bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double-Stranded RNA Interference of a Rice PI/GLO Paralog, OsMADS2, Uncovers Its Second-Whorl-Specific Function in Floral Organ Patterning
Authors: Prasad Kalika , Vijayraghavan Usha 
Published: April 2021

Abstract
Unlike many eudicot species, grasses have duplicated PI/GLO-like genes. Functional analysis of one of the rice PI/GLO paralogs, OsMADS2, is reported here. Our data demonstrate its essential role in lodicule development and implicate the second PI/GLO paralog, OsMADS4, to suffice for stamen specification. We provide the first evidence for differential contributions of grass PI/GLO paralogs in patterning second- and third-whorl floral organs.
Identification of Genetic Networks
Authors: Xiong Momiao , Li Jun , Fang Xiangzhong 
Published: April 2021

AbstractIn this report, we propose the use of structural equations as a tool for identifying and modeling genetic networks and genetic algorithms for searching the most likely genetic networks that best fit the data. After genetic networks are identified, it is fundamental to identify those networks influencing cell phenotypes. To accomplish this task we extend the concept of differential expression of the genes, widely used in gene expression data analysis, to genetic networks. We propose a definition for the differential expression of a genetic network and use the generalized T 2 statistic to measure the ability of genetic networks to distinguish different phenotypes. However, describing the differential expression of genetic networks is not enough for understanding biological systems because differences in the expression of genetic networks do not directly reflect regulatory strength between gene activities. Therefore, in this report we also introduce the concept of differentially regulated genetic networks, which has the potential to assess changes of gene regulation in response to perturbation in the environment and may provide new insights into the mechanism of diseases and biological processes. We propose five novel statistics to measure the differences in regulation of genetic networks. To illustrate the concepts and methods for reconstruction of genetic networks and identification of association of genetic networks with function, we applied the proposed models and algorithms to three data sets.
Effect of Breeding Structure on Population Genetic Parameters in Drosophila
Authors: Gravot Emmanuelle , Huet Michèle , Veuille Michel 
Published: April 2021

Abstract
The breeding structure of populations has been neglected in studies of Drosophila, even though Wright and Dobzhansky’s pioneering work on the genetics of natural populations was an attempt to tackle what they regarded as an essential factor in evolution. We compared the breeding structure of sympatric populations of D. melanogaster and D. simulans, two sibling species that are widely used in evolutionary studies. We recorded changes in population density and microsatellite variation patterns for 3 years in a temperate environment of southwestern France. Results were distinctively different in the two species. Maximum population levels in summer and in autumn were similar and fluctuated greatly over years, each species being in turn the most abundant. However, genetic data showed that D. melanogaster made up a continuous breeding population in time and space of practically infinite effective size. D. simulans was fragmented into isolates with a local effective size of between 50 and 350 individuals. A consequence of this was that, while a local sample provided a reliable estimate of regional genetic variability in D. melanogaster, a sample from the same area provided an underestimate of this parameter in D. simulans. In practical terms, this means that variations in breeding structure should be accounted for in sampling schemes and in designing evolutionary genetic models. More generally, this suggests the existence of differential reactions to local environments that might contribute to several genomic differences observed between these species.
Transposition of the Tol2 Element, an Ac-Like Element From the Japanese Medaka Fish Oryzias latipes, in Mouse Embryonic Stem Cells
Authors: Kawakami Koichi , Noda Tetsuo 
Published: April 2021

Abstract
The Tol2 transposable element of the Japanese medaka fish belongs to the hAT family of transposons including hobo of Drosophila, Ac of maize, and Tam3 of snapdragon. To date, Tol2 is the only natural transposon in vertebrates that has ever been shown to encode a fully functional transposase. It has not been known, however, whether Tol2 can transpose in vertebrates other than fish. We report here transposition of Tol2 in mouse embryonic stem (ES) cells. We constructed a transposon donor plasmid containing a nonautonomous Tol2 element with the neomycin resistance gene and a helper plasmid capable of expressing the transposase and introduced the donor plasmid with various amounts of the helper plasmid by electroporation into mouse ES cells. The number of G418-resistant ES colonies increased as the amount of helper plasmid was increased, in a dose-dependent manner, indicating that the transposase activity elevated the integration efficiency. These G418-resistant ES colonies were cloned and the structure of the junction of the integrated Tol2 element and the genomic DNA was analyzed by inverse PCR. In those clones, Tol2 was surrounded by mouse genomic sequences and an 8-bp direct repeat was created adjacent to both ends of Tol2, indicating that Tol2 was integrated in the genome through transposition. The Tol2 transposon system is thus active in mouse as well as in fish. We propose that it should be used as a genetic tool to develop novel gene transfer, transgenesis, and mutagenesis methods in mammals.
Saccharomyces cerevisiae SSD1-V Confers Longevity by a Sir2p-Independent Mechanism
Authors: Kaeberlein Matt , Andalis Alex A , Liszt Gregory B , Fink Gerald R , Guarente Leonard 
Published: April 2021

