bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional evolution of the colony-stimulating factor 1 receptor (CSF1R) and its ligands in birds
Authors: Hume David A. , Gutowska-Ding Maria W. , Garcia-Morales Carla , Kebede Adebabay , Bamidele Oladeji , Trujillo Adriana Vallejo , Gheyas Almas A. , Smith Jacqueline 
Published: September 2019

Abstract
Macrophage colony-stimulating factor (CSF1 or M-CSF) and interleukin 34 (IL34) are secreted cytokines that control macrophage survival and differentiation. Both act through the CSF1 receptor (CSF1R), a type III transmembrane receptor tyrosine kinase. The functions of CSF1R and both ligands are conserved in birds. We have analyzed protein-coding sequence divergence among avian species. The intracellular tyrosine kinase domain of CSF1R was highly conserved in bird species as in mammals but the extracellular domain of avian CSF1R was more divergent in birds with multiple positively selected amino acids. Based upon crystal structures of the mammalian CSF1/IL34 receptor-ligand interfaces and structure-based alignments, we identified amino acids involved in avian receptor-ligand interactions. The contact amino acids in both CSF1 and CSF1R diverged among avian species. Ligand-binding domain swaps between chicken and zebra finch CSF1 confirmed the function of variants that confer species specificity on the interaction of CSF1 with CSF1R. Based upon genomic sequence analysis, we identified prevalent amino acid changes in the extracellular domain of CSF1R even within the chicken species that distinguished commercial broilers and layers and tropically adapted breeds. The rapid evolution in the extracellular domain of avian CSF1R suggests that at least in birds this ligand-receptor interaction is subjected to pathogen selection. We discuss this finding in the context of expression of CSF1R in antigen-sampling and antigen-presenting cells.
Developmental architecture of the nervous system in Themiste lageniformis (Sipuncula): New evidence from confocal laser scanning microscopy and gene expression
Authors: Carrillo‐Baltodano Allan M. , Boyle Michael J. , Rice Mary E. , Meyer Néva P. 
Published: September 2019

AbstractSipuncula is a clade of unsegmented marine worms that are currently placed among the basal radiation of conspicuously segmented Annelida. Their new location provides a unique opportunity to reinvestigate the evolution and development of segmented body plans. Neural segmentation is clearly evident during ganglionic ventral nerve cord (VNC) formation across Sedentaria and Errantia, which includes the majority of annelids. However, recent studies show that some annelid taxa outside of Sedentaria and Errantia have a medullary cord, without ganglia, as adults. Importantly, neural development in these taxa is understudied and interpretation can vary widely. For example, reports in sipunculans range from no evidence of segmentation to vestigial segmentation as inferred from a few pairs of serially repeated neuronal cell bodies along the VNC. We investigated patterns of pan‐neuronal, neuronal subtype, and axonal markers using immunohistochemistry and whole mount in situ hybridization (WMISH) during neural development in an indirect‐developing sipunculan, Themiste lageniformis. Confocal imaging revealed two clusters of 5HT+ neurons, two pairs of FMRF+ neurons, and Tubulin+ peripheral neurites that appear to be serially positioned along the VNC, similar to other sipunculans, to other annelids, and to spiralian taxa outside of Annelida. WMISH of a synaptotagmin1 ortholog in T. lageniformis (Tl‐syt1) showed expression throughout the centralized nervous system (CNS), including the VNC where it appears to correlate with mature 5HT+ and FMRF+ neurons. An ortholog of elav1 (Tl‐elav1) showed expression in differentiated neurons of the CNS with continuous expression in the VNC, supporting evidence of a medullary cord, and refuting evidence of ontogenetic segmentation during formation of the nervous system. Thus, we conclude that sipunculans do not exhibit any signs of morphological segmentation during development.
Radiomics and Machine Learning With Multiparametric Preoperative MRI May Accurately Predict the Histopathological Grades of Soft Tissue Sarcomas
Authors: Wang Hexiang , Chen Haisong , Duan Shaofeng , Hao Dapeng , Liu Jihua 
Published: September 2019

