bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic age acceleration of cervical squamous cell carcinoma converged to human papillomavirus 16/18 expression, immunoactivation, and favourable prognosis
Authors: Lu Xiaofan , Zhou Yujie , Meng Jialin , Jiang Liyun , Gao Jun , Fan Xiaole , Chen Yanfeng , Cheng Yu , Wang Yang , Zhang Bing , Yan Hangyu , Yan Fangrong 
Published: February 2020

Abstract
Background
Ageing-associated molecular changes have been assumed to trigger malignant transformations and the epigenetic clock, and the DNA methylation age has been shown to be highly correlated with chronological age. However, the associations between the epigenetic clock and cervical squamous cell carcinoma (CSCC) prognosis, other molecular characteristics, and clinicopathological features have not been systematically investigated. To this end, we computed the DNA methylation (DNAm) age of 252 CSCC patients and 200 normal samples from TCGA and three external cohorts by using the Horvath clock model. We characterized the differences in human papillomavirus (HPV) 16/18 expression, pathway activity, genomic alteration, and chemosensitivity between two DNAm age subgroups. We then used Cox proportional hazards regression and restricted cubic spline (RCS) analysis to assess the prognostic value of epigenetic acceleration.

Results
DNAm age was significantly associated with chronological age, but it was differentiated between tumour and normal tissue (P < 0.001). Two DNAm age groups, i.e. DNAmAge-ACC and DNAmAge-DEC, were identified; the former had high expression of the E6/E7 oncoproteins of HPV16/18 (P < 0.05), an immunoactive phenotype (all FDRs < 0.05 in enrichment analysis), CpG island hypermethylation (P < 0.001), and lower mutation load (P = 0.011), including for TP53 (P = 0.002). When adjusted for chronological age and tumour stage, every 10-year increase in DNAm age was associated with a 12% decrease in fatality (HR 0.88, 95% CI 0.78–0.99, P = 0.03); DNAmAge-ACC had a 41% lower mortality risk and 47% lower progression rate than DNAmAge-DEC and was more likely to benefit from chemotherapy. RCS revealed a positive non-linear association between DNAm age and both mortality and progression risk (both, P < 0.05).

Conclusions
DNAm age is an independent predictor of CSCC prognosis. Better prognosis, overexpression of HPV E6/E7 oncoproteins, and higher enrichment of immune signatures were observed in DNAmAge-ACC tumours.
Myocardial perfusion reserve of kidney transplant patients is well preserved
Authors: Päivärinta Johanna , Metsärinne Kaj , Löyttyniemi Eliisa , Teuho Jarmo , Tolvanen Tuula , Knuuti Juhani , Koivuviita Niina 
Published: February 2020

Abstract
Background
Chronic kidney disease (CKD) is associated with endothelial dysfunction and increased cardiovascular mortality. Endothelial dysfunction can be studied measuring myocardial perfusion reserve (MPR). MPR is the ratio of stress and rest myocardial perfusion (MP) and reflects the capacity of vascular bed to increase perfusion and microvascular responsiveness. In this pilot study, our aim was to assess MPR of 19 patients with kidney transplant (CKD stages 2–3) and of ten healthy controls with quantitative [15O]H2O positron emission tomography (PET) method.

Results
Basal MP was statistically significantly higher at rest in the kidney transplant patients than in the healthy controls [1.3 (0.4) ml/min/g and 1.0 (0.2) ml/min/g, respectively, p = 0.0015]. After correction of basal MP by cardiac workload [MPcorr = basal MP/individual rate pressure product (RPP) × average RPP of the healthy controls], the difference between the groups disappeared [0.9 (0.2)  ml/min/g and 1.0 (0.3) ml/min/g, respectively, p = 0.55)]. There was no difference in stress MP between the kidney transplant patients and the healthy subjects [3.8 (1.0) ml/min/g and 4.0 (0.9) ml/min/g, respectively, p = 0.53]. Although MPR was reduced, MPRcorr (stress MP/basal MPcorr) did not differ between the kidney transplant patients and the healthy controls [4.1 (1.1) and 4.3 (1.6), respectively, p = 0.8].

