bluuebunny/crossref_metadata_2025 huggingface dataset:
Palonosetron is nonsuperior to ondansetron in acute phase but provides superior antiemetic control in delayed phase for pediatric patients administered highly emetogenic chemotherapy
Authors: Tan Juan , Wang Shan , Liang Xiaohua , Li Chang‐Chun , Zhang Jun , Zhao Zhenzhen , Kong Xiang‐Ru , Deng Xiaobin , Peng Liang , Yang Chao
Published: September 2017

Purpose

Chemotherapy‐induced nausea and vomiting (CINV) in children remains to be a major side effect despite antiemetic treatment. Palonosetron is a new generation 5‐HT3 receptor antagonists effective against acute and delayed nausea and vomiting. This study aimed to compare the therapeutic values of palonosetron and ondansetron in preventing pediatric CINV.

Methods

A prospective, randomized, double‐blind, parallel controlled study was conducted in 0–18 years old cancer patients administered highly emetogenic chemotherapy, with different dosage of palonosetron or ondansetron, both followed by dexamethasone. The patients were observed for vomiting and nausea from 0 to 120 hr after chemotherapy initiation. All adverse events (AEs) during the study period were recorded. This study was registered with the Chinese Clinical Trial Registry, number ChiCTR‐TRC‐14004891.

Results

Between August 2014 and July 2016, 565 patients were randomly assigned to receive 5 μg/kg palonosetron (n = 185), 10 μg/kg palonosetron (n = 186), and 3 × 150 μg/kg ondansetron (n = 194), of whom 181, 185, and 189, respectively, were included in the efficacy analysis. Complete response (CR) rates during the acute phase were 69.1, 69.7, and 64.6%, respectively, in the 5 μg/kg palonosetron, 10 μg/kg palonosetron, and ondansetron groups. In the delayed phase, 10 μg/kg palonosetron (CR, 53.5%) showed superiority to 5 μg/kg palonosetron (CR, 39.8%) and ondansetron (CR, 32.8%) groups (P < 0.05). The most frequently observed drug‐related AEs were nervous system disorders, mainly headache, with an incidence of 2.8, 2.2, and 2.6% in each group, respectively.

Conclusion

Combination of palonosetron plus dexamethasone is highly effective in controlling acute and delayed CINV, with palonosetron superior to ondansetron.
Rheological, crystallization and electrical properties of poly vinylidene fluoride filled with micron iron
Authors: Zhang Lulu , Yang Bin , Xia Ru , Qian Jiasheng , Cao Ming , Miao Jibin , Su Lifen , Chen Peng
Published: September 2017

Micron iron was added into poly(vinylidene fluoride) (PVDF) via solution method to prepare the PVDF conductive composites. The electrical properties, non‐isothermal crystallization kinetics, crystal form, rheological, and thermal properties of PVDF/Fe composites were studied. Compared with neat PVDF, the PVDF/Fe composites had a higher crystallization rate, thermal stability and conductivity, but both crystallinity and flow property would decrease. The PVDF/Fe composites were subsequently treated by an alternating magnetic field. The percolation threshold value of the composites was found to reduce from 30 vol % to 11 vol %. The conductivity of the PVDF/Fe composites after alternating magnetic treatment increased by 8 orders of magnitude in comparison to neat PVDF, and the electrical conductivity of the PVDF/Fe composite with 30 vol % iron content was about 10−0.58S m−1. The iron particles were more likely to form a conductive network in the polymer matrix after the magnetic field treatment according to morphological observation. The present work will supply an insight into the design of PVDF conductive composites as well as the further studies on the relationship between structure and property of polymer composites. POLYM. COMPOS., 40:E88–E101, 2019. © 2017 Society of Plastics Engineers
Hierarchical carbon fiber‐SiO2 hybrid/polyimide composites with enhanced thermal, mechanical, and tribological properties
Authors: Chen Beibei , Li Xiaofang , Li Xiang , Jia Yuhan , Yang Jin , Li Changsheng
Published: September 2017

Hierarchical carbon fiber‐SiO2 hybrid (CF‐SiO2) was first fabricated and CF‐SiO2/polyimide composite (CF‐SiO2/PI) was subsequently prepared by typical solution casting and thermal imidization. The microstructure and enhancement of CF‐SiO2 hybrid on the thermal, mechanical, and tribological properties of PI were investigated. Results showed SiO2 particles with the size of ∼500 nm were coated onto CF surface successfully, which endowed CF possessed active sites and high surface roughness. The 5% weight loss temperatures (T–5 wt%) of PI was improved from 328.6°C to 499.2°C by the incorporation of CF‐SiO2 hybrid. Besides, the hardness and elastic modulus of CF‐SiO2/PI composite reached 0.411GPa and 4.904 GPa, that is, an improvement of 22% and 12.2%, respectively, compared to pure PI. More importantly, the friction coefficient and wear rate of CF‐SiO2/PI reached 0.32 and 5.35 × 10−5 mm3/Nm, which were much lower than that of PI or CF/PI. This was mainly attributed to the fact that SiO2 could not only improve the thermal and mechanical properties but also promote the load transferring effectively during the friction and wear process through enhancing the interfacial effect between CF and PI. POLYM. COMPOS., 39:E1626–E1634, 2018. © 2017 Society of Plastics Engineers
Plasticizer effect and electronic diffusive behavior of polyaniline‐modified clay in polystyrene nanocomposites
Authors: Pinto Camila P. , Pachekoski Wagner M. , Dalmolin Carla , Becker Daniela
Published: September 2017

