bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated bioinformatic analysis revealed biological processes and immune cells implicated in autoimmune hepatitis
Authors: Yu Kangkang , Yang Jingshu , Xie Wentao , Wu Feizhen , Wang Mei , Li Ning 
Published: February 2021

AbstractAutoimmune hepatitis (AIH) is an immune‐mediated inflammatory liver disease for which the pathogenesis remains incompletely understood. The current study aimed to reveal key biological processes and immune cells implicated in AIH by integrated bioinformatic analysis. The global gene expression in livers from wild‐type BALB/c mice, mice with Tgfb1 deficiency, and mice with both Tgfb1 and Ifng deficiency was assessed by microarray data analysis. Differentially expressed genes were identified and subjected to functional enrichment analysis. AIH mice with Tgfb1 deletion showed significantly enhanced immune responses but impaired metabolic processes, whereas increased T cell activation and cytokine production, but weakened organic acid and lipid metabolic processes were observed in mice with deletion of both Tgfb1 and Ifng. In addition, infiltration of immune cells was evaluated by CIBERSORT. Increased infiltration of T cells, macrophages, and natural killer cells, and decreased infiltration of neutrophils, eosinophils, plasma cells, and B cells were observed in AIH mice. In conclusion, we identified potential biological processes and immune cells that contributed to AIH; further investigations are needed to confirm these findings and thus provide a potential novel therapeutic target for AIH treatment.
The Pharmacology, Efficacy, and Safety of Rivaroxaban in Renally Impaired Patient Populations
Authors: Ashton Veronica , Kerolus‐Georgi Sylvia , Moore Kenneth T. 
Published: February 2021

AbstractRivaroxaban is a factor Xa inhibitor oral anticoagulant first approved for use in the United States in 2011. Under the drug class commonly termed direct oral anticoagulants, rivaroxaban is approved for the most indications within its class, 7 indications, which are: (1) reduction of risk of stroke and systemic embolism (SE) in nonvalvular atrial fibrillation, (2) treatment of deep vein thrombosis (DVT), (3) treatment of pulmonary embolism (PE), (4) reduction in the risk of recurrence of DVT and/or PE, (5) prophylaxis of DVT following hip or knee replacement surgery, (6) prophylaxis of venous thromboembolism in acutely ill medical patients at risk for thromboembolic complications not at high risk of bleeding, and (7) reduction of risk of major cardiovascular events in patients with chronic coronary artery disease or peripheral artery disease. Considering the relationship between cardiovascular disease, renal impairment, and the use of oral anticoagulants, the following targeted review was created. This review reports the results of the primary pharmacology, pharmacokinetic modeling, clinical safety and efficacy, and real‐world postmarketing effectiveness and safety of rivaroxaban in patients with various degrees of renal impairment. Based on these data, rivaroxaban is a viable option for when anticoagulation is needed in patients who have both cardiovascular disease and renal impairment. However, as with any therapy, the benefits and risks of intervention should be carefully assessed and balanced. Patients treated with rivaroxaban for several of its approved indications should have their kidney function assessed prior to and during continued therapy to ensure consistency with the drug label.
Preliminary assessment of viral metagenome from cancer tissue and blood from patients with lung adenocarcinoma
Authors: Cai Hua‐Zhong , Zhang Heteng , Yang Jie , Zeng Jian , Wang Hao 
Published: February 2021

AbstractIn this study, using a viral metagenomic method, we investigated the composition of virome in blood and cancer tissue samples that were collected from 25 patients with lung adenocarcinoma. Results indicated that virus sequences showing similarity to human pegivirus (HPgV), anellovirus, human endogenous retrovirus (HERV), and polyomavirus were recovered from this cohort. Three different complete genomes of HPgV were acquired from the blood samples and one complete genome of polyomavirus was determined from the cancer tissue sample. Phylogenetic analysis indicated that the three HPgV strains belonged to genotype 3 and the polyomavirus showed the highest sequence identity (99.73%) to trichodysplasia spinulosa‐associated polyomavirus. PCR screening results indicated that the three HPgVs were present in 5 out of the 25 blood samples and the polyomavirus only existed in a cancer tissue sample pool. Whether infections with viruses have an association with lung cancer needs further study with a larger size of sampling.
Exploring the relationship among dental caries, nutritional habits, and peri‐implantitis
Authors: Vilarrasa Javi , Peña Marta , Gumbau Laura , Monje Alberto , Nart José 
Published: February 2021

