bluuebunny/crossref_metadata_2025_split huggingface dataset:
DAS181 Treatment of Severe Lower Respiratory Tract Parainfluenza Virus Infection in Immunocompromised Patients: A Phase 2 Randomized, Placebo-Controlled Study
Authors: Chemaly Roy F , Marty Francisco M , Wolfe Cameron R , Lawrence Steven J , Dadwal Sanjeet , Soave Rosemary , Farthing Jason , Hawley Stephen , Montanez Paul , Hwang Jimmy , Ho Jennifer Hui-Chun , Lewis Stanley , Wang George , Boeckh Michael 
Published: February 2021

AbstractBackgroundThere are no antiviral therapies for parainfluenza virus (PIV) infections. DAS181, a sialidase fusion protein, has demonstrated activity in in vitro and in animal models of PIV.MethodsAdult immunocompromised patients diagnosed with PIV lower respiratory tract infection (LRTI) who required oxygen supplementation were randomized 2:1 to nebulized DAS181 (4.5 mg/day) or matching placebo for up to 10 days. Randomization was stratified by need for mechanical ventilation (MV) or supplemental oxygen (SO). The primary endpoint was the proportion of patients reaching clinical stability survival (CSS) defined as returning to room air (RTRA), normalization of vital signs for at least 24 hours, and survival up to day 45 from enrollment.ResultsA total of 111 patients were randomized to DAS181 (n = 74) or placebo (n = 37). CSS was achieved by 45.0% DAS181-treated patients in the SO stratum compared with 31.0% for placebo (P = .15), whereas patients on MV had no benefit from DAS181. The proportion of patients achieving RTRA was numerically higher for SO stratum DAS181 patients (51.7%) compared with placebo (34.5%) at day 28 (P = .17). In a post hoc analysis of solid organ transplant, hematopoietic cell transplantation within 1 year, or chemotherapy within 1 year, more SO stratum patients achieved RTRA on DAS181 (51.8%) compared with placebo (15.8%) by day 28 (P = .012).ConclusionsThe primary endpoint was not met, but post hoc analysis of the RTRA component suggests DAS181 may have clinical activity in improving oxygenation in select severely immunocompromised patients with PIV LRTI who are not on mechanical ventilation.Clinical Trials Registration. NCT01644877.
Comparison of Reverse-Transcription Polymerase Chain Reaction Cycle Threshold Values From Respiratory Specimens in Symptomatic and Asymptomatic Children With Severe Acute Respiratory Syndrome Coronavirus 2 Infection
Authors: Strutner John , Ramchandar Nanda , Dubey Shruti , Gamboa Mary , Vanderpool Michelle K , Mueller Teresa , Wang Wei , Cannavino Christopher , Tovar Padua Leidy , Malicki Denise , Pong Alice 
Published: February 2021

Abstract

Background
Understanding viral kinetics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is important to assess risk of transmission, manage treatment, and determine the need for isolation and protective equipment. The impact of viral load in asymptomatic infected children is important to understand transmission potential. We sought to determine whether children deemed to be asymptomatic had a difference in the polymerase chain reaction (PCR) cycle threshold (Ct) value of respiratory samples from symptomatic children with SARS-CoV-2 infection.

Methods
This was a retrospective cross-sectional study to compare PCR Ct values of children who tested positive for SARS-CoV-2 by respiratory samples collected over a 4-month period at a large tertiary care children’s hospital.

Results
We analyzed 728 children who tested positive for SARS-CoV-2 by reverse-transcription PCR (RT-PCR) from a respiratory sample over a 4-month period and for whom data were available in the electronic medical record. Overall, 71.2% of infected children were symptomatic. The mean Ct value for symptomatic patients (Ct mean, 19.9 [standard deviation, 6.3]) was significantly lower than for asymptomatic patients (Ct mean, 23.5 [standard deviation, 6.9]) (P &lt; .001; 95% confidence interval, 2.6–4.6). The mean PCR Ct value was lowest in children &lt;5 years of age.

