bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ionizing radiation regulates long non-coding RNAs in human peripheral blood mononuclear cells
Authors: Beer Lucian , Nemec Lucas , Wagner Tanja , Ristl Robin , Altenburger Lukas M. , Ankersmit Hendrik Jan , Mildner Michael 
Published: October 2016

AbstractLong non-coding RNAs (lncRNAs) are non-protein coding transcripts that modulate mRNA and microRNA (miRNA) expression, thereby controlling multiple cellular processes, including transcriptional regulation of gene expression, cell differentiation and apoptosis. Ionizing radiation (IR), a strong cellular stressor, is known to influence gene expression of irradiated cells, mainly by activation of oxidative processes. Whether and how IR also affects lncRNA expression in human peripheral blood mononuclear cells (PBMCs) is still poorly understood. Exposure of PBMCs to IR dose-dependently activated p53 and its downstream target p21, ultimately leading to cell-cycle arrest and/or apoptosis. Cleavage of caspase-3, a specific process during apoptotic cell death, was detectable at doses as low as 30 Gy. Transcriptome analysis of 60 Gy–irradiated PBMCs revealed a strong time-dependent regulation of a variety of lncRNAs. Among many unknown lncRNAs we also identified a significant upregulation of Trp53cor1, MEG3 and TUG1, which have been shown to be involved in the regulation of cell cycle and apoptotic processes mediated by p53. In addition, we found 177 miRNAs regulated in the same samples, including several miRNAs that are known targets of upregulated lncRNAs. Our data show that IR dose-dependently regulates the expression of a wide spectrum of lncRNAs in PBMCs, suggesting a crucial role for lncRNAs in the complex regulatory machinery activated in response to IR.
Developmental DNA methyltransferase expression in the fire ant Solenopsis invicta
Authors: Kay Sasha , Skowronski Daniel , Hunt Brendan G. 
Published: October 2016

AbstractDNA methylation is accomplished in animals by 2 classes of enzymes known as DNA methyltransferases, DNMT3 and DNMT1, which perform de novo methylation and maintenance methylation, respectively. Several studies of hymenopteran eusocial insects suggest that DNA methylation is capable of influencing developmental plasticity. However, fundamental questions remain about the patterning of DNA methylation during the course of insect development. In this study, we performed quantitative real‐time PCR (qPCR) on transcripts from the single‐copy orthologs of DNMT1 and DNMT3 in the red imported fire ant, Solenopsis invicta. In particular, we assessed the expression of S. invicta Dnmt1 and Dnmt3 mRNA during 7 stages of worker development, among behaviorally distinct adults, and among male and female gonads. Dnmt3 was most highly expressed during embryonic development, whereas Dnmt1 was similarly expressed throughout the course of development. Moreover, Dnmt1 and Dnmt3 were highly expressed in testes and ovaries. Neither Dnmt was significantly differentially expressed among heads of behaviorally distinct adult castes. Our results support the hypothesis that extensive patterning of DNA methylation occurs during gametogenesis and embryogenesis in the insect order Hymenoptera.
Impacts of Human Behavioral Heterogeneity on the Benefits of Probabilistic Flood Warnings: An Agent‐Based Modeling Framework
Authors: Du Erhu , Rivera Samuel , Cai Ximing , Myers Laura , Ernest Andrew , Minsker Barbara 
Published: October 2016

AbstractFlood forecasts and warnings are intended to reduce flood‐related property damages and loss of human life. Considerable research has improved flood forecasting accuracy (e.g., more accurate prediction of the occurrence of flood events) and lead time. However, the delivery of improved forecast information alone is not necessarily sufficient to reduce flood damage and loss of life, as people have varying responses and reactions to flood warnings. This study develops an agent‐based modeling framework that evaluates the impacts of heterogeneity in human behaviors (i.e., variation in behaviors in response to flood warnings), as well as residential density, on the benefits of flood warnings. The framework is coupled with a traffic model to simulate evacuation processes within a road network under various flood warning scenarios. The results show the marginal benefit associated with providing better flood warnings is significantly constrained if people behave in a more risk‐tolerant manner, especially in high‐density residential areas. The results also show significant impacts of human behavioral heterogeneity on the benefits of flood warnings, and thus stress the importance of considering human behavioral heterogeneity in simulating flood warning‐response systems. Further study is suggested to more accurately model human responses and behavioral heterogeneity, as well as to include more attributes of residential areas to estimate and improve the benefits of flood warnings.
Prospective Analysis of Behavioral Economic Predictors of Stable Moderation Drinking Among Problem Drinkers Attempting Natural Recovery
Authors: Tucker Jalie A. , Cheong JeeWon , Chandler Susan D. , Lambert Brice H. , Pietrzak Brittney , Kwok Heather , Davies Susan L. 
Published: October 2016

