bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatic tools for analysis of CLIP ribonucleoprotein data
Authors: De Supriyo , Gorospe Myriam 
Published: December 2016

Investigating the interactions of RNA‐binding proteins (RBPs) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques and the computational approaches to understand RBP–RNA (or ribonucleoprotein, RNP) interactions have advanced considerably over the past few years and numerous and diverse software tools have been developed to analyze these data. Accordingly, laboratories interested in RNP biology face the challenge of choosing adequately among the available software tools those that best address the biological problem they are studying. Here, we focus on state‐of‐the‐art molecular biology techniques that employ crosslinking and immunoprecipitation (CLIP) of an RBP to study and map RNP interactions. We review the different software tools and databases available to analyze the most widely used CLIP methods, HITS‐CLIP, PAR‐CLIP, and iCLIP. WIREs RNA 2017, 8:e1404. doi: 10.1002/wrna.1404This article is categorized under:

RNA Evolution and Genomics > Computational Analyses of RNA
RNA Evolution and Genomics > Ribonomics
RNA Methods > RNA Analyses In Vitro and In Silico
The Norwegian Cervical Arthroplasty Trial (NORCAT): 2-year clinical outcome after single-level cervical arthroplasty versus fusion—a prospective, single-blinded, randomized, controlled multicenter study
Authors: Sundseth Jarle , Fredriksli Oddrun Anita , Kolstad Frode , Johnsen Lars Gunnar , Pripp Are Hugo , Andresen Hege , Myrseth Erling , Müller Kay , Nygaard Øystein P. , Zwart John-Anker ,   On behalf of the NORCAT study group
Published: December 2016

Abstract
Purpose
Standard surgical treatment for symptomatic cervical disc disease has been discectomy and fusion, but the use of arthroplasty, designed to preserve motion, has increased, and most studies report clinical outcome in its favor. Few of these trials, however, blinded the patients. We, therefore, conducted the Norwegian Cervical Arthroplasty Trial, and present 2-year clinical outcome after arthroplasty or fusion.

Methods
This multicenter trial included 136 patients with single-level cervical disc disease. The patients were randomized to arthroplasty or fusion, and blinded to the treatment modality. The surgical team was blinded to randomization until nerve root decompression was completed. Primary outcome was the self-rated Neck Disability Index. Secondary outcomes were the numeric rating scale for pain and quality of life questionnaires Short Form-36 and EuroQol-5Dimension-3 Level.

Results
There was a significant improvement in the primary and all secondary outcomes from baseline to 2-year follow-up for both arthroplasty and fusion (P < 0.001), and no observed significant between-group differences at any follow-up times. However, linear mixed model analyses, correcting for baseline values, dropouts and missing data, revealed a difference in Neck Disability Index (P = 0.049), and arm pain (P = 0.027) in favor of fusion at 2 years. The duration of surgery was longer (P < 0.001), and the frequency of reoperations higher (P = 0.029) with arthroplasty.

Conclusion
The present study showed excellent clinical results and no significant difference between treatments at any scheduled follow-up. However, the rate of index level reoperations was higher and the duration of surgery longer with arthroplasty.

Trial registration
http://www.clinicaltrials.gov NCT 00735176.19.
Estimation of stature by using the dimensions of the right hand and right foot in Han Chinese adults
Authors: Zhang Xinghua , Wei Yu , Zheng Lianbin , Yu Keli , Zhao Dapeng , Bao Jinping , Li Yonglan , Lu Shunhua , Xi Huanjiu , Xu Guochang , Wen Youfeng 
Published: December 2016

AbstractThe Han Chinese people are the main ethnic group in China and the largest ethnic group in the world. The dimensions of the hands and feet have been successfully used for the estimation of stature. A total of 26,927 healthy adult subjects, comprising 13,221 men and 13,706 women, were recruited. The survey samples were chosen through random cluster sampling. The mean values were significantly higher in men than those in women for all measurements (P<0.001). All the measurements showed a statistically significant correlation with stature (P<0.01). The combination of the right hand length and the right foot length was the best predictor of stature because it had the lowest standard error of estimate. The use of multiple regression equations yielded better results than did the use of linear regression equations. The accuracy of stature prediction ranged from ±4.81 to ±6.39 cm. The present study was of great importance with regards to improving the physical anthropology database of ethnic groups in China.
A comparison of measurement methods of hippocampal atrophy rate for predicting Alzheimer's dementia in the Aberdeen Birth Cohort of 1936
Authors: Rana Arnab K. , Sandu Anca‐Larisa , Robertson Kenna L. , McNeil Christopher J. , Whalley Lawrence J. , Staff Roger T. , Murray Alison D. 
Published: December 2016

