bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implications of using two low-power continuous-wave lasers for polishing
Authors: Zhang Wenxuan , Wong Kiwan , Morales Miguel , Molpeceres Carlos , Arnold Craig B 
Published: May 2020

Abstract
Laser polishing is widely employed to reduce the surface roughness of products with complex geometries. Traditional laser polishing techniques use a single high-power Gaussian beam to melt and smooth a thin layer of surface material. However, the reliance on high power lasers can present practical challenges such as minimizing surface evaporation or reducing overall cost. In this work, we combined two identical low-power laser beams with a spatial offset in between them to construct an elliptical beam. By changing the spatial offset, combined beams with different lengths along the major axis can be created. We observe over 20% improvement in line roughness reduction using this approach compared to a single Gaussian laser beam with the same total power. Additionally, both experiment and simulation results suggest such improvement is because this dual-laser set-up can create a longer molten pool compared to a single laser.
Synthesis, microbial susceptibility and anti-cancerous properties of copper oxide nanoparticles- review
Authors: Sharma Manisha , Sharma Anurag , Majumder Sudip 
Published: May 2020

Abstract
Use of Nanoparticles in the diagnosis of cancer and treatment of Cancer is being rapidly studied and developed. The present cancer chemotherapy agents are not much selective in differentiating between cancer cells and normal cells and often lead to development of drug resistance and severe side effects. This has prompted the need to study other potential anticancer agents like metallic oxide nanoparticles, with emphasis on their synthesis and application s in the treatment of cancer by designing targeted delivery system to tumour and cancer cells [Vinardell and Mitjans 2015. Nanomaterials, 5, 1004–1021, Valodkar et al 2011. Mater Chem Phys, 128, 83–89]. In this review paper an attempt has been made to study various methods of preparation of Copper Oxide Nanoparticles, their characteristics and the detailed microbial activities and anti-cancerous properties of these differently synthesized Copper Oxide Nanoparticles.
Chemerin as a Driver of Hypertension: A Consideration
Authors: Ferland David J , Mullick Adam E , Watts Stephanie W 
Published: May 2020

Abstract
The protein chemerin (tazarotene-induced gene, TIG2; RARRES2) is a relatively new adipokine. Many studies support that circulating chemerin levels associate strongly and positively with body mass index, visceral fat, and blood pressure. Here, we focus on the specific relationship of chemerin and blood pressure with the goal of understanding whether and how chemerin drives (pathological) changes in blood pressure such that it could be interfered with therapeutically. We dissect the biosynthesis of chemerin and how current antihypertensive medications change chemerin metabolism. This is followed with a review of what is known about where chemerin is synthesized in the body and what chemerin and its receptors can do to the physiological function of organs important to blood pressure determination (e.g., brain, heart, kidneys, blood vessels, adrenal, and sympathetic nervous system). We synthesize from the literature our best understanding of the mechanisms by which chemerin modifies blood pressure, with knowledge that plasma/serum levels of chemerin may be limited in their pathological relevance. This review reveals several gaps in our knowledge of chemerin biology that could be filled by the collective work of protein chemists, biologists, pharmacologists, and clinicians.
Development of a Personal Aerosol Sampler for Monitoring the Particle–Vapour Fractionation of SVOCs in Workplaces
Authors: Dragan George C , Kohlmeier Vesta , Orasche Juergen , Schnelle-Kreis Juergen , Forbes Patricia B C , Breuer Dietmar , Zimmermann Ralf 
Published: May 2020

Abstract
Semi-volatile organic compounds (SVOCs), partitioned between particulates and vapours of an aerosol, require special attention. The toxicological effects caused by the inhalation of such aerosols may depend on the concentration and in which phase the organic compounds are found. A personal denuder-gas–particle separation aerosol sampler was developed to provide information about the partitioning of aerosols from organic compounds. The sampler was tested in a series of controlled laboratory experiments, which confirmed the capability and accuracy of the sampler to measure gas–particle mixtures. An average difference of 14.8 ± 4.8% was found between sampler and reference laboratory instruments. The obtained results showed that our sampler enables a more accurate measurement of the SVOC aerosols’ gas–particle fractionation, compared with that of conventional samplers.
DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites
Authors: Liu Quanzhong , Chen Jinxiang , Wang Yanze , Li Shuqin , Jia Cangzhi , Song Jiangning , Li Fuyi 
Published: May 2020