BackgroundAs interventions have expanded beyond clinical treatment to include brief interventions for persons with less severe alcohol problems, predicting who can achieve stable moderation drinking has gained importance. Recent behavioral economic (BE) research on natural recovery has shown that active problem drinkers who allocate their monetary expenditures on alcohol and saving for the future over longer time horizons tend to have better subsequent recovery outcomes, including maintenance of stable moderation drinking. This study compared the predictive utility of this money‐based “Alcohol‐Savings Discretionary Expenditure” (ASDE) index with multiple BE analogue measures of behavioral impulsivity and self‐control, which have seldom been investigated together, to predict outcomes of natural recovery attempts.MethodsCommunity‐dwelling problem drinkers, enrolled shortly after stopping abusive drinking without treatment, were followed prospectively for up to a year (N = 175 [75.4% male], M age = 50.65 years). They completed baseline assessments of preresolution drinking practices and problems, analogue behavioral choice tasks (Delay Discounting, Melioration‐Maximization, and Alcohol Purchase Tasks), and a Timeline Followback interview including expenditures on alcohol compared to voluntary savings (ASDE index) during the preresolution year.ResultsMultinomial logistic regression models showed that, among the BE measures, only the ASDE index predicted stable moderation drinking compared to stable abstinence or unstable resolutions involving relapse. As hypothesized, stable moderation was associated with more balanced preresolution allocations to drinking and savings (odds ratio = 1.77, 95% confidence interval = 1.02 to 3.08, p < 0.05), suggesting it is associated with longer‐term behavior regulation processes than abstinence.ConclusionsThe ASDE's unique predictive utility may rest on its comprehensive representation of contextual elements to support this patterning of behavioral allocation. Stable low‐risk drinking, but not abstinence, requires such regulatory processes.
A revision of the flat bark beetle genus Platisus Erichson, 1842 (Coleoptera: Cucujidae)
Authors: Marris John W M 
Published: October 2016

AbstractThe Platisus Erichson fauna of Australia and New Zealand is revised. Six species are recorded, described and illustrated. A key to species is provided. One new species, Platisus vespertinus sp. nov., is described from New South Wales, South Australia, Victoria and Western Australia. This is the first Platisus species known from Western Australia. Platisus bicolor (Olliff, 1885) is removed from synonomy with Platisus coloniarius (Olliff, 1885), which is reinstated in the genus Cucujus. Platisus integricollis Reitter, 1879 is synonymised with P. angusticollis Reitter, 1879. Cucujus coloniarius is provisionally synonymised with the Himalayan species Cucujus bicolor Smith, 1851. Lectotypes are designated for Platisus angusticollis Reitter, 1879, Platisus integricollis Reitter, 1879, Platisus obscurus Erichson, 1842, Ipsaphes bicolor Olliff, 1885, Ipsaphes moerosus Pascoe, 1863, and Cucujus coloniarius Olliff, 1885.
Genome‐wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds,
Authors: Keel B. N. , Keele J. W. , Snelling W. M. 
Published: October 2016

SummaryCopy number variations (CNVs) are large insertions, deletions or duplications in the genome that vary between members of a species and are known to affect a wide variety of phenotypic traits. In this study, we identified CNVs in a population of bulls using low coverage next‐generation sequence data. First, in order to determine a suitable strategy for CNV detection in our data, we compared the performance of three distinct CNV detection algorithms on benchmark CNV datasets and concluded that using the multiple sample read depth approach was the best method for identifying CNVs in our sequences. Using this technique, we identified a total of 1341 copy number variable regions (CNVRs) from genome sequences of 154 purebred sires used in Cycle VII of the USMARC Germplasm Evaluation Project. These bulls represented the seven most popular beef breeds in the United States: Hereford, Charolais, Angus, Red Angus, Simmental, Gelbvieh and Limousin. The CNVRs covered 6.7% of the bovine genome and spanned 2465 protein‐coding genes and many known quantitative trait loci (QTL). Genes harbored in the CNVRs were further analyzed to determine their function as well as to find any breed‐specific differences that may shed light on breed differences in adaptation, health and production.
Chinese Stock Market Return Predictability: Adaptive Complete Subset Regressions
Authors: Chen Keqi , Chen Rui , Zhang Xueyong , Zhu Min 
Published: October 2016

