bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeography of two closely related species of Allium endemic to East Asia: Population evolution in response to climate oscillations
Authors: Yang Jingtian , Zhou Songdong , Huang Deqing , He Xingjin 
Published: July 2018

AbstractThis study investigated the effects of climate oscillations on the evolution of two closely related Allium species, A. neriniflorum and A. tubiflorum. We sequenced three cp DNA (cpDNA) fragments (rps16, rpl32‐trnL, and trnD‐trnT, together approximately 2,500 bp in length) of two closely related Allium species, with samples from 367 individuals in 47 populations distributed across the total range of these species. The interspecific and intraspecific divergence times of the two species were in the Quaternary glaciation. The population divergence was high for the cpDNA variation, suggesting a significant phylogeographic structure (NST = 0.844, GST = 0.798, p < 0.05). Remarkable ecological differentiation was also revealed by Niche models and statistical analyses. Our results suggest the speciation event of the two species was triggered by violent climatic changes during the Quaternary glaciation.
Stochastic procedure for the simulation of synthetic main shock‐aftershock ground motion sequences
Authors: Hu Sheng , Gardoni Paolo , Xu Longjun 
Published: July 2018

SummaryAccording to the current seismic codes, structures are designed to resist the first damaging earthquake during their service life. However, after a strong main shock, a structure may still face damaging aftershocks. The main shock‐aftershock sequence may result in major damage and eventually the collapse of a structure. Current studies on seismic hazard mainly focus on the modeling and simulation of main shocks. This paper proposes a 3‐step procedure to generate main shock‐aftershock sequences of pairs of horizontal components of a ground motion at a site of interest. The first step generates ground motions for the main shock using either a source‐based or site‐based model. The second step generates sequences of aftershocks' magnitudes, locations, and times of occurrence using either a fault‐based or seismicity‐based model. The third step simulates pairs of ground motion components using a new empirical model proposed in this paper. We develop prediction equations for the controlling parameters of a ground motion model, where the predictors are the site condition and the aftershock characteristics from the second step. The coefficients in the prediction equations and the correlation between the model parameters (of the 2 horizontal components of 1 record and of several records in 1 sequence) are estimated using a database of aftershock accelerograms. A backward stepwise deletion method is used to simplify the initial candidate prediction equations and avoid overfitting the data. The procedure, based on easily identifiable engineering parameters, is a useful tool to incorporate effects of aftershocks into seismic analysis and design.
Convergent phenotypic evolution of the visual system via different molecular routes: How Neotropical cichlid fishes adapt to novel light environments
Authors: Härer Andreas , Meyer Axel , Torres-Dowdall Julián 
Published: July 2018

AbstractHow predictable is evolution? This remains a fundamental but contested issue in evolutionary biology. When independent lineages colonize the same environment, we are presented with a natural experiment that allows us to ask if genetic and ecological differences promote species-specific evolutionary outcomes or whether species phenotypically evolve in a convergent manner in response to shared selection pressures. If so, are the molecular mechanisms underlying phenotypic convergence the same? In Nicaragua, seven species of cichlid fishes concurrently colonized two novel photic environments. Hence, their visual system represents a compelling model to address these questions, particularly since the adaptive value of phenotypic changes is well-understood. By analyzing retinal transcriptomes, we found that differential expression of genes responsible for color vision (cone opsins and cyp27c1) produced rapid and mostly convergent changes of predicted visual sensitivities. Notably, these changes occurred in the same direction in all species although there were differences in underlying gene expression patterns illustrating nonconvergence at the molecular level. Adaptive phenotypes evolved deterministically, even when species differ substantially in ecology and genetic variation. This provides strong evidence that phenotypic evolution of the visual system occurred in response to similar selective forces of the photic environment.
Adaptive radiation along a deeply conserved genetic line of least resistance inAnolislizards
Authors: McGlothlin Joel W. , Kobiela Megan E. , Wright Helen V. , Mahler D. Luke , Kolbe Jason J. , Losos Jonathan B. , Brodie Edmund D. 
Published: July 2018

