bluuebunny/crossref_metadata_2025_split huggingface dataset:
rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments
Authors: Price Jonathan L , Ziv Omer , Pinckert Malte L , Lim Andrew , Miska Eric A 
Published: April 2024

Abstract

Summary
RNA (ribonucleic acid) molecules have secondary and tertiary structures in vivo which play a crucial role in cellular processes such as the regulation of gene expression, RNA processing and localization. The ability to investigate these structures will enhance our understanding of their function and contribute to the diagnosis and treatment of diseases caused by RNA dysregulation. However, there are no mature pipelines or packages for processing and analyzing complex in vivo RNA structural data. Here, we present rnaCrosslinkOO (RNA Crosslink Object-Oriented), a novel software package for the comprehensive analysis of data derived from the COMRADES (Crosslinking of Matched RNA and Deep Sequencing) method. rnaCrosslinkOO offers a comprehensive pipeline from raw sequencing reads to the identification and comparison of RNA structural features. It includes read processing and alignment, clustering of duplexes, data exploration, folding and comparisons of RNA structures. rnaCrosslinkOO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction.

Availability and implementation
rnaCrosslinkOO is freely available to noncommercial users and implemented in R, with the source code and documentation accessible at https://CRAN.R-project.org/package=rnaCrosslinkOO. The software is supported on Linux, macOS, and Windows platforms.
Specialist learning curves and clinical feasibility of introducing a new MRI grading system for skeletal maturity
Authors: De Luca Francesca , Finnbogason Thröstur , Kvist Ola 
Published: April 2024

Abstract

Objective
MRI is an emerging imaging modality to assess skeletal maturity. This study aimed to chart the learning curves of paediatric radiologists when using an unfamiliar MRI grading system of skeletal maturity and to assess the clinical feasibility of implementing said system.

Methods
958 healthy paediatric volunteers were prospectively included in a dual-facility study. Each subject underwent a conventional MRI scan at 1.5 T. To perform the image reading, the participants were grouped into five subsets (subsets 1-5) of equal size (n∼192) in chronological order for scan acquisition. Two paediatric radiologists (R1-2) with different levels of MRI experience, both of whom were previously unfamiliar with the study’s MRI grading system, independently evaluated the subsets to assess skeletal maturity in five different growth plate locations. Congruent cases at blinded reading established the consensus reading. For discrepant cases, the consensus reading was obtained through an unblinded reading by a third paediatric radiologist (R3), also unfamiliar with the MRI grading system. Further, R1 performed a second blinded image reading for all included subjects with a memory wash-out of 180 days. Weighted Cohen kappa was used to assess interreader reliability (R1 vs consensus; R2 vs consensus) at non-cumulative and cumulative time points, as well as interreader (R1 vs R2) and intrareader (R1 vs R1) reliability at non-cumulative time points.

Results
Mean weighted Cohen kappa values for each pair of blinded readers compared to consensus reading (interreader reliability, R1-2 vs consensus) were ≥0.85, showing a strong to almost perfect interreader agreement at both non-cumulative and cumulative time points and in all growth plate locations. Weighted Cohen kappa values for interreader (R1 vs R2) and intrareader reliability (R1 vs R1) were ≥0.72 at non-cumulative time points, with values ≥0.82 at subset 5.

Conclusions
Paediatric radiologists’ clinical confidence when introduced to a new MRI grading system for skeletal maturity was high from the outset of their learning curve, despite the radiologists’ varying levels of work experience with MRI assessment. The MRI grading system for skeletal maturity investigated in this study is a robust clinical method when used by paediatric radiologists and can be used in clinical practice.

