bluuebunny/crossref_metadata_2025_split huggingface dataset:
RBPTD: a database of cancer-related RNA-binding proteins in humans
Authors: Li Kun , Guo Zhi-Wei , Zhai Xiang-Ming , Yang Xue-Xi , Wu Ying-Song , Liu Tian-Cai 
Published: January 2020

Abstract
RNA-binding proteins (RBPs) play important roles in regulating the expression of genes involved in human physiological and pathological processes, especially in cancers. Many RBPs have been found to be dysregulated in cancers; however, there was no tool to incorporate high-throughput data from different dimensions to systematically identify cancer-related RBPs and to explore their causes of abnormality and their potential functions. Therefore, we developed a database named RBPTD to identify cancer-related RBPs in humans and systematically explore their functions and abnormalities by integrating different types of data, including gene expression profiles, prognosis data and DNA copy number variation (CNV), among 28 cancers. We found a total of 454 significantly differentially expressed RBPs, 1970 RBPs with significant prognostic value, and 53 dysregulated RBPs correlated with CNV abnormality. Functions of 26 cancer-related RBPs were explored by analysing high-throughput RNA sequencing data obtained by crosslinking immunoprecipitation, and the remaining RBP functions were predicted by calculating their correlation coefficient with other genes. Finally, we developed the RBPTD for users to explore functions and abnormalities of cancer-related RBPs to improve our understanding of their roles in tumorigenesis.
Database URL: http: //www.rbptd.com
Seasonal Population Dynamics, Sampling Distribution, and Fixed-Precision Sequential Sampling of Spectrobates ceratoniae (Lepidoptera: Pyralidae) in Pomegranate Orchards
Authors: Yaghobi Saeed , Rajabpour Ali , Zandi-Sohani Nooshin 
Published: January 2020

Abstract
The carob moth, Spectrobates ceratoniae Zeller, is the most destructive pest of pomegranate groves of Iran. Seasonal population dynamics of the pest was studied in pomegranate orchards of Sirvan, Ilam province, in southwestern Iran for 2 yr (2016/2017). Sampling distribution of the pest larvae on pomegranate fruits was evaluated by Taylor’s power law and Iwao’s patchiness index, and a fixed-precision sequential sampling plan of the pest was developed using Green’s model. The adult population peaked in June. The activity period of the larvae was observed from June to October and peaked in October. Sampling distribution of the larvae on pomegranate fruits was random. Estimated optimum sample sizes ranged from 1 to 44 and 1 to 16 fruits at precision levels of 0.25 and 0.1, respectively.
NOVEL ‘PHOTONEUTRON VOLUME DOSE EQUIVALENT’ HYPOTHESIS AND METHODOLOGY FOR SECOND PRIMARY CANCER RISK ESTIMATION IN HIGH-ENERGY X-RAY MEDICAL ACCELERATORS
Authors: Sohrabi Mehdi , Hakimi Amir 
Published: January 2020

Abstract
A novel ‘photoneutron (PN) volume dose equivalent’ methodology was hypothesized and applied for the first time for estimating PN second primary cancer (PN-SPC) risks in high-energy X-ray medical accelerators. Novel position-sensitive mega-size polycarbonate dosimeters with 10B converter (with or without cadmium covers) were applied for determining fast, epithermal and thermal PN dose equivalents at positions on phantom surface and depths. The methodology was applied to sites of tumors such as brain, stomach and prostate in 47 patients. The PN-SPC risks were estimated for specific organs/tissues using linear International Commission on Radiological Protection cancer risks and were compared with some available data. The corresponding PN-SPC risk estimates ranged from 1.450 × 10−3 to 1.901 cases per 10 000 persons per Gray. The method was applied to 47 patients for estimating PN-SPC risks in patients undergoing radiotherapy. The PN-SPC risk estimates well match those calculated by simulation but are comparatively different from those estimated by ‘PN point dose equivalent’ methods, as expected.
Economic Development, Market Transition, and Work Values in Post-Socialist China
Authors: Cao Yang 
Published: January 2020