AbstractOn microevolutionary timescales, adaptive evolution depends upon both natural selection and the underlying genetic architecture of traits under selection, which may constrain evolutionary outcomes. Whether such genetic constraints shape phenotypic diversity over macroevolutionary timescales is more controversial, however. One key prediction is that genetic constraints should bias the early stages of species divergence along “genetic lines of least resistance” defined by the genetic (co)variance matrix, G. This bias is expected to erode over time as species means and G matrices diverge, allowing phenotypes to evolve away from the major axis of variation. We tested for evidence of this signal in West Indian Anolis lizards, an iconic example of adaptive radiation. We found that the major axis of morphological evolution was well aligned with a major axis of genetic variance shared by all species despite separation times of 20–40 million years, suggesting that divergence occurred along a conserved genetic line of least resistance. Further, this signal persisted even as G itself evolved, apparently because the largest evolutionary changes in G were themselves aligned with the line of genetic least resistance. Our results demonstrate that the signature of genetic constraint may persist over much longer timescales than previously appreciated, even in the presence of evolving genetic architecture. This pattern may have arisen either because pervasive constraints have biased the course of adaptive evolution or because the G matrix itself has been shaped by selection to conform to the adaptive landscape.
Dermatofibrosarcoma protuberans with a novel COL6A3‐PDGFD fusion gene and apparent predilection for breast
Authors: Dickson Brendan C. , Hornick Jason L. , Fletcher Christopher D. M. , Demicco Elizabeth G. , Howarth David J. , Swanson David , Zhang Lei , Sung Yun‐Shao , Antonescu Cristina R. 
Published: July 2018

AbstractDermatofibrosarcoma protuberans is a locally aggressive superficial mesenchymal neoplasm. It typically occurs in adulthood, and has been reported to have a slight male predilection. Tumors have a characteristic histopathologic appearance, including: storiform architecture, infiltrative “honeycomb” growth within subcutaneous adipose tissue, and immunoreactivity for CD34. Virtually all molecularly characterized cases to date have been found to harbor a COL1A1‐PDGFB fusion product. Following identification of an index patient with a novel COL6A3‐PDGFD fusion gene, we undertook a molecular investigation, using a combination of RNA sequencing and fluorescence in situ hybridization (FISH), to assess the prevalence of PDGFD rearrangement in dermatofibrosarcoma protuberans (N = 63). Three additional patients were found to have balanced PDGFD rearrangements. Interestingly, all 4 tumors arose on the breast of females. As a result, we subsequently examined 16 additional cases of primary breast dermatofibrosarcoma protuberans, identifying 2 additional tumors with PDGFD rearrangement. The morphology and immunophenotype of all 6 cases was analogous to those with the canonical COL1A1‐PDGFB fusion; none of the cases showed fibrosarcomatous transformation. This study illustrates that the COL6A3‐PDGFD fusion product is rare in dermatofibrosarcoma protuberans, and associated with an apparent predilection for breast. An awareness of this variant is important for pathologists, as it will not be detected using conventional reverse transcription polymerase chain reaction or FISH‐based diagnostic assays for dermatofibrosarcoma protuberans.
Older men with bipolar disorder: Clinical associations with early and late onset illness
Authors: Almeida Osvaldo P. , Hankey Graeme J. , Yeap Bu B. , Golledge Jonathan , Flicker Leon 
Published: July 2018

ObjectivesOlder adults living with bipolar disorder (BD) include people with early and late onset of symptoms. This study aimed to clarify the cross‐sectional and longitudinal clinical associations of BD with early and late onset.MethodsCohort study of 38 173 men aged 65–85 years followed for up to 17.6 years. We used the Western Australian Data Linkage System to establish the presence of BD, as well as diabetes, cardiovascular and renal diseases, cancer, respiratory and gastrointestinal diseases, alcohol use disorder, dementia, and mortality. The causes of death were recorded according to the International Classification of Diseases. We defined late onset BD using 2 different cut‐points: 50 and 60 years.ResultsThe prevalence of medical morbidities was greater among participants with than without BD, and cardiovascular diseases were more frequent among those with onset before than after 50 years (odds ratio = 1.72, 95% confidence interval = 1.01, 2.94). Bipolar disorder was associated with increased hazard ratio of dementia and death, but there was no difference between early and late onset participants. Death by suicide or accidents occurred exclusively among BD participants with illness onset <60 years, whereas death associated with strokes and neurodegenerative diseases was more frequent among those with illness onset ≥60 years than in the general population (HR = 2.28, 95% confidence interval = 1.34, 3.88).ConclusionsOur results indicate that the clinical associations and outcomes of older adults living with BD are not markedly influenced by age of onset. However, mortality data suggest that differences between older adults with BD onset before and after age 60 years should continue to be explored.
Model for MHD viscoelastic nanofluid flow with prominence effects of radiation
Authors: Hussain Azad , Sarwar Lubna , Akbar Sobia , Malik M. Y. , Ghafoor Saadia 
Published: July 2018

