bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using the U.S. Climate Reference Network to Identify Biases in Near- and Subsurface Meteorological Fields in the High-Resolution Rapid Refresh (HRRR) Weather Prediction Model
Authors: Lee Temple R. , Leeper Ronald D. , Wilson Tim , Diamond Howard J. , Meyers Tilden P. , Turner David D. 
Published: April 2023

Abstract
The ability of high-resolution mesoscale models to simulate near-surface and subsurface meteorological processes is critical for representing land–atmosphere feedback processes. The High-Resolution Rapid Refresh (HRRR) model is a 3-km numerical weather prediction model that has been used operationally since 2014. In this study, we evaluated the HRRR over the contiguous United States from 1 January 2021 to 31 December 2021. We compared the 1-, 3-, 6-, 12-, 18-, 24-, 30-, and 48-h forecasts against observations of air and surface temperature, shortwave radiation, and soil temperature and moisture from the 114 stations of the U.S. Climate Reference Network (USCRN) and evaluated the HRRR’s performance for different geographic regions and land cover types. We found that the HRRR well simulated air and surface temperatures, but underestimated soil temperatures when temperatures were subfreezing. The HRRR had the largest overestimates in shortwave radiation under cloudy skies, and there was a positive relationship between the shortwave radiation mean bias error (MBE) and air temperature MBE that was stronger in summer than winter. Additionally, the HRRR underestimated soil moisture when the values exceeded about 0.2 m3 m−3, but overestimated soil moisture when measurements were below this value. Consequently, the HRRR exhibited a positive soil moisture MBE over the drier areas of the western United States and a negative MBE over the eastern United States. Although caution is needed when applying conclusions regarding HRRR’s biases to locations with subgrid-scale land cover variations, general knowledge of HRRR’s biases will help guide improvements to land surface models used in high-resolution weather forecasting models.

Significance Statement
Weather forecasters rely upon output from many different models. However, the models’ ability to represent processes happening near the land surface over short time scales is critical for producing accurate weather forecasts. In this study, we evaluated the High-Resolution Rapid Refresh (HRRR) model using observations from the U.S. Climate Reference Network, which currently includes 114 reference climate observing stations in the contiguous United States. These stations provide highly accurate measurements of air temperature, precipitation, soil temperature, and soil moisture. Our findings helped illustrate conditions when the HRRR performs well, but also conditions in which the HRRR can be improved, which we expect will motivate ongoing improvements to the HRRR and other weather forecasting models.
Effect of 2 Teams and Operative Time on Complications After Oral Cavity Free Flap Reconstruction
Authors: Shaikh Noah , Noor Kinza , Jafary Haseeb , Chung Jeffson , Fancy Tanya , Stokes William 
Published: April 2023

Objective: Evaluate the effects of operative time and 2 team approach on complications after soft tissue free flap reconstruction for oral tongue cancer. Methods: Patients with oncologic glossectomy with myocutaneous or fasciocutaneous free flap reconstruction were included from the 2015 to 2018 American College of Surgery National Surgical Quality Improvement Program. The primary predictive variables assessed were operative time and 2 team approach; control variables included age, sex, body mass index (BMI), 5-question-modified frailty index (mFI-5), American Society of Anesthesiologists (ASA) class, and total work relative value units (wRVU). Outcomes assessed included 30-day mortality, 30-day reoperation, hospital length of stay beyond 30 days, readmission, medical and surgical complications, and non-home discharge. Multivariable logistic/linear regression models were used to predict surgical outcomes. Results: Microvascular soft tissue free flap reconstruction of the oral cavity after glossectomy was performed on 839 patients. Operative time was independently associated with readmission, prolonged length of stay, surgical complications, medical complications, and non-home discharge. A 2-team approach was independently associated with prolonged length of stay and medical complications. The mean operative time of the 1-team and 2-team approach was 8.73 and 9.13 hours. The 1-team approach did not significantly increase operative time ( P = .16). Conclusions: In the largest study to date of operative time on post-surgical outcomes after glossectomy and soft tissue free flap reconstruction, we found longer operative times increased rates of postoperative complications and non-home discharge. The 1-team approach is non-inferior to the 2-team approach with respect to operating time and complications.
Intensive and Extensive Margins of Export Diversification as Strategies for Sustainable Economic Growth: Evidence from the Nigerian Economy
Authors: Young Ademola Obafemi 
Published: April 2023