Abstract
The SSD1 gene of Saccharomyces cerevisiae is a polymorphic locus that affects diverse cellular processes including cell integrity, cell cycle progression, and growth at high temperature. We show here that the SSD1-V allele is necessary for cells to achieve extremely long life span. Furthermore, addition of SSD1-V to cells can increase longevity independently of SIR2, although SIR2 is necessary for SSD1-V cells to attain maximal life span. Past studies of yeast aging have been performed in short-lived ssd1-d strain backgrounds. We propose that SSD1-V defines a previously undescribed pathway affecting cellular longevity and suggest that future studies on longevity-promoting genes should be carried out in long-lived SSD1-V strains.
The External Amino Acid Signaling Pathway Promotes Activation of Stp1 and Uga35/Dal81 Transcription Factors for Induction of the AGP1 Gene in Saccharomyces cerevisiae
Authors: Abdel-Sater Fadi , Iraqui Ismaïl , Urrestarazu Antonio , André Bruno 
Published: April 2021

Abstract
Yeast cells respond to the presence of amino acids in their environment by inducing transcription of several amino acid permease genes including AGP1, BAP2, and BAP3. The signaling pathway responsible for this induction involves Ssy1, a permease-like sensor of external amino acids, and culminates with proteolytic cleavage and translocation to the nucleus of the zinc-finger proteins Stp1 and Stp2, the lack of which abolishes induction of BAP2 and BAP3. Here we show that Stp1—but not Stp2—plays an important role in AGP1 induction, although significant induction of AGP1 by amino acids persists in stp1 and stp1 stp2 mutants. This residual induction depends on the Uga35/Dal81 transcription factor, indicating that the external amino acid signaling pathway activates not only Stp1 and Stp2, but also another Uga35/Dal81-dependent transcriptional circuit. Analysis of the AGP1 gene’s upstream region revealed that Stp1 and Uga35/Dal81 act synergistically through a 21-bp cis-acting sequence similar to the UASAA element previously found in the BAP2 and BAP3 upstream regions. Although cells growing under poor nitrogen-supply conditions display much higher induction of AGP1 expression than cells growing under good nitrogen-supply conditions, the UASAA itself is totally insensitive to nitrogen availability. Nitrogen-source control of AGP1 induction is mediated by the GATA factor Gln3, likely acting through adjacent 5′-GATA-3′ sequences, to amplify the positive effect of UASAA. Our data indicate that Stp1 may act in combination with distinct sets of transcription factors, according to the gene context, to promote induction of transcription in response to external amino acids. The data also suggest that Uga35/Dal81 is yet another transcription factor under the control of the external amino acid sensing pathway. Finally, the data show that the TOR pathway mediating global nitrogen control of transcription does not interfere with the external amino acid signaling pathway.
Investigating Factors of Active Aging Among Chinese Older Adults: A Machine Learning Approach
Authors: Yu Jiao , Huang Wenxuan , Kahana Eva 
Published: April 2021

Abstract

Background and Objectives
With the extension of healthy life expectancy, promoting active aging has become a policy response to rapid population aging in China. Yet, it has been inconclusive about the relative importance of the determinants of active aging. By applying a machine learning approach, this study aims to identify the most important determinants of active aging in 3 domains, i.e., paid/unpaid work, caregiving, and social activities, among Chinese older adults.

Research Design and Methods
Data were drawn from the first wave of the China Health and Retirement Longitudinal Study, which surveys a nationally representative sample of adults aged 60 years and older (N = 7,503). We estimated Random Forest and the least absolute shrinkage and selection operator regression models (LASSO) to determine the most important factors related to active aging.

