bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of the Thermo Scientific™ SARS-CoV-2 RT-PCR Detection Workflow for the Detection of SARS-CoV-2 from Stainless-Steel Environmental Surface Swabs: AOAC Performance Tested MethodSM 012103
Authors: Stephenson Patrick , Crabtree David , Evans Katharine , Salavirta Heikki , Brzoska Pius , Leonte Ana-Maria , Manolis Amanda , Sohier Daniele 
Published: April 2021

Abstract

Background
The Thermo Scientific™ SARS-CoV-2 reverse transcription–polymerase chain reaction (RT-PCR) Detection Workflow, packaged with Applied Biosystems™ TaqMan™ 2019-nCoV Assay Kit v1 targets three different SARS-CoV-2 genomic regions in a single RT-PCR reaction.

Objective
To validate the Thermo Scientific SARS-CoV-2 RT-PCR Workflow, for the detection of SARS-CoV-2 virus on stainless-steel surfaces as part of the AOAC Performance Tested MethodSM Emergency Response Validation program.

Method
The Applied Biosystems TaqMan 2019-nCoV Assay Kit v1, as part of the Thermo Scientific SARS-CoV-2 RT-PCR Workflow, was evaluated for specificity using in silico analysis of 15 764 SARS-CoV-2 sequences and 65 exclusivity organisms. The Thermo Scientific SARS-CoV-2 RT-PCR Workflow was evaluated in an unpaired study for one environmental surface (stainless steel) and compared to the U.S. Centers for Disease Control and Prevention 2019-Novel Coronavirus RT-PCR Diagnostic Panel, Instructions for Use (Revision 4, Effective 6/12/2020).

Results
In silico analysis showed that, of the 15 756 target SARS-CoV-2 genomes analyzed, 99% of the strains/isolates are perfectly matched to at least two of the three assays, and more than 90% have 100% homology to all three assays (ORF1ab, N-gene, S-gene) in the SARS-CoV-2 Kit. None of the 65 non-target strain genomes analyzed showed matching sequences. In the matrix study, the Thermo Scientific SARS-CoV-2 workflow showed comparable detection to the centers of disease control and prevention (CDC) method.

Conclusions
The Thermo Scientific SARS-CoV-2 RT-PCR Workflow is an effective procedure for detection of RNA from SARS-CoV-2 virus from stainless steel.

Highlights
The workflow provides equivalent performance results with the two tested RNA extraction platforms and the two tested RT-PCR instruments.
Natural diet of the endemic freshwater crab Aegla castro Schmitt, 1942 (Decapoda: Anomura: Aeglidae)
Authors: de Almeida Karin C R , Moreira João M N C , Páez Fernanda P , Marçal Ingrid C , Teixeira Gustavo M 
Published: April 2021

Abstract
We characterized the natural diet and feeding dynamics of Aegla castroSchmitt, 1942 (Aeglidae), an endemic freshwater crab. Research was undertaken on the trophic spectrum of the species by analyzing the stomach contents of individuals collected in a stream in southeastern Brazil, and evaluating the diet through the index of relative importance (IRI). Seasonal and circadian variations in diet composition were analyzed, and the feeding dynamics investigated through repletion index (RI) analysis. We analyzed a total of 240 stomachs and identified 20 main food categories of the diet, which were studied throughout the seasons. Aegla castro maintained a constant RI throughout the year, with a peak of food activity between midnight (00) and 0600. The species was characterized as an omnivorous generalist and opportunist. The high overlay in the diet composition of adults of both sexes and juveniles indicates that they share the same food resources, even though they seem to exploit them in different quantities and frequencies. Future research should focus on the species of Aegla whose diets have not yet been described, and use available data to inform trophic network analyses and models.
Histopathological atlas of desmoplastic reaction characterization in colorectal cancer
Authors: Ueno Hideki , Kajiwara Yoshiki , Ajioka Yoich , Sugai Tamotsu , Sekine Shigeki , Ishiguro Megumi , Takashima Atsuo , Kanemitsu Yukihide 
Published: April 2021

