bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic brain tissue segmentation in MR images using hybrid atlas forest based on confidence‐weighted probability matrix
Authors: Xu Lijun , Liu Hong , Song Enmin , Jin Renchao , Hung Chih‐Cheng 
Published: December 2018

AbstractThe segmentation of specific tissues in an MR brain image for quantitative analysis can assist the disease diagnosis and medical research. Therefore, a robust and accurate method for automatic segmentation is necessary. Atlas‐based‐method is a common and effective method of automatic segmentation where an atlas refers to a pair of image consist of an intensity image and its corresponding label image. Apart from the general multi‐atlas‐based methods, which propagate labels through the single atlas then fuse them, we proposed a hybrid atlas forest based on confidence‐weighted probability matrix to consider the atlases set as a whole and treat each voxel differently. In the framework, we first register the atlas to the image space of target and calculate the confidence of voxels in the registered atlas. Then, a confidence‐weighted probability matrix is generated and it augments to the intensity image of the atlas or target for providing spatial information of the target tissue. Third, a hybrid atlas forest is trained to gather the features and correlation information among the atlases in the dataset. Finally, the segmentation of the target tissues is predicted by the trained hybrid atlas forest. The segment performance and the components efficiency of the proposed method are evaluated on the two public datasets. Based on the experiment results and quantitative comparisons, our method can gather spatial information and correlation among the atlases to obtain an accurate segmentation.
Vitamin E: Regulatory role of metabolites
Authors: Birringer Marc , Lorkowski Stefan 
Published: December 2018

AbstractVitamin E plays an important role as a lipophilic antioxidant in cellular redox homeostasis. Besides this function, numerous non‐antioxidant properties of this vitamin have been discovered in the past. DNA microarray technology revealed a complex regulatory network influenced by the different vitamin E forms (Rimbach et al., Molecules, 15, 1746 (2010); Galli et al., Free Radic. Biol. Med., 102, 16 (2017)); however, little is known about the biological activity of vitamin E metabolites. A new chapter of vitamin E research was been opened when endogenous long‐chain tocopherol metabolites were identified and their high biological activity in vitro and in vivo was recognized (Schmölz et al., World J. Biol. Chem., 7, 14 (2016); Torquato et al., J. Pharm. Biomed. Anal., 124, 399 (2016)). Just recently, it was shown that an endogenous metabolite of vitamin E inhibits 5‐lipoxygenase at nanomolar concentrations, thereby limiting inflammation (Pein et al., Nat. Commun., 9, 3834 (2018)). Furthermore, long‐chain vitamin E metabolites (LCM) exhibit hormone‐like activities similar to the lipid soluble vitamins A and D (Galli et al., Free Radic. Biol. Med., 102, 16 (2017); Schubert et al., Antioxidants, 7 (2018)). This review aims at summarizing recent findings on the regulatory activities of vitamin E metabolites, especially of LCMs. © 2018 IUBMB Life, 71(4):479–486, 2019
New paradigm of functional regulation by DNA mimic proteins: Recent updates
Authors: Wang Hao‐Ching , Chou Chia‐Cheng , Hsu Kai‐Cheng , Lee Chi‐Hua , Wang Andrew H.‐J. 
Published: December 2018

AbstractFor many, “DNA mimic protein” (DMP) remains an unfamiliar term. The key feature of these proteins is their DNA‐like shape and charge distribution, and they affect the activity of DNA‐binding proteins by occupying their DNA‐binding domains. Functionally, DMPs regulate mechanisms such as gene expression, restriction, and DNA repair as well as the nucleosome package. Although a few DMPs, such as phage uracil DNA glycosylase inhibitor (UGI) and overcome classical restriction (Ocr), were reported about 20 years ago, only a small number of DMPs have been studied to date. In 2014, we reviewed the functional and structural features of 16 DMPs that were known at the time. Now, seven new DMPs, namely anti‐CRISPR suppressors AcrF2, AcrF10 and AcrIIA4, human immunodeficiency virus essential factor VPR, multi‐functional inhibitor anti‐restriction nuclease (Arn), translational regulator AbbA, and putative Z‐DNA mimic MBD3, have been reported. In addition, further study of two previously known DMPs, DMP19 and SAUGI, increased our knowledge of their importance and function. Here, we discuss these updated results and address how several characteristics of the structure/sequence of DMPs (e.g. the DNA‐like charge distribution and structural D/E‐rich repeats) might someday be used to identify new DMPs using bioinformatic approach. © 2018 IUBMB Life, 71(5):539–548, 2019
Dual‐modality optical projection tomography reconstruction method from fewer views
Authors: Dou Shaobin , Liu Jinhuai , Yang Lianghuai 
Published: December 2018

