bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis and association mapping reveal the genetic regulatory network response to cadmium stress in Populus tomentosa
Authors: Quan Mingyang , Liu Xin , Xiao Liang , Chen Panfei , Song Fangyuan , Lu Wenjie , Song Yuepeng , Zhang Deqiang 
Published: September 2020

Abstract
Long non-coding RNAs (lncRNAs) play essential roles in plant abiotic stress responses, but the response of lncRNA-mediated genetic networks to cadmium (Cd) treatment remain elusive in trees, the promising candidates for phytoremediation of Cd contamination. We identified 172 Cd-responsive lncRNAs and 295 differentially expressed target genes in the leaves of Cd-treated Populus tomentosa. Functional annotation revealed that these lncRNAs were involved in various processes, including photosynthesis, hormone regulation, and phenylalanine metabolism. Association studies identified 78 significant associations, representing 14 Cd-responsive lncRNAs and 28 target genes for photosynthetic and leaf physiological traits. Epistasis uncovered 83 pairwise interactions among these traits, revealing Cd-responsive lncRNA-mediated genetic networks for photosynthesis and leaf physiology in P. tomentosa. We focused on the roles of two Cd-responsive lncRNA–gene pairs, MSTRG.22608.1–PtoMYB73 and MSTRG.5634.1–PtoMYB27, in Cd tolerance of Populus, and detected insertions/deletions within lncRNAs as polymorphisms driving target gene expression. Genotype analysis of lncRNAs and heterologous overexpression of PtoMYB73 and PtoMYB27 in Arabidopsis indicated their effects on enhancing Cd tolerance, photosynthetic rate, and leaf growth, and the potential interaction mechanisms of PtoMYB73 with abiotic stresses. Our study identifies the genetic basis for the response of Populus to Cd treatment, facilitating genetic improvement of Cd tolerance in trees.
Evaluation of probabilistic photometric redshift estimation approaches for The Rubin Observatory Legacy Survey of Space and Time (LSST)
Authors: Schmidt S J , Malz A I , Soo J Y H , Almosallam I A , Brescia M , Cavuoti S , Cohen-Tanugi J , Connolly A J , DeRose J , Freeman P E , Graham M L , Iyer K G , Jarvis M J , Kalmbach J B , Kovacs E , Lee A B , Longo G , Morrison C B , Newman J A , Nourbakhsh E , Nuss E , Pospisil T , Tranin H , Wechsler R H , Zhou R , Izbicki R 
Published: September 2020

Abstract
Many scientific investigations of photometric galaxy surveys require redshift estimates, whose uncertainty properties are best encapsulated by photometric redshift (photo-z) posterior probability density functions (PDFs). A plethora of photo-z PDF estimation methodologies abound, producing discrepant results with no consensus on a preferred approach. We present the results of a comprehensive experiment comparing twelve photo-z algorithms applied to mock data produced forLarge Synoptic Survey Telescope The Rubin Observatory Legacy Survey of Space and Time (lsst) Dark Energy Science Collaboration (desc). By supplying perfect prior information, in the form of the complete template library and a representative training set as inputs to each code, we demonstrate the impact of the assumptions underlying each technique on the output photo-z PDFs. In the absence of a notion of true, unbiased photo-z PDFs, we evaluate and interpret multiple metrics of the ensemble properties of the derived photo-z PDFs as well as traditional reductions to photo-z point estimates. We report systematic biases and overall over/under-breadth of the photo-z PDFs of many popular codes, which may indicate avenues for improvement in the algorithms or implementations. Furthermore, we raise attention to the limitations of established metrics for assessing photo-z PDF accuracy; though we identify the conditional density estimate (CDE) loss as a promising metric of photo-z PDF performance in the case where true redshifts are available but true photo-z PDFs are not, we emphasize the need for science-specific performance metrics.
The R136 star cluster dissected with Hubble Space Telescope/STIS – II. Physical properties of the most massive stars in R136
Authors: Bestenlehner Joachim M , Crowther Paul A , Caballero-Nieves Saida M , Schneider Fabian R N , Simón-Díaz Sergio , Brands Sarah A , de Koter Alex , Gräfener Götz , Herrero Artemio , Langer Norbert , Lennon Daniel J , Maíz Apellániz Jesus , Puls Joachim , Vink Jorick S 
Published: September 2020

