bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic risk of osteoarthritis operates during human skeletogenesis
Authors: Rice Sarah J , Brumwell Abby , Falk Julia , Kehayova Yulia S , Casement John , Parker Eleanor , Hofer Ines M J , Shepherd Colin , Loughlin John 
Published: October 2022

Abstract
Osteoarthritis (OA) is a polygenic disease of older people resulting in the breakdown of cartilage within articular joints. Although it is a leading cause of disability, there are no disease-modifying therapies. Evidence is emerging to support the origins of OA in skeletogenesis. Whereas methylation quantitative trait loci (mQTLs) co-localizing with OA genome-wide association study signals have been identified in aged human cartilage and used to identify effector genes and variants, such analyses have never been conducted during human development. Here, for the first time, we have investigated the developmental origins of OA genetic risk at seven well-characterized OA risk loci, comprising 39 OA-mQTL CpGs, in human fetal limb (FL) and cartilage (FC) tissues using a range of molecular genetic techniques. We identified significant OA-mQTLs at 14 and 29 CpGs in FL and FC tissues, respectively, and compared our results with aged cartilage samples (AC). Differential methylation was observed at 26 sites between FC and AC, with the majority becoming actively hypermethylated in old age. Notably, 6/9 OA effector genes showed allelic expression imbalances during fetal development. Finally, we conducted ATAC-sequencing in cartilage from the developing and aged hip and knee to identify accessible chromatin regions and found enrichment for transcription factor binding motifs including SOX9 and FOS/JUN. For the first time, we have demonstrated the activity of OA-mQTLs and expression imbalance of OA effector genes during human skeletogenesis. We show striking differences in the spatiotemporal function of these loci, contributing to our understanding of OA aetiology, with implications for the timing and strategy of pharmacological interventions.
Covering by Planks and Avoiding Zeros of Polynomials
Authors: Glazyrin Alexey , Karasev Roman , Polyanskii Alexandr 
Published: October 2022

Abstract
We note that the recent polynomial proofs of the spherical and complex plank covering problems by Zhao and Ortega-Moreno give some general information on zeros of real and complex polynomials restricted to the unit sphere. As a corollary of these results, we establish several generalizations of the celebrated Bang plank covering theorem. We prove a tight polynomial analog of the Bang theorem for the Euclidean ball and an even stronger polynomial version for the complex projective space. Specifically, for the ball, we show that for every real nonzero $d$-variate polynomial $P$ of degree $n$, there exists a point in the unit $d$-dimensional ball at distance at least $1/n$ from the zero set of the polynomial $P$. Using the polynomial approach, we also prove the strengthening of the Fejes Tóth zone conjecture on covering a sphere by spherical segments, closed parts of the sphere between two parallel hyperplanes. In particular, we show that the sum of angular widths of spherical segments covering the whole sphere is at least $\pi $.
Homotopies of Constant Cuntz Class
Authors: Toms Andrew S 
Published: October 2022

Abstract
Let $A$ be a unital simple separable exact C$^{\ast }$-algebra that is approximately divisible and of real rank zero. We prove that the set of positive elements in $A$ with a fixed Cuntz class is path connected. This result applies in particular to irrational rotation algebras and approximately finite-dimensional (AF) algebras.
On the Existence of SRB Measures for ∞ Surface Diffeomorphisms
Authors: Buzzi Jérôme , Crovisier Sylvain , Sarig Omri 
Published: October 2022

AbstractWe give a proof of Viana’s [19] conjecture on physical measures, in the special case of $C^\infty $ surface diffeomorphisms, and using the analysis of entropy and Lyapunov exponents we developed in [5]. Burguet [3] has recently proved a stronger result, using a different method.
Potential for Emergence of Foodborne Trematodiases Transmitted by an Introduced Snail (Melanoides tuberculata) in California and Elsewhere in the United States
Authors: Metz Daniel C G , Turner Andrew V , Nelson Alexandria P , Hechinger Ryan F 
Published: October 2022