AbstractDNA N4-methylcytosine (4mC) is an important epigenetic modification that plays a vital role in regulating DNA replication and expression. However, it is challenging to detect 4mC sites through experimental methods, which are time-consuming and costly. Thus, computational tools that can identify 4mC sites would be very useful for understanding the mechanism of this important type of DNA modification. Several machine learning-based 4mC predictors have been proposed in the past 3 years, although their performance is unsatisfactory. Deep learning is a promising technique for the development of more accurate 4mC site predictions. In this work, we propose a deep learning-based approach, called DeepTorrent, for improved prediction of 4mC sites from DNA sequences. It combines four different feature encoding schemes to encode raw DNA sequences and employs multi-layer convolutional neural networks with an inception module integrated with bidirectional long short-term memory to effectively learn the higher-order feature representations. Dimension reduction and concatenated feature maps from the filters of different sizes are then applied to the inception module. In addition, an attention mechanism and transfer learning techniques are also employed to train the robust predictor. Extensive benchmarking experiments demonstrate that DeepTorrent significantly improves the performance of 4mC site prediction compared with several state-of-the-art methods.
Thymosin Alpha 1 Reduces the Mortality of Severe Coronavirus Disease 2019 by Restoration of Lymphocytopenia and Reversion of Exhausted T Cells
Authors: Liu Yueping , Pan Yue , Hu Zhenhong , Wu Ming , Wang Chenhui , Feng Zeqing , Mao Congzheng , Tan Yingjun , Liu Ying , Chen Li , Li Min , Wang Gang , Yuan Zilin , Diao Bo , Wu Yuzhang , Chen Yongwen 
Published: May 2020

Abstract

Background
Thymosin alpha 1 (Tα1) had been used in the treatment of viral infections as an immune response modifier for many years. However, clinical benefits and the mechanism of Tα1 treatment for COVID-19 patients are still unclear.

Methods
We retrospectively reviewed the clinical outcomes of 76 severe COVID-19 cases admitted to 2 hospitals in Wuhan, China, from December 2019 to March 2020. The thymus output in peripheral blood mononuclear cells from COVID-19 patients was measured by T-cell receptor excision circles (TRECs). The levels of T-cell exhaustion markers programmed death-1 (PD-1) and T-cell immunoglobulin and mucin domain protein 3 (Tim-3) on CD8+ T cells were detected by flow cytometry.

Results
Compared with the untreated group, Tα1 treatment significantly reduced the mortality of severe COVID-19 patients (11.11% vs 30.00%, P = .044). Tα1 enhanced blood T-cell numbers in COVID-19 patients with severe lymphocytopenia. Under such conditions, Tα1 also successfully restored CD8+ and CD4+ T-cell numbers in elderly patients. Meanwhile, Tα1 reduced PD-1 and Tim-3 expression on CD8+ T cells from severe COVID-19 patients compared with untreated cases. It is of note that restoration of lymphocytopenia and acute exhaustion of T cells were roughly parallel to the rise of TRECs.

Conclusions
Tα1 treatment significantly reduced mortality of severe COVID-19 patients. COVID-19 patients with counts of CD8+ T cells or CD4+ T cells in circulation less than 400/μL or 650/μL, respectively, gained more benefits from Tα1. Tα1 reversed T-cell exhaustion and recovered immune reconstitution through promoting thymus output during severe acute respiratory syndrome–coronavirus 2 infection.
Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure
Authors: Jackman Shaun D , Coombe Lauren , Warren René L , Kirk Heather , Trinh Eva , MacLeod Tina , Pleasance Stephen , Pandoh Pawan , Zhao Yongjun , Coope Robin J , Bousquet Jean , Bohlmann Joerg , Jones Steven J M , Birol Inanc 
Published: May 2020

Abstract
Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.
Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements
Authors: Hosseini Morteza , Pratas Diogo , Morgenstern Burkhard , Pinho Armando J 
Published: May 2020

Abstract

Background
The development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial owing to their role in chromosomal evolution, genetic disorders, and cancer.

Results
We present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between 2 DNA sequences. This computational solution extracts information contents of the 2 sequences, exploiting a data compression technique to find rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image.