AbstractThis study examines the macro-level determinants of work values in urban China. Drawing on Inglehart’s theory of postmaterialism and the institutional theory in sociology, I argue that economic development and market transition, two of the most prominent themes of China’s social change in the post-socialist era, exert opposite effects on work values. On the one hand, rapid economic growth has created unprecedented material affluence and a high level of existential security in some parts of China. According to Inglehart’s theory, this should lead individuals to focus less on material rewards and to prioritize postmaterialist goals in the work domain. On the other hand, China’s institutional change from socialist redistribution to markets has abolished lifetime employment and replaced it with a precarious labor market. This change, I argue, promotes a materialist orientation among Chinese workers and discourages them from embracing postmaterialist work values. Using data from a 2012 national labor force survey, multilevel regression analysis shows that, all else being equal, workers in China’s more developed provinces indeed place less importance on how well work meets their survival needs, whereas workers in more marketized provinces exhibit the opposite tendency. However, neither economic development nor marketization at the province level is a significant predictor of postmaterialist work values. These findings have direct implications for work value research and for understanding social change in post-socialist China.
Electromyographic Comparison of the Efficacy of Ultrasound-guided Suprainguinal and Infrainguinal Fascia Iliaca Compartment Block for Blockade of the Obturator Nerve in Total Knee Arthroplasty
Authors: Qian Yuying , Guo Zhiyuan , Huang Juanjuan , Zhang Qunying , An Xiaofeng , Hu Huansheng , Zhu Fengqin , Wang Xianghe 
Published: January 2020

Background and Objectives:
The knee is innervated by the femoral, obturator, and sciatic nerves. An infrainguinal fascia iliaca compartment block (FICB) is often used as a technique for pain management after hip and knee arthroplasty. This approach blocks the femoral nerve, lateral femoral cutaneous nerve, and obturator nerve. Previous studies show suprainguinal FICB achieves improved postoperative analgesia compared with infrainguinal FICB after hip fracture. However, the analgesic effects of suprainguinal or infrainguinal FICB on the obturator nerve after total knee arthroplasty (TKA) remain to be established. This study compared the efficacy of suprainguinal versus infrainguinal FICB for the blockade of the obturator nerve using electromyography and quantification of total opioid consumption during the 24 hours after TKA.

Methods:
This prospective, randomized controlled clinical study enrolled 74 patients scheduled to undergo TKA. Patients were randomized 1:1 to receive suprainguinal FICB (group S) or infrainguinal FICB (group I) with 30 mL of 0.375% ropivacaine. The primary endpoint was the mean amplitude of the adductor longus compound muscle action potential (CMAP) at 0 (before the block), 10, 20, and 30 minutes after FICB. The secondary endpoint was total opioid consumption during the 24 hours after TKA.

Results:
Data from 62 patients were included in the analysis. The mean amplitude of the adductor longus CMAP was significantly lower in group S compared with group I (repeated-measures analysis of variance; F=4.73, P=0.034). At 24 hours after TKA, mean (SD) total opioid consumption was significantly lower in group S, compared with group I (131.5±76.8 vs. 201.5±85.1 μg) (P=0.001).

Conclusions:
Suprainguinal FICB significantly increased the incidence of successful obturator nerve block and significantly decreased fentanyl consumption 24 hours after TKA compared with infrainguinal FICB.
Biological Mechanisms of Atropine Control of Myopia
Authors: Upadhyay Aradhana , Beuerman Roger W. 
Published: January 2020

Abstract:
Myopia is a global problem that is increasing at an epidemic rate in the world. Although the refractive error can be corrected easily, myopes, particularly those with high myopia, are susceptible to potentially blinding eye diseases later in life. Despite a plethora of myopia research, the molecular/cellular mechanisms underlying the development of myopia are not well understood, preventing the search for the most effective pharmacological control. Consequently, several approaches to slowing down myopia progression in the actively growing eyes of children have been underway. So far, atropine, an anticholinergic blocking agent, has been most effective and is used by clinicians in off-label ways for myopia control. Although the exact mechanisms of its action remain elusive and debatable, atropine encompasses a complex interplay with receptors on different ocular tissues at multiple levels and, hence, can be categorized as a shotgun approach to myopia treatment. This review will provide a brief overview of the biological mechanisms implicated in mediating the effects of atropine in myopia control.
Disconnects in global discourses—the unintended consequences of marine mammal protection on small-scale fishers
Authors: Davis Katrina J. , Alfaro-Shigueto Joanna , Arlidge William N.S. , Burton Michael , Mangel Jeffrey C. , Mills Morena , Milner-Gulland E.J. , Palma Duque José , Romero-de-Diego Cristina , Gelcich Stefan 
Published: January 2020

