bluuebunny/crossref_metadata_2025_split huggingface dataset:
A meta-analysis of neutron lifetime measurements
Authors: Rajan Ashwani , Desai Shantanu 
Published: November 2019

Abstract
We calculate the median as well as weighted mean central estimates for the neutron lifetime from a subset of measurements compiled in the 2019 update of the Particle Data Group (PDG). We then reconstruct the error distributions for the residuals using three different central estimates and then check for consistency with a Gaussian distribution. We find that although the error distributions using the weighted mean as well as median estimate are consistent with a Gaussian distribution, the Student’s $t$ and Cauchy distribution provide a better fit. This median statistic estimate of the neutron lifetime from these measurements is given by $881.5 \pm 0.47$ seconds. This can be used as an alternate estimate of the neutron lifetime. We also note that the discrepancy between beam and bottle-based measurements using median statistics of the neutron lifetime persists with a significance between 4 $\sigma$ and 8 $\sigma$, depending on which combination of measurements is used.
The Institutional Foundations of Religious Politics: Evidence from Indonesia*
Authors: Bazzi Samuel , Koehler-Derrick Gabriel , Marx Benjamin 
Published: November 2019

AbstractThis article explores the foundations of religious influence in politics and society. We show that an important Islamic institution fostered the entrenchment of Islamism at a critical juncture in Indonesia, the world’s largest Muslim country. In the early 1960s, rural elites transferred large amounts of land into waqf—inalienable charitable trusts in Islamic law—to avoid expropriation by the state. Regions facing a greater threat of expropriation exhibit more prevalent waqf land and Islamic institutions endowed as such, including mosques and religious schools. These endowments provided conservative forces with the capital needed to promote Islamist ideology and mobilize against the secular state. We identify lasting effects of the transfers on the size of the religious sector, electoral support for Islamist parties, and the adoption of local sharia laws. These effects are shaped by greater demand for religion in government but not by greater piety among the electorate. Waqf assets also impose costs on the local economy, particularly in agriculture, where these endowments are associated with lower productivity. Overall, our findings shed new light on the origins and consequences of Islamism.
Should we fund research randomly? An epistemological criticism of the lottery model as an alternative to peer review for the funding of science
Authors: Bedessem Baptiste 
Published: November 2019

Abstract
The way research is, and should be, funded by the public sphere is the subject of renewed interest for sociology, economics, management sciences, and more recently, for the philosophy of science. In this contribution, I propose a qualitative, epistemological criticism of the funding by lottery model, which is advocated by a growing number of scholars as an alternative to peer review. This lottery scheme draws on the lack of efficiency and of robustness of the peer-review-based evaluation to argue that the majority of public resources for basic science should be allocated randomly. I first differentiate between two distinct arguments used to defend this alternative funding scheme based on considerations about the logic of scientific research. To assess their epistemological limits, I then present and develop a conceptual frame, grounded on the notion of ‘system of practice’, which can be used to understand what precisely it means, for a research project, to be interesting or significant. I use this epistemological analysis to show that the lottery model is not theoretically optimal, since it underestimates the integration of all scientific projects in densely interconnected systems of conceptual, experimental, or technical practices which confer their proper interest to them. I also apply these arguments in order to criticize the classical peer-review process. I finally suggest, as a discussion, that some recently proposed models that bring to the fore a principle of decentralization of the evaluation and selection process may constitute a better alternative, if the practical conditions of their implementation are adequately settled.
First 12 years of tardigrade succession in the young soils of a quickly evolving ecosystem
Authors: Bingemer Jana , Pfeiffer Martin , Hohberg Karin 
Published: November 2019