AbstractPresent phenomenon is dedicated to analyze the problem of steady state flow of an incompressible fluid model pertained to as magnetohydrodynamics viscoelastic nanofluid through a permeable plate. Continuity, momentum, energy, and concentration expressions are elaborated to comprehend nature of the fluid flow. Numerical solutions are presented. The arising mathematical problem is governed by interesting parameters which include viscoelastic parameter, magnetic field parameter, nanofluid parameter, radiation parameter, skin friction, Prandtle number, and Sherwood number. Solutions for the dimensionless velocity, temperature, and concentration fields and the corresponding skin friction, Nusselt number, and Sherwood number are determined and canvassed with the help of graphs for the distinct values of pertinent parameters.
Drying‐Off Periods for Irrigated Sugarcane to Maximize Sucrose Yields Under Brazilian Conditions
Authors: Dias Henrique Boriolo , Sentelhas Paulo Cesar 
Published: July 2018

AbstractThe natural ripening process in sugarcane plants is influenced by several factors, including water stress. In irrigated sugarcane areas, water application is often withheld prior to harvest, a process called drying‐off, which is done to increase the sucrose content and yield, and to provide suitable conditions of soil moisture for mechanical harvesting. Based on this, the objective of this study was to determine the drying‐off periods for irrigated sugarcane in different Brazilian regions to maximize sucrose yields. The APSIM‐Sugarcane model was used to simulate 12‐month plant cane in 12 Brazilian sites for a long‐term period. Three soil types with different water‐holding capacities (low, medium and high) were adopted. The drying‐off periods were determined based on the relationship between relative stalk dry mass yield (dried‐off and fully irrigated) and days in which water was withheld prior to harvest, considering yield reduction up to 4% as a target. As expected, the drying‐off periods varied considerably according to locations, soil types and harvest dates, with the median ranging from 15 to 115 days. In general, more drying‐off days are required at the beginning and end of the harvesting season, when higher interannual variability is also observed. The results obtained are useful for planning and decision‐making in irrigated sugarcane areas, since they allow evaluation of the best strategy to maximize sucrose yield. © 2018 John Wiley & Sons, Ltd.
Computational and biochemical studies of isothiocyanates as inhibitors of proteasomal cysteine deubiquitinases in human cancer cells
Authors: Ahmed Zainab Sabry Othman , Li Xin , Li Feng , Cheaito Hassan Ali , Patel Kush , Mosallam El‐Sayed Mohammed , Elbargeesy Gehad Abd El‐Fattah Hassan , Dou Q Ping 
Published: July 2018

AbstractIsothiocyanates (ITCs) are natural chemoprotective products found abundantly in cruciferous vegetables. However, the cancer‐relevant targets and molecular mechanisms of ITCs remain unclear. We hypothesize that ITCs, as electrophiles, can interact with the catalytic triads (CYS, HIS, and ASP) of the proteasomal cysteine deubiquitinases USP14 and UCHL5, ultimately inhibiting their activities. In the current study, we exploited this possibility by performing both computational docking and biochemical validation assays using human breast and prostate cancer cell models. Docking results suggest that benzyl isothiocyanate, phenethyl isothiocyanate, and DL‐sulforaphane are more potent inhibitors of UCHL5 than USP14, and these ITCs could interact with the catalytic triads of UCHL5 and USP14. Indeed, ubiquitin vinyl sulfone assay confirmed the inhibitory activity of each ITC on the ubiquitin‐binding activity of UCHL5 and USP14. We also found that inhibition of USP‐14 and UCHL5 activities by the ITCs caused increased levels of USP14 and UCHL5 proteins, but not the third 19S‐deubiquitinating enzyme (DUB), POH1/RPN11, suggesting feedback loop activation and further supporting that ITCs are inhibitors of proteasomal cysteine DUBs. Associated with DUB inhibition by ITCs, ubiquitinated proteins were significantly increased, accompanied with induction of apoptosis, inhibition of proliferation and suppression of cell invasion. Our findings of ITCs as proteasomal cysteine DUB inhibitors should provide insightful information for designing, discovering and developing potent, specific 19S‐DUB inhibitors for cancer therapies.
Retracted: IL‐6/STAT3 pathway intermediates M1/M2 macrophage polarization during the development of hepatocellular carcinoma
Authors: Yin Zi , Ma Tingting , Lin Ye , Lu Xin , Zhang Chuanzhao , Chen Sheng , Jian Zhixiang 
Published: July 2018

