bluuebunny/crossref_metadata_2025_split huggingface dataset:
Liquid Biopsy for Invasive Mold Infections in Hematopoietic Cell Transplant Recipients With Pneumonia Through Next-Generation Sequencing of Microbial Cell-Free DNA in Plasma
Authors: Hill Joshua A , Dalai Sudeb C , Hong David K , Ahmed Asim A , Ho Carine , Hollemon Desiree , Blair Lily , Maalouf Joyce , Keane-Candib Jacob , Stevens-Ayers Terry , Boeckh Michael , Blauwkamp Timothy A , Fisher Cynthia E 
Published: October 2020

Abstract

Background
Noninvasive diagnostic options are limited for invasive mold infections (IMIs). We evaluated the performance of a plasma microbial cell-free DNA sequencing (mcfDNA-Seq) test for diagnosing pulmonary IMI after hematopoietic cell transplant (HCT).

Methods
We retrospectively assessed the diagnostic performance of plasma mcfDNA-Seq next-generation sequencing in 114 HCT recipients with pneumonia after HCT who had stored plasma obtained within 14 days of diagnosis of proven/probable Aspergillus IMI (n = 51), proven/probable non-Aspergillus IMI (n = 24), possible IMI (n = 20), and non-IMI controls (n = 19). Sequences were aligned to a database including &gt;400 fungi. Organisms above a fixed significance threshold were reported.

Results
Among 75 patients with proven/probable pulmonary IMI, mcfDNA-Seq detected ≥1 pathogenic mold in 38 patients (sensitivity, 51% [95% confidence interval {CI}, 39%–62%]). When restricted to samples obtained within 3 days of diagnosis, sensitivity increased to 61%. McfDNA-Seq had higher sensitivity for proven/probable non-Aspergillus IMI (sensitivity, 79% [95% CI, 56%–93%]) compared with Aspergillus IMI (sensitivity, 31% [95% CI, 19%–46%]). McfDNA-Seq also identified non-Aspergillus molds in an additional 7 patients in the Aspergillus subgroup and Aspergillus in 1 patient with possible IMI. Among 19 non-IMI pneumonia controls, mcfDNA-Seq was negative in all samples, suggesting a high specificity (95% CI, 82%–100%) and up to 100% positive predictive value (PPV) with estimated negative predictive values (NPVs) of 81%–99%. The mcfDNA-Seq assay was complementary to serum galactomannan index testing; in combination, they were positive in 84% of individuals with proven/probable pulmonary IMI.

Conclusions
Noninvasive mcfDNA-Seq had moderate sensitivity and high specificity, NPV, and PPV for pulmonary IMI after HCT, particularly for non-Aspergillus species.
Mediatization from Within: A Plea for Emic Approaches to Media-Related Social Change
Authors: Jansson André , Bengtsson Stina , Fast Karin , Lindell Johan 
Published: October 2020

AbstractBased on a literature review, this article shows that current mediatization scholarship is characterized by what Pike (1967) refers to as etic accounts. These accounts forward theoretical categories on media-related social change to conclude that our age is characterized by deepened and expanded media reliance. However, such theoretical extrapolation takes place not from, but at the expense of, people’s lived experiences, that is, emic accounts of mediatization in everyday life. This article is an attempt to insert the etic/emic distinction to mediatization research in order to develop more reflexive and composite accounts. Drawing on examples from a representative survey and qualitative interviews conducted over twenty years, the article problematizes etic-oriented conceptions of mediatization. Emic analyses expose how perceptions of media reliance shift over time and thus underscore the need to develop research strategies that simultaneously consider the objective structures of the social (mediatized) world and subjective meaning-making structures.
Myasthenia is a poor prognostic factor for perioperative outcomes after robotic thymectomy for thymoma
Authors: Kumar Arvind , Asaf Belal Bin , Pulle Mohan Venkatesh , Puri Harsh Vardhan , Sethi Nitin , Bishnoi Sukhram 
Published: October 2020

