bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Population Structure of African Cultivated Rice Oryza glaberrima (Steud.)
Authors: Semon Mande , Nielsen Rasmus , Jones Monty P , McCouch Susan R 
Published: November 2004

Abstract
Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown (1) by a lack of decay in LD among markers on the same chromosome and (2) by a strictly increasing composite likelihood function for the recombination parameter. This suggested that the elevation in LD was due not to physical linkage but to other factors, such as population structure. A Bayesian clustering analysis confirmed this hypothesis, indicating that the sample of O. glaberrima in this study was subdivided into at least five cryptic subpopulations. Two of these subpopulations clustered with control samples of O. sativa, subspecies indica and japonica, indicating that some O. glaberrima accessions represent admixtures. The remaining three O. glaberrima subpopulations were significantly associated with specific combinations of phenotypic traits—possibly reflecting ecological adaptation to different growing environments.
Lig4 and Rad54 Are Required for Repair of DNA Double-Strand Breaks Induced by P-Element Excision in DrosophilaThis article is dedicated to the memory of our colleague and friend Dr. Jan C. J. Eeken, who died unexpectedly on May 24, 2002.
Authors: Romeijn Ron J , Gorski Marcin M , van Schie Martijn A , Noordermeer Jasprina N , Mullenders Leon H , Ferro Wouter , Pastink Albert 
Published: November 2004

AbstractSite-specific double-strand breaks (DSBs) were generated in the white gene located on the X chromosome of Drosophila by excision of the whd P-element. To investigate the role of nonhomologous end joining (NHEJ) and homologous recombination (HR) in the repair of these breaks, the whd P-element was mobilized in flies carrying mutant alleles of either lig4 or rad54. The survival of both lig4- and rad54-deficient males was reduced to 25% in comparison to the wild type, indicating that both NHEJ and HR are involved in the repair P-induced gaps in males. Survival of lig4-deficient females was not affected at all, implying that HR using the homologous chromosome as a template can partially compensate for the impaired NHEJ pathway. In rad54 mutant females survival was reduced to 70% after whd excision. PCR analysis indicated that the undamaged homologous chromosome may compensate for the potential loss of the broken chromosome in rad54 mutant females after excision. Molecular analysis of the repair junctions revealed microhomology (2–8 bp)-dependent DSB repair in most products. In the absence of Lig4, the 8-bp target site duplication is used more frequently for repair. Our data indicate the presence of efficient alternative end-joining mechanisms, which partly depend on the presence of microhomology but do not require Lig4.
Interaction Between the oxa1 and rmp1 Genes Modulates Respiratory Complex Assembly and Life Span in Podospora anserina
Authors: Sellem Carole H , Lemaire Claire , Lorin Séverine , Dujardin Geneviève , Sainsard-Chanet Annie 
Published: November 2004

AbstractA causal link between deficiency of the cytochrome respiratory pathway and life span was previously shown in the filamentous fungus Podospora anserina. To gain more insight into the relationship between mitochondrial function and life span, we have constructed a strain carrying a thermosensitive mutation of the gene oxa1. OXA1 is a membrane protein conserved from bacteria to human. The mitochondrial OXA1 protein is involved in the assembly/insertion of several respiratory complexes. We show here that oxa1 is an essential gene in P. anserina. The oxa1ts mutant exhibits severe defects in the respiratory complexes I and IV, which are correlated with an increased life span, a strong induction of the alternative oxidase, and a reduction in ROS production. However, there is no causal link between alternative oxidase level and life span. We also show that in the oxa1ts mutant, the extent of the defects in complexes I and IV and the life-span increase depends on the essential gene rmp1. The RMP1 protein, whose function is still unknown, can be localized in the mitochondria and/or the cytosolic compartment, depending on the developmental stage. We propose that the RMP1 protein could be involved in the process of OXA1-dependent protein insertion.
The Genomes of Recombinant Inbred Lines
Authors: Broman Karl W 
Published: November 2004

AbstractRecombinant inbred lines (RILs) can serve as powerful tools for genetic mapping. Recently, members of the Complex Trait Consortium proposed the development of a large panel of eight-way RILs in the mouse, derived from eight genetically diverse parental strains. Such a panel would be a valuable community resource. The use of such eight-way RILs will require a detailed understanding of the relationship between alleles at linked loci on an RI chromosome. We extend the work of Haldane and Waddington on two-way RILs and describe the map expansion, clustering of breakpoints, and other features of the genomes of multiple-strain RILs as a function of the level of crossover interference in meiosis.
RNA Silencing in Aspergillus nidulans Is Independent of RNA-Dependent RNA Polymerases
Authors: Hammond T M , Keller N P 
Published: November 2004