AbstractHuman cancers, including hepatocellular carcinoma (HCC), are characterized by a high degree of drug resistance in chemotherapy. However, the underlying molecular mechanism remains unknown. To the role of interleukin‐6 (IL‐6)/signal transducer and activator of transcription 3 (STAT3) signaling pathway in the regulation of macrophage polarization, M1‐type and M2‐type macrophages were separately induced using lipopolysaccharide and interleukin‐4 (IL‐4), and we found that the IL‐6/STAT3 signaling pathway was inhibited in M1‐type macrophages but activated in M2‐type macrophages. After anti‐IL‐6‐treated macrophages were separately induced by lipopolysaccharide and IL‐4, we found that the inhibition of IL‐6/STAT3 signaling pathway turned macrophages into M1‐type. Co‐culture with M1‐type macrophages reduced HCC cell viability, proliferation, invasion, migration, drug resistance, but increased apoptosis. Co‐culture with M2‐type macrophages yielded reciprocal results. The inhibition of IL‐6/STAT3 signaling pathway mediated by anti‐IL6 was shown to significantly enhance the effects of M1‐type macrophages on HCC cells and rescue HCC cells from co‐culture with M2‐type macrophages. Tumor xenografts of co‐cultured HCC cells were established in nude mice and the results showed that the inhibition of IL‐6/STAT3 signaling pathway mediated by anti‐IL6 was found to reduce tumor formation of HCC cells co‐cultured with M1‐ or M2‐type macrophages and lung metastases. The current study reveals a novel mechanism of IL‐6/STAT3 signaling pathway in the regulation of macrophage polarization, thus contributing to HCC metastasis and drug resistance in chemotherapy.
Predictive accuracy of serum total calcium for both critically high and critically low ionized calcium in critical illness
Authors: Hu Zhi‐De , Huang Yuan‐Lan , Wang Mei‐Ying , Hu Ge‐Ji‐Le , Han Yan‐Qiu 
Published: July 2018

BackgroundThe accuracy of total calcium and its corrected value for predicting critically high and critically low ionized calcium in critical illness is controversial. The aim of this study was to investigate whether the concentration of total serum calcium, either corrected for albumin or not, could predict critically high or low values in critical illness.MethodsThis report describes a retrospective study using the Medical Information Mart for Intensive Care (MIMIC) III database. Test panels that contained serum albumin, total calcium, and ionized calcium (named ATI panels) with order time intervals of less than one hour were extracted. The predictive accuracy of total calcium, either corrected for albumin or not, was assessed using receiver operating characteristic (ROC) curve analysis.ResultsA total of 12 118 ATIs with 103 critically low and 92 critically high ionized calcium results were extracted. The areas under ROC curves (AUCs) of corrected and uncorrected total calcium for predicting critically low ionized calcium were 0.69 (95% CI: 0.61‐0.76) and 0.70 (95% CI: 0.63‐0.78), respectively. For predicting critically high ionized calcium, the AUCs were 0.98 (95% CI: 0.97‐1.00) and 0.97 (95% CI: 0.95‐1.00), respectively. With positive predictive values (PPVs) of 0.05 and 0.10, the sensitivities (both corrected and uncorrected) were approximately 0.50 for predicting critically low ionized calcium and 0.95 for predicting critically high ionized calcium.ConclusionsTotal calcium, either corrected for albumin or not, is not a reliable test to predict critically low ionized calcium in critical illness. Total calcium's predictive accuracy for critically high ionized calcium is high.
The SNP43 (G/A) polymorphism in CAPN10 gene confers an increased risk of cognitive impairment in cerebral small vessel disease
Authors: Wu Kai , Cai Ying 
Published: July 2018

