bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous Galerkin schemes for semiexplicit differential-algebraic equations
Authors: Altmann Robert , Herzog Roland 
Published: April 2021

Abstract
This paper studies a new class of integration schemes for the numerical solution of semiexplicit differential-algebraic equations of differentiation index 2 in Hessenberg form. Our schemes provide the flexibility to choose different discretizations in the differential and algebraic equations. At the same time they are designed to have a property called variational consistency, i.e., the choice of the discretization of the constraint determines the discretization of the Lagrange multiplier. For the case of linear constraints we prove convergence of order $r+1$, both for the state and the multiplier if piecewise polynomials of order $r$ are used. These results are also verified numerically.
Evaluation of the GENE-UP® EHEC Detection Method for the Detection of Enterohemorrhagic E. coli in Select Foods: Collaborative Study: First Action Method 2020.06
Authors: Johnson Ronald , Mills John , Pittet Jean-Louis , Rannou Maryse , Bird Patrick 
Published: April 2021

Abstract

Background
The GENE-UP® EHEC assay (Performance Tested MethodSM 121806) is a real-time PCR molecular detection method that utilizes fluorescence resonance energy transfer proprietary hybridization probes for the rapid detection of enterohemorrhagic Escherichia coli (EHEC) in select foods.

Objective
The purpose of this validation was to evaluate the method’s interlaboratory performance and submit the results to AOAC INTERNATIONAL for adoption as a First Action Official Method of AnalysisSM for the detection of EHEC in select foods.

Method
The GENE-UP method was evaluated in a multi-laboratory study as part of the MicroVal VALIDATION certification process using unpaired test portions for one food matrix, raw ground beef (85% lean). Collaborators evaluated the candidate method using either an automated or manual lysis procedure. The candidate method was compared to the ISO/TS 13136:2012 method. Data from 17 participants from 15 laboratories throughout the European Union were evaluated. Three levels of contamination were evaluated: a non-inoculated control level (0 CFU/test portion), a low contamination level (∼1 CFU/test portion), and a high contamination level (∼10 CFU/test portion). Data from the study were analyzed according to the probability of detection (POD) statistical model.

Results
The difference in laboratory probability of detection (dLPODC) values with 95% confidence interval between the candidate and reference method results were –0.01 (–0.04, 0.02), 0.23 (0.07, 0.39), and 0.06 (0.01, 0.12) for the non-inoculated, low, and high contamination levels, respectively.

Conclusions
For the candidate method, values obtained for repeatability and reproducibility were similar to the reference method and indicated minimal variation between samples or between laboratories. No discrepant results (false positive or false negative) were observed for each contamination. A statistical difference was calculated between the candidate and reference method at the low and high inoculation levels, with the candidate method detecting a higher number of positive samples indicating a higher sensitivity than the reference method. No differences in the recovery of the target analyte were observed between the manual and automated lysis procedures.

Highlights
The GENE-UP EHEC Detection Method provides end users a rapid, easy-to-use workflow for the detection of EHEC in food matrixes.
Changes in nutrient balance, methane emissions, physiologic biomarkers and production performance in goats fed different forage-to-concentrate ratios during lactation
Authors: Fernández Carlos , Hernández Alberto , Gomis-Tena Julio , Loor Juan J 
Published: April 2021

Abstract
The objective was to determine the effect forage to concentrate (F:C) ratio and stage of lactation on methane emissions, digestibility, nutrient balance, lactation performance, and metabolic responses in lactating goats. Twenty Murciano-Granadina dairy goats were used in an experiment divided into three periods: early (30 d), mid (100 d) and late (170 d) lactation. All goats were fed a diet with 35:65 F:C (FCL) during early-lactation. Then, one group (n = 10 goats) remained on FCL through mid and late-lactation while the other group (n = 10 goats) was fed a diet with 50:50 F:C at mid-lactation (FCM) and 65:35 (FCH) at late lactation. A greater proportion of concentrate in the diet was associated with greater overall intake and digestibility (P &lt; 0.05). Energy balance was negative in early-lactation (-77 kJ/kg of BW 0.75, on average) and positive for FCL at mid and late-lactation (13 and 35 kJ/kg of BW 0.75, respectively). Goats fed FCM and FCH maintained negative energy balance throughout lactation. Plasma concentrations of non-esterified fatty acids (NEFA) at mid-lactation were greater for FCM than FCL (680 mEq/L), and at late-lactation concentrations were greater for FCH and FCL (856 mEq/L). A similar response was detected for plasma ß-Hydroxybutyrate (BHB). Methane emission was greater (P &lt; 0.05) for FCM than FCH (1.7 g CH4/d). This study demonstrated that differences in F:C across stages of lactation lead to distinct metabolic responses at the level of the rumen and tissues.
Direct and biometrical estimates of the closing force of major claws of the sand fiddler crab Leptuca pugilator (Bosc, 1801) (Decapoda: Brachyura: Ocypodidae): Support for the weakening combatant hypothesis
Authors: Levinton Jeffrey S , Arena Brooke 
Published: April 2021

