bluuebunny/crossref_metadata_2025_split huggingface dataset:
The human impact on North American erosion, sediment transfer, and storage in a geologic context
Authors: Kemp David B. , Sadler Peter M. , Vanacker Veerle 
Published: November 2020

AbstractHumans are primary agents of geomorphic change, and rates of anthropogenic landscape change likely far exceed the pace of change expected from natural geologic processes. Nevertheless, our understanding of the impact of humans on the natural landscape is limited by difficulties in accurately comparing past and present rates of change across wide spatial and temporal scales. Here, we present a compilation of  >4000 rates of alluvial sediment accumulation that provide an indirect record of North American erosion, mass transfer and sediment storage from the late Pleistocene to the present day. Continent-wide rates of alluvium accumulation were broadly stable for ~40,000 years, but increased 10-fold during the rapid expansion of agriculture and river system modification associated with European colonization. Interpreted in terms of mass transfer, humans have moved as much sediment in North America in the past century as natural processes can transfer in 700–3000 years.
Distinct prefrontal top-down circuits differentially modulate sensorimotor behavior
Authors: Huda Rafiq , Sipe Grayson O. , Breton-Provencher Vincent , Cruz K. Guadalupe , Pho Gerald N. , Adam Elie , Gunter Liadan M. , Sullins Austin , Wickersham Ian R. , Sur Mriganka 
Published: November 2020

AbstractSensorimotor behaviors require processing of behaviorally relevant sensory cues and the ability to select appropriate responses from a vast behavioral repertoire. Modulation by the prefrontal cortex (PFC) is thought to be key for both processes, but the precise role of specific circuits remains unclear. We examined the sensorimotor function of anatomically distinct outputs from a subdivision of the mouse PFC, the anterior cingulate cortex (ACC). Using a visually guided two-choice behavioral paradigm with multiple cue-response mappings, we dissociated the sensory and motor response components of sensorimotor control. Projection-specific two-photon calcium imaging and optogenetic manipulations show that ACC outputs to the superior colliculus, a key midbrain structure for response selection, principally coordinate specific motor responses. Importantly, ACC outputs exert control by reducing the innate response bias of the superior colliculus. In contrast, ACC outputs to the visual cortex facilitate sensory processing of visual cues. Our results ascribe motor and sensory roles to ACC projections to the superior colliculus and the visual cortex and demonstrate for the first time a circuit motif for PFC function wherein anatomically non-overlapping output pathways coordinate complementary but distinct aspects of visual sensorimotor behavior.
Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing
Authors: Price Alexander M. , Hayer Katharina E. , McIntyre Alexa B. R. , Gokhale Nandan S. , Abebe Jonathan S. , Della Fera Ashley N. , Mason Christopher E. , Horner Stacy M. , Wilson Angus C. , Depledge Daniel P. , Weitzman Matthew D. 
Published: November 2020

AbstractAdenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to mRNAs. While m6A-modified adenoviral RNAs have been previously detected, the location and function of this mark within the infectious cycle is unknown. Since the complex adenovirus transcriptome includes overlapping spliced units that would impede accurate m6A mapping using short-read sequencing, here we profile m6A within the adenovirus transcriptome using a combination of meRIP-seq and direct RNA long-read sequencing to yield both nucleotide and transcript-resolved m6A detection. Although both early and late viral transcripts contain m6A, depletion of m6A writer METTL3 specifically impacts viral late transcripts by reducing their splicing efficiency. These data showcase a new technique for m6A discovery within individual transcripts at nucleotide resolution, and highlight the role of m6A in regulating splicing of a viral pathogen.
Rapid de novo evolution of lysis genes in single-stranded RNA phages
Authors: Chamakura Karthik R. , Tran Jennifer S. , O’Leary Chandler , Lisciandro Hannah G. , Antillon Sophia F. , Garza Kameron D. , Tran Elizabeth , Min Lorna , Young Ry 
Published: November 2020