BackgroundCognitive impairment, significantly reducing processing speed and executive function, is the critical consequence of cerebral small vessel disease (SVD), in which genetic variations have been studied. In this study, we explore the role of SNP43 (G/A) and SNP63 (C/T) polymorphism in the CAPN10 on cognitive impairment process in cerebral SVD.MethodsCerebral SVD patients (n = 224) and healthy controls (n = 187) were recruited. The relationship between frequency distribution of SNP43 (G/A) and SNP63 (T/C) genotype and allele in CAPN10 gene, and cognitive impairment was examined. The independent risk factors for cognitive impairment in SVD were determined by logistic regression analysis.ResultsAccordingly, the frequency distribution of genotype and allele at SNP43 (G/A) was significantly different between cerebral SVD patients and healthy controls. Cerebral SVD patients with GG genotype were more susceptible for cognitive impairment, whereas cerebral SVD patients with GA + AA genotype were less possible to suffer from cognitive impairment, compared with those with GG genotype. And also, cerebral SVD does not include SNP63 (C/T) to associate with cognitive impairment, and SNP43 (G/A), total cholesterol, triglyceride, low‐density lipoprotein, and high‐density lipoprotein were independent risk factors for cognitive impairment in SVD.ConclusionOur study provides evidence that SNP43 (G/A) in the CAPN10 gene increases the risk of cognitive impairment in SVD patients. Besides it is proven that, patients with G allele are more susceptible to suffer from cerebral SVD with worse cognitive impairment.
Advanced liver fibrosis effects on the response to sofosbuvir‐based antiviral therapies for chronic hepatitis C
Authors: Morio Kei , Imamura Michio , Kawakami Yoshiiku , Nakamura Yuki , Hatooka Masahiro , Morio Reona , Fujino Hatsue , Nakahara Takashi , Murakami Eisuke , Kawaoka Tomokazu , Tsuge Masataka , Hiramatsu Akira , Aikata Hiroshi , Hayes C. Nelson , Miki Daiki , Ochi Hidenori , Katamura Yoshio , Arataki Keiko , Moriya Takashi , Ito Hiroyuki , Tsuji Keiji , Kohno Hiroshi , Waki Koji , Tamura Toru , Nakamura Toshio , Chayama Kazuaki ,   Hiroshima Liver Study Group
Published: July 2018

BackgroundSustained virological response (SVR) rates for the treatment of chronic hepatitis C virus (HCV)–infected patients have drastically improved with the use of direct‐acting antiviral (DAA) therapies; however, a small minority of patients still fails to eradicate the virus. We analyzed factors associated with SVR in DAA therapy and the effect of age and liver fibrosis on treatment response.MethodsNine hundred and eighteen patients with chronic HCV infection were treated with 24 weeks of daclatasvir plus asunaprevir (DCV + ASV) or 12 weeks of sofosbuvir plus ledipasvir (SOF + LDV), ombitasvir, paritaprevir plus ritonavir (OMB + PTV + r) or sofosbuvir plus ribavirin (SOF + RBV). Multivariate logistic regression analysis was used to identify factors associated with SVR. The effect of age and liver fibrosis on SVR was analyzed.ResultsThe overall SVR rate was 95.4% (876 of 918 patients), and rates by DAA regimen were 93.4%, 95.7%, 100%, and 95.0% in DCV + ASV‐treated, SOF + LDV‐treated, OMB + PTV + r‐treated, and SOF + RBV‐treated patients, respectively. Patients older than 75 years achieved a similar SVR rate with those aged 75 years or younger (96.4% and 94.8%, respectively). Multivariate logistic regression analysis identified absence of DAA therapy history (odds ratio [OR], 3.868 for presence; P = 0.002) and FIB‐4 index of less than 3.25 (OR, 5.042 for ≥3.25; P = 0.001) as independent predictors for SVR. SVR rates were significantly lower in patients with FIB4 index of 3.25 or more compared with those with less than 3.25, especially in sofosbuvir‐based therapies such as SOF + LDV‐treated or SOF + RBV‐treated patients.ConclusionBoth older and younger patients respond similarly to DAA therapy. Advanced liver fibrosis affects the virological response to sofosbuvir‐based therapy.