Abstract
The versatility of RNA-dependent RNA polymerases (RDRPs) in eukaryotic gene silencing is perhaps best illustrated in the kingdom Fungi. Biochemical and genetic studies of Schizosaccharomyces pombe and Neurospora crassa show that these types of enzymes are involved in a number of fundamental gene-silencing processes, including heterochromatin regulation and RNA silencing in S. pombe and meiotic silencing and RNA silencing in N. crassa. Here we show that Aspergillus nidulans, another model fungus, does not require an RDRP for inverted repeat transgene (IRT)-induced RNA silencing. However, RDRP requirements may vary within the Aspergillus genus as genomic analysis indicates that A. nidulans, but not A. fumigatus or A. oryzae, has lost a QDE-1 ortholog, an RDRP associated with RNA silencing in N. crassa. We also provide evidence suggesting that 5′ → 3′ transitive RNA silencing is not a significant aspect of A. nidulans IRT-RNA silencing. These results indicate a lack of conserved kingdom-wide requirements for RDRPs in fungal RNA silencing.
An Active Transposable Element, Herves, From the African Malaria Mosquito Anopheles gambiaeSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession no. AY462096.
Authors: Arensburger Peter , Kim Yu-Jung , Orsetti Jamison , Aluvihare Channa , O'Brochta David A , Atkinson Peter W 
Published: November 2004

Abstract
Transposable elements have proven to be invaluable tools for genetically manipulating a wide variety of plants, animals, and microbes. Some have suggested that they could be used to spread desirable genes, such as refractoriness to Plasmodium infection, through target populations of Anopheles gambiae, thereby disabling the mosquito's ability to transmit malaria. To achieve this, a transposon must remain mobile and intact after the initial introduction into the genome. Endogenous, active class II transposable elements from An. gambiae have not been exploited as gene vectors/drivers because none have been isolated. We report the discovery of an active class II transposable element, Herves, from the mosquito An. gambiae. Herves is a member of a distinct subfamily of hAT elements that includes the hopper-we element from Bactrocera dorsalis and B. cucurbitae. Herves was transpositionally active in mobility assays performed in Drosophila melanogaster S2 cells and developing embryos and was used as a germ-line transformation vector in D. melanogaster. Herves displays an altered target-site preference from the distantly related hAT elements, Hermes and hobo. Herves is also present in An. arabiensis and An. merus with copy numbers similar to that found in An. gambiae. Preliminary data from an East African population are consistent with the element being transpositionally active in mosquitoes.
Traditional Atlantic Diet and Its Effect on Health and the Environment
Authors: Cambeses-Franco Cristina , Gude Francisco , Benítez-Estévez Alfonso J. , González-García Sara , Leis Rosaura , Sánchez-Castro Juan , Moreira María Teresa , Feijoo Gumersindo , Calvo-Malvar Mar 
Published: February 2024