AbstractLeviviruses are bacteriophages with small single-stranded RNA genomes consisting of 3-4 genes, one of which (sgl) encodes a protein that induces the host to undergo autolysis and liberate progeny virions. Recent meta-transcriptomic studies have uncovered thousands of leviviral genomes, but most of these lack an annotated sgl, mainly due to the small size, lack of sequence similarity, and embedded nature of these genes. Here, we identify sgl genes in 244 leviviral genomes and functionally characterize them in Escherichia coli. We show that leviviruses readily evolve sgl genes and sometimes have more than one per genome. Moreover, these genes share little to no similarity with each other or to previously known sgl genes, thus representing a rich source for potential protein antibiotics.
Spatial patterns of correlation between cortical amyloid and cortical thickness in a tertiary clinical population with memory deficit
Authors: Pillai Jagan A. , Larvie Mykol , Chen Jacqueline , Crawford Anna , Cummings Jeffery L. , Jones Stephen E. 
Published: November 2020

AbstractTo estimate regional Alzheimer disease (AD) pathology burden clinically, analysis methods that enable tracking brain amyloid or tau positron emission tomography (PET) with magnetic resonance imaging (MRI) measures are needed. We therefore developed a robust MRI analysis method to identify brain regions that correlate linearly with regional amyloid burden in congruent PET images. This method was designed to reduce data variance and improve the sensitivity of the detection of cortical thickness–amyloid correlation by using whole brain modeling, nonlinear image coregistration, and partial volume correction. Using this method, a cross-sectional analysis of 75 tertiary memory clinic AD patients was performed to test our hypothesis that regional amyloid burden and cortical thickness are inversely correlated in medial temporal neocortical regions. Medial temporal cortical thicknesses were not correlated with their regional amyloid burden, whereas cortical thicknesses in the lateral temporal, lateral parietal, and frontal regions were inversely correlated with amyloid burden. This study demonstrates the robustness of our technique combining whole brain modeling, nonlinear image coregistration, and partial volume correction to track the differential correlation between regional amyloid burden and cortical thinning in specific brain regions. This method could be used with amyloid and tau PET to assess corresponding cortical thickness changes.
Comprehensive corrective exercise program improves alignment, muscle activation and movement pattern of men with upper crossed syndrome: randomized controlled trial
Authors: Seidi Foad , Bayattork Mohammad , Minoonejad Hooman , Andersen Lars Louis , Page Phil 
Published: November 2020

AbstractUpper crossed syndrome (UCS) refers to the altered muscle activations and movement patterns in scapulae along with some abnormal alignment in the upper quarter, which may contribute to the dysfunction of the cervicothoracic and glenohumeral joints. The present study aimed to investigate the effectiveness of a comprehensive corrective exercise program (CCEP) and subsequent detraining on alignment, muscle activation, and movement pattern in men with the UCS. This randomized controlled trial included 24 men. The intervention group conducted CCEP (8 weeks), followed by four weeks of detraining and the control group maintained normal daily activities. Electromyography of selected muscles, scapular dyskinesis test, head, shoulder, and thoracic spine angle were measured at baseline, post-test, and follow-up. There were significant differences for Group x time interaction and also for within-group from pre-test to post-test and follow-up in all outcomes. Also, significant differences were observed in three outcomes at post-test and follow-up between the CCEP and control group in favor of the CCEP. In Conclusion, the present study demonstrates that the CCEP for individuals with UCS is feasible and effective, improving muscle activation imbalance, movement patterns, and alignment. Importantly, these improvements were maintained after four weeks of detraining, suggesting lasting neuromuscular re-training adaptations.
Effect of different levels of hydrolysable tannin intake on the reproductive hormones and serum biochemical indices in healthy female rats
Authors: Manzoor Faiza , Nisa Mahr Un , Hussain Hafiz Amjad , Ahmad Nazir , Umbreen Huma 
Published: November 2020