ABSTRACT
We present an optical analysis of 55 members of R136, the central cluster in the Tarantula Nebula of the Large Magellanic Cloud. Our sample was observed with STIS aboard the Hubble Space Telescope, is complete down to about 40 M⊙, and includes seven very massive stars with masses over 100 M⊙. We performed a spectroscopic analysis to derive their physical properties. Using evolutionary models, we find that the initial mass function of massive stars in R136 is suggestive of being top-heavy with a power-law exponent γ ≈ 2 ± 0.3, but steeper exponents cannot be excluded. The age of R136 lies between 1 and 2 Myr with a median age of around 1.6 Myr. Stars more luminous than log L/L⊙ = 6.3 are helium enriched and their evolution is dominated by mass-loss, but rotational mixing or some other form of mixing could be still required to explain the helium composition at the surface. Stars more massive than 40 M⊙ have larger spectroscopic than evolutionary masses. The slope of the wind–luminosity relation assuming unclumped stellar winds is 2.41 ± 0.13 which is steeper than usually obtained (∼1.8). The ionizing ($\log Q_0\, [{\rm ph/s}] = 51.4$) and mechanical ($\log L_{\rm SW}\, [{\rm erg/s}] = 39.1$) output of R136 is dominated by the most massive stars ($\gt 100\, \mathrm{ M}_{\odot }$). R136 contributes around a quarter of the ionizing flux and around a fifth of the mechanical feedback to the overall budget of the Tarantula Nebula. For a census of massive stars of the Tarantula Nebula region, we combined our results with the VLT-FLAMES Tarantula Survey plus other spectroscopic studies. We observe a lack of evolved Wolf–Rayet stars and luminous blue and red supergiants.
Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks
Authors: Casasa Sofia , Biddle Joseph F , Koutsovoulos Georgios D , Ragsdale Erik J 
Published: September 2020

AbstractDevelopmental polyphenism, the ability to switch between phenotypes in response to environmental variation, involves the alternating activation of environmentally sensitive genes. Consequently, to understand how a polyphenic response evolves requires a comparative analysis of the components that make up environmentally sensitive networks. Here, we inferred coexpression networks for a morphological polyphenism, the feeding-structure dimorphism of the nematode Pristionchus pacificus. In this species, individuals produce alternative forms of a novel trait—moveable teeth, which in one morph enable predatory feeding—in response to environmental cues. To identify the origins of polyphenism network components, we independently inferred coexpression modules for more conserved transcriptional responses, including in an ancestrally nonpolyphenic nematode species. Further, through genome-wide analyses of these components across the nematode family (Diplogastridae) in which the polyphenism arose, we reconstructed how network components have changed. To achieve this, we assembled and resolved the phylogenetic context for five genomes of species representing the breadth of Diplogastridae and a hypothesized outgroup. We found that gene networks instructing alternative forms arose from ancestral plastic responses to environment, specifically starvation-induced metabolism and the formation of a conserved diapause (dauer) stage. Moreover, loci from rapidly evolving gene families were integrated into these networks with higher connectivity than throughout the rest of the P. pacificus transcriptome. In summary, we show that the modular regulatory outputs of a polyphenic response evolved through the integration of conserved plastic responses into networks with genes of high evolutionary turnover.
Elements at the 5′ end of Xist harbor SPEN-independent transcriptional antiterminator activity
Authors: Trotman Jackson B , Lee David M , Cherney Rachel E , Kim Susan O , Inoue Kaoru , Schertzer Megan D , Bischoff Steven R , Cowley Dale O , Calabrese J Mauro 
Published: September 2020

AbstractThe Xist lncRNA requires Repeat A, a conserved RNA element located in its 5′ end, to induce gene silencing during X-chromosome inactivation. Intriguingly, Repeat A is also required for production of Xist. While silencing by Repeat A requires the protein SPEN, how Repeat A promotes Xist production remains unclear. We report that in mouse embryonic stem cells, expression of a transgene comprising the first two kilobases of Xist (Xist-2kb) causes transcriptional readthrough of downstream polyadenylation sequences. Readthrough required Repeat A and the ∼750 nucleotides downstream, did not require SPEN, and was attenuated by splicing. Despite associating with SPEN and chromatin, Xist-2kb did not robustly silence transcription, whereas a 5.5-kb Xist transgene robustly silenced transcription and read through its polyadenylation sequence. Longer, spliced Xist transgenes also induced robust silencing yet terminated efficiently. Thus, in contexts examined here, Xist requires sequence elements beyond its first two kilobases to robustly silence transcription, and the 5′ end of Xist harbors SPEN-independent transcriptional antiterminator activity that can repress proximal cleavage and polyadenylation. In endogenous contexts, this antiterminator activity may help produce full-length Xist RNA while rendering the Xist locus resistant to silencing by the same repressive complexes that the lncRNA recruits to other genes.
Exploring sleep disturbance among adults with primary or secondary malignant brain tumors and their caregivers
Authors: Jeon Megan S , Dhillon Haryana M , Koh Eng-Siew , Nowak Anna K , Hovey Elizabeth , Descallar Joseph , Miller Lisa , Marshall Nathaniel S , Agar Meera R 
Published: September 2020