AbstractThis paper proposes a new combination framework to explore the Chinese stock market return predictability. While most well‐known predictor variables and simple combinations fail to beat the historical average benchmark, our adaptive complete subset regressions deliver statistically and economically significant out‐of‐sample performance. The subset, in which each regression includes five predictors, produces a significant statistic of 8.00% for January 2006 to September 2014. A mean‐variance investor who uses the adaptive subset regressions forecasts, instead of the historical average forecasts, can obtain sizable utility gains of 7.60% per annum. The results of our paper suggest that there is significant predictability in the Chinese aggregate stock market portfolio.
Alpha‐gal is a possible target of IgE‐mediated reactivity to antivenom
Authors: Fischer J. , Eberlein B. , Hilger C. , Eyer F. , Eyerich S. , Ollert M. , Biedermann T. 
Published: October 2016

AbstractBackgroundAntivenoms are mammalian immunoglobulins with the ability to neutralize snake venom components and to mitigate the progression of toxic effects. Immediate hypersensitivity to antivenoms often occurs during the first administration of these heterologous antibodies. A comparable clinical situation occurred after introduction of cetuximab, a chimeric mouse–human antibody, for cancer treatment. The carbohydrate epitope galactose‐alpha‐1,3‐galactose, located on the Fab region of cetuximab, was identified as the target responsible for IgE reactivity.ObjectiveTo investigate whether serum IgE antibodies directed to the α‐gal epitope are associated with hypersensitivity to equine antivenoms.MethodsAntivenoms were screened for α‐gal epitopes via immunoblot and in comparison with cetuximab and pork kidney by IgE reactivity assays. Basophil activation tests were used to investigate reactivity to antivenoms in samples from 20 patients with specific IgE antibodies to α‐gal and 10 controls. Additional IgE detection, IgE inhibition, ImmunoCAP inhibition, and skin prick tests were performed using samples from selected patients.ResultsBoth antivenoms and cetuximab induced positive skin prick test results in patients with sIgE to α‐gal. Alpha‐gal epitopes were detected by immunoblotting on antivenoms. Measurements of IgE reactivity and ImmunoCAP inhibition indicated that the antivenoms contained lower α‐gal contents than cetuximab. Deglycosylation assays and IgE inhibition tests confirmed that IgE‐mediated reactivity to antivenom is associated with α‐gal. Antivenoms, pork kidney, and cetuximab activated basophils from patients with IgE to α‐gal.ConclusionAlpha‐gal is a potential target of IgE‐mediated reactivity to equine antivenom and a possible cause of the high incidence of hypersensitivity reactions during the first application of equine antivenom.
Dynamic changes of the intraocular pressure and the pressure of cerebrospinal fluid in nonglaucomatous neurological patients
Authors: González‐Camarena Pedro Iván , San‐Juan Daniel , González‐Olhovich Irene , Rodríguez‐Arévalo David , Lozano‐Elizondo David , Trenado Carlos , Anschel David J. 
Published: October 2016

AbstractPurposeTo describe the dynamic changes of the intraocular pressure (IOP) and intracranial pressure (ICP) with normal or pathological values (intracranial hypertension) in nonglaucomatous neurological patients during lumbar punction (LP).MethodsCase–control study, prospective measurement of tonometry in both groups referred for LP. Intraocular pressure, ICP and translaminar pressure difference (TPD) were compared pre‐ and post‐LP.ResultsThirty‐six patients (72 eyes) with mean age of 38.5 (16–64) years and BMI of 26.81 kg/m2 were analysed. The initial mean ICP was 12.81 (± 6.6) mmHg. The mean TPD before and after the LP was 1.48 mmHg and 0.65 mmHg, respectively. The mean IOP of both eyes decreased to 0.8 mmHg post‐LP in patients with pathological ICP (p = 0.0193) and normal ICP (p = 0.006).ConclusionsWe found a statistically significant decrease of the IOP post‐LP compared to the pre‐LP in both groups, being higher in patients with pathological ICP. There were no significant differences of the IOP in patients with normal versus pathological ICP pre‐LP/post‐LP; neither was found a correlation between ICP and IOP.
Retinal oxygen saturation before and after glaucoma surgery
Authors: Nitta Eri , Hirooka Kazuyuki , Shimazaki Takeru , Sato Shino , Ukegawa Kaori , Nakano Yuki , Tsujikawa Akitaka 
Published: October 2016