AbstractBackgroundA study was made of the prevalence, co‐occurrence and association among caries, nutritional habits, and peri‐implant disease, with an analysis of the influence of other patient and implant factors upon peri‐implant disease.MethodsThe included subjects underwent a clinical examination and were asked to complete a questionnaire. Demographic data and potential lifestyle/behavioral variables were collected. Clinical and radiographic assessment allowed calculation of the decayed, missing and filled teeth (DMFT) index and peri‐implant diagnosis. Uni‐ and multivariate multinomial logistic regression analyses were applied to identify predictors of peri‐implant disease.ResultsA total of 169 patients with 311 implants were studied. At patient level, 92.2% of the subjects presented at least one carious lesion, whereas 22.5% and 56.2% were diagnosed with peri‐implantitis and mucositis, respectively. Those patients with more than two caries had a higher risk of mucositis (OR = 3.33). Statistically significant associations for peri‐implantitis included full mouth periodontal indexes, sugar‐rich diets, keratinized mucosa width, number of missing teeth and interproximal untreated caries or fillings adjacent to implants.ConclusionHigh caries risk profiles and mucositis/peri‐implantitis tended to accumulate within subjects. A sugar‐enriched diet and untreated caries or fillings adjacent to implant sites may be further considered as risk indicators of peri‐implantitis.
High concentrations of sodium and chloride ions have opposing effects on the growth of the xerophyte Pugionium cornutum under saline conditions
Authors: Cui Yan-Nong , Wang Fang-Zhen , Yuan Jian-Zhen , Guo Huan , Wang Suo-Min , Ma Qing 
Published: February 2021

AbstractBackground: The research on plant salt tolerance has mainly focused on Na+, but Cl− has been relatively neglected. Previous studies have found that the xerophyte Pugionium cornutum, an important forage grass in the arid and semi‐arid regions of northwestern China, could synergistically accumulate high quintiles of Na+ and Cl− in its shoots under NaCl treatments. However, the separate effects of these ions on the adaptation of P. cornutum to saline conditions have not been investigated.Aims: In this study, the response of P. cornutum to Na+ and Cl− was analyzed.Methods: Four‐week‐old seedlings were treated with additional 50 mM NaCl, Na+‐specific solution containing 50 mM Na+ with a mix of
, H2
, and
as counter anions, and Cl−‐specific solution containing 50 mM Cl− with a mix of K+, Ca2+, and Mg2+ as counter cations.Results: Compared with the normal growth condition irrigated with Hoagland solution, the Na+‐specific solution severely impaired the growth and photosynthesis of P. cornutum due to the high accumulation of Na+ in shoots and the deterioration of tissue K+ homeostasis; while the Cl−‐specific solution significantly increased shoot fresh and dry biomass. The Cl−‐specific solution could also increase the turgor pressure in leaves for enhancing osmotic adjustment, which should be mainly attributed to the large accumulation of Cl−, since the concentrations of other ions, including K+, Mg2+, Ca2+, H2
, and
, in tissues under Cl−‐specific treatment were maintained at the same levels as those observed under the normal condition.Conclusions: P. cornutum displays an excellent tolerance to moderate Cl− but not to Na+, and the large accumulation of Cl− should play a positive role in stimulating the growth of P. cornutum under salt stress.
Incidence and Prognosis of Brain Metastases in Head and Neck Cancer Patients at Diagnosis
Authors: Messing Ian , Goyal Sharad , Sherman Jonathan H. , Thakkar Punam , Siegel Robert , Joshi Arjun , Goodman Joseph , Ojong‐Ntui Martin , Rao Yuan James 
Published: February 2021