In optical projection tomography (OPT), for longitudinal living model studies, multiple measurements of the same sample are required at different time points. It is important to decrease both the total acquisition time and the light dose to the sample. We improved the ordered subsets expectation maximization reconstruction algorithm for OPT, which reduces the acquisition time and number of projections greatly compared with filtered back projection (FBP), and obtained satisfactory reconstructed images. Using zebrafish, in transmission and fluorescence mode, we demonstrate the capability of the method to reconstruct image from downsampled projection subsets. The result shows that the reconstruction image quality of the proposed method using 30 projections is comparable to that of FBP using 720 projections. The total acquisition procedure can be finished in a few seconds. The method also provides OPT with the remarkable capability to resist noises and artifacts.Projection image and fused image of zebrafish.
Time‐dependent diffusion MRI to distinguish malignant from benign head and neck tumors
Authors: Iima Mami , Yamamoto Akira , Kataoka Masako , Yamada Yosuke , Omori Koichi , Feiweier Thorsten , Togashi Kaori 
Published: December 2018

BackgroundThere is growing interest in the effect of diffusion time on apparent diffusion coefficient (ADC) values in cancers; however, little evidence exists regarding its utility to differentiate malignant from benign head and neck tumors.PurposeTo investigate the utility of ADC value changes in distinguishing between malignant and benign head and neck tumors using the different diffusion times obtained from oscillating gradient spin‐echo (OGSE) and pulsed gradient spin‐echo (PGSE) MRI sequences.Study TypeProspective.SubjectsThirty‐one consecutive patients with suspected head and neck tumors and a phantom.Field Strength/Sequence3T MRI with diffusion‐weighted imaging (DWI) using OGSE (effective diffusion time: 4.3 msec) and PGSE (effective diffusion time: 82.6 msec) sequences and b‐values of 0 and 700 s/mm2.AssessmentADC values using OGSE (ADCOGSE) and PGSE (ADCPGSE) and relative ADC value changes between ADCOGSE and ADCPGSE.Statistical TestsWilcoxon test, Mann–Whitney test, and McNemar test.ResultsRelative ADC changes for each polyvinylpyrrolidone (PVP) and water in the phantom between OGSE and PGSE sequences were small (relative ADC change within 0.6%). Malignant tumors had significantly smaller ADCOGSE and ADCPGSE values than benign tumors (P < 0.001 and < 0.0001, respectively). Significantly larger relative ADC changes were observed in malignant compared with benign head and neck tumors (P < 0.0001). ADCPGSE values were significantly lower than ADCOGSE values in both malignant and benign head and neck tumors (0.97 vs. 1.28 × 10−3mm2/s: P < 0.0001 and 1.93 vs. 1.99 × 10−3mm2/s: P = 0.0056, respectively). Relative ADC change and ADCPGSE tended to have higher diagnostic performance than ADCOGSE, with area under the curve (AUC) values of 0.97, 0.96, and 0.89, respectively.Data ConclusionADC values obtained using the PGSE sequence were lower than those obtained with OGSE. This difference was larger for malignant than benign tumors, suggesting differences in tissue structure (diffusion hindrance) or cell permeability, revealed by changes in diffusion time. The results underline the potential importance of reporting diffusion time for interpretation of head and neck diffusion MRI.Level of Evidence: 1Technical Efficacy: Stage 2J. Magn. Reson. Imaging 2019;50:88–95.
Serum 25(OH)D is associated with an altered bone turnover marker response after a hip fracture
Authors: Stewart Christopher C. , O'Hara Nathan N. , Orwig Denise , Hochberg Marc C. , Sprague Sheila , Magaziner Jay , Slobogean Gerard P. 
Published: December 2018