ImportanceThe universal call to action for healthier and more sustainable dietary choices is the framework of the United Nations’s Sustainable Development Goals. The Atlantic diet, originating from the northwest of the Iberian Peninsula, represents an example of a traditional diet that aligns with these principles.ObjectiveTo explore a 6-month intervention based on the Atlantic diet’s effects on metabolic and environmental health, assessing metabolic syndrome (MetS) incidence and the carbon footprint.Design, Setting, and ParticipantsThe Galician Atlantic Diet study was a 6-month randomized clinical trial designed to assess the effects of this regional traditional diet on families’ eating habits. The study was conducted from March 3, 2014, to May 29, 2015, at a local primary health care center in the rural town of A Estrada in northwestern Spain and involved a multisectoral collaboration. Families were randomly selected from National Health System records and randomized 1:1 to an intervention or control group. This secondary analysis of the trial findings was performed between March 24, 2021, and November 7, 2023.InterventionsOver 6 months, families in the intervention group received educational sessions, cooking classes, written supporting material, and foods characteristic of the Atlantic diet, whereas those randomized to the control group continued with their habitual lifestyle.Main Outcomes and MeasuresThe main outcomes were MetS incidence, defined per National Cholesterol Education Program Adult Treatment Panel III guidelines, and carbon footprint emissions as an environmental metric using life cycle assessment with daily dietary intake as the functional unit.ResultsInitially, 250 families were randomized (574 participants; mean [SD] age, 46.8 [15.7] years; 231 males [40.2%] and 343 females [59.8%]). The intervention group included 126 families (287 participants) and the control group, 124 families (287 participants). Ultimately, 231 families completed the trial. The intervention significantly reduced the risk of incident cases of MetS (rate ratio, 0.32; 95% CI, 0.13-0.79) and had fewer MetS components (proportional odds ratio, 0.58; 95% CI, 0.42-0.82) compared with the control condition. The intervention group did not have a significantly reduced environmental impact in terms of carbon footprint emissions compared with the control group (−0.17 [95% CI, −0.46 to 0.12] kg CO2 equivalents/person/d).Conclusions and RelevanceThese findings provide important evidence that a family-focused dietary intervention based on a traditional diet can reduce the risk of incident MetS. Further research is needed to understand the underlying mechanisms and determine the generalizability to other populations, taking into account regional cultural and dietary variations.Trial RegistrationClinicalTrials.gov Identifier: NCT02391701
Machine Learning Models for Predicting Disability and Pain Following Lumbar Disc Herniation Surgery
Authors: Berg Bjørnar , Gorosito Martin A. , Fjeld Olaf , Haugerud Hårek , Storheim Kjersti , Solberg Tore K. , Grotle Margreth 
Published: February 2024

ImportanceLumber disc herniation surgery can reduce pain and disability. However, a sizable minority of individuals experience minimal benefit, necessitating the development of accurate prediction models.ObjectiveTo develop and validate prediction models for disability and pain 12 months after lumbar disc herniation surgery.Design, Setting, and ParticipantsA prospective, multicenter, registry-based prognostic study was conducted on a cohort of individuals undergoing lumbar disc herniation surgery from January 1, 2007, to May 31, 2021. Patients in the Norwegian Registry for Spine Surgery from all public and private hospitals in Norway performing spine surgery were included. Data analysis was performed from January to June 2023.ExposuresMicrodiscectomy or open discectomy.Main Outcomes and MeasuresTreatment success at 12 months, defined as improvement in Oswestry Disability Index (ODI) of 22 points or more; Numeric Rating Scale (NRS) back pain improvement of 2 or more points, and NRS leg pain improvement of 4 or more points. Machine learning models were trained for model development and internal-external cross-validation applied over geographic regions to validate the models. Model performance was assessed through discrimination (Cstatistic) and calibration (slope and intercept).ResultsAnalysis included 22 707 surgical cases (21 161 patients) (ODI model) (mean [SD] age, 47.0 [14.0] years; 12 952 [57.0%] males). Treatment nonsuccess was experienced by 33% (ODI), 27% (NRS back pain), and 31% (NRS leg pain) of the patients. In internal-external cross-validation, the selected machine learning models showed consistent discrimination and calibration across all 5 regions. TheCstatistic ranged from 0.81 to 0.84 (pooled random-effects meta-analysis estimate, 0.82; 95% CI, 0.81-0.84) for the ODI model. Calibration slopes (point estimates, 0.94-1.03; pooled estimate, 0.99; 95% CI, 0.93-1.06) and calibration intercepts (point estimates, −0.05 to 0.11; pooled estimate, 0.01; 95% CI, −0.07 to 0.10) were also consistent across regions. For NRS back pain, theCstatistic ranged from 0.75 to 0.80 (pooled estimate, 0.77; 95% CI, 0.75-0.79); for NRS leg pain, theCstatistic ranged from 0.74 to 0.77 (pooled estimate, 0.75; 95% CI, 0.74-0.76). Only minor heterogeneity was found in calibration slopes and intercepts.ConclusionThe findings of this study suggest that the models developed can inform patients and clinicians about individual prognosis and aid in surgical decision-making.
Presentation Acuity and Surgical Outcomes for Patients With Health Insurance Living in Highly Deprived Neighborhoods
Authors: Schmidt Susanne , Jacobs Michael A. , Kim Jeongsoo , Hall Daniel E. , Stitzenberg Karyn B. , Kao Lillian S. , Brimhall Bradley B. , Wang Chen-Pin , Manuel Laura S. , Su Hoah-Der , Silverstein Jonathan C. , Shireman Paula K. 
Published: February 2024