AbstractBackgroundEmerging evidence supports the clinical impact of sleep disturbance (SD) on cancer patients. This study aimed to determine the prevalence and predictors of SD in people with malignant brain tumors and caregivers, and explore any relationship between the patient-caregiver dyad’s sleep.MethodsEighty-one adults with primary malignant (91%) or metastatic (9%) brain tumors and their family caregivers (n = 44) completed a series of self-report questionnaires, including the Pittsburgh Sleep Quality Index (PSQI), the Insomnia Severity Index, and the drowsiness item of The MD Anderson Symptom Inventory-Brain Tumor in an Australian ambulatory neuro-oncology setting. Participants were grouped by the PSQI cutoff (SD &gt; 5), and binary logistic regression analyses were performed to identify risk factors.ResultsOf patients, 53% reported SD and 15% of those clinically significant insomnia, and 27% reported moderate to severe daytime drowsiness. Whereas anxiety, depression, fatigue, pain, neurocognitive symptoms, and antiemetic use were higher in patients with SD, fatigue and KPS were strong predictors of SD. In caregivers, 55% reported poor sleep and 13% clinical insomnia. Anxiety, caregiver burden, and comorbid illness were significantly associated with caregivers’ SD. The individual’s SD did not affect the chance of the other member of the patient-caregiver dyad experiencing SD.ConclusionsMore than half the sample had sleep disturbance, which was linked to many concomitant symptoms, such as fatigue in patients and anxiety in caregivers, potentially contributing to distress and functional impairment. Understanding underlying mechanisms of SD, the potential use of these clinical predictors in care settings, and options for management is warranted.
A functional MRI study of presurgical cognitive deficits in glioma patients
Authors: Schouwenaars Irena T , de Dreu Miek J , Rutten Geert-Jan M , Ramsey Nick F , Jansma Johan M 
Published: September 2020

Abstract

Background
The main goal of this functional MRI (fMRI) study was to examine whether cognitive deficits in glioma patients prior to treatment are associated with abnormal brain activity in either the central executive network (CEN) or default mode network (DMN).

Methods
Forty-six glioma patients, and 23 group-matched healthy controls (HCs) participated in this fMRI experiment, performing an N-back task. Additionally, cognitive profiles of patients were evaluated outside the scanner. A region of interest–based analysis was used to compare brain activity in CEN and DMN between groups. Post hoc analyses were performed to evaluate differences between low-grade glioma (LGG) and high-grade glioma (HGG) patients.

Results
In-scanner performance was lower in glioma patients compared to HCs. Neuropsychological testing indicated cognitive impairment in LGG as well as HGG patients. fMRI results revealed normal CEN activation in glioma patients, whereas patients showed reduced DMN deactivation compared to HCs. Brain activity levels did not differ between LGG and HGG patients.

Conclusions
Our study suggests that cognitive deficits in glioma patients prior to treatment are associated with reduced responsiveness of the DMN, but not with abnormal CEN activation. These results suggest that cognitive deficits in glioma patients reflect a reduced capacity to achieve a brain state necessary for normal cognitive performance, rather than abnormal functioning of executive brain regions. Solely focusing on increases in brain activity may well be insufficient if we want to understand the underlying brain mechanism of cognitive impairments in patients, as our results indicate the importance of assessing deactivation.
The Causal Effect of Opioid Agonist Treatment on Adherence to Direct-Acting Antiviral Treatment for Hepatitis C Virus
Authors: Min Jeong E , Pearce Lindsay A , Janjua Naveed Z , Ti Lianping , Nosyk Bohdan 
Published: September 2020

