bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical utilization of radiation therapy in Korea, 2016
Authors: Kim Eunji , Jang Won Il , Kim Mi-Sook , Paik Eun Kyung , Kim Hee Jin , Yoo Hyung Jun , Yang Kwangmo , Cho Chul Koo 
Published: January 2020

Abstract
Radiotherapy (RT) is one of the primary cancer treatment modalities. To estimate the actual utilization of RT and infrastructure in Korea, the current study was performed. Data from 2012 to 2016 were extracted from the Health Insurance Review and Assessment Service. In addition, a nationwide survey was conducted to collect the statistics of RT facilities, equipment and human resources in Korea. The total number of patients treated with RT was 72 563 in 2016. The five cancers that were most commonly treated with RT in 2016 were breast, lung, colorectal, liver and prostate cancer. According to analyses of specific treatment modalities, the number of patients treated with intensity-modulated radiotherapy (IMRT), stereotactic radiation therapy (SRT) and proton therapy increased from 6670, 6306 and 50 in 2012 to 21584, 9048 and 703 in 2016, respectively. Ninety radiation oncology centers were working in 2015 and there were a total of 213 megavoltage teletherapy machines. In 2015, 310 patients were treated per megavoltage RT machine, 246 patients per radiation oncologist, 501 patients per medical physicist and 111 patients per radiotherapy technologist. In conclusion, the number of patients who underwent RT in Korea has increased steadily from 2012 to 2016. The IMRT utilization rate remarkably increased in 2016, and the number of patients treated with advanced treatment modalities such as IMRT, SRT and proton therapy is expected to increase.
Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption
Authors: Luong Xuan G , Daldello Enrico Maria , Rajkovic Gabriel , Yang Cai-Rong , Conti Marco 
Published: January 2020

Abstract
During oocyte maturation, changes in gene expression depend exclusively on translation and degradation of maternal mRNAs rather than transcription. Execution of this translation program is essential for assembling the molecular machinery required for meiotic progression, fertilization, and embryo development. With the present study, we used a RiboTag/RNA-Seq approach to explore the timing of maternal mRNA translation in quiescent oocytes as well as in oocytes progressing through the first meiotic division. This genome-wide analysis reveals a global switch in maternal mRNA translation coinciding with oocyte re-entry into the meiotic cell cycle. Messenger RNAs whose translation is highly active in quiescent oocytes invariably become repressed during meiotic re-entry, whereas transcripts repressed in quiescent oocytes become activated. Experimentally, we have defined the exact timing of the switch and the repressive function of CPE elements, and identified a novel role for CPEB1 in maintaining constitutive translation of a large group of maternal mRNAs during maturation.
Effect of patient- and center-level characteristics on uptake of home dialysis in Australia and New Zealand: a multicenter registry analysis
Authors: Ethier Isabelle , Cho Yeoungjee , Hawley Carmel , Pascoe Elaine M , Roberts Matthew A , Semple David , Nadeau-Fredette Annie-Claire , Sypek Matthew P , Viecelli Andrea , Campbell Scott , van Eps Carolyn , Isbel Nicole M , Johnson David W 
Published: January 2020

Abstract

Background
Home-based dialysis therapies, home hemodialysis (HHD) and peritoneal dialysis (PD) are underutilized in many countries and significant variation in the uptake of home dialysis exists across dialysis centers. This study aimed to evaluate the patient- and center-level characteristics associated with uptake of home dialysis.

Methods
The Australia and New Zealand Dialysis and Transplant (ANZDATA) Registry was used to include incident dialysis patients in Australia and New Zealand from 1997 to 2017. Uptake of home dialysis was defined as any HHD or PD treatment reported to ANZDATA within 6 months of dialysis initiation. Characteristics associated with home dialysis uptake were evaluated using mixed effects logistic regression models with patient- and center-level covariates, era as a fixed effect and dialysis center as a random effect.