ImportanceInsurance coverage expansion has been proposed as a solution to improving health disparities, but insurance expansion alone may be insufficient to alleviate care access barriers.ObjectiveTo assess the association of Area Deprivation Index (ADI) with postsurgical textbook outcomes (TO) and presentation acuity for individuals with private insurance or Medicare.Design, Setting, and ParticipantsThis cohort study used data from the National Surgical Quality Improvement Program (2013-2019) merged with electronic health record data from 3 academic health care systems. Data were analyzed from June 2022 to August 2023.ExposureLiving in a neighborhood with an ADI greater than 85.Main Outcomes and MeasuresTO, defined as absence of unplanned reoperations, Clavien-Dindo grade 4 complications, mortality, emergency department visits/observation stays, and readmissions, and presentation acuity, defined as having preoperative acute serious conditions (PASC) and urgent or emergent cases.ResultsAmong a cohort of 29 924 patients, the mean (SD) age was 60.6 (15.6) years; 16 424 (54.9%) were female, and 13 500 (45.1) were male. A total of 14 306 patients had private insurance and 15 618 had Medicare. Patients in highly deprived neighborhoods (5536 patients [18.5%]), with an ADI greater than 85, had lower/worse odds of TO in both the private insurance group (adjusted odds ratio [aOR], 0.87; 95% CI, 0.76-0.99; P = .04) and Medicare group (aOR, 0.90; 95% CI, 0.82-1.00; P = .04) and higher odds of PASC and urgent or emergent cases. The association of ADIs greater than 85 with TO lost significance after adjusting for PASC and urgent/emergent cases. Differences in the probability of TO between the lowest-risk (ADI ≤85, no PASC, and elective surgery) and highest-risk (ADI &amp;gt;85, PASC, and urgent/emergent surgery) scenarios stratified by frailty were highest for very frail patients (Risk Analysis Index ≥40) with differences of 40.2% and 43.1% for those with private insurance and Medicare, respectively.Conclusions and RelevanceThis study found that patients living in highly deprived neighborhoods had lower/worse odds of TO and higher presentation acuity despite having private insurance or Medicare. These findings suggest that insurance coverage expansion alone is insufficient to overcome health care disparities, possibly due to persistent barriers to preventive care and other complex causes of health inequities.
Efficient Preparation of Biomass‐Based Ultra‐Thin 2D Porous Carbon Materials by In Situ Template‐Activation And Its Application in Sodium Ion Capacitors
Authors: Yang Zijian , Liu Xiaohao , Ma Xiaotong , Cao Taoding , Xu Jiawei , Feng Hao , Diao Rui , Qi Fenglei , Huang Haijian , Ma Peiyong 
Published: February 2024

Abstract2D porous carbon materials have demonstrated immense potential in electrochemical energy storage, whereas the challenge of achieving their efficient preparation remains substantial. Herein, 2D carbon materials with high specific surface area (SSA), well‐developed porous structures, and controllable carbon layer thickness are successfully prepared by direct co‐pyrolysis of agroforestry biomass with potassium oxalate. It is found that the potassium oxalate acts as reactant and its decomposition product potassium carbonate acts as in situ template and activator. The potassium carbonate in the core activates the outer carbon structure to form nanopores, and regulates the thickness and the graphitization degree of the carbon material. Moreover, the N‐doping strategy seriously affects the structure of the materials. CSAN‐800 prepared with 0.2 vol.% NH3 addition can achieve N doping and SSA improvement (1802 m2 g−1) without damaging the ultra‐thin 2D structure. As a cathode material of sodium ion capacitors, CSAN‐800 exhibits excellent electrochemical with particularly a high‐capacity retention (90.3%) achieved (0.1 A g−1–2 A g−1). The 2D porous structure, high SSA, and rich pyridine‐N content significantly enhance the ion transport, storage, and optimize the charge carrier's adsorption and desorption. This study provides a low‐cost and eco‐friendly preparation strategy for ultra‐thin 2D porous carbon materials.
A Comprehensive, Multidimensional First‐Principles Model for Free‐Radical Photopolymerizations in Bulk and Thin Films
Authors: Dobson Adam L. , Bowman Christopher N. 
Published: February 2024

