bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post-fire seed dispersal of a wind-dispersed shrub declined with distance to seed source, yet had high levels of unexplained variation
Authors: Applestein Cara , Caughlin T Trevor , Germino Matthew J 
Published: October 2022

AbstractPlant-population recovery across large disturbance areas is often seed-limited. An understanding of seed dispersal patterns is fundamental for determining natural-regeneration potential. However, forecasting seed dispersal rates across heterogeneous landscapes remains a challenge. Our objectives were to determine (i) the landscape patterning of post-disturbance seed dispersal, and underlying sources of variation and the scale at which they operate, and (ii) how the natural seed dispersal patterns relate to a seed augmentation strategy. Vertical seed trapping experiments were replicated across 2 years and five burned and/or managed landscapes in sagebrush steppe. Multi-scale sampling and hierarchical Bayesian models were used to determine the scale of spatial variation in seed dispersal. We then integrated an empirical and mechanistic dispersal kernel for wind-dispersed species to project rates of seed dispersal and compared natural seed arrival to typical post-fire aerial seeding rates. Seeds were captured across the range of tested dispersal distances, up to a maximum distance of 26 m from seed-source plants, although dispersal to the furthest traps was variable. Seed dispersal was better explained by transect heterogeneity than by patch or site heterogeneity (transects were nested within patch within site). The number of seeds captured varied from a modelled mean of ~13 m−2 adjacent to patches of seed-producing plants, to nearly none at 10 m from patches, standardized over a 49-day period. Maximum seed dispersal distances on average were estimated to be 16 m according to a novel modelling approach using a ‘latent’ variable for dispersal distance based on seed trapping heights. Surprisingly, statistical representation of wind did not improve model fit and seed rain was not related to the large variation in total available seed of adjacent patches. The models predicted severe seed limitations were likely on typical burned areas, especially compared to the mean 95–250 seeds per m2 that previous literature suggested were required to generate sagebrush recovery. More broadly, our Bayesian data fusion approach could be applied to other cases that require quantitative estimates of long-distance seed dispersal across heterogeneous landscapes.
Reciprocal best structure hits: using AlphaFold models to discover distant homologues
Authors: Monzon Vivian , Paysan-Lafosse Typhaine , Wood Valerie , Bateman Alex 
Published: October 2022

Abstract

Motivation
The conventional methods to detect homologous protein pairs use the comparison of protein sequences. But the sequences of two homologous proteins may diverge significantly and consequently may be undetectable by standard approaches. The release of the AlphaFold 2.0 software enables the prediction of highly accurate protein structures and opens many opportunities to advance our understanding of protein functions, including the detection of homologous protein structure pairs.

Results
In this proof-of-concept work, we search for the closest homologous protein pairs using the structure models of five model organisms from the AlphaFold database. We compare the results with homologous protein pairs detected by their sequence similarity and show that the structural matching approach finds a similar set of results. In addition, we detect potential novel homologs solely with the structural matching approach, which can help to understand the function of uncharacterized proteins and make previously overlooked connections between well-characterized proteins. We also observe limitations of our implementation of the structure-based approach, particularly when handling highly disordered proteins or short protein structures. Our work shows that high accuracy protein structure models can be used to discover homologous protein pairs, and we expose areas for improvement of this structural matching approach.

Availability and Implementation
Information to the discovered homologous protein pairs can be found at the following URL: https://doi.org/10.17863/CAM.87873. The code can be accessed here: https://github.com/VivianMonzon/Reciprocal_Best_Structure_Hits.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Cortical theta–gamma coupling governs the adaptive control of motor commands
Authors: Spooner Rachel K , Wilson Tony W 
Published: October 2022

