bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individual-specific levels of CTG•CAG somatic instability are shared across multiple tissues in myotonic dystrophy type 1
Authors: Morales Fernando , Corrales Eyleen , Vásquez Melissa , Zhang Baili , Fernández Huberth , Alvarado Fernando , Cortés Sergio , Santamaría-Ulloa Carolina , Initiative-MMDBDI Marigold Myotonic Dystrophy Biomarkers Discovery , Krahe Ralf , Monckton Darren G 
Published: September 2022

Abstract
Myotonic dystrophy type 1 is a complex disease caused by a genetically unstable CTG repeat expansion in the 3′-untranslated region of the DMPK gene. Age-dependent, tissue-specific somatic instability has confounded genotype–phenotype associations, but growing evidence suggests that it also contributes directly toward disease progression. Using a well-characterized clinical cohort of DM1 patients from Costa Rica, we quantified somatic instability in blood, buccal cells, skin and skeletal muscle. Whilst skeletal muscle showed the largest expansions, modal allele lengths in skin were also very large and frequently exceeded 2000 CTG repeats. Similarly, the degree of somatic expansion in blood, muscle and skin were associated with each other. Notably, we found that the degree of somatic expansion in skin was highly predictive of that in skeletal muscle. More importantly, we established that individuals whose repeat expanded more rapidly than expected in one tissue (after correction for progenitor allele length and age) also expanded more rapidly than expected in other tissues. We also provide evidence suggesting that individuals in whom the repeat expanded more rapidly than expected in skeletal muscle have an earlier age at onset than expected (after correction for the progenitor allele length). Pyrosequencing analyses of the genomic DNA flanking the CTG repeat revealed that the degree of methylation in muscle was well predicted by the muscle modal allele length and age, but that neither methylation of the flanking DNA nor levels of DMPK sense and anti-sense transcripts could obviously explain individual- or tissue-specific patterns of somatic instability.
A genome for Cissus illustrates features underlying its evolutionary success in dry savannas
Authors: Xin Haiping , Wang Yi , Li Qingyun , Wan Tao , Hou Yujun , Liu Yuanshuang , Gichuki Duncan Kiragu , Zhou Huimin , Zhu Zhenfei , Xu Chen , Zhou Yadong , Liu Zhiming , Li Rongjun , Liu Bing , Lu Limin , Jiang Hongsheng , Zhang Jisen , Wan Junnan , Aryal Rishi , Hu Guangwan , Chen Zhiduan , Gituru Robert Wahiti , Liang Zhenchang , Wen Jun , Wang Qingfeng 
Published: September 2022

Abstract
Cissus is the largest genus in Vitaceae and is mainly distributed in the tropics and subtropics. Crassulacean acid metabolism (CAM), a photosynthetic adaptation to the occurrence of succulent leaves or stems, indicates that convergent evolution occurred in response to drought stress during species radiation. Here we provide the chromosomal level assembly of Cissus rotundifolia (an endemic species in Eastern Africa) and a genome-wide comparison with grape to understand genome divergence within an ancient eudicot family. Extensive transcriptome data were produced to illustrate the genetics underpinning C. rotundifolia’s ecological adaption to seasonal aridity. The modern karyotype and smaller genome of C. rotundifolia (n = 12, 350.69 Mb/1C), which lack further whole-genome duplication, were mainly derived from gross chromosomal rearrangements such as fusions and segmental duplications, and were sculpted by a very recent burst of retrotransposon activity. Bias in local gene amplification contributed to its remarkable functional divergence from grape, and the specific proliferated genes associated with abiotic and biotic responses (e.g. HSP-20, NBS-LRR) enabled C. rotundifolia to survive in a hostile environment. Reorganization of existing enzymes of CAM characterized as diurnal expression patterns of relevant genes further confer the ability to thrive in dry savannas.
An access and transfer right to data—from a competition law perspective
Authors: Lundqvist Björn 
Published: September 2022

