bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic regulation of anthocyanin biosynthesis at different light intensities by the BT2-TCP46-MYB1 module in apple
Authors: An Jian-Ping , Liu Ya-Jing , Zhang Xiao-Wei , Bi Si-Qi , Wang Xiao-Fei , You Chun-Xiang , Hao Yu-Jin 
Published: January 2020

AbstractTeosinte branched1/cycloidea/proliferating (TCP) transcription factors play a broad role in plant growth and development, but their involvement in the regulation of anthocyanin biosynthesis is currently unclear. In this study, anthocyanin biosynthesis induced by different light intensities in apple (Malus domestica) was found to be largely dependent on the functions of the MdMYB1 and MdTCP46 transcription factors. The expression of MdTCP46 was responsive to high light intensity, and under these conditions it promoted anthocyanin biosynthesis by direct interactions with MdMYB1 that enhanced the binding of the latter to its target genes. MdTCP46 also interacted with a bric-a-brac/tramtrack/broad (BTB) protein, MdBT2, that is responsive to high light intensity, which ubiquitinated MdTCP46 and mediated its degradation via the 26S proteasome pathway. Our results demonstrate that the dynamic regulatory module MdBT2-MdTCP46-MdMYB1 plays a key role in modulating anthocyanin biosynthesis at different light intensities in apple, and provides new insights into the post-transcriptional regulation of TCP proteins.
Statistical approaches in literature: An application of principal component analysis and factor analysis to analyze the different arrangements about the Quran’s Suras
Authors: Wang Yanwen , Garjami Javad , Tsvetkova Milena , Huu Hau Nguyen , Pho Kim-Hung 
Published: January 2020

AbstractData mining, statistics, and data analysis are popular techniques to study datasets and extract knowledge from them. In this article, principal component analysis and factor analysis were applied to cluster thirteen different given arrangements about the Suras of the Holy Quran. The results showed that these thirteen arrangements can be categorized in two parts such that the first part includes Blachère, Davood, Grimm, Nöldeke, Bazargan, E’temad-al-Saltane and Muir, and the second part includes Ebn Nadim, Jaber, Ebn Abbas, Hazrat Ali, Khazan, and Al-Azhar.
On aggregating probabilistic evidence
Authors: Artemov Sergei 
Published: January 2020

Abstract
Imagine a database—a set of propositions $\varGamma =\{F_1,\ldots ,F_n\}$ with some kind of probability estimates and let a proposition $X$ logically follow from $\varGamma $. What is the best justified lower bound of the probability of $X$? The traditional approach, e.g. within Adams’ probability logic, computes the numeric lower bound for $X$ corresponding to the worst-case scenario. We suggest a more flexible parameterized approach by assuming probability events $u_1,u_2,\ldots ,u_n$ that support $\varGamma $ and calculating aggregated evidence$e(u_1,u_2,\ldots ,u_n)$ for $X$. The probability of $e$ provides a tight lower bound for any, not only a worst-case, situation. The problem is formalized in a version of justification logic and the conclusions are supported by corresponding completeness theorems. This approach can handle conflicting and inconsistent data and allows the gathering both positive and negative evidence for the same proposition.
The cosmic atomic hydrogen mass density as a function of mass and galaxy hierarchy from spectral stacking
Authors: Hu Wenkai , Catinella Barbara , Cortese Luca , Staveley-Smith Lister , Lagos Claudia del P , Chauhan Garima , Oosterloo Tom , Chen Xuelei 
Published: January 2020