AbstractThe present work aimed to find out the effect of different levels of hydrolysable tannin (HT) on serum hormonal profile, biochemical indices, lipid profile, apparent digestibility of nutrients and body weight gain in healthy female rats. Forty five adult healthy female rats of 8 weeks old were randomly divided into five equal groups. Different doses of HT 0, 0.5, 1, 1.5 and 2% were administered daily to each rats group on the body weight basis for 6 weeks. The results had shown the reduction trend (p < 0.05) in the blood glucose, serum cholesterol, low density lipoprotein, testosterone, prolactin, ghrelin, total oxidative stress and serum iron levels; while an improvement (p < 0.05) was seen in serum follicle stimulating hormone, progesterone, luteinizing hormone, high density lipoprotein, IgM and total antioxidant capacity. However, no effect (p > 0.05) was noticed in serum IgG, protein, estrogen and calcium levels. A significant reduction (p < 0.05) was seen in the apparent nutrient digestibility and body weight gain. The results had shown improvement in the feed conversion ratio (p < 0.05) but non-significant decrease (p > 0.05) in the feed intake. The findings showed that HT had healthy effects on the serum biochemical indices and reproductive hormonal profile but had a negative impact on the nutrient digestibility. Thus, the study concluded that HT could be used as an herbal medicine for the treatment of leading metabolic and infertility diseases like obesity and polycystic ovarian syndrome in females.
Premature termination codons in SOD1 causing Amyotrophic Lateral Sclerosis are predicted to escape the nonsense-mediated mRNA decay
Authors: Guissart Claire , Mouzat Kevin , Kantar Jovana , Louveau Baptiste , Vilquin Paul , Polge Anne , Raoul Cédric , Lumbroso Serge 
Published: November 2020

AbstractAmyotrophic lateral sclerosis (ALS) is the most common and severe adult-onset motoneuron disease and has currently no effective therapy. Approximately 20% of familial ALS cases are caused by dominantly-inherited mutations in the gene encoding Cu/Zn superoxide dismutase (SOD1), which represents one of the most frequent genetic cause of ALS. Despite the overwhelming majority of ALS-causing missense mutations in SOD1, a minority of premature termination codons (PTCs) have been identified. mRNA harboring PTCs are known to be rapidly degraded by nonsense-mediated mRNA decay (NMD), which limits the production of truncated proteins. The rules of NMD surveillance varying with PTC location in mRNA, we analyzed the localization of PTCs in SOD1 mRNA to evaluate whether or not those PTCs can be triggered to degradation by the NMD pathway. Our study shows that all pathogenic PTCs described in SOD1 so far can theoretically escape the NMD, resulting in the production of truncated protein. This finding supports the hypothesis that haploinsufficiency is not an underlying mechanism of SOD1 mutant-associated ALS and suggests that PTCs found in the regions that trigger NMD are not pathogenic. Such a consideration is particularly important since the availability of SOD1 antisense strategies, in view of variant treatment assignment.
An enzyme free fluorescence resonance transfer strategy based on hybrid chain reaction and triplex DNA for Vibrio parahaemolyticus
Authors: Tan Xiao-Hui , Li Yu-Bin , Liao Yan , Liu Hua-Zhong 
Published: November 2020

AbstractIn this work, an enzyme-free fluorescence resonance energy transfer (FRET) strategy was established for rapid and specific detection of the DNA sequence from Vibrio parahaemolyticus (VP) using hybridization chain reaction (HCR) amplification and triplex DNA. The triplex forming oligonucleotide (TFO) was labelled with carboxyfluorescein (FAM) as fluorescence donor, and hairpin sequence H1 was labelled by tetramethylrhodamine (TAMRA) as fluorescence receptor. In the present target VP DNA, the hairpin structure of molecular beacon (MB) was opened, the free end was released and hybridized with H1-TAMRA, and the HCR reaction was triggered by the alternate supplementation of H1-TAMRA and H2 to produce the notch double helix analogue. After the addition of TFO-FAM, a triplex structure was formed between HCR products (H1-TAMRA/H2) and TFO-FAM. A close contact between the donor and the receptor resulted in FRET. Under the optimal conditions, the fluorescence quenching value was inversely proportional to the concentration of target VP DNA in the range of 0.1–50 nmol L−1, and the detection limit was 35 pmol L−1.
Predicting clinical resistance prevalence using sewage metagenomic data
Authors: Karkman Antti , Berglund Fanny , Flach Carl-Fredrik , Kristiansson Erik , Larsson D. G. Joakim 
Published: November 2020