Advances in knowledge
Radiologists with fellowship training in paediatric radiology experienced no learning curve progress when introduced to a new MRI grading system for skeletal maturity and achieved desirable agreement from the first time point of the learning curve. The robustness of the investigated MRI grading system was not affected by the earlier different levels of MRI experience among the readers.
Propofol and salvianolic acid A synergistically attenuated cardiac ischemia–reperfusion injury in diabetic mice via modulating the CD36/AMPK pathway
Authors: Zhou Jiaqi , Xia Weiyi , Chen Jiajia , Han Kaijia , Jiang Yuxin , Zhang Anyuan , Zhou Dongcheng , Liu Danyong , Lin Jiefu , Cai Yin , Chen Guanghua , Zhang Liangqing , Xu Aimin , Xu Youhua , Han Ronghui , Xia Zhengyuan 
Published: April 2024

Abstract

Background
Prevention of diabetic heart myocardial ischemia–reperfusion (IR) injury (MIRI) is challenging. Propofol attenuates MIRI through its reactive oxygen species scavenging property at high doses, while its use at high doses causes hemodynamic instability. Salvianolic acid A (SAA) is a potent antioxidant that confers protection against MIRI. Both propofol and SAA affect metabolic profiles through regulating Adenosine 5‘-monophosphate-activated protein kinase (AMPK). The aim of this study was to investigate the protective effects and underlying mechanisms of low doses of propofol combined with SAA against diabetic MIRI.

Methods
Diabetes was induced in mice by a high-fat diet followed by streptozotocin injection, and MIRI was induced by coronary artery occlusion and reperfusion. Mice were treated with propofol at 46 mg/kg/h without or with SAA at 10 mg/kg/h during IR. Cardiac origin H9c2 cells were exposed to high glucose (HG) and palmitic acid (PAL) for 24 h in the absence or presence of cluster of differentiation 36 (CD36) overexpression or AMPK gene knockdown, followed by hypoxia/reoxygenation (HR) for 6 and 12 h.

Results
Diabetes-exacerbated MIRI is evidenced as significant increases in post-ischemic infarction with reductions in phosphorylated (p)-AMPK and increases in CD36 and ferroptosis. Propofol moderately yet significantly attenuated all the abovementioned changes, while propofol plus SAA conferred superior protection against MIRI to that of propofol. In vitro, exposure of H9c2 cells under HG and PAL decreased cell viability and increased oxidative stress that was concomitant with increased levels of ferroptosis and a significant increase in CD36, while p-AMPK was significantly reduced. Co-administration of low concentrations of propofol and SAA at 12.5 μM in H9c2 cells significantly reduced oxidative stress, ferroptosis and CD36 expression, while increasing p-AMPK compared to the effects of propofol at 25 μM. Moreover, either CD36 overexpression or AMPK silence significantly exacerbated HR-induced cellular injuries and ferroptosis, and canceled propofol- and SAA-mediated protection. Notably, p-AMPK expression was downregulated after CD36 overexpression, while AMPK knockdown did not affect CD36 expression.

Conclusions
Combinational usage of propofol and SAA confers superior cellular protective effects to the use of high-dose propofol alone, and it does so through inhibiting HR-induced CD36 overexpression to upregulate p-AMPK.
COVID-19 Vaccine Efficacy in Participants With Weakened Immune Systems From 4 Randomized Controlled Trials
Authors: Sherman Amy C , Tuan Jessica , Cantos Valeria D , Adeyiga Oladunni , Mahoney Scott , Ortega-Villa Ana M , Tillman Amy , Whitaker Jennifer , Woodward Davis Amanda S , Leav Brett , Hirsch Ian , Sadoff Jerald , Dunkle Lisa M , Gilbert Peter B , Janes Holly E , Kublin James G , Goepfert Paul A , Kotloff Karen , Rouphael Nadine , Falsey Ann R , El Sahly Hana M , Sobieszczyk Magdalena E , Huang Yunda , Neuzil Kathleen M , Corey Lawrence , Grinsztejn Beatriz , Gray Glenda , Nason Martha , Baden Lindsey R , Gay Cynthia L 
Published: April 2024

Abstract

Background
Although the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are highly efficacious at preventing severe disease in the general population, current data are lacking regarding vaccine efficacy (VE) for individuals with mild immunocompromising conditions.