ABSTRACT
We use spectral stacking to measure the contribution of galaxies of different masses and in different hierarchies to the cosmic atomic hydrogen (H i) mass density in the local Universe. Our sample includes 1793 galaxies at z &lt; 0.11 observed with the Westerbork Synthesis Radio Telescope, for which Sloan Digital Sky Survey spectroscopy and hierarchy information are also available. We find a cosmic H i mass density of $\Omega _{\rm H\, \small {I} } = (3.99 \pm 0.54)\times 10^{-4} \, h_{70}^{-1}$ at 〈 z〉 = 0.065. For the central and satellite galaxies, we obtain $\Omega _{\rm H\, {\small {I}}}$ of $(3.51 \pm 0.49)\times 10^{-4} \, h_{70}^{-1}$ and $(0.90 \pm 0.16)\times 10^{-4} \, h_{70}^{-1}$, respectively. We show that galaxies above and below stellar masses of ∼109.3 M⊙ contribute in roughly equal measure to the global value of $\Omega _{\rm H\, \small {I} }$. While consistent with estimates based on targeted H i surveys, our results are in tension with previous theoretical work. We show that these differences are, at least partly, due to the empirical recipe used to set the partition between atomic and molecular hydrogen in semi-analytical models. Moreover, comparing our measurements with the cosmological semi-analytic models of galaxy formation Shark and GALFORM reveals gradual stripping of gas via ram pressure works better to fully reproduce the properties of satellite galaxies in our sample than strangulation. Our findings highlight the power of this approach in constraining theoretical models and confirm the non-negligible contribution of massive galaxies to the H i mass budget of the local Universe.
The connection between the UV/optical and X-ray emission in the neutron star low-mass X-ray binary Aql X-1
Authors: López-Navas E , Degenaar N , Parikh A S , Hernández Santisteban J V , van den Eijnden J 
Published: January 2020

ABSTRACT
Accreting neutron stars and black holes in low-mass X-ray binaries (LMXBs) radiate across the electromagnetic spectrum. Linking the emission produced at different wavelengths can provide valuable information about the accretion process and any associated outflows. In this work, we study simultaneous X-ray and ultraviolet (UV)/optical observations of the neutron star LMXB Aql X-1, obtained with the Neil Gehrels Swift Observatory during its 2013, 2014, and 2016 accretion outbursts. We find that the UV/optical and X-ray emission are strongly correlated during all three outbursts. For the 2013 and 2014 episodes, which had the best Swift sampling, we find that the correlation between the UV/optical and X-ray fluxes is significantly steeper during the decay (soft state) of the outburst than during the rise (hard-to-soft state). We observe a UV/optical hysteresis behaviour that is likely linked to the commonly known X-ray spectral hysteresis pattern. For the decays of the three outbursts, we obtain a correlation index that cannot be directly explained by any single model. We suspect that this is a result of multiple emission processes contributing to the UV/optical emission, but we discuss alternative explanations. Based on these correlations, we discuss which mechanisms are likely dominating the UV/optical emission of Aql X-1.
Kinetic turbulence in shining pair plasma: intermittent beaming and thermalization by radiative cooling
Authors: Zhdankin Vladimir , Uzdensky Dmitri A , Werner Gregory R , Begelman Mitchell C 
Published: January 2020

ABSTRACTHigh-energy astrophysical systems frequently contain collision-less relativistic plasmas that are heated by turbulent cascades and cooled by emission of radiation. Understanding the nature of this radiative turbulence is a frontier of extreme plasma astrophysics. In this paper, we use particle-in-cell simulations to study the effects of external inverse Compton radiation on turbulence driven in an optically thin, relativistic pair plasma. We focus on the statistical steady state (where injected energy is balanced by radiated energy) and perform a parameter scan spanning from low magnetization to high magnetization (0.04 ≲ σ ≲ 11). We demonstrate that the global particle energy distributions are quasi-thermal in all simulations, with only a modest population of non-thermal energetic particles (extending the tail by a factor of ∼2). This indicates that non-thermal particle acceleration (observed in similar non-radiative simulations) is quenched by strong radiative cooling. The quasi-thermal energy distributions are well fit by analytic models in which stochastic particle acceleration (due to, e.g. second-order Fermi mechanism or gyroresonant interactions) is balanced by the radiation reaction force. Despite the efficient thermalization of the plasma, non-thermal energetic particles do make a conspicuous appearance in the anisotropy of the global momentum distribution as highly variable, intermittent beams (for high magnetization cases). The beamed high-energy particles are spatially coincident with intermittent current sheets, suggesting that localized magnetic reconnection may be a mechanism for kinetic beaming. This beaming phenomenon may explain rapid flares observed in various astrophysical systems (such as blazar jets, the Crab nebula, and Sagittarius A*).
Evolution of the Autism-Associated Neuroligin-4 Gene Reveals Broad Erosion of Pseudoautosomal Regions in Rodents
Authors: Maxeiner Stephan , Benseler Fritz , Krasteva-Christ Gabriela , Brose Nils , Südhof Thomas C 
Published: January 2020