Abstract
Many conclusions concerning the functional biology of crab claws rely upon biometrical estimates of closing force, based upon measures of muscle cross-sectional area and mechanical advantage. Fiddler crab closing force patterns show variation with body size, claw size, location of the opposing claw tips, and physiological condition, so we have measured closing force of the sand fiddler crab Leptuca pugilator (Bosc, 1801) as a function of claw size, force exerted at claw tips, and at the commonly well-developed pollex tooth. Leptuca pugilator has an elongated claw with gracile dactyl and pollex. As predicted by biometrical proportions, closing force is greater at the pollex tooth than at the claw tip. The pollex tooth does shift with increasing claw size in relative position toward the claw hinge. Mechanical advantage at the pollex tooth and dactyl tip both decline with increasing claw length. But there is no difference in slope of log closing force as a function of log claw length between the pollex position and terminus of the dactyl, which demonstrates that force exerted at the pollex tooth has no impact on proportional change in closing force with increasing claw size. The log-log slope is ~0.9, reflecting the proportionally decreasing muscle cross-sectional area and lowering mechanical advantage with increasing claw size. For both the pollex tooth and the claw tip, mechanical advantage decreases very slightly with increasing claw size, but closing force proportionally decreases with increasing claw size, supporting the weakening combatant hypothesis for this species.
Alternative Formulations of Trap Lures for Operational Detection, Population Monitoring, and Outbreak Forecasting of Southern Pine Beetle in the United States
Authors: Sullivan Brian T , Shepherd William P , Nowak John T , Clarke Stephen R , Merten Paul R , Billings Ronald F , Upton William W , Riggins John J , Brownie Cavell 
Published: April 2021

Abstract
The southern pine beetle, Dendroctonus frontalis Zimmermann (Coleoptera: Curculionidae: Scolytinae) is a major destructive pest of Pinus L. In the southeastern United States, numbers of this species and a major predator, Thanasimus dubius (Fabricius) (Coleoptera: Cleridae), captured during an annual springtime trapping survey are used to make forecasts of the likelihood and severity of an outbreak during the following summer. We investigated responses by both species to six lure formulations to evaluate their suitability for the survey and allow integration of historical data sets produced with differing lure compositions. Trapping trials were performed at four locations across three states (Louisiana, Mississippi, and Alabama) during spring, and at these and one additional location (North Carolina) in fall 2016. All lures included the pheromone component frontalin. Southern pine beetle preferred lures that additionally included the pheromone component endo-brevicomin and turpentine as a source of host odors (rather than a 7:3 mixture of monoterpenes alpha- and beta-pinene). Thanasimus dubius displayed little discrimination among lure compositions. Lure preferences by southern pine beetle did not differ significantly among locations in spring but were influenced by season. Gas chromatography (GC)-electroantennographic detection analyses with southern pine beetle and GC-mass spectrometry identified numerous known and potential semiochemicals that distinguished volatiles released by the tested host odor devices. The lure combination that included endo-brevicomin and alpha/beta-pinene is recommended for the trapping survey because of its high sensitivity for southern pine beetle and potential for greater data integrity resulting from its reproducible composition.
A Special Collection: Drones to Improve Insect Pest Management
Authors: Moses-Gonzales Nathan , Brewer Michael J 
Published: April 2021