Abstract
Motor control requires the adaptive updating of internal models to successfully target desired outcomes. This adaptive control can be proactive, such that imminent actions and corresponding sensorimotor programmes are anticipated prior to movement, or reactive, such that online error correction is necessary to adjust to sudden changes. While substantial evidence implicates a distributed cortical network serving adaptive control when behavioural changes are required (e.g. response inhibition), the neural dynamics serving such control when the target motor commands are to remain intact are poorly understood. To address this, we developed a novel proactive–reactive cued finger tapping paradigm that was performed during magnetoencephalography by 25 healthy adults. Importantly, to ensure condition-wise differences in adaptive cueing were not attributable to changes in movement kinematics, motor selection and planning processes were held constant despite changes in task demands. All data were imaged in the time-frequency domain using a beamformer to evaluate the effect of proactive and reactive cues on movement-related oscillations and subsequent performance. Our results indicated spectrally specific increases in low (i.e. theta) and high (i.e. gamma) frequency oscillations during motor execution as a function of adaptive cueing. Additionally, we observed robust cross-frequency coupling of theta and gamma oscillatory power in the contralateral motor cortex and further, the strength of this theta–gamma coupling during motor execution was differentially predictive of behavioural improvements and decrements during reactive and proactive trials, respectively. These data indicate that functional oscillatory coupling may govern the adaptive control of movement in the healthy brain and importantly, may serve as effective proxies for characterizing declines in motor function in clinical populations in the future.
Squid Game’s foreigners: Orientalism, Occidentalism, sub-imperialism
Authors: Fedorenko Olga 
Published: October 2022

AbstractThis article considers foreigners that appear in Squid Game and interrogates how the show both critiques and reproduces the racialized politics of oppression in global capitalism. It is argued that deploying stereotyped foreigners as the extremes of both precarity and privilege is lodged in South Korean sub-imperialist triumphalism and reproduces ideologies of othering that support structures of exploitation and oppression.
Heroin Use Is Associated With Vascular Inflammation in Human Immunodeficiency Virus
Authors: Hileman Corrilynn O , Durieux Jared C , Janus Scott E , Bowman Emily , Kettelhut Aaren , Nguyen Trong-Tuong , Avery Ann K , Funderburg Nicholas , Sullivan Claire , McComsey Grace A 
Published: October 2022

Abstract

Background
Heroin use may work synergistically with human immunodeficiency virus (HIV) infection to cause greater immune dysregulation than either factor alone. Unraveling how this affects end-organ disease is key as it may play a role in the excess mortality seen in people with HIV (PWH) who use heroin despite access to care and antiretroviral therapy.

Methods
This is a prospectively enrolled, cross-sectional study of adults with and without HIV who use and do not use heroin using (18)F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) to compare tissue-specific inflammation including aortic (target-to-background ratio [TBR]), splenic, and bone marrow (standardized uptake value [SUV]).

Results
A total of 120 participants were enrolled. The unadjusted mean difference in aortic TBR was 0.43 between HIV-positive [HIV+] heroin+ and HIV+ heroin-negative [heroin−] (P = .02); however, among HIV−, aortic TBR was similar regardless of heroin-use status. Further, HIV-by-heroin-use status interaction was significant (P = .02), indicating that the relationship between heroin use and higher aortic TBR depended on HIV status. On the other hand, both HIV (1.54 vs 1.68; P = .04, unadjusted estimated means for HIV+ vs HIV−) and heroin use were associated with lower bone marrow SUV, although the effect of heroin depended on sex (heroin-use-by-sex interaction, P = .03). HIV-by-heroin-use interaction was not significant for splenic or bone marrow SUV.

Conclusions
Aortic inflammation was greatest in PWH who use heroin, but paradoxically, bone marrow activity was the least in this group, suggesting complex and possibly divergent pathophysiology within these different end organs.
Strategies for Using Antigen Rapid Diagnostic Tests to Reduce Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in Low- and Middle-Income Countries: A Mathematical Modelling Study Applied to Zambia
Authors: Han Alvin X , Girdwood Sarah J , Khan Shaukat , Sacks Jilian A , Toporowski Amy , Huq Naushin , Hannay Emma , Russell Colin A , Nichols Brooke E 
Published: October 2022