AbstractWe document that 3 human-infectious trematodes and their introduced first intermediate host snail (Melanoides tuberculata) are widespread throughout southern California. We surveyed 41 fishing localities, 19 of which harbored snails infected with zoonotic trematodes. Two of the parasites, Haplorchis pumilio and Centrocestus formosanus, are fishborne intestinal trematodes recognized as being important human pathogens in other areas of the world; the third, Philophthalmus gralli, can infect the human eye. An additional 5 species detected infecting M. tuberculata are likely of little direct threat to people; however, they may be recently introduced to the Americas, highlighting the risk that additional pathogenic trematodes transmitted by the snail in its native range could be introduced to the United States. The current, possible human-infection risk in California clarifies the need to consider the introduced snail and its parasites from a public health perspective anywhere in the United States the snail has been introduced.
In utero hyperthermia in late gestation derails dairy calf early-life mammary development
Authors: Dado-Senn Bethany M , Field Sena L , Davidson Brittney D , Dahl Geoffrey E , Laporta Jimena 
Published: October 2022

Abstract
Prenatal hyperthermia has immediate and long-term consequences on dairy cattle growth, immunity, and productivity. While changes in the molecular architecture are reported in the mature mammary gland (MG), any influence on early-life mammary development is unknown. Herein, we characterize the impact of late-gestation in utero heat stress on heifer mammary gross and cellular morphology at early-life developmental stages (i.e., birth and weaning). During summer, pregnant dams were exposed to environmental heat stress (shade of a free-stall barn) or offered active cooling (shade, fans, and water soakers) for 54 ± 5 d before parturition (avg. temperature–humidity index = 79). Heifer calves born to these dams were either in utero heat-stressed (IU-HT; n = 36) or in utero cooled (IU-CL; n = 37) and were managed as a single cohort thereafter. A subset of heifers was euthanized at birth (d0; n = 8/treatment; 4.6 ± 2.3 h after birth) and after weaning (d63; n = 8/treatment; 63.0 ± 1.5 d) to harvest the whole MG. An ultrasound of rear mammary parenchyma (MPAR) was taken prior to d63 and correlated to harvested MPAR cross-sectional area and weight. Portions of mammary fat pad (MFP) and MPAR were preserved for compositional and histological analysis, including ductal structure number and cross-sectional area, connective tissue area, and adipocyte number and cross-sectional area. Cellular proliferation in MPAR was assessed via Ki-67 immunohistochemistry. Relative to IU-CL heifers, the MGs of IU-HT heifers were shorter in length at d0 and d63 (P ≤ 0.02). There were moderate correlations between d63 ultrasound and harvest measures. The IU-HT heifers had reduced MG and MFP mass at d0 and d63 (P ≤ 0.05), whereas MPAR mass was reduced only at d0 (P = 0.01). IU-HT heifers had greater MPAR protein and DNA content at d63 (P ≤ 0.04), but there were no MFP compositional differences (P ≥ 0.12). At d0, IU-HT heifers had fewer MPAR ductal structures (P ≤ 0.06), but there were no differences at d63. Yet, MPAR luminal and total ductal structure cross-sectional areas of IU-HT heifers were reduced at both d0 and d63 (P ≤ 0.01). The MFP adipocytes of IU-HT heifers were smaller at d0 (P ≤ 0.01), but differences were not detected at d63. The IU-HT heifers had diminished MPAR total, stromal, and epithelial cellular proliferation at both d0 and d63 (P &lt; 0.01). Prenatal hyperthermia derails dairy calf early-life mammary development with potential carry-over consequences on future synthetic capacity.
Nutritive value, silage fermentation characteristics, and aerobic stability of grass-legume round-baled silages at differing moisture concentrations with and without manure fertilization and microbial inoculation
Authors: Coblentz Wayne K , Akins Matthew S , Jaramillo David M , Cavadini Jason S 
Published: October 2022

