bluuebunny/crossref_metadata_2025_split huggingface dataset:
Students Matriculating into Integrated Plastic Surgery: Are all Medical Schools Equal?
Authors: Yau Alice , Lentskevich Marina A. , Reddy Narainsai K. , Gutowski Kristof S. , Yau Irene , Gosain Arun K. 
Published: June 2024

Introduction
Becoming a craniofacial/pediatric plastic surgeon depends on completing a plastic surgery (PS) residency. As medical school curricula for PS exposure are highly inconsistent, the authors investigated whether there was an association between the presence of PS elective rotations and/or home programs in medical schools with the proportion of students matriculating into integrated PS residency.

Methods:
A list of 198 medical schools was compiled from the Association for American Medical Colleges and the American Association of Colleges of Osteopathic Medicine. Plastic surgery residency programs were identified by the American Society of Plastic Surgery and the American Council of Educators in Plastic Surgery. Plastic surgery elective rotation offerings and recent matches (2021–2022) were obtained from school websites. Mean proportions of students matriculating into PS between schools that did versus did not have PS elective rotations and/or home PS residency programs were compared.

Results:
One hundred fifty-nine medical schools were included. Seventy-seven of 159 (48%) had both PS elective rotations and home program(s), 63/159 (40%) offered PS elective rotations only, and 19/159 (12%) had neither. The mean proportions of students matriculating differed significantly (P<0.001) among schools without PS electives or a home program [0.09%, 95% confidence interval (CI): −0.04% to 0.21%), PS elective only (0.51%, 95% CI: 0.25%–0.77%), and both PS elective and home program(s) (1.14%, 95% CI: 0.92%–1.37%).

Conclusion:
The presence of elective PS rotations and a home PS residency program significantly increase the chances of matriculation into integrated PS residency programs.
Middle Meningeal Arterial Embolization Combined With Drilling in the Treatment of Acute Epidural Hematoma
Authors: Wang Henglu , Wang Qingbo , Li Zefu 
Published: June 2024

Objective:
The purpose of this study was to determine the technical feasibility and safety of middle meningeal arterial (MMA) embolization combined with drilling drainage in the treatment of acute epidural hematoma (AEDH) by comparing it with traditional craniotomy in the treatment.

Methods:
One hundred seventeen patients with AEDH treated for MMA embolization combined with drilling and drainage or craniotomy hematoma removal from January 2017 to September 2020 were retrospectively analyzed and divided into a craniotomy group (n=85) and a minimally invasive group (n=32). Hematoma removal was performed in the craniotomy group, and MMA embolization combined with drilling and drainage was performed in the minimally invasive group. The general clinical data, imaging data, surgery, and follow-up of the 2 groups were compared and analyzed.

Results:
Compared with the craniotomy group, the residual hematoma volume in the minimally invasive group was higher than in the craniotomy group. The average postoperative drainage duration in the minimally invasive group was longer than in the craniotomy group. Compared with the craniotomy group, the minimally invasive group was associated with shorter operative time, less intraoperative bleeding, and lower rates of postoperative rebleeding. In addition, the incidence of postoperative complications and length of hospitalization in the minimally invasive group were significantly shortened.

Conclusion:
Middle meningeal arterial embolization combined with drilling and drainage in the treatment of AEDH caused by MMA active bleeding is safe, effective, and more minimally invasive, and can be promoted and applied.
EnderScope: a low-cost 3D printer-based scanning microscope for microplastic detection
Authors: Burke Niamh , Müller Gesine , Saggiomo Vittorio , Hassett Amy Ruth , Mutterer Jérôme , Ó Súilleabháin Patrick , Zakharov Daniel , Healy Donal , Reynaud Emmanuel G. , Pickering Mark 
Published: June 2024

