bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupling of microRNA‐directed phased small interfering RNA generation from long noncoding genes with alternative splicing and alternative polyadenylation in small RNA‐mediated gene silencing
Authors: Ma Wuqiang , Chen Chengjie , Liu Yuanlong , Zeng Ming , Meyers Blake C. , Li Jianguo , Xia Rui 
Published: December 2017

Summary

MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play vital regulatory roles in plant growth and development. Little is known about these small RNAs in litchi (Litchi chinensis), an economically important fruit crop widely cultivated in Southeast Asia.

We profiled the litchi small RNA population with various deep‐sequencing techniques and in‐depth bioinformatic analyses.

The genome‐wide identification of miRNAs, their target genes, and phasiRNA‐generating (PHAS) genes/loci showed that the function of miR482/2118 has expanded, relative to its canonical function. We also discovered that, for 29 PHAS loci, miRNA‐mediated phasiRNA production was coupled with alternative splicing (AS) and alternative polyadenylation (APA). Most of these loci encoded long noncoding RNAs. An miR482/2118 targeted locus gave rise to four main transcript isoforms through AS/APA, and diverse phasiRNAs generated from these isoforms appeared to target long terminal repeat (LTR) retrotransposons and other unrelated genes. This coupling enables phasiRNA production from different exons of noncoding PHAS genes and yields diverse phasiRNA populations, both broadening and altering the range of downstream phasiRNA‐regulated genes.

Our results reveal the diversity of miRNA and phasiRNA in litchi, and demonstrate AS/APA as a new layer of regulation in small RNA‐mediated gene silencing.
Sorting the Left from the Rest: The Communitarian Religious Perspective and Liberal Economic Attitudes
Authors: Ledet Richard 
Published: December 2017

In this article, the argument is made that the religious activity generated by churches, which tends to focus an individual's attention either outward toward the larger community or inward toward one's self, can influence parishioners’ economic attitudes. Using survey data obtained during the 2008 presidential election cycle, this article tests the merits of that argument by examining the effect of multiple aspects of religion on economic attitudes. Evidence indicates that, along with some of the conventional religiosity measures, there is a previously noticed but understudied “communitarian” dimension of religion that explains variation in social welfare attitudes. Additional tests conducted on subsamples of denominational groups reveal that the communitarian religious perspective is a significant predictor of liberal welfare attitudes among Mainline Protestants. These findings shed light on characteristics associated with the “religious left,” and provide a clearer picture of how religion, in different measurable forms, is related to economic attitudes.Related Articles

Rugeley, Cynthia R., and
John David Gerlach. 2012. “.” Politics & Policy 40 (): 444‐470. http://onlinelibrary.wiley.com/doi/10.1111/j.1747-1346.2012.00352.x/full

Butz, Adam M., and
Jason E. Kehrberg. 2015. “.” Politics & Policy 43 (): 256‐286. http://onlinelibrary.wiley.com/doi/10.1111/polp.12115/full

Ertas, Nevbahar. 2015. “.” Politics & Policy 43 (): 426‐451. http://onlinelibrary.wiley.com/doi/10.1111/polp.12120/abstract
Related Media
. n.d. “The Henry Institute National Survey of Religion and Public Life, 2008.” http://www.thearda.com/Archive/Files/Descriptions/NSRPL.asp

. 2017. Calvin College. Home Page. https://calvin.edu/centers-institutes/henry-institute/
Variable Implementation of Sexuality Education in Three Nigerian States
Authors: Kunnuji Michael O. N. , Robinson Rachel Sullivan , Shawar Yusra Ribhi , Shiffman Jeremy 
Published: December 2017

AbstractIn 2003, Nigeria adopted the Family Life and HIV Education (FLHE) sexuality education curriculum. Our analysis interrogates variation in sub‐national implementation. We conducted 52 interviews with persons knowledgeable about the curriculum in three states—Kano, Lagos, and Niger—and reviewed publications on FLHE. In Kano, the socio‐cultural context impeded implementation, but the persistence of innovative local champions resulted in some success. In Lagos, the cosmopolitan context, effective champions, funding by international donors, and a receptive government bureaucracy led to successful implementation. In Niger, despite a relatively conservative socio‐cultural context, state bureaucratic bottlenecks overwhelmed proponents’ efforts. In summary, the interaction of socio‐cultural context, domestic champions, adaptive capacity of state bureaucracies, and international funders explains variable implementation of FLHE. The Nigerian experience highlights the need for sexuality education proponents to anticipate and prepare for local opposition and bureaucratic barriers.
Putting It Off for Later: Procrastination and End of Fiscal Year Spending Spikes
Authors: Baumann Stuart 
Published: December 2017

