bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using historical fisheries data to predict tuna distribution within the British Indian Ocean Territory Marine Protected Area, and implications for its management
Authors: Dunn Nicholas , Curnick David 
Published: August 2019

Abstract

Recently, several large marine protected areas (MPAs) have been established globally, and it is hoped that they will aid the recovery of populations of highly mobile, large pelagic species. Understanding the distribution of these species within MPAs is key to delivering effective management, but monitoring can be challenging over such vast areas of open ocean.
Historical fisheries data, collected prior to MPA establishment, can provide an insight into the past distributions of target species. We investigated the spatial and temporal distribution of yellowfin (Thunnus albacares) and skipjack (Katsuwonus pelamis) tuna catch using logbook data from the purse seine fishery in the British Indian Ocean Territory from 1996 to 2010, before it was established as an MPA in April 2010.
Generalized additive models were used to predict tuna presence and relative abundance from fishing records in relation to temporal and environmental variables. Significant variables included sea salinity, temperature, and water velocity.
Predictions from the models identified a distinct hotspot for large yellowfin tuna within the MPA, and areas of high predicted relative abundance of skipjack tuna. We recommend that these areas are used as focal points from which populations can be monitored and investigations into tuna residency time can occur, so that the effectiveness of the MPA in conserving highly mobile pelagic fish can be determined.
Timing of Elevations of Autoantibody Isotypes Prior to Diagnosis of Rheumatoid Arthritis
Authors: Kelmenson Lindsay B. , Wagner Brandie D. , McNair Bryan K. , Frazer‐Abel Ashley , Demoruelle M. Kristen , Bergstedt Dylan T. , Feser Marie L. , Moss Laura K. , Parish Mark C. , Mewshaw Elizabeth A. , Mikuls Ted R. , Edison Jess D. , Holers V. Michael , Deane Kevin D. 
Published: August 2019

ObjectiveTo evaluate patterns of elevations of isotypes of rheumatoid factor (RF) and anti–citrullinated protein antibodies (ACPAs) pre–rheumatoid arthritis (RA) diagnosis and post–RA diagnosis.MethodsUsing the Department of Defense Serum Repository we identified 214 RA cases and 210 matched controls. Up to 3 pre–RA diagnosis and 1 post–RA diagnosis serum samples per subject were tested for RF and for IgA, IgG, and IgM ACPAs. The timing and trajectories of elevations of autoantibodies were evaluated.ResultsAutoantibody levels were elevated in cases versus controls a mean of 17.9 years before RA diagnosis for IgG ACPA, 14.2 years for IgA‐RF, 7.2 years for IgM‐RF, 6.2 years for IgA ACPA, and 5.0 years for both IgM ACPA and IgG‐RF (P < 0.01 for all comparisons). There were similar relationships for positive or negative autoantibody status, with cases first showing positivity for IgG ACPA 1.9 years pre‐RA and for IgA‐RF 1.7 years pre‐RA, followed by the other isotypes. Only IgA ACPA positivity was significantly increased in post–RA diagnosis samples (19% 0–2 years pre‐RA versus 39% >2 years post–RA diagnosis; P = 0.04). All autoantibody levels demonstrated an early initial elevation, a period of stability, then an increase immediately before RA diagnosis. A pre‐RA endotype of early elevation of autoantibodies was associated with increased use of biologic therapy, and a higher prevalence of sicca symptoms and lung disease post–RA diagnosis.ConclusionDifferences in patterns of elevations of autoantibody isotypes have implications for understanding the pathophysiology of RA development. These include understanding what factors drive initial autoantibody elevations compared to what factors (including mucosal) drive later increases in autoantibody levels and a transition to clinically apparent RA, and how pre‐RA endotypes may influence post–RA diagnosis phenotypes.
Octa[4‐(9‐carbazolyl)phenyl]silsesquioxane‐Based Porous Material for Dyes Adsorption and Sensing of Nitroaromatic Compounds
Authors: Li Wanli , Jiang Chundong , Liu Huanhuan , Yan Yehao , Liu Hongzhi 
Published: August 2019