AbstractBackgroundOpioid agonist treatment (OAT) supports adherence in medication regimens for other concurrent conditions. However, sparse evidence is available on its effect on promoting retention to direct-acting antivirals (DAAs) for people with opioid use disorder (PWOUD) with concurrent hepatitis C virus (HCV). Our objective was to determine the causal impact of OAT exposure on DAA adherence among HCV-positive PWOUD.MethodsWe executed a retrospective study using linked population-level data for British Columbia, Canada (January 1996–September 2018). We estimated the effect of OAT on DAA adherence using generalized estimating equations (GEEs) and marginal structural modeling (MSM) for time-varying confounding. The primary outcome was 85% DAA adherence (minimum 6 of 7 days).ResultsWe included 2820 HCV-positive PWOUD who initiated a DAA regimen (32.6% female, 83.9% previously accessing OAT), with 2410 (95% among uncensored episodes) completing the regimen. The GEE-adjusted odds ratio of DAA adherence after OAT exposure was 1.05 (0.89–1.23), whereas the MSM-adjusted odds ratio was 0.97 (0.78–1.22).ConclusionsIn a setting with universal healthcare and widespread access to OAT and DAA treatment, DAA regimen completion rates were high regardless of OAT, and engagement in OAT did not increase DAA adherence. Nonengagement in OAT should not preclude DAA treatment for PWOUD.
Climate change and monetary policy: issues for policy design and modelling
Authors: McKibbin Warwick J , Morris Adele C , Wilcoxen Peter J , Panton Augustus J 
Published: September 2020

Abstract
This paper explores the interaction of monetary policy and climate change as they jointly influence macroeconomic outcomes, connecting policy and outcomes in each realm to the implications of the other. It also explores the nature of the macroeconomic model that would be required to explore the links between monetary policy and climate policy. The paper has four parts. First, it reviews the relevant macroeconomic outcomes of emissions mitigation policy and climatic disruption, exploring how negative supply shocks can affect central banks’ ability to forecast and manage inflation. Second, the paper reviews basic approaches to monetary policy, including inflation and output targeting, and other responsibilities that may fall to central bankers. Third, we bring together the two sets of issues to consider the appropriate monetary framework in a carbon-constrained and climatically disrupted world and to highlight the climate policy frameworks that can make monetary policies more efficient and effective. We then summarize the nature of the macroeconomic modelling framework that is needed to better analyse climate and monetary policy interactions. We conclude that policy responses to climate change can have important implications for monetary policy and vice versa and that, in light of the urgency of ambitious climate action, these policy spheres should be brought together more explicitly and more appropriate macroeconomic modelling frameworks developed.
Growth and ingestion rates of the freshwater jellyfish Craspedacusta sowerbii
Authors: Marchessaux Guillaume , Bejean Mickaël 
Published: September 2020

Abstract
The invasive freshwater hydromedusa Craspedacusta sowerbii Lankester, 1880 (phylum Cnidaria, class Hydrozoa, family Olindiidae) is native from East Asia but for more than 20 years, reports of this species have been increasing in Europe, North America, and Australia. Due to the sporadic presence of the medusa stage and difficulties in the sample polyp stage, there is a lack of data on the physiological parameters of C. sowerbii and its potential impact. We present data on growth and ingestion rates of the medusa stage measured at 29°C, temperature at which polyps are maintained in the Cinéaqua Aquarium (Paris). Medusa growth increased from 0.60 ± 0.08 to 9.0 ± 2.1 mm (mean: 0.28 ± 0.26 mm d−1), and gonads appeared after 11.5 ± 3.0 days. Ingestion rates increased significantly from 28 ± 16 prey ind−1 d−1 (&lt;1 mm) to 442 ± 170 prey ind−1 d−1 (&gt;7 mm).
Dry Needling of a Healthy Rat Achilles Tendon Increases Its Gene Expressions: A Pilot Study
Authors: Calderón-Díez Laura , Sánchez-Sánchez José Luis , Herrero-Turrión Javier , Cleland Joshua , Arias-Buría José L , Fernández-de-las-Peñas César 
Published: September 2020

Abstract

Background
Tendon dry needling is a potential treatment for tendinopathies. Several hypotheses have been proposed to explain its underlying mechanisms. No studies (to the best of our knowledge) have investigated changes in gene expression.

Objective
To investigate histological and gene expression changes after the application of dry needling to the healthy Achilles tendons of rats.