Conclusions
MP during stress is preserved in kidney transplant patients with CKD stage 2–3. The reduced MPR appears to be explained by increased resting MP. This is likely linked with increased cardiac workload due to sympathetic overactivation in kidney transplant patients.
Effects of torrefied wood chip and vermicompost application on vegetation growth and nutrient uptake in the Saemangeum reclaimed land
Authors: Aung Aung , Seo Jeong Min , Han Si Ho , An Ji Young , Dao Huong Thi Thuy , Youn Woo Bin , Park Byung Bae 
Published: February 2020

Abstract
Background
In reclaimed land, the growth environment for plants may be unfavorable and the initial establishment and growth of seedlings could be limited because of low nutrient and water availability. Fertilization and control of understory vegetation that competes with seedlings may be of help in ameliorating soil physical and chemical properties, resulting in better seedling growth and reclamation success. However, the amount of nutrients understory vegetation absorbs in this ecological process has been rarely studied. Thus, we aimed to investigate the effect of soil amendment on biomass production and nutrient uptake by weeds in the nutrient-poor reclaimed area. We applied three levels of torrefied wood chip (TWC; 0, 2.5, and 5 Mg ha−1) and two levels of vermicompost (VC; 0 and 2.7 Mg ha−1) as soil physical improvements and organic soil amendments in reclaimed land in the Republic of Korea, with Populus euramericana used as the crop tree.

Results
TWC did not influence weed biomass, but 2.7 Mg ha−1 VC significantly increased weed biomass by 21% compared to 0 Mg ha−1 VC treatments. Nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sodium (Na) concentrations in weeds were the highest in control, but there was no statistical difference among treatments. However, VC treatment did marginally increase nutrient uptake in weeds, especially P, K, Ca, and Na. No treatments influenced crop tree height.

Conclusion
We conclude that VC can be used as an organic source of nutrients in reclaimed soil and that weed management is necessary to increase treatment effects on crop trees in this salt-affected reclaimed land.
Flexural Behavior of Circular Hollow RC Piers with Reduced Amounts of Inner Hoops
Authors: Li Zhong-Xian , Du Chun-yu , Liang Xiao , Zhao Bo 
Published: February 2020

AbstractReversed cyclic loading tests of two circular hollow RC piers were conducted in this study to investigate the effect of different amounts of inner and outer circular hoops on their flexural behavior. The test results showed that the column with a smaller amount of inner circular hoops presented better flexural response than the as-built column with an equal amount of inner and outer circular hoops. Also, the demand developed on the inner circular hoops was smaller than the outer one within the plastic hinge regions, which verified that using a smaller amount of inner circular hoops was reasonable and effective. By examining the confining stress experienced by the concrete in the radial and circumferential directions based on a detailed theoretical analysis, a modeling approach was proposed to take the confinement effect in circular hollow RC piers into consideration. The proposed modeling approach was validated through comparisons with the experimental study and satisfactory agreement was found.
Circulating basophil count as a prognostic marker of tumor aggressiveness and survival outcomes in colorectal cancer
Authors: Liu Qi , Luo Dakui , Cai Sanjun , Li Qingguo , Li Xinxiang 
Published: February 2020

AbstractBackgroundAccumulating evidence demonstrated immune/inflammation‐related implications of basophils in affecting tissue microenvironment that surrounded a tumor, and this study aimed to elucidate the clinical value of serum basophil count level.MethodsBetween December 2007 and September 2013, 1029 patients diagnosed with stage I–III CRC in Fudan University Shanghai Cancer Center meeting the essential criteria were identified. The Kaplan–Meier method was used to construct the survival curves. Several Cox proportional hazard models were constructed to assess the prognostic factors. A simple predictor (CB classifier) was generated by combining serum basophil count and serum carcinoembryonic antigen (CEA) level which had long been accepted as the most important and reliable prognostic factor in CRC.ResultsThe preoperative basophils count < 0.025*109/L was strongly associated with higher T stage, higher N stage, venous invasion, perineural invasion, elevated serum CEA level, and thus poor survival (P < 0.05). Moreover, multivariate Cox analysis showed that patients with low level of preoperative basophils count had an evidently poorer DFS [Hazard ratio (HR) = 2.197, 95% CI 1.868–2.585].ConclusionsAs a common immune/inflammation‐related biomarker available from the blood routine examination, low level of preoperative serum basophil count was associated with aggressive biology and indicated evidently poor survival. Preoperative serum basophil count would be a useful and simple marker for the management of CRC patients.
Glycated hemoglobin and glycated albumin in patients with diabetes undergoing hemodiafiltration
Authors: Kitajima Yukie , Urabe Shunichiro , Hosono Takashi , Yoshikawa Satoshi , Sato Yuzuru , Hyodo Toru 
Published: February 2020

Abstract
Background
Online hemodiafiltration (OHDF), which results in high albumin leakage, is now widely used in Japan for dialysis, since the national insurance system began reimbursing its costs in 2012. Glycated albumin (GA) levels are affected by albumin leakage into effluent dialysate fluid. Therefore, GA levels in patients requiring diabetes-related dialysis undergoing OHDF require monitoring. However, there have been no previous reports on glycemic control indicators of patients with diabetes undergoing OHDF. We aimed to develop a glycemic control index for patients requiring diabetes-related dialysis undergoing OHDF.