AbstractA new fluorescent hybrid porous polymer (HPP) is synthesized by an anhydrous FeCl3‐mediated oxidative coupling reaction of octa[4‐(9‐carbazolyl)phenyl]silsesquioxane (OCPS). The polymer possesses a surface area of 1741 m2 g−1 and hierarchical bimodal micropores (1.41 and 1.69 nm) and mesopores (2.65 nm). The material serves as an excellent adsorbent for CO2 and dyes with high adsorption capacity for CO2 (8.53 wt %,1.94 mmol g−1), congo red (1715 mg g−1) and rhodamine B (1501 mg g−1). In addition, the presence of peripheral cabozolyl groups with extended π‐conjugation in the crosslinked framework imparts luminescent character to the polymer and offers the detection of nitroaromatic compounds.
Large‐scale meteorological control on the spatial pattern of wintertime PM2.5 pollution over China
Authors: Wang Ziwei , Chen Gang , Gu Yu , Zhao Bin , Ma Qiao , Wang Shuxiao , Liou Kuo‐Nan 
Published: August 2019

AbstractThe frequent episodes of severe air pollution over China during recent years have posed serious health threats to densely populated eastern China. Although several studies investigated the linkage between enhanced severity and frequency of air pollution and the large‐scale weather patterns over China, the day‐to‐day covariability between them, as well as its local and remote mechanisms, has not been systematically documented. The wintertime synoptic covariability between PM2.5 and large‐scale meteorological fields is studied using surface observations of PM2.5 in 2013/2014–2016/2017 and ERA‐Interim meteorological fields through maximum covariance analysis (MCA). The first MCA mode (MCA1) suggests a consistent accumulation of ambient PM2.5 as a result of weakened winds that block the pollutant removal passage in heavily polluted areas of eastern China, as well as moist air from southeast coast favoring haze formation. A northeast–southwest belt that extends into northeastern China and central China on each end is more sensitive to MCA1. The second MCA mode (MCA2) shows a north–south dipole in PM2.5 linked to the contrast of boundary layer height and surface wind speed between northern and southern regions of China. Spatial patterns of both modes are supported by the GEOS‐Chem chemistry transport model with realistic emission inventory. The spatial patterns of the two modes are robust on the interannual time scales. Based on that, we investigate the variability of the first two modes of the identified modes on the multidecadal scale by projecting GPM_500 pattern to 1981–2010. Correlation analysis of the projected time series and climate indices over 30 years indicates the possible linkage of Arctic oscillation, ENSO indices, Pacific decadal oscillation and east Atlantic/western Russia to regional air pollution patterns over China.
Familial confounding of the association between maternal smoking in pregnancy and autism spectrum disorder in offspring
Authors: Kalkbrenner Amy E. , Meier Sandra M. , Madley‐Dowd Paul , Ladd‐Acosta Christine , Fallin Margaret Daniele , Parner Erik , Schendel Diana 
Published: August 2019

Evidence supports no link between maternal smoking in pregnancy and autism spectrum disorder (autism) overall. To address remaining questions about the unexplained heterogeneity between study results and the possibility of risk for specific autism sub‐phenotypes, we conducted a whole‐population cohort study in Denmark. We followed births 1991–2011 (1,294,906 persons, including 993,301 siblings in 728,271 families), from 1 year of age until an autism diagnosis (13,547), death, emigration, or December 31, 2012. Autism, with and without attention deficit hyperactivity disorder (ADHD) and with and without intellectual disability (ID) were based on ICD‐8 and ICD‐10 codes from Danish national health registers, including 3,319 autism + ADHD, 10,228 autism − no ADHD, 2,205 autism + ID, and 11,342 autism − no ID. We estimated hazard ratios (HRs) and 95% confidence intervals (95% CIs) between any maternal smoking (from birth records) and autism (or sub‐phenotypes) using survival models with robust standard errors, stratifying by birth year and adjusting for child sex, parity, and parental age, education, income, and psychiatric history. To additionally address confounding using family designs, we constructed a maternal cluster model (adjusting for the smoking proportion within the family), and a stratified sibling model. Associations with maternal smoking and autism were elevated in conventional adjusted analyses (HR of 1.17 [1.13–1.22]) but attenuated in the maternal cluster (0.98 [0.88–1.09]) and sibling (0.86 [0.64–1.15]) models. Similarly, risks of autism sub‐phenotypes with maternal smoking were attenuated in the family‐based models. Together these results support that smoking in pregnancy is not linked with autism or select autism comorbid sub‐phenotypes after accounting for familial confounding. Autism Res 2020, 13: 134–144. © 2019 International Society for Autism Research, Wiley Periodicals, Inc.Lay SummarySmoking during pregnancy has many harmful impacts, which may include harming the baby's developing brain. However, in a study of thousands of families in Denmark, it does not appear that smoking in pregnancy leads to autism or autism in combination with intellectual problems or attention deficits, once you account for the way smoking patterns and developmental disabilities run in families.
Association between giant cell glioblastoma and glioblastoma multiforme in the United States: A retrospective cohort study
Authors: Bin Abdulrahman Amro K. , Bin Abdulrahman Khalid A. , Bukhari Yousef R. , Faqihi Abdulaziz M. , Ruiz Juan Gabriel 
Published: August 2019

