bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-Antibody Evaluation of T-Cell Receptor β Constant Chain Monotypia by Flow Cytometry Facilitates the Diagnosis of T-Cell Large Granular Lymphocytic Leukemia
Authors: Horna Pedro , Olteanu Horatiu , Jevremovic Dragan , Otteson Gregory E , Corley Heidi , Ding Wei , Parikh Sameer A , Shah Mithun V , Morice William G , Shi Min 
Published: September 2020

Abstract

Objectives
The diagnosis of T-cell large granular lymphocytic leukemia (T-LGLL) is challenging because of overlapping immunophenotypic features with reactive T cells and limitations of T-cell clonality assays. We studied whether adding an antibody against T-cell receptor β constant region 1 (TRBC1) to a comprehensive flow cytometry panel could facilitate the diagnosis of T-LGLL.

Methods
We added TRBC1 antibody to the standard T-cell and natural killer (NK) cell panel to assess T-cell clonality in 56 T-LGLLs and 34 reactive lymphocytoses. In addition, 20 chronic lymphoproliferative disorder of NK cells (CLPD-NKs) and 10 reactive NK-cell lymphocytoses were analyzed.

Results
Clonal T cells were detected in all available T-LGLLs by monotypic TRBC1 expression and clonal/equivocal T-cell receptor gene rearrangement (TCGR) studies, compared with only 27% of T-LGLLs by killer-cell immunoglobulin-like receptor (KIR) restriction. Overall, 85% of T-LGLLs had a blood tumor burden greater than 500 cells/µL. Thirty-four reactive cases showed polytypic TRBC1 expression, except for 5 that revealed small T-cell clones of uncertain significance. All CLPD-NKs showed expected clonal KIR expression and negative TRBC1 expression.

Conclusions
Addition of TRBC1 antibody to the routine flow cytometry assay could replace the TCGR molecular study and KIR flow cytometric analysis to assess clonality, simplifying the diagnosis of T-LGLL.
Precise uncertain significance prediction using latent space matrix factorization models: genomics variant and heterogeneous clinical data-driven approaches
Authors: Abdollahi Sina , Lin Peng-Chan , Shen Meng-Ru , Chiang Jung-Hsien 
Published: September 2020

Abstract
Several studies to date have proposed different types of interpreters for measuring the degree of pathogenicity of variants. However, in predicting the disease type and disease–gene associations, scholars face two essential challenges, namely the vast number of existing variants and the existence of variants which are recognized as variant of uncertain significance (VUS). To tackle these challenges, we propose algorithms to assign a significance to each gene rather than each variant, describing its degree of pathogenicity. Since the interpreters identified most of the variants as VUS, most of the gene scores were identified as uncertain significance. To predict the uncertain significance scores, we design two matrix factorization-based models: the common latent space model uses genomics variant data as well as heterogeneous clinical data, while the single-matrix factorization model can be used when heterogeneous clinical data are unavailable. We have managed to show that the models successfully predict the uncertain significance scores with low error and high accuracy. Moreover, to evaluate the effectiveness of our novel input features, we train five different multi-label classifiers including a feedforward neural network with the same feature set and show they all achieve high accuracy as the main impact of our approach comes from the features. Availability: The source code is freely available at https://github.com/sabdollahi/CoLaSpSMFM.
Predictive risk modelling and the mistaken equation of socio-economic disadvantage with risk of maltreatment
Authors: Vannier Ducasse Hélène 
Published: September 2020

Abstract
In England, the involvement of the state in private family life has significantly changed since 1989, and is about to undergo yet further transformation with the adoption of predictive risk modelling. Its implementation by at least eight local authorities and promotion by the central government operates an ontological and methodological revolution in child protection policies and practice. This article particularly discusses the conceptual and empirical limits to their use. It makes the case that the data fed to risk models, and the institutional structures through which they are run, limit the understanding of maltreatment. Based on misleading evidence, risk models are set to mistakenly equate socio-economic disadvantage with risks, thus threatening to automatise the discrimination and alienation of the poorest sections of the population.
Relation of outcomes to ABC (Atrial Fibrillation Better Care) pathway adherent care in European patients with atrial fibrillation: an analysis from the ESC-EHRA EORP Atrial Fibrillation General Long-Term (AFGen LT) Registry
Authors: Proietti Marco , Lip Gregory Y H , Laroche Cécile , Fauchier Laurent , Marin Francisco , Nabauer Michael , Potpara Tatjana , Dan Gheorghe-Andrei , Kalarus Zbigniew , Tavazzi Luigi , Maggioni Aldo Pietro , Boriani Giuseppe ,   the ESC-EORP Atrial Fibrillation General Long-Term Registry Investigators Group
Published: September 2020