Abstract
While business users face difficulties accessing and porting data on platforms, the Digital Markets Act has been hailed as the legislative tool enabling business users access and transfer the data they have generated on platforms controlled by gatekeepers. The tool provided by the Digital Markets Act is discussed in this article and the author argue that business users should have a more elaborated right to first access the data they produce on platforms and in ecosystems, and secondly transfer such data from platform to platform, cloud to cloud, thing to thing or in-house. A right to access and transfer data could have several benefits; it benefits dissemination of data, creativity and innovation in connected markets and it promotes competition between platforms, clouds and ecosystem providers. Creativity will be enhanced because necessary data—being the raw material for new innovations—will be more broadly disbursed. It will also benefit consumers having a disbursed and disseminated data commons for the development of ideas, innovations, and the exchange of knowledge.
Reference genome of the color polymorphic desert annual plant sandblossoms, Linanthus parryae
Authors: Anghel Ioana G , Jacobs Sarah J , Escalona Merly , Marimuthu Mohan P A , Fairbairn Colin W , Beraut Eric , Nguyen Oanh , Toffelmier Erin , Shaffer H Bradley , Zapata Felipe 
Published: September 2022

Abstract
Sandblossoms, Linanthus parryae is a widespread annual plant species found in washes and sandy open habitats across the Mojave Desert and Eastern Sierra Nevada of California. Studies in this species have played a central role in evolutionary biology, serving as the first test cases of the shifting balance theory of evolution, models of isolation by distance, and metrics to describe the genetic structure of natural populations. Despite the importance of L. parryae in the development of landscape genetics and phylogeography, there are no genomic resources available for the species. Through the California Conservation Genomics Project, we assembled the first genome in the genus Linanthus. Using PacBio HiFi long reads and Hi-C chromatin conformation capture, we assembled 123 scaffolds spanning 1.51 Gb of the 1.96 Gb estimated genome, with a contig N50 of 18.7 Mb and a scaffold N50 of 124.8 Mb. This assembly, with a BUSCO completeness score of 88.7%, will allow us to revisit foundational ideas central to our understanding of how evolutionary forces operate in a geographic landscape. In addition, it will be a new resource to uncover adaptations to arid environments in the fragile desert habitat threatened by urban and solar farm development, climate change, and off-road vehicles.
The SLIM1 transcription factor affects sugar signaling during sulfur deficiency in Arabidopsis
Authors: Wawrzyńska Anna , Piotrowska Justyna , Apodiakou Anastasia , Brückner Franziska , Hoefgen Rainer , Sirko Agnieszka 
Published: September 2022

AbstractThe homeostasis of major macronutrient metabolism needs to be tightly regulated, especially when the availability of one or more nutrients fluctuates in the environment. Both sulfur metabolism and glucose signaling are important processes throughout plant growth and development, as well as during stress responses. Still, very little is known about how these processes affect each other, although they are positively connected. Here, we showed in Arabidopsis that the crucial transcription factor of sulfur metabolism, SLIM1, is involved in glucose signaling during shortage of sulfur. The germination rate of the slim1_KO mutant was severely affected by high glucose and osmotic stress. The expression of SLIM1-dependent genes in sulfur deficiency appeared to be additionally induced by a high concentration of either mannitol or glucose, but also by sucrose, which is not only the source of glucose but another signaling molecule. Additionally, SLIM1 affects PAP1 expression during sulfur deficiency by directly binding to its promoter. The lack of PAP1 induction in such conditions leads to much lower anthocyanin production. Taken together, our results indicate that SLIM1 is involved in the glucose response by modulating sulfur metabolism and directly controlling PAP1 expression in Arabidopsis during sulfur deficiency stress.
Three tRNA nuclear exporters in S. cerevisiae: parallel pathways, preferences, and precision
Authors: Chatterjee Kunal , Marshall William A , Hopper Anita K 
Published: September 2022

