bluuebunny/crossref_metadata_2025 huggingface dataset:
circtools—a one-stop software solution for circular RNA research
Authors: Jakobi Tobias , Uvarovskii Alexey , Dieterich Christoph
Published: November 2018

Motivation

Circular RNAs (circRNAs) originate through back-splicing events from linear primary transcripts, are resistant to exonucleases, are not polyadenylated and have been shown to be highly specific for cell type and developmental stage. CircRNA detection starts from high-throughput sequencing data and is a multi-stage bioinformatics process yielding sets of potential circRNA candidates that require further analyses. While a number of tools for the prediction process already exist, publicly available analysis tools for further characterization are rare. Our work provides researchers with a harmonized workflow that covers different stages of in silico circRNA analyses, from prediction to first functional insights.

Results

Here, we present circtools, a modular, Python-based framework for computational circRNA analyses. The software includes modules for circRNA detection, internal sequence reconstruction, quality checking, statistical testing, screening for enrichment of RBP binding sites, differential exon RNase R resistance and circRNA-specific primer design. circtools supports researchers with visualization options and data export into commonly used formats.

Availability and implementation

circtools is available via https://github.com/dieterich-lab/circtools and http://circ.tools under GPLv3.0.

Supplementary information

Supplementary data are available at Bioinformatics online.
Blue care: a systematic review of blue space interventions for health and wellbeing
Authors: Britton Easkey , Kindermann Gesche , Domegan Christine , Carlin Caitriona
Published: November 2018

There is increasing interest in the potential use of outdoor water environments, or blue space, in the promotion of human health and wellbeing. However, therapeutic nature-based practices are currently outpacing policy and the evidence base for health or wellbeing benefits of therapeutic interventions within blue space has not been systematically assessed. This systematic review aims to address the gap in understanding the impacts of blue space within existing interventions for targeted individuals. A systematic review was carried out, searching Google Scholar, SCOPUS, PubMed, etc. through to August 2017. Only blue space interventions were included that were specifically designed and structured with a therapeutic purpose for individuals with a defined need and did not include nature-based promotion projects or casual recreation in the outdoors. Thirty-three studies met the inclusion criteria and were assessed. Overall, the studies suggest that blue care can have direct benefit for health, especially mental health and psycho-social wellbeing. The majority of papers found a positive or weak association between blue care and health and wellbeing indicators. There was also some evidence for greater social connectedness during and after interventions, but results were inconsistent and mixed across studies with very few findings for physical health. This is the first systematic review of the literature on blue care. In summary, it has been shown that mental health, especially psycho-social wellbeing, can be improved with investment in blue spaces. Key areas for future research include improving understanding of the mechanisms through which blue care can improve public health promotion.
Malignant Meningioma: An International Multicentre Retrospective Study
Authors: Champeaux Charles , Jecko Vincent , Houston Deborah , Thorne Lewis , Dunn Laurence , Fersht Naomi , Khan Akbar Ali , Resche-Rigon Matthieu
Published: November 2018

BACKGROUND

In contrast to benign meningiomas, malignant meningiomas (MM) are rare and associated with an unfavourable prognosis. Reports on MM concern fairly small cohorts, often comprising less than 30 cases.

OBJECTIVE

To describe the outcome MM and identify factors that may influence survival.

METHODS

Pathology reports and clinical data of 178 patients treated between 1989 and 2017 for a MM at 6 different international institutions were retrospectively reviewed. Seventy-six patients (42.7%) had a previous history of grade I or grade II meningioma. The patients underwent a total of 380 surgical resections and 72.5% received radiotherapy. Median follow-up was 4.5 yr.

RESULTS

At data collection, 111 patients were deceased (63.4%) and only 23 patients (13.7%) were alive without any residual tumor on the most recent scan. Median overall survival was 2.9 yr, 95% confidence interval [CI; 2.4, 4.5]. Overall survival rates at 1, 5, and 10 yr, respectively, were: 77.7%, 95% CI [71.6, 84.3], 40%, 95% CI [32.7, 49], and 27.9%, 95% CI [20.9, 37.3]. In the multivariable analysis, age at MM surgery <65 yr (hazard ratio [HR] = 0.44, 95% CI [0.29, 0.67], P < .001), previous benign or atypical meningioma surgery (HR = 1.9, 95% CI [1.23, 2.92], P = .004), completeness of resection (HR = 0.51, 95% CI [0.34, 0.78], P = .002), and adjuvant radiotherapy (HR = 0.64, 95% CI [0.42, 0.98], P = .039) were established as independent prognostic factors for survival.

