bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term lichen trends in a rust belt region
Authors: Warren Robert J , Casterline Shannon , Goodman Madeson , Kocher Megan , Zaluski Rachel , Battaglia Jim H 
Published: August 2019

AbstractDeindustrialization and national air pollution standards greatly reduced air pollution in the USA since the mid-20th century, particularly in the ‘rust belt’ industrial cities of the Great Lakes and Northeastern regions. Still, sprawling urbanization, vehicular traffic and coal-fired power plants may maintain regional heat islands and NOx and SO2 pollution. Lichens are one of the first, and longest used, bioindicators of urban heat island effects and atmospheric pollution, but there are few long-term studies of lichen bioindications. We examined herbaria records for lichens collected between 1869 and 2016 in the Western New York (WNY) region (USA). We hypothesized a long-term trend of increasing pollution-sensitive lichens in the region as well as increased desiccation-tolerant species from urban heat island effects. We also evaluated local (urban and tree land use cover) and regional (ecological zones) influences on pollution-sensitive and desiccation-tolerant lichens. We found that the WNY lichen communities appear to be shaped by urbanization with desiccation- and pollution-tolerant species dominating areas adjacent to the urbanized/industrialized core, and direct local effects of the urban heat island and vehicle traffic within the urban core. These results suggest that despite deindustrialization and tighter air quality standards, an industrial imprint remains on the lichen communities of WNY. However, despite urban filtering toward desiccation- and pollution-tolerant lichen species, the urban landscape contributed unique lichen species to the region, increasing WNY’s overall lichen biodiversity as much as the relatively pristine Allegheny Plateau. Hence, the urbanized areas of WNY contribute unique species to the regional lichen flora.
KSHV RNA-binding protein ORF57 inhibits P-body formation to promote viral multiplication by interaction with Ago2 and GW182
Authors: Sharma Nishi R , Majerciak Vladimir , Kruhlak Michael J , Yu Lulu , Kang Jeong Gu , Yang Acong , Gu Shuo , Fritzler Marvin J , Zheng Zhi-Ming 
Published: August 2019

Abstract
Cellular non-membranous RNA-granules, P-bodies (RNA processing bodies, PB) and stress granules (SG), are important components of the innate immune response to virus invasion. Mechanisms governing how a virus modulates PB formation remain elusive. Here, we report the important roles of GW182 and DDX6, but not Dicer, Ago2 and DCP1A, in PB formation, and that Kaposi’s sarcoma-associated herpesvirus (KSHV) lytic infection reduces PB formation through several specific interactions with viral RNA-binding protein ORF57. The wild-type ORF57, but not its N-terminal dysfunctional mutant, inhibits PB formation by interacting with the N-terminal GW-domain of GW182 and the N-terminal domain of Ago2, two major components of PB. KSHV ORF57 also induces nuclear Ago2 speckles. Homologous HSV-1 ICP27, but not EBV EB2, shares this conserved inhibitory function with KSHV ORF57. By using time-lapse confocal microscopy of HeLa cells co-expressing GFP-tagged GW182, we demonstrated that viral ORF57 inhibits primarily the scaffolding of GW182 at the initial stage of PB formation. Consistently, KSHV-infected iSLK/Bac16 cells with reduced GW182 expression produced far fewer PB and SG, but 100-fold higher titer of infectious KSHV virions when compared to cells with normal GW182 expression. Altogether, our data provide the first evidence that a DNA virus evades host innate immunity by encoding an RNA-binding protein that promotes its replication by blocking PB formation.
TrmB, a tRNA m7G46 methyltransferase, plays a role in hydrogen peroxide resistance and positively modulates the translation of katA and katB mRNAs in Pseudomonas aeruginosa
Authors: Thongdee Narumon , Jaroensuk Juthamas , Atichartpongkul Sopapan , Chittrakanwong Jurairat , Chooyoung Kamonchanok , Srimahaeak Thanyaporn , Chaiyen Pimchai , Vattanaviboon Paiboon , Mongkolsuk Skorn , Fuangthong Mayuree 
Published: August 2019