Methods
This study comprised 133 diabetic patients undergoing OHDF. We examined the correlation between GA and glycated hemoglobin (HbA1c) levels. We analyzed effluent dialysate fluid samples from 41 patients classified into 3 groups, namely, group A, non-protein-leaking OHDF (n = 20); group B, protein-leaking OHDF (n = 14); and group C, highly efficient protein-leaking OHDF (n = 7). We examined the association between GA and HbA1c levels in each group and among patients.

Results
A significant positive correlation was observed between GA and HbA1c levels (r = 0.562, p < 0.0001). There was no significant correlation between pre-dialysis blood glucose levels and HbA1c or GA levels as observed on regular blood tests performed under non-fasting conditions. Patients were classified into 2 groups based on their mean albumin levels (3.4 g/dL cutoff). The correlation between HbA1c and GA levels was found to be weaker in the 51 patients with mean albumin levels < 3.4 g/dL (r = 0.399, p = 0.0037) than in the 82 patients with mean albumin levels ≥ 3.4 g/dL (r = 0.674, p < 0.0001). When the hemodiafilter performance was assessed, no correlation was observed between HbA1c and GA levels in group C patients.

Conclusions
GA levels may be underestimated in patients undergoing OHDF because of the effect of albumin leakage into the effluent dialysate fluid. If a stable hemoglobin value can be maintained during OHDF therapy, then GA and HbA1c levels should be used as a glycemic control index for patients requiring diabetes-related dialysis, considering the dialysis treatment method and protein permeability of the dialyzers and hemodiafilters.
Breast ultrasound: automated or hand-held? Exploring patients’ experience and preference
Authors: Mussetto Ilaria , Gristina Licia , Schiaffino Simone , Tosto Simona , Raviola Edoardo , Calabrese Massimo 
Published: February 2020

Abstract
Background
Our aim was to compare women’s experience with automated breast ultrasound (ABUS) versus breast hand-held ultrasound (HHUS) and to evaluate their acceptance rate.

Methods
After ethical approval, from October 2017 to March 2018, 79 consecutive patients were enrolled in this prospective study. On the same day, patients underwent HHUS followed by ABUS. Each patient’s experience was assessed using the modified testing morbidities index (TMI) (the lower the score, the better is the experience). Nine items were assessed for both techniques: seven directly related to the examination technique (pain or discomfort immediately before (preparation), during and after testing, fear or anxiety immediately before (preparation) and during testing, physical and mental function after testing) and two indirectly related to the examination technique (embarrassment during testing and overall satisfaction). Finally, we asked patients to choose between the two techniques for a potential next breast examination. Wilcoxon signed ranks test was used.

Results
The median TMI score for the seven items was found to be significantly better for HHUS (8, interquartile range [IQR] 7–11) compared to ABUS (9, IQR 8–12) (p = 0.003). The item ‘pain/discomfort during the test’ (p < 0.001) was significantly higher for ABUS compared to HHUS. Instead, the item ‘fear/anxiety before the test’ was higher for HHUS (p = 0.001). Overall, 40.5% of the patients chose HHUS, 29.1% chose ABUS, and 30.4% were unable to choose.

Conclusions
ABUS and HHUS exams were well tolerated and accepted. However, HHUS was perceived to be less painful than ABUS.
The prevalence and the adding value of fetal MRI imaging in midline cerebral anomalies
Authors: Raafat Rehab M. E. , Abdelrahman Tamer M. , Hafez Mona A. F. 
Published: February 2020

Abstract
Background
Foetal MR imaging is widely accepted as an adjunct to foetal ultrasonography; however, there are many controversies regarding its importance and indications. Therefore, this study aimed to evaluate foetuses with different midline cerebral abnormalities, to determine the prevalence of these anomalies, to define the role of foetal MRI, and to compare MRI and ultrasound (US) result with postnatal MRI findings. Seventy-eight pregnant women who had foetuses with CNS abnormalities detected by sonogram were included. Foetuses with midline anomalies were selected and evaluated by anomaly scan foetal US, pre- and postnatal MRI.

