bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform
Authors: Szarvas Judit , Ahrenfeldt Johanne , Cisneros Jose Luis Bellod , Thomsen Martin Christen Frølund , Aarestrup Frank M. , Lund Ole 
Published: March 2020

AbstractPublic health authorities whole-genome sequence thousands of isolates each month for microbial diagnostics and surveillance of pathogenic bacteria. The computational methods have not kept up with the deluge of data and the need for real-time results. We have therefore created a bioinformatics pipeline for rapid subtyping and continuous phylogenomic analysis of bacterial samples, suited for large-scale surveillance. The data is divided into sets by mapping to reference genomes, then consensus sequences are generated. Nucleotide based genetic distance is calculated between the sequences in each set, and isolates are clustered together at 10 single-nucleotide polymorphisms. Phylogenetic trees are inferred from the non-redundant sequences and the clustered isolates are added back. The method is accurate at grouping outbreak strains together, while discriminating them from non-outbreak strains. The pipeline is applied in Evergreen Online, which processes publicly available sequencing data from foodborne bacterial pathogens on a daily basis, updating phylogenetic trees as needed.
Linear programs for entanglement and key distribution in the quantum internet
Authors: Bäuml Stefan , Azuma Koji , Kato Go , Elkouss David 
Published: March 2020

AbstractQuantum networks will allow to implement communication tasks beyond the reach of their classical counterparts. A pressing and necessary issue for the design of quantum network protocols is the quantification of the rates at which these tasks can be performed. Here, we propose a simple recipe that yields efficiently computable lower and upper bounds on the maximum achievable rates. For this we make use of the max-flow min-cut theorem and its generalization to multi-commodity flows to obtain linear programs. We exemplify our recipe deriving the linear programs for bipartite settings, settings where multiple pairs of users obtain entanglement in parallel as well as multipartite settings, covering almost all known situations. We also make use of a generalization of the concept of paths between user pairs in a network to Steiner trees spanning a group of users wishing to establish Greenberger-Horne-Zeilinger states.
HST calculation of a 10 kV oil‐immersed transformer with 3D coupled‐field method
Authors: Ruan Jiangjun , Deng Yongqing , Huang Daochun , Duan Cihan , Gong Ruohan , Quan Yu , Hu Yuanchao , Rong Qingyu 
Published: March 2020

Transformer winding hot‐spot temperature (HST) is one of the important factors affecting transformer oil–paper insulation deterioration. This study presents a three‐dimensional coupled electromagnetic‐fluid‐thermal analysis method for HST calculation in a 10 kV oil‐immersed distribution transformer, the influence of the transformer internal metal structure parts on the HST of the winding is considered in the simulation. Combining electromagnetic‐field calculation with no‐load test and load test of the transformer provides a more accurate method to determine internal losses of the transformer. Taking those power losses as heat sources, the transformer fluid‐thermal field analysis is conducted with the finite volume method. The variation of physical parameters of transformer oil with temperature is considered in the simulation. On the basis of the equivalent thermal resistance theory, the equivalent thermal conductivities of transformer windings are obtained. The simulation results deduced from the proposed method agree well with the experimental ones, which are obtained with fibre optic temperature sensors during the transformer temperature rise test, the maximum temperature difference is <3°C. The results validated the validity and accuracy of the proposed transformer HST calculation method.
Sensorless flux adaption DTFC of an IPMSM based on an active flux‐based MTPA and an adaptive second‐order sliding mode observer
Authors: Chen Junlei , Wu Xiang , Chen Shuo , Tan Guojun 
Published: March 2020