AbstractVariants in genes encoding synaptic adhesion proteins of the neuroligin family, most notably neuroligin-4, are a significant cause of autism spectrum disorders in humans. Although human neuroligin-4 is encoded by two genes, NLGN4X and NLGN4Y, that are localized on the X-specific and male-specific regions of the two sex chromosomes, the chromosomal localization and full genomic sequence of the mouse Nlgn4 gene remain elusive. Here, we analyzed the neuroligin-4 genes of numerous rodent species by direct sequencing and bioinformatics, generated complete drafts of multiple rodent neuroligin-4 genes, and examined their evolution. Surprisingly, we find that the murine Nlgn4 gene is localized to the pseudoautosomal region (PAR) of the sex chromosomes, different from its human orthologs. We show that the sequence differences between various neuroligin-4 proteins are restricted to hotspots in which rodent neuroligin-4 proteins contain short repetitive sequence insertions compared with neuroligin-4 proteins from other species, whereas all other protein sequences are highly conserved. Evolutionarily, these sequence insertions initiate in the clade eumuroidea of the infraorder myomorpha and are additionally associated with dramatic changes in noncoding sequences and gene size. Importantly, these changes are not exclusively restricted to neuroligin-4 genes but reflect major evolutionary changes that substantially altered or even deleted genes from the PARs of both sex chromosomes. Our results show that despite the fact that the PAR in rodents and the neuroligin-4 genes within the rodent PAR underwent massive evolutionary changes, neuroligin-4 proteins maintained a highly conserved core structure, consistent with a substantial evolutionary pressure preserving its physiological function.
Bending and looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid
Authors: Heenan Patrick R , Wang Xueyin , Gooding Anne R , Cech Thomas R , Perkins Thomas T 
Published: January 2020

Abstract
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene silencing, cellular differentiation and the formation of facultative heterochromatin. It can also promote or inhibit oncogenesis. Despite this importance, the molecular mechanisms by which PRC2 compacts chromatin are relatively understudied. Here, we visualized the binding of PRC2 to naked DNA in liquid at the single-molecule level using atomic force microscopy. Analysis of the resulting images showed PRC2, consisting of five subunits (EZH2, EED, SUZ12, AEBP2 and RBBP4), bound to a 2.5-kb DNA with an apparent dissociation constant ($K_{\rm{D}}^{{\rm{app}}}$) of 150 ± 12 nM. PRC2 did not show sequence-specific binding to a region of high GC content (76%) derived from a CpG island embedded in such a long DNA substrate. At higher concentrations, PRC2 compacted DNA by forming DNA loops typically anchored by two or more PRC2 molecules. Additionally, PRC2 binding led to a 3-fold increase in the local bending of DNA’s helical backbone without evidence of DNA wrapping around the protein. We suggest that the bending and looping of DNA by PRC2, independent of PRC2’s methylation activity, may contribute to heterochromatin formation and therefore epigenetic gene silencing.
A conserved sequence signature is essential for robust plant miRNA biogenesis
Authors: Narjala Anushree , Nair Ashwin , Tirumalai Varsha , Hari Sundar G Vivek , Shivaprasad Padubidri V 
Published: January 2020

Abstract
Micro (mi)RNAs are 20–22nt long non-coding RNA molecules involved in post-transcriptional silencing of targets having high base-pair complementarity. Plant miRNAs are processed from long Pol II-transcripts with specific stem-loop structures by Dicer-like (DCL) 1 protein. Although there were reports indicating how a specific region is selected for miRNA biogenesis, molecular details were unclear. Here, we show that the presence of specific GC-rich sequence signature within miRNA/miRNA* region is required for the precise miRNA biogenesis. The involvement of GC-rich signatures in precise processing and abundance of miRNAs was confirmed through detailed molecular and functional analysis. Consistent with the presence of the miRNA-specific GC signature, target RNAs of miRNAs also possess conserved complementary sequence signatures in their miRNA binding motifs. The selection of these GC signatures was dependent on an RNA binding protein partner of DCL1 named HYL1. Finally, we demonstrate a direct application of this discovery for enhancing the abundance and efficiency of artificial miRNAs that are popular in plant functional genomic studies.
Early net ultrafiltration rate and mortality in critically ill patients receiving continuous renal replacement therapy
Authors: Naorungroj Thummaporn , Neto Ary Serpa , Zwakman-Hessels Lara , Yanase Fumitaka , Eastwood Glenn , Murugan Raghavan , Kellum John A , Bellomo Rinaldo 
Published: January 2020

Abstract

Background
In patients treated with continuous renal replacement therapy (CRRT), early net ultrafiltration (NUF) rates may be associated with differential outcomes. We tested whether higher early NUF rates are associated with increased mortality in CRRT patients.