Results
Midline brain anomalies were found in 47.4% of foetuses with brain anomalies. Holoprosencephaly was found in 24.3% of midline anomaly foetuses, corpus callosum abnormalities (ACC) were detected in 40.5%, midline intracranial mass lesions in 2.7%, and midline posterior fossa anomalies in 32.4%. An agreement between MRI and US in the main diagnosis was in 56.76% of cases; MRI added information to US findings in 43.2% of cases, and US added information to MRI findings in 8.1% of cases.

Conclusion
In evaluating midline cerebral anomalies, US and MRI are complementary techniques. US is the primary survey, and MRI can add additional information and/or change the main diagnosis.
Dynamic economic dispatch using hybrid metaheuristics
Authors: Santra Dipankar , Mukherjee Anirban , Sarker Krishna , Mondal Subrata 
Published: February 2020

AbstractDynamic economic dispatch problem or DED is an extension of static economic dispatch problem or SED which is used to determine the generation schedule of the committed units so as to meet the predicted load demand over a time horizon at minimum operating cost under ramp rate constraints and other constraints. This work presents an efficient hybrid method based on particle swarm optimization (PSO) and termite colony optimization (TCO) for solving DED problem. The hybrid method employs PSO for global search and TCO for local search in an interleaved mode towards finding the optimal solution. After the first round iteration of local search by TCO, the best local solutions are considered by PSO to update the schedules globally. In the next round, TCO performs local search around each solution found by PSO. This paper reports the methodology and result of application of PSO–TCO hybrid to 5-unit, 10-unit and 30-unit power dispatch problems; the result shows that the PSO–TCO (HPSTCO) gives improved solution compared to PSO or TCO (when applied separately) and also other hybrid methods.
The Rheb-TORC1 signaling axis functions as a developmental checkpoint
Authors: Duong Tam , Rasmussen Neal R. , Ballato Elliot , Mote F. Sefakor , Reiner David J. 
Published: February 2020

ABSTRACT
In many eukaryotes, the small GTPase Rheb functions as a switch to toggle activity of TOR complex 1 (TORC1) between anabolism and catabolism, thus controlling lifespan, development and autophagy. Our CRISPR-generated, fluorescently tagged endogenous Caenorhabditis elegans RHEB-1 and DAF-15/Raptor are expressed ubiquitously and localize to lysosomes. LET-363/TOR and DAF-15/Raptor are required for development beyond the third larval stage (L3). We observed that deletion of RHEB-1 similarly conferred L3 arrest. Unexpectedly, robust RNAi-mediated depletion of TORC1 components caused arrest at stages prior to L3. Accordingly, conditional depletion of endogenous DAF-15/Raptor in the soma revealed that TORC1 is required at each stage of the life cycle to progress to the next stage. Reversal of DAF-15 depletion permits arrested animals to recover to continue development. Our results are consistent with TORC1 functioning as a developmental checkpoint that governs the decision of the animal to progress through development.
Oxidative stress regulates progenitor behavior and cortical neurogenesis
Authors: Chui Angela , Zhang Qiangqiang , Dai Qi , Shi Song-Hai 
Published: February 2020

ABSTRACT
Orderly division of radial glial progenitors (RGPs) in the developing mammalian cerebral cortex generates deep and superficial layer neurons progressively. However, the mechanisms that control RGP behavior and precise neuronal output remain elusive. Here, we show that the oxidative stress level progressively increases in the developing mouse cortex and regulates RGP behavior and neurogenesis. As development proceeds, numerous gene pathways linked to reactive oxygen species (ROS) and oxidative stress exhibit drastic changes in RGPs. Selective removal of PRDM16, a transcriptional regulator highly expressed in RGPs, elevates ROS level and induces expression of oxidative stress-responsive genes. Coinciding with an enhanced level of oxidative stress, RGP behavior was altered, leading to abnormal deep and superficial layer neuron generation. Simultaneous expression of mitochondrially targeted catalase to reduce cellular ROS levels significantly suppresses cortical defects caused by PRDM16 removal. Together, these findings suggest that oxidative stress actively regulates RGP behavior to ensure proper neurogenesis in the mammalian cortex.
Rnd3 interacts with TAO kinases and contributes to mitotic cell rounding and spindle positioning
Authors: Garg Ritu , Koo Chuay-Yeng , Infante Elvira , Giacomini Caterina , Ridley Anne J. , Morris Jonathan D. H. 
Published: February 2020