AbstractIntroductionVarious methods are available to measure hippocampal atrophy rate. We compared methods to predict Alzheimer's dementia.MethodsParticipants with brain imaging at ages 69 and 73 years were identified from a previous study. Simple manual measures and computationally automated volumetry were performed. Receiver operating characteristics assessed the predictive ability of each method at baseline and on logit regression analysis of two serial scans.ResultsTen of 149 participants developed Alzheimer's dementia and had lower baseline volumes (3647 vs. 4194 mm3 P = .002), rates of volume loss (−126 vs. −36 mm3/y; P = .001), and rates of loss in hippocampal fraction (−8.55 vs. −2.35 x 10−5/y; P = .001). Baseline volume with a rate of change gave the highest area under the curve value of 0.96.DiscussionAutomated volumetry measuring hippocampal size at age 69 years and subsequent rate of change predicts Alzheimer's dementia development.
Synergistic interaction between amyloid and tau predicts the progression to dementia
Authors: Pascoal Tharick A. , Mathotaarachchi Sulantha , Shin Monica , Benedet Andrea L. , Mohades Sara , Wang Seqian , Beaudry Tom , Kang Min Su , Soucy Jean‐Paul , Labbe Aurelie , Gauthier Serge , Rosa‐Neto Pedro 
Published: December 2016

AbstractIntroductionRecent literature proposes that amyloid β (Aβ) and phosphorylated tau (p‐tau) synergism accelerates biomarker abnormalities in controls. Yet, it remains to be answered whether this synergism is the driving force behind Alzheimer disease (AD) dementia.MethodsWe stratified 314 mild cognitive impairment individuals using [18F]florbetapir positron emission tomography Aβ imaging and cerebrospinal fluid p‐tau. Regression and voxel‐based logistic regression models with interaction terms evaluated 2‐year changes in cognition and clinical status as a function of baseline biomarkers.ResultsWe found that the synergism between [18F]florbetapir and p‐tau, rather than their additive effects, was associated with the cognitive decline and progression to AD. Furthermore, voxel‐based analysis revealed that temporal and inferior parietal were the regions where the synergism determined an increased likelihood of developing AD.DiscussionTogether, the present results support that progression to AD dementia is driven by the synergistic rather than a mere additive effect between Aβ and p‐tau proteins.
Metastasis of colon adenocarcinoma to the mandible: A case report
Authors: Kameta Ayako , Oda Takaaki , Ogura Ichiro , Ono Junya , Kanri Yoriaki , Okada Yasuo , Tsuchimochi Makoto 
Published: December 2016

AbstractMetastatic tumors to the oral cavity are uncommon. In this article, we report a case of metastatic adenocarcinoma of the colon to the mandible with imaging features. A 73‐year‐old man with a history of colon cancer and liver metastasis was referred to our hospital with a chief complaint of swelling and pain in the right mandible. Panoramic radiograph revealed a radiolucency with ill‐defined margin. Computed tomography showed an osteolytic lesion with cortical bone destruction. Magnetic resonance imaging showed a round‐shaped homogeneous intensity mass expanding from the mandible. Histopathological diagnosis revealed metastatic adenocarcinoma of the colon.
Toxic effects of insecticides on the life table and development of Earias vittella (Lepidoptera: Noctuidae) on okra
Authors: Ahmad Salman , Ansari M. Shafiq , Khan Nadeem , Hasan Fazil 
Published: December 2016

AbstractOkra,Abelmoschus esculentus(L.) Moench, is an important vegetable crop grown throughout the tropical and temperate regions of the world. Spotted bollworm,Earias vittella(Fab.), is one of the most important insect pests of okra. The effects of insecticides (cypermethrin, imidacloprid, carbaryl and neem oil) were studied on the fitness of the F1 generation ofE. vittellaby a demographic method. Life table was constructed from the eggs obtained by the surviving individuals that had ingested insecticides. Survivorship and expectancy was highest with the commencement of age and gradually decreased with the progression of age in the treatment groups and control. However, it was reduced in the treatment groups in comparison to control groups. Highest numbers of unhatched eggs (17%) were recorded with imidacloprid and cypermethrin treatments, whereas all the eggs hatched in control groups. Larval mortality was high in the initial instars as compared to late instars. Potential fecundity was significantly reduced to 94 females/female/generation treated with cypermethrin as compared to 256 in the untreated females. Developmental time of pre-pupa and pupa was significantly decreased with cypermethrin treatment. The intrinsic rate of increase was reduced to 0.0201 females/female/day in cypermethrin groups as compared to 0.046 in the control groups. The generation time was 33.27 days in the control, which was reduced to 26.78 days with carbaryl treatment and was increased to 37.5 days with neem oil. Insecticides cause adverse effect on the surviving generation ofE. vittella, and may be incorporated as a valuable component in the integrated management ofE. vittellaon okra.
Smad3-related miRNAs regulated oncogenic TRIB2 promoter activity to effectively suppress lung adenocarcinoma growth
Authors: Zhang Yan-Xia , Yan Yun-Fei , Liu Yue-Mei , Li You-Jie , Zhang Han-Han , Pang Min , Hu Jin-Xia , Zhao Wei , Xie Ning , Zhou Ling , Wang Ping-Yu , Xie Shu-Yang 
Published: December 2016