Two opposite strands of literature analysing export diversification’s role in promoting sustainable growth have evolved in international economics and development, namely, the intensive and extensive margins of exports. This study empirically investigates which of the margin is more useful towards promoting sustainable growth using annual time series data of Nigeria for the period 1960–2021. Autoregressive distributed lag (ARDL) and innovative accounting procedure were employed. The ARDL results reveal that both margins significantly enhance growth in short and long run. However, importance of the extensive margin, in aggregate, dominates that of the intensive margin. Likewise, the results from innovative accounting procedures reveal that although both margins contribute positively to growth, the contribution to growth of extensive margin dominates over that of the intensive margin. These results, thus, lend credence to the extensive-margin exposition, which postulates that the export of extant commodities to new market destinations or export of new commodities to new and/or old market destinations plays a relatively more important role in export growth/diversification and, ultimately, sustainable growth. The study recommends that governments should develop and implement economic policies aimed at enhancing exports of value-added commodities—due to their relatively high income and price elasticities over primary commodities—to maximise the benefits in the extensive margin. JEL Codes: F10, F14, O10, O12, O50, O55
Multilevel power structure and local compliance with government transparency mandates: evidence from China's environmental transparency reform
Authors: Li Jin , Chen Shaowei 
Published: April 2023

Despite the ample literature on government transparency, our knowledge about how the vertical power structure of governments shapes local compliance with government transparency mandates is still limited. This study sets out to address this gap. Specifically, we investigate how the central government's environmental information disclosure (EID) signal and provincial governments’ conflicting signal of economic growth affect, independently and interactively, city governments’ compliance with central EID mandates in the center-province-city hierarchical structure in China. We argue that the central EID signal positively affects city compliance, while the provincial signal of economic growth reduces it. Moreover, the provincial signal of economic growth negatively moderates the impact of the central EID signal. Empirically, with a panel dataset for city-level governments from 2008 to 2018, we found robust evidence strongly supporting our theoretical hypotheses. Points for practitioners This research reveals the influences of the complex dynamics among governments at different levels on local compliance with government transparency mandates. The findings suggest that the maneuvers of middle-level governments in a multilevel power structure and the interactions among multiple conflicting policy goals should be taken seriously by practitioners when designing policies to promote government transparency reforms.
Regional Alterations of Macroscopy and Histology in Meniscus in an ACL Transection Rabbit Model
Authors: Huang Mingru , Sheng Huaixuan , Gao Han , Feng Sijia , Sun Luyi , Chen Jun , Li Yunxia 
Published: April 2023