ObjectivesLimited data is available on head and neck cancer (HNC) patients presenting with brain metastases (BM) at initial diagnosis. We sought to evaluate the incidence, management, and treatment outcomes of these patients using the National Cancer Database (NCDB).MethodsWe identified 465,925 patients diagnosed with HNC between 2010 and 2015 in the NCDB. 14,583 of these patients presented with metastatic disease to any site. 440 of these patients had BM at the time of initial diagnosis. Overall survival was compared using the Kaplan–Meier method. Cox proportional hazard modeling, propensity score matching, and subgroup analyses were performed.ResultsThe median age overall was 62.0 years. Nasopharynx NOS (13.2%) and Parotid Gland (10.9%) were the most common anatomical sites with the highest frequency of BM. The overall median survival time was 7.1 months. Predictors for the presence of BM included distant metastasis to the bone, liver, or lung on univariate analysis, and bone or lung on multivariate analysis. High‐risk Human Papilloma Virus status was associated with a lower chance of BM. No pattern was determined when comparing lymph node level involvement and BM. The median survival for patients receiving radiation therapy and multi‐agent chemotherapy was 8.4 and 11.7 months, respectively. Immunotherapy administered as first course therapy did not influence median survival. Most patients received radiation (62.7%) therapy and chemotherapy (50.2%).ConclusionsThe data extracted and analyzed from the NCDB should work to aid in the surveillance and management of BM in patients with HNC.Level of Evidence4 Laryngoscope, 131:E2543–E2552, 2021
Submarine groundwater discharge drives nitrous oxide source/sink dynamics in a metropolitan estuary
Authors: Reading Michael J. , Tait Douglas R. , Maher Damien T. , Jeffrey Luke C. , Correa Rogger E. , Tucker James P. , Shishaye Haile A. , Santos Isaac R. 
Published: February 2021

AbstractCoastal waterways can be significant sources of the potent greenhouse gas nitrous oxide (N2O) due to nitrogen inputs and eutrophication. Here, we quantify groundwater derived N2O inputs and atmospheric emissions within a modified urban embayment (Sydney Harbour, Australia). Overall, we found low N2O saturation (91–171%) and air–water fluxes (−2.2 to 24.6 μmol m−2 d−1). Concentrations were highest in upstream brackish areas and a commercial/industrial subembayment. Dissolved inorganic nitrogen concentrations were low and inversely correlated to N2O throughout the harbor. N2O surface water dynamics were apparently driven by saline submarine groundwater discharge, as quantified by the radioisotope tracer radon‐222. Groundwater discharge was highest within the embayments and mangrove‐lined upper estuary. While groundwater was a net N2O source to surface waters, two upstream sub‐embayments featured groundwater N2O concentrations lower than surface water, suggesting a sink driven by surface waters recirculating in intertidal sediments. Surface‐water N2O was undersaturated within one upstream embayment, likely due to N2O consumption within sediments. Contrastingly, the downstream embayments featured higher groundwater N2O and accounted for 45% ± 21% of the groundwater N2O flux. Sydney Harbour was a net source of N2O to the atmosphere (mean 0.6 ± 0.3 μmol m−2 d−1) with larger N2O fluxes occurring from relatively small areas. N2O emissions (expressed in CO2 equilivents) were equivalent to 17% of CO2 emission estimates from previous studies. The low N2O emissions in Sydney Harbour contrast with other modified estuaries which often emit higher N2O fluxes due to larger nitrogen inputs.
XPM‐Induced Vector Asymmetrical Soliton with Spectral Period Doubling in Mode‐Locked Fiber Laser
Authors: Cui Yudong , Zhang Yusheng , Song Youjian , Huang Lin , Tong Limin , Qiu Jianrong , Liu Xueming 
Published: February 2021