AbstractMicroRNAs (miRNAs) and Smad3, as key transcription factors in transforming growth factor-β1 (TGF-β1) signaling, help regulate various physiological and pathological processes. We investigated the roles of Smad3-regulated miRNAs with respect to lung adenocarcinoma cell apoptosis, proliferation, and metastasis. We observed that Smad3 and phospho-SMAD3 (p-Smad3) were decreased in miR-206- (or miR-140)-treated cells and there might be a feedback loop between miR-206 (or miR-140) and TGF-β1 expression. Smad3-related miRNAs affected tribbles homolog 2 (TRIB2) expression by regulating trib2 promoter activity through the CAGACA box. MiR-206 and miR-140 inhibited lung adenocarcinoma cell proliferation in vitro and in vivo by suppressing p-Smad3/Smad3 and TRIB2. Moreover, lung adenocarcinoma data supported a suppressive role for miR-206/miR-140 and an oncogenic role for TRIB2—patients with higher TRIB2 levels had poorer survival. In summary, miR-206 and miR-140, as tumor suppressors, induced lung adenocarcinoma cell death and inhibited cell proliferation by modifying oncogenic TRIB2 promoter activity through p-Smad3. MiR-206 and miR-140 also suppressed lung adenocarcinoma cell metastasis in vitro and in vivo by regulating EMT-related factors.
Ultrafast infrared observation of exciton equilibration from oriented single crystals of photosystem II
Authors: Kaucikas Marius , Maghlaoui Karim , Barber Jim , Renger Thomas , van Thor Jasper J. 
Published: December 2016

AbstractIn oxygenic photosynthesis, two photosystems work in series. Each of them contains a reaction centre that is surrounded by light-harvesting antennae, which absorb the light and transfer the excitation energy to the reaction centre where electron transfer reactions are driven. Here we report a critical test for two contrasting models of light harvesting by photosystem II cores, known as the trap-limited and the transfer-to-the trap-limited model. Oriented single crystals of photosystem II core complexes of Synechococcus elongatus are excited by polarized visible light and the transient absorption is probed with polarized light in the infrared. The dichroic amplitudes resulting from photoselection are maintained on the 60 ps timescale that corresponds to the dominant energy transfer process providing compelling evidence for the transfer-to-the-trap limitation of the overall light-harvesting process. This finding has functional implications for the quenching of excited states allowing plants to survive under high light intensities.
Tumor cell-intrinsic PD-L1 promotes tumor-initiating cell generation and functions in melanoma and ovarian cancer
Authors: Gupta Harshita B , Clark Curtis A , Yuan Bin , Sareddy Gangadhara , Pandeswara Srilakshmi , Padron Alvaro S , Hurez Vincent , Conejo-Garcia José , Vadlamudi Ratna , Li Rong , Curiel Tyler J 
Published: December 2016

AbstractAs tumor PD-L1 provides signals to anti-tumor PD-1+ T cells that blunt their functions, αPD-1 and αPD-L1 antibodies have been developed as anti-cancer immunotherapies based on interrupting this signaling axis. However, tumor cell-intrinsic PD-L1 signals also regulate immune-independent tumor cell proliferation and mTOR signals, among other important effects. Tumor-initiating cells (TICs) generate carcinomas, resist treatments and promote relapse. We show here that in murine B16 melanoma and ID8agg ovarian carcinoma cells, TICs express more PD-L1 versus non-TICs. Silencing PD-L1 in B16 and ID8agg cells by shRNA (‘PD-L1lo’) reduced TIC numbers, the canonical TIC genes nanog and pou5f1 (oct4), and functions as assessed by tumorosphere development, immune-dependent and immune-independent tumorigenesis, and serial transplantability in vivo. Strikingly, tumor PD-L1 sensitized TIC to interferon-γ and rapamycin in vitro. Cell-intrinsic PD-L1 similarly drove functional TIC generation, canonical TIC gene expression and sensitivity to interferon-γ and rapamycin in human ES2 ovarian cancer cells. Thus, tumor-intrinsic PD-L1 signals promote TIC generation and virulence, possibly by promoting canonical TIC gene expression, suggesting that PD-L1 has novel signaling effects on cancer pathogenesis and treatment responses.
Translocation of the thioesterase domain for the redesign of plipastatin synthetase
Authors: Gao Ling , Liu Hongxia , Ma Zhi , Han Jinzhi , Lu Zhaoxin , Dai Chen , Lv Fengxia , Bie Xiaomei 
Published: December 2016