AbstractBackgroundIncreasing the availability of antigen rapid diagnostic tests (Ag-RDTs) in low- and middle-income countries (LMICs) is key to alleviating global SARS-CoV-2 testing inequity (median testing rate in December 2021–March 2022 when the Omicron variant was spreading in multiple countries: high-income countries = 600 tests/100 000 people/day; LMICs = 14 tests/100 000 people/day). However, target testing levels and effectiveness of asymptomatic community screening to impact SARS-CoV-2 transmission in LMICs are unclear.MethodsWe used Propelling Action for Testing and Treating (PATAT), an LMIC-focused agent-based model to simulate coronavirus disease 2019 (COVID-19) epidemics, varying the amount of Ag-RDTs available for symptomatic testing at healthcare facilities and asymptomatic community testing in different social settings. We assumed that testing was a function of access to healthcare facilities and availability of Ag-RDTs. We explicitly modelled symptomatic testing demand from individuals without SARS-CoV-2 and measured impact based on the number of infections averted due to test-and-isolate.ResultsTesting symptomatic individuals yields greater benefits than any asymptomatic community testing strategy until most symptomatic individuals who sought testing have been tested. Meeting symptomatic testing demand likely requires at least 200–400 tests/100 000 people/day, on average, as symptomatic testing demand is highly influenced by individuals without SARS-CoV-2. After symptomatic testing demand is satisfied, excess tests to proactively screen for asymptomatic infections among household members yield the largest additional infections averted.ConclusionsTesting strategies aimed at reducing transmission should prioritize symptomatic testing and incentivizing test-positive individuals to adhere to isolation to maximize effectiveness.
Evaluation of rhomboid intercostal and subserratus plane block under direct vision for postoperative analgesia in thoracic surgeries: a prospective, randomized controlled trial
Authors: Kozanhan Betul , Semerkant Tolga , Esme Hıdır , Canitez Ahmet , İyisoy Mehmet Sinan 
Published: October 2022

Abstract

OBJECTIVES
This study is designed to evaluate the efficacy of rhomboid intercostal and subserratus plane (RISS) block under the surgeon’s direct vision for providing postoperative pain relief after thoracic surgeries.

METHODS
Forty patients who underwent thoracotomy were prospectively recruited and randomly assigned to group R (intravenous patient-controlled analgesia + continued RISS block; n = 20) and group C (intravenous patient-controlled analgesia; n = 20). Numeric rating scale at rest and cough, at post-anaesthetic care unit, 1, 2, 6, 9, 12, 24 and 48 h, was used as the primary outcome measure. Secondary outcome measures were the amount of tramadol consumption, the number of patients required rescue analgesia, the occurrence of postoperative adverse effects, pulmonary functions and the overall satisfaction with pain management.

RESULTS
Numeric rating scale scores both at rest and during coughing were significantly lower in group R than in group C at all time intervals (P &lt; 0.001 in each). Tramadol consumption at 24 and 48 h was significantly lower in the group R block than in group C (P &lt; 0.001 for each). None of the patients in group R requires rescue analgesia. The incidence of nausea and vomiting was similar among the groups. Compared with group C, change in lung function from baseline levels was significantly less in group R (P = 0.047 and P = 0.04 for FEV1 and FVC, respectively). The satisfaction scores in group R were significantly higher than that in group C (P &lt; 0.001).

CONCLUSIONS
Continuous RISS block improved postoperative outcomes of thoracic surgery in terms of reduced postoperative pain scores, sparing opioid consumption, pulmonary function and patient satisfaction.
Estimating individual lifetime risk of incident cardiovascular events in adults with Type 2 diabetes: an update and geographical calibration of the DIAbetes Lifetime perspective model (DIAL2)
Authors: Østergaard Helena Bleken , Hageman Steven H J , Read Stephanie H , Taylor Owen , Pennells Lisa , Kaptoge Stephen , Petitjean Carmen , Xu Zhe , Shi Fanchao , McEvoy John William , Herrington William , Visseren Frank L J , Wood Angela , Eliasson Björn , Sattar Naveed , Wild Sarah , Di Angelantonio Emanuele , Dorresteijn Jannick A N 
Published: October 2022

Abstract

Aims
The 2021 European Society of Cardiology cardiovascular disease (CVD) prevention guidelines recommend the use of (lifetime) risk prediction models to aid decisions regarding intensified preventive treatment options in adults with Type 2 diabetes, e.g. the DIAbetes Lifetime perspective model (DIAL model). The aim of this study was to update the DIAL model using contemporary and representative registry data (DIAL2) and to systematically calibrate the model for use in other European countries.