AbstractObjectivesThe current study aims to find the differences between glioblastoma multiforme (GBM) and giant cell glioblastoma (GCG) regarding mortality and prognosis among adults and elderly patients in the U.S.Methods and MaterialsThis study is a historical cohort type of study and is conducted on adults and elderly individuals with GBM or GCG from the years 1985–2014 in the U.S. Data were collected from the Surveillance, Epidemiology, and End Results Program (SEER) database. The study exposure was GBM or GCG and the outcome was mortality. The potential confounders were age, sex, race, ethnicity, year of diagnosis, primary site, brain overlap, and surgery. A chi‐square test was used for categorical data. A univariate analysis was used for variables having a p‐value <.05. Potential confounders were selected and evaluated using multivariate logistic regression models to calculate the odds ratio with stepwise selection.ResultsThe study sample was 25,117. The incidences of GBM and GCG were not similar in relation to age group. Also, Spanish–Hispanic ethnicity was independently protective of GBM and GCG as compared to Non‐Spanish–Hispanic ethnicity patients with GBM have a higher mortality rate than do GCG patients. The mortality rate was higher among patients diagnosed before 2010.ConclusionGCG was not statistically significant in association to reduced mortality. Non‐Spanish–Hispanics with GBM or GCG had a higher mortality rate than did Spanish–Hispanics. Factors such as being female, being age 59–65, and having a year of diagnosis before 2010 were independently associated with increased mortality.
RIG‐I promotes IFN/JAK2 expression and the endoplasmic reticulum stress response to inhibit chemoradiation resistance in nasopharyngeal carcinoma
Authors: Jing Di , Zhou Weibing , Shen Lin , Zhang Qian , Xie Wang‐Ti , Shen Erdong , Li Zhi , Shen Liang‐Fang , Sun Lun‐Quan 
Published: August 2019

AbstractRIG‐I is associated with the occurrence and development of many tumors. However, the role of RIG‐I in radiotherapy and chemotherapy in NPC has not been reported to date. In our study, RIG‐I expression was significantly reduced in chemoradiotherapy‐resistant NPC tissues and cells compared with that in therapy‐sensitive tissues and cells. RIG‐I expression increased in nonresistant NPC cells, including CNE1 and CNE2, in a dose‐dependent manner with increasing chemotherapy drug concentration or radiotherapy dose. RIG‐I overexpression promoted radiotherapy and chemotherapy sensitivity in NPC cells, leading to cellular apoptosis and increased expression of the proapoptotic factors BAX and caspase‐3. Similarly, RIG‐I knockdown in NPC cells promoted chemoradiotherapy resistance and reduced apoptosis. Analysis of microarray data indicated that the expression of IFN/JAK2 and endoplasmic reticulum (ER) stress response markers, such as JAK2, STAT1, IRF9, IFNB1, IRF3, p‐IRF3, XBP1, ATF6, IFIT2, and ISG15, was inhibited in chemoradiotherapy‐resistant cells compared with that in sensitive cells. Conversely, activation of IFN/JAK2 and ER stress response pathways in NPC cells reduced paclitaxel resistance and increased apoptosis. RIG‐I promotes IFN/JAK2 and ER stress response‐mediated apoptosis to inhibit chemoradiation resistance in nasopharyngeal carcinoma.
Prognostic factors among single primary gliosarcoma cases: A study using Surveillance, Epidemiology, and End Results data from 1973–2013
Authors: Chen Bin , Liu Bin , Wu Chao , Wang Zhenyu 
Published: August 2019