Abstract
Emergent scientific evidence indicates the central role of cancer-associated fibroblasts in determining whether the microenvironment of cancer works as friend or foe of the host; however, there is no unified histological evaluation framework of fibrotic stroma in colorectal cancers. Myxoid stroma and keloid-like collagen are site-specific histopathological features generated by cancer-associated fibroblasts, which appear exclusively in the tumor front during desmoplastic reaction. On the basis of these two stromal components, desmoplastic reaction is categorized into three patterns—immature, intermediate and mature—using hematoxylin and eosin staining. In January 2020, a prospective randomized clinical trial, JCOG1805, to elucidate the value of adjuvant chemotherapy in stage II colorectal cancer patients with pathological risk factors of recurrence was launched in Japan, in which intermediate/immature desmoplastic reaction is one of the four risk factors selected as inclusion criteria. This paper covers the diagnostic criteria for the desmoplastic reaction classification being used in the JCOG1805 study.
Comparative Effectiveness of Digital Breast Tomosynthesis for Breast Cancer Screening Among Women 40-64 Years Old
Authors: Richman Ilana B , Long Jessica B , Hoag Jessica R , Upneja Akhil , Hooley Regina , Xu Xiao , Kunst Natalia , Aminawung Jenerius A , Kyanko Kelly A , Busch Susan H , Gross Cary P 
Published: April 2021

Abstract

Background
Digital breast tomosynthesis (DBT) may have a higher cancer detection rate and lower recall compared with 2-dimensional (2 D) mammography for breast cancer screening. The goal of this study was to evaluate screening outcomes with DBT in a real-world cohort and to characterize the population health impact of DBT as it is widely adopted.

Methods
This observational study evaluated breast cancer screening outcomes among women screened with 2 D mammography vs DBT. We used deidentified administrative data from a large private health insurer and included women aged 40-64 years screened between January 2015 and December 2017. Outcomes included recall, biopsy, and incident cancers detected. We used 2 complementary techniques: a patient-level analysis using multivariable logistic regression and an area-level analysis evaluating the relationship between population-level adoption of DBT use and outcomes. All statistical tests were 2-sided.

Results
Our sample included 7 602 869 mammograms in 4 580 698 women, 27.5% of whom received DBT. DBT was associated with modestly lower recall compared with 2 D mammography (113.6 recalls per 1000 screens, 99% confidence interval [CI] = 113.0 to 114.2 vs 115.4, 99% CI = 115.0 to 115.8, P &lt; .001), although younger women aged 40-44 years had a larger reduction in recall (153 recalls per 1000 screens, 99% CI = 151 to 155 vs 164 recalls per 1000 screens, 99% CI = 163 to 166, P &lt; .001). DBT was associated with higher biopsy rates than 2 D mammography (19.6 biopsies per 1000 screens, 99% CI = 19.3 to 19.8 vs 15.2, 99% CI = 15.1 to 15.4, P &lt; .001) and a higher cancer detection rate (4.9 incident cancers per 1000 screens, 99% CI = 4.7 to 5.0 vs 3.8, 99% CI = 3.7 to 3.9, P &lt; .001). Point estimates from the area-level analysis generally supported these findings.

Conclusions
In a large population of privately insured women, DBT was associated with a slightly lower recall rate than 2 D mammography and a higher cancer detection rate. Whether this increased cancer detection improves clinical outcomes remains unknown.
Wedding of Molecular Alterations and Immune Checkpoint Blockade: Genomics as a Matchmaker
Authors: Fountzilas Elena , Kurzrock Razelle , Vo Henry Hiep , Tsimberidou Apostolia-Maria 
Published: April 2021

Abstract
The development of checkpoint blockade immunotherapy has transformed the medical oncology armamentarium. But despite its favorable impact on clinical outcomes, immunotherapy benefits only a subset of patients, and a substantial proportion of these individuals eventually manifest resistance. Serious immune-related adverse events and hyperprogression have also been reported. It is therefore essential to understand the molecular mechanisms and identify the drivers of therapeutic response and resistance. In this review, we provide an overview of the current and emerging clinically relevant genomic biomarkers implicated in checkpoint blockade outcome. US Food and Drug Administration–approved molecular biomarkers of immunotherapy response include mismatch repair deficiency and/or microsatelliteinstability and tumor mutational burden of at least 10 mutations/megabase. Investigational genomic-associated biomarkers for immunotherapy response include alterations of the following genes/associated pathways: chromatin remodeling (ARID1A, PBRM1, SMARCA4, SMARCB1, BAP1), major histocompatibility complex, specific (eg, ultraviolet, APOBEC) mutational signatures, T-cell receptor repertoire, PDL1, POLE/POLD1, and neo-antigens produced by the mutanome, those potentially associated with resistance include β2-microglobulin, EGFR, Keap1, JAK1/JAK2/interferon-gamma signaling, MDM2, PTEN, STK11, and Wnt/Beta-catenin pathway alterations. Prospective clinical trials are needed to assess the role of a composite of these biomarkers to optimize the implementation of precision immunotherapy in patient care.
Excision of an unusual tumour of oncocytic origin: a case report
Authors: Howden William B , Gunaratne Dakshika A , Gallagher Richard M 
Published: April 2021