Conclusions
Tested on several synthetic and real DNA sequences from bacteria, fungi, Aves, and Mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions were in accordance with previous studies, which took alignment-based approaches or performed FISH (fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was ~1 GB, which makes Smash++ feasible to run on present-day standard computers.
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome
Authors: Marrano Annarita , Britton Monica , Zaini Paulo A , Zimin Aleksey V , Workman Rachael E , Puiu Daniela , Bianco Luca , Pierro Erica Adele Di , Allen Brian J , Chakraborty Sandeep , Troggio Michela , Leslie Charles A , Timp Winston , Dandekar Abhaya , Salzberg Steven L , Neale David B 
Published: May 2020

Abstract

Background
The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes.

Findings
Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars.

Conclusion
Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.
Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy
Authors: Lai Christopher K C , Ng Rita W Y , Wong Martin C S , Chong Ka Chun , Yeoh Yun Kit , Chen Zigui , Chan Paul K S 
Published: May 2020

Abstract

Background
Hong Kong (HK) is a densely populated city near the epicentre of the coronavirus disease 2019 (COVID-19) outbreak. Stringent border control together with aggressive case finding, contact tracing, social distancing and quarantine measures were implemented to halt the importation and spread of the virus.

Methods
We performed an epidemiological study using government information covering the first 100 confirmed cases to examine the epidemic curve, incidence, clusters, reproduction number (Rt), incubation period and time to containment.

Results
A total of 93 of the 100 cases were HK residents (6 infected in Mainland China, 10 on the Diamond Princess Cruise). Seven were visitors infected in Mainland China before entering HK. The majority (76%) were aged ≥45 years, and the incidence increased with age (P &lt; 0.001). Escalation of border control measures correlated with a decrease in the proportion (62.5% to 0%) of cases imported from Mainland China, and a reduction in Rt (1.07 to 0.75). The median incubation period was 4.2 days [95% confidence interval (CI), 4.0–4.5; 5th and 95th percentiles: 1.3 and 14.0). Most clusters with identifiable epidemiological links were households involving 2–4 people. Three medium-spreading events were identified: two from New Year gatherings (6–11 people), and another from environmental contamination of a worship hall (12 people). Despite intensified contact tracing, containment was delayed in 78.9% of cases (mean = 5.96 days, range = 0–24 days). An unusual transmission in a multi-storey building via faulty toilet plumbing was suspected with &gt;100 residents evacuated overnight. Our analysis indicated that faulty plumbing was unlikely to be the source of this transmission.

Conclusion
Timely stringent containment policies minimized the importation and transmission of COVID-19 in HK.
Detecting carbapenemase-producing Enterobacterales (CPE): an evaluation of an enhanced CPE infection control and screening programme in acute care
Authors: Otter Jonathan A , Mookerjee Siddharth , Davies Frances , Bolt Frances , Dyakova Eleonora , Shersing Yeeshika , Boonyasiri Adhiratha , Weiße Andrea Y , Gilchrist Mark , Galletly Tracey J , Brannigan Eimear T , Holmes Alison H 
Published: May 2020

AbstractObjectivesThe transmission of carbapenemase-producing Enterobacterales (CPE) poses an increasing healthcare challenge. A range of infection prevention activities, including screening and contact precautions, are recommended by international and national guidelines. We evaluated the introduction of an enhanced screening programme in a multisite London hospital group.MethodsIn June 2015, an enhanced CPE policy was launched in response to a local rise in CPE detection. This increased infection prevention measures beyond the national recommendations, with enhanced admission screening, contact tracing and environmental disinfection, improved laboratory protocols and staff/patient education. We report the CPE incidence and trends of CPE in screening and clinical cultures and the adoption of enhanced CPE screening. All non-duplicate CPE isolates identified between April 2014 and March 2018 were included.ResultsThe number of CPE screens increased progressively, from 4530 in July 2015 to 10 589 in March 2018. CPE detection increased from 18 patients in July 2015 (1.0 per 1000 admissions) to 50 patients in March 2018 (2.7 per 1000 admissions). The proportion of CPE-positive screening cultures remained at approximately 0.4% throughout, suggesting that whilst the CPE carriage rate was unchanged, carrier identification increased. Also, 123 patients were identified through positive CPE clinical cultures over the study period; there was no significant change in the rate of CPE from clinical cultures per 1000 admissions (P = 0.07).ConclusionsOur findings suggest that whilst the enhanced screening programme identified a previously undetected reservoir of CPE colonization in our patient population, the rate of detection of CPE in clinical cultures did not increase.
A Bolognese collector rediscovered: Count Ludovico Caprara (1621–1695) and the seventeenth-century art market
Authors: Iseppi Giulia 
Published: May 2020