Abstract OBJECTIVESThe goal of this study was to compare the early and intermediate surgical outcomes, including the survival of those with and without myasthenic thymoma, following robotic thymectomy.METHODSThis is a retrospective analysis of prospectively maintained data of 111 patients who underwent robotic thymectomy for thymoma over 7 years in a thoracic surgery centre in India. We performed a comparative analysis of demographics, intraoperative variables and postoperative outcomes including survival of those with and without myasthenic thymoma.RESULTSOf 111 patients, 68 patients were myasthenic and 43 were non-myasthenic. The need to resect surrounding structures and conversions was greater in the myasthenic group (P = 0.02, P = 0.04). Postoperative complications were significantly higher in the myasthenic group (P = 0.02). No differences were observed in intensive care unit stay, the need for postoperative ventilation and the hospital stay. On correlation, a higher Masaoka stage [odds ratio 1.96, 95% confidence interval (CI) 1.22–3.15] and an aggressive World Health Organization histological diagnosis (odds ratio 1.58, 95% CI 1.10–2.26) were more likely in patients with myasthenia gravis. A total of 7 deaths (6.3%) occurred during the median follow-up of 4.2 years, 5 among those with myasthenic thymoma and 2 among patients with non-myasthenic thymoma. Due to the small number of deaths, there is insufficient evidence to draw any conclusion about the effect of myasthenia gravis on survival after surgery (hazard ratio 0.51, 95% CI 0.09–2.71; P = 0.43).CONCLUSIONSThe presence of myasthenia with thymoma is associated with more adjacent structure resection, higher postoperative complications and more conversions. The use of robotic surgery for thymoma resection in patients with myasthenia could not overcome the early postoperative problems related to myasthenia gravis.
Cardiopulmonary bypass increases endothelial dysfunction after pulmonary ischaemia-reperfusion in an animal model
Authors: Selim Jean , Hamzaoui Mouad , Boukhalfa Inès , Djerada Zoubir , Chevalier Laurence , Piton Nicolas , Genty Damien , Besnier Emmanuel , Clavier Thomas , Dumesnil Anaïs , Renet Sylvanie , Mulder Paul , Doguet Fabien , Tamion Fabienne , Veber Benoît , Richard Vincent , Baste Jean-Marc 
Published: October 2020

Abstract

OBJECTIVES
Endothelial dysfunction during ischaemia-reperfusion (IR) is a major cause of primary graft dysfunction during lung transplantation. The routine use of cardiopulmonary bypass (CPB) during lung transplantation remains controversial. However, the contribution of CPB to pulmonary endothelial dysfunction remains unclear. The objective was to investigate the impact of CPB on endothelial dysfunction in a lung IR rat model.

METHODS
Rats were allocated to 4 groups: (i) Sham, (ii) IR, (iii) CPB and (iv) IR-CPB. The primary outcome was the study of pulmonary vascular reactivity by wire myograph. We also assessed glycocalyx degradation by enzyme-linked immunosorbent assay and electron microscopy and both systemic and pulmonary inflammation by enzyme-linked immunosorbent assay and immunohistochemistry. Rats were exposed to 45 min of CPB and IR. We used a CPB model allowing femoro-femoral support with left pulmonary hilum ischaemia for IR.

RESULTS
Pulmonary endothelium-dependent relaxation to acetylcholine was markedly reduced in the IR-CPB group (10.7 ± 9.1%) compared to the IR group (50.5 ± 5.2%, P &lt; 0.001), the CPB group (54.1 ± 4.7%, P &lt; 0.001) and the sham group (80.8 ± 6.7%, P &lt; 0.001), suggesting that the association of pulmonary IR and CPB increases endothelial dysfunction. In IR-CPB, IR and CPB groups, vasorelaxation was completely abolished when inhibiting nitric oxide synthase, suggesting that this relaxation process was mainly mediated by nitric oxide. We observed higher syndecan-1 plasma levels in the IR-CPB group in comparison with the other groups, reflecting an increased degradation of glycocalyx. We also observed higher systemic inflammation in the IR-CPB group as shown by the increased plasma levels of IL-1β, IL-10.