AbstractFor baled silages, production of clostridial fermentation products can be exacerbated by exceeding normal moisture targets (45% to 55%), and/or by the application of dairy slurry before harvest. Our objectives were to test a microbial inoculant as a mitigant of clostridial products in high-moisture, grass-legume (52% ± 13.8% cool-season grasses, 44.0% ± 14.0% legumes [predominately alfalfa]) baled silages in swards that were fertilized with dairy slurry. A secondary objective was to examine the effects of bale moisture and inoculation on the aerobic stability of these fermented silages following exposure to air. After the first-cutting was removed, three manure treatments were applied as a whole-plot factor: 1) control (no manure); 2) slurry applied immediately to stubble (63,250 L/ha); or 3) slurry applied after a 1-wk delay (57,484 L/ha). An interactive arrangement of bale moisture (64.1% or 48.4%) and inoculation (yes or no) served as a subplot term in the experiment. The inoculant contained both homolactic (Lactococcus lactis 0224) and heterolactic (Lactobacillus buchneri LB1819) bacteria. The experimental design was analyzed as a randomized complete block with four replications, and the study included 48 experimental units (1.2 × 1.2-m round bales). Total fermentation acids were affected (P ≤ 0.021) by slurry application strategies, but this was likely related to inconsistent bale moisture across slurry-application treatments. Concentrations of butyric acid were low, and there were no detectable contrasts comparing manure treatments (mean = 0.05%; P ≥ 0.645). Bale moisture affected all measures of fermentation, with bales made at 64.1% moisture exhibiting a more acidic final pH (4.39 vs. 4.63; P &lt; 0.001), less residual water-soluble carbohydrates (2.1% vs. 5.1%; P &lt; 0.001), as well as greater lactic acid (4.64% vs. 2.46%; P &lt; 0.001), acetic acid (2.26% vs. 1.32%; P &lt; 0.001), and total fermentation acids (7.37% vs. 3.97%; P &lt; 0.001). Inoculation also reduced pH (4.47 vs. 4.56; P = 0.029), and increased acetic acid (1.97% vs. 1.61%; P &lt; 0.001) and 1,2-propanediol (1.09% vs. 0.72%; P &lt; 0.001) compared to controls. During a 34-d aerobic exposure period, maximum surface bale temperatures were not affected (P ≥ 0.186) by any aspect of treatment, likely due to the prevailing cool ambient temperatures; however, yeast counts were numerically lower in response to greater (P &lt; 0.001) production of acetic acid that was stimulated by both high bale moisture and inoculation.
Characterization of KDM5 lysine demethylase family substrate preference and identification of novel substrates
Authors: Hoekstra Matthew , Ridgeway Nashira H , Biggar Kyle K 
Published: October 2022

Abstract
The KDM5/JARID1 sub-family are 2-oxoglutarate and Fe(II)-dependent lysine-specific histone demethylases that are characterized by their Jumonji catalytic domains. The KDM5 family is known to remove tri-/di-methyl modifications from lysine-4 of histone H3 (i.e. H3-K4me2/3), a mark associated with active gene expression. As a result, studies to date have revolved around the influence of KDM5 on disease through their ability to regulate H3-K4me2/3. Recent evidence demonstrates that KDM5 may influence disease beyond H3-K4 demethylation, making it critical to further investigate KDM5-mediated demethylation of non-histone proteins. To help identify potential non-histone substrates for the KDM5 family, we developed a library of 180 permutated peptide substrates, with sequences that are systematically altered from the wild-type H3-K4me3 substrate. From this library, we characterized recombinant KDM5A/B/C/D substrate preference and developed recognition motifs for each KDM5 demethylase. The recognition motifs developed were used to predict potential substrates for KDM5A/B/C/D and profiled to generate a list of high-ranking and medium/low-ranking substrates for further in vitro validation. Through this approach, we identified 66 high-ranking substrates in which KDM5 demethylases displayed significant in vitro activity towards.
An Assessment of American Indian Forestry Research, Information Needs, and Priorities
Authors: Dockry Michael J , Hoagland Serra J , Leighton Adrian D , Durglo James R , Pradhananga Amit 
Published: October 2022