This study proposes a sensorless flux adaption direct torque and flux control (DTFC) for an interior permanent magnet synchronous motor (IPMSM), in which an maximum torque per ampere (MTPA) based on active flux and an adaptive second‐order sliding mode observer (SOSMO) are adopted. Flux adaption DTFC is proposed based on the existing active flux concept. Thus, the stator current amplitude can be minimised in both steady state and transient state. Furthermore, to realise the sensorless control of the IPMSM, an adaptive SOSMO is proposed. Compared with constant gains SOSMO, the gains of the adaptive SOSMO can be adjusted adaptively with the motor speed changing. Then, the precision of position estimation is enhanced effectively in a wide speed range. Numerical simulations and experiments with a 60 kW IPMSM are implemented. In addition, the results validate the capability of the proposed sensorless flux adaption DTFC scheme.
Fe7S8 nanoparticles encapsulated in porous N, S co‐doped carbon as an efficient bifunctional electrocatalyst for Zn‐air battery
Authors: Jiang Tongzhou , Dai Peng , Zhang Wen 
Published: March 2020

The development of low‐cost and highly active bifunctional electrocatalysts for oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) is of great significance to promote the practical application of Zn‐air battery (ZAB). Herein, the authors report a facile strategy for the fabrication of Fe7S8 nanoparticles embedded in the N, S co‐doped porous carbon (NSC) network that served as an efficient bifunctional catalyst. The obtained Fe7S8/NSC shows remarkable oxygen electrocatalytic activity, in terms of superior ORR activity to commercial Pt/C as well as comparable OER capability to RuO2. Besides, when evaluated as the cathode catalyst for a homemade ZAB, Fe7S8/NSC also displays a superior peak power density of 135 mA cm−2 and high cycling stability over 65 h (195 cycles).
Combining friend-of-friend and halo-based algorithms for the identification of galaxy groups
Authors: Rodriguez Facundo , Merchán Manuel 
Published: March 2020

Context. Galaxy groups provide the means for a great diversity of studies that contribute to a better understanding of the structure of the universe on a large scale and allow the properties of galaxies to be linked to those of the host halos. However, the identification of galaxy systems is a challenging task and therefore it is necessary to improve the techniques involved as much as possible.
Aims. In view of the large present and forthcoming galaxy catalogues, we propose, implement, and evaluate an algorithm that combines the two most popular techniques used to identify galaxy systems. The algorithm can be easily applied to any spectroscopic galaxy catalogue, but here we demonstrate its use on the Sloan Digital Sky Survey.
Methods. Assuming that a galaxy group is a gravitationally bounded system that has at least one bright galaxy, we begin by identifying groups with a friends-of-friends algorithm adapted to fit this definition. In view of the shortcomings of this method, particularly the lack of ability to identify low-number groups, and consequently the inability to study the occupation of halos throughout the mass range, we improve it by adding a halo-based procedure. To assess the performance, we construct a mock catalogue from a semi-analytical model to compare the groups identified using our method with those obtained from the simulation.
Results. The comparison of groups extracted using our method with those of a mock catalogue shows that the proposed algorithm provides excellent results. The modifications introduced to the friends-of-friends algorithm in the first part of the procedure to fit the adopted group definition gave reliable groups. Furthermore, incorporation of the halo-based method reduces the interlopers while more accurately reproducing the number of galaxies per group. As a specific application, we use the algorithm to extract groups from the Sloan Digital Sky Survey.
The Population Pharmacokinetics of Rifampicin in Japanese Pulmonary Tuberculosis Patients
Authors: Nishimura Takahiro , Kohno Haruichi , Nagai Hideaki , Maruoka Daisuke , Koike Yuichi , Kobayashi Masahiro , Atsuda Koichiro 
Published: March 2020