AbstractAntibiotic resistance surveillance through regional and up-to-date testing of clinical isolates is a foundation for implementing effective empirical treatment. Surveillance data also provides an overview of geographical and temporal changes that are invaluable for guiding interventions. Still, due to limited infrastructure and resources, clinical surveillance data is lacking in many parts of the world. Given that sewage is largely made up of human fecal bacteria from many people, sewage epidemiology could provide a cost-efficient strategy to partly fill the current gap in clinical surveillance of antibiotic resistance. Here we explored the potential of sewage metagenomic data to assess clinical antibiotic resistance prevalence using environmental and clinical surveillance data from across the world. The sewage resistome correlated to clinical surveillance data of invasive Escherichia coli isolates, but none of several tested approaches provided a sufficient resolution for clear discrimination between resistance towards different classes of antibiotics. However, in combination with socioeconomic data, the overall clinical resistance situation could be predicted with good precision. We conclude that analyses of bacterial genes in sewage could contribute to informing management of antibiotic resistance.
Waste-minimized synthesis of C2 functionalized quinolines exploiting iron-catalysed C–H activation
Authors: Ferlin Francesco , Zangarelli Agnese , Lilli Simone , Santoro Stefano , Vaccaro Luigi 
Published: November 2020

Herein we present an efficient and regioselective iron-catalyzed methodology for the external oxidant-free C–H activation of quinoline N-oxide.
Estimation of transmission line parameters by using two least‐squares methods
Authors: Albuquerque Felipe P. , Costa Eduardo C. Marques , Liboni Luísa H. B. , Pereira Ronaldo F. Ribeiro , de Oliveira Maurício C. 
Published: November 2020

AbstractThis work proposes two new approaches based on the ordinary least‐squares method and the total least‐squares method to estimate the parameters of a balanced three‐phase transmission line using voltage and current measurements from phasor measurement unit. First, a new model for the steady‐state phasorial equations of a medium‐length transmission line is proposed. Then, the noises acting upon each measurement on the ordinary least‐squares setup are considered, and for the total least‐squares setup, noise acting upon the observation matrix in order to account for model uncertainties and non‐linearities is also considered. The methods are tested in simulation data of a real medium‐size transmission line.s The main goal is to compare both methods and show their complexities. The results show good performances for both methods and, indeed, the total least‐squares setup had better performance than other reported total least‐squares estimators, which use a different phasorial set of equations and oversimplified noise modelling. It is concluded that for the ordinary least‐squares, the solution is well known and its behavior is predictable. While for the total least‐squares, the solution requires more sophisticated methods of matrix decomposition and its behavior is not as predictable. Therefore the implications of these new approaches, where new considerations about the modelling of the noises are made and where a new phasorial set of equations is used are significant, given that the many works in the literature make use of these common‐place tools.
TOI-519 b: A short-period substellar object around an M dwarf validated using multicolour photometry and phase curve analysis
Authors: Parviainen H. , Palle E. , Zapatero-Osorio M. R. , Nowak G. , Fukui A. , Murgas F. , Narita N. , Stassun K. G. , Livingston J. H. , Collins K. A. , Hidalgo Soto D. , Béjar V. J. S. , Korth J. , Monelli M. , Montanes Rodriguez P. , Casasayas-Barris N. , Chen G. , Crouzet N. , de Leon J. P. , Hernandez A. , Kawauchi K. , Klagyivik P. , Kusakabe N. , Luque R. , Mori M. , Nishiumi T. , Prieto-Arranz J. , Tamura M. , Watanabe N. , Gan T. , Collins K. I. , Jensen E. L. N. , Barclay T. , Doty J. P. , Jenkins J. M. , Latham D. W. , Paegert M. , Ricker G. , Rodriguez D. R. , Seager S. , Shporer A. , Vanderspek R. , Villaseñor J. , Winn J. N. , Wohler B. , Wong I. 
Published: November 2020

