bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Wide Analysis of Biosynthetic Gene Cluster Reveals Correlated Gene Loss with Absence of Usnic Acid in Lichen-Forming Fungi
Authors: Pizarro David , Divakar Pradeep K , Grewe Felix , Crespo Ana , Dal Grande Francesco , Lumbsch Helge Thorsten 
Published: September 2020

AbstractLichen-forming fungi are known to produce a large number of secondary metabolites. Some metabolites are deposited in the cortical layer of the lichen thallus where they exert important ecological functions, such as UV filtering. The fact that closely related lineages of lichen-forming fungi can differ in cortical chemistry suggests that natural product biosynthesis in lichens can evolve independent from phylogenetic constraints. Usnic acid is one of the major cortical pigments in lichens. Here we used a comparative genomic approach on 46 lichen-forming fungal species of the Lecanoromycetes to elucidate the biosynthetic gene content and evolution of the gene cluster putatively responsible for the biosynthesis of usnic acid. Whole-genome sequences were gathered from taxa belonging to different orders and families of Lecanoromycetes, where Parmeliaceae is the most well-represented taxon, and analyzed with a variety of genomic tools. The highest number of biosynthetic gene clusters was found in Evernia prunastri, Pannoparmelia angustata, and Parmotrema austrosinense, respectively, and lowest in Canoparmelia nairobiensis, Bulbothrix sensibilis, and Hypotrachyna scytodes. We found that all studied species producing usnic acid contain the putative usnic acid biosynthetic gene cluster, whereas the cluster was absent in all genomes of species lacking usnic acid. The absence of the gene cluster was supported by an additional unsuccessful search for ß-ketoacylsynthase, the most conserved domain of the gene cluster, in the genomes of species lacking usnic acid. The domain architecture of this PKS cluster—homologous to the already known usnic acid PKS cluster (MPAS) and CYT450 (MPAO)—varies within the studied species, whereas the gene arrangement is highly similar in closely related taxa. We hypothesize that the ancestor of these lichen-forming fungi contained the putative usnic acid producing PKS cluster and that the gene cluster was lost repeatedly during the evolution of these groups. Our study provides insight into the genomic adaptations to the evolutionary success of these lichen-forming fungal species and sets a baseline for further exploration of biosynthetic gene content and its evolutionary significance.
What Determines Cognitive Functioning in the Oldest-Old? The EMIF-AD 90+ Study
Authors: Legdeur Nienke , Badissi Maryam , Yaqub Maqsood , Beker Nina , Sudre Carole H , ten Kate Mara , Gordon Mark Forrest , Novak Gerald , Barkhof Frederik , van Berckel Bart N M , Holstege Henne , Muller Majon , Scheltens Philip , Maier Andrea B , Visser Pieter Jelle 
Published: September 2020

Abstract

Objectives
Determinants of cognitive functioning in individuals aged 90 years and older, the oldest-old, remain poorly understood. We aimed to establish the association of risk factors, white matter hyperintensities (WMHs), hippocampal atrophy, and amyloid aggregation with cognition in the oldest-old.

Method
We included 84 individuals without cognitive impairment and 38 individuals with cognitive impairment from the EMIF-AD 90+ Study (mean age 92.4 years) and tested cross-sectional associations between risk factors (cognitive activity, physical parameters, nutritional status, inflammatory markers, and cardiovascular risk factors), brain pathology biomarkers (WMH and hippocampal volume on magnetic resonance imaging, and amyloid binding measured with positron emission tomography), and cognition. Additionally, we tested whether the brain pathology biomarkers were independently associated with cognition. When applicable, we tested whether the effect of risk factors on cognition was mediated by brain pathology.

Results
Lower values for handgrip strength, Short Physical Performance Battery (SPPB), nutritional status, HbA1c, and hippocampal volume, and higher values for WMH volume and amyloid binding were associated with worse cognition. Higher past cognitive activity and lower body mass index were associated with increased amyloid binding, lower muscle mass with more WMH, and lower SPPB scores with more WMH and hippocampal atrophy. The brain pathology markers were independently associated with cognition. The association of SPPB with cognition was partially mediated by hippocampal volume.