Methods
We performed a retrospective, observational study of all patients treated with CRRT within 14 days of intensive care unit admission. We defined the early (first 48 h) NUF rate as the volume of fluid removed per hour adjusted for patient body weight and analysed as a categorical variable (&gt;1.75, 1.01–1.75 and &lt;1.01 mL/kg/h). The primary outcome was 28-day mortality. To deal with competing risk, we also compared different time epochs.

Results
We studied 347 patients {median age 64 [interquartile range (IQR) 53–71] years and Acute Physiology and Chronic Health Evaluation III score 73 [IQR 54–90]}. Compared with NUF rates &lt;1.01 mL/kg/h, NUF rates &gt;1.75 mL/kg/h were associated with greater mortality rates in each epoch: Days 0–5, adjusted hazard ratio (aHR) 1.27 [95% confidence interval (CI) 1.21–1.33]; Days 6–10, aHR 1.62 (95% CI 1.55–1.68); Days 11–15, aHR 1.87 (95% CI 1.79–1.94); Days 16–26, aHR 1.92 (95% CI 1.84–2.01) and Days 27–28, aHR 4.18 (95% CI 3.98–4.40). For every 0.5 mL/kg/h NUF rate increase, mortality similarly increased during these epochs.

Conclusion
Compared with early NUF rates &lt;1.01 mL/kg/h, NUF rates &gt;1.75 mL/kg/h are associated with increased mortality. These observations provide the rationale for clinical trials to confirm or refute these findings.
Surface Perturbation Training to Prevent Falls in Older Adults: A Highly Pragmatic, Randomized Controlled Trial
Authors: Lurie Jon D , Zagaria Alexandra B , Ellis Lisa , Pidgeon Dawna , Gill-Body Kathleen M , Burke Christina , Armbrust Kurt , Cass Sharil , Spratt Kevin F , McDonough Christine M 
Published: January 2020

Abstract

Background
Falls are the leading cause of injuries among older adults, and trips and slips are major contributors to falls.

Objective
The authors sought to compare the effectiveness of adding a component of surface perturbation training to usual gait/balance training for reducing falls and fall-related injury in high-risk older adults referred to physical therapy.

Design
This was a multi-center, pragmatic, randomized, comparative effectiveness trial.

Setting
Treatment took place within 8 outpatient physical therapy clinics.

Patients
This study included 506 patients 65+ years of age at high fall risk referred for gait/balance training.

Intervention
This trial evaluated surface perturbation treadmill training integrated into usual multimodal exercise-based balance training at the therapist’s discretion versus usual multimodal exercise-based balance training alone.

Measurements
Falls and injurious falls were assessed with a prospective daily fall diary, which was reviewed via telephone interview every 3 months for 1 year.
A total of 211/253 (83%) patients randomized to perturbation training and 210/253 (83%) randomized to usual treatment provided data at 3-month follow-up. At 3 months, the perturbation training group had a significantly reduced chance of fall-related injury (5.7% versus 13.3%; relative risk 0.43) but no significant reduction in the risk of any fall (28% versus 37%, relative risk 0.78) compared with usual treatment. Time to first injurious fall showed reduced hazard in the first 3 months but no significant reduction when viewed over the entire first year.

Limitations
The limitations of this trial included lack of blinding and variable application of interventions across patients based on pragmatic study design.

Conclusion
The addition of some surface perturbation training to usual physical therapy significantly reduced injurious falls up to 3 months posttreatment. Further study is warranted to determine the optimal frequency, dose, progression, and duration of surface perturbation aimed at training postural responses for this population.
Controlling parenting and perfectionism is associated with an increased error-related negativity (ERN) in young adults
Authors: Meyer Alexandria , Wissemann Karl 
Published: January 2020