AbstractCellular response to oxidative stress is a crucial mechanism that promotes the survival of Pseudomonas aeruginosa during infection. However, the translational regulation of oxidative stress response remains largely unknown. Here, we reveal a tRNA modification-mediated translational response to H2O2 in P. aeruginosa. We demonstrated that the P. aeruginosa trmB gene encodes a tRNA guanine (46)-N7-methyltransferase that catalyzes the formation of m7G46 in the tRNA variable loop. Twenty-three tRNA substrates of TrmB with a guanosine residue at position 46 were identified, including 11 novel tRNA substrates. We showed that loss of trmB had a strong negative effect on the translation of Phe- and Asp-enriched mRNAs. The trmB-mediated m7G modification modulated the expression of the catalase genes katA and katB, which are enriched with Phe/Asp codons at the translational level. In response to H2O2 exposure, the level of m7G modification increased, consistent with the increased translation efficiency of Phe- and Asp-enriched mRNAs. Inactivation of trmB led to decreased KatA and KatB protein abundance and decreased catalase activity, resulting in H2O2-sensitive phenotype. Taken together, our observations reveal a novel role of m7G46 tRNA modification in oxidative stress response through translational regulation of Phe- and Asp-enriched genes, such as katA and katB.
The autoregulator Aca2 mediates anti-CRISPR repression
Authors: Birkholz Nils , Fagerlund Robert D , Smith Leah M , Jackson Simon A , Fineran Peter C 
Published: August 2019

AbstractCRISPR-Cas systems are widespread bacterial adaptive defence mechanisms that provide protection against bacteriophages. In response, phages have evolved anti-CRISPR proteins that inactivate CRISPR-Cas systems of their hosts, enabling successful infection. Anti-CRISPR genes are frequently found in operons with genes encoding putative transcriptional regulators. The role, if any, of these anti-CRISPR-associated (aca) genes in anti-CRISPR regulation is unclear. Here, we show that Aca2, encoded by the Pectobacterium carotovorum temperate phage ZF40, is an autoregulator that represses the anti-CRISPR–aca2 operon. Aca2 is a helix-turn-helix domain protein that forms a homodimer and interacts with two inverted repeats in the anti-CRISPR promoter. The inverted repeats are similar in sequence but differ in their Aca2 affinity, and we propose that they have evolved to fine-tune, and downregulate, anti-CRISPR production at different stages of the phage life cycle. Specific, high-affinity binding of Aca2 to the first inverted repeat blocks the promoter and induces DNA bending. The second inverted repeat only contributes to repression at high Aca2 concentrations in vivo, and no DNA binding was detectable in vitro. Our investigation reveals the mechanism by which an Aca protein regulates expression of its associated anti-CRISPR.
Estimating glomerular filtration rate in patients with acute kidney injury: a prospective multicenter study of diagnostic accuracy
Authors: Pelletier Karyne , Lafrance Jean-Philippe , Roy Louise , Charest Mathieu , Bélanger Marie-Claire , Cailhier Jean-François , Albert Martin , Duca Anatolie , Elftouh Naoual , Bouchard Josée 
Published: August 2019

Abstract

Background
Estimating glomerular filtration rate (GFR) in acute kidney injury (AKI) is challenging, with limited data comparing estimated and gold standard methods to assess GFR. The objective of our study was to assess the performance of the kinetic estimated GFR (KeGFR) and Jelliffe equations to estimate GFR in AKI, using a radioisotopic method (technetium-diethylenetriaminepentaacetic acid) as a reference measure.

Methods
We conducted a prospective multicenter observational study in hospitalized patients with AKI. We computed the Jelliffe and KeGFR equations to estimate GFR and compared these estimations to measured GFR (mGFR) by a radioisotopic method. The performances were assessed by correlation, Bland–Altman plots and smoothed and linear regressions. We conducted stratified analyses by age and chronic kidney disease (CKD).

Results
The study included 119 patients with AKI, mostly from the intensive care unit (63%) and with Stage 1 AKI (71%). The eGFR obtained from the Jelliffe and KeGFR equations showed a good correlation with mGFR (r = 0.73 and 0.68, respectively). The median eGFR by the Jelliffe and KeGFR equations was less than the median mGFR, indicating that these equations underestimated the mGFR. On Bland–Altman plots, the Jelliffe and KeGFR equations displayed a considerable lack of agreement with mGFR, with limits of agreement &gt;40 mL/min/1.73 m2. Both equations performed better in CKD and the KeGFR performed better in older patients. Results were similar across AKI stages.