Abstract
The Special Collection Drones to Improve Insect Pest Management presents research and development of unmanned (or uncrewed) aircraft system (UAS, or drone) technology to improve insect pest management. The articles bridge from more foundational studies (i.e., evaluating and refining abilities of drones to detect pest concerns or deliver pest management materials) to application-oriented case studies (i.e., evaluating opportunities and challenges of drone use in pest management systems). The collection is composed of a combination of articles presenting information first-time published, and a selection of articles previously published in Journal of Economic Entomology (JEE). Articles in the Collection, as well as selected citations of articles in other publications, reflect the increase in entomology research using drones that has been stimulated by advancement in drone structural and software engineering such as autonomous flight guidance; in- and post-flight data storage and processing; and companion advances in spatial data management and analyses including machine learning and data visualization. The Collection is also intended to stimulate discussion on the role of JEE as a publication venue for future articles on drones as well as other cybernectic-physical systems, big data analyses, and deep learning processes. While these technologies have their genesis in fields arguably afar from the discipline of entomology, we propose that interdisciplinary collaboration is the pathway for applications research and technology transfer leading to an acceleration of research and development of these technologies to improve pest management.
Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field
Authors: Schweizer Rena M , Saarman Norah , Ramstad Kristina M , Forester Brenna R , Kelley Joanna L , Hand Brian K , Malison Rachel L , Ackiss Amanda S , Watsa Mrinalini , Nelson Thomas C , Beja-Pereira Albano , Waples Robin S , Funk W Chris , Luikart Gordon 
Published: April 2021

AbstractA current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors—and beyond—to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.
Tarski’s Undefinability Theorem and the Diagonal Lemma
Authors: Salehi Saeed 
Published: April 2021

AbstractWe prove the equivalence of the semantic version of Tarski’s theorem on the undefinability of truth with the semantic version of the diagonal lemma and also show the equivalence of a syntactic version of Tarski’s undefinability theorem with a weak syntactic diagonal lemma. We outline two seemingly diagonal-free proofs for these theorems from the literature and show that the syntactic version of Tarski’s theorem can deliver Gödel–Rosser’s incompleteness theorem.
Outcomes of salvage fractionated re-irradiation combined with bevacizumab for recurrent high-grade gliomas that progressed after bevacizumab treatment**
Authors: Yonezawa Hajime , Ohno Makoto , Igaki Hiroshi , Miyakita Yasuji , Takahashi Masamichi , Tamura Yukie , Shima Satoshi , Matsushita Yuko , Ichimura Koichi , Narita Yoshitaka 
Published: April 2021

Abstract

Background
There is no standard treatment for patients with recurrent high-grade gliomas who progress after bevacizumab treatment. We evaluated the outcomes of re-irradiation combined with bevacizumab for patients refractory to bevacizumab.

Methods
Between January 2015 and September 2019, patients with progression after bevacizumab treatment were treated with re-irradiation combined with bevacizumab (25 Gy in five fractions).

Results
Fourteen patients [glioblastoma, isocitrate dehydrogenase (IDH) wild type (N = 6), glioblastoma, IDH mutant (N = 4), anaplastic astrocytoma, IDH wild type (N = 1), anaplastic astrocytoma, IDH mutant (N = 1), glioblastoma, not otherwise specified (N = 1) and radiologically diagnosed brainstem glioma (N = 1)] were included in this study. The median survival and progression-free survival times after re-irradiation combined with bevacizumab were 6.1 and 3.8 months, respectively. The 6-month survival and progression-free survival rates were 54.5 and 15.7%, respectively. Patients with a Karnofsky performance status of ≥70 tended to have longer median survival time (9.3 vs. 5.4 months, respectively; P = 0.058) and had a significantly longer median progression-free survival time (4.2 vs. 3.7 months, respectively; P = 0.046) than those with a Karnofsky performance status of &lt;70. Four patients (28.6%) achieved a complete or partial radiological response, and three patients (21.4%) had an improved Karnofsky performance status after re-irradiation combined with bevacizumab. Grade 3/4 toxicities included leukopenia in four patients (28.6%), hypertension in three (21.4%), proteinuria in one (7.1%) and gastrointestinal hemorrhage in one (7.1%).

Conclusions
Re-irradiation combined with bevacizumab for patients with recurrent high-grade gliomas who progress after bevacizumab treatment was feasible. Re-irradiation combined with bevacizumab is a potential treatment option, especially for patients with a Karnofsky performance status of ≥70.
The stellar mass function and evolution of the density profile of galaxy clusters from the Hydrangea simulations at 0 &lt; z &lt; 1.5
Authors: Ahad Syeda Lammim , Bahé Yannick M , Hoekstra Henk , van der Burg Remco F J , Muzzin Adam 
Published: April 2021