Discussion
In the oldest-old, physical parameters, nutritional status, HbA1c, WMH, hippocampal atrophy, and amyloid binding are associated with cognitive impairment. Physical performance may affect cognition through hippocampal atrophy. This study highlights the importance to consider multiple factors when assessing cognition in the oldest-old.
Age-Related Attributions of Experienced Changes in Life: Origins and Implications
Authors: Rothermund Klaus , de Paula Couto Maria Clara Pinheiro , Fung Helene H , Graf Sylvie , Hess Thomas M , Liou Shyhnan , Nikitin Jana 
Published: September 2020

Abstract

Objectives
Attributing life changes to age represents a core marker of the subjective experience of aging. The aims of our study were to investigate views on aging (VA) as origins of age-related attributions of life changes and to investigate the implications of these age-related attributions for personal control (PC) and life satisfaction (LS).

Methods
Life changes and the attribution of life changes to age were independently assessed on a large international sample of older adults (N = 2,900; age range 40–90 years) from the Ageing as Future project. The valence of VA, PC, and LS were also assessed to investigate possible determinants (VA) and consequences (PC and LS) of age-related attributions of life changes.

Results
Attributions to age were shown to depend on the valence of experienced life changes, with more negative changes being linked to more age-related attributions. This relation was moderated by the valence of personally held VA, with more negative VA amplifying the relation between negative life changes and age-related attributions. Age-related attributions predicted reduced PC and lower LS and were found to exacerbate the effects of negative life changes on LS, especially for the older cohorts of our sample.

Discussion
Our findings help to better understand what determines age-related attributions of life changes and highlight the negative consequences of attributing them to aging. Age-related attributions of change are a major factor that worsens the subjective aging experience. Methodologically, our study emphasizes the necessity to separately assess changes and their attributions to age.
A Bayesian 3-D linear gravity inversion for complex density distributions: application to the Puysegur subduction system
Authors: Hightower Erin , Gurnis Michael , Van Avendonk Harm 
Published: September 2020

SUMMARY
We have developed a linear 3-D gravity inversion method capable of modelling complex geological regions such as subduction margins. Our procedure inverts satellite gravity to determine the best-fitting differential densities of spatially discretized subsurface prisms in a least-squares sense. We use a Bayesian approach to incorporate both data error and prior constraints based on seismic reflection and refraction data. Based on these data, Gaussian priors are applied to the appropriate model parameters as absolute equality constraints. To stabilize the inversion and provide relative equality constraints on the parameters, we utilize a combination of first and second order Tikhonov regularization, which enforces smoothness in the horizontal direction between seismically constrained regions, while allowing for sharper contacts in the vertical. We apply this method to the nascent Puysegur Trench, south of New Zealand, where oceanic lithosphere of the Australian Plate has underthrust Puysegur Ridge and Solander Basin on the Pacific Plate since the Miocene. These models provide insight into the density contrasts, Moho depth, and crustal thickness in the region. The final model has a mean standard deviation on the model parameters of about 17 kg m–3, and a mean absolute error on the predicted gravity of about 3.9 mGal, demonstrating the success of this method for even complex density distributions like those present at subduction zones. The posterior density distribution versus seismic velocity is diagnostic of compositional and structural changes and shows a thin sliver of oceanic crust emplaced between the nascent thrust and the strike slip Puysegur Fault. However, the northern end of the Puysegur Ridge, at the Snares Zone, is predominantly buoyant continental crust, despite its subsidence with respect to the rest of the ridge. These features highlight the mechanical changes unfolding during subduction initiation.
Fully discrete finite element approximation of the stochastic Cahn–Hilliard–Navier–Stokes system
Authors: Deugoué G , Moghomye B Jidjou , Tachim Medjo T 
Published: September 2020

Abstract
In this paper we study the numerical approximation of the stochastic Cahn–Hilliard–Navier–Stokes system on a bounded polygonal domain of $\mathbb{R}^{d}$, $d=2,3$. We propose and analyze an algorithm based on the finite element method and a semiimplicit Euler scheme in time for a fully discretization. We prove that the proposed numerical scheme satisfies the discrete mass conservative law, has finite energies and constructs a weak martingale solution of the stochastic Cahn–Hilliard–Navier–Stokes system when the discretization step (both in time and in space) tends to zero.
A Class of Fully Nonlinear Equations Arising in Conformal Geometry
Authors: Chen Li , Guo Xi , He Yan 
Published: September 2020