Conclusions
In our study, the Jelliffe and KeGFR equations had good correlations with mGFR; however, they had wide limits of agreement. Further studies are needed to optimize the prediction of mGFR with estimatation equations.
A Positive Feedback Loop Comprising LHW–TMO5 and Local Auxin Biosynthesis Regulates Initial Vascular Development in Arabidopsis Roots
Authors: Ohashi-Ito Kyoko , Iwamoto Kuninori , Nagashima Yoshinobu , Kojima Mikiko , Sakakibara Hitoshi , Fukuda Hiroo 
Published: August 2019

Abstract
The phytohormone auxin governs various developmental processes in plants including vascular formation. Auxin transport and biosynthesis are important factors in determining auxin distribution in tissues. Although the role of auxin transport in vein pattern formation is widely recognized, that of auxin biosynthesis in vascular development is poorly understood. Heterodimer complexes comprising two basic helix–loop–helix protein families, LONESOME HIGHWAY (LHW) and TARGET OF MONOPTEROS5 (TMO5)/TMO5-LIKE1 (T5L1), are master transcriptional regulators of the initial process of vascular development. The LHW–TMO5/T5L1 dimers regulate vascular initial cell production, vascular cell proliferation and xylem fate determination in the embryo and root apical meristem (RAM). In this study, we investigated the function of local auxin biosynthesis in initial vascular development in RAM. Results showed that LHW–T5L1 upregulated the expression of YUCCA4 (YUC4), a key auxin biosynthesis gene. The expression of YUC4 was essential for promoting xylem differentiation and vascular cell proliferation in RAM. Conversely, auxin biosynthesis was required for maintaining the expression levels of LHW, TMO5/T5L1 and their targets. Our results suggest that local auxin biosynthesis forms a positive feedback loop for fine-tuning the level of LHW–TMO5/T5L1, which is necessary for initiating vascular development.
In Vitro Enzymatic Activity Assays Implicate the Existence of the Chlorophyll Cycle in Chlorophyll b-Containing Cyanobacteria
Authors: Lim HyunSeok , Tanaka Ayumi , Tanaka Ryouichi , Ito Hisashi 
Published: August 2019

Abstract
In plants, chlorophyll (Chl) a and b are interconvertible by the action of three enzymes—chlorophyllide a oxygenase, Chl b reductase (CBR) and 7-hydroxymethyl chlorophyll a reductase (HCAR). These reactions are collectively referred to as the Chl cycle. In plants, this cyclic pathway ubiquitously exists and plays essential roles in acclimation to different light conditions at various developmental stages. By contrast, only a limited number of cyanobacteria species produce Chl b, and these include Prochlorococcus, Prochloron, Prochlorothrix and Acaryochloris. In this study, we investigated a possible existence of the Chl cycle in Chl b synthesizing cyanobacteria by testing in vitro enzymatic activities of CBR and HCAR homologs from Prochlorothrix hollandica and Acaryochloris RCC1774. All of these proteins show respective CBR and HCAR activity in vitro, indicating that both cyanobacteria possess the potential to complete the Chl cycle. It is also found that CBR and HCAR orthologs are distributed only in the Chl b-containing cyanobacteria that habitat shallow seas or freshwater, where light conditions change dynamically, whereas they are not found in Prochlorococcus species that usually habitat environments with fixed lighting. Taken together, our results implicate a possibility that the Chl cycle functions for light acclimation in Chl b-containing cyanobacteria.
Phylogeography of Neomysis americana (Crustacea, Mysida), focusing on the St. Lawrence system
Authors: Cortial GrÉgoire , Woodland Ryan , Lasley-Rasher Rachel , Winkler Gesche 
Published: August 2019

AbstractSpecies characterized by low dispersal capacities, such as mysids, usually show evidence of genetic differentiation. Many mysids are broadly distributed and often show eurythermal and euryhaline traits. This study aimed to describe intraspecific genetic structure and the phylogeography of Neomysis americana, a key species of estuarine food webs in northwest Atlantic, using the mitochondrial cytochrome c oxidase subunit I gene. We sampled 26 populations across the St. Lawrence system (SLS) and two along the east coast of North America [Penobscot and Chesapeake Bay (CB)]. Sequencing of 420 individuals revealed three divergent (&gt;3%) lineages (LA, LB, LC) across the sampling area suggesting that N. americana represents a cryptic species complex. The distribution of the lineages was geographically structured. LC occurred in the CB only, whereas LA and LB co-occurred along the SLS and Penobscot Bay. This suggests secondary contact after the last glacial maximum. In the SLS the lineage LA dominated the estuarine transition zone and the Gulf of St. Lawrence, whereas the lineage LB was prevalent in the lower St. Lawrence Estuary, potentially due to different eco-physiological preferences. These results might help to define reasonable entities for research and management.
Effectiveness of Deep Dry Needling vs Ischemic Compression in the Latent Myofascial Trigger Points of the Shortened Triceps Surae from Triathletes on Ankle Dorsiflexion, Dynamic, and Static Plantar Pressure Distribution: A Clinical Trial
Authors: Benito-de-Pedro María , Becerro-de-Bengoa-Vallejo Ricardo , Elena Losa-Iglesias Marta , Rodríguez-Sanz David , López-López Daniel , Palomo-López Patricia , Mazoteras-Pardo Victoria , Calvo-Lobo and César 
Published: August 2019

Abstract

Objective
To determine the immediate efficacy of a single session of deep dry needling (DDN) vs ischemic compression (ICT) in a latent myofascial trigger point (MTrP) of the shortened triceps surae from triathletes for ankle dorsiflexion and redistribution of plantar pressures and stability.