AbstractBackgroundPrognostic factors for single primary gliosarcoma (PGS) remain unknown.ObjectiveThe purpose of our study was to examine patient, tumor, and treatment characteristics as potential predictors of survival using Surveillance, Epidemiology, and End Results (SEER) program data (1973‐2013).MethodsThe patients of single PGS were selected based on the exclusion criteria from SEER. Kaplan‐Meier survival analysis, log‐rank test and Cox proportional hazards models were used to analyze all the data.ResultsSingle PGS has an apparent popularity for the temporal lobe (35.2%, hazard ratio [HR] = 0.440, 95%CI = 0.251‐0.770) and frontal lobe (20.9%, HR = 0.408, 95%CI = 0.231‐0.720) which could achieve a better survival rate than cerebrum (P = .034). The mean age at diagnosis was 60.07 ± 14.161. The overall 6‐month, 1‐year, 2‐year, and 5‐year survival was 55.40%, 29.58%, 10.01%, and 2.73%. Age at diagnosis was proved to be a significant predictor of overall survival (OS) (P < .001). There is no significant difference in race, marital status, or grade. Patients' tumor size which is located in 41‐60 mm (P = .047, HR = 1.468, 95%CI = 1.004‐2.147) and >60 mm (P= .003, HR = 1.899, 95%CI = 1.244‐2.901) showed a higher risk of death. Surgery played a critical role in OS (P < .001). Radiation after surgery was another predictor of OS of PGS (P < .001). Among all the radiation methods, combination of beam with implants or isotopes (P = .000, HR = 0.491, 95%CI = 0.412‐0.585) or radiation NOS (P = .027, HR = 0.362, 95%CI = 0.148‐0.889) were more beneficial to patients.ConclusionThis study indicated that single PGS has a poor prognosis. Prognosis of single PGS would become poorer along with patients' age and tumor size (>40 mm). Surgery intervention and radiation therapy were beneficial factors.
Parenchymal‐sparing versus extended hepatectomy for colorectal liver metastases: A systematic review and meta‐analysis
Authors: Deng Gang , Li Hui , Jia Gui‐qing , Fang Dan , Tang You‐yin , Xie Jie , Chen Ke‐fei , Chen Zhe‐yu 
Published: August 2019

AbstractAimsTo assess the safety and efficacy of parenchymal‐sparing hepatectomy (PSH) as a treatment of colorectal liver metastases (CLM).MethodsA comprehensive medical literature search was performed. Perioperative and long‐term survival outcomes were pooled. Subgroup analysis and meta‐regression analysis were performed to identify potential sources of heterogeneity.ResultsA total of 18 studies comprising 7081 CLM patients were eligible for this study. The PSH was performed on 3974 (56.1%) patients. We found that the OS (overall survival; hazard ratio [HR] = 1.01, 95% confidence interval [CI]: 0.94‐1.08) and RFS (recurrence‐free survival; HR = 1.00, 95% CI: 0.94‐1.07) were comparable between non‐PSH and PSH group. The perioperative outcomes were better in PSH than in non‐PSH group. Non‐PSH group was significantly associated with longer operative time (standard mean difference [SMD] = 1.17, 95% CI: 0.33‐2.00), increased estimated blood loss (SMD = 1.36, 95% CI: 0.64‐2.07), higher intraoperative transfusion rate (risk ratio [RR] = 2.27, 95% CI: 1.60‐3.23), and more postoperative complications (RR = 1.39, 95% CI: 1.16‐1.66). Meta‐regression analyses revealed that no variable influenced the association between surgical types and the survival outcomes.ConclusionsThis study shows that PSH is associated with better perioperative outcomes without compromising oncological outcomes. Given the increasing incidence of hepatic parenchyma, the PSH treatment offers a greater opportunity of repeat resection for intrahepatic recurrent tumors. It should be considered as an effective surgical approach for CLM.
Assignment of Vibrational Circular Dichroism Cross‐Referenced Electronic Circular Dichroism Spectra of Flexible Foldamer Building Blocks: Towards Assigning Pure Chiroptical Properties of Foldamers
Authors: Farkas Viktor , Nagy Adrienn , Menyhárd Dóra K. , Perczel András 
Published: August 2019