CONCLUSION

This large series confirms the poor prognosis associated with MM, the treatment of which remains challenging. Patients under 65-yr-old with primary MM may live longer after complete resection and postoperative radiotherapy. Even with aggressive treatments, local control remains difficult to achieve.
Rev-erb Agonist Inhibits Chikungunya and O’nyong’nyong Virus Replication
Authors: Hwang Jesse , Jiang Alfred , Fikrig Erol
Published: November 2018

Chikungunya virus (CHIKV), an alphavirus spread by Aedes spp. mosquitos, causes severe inflammation and joint pain, progressing to a chronic arthralgic state in a subset of patients. Due to recent global epidemics of CHIKV and the potential for related viruses to cause outbreaks, multiple approaches to combat these pathogens are of interest. We report that SR9009, a synthetic agonist of nuclear receptors Rev-erb α/β, inhibits replication of multiple alphaviruses (CHIKV and O’nyong’nyong virus) mainly by suppressing structural protein synthesis, although viral RNA accumulation is relatively unimpeded. Furthermore, SR9009 reduces the inflammatory response in cultured murine macrophages exposed to alphavirus-infected cells.
House Price Beliefs And Mortgage Leverage Choice
Authors: Bailey Michael , Dávila Eduardo , Kuchler Theresa , Stroebel Johannes
Published: November 2018

We study the relationship between homebuyers’ beliefs about future house price changes and their mortgage leverage choices. Whether more pessimistic homebuyers choose higher or lower leverage depends on their willingness and ability to reduce the size of their housing market investments. When households primarily maximize the levered return of their property investments, more pessimistic homebuyers reduce their leverage to purchase smaller houses. On the other hand, when considerations such as family size pin down the desired property size, pessimistic homebuyers reduce their financial exposure to the housing market by making smaller downpayments to buy similarly-sized homes. To determine which scenario better describes the data, we investigate the cross-sectional relationship between house price beliefs and mortgage leverage choices in the U.S. housing market. We use plausibly exogenous variation in house price beliefs to show that more pessimistic homebuyers make smaller downpayments and choose higher leverage, in particular in states where default costs are relatively low, as well as during periods when house prices are expected to fall on average. Our results highlight the important role of heterogeneous beliefs in explaining households’ financial decisions.
Bonds of Kinship and Care: RAMC Photographic Albums and the Making of ‘Other’ Domestic Lives
Authors: Bate Jason
Published: November 2018

This article critically interrogates the nature of facial wounds themselves, their visceral, dehumanising quality, visibility, and social meaning. Little attention has been paid to the cultural ramifications and difficult questions concerning the futures of facially injured soldiers that Britain had to address in the post-war era. Focusing on photograph albums as socially salient objects, this article challenges medical photographic archives. Building on unexplored family archives, it revises understandings of the difficulties of veterans' homecoming, and how they achieved a level of emotional recovery as they tried to find a place in the post-war social fabric. The article argues that family photographic collections show the less obvious way that the war lived on for veterans and families, its damage and how it was passed on. These private collections offer new revelations on the success or failure of the surgical interventions in their aesthetic aims.
Zucchini yellow mosaic virus Genomic Sequences from Papua New Guinea: Lack of Genetic Connectivity with Northern Australian or East Timorese Genomes, and New Recombination Findings
Authors: Maina Solomon , Barbetti Martin J. , Edwards Owain R. , Minemba David , Areke Michael W. , Jones Roger A. C.
Published: November 2018

Zucchini yellow mosaic virus (ZYMV) isolates were obtained in Papua New Guinea (PNG) from cucumber (Cucumis sativus) or pumpkin (Cucurbita spp.) plants showing mosaic symptoms growing at Kongop in the Mount Hagen District, Western Highlands Province, or Zage in the Goroka District, Eastern Highlands Province. The samples were blotted onto FTA cards, which were sent to Australia, where they were subjected to high-throughput sequencing. When the coding regions of the nine new ZYMV genomic sequences found were compared with those of 64 other ZYMV sequences from elsewhere, they grouped together, forming new minor phylogroup VII within ZYMV’s major phylogroup A. Genetic connectivity was lacking between ZYMV genomic sequences from PNG and its neighboring countries, Australia and East Timor; the closest match between a PNG and any other genomic sequence was a 92.8% nucleotide identity with a sequence in major phylogroup A’s minor phylogroup VI from Japan. When the RDP5.2 recombination analysis program was used to compare 66 ZYMV sequences, evidence was obtained of 30 firm recombination events involving 41 sequences, and all isolates from PNG were recombinants. There were 21 sequences without recombination events in major phylogroup A, whereas there were only 4 such sequences within major phylogroup B. ZYMV’s P1, Cl, N1a-Pro, P3, CP, and NIb regions contained the highest evidence of recombination breakpoints. Following removal of recombinant sequences, seven minor phylogroups were absent (I, III, IV, V, VI, VII, and VIII), leaving only minor phylogroups II and IX. By contrast, when a phylogenetic tree was constructed using recombinant sequences with their recombinationally derived tracts removed before analysis, five previous minor phylogroups remained unchanged within major phylogroup A (II, III, IV, V, and VII) while four formed two new merged phylogroups (I/VI and VIII/IX). Absence of genetic connectivity between PNG, Australian, and East Timorese ZYMV sequences, and the 92.8% nucleotide identity between a PNG sequence and the closest sequence from elsewhere, suggest that a single introduction may have occurred followed by subsequent evolution to adapt to the PNG environment. The need for enhanced biosecurity measures to protect against potentially damaging virus movements crossing the seas separating neighboring countries in this region of the world is discussed.
A database of egg size and shape from more than 6,700 insect species
Authors: Church Samuel H. , Donoughe Seth , de Medeiros Bruno A. S. , Extavour Cassandra G.
Published: November 2018