Results
Overall, 54 773 patients were included. Uptake of home-based dialysis was reported in 24 399 (45%) patients but varied between 0 and 87% across the 76 centers. Patient-level factors associated with lower uptake included male sex, ethnicity (particularly indigenous peoples), older age, presence of comorbidities, late referral to a nephrology service, remote residence and obesity. Center-level predictors of lower uptake included small center size, smaller proportion of patients with permanent access at dialysis initiation and lower weekly facility hemodialysis hours. The variation in odds of home dialysis uptake across centers increased by 3% after adjusting for the era and patient-level characteristics but decreased by 24% after adjusting for center-level characteristics.

Conclusion
Center-specific factors are associated with the variation in uptake of home dialysis across centers in Australia and New Zealand.
Salt-Induced Stability ofSR1/CAMTA3mRNA Is Mediated by Reactive Oxygen Species and Requires the 3’ End of Its Open Reading Frame
Authors: Abdel-Hameed Amira A E , Prasad Kasavajhala V S K , Jiang Qiyan , Reddy Anireddy S N 
Published: January 2020

AbstractSoil salinity, a prevalent abiotic stress, causes enormous losses in global crop yields annually. Previous studies have shown that salt stress-induced reprogramming of gene expression contributes to the survival of plants under this stress. However, mechanisms regulating gene expression in response to salt stress at the posttranscriptional level are not well understood. In this study, we show that salt stress increases the level of Signal Responsive 1 (SR1) mRNA, a member of signal-responsive Ca2+/calmodulin-regulated transcription factors, by enhancing its stability. We present multiple lines of evidence indicating that reactive oxygen species generated by NADPH oxidase activity mediate salt-induced SR1 transcript stability. Using mutants impaired in either nonsense-mediated decay, XRN4 or mRNA decapping pathways, we show that neither the nonsense-mediated mRNA decay pathway, XRN4 nor the decapping of SR1 mRNA is required for its decay. We analyzed the salt-induced accumulation of eight truncated versions of the SR1 coding region (∼3 kb) in the sr1 mutant background. This analysis identified a 500-nt region at the 3’ end of the SR1 coding region to be required for the salt-induced stability of SR1 mRNA. Potential mechanisms by which this region confers SR1 transcript stability in response to salt are discussed.
Polygenic Risk for Depression is Associated with the Severity and Rate of Change in Depressive Symptoms Across Adolescence
Authors: Kwong Alex S. F. , Morris Tim T. , Pearson Rebecca M. , Timpson Nicholas J. , Rice Frances , Stergiakouli Evie , Tilling Kate 
Published: January 2020

AbstractAdolescence marks a period where depression will commonly onset and previous research using twin studies has suggested that genetic influences play a role in how depression develops and changes across adolescence. Recent genome-wide association studies have also shown that common genetic variants – which can be combined into a polygenic risk score (PRS) – are also implicated in depression. However, the role of PRS in adolescent depression and changes in adolescent depression is not yet understood. We aimed to examine the association between a PRS for depressive symptoms and depressive symptoms across adolescence and young adulthood, and how polygenic risk is associated with changes in depressive symptoms using two methods: cross-sectional analysis and multilevel growth curve modelling to examine the rate of change over time. Using data from over 6000 participants of the Avon Longitudinal Study of Parents and Children (ALSPAC) we examined associations between genetic liability to depressive symptoms (PRS for depressive symptoms) and self-reported depressive symptoms (short mood and feelings questionnaire over 9 occasions from 10-24 years). We examined cross-sectional associations at each age and longitudinal trajectories of depressive symptoms in a repeated measures framework using growth curve analysis. The PRS was associated with depressive symptoms throughout adolescence and young adulthood in cross-sectional and growth curve analyses, though associations were stronger in the latter analyses. Growth curve analyses also provided additional insights, demonstrating that individuals with a higher PRS had steeper trajectories of depressive symptoms across adolescence with a greater increasing rate of change. These results show that common genetics variants as indexed by a PRS for depressive symptoms influence both the severity and rate of change in adolescent depressive symptoms. Longitudinal data that make use of repeated measures designs have the potential to provide greater insights into the factors that influence the onset and persistence of adolescent depression.
Prevalence, Characteristics, and Associated Factors of Workplace Violence Against Healthcare Professionals in India: A Systematic Review and Meta-analysis
Authors: Hossain Md Mahbub , Sharma Rachit , Tasnim Samia , Al Kibria Gulam Muhammed , Sultana Abida , Saxena Tanjul 
Published: January 2020