AbstractMany governments around the world exhibit heightened spending at the end of the fiscal year. These end of fiscal year spending spikes often concern policy makers due to their tendency to result in lower quality spending. This paper uses UK data to offer evidence against the precautionary savings explanation for spending spikes. An alternative explanation is offered with procrastination driving heightened end of fiscal year spending. A new technique of time‐variant budgetary taxes is calibrated to the model, and it is shown to be effective for smoothing spending and improving spending efficiency throughout the fiscal year.
Power Variations and Testing for Co‐Jumps: The Small Noise Approach
Authors: Kurisu Daisuke 
Published: December 2017

AbstractIn this paper, we study the effects of noise on bipower variation, realized volatility (RV) and testing for co‐jumps in high‐frequency data under the small noise framework. We first establish asymptotic properties of bipower variation in this framework. In the presence of the small noise, RV is asymptotically biased, and the additional asymptotic conditional variance term appears in its limit distribution. We also propose consistent estimators for the asymptotic variances of RV. Second, we derive the asymptotic distribution of the test statistic proposed in (Ann. Stat. 37, 1792‐1838) under the presence of small noise for testing the presence of co‐jumps in a two‐dimensional Itô semimartingale. In contrast to the setting in (Ann. Stat. 37, 1792‐1838), we show that the additional asymptotic variance terms appear and propose consistent estimators for the asymptotic variances in order to make the test feasible. Simulation experiments show that our asymptotic results give reasonable approximations in the finite sample cases.
Potential of saprophage Diptera to acquire culturable livestock‐associated antibiotic‐resistant bacteria
Authors: Russell S. M. , Chittick V. A. , Sangweme D. T. , Lampert E. C. 
Published: December 2017

SummaryThe increasing prevalence of antibiotic resistance among bacteria is one of the most intractable challenges in 21st‐century public health. Dipterans that associate with livestock, livestock waste products and cadavers have the potential to acquire livestock‐associated antibiotic‐resistant bacteria (LA‐ARB) and transmit them to humans. In this study, piglet cadavers were used to attract saprophage dipterans from the environment and those dipterans were sampled for the presence of LA‐ARB. In the first trial, culturable microbes resistant to both aminoglycoside and β‐lactam antibiotics were found in all cadavers and masses of dipteran larvae, and in three‐quarters of adult dipterans. In the second trial, over 130 culturable bacterial colonies resistant to β‐lactams were isolated from the cadavers, larval and adult dipterans. Over 100 of those colonies were coliform or metabolically similar bacteria. Adult dipterans carried β‐lactam resistant staphylococci, whereas those bacterial types were absent from larval dipterans and cadavers, suggesting they were picked up from elsewhere in the environment. This research indicates that LA‐ARB are ubiquitous in pig farms, and dipterans have the potential to carry medically important microbes. Further research is encouraged to determine the extent to which dipterans acquire microbes from animal agriculture relative to other environments.
Aerobic Transformation of 2,4-Dinitrotoluene by Escherichia coli and Its Implications for the Detection of Trace Explosives
Authors: Shemer Benjamin , Yagur-Kroll Sharon , Hazan Carina , Belkin Shimshon 
Published: December 2017

ABSTRACT

DNT (2,4-dinitrotoluene), a volatile impurity in military-grade 2,4,6-trinitrotoluene (TNT)-based explosives, is a potential tracer for the detection of buried landmines and other explosive devices. We have previously described an
Escherichia coli
bioreporter strain engineered to detect traces of DNT and have demonstrated that the
yqjF
gene promoter, the sensing element of this bioreporter, is induced not by DNT but by at least one of its transformation products. In the present study, we have characterized the initial stages of DNT biotransformation in
E. coli
, have identified the key metabolic products in this reductive pathway, and demonstrate that the main DNT metabolite that induces
yqjF
is 2,4,5-trihydroxytoluene. We further show that
E. coli
cannot utilize DNT as a sole carbon or nitrogen source and propose that this compound is metabolized in order to neutralize its toxicity to the cells.