1

Offspring size is a fundamental trait in disparate biological fields of study. This trait can be measured as the size of plant seeds, animal eggs, or live young, and it influences ecological interactions, organism fitness, maternal investment, and embryonic development. Although multiple evolutionary processes have been predicted to drive the evolution of offspring size, the phylogenetic distribution of this trait remains poorly understood, due to the difficulty of reliably collecting and comparing offspring size data from many species. Here we present a database of 10,449 morphological descriptions of insect eggs, with records for 6,706 unique insect species and representatives from every extant hexapod order. The dataset includes eggs whose volumes span more than eight orders of magnitude. We created this database by partially automating the extraction of egg traits from the primary literature. In the process, we overcame challenges associated with large-scale phenotyping by designing and employing custom bioinformatic solutions to common problems. We matched the taxa in this database to the currently accepted scientific names in taxonomic and genetic databases, which will facilitate the use of this data for testing pressing evolutionary hypotheses in offspring size evolution.
Origin of the mobile di-hydro-pteroate synthase gene determining sulfonamide resistance in clinical isolates
Authors: Sánchez-Osuna Miquel , Cortés Pilar , Barbé Jordi , Erill Ivan
Published: November 2018

Sulfonamides are synthetic chemotherapeutic agents that work as competitive inhibitors of the di-hydro-pteroate synthase (DHPS) enzyme, encoded by the folP gene. Resistance to sulfonamides is widespread in the clinical setting and predominantly mediated by plasmid- and integron-borne sul1-3 genes encoding mutant DHPS enzymes that do not bind sulfonamides. In spite of their clinical importance, the genetic origin of sul1-3 genes remains unknown. Here we analyze sul genes and their genetic neighborhoods to uncover sul signature elements that enable the elucidation of their genetic origin. We identify a protein sequence Sul motif associated with sul-encoded proteins, as well as consistent association of a phosphoglucosamine mutase gene (glmM) with the sul2 gene. We identify chromosomal folP genes bearing these genetic markers in two bacterial families: the Rhodobiaceae and the Leptospiraceae. Bayesian phylogenetic inference of FolP/Sul and GlmM protein sequences clearly establishes that sul1-2 and sul3 genes originated as a mobilization of folP genes present in, respectively, the Rhodobiaceae and the Leptospiraceae, and indicate that the Rhodobiaceae folP gene was transferred from the Leptospiraceae. Analysis of %GC content in folP/sul gene sequences supports the phylogenetic inference results and indicates that the emergence of the Sul motif in chromosomally-encoded FolP proteins is ancient and considerably predates the clinical introduction of sulfonamides. In vitro assays reveal that both the Rhodobiaceae and the Leptospiraceae, but not other related chromosomally-encoded FolP proteins confer resistance in a sulfonamide-sensitive Escherichia coli background, indicating that the Sul motif is associated with sulfonamide resistance. Given the absence of any known natural sulfonamides targeting DHPS, these results provide a novel perspective on the emergence of resistance to synthetic chemotherapeutic agents, whereby preexisting resistant variants in the vast bacterial pangenome may be rapidly selected for and mobilized upon the clinical introduction of novel chemotherapeuticals.
Race modifies default mode network connectivity in Alzheimer’s disease
Authors: Misiura Maria B. , Wu Junjie , Qiu Deqiang , Howell Jennifer C. , Parker Monica W. , Turner Jessica A. , Hu William T.
Published: November 2018

Objective

To determine if resting state functional MRI biomarkers of Alzheimer’s disease (AD) differ between older African Americans and Caucasians.

Methods

We analyzed MRI profiles from 78 individuals (31 African Americans, 47 Caucasians) with normal cognition (n=36) or mild cognitive impairment/mild AD dementia (MCI/AD, n=42). We compared AD-associated intra-network functional connectivity of the default mode network (DMN) according to race, and correlated domain-specific cognitive functions with functional connectivity which differed between the racial groups.

Results

We identified key differences in DMN functional connectivity associated with AD between the races. Whereas MCI/AD was associated with decreased functional connectivity within the midline core DMN subsystem in older Caucasians, MCI/AD was instead associated with increased functional connectivity within the same subsystem of older African Americans. This is despite decreased functional connectivity in the medial temporal lobe DMN subsystem in both races. Memory function was also positively associated with connectivity between the precuneus and the posterior cingulate/inferior parietal lobule within the midline core subsystem, in keeping with a less amnestic-profile in older African Americans with MCI/AD.

Conclusions

These findings provide structural support that race modifies the AD phenotypes downstream from cerebral amyloid deposition, and suggests a rsf-MRI correlate of African American’s less amnestic neuropsychological profile in MCI/AD.
Optogenetic and transcriptomic interrogation of enhanced muscle function in the paralyzed mouse whisker pad
Authors: Vajtay Thomas J. , Bandi Akhil , Upadhyay Aman , Swerdel Mavis. R. , Hart Ronald P. , Lee Christian R. , Margolis David J.
Published: November 2018

The functional state of denervated muscle is a critical factor in the ability to restore movement after injury- or disease-related paralysis. Here we used peripheral optogenetic stimulation and transcriptome profiling in the mouse whisker system to investigate the time course of changes in neuromuscular function following complete unilateral facial nerve transection. While most skeletal muscles rapidly lose functionality after lower motor neuron denervation, optogenetic muscle stimulation of the paralyzed whisker pad revealed sustained increases in the sensitivity, velocity, and amplitude of whisker movements, and reduced fatigability, starting 48 h after denervation. RNA-seq analysis showed distinct regulation of multiple gene families in denervated whisker pad muscles compared to the atrophy-prone soleus, including prominent changes in ion channels and contractile fibers. Together, our results define the unique functional and transcriptomic landscape of denervated facial muscles, and have general implications for restoring movement after neuromuscular injury or disease.

