bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population-based Influenza and Respiratory Syncytial Virus Hospitalizations and In-hospital Mortality Rates Among Mexican Children Less Than Five Years of Age
Authors: Mata-Moreno Gabriel , Bernal-Silva Sofía , García-Sepúlveda Christian A. , González-Ortíz Ana María , Ochoa-Pérez Uciel R. , Medina-Serpa Aldo Uzziel , Pérez-González Luis Fernando , Noyola Daniel E. 
Published: February 2024

Background:
Population-based information regarding the impact of respiratory syncytial virus (RSV) and influenza on hospital admissions and mortality is scant for many countries.

Methods:
Prospective testing of RSV and influenza virus was undertaken in patients <5 years old admitted to hospital with acute respiratory infection (ARI) between July, 2014 and June, 2015, and mortality rates for children living in 3 municipalities in the state of San Luis Potosí were calculated.

Results:
During the 12-month study period, 790 children living in these municipalities were admitted with ARI. RSV was detected in 245 (31%) and influenza in 47 (5.9%). History of preterm birth was recorded for 112 children on admission. For children <5 years old, ARI-, RSV- and influenza-associated admission rates were 23.2, 7.2 and 1.4 (per 1000 population), respectively. The corresponding admission rates per 1000 infants <1 year old were 78, 25.2 and 4.4. Preterm infant admission rates were 2 times higher than those of term infants. Six children died; RSV was detected in 4 (66.6%) of the deceased, while no deaths were associated with influenza. ARI and RSV in-hospital mortality rates for children <5 years were 0.18 and 0.12 per 1000 population. ARI and RSV mortality rates in preterm infants were 7 and 14 times higher than in term infants, respectively.

Conclusions:
RSV was associated with both high admission and in-hospital mortality rates in children <5 years old. Specific interventions, such as active or passive immunization, to prevent RSV infections are required to reduce ARI-associated infant mortality.
Diagnosis of Fever Source Following Tonsillectomy and Adenoidectomy in the Pediatric Emergency Department
Authors: Yanai Milshtein Nili , Pres Shir , Derowe Ari , Rimon Ayelet 
Published: February 2024

Objectives
This study aimed to describe the epidemiology and diagnoses of children with postoperative fever (a temperature of 38°C or higher) during the week after tonsillectomy and/or adenoidectomy and to assess the yield of the laboratory tests and otolaryngologist consultations of these patients in the pediatric emergency department (ED).

Methods
We conducted a retrospective cohort study that included all children who presented with fever to the pediatric ED of a tertiary university-affiliated medical center between May 2017 and April 2020 during the week after a tonsillectomy and/or adenoidectomy.

Results
There were 94 patients who fulfilled study entry criteria during the 3-year study period, representing a 6% rate of postoperative fever for combined tonsillectomy and adenoidectomy and 3% for adenoidectomy alone. Only 9 patients (<10% of the total) were classified as having bacterial infection, whereas the most common cause for the fever was pneumonia diagnosed by chest radiography. None had surgical site infection. There was no significant difference in blood test findings of patients diagnosed with a bacterial infection and patients with a presumed viral infection or an inflammatory response to surgery.

Conclusions
The results of this investigation revealed that the source of fever of the overwhelming majority of children who were referred to the pediatric ED for fever after undergoing tonsillectomy and/or adenoidectomy was pneumonia as determined by chest radiography, which can be performed in an outpatient setting. Blood tests and otolaryngologist consultations were not contributory in classifying the source of fever, questioning the value of their routine use in these patients.
Point-of-Care Ultrasound of a Nasal Septal Abscess
Authors: Marin Acevedo Paula , Wise Tyler , Mayer Jeffrey , Lin Sophia 
Published: February 2024