Design
A randomized simple blind clinical trial (NCT03273985).

Setting
An outpatient clinic.

Subjects
Thirty-four triathletes with a latent MTrP in the shortened gastrocnemius.

Methods
Triathletes were randomized to receive a single session of DDN (N = 17) or ICT (N = 17) in a latent MTrP of the shortened triceps surae. The primary outcome was ankle dorsiflexion range of motion (ROM) by a universal goniometer. Secondary objectives were distribution of dynamic and static plantar pressures by T-Plate platform pressure, with measurements both before and after five, 10, 15, 20, and 25 minutes of treatment.

Results
There were no statistically significant differences (P &gt; 0.05) for ankle dorsiflexion ROM or dynamic and static plantar pressures between the experimental group treated with DDN and the control group treated with ICT before and after treatment.

Conclusions
DDN vs ICT carried out in latent MTrPs of the shortened gastrocnemius of triathletes did not present differences in terms of dorsiflexion ROM of the tibiofibular-talar joint or in static and dynamic plantar pressure changes before and immediately after treatment.
Homeless people and health: a qualitative enquiry into their practices and perceptions
Authors: Mc Conalogue Dave , Maunder Nicky , Areington Angelika , Martin Katherine , Clarke Vikki , Scott Sarah 
Published: August 2019

ABSTRACT

Background
Homeless people experience poorer health and shorter life expectancies than the UK average, but their health needs and expectations have received little attention in research. This study aims to understand homeless people’s health perceptions and experiences.

Methods
Semi-structured interviews took place with 28 homeless people in Gloucestershire. The transcripts were thematically analysed drawing out key themes.

Results
Homelessness was often rooted in early trauma or an unstable family unit. Participants described poor support on leaving prison, termination of a cohabiting relationship or financial issues as factors precipitating homelessness. There was an expansive and positive understanding of health and its determinants. Mental health issues were common, often linked to traumatic life-events. Substance misuse issues were expressed as a mechanism to manage mental health issues. Participants were frustrated that this co-dependency was not recognized by support services. Participants’ living situation curtailed their ability to make health-enhancing choices, which was compounded by issues accessing mainstream healthcare services.

Conclusions
Mental health in homeless people must be recognized in the context of substance misuse and early trauma. Dealing with housing and addiction are critical to enable prioritisation of healthy behaviours. Healthcare services should recognize the chaotic nature of homeless people and their competing issues.
Mental wellbeing among people in prison in Scotland: an analysis of repeat cross-sectional surveys
Authors: Tweed Emily J , Gounari Xanthippi , Graham Lesley 
Published: August 2019

ABSTRACT

Background
Mental wellbeing among people in prison is poorly studied, despite featuring in many health and justice policies. We aimed to describe for the first time mental wellbeing among an unselected national prison sample.

Methods
Since 2013, the Scottish Prisoner Survey—a biennial survey of people in custody in Scotland—has included the Warwick-Edinburgh mental wellbeing scale (WEMWBS), a 14-item scale with higher scores indicating greater wellbeing. We analysed data from sweeps in 2013 (n = 3158), 2015 (n = 2892) and 2017 (n = 2405) using Student’s t-test, ANOVA and multiple linear regression. We also used WEMWBS data from the Scottish Health Survey stratified by age, gender and deprivation to compare with the population at liberty.

Results
Mean WEMWBS scores overall were 43.4 in 2013 (SD = 12.2), 41.8 (SD = 11.9) in 2015 and 41.2 (SD = 12.3) in 2017. Mean scores were lower among people on remand and with multiple prison episodes. Age-standardized mean scores were lower among people in prison than their peers at liberty.