Montmorillonite clay (MMT) was modified with polyaniline (Pani) and used to produce nanocomposites in a polystyrene (PS) matrix. MMT/Pani particles were evaluated by Infrared Spectroscopy (FT‐IR), where groups of both MMT and Pani were found; and by XRD, where an increase in the interlamellar distance was detected, changes on the resistive electrical behavior of MMT to a diffusive one for MMT/Pani were identified by Electrochemical Impedance Spectroscopy (EIS). Nanocomposites of PS with MMT‐Pani were produced by melt intercalation in the proportions of 1%, 3%, 5%, and 10%. They were characterized by Transmission Electron Microscopy (TEM), Differential Scanning Calorimetry (DSC), Thermogravimetry (TG), and EIS. Main results showed a decrease in the glass transition temperature and in the onset temperature according to the amount of MMT‐Pani. Analyses by EIS demonstrated a capacitive behavior (polarization) for nanocomposites containing smaller amounts of MMT‐Pani and diffusive behavior for the largest proportions, which were explained by a model of electronic diffusion in the Pani polymeric chain due to the chain intercalation observed by TEM in samples with higher concentration of MMT‐Pani. Therefore, the results suggest that the addition of MMT‐Pani alters some properties of the polystyrene matrix, changing its degradation and transition temperature, and its electrical behavior. POLYM. COMPOS., 40:37–45, 2019. © 2017 Society of Plastics Engineers
Influence of the mold temperature on the material properties and the vibration welding process of crosslinked polyamide 66
Authors: Leisen Christoph , Wolf Michael , Drummer Dietmar
Published: September 2017

Radiation crosslinking of polyamide 66 with electron beams alters the material characteristics. This leads to a varied relationship between the process, the structure, and properties for vibration welding crosslinked polyamide 66. A three‐dimensional network of covalent bonds in the amorphous areas results in an impeded melt flow and altered welding characteristics. A possible way to influence this three‐dimensional network is to change the mold temperature during the injection molding process. At higher mold temperatures, the degree of crystallinity increases and leads to a decrease in the resulting covalent bonds in the amorphous area. The altered degree of covalent bonds influences the vibration welding process. Higher temperatures during the process can be achieved. The scope of this article is to show how the mold temperature influences the material characteristics and, by extension, the resulting processing and welding characteristics of radiation crosslinked polyamide 66. Optical, thermal, mechanical and chemical investigations serve to highlight the influence of the mold temperature on the material and the welding process of radiation crosslinked polyamide 66. POLYM. ENG. SCI., 58:E207–E214, 2018. © 2017 Society of Plastics Engineers
Dynamic Changes in Brain Mesenchymal Perivascular Cells Associate with Multiple Sclerosis Disease Duration, Active Inflammation, and Demyelination
Authors: Iacobaeus Ellen , Sugars Rachael V. , Törnqvist Andrén Anton , Alm Jessica J. , Qian Hong , Frantzen Janek , Newcombe Jia , Alkass Kanar , Druid Henrik , Bottai Matteo , Röyttä Matias , Le Blanc Katarina
Published: September 2017

Vascular changes, including blood brain barrier destabilization, are common pathological features in multiple sclerosis (MS) lesions. Blood vessels within adult organs are reported to harbor mesenchymal stromal cells (MSCs) with phenotypical and functional characteristics similar to pericytes. We performed an immunohistochemical study of MSCs/pericytes in brain tissue from MS and healthy persons. Post-mortem brain tissue from patients with early progressive MS (EPMS), late stage progressive MS (LPMS), and healthy persons were analyzed for the MSC and pericyte markers CD146, platelet-derived growth factor receptor beta (PDGFRβ), CD73, CD271, alpha-smooth muscle actin, and Ki67. The MS samples included active, chronic active, chronic inactive lesions, and normal-appearing white matter. MSC and pericyte marker localization were detected in association with blood vessels, including subendothelial CD146+PDGFRβ+Ki67+ cells and CD73+CD271+PDGFRβ+Ki67– cells within the adventitia and perivascular areas. Both immunostained cell subpopulations were termed mesenchymal perivascular cells (MPCs). Quantitative analyses of immunostainings showed active lesions containing increased regions of CD146+PDGFRβ+Ki67+ and CD73+CD271+PDGFRβ+Ki67– MPC subpopulations compared to inactive lesions. Chronic lesions presented with decreased levels of CD146+PDGFRβ+Ki67+ MPC cells compared to control tissue. Furthermore, LPMS lesions displayed increased numbers of blood vessels harboring greatly enlarged CD73+CD271+ adventitial and perivascular areas compared to control and EPMS tissue. In conclusion, we demonstrate the presence of MPC subgroups in control human brain vasculature, and their phenotypic changes in MS brain, which correlated with inflammation, demyelination and MS disease duration. Our findings demonstrate that brain-derived MPCs respond to pathologic mechanisms involved in MS disease progression and suggest that vessel-targeted therapeutics may benefit patients with progressive MS.
Surgical Site Infections in Emergency Abdominal Surgery at Tamale Teaching Hospital, Ghana
Authors: Tabiri Stephen , Yenli Edwin , Kyere Martin , Anyomih Theophilus T. K.
Published: September 2017