ABSTRACTC‐terminal telopeptide of type I collagen (CTX) and procollagen type 1 N‐terminal propeptide (P1NP) are bone turnover markers (BTMs) that are promising surrogate measures of fracture healing; however, it is unknown if their response is affected by other bone healing metabolites. Since 70% of fracture patients are reported to have insufficient serum vitamin D, we sought to determine if serum 25(OH)D levels are associated with differential changes in CTX and P1NP concentrations after hip fracture. This prospective cohort included hip fracture patients 65 years of age or older admitted to one of eight Baltimore‐area hospitals. Serum samples were collected at baseline, 2‐, 6‐, and 12‐month post‐fracture. A mixed‐effects repeated‐measures analysis was used to determine the longitudinal association between vitamin D deficiency (25(OH)D < 20 ng/ml) and CTX and P1NP. Baseline lab values were obtained for 296 participants (mean age, 80.8 years; 51% male; 55% 25(OH)D < 20 ng/ml). During the acute fracture healing period P1NP concentrations increased by 14% (95%CI: 7–21%, p < 0.01) while CTX levels did not change (p = 0.07). Both CTX and P1NP decreased below baseline at 6 and 12 months. CTX levels were higher in participants with baseline 25(OH)D < 20 ng/ml (p = 0.01). There was no association between 25(OH)D < 20 ng/ml and P1NP levels over the study duration (p = 0.33). Data from this large, longitudinal cohort support claims that CTX and P1NP concentrations change during fracture healing; however, the differential response of CTX among vitamin D deficient patients highlights important questions for its utility as a reliable surrogate marker of fracture healing. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res
Genetic modification of scAAV‐equine‐BMP‐2 transduced bone‐marrow‐derived mesenchymal stem cells before and after cryopreservation: An “off‐the‐shelf” option for fracture repair
Authors: Ball Alyssa N. , Phillips Jennifer N. , McIlwraith C. Wayne , Kawcak Christopher E. , Samulski Richard J. , Goodrich Laurie R. 
Published: December 2018

ABSTRACTOptimizing the environment of complex bone healing and improving treatment of catastrophic bone fractures and segmental bone defects remains an unmet clinical need both human and equine veterinary medical orthopaedics. The objective of this study was to determine whether scAAV‐equine‐BMP‐2 transduced cells would induce osteogenesis in equine bone marrow derived mesenchymal stem cells (BMDMSCs) in vitro, and if these cells could be cryopreserved in an effort to osteogenically prime them as an “off‐the‐shelf” gene therapeutic approach for fracture repair. Our study found that transgene expression is altered by cell expansion, as would be expected by a transduction resulting in episomal transgene expression, and that osteoinductive levels could still be achieved 5 days after recovery, and protein expression would continue up to 14 days after transduction. This is the first evidence that cryopreservation of genetically modified BMDMSCs would not alter the osteoinductive potential or clinical use of allogeneic donor cells in cases of equine fracture repair. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:1310–1317, 2019.
Buccal bone thickness adjacent to virtual dental implants following guided bone regeneration
Authors: Phillips Daniel J. , Swenson Dane T. , Johnson Thomas M. 
Published: December 2018

AbstractBackgroundCrestal bone thickness is a critical determinant of peri‐implant tissue stability. This retrospective observational study sought to quantify the buccal bone thickness achieved adjacent to virtual dental implants following guided bone regeneration (GBR) surgery and evaluate the influence of patient‐ and procedure‐related variables on buccal bone thickness.MethodsCone‐beam computed tomography (CBCT) images acquired from patients who had undergone GBR surgery between July 1, 2012, and November 7, 2016, were used for this analysis. In all cases, the GBR procedure involved a dense polytetrafluoroethylene (dPTFE) barrier membrane and a mineralized cortical particulate freeze‐dried bone allograft (FDBA). Eighty‐four virtual dental implants were placed at planned locations using CBCT images from 84 patients, and the adjacent buccal bone thickness was measured at each site. The effects of sex, age, estimated baseline ridge width, number of missing teeth in site, site type (tooth‐bounded versus terminal position in arch), dental arch (mandibular or maxillary), arch location (anterior or posterior), smoking status, titanium reinforcement in the membrane, membrane fixation, and tenting screw use were assessed.ResultsThe mean post‐GBR buccal bone thickness adjacent to virtual dental implants was 2.24 ± 1.01 mm. Fifty‐nine of 84 virtual implants (70%) exhibited buccal bone thickness > 1.9 mm. GBR sites using membrane fixation produced significantly greater virtual implant buccal bone thickness than those without membrane fixation (2.31 ± 0.96 versus 1.15 ± 1.25 mm, P = 0.012). Virtual implant buccal bone thickness also exhibited moderate correlation with estimated initial ridge width (r = 0.43, P < 0.0001). The alveolar ridge at 81 virtual implant sites (96%) was classified as good or satisfactory, meaning dental implants were actually placed at these sites, with or without additional grafting at implant placement.ConclusionsObservations in this study suggest GBR procedures using dPTFE membranes and FDBA result in favorable ridge dimensions for dental implant placement in most cases. However, additional augmentation at implant surgery may be necessary at ≈ 30% of sites, if buccal bone thickness > 1.9 mm is intended.
Effect of Texel crossbreeding on productive traits, carcass and meat quality of Segureña lambs
Authors: Blasco Miguel , Campo María M , Balado Javier , Sañudo Carlos 
Published: December 2018