AbstractBackgroundWorkplace violence (WPV) against doctors, nurses, and other healthcare professionals is a growing public health concern affecting health systems in low- and middle-income countries. In India, incidents of WPV against health workforce have become common in recent years. However, there is no synthesized evidence on the nationwide burden of WPV in healthcare. This study aims to systematically evaluate the current evidence on the prevalence, characteristics, and associated factors of WPV against healthcare professionals in India.MethodsWe systematically searched seven major databases and additional sources to retrieved published literature on WPV in India. We included empirical studies without any time restriction, which reported the prevalence of WPV against healthcare professionals in India. Following data extraction, we estimated the pooled prevalence of WPV using random-effects model in meta-analysis. The characteristics and associated factors of WPV were narratively synthesized from these empirical studies.ResultsAmong 1065 articles retrieved from multiple sources, 15 studies met our inclusion and exclusion criteria. The pooled prevalence of WPV among 2849 participants in those 15 studies was 63% (95% confidence interval [CI], 54%-72%). In the subgroup analyses, the pooled prevalence for male and female was 64% (95% CI, 51%-78%) and 54% (95% CI, 47%-62%) respectively. Moreover, pooled prevalence in 12-months and lifetime was 55% (95% CI, 43%-67%) and 69% (95% CI, 61%-78%) respectively. Among the participants, the prevalence of verbal violence (52%; 95% CI, 45%-60%) was higher than physical violence (8%; 95% CI, 5%-11%). The emergency department was a common location of WPV, whereas the patients’ attendants were perpetrators in most studies. Major factors associated with WPV included ineffective patient-provider communication, less experience of the healthcare professionals, overcrowding, shortage of resources, long waiting hours, lack of security measures, dissatisfaction about health services, high cost of care, the negative role of media, and other socio-behavioral problems among the patients and healthcare professionals.ConclusionWPV is highly prevalent among healthcare professionals in India. Critical challenges within the healthcare and social context necessitate further research, better policymaking, and multipronged interventions to address the same and prevent WPV against healthcare professionals in India.
Brief exposure to a diverse range of environmental stress enhances stress tolerance in the polyextremophilic Antarctic midge,Belgica antarctica
Authors: Gantz J. D. , Philip B. N. , Teets N. M. , Kawarasaki Y. , Potts L. J. , Spacht D. E. , Benoit J. B. , Denlinger D. L. , Lee R. E 
Published: January 2020

AbstractInsects use rapid acclimation to enhance their tolerance of abiotic stresses within minutes to hours. These responses are critical adaptations for insects and other small ectotherms to tolerate drastic changes in temperature, hydration, or other factors that can fluctuate precipitously with ambient conditions or as a result of behavior. Rapid cold-hardening, where insects use brief exposure to modest chilling as a cue to enhance their cold tolerance, is the most thoroughly-studied of these responses and relatively little is known about rapid acclimation that is either triggered by or enhances tolerance of other abiotic stresses. Here, we used larvae of the Antarctic midge,Belgica antarctica, a polar extremophile that routinely experiences numerous stresses in nature, to investigate how 2 h exposure to modest environmental stresses affect stress tolerance in insects. Brief pretreatment by various stresses, including hyperosmotic challenge, hypoosmotic challenge, acidity, basicity, and UV irradiation enhanced stress tolerance inB. antarcticalarvae relative to untreated controls. These results indicate that numerous environmental cues can trigger rapid acclimation in insects and that these responses can enhance tolerance of multiple stresses.
Epitope-tagging of the endogenous murine BiP/GRP78/Hspa5locus allows direct analysis of the BiP interactome and protein misfoldingin vivo
Authors: Peng Yunqian , Chen Zhouji , Jang Insook , Arvan Peter , Kaufman Randal J. 
Published: January 2020