BackgroundPreoperative prediction of the grade of soft tissue sarcomas (STSs) is important because of its effect on treatment planning.PurposeTo assess the value of radiomics features in distinguishing histological grades of STSs.Study TypeRetrospective.PopulationIn all, 113 patients with pathology‐confirmed low‐grade (grade I), intermediate‐grade (grade II), or high‐grade (grade III) soft tissue sarcoma were collected.Field Strength/SequenceThe 3.0T axial T1‐weighted imaging (T1WI) with 550 msec repetition time (TR); 18 msec echo time (TE), 312 × 312 matrix, fat‐suppressed fast spin‐echo T2WI with 4291 msec TR, 85 msec TE, 312 × 312 matrix.AssessmentMultiple machine‐learning methods were trained to establish classification models for predicting STS grades. Eighty STS patients (18 low‐grade [grade I]; 62 high‐grade [grades II–III]) were enrolled in the primary set and we tested the model with a validation set with 33 patients (7 low‐grade, 26 high‐grade).Statistical Tests1) Student's t‐tests were applied for continuous variables and the χ2 test were applied for categorical variables between low‐grade STS and high‐grade STS groups. 2) For feature subset selection, either no subset selection or recursive feature elimination was performed. This technology was combined with random forest and support vector machine‐learning methods. Finally, to overcome the disparity in the frequencies of the STS grades, each machine‐learning model was trained i) without subsampling, ii) with the synthetic minority oversampling technique, and iii) with random oversampling examples, for a total of 12 combinations of machine‐learning algorithms that were assessed, trained, and tested in the validation cohort.ResultsThe best classification model for the prediction of STS grade was a combination of features selected by recursive feature elimination and random forest classification algorithms with a synthetic minority oversampling technique, which had an area under the curve of 0.9615 (95% confidence interval 0.8944–1.0) in the validation set.Data ConclusionRadiomics feature‐based machine‐learning methods are useful for distinguishing STS grades.Level of Evidence: 3Technical Efficacy: Stage 2J. Magn. Reson. Imaging 2020;51:791–797.
Climate projections for glacier change modelling over the Himalayas
Authors: Jury Martin W. , Mendlik Thomas , Tani Satyanarayana , Truhetz Heimo , Maraun Douglas , Immerzeel Walter W. , Lutz Arthur F. 
Published: September 2019

AbstractGlaciers are of key importance to freshwater supplies in the Himalayan region. Their growth or decline is among other factors determined by an interaction of 2‐m air temperature (TAS) and precipitation rate (PR) and thereof derived positive degree days (PDD) and snow and ice accumulation (SAC). To investigate determining factors in climate projections, we use a model ensemble consisting of 36 CMIP5 general circulation models (GCMs) and 13 regional climate models (RCMs) of two Asian CORDEX domains for two different representative concentration pathways (RCP4.5 and RCP8.5). First, we downsize the ensemble in respect to the models' ability to correctly reproduce dominant circulation patterns (i.e., the Indian summer monsoon [ISM] and western disturbances [WDs]) as well as elevation‐dependent trend signals in winter. Within this evaluation, a newly produced data set for the Indus, Ganges and Brahmaputra catchments is used as observational data. The reanalyses WFDEI, ERA‐Interim, NCEP/NCAR and JRA‐55 are used to further account for observational uncertainty. In a next step, remaining TAS and PR data are bias corrected applying a new bias adjustment method, scale distribution mapping, and subsequently PDD and SAC computed. Finally, we identify and quantify projected climate change effects. Until the end of the century, the ensemble indicates a rise of PDD, especially during summer and for lower altitudes. Also TAS is rising, though the highest increases are shown for higher altitudes and between December and April (DJFMA). PRs connected to the ISM are projected to robustly increase, while signals for PR changes during DJFMA show a higher level of uncertainty and spatial heterogeneity. However, a robust decline in solid precipitation is projected over our research domain, with the exception of a small area in the high mountain Indus catchment where no clear signal emerges.
Towards the integration of lean principles and optimization for agricultural production systems: a conceptual review proposition
Authors: Caicedo Solano Nestor E , García Llinás Guisselle A , Montoya‐Torres Jairo R 
Published: September 2019