Abstract

Aims
There has been an increasing focus on integrated, multidisciplinary, and holistic care in the treatment of atrial fibrillation (AF). The ‘Atrial Fibrillation Better Care’ (ABC) pathway has been proposed to streamline integrated care in AF. We evaluated the impact on outcomes of an ABC adherent management in a contemporary real-life European-wide AF cohort.

Methods and results
Patients enrolled in the ESC-EHRA EURObservational Research Programme in AF General Long-Term Registry with baseline data to evaluate ABC criteria and available follow-up data were considered for this analysis. Among the original 11 096 AF patients enrolled, 6646 (59.9%) were included in this analysis, of which 1996 (30.0%) managed as ABC adherent. Patients adherent to ABC care had lower CHA2DS2-VASc and HAS-BLED scores (mean ± SD, 2.68 ± 1.57 vs. 3.07 ± 1.90 and 1.26 ± 0.93 vs. 1.58 ± 1.12, respectively; P &lt; 0.001). At 1-year follow-up, patients managed adherent to ABC pathway compared to non-adherent ones had a lower rate of any thromboembolic event (TE)/acute coronary syndrome (ACS)/cardiovascular (CV) death (3.8% vs. 7.6%), CV death (1.9% vs. 4.8%), and all-cause death (3.0% vs. 6.4%) (all P &lt; 0.0001). On Cox multivariable regression analysis, ABC adherent care showed an association with a lower risk of any TE/ACS/CV death [hazard ratio (HR): 0.59, 95% confidence interval (CI): 0.44–0.79], CV death (HR: 0.52, 95% CI: 0.35–0.78), and all-cause death (HR: 0.57, 95% CI: 0.43–0.78).

Conclusion
In a large contemporary cohort of European AF patients, a clinical management adherent to ABC pathway for integrated care is associated with a significant lower risk for cardiovascular events, CV death, and all-cause death.
Brief alcohol intervention at a municipal registry office: reach and retention
Authors: Enders Caroline E , Staudt Andreas , Freyer-Adam Jennis , Meyer Christian , Ulbricht Sabina , John Ulrich , Baumann Sophie 
Published: September 2020

Abstract

Background
The aim was to investigate the suitability of a municipal registry office for alcohol screening and brief intervention. We analyzed whether trial participation and retention differ by alcohol- and health-related, demographic and socio-economic participant characteristics.

Methods
Over 3 months, all 18- to 64-year-old visitors of a registry office were systematically screened. Persons with alcohol consumption in the past 12 months (N = 1646) were randomized to brief alcohol intervention (BAI) or assessment only. BAI was delivered by computer-generated individualized feedback letters at baseline, 3 and 6 months. Logistic and ordered logistic regression models were used to investigate whether the odds of trial participation and retention depended on participant characteristics. Models were rerun separately for low-risk and at-risk drinkers with Alcohol Use Disorder Identification Test-Consumption scores ≥4/≥5 for women/men indicating at-risk drinking.

Results
The trial participation rate was 67% with higher odds of participation in younger adults (P &lt; 0.001). Retention rates at 3 and 6 months were 85% and 81%, respectively. Higher retention was associated with older age, higher level of school education and non-smoking (all p-values ≤0.05). Low-risk drinkers were more likely to participate in the trial (P &lt; 0.01) and in post-baseline assessments (P &lt; 0.05) than at-risk drinkers.