Background

Surgical site infections (SSIs) result in delayed wound healing, increased use of antibiotics and increased length of hospital stay, putting remarkable physical and financial burden on patients, their relatives and the healthcare facilities. Patient‐related factors, such as pre‐existing colonization with antibiotic‐resistant bacteria, and clinical‐related factors, such as adherence to sterile techniques, contribute to the development of SSIs. The objective of this study, therefore, was to determine the SSI rate and risk factors for emergency abdominal surgeries at Tamale Teaching Hospital, Ghana.

Methods

The study population was composed of patients undergoing emergency abdominal surgery at the Tamale Teaching Hospital between June 2010 and June 2015. Demographic and clinical data were collected and included, but was not limited to, patient age and sex, type of procedure performed, wound class (dirty or contaminated), receipt of perioperative blood transfusion, American Society of Anesthesiologists (ASA) score, presence of SSI, length of hospital stay and outcome of surgery. Standard multiple regression was used to statistically assess the independent variables for their association with SSI, and Pearson correlation coefficient was used to determine the strength of association. The beta (β) values, which had the greatest influence on the overall SSI, indicated the relative influence of the entered variable(s).

Results

A total of 1011 patients underwent various emergency abdominal surgical procedures during the period of study. The β values were 0.008 for perioperative blood transfusion, 0.050 for sex, − 0.048 for ASA risk, − 0.001 for having health insurance, 0.037 for being referred from another health facility and 0.034 for age. Sex was the most distinctive contributor to SSI, while perioperative blood transfusion showed the least influence. Sex and ASA score were the best predictors of SSI occurrence. The coefficients of the P values for wound class and serum haemoglobin level (g/dL) were 0.000 and 0.032, respectively. The outcome of surgery was significantly and strongly associated with overall SSI and vice versa (r = 0.088, P < 0.01 two‐tailed).

Conclusion

Sex, ASA score, perioperative blood transfusion, wound class and haemoglobin level can predispose to SSI.
Annual variability in acorn production and pre‐dispersal damage to acorns of four fagaceous species in two adjacent forest stands with different mixed ratios in western Japan
Authors: Hirayama Kimiko , Imai Tatsuo , Enomoto Kosaku , Tachikawa Chieri
Published: September 2017

We investigated the relationships between the annual variation in acorn production and pre‐dispersal insect damage to acorns for 6 years in co‐occurring fagaceous species (Quercus variabilis, Q. serrata, Q. glauca, and Castanopsis cuspidata) in two adjacent forest stands that had different mixed ratios due to succession: a deciduous broad‐leaved forest stand (DB), and an evergreen broad‐leaved forest stand (EB). In C. cuspidata, the annual number of sound acorns correlated with that of female flowers. In contrast, for three Quercus species, the annual variability in sound acorn production was not correlated with that in female flowers, but was affected by the annual fluctuation in the percentage of insect damage in both the stands. For the three Quercus species, the dominant types of insect damage were different among the species, but similar between the two stands: damaged by moth larvae in Q. variabilis, and sap suction by adult weevils in Q. serrata and Q. glauca. Key factor analyses showed that the contribution of the dominant type of insect damage was similar between the two stands for the reproductive loss in Q. variabilis, but was different between the stands in Q. serrata and Q. glauca. Different mixed ratios of fagaceous species might affect the annual variability in sound acorn production via changes in the impact of a particular type of insect damage, even between adjacent stands.
Working with the Hmong Population in a Genetics Setting: an Interpreter Perspective
Authors: Krieger Meghan , Agather Aime , Douglass Kathryn , Reiser Catherine A. , Petty Elizabeth M.
Published: September 2017