Abstract
Although nasal septal abscesses (NSA) are rare, complications can be significant and devastating. Thus, timely diagnosis of NSA is critical. In this case report, we describe the use of point-of-care ultrasound in diagnosing NSA in a healthy boy presenting with viral upper respiratory infection symptoms and fever. Point-of-care ultrasound findings resulted in expediting this patient's treatment and transfer to a quaternary care center for definitive treatment.
Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR
Authors: Endelman Jeffrey B. , Kante Moctar , Lindqvist-Kreuze Hannele , Kilian Andrzej , Shannon Laura M. , Caraza-Harter Maria V. , Vaillancourt Brieanne , Mailloux Kathrine , Hamilton John P. , Buell C. Robin 
Published: February 2024

ABSTRACTMid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTagTMtechnology and later expanded to 4K targets. Genomic markers were selected from the potato InfiniumTMSNP array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N=85), which was significantly lower than the RMSE of 0.42 with the Random Forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics.Core IdeasA mid-density, targeted genotyping-by-sequencing (GBS) assay was developed for potato.The GBS assay includes markers for resistance to potato virus Y, golden cyst nematode, and potato wart.The GBS assay includes multi-allelic markers for potato maturity and tuber shape.The polyBreedR software has functions for manipulating and imputing polyploid marker data in Variant Call Format.Linkage Analysis was more accurate than the Random Forest method when imputing from 2K to 10K markers.
Leaf functional trait evolution and its putative climatic drivers in AfricanCoffeaspecies
Authors: Hendrickx Aiden , Hatangi Yves , Honnay Olivier , Janssens Steven B. , Stoffelen Piet , Vandelook Filip , Depecker Jonas 
Published: February 2024

AbstractBackground and AimsLeaf traits are known to be strong predictors of plant performance and can be expected to (co)vary along environmental gradients. We investigated the variation, integration, environmental relationships, and evolutionary history of leaf functional traits in the genusCoffeaL., typically a rainforest understory shrub, across Africa. A better understanding of the adaptive processes involved in leaf trait evolution can inform the use and conservation of coffee genetic resources in a changing climate.MethodsWe used phylogenetic comparative methods to investigate the evolution of six leaf traits measured from herbarium specimens of 58 AfricanCoffeaspecies. We added environmental data and data on maximum plant height for each species to test trait-environment correlations in various (sub)clades, and we compared continuous trait evolution models to identify variables driving trait diversification.Key ResultsA substantial leaf trait variation was detected across the genusCoffeain Africa, which was mostly interspecific. Of these traits, stomatal size and stomatal density exhibited a clear trade-off. We observed low densities of large stomata in early branching lineages and higher densities of smaller stomata in more recent taxa, which we hypothesise to be related to declining CO2levels since the mid-Miocene. Brownian Motion evolution was rejected in favour of White Noise or Ornstein-Uhlenbeck models for all traits, implying these traits are adaptively significant rather than driven by pure drift. The evolution of leaf area was likely driven by precipitation, with smaller leaves in dryer climates across the genus.ConclusionsGenerally,Coffealeaf traits appear to be evolutionarily labile and governed by stabilising selection, though evolutionary patterns and correlations differ depending on the traits and clades considered. Our study highlights the importance of a phylogenetic perspective when studying trait relationships across related taxa, as well as the consideration of various taxonomic ranges.
Multiple horizontal mini-chromosome transfers drive genome evolution of clonal blast fungus lineages
Authors: Barragan A. Cristina , Latorre Sergio M. , Malmgren Angus , Harant Adeline , Win Joe , Sugihara Yu , Burbano Hernán A. , Kamoun Sophien , Langner Thorsten 
Published: February 2024