ABSTRACTBiP/GRP78, encoded by theHspa5gene, is the major HSP70 family member in the endoplasmic reticulum (ER) lumen, and controls ER protein folding. The essential functions of BiP in facilitating proper protein folding are mainly mediated through its dynamic interaction with unfolded or misfolded client proteins, and by serving as a negative regulator of the Unfolded Protein Response. A mechanistic understanding of the dynamics of BiP interaction with its protein partners is essential to understand ER biology, and therefore, we have sought to develop a tractable model to study misfolded protein interaction with BiP. For this purpose, we have used homologous recombination to insert a 3xFLAG epitope tag into the endogenous murineHspa5 gene, just upstream from the essential KDEL signal necessary for ER localization of BiP. Tagging BiP in this way did not alterHspa5expression under basal or ER-stress induced conditions in hepatocytesex vivoor in fibroblasts. Furthermore, the tag did not alter the cellular localization of BiP or its functionality. All of these findings in primary tissue culture were also confirmedin vivoin livers of heterozygous mice harboring one WT and one FLAG-taggedHspa5allele. Hepatocyte-specific BiP-FLAG modification did not alter liver function or UPR signaling. Importantly, immunoprecipitation with anti-FLAG antibody completely pulled down FLAG-tagged BiP from lysates of BiP-FLAG expressing livers. Affinity purification-mass spectrometry (AP-MS) of BiP-FLAG protein complexes isolated from the BiP-FLAG-expressing livers of tunicamycin (TM)- and vehicle-treated mice revealed a marked increase in interaction of glycoproteins with BiP-FLAG in response to inhibition of N-glycosylation due to TM-treatment, validating utility of our BiP-Flag mice as a tool to identify ER misfolded proteinsin vivo. Significantly, our AP-MS analysis also providedin vivoevidence demonstrating that BiP-FLAG binds to UPR transducers IRE1α and PERK under basal conditions but is released upon TM-treatment to activate UPR. We have also employed this mouse model to demonstrate that proinsulin in pancreatic β cells misfolds and interacts with BiP-FLAG in healthy mice. In summary, we generated a novel model that can be used to investigate the BiP interactomein vivounder physiological and pathophysiological conditions in a cell type-specific manner. This tool provides, for the first time, an unbiased approach to identify unfolded and misfolded BiP-client proteins, and a new approach to study ER protein misfolding in a cell-type and temporal manner to uncover the role of BiP in many essential ER processes.
Mitochondrial fostering: the mitochondrial genome may play a role in plant orphan gene evolution
Authors: O’Conner Seth , Li Ling 
Published: January 2020

AbstractPlant mitochondrial genomes exhibit odd evolutionary patterns. They have a high rearrangement but low mutation rate, and a large size. Based on massive mitochondrial DNA transfers to the nucleus as well as the mitochondrial unique evolutionary traits, we propose a “Mitochondrial Fostering” theory where the organelle genome plays an integral role in the arrival and development of orphan genes (genes with no homologues in other lineages). Two approaches were used to test this theory: 1) bioinformatic analysis of nuclear mitochondrial DNA (Numts: mitochondrial originating DNA that has migrated to the nucleus) at the genome level, and 2) bioinformatic analysis of particular orphan sequences present in both the mitochondrial genome and the nuclear genome ofArabidopsis thaliana. One study example is given about one orphan sequence that codes for two unique orphan genes: one in the mitochondrial genome and another one in the nuclear genome. DNA alignments show regions of thisA. thalianaorphan sequence exist scattered throughout other land plant mitochondrial genomes. This is consistent with the high recombination rates of mitochondrial genomes in land plants. This may also enable the creation of novel coding sequences within the orphan loci, which can then be transferred to the nuclear genome and become exposed to new evolutionary pressures. Our study also reveals a high correlation between mitochondrial DNA rate transferred to the nuclear genome and number of orphan genes in land plants. All the data suggests the mitochondrial genome may play a role in nuclear orphan gene evolution in land plants.
VIPR: Vectorial Implementation of Phase Retrieval for fast and accurate microscopic pixel-wise pupil estimation
Authors: Ferdman Boris , Nehme Elias , Weiss Lucien E. , Orange Reut , Alalouf Onit , Shechtman Yoav 
Published: January 2020