AbstractGlobally, the populations of many marine mammals remain of critical concern after centuries of exploitation and hunting. However, some marine mammal populations (e.g. pinnipeds) have largely recovered from exploitation, and interactions between these species and fisheries—particularly small-scale fisheries—is once again of concern globally. The large scope and widespread scale of interactions highlights the local disconnect between two global policies: marine mammal conservation and small-scale fisheries protection. In this research, we explore these conflicting global policies by assessing the perceptions of coastal small-scale fishers in Peru and Chile regarding their interactions with pinnipeds, including the South American sea lion (Otaria flavescens) and South American fur seal (Arctocephalus australis). We surveyed 301 gill net fishers and assess perceptions using a best-worst scaling methodology. We find that fishers are chiefly concerned with the increase in pinniped populations, perceive that their interactions with pinnipeds have significantly increased over the past 80 years, and report pinniped-driven catch and income losses ≥ 26 per cent. Surprisingly, fishers do not believe that compensation schemes will resolve this issue—instead they overwhelmingly call for pinniped population culls. The reported number of pinnipeds illegally killed by fishers suggests the potential for large negative impacts on these protected species, and a loss of legitimacy in marine regulation. Collectively, our results portray a sense of marginalisation from fishers’—that global policy treats them as less “important” than marine mammals. Our results highlight the increasing disconnect in global policy, which on one hand seeks to protect threatened marine mammal populations, and on the other seeks to promote the welfare of small-scale fishers.
Elevated phosphate mediates extensive cellular toxicity: from abnormal proliferation to excessive cell death
Authors: He Ping , Mann-Collura Olivia , Fling Jacob , Edara Naga , Razzaque Mohammed S. 
Published: January 2020

AbstractInorganic phosphate (Pi) is an essential nutrient for human health. Due to our change in dietary pattern, dietary Pi overload engenders systematic phosphotoxicity, including excessive Pi related vascular calcification and chronic tissue injury. The molecular mechanisms of the seemingly distinct phenotypes remain elusive. In this study, we found that Pi directly mediates diverse cellular toxicity in a dose-dependent manner on a cell-based model. At moderately higher than physiological level, extracellular Pi promotes cell proliferation by activating AKT and extracellular signal-regulated kinase 1/2 (ERK1/2) cascades. By introducing additional Pi, we observed significant cell damage caused by the interwoven Pi related biological processes, including activation of mitogen-activated protein kinase (MAPK) signaling, endoplasmic reticulum (ER) stress, epithelial-mesenchymal transition (EMT) and apoptosis. Taken together, elevated extracellular Pi results in a broad spectrum of toxicity by rewiring complicated signaling networks that control cell growth, cell death, ER stress, and cell mobility.
Molecular mechanism underlying venation patterning in butterflies
Authors: Banerjee Tirtha Das , Monteiro Antónia 
Published: January 2020

AbstractThe mechanism of wing vein differentiation inDrosophilais a classic text-book example of pattern formation using a system of positional-information, yet very little is known about how this mechanism differs in species with a different number of veins and how insect venation patterns evolved. Here, we examine the expression patterns of genes previously implicated in vein differentiation inDrosophilain two butterfly species with more complex venation, the African squinting bush brownBicyclus anynanaand the Asian cabbage white,Pieris canidia. We also test the function of one of these genes,spalt (sal), with CRISPR-Cas9 inB. anynana. We identify both conserved as well as new domains ofdecapentaplegic (dpp), engrailed (en),invected (inv)andsalgene expression inB. anynana, and propose how the simplified venation inDrosophilamight have evolved via loss ofdppandsalgene expression domains, silencing of vein inducing programs at Sal-expression boundaries, and changes in gene expression of vein maintenance genes.Summary statementThe paper describes new domains of venation patterning genes in butterflies and proposes how simplified venation in other insect lineages might have evolved.
Bmf Facilitates Protein Degradation and Reduces Beclin1 Ubiquitination to Inhibit Autophagy Independent of mTOR
Authors: Delgado-Vergas Monica , Fort Susan , Tassew Dereje , Tesfaigzi Yohannes 
Published: January 2020