AbstractNon-ribosomal peptide synthetases (NRPSs) are large enzymatic complexes that catalyse the synthesis of biologically active peptides in microorganisms. Genetic engineering has recently been applied to reprogram NRPSs to produce lipopeptides with a new sequence. The carboxyl-terminal thioesterase (TE) domains from NRPSs catalyse cleavage products by hydrolysis or complex macrocyclization. In this study, we modified plipastatin synthetase by moving the intrinsic TE region to the end of the internal thiolation (T) domains, thus generating Bacillus subtilis strains that could produce new truncated cyclic or linear peptides of the predicted sequence, which further provided an important insight into the regioselectivity of plipastatin TE. The TE was capable of recognizing and catalysing the lactone formation between L-Try3 with the last few residues L-Pro7 and L-Gln8 at the C-terminus. Additionally, the unmatched linkers connecting the TE region and T domain resulted in nonproduction strains, suggesting that the native T–TE linker is necessary and sufficient for the TE domain to release the products from the hybrid enzymes. This is the first report to demonstrate truncated cyclic lipopeptides production and module skipping by simply moving the TE domain forward in an NRPS system.
Super-Spreader Identification Using Meta-Centrality
Authors: Madotto Andrea , Liu Jiming 
Published: December 2016

AbstractSuper-spreaders are the nodes of a network that can maximize their impacts on other nodes, e.g., in the case of information spreading or virus propagation. Many centrality measures have been proposed to identify such nodes from a given network. However, it has been observed that the identification accuracy based on those measures is not always satisfactory among different types of networks. In addition, the nodes identified by using single centrality are not always placed in the top section, where the super-spreaders are supposed to be, of the ranking generated by simulation. In this paper we take a meta-centrality approach by combining different centrality measures using a modified version of Borda count aggregation method. As a result, we are able to improve the performance of super-spreader identification for a broad range of real-world networks. While doing so, we discover a pattern in the centrality measures involved in the aggregation with respect to the topological structures of the networks used in the experiments. Further, we study the eigenvalues of the Laplacian matrix, also known as Laplacian spectrum, and by using the Earth Mover’s distance as a metric for the spectrum, we are able to identify four clusters to explain the aggregation results.
Inhibition of farnesyl pyrophosphate synthase improves pressure overload induced chronic cardiac remodeling
Authors: Zhao Chen-Ze , Zhao Xu-Ming , Yang Jian , Mou Yun , Chen Bin , Wu Huan-Dong , Dai Dong-Pu , Ding Jie , Hu Shen-Jiang 
Published: December 2016

AbstractFarnesyl pyrophosphate synthase (FPPS) is a key enzyme in the mevalonate pathway. In our previous studies, we find that inhibition of FPPS attenuates angiotensin II-induced cardiac hypertrophy and fibrosis by suppressing RhoA while FPPS and Ras are up-regulated in pressure overload rats. In this study, we evaluate the effects and mechanisms of FPPS inhibition in pressure overload mice. Male FPPS-small interfering RNA (SiRNA) transgenic (Tg) mice and non-transgenic littermate control (NLC) were randomly divided into suprarenal abdominal aortic constriction (AAC) group and sham operation group. 12 weeks following AAC, mice were sacrificed by cervical dislocation. Histological and echocardiographic assessments showed that inhibition of FPPS improved chronic cardiac remodeling which was induced by AAC. The reductions of Ras farnesylation and GTP-Ras, as well as their downstream extracellular signal-related kinases 1/2 (ERK1/2) expression were observed in the heart of Tg-AAC mice compared with NLC-AAC mice, along with the reduction of fetal gene expression. We provide here important experimental evidence that inhibition of FPPS improves AAC induced chronic cardiac remodeling and fibrosis by the reduction of farnesylated Ras and the downregulation of Ras-ERK1/2 pathway.
Sodium selenate regulates the brain ionome in a transgenic mouse model of Alzheimer’s disease
Authors: Zheng Lin , Zhu Hua-Zhang , Wang Bing-Tao , Zhao Qiong-Hui , Du Xiu-Bo , Zheng Yi , Jiang Liang , Ni Jia-Zuan , Zhang Yan , Liu Qiong 
Published: December 2016

