (8.8%). Six patients (17.1%) with in-stent restenosis were symptomatic. The stenotic length was the only significant (P = 0.026 and 0.024, respectively) independent risk factor for 1 year stroke or death events and in-stent restenosis.

Conclusion
The Enterprise stent can be safely and efficaciously applied in the treatment of symptomatic severe posterior circulation atherosclerotic stenosis, with a relatively low rate of in-stent restenosis and recurrent stroke within 1 year. The stenotic length was the only significant independent risk factor for 1 year stroke or death events and in-stent restenosis.
Research methods for heritage cotton fibres: case studies from archaeological and historical finds in a Finnish context
Authors: Suomela Jenni A. , Viljanen Mira , Svedström Kirsi , Wright Krista , Lipkin Sanna 
Published: August 2023

Abstract
Cotton (Gossypium species) was used as textile fibre already in the early Indus culture, and since then it has been cultivated in Tropical and Subtropical regions around the whole planet. The species G. hirsutum is nowadays the dominant cotton crop with more than 90% of the world market, while G. barbadense, G. herbaceum and G. arboreum combined, the other cultivated species of Gossypium genus total a minor part of world’s cotton production. Even in places where cotton was not cultivated, it could be an important trade item and income source for local textile centres, with the imported raw cotton lint being spun, woven and for some part exported from such sites around the globe. This all occurred far away from Finland, until changes brought by the development of long-distance trade and the Industrial Revolution. Based on archaeological finds, cotton as a textile material reached Finland relatively late, in the early Middle Ages. The article focuses on the problematic nature of identifying these cotton finds: whereas modern cotton fibres are easy to identify, the archaeological finds can at first sight be confused with bast or un-degummed silk fibres. This issue will be approached through reviewing recent Finnish cotton finds in heritage textiles. Additionally, the article examines whether the four cultivated cotton species could be differentiated using both classical and newly developed fibre identification methods, such as optical microscopy methods, a Scanning Electron Microscope (SEM), Fourier-transform infrared spectroscopy (FTIR) or Wide-Angle X-ray Scattering (WAXS).
Effect of a music intervention on anxiety in adult critically ill patients: a multicenter randomized clinical trial
Authors: Kakar Ellaha , Ottens Thomas , Stads Susanne , Wesselius Sanne , Gommers Diederik A. M. P. J. , Jeekel Johannes , van der Jagt Mathieu 
Published: August 2023

Abstract
Background
Previous studies show positive effect of music on reducing anxiety, pain, and medication requirement. Anxiety has become a more pertinent issue in the intensive care unit (ICU) since wakefulness is preferred according to recent guidelines. Nevertheless, evidence on the effect of music in ICU patients is scarce. Therefore, we studied the effect of music intervention on anxiety in ICU patients.

Methods
A multicenter randomized clinical trial was conducted between August 2020 and December 2021 in ICU’s at an academic medical centre and two regional hospitals. Adult critically ill patients were eligible when hemodynamically stable and able to communicate (Richmond agitation-sedation scale (RASS) of at least − 2). Patients in the intervention arm were offered music twice daily during three days for at least 30 min per session. Patients in the control group received standard care. The primary outcome was anxiety level assessed with the visual analogue scale for anxiety [VAS-A; range 0–10] twice daily (morning and evening). Secondary outcomes included; 6-item state-trait anxiety inventory (STAI-6), sleep quality, delirium, heart rate, mean arterial pressure, pain, RASS, medication, ICU length of stay, patients’ memory and experience of ICU stay.

Results
94 patients were included in the primary analysis. Music did not significantly reduce anxiety (VAS-A in the intervention group; 2.5 (IQR 1.0–4.5), 1.8 (0.0–3.6), and 2.5 (0.0–3.6) on day 1, 2, and 3 vs. 3.0 (0.6–4.0), 1.5 (0.0–4.0), and 2.0 (0.0–4.0) in the control group; p > 0.92). Overall median daily VAS-A scores ranged from 1.5 to 3.0. Fewer patients required opioids (21 vs. 29, p = 0.03) and sleep quality was lower in the music group on study day one [5.0 (4.0–6.0) vs. 4.5 (3.0–5.0), p = 0.03]. Other outcomes were similar between groups.

Conclusions
Anxiety levels in this ICU population were low, and music during 3 days did not decrease anxiety. This study indicates that efficacy of music is context and intervention-dependent, given previous evidence showing decreased anxiety.
Trial registration Netherlands Trial Register: NL8595, Registered, 1 April 2020. ClinicalTrials.gov ID: NCT04796389, Registered retrospectively, 12 March 2021
Spatial transcriptomics: recent developments and insights in respiratory research
Authors: Wang Wen-Jia , Chu Liu-Xi , He Li-Yong , Zhang Ming-Jing , Dang Kai-Tong , Gao Chen , Ge Qin-Yu , Wang Zhou-Guang , Zhao Xiang-Wei 
Published: August 2023

AbstractThe respiratory system’s complex cellular heterogeneity presents unique challenges to researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have provided insights into cell types and heterogeneity in the respiratory system, the relevant specific spatial localization and cellular interactions have not been clearly elucidated. Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies. This review focuses on the latest iterative technology of ST in recent years, summarizing how ST can be applied to the physiological and pathological processes of the respiratory system, with emphasis on the lungs. Finally, the current challenges and potential development directions are proposed, including high-throughput full-length transcriptome, integration of multi-omics, temporal and spatial omics, bioinformatics analysis, etc. These viewpoints are expected to advance the study of systematic mechanisms, including respiratory studies.