AbstractPurposeThis study compared retinal vessel oxygen saturation before and after glaucoma surgery.MethodsRetinal oxygen saturation in glaucoma patients was measured using a non‐invasive spectrophotometric retinal oximeter. Adequate image quality was found in 49 of the 108 consecutive glaucoma patients recruited, with 30 undergoing trabeculectomy, 11 EX‐PRESS and eight trabeculotomy. Retinal oxygen saturation measurements in the retinal arterioles and venules were performed at 1 day prior to and at approximately 10 days after surgery. Statistical analysis was performed using a Student's t‐test.ResultsAfter glaucoma surgery, intraocular pressure (IOP) decreased from 19.8 ± 7.7 mmHg to 9.0 ± 5.7 mmHg (p < 0.001). Although oxygen saturation in retinal arterioles remained unchanged before and after surgery (104.7 ± 10.6% before and 105.4 ± 9.3% after surgery, p = 0.58), the oxygen saturation in the venules increased from 54.9 ± 7.4% to 57.4 ± 5.7% (p = 0.01).ConclusionIntraocular pressure (IOP) decreases caused by glaucoma surgery had an effect on the retinal venous oxygen saturation.
Reader Reaction on Estimation of Treatment Effects in All-Comers Randomized Clinical Trials with a Predictive Marker
Authors: Korn Edward L. , Freidlin Boris 
Published: October 2016

Summary
For a fallback randomized clinical trial design with a marker, Choai and Matsui (2015, Biometrics 71, 25–32) estimate the bias of the estimator of the treatment effect in the marker-positive subgroup conditional on the treatment effect not being statistically significant in the overall population. This is used to construct and examine conditionally bias-corrected estimators of the treatment effect for the marker-positive subgroup. We argue that it may not be appropriate to correct for conditional bias in this setting. Instead, we consider the unconditional bias of estimators of the treatment effect for marker-positive patients.
A Subgroup Cluster-Based Bayesian Adaptive Design for Precision Medicine
Authors: Guo Wentian , Ji Yuan , Catenacci Daniel V. T. 
Published: October 2016

SummaryIn precision medicine, a patient is treated with targeted therapies that are predicted to be effective based on the patient's baseline characteristics such as biomarker profiles. Oftentimes, patient subgroups are unknown and must be learned through inference using observed data. We present SCUBA, a Subgroup ClUster-based Bayesian Adaptive design aiming to fulfill two simultaneous goals in a clinical trial, 1) to treatments enrich the allocation of each subgroup of patients to their precision and desirable treatments and 2) to report multiple subgroup-treatment pairs (STPs). Using random partitions and semiparametric Bayesian models, SCUBA provides coherent and probabilistic assessment of potential patient subgroups and their associated targeted therapies. Each STP can then be used for future confirmatory studies for regulatory approval. Through extensive simulation studies, we present an application of SCUBA to an innovative clinical trial in gastroesphogeal cancer.
Alternating Logistic Regressions with Improved Finite Sample Properties
Authors: Perin Jamie , Preisser John S. 
Published: October 2016

Summary
Alternating logistic regressions is an estimating equations procedure used to model marginal means of correlated binary outcomes while simultaneously specifying a within-cluster association model for log odds ratios of outcome pairs. A recent generalization of alternating logistic regressions, known as orthogonalized residuals, is extended to incorporate finite sample adjustments in the estimation of the log odds ratio model parameters for when there is a moderately small number of clusters. Bias adjustments are made both in the sandwich variance estimators and in the estimating equations for the association parameters. The proposed methods are demonstrated in a repeated cross-sectional cluster trial to reduce underage drinking in the United States, and in an analysis of dental caries incidence in a cluster randomized trial of 30 aboriginal communities in the Northern Territory of Australia. A simulation study demonstrates improved performance with respect to bias and coverage of their estimators relative to those based on the uncorrected orthogonalized residuals procedure.
Towards an event stratigraphy for Baltic Sea sediments deposited since AD 1900: approaches and challenges
Authors: Moros Matthias , Andersen Thorbjørn J. , Schulz‐Bull Detlef , Häusler Katharina , Bunke Dennis , Snowball Ian , Kotilainen Aarno , Zillén Lovisa , Jensen Jørn B. , Kabel Karoline , Hand Ines , Leipe Thomas , Lougheed Bryan C. , Wagner Bernd , Arz Helge W. 
Published: October 2016