Methods
A post hoc, cross-protocol analysis of participant-level data from the blinded phase of four randomized, placebo-controlled, coronavirus disease 2019 (COVID-19) vaccine phase 3 trials (Moderna, AstraZeneca, Janssen, and Novavax) was performed. We defined a “tempered immune system” (TIS) variable via a consensus panel based on medical history and medications to determine VE against symptomatic and severe COVID-19 cases in TIS participants versus non-TIS individuals starting at 14 days after completion of the primary series through the blinded phase for each of the 4 trials. An analysis of participants living with well-controlled human immunodeficiency virus was conducted using the same methods.

Results
A total of 3852/30 351 (12.7%) Moderna participants, 3088/29 868 (10.3%) Novavax participants, 3549/32 380 (11.0%) AstraZeneca participants, and 5047/43 788 (11.5%) Janssen participants were identified as having a TIS. Most TIS conditions (73.9%) were due to metabolism and nutritional disorders. Vaccination (vs placebo) significantly reduced the likelihood of symptomatic and severe COVID-19 for all participants for each trial. VE was not significantly different for TIS participants versus non-TIS for either symptomatic or severe COVID-19 for each trial, nor was VE significantly different in the symptomatic endpoint for participants with human immunodeficiency virus.

Conclusions
For individuals with mildly immunocompromising conditions, there is no evidence of differences in VE against symptomatic or severe COVID-19 compared with those with non-TIS in the 4 COVID-19 vaccine randomized controlled efficacy trials.
The problems of macroeconomics as institutional problems: complementing the ‘what went wrong’ story with a social epistemology perspective
Authors: Lari Teemu 
Published: April 2024

Abstract
After the financial crisis of 2008, many economists expressed dissatisfaction with the state of macroeconomics. They criticised deficiencies in the dominant dynamic stochastic general equilibrium modelling approach and conceptions of good macroeconomic research behind that dominance. This paper argues that there is a deeper problem in macroeconomics, which remains unaddressed. I connect existing literature critical of the institutions of macroeconomics and of economics in general to the institutional preconditions of effective criticism outlined by the philosopher Helen Longino. I find that as an epistemic community, macroeconomics does not function in a way that adequately supports critical evaluation of established beliefs, norms and practices. This failure may partly explain why many views on macroeconomic modelling, the tenability of which economists questioned after the crisis, were able to persist for so long. My analysis gives additional support to several recent proposals for institutional reforms in economics.
Sexual differences in bite force are not related to testosterone level in the wild-derived red junglefowl
Authors: Rao Xiaodong , Wang Daiping , Liang Wei 
Published: April 2024

Abstract
Bite force is an important performance indicator of individual fitness that is closely related to food acquisition, male competition, and mating selection. It is also affected by a variety of factors and different mechanisms. Therefore, it is relatively difficult to understand the evolutionary driving forces of changes in bite force. In this study, the driving factors affecting the bite force of wild-derived red junglefowl (Gallus gallus jabouillei) were investigated from the aspects of morphological indicators and physiological characteristics. Results showed that the bite force of wild-derived red junglefowl was directly related to sex, showing obvious sexual differences. However, there was no correlation between the plasma testosterone level and bite force. The bite force of males was significantly greater than that of females, and the body index (i.e., PC1 of five body measures, namely body mass, body length, wing length, tail length, and tarsus length), the grasp index (i.e., tomial length × bill width) of males were significantly greater than those of females. Sexual selection may have played a key role in the evolution of bite force in the red junglefowl. Future studies should examine other key factors affecting changes in bite force to verify the correlation between secondary sexual characteristics and bite force in red junglefowls.
Physical Activity is Associated with a Decreased Risk of Developing Inflammatory Bowel Disease: A Systematic Review and Meta-analysis
Authors: Tiong Ho Tuan , Fan Dali , Frampton Chris , Ananthakrishnan Ashwin N , Gearry Richard B 
Published: April 2024

Abstract

Background and Aims
Modifiable risk factors in inflammatory bowel disease [IBD], such as physical activity, may be used as prevention strategies. However, the findings of previous studies on the association between physical activity and IBD risk have been inconsistent. We aimed to perform a systematic review and meta-analysis to estimate the effect of physical activity on IBD risk.