Abstract
This case presents a 46-year-old woman presented with a 5-month history of a gradually enlarging, non-painful swelling her right medial canthus, with magnetic resonance imaging demonstrating a large tumour of her lacrimal sac. The lesion was subsequently excised and the histopathological diagnosis made of a rare primary oncocytoma of the lacrimal sac.
MYB transcription factors GmMYBA2 and GmMYBR function in a feedback loop to control pigmentation of seed coat in soybean
Authors: Gao Ruifang , Han Taotao , Xun Hongwei , Zeng Xiangsheng , Li Penghui , Li Yueqing , Wang Yanan , Shao Yan , Cheng Xin , Feng Xianzhong , Zhao Jian , Wang Li , Gao Xiang 
Published: April 2021

Abstract
Soybean has undergone extensive selection pressures for seed nutrient composition and seed color during domestication, but the major genetic loci controlling seed coat color have not been completely understood, and the transcriptional regulation relationship among the loci remains elusive. Here, two major regulators, GmMYBA2 and GmMYBR, were functionally characterized as an anthocyanin activator and repressor, respectively. Ectopic expression of GmMYBA2 in soybean hairy roots conferred the enhanced accumulation of delphinidin and cyanidin types of anthocyanins in W1t and w1T backgrounds, respectively, through activating anthocyanin biosynthetic genes in the reported loci. The seed coat pigmentation of GmMYBA2-overexpressing transgenic plants in the W1 background mimicked the imperfect black phenotype (W1/w1, i, R, t), suggesting that GmMYBA2 was responsible for the R locus. Molecular and biochemical analysis showed that GmMYBA2 interacted with GmTT8a to directly activate anthocyanin biosynthetic genes. GmMYBA2 and GmMYBR might form a feedback loop to fine-tune seed coat coloration, which was confirmed in transgenic soybeans. Both GmTT8a and GmMYBR that were activated by GmMYBA2 in turn enhanced and obstructed the formation of the GmMYBA2–GmTT8a module, respectively. The results revealed the sophisticated regulatory network underlying the soybean seed coat pigmentation loci and shed light on the understanding of the seed coat coloration and other seed inclusions.
Transcriptomic, proteomic, and physiological studies reveal key players in wheat nitrogen use efficiency under both high and low nitrogen supply
Authors: Meng Xiaodan , Wang Xiaochun , Zhang Zhiyong , Xiong Shuping , Wei Yihao , Guo Jianbiao , Zhang Jie , Wang Lulu , Ma Xinming , Tegeder Mechthild 
Published: April 2021

AbstractThe effective use of available nitrogen (N) to improve crop grain yields provides an important strategy to reduce environmental N pollution and promote sustainable agriculture. However, little is known about the common genetic basis of N use efficiency (NUE) at varying N availability. Two wheat (Triticum aestivum L.) cultivars were grown in the field with high, moderate, and low N supply. Cultivar Zhoumai 27 outperformed Aikang 58 independent of the N supply and showed improved growth, canopy leaf area index, flag leaf surface area, grain number, and yield, and enhanced NUE due to both higher N uptake and utilization efficiency. Further, transcriptome and proteome analyses were performed using flag leaves that provide assimilates for grain growth. The results showed that many genes or proteins that are up- or down-regulated under all N regimes are associated with N and carbon metabolism and transport. This was reinforced by cultivar differences in photosynthesis, assimilate phloem transport, and grain protein/starch yield. Overall, our study establishes that improving NUE at both high and low N supply requires distinct adjustments in leaf metabolism and assimilate partitioning. Identified key genes/proteins may individually or concurrently regulate NUE and are promising targets for maximizing crop NUE irrespective of the N supply.
Modelling synchrotron self-Compton and Klein–Nishina effects in gamma-ray burst afterglows
Authors: Jacovich Taylor E , Beniamini Paz , van der Horst Alexander J 
Published: April 2021

ABSTRACT
We present an implementation of a self-consistent way of modelling synchrotron self-Compton (SSC) effects in gamma-ray burst afterglows, with and without approximated Klein–Nishina suppressed scattering for the afterglow modelling code boxfit, which is currently based on pure synchrotron emission. We discuss the changes in spectral shape and evolution due to SSC effects, and comment on how these changes affect physical parameters derived from broad-band modelling. We show that SSC effects can have a profound impact on the shape of the X-ray light curve using simulations including these effects. This leads to data that cannot be simultaneously fit well in both the X-ray and radio bands when considering synchrotron-only fits, and an inability to recover the correct physical parameters, with some fitted parameters deviating orders of magnitude from the simulated input parameters. This may have a significant impact on the physical parameter distributions based on previous broad-band modelling efforts.
The rare X-ray flaring activity of the ultraluminous X-ray source NGC 4559 X7
Authors: Pintore Fabio , Motta S , Pinto C , Bernardini M G , Rodriguez-Castillo G , Salvaterra R , Israel G L , Esposito P , Ambrosi E , Salvaggio C , Zampieri L , Wolter A 
Published: April 2021