Reconstructions of environmental changes at sub‐decadal to decadal resolution based on central Baltic Sea sediments rely on accurate and precise high‐resolution sediment depth/age relationships. A model chronology for Baltic Sea sediments is presented here based on established historical records of anthropogenic radionuclides (137Cs/241Am/bomb14C), polychlorinated biphenyls (PCBs), lead (Pb) and stable lead isotope (206/207Pb ratios), and radionuclide 210Pb and 14C decay dating methods. Marker horizons consisting of chemical precipitates formed by documented Major Baltic Inflow (MBIs) events and an extended diatom bloom period were also integrated into the model. The main time markers in Baltic Sea sediments that formed during the last 120 years were the following: (i) the deepest observation of 210Pbunsupp. (marking the 210Pb dating horizon) and departure of Hg from natural background levels at c. AD 1900; (ii) first detectable presence of PCBs at AD 1935; (iii) radionuclide production (i.e. 241Am) due to nuclear weapons testing between AD 1954 and AD 1975, with a peak in AD 1963; (iv) maximum heavy metal and PCB concentrations in the AD 1960s/1970s; (v) the Chernobyl nuclear accident in AD 1986 as a sharp 137Cs increase; (vi) exceptionally strong diatom blooms with a massive diatom layer found in the Eastern Gotland Basin in AD 1988–1990; and (vii) characteristic manganese‐carbonate layers in the deeper central basins formed by MBIs in AD 1993 and AD 2003. A precise and accurate sediment depth/age relationship can only be achieved in restricted areas of the Baltic Sea where continuous sedimentation has prevailed and there has been limited postdepositional disturbance. We demonstrate that parallel Hg and 137Cs measurements can be used to assess the quality of sediment sequences for high‐resolution environmental reconstructions. We show examples of sediment profiles that conform to the historical record, and examples from Western Baltic Sea areas where it appears to be impossible to establish accurate geochronologies.
The suppression of bromodomain and extra‐terminal domain inhibits vascular inflammation by blocking NF‐κB and MAPK activation
Authors: Huang Mingcheng , Zeng Shan , Zou Yaoyao , Shi Maohua , Qiu Qian , Xiao Youjun , Chen Guoqiang , Yang Xiuyan , Liang Liuqin , Xu Hanshi 
Published: October 2016

Background and PurposeThere is increasing evidence indicating that bromodomain and extra‐terminal domain (BET) proteins play a critical role in the regulation of immune and inflammatory responses; however, their contribution to vascular inflammation has not yet been elucidated. In this study, we investigated the effect of inhibiting BET bromodomain on vascular inflammation and the underlying mechanisms.Experimental ApproachHUVECs were isolated from fresh umbilical cords. JQ1, a specific BET bromodomain inhibitor, and Brd shRNA were used to evaluate the regulation of the BET proteins in vascular inflammation. Leukocyte adhesion to HUVECs was measure by an adhesion assay. Western blot or immunohistochemical analysis was used to detect the protein expression. Real‐time PCR was used to evaluate mRNA expression. Leukocyte accumulation in vivo was determined by an acute lung inflammation model.Key ResultsBET bromodomain inhibition suppressed the expression of adhesion molecules induced by TNF‐α‐ or LPS, including ICAM‐1, VCAM‐1 and E‐selectin, and inhibited leukocyte adhesion to activated HUVEC monolayers. Treatment with JQ1 also attenuated the LPS‐induced accumulation of leukocytes and expression of endothelial adhesion molecules in the acute lung inflammation model in vivo. Furthermore, BET bromodomain inhibition reduced the activity of p38 and JNK MAPKs and NF‐κB in TNF‐α‐stimulated HUVECs. TNF‐α‐induced NF‐κB activation was also blocked by inhibitors of p38 (SB203580) or JNK (SP600125).Conclusions and ImplicationsBET bromodomain is important for regulating endothelial inflammation. Strategies targeting endothelial BET bromodomain may provide a new therapeutic approach for controlling inflammatory‐related diseases.