Methods and results
The DIAL2 model was derived in 467 856 people with Type 2 diabetes without a history of CVD from the Swedish National Diabetes Register, with a median follow-up of 7.3 years (interquartile range: 4.0–10.6 years) and comprising 63 824 CVD (including fatal CVD, non-fatal stroke and non-fatal myocardial infarction) events and 66 048 non-CVD mortality events. The model was systematically recalibrated to Europe’s low- and moderate-risk regions using contemporary incidence data and mean risk factor distributions. The recalibrated DIAL2 model was externally validated in 218 267 individuals with Type 2 diabetes from the Scottish Care Information—Diabetes (SCID) and Clinical Practice Research Datalink (CPRD). In these individuals, 43 074 CVD events and 27 115 non-CVD fatal events were observed. The DIAL2 model discriminated well, with C-indices of 0.732 [95% confidence interval (CI) 0.726–0.739] in CPRD and 0.700 (95% CI 0.691–0.709) in SCID.

Conclusion
The recalibrated DIAL2 model provides a useful tool for the prediction of CVD-free life expectancy and lifetime CVD risk for people with Type 2 diabetes without previous CVD in the European low- and moderate-risk regions. These long-term individualized measures of CVD risk are well suited for shared decision-making in clinical practice as recommended by the 2021 CVD ESC prevention guidelines.
Co-occurrences enhance our understanding of aquatic fungal metacommunity assembly and reveal potential host–parasite interactions
Authors: Vass Máté , Eriksson Karolina , Carlsson-Graner Ulla , Wikner Johan , Andersson Agneta 
Published: October 2022

ABSTRACTOur knowledge of aquatic fungal communities, their assembly, distributions and ecological roles in marine ecosystems is scarce. Hence, we aimed to investigate fungal metacommunities of coastal habitats in a subarctic zone (northern Baltic Sea, Sweden). Using a novel joint species distribution model and network approach, we quantified the importance of biotic associations contributing to the assembly of mycoplankton, further, detected potential biotic interactions between fungi–algae pairs, respectively. Our long-read metabarcoding approach identified 493 fungal taxa, of which a dominant fraction (44.4%) was assigned as early-diverging fungi (i.e. Cryptomycota and Chytridiomycota). Alpha diversity of mycoplankton declined and community compositions changed along inlet–bay–offshore transects. The distributions of most fungi were rather influenced by environmental factors than by spatial drivers, and the influence of biotic associations was pronounced when environmental filtering was weak. We found great number of co-occurrences (120) among the dominant fungal groups, and the 25 associations between fungal and algal OTUs suggested potential host–parasite and/or saprotroph links, supporting a Cryptomycota-based mycoloop pathway. We emphasize that the contribution of biotic associations to mycoplankton assembly are important to consider in future studies as it helps to improve predictions of species distributions in aquatic ecosystems.
Investigating Biological Pathways Underpinning the Longitudinal Association Between Loneliness and Cognitive Impairment
Authors: Yu Kexin , Siang Ng Ted Kheng 
Published: October 2022