Background: Although meniscal injury is common after anterior cruciate ligament (ACL) injury, the underlying process in different meniscal regions remains unclear. Purpose: To investigate macroscopic and histological alterations in different meniscal regions in an ACL transection (ACLT) rabbit model. Study Design: Controlled laboratory study. Methods: ACLT was performed on New Zealand White rabbits. Both the medial meniscus (MM) and the lateral meniscus (LM) of the ACLT knees were obtained at 8 (n = 6) and 26 (n = 6) weeks postoperatively. MM and LM collected from nonoperated knees were considered 0 weeks (n = 6) postoperatively. Menisci were then divided into posterior, central, and anterior regions for macroscopic (width) and histological (hematoxylin and eosin, safranin O/fast green, collagen type 2 [COL2]) analysis. Results: The macroscopic widths of MM and LM increased and then decreased over 26 weeks postoperatively, with all 3 MM widths at 8 weeks significantly wider than at 0 weeks (posterior: P < .01; central: P < .05; anterior: P < .05). In the MM, chondrocyte-like cell density increased and then decreased postoperatively, whereas in the LM, it decreased and then remained almost unchanged. Cell density was significantly higher in the central MM region at 8 weeks than at 0 weeks ( P < .05). Glycosaminoglycan (GAG) and COL2 percentages of MM and LM decreased from 0 to 8 weeks and then returned to nearly normal levels at 26 weeks postoperatively. In the MM, the GAG percentage in the posterior ( P < .05) and central ( P < .01) regions and the COL2 percentage in the posterior region ( P < .05) was significantly lower at 8 weeks than at 0 weeks. Conclusion: After ACLT in rabbit meniscus, the extracellular matrix (ECM) initially decreased and then increased to almost normal. Additionally, there were significant differences in the ECM percentage in the posterior and central regions of the MM in comparison with other meniscal regions between 0 and 8 weeks postoperatively. Clinical Relevance: The results indicate that the time for meniscal injury after ACL injury is important, and attention should be paid to the posterior and central regions of the MM after ACLT.
The Herbal Medicine Suanzaoren (Ziziphi Spinosae Semen) for Sleep Quality Improvements: A Systematic Review and Meta-analysis
Authors: Yang Mingxiao , Wang Hui , Zhang Yi Lily , Zhang Furong , Li Xiaotong , Kim Soo-Dam , Chen Yalan , Chen Jiyao , Chimonas Susan , Korenstein Deborah , Mao Jun J. 
Published: April 2023

Background: Sleep disturbances are common and bothersome among cancer and noncancer populations. Suanzaoren ( Ziziphi Spinosae Semen) is commonly used to improve sleep, yet its efficacy and safety are unclear. Methods: We systematically searched PubMed, Cochrane Library, and EMBASE from inception through October 5, 2021, to identify randomized trials of Suanzaoren. We included randomized trials comparing Suanzaoren to placebo, medications, cognitive behavioral therapy (CBT), or usual care for improving sleep outcomes in cancer and noncancer patients with insomnia or sleep disturbance. We performed a risk of bias analysis following Cochrane guidelines. Depending on heterogeneity, we pooled studies with similar comparators using fixed- and random-effects models. Results: We included participants with insomnia disorder (N = 785) or sleep disturbance (N = 120) from 9 trials. Compared with placebo, Suanzaoren led to significant subjective sleep quality improvements in participants with insomnia and patients with sleep disturbance combined (standard mean difference −0.58, 95% CI −1.04, −0.11; P < .01); Compared with benzodiazepines or CBT, Suanzaoren was associated with a significant decrease in insomnia severity (mean difference −2.68 points, 95% CI −5.50, −0.22; P = .03) at 4 weeks in the general population and cancer patients. The long-term effects of Suanzaoren were mixed among trials. Suanzaoren did not increase the incidence of major adverse events. The placebo-controlled studies had a low risk of bias. Conclusion: Suanzaoren is associated with short-term patient-reported sleep quality improvements among individuals with insomnia or sleep disturbance. Due to the small sample size and variable study quality, the clinical benefits and harms of Suanzaoren, particularly in the long term, should be further assessed in a sufficiently powered randomized trial. Registration: PROSPERO CRD42021281943
Blood-based liquid biopsy: insights into early detection, prediction, and treatment monitoring of bladder cancer
Authors: Li Shijie , Xin Kerong , Pan Shen , Wang Yang , Zheng Jianyi , Li Zeyu , Liu Xuefeng , Liu Bitian , Xu Zhenqun , Chen Xiaonan 
Published: April 2023