Low-cost and scalable technologies that allow people to measure microplastics in their local environment could facilitate a greater understanding of the global problem of marine microplastic pollution. A typical way to measure marine microplastic pollution involves imaging filtered seawater samples stained with a fluorescent dye to aid in the detection of microplastics. Although traditional fluorescence microscopy allows these particles to be manually counted and detected, this is a resource- and labour-intensive task. Here, we describe a novel, low-cost microscope for automated scanning and detection of microplastics in filtered seawater samples—the EnderScope. This microscope is based on the mechanics of a low-cost 3D printer (Creality Ender 3). The hotend of the printer is replaced with an optics module, allowing for the reliable and calibrated motion system of the 3D printer to be used for automated scanning over a large area (>20 × 20 cm). The EnderScope is capable of both reflected light and fluorescence imaging. In both configurations, we aimed to make the design as simple and cost-effective as possible, for example, by using low-cost LEDs for illumination and lighting gels as emission filters. We believe this tool is a cost-effective solution for microplastic measurement.
This article is part of the Theo Murphy meeting issue 'Open, reproducible hardware for microscopy'.
Open instrumentation, like open data, is key to reproducible science. Yet, without incentives it won’t thrive
Authors: Stirling Julian 
Published: June 2024

There is far more to open science than simply not shutting away your work. For example, a significant time investment must be made to collate, curate, explain and document precisely how an experiment can be reproduced or data can be reused. This time investment is currently poorly rewarded in our current model of open science where a bare minimum of openness is mandated, but further work is not recognized. As the open science movement looks beyond open access publications and open data towards ongoing detailed work such as open source software and open source hardware, it needs to consider how to properly encourage the extra work that is needed to properly document these projects. Without detailed documentation, the work cannot be replicated, reused and continually improved. If the work cannot be replicated or reused, is it really even open?
This article is part of the Theo Murphy meeting issue ‘Open, reproducible hardware for microscopy’.
Microbial-Derived Exerkines Prevent Skeletal Muscle Atrophy
Authors: Valentino Taylor R. , Burke Benjamin I. , Kang Gyumin , Goh Jensen , Dungan Cory M. , Ismaeel Ahmed , Mobley C. Brooks , Flythe Michael D. , Wen Yuan , McCarthy John J. 
Published: June 2024

AbstractRegular exercise yields a multitude of systemic benefits, many of which may be mediated through the gut microbiome. Here, we report that cecal microbial transplants (CMTs) from exercise-trained vs. sedentary mice have modest benefits in reducing skeletal muscle atrophy using a mouse model of unilaterally hindlimb-immobilization. Direct administration of top microbial-derived exerkines from an exercise-trained gut microbiome preserved muscle function and prevented skeletal muscle atrophy.
Comprehensive Analysis of Juvenile Nasopharyngeal Angiofibromas via Whole Exome Sequencing
Authors: Kumari Kiran , Afroj Shariya , Madhry Deeksha , Verma Yash , Kairo Arvind K. , Thakar Alok , Sikka Kapil , Verma Hitesh , Verma Bhupendra 
Published: June 2024

ABSTRACTObjectivesThe molecular basis and mechanisms of Juvenile Nasopharyngeal Angiofibromas (JNA) pathogenesis are still unknown. Despite being a rare and benign neoplasm, JNA is a locally aggressive and potentially destructive neoplasm among head and neck tumors, typically diagnosed in young males. The advancement of genome technologies and analytical tools has provided an unparalleled opportunity to explore the intricacy of JNA. The present study provides the first evidence of the involvement of chromosome Y genes in JNA.MethodsThirteen JNA patients at an advanced disease stage and 5 age-matched male controls were registered for this study. Whole-exome sequencing (WES) analysis was conducted followed by functional analysis to understand the molecular mechanism of the JNA.ResultsWES analysis revealed a high prevalence of mutations in 14 genes within the protein-coding, Male-Specific Region of the Y-chromosome of young males (mean age: 13.8 ± 2.4) with JNA. These mutations, occurring at 28 distinct positions, were characterized as moderate to high impact and were prevalent in 9 JNA patients but not in the control group. The most frequently mutated genes were USP9Y and UTY, followed by KDM5D, DDX3Y and TSPY4. The expression of USP9Y, UTY and DDX3Y was found to be co-modulated, implying their coordinated regulation as a complex. Furthermore, somatic mutations were detected in genes previously linked to JNA.ConclusionThe wide array of genetic and somatic mutations identified in JNA provides novel insight into JNA pathophysiology.
Continent-wide drivers of spatial synchrony in age structure across wild great tit populations
Authors: Woodman Joe P. , Vriend Stefan J. G. , Adriaensen Frank , Álvarez Elena , Artemyev Alexander , Barba Emilio , Burgess Malcolm D. , Caro Samuel P. , Cauchard Laure , Charmantier Anne , Cole Ella F. , Dingemanse Niels , Doligez Blandine , Eeva Tapio , Evans Simon R. , Grégoire Arnaud , Lambrechts Marcel , Leivits Agu , Liker András , Matthysen Erik , Orell Markku , Park John S. , Rytkõnen Seppo , Senar Juan Carlos , Seress Gábor , Szulkin Marta , van Oers Kees , Vatka Emma , Visser Marcel E. , Firth Josh A. , Sheldon Ben C. 
Published: June 2024