New & Noteworthy

Optogenetic activation of muscle can be used to non-invasively induce movements and probe muscle function. We used this technique in mice to investigate changes in whisker movements following facial nerve transection. We found unexpectedly enhanced functional properties of whisker pad muscle following denervation, accompanied by unique transcriptomic changes. Our findings highlight the utility of the mouse whisker pad for investigating the restoration of movement after paralysis.
A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase
Authors: Sun Song , Weile Jochen , Verby Marta , Cote Atina G. , Wu Yingzhou , Fotiadou Iosifina , Kitaygorodsky Julia , Rine Jasper , Ješina Pavel , Kožich Viktor , Roth Frederick P.
Published: November 2018

Success in precision medicine depends on our ability to determine which rare human genetic variants have functional effects. Classical homocystinuria—characterized by elevated homocyst(e)ine in plasma and urine—is caused by primarily-rare variants in the cystathionine beta-synthase (CBS) gene. About half of patients respond to vitamin B6therapy. With early detection in newborns, existing therapies are highly effective. FunctionalCBSvariants, especially those that respond to vitamin B6, can be detected based on their ability to restore growth in yeast cells lackingCYS4 (the yeast ortholog ofCBS). This assay has previously been carried out only ‘reactively’ after first observation of a variant in patients. Here we describe a ‘proactive’ comprehensive missense variant effect map for human CBS. Together, saturation codon-replacement mutagenesis,en massegrowth selection at different vitamin B6levels, and sequencing yielded a ‘look-up table’ for CBS missense variant function and vitamin B6-remediability in yeast. The CBS variant effect map identified disease variants and predicted both disease severity (r= 0.82) and human clinical response to vitamin B6(r= 0.89). Thus, highly-multiplexed cell-based assays can yield proactive maps of variant function and patient response to therapy, even for rare variants not previously seen in the clinic.
Rac-dependent signaling from keratinocytes promotes differentiation of intradermal white adipocytes
Authors: Ueyama Takehiko , Sakuma Megumi , Nakatsuji Mio , Uebi Tatsuya , Hamada Takeshi , Aiba Atsu , Saito Naoaki
Published: November 2018

Rac signaling affects numerous downstream targets; however, few studies have established in vivo levels. We generated mice with a single knockout (KO) of Rac1 (Keratin5 (K5)-Cre;Rac1flox/flox, Rac1-KO) and double KO of Rac1 and Rac3 (K5-Cre;Rac1flox/flox;Rac3−/−, Rac1/Rac3-DKO) in keratinocytes. Strikingly, Rac1-KO mice exhibited thinner dermal white adipose tissue, which was considerably further reduced in Rac1/Rac3-DKO mice. DNA microarray using primary keratinocytes from Rac1/Rac3-DKO mice exhibited decreased mRNA levels of Bmp2, Bmp5, Fgf20, Fgf21, Fgfbp1, and Pdgfα. Combinational treatment with BMP2 and FGF21 or BMP2 and FGF20 in culture medium, but not individual purified recombinant proteins, could differentiate 3T3-L1 fibroblasts into adipocytes, as could culture media obtained from primary keratinocytes. Conversely, addition of anti-BMP2 or anti-FGF21 antibodies into the culture medium inhibited fibroblast differentiation. Furthermore, combinational treatment with BMP2 and FGF21 promoted adipocyte differentiation only of rat primary white, but not brown, adipocyte precursors. Notably, brown adipogenesis by FGF21 was inhibited by BMP2. Thus, we proposed novel paracrine pathways from keratinocytes to intradermal pre-adipocytes, which function as Rac-dependent modulators of white adipogenesis, but also brown adipogenesis.
Elevation of intracellular levels of nitric oxide in SHR attenuates hyperproliferation of vascular smooth muscle cells through the inhibition of AT1 receptor expression and c-Src/growth factor receptor signaling pathways
Authors: Hossain Ekhtear , Sarkar Oli , Li Yuan , Anand-Srivastava Madhu B.
Published: November 2018

We previously showed that decreased levels of intracellular nitric oxide (NO) contribute to the hyperproliferation of vascular smooth muscle cells (VSMC) from spontaneously hypertensive rats (SHR). The present study investigates if elevation of intracellular levels of NO by in vivo treatment of SHR with NO donor, sodium nitroprusside (SNP) that was shown to attenuate hypertension could attenuate the hyperproliferation of VSMC and identify the molecular mechanisms. Intraperitoneal injection of SNP (0.5 mg/kg BW) into 8-week-old SHR and WKY rats twice a week for two weeks increased significantly the intracellular levels of NO in aortic VSMC and resulted in the attenuation of hyperproliferation of VSMC from SHR to control levels. The antiproliferative effect of SNP was associated with the restoration of the overexpression of cell cycle proteins, cyclins D1, E, Cdk2, Cdk4, phosphorylated pRB and decreased expression of Cdk inhibitors p21Cip1 and p27Kip1 towards control levels. In addition, SNP treatment also attenuated the overexpression of angiotensin II receptor type 1 (AT1) receptor, phosphorylation of c-Src, EGF-R, PDGF-R, IGF-IR and ERK1/2 in VSMC from SHR to control levels. These results suggest that the augmentation of intracellular levels of NO elicits antiproliferative effect that may be mediated through its ability to inhibit the enhanced expression of AT1 receptor, activation of c- Src, growth factor receptors and MAP kinase signaling and overexpression of cell cycle proteins.
The idiosyncratic drivers of correlated evolution
Authors: Dench Jonathan , Hinz Aaron , Aris-Brosou Stéphane , Kassen Rees
Published: November 2018