AbstractOpen-cast coal-mining creates a severe disturbance of ecological systems, resulting in post-mining areas that have lost their soils entirely and are exposed to extreme conditions. Nonetheless, these areas allow us to investigate the process of primary succession. We studied the first 12 years of soil tardigrade succession at ‘Chicken Creek’, an experimental site within the open-cast coal-mining area in Welzow Süd, Germany. A total of ten tardigrade genera and 13 species or species groups were identified at the site. Over time, the organic carbon content, proportion of silt and nutrient availability in the soil increased, and the soil particle size distribution and pH value changed significantly. The vegetation cover and nematode abundance increased, whereas tardigrade densities peaked in 2008 and decreased thereafter, as did their mean body size. Species replacement was obvious within this 12 year study period, and tardigrade species diversity increased, indicating that ecological niche diversity also increased throughout this time. Vegetation cover, soil particle size distribution and time were the most important factors influencing the tardigrade community. We also discuss further potential factors and the ability of terrestrial tardigrades to persist despite many environmental constraints, such as fluctuations in pH and moisture, and to colonize new habitats faster than most other animal groups.
Corin plays a protective role via upregulating MAPK and downregulating eNOS in diabetic nephropathy endothelial dysfunction
Authors: Xue Meiting , Shi Yue , Pang Aiming , Men Li , Hu Yahui , Zhou Pengfei , Long Guangfeng , Tian Xin , Wang Rong , Zhao Yonghua , Liao Xudong , Shen Yanna , Cui Yujie 
Published: November 2019

AbstractDiabetic nephropathy (DN) is one of the leading causes of mortality in diabetic patients, but its pathogenesis is unclear. We aimed to study the role of the pro‐ANP convertase Corin in the pathogenesis of DN. Corin and ANP expression in DN rat kidneys and high‐glucose‐treated HK‐2 cells was analyzed by real‐time PCR, western blotting, and immunohistochemical staining. The effect of Corin‐siRNA or ANP‐siRNA HK‐2 cells on EA.hy926 cell migration was determined by scratch‐wound healing assay. The expression of mitogen‐activated protein kinase (MAPK) and endothelial NO synthase (eNOS) in EA.hy926 cells treated with conditioned medium from Corin‐siRNA‐ or ANP‐siRNA‐transfected HK‐2 cells was determined by western blotting. We found a significant reduction in Corin and ANP expression in DN rat kidneys. These results were recapitulated in HK‐2 cells treated with high glucose. EA.hy926 cells treated with conditioned medium from Corin‐deficient HK‐2 cells had inhibited migration, increased MAPK activity, and decreased eNOS activity. Similar effects were observed with ANP‐siRNA transfection. Finally, adding ANP to the Corin‐deficient HK‐2 conditioned medium rescued the above defects, indicating that Corin mediates its effects through ANP. In conclusion, Corin plays a renoprotective role through pro‐ANP processing, and defects in Corin cause endothelial dysfunction through MAPK and eNOS signaling in DN.
Wnt4‐modified NSC transplantation promotes functional recovery after spinal cord injury
Authors: Li Xiang , Peng Zhiming , Long Lingli , Tuo Ying , Wang Liqin , Zhao Xiaoyang , Le Wang , Wan Yong 
Published: November 2019

AbstractSpinal cord injury (SCI) can lead to severe motor and sensory dysfunction, yet there are no effective therapies currently due to the failure of reconstructing the interruption of the neuroanatomical circuit. While neural stem cell (NSC) transplantation has been considered a potential strategy to repair the neural circuit after SCI, the efficacy of this strategy remains unproven. The main reason is that most of the transplanted NSC differentiates into astrocyte rather than neuron in the microenvironment of SCI. Our results demonstrated that Wnt4 significantly promotes the differentiation of NSC into neuron by activating both β‐catenin and MAPK/JNK pathways and suppressing the activation of Notch signaling, which is acknowledged as prevention of NSC differentiation into neuron, through downregulating NICD expression, translocating and preventing the combination of NICD and RbpJ in nucleus. In addition, Wnt4 rescues the negative effect of Jagged, the ligand of Notch signaling, to promote neuronal differentiation. Moreover, in vivo study, transplantation of Wnt4‐modified NSC efficaciously repairs the injured spinal cord and recovers the motor function of hind limbs after SCI. This study sheds new light into mechanisms that Wnt4‐modified NSC transplantation is sufficient to repair the injured spinal cord and recover the motor dysfunction after SCI.
METTL3 regulates inflammatory pain by modulating m6A‐dependent pri‐miR‐365‐3p processing
Authors: Zhang Chenjing , Wang Yin , Peng Yunan , Xu Hongjiao , Zhou Xuelong 
Published: November 2019