Conclusion
Our data suggest that registry offices could be a suitable setting to reach people from the general population for BAI. Especially the understudied group of low-risk drinkers was well reached through BAI and showed high adherence. BAI that addresses alcohol consumers beyond those at risk may be well accepted in proactively recruited people from the general population.
Stochastic processes dominate marine free-living Vibrio community assembly in a subtropical gulf
Authors: Li Nan , Dong Ke , Jiang Gonglingxia , Tang Jinli , Xu Qiangsheng , Li Xiaoli , Kang Zhenjun , Zou Shuqi , Chen Xing , Adams Jonathan M , Zhao Huaxian 
Published: September 2020

ABSTRACT
Understanding the effects of eutrophication on heterotrophic bacteria, a primary responder to eutrophication, is critical for predicting the responses of ecosystems to marine environmental pollution. Vibrio are indigenous in coastal water and of significance to geochemical cycling and public health. In this study, we investigated the diversity and assembly features of Vibrio, as well as their relationship with the environmental factors in the subtropical Beibu Gulf. We found that the alpha diversity of Vibrio increased in parallel with the trophic state they occupy. A Mantel test indicated that the trophic state was correlated to Vibrio beta diversity and the correlation gradually strengthened at higher trophic states. Variation partitioning analysis suggested that the geographic distance was an important factor impacting the variables of Vibrio communities in all the samples, but nutrients exerted more influence in the more highly eutrophic samples. Our results demonstrated that stochastic processes govern the turnover of marine Vibrio communities in the Beibu Gulf and that ecological drift was the most important process for assembly of the Vibrio communities.
Evolution of a Record-Setting AT-Rich Genome: Indel Mutation, Recombination, and Substitution Bias
Authors: Nguyen Duong T , Wu Baojun , Xiao Shujie , Hao Weilong 
Published: September 2020

AbstractGenome-wide nucleotide composition varies widely among species. Despite extensive research, the source of genome-wide nucleotide composition diversity remains elusive. Yeast mitochondrial genomes (mitogenomes) are highly A + T rich, and they provide a unique opportunity to study the evolution of AT-biased landscape. In this study, we sequenced ten complete mitogenomes of the Saccharomycodes ludwigii yeast with 8% G + C content, the lowest genome-wide %(G + C) in all published genomes to date. The S. ludwigii mitogenomes have high densities of short tandem repeats but severely underrepresented mononucleotide repeats. Comparative population genomics of these record-setting A + T-rich genomes shows dynamic indel mutations and strong mutation bias toward A/T. Indel mutations play a greater role in genomic variation among very closely related strains than nucleotide substitutions. Indels have resulted in presence–absence polymorphism of tRNAArg (ACG) among S. ludwigii mitogenomes. Interestingly, these mitogenomes have undergone recombination, a genetic process that can increase G + C content by GC-biased gene conversion. Finally, the expected equilibrium G + C content under mutation pressure alone is higher than observed G + C content, suggesting existence of mechanisms other than AT-biased mutation operating to increase A/T. Together, our findings shed new lights on mechanisms driving extremely AT-rich genomes.
Stability of delayed switched systems via Razumikhin technique and application to switched neural networks
Authors: Sun Dihua , Liu Chao , Yang Zheng , Liu Xiaoyang , Yang Hongyu , Huang Junjian 
Published: September 2020

Abstract
This paper investigates the globally exponential stability of delayed switched systems via Razumikhin technique. According to mode-dependent dwell average time and multiple Lyapunov functions, new Razumikhin-type stability results are deduced. In contrast to the existing Rzumikhin-type results, the proposed ones are less conservative. In order to demonstrate the applicability, some stability and stabilization results for switched neural networks with time-varying delays are also derived. Several numerical examples are also employed to show the effectiveness and superiority of the obtained results.
Optimizing Caneberry Spray Coverage for Drosophila suzukii (Diptera: Drosophilidae) Management on Diversified Fruit Farms
Authors: Lewis Margaret T , Hamby Kelly A 
Published: September 2020