Abstract
tRNAs that are transcribed in the nucleus are exported to the cytoplasm to perform their iterative essential function in translation. However, the complex set of tRNA post-transcriptional processing and subcellular trafficking steps are not completely understood. In particular, proteins involved in tRNA nuclear export remain unknown since the canonical tRNA nuclear exportin, Los1/Exportin-t, is unessential in all tested organisms. We previously reported that budding yeast Mex67-Mtr2, a mRNA nuclear exporter, co-functions with Los1 in tRNA nuclear export. Here we employed in vivo co-purification of tRNAs with endogenously expressed nuclear exporters to document that Crm1 also is a bona fide tRNA nuclear exporter. We document that Los1, Mex67-Mtr2 and Crm1 possess individual tRNA preferences for forming nuclear export complexes with members of the 10 families of intron-containing pre-tRNAs. Remarkably, Mex67-Mtr2, but not Los1 or Crm1, is error-prone, delivering tRNAs to the cytoplasm prior to 5′ leader removal. tRNA retrograde nuclear import functions to monitor the aberrant leader-containing spliced tRNAs, returning them to the nucleus where they are degraded by 3′ to 5′ exonucleases. Overall, our work identifies a new tRNA nuclear exporter, uncovers exporter preferences for specific tRNA families, and documents contribution of tRNA nuclear import to tRNA quality control.
Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides
Authors: Todisco Marco , Szostak Jack W 
Published: September 2022

Abstract
Hybridization and strand displacement kinetics determine the evolution of the base paired configurations of mixtures of oligonucleotides over time. Although much attention has been focused on the thermodynamics of DNA and RNA base pairing in the scientific literature, much less work has been done on the time dependence of interactions involving multiple strands, especially in RNA. Here we provide a study of oligoribonucleotide interaction kinetics and show that it is possible to calculate the association, dissociation and strand displacement rates displayed by short oligonucleotides (5nt–12nt) that exhibit no expected secondary structure as simple functions of oligonucleotide length, CG content, ΔG of hybridization and ΔG of toehold binding. We then show that the resultant calculated kinetic parameters are consistent with the experimentally observed time dependent changes in concentrations of the different species present in mixtures of multiple competing RNA strands. We show that by changing the mixture composition, it is possible to create and tune kinetic traps that extend by orders of magnitude the typical sub-second hybridization timescale of two complementary oligonucleotides. We suggest that the slow equilibration of complex oligonucleotide mixtures may have facilitated the nonenzymatic replication of RNA during the origin of life.
Genomic and geographic diversification of a “great-speciator” (Rhipidura rufifrons)
Authors: Klicka Lukas B , Campillo Luke C , Manthey Joseph D , Andersen Michael J , Dumbacher John P , Filardi Christopher E , Joseph Leo , Uy J Albert C , Weidemann Douglas E , Moyle Robert G 
Published: September 2022

AbstractThe radiation of so-called “great speciators” represents a paradox among the myriad of avian radiations endemic to the southwest Pacific. In such radiations, lineages otherwise capable of dispersing across vast distances of open ocean differentiate rapidly and frequently across relatively short geographic barriers. Here, we evaluate the phylogeography of the Rufous Fantail (Rhipidura rufifrons). Although a presumed “great-speciator”, no formal investigations across its range have been performed. Moreover, delimitation of lineages within R. rufifrons, and the biogeographic implications of those relationships, remain unresolved. To investigate whether R. rufifrons represents a great speciator we identified thousands of single nucleotide polymorphisms for 89 individuals, representing 19 described taxa. Analyses recovered 7 divergent lineages and evidence of gene flow between geographically isolated populations. We also found plumage differences to be a poor proxy for evolutionary relationships. Given the relatively recent divergence dates for the clade (1.35–2.31 mya), rapid phenotypic differentiation, and evidence for multiple independent lineages within the species complex, we determine that R. rufifrons possesses the characteristics of a great speciator.
Perioperative Coagulation Changes in Total Pancreatectomy and Islet Autotransplantation
Authors: Bergman Zachary R. , Robbins Alexandria J. , Alwan Fatima S. , Bellin Melena D. , Kirchner Varvara A. , Pruett Timothy L. , Mulier Kristine E. , Boucher Alex A. , Lusczek Elizabeth R. , Beilman Greg J. 
Published: September 2022

Objectives
Thrombotic complications after total pancreatectomy with islet autotransplantation (TPIAT) are common. However, the systemic changes to coagulation in the perioperative period have not been well studied. Our objective was to evaluate the derangements in coagulation in the perioperative period for this procedure.

Methods
This was a prospective observational study of patients undergoing elective TPIAT for chronic pancreatitis. Multiple methods of evaluating coagulation, including 2 viscoelastic assays and standard laboratory assays were obtained at defined intraoperative and postoperative intervals.