The ultimate causes of correlated evolution among sites in a genome remain difficult to tease apart. To address this problem directly, we performed a high-throughput search for correlated evolution among sites associated with resistance to a fluoroquinolone antibiotic using whole genome data from clinical strains ofPseudomonas aeruginosa, before validating our computational predictions experimentally. We show that for at least two sites, this correlation is underlain by epistasis. Our analysis also revealed eight additional pairs of synonymous substitutions displaying correlated evolution underlain by physical linkage, rather than selection associated with antibiotic resistance. Our results provide direct evidence that both epistasis and physical linkage among sites can drive the correlated evolution identified by high throughput computational tools. In other words, the observation of correlated evolution is not by itself sufficient evidence to guarantee that the sites in question are epistatic; such a claim requires additional evidence, ideally coming from direct estimates of epistasis, based on experimental evidence.
Real exchange rate misalignment and economy
Authors: Wong Hock Tsen
Published: November 2018

Purpose

The purpose of this paper is to examine the impact of real exchange rate misalignment on economy and economic sectors, namely construction, manufacturing and mining and quarrying in Malaysia.

Design/methodology/approach

The equilibrium real exchange rate and economic models are estimated using the autoregressive distributed lag approach.

Findings

An increase in productivity differential or reserve differential will lead to an appreciation of real exchange rate in the long run. An increase in positive (negative) real exchange rate misalignment will lead to an increase (decrease) in economy. An increase in long-run real exchange rate misalignment will lead to a decrease in economy. Real exchange rate misalignment or long-run real exchange rate misalignment can influence the manufacturing sector in Malaysia. More specifically, undervaluation will promote whereas overvaluation will hurt the manufacturing sector.

Originality/value

Real exchange rate misalignment can be a policy to influence economy but may not be the best choice.
Environmental Kuznets curve for CO2 emissions: a literature survey
Authors: Shahbaz Muhammad , Sinha Avik
Published: November 2018

Purpose

The purpose of this paper is to provide a survey of the empirical literature on environmental Kuznets curve (EKC) estimation of carbon dioxide (CO2) emissions over the period of 1991–2017.

Design/methodology/approach

This survey categorizes the studies on the basis of power of income in empirical models of EKC. It has been hypothesized that the EKC shows an inverted U-shaped association between economic growth and CO2 emissions.

Findings

For all the contexts, the results of EKC estimation for CO2 emissions are inconclusive in nature. The reasons behind this discrepancy can be attributed to the choice of contexts, time period, explanatory variables, and methodological adaptation.

Research limitations/implications

The future studies in this context should not only consider new set of variables (e.g. corruption index, social indicators, political scenario, energy research and development expenditures, foreign capital inflows, happiness, population education structure, public investment toward alternate energy exploration, etc.), but also the data set should be refined, so that the EKC estimation issues raised by Stern (2004) can be addressed.

Originality/value

By far, no study in the literature of ecological economics has focused on the empirical estimation of EKC for CO2 emissions. This particular context has been used for this study, as CO2 is one of the highest studied pollutants in the ecological economics, and especially within the EKC hypothesis framework.
West African strangers and the politics of inhumanity in Angola
Authors: GAIBAZZI PAOLO
Published: November 2018

Since 2002, Angola has increasingly resorted to illegalization, deportation, and predatory policing to manage immigration. The resulting abuses lead Muslim West African migrants, especially those from the Mande ethnolinguistic area, to denounce Angola's lack of “humanity.” Their takes on inhumanity cannot be sufficiently explained by either conventional understandings of human rights or biopolitical theories of legal exclusion and bare life. Instead, Mande notions of hospitality, empathy, and the “human right” to survival enable migrants to navigate Angola's regimes of clientelism. Inhumanity results from the state's repression and predation, which prevent migrants from negotiating with their “hosts” on affective‐ethical grounds rather than solely on legal ones. Departing from Western Enlightenment, Mande humanism provides an alternative perspective from the South for analyzing how life and politics connect. [empathy, migrant illegality, deportation, humanism, hospitality, human rights, West African traders, Mande, Angola]
Systematic review of the applications of three‐dimensional printing in colorectal surgery
Authors: Emile S. H. , Wexner S. D.
Published: November 2018

Aim

Three‐dimensional (3D) printing has been recognized as a revolutionary technological innovation that has benefitted numerous disciplines, including medicine. The present systematic review aimed to demonstrate the current applications of 3D printing in colorectal surgery along with the limitations and potential future applications of this innovation.

Method

A PRISMA‐compliant systematic literature search of studies that applied 3D printing in colorectal surgery in the period from January 1990 to July 2018 was conducted. Electronic databases including PubMed/Medline, Scopus and the Cochrane Library were searched. All full‐text original articles were eligible for inclusion.