Results
Health has a generic effect on all outcomes of active aging. Our findings also identified the domain-specific determinants of active aging. Urban/rural residency is among the most important factors determining the likelihood of engaging in paid/unpaid work. Living in a multigenerational household is especially important in predicting caregiving activities. Neighborhood infrastructure and facilities have the strongest influence on older adults’ participation in social activities.

Discussion and Implications
The application of feature selection models provides a fruitful first step in identifying the most important determinants of active aging among Chinese older adults. These results provide evidence-based recommendations for policies and practices promoting active aging.
Genetic meta-analysis of twin birth weight shows high genetic correlation with singleton birth weight
Authors: Beck Jeffrey J , Pool René , van de Weijer Margot , Chen Xu , Krapohl Eva , Gordon Scott D , Nygaard Marianne , Debrabant Birgit , Palviainen Teemu , van der Zee Matthijs D , Baselmans Bart , Finnicum Casey T , Yi Lu , Lundström Sebastian , van Beijsterveldt Toos , Christiansen Lene , Heikkilä Kauko , Kittelsrud Julie , Loukola Anu , Ollikainen Miina , Christensen Kaare , Martin Nicholas G , Plomin Robert , Nivard Michel , Bartels Meike , Dolan Conor , Willemsen Gonneke , de Geus Eco , Almqvist Catarina , Magnusson Patrik K E , Mbarek Hamdi , Ehli Erik A , Boomsma Dorret I , Hottenga Jouke-Jan 
Published: April 2021

Abstract
Birth weight (BW) is an important predictor of newborn survival and health and has associations with many adult health outcomes, including cardiometabolic disorders, autoimmune diseases and mental health. On average, twins have a lower BW than singletons as a result of a different pattern of fetal growth and shorter gestational duration. Therefore, investigations into the genetics of BW often exclude data from twins, leading to a reduction in sample size and remaining ambiguities concerning the genetic contribution to BW in twins. In this study, we carried out a genome-wide association meta-analysis of BW in 42 212 twin individuals and found a positive correlation of beta values (Pearson’s r = 0.66, 95% confidence interval [CI]: 0.47–0.77) with 150 previously reported genome-wide significant variants for singleton BW. We identified strong positive genetic correlations between BW in twins and numerous anthropometric traits, most notably with BW in singletons (genetic correlation [rg] = 0.92, 95% CI: 0.66–1.18). Genetic correlations of BW in twins with a series of health-related traits closely resembled those previously observed for BW in singletons. Polygenic scores constructed from a genome-wide association study on BW in the UK Biobank demonstrated strong predictive power in a target sample of Dutch twins and singletons. Together, our results indicate that a similar genetic architecture underlies BW in twins and singletons and that future genome-wide studies might benefit from including data from large twin registers.
Clinical and Host Biological Factors Predict Colectomy Risk in Children Newly Diagnosed With Ulcerative Colitis
Authors: Hyams Jeffrey S , Brimacombe Michael , Haberman Yael , Walters Thomas , Gibson Greg , Mo Angela , Mack David , Griffiths Anne , Boyle Brendan , LeLeiko Neal , Markowitz James , Rosh Joel , Patel Ashish , Shah Sapana , Baldassano Robert , Pfefferkorn Marian , Sauer Cary , Dailey Joelynn , Venkateswaran Suresh , Kugathasan Subra , Denson Lee A 
Published: April 2021