Abstract
In this paper, we consider the equations of Krylov type in conformal geometry on closed smooth Riemannian manifolds, which can be viewed as an extension of $\sigma _k$-Yamabe equation. Moreover, we prove local gradient and 2nd-derivative estimates for solutions to these equations and establish an existence result.
Optimizing a literature surveillance strategy to retrieve sound overall prognosis and risk assessment model papers
Authors: Kavanagh Patricia L , Frater Francine , Navarro Tamara , LaVita Peter , Parrish Rick , Iorio Alfonso 
Published: September 2020

Abstract

Objective
Our aim was to develop an efficient search strategy for prognostic studies and clinical prediction guides (CPGs), optimally balancing sensitivity and precision while independent of MeSH terms, as relying on them may miss the most current literature.

Materials and Methods
We combined 2 Hedges-based search strategies, modified to remove MeSH terms for overall prognostic studies and CPGs, and ran the search on 269 journals. We read abstracts from a random subset of retrieved references until ≥ 20 per journal were reviewed and classified them as positive when fulfilling standardized quality criteria, thereby assembling a standard dataset used to calibrate the search strategy. We determined performance characteristics of our new search strategy against the Hedges standard and performance characteristics of published search strategies against the standard dataset.

Results
Our search strategy retrieved 16 089 references from 269 journals during our study period. One hundred fifty-four journals yielded ≥ 20 references and ≥ 1 prognostic study or CPG. Against the Hedges standard, the new search strategy had sensitivity/specificity/precision/accuracy of 84%/80%/2%/80%, respectively. Existing published strategies tested against our standard dataset had sensitivities of 36%–94% and precision of 5%–10%.

Discussion
We developed a new search strategy to identify overall prognosis studies and CPGs independent of MeSH terms. These studies are important for medical decision-making, as they identify specific populations and individuals who may benefit from interventions.

Conclusion
Our results may benefit literature surveillance and clinical guideline efforts, as our search strategy performs as well as published search strategies while capturing literature at the time of publication.
Fine mapping genetic variants associated with age at puberty and sow fertility using SowPro90 genotyping array
Authors: Wijesena Hiruni R , Kachman Stephen D , Lents Clay A , Riethoven Jean-Jack , Trenhaile-Grannemann Melanie D , Safranski Tim J , Spangler Matthew L , Ciobanu Daniel C 
Published: September 2020

Abstract
Sow fertility traits, such as litter size and the number of lifetime parities produced (reproductive longevity), are economically important. Selection for these traits is difficult because they are lowly heritable and expressed late in life. Age at puberty (AP) is an early indicator of reproductive longevity. Here, we utilized a custom Affymetrix single-nucleotide polymorphisms (SNPs) array (SowPro90) enriched with positional candidate genetic variants for AP and a haplotype-based genome-wide association study to fine map the genetic sources associated with AP and other fertility traits in research (University of Nebraska-Lincoln [UNL]) and commercial sow populations. Five major quantitative trait loci (QTL) located on four Sus scrofa chromosomes (SSC2, SSC7, SSC14, and SSC18) were discovered for AP in the UNL population. Negative correlations (r = −0.96 to −0.10; P &lt; 0.0001) were observed at each QTL between genomic estimated breeding values for AP and reproductive longevity measured as lifetime number of parities (LTNP). Some of the SNPs discovered in the major QTL regions for AP were located in candidate genes with fertility-associated gene ontologies (e.g., P2RX3, NR2F2, OAS1, and PTPN11). These SNPs showed significant (P &lt; 0.05) or suggestive (P &lt; 0.15) associations with AP, reproductive longevity, and litter size traits in the UNL population and litter size traits in the commercial sows. For example, in the UNL population, when the number of favorable alleles of an SNP located in the 3′ untranslated region of PTPN11 (SSC14) increased, AP decreased (P &lt; 0.0001), while LTNP increased (P &lt; 0.10). Additionally, a suggestive difference in the observed NR2F2 isoforms usage was hypothesized to be the source of the QTL for puberty onset mapped on SSC7. It will be beneficial to further characterize these candidate SNPs and genes to understand their impact on protein sequence and function, gene expression, splicing process, and how these changes affect the phenotypic variation of fertility traits.
Reimagining disability: the screening of donor gametes and embryos in IVF
Authors: Karpin Isabel , Mykitiuk Roxanne 
Published: September 2020