AbstractIn Japan, tuberculosis has been recognized as one of the major infections requiring urgent measures because of its high morbidity rate even now especially in elderly people suffering from tuberculosis during the past epidemic and its reactivation. Hence, many Japanese clinicians have made efforts to suppress the onset of tuberculosis and treat it effectively. The objectives of this study are to (1) identify covariate(s) that may explain the variation of rifampicin, which is the key antitubercular agent, under the steady-state by evaluating its population pharmacokinetics and (2) to propose an appropriate dosing method of rifampicin to Japanese patients. For this purpose, serum concentration–time data were obtained from 138 patients receiving rifampicin (300–450 mg) and isoniazid (300–400 mg) every day over 14 days, and analyzed using nonlinear mixed effects model. Thereby, population pharmacokinetic parameters were estimated followed by elucidating relations between the parameters and statistical factors. The analysis adopted one-compartment model including Lag-time by assuming that the absorption process is 0+1st order. The analyses demonstrate that meal affected the bioavailability, primary absorption rate constant, and zero order absorption time in the constructed model. A body weight calculated from the power model was selected as the covariate by the Stepwise Covariate Model method and found to highly affect the clearance in the range from −31.6% to 47.4%. We conclude that the dose in Japanese tuberculous patients can be well estimated by the power model formula and should be taken into consideration when rifampicin is administered.
Psychometric Properties of the Fear of Progression Questionnaire for
Children (FoP-Q-SF/C)
Authors: Luz Johanne Katrin , Martini Julia , Clever Katharina , Herschbach Peter , Christiansen Holger , Schepper Florian 
Published: March 2020

Abstract
Background Recent research shows that parents of children suffer from
fear of progression (FoP), the fear of further disease progression. It is most
possible that children also develop FoP, which could impair treatment and
psychological health. The aim of this study is to adapt the adult’s
version of the Fear of Progression Questionnaire – Short Form (FoP-Q-SF)
for children and to examine the psychometric properties in pediatric cancer
patients.
Patients 32 pediatric cancer patients between 10 and 18 years with
different diagnoses and in different treatment states participated in this
study.
Method In the cross-sectional study participants completed the adapted
Fear of Progression Questionnaire – Short Form for Children
(FoP-Q-SF/C) and self-report measures assessing quality of life,
depression, fear and coping satisfaction.
Results The questionnaire (FoP-Q-SF/C) showed adequate
psychometric properties (Cronbachs α=0.86) and good results for
construct validity. Significant medium to large correlations of
children’s FoP was observed with quality of life
(r=− 0.37), depression (r=0.52), fear
(r=0.33 – 0.76), and satisfaction with coping
(r=− 0.44). One-fifth of the sample was classified as
having high FoP with values over 37.
Conclusions The FoP-Q-SF/C is a short, economic questionnaire
that is applicable in children with cancer. Clinicians can use the questionnaire
to explore specific fear and the need for psychosocial support. Further research
for specific treatment approaches for FoP in pediatric cancer patients are
warranted.
A Study of Executive Function in Patients with Chronic Kidney Disease before and after a Single Session of Hemodialysis
Authors: Murthy Vasantmeghna S. , Shukla Vedant S. 
Published: March 2020

Abstract

Background Executive functions (EFs) are critical to daily life and sensitive to our physiological functioning and emotional states. The number of people living with chronic kidney disease (CKD) on hemodialysis (HD) globally is increasing steadily. We aimed to determine the impact of a single session of HD on EFs in patients with CKD receiving maintenance HD (MHD).

Methods This was a quasi-experimental study conducted at the department of psychiatry and dialysis unit of a tertiary hospital. Patients undergoing MHD underwent screening to rule out delirium, using the Confusion Assessment Method prior to EF testing. The tests of EF used were the Trail-Making Test—Part B (TMT-B) and Frontal Assessment Battery (FAB), both of which were administered before and after a session of HD. Statistical tests used were Wilcoxon matched pairs signed ranks test, paired t-test, single sample t-test, and correlation analyses.

Results The mean time taken on TMT-B before HD was 195.36 seconds and after HD, 171.1 seconds; difference is significant (p = 0.0001). The mean FAB score was 13.19 before HD and 14.83 after HD; the difference is significant (p < 0.0001). Significant differences were observed on similarities (p = 0.003), lexical fluency (p = 0.02), and go–no go (p = 0.003) subtests of FAB. Mean TMT-B scores before and after HD differed significantly from that of a reference study (reference TMT-B 150.69 seconds), p = 0.0002 and 0.04, respectively.