AbstractBackgroundDevelop a clinical and biological predictive model for colectomy risk in children newly diagnosed with ulcerative colitis (UC).MethodsThis was a multicenter inception cohort study of children (ages 4-17 years) newly diagnosed with UC treated with standardized initial regimens of mesalamine or corticosteroids (CS) depending upon initial disease severity. Therapy escalation to immunomodulators or infliximab was based on predetermined criteria. Patients were phenotyped by clinical activity per the Pediatric Ulcerative Colitis Activity Index (PUCAI), disease extent, endoscopic/histologic severity, and laboratory markers. In addition, RNA sequencing defined pretreatment rectal gene expression and high density DNA genotyping by the Affymetrix UK Biobank Axiom Array. Coprimary outcomes were colectomy over 3 years and time to colectomy. Generalized linear models, Cox proportional hazards multivariate regression modeling, and Kaplan-Meier plots were used.ResultsFour hundred twenty-eight patients (mean age 13 years) started initial theapy with mesalamine (n = 136), oral CS (n = 144), or intravenous CS (n = 148). Twenty-five (6%) underwent colectomy at ≤1 year, 33 (9%) at ≤2 years, and 35 (13%) at ≤3 years. Further, 32/35 patients who had colectomy failed infliximab. An initial PUCAI ≥ 65 was highly associated with colectomy (P = 0.0001). A logistic regression model predicting colectomy using the PUCAI, hemoglobin, and erythrocyte sedimentation rate had a receiver operating characteristic area under the curve of 0.78 (95% confidence interval [0.73, 0.84]). Addition of a pretreatment rectal gene expression panel reflecting activation of the innate immune system and response to external stimuli and bacteria to the clinical model improved the receiver operating characteristic area under the curve to 0.87 (95% confidence interval [0.82, 0.91]).ConclusionsA small group of children newly diagnosed with severe UC still require colectomy despite current therapies. Our gene signature observations suggest additional targets for management of those patients not responding to current medical therapies.
Combatting malfunction or optimizing democracy? Lessons from Germany for a comparative political process theory
Authors: Hailbronner Michaela 
Published: April 2021

Abstract
Ely’s representation-reinforcing theory of judicial review is little known in German public law. Where it is mentioned, it is most often to contest its relevance to German debates. Yet both German jurisprudence and scholarship have a long tradition of taking process-related issues seriously independently of Ely. This makes Germany an interesting place not only to examine the reception of Ely’s work but also to analyze how and where Elyian arguments surface and in what forms. In the context of the German Constitutional Court’s robust understanding of its own role and the character of the Basic Law as a set of substantive values or principles, such arguments often do not appear as part of a broader theory of relative trust and distrust, but rather serve standardly to justify judicial intervention. The German experience also speaks to the problem noted by Ely’s US critics of operationalizing the idea of malfunction, which lies at the heart of his argument and ensures not only its survival but its current popularity. It suggests that malfunction is often not something we can define in the abstract, but that Ely’s theory is nevertheless important for confronting us with the question of not only when distrust warrants intervention but also when the evidence for trust does not.
Shifting Patterns of Respiratory Virus Activity Following Social Distancing Measures for Coronavirus Disease 2019 in South Korea
Authors: Park Sangshin , Michelow Ian C , Choe Young June 
Published: April 2021

Abstract

Background
We hypothesized that nationwide social distancing and other preventive measures for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were associated with reduced detection of other respiratory viruses in South Korea.

Methods
We analyzed national surveillance data to compare incidence of respiratory viruses during 2016–2019 vs 2020. Results of multiplex reverse-transcription polymerase chain reaction assays for 8 respiratory viruses were included: adenovirus (ADV), parainfluenza virus (PIV), respiratory syncytial virus (RSV), influenza virus (IFV), human coronavirus (HCoV; non–SARS-CoV-2), human rhinovirus (HRV), human bocavirus (HBoV), and human metapneumovirus (HMPV).

Results
During 2016–2019, rates of detection of respiratory viruses were relatively stable: ADV, 3.7%–9.2%; PIV, 1.4%–17.0%; RSV, 0.3%–15.3%; IFV, 0.4%–35.6%; HCoV, 1.5%–8.4%; HRV, 7.0%–25.1%; HBoV, 0.6%–6.3%; and HMPV, 0.7%–14.5%. Following implementation of social distancing in February 2020, rates of detection of enveloped viruses (HCoV, HMPV, IFV, PIV, and RSV) were significantly reduced by up to 100%. However, nonenveloped viruses (ADV, HRV, and HBoV) persisted throughout 2020, and HRV rates in hospitalized patients significantly increased.

Conclusions
After implementation of social distancing for SARS-CoV-2 in South Korea, rates of detection of enveloped respiratory viruses decreased significantly, whereas nonenveloped viruses persisted, suggesting that enhanced infection prevention strategies are required to mitigate spread of these viruses.
Discrepancy between patient-reported and clinician-documented symptoms for myocardial perfusion imaging: initial findings from a prospective registry
Authors: Schwartz Cody , Winchester David E 
Published: April 2021

Abstract

Background
Occasionally, the symptoms reported by patients disagree with those documented in the medical record. We designed the Patient Centered Assessment of Symptoms (PCAS) registry to measure discrepancies between patient-reported and clinician-documented symptoms.

Objective
Use patient-derived symptoms data to measure discrepancies with clinical documentation.