AbstractN6‐methyladenosine (m6A) modification in RNA has been implicated in diverse biological processes. However, very little is currently known about its role in nociceptive modulation. Here, we found that the level of spinal m6A modification was significantly increased in a mouse model of Complete Freund's Adjuvant (CFA)‐induced chronic inflammatory pain, which was accompanied with the augmentation of methyltransferase‐like 3 (METTL3) expression in the spinal cord. Knockdown of spinal METTL3 prevented and reversed CFA‐induced pain behaviors and spinal neuronal sensitization. In contrast, overexpression of spinal METTL3 produced pain behaviors and neuronal sensitization in naive mice. Moreover, we found that METTL3 positively modulated the pri‐miR‐65‐3p processing in a microprocessor protein DiGeorge critical region 8‐dependent manner. Collectively, our findings reveal an important role of METTL3‐mediated m6A modification in nociceptive sensitization and provide a novel perspective on m6A modification in the development of pathological pain.
Conditional knockout of kisspeptin signaling in brown adipose tissue increases metabolic rate and body temperature and lowers body weight
Authors: Tolson Kristen P. , Marooki Nuha , De Bond Julie‐Ann P. , Walenta Evelyn , Stephens Shannon B.Z. , Liaw Reanna B. , Savur Rishi , Wolfe Andrew , Oh Da Young , Smith Jeremy T. , Kauffman Alexander S. 
Published: November 2019

AbstractThe peptide kisspeptin and its receptor, Kiss1r, act centrally to stimulate reproduction. Evidence indicates that kisspeptin signaling is also important for body weight (BW) and metabolism. We recently reported that Kiss1r KO mice develop obesity, along with reduced metabolism and energy expenditure, independent of estradiol levels. Outside the brain, Kiss1r is expressed in several metabolic tissues, including brown adipose tissue (BAT), but it is unknown which specific tissue is responsible for the metabolic phenotype in Kiss1r KOs. We first determined that global Kiss1r KO mice have significant alterations in body temperature and BAT thermogenic gene expression, perhaps contributing to their obesity. Next, to test whether kisspeptin signaling specifically in BAT influences BW, metabolism, or body temperature, we used Cre/lox technology to generate conditional Kiss1r knockout exclusively in BAT (BAT‐Kiss1r KO). Unlike global Kiss1r KOs, BAT‐Kiss1r KOs (lacking Kiss1r in just BAT) were not hypogonadal, as expected. Surprisingly, however, BAT‐Kiss1r KOs of both sexes displayed significantly lower BW and adiposity than controls. This novel BAT‐Kiss1r KO phenotype was of greater magnitude in females and was associated with improved glucose tolerance, increased metabolism, energy expenditure, and locomotor activity, along with increased body temperature and BAT gene expression, specifically Cox8b. Our findings suggest that the previously observed obesity and decreased metabolism in global Kiss1r KOs reflect impaired kisspeptin signaling in non‐BAT tissues. However, the novel finding of increased metabolism and body temperature and lower BW in BAT‐Kiss1r KOs reveal a previously unidentified role for endogenous kisspeptin signaling in BAT in modulating metabolic and thermogenic physiology.
Neural Closed Loop Deep Brain Stimulation for Freezing of Gait
Authors: Petrucci Matthew N. , Neuville Raumin S. , Afzal M. Furqan , Velisar Anca , Anidi Chioma M. , Anderson Ross W. , Parker Jordan E. , O’Day Johanna J. , Wilkins Kevin B. , Bronte-Stewart Helen M. 
Published: November 2019

AbstractFreezing of gait (FOG), a devastating symptom of Parkinson’s disease (PD), can be refractory to current treatments such as medication and open-loop deep brain stimulation (olDBS). Recent evidence suggests that closed-loop DBS (clDBS), using beta local field potential power from the subthalamic nucleus (STN) as the control variable, can improve tremor and bradykinesia; however, no study has investigated the use of clDBS for the treatment of FOG. In this study, we provide preliminary evidence that clDBS was superior to olDBS in reducing percent time freezing and in reducing freezing behavior (gait arrhythmicity) in a person with PD and FOG. These findings warrant further investigation into the use of clDBS to treat FOG while also minimizing the total energy delivered to maintain a therapeutic effect.
Risk of Inflammatory Bowel Disease in Psoriasis Patients Treated with Anti-Interleukin-17 Agents: A Bayesian Metaanalysis
Authors: Gill N. , Pietrosanu M. , Gniadecki R. 
Published: November 2019