AbstractCross phase modulation (XPM) can induce soliton trapping in nonlinear medium, which has been employed to achieve vector soliton, optical switching, and optical analog of gravity‐like potentials. Here, the first observation of a novel soliton operation is reported whose wavelength exhibits redshift and blueshift periodically in a mode‐locked fiber laser under appropriate birefringence and dispersion map. XPM dominates the dynamics by inducing and sustaining the vector asymmetrical soliton (VAS) with spectral period doubling, and exhibits a unique trajectory of pulse trapping. The XPM‐induced VAS is an idiosyncratic steady state featured with asymmetry in the model based on the coupled Ginzburg–Landau equation, which depicts the distinct pulse features in comparison with vector soliton, soliton molecule, and traditional period‐doubling evolutions. The two orthogonal polarized directions of mode‐locked fiber laser can be regarded as the XPM‐coupled dissipative resonators guiding the further study of the optical nonlinear dynamics and chaos for soliton, which is helpful to laser design and brings useful insights into nonlinear science and applications.
Gut Microbial and Metabolic Profiling Reveal the Lingering Effects of Infantile Iron Deficiency Unless Treated with Iron
Authors: Mayneris‐Perxachs Jordi , Amaral Wellington , Lubach Gabriele R. , Lyte Mark , Phillips Gregory J. , Posma Joram M. , Coe Christopher L. , Swann Jonathan R. 
Published: February 2021

ScopeIron deficiency (ID) compromises the health of infants worldwide. Although readily treated with iron, concerns remain about the persistence of some effects. Metabolic and gut microbial consequences of infantile ID were investigated in juvenile monkeys after natural recovery (pID) from iron deficiency or post‐treatment with iron dextran and B vitamins (pID+Fe).Methods and ResultsMetabolomic profiling of urine and plasma is conducted with 1H nuclear magnetic resonance (NMR) spectroscopy. Gut microbiota are characterized from rectal swabs by amplicon sequencing of the 16S rRNA gene. Urinary metabolic profiles of pID monkeys significantly differed from pID+Fe and continuously iron‐sufficient controls (IS) with higher maltose and lower amounts of microbial‐derived metabolites. Persistent differences in energy metabolism are apparent from the plasma metabolic phenotypes with greater reliance on anaerobic glycolysis in pID monkeys. Microbial profiling indicated higher abundances of Methanobrevibacter, Lachnobacterium, and Ruminococcus in pID monkeys and any history of ID resulted in a lower Prevotella abundance compared to the IS controls.ConclusionsLingering metabolic and microbial effects are found after natural recovery from ID. These long‐term biochemical derangements are not present in the pID+Fe animals emphasizing the importance of the early detection and treatment of early‐life ID to ameliorate its chronic metabolic effects.
Lean Thinking to manage a national working group on physics aspects of Stereotactic Body Radiation Therapy
Authors: Mancosu Pietro , Russo Serenella , Antonucci Adriana Rossella , Stasi Michele 
Published: February 2021

PurposeTo report how the adoption of a Lean Thinking mindset in the management of a national working group (WG) on the physics of stereotactic body radiation therapy (SBRT) contributed to achieve SBRT standardization objectives.MethodsVision for the WG has been established as fragmentation reduction and process harmonization enhancement in SBRT for Italian centers. Two main research themes of the technical aspects of SBRT emerged as areas with major standardization improvement needs, small field dosimetry and SBRT planning comparisons, to be investigated through multi‐institutional studies. The management of the WG leveraged on the Lean concept of fostering self‐organization in a non‐hierarchical environment. Four progressive involvement levels were defined for each study. No specific “scientific” pre‐experience was required to propose and coordinate a project, just requiring a voluntary commitment. People engagement was measured in terms of number of published articles. The standardization goals have been conducted through a simplified “5S” (Sort, Set in Order, Shine, Standardize, and Sustain) methodology, first considering a phase of awareness (the first three “S”), then identifying and implementing standardization actions (the last two “S”).ResultsSince the beginning, 157 medical physicists joined the AIFM/SBRT‐WG. Twenty‐four papers/reviews/letters have been published in the period 2014–2019 on major radiation oncology journals, authored by >100 physicists (>50% working in small hospitals). Six over 12 first authors worked in peripheral/small hospitals, with no prior publication as first author. These studies contributed to the awareness and standardization phases for both small‐field dosimetry and planning. In particular, errors in small‐field measurements in 8% of centers were detected thanks to a generalized output factor curve in function of the effective field size created by averaging data available from different Linacs. Furthermore, planner’s experience in SBRT was correlated with dosimetric parameters in the awareness phase; while sharing median dose volume histograms (DVHs) reduced variability among centers while keeping the same level of plan complexity. Finally, all the dosimetric parameters statistically significant to the planner experience during the awareness phase, were no longer significantly different in the standardization phase.ConclusionsThe experience of our SBRT‐WG has shown how a Lean Thinking mindset could foster the SBRT procedure standardization and spread the physics of SBRT knowledge, enhancing personal growth. Our expectation is to inspire other scientific societies that have to deal with fragmented contexts or pursue processes harmonization through Lean principles.
Modularized data‐driven reconstruction framework for nonideal focal spot effect elimination in computed tomography
Authors: Zhang Zhicheng , Yu Lequan , Zhao Wei , Xing Lei 
Published: February 2021