The aim of this pilot qualitative study was to describe the experiences and beliefs of medical interpreters when working with genetic counselors and other genetic providers caring for Hmong patients who are not native English speakers. Specific goals were to identify interpreters’ thoughts and perceptions on (a) their roles during sessions, (b) unique challenges in a genetics session, (c) knowledge genetics providers need when working with Hmong patients and interpreters, and (d) supports and training needed to effectively interpret in a genetics setting. Hmong medical interpreters from Wisconsin and Minnesota were invited by email to participate in the study. Six were interviewed by telephone. Participants had worked with a variety of providers including geneticists, genetic counselors, primary care physicians, and oncologists. Factors identified by Hmong interpreters that made interpretation of content difficult in clinical genetics sessions included: time constraints, technical terms, and unique cultural perspectives of Hmong patients. While all respondents felt their primary role was to interpret session content as close to verbatim as possible, there was notable variation in the description of their interpretation style and other perceived roles in the genetic counseling session. Cultural issues genetics providers could consider when working with Hmong patients and different style issues when working with Hmong interpreters are discussed. Ideas for future studies and suggestions to improve communication with Hmong patients are explored.
Decay rate of iterated integrals of branched rough paths
Authors: Boedihardjo Horatio
Published: September 2017

Iterated integrals of paths arise frequently in the study of the Taylor's expansion for controlled differential equations. We will prove a factorial decay estimate, conjectured by M. Gubinelli, for the iterated integrals of non-geometric rough paths. We will explain, with a counter example, why the conventional approach of using the neoclassical inequality fails. Our proof involves a concavity estimate for sums over rooted trees and a non-trivial extension of T. Lyons' proof in 1994 for the factorial decay of iterated Young's integrals.
Factors associated with abdominal pain in patients submitted to colonoscopy
Authors: Bellei Amanda Colpani , Dacoregio Daniela Ghizoni , Bianchini Flávio , Souza Jaime César Gelosa , Bello João Martiniano Lamim , Kock Kaiser de Souza
Published: September 2017

Objective The study evaluated factors associated with abdominal pain during colonoscopy.

Methods This was a cross-sectional observational study that evaluated patients who underwent colonoscopy between February 2014 and February 2015. Physical characteristics, surgical history and previous colonoscopies, indication and current examination conditions, fentanyl and midazolam dose, and pain level were analyzed. Significance level adopted: p
< 0.05. Chi-squared test was used for association of categorical variables, Student's t-test was applied for comparison of means, and Spearman's coefficient was used for correlation.

Results A total of 566 women and 391 men with mean age of 54.81 years and mean BMI of 27,064 were evaluated. Of the total, 29 (3.0%) had mild pain, 42 (4.4%) had moderate pain, and 18 (1.9%) had severe pain. Women were less tolerant (p = 0.011) and had longer cecal intubation times (p = 0.001). Mean duration of colonoscopy and mean dose of midazolam were higher in patients with pain (p = 0.001), (p < 0.001*). Among the 39 patients with an incomplete examination, 8 reported pain (p = 0.049).

Conclusion Female gender and prolonged intubation time were significantly associated with abdominal pain during colonoscopy. Patients with discomfort had a higher failure rate on the exam. Additional doses of midazolam given to patients with pain were not effective.
The River Basin’s Tale: Carbon Transport Along the Thames
Authors: Witman Sarah
Published: September 2017

A study finds that population growth during urbanization and World War II–era plowing fed additional carbon into the Thames River Basin.
A new phase-matchable nonlinear optical silicate: Rb2ZnSi3O8
Authors: Zhao Bingqing , Yang Yi , Zhao Sangen , Shen Yaoguo , Li Xianfeng , Li Lina , Ji Chengmin , Lin Zheshuai , Luo Junhua
Published: September 2017

A new asymmetric silicate Rb2ZnSi3O8with a three-dimensional structure shows phase-matchability and enhanced second-harmonic generation as compared with α-SiO2.
A novel long noncoding RNA linc00460 up-regulated by CBP/P300 promotes carcinogenesis in esophageal squamous cell carcinoma
Authors: Liang Yan , Wu Yuanyuan , Chen Xuedan , Zhang Shixin , Wang Kai , Guan Xingying , Yang Kang , Li Juan , Bai Yun
Published: September 2017

Esophageal cancer is one of the leading causes of cancer-related mortality because of poor prognosis. Long noncoding RNAs (lncRNAs) have been gradually demonstrated to play critical roles in cancer development. We identified a novel long noncoding RNA named linc00460 by microarray analysis using esophageal squamous cell carcinoma (ESCC) clinical samples, which has not been studied before. Our research indicated that linc00460 was overexpressed in the majority of tumor tissues and ESCC cell lines. Linc00460 expression was positively correlated with ESCC TNM stage, lymph node metastasis, and predicted poor prognosis. In vitro experiments showed that linc00460 depletion suppressed ESCC cell growth through regulating cell proliferation and cell cycle; in additional, linc00460 depletion accelerated ESCC cell apoptosis. We further revealed that linc00460 overexpression was manipulated by transcriptional co-activator CBP/P300 through histone acetylation. Given the high expression and important biological functions of linc00460, we suggest that linc00460 works as an oncogene and might be a valuable prognostic biomarker for ESCC diagnosis and treatment.
Long and small noncoding RNAs during oocyte-to-embryo transition in mammals
Authors: Svoboda Petr
Published: September 2017