Methods
A search was conducted for relevant studies published before April 2023 that assessed the effect of pre-IBD diagnosis levels of physical activity on IBD incidence. Individual summary statistics [relative risks; RR], and confidence intervals [CI] were extracted with forest plots generated. We used the Grading of Recommendations Assessment, Development and Evaluation [GRADE] approach to assess the quality of evidence.

Results
Ten observational studies were included. For cohort studies, there were 1182 Crohn’s disease [CD] and 2361 ulcerative colitis [UC] patients, with 860 992 participants without IBD. For case-control studies, there were 781 CD to 2636 controls, and 1127 UC to 3752 controls. Compared with individuals with low physical activity levels, the RRs of CD in individuals with high physical activity levels for cohort and case-control studies were 0.78 [95% CI 0.68-0.88, p = 0.0001] and 0.87 [95% CI 0.79-0.95, p = 0.003], respectively. For UC, the RRs were 0.62 [95% CI 0.43-0.88, p = 0.008] and 0.74 [95% CI 0.51-1.07, p = 0.11].

Conclusion
This meta-analysis suggests that physical activity is inversely associated with the risk of developing IBD, more so in CD than in UC.
A New Stocking Guide Formulation Applied to Eastern White Pine
Authors: Seymour Robert S. , Smith David M. 
Published: April 2024

Abstract
A procedure is described for incorporating stand age, or stage in development, into the widely used stocking guides based on the crown competition factor (CCF). A simple model that predicts dbh of individual trees from crown projection area and total height is derived from a three-dimensional relationship between cumulative foliage production (crown volume) and total volume of the main stem. Procedures employed by previous researchers to prepare CCF-based stocking guides are then used to convert this individual-tree model to stand basal areas and numbers of trees per unit area at successive stages in development denoted by stand heights. An equation relating crown width to crown length and height is derived and used to predict growth under conventional and low-density thinning schedules for eastern white pine. An example shows that complete crown closure can occur well below the CCF-based B level if early thinnings are heavy enough to permit development of large crowns. Because CCF-based stocking guides assume that the crown width-dbh relationship is independent of height, they may, in some cases, overestimate the number of trees required for full crown closure. For. Sci. 33(2):469-484.
Effects of Light Intensity and Temperature on the Growth of Douglas-Fir and Incense-Cedar Seedlings
Authors: Minore Don 
Published: April 2024

Abstract
Seedlings of Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) and incense-cedar (Calocedrus decurrens [Torr.] Florin) were grown together in six moist growth-chamber environments to compare growth in warm and cool temperatures, determine relative shade tolerances, and investigate the effects of temperature on shade tolerance. Incense-cedar grew larger than Douglas-fir in cool temperatures under all three light intensities used (5, 24, and 420 μE.m-2.s-1), but Douglas-fir grew as large or larger than incense-cedar in warm temperatures under light intensities of 24 and 420 μE. The relative allocation of growth to shoots and roots was allometric and similar for warm and cool temperatures under 24 and 420 μE in the incense-cedar seedlings but not in the Douglas-fir seedlings. Incense-cedar seedlings were more shade tolerant than Douglas-fir seedlings. High temperatures reduced the shade tolerances of both species. For. Sci. 34(1):215-223.
Do One Percent of the Forest Fires Cause Ninety-Nine Percent of the Damage?
Authors: Strauss David , Bednar Larry , Mees Romain 
Published: April 2024

Abstract
A relatively small number of forest fires are responsible for a very high proportion of the total damage. The proportion due to the fraction p of largest fires, when plotted against p, is a measure of variability of fire sizes that is especially sensitive to the important extreme events. We find the theoretical form of the plot for several commonly used distributions and show how the results can be used in the analysis of empirical plots from actual fire size distributions. Some simple graphical methods are suggested for the fitting of truncated Pareto and lognormal distributions to empirical data. We use the plots to compare the firesize heterogeneity of several fire climate regions of the western United States; the proportion of area burned by the 1% of largest fires ranges from 80%-96%. We also compare patterns of the larger fires for Southern California and Baja California. For. Sci 35(2):319-328.
Spatial and Temporal Variability of Nitrogen Cycling in Northern Lower Michigan
Authors: Zak Donald R. , Pregitzer Kurt S. 
Published: April 2024