IMPORTANCE
The information provided in this article sheds new light both on the microbial biodegradability of nitroaromatic compounds and on the metabolic capabilities of
E. coli
. By doing so, it also clarifies the pathway leading to the previously unexplained induction of the
E. coli yqjF
gene by 2,4-dinitrotoluene, an impurity that accompanies 2,4,6-trinitrotoluene (TNT)-based explosives. Our improved understanding of these processes will serve to molecularly enhance the performance of a previously described microbial bioreporter of buried landmines and other explosive devices, in which the
yqjF
gene promoter serves as the sensing element.
Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach
Authors: Lugli Gabriele Andrea , Milani Christian , Duranti Sabrina , Mancabelli Leonardo , Mangifesta Marta , Turroni Francesca , Viappiani Alice , van Sinderen Douwe , Ventura Marco 
Published: December 2017

ABSTRACT

For decades, bacterial taxonomy has been based on
in vitro
molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species to reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus
Bifidobacterium
and identify apparent misclassifications in current bifidobacterial taxonomy. The developed method was validated by the classification of seven novel taxa belonging to the genus
Bifidobacterium
by employing their overall genetic content. The results of this study demonstrate the potential of this whole-genome approach to become the gold standard for phylogenomics-based taxonomic classification of bacteria.

IMPORTANCE
Nowadays, next-generation sequencing has given access to genome sequences of the currently known bacterial taxa. The public databases constructed by means of these new technologies allowed comparison of genome sequences between microorganisms, providing information to perform genomic, phylogenomic, and evolutionary analyses. In order to avoid misclassifications in the taxonomy of novel bacterial isolates, new (bifido)bacterial taxons should be validated with a phylogenomic assessment like the approach presented here.
Origin, History, and Meanings of the WordTransmission
Authors: Villalba Joaquín , Navarro Fernando A. , Cortés Francisco 
Published: December 2017

ABSTRACTThe origin of the wordstransmitandtransmissionand their derivatives can be traced to the Latintransmittere, in turn formed by prefixing the prepositiontrans(“across or beyond”) to the verbmittere(“to let go or to send”). From the times of Ancient Rome in the 3rd centuryb.c.e., the Latin wordtransmissiohas been “transmitted” (through Romance languages such as French, Italian, Spanish, and Portuguese) to all the major languages of culture, English among them. And through English, the international language of biomedical science in the 21st century, the termtransmissionis increasingly present today in some of the most dynamic disciplines of modern natural science, including genomics, molecular microbiology, hospital epidemiology, molecular genetics, biotechnology, evolutionary biology, and systems biology.
Case–control study to assess the association between colorectal cancer and selected occupational agents using INTEROCC job exposure matrix
Authors: El-Zaemey Sonia , Anand TN , Heyworth Jane Shirley , Boyle Terry , van Tongeren Martie , Fritschi Lin 
Published: December 2017

BackgroundColorectal cancer is the third most prevalent cancer in the world and is twice as common in developed countries when compared with low-income and middle-income countries. Few occupational risk factors for colorectal cancer have been identified. This case–control study aimed to assess the association between colorectal cancer and occupational exposure to selected solvents, combustion products, metals, dusts and other agents.MethodsCases (n=918) were enrolled from the Western Australian Cancer Registry from June 2005 to August 2007. Controls (n=1021) were randomly selected from the Western Australian electoral roll. We collected lifetime occupational history from cases and controls, in addition to their demographic and lifestyle characteristics. We applied the INTEROCC job exposure matrix to convert the occupational history to occupational exposure for 18 selected agents. Three exposure indices were developed: (1) exposed versus non-exposed; (2) lifetime cumulative exposure; and (3) total duration of exposure. The associations between colorectal cancer and the selected agents were estimated using logistic regression models adjusting for sex and age.ResultsNone of the 18 selected agents showed an association with colorectal cancer. No dose–response relationships with lifetime cumulative exposure or duration of exposure were observed.ConclusionThere was no evidence to suggest that occupational exposure to 18 selected agents increased the risk of colorectal cancer.
Quasi-distribution amplitudes for pion and kaon via the nonlocal chiral-quark model
Authors: Nam Seung-il 
Published: December 2017