AbstractBACKGROUNDThe present study aimed to assess the effect of crossbreeding a local breed (Segureña, S × S) with Texel as the sire line (Texel × Segureña crossbred, T × S) on productive traits and meat quality attributes. Sixty‐eight lambs (both males and females) from each genotype, weaned at about 45 days old and intensively fed with concentrates and cereal straw ad libitum until they were 72 days old, were used to assess productive traits, and ten animals from each genotype were used to assess meat quality.RESULTSThe crossbreeding with Texel improves productivity, with a greater weight at birth (+1 kg) and at slaughter (+3 kg) and a greater average daily gain (+29 g). T × S lambs had a better conformation, less carcass fatness, and higher content of muscle (+45 g kg−1) as opposed to a lower fat content (−50.6 g kg−1). With regard to meat quality, crossbreeding with Texel provided a meat with a higher protein content (+4 g kg−1) and a lower oleic acid content (21% less), although the differences were very scarce from a sensory point of view, and non‐existent with respect to instrumental quality.CONCLUSIONCrossbreeding could comprise a useful tool in the production of ovine meat in local breeds, such as Segureña, within the Mediterranean Area, and, consequently, a way of increasing the profitability of the farms. © 2018 Society of Chemical Industry
Synergistic effect of natural antifungal agents for postharvest diseases of blackberry fruits
Authors: Liu Hongxia , Zhao Huifang , Lyu Lianfei , Huang Zhengjin , Fan Sufan , Wu Wenlong , Li Weilin 
Published: December 2018

AbstractBACKGROUNDBlackberry postharvest diseases are caused by fungal pathogens, and treatment of fruits with edible, natural products could reduce the postharvest losses and contribute to food sustainability. Based on the hypothesis that inhibition of fungal pathogens will significantly extend the shelf‐life of food products, the effects of natural antifungal agents on fungal pathogens were tested.RESULTSTwo pathogenic fungal isolates, Aspergillus japonicus and Gilbertella persicaria, from infected blackberry fruits were identified morphologically using scanning electron microscopy and confirmed by DNA sequence analysis. The inhibitory effects and synergistic action of natural antifungal agents against the two fungal isolates were investigated. The results obtained demonstrated that the natamycin, chitosan and ferulic acid exhibited significant antifungal activities against the tested strains based on the calculated minimum inhibitory concentration. The best antifungal activity was obtained using a combination of ferulic acid and natamycin, which generated a total synergistic effect on both tested strains with a fractional inhibitory concentration index of 0.281. Application of the selected agents on postharvest blackberry fruits reduced the rot ratio and weight loss and also increased fruit firmness. In addition, the shelf‐life of fresh blackberry fruits was extended up to 12–15 days at 4 °C and 90 ± 5% relative humidity.CONCLUSIONThe combined utilization of ferulic acid and natamycin showed synergistic antifungal activity against two pathogenic fungal isolates, and extended the shelf life of fresh blackberry fruits up to 12–15 days. © 2018 Society of Chemical Industry
Construct validity of a low‐cost medium‐fidelity endoscopic sinus surgery simulation model
Authors: Yoshiyasu Yuki , Chang Daniel R. , Bunegin Leon , Lin Ryan P. , Aden James K. , Prihoda Thomas J. , Weitzel Erik K. , McMains Kevin C. , Malekzadeh Sonya , Bowe Sarah N. , Chen Philip G. 
Published: December 2018