Conclusion We conclude that patients with CKD on MHD, in general, have worse executive cognitive functioning compared with healthy populations. A session of HD results in significant improvement in these functions.
Can Prolactinemia Cause Coronary Thrombosis
Authors: Akidi Goutham 
Published: March 2020

AbstractThere is an increasing trend of myocardial infarction (MI) among the young population. There exist various causes for this trend, as the pathogenesis of increased MI could be atheromatous, nonatheromatous, or hypercoagulable, and involve substance misuse. Here, we report a case of a 32-year-old female patient presented with coronary thrombosis; on evaluation, she was found to have hyperprolactinemia with no other causes of coronary thrombosis. Hyperprolactinemia is a rare cause of recurrent coronary thrombosis. Prolactin levels are even elevated in MI but they return to normal values in 2 to 4 weeks; however, this patient experienced a persistent elevation of prolactin levels with no signs of pituitary adenoma, so there is a possibility that elevated prolactin levels could cause coronary thrombosis.
Individual homogenization in large-scale systems: on the politics of computer and social architectures
Authors: Bürger Jens , Laguna-Tapia Andrés 
Published: March 2020

AbstractOne determining characteristic of contemporary sociopolitical systems is their power over increasingly large and diverse populations. This raises questions about power relations between heterogeneous individuals and increasingly dominant and homogenizing system objectives. This article crosses epistemic boundaries by integrating computer engineering and a historicalphilosophical approach making the general organization of individuals within large-scale systems and corresponding individual homogenization intelligible. From a versatile archeological-genealogical perspective, an analysis of computer and social architectures is conducted that reinterprets Foucault’sdisciplinesandpolitical anatomyto establish the notion of politics for a purely technical system. This permits an understanding of system organization as modern technology with application to technical and social systems alike. Connecting to Heidegger’s notions of theenframing(Gestell) and a moreprimal truth(anfänglicheren Wahrheit), the recognition of politics in differently developing systems then challenges the immutability of contemporary organization. Following this critique of modernity and within the conceptualization of system organization, Derrida’sdemocracy to come (à venir)is then reformulated more abstractly asorganizations to come. Through the integration of the discussed concepts, the framework ofLarge-Scale Systems Composed of Homogeneous Individuals(LSSCHI) is proposed, problematizing the relationships between individuals, structure, activity, and power within large-scale systems. The LSSCHI framework highlights the conflict of homogenizing system-level objectives and individual heterogeneity, and outlines power relations and mechanisms of control shared across different social and technical systems.
Transcriptional suppression of AMPKα1 promotes breast cancer metastasis upon oncogene activation
Authors: Yi Yong , Chen Deshi , Ao Juan , Zhang Wenhua , Yi Jianqiao , Ren Xiaokun , Fei Junjie , Li Fengtian , Niu Mengmeng , Chen Hu , Luo Yangkun , Luo Zhijun , Xiao Zhi-Xiong Jim 
Published: March 2020

Significance
Oncogenic hotspot mutations in PIK3CA and overexpression of HER2 are known as a driving force for human breast cancer metastasis. AMPK is pivotal in maintaining cellular energy homeostasis. In this study, we demonstrate that transcription inhibition of AMPKα1 is critically important in human advanced breast cancer with poor clinical outcomes, that AMPKα1 is transcriptionally inhibited in response to activation of PI3K/HER2, and that ΔNp63α, a tumor metastasis suppressor, is a direct transcriptional factor mediating oncogenic PI3K/HER2-induced transcriptional suppression of AMPKα1. In addition, inhibition of AMPK leads to disruption of cell–cell adhesion and promotes cancer metastasis. This study highlights a critical role for AMPK in the connection of cell–cell adhesion and cancer metastasis.
Host membrane lipids are trafficked to membranes of intravacuolar bacteriumEhrlichia chaffeensis
Authors: Lin Mingqun , Grandinetti Giovanna , Hartnell Lisa M. , Bliss Donald , Subramaniam Sriram , Rikihisa Yasuko 
Published: March 2020