PurposeHigh‐performance computed tomography (CT) plays a vital role in clinical decision‐making. However, the performance of CT imaging is adversely affected by the nonideal focal spot size of the x‐ray source or degraded by an enlarged focal spot size due to aging. In this work, we aim to develop a deep learning‐based strategy to mitigate the problem so that high spatial resolution CT images can be obtained even in the case of a nonideal x‐ray source.MethodsTo reconstruct high‐quality CT images from blurred sinograms via joint image and sinogram learning, a cross‐domain hybrid model is formulated via deep learning into a modularized data‐driven reconstruction (MDR) framework. The proposed MDR framework comprises several blocks, and all the blocks share the same network architecture and network parameters. In essence, each block utilizes two sub‐models to generate an estimated blur kernel and a high‐quality CT image simultaneously. In this way, our framework generates not only a final high‐quality CT image but also a series of intermediate images with gradually improved anatomical details, enhancing the visual perception for clinicians through the dynamic process. We used simulated training datasets to train our model in an end‐to‐end manner and tested our model on both simulated and realistic experimental datasets.ResultsOn the simulated testing datasets, our approach increases the information fidelity criterion (IFC) by up to 34.2%, the universal quality index (UQI) by up to 20.3%, the signal‐to‐noise (SNR) by up to 6.7%, and reduces the root mean square error (RMSE) by up to 10.5% as compared with FBP. Compared with the iterative deconvolution method (NSM), MDR increases IFC by up to 24.7%, UQI by up to 16.7%, SNR by up to 6.0%, and reduces RMSE by up to 9.4%. In the modulation transfer function (MTF) experiment, our method improves the MTF50% by 34.5% and MTF10% by 18.7% as compared with FBP, Similarly remarkably, our method improves MTF50% by 14.3% and MTF10% by 0.9% as compared with NSM. Also, our method shows better imaging results in the edge of bony structures and other tiny structures in the experiments using phantom consisting of ham and a bottle of peanuts.ConclusionsA modularized data‐driven CT reconstruction framework is established to mitigate the blurring effect caused by a nonideal x‐ray source with relatively large focal spot. The proposed method enables us to obtain high‐resolution images with less ideal x‐ray source.
NMR visibility of deuterium‐labeled liver glycogen in vivo
Authors: De Feyter Henk M. , Thomas Monique A. , Behar Kevin L. , de Graaf Robin A. 
Published: February 2021

PurposeDeuterium metabolic imaging (DMI) combined with [6,6’‐2H2]‐glucose has the potential to detect glycogen synthesis in the liver. However, the similar chemical shifts of [6,6’‐2H2]‐glucose and [6,6’‐2H2]‐glycogen in the 2H NMR spectrum make unambiguous detection and separation difficult in vivo, in contrast to comparable approaches using 13C MRS. Here the NMR visibility of 2H‐labeled glycogen is investigated to better understand its potential contribution to the observed signal in liver following administration of [6,6’‐2H2]‐glucose.MethodsMice were provided drinking water containing 2H‐labeled glucose. High‐resolution NMR analyses was performed of isolated liver glycogen in solution, before and after the addition of the glucose‐releasing enzyme amyloglucosidase.Results2H‐labeled glycogen was barely detectable in solution using 2H NMR because of the very short T2 (<2 ms) of 2H‐labeled glycogen, giving a spectral line width that is more than five times as broad as that of 13C‐labeled glycogen (T2 = ~10 ms).Conclusion2H‐labeled glycogen is not detectable with 2H MRS(I) under in vivo conditions, leaving 13C MRS as the preferred technique for in vivo detection of glycogen.