Oocyte-to-embryo transition is a process during which an oocyte ovulates, is fertilized, and becomes a developing embryo. It involves the first major genome reprogramming event in life of an organism where gene expression, which gave rise to a differentiated oocyte, is remodeled in order to establish totipotency in blastomeres of an early embryo. This remodeling involves replacement of maternal RNAs with zygotic RNAs through maternal RNA degradation and zygotic genome activation. This review is focused on expression and function of long noncoding RNAs (lncRNAs) and small RNAs during oocyte-to-embryo transition in mammals. LncRNAs are an assorted rapidly evolving collection of RNAs, which have no apparent protein-coding capacity. Their biogenesis is similar to mRNAs including transcriptional control and post-transcriptional processing. Diverse molecular and biological roles were assigned to lncRNAs although most of them probably did not acquire a detectable biological role. Since some lncRNAs serve as precursors for small noncoding regulatory RNAs in RNA silencing pathways, both types of noncoding RNA are reviewed together.
Detailed modelling and parameters optimisation analysis on governing system of hydro‐turbine generator unit
Authors: Zhang Changbing , Yang Mengjiao , Li Jinyao
Published: September 2017

Aiming at the mutual influence of hydraulic, mechanical, and electrical factors in a hydropower station, a detailed mathematical model for the governing system of a hydro‐turbine generator unit was presented here. An object‐oriented approach was used to write the computational program in Matlab/Simulink platform, and then it was verified by the prototype tests. The parameters of the governing system were optimised by the experimental test and this model, and evaluated by using the amplitude frequency characteristic method under no‐load frequency control mode, load frequency control mode, and load opening control mode. The characteristics of the waveform of the transient process and the influence degree of hydraulic, mechanical, and electrical factors were obtained. The computational results of the transient process show that the load rejection as an electrical disturbance leads to the water hammer, and the water‐level fluctuation in the surge chamber becomes one of the reasons of the low‐frequency oscillations in the power grid, especially under the load frequency control mode.
Does Index Insurance Help Households Recover from Disaster? Evidence from IBLI Mongolia
Authors: Bertram‐Huemmer Veronika , Kraehnert Kati
Published: September 2017

This article investigates the impact that indemnity payments from index insurance have on the asset recovery of households following a catastrophic weather disaster. Our focus is on the Index‐Based Livestock Insurance (IBLI) in Mongolia. We analyze the effect of IBLI indemnity payments after a once‐every‐50‐year winter disaster struck Mongolia over the winter of 2009/2010. The analysis is based on three waves of a household panel survey implemented in western Mongolia two to five years after the shock. We employ the bias‐corrected matching estimator to account for selection into purchasing IBLI. Results indicate that pastoralist households purchasing IBLI before the shock recover faster from shock‐induced asset losses than comparable uninsured households. We find a significant, positive, and economically large effect of IBLI indemnity payments on herd size one to three years after the shock. Four years after the shock, the effect vanishes. Results are robust to defining post‐shock livestock recovery in various ways, as well as the choice of covariates and the use of alternative propensity score estimators. An analysis of shock‐coping strategies suggests that IBLI appears to have relieved households from credit constraints. In addition, indemnity payments helped herders avoid selling and slaughtering animals, thus smoothing their productive asset base. Our article is among the first to provide evidence on the beneficial effects of index insurance after a weather shock in a developing economy.
Phandango: an interactive viewer for bacterial population genomics
Authors: Hadfield James , Croucher Nicholas J , Goater Richard J , Abudahab Khalil , Aanensen David M , Harris Simon R
Published: September 2017

Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner.

Availability and implementation

Phandango is a web application freely available for use at www.phandango.net and includes a diverse collection of datasets as examples. Source code together with a detailed wiki page is available on GitHub at https://github.com/jameshadfield/phandango.
Domination, Authority, and the Forms of Chinese Power
Authors: Lake David A
Published: September 2017

The debate about China’s rise and future United States–China relations has focused on the purpose to which China’s growing international power will be put. This article focuses on the form of China’s power, distinguishing between domination and authority. Different great powers have, at different times, chosen one, the other, or more commonly differing mixes of the two forms. How China chooses now and in the future will have a significant effect on its relationships with other states, and through them on its relationship with the United States. The first section explores the differences between domination and authority as strategies for the exercise of international power. The second section summarizes a theory of authority with particular relevance to China today. Though necessarily speculative, this section identifies where China is most likely to choose one strategy over the other as its international influence expands. The final section examines the domestic impediments in China to the choice of authority. While both China and the United States might be better off in a world in which the former constructs an international hierarchy to parallel the latter’s, the conclusion draws a relatively pessimistic assessment of the prospects for cooperation between the two emerging superpowers.
Image Desecration in Spilamberto: Jews and Christian Images in Seventeenth-Century Italy
Authors: Aron-Beller Katherine
Published: September 2017