AbstractDecades of advances in understanding and simulating the polymerization kinetics and structural evolution that arises in free‐radical photopolymerizations of multifunctional monomers are combined into a single, first‐principles 3D model. The model explicitly accounts for polymerization features including diffusion‐controlled kinetics, oxygen inhibition, light attenuation, chain‐length dependent termination, reaction‐diffusion termination, heat transfer, composition and conversion‐dependent material properties, crosslinking effects, and species diffusion. Using the homopolymerization of 1,6‐hexanediol diacrylate as a model system, a minimum of two kinetics experiments performed at different initiation rates are required to fit model parameters. The model accurately predicts known relationships regarding oxygen inhibition, light intensity, and curing temperature for samples of different geometries and boundary conditions. The emphasis of the results herein is placed on the interactions between polymerization features, motivating the importance of a model that accommodates these features all in one simulation. The model is shown to be robust in its handling of thermal boundary conditions, alternative polymerization techniques or mechanisms, and characteristics of 3D voxel formation. The model in this work provides a useful tool for property prediction in a wide variety of applications, most notably coatings, dental materials, industrial photocuring processes, additive manufacturing, and holography, where complex interactions of the various features of polymerization play a substantial role.
Polymorphic Kondo Effects Driven by Spin Lattice Coupling in VTe2
Authors: Won Dongyeun , Kiem Do Hoon , Cho Woohyun , Yang Sang‐Hyeok , Kim Young‐Hoon , Kim Young‐Min , Cho Suyeon , Han Myung Joon , Yang Heejun 
Published: February 2024

AbstractPolymorphism in transition metal dichalcogenides (TMDs) allows unique physical properties to be controlled, such as artificial heavy fermion phenomena, the quantum spin Hall effect, and optimized device operations with 2D materials. Besides lattice structural and metal‐semiconductor polymorphs, intriguing charge density wave (CDW) states with different electronic and magnetic phases are demonstrated in TMDs. Typically, the “normal” state is stabilized at high temperature above the CDW energy scale, and therefore, is not relevant to many low‐temperature quantum phenomena, such as magnetic ordering and the heavy fermion Kondo state. Here, a local and robust phase manipulation of the normal (1T) and CDW (1T’) states of VTe2 is reported by laser irradiation, and polymorphic Kondo effects are demonstrated with the two phases at low temperatures. The theoretical calculations show that Kondo screening of vanadium 3d electron moments is markedly enhanced in 1T’‐VTe2, which is responsible for the observed transport properties distinct from its 1T counterpart. Controlling the spin‐lattice coupling and Kondo physics via laser‐driven CDW phase patterning allows the design of correlated electronic and magnetic properties in TMDs.
Amorphous Cellulose Electrolyte for Long Life and Mechanically Robust Aqueous Structural Batteries
Authors: Lim Gwendolyn J.H. , Koh J. Justin , Chan Kwok Kiong , Verma Vivek , Chua Rodney , Koh Xue Qi , Kidkhunthod Pinit , Sutrisnoh Nur Ayu Afira , Srinivasan Madhavi 
Published: February 2024

AbstractAqueous zinc (Zn)‐based structural batteries capable of both electrochemical energy storage and mechanical load‐bearing capabilities are attractive for next‐generation energy storage for future electric vehicles due to their eco‐friendliness, non‐toxic, and safe nature. However, parasitic free water activities plague aqueous Zn‐based batteries, detrimental to the electrochemical performance and longevity of the cell. Developing polymer gel electrolytes is a notable potential solution, but they usually have poor electrode interfacial interactions and inadequate mechanical properties. This article introduces a novel non‐fibrous highly amorphous cellulose polymer electrolyte “Cellyte” for aqueous structural Zn‐based batteries. Cellyte exhibits a high strength of ≈24 MPa and Young's modulus of ≈380 MPa, along with the ability to suppress parasitic water activity. The symmetric Zn||Cellyte||Zn cell therefore demonstrates excellent cycling stability of over ≈3000 h. Cellyte can also serve as the binder for the structural cathode material, creating a continuous polymer electrolyte–cathode interface, thereby increasing mechanical robustness and decreasing interfacial resistances of the battery, allowing the structural Zn||Cellyte||LMO‐CF battery to achieve high electrochemical performance with excellent cycling stability over 1200 h with ≈91.5% capacity retention. This provides a pathway to design mechanically robust, electrochemically performing, and safe structural batteries.