AbstractSpatio-temporal variation in age structure influences population dynamics, yet we have limited understanding of the spatial scale at which its fluctuations are synchronised between populations. Using 32 great tit populations, spanning 3200km and>130,000 birds across 67 years, we quantify spatial synchrony in breeding age structure and its drivers. We show that larger clutch sizes, colder winters and summers, and larger beech crops lead to younger populations. We report distant-dependent spatial synchrony of age structure, which is maintained at approximately 650km. Despite covariation with age structure, reproductive and environmental variables do not influence the scale of synchrony, except for a moderate effect of beech masting. We suggest that local ecological and density-dependent dynamics impact how environmental variation interacts with age structure, influencing estimates of the environment’s effect on spatial synchrony. Our analyses demonstrate the operation of synchrony in age structure over large scales, with implications for age-dependent demography in populations.
Dietary isoleucine content defines the metabolic and molecular response to a Western diet
Authors: Trautman Michaela E. , Green Cara L. , MacArthur Michael R. , Chaiyakul Krittisak , Alam Yasmine H. , Yeh Chung-Yang , Babygirija Reji , James Isabella , Gilpin Michael , Zelenovskiy Esther , Green Madelyn , Marshall Ryan N. , Sonsalla Michelle M. , Flores Victoria , Simcox Judith A. , Ong Irene M. , Malecki Kristen C. , Jang Cholsoon , Lamming Dudley W. 
Published: June 2024

AbstractThe amino acid composition of the diet has recently emerged as a critical regulator of metabolic health. Consumption of the branched-chain amino acid isoleucine is positively correlated with body mass index in humans, and reducing dietary levels of isoleucine rapidly improves the metabolic health of diet-induced obese male C57BL/6J mice. However, it is unknown how sex, strain, and dietary isoleucine intake may interact to impact the response to a Western Diet (WD). Here, we find that although the magnitude of the effect varies by sex and strain, reducing dietary levels of isoleucine protects C57BL/6J and DBA/2J mice of both sexes from the deleterious metabolic effects of a WD, while increasing dietary levels of isoleucine impairs aspects of metabolic health. Despite broadly positive responses across all sexes and strains to reduced isoleucine, the molecular response of each sex and strain is highly distinctive. Using a multi-omics approach, we identify a core sex- and strain-independent molecular response to dietary isoleucine, and identify mega-clusters of differentially expressed hepatic genes, metabolites, and lipids associated with each phenotype. Intriguingly, the metabolic effects of reduced isoleucine in mice are not associated with FGF21 – and we find that in humans plasma FGF21 levels are likewise not associated with dietary levels of isoleucine. Finally, we find that foods contain a range of isoleucine levels, and that consumption of dietary isoleucine is lower in humans with healthy eating habits. Our results demonstrate that the dietary level of isoleucine is critical in the metabolic and molecular response to a WD, and suggest that lowering dietary levels of isoleucine may be an innovative and translatable strategy to protect from the negative metabolic consequences of a WD.
Human skeletal muscle possesses an epigenetic memory of high intensity interval training
Authors: Pilotto AM , Turner DC , Crea E , Mazzolari R , Brocca L , Pellegrino MA , Miotti D , Bottinelli R , Sharples AP , Porcelli S 
Published: June 2024