This article explores a series of incidents that took place near Modena between 1632 and 1635, in which members of a Jewish family were accused of desecrating Christian devotional images. It is based on a file in the inquisitorial archive in Modena, with additional information culled from the Archivio della Congregazione per la Dottrina della Fede in Rome. The principal locale of the story is a silk mill which was leased to Simon Sanguinetti and his four sons in 1632, a year after plague had devastated the region. The Sanguinetti were encouraged to take on this enterprise by the mill-owner, Baldassare Rangone, who clearly hoped that an injection of Jewish capital would result in the revival of the business. However, the Jewish tenants-cum-managers were soon accused of desecrating two types of Catholic images—a painted panel and cheap prints of religious subjects. During the investigations, three Jewish suspects were imprisoned for periods of up to four months, and two of them were tortured. The main focus of this article is on the two types of images, their religious and social significance, the Jewish–Christian tensions that were created by them, and their supposed desecration. It illustrates an unstudied aspect of hidden Jewish violence and the actualisation of emotions that might otherwise have remained unnoticed.
TC3A: The Cancer 3′ UTR Atlas
Authors: Feng Xin , Li Lei , Wagner Eric J , Li Wei
Published: September 2017

Widespread alternative polyadenylation (APA) occurs during enhanced cellular proliferation and transformation. Recently, we demonstrated that CFIm25-mediated 3′ UTR shortening through APA promotes glioblastoma tumor growth in vitro and in vivo, further underscoring its significance to tumorigenesis. Here, we report The Cancer 3′ UTR Atlas (TC3A), a comprehensive resource of APA usage for 10,537 tumors across 32 cancer types. These APA events represent potentially novel prognostic biomarkers and may uncover novel mechanisms for the regulation of cancer driver genes. TC3A is built on top of the now de facto standard cBioPortal. Therefore, the large community of existing cBioPortal users and clinical researchers will find TC3A familiar and immediately usable. TC3A is currently fully functional and freely available at http://tc3a.org.
Database Resources of the BIG Data Center in 2018
Authors:   BIG Data Center Members, Xu Xingjian , Hao Lili , Zhu Junwei , Tang Bixia , Zhou Qing , Song Fuhai , Chen Tingting , Zhang Sisi , Dong Lili , Lan Li , Wang Yanqing , Sang Jian , Hao Lili , Liang Fang , Cao Jiabao , Liu Fang , Liu Lin , Wang Fan , Ma Yingke , Xu Xingjian , Zhang Lijuan , Chen Meili , Tian Dongmei , Li Cuiping , Dong Lili , Du Zhenglin , Yuan Na , Zeng Jingyao , Zhang Zhewen , Wang Jinyue , Shi Shuo , Zhang Yadong , Pan Mengyu , Tang Bixia , Zou Dong , Song Shuhui , Sang Jian , Xia Lin , Wang Zhennan , Li Man , Cao Jiabao , Niu Guangyi , Zhang Yang , Sheng Xin , Lu Mingming , Wang Qi , Xiao Jingfa , Zou Dong , Wang Fan , Hao Lili , Liang Fang , Li Mengwei , Sun Shixiang , Zou Dong , Li Rujiao , Yu Chunlei , Wang Guangyu , Sang Jian , Liu Lin , Li Mengwei , Li Man , Niu Guangyi , Cao Jiabao , Sun Shixiang , Xia Lin , Yin Hongyan , Zou Dong , Xu Xingjian , Ma Lina , Chen Huanxin , Sun Yubin , Yu Lei , Zhai Shuang , Sun Mingyuan , Zhang Zhang , Zhao Wenming , Xiao Jingfa , Bao Yiming , Song Shuhui , Hao Lili , Li Rujiao , Ma Lina , Sang Jian , Wang Yanqing , Tang Bixia , Zou Dong , Wang Fan
Published: September 2017

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn.
Synthesis of tetraphenylene derivatives and their recent advances
Authors: Han Jian-Wei , Peng Xiao-Shui , Wong Henry N C
Published: September 2017

The synthetic strategies towards tetraphenylene derivatives are comprehensively summarized in this review. Recent advances in the functionalized tetraphenylene skeleton for research into their structurally unique properties are described together with their potential applications.
Food environments and obesity – can’t see the fat for the restaurants?
Authors: Speakman John R , Mazidi Mohsen
Published: September 2017

We recently showed that across the mainland USA there is no association between the density of fast food and full service restaurants and the prevalence of obesity. In a recent editorial it was suggested there are 4 problems with our analysis. The suggested problems were the area of analysis may not reflect adequately the exposure to different outlets, using the absolute numbers of restaurants rather than their ratio, using a global model which assumes the same relationship across all sites and finally the potential for residual confounding. In this short note we address all four of these issues and provide some new analysis of the impact of the ratio of restaurant types on obesity prevalence showing there is only a very weak association (r2= 0.006). We conclude that none of the supposed weaknesses in our original analysis are valid.
Integrative genomics analysis identifiesACVR1Bas a candidate causal gene of emphysema distribution in non-alpha 1-antitrypsin deficient smokers
Authors: Boueiz Adel , Chase Robert , Lamb Andrew , Lee Sool , Naing Zun Zar Chi , Cho Michael H. , Parker Margaret M. , Hersh Craig P. , Crapo James D. , Stergachis Andrew B. , Tal-Singer Ruth , DeMeo Dawn L. , Silverman Edwin K. , Castaldi Peter J. ,   for the COPDGene investigators
Published: September 2017