AbstractBackgroundUse of interleukin-17 inhibitors (IL-17i) in psoriasis has been associated with an increased risk of inflammatory bowel disease (IBD). However, the clinical significance of this association is not understood.ObjectivesTo quantify the absolute risk of IBD in patients with psoriasis treated with IL-17i, stratified by known IBD risk factors.MethodsLiterature searches were performed to identify known IBD risk factors and the prevalences were quantified by a meta-analysis of proportions. The Bayesian model was used to estimate the probability of a new-onset or a flare of IBD in patients with psoriasis.ResultsThe prevalence of Crohn’s disease (CD) or ulcerative colitis (UC) in the general psoriasis population was 0.0010. Use of IL-17i increased the risk of CD to 0.0037 and UC to 0.0028, translating to a number needed to harm (NNH) of 373 for CD and 564 for UC. In patients who had concomitant hidradenitis suppurativa, the use of IL-17i was associated with a decrease in NNH for CD and UC to 18 and 76, respectively, whereas for patients with a family history of IBD, the NNH values were 6 (for CD) and 10 (for UC).ConclusionsIn patients with no risk factors, the probability of IBD flare or onset during IL-17i treatment is negligible and additional IBD screening procedures are not indicated. In contrast, the patients with psoriasis who have hidradenitis suppurativa or first-degree family history of IBD as risk factors should be monitored for signs and symptoms of CD and UC during IL-17i therapy.
Comprehensive biological interpretation of gene signatures using semantic distributed representation
Authors: Okuzono Yuumi , Hoshino Takashi 
Published: November 2019

AbstractRecent rise of microarray and next-generation sequencing in genome-related fields has simplified obtaining gene expression data at whole gene level, and biological interpretation of gene signatures related to life phenomena and diseases has become very important. However, the conventional method is numerical comparison of gene signature, pathway, and gene ontology (GO) overlap and distribution bias, and it is not possible to compare the specificity and importance of genes contained in gene signatures as humans do.This study proposes the gene signature vector (GsVec), a unique method for interpreting gene signatures that clarifies the semantic relationship between gene signatures by incorporating a method of distributed document representation from natural language processing (NLP). In proposed algorithm, a gene-topic vector is created by multiplying the feature vector based on the gene’s distributed representation by the probability of the gene signature topic and the low frequency of occurrence of the corresponding gene in all gene signatures. These vectors are concatenated for genes included in each gene signature to create a signature vector. The degrees of similarity between signature vectors are obtained from the cosine distances, and the levels of relevance between gene signatures are quantified.Using the above algorithm, GsVec learned approximately 5,000 types of canonical pathway and GO biological process gene signatures published in the Molecular Signatures Database (MSigDB). Then, validation of the pathway database BioCarta with known biological significance and validation using actual gene expression data (differentially expressed genes) were performed, and both were able to obtain biologically valid results. In addition, the results compared with the pathway enrichment analysis in Fisher’s exact test used in the conventional method resulted in equivalent or more biologically valid signatures. Furthermore, although NLP is generally developed in Python, GsVec can execute the entire process in only the R language, the main language of bioinformatics.
Nutritional Programming Improves Dietary Plant Protein Utilization in Zebrafish Danio rerio
Authors: Kwasek Karolina , Wojno Michal , Terova Genciana , McCracken Vance J. , Molinari Giovanni S. , Iannini Federica 
Published: November 2019

AbstractNutritional Programming (NP) has been shown to counteract the negative effects of dietary plant protein (PP) by introducing PP at an early age towards enhancement of PP utilization during later life stages. This study explored the effect of NP and its induction time on growth, expression of appetite-stimulating hormones, and any morphological changes in the gut possibly responsible for improved dietary PP utilization. At 3 days post-hatch (dph) zebrafish were distributed into 12 (3 L) tanks, 100 larvae per tank. This study included four groups: 1) The control (NP-FM) group received fishmeal (FM)-based diet from 13-36 dph and was challenged with PP-based diet during 36-66 dph; 2) The NP-PP group received NP with dietary PP in larval stage via live food enrichment during 3-13 dph followed by FM diet during 13-36 dph and PP diet during 36-66 dph; 3) The T-NP group received NP between 13-23 dph through PP diet followed by FM diet during 23-36 dph and PP diet during 36-66 dph; and 4) The PP group received PP diet from 13-66 dph. During the PP challenge the T-NP group achieved the highest weight gain compared to control and PP. Ghrelin expression in the brain was higher in T-NP compared to NP-FM and NP-PP, while in the gut it was reduced in both NP-PP and T-NP groups. Cholecystokinin expression showed an opposite trend to ghrelin. The brain neuropeptide Y expression was lower in NP-PP compared to PP but not different with NP-FM and T-NP groups. The highest villus length to width ratio in the middle intestine was found in T-NP compared to all other groups. The study suggests that NP induced during juveniles stages improves zebrafish growth and affects digestive hormone regulation and morphology of the intestinal lining – possible mechanisms behind the improved PP utilization in pre-adult zebrafish stages.
Comparative of probiotics reveals cecal microbial component associated with performance parameters in broilers
Authors: Rodrigues D.R. , Briggs W. , Duff A. , Chasser K. , Murugesan R. , Pender C. , Ramirez S. , Valenzuela L. , Bielke L.R. 
Published: November 2019