Results
Fifteen patients were enrolled. Laboratory values demonstrated initial intraoperative hypercoagulability before significant systemic anticoagulation after islet infusion with heparin. Hypercoagulability is again seen at postoperative days 3 and 7. Subgroup analysis did not identify any major coagulation parameters associated with portal vein thrombosis formation.

Conclusions
Apart from the immediate period after islet cell and heparin infusion, patients undergoing TPIAT are generally hypercoagulable leading to a high rate of thrombotic complications. Portal vein thrombosis development had minimal association with systemic derangements in coagulation as it is likely driven by localized inflammation at the time of islet cell infusion. This study may provide the groundwork for future studies to identify improvements in thrombotic complications.
An Examination of Donor Factors That Impact the Results of the Glucagon Stimulation Test as an Assessment of the Pancreatic Graft Endocrine Function
Authors: Ito Taihei , Kenmochi Takashi , Aida Naohiro , Hiratsuka Izumi , Matsushima Hajime , Kurihara Kei , Suzuki Atsushi , Shibata Megumi , Kusaka Mamoru , Hasegawa Midori , Ishihara Takuma , Go Hirofumi , Yabusaki Kohei , Shintani Ayumi 
Published: September 2022

Objectives
Delta C-peptide derived by the glucagon stimulation test is a reliable value for the evaluation of the pancreatic endocrine function after pancreas transplantation. We examined the associations between delta C-peptide as pancreatic graft endocrine function and donor background factors.

Methods
Sixty-five cases of pancreatic transplantation from brain-dead donors, which were performed in our facility, were enrolled in this study. Enrolled recipients underwent a glucagon stimulation test within 1 to 3 months after transplantation to evaluate the pancreatic graft endocrine function with delta C-peptide to compare donor background factors.

Results
The following factors were associated with significant deterioration of the delta C-peptide: age of 50 years or greater, death from cerebrovascular accident, hemoglobin A1c level of 5.6% or greater, creatinine level of 1.0 mg/dL or greater, C-reactive protein level of 25 mg/dL or greater, and sodium level of 150 mmol/L or greater. In addition, increased numbers of these donor factors indicated significantly greater deterioration of the posttransplant pancreatic endocrine function (P < 0.001).

Conclusions
To secure insulin independence after pancreas transplantation, which means maintaining a delta C-peptide level of 1.0 ng/mL or greater on a glucagon stimulation test, the utilization of donors, who possesses more than equal to 3 of the donor factors identified in this study, should be carefully considered.
Work Environment and Operational Failures Associated With Nurse Outcomes, Patient Safety, and Patient Satisfaction
Authors: Riman Kathryn A. , Harrison Jordan M. , Sloane Douglas M. , McHugh Matthew D. 
Published: September 2022

Background
Operational failures, defined as the inability of the work system to reliably provide information, services, and supplies needed when, where, and to who, are a pervasive problem in U.S. hospitals that disrupt nurses’ ability to provide safe and effective care.

Objectives
We examined the relationship between operational failures, patient satisfaction, nurse-reported quality and safety, and nurse job outcomes (e.g., burnout and job satisfaction) and whether differences in hospital work environments explained the relationship.

Methods
We conducted a cross-sectional analysis using population-based survey data from 11,709 registered nurses in 415 hospitals who participated in the RN4CAST-US nurse survey (2015–2016) and the 2016 Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey. The RN4CAST-US nurse survey focused on hospital quality and safety, job outcomes, and hospital work environments. The HCAHPS survey collected publicly reported patient data on their satisfaction with their care. Operational failures were evaluated using an eight-item composite measure that assessed missing supplies, orders, medication, missing/wrong patient diet, electronic documentation problems, insufficient staff, and time spent on workarounds and nonnursing tasks. Multilevel regression models were used to test the hypothesized relationships.

Results
Operational failures were associated with low patient satisfaction scores, poor quality and safety outcomes, and poor nurse job outcomes, and those associations were partly accounted for by hospital work environments.