CONCLUSIONS
CPB significantly increased the IR-mediated effects on pulmonary endothelial dysfunction. Therefore, the use of CPB during lung transplantation could be deleterious, by increasing endothelial dysfunction.
Plant components affect bacterial biofilm development by altering their cell surface physicochemical properties: a predictability study using Actinomyces naeslundii
Authors: Wang Yi , Samaranayake Lakshman P , Dykes Gary A 
Published: October 2020

Abstract
We hypothesized that the initial events leading to biofilm formation by bacteria, in general, are predominantly mediated by cell surface physicochemical interactions, and that natural products can impact the process by altering cell surface physicochemical properties. We exemplified this phenomenon using Actinomyces naeslundii as the model organism, and using tea products to modify its cell surface physicochemical properties. To test the hypothesis, a non-linear multiple regression model incorporating a normal distribution curve was constructed to explain the impact of tea extracts on the physiochemical processes of biofilm formation by A. naeslundii. The model utilized tea extract-induced changes in cell surface physicochemical properties as independent variables, and the corresponding biofilm formation as a dependent variable. Five different tea extracts were used to treat A. naeslundii, and their impact on the cell surface hydrophobicity, charge, auto-aggregation, attachment and biofilm formation on four different hard surfaces were measured and the data were used to construct the model. The established model was then tested in independent experiments involving other plant extracts and purified phytochemicals. Experimental results showed that the tea extracts significantly reduced cell surface hydrophobicity (by up to 21.3%), increased cell surface charge and auto-aggregation (by up to 4.5 mV and 14.9%, respectively), inhibited attachment (by 0.6–2.5 log CFU cm−2) and affected biofilm formation (by up to 0.6 log CFU cm−2). The model indicated that both cell surface hydrophobicity and charge played an important role in bacterial auto-aggregation and attachment, and that the latter two phenomena significantly correlated with subsequent biofilm development. The accuracy of the model construct was approximately 64%. This modelling approach can be employed for other microbial colonization systems to predict biofilm formation, and to study the impact of cell surface physicochemical properties in biofilm development.
Three-dimensional forward modelling of gravity field vector and its gradient tensor using the compact difference schemes
Authors: Pan Kejia , Zhang Zhihao , Hu Shuanggui , Ren Zhengyong , Guo Rongwen , Tang Jingtian 
Published: October 2020

SUMMARY
The traditional gravity forward modelling methods for solving partial differential equations (PDEs) only can yield second-order accuracy. When computing the gravity field vector and gradient tensor from the obtained potential, those numerical differentiation approaches will inevitably lose accuracy. To mitigate this issue, we propose an efficient and accurate 3-D forward modelling algorithm based on a fourth-order compact difference scheme. First, a 19-point fourth-order compact difference scheme with general meshsizes in x-, y- and z-directions is adopted to discretize the governing 3-D Poisson’s equation. The resulting symmetric positive-definite linear systems are solved by the pre-conditioned conjugate gradient algorithm. To obtain the first-order (i.e. the gravity field vector) and second-order derivatives (i.e. the gravity gradient tensor) with fourth-order accuracy, we seek to solve a sequence of tridiagonal linear systems resulting from the above mentioned finite difference discretization by using fast Thomas algorithm. Finally, two synthetic models and a real topography relief are used to verify the accuracy of our method. Numerical results show that our method can yield a nearly fourth-order accurate approximation not only to the gravitational potential, but also to the gravity field vector and its gradient tensor, which clearly demonstrates its superiority over the traditional PDE-based methods.
Investigation of acidic free-glycans in urine and their alteration in cancer
Authors: Hanzawa Ken , Tanaka-Okamoto Miki , Murakami Hiroko , Mukai Mikio , Takahashi Hidenori , Omori Takeshi , Ikezawa Kenji , Ohkawa Kazuyoshi , Ohue Masayuki , Miyamoto Yasuhide 
Published: October 2020