Methods
Six Sprague-Dawley male rats were randomly divided into two groups: no intervention or dry needling. Dry needling consisted of three sessions (once per week) to the Achilles tendon. Molecular expression of several genes involved in tendon repair and remodeling (e.g., Cox2, Mmp2, Mmp9, Col1a1, Col3a1, Vefg, and Scx) was assessed 7 days after the last needling session (day 28) or 28 days after for the no-intervention group. Histological tissue changes were determined with hematoxylin-eosin analyses.

Results
The hematoxylin-eosin–stained images revealed no substantial differences in collagen structure or the presence of inflammatory cells between the dry needling and no-intervention groups. A significant increase in the molecular expression of Cox2, Mmp2, Col3a1, and Scx genes was observed in Achilles tendons treated with dry needling when compared with the no-intervention group.

Conclusion
This animal pilot study found that the application of dry needling to the healthy Achilles tendons of rats is able to increase the expression of genes associated with collagen regeneration and tissue remodeling of the extracellular matrix with no further histological damage to the tendon.
Michigan Initiative for Anterior Cruciate Ligament Rehabilitation (MiACLR): A Protocol for a Randomized Clinical Trial
Authors: Rodriguez Kazandra , Garcia Steven A , Spino Cathie , Lepley Lindsey K , Pang Yuxi , Wojtys Edward , Bedi Asheesh , Angelini Mike , Ruffino Bethany , Bolley Tyler , Block Corey , Kellum Jessica , Swartout Andrew , Palmieri-Smith Riann M 
Published: September 2020

Abstract

Objective
Restoring quadriceps muscle strength following anterior cruciate ligament reconstruction (ACLR) may prevent the posttraumatic osteoarthritis that affects over 50% of knees with ACLR. However, a fundamental gap exists in our understanding of how to maximize muscle strength through rehabilitation. Neurological deficits and muscle atrophy are 2 of the leading mechanisms of muscle weakness after ACLR. High-intensity neuromuscular electrical stimulation (NMES) and eccentric exercise (ECC) have been shown to independently target these mechanisms. If delivered in succession, NMES and then ECC may be able to significantly improve strength recovery. The objectives of this study were to evaluate the ability of NMES combined with ECC to restore quadriceps strength and biomechanical symmetry and maintain cartilage health at 9 and 18 months after ACLR.

Methods
This study is a randomized, double-blind, placebo-controlled, single-center clinical trial conducted at the University of Michigan. A total of 112 participants between the ages of 14 and 45 years and with an anterior cruciate ligament rupture will be included. Participants will be randomly assigned 1:1 to NMES combined with ECC or NMES placebo combined with ECC placebo. NMES or NMES placebo will be delivered 2 times per week for 8 weeks beginning 10 to 14 days postoperatively and will be directly followed by 8 weeks of ECC or ECC placebo delivered 2 times per week. The co-primary endpoints are change from baseline to 9 months and change from baseline to 18 months after ACLR in isokinetic quadriceps strength symmetry. Secondary outcome measures include isometric quadriceps strength, quadriceps activation, quadriceps muscle morphology (cross-sectional area), knee biomechanics (sagittal plane knee angles and moments), indexes of patient-reported function, and cartilage health (T1ρ and T2 relaxation time mapping on magnetic resonance imaging).

Impact
The findings from this study might identify an intervention capable of targeting the lingering quadriceps weakness after ACLR and in turn prevent deterioration in cartilage health after ACLR, thereby potentially improving function in this patient population.
Moduli Spaces of Generalized Hyperpolygons
Authors: Rayan Steven , Schaposnik Laura P 
Published: September 2020

Abstract
We introduce the notion of generalized hyperpolygon, which arises as a representation, in the sense of Nakajima, of a comet-shaped quiver. We identify these representations with rigid geometric figures, namely pairs of polygons: one in the Lie algebra of a compact group and the other in its complexification. To such data, we associate an explicit meromorphic Higgs bundle on a genus-g Riemann surface, where g is the number of loops in the comet, thereby embedding the Nakajima quiver variety into a Hitchin system on a punctured genus-g Riemann surface (generally with positive codimension). We show that, under certain assumptions on flag types, the space of generalized hyperpolygons admits the structure of a completely integrable Hamiltonian system of Gelfand–Tsetlin type, inherited from the reduction of partial flag varieties. In the case where all flags are complete, we present the Hamiltonians explicitly. We also remark upon the discretization of the Hitchin equations given by hyperpolygons, the construction of triple branes (in the sense of Kapustin–Witten mirror symmetry), and dualities between tame and wild Hitchin systems (in the sense of Painlevé transcendents).