AbstractProbiotics have become increasingly popular in poultry industry as a promising nutritional intervention to promote modulation of intestinal microbiota as a means of improving health and performance. This study aimed to determine the effects of different probiotic formulations on the cecal microbial communities and performance in 21 and 42 day-old-broilers, as well as to define associations between ceca microbial profile and growth parameters. Probiotics investigated included a synbiotic (SYNBIO), a yeast-based probiotic (YEAST), and three single-strain formulations of spore-formingBacillus amyloliquefaciens(SINGLE1),B. subtilis(SINGLE2) andB. licheniformis(SINGLE3). Dietary inclusion of SYNBIO, YEAST, and SINGLE2 increased body weight (BW) by 7, 14, and 21d (p<0.05) compared to a basal diet without probiotics (CON). The treatments SYNBIO, and YEAST decreased mortality by 21d, while SYNBIO reduced the overall mortality rate by 42d (p<0.05). Bifidobacteriales had the highest (p<0.05) population in SINGLE2, whereas Clostridiales was reduced compared to CON, SINGLE1, and SINGLE3. The addition of SYNBIO into diet mainly stimulated (p<0.05) the cecal relative abundance of Lactobacillales by 21d. Besides, Spearman’s correlation analyses revealed that population of Lactobacillales was associated with lower Enterobacteriales, higher BW, and lower mortality of growing broilers. These results suggest that the modulation of ceca microbiota and the greatest productive parameters were achieved by supplementation of specific probiotic mixture. The selection of probiotics by their ability to drive cecal microbiota towards lactic acid bacteria colonization may be a strategic approach to improve the indicators of performance in broilers.
Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved AS-NMD pathways
Authors: Kovalak Carrie , Donovan Scott , Bicknell Alicia A. , Metkar Mihir , Moore Melissa J. 
Published: November 2019

AbstractBackgroundAlternative splicing (AS), which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression. The flux through competing AS pathways cannot be determined by traditional RNA-Seq, however, because different mRNA isoforms can have widely differing decay rates. Indeed, some mRNA isoforms with extremely short half-lives, such as those subject to translation-dependent nonsense-mediated decay (AS-NMD), may be completely overlooked in even the most extensive RNA-Seq analyses.ResultsRNA immunoprecipitation in tandem (RIPiT) of exon junction complex (EJC) components allows for purification of post-splicing mRNA-protein particles (mRNPs) not yet subject to translation (pre-translational mRNPs) and, therefore, translation-dependent mRNA decay. Here we compared EJC RIPiT-Seq to whole cell RNA-Seq data from HEK293 cells. Consistent with expectation, the flux through known AS-NMD pathways is substantially higher than that captured by RNA-Seq. Our EJC RIPiT-Seq also definitively demonstrates that the splicing machinery itself has no ability to detect reading frame. We identified thousands of previously unannotated splicing events; while many can be attributed to “splicing noise”, others are evolutionarily-conserved events that produce new AS-NMD isoforms likely involved in maintenance of protein homeostasis. Several of these occur in genes whose overexpression has been linked to poor cancer prognosis.ConclusionsDeep sequencing of RNAs in post-splicing, pre-translational mRNPs provides a means to identify and quantify splicing events without the confounding influence of differential mRNA decay. For many known AS-NMD targets, the NMD-linked AS pathway predominates. EJC RIPiT-Seq also enabled identification of numerous conserved but previously unannotated AS-NMD events.