AbstractIn microscopy, proper modeling of the image formation has a substantial effect on the precision and accuracy in localization experiments and facilitates the correction of aberrations in adaptive optics experiments. The observed images are subject to polarization effects, refractive index variations and system specific constraints. Previously reported techniques have addressed these challenges by using complicated calibration samples, computationally heavy numerical algorithms, and various mathematical simplifications. In this work, we present a phase retrieval approach based on an analytical derivation of the vectorial diffraction model. Our method produces an accurate estimate of the system phase information (without any prior knowledge) in under a minute.
Interleukin-22 drives a metabolic adaptive reprogramming to maintain mitochondrial fitness and treat liver injury
Authors: Chen Wei , Zai Wenjing , Fan Jiajun , Zhang Xuyao , Luan Jingyun , Wang Yichen , Shen Yilan , Wang Ziyu , Dai Shixuan , Fang Si , Ju Dianwen 
Published: January 2020

AbstractInterleukin 22 (IL-22) is an epithelial survival cytokine that is at present being explored as therapeutic agents for acute and chronic liver injury. However, its molecular basis of protective activities remains poorly understood. Here we demonstrate that IL-22 inhibits the deteriorating metabolic states induced by stimuli in hepatocytes. Specifically, we provide evidence that IL-22 promotes oxidative phosphorylation (OXPHOS) and glycolysis and regulates the metabolic reprogramming related transcriptional responses. IL-22 controls metabolic regulators and enzymes activity through the induction of AMP-activated protein kinase (AMPK), AKT and mammalian target of rapamycin (mTOR), thereby ameliorating mitochondrial. The upstream effector lncRNA H19 also participates in the controlling of these metabolic processes in hepatocytes. Importantly, amelioration of liver injury by IL-22 through activation of metabolism relevant signaling and regulation of mitochondrial function are further demonstrated in cisplatin-induced liver injury and steatohepatitis. Collectively, our results reveal a novel mechanism underscoring the regulation of metabolic profiles of hepatocytes by IL-22 during liver injury, which might provide useful insights from the bench to the clinic in treating and preventing liver diseases.Graphical AbstractOur works demonstrate a critical role of IL-22 in regulating hepatocellular metabolism to treat liver injury via activating STAT3-lncRNA H19-AMPK-AKT-mTOR axis. These findings describe a novel mechanism underscoring the regulation of metabolic states of hepatocytes by IL-22 during liver injury with potentially broad therapeutic insights.
Three previously characterized resistances to yellow rust are encoded by a single locusWtk1
Authors: Klymiuk Valentyna , Fatiukha Andrii , Raats Dina , Bocharova Valeria , Huang Lin , Feng Lihua , Jaiwar Samidha , Pozniak Curtis , Coaker Gitta , Dubcovsky Jorge , Fahima Tzion 
Published: January 2020

AbstractThe wild emmer wheat (Triticum turgidumssp.dicoccoides; WEW) yellow (stripe) rust resistance genesYr15, YrG303andYrH52were discovered in natural populations from different geographic locations. They all localize to chromosome 1B but were thought to be non-allelic based on differences in resistance response. We recently clonedYr15as aWheat Tandem Kinase 1(WTK1) and showed here that these three resistance loci co-segregate in fine-mapping populations and share identical full-length genomic sequence of functionalWtk1. Independent EMS mutagenized susceptibleyrG303andyrH52lines carried single nucleotide mutations inWtk1that disrupted function. A comparison of the mutations foryr15, yrG303andyrH52mutants showed that while key conserved residues were intact, other conserved regions in critical kinase subdomains were frequently affected. Thus, we concluded thatYr15-, YrG303-andYrH52-mediated resistances to yellow rust are encoded by a single locusWtk1. Introgression ofWtk1into multiple genetic backgrounds resulted in variable phenotypic responses, confirming thatWtk1-mediated resistance is part of a complex immune response network. WEW natural populations subjected to natural selection and adaptation have potential to serve as a good source for evolutionary studies of different traits and multifaceted gene networks.HighlightWe demonstrate thatYr15, YrG303andYrH52resistances are encoded by theWtk1locus, but express variable resistance responses to yellow rust in a genetic background dependent manner.