AbstractAssignment of the most established electronic circular dichroism (ECD) spectra of polypeptides and foldamers is either “evidence based” or relies on the 3D structures of longer oligomers of limited internal dynamics, which are derived from NMR spectroscopy (or X‐ray) data. Critics warn that the use of NMR spectroscopy and ECD side by side has severe limitations for flexible molecules because explicit knowledge of conformational ensembles is a challenge. Herein, an old–new method of comparing ab initio computed and measured vibrational circular dichroism (VCD) data is presented to validate both the structures (conf(i)) and their relative weights (c(i)) that make up the conformational ensemble. Based on the array of {conf(i), c(i)}, the pure ECD spectra, g(i)conf(i), can be ab initio calculated. The reconstructed spectrum Σc(i)g(i)conf(i) can thus help to assign any experimental ECD counterparts. Herein, such a protocol is successfully applied to flexible foldamer building blocks of sugar β‐amino acid diamides. The epimeric pair of the model system was selected because these molecules were conformationally tunable by simple chemical modification, and thus, the robustness of the current approach could be probed. The initial hydrogen bond (NH⋅⋅⋅O) eliminated by N‐methylation reorients the amide plain, which influences the chiroptical properties of the foldamer building block; this structural change is successfully monitored by changes to the VCD and ECD transitions, which are now assigned to pure conformers. The current method seems to be general and effective without requiring extensive CPU and spectroscopic resources.
FOXC2 expression and epithelial–mesenchymal phenotypes are associated with castration resistance, metastasis and survival in prostate cancer
Authors: Børretzen Astrid , Gravdal Karsten , Haukaas Svein A , Beisland Christian , Akslen Lars A , Halvorsen Ole J 
Published: August 2019

AbstractEpithelial–mesenchymal transition (EMT) is important for tumour cell invasion and metastasis and is a feature of aggressive carcinomas. EMT is characterised by reduced E‐cadherin and increased N‐cadherin expression (EN‐switch), and increased expression of the EMT‐regulating transcription factor Forkhead box protein C2 (FOXC2) has been associated with progression and poor prognosis in various malignancies. FOXC2 was recently highlighted as a novel therapy target in prostate cancer, but survival data on FOXC2 are lacking. This study evaluates the expression of FOXC2, E‐cadherin and N‐cadherin in different prostatic tissues focusing on EMT, clinico‐pathological phenotype, recurrence and patient survival. Tissue microarray sections from 338 radical prostatectomies (1986–2007) with long and complete follow‐up, 33 castration resistant prostate cancers, 33 non‐skeletal metastases, 13 skeletal metastases and 41 prostatic hyperplasias were stained immunohistochemically for FOXC2, E‐cadherin and N‐cadherin. FOXC2 was strongly expressed in primary carcinomas, including castration resistant tumours and metastatic lesions as compared to benign prostatic hyperplasia. A hybrid epithelial–mesenchymal phenotype, with co‐expression of E‐cadherin and N‐cadherin, was found in the majority of skeletal metastases and in a substantial proportion of castration resistant tumours. In localised carcinomas, the EN‐switch was associated with adverse clinico‐pathological variables, such as extra‐prostatic extension, high pathological stage and lymph node infiltration. In univariate survival analyses of the clinically important, large subgroup of 199 patients with Gleason score 7, high FOXC2 expression and EN‐switching were significantly associated with shorter time to clinical recurrence, skeletal metastases and cancer specific death. In multivariate Cox' survival analysis, high FOXC2 and the EN‐switch, together with Gleason grade group (GG3 versus GG2), were independent predictors of time to these end‐points. High FOXC2 gene expression (mRNA) was also related to patient outcome, validating our immunohistochemical findings. FOXC2 and factors signifying EMT or its intermediate states may prove important as biomarkers for aggressive disease and are potential novel therapy targets in prostate cancer.
Using analysis information in the synchronization‐free GPU solution of sparse triangular systems
Authors: Dufrechou Ernesto , Ezzatti Pablo 
Published: August 2019

SummaryThe solution of sparse triangular linear systems is one of the most important building blocks for a large number of science and engineering problems. For these reasons, it has been studied steadily for several decades, principally in order to take advantage of emerging parallel platforms. In the context of massively parallel platforms such as GPUs, the standard strategy of parallel solution is based on performing a level‐set analysis of the sparse matrix, and the kernel included in the nVidia cuSparse library is the most prominent example of this approach. However, a weak spot of this implementation is the costly analysis phase and the constant synchronizations with the CPU during the solution stage. In previous work, we presented a self‐scheduled and synchronization‐free GPU algorithm that avoided the analysis phase and the synchronizations of the standard approach. Here, we extend this proposal and show how the level‐set information can be leveraged to improve its performance. In particular, we present new GPU solution routines that attack some of the weak spots of the self‐scheduled solver, such as the under‐utilization of the GPU resources in the case of highly sparse matrices. The experimental evaluation reveals a sensible runtime reduction over cuSparse and the state‐of‐the‐art synchronization‐free method.