ABSTRACT
Galaxy clusters are excellent probes to study the effect of environment on galaxy formation and evolution. Along with high-quality observational data, accurate cosmological simulations are required to improve our understanding of galaxy evolution in these systems. In this work, we compare state-of-the-art observational data of massive galaxy clusters ($\gt 10^{14}\, \textrm {M}_{\odot }$) at different redshifts (0 &lt; z &lt; 1.5) with predictions from the Hydrangea suite of cosmological hydrodynamic simulations of 24 massive galaxy clusters ($\gt 10^{14}\, \textrm {M}_{\odot }$ at z = 0). We compare three fundamental observables of galaxy clusters: the total stellar mass-to-halo mass ratio, the stellar mass function, and the radial mass density profile of the cluster galaxies. In the first two of these, the simulations agree well with the observations, albeit with a slightly too high abundance of $M_\star \lesssim 10^{10} \, \mathrm{M}_\odot$ galaxies at z ≳ 1. The Navarro–Frenk–White concentrations of cluster galaxies increase with redshift, in contrast to the decreasing dark matter (DM) halo concentrations. This previously observed behaviour is therefore due to a qualitatively different assembly of the smooth DM halo compared to the satellite population. Quantitatively, we, however, find a discrepancy in that the simulations predict higher stellar concentrations than observed at lower redshifts (z &lt; 0.3), by a factor of ≈2. This may be due to selection bias in the simulations, or stem from shortcomings in the build-up and stripping of their inner satellite halo.
Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes
Authors: Wang Jianhua , Han Guan-Zhu 
Published: April 2021

Abstract
LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.
Reverse Plasticity Underlies Rapid Evolution by Clonal Selection within Populations of Fibroblasts Propagated on a Novel Soft Substrate
Authors: Purkayastha Purboja , Pendyala Kavya , Saxena Ayush S , Hakimjavadi Hesamedin , Chamala Srikar , Dixit Purushottam , Baer Charles F , Lele Tanmay P 
Published: April 2021

Abstract
Mechanical properties such as substrate stiffness are a ubiquitous feature of a cell’s environment. Many types of animal cells exhibit canonical phenotypic plasticity when grown on substrates of differing stiffness, in vitro and in vivo. Whether such plasticity is a multivariate optimum due to hundreds of millions of years of animal evolution, or instead is a compromise between conflicting selective demands, is unknown. We addressed these questions by means of experimental evolution of populations of mouse fibroblasts propagated for approximately 90 cell generations on soft or stiff substrates. The ancestral cells grow twice as fast on stiff substrate as on soft substrate and exhibit the canonical phenotypic plasticity. Soft-selected lines derived from a genetically diverse ancestral population increased growth rate on soft substrate to the ancestral level on stiff substrate and evolved the same multivariate phenotype. The pattern of plasticity in the soft-selected lines was opposite of the ancestral pattern, suggesting that reverse plasticity underlies the observed rapid evolution. Conversely, growth rate and phenotypes did not change in selected lines derived from clonal cells. Overall, our results suggest that the changes were the result of genetic evolution and not phenotypic plasticity per se. Whole-transcriptome analysis revealed consistent differentiation between ancestral and soft-selected populations, and that both emergent phenotypes and gene expression tended to revert in the soft-selected lines. However, the selected populations appear to have achieved the same phenotypic outcome by means of at least two distinct transcriptional architectures related to mechanotransduction and proliferation.
Transcriptome Analysis in Yeast Reveals the Externality of Position Effects
Authors: Gui Qian , Deng Shuyun , Zhou ZhenZhen , Cao Waifang , Zhang Xin , Shi Wenjun , Cai Xiujuan , Jiang Wenbing , Cui Zifeng , Hu Zheng , Chen Xiaoshu 
Published: April 2021

Abstract
The activity of a gene newly integrated into a chromosome depends on the genomic context of the integration site. This “position effect” has been widely reported, although the other side of the coin, that is, how integration affects the local chromosomal environment, has remained largely unexplored, as have the mechanism and phenotypic consequences of this “externality” of the position effect. Here, we examined the transcriptome profiles of approximately 250 Saccharomyces cerevisiae strains, each with GFP integrated into a different locus of the wild-type strain. We found that in genomic regions enriched in essential genes, GFP expression tended to be lower, and the genes near the integration site tended to show greater expression reduction. Further joint analysis with public genome-wide histone modification profiles indicated that this effect was associated with H3K4me2. More importantly, we found that changes in the expression of neighboring genes, but not GFP expression, significantly altered the cellular growth rate. As a result, genomic loci that showed high GFP expression immediately after integration were associated with growth disadvantages caused by elevated expression of neighboring genes, ultimately leading to a low total yield of GFP in the long run. Our results were consistent with competition for transcriptional resources among neighboring genes and revealed a previously unappreciated facet of position effects. This study highlights the impact of position effects on the fate of exogenous gene integration and has significant implications for biological engineering and the pathology of viral integration into the host genome.