Abstract
Alterations to glycans in cancer patients have been used to identify novel tumor biomarkers. Most of these studies have focused on protein glycosylation but less attention has been paid to free-glycans. Here, we analyzed acidic free-glycans in the urine of cancer patients to identify novel tumor marker candidates. Specifically, urine samples were collected from patients with gastric cancer, pancreatic cancer and cholangiocarcinoma as well as normal controls. The free-glycans were extracted from creatinine-adjusted urine and fluorescently labeled with 2-aminopyridine. Initially, we performed profiling of urinary free-glycans by high-performance liquid chromatography and mass spectrometry with enzymatic and chemical degradation. More than 100 glycans, including novel structures, were identified. The chromatographic peaks suggested some of these glycans were present at elevated levels in cancer patients. To verify cancer-associated alterations, we compared the glycan levels between cancer patients and normal controls by selected reaction monitoring. Representative structures of glycans with elevated levels in cancer patients included the following: small glycans related to sialyllactose; sialyl Lewis X; lactose- and N-acetyllactosamine (LacNAc) type-II-core glycans with LacNAc (type-I or II)-extensions and modifications of α1,3/4-fucose and/or 6-sulfate on the Glc/GlcNAc; free-N-glycans containing sialylation or β1,6-branch of 6-sulfo Lewis X; novel NeuAcα2-3Galβ1-4(+/−Fucα1-3) Xylα1-3Glc glycans. Our results provide further insight into urinary free-glycans and suggest the potential utility of these compounds as tumor markers.
Economic evaluation of interventions to address undernutrition: a systematic review
Authors: Ramponi Francesco , Tafesse Wiktoria , Griffin Susan 
Published: October 2020

Abstract
Strategies to address undernutrition in low- and middle-income countries (LMICs) include various interventions implemented through different sectors of the economy. Our aim is to provide an overview of published economic evaluations of such interventions and to compare and contrast evaluations of interventions in different areas. We reviewed economic evaluations of nutrition interventions in LMICs published since 2015 and/or included in the Tufts Global registry or Disease Control Priorities 3rd edition. We categorized the studies by intervention type (preventive; therapeutic; fortification; delivery platforms), nutritional deficiency addressed and characteristics of the economic evaluation (e.g. type of model, costs and outcomes included). Of the 62 economic evaluations identified, 56 (90%) were cost-effectiveness analyses. Twenty-two (36%) evaluations investigated fortification and 23 (37%) preventive interventions. Forty-three percent of the evaluations of preventive interventions did not include a model, whereas most of fortification strategies used the same reference model. We identified different trends in cost categories and inclusion of health and non-health outcomes across evaluations in the four different topic areas. To illustrate the implications of such trends for decision-making, we compared a set of studies evaluating alternative strategies to combat zinc deficiency. We showed that the use of ‘off-the-shelf’ models and tools can potentially conceal what outcomes and costs and value judgements are used. Comparing interventions across different areas is fundamental to assist decision-makers in developing their nutrition strategy. Systematic differences in the economic evaluations of interventions delivered within and outside the health sector can undermine the ability to prioritize alternative nutrition strategies.
Demographic history and admixture dynamics in African Sahelian populations
Authors: Černý Viktor , Fortes-Lima Cesar , Tříska Petr 
Published: October 2020

AbstractThe Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterized by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure and the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.
Impact of immunohistochemistry-based molecular subtype on predicting chemotherapy response and survival in patients with T1 stage bladder cancer after bladder-preserving treatment
Authors: Lu Jiangli , Zhang Yijun , Wu Chenyan , Chu Chengbiao , Liu Zhuowei , Cao Yun 
Published: October 2020

Abstract

Objective
To explore the immunohistochemistry-based molecular subtypes of bladder cancer, and their impact on the prognosis and the chemotherapy response between gemcitabine plus cisplatin intra-arterial chemotherapy and epirubicin-inducted intravesical chemotherapy, in patients with T1 stage bladder cancer after bladder-preserving treatment.

Methods
One hundred and seventy-six patients with T1 stage bladder cancer were selected for this study. Thirty-three patients underwent radical cystectomy, 43 received gemcitabine plus cisplatin intra-arterial chemotherapy and 100 received intravesical chemotherapy. The markers labeled with luminal (GATA3, Uroplakin II, CK20) and basal (CK5/6, CK14, CD44) phenotypes were chosen as candidate markers.

Results
One hundred and seventy-six patients were divided into 76 patients as basal/squamous (BASQ), 45 as the luminal A and 55 as the luminal B. Compared with the luminal B and BASQ tumors, the luminal A tumors showed a trend for better recurrence-free survival (P = 0.105) and progression-free survival (P = 0.093). The combination of CK20 and GATA3 was practical to identify the molecular phenotypes with total 84.9% accuracy and significantly associated with recurrence-free survival (P = 0.025) and progression-free survival (P = 0.004). The patient with BASQ tumors who received intravesical chemotherapy showed a trend for worse progression-free survival than the patient who received gemcitabine plus cisplatin intra-arterial chemotherapy or radical cystectomy. Furthermore, the patients with BASQ tumors experienced a significant improvement in progression-free survival after gemcitabine plus cisplatin intra-arterial chemotherapy compared with the patients who received intravesical chemotherapy (P = 0.011).