Background

Several genetic risk loci associated with emphysema apico-basal distribution (EABD) have been identified through genome-wide association studies (GWAS), but the biological functions of these variants are unknown. To characterize gene regulatory functions of EABD-associated variants, we integrated EABD GWAS results with 1) a multi-tissue panel of expression quantitative trait loci (eQTL) from subjects with COPD and the GTEx project and 2) epigenomic marks from 127 cell types in the Roadmap Epigenomics project. Functional validation was performed for a variant nearACVR1B.

Results

SNPs from 168 loci with P-values<5x10-5in the largest GWAS meta-analysis of EABD(Boueiz A. et al, AJRCCM 2017)were analyzed. 54 loci overlapped eQTL regions from our multi-tissue panel, and 7 of these loci showed a high probability of harboring a single, shared GWAS and eQTL causal variant (colocalization posterior probability≥0.9). 17 cell types exhibited greater than expected overlap between EABD loci and DNase-I hypersensitive peaks, DNaseI hotspots, enhancer marks, or digital DNaseI footprints (permutation P-value < 0.05), with the strongest enrichment observed in CD4+, CD8+, and regulatory T cells. A region nearACVR1Bdemonstrated significant colocalization with a lung eQTL and overlapped DNase-I hypersensitive regions in multiple cell types, and reporter assays in human bronchial epithelial cells confirmed allele-specific regulatory activity for the lead variant, rs7962469.

Conclusions

Integrative analysis highlights candidate causal genes, regulatory variants, and cell types that may contribute to the pathogenesis of emphysema distribution. These findings will enable more accurate functional validation studies and better understanding of emphysema distribution biology.
Combining radiomics and mathematical modeling to elucidate mechanisms of resistance to immune checkpoint blockade in non-small cell lung cancer
Authors: Saeed-Vafa Daryoush , Bravo Rafael , Dean Jamie A. , El-Kenawi Asmaa , Mon Père Nathaniel , Strobl Maximilian , Daniels Charlie , Stringfield Olya , Damaghi Mehdi , Tunali Ilke , Brown Liam V. , Curtin Lee , Nichol Daniel , Peck Hailee , Gillies Robert J. , Gallaher Jill A.
Published: September 2017

Immune therapies have shown promise in a number of cancers, and clinical trials using the anti-PD-L1/PD-1 checkpoint inhibitor in lung cancer have been successful for a number of patients. However, some patients either do not respond to the treatment or have cancer recurrence after an initial response. It is not clear which patients might fall into these categories or what mechanisms are responsible for treatment failure. To explore the different underlying biological mechanisms of resistance, we created a spatially explicit mathematical model with a modular framework. This construction enables different potential mechanisms to be turned on and off in order to adjust specific tumor and tissue interactions to match a specific patient's disease. In parallel, we developed a software suite to identify significant computed tomography (CT) imaging features correlated with outcome using data from an anti-PDL-1 checkpoint inhibitor clinical trial for lung cancer and a tool that extracts these features from both patient CT images and “virtual CT” images created from the cellular density profile of the model. The combination of our two toolkits provides a framework that feeds patient data through an iterative pipeline to identify predictive imaging features associated with outcome, whilst at the same time proposing hypotheses about the underlying resistance mechanisms.
Selection bias in instrumental variable analyses
Authors: Hughes Rachael A. , Davies Neil M. , Davey Smith George , Tilling Kate
Published: September 2017

Participants in epidemiological and genetic studies are rarely true random samples of the populations they are intended to represent, and both known and unknown factors can influence participation in a study (known as selection into a study). The circumstances in which selection causes bias in an instrumental variable (IV) analysis are not widely understood by practitioners of IV analyses. We use directed acyclic graphs (DAGs) to depict assumptions about the selection mechanism (factors affecting selection) and show how DAGs can be used to determine when a two-stage least squares (2SLS) IV analysis is biased by different selection mechanisms. Via simulations, we show that selection can result in a biased IV estimate with substantial confidence interval undercoverage, and the level of bias can differ between instrument strengths, a linear and nonlinear exposure-instrument association, and a causal and noncausal exposure effect. We present an application from the UK Biobank study, which is known to be a selected sample of the general population. Of interest was the causal effect of education on the decision to smoke. The 2SLS exposure estimates were very different between the IV analysis ignoring selection and the IV analysis which adjusted for selection (e.g., 1.8 [95% confidence interval −1.5, 5.0] and −4.5 [−6.6, −2.4], respectively). We conclude that selection bias can have a major effect on an IV analysis and that statistical methods for estimating causal effects using data from nonrandom samples are needed.
The neurobiology of agrammatic sentence comprehension: a lesion study
Authors: Rogalsky Corianne , LaCroix Arianna N. , Chen Kuan-Hua , Anderson Steven W. , Damasio Hanna , Love Tracy , Hickok Gregory
Published: September 2017