AbstractOperative planning in agricultural production has historically had the objective of improving yields and quality. Sowing, cropping, and harvesting are usually treated independently, and waste and the sustainability of operations are generally not integrated into operational planning methodologies for agricultural production. This study shows the need to have a clear and precise methodology to minimize waste in agricultural production systems to ensure sustainability. This need is addressed with a novel methodological guide to minimizing waste in agricultural operations, crop maintenance, and harvesting. The proposed methodology is founded on the use of lean manufacturing as a waste‐management tool. Lean manufacturing principles allow agricultural operations and the variables that represent wastes to be identified, mathematical models to be built, constraints to be defined, and the cost of waste to be illustrated, as well as its minimization through an objective function. To guide implementation, we propose a conceptual model to explain the construction of a mathematical model that represents the development of decision variables on agricultural operations with the elements to consider and the constraints and theoretical proposal of the necessary objective function. The proposed conceptual model and the constructed methodology constitute a novel development within agricultural production systems that could be used by decision makers and farmers. © 2019 Society of Chemical Industry
Hypo‐vascular hepatocellular carcinoma and liver transplantation: Morphological characteristics and implications on outcomes
Authors: Aggarwal Alok , Horwitz Julian K. , Dolan Dan , Kamath Amita , Lewis Sara , Facciuto Matias , Grewal Priya , Fiel Maria Isabel , Schiano Thomas , Facciuto Marcelo E. 
Published: September 2019

AbstractBackgroundThe clinical importance of hypovascular liver lesions in cirrhotic patients awaiting liver transplantation (LT) has not been fully investigated. The objective of this study was to characterize the clinicopathologic features and management of these tumors and to assess their impact on post‐LT outcomes.MethodsWe performed a retrospective review of cirrhotic patients with lesions suspicious for hypovascular hepatocellular carcinoma (HCC) who underwent LT at a single institution from 2011‐ 2017.ResultsWe identified 22 pre‐LT patients with radiologic diagnosis of a lesion(s) suspicious for hypovascular HCC. There were 28 hypovascular lesions within the 22 patient cohort; 9 lesions (32%) converted to hypervascular HCC before LT and 19 lesions remained hypovascular at LT. 88% of hypovascular lesions were HCC on explant pathology. Compared to patients with hyper‐vascular HCC lesions, hypovascular HCC lesions underwent less preoperative tumor ablation (58% vs 89%; P < .01). Hypovascular HCC were more likely to be well‐differentiated (67% vs 11%; P < .01), but there were no differences in the microvascular invasion, tumor recurrence, or survival post‐LT.ConclusionsHypovascular HCC has similar clinical outcomes and needs for transplantation as hypervascular HCC. The high prevalence of HCC within suspicious hypovascular lesions supports a similar monitoring and locoregional therapy strategy as for hypervascular HCC.
A propensity‐score matched analysis of limb salvage vs amputation for osteosarcoma
Authors: Traven Sophia A. , Brinton Daniel L. , Walton Zeke J. , Leddy Lee R. 
Published: September 2019

AbstractBackground and ObjectivesWith recent advances in chemotherapy and surgical techniques, the trend in the treatment of osteosarcoma continues to progress towards limb salvage. However, studies comparing limb salvage with amputation continue to be limited by selection bias and small sample sizes. This study utilized propensity‐score matching to minimize potential confounders and selection bias to compare the survival rates in patients with osteosarcoma that were treated with amputation vs limb salvage surgery.MethodsThe Surveillance, Epidemiology, and End Results Program was utilized to identify all patients with a diagnosis of extremity osteosarcoma. Patients were matched with demographics, tumor characteristics, and treatment information. These variables were then fitted in a multivariate model and hazard ratios (HR) for overall‐ and disease‐specific mortality was calculated.ResultsA total of 4107 patients were identified, of which, 1538 were left after propensity‐score matching. Older age, Black race, upper extremity location, and higher American joint committee on cancer (AJCC) class were associated with worse overall‐ and disease‐specific mortality rates (P ≤ .0389). Compared with their matched counterparts, patients treated with amputation had higher overall mortality (HR 1.677; P < .0001) and higher disease‐specific mortality (HR 1.678; P < .0001).ConclusionPatients whose tumor characteristics preclude limb salvage have significantly higher overall‐ and disease‐specific mortality rates.
Fast analysis of 19 anabolic steroids in bovine tissues by high performance liquid chromatography with tandem mass spectrometry
Authors: Wozniak Barbara , Matraszek–Zuchowska Iwona , Klopot Alicja , Posyniak Andrzej 
Published: September 2019