AbstractBladder cancer (BC) is a clinical challenge worldwide with late clinical presentation, poor prognosis, and low survival rates. Traditional cystoscopy and tissue biopsy are routine methods for the diagnosis, prognosis, and monitoring of BC. However, due to the heterogeneity and limitations of tumors, such as aggressiveness, high cost, and limited applicability of longitudinal surveillance, the identification of tumor markers has attracted significant attention in BC. Over the past decade, liquid biopsies (e.g., blood) have proven to be highly efficient methods for the discovery of BC biomarkers. This noninvasive sampling method is used to analyze unique tumor components released into the peripheral circulation and allows serial sampling and longitudinal monitoring of tumor progression. Several liquid biopsy biomarkers are being extensively studied and have shown promising results in clinical applications of BC, including early detection, detection of microscopic residual disease, prediction of recurrence, and response to therapy. Therefore, in this review, we aim to provide an update on various novel blood-based liquid biopsy markers and review the advantages and current limitations of liquid biopsy in BC therapy. The role of blood-based circulating tumor cells, circulating tumor DNA, cell-free RNA, exosomes, metabolomics, and proteomics in diagnosis, prognosis, and treatment monitoring, and their applicability to the personalized management of BC, are highlighted.
Role of muscle FOXO gene in exercise against the skeletal muscle and cardiac age-related defects and mortality caused by high-salt intake in Drosophila
Authors: Wen Deng-tai , Gao Ying-hui , Wang Jingfeng , Wang Shijie , Zhong Qi , Hou Wen-qi 
Published: April 2023

AbstractFOXO has long been associated with aging, exercise, and tissue homeostasis, but it remains unclear what the role is of the muscle FOXO gene in E against high-salt intake(HSI)-induced age-related defects of the skeletal muscle, heart, and mortality. In this research, overexpression and RNAi of the FOXO gene in the skeletal and heart muscle of Drosophila were constructed by building Mhc-GAL4/FOXO-UAS-overexpression and Mhc-GAL4/FOXO-UAS-RNAi system. The skeletal muscle and heart function, the balance of oxidation and antioxidant, and mitochondrial homeostasis were measured. The results showed that exercise reversed the age-related decline in climbing ability and downregulation of muscle FOXO expression induced by HSI. Muscle-specific FOXO-RNAi (FOXO-RNAi) and -overexpression (FOXO-OE) promoted or slowed the age-related decline in climbing ability, heart function, and skeletal muscle and heart structure damage, which was accompanied by the inhibition or activation of FOXO/PGC-1α/SDH and FOXO/SOD pathway activity, and oxidative stress (ROS) increased or decreased in both skeletal muscle and heart. The protective effect of exercise on the skeletal muscle and heart was blocked by FOXO-RNAi in aged HSI flies. FOXO-OE prolonged its lifespan, but it did not resist the HSI-induced lifespan shortening. Exercise did not improve HSI-induced lifespan shortening in FOXO-RNAi flies. Therefore, current results confirmed that the muscle FOXO gene played a vital role in exercise against age-related defects of the skeletal muscle and heart induced by HSI because it determined the activity of muscle FOXO/SOD and FOXO/PGC-1α/SDH pathways. The muscle FOXO gene also played an important role in exercise against HSI-induced mortality in aging flies.
Shine: A novel strategy to extract specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets
Authors: Ji Cong , Shao Junbin 
Published: April 2023

Abstract
Background
Concentrations of the pathogenic microorganisms’ DNA in biological samples are typically low. Therefore, DNA diagnostics of common infections are costly, rarely accurate, and challenging. Limited by failing to cover updated epidemic testing samples, computational services are difficult to implement in clinical applications without complex customized settings. Furthermore, the combined biomarkers used to maintain high conservation may not be cost effective and could cause several experimental errors in many clinical settings. Given the limitations of recent developed technology, 16S rRNA is too conserved to distinguish closely related species, and mosaic plasmids are not effective as well because of their uneven distribution across prokaryotic taxa.

Results
Here, we provide a computational strategy, Shine, that allows extraction of specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets. Distinguished with simple concatenations with blast-based filtering, our method involves a de novo genome alignment-based pipeline to explore the original and specific repetitive biomarkers in the defined population. It can cover all members to detect newly discovered multicopy conserved species-specific or even subspecies-specific target probes and primer sets. The method has been successfully applied to a number of clinical projects and has the overwhelming advantages of automated detection of all pathogenic microorganisms without the limitations of genome annotation and incompletely assembled motifs. Using on our pipeline, users may select different configuration parameters depending on the purpose of the project for routine clinical detection practices on the website https://bioinfo.liferiver.com.cn with easy registration.