Conclusions
In this retrospective review of children who tested positive by RT-PCR for SARS-CoV-2, the mean Ct was significantly lower in symptomatic children and was lowest in children &lt;5 years of age, indicating that symptomatic children and younger children infected with SARS-CoV-2 may have a higher viral load in the nasopharynx compared to asymptomatic children. Further studies are needed to assess the transmission potential from asymptomatic children.
Real-World Effectiveness and Safety of Ustekinumab for Ulcerative Colitis From 2 Tertiary IBD Centers in the United States
Authors: Hong Simon J , Krugliak Cleveland Noa , Akiyama Shintaro , Zullow Samantha , Yi Yangtian , Shaffer Seth R , Malter Lisa B , Axelrad Jordan E , Chang Shannon , Hudesman David P , Rubin David T 
Published: February 2021

AbstractBackgroundUstekinumab has been recently approved for the treatment of moderately to severely active ulcerative colitis (UC). The registry trials for ustekinumab in UC demonstrated efficacy and safety, but data on real-world outcomes are limited. We describe the effectiveness and safety of ustekinumab in patients with UC from 2 US tertiary inflammatory bowel disease centers.MethodsPatients with moderately to severely active UC treated with ustekinumab at NYU Langone Health (New York, New York) and University of Chicago Medical Center (Chicago, Illinois) between January 2016 and March 2020 were retrospectively included. The primary outcome was clinical remission at 3 and 12 months, defined as a partial Mayo score of ≤2, with a combined rectal bleeding and stool frequency subscore of ≤1.ResultsSixty-six UC patients were included. Ninety-two percent of patients had prior exposure to biologics or tofacitinib. Forty-three percent and 45% of patients achieved clinical remission by 3 and 12 months, respectively. Anti-TNF nonresponse and endoscopic Mayo score of 3 were negative predictors of clinical remission. Thirty-three percent of those followed for a year achieved concurrent endoscopic and histologic healing, which was significantly associated with lower partial Mayo score (P &lt; 0.01) and lower stool frequency (P = 0.02). Serious adverse events occurred in 4 (6%) patients (3 UC exacerbations, 1 vasculitis).ConclusionsIn this cohort of mostly biologic-refractory UC patients, treatment with ustekinumab achieved remission in nearly half of them at 12 months, and was associated with an overall favorable safety profile. These results are modestly better than the pivotal trials.
Phylogeny of drepanosiphine aphids sensu lato (Hemiptera, Aphidoidea) inferred from molecular and morphological data
Authors: Du Congcong , Chen Jing , Jiang Liyun , Qiao Gexia 
Published: February 2021

AbstractAs the second largest and most diverse group in the superfamily Aphidoidea, the phylogeny of drepanosiphine aphids sensu lato (s.l.) is critical for discussing the evolution of aphids. However, the taxa composition and phylogenetic relationships of drepanosiphine aphids s.l. have not been fully elucidated to date. In this study, based on total-evidence analyses combining 4 molecular genes (3 mitochondrial, COI, tRNA-Leu/COII, and CytB; 1 nuclear, EF-1ɑ) and 64 morphological and biological characteristics, the phylogeny of this group was reconstructed for the first time at the subfamily level using different datasets, parsimonies and model-based methods. All of our phylogenetic inferences clearly indicated that the drepanosiphine aphids s.l. was not a monophyletic group and seemed to support the division of the drepanosiphine aphids s.l. into different groups classified at the subfamily level. Calaphidinae was also not a monophyletic group, and Saltusaphidinae was nested within this subfamily. Drepanosiphinae was not clustered with Chaitophorinae, which was inconsistent with the previous hypothesis of a close relationship between them, illustrating that their phylogeny remains controversial. Overall, some groups of drepanosiphine aphids s.l., including Phyllaphidinae, Macropodaphidinae, Pterastheniinae, Lizeriinae, Drepanosiphinae, Spicaphidinae, Saltusaphidinae, and Calaphidinae, clustered together and might constitute the actual drepanosiphine aphids s.l. To a certain extent, our results clarified the phylogenetic relationships among drepanosiphine aphids s.l. and confirmed their taxonomic status as subfamilies.
Teacher talk in EAP classes: transition to post-liminal understanding
Authors: Pourhaji Mostafa , Sadeghi Michael 
Published: February 2021