AbstractFor the detection of 19 steroid hormones in bovine muscle, a fast and sensitive liquid chromatography with electrospray ionization tandem mass spectrometry method was developed using both positive and negative ionization mode. Chromatographic separation on Poroshell 120‐EC C18 column was achieved in less than 10 min using isocratic elution of mobile phase of acetonitrile/methanol/water. The compounds were extracted from muscle tissue using ethyl acetate and quick, easy, cheap, effective, rugged, and safe technique. The purification of the obtained extract was performed by dispersive solid‐phase extraction with sorbents C18, primary secondary amine and magnesium sulphate. The method was validated in accordance with the Commission Decision 2002/657/EC. For all steroids tested good recoveries were obtained (from 51.2 to 121.4%) in the concentration range from decision limits until 5 µg/kg. The values of decision limits and the detection capabilities for individual compounds were in the range 0.10–0.48 and 0.17–0.95 µg/kg, respectively. The method was characterized by satisfactory linearity for most compounds (correlation coefficients > 0.99) and the reproducibility was lower than 35%. The elaborated procedure has met the criteria for confirmatory methods and is currently used in the official control of hormones.
Prediction of lateral neck lymph node metastasis according to preoperative calcitonin level and tumor size for medullary thyroid carcinoma
Authors: Bae Soo Y. , Jung Seung P. , Choe Jun‐Ho , Kim Jee S. , Kim Jung H. 
Published: September 2019

AbstractMedullary thyroid carcinoma (MTC) accounts up to 10% of all thyroid cancers, but is responsible for a disproportionate number of deaths. While surgery is the only curative treatment for MTC, indications for lateral neck lymph node (LLN) dissection are controversial. We performed a retrospective review to describe clinical outcomes in 93 MTC patients from July 1995 to March 2015. We analyzed their clinicopathologic factors, and cut‐off values of tumor size and calcitonin levels were calculated using a receiver operating characteristic curve. Using the instances of lymph node metastases, the tumor size cut‐off value was 0.95 cm (area under curve, AUC = 0.697) in patients with ipsilateral central lymph node (CLN) metastases, 2.25 cm (AUC = 0.793) in contralateral CLN metastases, and 1.75 cm (AUC = 0.753) in ipsilateral LLN metastases. The cut‐off values of preoperative calcitonin levels were 226.6 pg/mL (AUC = 0.746) in ipsilateral CLN, 755.0 pg/mL (AUC = 0.840) in contralateral CLN metastases, and 237.0 pg/mL (AUC = 0.775) in ipsilateral LLN metastases. This study supports the notion that ipsilateral LLN metastases occur before contralateral CLN metastases. Therefore, ipsilateral LLN dissection should be considered in patients with contralateral CLN metastases. The extent of surgery should be based on the status of LN metastases, preoperative basal calcitonin level, and tumor size to help individualize the extent of surgery.
Respiratory Epithelial Adenomatoid Hamartoma is Frequent in Olfactory Cleft After Nasalization
Authors: Nguyen Duc Trung , Jankowski Roger , Bey Ayoub , Gauchotte Guillaume , Casse Jean Matthieu , Gondim Teixeira Pedro Augusto , Gallet Patrice , Rumeau Cécile 
Published: September 2019

ObjectivesTo assess the site and histopathology of polyps at the first revision surgery for recurrent nasal polyposis (NP) after radical ethmoidectomy (nasalization).Study DesignRetrospective study.MethodsBetween January 2008 and December 2015, a total of 62 patients having undergone revision surgery for recurrent NP after nasalization were included. The site and histology of the recurrence of polyps were analyzed according to operative and pathological reports.ResultsHistology showed classical inflammatory nasal polyps (CINP) in 91% of nasal cavities at primary surgery versus respiratory epithelial adenomatoid hamartoma (REAH) or REAH associated to CINP in 54.8% at revision surgery (P < .0001). Polyps were principally observed in the ethmoidal complex in 70% of nasal cavities during primary surgery and in the olfactory clefts in 88.7% during revision surgery (P < .0001). The mean interval between nasalization and first revision surgery was 8.8 ± 4.4 years (0.4–21.7 years). This interval was significantly shorter for grade 3 polyps, polyps removed from both ethmoidal complex and olfactory cleft at primary surgery, association of CINP and REAH at primary surgery, and when primary surgery had preserved the middle turbinates.ConclusionPolyp recurrences after nasalization were mainly observed in the olfactory clefts and can be different histological features: inflammatory polyps, respiratory epithelial adenomatoid hamartoma, or a combination of both.Level of Evidence4 Laryngoscope, 130:2098–2104, 2020
KLF3 is a crucial regulator of metastasis by controlling STAT3 expression in lung cancer
Authors: Sun Wei , Hu Shan , Zu Yukun , Deng Yu 
Published: September 2019