Results

Nine studies including 58 patients with a median age of 60.7 years were reviewed. The studies assessed 3D printing in patients with planned stoma construction, colon cancer with liver metastasis, right colon cancer, rectal cancer, intractable constipation and anal fistula. The applications of 3D printing were classified into three categories: patient education, preoperative planning and evaluation of response of colorectal liver metastasis to chemotherapy. 3D printed models aided in planning resection of colorectal liver metastasis, facilitating D3 lymphadenectomy in complete mesocolic excision, improving the understanding of pelvic anatomy in laparoscopic rectal cancer treatment, guiding electrode implantation in sacral neuromodulation for intractable constipation, and elucidating the morphology of anal fistula tract and anal sphincter muscles.

Conclusion

Colorectal surgery may benefit from 3D printing in enhancing patient education before stoma construction, preoperative planning and evaluation of the response of liver metastasis to chemotherapy using 3D ultrasonography.
Repeated blast model of mild traumatic brain injury alters oxycodone self‐administration and drug seeking
Authors: Nawarawong Natalie N. , Slaker Megan , Muelbl Matt , Shah Alok S. , Chiariello Rachel , Nelson Lindsay D. , Budde Matthew D. , Stemper Brian D. , Olsen Christopher M.
Published: November 2018

Each year, traumatic brain injuries (TBI) affect millions worldwide. Mild TBIs (mTBI) are the most prevalent and can lead to a range of neurobehavioral problems, including substance abuse. A single blast exposure, inducing mTBI alters the medial prefrontal cortex, an area implicated in addiction, for at least 30 days post injury in rats. Repeated blast exposures result in greater physiological and behavioral dysfunction than single exposure; however, the impact of repeated mTBI on addiction is unknown. In this study, the effect of mTBI on various stages of oxycodone use was examined. Male Sprague Dawley rats were exposed to a blast model of mTBI once per day for 3 days. Rats were trained to self‐administer oxycodone during short (2 h) and long (6 h) access sessions. Following abstinence, rats underwent extinction and two cued reinstatement sessions. Sham and rbTBI rats had similar oxycodone intake, extinction responding and cued reinstatement of drug seeking. A second group of rats were trained to self‐administer oxycodone with varying reinforcement schedules (fixed ratio (FR)‐2 and FR‐4). Under an FR‐2 schedule, rbTBI‐exposed rats earned fewer reinforcers than sham‐exposed rats. During 10 extinction sessions, the rbTBI‐exposed rats exhibited significantly more seeking for oxycodone than the sham‐injured rats. There was a positive correlation between total oxycodone intake and day 1 extinction drug seeking in sham, but not in rbTBI‐exposed rats. Together, this suggests that rbTBI‐exposed rats are more sensitive to oxycodone‐associated cues during reinstatement than sham‐exposed rats and that rbTBI may disrupt the relationship between oxycodone intake and seeking.
Connecting the public with soil to improve human health
Authors: Brevik Eric C. , Steffan Joshua J. , Rodrigo‐Comino Jesús , Neubert Darrell , Burgess Lynn C. , Cerdà Artemi
Published: November 2018

Despite the definite links between soil and human health, it is likely that most people do not think about soil when considering human health. There is a disconnect between most people in our modern society and soil, and when people notice soil it is often in a negative context. People care for things that matter to them, and creating a more positive public image of soil could improve human health by leading to better treatment and understanding of the soil resource. There are a number of concepts that may be able to connect people to the soil, including terroir, soil health and soil security. While terroir originally established a connection between those who appreciate wine and the soils that produce those wines, the concept has been expanded to many additional products. It might be possible to provide a terroir link to human health benefits if they can be shown to be characteristic of a given soil environment. The concept of soil health has caught on with many farmers, policymakers, scientists and the general public, thus providing another possible approach to improve peoples’ connection with soil. Soil security is a recent concept that has been advanced as a way to take advantage of the connection that concepts such as energy, food and water security have made with policymakers. Therefore, we advocate a concerted effort to investigate terroir, soil health and soil security as concepts to improve overall human health. Soil health and soil security might have the most promise, and some social marketing campaigns that include soil health are ongoing.

Highlights

Soil is important to human health.

A disconnect exists between the urban population and soil.

Education about soil can rebuild these connections.

Concepts such as terroir, soil health or soil security might help make connections.
Selection and optimization of a suitable pretreatment method for miscanthus and poplar raw material
Authors: Seibert‐Ludwig Daniel , Hahn Thomas , Hirth Thomas , Zibek Susanne
Published: November 2018

Miscanthus and poplar are very promising second‐generation feedstocks due to the high growth rates and low nutrient demand. The aim of the study was to develop a systematic approach for choosing suitable pretreatment methods evaluated with the modified severity factor (log ). Optimal pretreatment results in a high delignification grade, low cellulose solubilization and increased accessibility for enzymatic hydrolysis while revealing minimal log values. In order to do so, several reaction approaches were compared. Acid‐catalyzed organosolv processing carried out for miscanthus and poplar revealed the highest delignification grade leading to a relatively high glucose yield after enzymatic saccharification. In both cases, a design of experiments approach was used to study the influence of relevant parameters. Modeling the data resulted in the identification of optimum pretreatment conditions for miscanthus with concentrations of 0.16% H2SO4 and 50% EtOH at 185°C for a retention time of 60 min. Experimental validation of these conditions revealed an even higher delignification degree (88%) and glucose yield (85%) than predicted. 0.19% H2SO4 and 50% EtOH were determined as optimum concentrations, 182°C and 48 min identified as optimum pretreatment conditions for poplar; the delignification degree was 84% and the resulting glucose yield 70%.
An evaluation of mainstream type 2 diabetes educational programmes in relation to the needs of people with intellectual disabilities: A systematic review of the literature
Authors: Maine Andrew , Brown Michael J. , Dickson Adele , Truesdale Maria
Published: November 2018