AbstractEffective teacher talk has been reported to be dependent upon the teacher having post-liminal (higher levels of) understanding and has been operationalized as aligning one’s talk with the pedagogic purpose. In EAP classes, however, there are some instances where enacting effective teacher talk can be challenging. This article reports on one such instance by drawing on fifty-one hours of classroom video-recordings and seventeen hours of reflective meetings. It explores EAP teachers’ responses to learner initiatives, tapping into the teachers’ subject knowledge deficit. It also examines the potential of data-led dialogic reflective practice to enable teachers to skilfully manage the interacting influences of face, authority, ethics, input, and learner participation in EAP classes.
Use and non-use values to explain farmers’ motivation for the provision of animal welfare
Authors: Owusu-Sekyere Enoch , Hansson Helena , Telezhenko Evgenij 
Published: February 2021

AbstractThis paper examines how differences in motivation in terms of use and non-use values affect the choice of animal welfare improvement practices. The application is focused on Swedish dairy farmers’ preferences for different flooring systems’ attributes. Using multiple indicators and multiple causes and hybrid latent class models, the findings demonstrate that dairy farmers who favour flooring solutions that enhance farm animal welfare are motivated by a complex set of both use values relating to internal and external pressures and non-use values linked to animal freedom, ethical codes of farmers and building business-to-customer relationships. The findings imply that measures to stimulate more uptake of animal welfare improvement practices can be better targeted by using insights into motivational constructs of farmers and by adopting policy communication that captures the whole breadth of use and non-use motivational constructs held by farmers.
Stand Assessment through Lidar-Based Forest Visualization Using Immersive Virtual Environment Technology
Authors: Fujisaki Ikuko , Evans David L. , Moorhead Robert J. , Irby Derek W. , Mohammadi-Aragh Mahnas Jean , Roberts Scott D. , Gerard Patrick D. 
Published: February 2021

Abstract
This study examined the utility of light detection and ranging (lidar) remote sensing combined with immersive virtual environment technology for timber stand assessment. Lidar data were used to identify locations and extract dimensional information of trees in immature and mature loblolly pine (Pinas taeda, L) stands in northeast Mississippi. Computer visualized stands were built on the basis of lidar measurements and were projected with an interactive room-size stereoscopic display. Representational quality of lidar-based virtual forests was assessed through stand descriptions made by human subjects recruited from the Department of Forestry at Mississippi State University. Subjects examined either field-recorded videos or computer visualizations of immature and mature stands and estimated stocking, tree size class, height class, rotation stage, stand structure, and hardwood competition of each stand. Estimated stand characteristics by the two groups were compared. Significant viewer group differences were found in height class and rotation stage but not in other characteristics. Discussion includes how the immersive virtual environment technologies are potentially useful in natural resources management. Further study of economic aspects and interface development would be required to promote these technologies to an operational system.
Deriving Tree Diameter Growth and Probability of Survival Equations from Successive Diameter Distributions
Authors: Matney Thomas G. , Schultz Emily B. 
Published: February 2021

Abstract
Many growth and yield models have used statistical probability distributions to estimate the diameter distribution of a stand at any age. Equations for approximating individual tree diameter growth and survival probabilities from dbh can be derived from these models. A general procedure for determining the functions is discussed and illustrated using a loblolly pine spacing study. The results from the spacing study show that it is possible to define tree diameter growth and survival probability functions from diameter distributions with an accuracy sufficient to obtain a link between the individual tree and diameter growth and yield models.
Stand-Level Forest Structure and Avian Habitat: Scale Dependencies in Predicting Occurrence in a Heterogeneous Forest
Authors: Smith Katherine Manaras , Keeton William S. , Donovan Therese M. , Mitchell Brian 
Published: February 2021

Abstract
We explored the role of stand-level forest structure and spatial extent of forest sampling in models of avian occurrence in northern hardwood-conifer forests for two species: black-throated blue warbler (Dendroica caerulescens) and ovenbird (Seiurus aurocapillus). We estimated site occupancy from point counts at 20 sites and characterized the forest structure at these sites at three spatial extents (0.2, 3.0, and 12.0 ha). Weight of evidence was greatest for habitat models using forest stand structure at the 12.0-ha extent and diminished only slightly at the 3.0-ha extent, a scale that was slightly larger than the average territory size of both species. Habitat models characterized at the 0.2-ha extent had low support, yet are the closest in design to those used in many of the habitat studies we reviewed. These results suggest that the role of stand-level vegetation may have been underestimated in the past, which will be of interest to land managers who use habitat models to assess the suitability of habitat for species of concern.
Modeling Airtanker Flight Distance between Concurrent Fires: The Development and Use of Statistical Distribution Parameters
Authors: Greulich Francis E. 
Published: February 2021