ABSTRACTINTRODUCTIONHuman skeletal muscle displays an epigenetic memory of resistance exercise induced by hypertrophy. It is unknown, however, whether high-intensity interval training (HIIT) also evokes an epigenetic muscle memory. This study employed repeated training intervention interspersed with a detraining period to assess epigenetic memory of HIIT.METHODSTwenty healthy subjects (25±5yrs) completed two HIIT interventions (training and retraining) lasting 2 months, separated by 3 months of detraining. Measurements at baseline, after training, detraining and retraining included maximal oxygen consumption (V̇O2max). Vastus lateralis biopsies were taken for genome-wide DNA methylation and targeted gene expression analyses. RESULTS: V̇O2maximproved during training and retraining (p<0.001) without differences between interventions (p>0.58). Thousands of differentially methylated positions (DMPs) predominantly demonstrated a hypomethylated state after training, retained even after 3-months exercise cessation and into retraining. Five genes; ADAM19, INPP5a, MTHFD1L, CAPN2, SLC16A3 possessed differentially methylated regions (DMRs) with retained hypomethylated memory profiles and increased gene expression. The retained hypomethylation during detraining was associated with an enhancement in expression of the same genes even after 3 months of detraining. SLC16A3, INPP5a, CAPN2 are involved in lactate transport and calcium signaling.CONCLUSIONSDespite similar physiological adaptations between training and retraining, memory profiles were found at epigenetic and gene expression level, characterized by retained hypomethylation and increased gene expression after training into long-term detraining and retraining. These genes were associated with calcium signaling and lactate transport. Whilst significant memory was not observed in physiological parameters, our novel findings indicate that human skeletal muscle possesses an epigenetic memory of HIIT.
High-dimensional multi-omics measured in controlled conditions are useful for maize platform and field trait predictions
Authors: Baber Ali , Bertrand Huguenin-Bizot , Maxime Laurent , François Chaumont , Maistriaux Laurie C , Stéphane Nicolas , Hervé Duborjal , Claude Welcker , François Tardieu , Tristan Mary-Huard , Laurence Moreau , Alain Charcosset , Daniel Runcie , Renaud Rincent 
Published: June 2024

AbstractThe effects of climate change in the form of drought, heat stress, and irregular seasonal changes threaten global crop production. The ability of multi-omics data, such as transcripts and proteins, to reflect a plant’s response to such climatic factors can be capitalized in prediction models to maximize crop improvement. Implementing multi-omics characterization in routine field evaluations is challenging due to high costs. It is, however, possible to do it on reference genotypes in controlled conditions. Using omics measured on a platform, we tested different multi-omics-based prediction approaches, with and without pedo-climatic data, using a high dimensional linear mixed model (MegaLMM) to predict genotypes for platform traits and agronomic field traits in a hybrid panel of 244 maize Dent lines crossed to a Flint tester. We considered two prediction scenarios: in the first one, new hybrids are predicted (CV1), and in the second one, partially observed hybrids are predicted (CV2). For both scenarios, all hybrids were characterized for omics on the platform. We observed that omics can predict both additive and non-additive genetic effects for the platform traits, resulting in much higher predictive abilities than GBLUP. This highlights their efficiency in capturing regulation processes in relation to the growth conditions. For the field traits, we observed that only the additive components of omics were useful and only slightly improved predictive abilities for predicting new hybrids (CV1, model MegaGAO) and for predicting partially observed hybrids (CV2, model GAOxW-BLUP) in comparison to GBLUP. We conclude that measuring the omics in the fields would be of considerable interest for predicting productivity, if the omics costs were to drop significantly. Our study confirms the potential of omics to predict additive and non-additive genetic effects, resulting in a potentially high increase in predictive abilities compared to standard genomic prediction models.Key MessageTranscriptomics and proteomics information collected on a platform can predict additive and non-additive effects for platform traits and additive effects for field traits.
Systemic mRNA transport depends on m5C methylation, nuclear mRNA export factors and developmental phase changes
Authors: Xu Ying , Székely András , Ostendorp Steffen , Gupta Saurabh , Tomkins Melissa , Yang Lei , Apelt Federico , Zhao Yan , Mavrothalassiti Eleni , Wansing Linda , Kehr Julia , Saplaoura Eleftheria , Kragler Friedrich 
Published: June 2024