AbstractCrop disease pandemics are often driven by clonal lineages of plant pathogens that reproduce asexually. How these clonal pathogens continuously adapt to their hosts despite harboring limited genetic variation, and in absence of sexual recombination remains elusive. Here, we reveal multiple instances of horizontal chromosome transfer within pandemic clonal lineages of the blast fungusMagnaporthe(Syn.Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb supernumerary mini-chromosome which is remarkably conserved betweenM. oryzaeisolates from both the rice blast fungus lineage and the lineage infecting Indian goosegrass (Eleusine indica), a wild grass that often grows in the proximity of cultivated cereal crops. Furthermore, we show that this mini-chromosome was horizontally acquired by clonal rice blast isolates through at least nine distinct transfer events over the past three centuries. These findings establish horizontal mini-chromosome transfer as a mechanism facilitating genetic exchange among different host-associated blast fungus lineages. We propose that blast fungus populations infecting wild grasses act as genetic reservoirs that drive genome evolution of pandemic clonal lineages that afflict cereal crops.
Recurrent loss of crossover interference punctuates the recombination landscape across yeast species
Authors: Dutta Abhishek , Dutreux Fabien , Garin Marion , Caradec Claudia , Friedrich Anne , Brach Gauthier , Thiele Pia , Llorente Bertrand , Schacherer Joseph 
Published: February 2024

AbstractMeiotic recombination is essential for the accurate chromosome segregation and the generation of genetic diversity through crossover and gene conversion events. Although this process has been studied extensively in a few selected model species, understanding how its properties vary across species remains limited. In this context, we first characterized the meiotic recombination landscape and properties of theKluyveromyces lactisbudding yeast. We then conducted a comprehensive analysis of 28,897 recombination events spanning 567 meioses in five budding yeast species includingSaccharomyces cerevisiae,Saccharomyces paradoxus,Lachancea kluyveri,Lachancea waltiiandK. lactis. We observed variations in the recombination landscapes and properties across these species. TheSaccharomycesyeasts displayed higher recombination rates compared to the non-Saccharomycesyeasts. In addition, bona fide crossover interference and associated crossover homeostasis were found in theSaccharomycesspecies only. The evolutionarily conserved ZMM pathway, essential for generating interference-dependent crossovers, has undergone multiple losses throughout evolution, suggesting variations in the regulation of crossover formation. Finally, recombination hotspots, although highly conserved within theSaccharomycesyeasts are not conserved beyond theSaccharomycesgenus. Overall, these results highlight great variability and evolution in the recombination landscape between species.
Canine major histocompatibility complex class I (MHC-I) diversity landscape
Authors: Feng Yuan , Ho Kun-Lin , Zhang Mengyuan , Sundaresha Nikitha Brahmasamudra , Cavanagh Hannah Lorelle , Zhao Shaying 
Published: February 2024

AbstractThe genes of the Major Histocompatibility Complex class I (MHC-I) are among the most diverse in the mammalian genome, playing a crucial role in immunology. Understanding the diversity landscape of MHC-I is therefore of paramount importance. The dog is a key translational model in various biomedical fields. However, our understanding of the canine MHC-I diversity landscape lags significantly behind that of humans. To address this deficiency, we used our newly developed software, KPRde novoassembler and genotyper, to genotype 1,325 samples from 1,025 dogs with paired-end RNA-seq data from 43 BioProjects, after extensive quality control. Among 926 dogs that pass the QC, 591 dogs (64%) have at least one allele genotyped, and a total of 97 known alleles and 52 putative new alleles were identified. Further analysis reveals that DLA-I gene expression levels vary among the tissues, with lowest for testis and brain tissues and highest for blood, corpus luteum, and spleen. We identified dominant alleles in each of the 17 canine breeds, as well as among the entire canine population. Furthermore, our analysis also identifies breed-specific alleles and mutually co-occurred/exclusive alleles. Our study indicates that canine DLA-88 is as diversified as human HLA-A/B/C genes within the entire population, but less diversified within a breed than with HLA-A/B/C within an ethnic group. Lastly, we examined the hypervariable regions (HVR) within or across human/canine MHC-I alleles and found that 80% of the HVRs overlap between the two species. We further noted that 80% of the HVRs are within 4A contact with the peptides, and that the dog-human difference overlaps with only 20% HVRs. Our research offers valuable insights for immunological studies involving dogs.
Differential GTP-dependentin-vitropolymerization of recombinant Physcomitrella FtsZ proteins
Authors: Milferstaedt Stella W. L. , Joest Marie , Bohlender Lennard L. , Hoernstein Sebastian N. W. , Özdemir Buğra , Decker Eva L. , van der Does Chris , Reski Ralf 
Published: February 2024