ABSTRACT
Ultraluminous X-ray sources are considered amongst the most extremely accreting objects in the local Universe. The recent discoveries of pulsating neutron stars in ULXs strengthened the scenario of highly super-Eddington accretion mechanisms on stellar mass compact objects. In this work, we present the first long-term light curve of the source NGC 4559 X7 using all the available Swift/XRT, XMM–Newton, Chandra, and NuSTAR data. Because of the high quality 2019 XMM–Newton and NuSTAR observations, we investigated in an unprecedented way the spectral and temporal properties of NGC 4559 X7. The source displayed flux variations of up to an order of magnitude and an unusual flaring activity. We modelled the spectra from NGC 4559 X7 with a combination of two thermal components, testing also the addition of a further high energy cut-off power law. We observed a spectral hardening associated with a luminosity increase during the flares, and a spectral softening in the epochs far from the flares. Narrow absorption and emission lines were also found in the RGS spectra, suggesting the presence of an outflow. Furthermore, we measured hard and (weak) soft lags with magnitudes of a few hundreds of seconds whose origin is possibly due to the accretion flow. We interpret the source properties in terms of a super-Eddington accretion scenario assuming the compact object is either a light stellar mass black hole or a neutron star.
Large dust fractions can prevent the propagation of soundwaves
Authors: David-Cléris Timothée , Laibe Guillaume 
Published: April 2021

ABSTRACT
Dust plays a central role in several astrophysical processes. Hence, the need of dust/gas numerical solutions, and analytical problems to benchmark them. In the seminal dustywave problem, we discover a regime where sound waves cannot propagate through the mixture above a large critical dust fraction. We characterize this regime analytically, making it of use for testing accuracy of numerical solvers at large dust fractions.
Physical origin of the non-physical spin evolution of MAXI J1820 + 070
Authors: Guan J , Tao L , Qu J L , Zhang S N , Zhang W , Zhang S , Ma R C , Ge M Y , Song L M , Lu F J , Li T P , Xu Y P , Chen Y , Cao X L , Liu C Z , Zhang L , Wang Y N , Chen Y P , Bu Q C , Cai C , Chang Z , Chen L , Chen T X , Chen Y B , Cui W W , Du Y Y , Gao G H , Gao H , Gu Y D , Guo C C , Han D W , Huang Y , Huo J , Jia S M , Jiang W C , Jin J , Kong L D , Li B , Li C K , Li G , Li W , Li X , Li X B , Li X F , Li Z W , Liang X H , Liao J Y , Liu B S , Liu H W , Liu H X , Liu X J , Lu X F , Luo Q , Luo T , Ma X , Meng B , Nang Y , Nie J Y , Ou G , Ren X Q , Sai N , Song X Y , Sun L , Tan Y , Wang C , Wang L J , Wang P J , Wang W S , Wang Y S , Wen X Y , Wu B B , Wu B Y , Wu M , Xiao G C , Xiao S , Xiong S L , Yang R J , Yang S , Yang Y J , Yang Y J , Yi Q B , Yin Q Q , You Y , Zhang F , Zhang H M , Zhang J , Zhang P , Zhang W C , Zhang Y F , Zhang Y H , Zhao H S , Zhao X F , Zheng S J , Zheng Y G , Zhou D K 
Published: April 2021

ABSTRACT
We report on the Insight-HXMT observations of the new black hole X-ray binary MAXI J1820+070 during its 2018 outburst. Detailed spectral analysis via the continuum fitting method shows an evolution of the inferred spin during its high soft sate. Moreover, the hardness ratio, the non-thermal luminosity and the reflection fraction also undergo an evolution, exactly coincident to the period when the inferred spin transition takes place. The unphysical evolution of the spin is attributed to the evolution of the inner disc, which is caused by the collapse of a hot corona due to condensation mechanism or may be related to the deceleration of a jet-like corona. The studies of the inner disc radius and the relation between the disc luminosity and the inner disc radius suggest that, only at a particular epoch, did the inner edge of the disc reach the innermost stable circular orbit and the spin measurement is reliable. We then constrain the spin of MAXI J1820 + 070 to be $a_*=0.2^{+0.2}_{-0.3}$. Such a slowly spinning black hole possessing a strong jet suggests that its jet activity is driven mainly by the accretion disc rather than by the black hole spin.
Impact of CYP2A6 Activity on Nicotine Reinforcement and Cue-Reactivity in Daily Smokers
Authors: Butler Kevin , Chenoweth Meghan J , El-Boraie Ahmed , Giratallah Haidy , Kowalczyk William J , Heishman Stephen J , Tyndale Rachel F , Le Foll Bernard 
Published: April 2021