Background

Risk reduction and self‐management programs for type 2 diabetes (T2D) are commonplace. However, little is known about their appropriateness for people with intellectual disabilities (ID). This review evaluates successful components and theoretical basis of interventions and preventions in relation to the needs of people with ID with or at risk of T2D.

Method

Characteristics of 23 randomised controlled trialled T2D educational programs were systematically assessed alongside the needs of people with ID, and evaluated in terms of study design and theoretical application.

Results

Successful components of programs align to the needs of people with ID. Further adaptations are required to ensure accessibility of materials and social support to enable reflection on illness perceptions and self‐efficacy, as underpinned by Self‐regulation and Social‐cognitive theories.

Conclusions

Support is provided for further trials of self‐management and preventative adaptations under development. Impact may be enhanced through preventions aimed at younger groups in educational settings.
Exercise during transition from compensated left ventricular hypertrophy to heart failure in aortic stenosis rats
Authors: Reyes David R. A. , Gomes Mariana J. , Rosa Camila M. , Pagan Luana U. , Zanati Silmeia G. , Damatto Ricardo L. , Rodrigues Eder A. , Carvalho Robson F. , Fernandes Ana A. H. , Martinez Paula F. , Lima Aline R. R. , Cezar Marcelo D. M. , Carvalho Luiz E. F. M. , Okoshi Katashi , Okoshi Marina P.
Published: November 2018

We evaluated the influence of aerobic exercise on cardiac remodelling during the transition from compensated left ventricular (LV) hypertrophy to clinical heart failure in aortic stenosis (AS) rats. Eighteen weeks after AS induction, rats were assigned into sedentary (AS) and exercised (AS‐Ex) groups. Results were compared to Sham rats. Exercise was performed on treadmill for 8 weeks. Exercise improved functional capacity. Echocardiogram showed no differences between AS‐Ex and AS groups. After exercise, fractional shortening and ejection fraction were lower in AS‐Ex than Sham. Myocyte diameter and interstitial collagen fraction were higher in AS and AS‐Ex than Sham; however, myocyte diameter was higher in AS‐Ex than AS. Myocardial oxidative stress, evaluated by lipid hydroperoxide concentration, was higher in AS than Sham and was normalized by exercise. Gene expression of the NADPH oxidase subunits NOX2 and NOX4, which participate in ROS generation, did not differ between groups. Activity of the antioxidant enzyme superoxide dismutase was lower in AS and AS‐Ex than Sham and glutathione peroxidase was lower in AS‐Ex than Sham. Total and reduced myocardial glutathione, which is involved in cellular defence against oxidative stress, was lower in AS than Sham and total glutathione was higher in AS‐Ex than AS. The MAPK JNK was higher in AS‐Ex than Sham and AS groups. Phosphorylated P38 was lower in AS‐Ex than AS. Despite improving functional capacity, aerobic exercise does not change LV function in AS rats. Exercise restores myocardial glutathione, reduces oxidative stress, impairs JNK signalling and further induces myocyte hypertrophy.
Ghrelin receptor deletion reduces binge‐like alcohol drinking in rats
Authors: Zallar Lia J. , Beurmann Silvia , Tunstall Brendan J. , Fraser Claire M. , Koob George F. , Vendruscolo Leandro F. , Leggio Lorenzo
Published: November 2018

Ghrelin is a gastric hormone that has been implicated in the neurobiology of alcohol drinking. We have recently developed a ghrelin receptor (growth hormone secretagogue receptor; GHSR) knockout (KO) rat model, which exhibits reduced food consumption and body weight. In addition, recent preliminary work suggests that the gut‐microbiome, which appears to interact with the ghrelin system, may modulate alcohol drinking. In the present study, we investigated the effects of GHSR deletion on alcohol consumption utilising GHSR KO and wild‐type (WT) rats in three separate alcohol consumption paradigms: (i) operant self‐administration (30‐minute sessions); (ii) drinking in the dark (DID) (4‐hour sessions); and (iii) intermittent access (24‐hour sessions). These paradigms model varying degrees of alcohol consumption. Furthermore, we aimed to investigate the gut‐microbiome composition of GHSR KO and WT rats before and after alcohol exposure. We found that the GHSR KO rats self‐administered significantly less alcohol compared to WT rats in the operant paradigm, and consumed less alcohol than WT in the initial stages of the DID paradigm. No genotype differences were found in the intermittent access test. In addition, we found a significant decrease in gut‐microbial diversity after alcohol exposure in both genotypes. Thus, the present results indicate that the ghrelin system may be involved in drinking patterns that result in presumably increased alcohol exposure levels. Furthermore, GHSR may constitute a potential pharmacological target for the reduction of binge‐alcohol consumption. The potential functional role of the gut‐microbiome in alcohol drinking, as well as interaction with the ghrelin system, is an interesting topic for further investigation.
International comparison of trends in patients commencing renal replacement therapy by primary renal disease
Authors: Stel Vianda S , Awadhpersad Ryan , Pippias Maria , Ferrer‐Alamar Manuel , Finne Patrik , Fraser Simon D , Heaf James G , Hemmelder Marc H , Martínez‐Castelao Alberto , de Meester Johan , Palsson Runolfur , Prischl Friedrich C , Segelmark Mårten , Traynor Jamie P , Santamaria Rafael , Reisæter Anna Varberg , Massy Ziad A , Jager Kitty J
Published: November 2018