Abstract
Spray coverage may influence the efficacy of insecticides targeting the invasive vinegar fly Drosophila suzukii (Matsumura), a primary pest of raspberries and blackberries. In commercially managed caneberries, spray coverage is typically lowest in the inner and lower plant canopy, regions that overlap with higher levels of adult D. suzukii activity. To understand how spray coverage of fruit impacts efficacy against D. suzukii, laboratory bioassays were conducted using raspberries. In laboratory bioassays, higher spray coverage did not impact larval infestation rates but did increase adult mortality, indicating that flies can avoid a lethal dose of insecticide when applications do not achieve adequate coverage. We also evaluated how carrier water volume impacts spray coverage patterns throughout the canopy of raspberry and blackberry plants using both airblast and CO2 backpack sprayers. Increasing carrier water volume generally improved spray coverage in the lower plant canopy. However, effects in the upper plant canopy were inconsistent and varied between sprayer types. In addition to carrier water volume, other approaches, including adjusting the pesticide sprayer equipment used and/or sprayer calibration, should also be explored to improve coverage. Growers should evaluate spray coverage in their caneberries to identify and troubleshoot coverage issues. Results from this study indicate that taking the time to optimize this aspect of pesticide application may improve chemical management of D. suzukii and will likely also improve control of other important caneberry pests.
An Evaluation of Characters for the Separation of Two Culex Species (Diptera: Culicidae) Based on Material From the Upper Midwest
Authors: Ferreira-de-Freitas Lílian , Thrun Nicholas B , Tucker Bradley J , Melidosian Lauren , Bartholomay Lyric C 
Published: September 2020

Abstract
Mosquitoes (Diptera: Culicidae) in the Culex pipiens complex play a key role in the transmission and therefore epidemiology of a number of human and animal pathogens globally. These mosquitoes, and sympatric species of the genus Culex Linnaeus that are not within the Cx. pipiens complex, are often considered ‘impossible’ to distinguish by morphology in the adult female stage. In the United States, this is particularly true for Culex pipiens s.l. and Culex restuans Theobald, both of which are competent vectors of West Nile virus, but likely play different roles in the transmission cycle. Therefore, we undertook an in-depth morphological evaluation of matched larval exuviae and adult specimens that revealed five useful morphological characters that are informative to distinguish Cx. pipiens s.l. from Cx. restuans in the adult stage. Herein, we provide a comprehensive review of the literature on these species of interest, and four additional, morphologically similar, Culex species, and a proposed key to adult female specimens.
Identification of a Novel BRCA1 Alteration in Recurrent Melanocytoma Resulting in Increased Proliferation
Authors: San-Miguel Teresa , Navarro Lara , Sánchez-Sendra Beatriz , Megías Javier , Muñoz-Hidalgo Lisandra , Santonja Nuria , López-Ginés Concha , Cerdá-Nicolas Miguel 
Published: September 2020

Abstract
Primary meningeal melanocytomas are rare tumors of the central nervous system. Although they are considered benign neoplasms, some reports describe recurrent rates up to 45%. Little is known about their genetic and epigenetic landscape because of their infrequency. Even less has been described about markers with prognostic value. Here we describe a patient who developed a primary meningeal melanocytoma, suffered 3 recurrences in a period of 6 years and died of the tumor. The genetic and epigenetic changes explored confirmed GNAQ mutation as an initiating event. We found an epigenetic alteration of GSTP1, a feature that has recently been described in meningiomas, from the beginning of the disease. In addition, there was loss of heterozygosity in BRCA1 beginning in the second recurrence that was linked to an increase in the proliferation index; this suggested a progression pathway similar to the one described in uveal melanomas. These findings underscore the necessity of further research focused on these tumors.
Changes in peripheral immune cells after intraoperative radiation therapy in low-risk breast cancer
Authors: Linares-Galiana Isabel , Berenguer-Frances Miguel Angel , Cañas-Cortés Rut , Pujol-Canadell Monica , Comas-Antón Silvia , Martínez Evelyn , Laplana Maria , Pérez-Montero Héctor , Pla-Farnós María Jesús , Navarro-Martin Arturo , Nuñez Miriam , Both Brigitte , Guedea Ferran 
Published: September 2020

Abstract
A detailed understanding of the interactions and the best dose-fractionation scheme of radiation to maximize antitumor immunity have not been fully established. In this study, the effect on the host immune system of a single dose of 20 Gy through intraoperative radiation therapy (IORT) on the surgical bed in low-risk breast cancer patients undergoing conserving breast cancer has been assessed. Peripheral blood samples from 13 patients were collected preoperatively and at 48 h and 3 and 10 weeks after the administration of radiation. We performed a flow cytometry analysis for lymphocyte subpopulations, natural killer cells (NK), regulatory T cells (Treg) and myeloid-derived suppressor cells (MDSCs). We observed that the subpopulation of NK CD56+high CD16+ increased significantly at 3 weeks after IORT (0.30–0.42%, P &lt; 0.001), while no changes were found in immunosuppressive profile, CD4+CD25+Foxp3+Helios+ Treg cells, granulocytic MDSCs (G-MDSCs) and monocytic MDSCs (Mo-MDSCs). A single dose of IORT may be an effective approach to improve antitumor immunity based on the increase in NK cells and the non-stimulation of immunosuppressive cells involved in immune escape. These findings support future combinations of IORT with immunotherapy, if they are confirmed in a large cohort of breast cancer patients.
The anomalous atmospheric structure of the strongly magnetic Ap star HD 166473
Authors: Järvinen S P , Hubrig S , Mathys G , Khalack V , Ilyin I , Adigozalzade H 
Published: September 2020