AbstractPrevious observations suggested that Bcl-2 modifying factor (Bmf) affects autophagy but the underlying mechanisms were unknown. The present studies show that Bmf inhibited the initiation and flux of autophagy in a manner that is independent of the mTOR pathway and inhibition of mTOR increased Bmf expression to temper the autophagic cell death. In mice, emphysema was observed in Bmf-deficient mice, suggesting that Bmf suppresses autophagic cell death of alveolar type II cells. Bmf deficiency increased ubiquitination of Beclin1 with K63 chains and released Beclin1 from Bcl-2. However, Bmf deficiency also increased the levels of polyubiquitinated proteins in general. In mice, Bmf-deficiency robustly increased p62 levels in all tissues analyzed, but LC3-II levels were reduced only in the hearts of old mice. Also, Bmf-deficiency caused persistent mucous cell metaplasia in mice exposed to allergen and increased levels of polyubiquitinated Muc5ac in differentiated airway epithelial cells. The reduction of ubiquitinated proteins was mediated by the BH3- and dynein binding-domains of Bmf. Together, these findings show that the primary role of Bmf is to reduce protein levels and affects K63- and K48-ubiqutination.
CXCR4-binding PET tracers link monocyte recruitment and endothelial injury in murine atherosclerosis
Authors: Baba Osamu , Elvington Andrew , Szpakowska Martyna , Sultan Deborah , Heo Gyu Seong , Zhang Xiaohui , Luehmann Hannah , Detering Lisa , Chevigné Andy , Liu Yongjian , Randolph Gwendalyn J. 
Published: January 2020

AbstractViral macrophage inflammatory protein 2 (vMIP-II/vCCL2) binds to multiple chemokine receptors, and vMIP-II based PET tracer (64Cu-DOTA-vMIP-II: vMIP-II tracer) accumulates at atherosclerotic lesions in mice. The magnitude of64Cu-DOTA-vMIP-II accumulation correlated with monocyte recruitment, asApoe-/-mice treated with AAV-mApoE showed PET signal declining as monocyte recruitment subsided. Unexpectedly, monocytes themselves were not the major target of the64Cu-DOTA-vMIP-II tracer. Using fluorescence-tagged vMIP-II tracer, competitive receptor blocking with CXCR4 antagonists, CXCR4-specific tracer64Cu-DOTA-FC131, or CXCR4 staining during disease progression and regression, endothelial cell expression of CXCR4 proved to be the main target of64Cu-DOTA-vMIP-II imaging. Expression of CXCR4 was low in non-plaque areas, but strongly detected on endothelium at the edges of progressing plaques, corresponding to a population of proliferating endothelium and to the location in plaques where monocyte recruitment occurred. Thus, endothelial injury status of plaques is marked by CXCR4 expression and that this injury correlates with the tendency of such plaques to recruit monocytes. Furthermore, our findings suggest PET tracers that, through binding CXCR4, may be useful to monitor plaque injury status.
A plug and play microfluidic platform for standardized sensitive low-input Chromatin Immunoprecipitation
Authors: Dirks René A.M. , Thomas Peter , Jones Robert C. , Stunnenberg Hendrik G. , Marks Hendrik 
Published: January 2020

AbstractEpigenetic profiling by ChIP-Seq has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks and for screening for biomarkers. However, the ChIP-Seq protocol for low-input samples is laborious, time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput. Although prototypic microfluidic ChIP-Seq platforms have been developed, these are poorly transferable as they require sophisticated custom-made equipment and in-depth microfluidic and ChIP expertise, while lacking parallelisation. To enable standardized, automated ChIP-Seq profiling of low-input samples, we constructed PDMS-based plates containing microfluidic Integrated Fluidic Circuits capable of performing 24 sensitive ChIP reactions within 30 minutes hands-on time. These disposable plates can conveniently be loaded into a widely available controller for pneumatics and thermocycling, making the ChIP-Seq procedure Plug and Play (PnP). We demonstrate high-quality ChIP-seq on hundreds to few thousands of cells for multiple widely-profiled post-translational histone modifications, together allowing genome-wide identification of regulatory elements. As proof of principle, we managed to generate high-quality epigenetic profiles of rare totipotent subpopulations of mESCs using our platform. In light of the ready-to-go ChIP plates and the automated workflow, we named our procedure PnP-ChIP-Seq. PnP-ChIP-Seq allows non-expert labs worldwide to conveniently run robust, standardized ChIP-Seq, while its high-throughput, consistency and sensitivity paves the way towards large-scale profiling of precious sample types such as rare subpopulations of cells or biopsies.Reviewer link to dataAll sequencing data has been submitted to the NCBI GEO database. Reviewer link:http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=klwnocicrpaxrkv&acc=GSE120673
Estimating invasion dynamics with geopolitical-unit level records: performance and similarity of common methods using both simulated data and a real case
Authors: Liang Wanwan , Tran Liem , Wiggins Gregory , Grant Jerome 
Published: January 2020