ObjectiveAssess construct validity of a low‐cost medium‐fidelity silicone injection molded model task trainer for endoscopic sinus surgery (ESS) training.MethodsFellowship‐trained rhinologists, otolaryngology attendings, and otolaryngology residents at various levels of training performed sinus endoscopy and seven procedures on the model. Construct validity was evaluated by comparing novice to various levels of experienced performance using a validated checklist.ResultsThirty‐two subjects participated in this study. Otolaryngology attendings and postgraduate year (PGY) 3 to 5 otolaryngology residents significantly outperformed PGY 1 to 2 otolaryngology residents on most tasks in the task‐specific checklist.ConclusionsThis study demonstrated the construct validity of the low‐cost medium‐fidelity ESS model.Level of EvidenceNALaryngoscope, 129:1505–1509, 2019
Evaluation of spin in the abstracts of otolaryngology randomized controlled trials
Authors: Cooper Craig M. , Gray Harrison M. , Ross Andrew E. , Hamilton Tom A. , Bea Downs Jaye , Wayant Cole , Vassar Matt 
Published: December 2018

ObjectiveSpin, the misrepresentation and distortion of research findings, has been shown to affect clinical decision making. Spin has been found in randomized controlled trials (RCTs) published in various fields of medicine, but no study has tested for the presence of spin in otolaryngology RCTs. The purpose of this study is to evaluate the abstracts of RCTs found in the otolaryngology literature for spin.MethodsIn this cross‐sectional analysis, we analyzed the abstracts of RCTs for spin using a pilot‐tested form. Double data extraction was performed by two blinded authors, and discrepancies were resolved using mutual discussion.ResultsOut of the 534 PubMed citations retrieved by our search string, 162 parallel‐group RCTs with clearly defined primary and secondary endpoints were identified. Further analysis identified 47 trials with nonsignificant primary outcomes, which were then evaluated for spin. Spin was identified in 33 of the 47 (70%) abstracts. Spin was found in the results sections of 25 (53%) of the included abstracts and was found in the conclusion section of 27 (57%) of the abstracts. Spin was not present in the titles of any of the included studies.ConclusionSpin was common in our sample of otolaryngology RCTs. Spin may potentially create false impressions about the true validity of a drug or intervention. Further research needs to test for potential clinical implications of spin in the otolaryngology literature.Level of EvidenceNALaryngoscope, 129:2036–2040, 2019
Naringenin Supplementation to a Chow Diet Enhances Energy Expenditure and Fatty Acid Oxidation, and Reduces Adiposity in Lean, Pair‐Fed Ldlr−/− Mice
Authors: Burke Amy C. , Telford Dawn E. , Edwards Jane Y. , Sutherland Brian G. , Sawyez Cynthia G. , Huff Murray W. 
Published: December 2018

ScopeNaringenin is a citrus‐derived flavonoid that has potent lipid‐lowering and insulin‐sensitizing effects in obese mouse models of metabolic dysfunction. However, in these models, a significant effect of naringenin supplementation is the prevention of weight gain, which in itself can confer metabolic protection. Therefore, in the present study, the effect of naringenin supplementation in lean, chow‐fed Ldlr−/− mice is investigated.Methods and resultsIn Ldlr−/− mice with isocaloric food consumption, treatment with naringenin for 8 weeks reduces body weight and adiposity compared to littermate controls pair‐fed the chow diet alone. Furthermore, naringenin treatment reduces plasma lipids and enhances insulin sensitivity compared to chow‐fed controls. Metabolic cage studies reveal that naringenin‐treated mice have elevated energy expenditure with no change in ambulatory activity. Additionally, naringenin‐treated mice have an increased respiratory exchange ratio and food consumption during the dark cycle. Treatment increases the expression of fatty acid oxidation genes in liver, and increased β‐hydroxybutyrate concentrations in plasma, indicating that one mechanism through which naringenin mediates metabolic improvement is enhanced hepatic fatty acid oxidation.ConclusionsThese studies highlight the potential therapeutic utility of naringenin and suggest that this flavonoid maintains potent metabolic properties in the absence of obesity or a high‐fat diet.