Conclusions
Poor mental wellbeing is an important, under-studied facet of the extreme health inequalities associated with imprisonment. These results identify that people on remand or with multiple episodes are particularly disadvantaged and provide a baseline for monitoring impacts of service or policy interventions.
Long-term outcomes in elderly patients with ANCA-associated vasculitis
Authors: McGovern Dominic , Williams Sam P , Parsons Katrina , Farrah Tariq E , Gallacher Peter J , Miller-Hodges Eve , Kluth David C , Hunter Robert W , Dhaun Neeraj 
Published: August 2019

AbstractObjectiveANCA-associated vasculitis (AAV) is a small vessel vasculitis that commonly presents in the elderly. However, there are few long-term outcome data for these patients. Here, we assessed long-term outcomes in a single-centre cohort of elderly patients with AAV. Additionally, we tested whether a pre-morbid frailty score could aid prognosis.MethodsUsing a prospectively-compiled dataset, we investigated patients over the age of 65 who presented with AAV between 2005 and 2017 to a regional vasculitis centre. We used a Cox model to determine the factors associated with mortality. We also compared outcomes in pre-specified subgroups stratified by baseline frailty score, ANCA serotype and induction immunosuppression (with cyclophosphamide, rituximab or mycophenolate mofetil used as the main glucocorticoid-sparing agent).Results83 patients were included in the study and were followed for a median of 1203 days. Median age was 74 years (range 65–92). Two- and five-year survival in the overall cohort were 83% (95% CI 75, 92%) and 75% (95% CI 65, 86%), respectively. The median cumulative dose of oral prednisolone was 2030 mg during the first three months. Only one patient received intravenous glucocorticoids. Age, frailty score and CRP at presentation were independently associated with mortality; all deaths occurred in patients aged over 75 at presentation. Patients treated with a cyclophosphamide-based induction regimen tended to be younger than those treated with rituximab or mycophenolate mofetil. Survival was better in the cyclophosphamide-treated group.ConclusionIn the contemporary era, the overall prognosis of AAV in elderly patients is good. Baseline frailty associates with disease outcomes including mortality. A low-dose glucocorticoid regimen (avoiding intravenous methylprednisolone) can be used to treat AAV effectively in elderly patients.
The performance of dual-energy CT in the classification criteria of gout: a prospective study in subjects with unclassified arthritis
Authors: Gamala Mihaela , Jacobs Johannes W G , Linn-Rasker Suzanne F , Nix Maarten , Heggelman Ben G F , Pasker-de Jong Pieternel C M , van Laar Jaap M , Klaasen Ruth 
Published: August 2019

Abstract

Objective
To establish the performance of (subsets of) the 2015 ACR/EULAR gout classification criteria in patients with unclassified arthritis, and to determine the value of dual-energy CT (DECT) herein. Reference was the MSU crystal detection result in SF at polarization microscopy.

Methods
We included subjects with acute, unclassified mono or oligoarthritis, who underwent SF analysis and DECT. Performance was assessed by calculating area under the receiver operating characteristic curve of (i) the clinical criteria subset, (ii) the clinical+serum urate subset and (iii) the full set (including DECT).

Results
Of the 89 subjects enrolled, 40 met the clinical+serum urate subset criteria, and 49 (55%) subjects did not. Of these 49, 30 had a negative microscopy result, of whom 15 had positive DECT; of these 15, 14 met the full set criteria only after adding the positive DECT result. For the clinical-only subset, the areas under the curves (AUCs) were 0.68 and 0.69 without and with DECT result, respectively, and for the clinical+serum urate subset without and with DECT, AUCs were 0.81 and 0.81, respectively (results not significant).

Conclusion
Adding the serum urate results to the clinical subset improves the performance, but adding the DECT result does not, neither does adding the DECT results to the clinical+serum urate subset. However, DECT seems to have an additive value in gout classification, especially when microscopy of SF is negative; 14/89 of patients (16%) only met the classification criteria with the use of DECT.

Trial registration
ClinicalTrials.gov, http://clinicaltrials.gov, NCT03038386.
Gender Attitudes in Africa: Liberal Egalitarianism Across 34 Countries
Authors: Charles Maria 
Published: August 2019

AbstractThis study provides a first descriptive mapping of support for women’s equal rights in 34 African countries and assesses diverse theoretical explanations for variability in this support. Contrary to stereotypes of a homogeneously tradition-bound continent, African citizens report high levels of agreement with gender equality that are more easily understood with reference to global processes of ideational diffusion than to country-level differences in economic modernization or women’s public-sphere roles. Multivariate analyses suggest, however, that gender liberalism in Africa may be spreading through mechanisms not typically considered by world-society scholars: Support for equal rights is largely unrelated to countries’ formal ties to the world system, but it is stronger among persons who are more exposed to extra-local culture, including through internet and mobile phone usage, news access, and urban residency. Forces for gender liberalism are conditioned, moreover, by local religious cultures and gender structures.