1.AbstractBacterial cell division and plant chloroplast division require self-assembling Filamentous temperature-sensitive Z (FtsZ) proteins. FtsZ proteins are GTPases sharing structural and biochemical similarities with eukaryotic tubulin. In the moss Physcomitrella, the morphology of the FtsZ polymer networks varies between the different FtsZ isoforms. The underlying mechanism and foundation of the distinct networks is unknown. Here, we investigated the interaction of Physcomitrella FtsZ2-1 with FtsZ1 isoformsviaco-immunoprecipitation and mass spectrometry, and found protein-protein interactionin vivo. We tagged FtsZ1-2 and FtsZ2-1 with different fluorophores and expressed both inE. coli, which led to the formation of defined structures within the cells and to an influence on bacterial cell division and morphology. Furthermore, we have optimized the purification protocols for FtsZ1-2 and FtsZ2-1 expressed inE. coliand characterized their GTPase activity and polymerizationin vitro. Both FtsZ isoforms showed GTPase activity. Stoichiometric mixing of both proteins led to a significantly increased GTPase activity, indicating a synergistic interaction between them. In light scattering assays, we observed GTP-dependent assembly of FtsZ1-2 and of FtsZ2-1 in a protein concentration dependent manner. Stoichiometric mixing of both proteins resulted in significantly faster polymerization, again indicating a synergistic interaction between them. Under the same conditions used for GTPase and light scattering assays both FtsZ isoforms formed filaments in a GTP-dependent manner as visualized by transmission electron microscopy (TEM). Taken together, our results reveal that Physcomitrella FtsZ1-2 and FtsZ2-1 are functionally different, can synergistically interactin vivoandin vitro, and differ in their properties from FtsZ proteins from bacteria, archaea and vascular plants.
Translational response to mitochondrial stresses is orchestrated by tRNA modifications
Authors: Rashad Sherif , Al-Mesitef Shadi , Mousa Abdulrahman , Zhou Yuan , Ando Daisuke , Sun Guangxin , Fukuuchi Tomoko , Iwasaki Yuko , Xiang Jingdong , Byrne Shane R , Sun Jingjing , Maekawa Masamitsu , Saigusa Daisuke , Begley Thomas J , Dedon Peter C , Niizuma Kuniyasu 
Published: February 2024

AbstractMitochondrial stress and dysfunction play important roles in many pathologies. However, how cells respond to mitochondrial stress is not fully understood. Here, we examined the translational response to electron transport chain (ETC) inhibition and arsenite induced mitochondrial stresses. Our analysis revealed that during mitochondrial stress, tRNA modifications (namely f5C, hm5C, queuosine and its derivatives, and mcm5U) dynamically change to fine tune codon decoding, usage, and optimality. These changes in codon optimality drive the translation of many pathways and gene sets, such as the ATF4 pathway and selenoproteins, involved in the cellular response to mitochondrial stress. We further examined several of these modifications using targeted approaches. ALKBH1 knockout (KO) abrogated f5C and hm5C levels and led to mitochondrial dysfunction, reduced proliferation, and impacted mRNA translation rates. Our analysis revealed that tRNA queuosine (tRNA-Q) is a master regulator of the mitochondrial stress response. KO of QTRT1 or QTRT2, the enzymes responsible for tRNA-Q synthesis, led to mitochondrial dysfunction, translational dysregulation, and metabolic alterations in mitochondria-related pathways, without altering cellular proliferation. In addition, our analysis revealed that tRNA-Q loss led to a domino effect on various tRNA modifications. Some of these changes could be explained by metabolic profiling. Our analysis also revealed that utilizing serum deprivation or alteration with Queuine supplementation to study tRNA-Q or stress response can introduce various confounding factors by altering many other tRNA modifications. In summary, our data show that tRNA modifications are master regulators of the mitochondrial stress response by driving changes in codon decoding.
Inelastic and elastic parton scattering in the strongly interacting quark-gluon plasma
Authors: Grishmanovskii Ilia , Soloveva Olga , Song Taesoo , Greiner Carsten , Bratkovskaya Elena 
Published: February 2024