AbstractNative American and Alaska Native tribes manage millions of acres of land and are leaders in forestry and fire management practices despite inadequate and inequitable funding. Native American tribes are rarely considered as research partners due to historically poor relationships with non-native scientists, tribal mistrust of research, differences between Indigenous values and scientific methods, and low Indigenous representation at research institutions. Understanding tribal research needs is critical to foster successful research partnerships with underserved tribal communities. This study expands on a 2011 tribal research needs assessment with a survey to identify tribal natural resource professionals’ research needs, access to research findings, and interest in participating in research. Information needs identified in our survey includes forest health, water quality, culturally significant species, workforce and tribal youth development, cultural importance of water, and invasive species. Additionally, postfire response and valuation, resilience and long-term forestry, protecting and curating tribal data, and Indigenous burning were more important research needs for tribal members than for nontribal members. This study can inform forestry research planning efforts and establish ­research priorities and collaborations that are aligned with needs identified by tribal natural resource managers.Study Implications: There is a growing desire to broaden forestry research to support tribal forest management. This study shows that tribal research priorities include forest health, water quality, culturally significant species, workforce development/training, tribal youth development, cultural importance of water, and invasive species. Additionally, postfire response and valuation, resilience and long-term forestry, protecting and curating tribal data, and Indigenous burning were ranked of higher importance by tribal members than nontribal members. This study can inform federal research entities, universities, and natural resource management agencies in planning and establishing research priorities that are aligned with the needs identified by tribal resource managers.
3D photon conserving code for time-dependent general relativistic radiative transfer: CARTOON
Authors: Takahashi Mikiya M , Ohsuga Ken , Takahashi Rohta , Ogawa Takumi , Umemura Masayuki , Asahina Yuta 
Published: October 2022

ABSTRACT
We develop the three-dimensional general relativistic radiative transfer code: CARTOON (Calculation code of Authentic Radiative Transfer based On phOton Number conservation in curved space–time) which is improved from the two-dimensional code: ARTIST developed by Takahashi & Umemura (2017). In CARTOON, the frequency-integrated general relativistic radiative transfer equation is solved in a photon number-conserving manner, and the isotropic and coherent scattering in the zero angular momentum observers (ZAMO) frame and the fluid rest frame is incorporated. By calculating the average energy of photons, energy conservation of the radiation is also guaranteed. With the test calculations in two-dimensional and three-dimensional space, we have demonstrated that the wavefront propagation in black hole space–time can be correctly solved in CARTOON conserving photon numbers. The position of the wavefront coincides with the analytical solution and the number of photons remains constant until the wavefront reaches the event horizon. We also solve the radiative transfer equation on the geodesic reaching the observer’s screen. The time variation of the intensity map on the observer’s screen can be simultaneously and consistently calculated with the time variation of the radiation field around the black hole. In addition, the black hole shadow can be reproduced in moderately optically thin situations.
Consequences of dynamically unstable moons in extrasolar systems
Authors: Hansen Bradley M S 
Published: October 2022

ABSTRACT
Moons orbiting rocky exoplanets in compact orbits about other stars experience an accelerated tidal evolution, and can either merge with their parent planet or reach the limit of dynamical instability within a Hubble time. We review the parameter space over which moons become unbound, including the effects of atmospheric tides on the planetary spin. We find that such tides can change the final outcome from merger to escape, albeit over a limited parameter space. We also follow the further evolution of unbound moons, and demonstrate that the overwhelmingly most likely long-term outcome is that the unbound moon returns to collide with its original parent planet. The dust released by such a collision is estimated to reach optical depths $\sim 10^{-3}$, exhibit characteristic temperatures of a few hundred degrees kelvin, and last for a few thousand years. These properties make such events an attractive model for the emerging class of middle-aged main-sequence stars that are observed to show transient clouds of warm dust. Furthermore, a late collision between a planet and a returning moon on a hyperbolic orbit may sterilize an otherwise habitable planet.
A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles
Authors: Raskó Tamás , Pande Amit , Radscheit Kathrin , Zink Annika , Singh Manvendra , Sommer Christian , Wachtl Gerda , Kolacsek Orsolya , Inak Gizem , Szvetnik Attila , Petrakis Spyros , Bunse Mario , Bansal Vikas , Selbach Matthias , Orbán Tamás I , Prigione Alessandro , Hurst Laurence D , Izsvák Zsuzsanna 
Published: October 2022