Conclusions
The proposed strategy is suitable for identifying shared phylogenetic markers while featuring low rates of false positive or false negative. This technology is suitable for the automatic design of minimal and efficient PCR primers and other types of detection probes.
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
Authors: Fallon Timothy R. , Čalounová Tereza , Mokrejš Martin , Weng Jing-Ke , Pluskal Tomáš 
Published: April 2023

Abstract
Background
RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore presents a major barrier for researchers to adopt best-practice methods and up-to-date versions of software.

Results
Here we present a streamlined and universal de novo transcriptome assembly and annotation pipeline, transXpress, implemented in Snakemake. transXpress supports two popular assembly programs, Trinity and rnaSPAdes, and allows parallel execution on heterogeneous cluster computing hardware.

Conclusions
transXpress simplifies the use of best-practice methods and up-to-date software for de novo transcriptome assembly, and produces standardized output files that can be mined using SequenceServer to facilitate rapid discovery of new genes and proteins in non-model organisms.
Identification of candidate genes responsible for chasmogamy in wheat
Authors: Szeliga Magdalena , Bakera Beata , Święcicka Magdalena , Tyrka Mirosław , Rakoczy-Trojanowska Monika 
Published: April 2023

Abstract
Background
The flowering biology of wheat plants favours self-pollination which causes obstacles in wheat hybrid breeding. Wheat flowers can be divided into two groups, the first one is characterized by flowering and pollination within closed flowers (cleistogamy), while the second one possesses the ability to open flowers during processes mentioned above (chasmogamy). The swelling of lodicules is involved in the flowering of cereals and among others their morphology, calcium and potassium content differentiate between cleistogamic and non-cleistogamous flowers. A better understanding of the chasmogamy mechanism can lead to the development of tools for selection of plants with the desired outcrossing rate. To learn more, the sequencing of transcriptomes (RNA-Seq) and Representational Difference Analysis products (RDA-Seq) were performed to investigate the global transcriptomes of wheat lodicules in two highly chasmogamous (HCH, Piko and Poezja) and two low chasmogamous (LCH, Euforia and KWS Dacanto) varieties at two developmental stages—pre-flowering and early flowering.

Results
The differentially expressed genes were enriched in five, main pathways: “metabolism”, “organismal systems”, “genetic information processing”, “cellular processes” and “environmental information processing”, respectively. Important genes with opposite patterns of regulation between the HCH and LCH lines have been associated with the lodicule development i.e. expression levels of MADS16 and MADS58 genes may be responsible for quantitative differences in chasmogamy level in wheat.

Conclusions
We conclude that the results provide a new insight into lodicules involvement in the wheat flowering process. This study generated important genomic information to support the exploitation of the chasmogamy in wheat hybrid breeding programs.
The genetic basis of wing spots in Pieris canidia butterflies
Authors: Wee Jocelyn Liang Qi , Murugesan Suriya Narayanan , Wheat Christopher W. , Monteiro Antónia 
Published: April 2023

AbstractSpots in pierid butterflies and eyespots in nymphalid butterflies are likely non-homologous wing colour pattern elements, yet they share a few features in common. Both develop black scales that depend on the function of the gene spalt, and both might have central signalling cells. This suggests that both pattern elements may be sharing common genetic circuitry. Hundreds of genes have already been associated with the development of nymphalid butterfly eyespot patterns, but the genetic basis of the simpler spot patterns on the wings of pierid butterflies has not been investigated. To facilitate studies of pierid wing patterns, we report a high-quality draft genome assembly for Pieris canidia, the Indian cabbage white. We then conducted transcriptomic analyses of pupal wing tissues sampled from the spot and non-spot regions of P. canidia at 3-6 h post-pupation. A total of 1352 genes were differentially regulated between wing tissues with and without the black spot, including spalt, Krüppel-like factor 10, genes from the Toll, Notch, TGF-β, and FGFR signalling pathways, and several genes involved in the melanin biosynthetic pathway. We identified 14 genes that are up-regulated in both pierid spots and nymphalid eyespots and propose that spots and eyespots share regulatory modules despite their likely independent origins.