Methods
The PCAS registry captured data from a prospective cohort of patients undergoing myocardial perfusion imaging (MPI) and includes free response and structured questions to gauge symptoms. Clinician-documented symptoms were extracted from the patients’ medical records. The appropriateness of testing was determined twice: once using the patient-reported symptoms and once using the clinician-documented symptoms.

Results
A total of 90 subjects were enrolled, among whom diabetes (36.7%), prior coronary disease (28.9%), hypertension (80.0%) and hyperlipidemia (85.6%) were common. Percentage of patient-reported symptoms compared to clinician-documented symptoms and agreement were as follows: chest pain (patient 29.0%, clinician 36.6%, moderate [kappa = 0.54]), chest pressure (patient 18.3%, clinician 10.8%, fair [kappa = 0.27]), dyspnea (patient 41.0%, clinician 36.6%, fair [kappa = 0.28]), onset with exertion (patient 61.7%, clinician 59.6%, slight [kappa = 0.17]), symptoms same as prior coronary artery disease (patient 46.2%, clinician 15.3%, slight [kappa = 0.01]). As a result of these inconsistencies, appropriateness ratings were different for 13.3% (n = 12) subjects.

Conclusion
In this prospective registry of patients undergoing MPI, we observed substantial disagreements between patient-reported and clinician-documented symptoms. Disagreement resulted in a considerable proportion of MPI appropriateness ratings also being incongruous.
Economic Decline, Social Identity, and Authoritarian Values in the United States
Authors: Ballard-Rosa Cameron , Jensen Amalie , Scheve Kenneth 
Published: April 2021

AbstractWhy does the contemporary backlash against globalization in the United States have such a substantial authoritarian character? We argue that sustained economic decline has a negative effect on the social identity of historically dominant groups. These losses lead individuals to be more likely to want to enforce social norm conformity—that is, adopt more authoritarian values—as a way to preserve social status and this effect is greater the larger the size of other groups in the population. Central to our account is the expectation of an interactive effect of local economic and demographic conditions in forging value responses to economic decline. The article evaluates this argument using an original 2017 representative survey in the United States. We find that individuals living in relatively diverse regions facing more intense competition from Chinese imports have more authoritarian values. We further find that the greater effect of globalization-induced labor market decline in more diverse areas is also evident for vote choice in the 2016 Presidential election.
Comparison of Arterial-Venous Balance and Tracer Incorporation Methods for Measuring Muscle Fractional Synthesis and Fractional Breakdown Rates
Authors: Hudson Joshua L , Cotter Matthew , Herndon David N , Wolfe Robert R , Børsheim Elisabet 
Published: April 2021

Abstract
Loss of muscle mass in response to injury or immobilization impairs functional capacity and metabolic health, thus hindering rehabilitation. Stable isotope techniques are powerful in determining skeletal muscle protein fluxes. Traditional tracer incorporation methods to measure muscle protein synthesis and breakdown are cumbersome and invasive to perform in vulnerable populations such as children. To circumvent these issues, a two-bolus stable isotope amino acid method has been developed; although, measured rates of protein synthesis and breakdown have not been validated simultaneously against an accepted technique such as the arterial-venous balance method. The purpose of the current analysis was to provide preliminary data from the simultaneous determination of the arteriovenous balance and two-bolus tracer incorporation methods on muscle fractional synthesis and breakdown rates in children with burns. Five were administered a primed-constant infusion of L-[15N]Threonine for 180 minutes (Prime: 8 µmol/kg; constant: 0.1 µmol·kg-1·minute-1). At 120 and 150 minutes, bolus injections of L-[ring-13C6]Phenylalanine and L-[15N]Phenylalanine (50 µmol/kg each) were administered, respectively. Blood and muscle tissue samples were collected to assess mixed muscle protein synthesis and breakdown rates. The preliminary results from this study indicate that there is no difference in either fractional synthesis rate (mean ± SD; arteriovenous balance: 0.19 ± 0.17 %/h; tracer incorporation: 0.14 ± 0.08 %/h; P = .42) or fractional breakdown rate (arteriovenous balance: 0.29 ± 0.22 %/h; tracer incorporation: 0.23 ± 0.14 %/h; P = .84) between methods. These data support the validity of both methods in quantifying muscle amino acid kinetics; however, the results are limited and adequately powered research is still required.