AbstractLung cancer is one of the most common causes of cancer‐related mortality worldwide, which is partially due to its metastasis. However, the mechanism underlying its metastasis remains elusive. In this study, we showed that a low Krüppel‐like factor 3 (KLF3) expression level is correlated with a poor prognosis and TNM stages in clinical patients with lung cancer and further demonstrated that KLF3 expression is downregulated in lung cancer tissues compared with adjacent normal samples. In addition, bioinformatics analysis results showed that KLF3 expression is related to lung cancer epithelial‐mesenchymal transition (EMT). In vitro and in vivo experiments also showed that KLF3 silencing promotes lung cancer EMT and enhances lung cancer metastasis. More importantly, bioinformatics analysis and in vitro experiments indicated that the role of KLF3 in lung cancer metastasis is dependent on the STAT3 signaling pathway. Overall, our data indicated the crucial function of KLF3 in lung cancer metastasis and suggested opportunities to improve the therapy of patients with lung cancer.
p53 Promotes chemoresponsiveness by regulating hexokinase II gene transcription and metabolic reprogramming in epithelial ovarian cancer
Authors: Han Chae Young , Patten David A. , Lee Seung Gee , Parks Robin J. , Chan David W. , Harper Mary‐Ellen , Tsang Benjamin K. 
Published: September 2019

AbstractMetabolic reprogramming (including the Warburg effect) is a hallmark of cancer, yet the association between the altered metabolism and chemoresistance remains elusive. Hexokinase II (HKII) is a key metabolic enzyme and is upregulated in multiple cancers. In this study, we examined the impact of targeting metabolism via silencing of HKII on chemoresistance in ovarian cancer (OVCA). In addition, the regulatory molecular mechanism of tumor metabolism was examined using gain‐ and loss‐of‐function approaches in epithelial OVCA cell lines of various histological subtypes. We demonstrated that cisplatin (CDDP)‐induced p53‐mediated HKII downregulation is a determinant of chemosensitivity in OVCA. Silencing of HKII sensitized chemoresistant OVCA cells to apoptosis in a p53‐dependent manner. As a negative regulator, p53 suppressed HKII transcription by promoter binding and decreased glycolysis. Pyruvate dehydrogenase kinase‐1 (PDK1) is a key regulator of cell proliferation involved in Akt signaling axis. Our Gene Expression Profiling Interactive Analysis (GEPIA) and molecular studies also revealed that PDK1, an upstream activator strongly correlates with HKII expression and regulates its metabolic activity. Finally, we demonstrated that the clinically approved drug metformin sensitizes chemoresistant OVCA cells to CDDP via PDK1‐HKII pathway. Collectively, our data implicate that p53‐‐PDK1‐HKII axis is a central regulatory component of metabolism conferring chemoresistance in OVCA.
Understanding the Links Between Cardiovascular Disease and Parkinson's Disease
Authors: Potashkin Judy , Huang Xuemei , Becker Claudia , Chen Honglei , Foltynie Thomas , Marras Connie 
Published: September 2019

AbstractStudies investigating the associations between genetic or environmental factors and Parkinson's disease (PD) have uncovered a number of factors shared with cardiovascular disease, either as risk factors or manifestations of cardiovascular disease itself. Older age, male sex, and possibly type 2 diabetes are examples. On the other hand, coffee consumption and physical activity are each associated with a lower risk of both PD and cardiovascular disease. This observation raises questions about the underlying pathophysiological links between cardiovascular disease and PD. There is evidence for common mechanisms in the areas of glucose metabolism, cellular stress, lipid metabolism, and inflammation. On the other hand, smoking and total/low‐density lipoprotein cholesterol appear to have opposite associations with cardiovascular disease and PD. Thus, it is uncertain whether the treatment of cardiovascular risk factors will impact on the onset or progression of PD. The available data suggest that a nuanced approach is necessary to manage risk factors such as cholesterol levels once the associations are better understood. Ultimately, the choice of therapy may be tailored to a patient's comorbidity profile. This review presents the epidemiological evidence for both concordant and discordant associations between cardiovascular disease and PD, discusses the cellular and metabolic processes that may underlie these links, and explores the implications this has for patient care and future research. © 2019 International Parkinson and Movement Disorder Society