Abstract
Net N mineralization and nitrification were studied in three forest ecosystems to gain an understanding of the spatial and temporal variability of N transformations. The upland forests studied were two sugar maple ecosystems that differed in overstory associates and ground flora composition, and an oak ecosystem. Three stands in each ecosystem were sampled to provide spatial replication within a 250,000 ha area in northwestern Lower Michigan. Overstory biomass and annual increment were estimated using species-specific allometric biomass equations. Net N mineralization and nitrification were determined by an in situ buried polyethylene bag technique in which surface soil samples were incubated at monthly intervals for one year. Litter was collected during autumn in each ecosystem from one randomly selected stand.
Aboveground biomass was lowest in the oak ecosystem (151 t ha-1) and greatest in the sugar maple-basswood/Osmorhiza ecosystem (209 t ha-1). Net annual N mineralization was 313 μg N g-1 yr-1 in the oak ecosystem and was significantly less than annual mineralization in the two sugar maple ecosystems. Mineral N production in the sugar maple-basswood/Osmorhiza and sugar maple-red oak/Maianthemum ecosystems was 426 and 382 μg N g-1 yr-1, respectively. Nitrification was greatest in the sugar maple-basswood/Osmorhiza ecosystem where 85% of mineral N was oxidized to NO3- (364 μg N g-1 yr-1). Nitrification was minimal in the oak forest, totaling 6% of annual mineralization (18 μg N g-1 yr-1). Results suggest that ecosystem types may be used to predict spatial patterns of N transformations at regional scales. For. Sci. 36(2):367-380.
A Carbon Balance Model of Growth and Self-Pruning in Trees Based on Structural Relationships
Authors: Mäkelä Annikki 
Published: April 2024

Abstract
A tree growth model is formulated based on structural relationships in a carbon balance framework. Three relationships are applied: (1) an allometric relationship between crown surface area and foliage area, (2) the principle of functional balance, and (3) the pipe-model theory. These assumptions lead to a model where the sizes of the functional parts of the tree are derivable from foliage weight, except for the pruning height of the crown. This is determined by defining a "self-pruning coefficient," which controls the allocation of growth between height growth and foliage growth. The tree model is applied to an average-tree based stand growth model where both the self-pruning coefficient and tree mortality are made functions of crown coverage. The model is quantified for Scots pine growing in southern Fenno-Scandia. The overall behavior of the model is realistic. The model responds to stocking density through the rate of self-pruning, lower stocking densities leading to larger crown ratios. It also responds to changes in parameters describing site quality in a realistic way, although the differences in stand density are not as large as expected. The predicted development of the biomass compartments in individual trees agrees well with data on dominant Scots pine trees in Finland. For. Sci. 43(1):7-24.
Monitoring Hemlock Forest Health in New Jersey Using Landsat TM Data and Change Detection Techniques
Authors: Royle Denise D. , Lathrop Richard G. 
Published: April 2024

Abstract
Defoliation of eastern hemlock (Tsuga canadensis Carriere) forest caused mainly by the hemlock woolly adelgid (Adelges tsugae Annand) was detected, quantified, and mapped for a 1,267 km² study area in the New Jersey Highlands using anniversary dates of Landsat Thematic Mapper data (1984 and 1994). A model relating estimates of canopy condition to the temporal difference in near infrared/red reflectance (i.e., the vegetative index difference) was developed to predict and map four classes of hemlock condition across the study area. Data from 105 circular ground plots (90 m diameter) were used to develop the regression model, while data from 50 plots were reserved for accuracy assessment. The vegetative index difference was highly correlated to hemlock damage as measured on the ground (R² = 0.73). Lightly defoliated hemlock canopy did not differ spectrally from healthy hemlock; thus, these two classes were joined together. Accuracy assessment showed that hemlock condition can be predicted within one-half damage class with an overall accuracy of 64% for four damage classes, 70-72% for three classes, and 78-92% for two classes. Of the 7,735 ha of hemlock forest in 1984, 47% remained healthy to lightly defoliated, 44% had experienced moderate to severe defoliation, and 9% were dead by 1994. For. Sci. 43(3):327-335.