AbstractMany studies have shown that imbalance of mineral metabolism may play an important role in Alzheimer’s disease (AD) progression. It was recently reported that selenium could reverse memory deficits in AD mouse model. We carried out multi-time-point ionome analysis to investigate the interactions among 15 elements in the brain by using a triple-transgenic mouse model of AD with/without high-dose sodium selenate supplementation. Except selenium, the majority of significantly changed elements showed a reduced level after 6-month selenate supplementation, especially iron whose levels were completely reversed to normal state at almost all examined time points. We then built the elemental correlation network for each time point. Significant and specific elemental correlations and correlation changes were identified, implying a highly complex and dynamic crosstalk between selenium and other elements during long-term supplementation with selenate. Finally, we measured the activities of two important anti-oxidative selenoenzymes, glutathione peroxidase and thioredoxin reductase, and found that they were remarkably increased in the cerebrum of selenate-treated mice, suggesting that selenoenzyme-mediated protection against oxidative stress might also be involved in the therapeutic effect of selenate in AD. Overall, this study should contribute to our understanding of the mechanism related to the potential use of selenate in AD treatment.
Deficiency of Mkrn2 causes abnormal spermiogenesis and spermiation, and impairs male fertility
Authors: Qian Xu , Wang Lin , Zheng Bo , Shi Zhu-Mei , Ge Xin , Jiang Cheng-Fei , Qian Ying-Chen , Li Dong-Mei , Li Wei , Liu Xue , Yin Yu , Zheng Ji-Tai , Shen Hua , Wang Min , Guo Xue-Jiang , He Jun , Lin Marie , Liu Ling-Zhi , Sha Jia-Hao , Jiang Bing-Hua 
Published: December 2016

AbstractAlthough recent studies have shed insights on some of the potential causes of male infertility, new underlining molecular mechanisms still remain to be elucidated. Makorin-2 (Mkrn2) is an evolutionarily conserved gene whose biological functions are not fully known. We developed an Mrkn2 knockout mouse model to study the role of this gene, and found that deletion of Mkrn2 in mice led to male infertility. Mkrn2 knockout mice produced abnormal sperms characterized by low number, poor motility, and aberrant morphology. Disruption of Mkrn2 also caused failure of sperm release (spermiation failure) and misarrangement of ectoplasmic specialization (ES) in testes, thus impairing spermiogenesis and spermiation. To understand the molecular mechanism, we found that expression of Odf2, a vital protein in spermatogenesis, was significantly decreased. In addition, we found that expression levels of Odf2 were decreased in Mkrn2 knockout mice. We also found that MKRN2 was prominently expressed in the sperm of normal men, but was significantly reduced in infertile men. This result indicates that our finding is clinically relevant. The results of our study provided insights into a new mechanism of male infertility caused by the MKRN2 downregulation.
Effect of omega-3 fatty acid supplementation on serum lipids and vascular inflammation in patients with end-stage renal disease: a meta-analysis
Authors: Xu Tianhua , Sun Yiting , Sun Wei , Yao Li , Sun Li , Liu Linlin , Ma Jianfei , Wang Lining 
Published: December 2016

AbstractOmega-3 fatty acids (O3FAs) are associated with lower cardiovascular disease (CVD) risk in adults. However, this association in patients with end-stage renal disease (ESRD) remains controversial prompting the need for investigation into the role of O3FAs on serum lipids and vascular inflammation markers. The present meta-analysis summarized the effects of O3FA supplementation on serum lipids and vascular inflammatory markers in patients with ESRD. PubMed, EmBase, and the Cochrane Library were searched to identify randomized controlled trials (RCTs) focused on serum lipids and vascular inflammation markers in patients with ESRD. Standard mean differences (SMD) were used to measure the effect of O3FA supplementation on serum lipids and vascular inflammatory markers. The final pooled analysis included 20 RCTs involving 1,461 patients with ESRD. The results indicated that O3FA supplementation reduced TG by 0.61, LDL by 0.35 and CRP by 0.56. However, O3FA had no significant effect on TC, HDL, albumin, hemoglobin, homocysteine, DBP, glucose, lipoprotein(a), and ferritin. O3FA supplementation is associated with lower several serum lipids and vascular inflammation markers in patients with ESRD.