Broca’s area has long been implicated in sentence comprehension. Damage to this region is thought to be the central source of “agrammatic comprehension” in which performance is substantially worse (and near chance) on sentences with noncanonical word orders compared to canonical word order sentences (in English). This claim is supported by functional neuroimaging studies demonstrating greater activation in Broca’s area for noncanonical versus canonical sentences. However, functional neuroimaging studies also have frequently implicated the anterior temporal lobe (ATL) in sentence processing more broadly, and recent lesion-symptom mapping studies have implicated the ATL and mid temporal regions in agrammatic comprehension. The present study investigates these seemingly conflicting findings in 66 left hemisphere patients with chronic focal cerebral damage. Patients completed two sentence comprehension measures, sentence-picture matching and plausibility judgments. Patients with damage including Broca’s area (but excluding the temporal lobe; n=11) on average did not exhibit the expected agrammatic comprehension pattern, e.g. their performance was > 80% on noncanonical sentences in the sentence-picture matching task. Patients with ATL damage (n=18) also did not exhibit an agrammatic comprehension pattern. Across our entire patient sample, the lesions of patients with agrammatic comprehension patterns in either task had maximal overlap in posterior superior temporal and inferior parietal regions. Using voxel-based lesion symptom mapping (VLSM), we find that lower performances on canonical and noncanonical sentences in each task are both associated with damage to a large left superior temporal-inferior parietal network including portions of the ATL, but not Broca’s area. Notably however, response bias in plausibility judgments was significantly associated with damage to inferior frontal cortex, including gray and white matter in Broca’s area, suggesting that the contribution of Broca’s area to sentence comprehension may be related to task-related cognitive demands.
A near complete haplotype-phased genome of the dikaryotic wheat stripe rust fungusPuccinia striiformisf. sp.triticireveals high inter-haplotype diversity
Authors: Schwessinger Benjamin , Sperschneider Jana , Cuddy William S. , Garnica Diana P. , Miller Marisa E. , Taylor Jennifer M. , Dodds Peter N. , Figueroa Melania , Robert Park F. , Rathjen John
Published: September 2017

A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here we present a diploidaware assembly of the wheat stripe rust fungusPuccinia striiformisf. sp.triticibased on long-reads using the FALCON-Unzip assembler. RNA-seq datasets were used to infer high quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most completePuccinia striiformisf. sp.triticigenome assembly to date (83 Mb, 156 contigs, N50 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high inter-haplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When investigating genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors, and are less likely to be evolutionarily conserved within theP. striiformisspecies complex andPucciniales. In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant pathogenic fungus previously hidden in collapsed and fragmented genome assemblies.

Importance

Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism’s evolutionary potential and ability to adapt to stress conditions. Yet it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which leads to allelic variation and the presence of genes lacking allelic counterparts. Non-allelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
Dysconnection of right parietal and frontal cortex in neglect syndrome
Authors: Dietz Martin J. , Nielsen Jørgen F. , Roepstorff Andreas , Garrido Marta I.
Published: September 2017

A lesion to the right hemisphere of the brain often leads to perceptual neglect of the left side of the sensorium. The fact that lesions to different cortical regions lead to the same symptoms points to neglect as a dysconnection syndrome that may result from the dysconnection of a distributed network, rather than a disruption of computation in any particular brain region. To test this hypothesis, we used Bayesian analysis of effective connectivity based on electroencephalographic recordings in patients with left-sided neglect after a right-hemisphere lesion. While age-matched healthy controls showed a contralateral increase in connection strength between parietal and frontal cortex with respect to the laterality of the stimuli, neglect patients showed a dysconnection between parietal and frontal cortex in the right hemisphere when stimuli appeared on their neglected side, but preserved connectivity in the left hemisphere when stimuli appeared on their right. Crucially, this parieto-frontal feedback connectivity was aggravated in patients with more severe symptoms. In contrast, patients and controls did not show differences in the local connectivity within regions. These findings suggest that the aetiology of neglect may lie in the dysconnection of a distributed network, rather than the disruption of any particular brain region.
Social behavior in bees influences the abundance ofSodalis(Enterobacteriaceae) symbionts
Authors: Rubin Benjamin E. , Sanders Jon G. , Turner Kyle M. , Pierce Naomi E. , Kocher Sarah D.
Published: September 2017

Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviors and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both social and solitary bee species within the behaviorally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms, and most halictid species appear to share similar gut bacterial communities. However, several strains ofSodalis,a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between social and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate thatSodalishas independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting thatSodalisstrains compete for access to hosts.De novogenome assemblies indicate that these three lineages are subject to widespread relaxed selection and thatSodalisis undergoing genome degeneration during the colonization of these hosts.