Conclusions
The immunohistochemistry-based molecular subtypes could predict the patient’s prognosis and clinically different chemotherapeutic survival outcomes in patients with T1 stage bladder cancer after bladder-preserving treatment.
Bayesian AGN Decomposition Analysis for SDSS spectra: a correlation analysis of [O iii] λ5007 outflow kinematics with AGN and host galaxy properties
Authors: Sexton Remington O , Matzko William , Darden Nicholas , Canalizo Gabriela , Gorjian Varoujan 
Published: October 2020

ABSTRACT
We present Bayesian active galactic nucleus (AGN) Decomposition Analysis for Sloan Digital Sky Survey (SDSS) Spectra, an open source spectral analysis code designed for automatic detailed deconvolution of AGN and host galaxy spectra, implemented in python, and designed for the next generation of large-scale surveys. The code simultaneously fits all spectral components, including power-law continuum, stellar line-of-sight velocity distribution, Fe ii emission, as well as forbidden (narrow), permitted (broad), and outflow emission line features, all performed using Markov chain Monte Carlo to obtain robust uncertainties and autocorrelation analysis to assess parameter convergence. Our code also utilizes multiprocessing for batch fitting large samples of spectra while efficiently managing memory and computation resources and is currently being used in a cluster environment to fit thousands of SDSS spectra. We use our code to perform a correlation analysis of 63 SDSS type 1 AGNs with evidence of strong non-gravitational outflow kinematics in the [O iii] λ5007 emission feature. We confirm findings from previous studies that show the core of the [O iii] profile is a suitable surrogate for stellar velocity dispersion σ*, however there is evidence that the core experiences broadening that scales with outflow velocity. We find sufficient evidence that σ*, [O iii] core dispersion, and the non-gravitational outflow dispersion of the [O iii] profile form a plane whose fit results in a scatter of ∼0.1 dex. Finally, we discuss the implications, caveats, and recommendations when using the [O iii] dispersion as a surrogate for σ* for the MBH−σ* relation.
Influence of the input-stage architecture on the in-laboratory test of a mid-infrared interferometer: application to the ALOHA up-conversion interferometer in the L band
Authors: Magri Julie , Lehmann Lucien , Grossard Ludovic , Delage Laurent , Reynaud François , Chauvet Mathieu , Bassignot Florent , Krawczyk Rodolphe , Le Duigou Jean-Michel 
Published: October 2020

ABSTRACT
In the framework of the Astronomical Light Optical Hybrid Analysis (ALOHA) laboratory mid-infrared (MIR) up-conversion fibred interferometer in the L band, we report on the influence of the input-stage architecture. Using an amplitude division set-up in the visible or near-infrared is a straightforward choice in most cases. In the MIR context, the results are slightly different and we show that a wavefront division set-up is needed. These in-laboratory principle experiments allow us to measure a reliable 88 per cent instrumental contrast with high flux and to obtain fringes from faint sources at 3.5 μm with a spectral bandwith of 37 nm converted to 817 nm. An equivalent limiting L-band magnitude around 3.9, equivalent to 3.0 fW nm−1, could be demonstrated on 1 m class telescopes. This opens the possibility of planning future on-sky tests at the Center for High Angular Resolution Astronomy (CHARA) array and of predicting the performance attained.
Streaming instability on different scales – I. Planetesimal mass distribution variability
Authors: Rucska J J , Wadsley J W 
Published: October 2020

ABSTRACT
We present numerical simulations of dust clumping and planetesimal formation initiated by the streaming instability (SI) with self-gravity. We examine the variability in the planetesimal formation process by employing simulation domains with large radial and azimuthal extents and a novel approach of re-running otherwise identical simulations with different random initializations of the dust density field. We find that the planetesimal mass distribution and the total mass of dust that is converted into planetesimals can vary substantially between individual small simulations and within the domains of larger simulations. Our results show that the non-linear nature of the developed SI introduces substantial variability in the planetesimal formation process that has not been previously considered and suggests larger scale dynamics may affect the process.