Abstract
A substantial amount of research focuses on the error-related negativity (ERN)—a negative deflection in the event-related potential waveform that occurs when individuals commit errors on lab-based tasks. The ERN has been link to concurrent and prospective risk for psychopathology and is thought to index sensitivity or reactivity to errors. The ERN can be potentiated in the lab with punishment and has been shown to be increased among offspring of harsh or controlling parents. A separate line of work has demonstrated that the ERN is increased among individuals high in perfectionism. In the current study, we integrate these separate lines of work by examining parenting styles, perfectionism and the ERN in a sample of young adults. Results suggest that the ERN is increased among offspring of controlling parents (both maternal and paternal). Additionally, the ERN is increased among individuals who report being high in perfectionism—specifically, the concerns over mistake and the personal standard perfectionism subscales of the Frost Multidimensional Perfectionism Scale. Moreover, results supported a mediation model wherein the indirect pathway from controlling parenting style to perfectionism (personal standard subscale) was mediated by the ERN—for paternal parenting.
Approaching intellectual property scholarship differently: A qualitative research review and agenda
Authors: Parthasarathy Shobita 
Published: January 2020

AbstractSocial and policy interest in intellectual property, and patents, in particular, is growing. This is reflected in the rise of scholarly inquiry on the topic beyond the legal community, including among social scientists and humanists. In this article, I advocate for expanding qualitative research on patents and intellectual property related to innovation, arguing that it is essential for political and policy discussion. I review existing work and suggest avenues forward along four lines of inquiry: the political economy of intellectual property, the relationship between patents and innovation, the broader implications of intellectual property for social and political orders, and public participation in intellectual property law and policy. Throughout, I use the emerging field of precision medicine—and specifically, efforts to create intellectual property policies that promote open science and innovation—to explore how qualitative methodologies can help us understand the context and consequences of intellectual property law and policy and, ultimately, make better decisions to govern innovation.
Effects of supplementing late-gestation sow diets with zinc on preweaning mortality of pigs under commercial rearing conditions1
Authors: Holen Julia P , Urriola Pedro E , Schwartz Mark , Jang Jae-Cheol , Shurson Gerald C , Johnston Lee J 
Published: January 2020

Abstract
The objective of this experiment was to determine preweaning survival of pigs when sows were supplemented with 3 dietary levels of zinc (Zn) in late gestation. Gilts and sows (n = 339) were assigned to 1 of 3 dietary treatments based on parity. Dietary treatments were 1) Control—sows fed a corn–soybean meal-based diet containing 125 ppm total supplemental Zn supplied by ZnSO4 (75 ppm Zn) and AvailaZn (50 ppm Zn, CON); 2) Intermediate—as Control + 240 ppm supplemental Zn as ZnSO4 (INT); and 3) High—as Control + 470 ppm supplemental Zn as ZnSO4 (HI). Final supplemental Zn concentrations of the 3 dietary treatments were 1) CON—125 ppm; 2) INT—365 ppm; and 3) HI—595 ppm. Sows received dietary treatments from about day 85 of gestation until farrowing. Individual piglet birth weights were recorded within 12 h of parturition. Instances of piglet mortality were recorded daily. The statistical model considered fixed effects of treatment and random effects of parity. Piglets from sows fed the INT diet had heavier (P &lt; 0.05) birth weights than those fed CON (1.42 vs. 1.38 kg, respectively), while offspring from sows fed HI tended to have heavier (P &lt; 0.10) birth weights (1.40 kg) than pigs from INT sows. Furthermore, incidence of low birth weight pigs was less (P &lt; 0.05) for sows consuming INT compared with sows fed CON and HI. Despite differences in birth weight, there were no differences (P &gt; 0.05) in total pigs born, born alive, or weaned, nor differences in individual piglet gain or weaning weight across treatments. Mortality of low birth weight pigs was lowest (P &lt; 0.05) for offspring from sows fed HI (28.1%) compared with offspring from sows fed INT (36.1%) and CON (38.3%). Similarly, overall piglet mortality tended to decrease (P &lt; 0.10) as dietary Zn content increased (CON: 15.0%, INT: 13.2%, and HI: 12.2%). A subset of pigs (n = 420, n = 140/treatment) were selected at weaning to evaluate effects of dietary treatment on postweaning performance. There were no significant effects of sow Zn supplementation on final body weight, days to market, or carcass characteristics of market pigs. Overall, effects of supplemental dietary Zn at 365 and 595 ppm in late gestation improved preweaning survival of low birth weight piglets and reduced overall preweaning mortality of piglets.