Discussion
Operational failures prevent high-quality care and positive patient and nurse outcomes. Operational failures and the hospital work environment should be targeted simultaneously to maximize quality improvement efforts. Hospital leadership should work with frontline staff to identify and target the sources of operational failures in nursing units. Improvements to hospital work environments may reduce the occurrence of operational failures.
Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells
Authors: Sun Tongyu , Xu Yueyuan , Xiang Yu , Soderblom Erik J , Diao Yarui 
Published: September 2022

ABSTRACTTransposable elements (TEs) are parasitic DNA sequences accounting for over half of the human genome. Tight control of the repression and activation states of TEs is critical for genome integrity, development, immunity, and diseases, including cancer. However, precisely how this regulation is achieved remains unclear. To address this question, we develop a targeted proteomic proximity labeling approach to capture TE-associated proteins in human embryonic stem cells (hESCs). We find that the RNA N6-methyladenosine(m6A)-reader, YTHDC2, occupies genomic loci of the primate-specific TE, LTR7/HERV-H, specifically through its interaction with m6A-modified HERV-H RNAs. Unexpectedly, YTHDC2 recruits the DNA 5-methylcytosine(5mC)-demethylase, TET1, to remove 5mC from LTR7/HERV-H and prevent epigenetic silencing. Functionally, the YTHDC2/LTR7-axis inhibits neural differentiation of hESCs. Our results reveal both an underappreciated crosstalk between RNA m6A and DNA 5mC, the most abundant regulatory modifications of RNA and DNA in eukaryotes, and the fact that in hESCs this interplay controls TE activity and cell fate.
Temperature and dietary energy content influence female maturation age and egg nutritional content in Atlantic salmon
Authors: Maamela Katja S. , Åsheim Eirik R. , Debes Paul V. , House Andrew H. , Erkinaro Jaakko , Liljeström Petra , Primmer Craig R. , Mobley Kenyon B. 
Published: September 2022

AbstractThe environment experienced by a female influences reproductive traits in many species of fish. Environmental factors such as temperature and diet are not only important mediators of female maturation and reproduction but also of egg traits and offspring fitness through maternal provisioning. In this study, we use three-year-old, tank-reared, Atlantic salmon from two Finnish populations to investigate the effect of temperature and diet on maturation and egg traits. We show that a temperature difference of 2°C is sufficient to delay maturation in female Atlantic salmon whereas a 22% reduction in dietary energy content had no effect on maturation. Diet did not influence the body size, condition, or fecundity of the mature females or the size or protein content of the eggs. However, a higher energy diet increased egg lipid content. Neither female body size nor condition were associated with egg size or fat/protein composition. Our results indicate that female salmon that have a poorer diet in terms of energy content may have a reproductive disadvantage due to lower energy provisioning of eggs. This disadvantage has the potential to translate into fitness consequences for their offspring.
Increased conductance associated with higher photosynthesis in leaves and green stems of avocado exposed to diffuse light
Authors: Berry Z. Carter , Ávila-Lovera Eleinis , Ellertson Kendra , Goldsmith Gregory R. 
Published: September 2022

AbstractResearch has demonstrated that diffuse light drives changes in leaf photosynthesis, with the direction and magnitude varying across species; however, our understanding of the relationship between diffuse light and plant gas exchange, as well as the mechanisms driving these relationships remain unresolved. We studied the effects of diffuse light on plant function in potted individuals ofPersea americana(avocado). We first measured leaf gas exchange subject to varying proportions of direct and diffuse light, as well as photosynthetic response to varying CO2(A-Cicurves) in predominantly direct and predominantly diffuse light. We find that leaf photosynthetic rates increase as the proportion of diffuse light increases and that those changes are associated with stomatal conductance, rather than photosynthetic biochemistry. Given that avocados have green stems, we then measured stem gas exchange in predominantly direct compared to predominantly diffuse light. While we also observed an increase in conductance in stems subject to diffuse light, there was not an increase in photosynthetic rate, effectively decoupling gas flux from carbon gain. Finally, by scaling measurements of gas exchange to the plant, we demonstrate that stem bark conductance contributes proportionally more to whole-plant conductance under diffuse light. Our results add to our understanding of the potential mechanisms that govern how plant function varies in response to changes in light quality, the first paper to demonstrate mechanisms to explain increases under diffuse light. As diffuse light increases globally, this variable needs to be integrated into our understanding of plant carbon-water tradeoffs in response to climate change.