AbstractBackgroundLoneliness precedes the onset of cognitive impairment (CI) in older adults. Although the mechanisms through which loneliness “gets under the skin” to influence the risk of developing CI have been conceptually proposed, they are rarely empirically examined. The Evolutionary Theory of Loneliness posits that loneliness as a stressor could cause dysregulations in multiple physiological systems. The current study investigated whether inflammatory, cardiovascular, and kidney biomarkers mediate the longitudinal association between loneliness and CI.MethodsCross-lagged panel models were used to examine the hypothesized relationships, using 2006, 2010, and 2014 waves of data from the Health and Retirement Study (N = 7,037). Loneliness was measured with the 3-item UCLA loneliness scale. CI was assessed with the modified telephone interview for cognitive status. Biomarkers included HbA1C, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, C-reactive protein, and Cystatin C. Using a stepwise model-building approach, first, the model included only loneliness, CI, and biomarker variables; then, sociodemographic covariates were added; lastly, health status were controlled for.ResultsIn unadjusted and partially adjusted models, loneliness was associated with higher odds of worse cognitive status in an 8-year follow-up. Only HbA1C mediated the longitudinal association between loneliness and CI. However, after further controlling for health status, all associations became nonsignificant.ConclusionsExamining a large number of participants and linking a limited number of biological markers with cognition and loneliness longitudinally, our empirical data did not support theoretical propositions, highlighting the critical importance of controlling for confounders in future studies examining longitudinal mediational relationships underlying loneliness and CI.
Observed versus expected morbidity and mortality in patients undergoing mitral valve repair
Authors: Newell Paige , Tartarini Richard , Hirji Sameer , Harloff Morgan , McGurk Siobhan , Cherkasky Olena , Kaneko Tsuyoshi 
Published: October 2022

Abstract

OBJECTIVES
Mitral valve repair (MVP) is the gold standard treatment for degenerative mitral regurgitation. With the expansion of transcatheter technologies, this study compares the outcome of MVP in low-risk and non-low-risk patients to serve as a benchmark.

METHODS
This retrospective, single-institution study examined all patients who underwent MVP for primary mitral regurgitation from 2005 to 2018. Patients were stratified into 2 risk categories: low-risk [Society of Thoracic Surgeons (STS) Predicted Risk of Mortality (STS-PROM) ≤2%] and non-low risk (STS-PROM &gt; 2% or age &gt; 75), with a subgroup of very low risk (STS-PROM ≤1%, age &lt;75).

RESULTS
A total of 1207 patients were included, and 1053 patients were classified as low risk and 154 as non-low risk. The non-low-risk group was significantly older, more likely to be female, and had a higher comorbidity burden than the low-risk group (all P &lt; 0.01). For the low-risk group, the observed-to-expected (O:E) STS mortality ratio was 0.4 and the composite morbidity and mortality ratio was 0.6, whereas for the non-low risk, the O:E mortality was 1.5 and the composite morbidity and mortality was 0.9. When the subgroup of very low-risk group was assessed, the mortality O:E ratio was 0.

CONCLUSIONS
The observed composite morbidity and mortality of patients undergoing MVP were persistently lower in low-risk patients, mainly driven by the very low-risk group. The excellent outcome of MVP in low-risk patients should be validated on a national level to determine how transcatheter technologies can be utilized in these patients.
Recognition as Transitional Justice ‘From Below’: Analysing Victims’ Grassroots Activism in Postconflict Colombia
Authors: Tamayo Gomez Camilo 
Published: October 2022

ABSTRACT
The framework of transitional justice ‘from below’ is often used to explore perspectives where victims are addressed as subjects with their own agency and organizational capability in temporal and normative aspects. Using qualitative research techniques to analyse victims’ organizations in Colombia, this article establishes the notion of recognition as crucial to comprehending ‘from below’ perspectives of transitional justice. It explores the cases of the Never Again Museum and the Trails for Life and Reconciliation in Eastern Antioquia. It examines victims’ efforts to create processes of ‘democratization of pain’ (the transformation of personal experiences of loss into common public knowledge) as expressions of recognition. The article’s main contribution rests in the idea that by scrutinizing victims’ initiatives as expressions of recognition, the normative idea of transitional justice ‘from below’ can be reinvigorated. It demonstrates that the concept of transitional justice ‘from below’ constitutes an abstract ideal that needs to be redefined by bringing into consideration the function and particularities of victims’ grassroots activism.