Abstract
Airtankers, while actively engaging in initial attack, are sometimes reassigned and flown directly to another randomly occurring initial attack fire. Airtanker system planning that means to incorporate this fire-to-fire transfer activity needs information about the flight distance between these randomly located fires. Moments of the distance distribution, derived in this article, can be used to characterize and evaluate fire-to-fire airtanker dispatch within and between protection areas. A hypothetical example illustrates how a proposed change in an airtanker protection zone can affect not only airbase-to-fire flight distance but also fire-to-fire flight distance. In this example, the expected airbase-to-fire distance and the expected total transfer-flight distance are both significantly reduced, but at the same time, somewhat unexpectedly, the average fire-to-fire flight distance actually increases. The discovery and quantification of such unanticipated results can potentially influence airtanker system design. These key system design parameters can now be obtained through the exceedingly fast and accurate analytical methods presented here.
Investigation of Some Sector Sampling Statistical Properties
Authors: Smith Nick J. , Iles Kim , Raynor Kurt 
Published: February 2021

Abstract
Sector sampling is designed to sample objects in clusters or small, irregularly shaped polygons, such as variable retention patches and associated harvested areas. A number of statistical aspects of sector sampling were examined by using real data and a resampling framework. When the sector angle is selected at random, the probability of sampling each tree is the same; thus, a simple expansion factor method is all that is required to calculate tract totals and mean tree values. Standard variance formulas can then be used. For unit area estimates (such as basal area per hectare) a ratio-of-means estimator balances the areas in different-sized sectors. However, both the ratio-of-means mean and variance may be underestimated. An empirical correction to the biased variance estimator was derived. Alternatively, an unbiased and also more efficient unit area estimate can be made using a random point sector angle selection with a mean-of-ratios method. In this case standard variance formulas can again be used. A systematic sector arrangement reduced variance under an expansion factor but did not reduce variance using a ratio-of-means approach where sector area was already considered.
Artificial Regeneration of Major Oak (Quercus) Species in the Eastern United States—A Review of the Literature
Authors: Dey Daniel C. , Jacobs Douglass , McNabb Ken , Miller Gary , Baldwin V. , Foster G. 
Published: February 2021

Abstract
Although natural regeneration is often the best method for establishing new oak (Quercus spp.) stands, there are increasingly more situations in which high potential for oak regeneration failure dictates the use of artificial regeneration including direct seeding and planting seedlings. Additionally, afforestation planting programs frequently incorporate oak species. Artificial regeneration of oak stands is challenging for numerous reasons. In this article we synthesize the current state of knowledge regarding growing and planting the major oak species in the eastern United States, point out critical research gaps, and provide some general growing, planting, and stand tending guidelines and recommendations. Adequate site preparation, careful planting of healthy, genetically adapted seed or seedlings of high morphological and physiological quality, and subsequent control of competing vegetation and browse damage are necessary actions to assure regeneration success. Oak seedling survival in the early years after planting or seeding is a poor indicator of regeneration success. Successful regeneration may be defined as having a desired proportion of the oak planting stock reach dominant/codominant status in the stand. The costs of all activities required to produce a successful oak tree in the future stand should be considered in economic comparison of alternative prescriptions for oak regeneration.
Trans-acting genetic variation affects the expression of adjacent genes
Authors: Van Dyke Krisna , Lutz Sheila , Mekonnen Gemechu , Myers Chad L , Albert Frank W 
Published: February 2021