ABSTRACT
Rnd3 is an atypical Rho family protein that is constitutively GTP bound, and acts on membranes to induce loss of actin stress fibers and cell rounding. Phosphorylation of Rnd3 promotes 14-3-3 binding and its relocation to the cytosol. Here, we show that Rnd3 binds to the thousand-and-one amino acid kinases TAOK1 and TAOK2 in vitro and in cells. TAOK1 and TAOK2 can phosphorylate serine residues 210, 218 and 240 near the C-terminus of Rnd3, and induce Rnd3 translocation from the plasma membrane to the cytosol. TAOKs are activated catalytically during mitosis and Rnd3 phosphorylation on serine 210 increases in dividing cells. Rnd3 depletion by RNAi inhibits mitotic cell rounding and spindle centralization, and delays breakdown of the intercellular bridge between two daughter cells. Our results show that TAOKs bind, phosphorylate and relocate Rnd3 to the cytosol and that Rnd3 contributes to mitotic cell rounding, spindle positioning and cytokinesis. Rnd3 can therefore participate in the regulation of early and late mitosis and may also act downstream of TAOKs to affect the cytoskeleton.
Rab10, Crag and Ehbp1 regulate the basolateral transport of Na+K+ATPase in Drosophila photoreceptors
Authors: Nakamura Yuri , Ochi Yuka , Satoh Takunori , Satoh Akiko K. 
Published: February 2020

ABSTRACT
Cells in situ are often polarized and have multiple plasma membrane domains. To establish and maintain these domains, polarized transport is essential, and its impairment results in genetic disorders. Nevertheless, the underlying mechanisms of polarized transport have not been elucidated. Drosophila photoreceptor offers an excellent model for studying this. We found that Rab10 impairment significantly reduced basolateral levels of Na+K+ATPase, mislocalizing it to the stalk membrane, which is a domain of the apical plasma membrane. Furthermore, the shrunken basolateral and the expanded stalk membranes were accompanied with abnormalities in the Golgi cisternae of Rab10-impaired retinas. The deficiencies of Rab10-GEF Crag or the Rab10 effector Ehbp1 phenocopied Rab10 deficiency, indicating that Crag, Rab10 and Ehbp1 work together for polarized trafficking of membrane proteins to the basolateral membrane. These phenotypes were similar to those seen upon deficiency of AP1 or clathrin, which are known to be involved in the basolateral transport in other systems. Additionally, Crag, Rab10 and Ehbp1 colocalized with AP1 and clathrin on the trans-side of Golgi stacks. Taken together, these results indicate that AP1 and clathrin, and Crag, Rab10 and Ehbp1 collaborate in polarized basolateral transport, presumably in the budding process in the trans-Golgi network.
High aerodynamic lift from the tail reduces drag in gliding raptors
Authors: Usherwood James R. , Cheney Jorn A. , Song Jialei , Windsor Shane P. , Stevenson Jonathan P. J. , Dierksheide Uwe , Nila Alex , Bomphrey Richard J. 
Published: February 2020

ABSTRACT
Many functions have been postulated for the aerodynamic role of the avian tail during steady-state flight. By analogy with conventional aircraft, the tail might provide passive pitch stability if it produced very low or negative lift. Alternatively, aeronautical principles might suggest strategies that allow the tail to reduce inviscid, induced drag: if the wings and tail act in different horizontal planes, they might benefit from biplane-like aerodynamics; if they act in the same plane, lift from the tail might compensate for lift lost over the fuselage (body), reducing induced drag with a more even downwash profile. However, textbook aeronautical principles should be applied with caution because birds have highly capable sensing and active control, presumably reducing the demand for passive aerodynamic stability, and, because of their small size and low flight speeds, operate at Reynolds numbers two orders of magnitude below those of light aircraft. Here, by tracking up to 20,000, 0.3 mm neutrally buoyant soap bubbles behind a gliding barn owl, tawny owl and goshawk, we found that downwash velocity due to the body/tail consistently exceeds that due to the wings. The downwash measured behind the centreline is quantitatively consistent with an alternative hypothesis: that of constant lift production per planform area, a requirement for minimizing viscous, profile drag. Gliding raptors use lift distributions that compromise both inviscid induced drag minimization and static pitch stability, instead adopting a strategy that reduces the viscous drag, which is of proportionately greater importance to lower Reynolds number fliers.