ABSTRACT
High-resolution spectropolarimetric observations of the strongly magnetic, superslowly rotating rapidly oscillating Ap star HD 166473 are used to investigate the implications of the presence of a variable strong magnetic field on the vertical and surface horizontal distribution of various chemical elements. The analysis of the calculated least-squares deconvolution Stokes I and V profiles confirms the previously reported detection of non-uniform horizontal surface distribution of several chemical elements. To test the vertical abundance stratification of iron peak and rare earth elements, magnetic field measurements were carried out using spectral lines of these elements belonging to neutral and ionized stages. We find clear indication of the existence of a relation between the magnetic field strength and its orientation and vertical element stratification: magnetic field values obtained for elements in different stages close to the magnetic equator are rather similar, whereas the dispersion in field strengths is remarkably large in the regions close to magnetic field poles. At the phases of negative and positive extrema the mean longitudinal field strength determined from the analysis of the rare-earth element lines is usually stronger than when using Fe and Cr. The strongest mean longitudinal magnetic field, up to −4160 ± 226 G, is detected using the La ii line list at the negative extremum, followed by the measurements using the Pr iii lines with 〈Bz〉=−3740 ± 343 G and the Ce ii lines with 〈Bz〉 = −3372 ± 247 G. The strongest mean longitudinal magnetic field of positive polarity, up to 3584 ± 354 G is detected using the Pr iii lines, followed by the measurement 〈Bz〉 = 2517 ± 249 G using the Ce ii lines.
A possible γ-ray quasi-periodic oscillation of ∼314 days in the blazar OJ 287
Authors: Kushwaha Pankaj , Sarkar Arkadipta , Gupta Alok C , Tripathi Ashutosh , Wiita Paul J 
Published: September 2020

ABSTRACT
We report the detection of a probable γ-ray quasi-periodic oscillation (QPO) of around 314 d in the monthly binned 0.1–300 GeV γ-ray Fermi-Large Area Telescope light curve of the well-known BL Lacertae blazar OJ 287. To identify and quantify the QPO nature of the γ-ray light curve of OJ 287, we used the Lomb–Scargle periodogram (LSP), REDFIT, and weighted wavelet Z-transform (WWZ) analyses. We briefly discuss possible emission models for radio-loud active galactic nuclei that can explain a γ-ray QPO of such a period in a blazar.
Systematic errors in dust mass determinations: insights from laboratory opacity measurements
Authors: Fanciullo Lapo , Kemper Francisca , Scicluna Peter , Dharmawardena Thavisha E , Srinivasan Sundar 
Published: September 2020

ABSTRACTThe thermal emission of dust is one of the most important tracers of the interstellar medium: multiwavelength photometry in the far-infrared (FIR) and submillimetre (submm) can be fitted with a model, providing estimates of the dust mass. The fit results depend on the assumed value for FIR/submm opacity, which in most models – due to the scarcity, until recently, of experimental measurements – is extrapolated from shorter wavelengths. Lab measurements of dust analogues, however, show that FIR opacities are usually higher than the values used in models and depend on temperature, which suggests that dust mass estimates may be biased. To test the extent of this bias, we create multiwavelength synthetic photometry for dusty galaxies at different temperatures and redshifts, using experimental results for FIR/submm dust opacity and then we fit the synthetic data using standard dust models. We find that the dust masses recovered by typical models are overestimated by a factor of 2–20, depending on how the experimental opacities are treated. If the experimental dust samples are accurate analogues of interstellar dust, therefore, current dust masses are overestimated by up to a factor of 20. The implications for our understanding of dust, both Galactic and at high redshift, are discussed.