Abstract
Gene expression differences among individuals are shaped by trans-acting expression quantitative trait loci (eQTLs). Most trans-eQTLs map to hotspot locations that influence many genes. The molecular mechanisms perturbed by hotspots are often assumed to involve “vertical” cascades of effects in pathways that can ultimately affect the expression of thousands of genes. Here, we report that trans-eQTLs can affect the expression of adjacent genes via “horizontal” mechanisms that extend along a chromosome. Genes affected by trans-eQTL hotspots in the yeast Saccharomyces cerevisiae were more likely to be located next to each other than expected by chance. These paired hotspot effects tended to occur at adjacent genes that also show coexpression in response to genetic and environmental perturbations, suggesting shared mechanisms. Physical proximity and shared chromatin state, in addition to regulation of adjacent genes by similar transcription factors, were independently associated with paired hotspot effects among adjacent genes. Paired effects of trans-eQTLs can occur at neighboring genes even when these genes do not share a common function. This phenomenon could result in unexpected connections between regulatory genetic variation and phenotypes.
Innate immunity to yeast prions: Btn2p and Cur1p curing of the [URE3] prion is prevented by 60S ribosomal protein deficiency or ubiquitin/proteasome system overactivity
Authors: Bezsonov Evgeny E , Edskes Herman K , Wickner Reed B 
Published: February 2021

Abstract[URE3] is an amyloid-based prion of Ure2p, a negative regulator of poor nitrogen source catabolism in Saccharomyces cerevisiae. Overproduced Btn2p or its paralog Cur1p, in processes requiring Hsp42, cure the [URE3] prion. Btn2p cures by collecting Ure2p amyloid filaments at one place in the cell. We find that rpl4aΔ, rpl21aΔ, rpl21bΔ, rpl11bΔ, and rpl16bΔ (large ribosomal subunit proteins) or ubr2Δ (ubiquitin ligase targeting Rpn4p, an activator of proteasome genes) reduce curing by overproduced Btn2p or Cur1p. Impaired curing in ubr2Δ or rpl21bΔ is restored by an rpn4Δ mutation. No effect of rps14aΔ or rps30bΔ on curing was observed, indicating that 60S subunit deficiency specifically impairs curing. Levels of Hsp42p, Sis1p, or Btn3p are unchanged in rpl4aΔ, rpl21bΔ, or ubr2Δ mutants. Overproduction of Cur1p or Btn2p was enhanced in rpn4Δ and hsp42Δ mutants, lower in ubr2Δ strains, and restored to above wild-type levels in rpn4Δ ubr2Δ strains. As in the wild-type, Ure2N-GFP colocalizes with Btn2-RFP in rpl4aΔ, rpl21bΔ, or ubr2Δ strains, but not in hsp42Δ. Btn2p/Cur1p overproduction cures [URE3] variants with low seed number, but seed number is not increased in rpl4aΔ, rpl21bΔ or ubr2Δ mutants. Knockouts of genes required for the protein sorting function of Btn2p did not affect curing of [URE3], nor did inactivation of the Hsp104 prion-curing activity. Overactivity of the ubiquitin/proteasome system, resulting from 60S subunit deficiency or ubr2Δ, may impair Cur1p and Btn2p curing of [URE3] by degrading Cur1p, Btn2p or another component of these curing systems.
Seismicity in the central and southeastern United States due to upper mantle heterogeneities
Authors: Saxena Arushi , Choi Eunseo , Powell Christine A , Aslam Khurram S 
Published: February 2021

SUMMARYSources of stress responsible for earthquakes occurring in the Central and Eastern United States (CEUS) include not only far-field plate boundary forces but also various local contributions. In this study, we model stress fields due to heterogeneities in the upper mantle beneath the CEUS including a high-velocity feature identified as a lithospheric drip in a recent regional P-wave tomography study. We calculate velocity and stress distributions from numerical models for instantaneous 3-D mantle flow. Our models are driven by the heterogeneous density distribution based on a temperature field converted from the tomography study. The temperature field is utilized in a composite rheology, assumed for the numerical models. We compute several geodynamic quantities with our numerical models: dynamic topography, rate of dynamic topography, gravitational potential energy (GPE), differential stress, and Coulomb stress. We find that the GPE, representative of the density anomalies in the lithosphere, is an important factor for understanding the seismicity of the CEUS. When only the upper mantle heterogeneities are included in a model, differential and Coulomb stress for the observed fault geometries in the CEUS seismic zones acts as a good indicator to predict the seismicity distribution. Our modelling results suggest that the upper mantle heterogeneities and structure below the CEUS have stress concentration effects and are likely to promote earthquake generation at preexisting faults in the region’s seismic zones. Our results imply that the mantle flow due to the upper-mantle heterogeneities can cause stress perturbations, which could help explain the intraplate seismicity in this region.