Aim

To examine international time trends in the incidence of renal replacement therapy (RRT) for end‐stage renal disease (ESRD) by primary renal disease (PRD).

Methods

Renal registries reporting on patients starting RRT per million population for ESRD by PRD from 2005 to 2014, were identified by internet search and literature review. The average annual percentage change (AAPC) with a 95% confidence interval (CI) of the time trends was computed using Joinpoint regression.

Results

There was a significant decrease in the incidence of RRT for ESRD due to diabetes mellitus (DM) in Europe (AAPC = −0.9; 95%CI −1.3; −0.5) and to hypertension/renal vascular disease (HT/RVD) in Australia (AAPC = −1.8; 95%CI −3.3; −0.3), Canada (AAPC = −2.9; 95%CI −4.4; −1.5) and Europe (AAPC = −1.1; 95%CI −2.1; −0.0). A decrease or stabilization was observed for glomerulonephritis in all regions and for autosomal dominant polycystic kidney disease (ADPKD) in all regions except for Malaysia and the Republic of Korea. An increase of 5.2–16.3% was observed for DM, HT/RVD and ADPKD in Malaysia and the Republic of Korea.

Conclusion

Large international differences exist in the trends in incidence of RRT by primary renal disease. Mapping of these international trends is the first step in defining the causes and successful preventative measures of CKD.
Epiphytic lichen synusiae and functional trait groups in boreo‐nemoral deciduous forests are influenced by host tree and environmental factors
Authors: Jüriado Inga , Paal Jaanus
Published: November 2018

Deciduous forests with temperate broad‐leaved tree species are particularily important in terms of biodiversity and its protection, but are threatened habitats in northern Europe. Using multivariate analyses we studied the effect of forest site type, environmental variables and host tree properties on epiphytic lichen synusiae as well as on the composition of species‐specific functional traits. Epiphytic lichens were examined on Acer platanoides, Fraxinus excelsior, Quercus robur, Tilia cordata, Ulmus glabra and U. laevis in two types of forests: Humulus‐type floodplain forests and Lunaria‐type boreo‐nemoral forests on the talus slopes of limestone escarpment (klint forests). Klint forests located near the seashore were under greater maritime influence compared to floodplain forests located in inland Estonia which experience stronger air temperature contrasts. In addition to stand level and climatic variables, tree level factors (bark pH, trunk circumference and cover of bryophytes) considerably affected the species composition of the lichen synusiae. Overall, 137 lichen species were recorded, including 14 red‐listed species characteristic of deciduous trees. We defined 13 lichen societies and showed their preference to forests of a specific site type and/or host tree properties. In forests of both types, most of the epiphytic lichens were crustose, and had apothecia as the fruit bodies and chlorococcoid algae as the photobiont. However, the proportion of lichens with a foliose or fruticose growth form, as well as the proportion of lichens with vegatative diaspores, were higher in floodplain forests. In klint forests with a stronger influence from the wind, crustose species completely dominated, while species with vegetative diaspores were rare and most species dispersed sexually. Lichens with Trentepohlia as the photobiont were characteristic of these forests, and lichens with lirellate ascomata were prevailing, indicating the great uniqueness of the kint forests for epiphytic lichens in the boreo‐nemoral region.
Cold hardiness in immature stages and adults in the adult‐diapausing spider mite Stigmaeopsis longus
Authors: Ito Katsura , Chae Younghae
Published: November 2018

The cold hardiness of arthropods is an important characteristic associated with overwintering success. Cold‐tolerant stages affect overwintering strategy, especially in arthropods that continuously feed on evergreen host plants in temperate regions. However, cold hardiness to mildly low temperature is rarely investigated. In the present study, we estimate the stage‐specific cold hardiness of a population of the spider mite Stigmaeopsis longus (Saito) (Acari: Tetranychidae) occurring on evergreen Sasa bamboo in a temperate area (Kochi City, southwestern Japan). Individuals of each stage developing under diapause‐inducing conditions (LD 10 : 14 h at 20 °C) are maintained at 4 °C (approximating the mean daily minimum temperature for December in Kochi City) for 30 days (eggs are cooled immediately, without short‐day development first). They are then returned to the initial conditions to assess survival rates. The survival rate of adult females (i.e. the diapausing stage) is high (99.5%), as is that of adult males and deutonymphs of both sexes (84.2–98.7% and 89.7–89.8%, respectively). The survival rate of mobile immature stages tends to increase toward adulthood in both sexes, whereas the survival rate of the eggs and quiescent stages is extremely low (16–23% and 0–20%, respectively). The poor cold hardiness of the eggs and quiescent stages presumably prevents the normal development of immature individuals during winter.