We investigate the pseudoscalar (PS) meson ([Formula: see text] and [Formula: see text]) quasi-distribution amplitude (QDA), which is supposed to be an asymptotic analog to the meson distribution amplitude (DA) [Formula: see text] in the limit of the large longitudinal PS-meson momentum, i.e. [Formula: see text], in the non-perturbative (NP) region. For this purpose, we employ the nonlocal chiral-quark model (NLChQM) in the light-front (LF) formalism with a minimal Fock-state for the mesons [Formula: see text][Formula: see text][Formula: see text] at the low-energy scale parameter of the model [Formula: see text][Formula: see text][Formula: see text][Formula: see text]1 GeV. As a trial, we extract the transverse-momentum distribution amplitude (TMDA) from the light-front wave function (LFWF) within the model, and convert it to QDA with help of the virtuality-distribution amplitude (VDA). By doing that, we derive an analytical expression for the NP QDA with the current-quark mass correction up to [Formula: see text]. Numerically, we confirm that the obtained TMDA reproduces the experimental data for the photon-pion transition form factor [Formula: see text] at the low-[Formula: see text] qualitatively well. We also observe that the obtained QDA approaches to DA as [Formula: see text] increases, showing the symmetric and asymmetric curves with respect to [Formula: see text] for the pion and kaon, respectively, due to the current-quark mass difference [Formula: see text]. Assigning [Formula: see text], the moments [Formula: see text] are computed, using the pion and kaon QDAs, and there appear only a few percent deviations in the moments for [Formula: see text] in comparison to the values calculated directly from DAs. It turns out that the higher moments are more sensitive to the change of [Formula: see text], whereas the lower ones depend less on it.
Theory and calculation of colloidal depletion interaction
Authors: Ma Hongru 
Published: December 2017

Colloidal dispersion is composed of particles with size ranging from 1 nm to [Formula: see text]m dispersed in solvents. There are the volume exclusion interaction and other interactions between colloidal particles, of which the former interaction causes the depletion effect. When a big sphere is immersed in the colloidal system of small spheres, there is a depletion layer around the big sphere where the center of small sphere cannot enter. The depletion layers of two big spheres overlap if they are close to each other, increasing the free volume accessed by small spheres and thereby enlarging the entropy of the system. As a result, an effective interaction between the two big spheres is resulted from the change of entropy as a function of their distance, which is referred to as the depletion interaction. This paper first introduces the concept and scenario of the depletion interaction in colloidal systems. Then we briefly introduce various numerical or simulations methods of the depletion interaction of hard sphere systems, such as the acceptance ratio method, Wang–Landau method, and the density functional theory method. Taking the Asakura–Oosawa model as an example, we introduce a useful approximation method, Derjaguin approximation as well as the derivation of some approximate formula for the depletion interaction of different hardcore colloidal systems, such as between a pair of spheres in mono-disperse small spheres, between a hard sphere and a hard wall in a liquid of small spheres, and between a pair of hard spheres in a liquid of thin rods and thin disks.
A REVIEW ON BIOMECHANICAL ASPECTS OF VERTEBROPLASTY AND KYPHOPLASTY USING FINITE ELEMENT MODELING-BASED METHODS
Authors: JAMSHIDI NIMA , FARADONBEH SEYED AREF HOSSEINI 
Published: December 2017