Abstract
Although new genes can arrive from modes other than duplication, few examples are well characterized. Given high expression in some human brain subregions and a putative link to psychological disorders [e.g., schizophrenia (SCZ)], suggestive of brain functionality, here we characterize piggyBac transposable element-derived 1 (PGBD1). PGBD1 is nonmonotreme mammal-specific and under purifying selection, consistent with functionality. The gene body of human PGBD1 retains much of the original DNA transposon but has additionally captured SCAN and KRAB domains. Despite gene body retention, PGBD1 has lost transposition abilities, thus transposase functionality is absent. PGBD1 no longer recognizes piggyBac transposon-like inverted repeats, nonetheless PGBD1 has DNA binding activity. Genome scale analysis identifies enrichment of binding sites in and around genes involved in neuronal development, with association with both histone activating and repressing marks. We focus on one of the repressed genes, the long noncoding RNA NEAT1, also dysregulated in SCZ, the core structural RNA of paraspeckles. DNA binding assays confirm specific binding of PGBD1 both in the NEAT1 promoter and in the gene body. Depletion of PGBD1 in neuronal progenitor cells (NPCs) results in increased NEAT1/paraspeckles and differentiation. We conclude that PGBD1 has evolved core regulatory functionality for the maintenance of NPCs. As paraspeckles are a mammal-specific structure, the results presented here show a rare example of the evolution of a novel gene coupled to the evolution of a contemporaneous new structure.
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex
Authors: Patterson Angela , White Aidan , Waymire Elizabeth , Fleck Sophie , Golden Sarah , Wilkinson Royce A , Wiedenheft Blake , Bothner Brian 
Published: October 2022

Abstract
CRISPR RNA-guided detection and degradation of foreign DNA is a dynamic process. Viruses can interfere with this cellular defense by expressing small proteins called anti-CRISPRs. While structural models of anti-CRISPRs bound to their target complex provide static snapshots that inform mechanism, the dynamics and thermodynamics of these interactions are often overlooked. Here, we use hydrogen deuterium exchange-mass spectrometry (HDX-MS) and differential scanning fluorimetry (DSF) experiments to determine how anti-CRISPR binding impacts the conformational landscape of the type IF CRISPR RNA guided surveillance complex (Csy) upon binding of two different anti-CRISPR proteins (AcrIF9 and AcrIF2). The results demonstrate that AcrIF2 binding relies on enthalpic stabilization, whereas AcrIF9 uses an entropy driven reaction to bind the CRISPR RNA-guided surveillance complex. Collectively, this work reveals the thermodynamic basis and mechanistic versatility of anti-CRISPR-mediated immune suppression. More broadly, this work presents a striking example of how allosteric effectors are employed to regulate nucleoprotein complexes.
Effect of Blood Culture Contamination on Antibiotic Use in an Institution With Rapid Laboratory Methods and Phone-Based Clinical Follow-up of Blood Culture Results
Authors: Bloomfield Max G , O’Connor Michael J Q , Balm Michelle N D , Blackmore Tim K 
Published: October 2022

Abstract
In a multivariate analysis of 30 574 blood culture (BC) results, BC contamination was associated with only a small increase in antibiotic length of therapy compared to no-growth BCs (difference, 0.36 days [95% confidence interval, .05–.67]; P = .02). Stewardship processes at our institution appear to be effective in reducing the impact of BC contamination.
A new long-term measure of sustainable growth under uncertainty
Authors: Okabe Takuya , Yoshimura Jin 
Published: October 2022

Abstract
The trade-off between short-term success and long-term sustainability is a common subject of great importance both in the biological evolution of organisms and in the economic activities of human beings. In evolutionary biology, bet-hedging theories have described it as the trade-off between the (within-generation) arithmetic mean fitness and the (between-generation) geometric mean fitness of a genotype. Accordingly, bet-hedging strategies observed in various organisms are regarded as optimizing the geometric mean fitness. To increase the geometric mean fitness signifies to suppress the between-generation variance in the mean fitness. Thus, this view is consistent with mean-variance portfolio analysis in which the standard deviation of a portfolio is regarded as a measure of risk. In the present study, we provide yet another measure of long-term sustainability, which is based on minimization of the probability of extinction/bankruptcy that randomly varying population/asset size after a long time becomes less than a certain small value. We present results for representative examples to show that the present criterion gives a qualitatively similar but quantitatively different prediction from the traditional ones. In particular, we emphasize that maximizing survival probability (i.e. minimizing extinction probability) is equivalent neither to maximizing geometric mean fitness nor to minimizing variance in mean fitness, while these three are consistently related to each other.