Context. We report the discovery of TOI-519 b (TIC 218795833), a transiting substellar object (R = 1.07 RJup) orbiting a faint M dwarf (V = 17.35) on a 1.26 d orbit. Brown dwarfs and massive planets orbiting M dwarfs on short-period orbits are rare, but more have already been discovered than expected from planet formation models. TOI-519 is a valuable addition to this group of unlikely systems, and it adds towards our understanding of the boundaries of planet formation.
Aims. We set out to determine the nature of the Transiting Exoplanet Survey Satellite (TESS) object of interest TOI-519 b.
Methods. Our analysis uses a SPOC-pipeline TESS light curve from Sector 7, multicolour transit photometry observed with MuSCAT2 and MuSCAT, and transit photometry observed with the LCOGT telescopes. We estimated the radius of the transiting object using multicolour transit modelling, and we set upper limits for its mass, effective temperature, and Bond albedo using a phase curve model that includes Doppler boosting, ellipsoidal variations, thermal emission, and reflected light components.
Results. TOI-519 b is a substellar object with a radius posterior median of 1.07 RJup and 5th and 95th percentiles of 0.66 and 1.20 RJup, respectively, where most of the uncertainty comes from the uncertainty in the stellar radius. The phase curve analysis sets an upper effective temperature limit of 1800 K, an upper Bond albedo limit of 0.49, and a companion mass upper limit of 14 MJup. The companion radius estimate combined with the Teff and mass limits suggests that the companion is more likely a planet than a brown dwarf, but a brown-dwarf scenario is a priori more likely given the lack of known massive planets in ≈ 1 day orbits around M dwarfs with Teff < 3800 K, and given the existence of some (but few) brown dwarfs.
Identification of coherent structures in space plasmas: the magnetic helicity–PVI method
Authors: Pecora F. , Servidio S. , Greco A. , Matthaeus W. H. 
Published: November 2020

Context. Plasma turbulence can be viewed as a magnetic landscape populated by large- and small-scale coherent structures. In this complex network, large helical magnetic tubes might be separated by small-scale magnetic reconnection events (current sheets). However, the identification of these magnetic structures in a continuous stream of data has always been a challenging task.
Aims. Here, we present a method that is able to characterize both the large- and small-scale structures of the turbulent solar wind, based on the combined use of a filtered magnetic helicity (Hm) and the partial variance of increments (PVI).
Methods. This simple, single-spacecraft technique was first validated via direct numerical simulations of plasma turbulence and then applied to data from the Parker Solar Probe mission.
Results. This novel analysis, combining Hm and PVI methods, reveals that a large number of flux tubes populate the solar wind and continuously merge in contact regions where magnetic reconnection and particle acceleration may occur.
Interdisciplinary Surveillance of Ocular Melanomas: Experiences in a German Tertiary Centre
Authors: Mor Joel M. , Rokohl Alexander C. , Mauch Cornelia , Heindl Ludwig M. 
Published: November 2020

Abstract
Background In contrast to cutaneous melanoma, there are no uniform guidelines regarding surveillance of ocular (uveal, conjunctival) melanomas. A consented standard operating procedure (SOP) by the “Netzwerk onkologische Spitzenzentren” Germany only exists for conjunctival melanoma but not for uveal melanoma. Surveillance is partially based on German S3-guidelines for cutaneous melanoma and is carried out by oncologic centres in a multidisciplinary approach. This study aims to evaluate patientsʼ adherence to surveillance programs and whether surveillance recommendations (examinations, intervals) can be realised.
Methods Retrospective analysis of all ocular melanoma patients overseen at the University Hospital of Cologne between 2008 and 2019. The study evaluates rates of successful patient integration into a standardized surveillance program and patientsʼ surveillance adherence, subject to age, gender, primary therapy and tumour entity, respectively.
Results 99 patients were included (56 female, 43 male), 83 of which had uveal melanomas and 16 conjunctival melanomas. Mean follow-up was 59 months. 81% of patients were integrated into a surveillance program. Surveillance was performed according to published recommendations in 78%. 13% of patients dropped out of the surveillance program after a mean period of 38 months.
Conclusions Our data show a growing number of patients in standardized surveillance. However, there are still gaps. There is a need for guidelines specifically designed for ocular melanomas, allowing centres to offer patients an individualized approach.