AbstractEstimating invasion dynamic is important to the management of invasive species, and geopolitical-unit level data are usually the most abundant and available records of invasive species. Here, for the first time we evaluated performances and similarities of eight common methods to estimate spread pattern and spread dynamic of invasive species with geopolitical-unit level data, and assessed impacts of variations in geopolitical-units on each method using simulated spread data. We also formulated a concave hull boundary displacement method (i.e., CEB) and an area-based regression method (i.e., AER) for estimating spread with geopolitical-unit data. Three regions with different sized counties in the United States (U.S.) were selected to conduct simulations and three spread scenarios were simulated. R2and root mean square error were used to evaluate the abilities of all methods to estimate spread. Correlation coefficients were used to assess the similarity pattern of all methods. Finally, kudzu bugMegacopta cribraria, an invasive insect in the U.S., was used as a case study to test the generality of some results concluded from the simulated research. We found the CEB and two regression methods consistently estimated the right expansion patterns. Two boundary displacement and two area-based regression methods estimated highly correlated spread and were the best four methods, among which CEB had the best estimation. Distance-based regression methods are sensitive to irregularity and stochasticity in spread, and the minimum spread distance method had low ability to estimate spread. The case study showed consistent results with the simulated research. Both regression and boundary displacement methods can estimate spread patterns, overall rate, and spread dynamics of invasive species. Boundary displacement methods best estimate spread rates and dynamics; however, for spread without clear infestation outlines, area-based regression methods can be good alternatives.
Chop/Ddit3depletion in β-cells alleviates ER stress and corrects hepatic steatosis
Authors: Yong Jing , Parekh Vishal S. , Nayak Jonamani , Chen Zhouji , Lebeaupin Cynthia , Zhang Jiangwei , Prakash Thazha P. , Murray Sue , Guo Shuling , Ayala Julio E. , Satin Leslie S. , Kaufman Randal J. 
Published: January 2020

AbstractType 2 diabetes (T2D) is a metabolic disorder characterized by hyperglycemia, hyperinsulinemia and insulin resistance (IR). During the early phase of T2D, insulin synthesis and secretion by pancreatic β cells is enhanced, which can lead to proinsulin (ProIns) misfolding that aggravates endoplasmic reticulum (ER) homeostasis in β cells. Moreover, increased insulin in the circulation may contribute to fatty liver disease. Medical interventions aimed at alleviating ER stress in β cells while maintaining optimal insulin secretion are therefore an attractive therapeutic strategy for T2D. Previously, we demonstrated that germlineChopgene deletion preserved β cells in high fat diet (HFD) fed mice and in leptin receptor-deficientdb/dbmice. In the current study, we further investigated whether targetingChop/Ddit3specifically in murine β cells confers therapeutic benefits. First, we show thatChopdeletion in β cells alleviates β cell ER stress and delays glucose-stimulated insulin secretion (GSIS) in HFD fed mice. Second, importantly, β cell-specificChopdeletion prevented liver steatosis and hepatomegaly in aged HFD fed mice without affecting basal glucose homeostasis. Third, we provide the first mechanistic evidence that ER remodeling secondary toChopdeletion modulates glucose-induced islet Ca2+oscillations. Finally, using state-of-the-art GLP1-conjugatedChopAntiSense Oligonucleotides (GLP1-ChopASO), we demonstrated that theChopdeletion induced GSIS change is a long term complex event in β cells. In summary, our results demonstrate thatChopdepletion in β cells is a new therapeutic strategy to alleviate dysregulated insulin secretion and the consequently fatty liver disease in T2D.