ABSTRACT
In this article, we examine how disability is figured in the imaginaries that are given shape by the reproductive projects and parental desires facilitated by the bio-medical techniques and practices of assisted reproductive technologies (ARTs) that involve selection and screening for disability. We investigate how some users of ARTs understand and deploy these imaginaries in ways that are both concordant with and resistant to the understanding of disability embedded within the broader sociotechnical and social imaginaries. It is through users’ deliberations, choices, responses, and expectations that we come to understand how these imaginaries are perpetuated and resisted, and how maintaining them is also dependent upon the individual actions and actors who have internalized them. Our examination is grounded in a close analysis of a small selection of interviews drawn from data gathered during a 4-year project funded by the Australian Research Council exploring the Australian experience of cross border reproductive treatment, looking particularly at surrogacy, and gamete and embryo donation. Our interviewees were individuals or couples who used gamete or embryo donation, coupled at times with surrogacy in attempting to have a child. Participants discussed their views on testing, screening, and future disability.
Serum Concentrations of Per- and Polyfluoroalkyl Substances and Risk of Renal Cell Carcinoma
Authors: Shearer Joseph J , Callahan Catherine L , Calafat Antonia M , Huang Wen-Yi , Jones Rena R , Sabbisetti Venkata S , Freedman Neal D , Sampson Joshua N , Silverman Debra T , Purdue Mark P , Hofmann Jonathan N 
Published: September 2020

Abstract

Background
Per- and polyfluoroalkyl substances (PFAS) are highly persistent chemicals that have been detected in the serum of over 98% of the US population. Studies among highly exposed individuals suggest an association with perfluorooctanoic acid (PFOA) exposure and kidney cancer. It remains unclear whether PFOA or other PFAS are renal carcinogens or if they influence risk of renal cell carcinoma (RCC) at concentrations observed in the general population.

Methods
We measured prediagnostic serum concentrations of PFOA and 7 additional PFAS in 324 RCC cases and 324 individually matched controls within the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. Multivariable conditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CIs) relating serum PFAS concentrations and RCC risk. Individual PFAS were modeled continuously (log2-transformed) and categorically, with adjustment for kidney function and additional potential confounders. All statistical tests were 2-sided.

Results
We observed a positive association with RCC risk for PFOA (doubling in serum concentration, ORcontinuous = 1.71, 95% CI = 1.23 to 2.37, P = .002) and a greater than twofold increased risk among those in the highest quartile vs the lowest (OR = 2.63, 95% CI = 1.33 to 5.20, Ptrend = .007). The association with PFOA was similar after adjustment for other PFAS (ORcontinuous = 1.68, 95% CI = 1.07 to 2.63, P = .02) and remained apparent in analyses restricted to individuals without evidence of diminished kidney function and in cases diagnosed 8 or more years after phlebotomy.

Conclusions
Our findings add substantially to the weight of evidence that PFOA is a renal carcinogen and may have important public health implications for the many individuals exposed to this ubiquitous and highly persistent chemical.
Predicted Chemotherapy Benefit for Breast Cancer Patients With Germline Pathogenic Variants in Cancer Susceptibility Genes
Authors: Kurian Allison W , Ward Kevin C , Abrahamse Paul , Hamilton Ann S , Katz Steven J 
Published: September 2020

Abstract
Breast cancer patients increasingly undergo genetic testing. To examine chemotherapy indications for germline pathogenic variant (PV) carriers, we linked results of germline testing to Georgia and California Surveillance, Epidemiology, and End Results registry records, including 21-gene recurrence score (RS) results, for breast cancer patients diagnosed in 2013-2017. All statistical tests were 2-sided. Patients (N=37 349) had RS results of whom 714 had BRCA1, BRCA2, CHEK2, ATM, PALB2, or Lynch syndrome (MLH1, MSH2, MSH6, PMS2) PVs. For women aged 50 years or older at breast cancer diagnosis, RS often exceeded the chemotherapy benefit threshold (≥26) with BRCA1 (71.7% vs 14.4% with none; P &lt;.001), PALB2 (37.1%; P = .001), and BRCA2 (44.3%; P &lt; .001) PVs. Results were similar for women diagnosed at younger than 50 years of age. PVs in BRCA1, but not BRCA2, PALB2, ATM, CHEK2, or Lynch syndrome genes, were associated with elevated RS on multivariable analysis (P &lt; .001). Results may inform RS testing decisions in breast cancer patients with PVs.
LncRNA BC083743 Promotes the Proliferation of Schwann Cells and Axon Regeneration Through miR-103-3p/BDNF After Sciatic Nerve Crush
Authors: Gao Lin , Feng Aiqin , Yue Peijian , Liu Yue , Zhou Qiaoyu , Zang Qiuling , Teng Junfang 
Published: September 2020