AbstractIn Arabidopis a high number of distinct mRNAs move from shoot to root. We previously reported on the correlation of m5C-methylation and lack of mRNA transport in juvenile plants depending on the RNA methyltransferasesDNMT2 NSUN2B. However, to our surprise we uncovered that lack ofDNMT2 NSUN2B(writer) activity did not abolished transport ofTCTP1andHSC70.1transcripts in flowering plants. We uncovered that transport of both transcripts is reinstated indnmt2 nsun2bmutants after commitment to flowering. This finding suggests that additional factors are seemingly involved in regulating / mediating mRNA transport. In search of such candidates, we identified the two ALY2 and ALY4 nuclear mRNA export factors belonging to the ALYREF family as bona fide m5C readers mediating mRNA transport. We show that both proteins are allocated along the phloem and that they bind preferentially to mobile mRNAs. MST measurements indicate that ALY2 and ALY4 bind to mobile mRNAs with relative high affinity with ALY4 showing higher affinity towards m5C-methylated mobile mRNAs. An analysis of the graft-mobile transcriptome of juvenile heterografted-grafted wild type,dnmt2 nsun2b,aly2andaly4mutants revealed that the nuclear export factors are key regulators of mRNA transport. We suggest that depending on the developmental stage m5C methylation has a negative and positive regulatory function in mRNA transport and acts together with ALY2 and ALY4 to facilitate mRNA transport in both juvenile and flowering plants.
TMAO miscompartmentalization is a reversible driver of autism pathophysiology
Authors: Launay Jean-Marie , Vodovar Nicolas 
Published: June 2024

AbstractAutism spectrum disorder (ASD) is a complex and heterogeneous neurodevelopmental disorder. Contrary to what has been reported for genetics and gut dysbiosis, ASD appears to be very homogeneous when considering tryptophan metabolism. Indeed, multiple biochemical anomalies have been observed in most individuals with ASD. Following up on these findings, we found that ASD is strongly associated with the miscompartmentalization of the chemical chaperone trimethylamineN-oxide (TMAO). Intracellular TMAO was markedly reduced in individuals with ASD as a result of altered fluid/electrolyte homeostasis and was responsible for numerous biochemical anomalies described in ASD. Administration of urea in a rat model of ASD that recapitulates the biochemical anomalies observed in humans not only restored biochemical parameters but also broadly improved all behaviours. Our results demonstrate the major role of TMAO in the pathophysiology of ASD and cellular physiology, although TMAO miscompartmentalization is not causal for ASD. We anticipate that urea, which is already clinically approved, offers a breakthrough therapeutic opportunity for ASD.
Lessons from combined metabolic model of mesophyll and guard cells
Authors: Sarkar Devlina , Kundu Sudip 
Published: June 2024

SummaryUnderstanding of overall metabolisms of guard cell (GC) and mesophyll cell (MC), their possible interactions and roles in stomatal movement will help in designing crop plants with higher water use efficiencies. Although, previous constraint based modelling and analyses correctly predicted some known metabolic patterns of isolated C3MC, GC and Crassulacean Acid Metabolism (CAM) MC, quantitative estimations of combined metabolism of GC and MC and detailed analysis of GC metabolism in CAM are still awaiting. A six phase diel combined model of GC and MC is constructed integrating existing models of two different cell types with necessary modifications guided by known physiology. It is used to predict the similarities and dissimilarities of GC and MC metabolisms. In addition to previously predicted results, analysis of this new two-cell model successfully shows higher activities of some experimentally observed C4like enzymes in GC than MC in C3, the possible storage patterns of the osmolytes like K+, malate2-, sucrose etc., in CAM GC. Results also show different patterns of starch synthesis and accumulation, ATP production and utilization in GC and MC of C3and CAM. This combined model integrates stomatal opening, gaseous exchange and GC-MC metabolisms. It is a significant step towards understanding and quantitative estimation of the whole leaf tissue metabolism linking gaseous exchange with environment.Significance statementOur time-resolved combined metabolic model of guard and mesophyll cells integrates stomatal opening, gaseous exchange and cellular metabolisms in C3, CAM and partial CAM conditions; their analyses provide quantitative estimations of metabolic fluxes, ATP production and utilization, and different metabolic patterns of starch synthesis and accumulation of both the cells. It is a significant step towards understanding and quantitative estimation of the whole leaf tissue metabolism linking gaseous exchange with environment and phloem loading.