Abstract

Introduction
Variation in CYP2A6, the primary enzyme responsible for nicotine metabolism, is associated with nicotine dependence, cigarette consumption, and abstinence outcomes in smokers. The impact of CYP2A6 activity on nicotine reinforcement and tobacco cue-reactivity, mechanisms that may contribute to these previous associations, has not been fully evaluated.

Aims and Methods
CYP2A6 activity was indexed using 3 genetic approaches in 104 daily smokers completing forced-choice and cue-induced craving tasks assessing nicotine reinforcement and tobacco cue-reactivity, respectively. First, smokers were stratified by the presence or absence of reduced/loss-of-function CYP2A6 gene variants (normal vs. reduced metabolizers). As nicotine metabolite ratio (NMR) is a reliable biomarker of CYP2A6 activity, our second and third approaches used additional genetic variants identified in genome-wide association studies of NMR to create a weighted genetic risk score (wGRS) to stratify smokers (fast vs. slow metabolizers) and calculate a wGRS-derived NMR.

Results
Controlling for race and sex, normal metabolizers (vs. reduced) selected a greater proportion of puffs from nicotine-containing cigarettes (vs. denicotinized) on the forced-choice task (p = .031). In confirmatory analyses, wGRS-based stratification (fast vs. slow metabolizers) produced similar findings. Additionally, wGRS-derived NMR, which correlated with actual NMR assessed in a subset of participants (n = 55), was positively associated with the proportion of puffs from nicotine-containing cigarettes controlling for race and sex (p = .015). None of the CYP2A6 indices were associated with tobacco cue-reactivity in minimally deprived smokers.

Conclusions
Findings suggest increased nicotine reinforcement is exhibited by smokers with high CYP2A6 activity, which may contribute to heavier smoking and poorer cessation outcomes previously reported in faster metabolizers.

Implications
CYP2A6 activity is a key determinant of smoking behavior and outcomes. Therefore, these findings support the targeting of CYP2A6 activity, either therapeutically or as a clinically relevant biomarker in a precision medicine approach, for tobacco use disorder treatment.
Circadian Clock inArabidopsis thalianaDetermines Flower Opening Time Early in the Morning and Dominantly Closes Early in the Afternoon
Authors: Muroya Mitsuhiko , Oshima Haruka , Kobayashi Shoko , Miura Aya , Miyamura Yohei , Shiota Hajime , Onai Kiyoshi , Ishiura Masahiro , Manabe Katsushi , Kutsuna Shinsuke 
Published: April 2021

AbstractMany plant species exhibit diurnal flower opening and closing, which is an adaptation influenced by the lifestyle of pollinators and herbivores. However, it remains unclear how these temporal floral movements are modulated. To clarify the role of the circadian clock in flower movement, we examined temporal floral movements in Arabidopsis thaliana. Wild-type (accessions; Col-0, Ler-0 and Ws-4) flowers opened between 0.7 and 1.4 h in a 16-h light period and closed between 7.5 and 8.3 h in a diurnal light period. In the arrhythmic mutants pcl1-1 and prr975, the former flowers closed slowly and imperfectly and the latter ones never closed. Under continuous light conditions, new flowers emerged and opened within a 23–26 h window in the wild-type, but the flowers in pcl1-1 and prr975 developed straight petals, whose curvatures were extremely small. Anti-phasic circadian gene expression of CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYLE (LHY) and TIMING OF CAB EXPRESSION 1 (TOC1) occurred in wild-type flowers, but non-rhythmic expression was observed in pcl1-1 and prr975 mutants. Focusing on excised petals, bioluminescence monitoring revealed rhythmic promoter activities of genes expressed (CCA1, LHY and PHYTOCLOCK 1/LUX ARRHYTHMO, PCL1/LUX) in the morning and evening. These results suggest that the clock induces flower opening redundantly with unknown light-sensing pathways. By contrast, flower closing is completely dependent on clock control. These findings will lead to further exploration of the molecular mechanisms and evolutionary diversity of timing in flower opening and closing.