Abstract
To investigate the underlying mechanism of lncRNA BC083743 in regulating the proliferation of Schwann cells (SCs) and axon regeneration after sciatic nerve crush (SNC), we used a rat model. Sciatic function index and the atrophy ratio of gastrocnemius muscle were evaluated. The relationship among BC083743, miR-103-3p, and brain-derived neurotrophic factor (BDNF) and their regulation mechanism in the repair of SNC were investigated using in vivo and in vitro experiments. The expression changes of BC083743 were positively associated with that of BDNF following SNC, but the expression changes of miR-103-3p were inversely associated with that of BDNF. The SC proliferation and BDNF expression could be promoted by overexpression of BC083743, while they were inhibited by a miR-103-3p mimic. In addition, BC083743 interacted with and regulated miR-103-3p, thereby promoting BDNF expression and SC proliferation. BC083743 overexpression also promoted axon regeneration through miR-103-3p. In vivo experiments also indicated that BC083743 overexpression promoted the repair of SNC. In conclusion, LncRNA BC083743 promotes SC proliferation and the axon regeneration through miR-103-3p/BDNF after SNC.
A dummy-run evaluation of postoperative hypofractionated intensity-modulated radiation therapy (POHIM-RT) trials for cervical cancer
Authors: Cho Won Kyung , Kim Heejung , Park Won , Kim Sang-Won , Kim Jongwon , Lee Kang Kyu , Oh Jeong Geun , Yoon Mee Sun , Song Ju-Young , Ahn Ki Jung , Park Sung Kwang , Choi Jin Hwa , Bak Jino 
Published: September 2020

Abstract
The postoperative hypofractionated intensity-modulated radiation therapy (POHIM-RT) trial is a phase II study to evaluate toxicity following hypofractionated intensity modulated radiation therapy (IMRT) for cervical cancer. This study describes the results of a benchmark procedure for RT quality assurance of the POHIM-RT trial. Six participating institutions were provided computed tomography for RT planning and an IMRT plan for a sample and were instructed to delineate volumes, create a treatment plan and quality assurance (QA) plan, and submit the results of all procedures. The inter-institutional agreements on RT volume and plan results were evaluated using the kappa value and dice similarity coefficients. The simultaneous truth and performance level estimation (STAPLE) method was employed to generate a consensus target volume. The treatment volumes, organs-at-risk volumes, and results of the RT plan and QA reported by the institutions were acceptable and adhered well to the protocol. In terms of clinical target volume (CTV) delineation, there were differences between the institutions, particularly in vaginal cuff and paracolpium subsites. Consensus CTV was generated from the collected CTVs with the STAPLE method. The participating institutions showed considerable agreement regarding volume, dose and QA results. To improve CTV agreement in CTV, we provided feedback with images of the consensus target volume and detailed written guidelines for specific subsites that were the most heterogeneous.
A rare and severe case of pronator teres syndrome
Authors: Moura Francisco Serra E , Agarwal Anil 
Published: September 2020

Abstract
We present the case of a patient with severe symptoms of proximal forearm median nerve neuropathy. Over the course of 5 years his condition progressed to encompass rare features of combined pronator teres syndrome (PTS) and anterior interosseous nerve syndrome (AINS). The aetiology was found to be pronator teres compression and was managed successfully by surgical decompression. Proximal forearm median nerve compression should be considered as a continuum with two classic endpoints. At one end of the spectrum pure PTS presents with solely or mainly sensory symptoms, whereas at the other end AINS presents with pure motor symptoms. Hence, all possible anatomical sites of compression must be surgically explored in all cases of PTS or AINS, regardless of symptomatology. Timely referral to an experienced specialist is encouraged to ensure good outcomes, whenever a primary care practitioner encounters an atypical carpal tunnel syndrome-like presentation.