The vertebroplasty (VP) and kyphoplasty (KP) are two minimally invasive surgeries using cement augmentation to treat the osteoporotic vertebrae in elderlies in order to relieve pain and prevent the continuation of microfractures. Biomechanists have always tried to assess the mechanical behavior of vertebrae after cement augmentation by using both the experimental and theoretical methods such as finite element modeling (FEM). In this study, 31 related articles using FEM in analyzing the VP and KP have been reviewed. This study included two main categories of spinal load distribution and tension in vertebrae after the VP and KP operations. This could be obtained by conducting FEM on the whole spine or other sectors of it such as intervertebral disc (IVD) or end plates (EPs). This study also referred to articles predicting the probability of adjacent fractures following VP and KP. The most common software employed in FEM was ABAQUS, applied for static and dynamic loads’ analyses. It was found that most of the reviewed articles adopted reverse engineering techniques by converting 2D computed tomography (CT) scan images into 3D reconstructed models. The material properties were generally taken from the literature. In more than 80% of studies, the model geometry was based on CT data of the spine. Almost 45% of the studies have attempted to compare the simulated vertebra after augmentation with experimental results taken from the literature (5% of the reviewed articles) or their own experimental tests (40% of the reviewed articles).
Diagnostic Ureteroscopy Prior to Radical Nephroureterectomy for Upper Tract Urothelial Carcinoma Increased the Risk of Intravesical Recurrence
Authors: Tan Ping , Xie Nan , Yang Lu , Liu Liangren , Tang Zhuang , Wei Qiang 
Published: December 2017

<b><i>Objective:</i></b> To assess the impact of diagnostic ureteroscopy (URS) prior to radical nephroureterectomy (RNU) on intravesical recurrence (IVR) in patients with upper tract urothelial carcinoma (UTUC). <b><i>Materials and Methods:</i></b> A systematic literature search of the Medline, Embase, PubMed, and Cochrane library was performed in August 2017. Cumulative analyses of available hazard ratios (HRs) and their 95% CI were conducted using Stata version 12.0. <b><i>Results:</i></b> Eleven studies including 4,057 participants were included, with a total of 1,403 patients diagnosed with IVR during the follow-up period. The pooled HRs of eight studies suggested that diagnostic URS prior to RNU significantly increased the IVR risk after RNU (HR 1.53, 95% CI 1.31–1.77; <i>p</i> &#x3c; 0.001). However, the preoperative diagnostic URS was not associated with cancer-specific survival (HR 0.72; <i>p</i> = 0.11), metastasis-free survival (HR 1.09; <i>p</i> = 0.60) or overall survival (HR 1.12; <i>p</i> = 0.73). No publication bias was observed (Begg, <i>p</i> = 0.90; Egger, <i>p</i> = 0.71). <b><i>Conclusions:</i></b> Regardless, the diagnostic URS prior to RNU might increase the IVR risk in patients with UTUC. As ureteroscopy provides important prognostic and therapeutic value and guides decisions in UTUC, more future studies should be performed to find a novel way to mitigate the potential risk of IVR after RNU, such as chemoprophylaxis after endoscopy.
Impact of Palliative Chemotherapy and Travel Distance on Hospice Referral in Patients With Stage IV Pancreatic Cancer: A Retrospective Analysis Within a Veterans Administration Medical Center
Authors: Duff Jennifer M. , Thomas Ryan M. 
Published: December 2017

Background: Metastatic pancreatic ductal adenocarcinoma (mPDAC) has a poor prognosis despite chemotherapy advancements. Although hospice utilization has increased, timing of referral is not always optimal. Aim: To investigate whether palliative chemotherapy and travel distance to the treatment center impact hospice referral patterns in veterans of the US military in order to identify potential areas for improving referral timing. Design: Demographic and clinical data were collected retrospectively according to the timing of hospice referral. Settings/Participants: Patients with mPDAC within a Veterans Administration Medical Center from 2005 to 2014. Results: Of 58 patients identified, 52 were referred to hospice. The median time from diagnosis to referral and referral to death was 2.4 and 3.1 weeks, respectively. Palliative chemotherapy was administered to 22 (42.3%) patients, with 30 (57.7%) patients not treated due to poor functional status (n = 16, 53.3%) or patient refusal (n = 14, 46.7%). Subset analysis for those travelling >60 miles versus <60 miles to the treatment center showed the median time to hospice referral was 1.7 versus 4.7 weeks. With no significant differences between groups, univariate analysis demonstrated that those referred to hospice >2.4 weeks from diagnosis more often received chemotherapy ( P < .001) and lived <60 miles from the treatment center ( P = .05). Conclusion: Receipt of palliative chemotherapy and proximity to the treatment center appear to delay referral to hospice in patients with mPDAC. Increasing physician awareness of such factors that may impact the decision to involve hospice is necessary for delivering optimal oncology care.