SignificanceBiological membranes are essential for life. Although bacteria and eukaryotic cells have evolved to produce membranes of different compositions, several bacterial pathogens can hijack and utilize host-synthesized membrane lipids. Here, we show that an obligatory intracellular pathogen,Ehrlichia chaffeensis, deficient in biosynthesis of cholesterol and some glycerophospholipids, actively acquires host-derived membrane components within membrane-bound inclusions (vacuoles). The trafficking of host membrane components toEhrlichiaand membrane-bound inclusions appears to occur via endocytosis and autophagy induced by a bacteria-secreted protein. Numerous intraluminal vesicles were found inEhrlichiainclusions that may function as a membrane reserve for rapid proliferation ofEhrlichia. Our findings provide insights into host membrane assimilation by an intracellular pathogen, which can be exploited for antibacterial therapy.
Las metafunciones de Halliday en traducción
Authors: Chatzikoumi Eirini 
Published: March 2020

Abstract
This article addresses the contribution of Systemic Functional Linguistics (SFL) to translation and, specifically,
the use of Halliday’s metafunctions in translation studies research. The aim is to provide the state of the art of the main
findings and proposals of these studies regarding the role of metafunctions in translation and translation teaching, thus
evaluating their relevance and applicability in this field. In order to achieve this, six studies were reviewed, three of them
dedicated to metafunctional shifts and three to the use of metafunctions in translation teaching and evaluation. This critical
bibliographic review allowed for the corroboration of the contribution of SFL to the field of translation, and for the deduction
of relevant aspects for future research and teaching proposals. More precisely, the relevance of the incorporation of semantic
metafunctions in translator training and evaluation is confirmed, and the possibility of a distinction between obligatory and
optional metafunctional translation shifts is suggested.
Constructions, generalizations, and the unpredictability of language
Authors: Herbst Thomas 
Published: March 2020

AbstractAttempts at predicting syntactic behavior from semantic or other generalizations are often unsatisfactory. It is argued that the notion of competition as used byGoldberg (2019)can serve as an explanation for unpredictability in language because established formulations that are preferred over others automatically distort the collocational profiles of verbs in argument structure constructions. As a consequence of this, an approach of seeing items as items-in-constructions (and not as elements attracted to them) is argued for. It is then shown how this items-in-constructions view can be applied to designing models of reference constructicons and mental constructicons.
Dendrochronology of U.S. immigration
Authors: Cruz Pedro , Wihbey John , Ghael Avni , Shibuya Felipe , Costa Stephen 
Published: March 2020

Abstract
Immigrants are central to the identity of the United States, the population of which has grown in number and diversity as
a function of new arrivals from around the globe. This article describes a visualization project that uses the visual metaphor of tree rings
to explore the contribution of immigrants to the country’s population. Immigrants and native-born persons are represented and differentiated
as cells in trees, with layered annual rings capturing patterns of population growth. These rings register, in their shape and color,
certain environmental conditions. In order to mimic the natural process by which growth rings are formed, we devised a computational system
that simulates the growth of trees as if cells were data-units. Dendrochronology involves dating certain events by analyzing patterns of
growth in trees. Analogously, in our visualizations the rings can be counted and dated, showing the chronological evolution of the
population. The dendrochronology theme is a poetic take on the data, yet it is also a functional and conceptual space that is used to
construct language and rationales on that data. The tree-growth process not only inspires the appearance of the visualizations but also
informs the rules of the computational system that creates them.
Feeling numbers
Authors: Campbell Sarah , Offenhuber Dietmar 
Published: March 2020

AbstractFor means of communication, persuasion is a natural and critical part of conveying a message. Data visualizations, being means of communication themselves, are used as rhetorical instruments, but how they persuade has yet to be fully understood. Based on George Campbell’s rhetorical theory, this paper presents the results of an empirical study testing the effectiveness of appeals to emotion through proximity techniques – the contextual framing of a visualization. The findings indicate that people feel greater interest towards a topic when the visualized data are more relevant to them, and that data representing events closer in time are more affecting.