We investigate the role of inelastic processes in the strongly interacting quark-gluon plasma (sQGP) based on the effective dynamical quasiparticle model (DQPM). In the DQPM the nonperturbative properties of the sQGP at finite temperature T and baryon chemical potential μB are described in terms of strongly interacting off-shell partons (quarks and gluons) with dynamically generated spectral functions whose properties are adjusted to reproduce the lattice QCD equation of state for the quark-gluon plasma in thermodynamic equilibrium. For the first time the massive gluon radiation processes from the off-shell quark-quark (q+q) and quark-gluon (q+g) scatterings are calculated explicitly within leading-order Feynman diagrams with effective propagators and vertices from the DQPM without any further approximations. We present the results for the energy and temperature dependencies of the total and differential radiative cross sections and compare them to the corresponding elastic cross sections. We show that our results reproduce the perturbative QCD calculations in the limit of zero masses and widths of quasiparticles. Also we study the μB dependence of the inelastic cross sections. Moreover, we present estimates for the transition rate and relaxation time of radiative versus elastic scatterings in the sQGP.

Published by the American Physical Society
2024
Yukawa potential under weak magnetic field
Authors: Braghin Fábio L. , Loewe Marcelo , Villavicencio Cristian 
Published: February 2024

Weak magnetic field induced corrections for the Yukawa potential due to one pion exchange between two constituent quarks (nucleons) are presented. For that, the constant magnetic field effect on the pion propagator and on the pion form factor are taken into account. An effective gluon propagator parametrized with an effective gluon mass (Mg∼0.5  GeV) is considered. In the limit of magnetic field that is weak with respect to the constituent quark mass and pion mass, analytical and semianalytical expressions can be obtained. Different types of contributions are found, isotropic or anisotropic, dependent on the pion mass and also on the constituent quark and effective gluon masses. Overall the corrections are of the order of 2% to 5% of the Yukawa potential at distances close to 2 fm, and they decrease slower than the Yukawa potential. The anisotropic corrections are considerably smaller than the isotropic components. A sizable splitting between results due to the magnetic field dependent neutral or charged pion mass is found.

Published by the American Physical Society
2024
Generalized parton distributions from lattice QCD with asymmetric momentum transfer: Axial-vector case
Authors: Bhattacharya Shohini , Cichy Krzysztof , Constantinou Martha , Dodson Jack , Gao Xiang , Metz Andreas , Miller Joshua , Mukherjee Swagato , Petreczky Peter , Steffens Fernanda , Zhao Yong 
Published: February 2024

Recently, we made significant advancements in improving the computational efficiency of lattice QCD calculations for generalized parton distributions (GPDs). This progress was achieved by adopting calculations of matrix elements in asymmetric frames, deviating from the computationally-expensive symmetric frame typically used, and allowing freedom in the choice for the distribution of the momentum transfer between the initial and final states. A crucial aspect of this approach involves the adoption of a Lorentz covariant parametrization for the matrix elements, introducing Lorentz-invariant amplitudes. This approach also allows us to propose an alternative definition of quasi-GPDs, ensuring frame independence and potentially reduce power corrections in matching to light cone GPDs. In our previous work, we presented lattice QCD results for twist-2 unpolarized GPDs (H and E) of quarks obtained from calculations performed in asymmetric frames at zero skewness. Building upon this work, we now introduce a novel Lorentz covariant parametrization for the axial-vector matrix elements. We employ this parametrization to compute the axial-vector GPD H˜ at zero skewness, using an Nf=2+1+1 ensemble of twisted mass fermions with clover improvement. The light-quark masses employed in our calculations correspond to a pion mass of approximately 260 MeV.

Published by the American Physical Society
2024