Abstract
This study concerns the discovery of a new figure in the field of seventeenth-century art collecting: Count Ludovico Caprara, a general under Ferdinand II de’ Medici. Newly discovered archival documents reveal that the Caprara family had one of the richest collections of paintings in Bologna, displayed in a palace close to the Piazza Maggiore; most of these works, however, remain untraced. Ludovico collected more than a hundred canvases, mostly portraits of contemporary painters. The discovery of a purchase note and an inventory of the picture gallery have allowed the role of Ludovico in contemporary collecting and his contacts with personalities in the art market of Seicento Bologna to be established. An attempt is made here to identify several paintings by Giovanni Andrea Sirani, Francesco Gessi and others, and to clarify certain aspects of Ludovico’s taste, especially his preference for the Bolognese school, despite spending his life at the Medici court.
HAGLROS is overexpressed and promotes non-small cell lung cancer migration and invasion
Authors: Chen Ying , Shen Tianle , Ding Xuping , Cheng Lei , Sheng Liming , Du Xianghui 
Published: May 2020

Abstract

Introduction
Non-small cell lung cancer was one of the most common and deadly cancers worldwide. Long non-coding RNAs had been implicated in multiple human cancers, including non-small cell lung cancer. In this study, we focused on a novel long non-coding RNA, HAGLROS, in non-small cell lung cancer.

Material and methods
In this study, we used GEPIA dataset to analyse the expression levels of HAGLROS in non-small cell lung cancer samples and normal tissues. Then, we analysed Kaplan–Meier Plotter database to reveal the association between HAGLROS expression and overall survival time in patients with non-small cell lung cancer. Moreover, we used small interfering RNA-mediated knockdown to reduce HAGLROS expression in A549 and H1299 cells. Cell Counting Kit-8 assay was used to detect the effect of HAGLROS on cell proliferation. Transwell assays were used to determine the effect of HAGLROS on cell migration and invasion. Co-expression analysis and bioinformatics analysis were conducted to predict the potential functions of HAGLROS in non-small cell lung cancer.

Results
We identified HAGLROS was significantly overexpressed in non-small cell lung cancer samples compared to normal tissues. Higher expression of HAGLROS was significantly associated with shorter overall survival time in patients with non-small cell lung cancer. Moreover, we found knockdown of HAGLROS in non-small cell lung cancer cells remarkably suppressed tumour proliferation, migration and invasion. By conducting bioinformatics analysis, we found HAGLROS was involved in regulating multiple cancer-related pathways, including Spliceosome, DNA replication, cell cycle, chromosome segregation and sister chromatid segregation.

Conclusions
Our results for the first time demonstrated HAGLROS may serve as a target for new therapies in non-small cell lung cancer.
Voronoi volume function: a new probe of cosmology and galaxy evolution
Authors: Paranjape Aseem , Alam Shadab 
Published: May 2020

ABSTRACT
We study the Voronoi volume function (VVF) – the distribution of cell volumes (or inverse local number density) in the Voronoi tessellation of any set of cosmological tracers (galaxies/haloes). We show that the shape of the VVF of biased tracers responds sensitively to physical properties such as halo mass, large-scale environment, substructure, and redshift-space effects, making this a hitherto unexplored probe of both primordial cosmology and galaxy evolution. Using convenient summary statistics – the width, median, and a low percentile of the VVF as functions of average tracer number density – we explore these effects for tracer populations in a suite of N-body simulations of a range of dark matter models. Our summary statistics sensitively probe primordial features such as small-scale oscillations in the initial matter power spectrum (as arise in models involving collisional effects in the dark sector), while being largely insensitive to a truncation of initial power (as in warm dark matter models). For vanilla cold dark matter (CDM) cosmologies, the summary statistics display strong evolution and redshift-space effects, and are also sensitive to cosmological parameter values for realistic tracer samples. Comparing the VVF of galaxies in the Galaxies & Mass Assembly (GAMA) survey with that of abundance-matched CDM (sub)haloes tentatively reveals environmental effects in GAMA beyond halo mass (modulo unmodelled satellite properties). Our exploratory analysis thus paves the way for using the VVF as a new probe of galaxy evolution physics as well as the nature of dark matter and dark energy.
A new class of discontinuous solar wind solutions
Authors: Shergelashvili Bidzina M , Melnik Velentin N , Dididze Grigol , Fichtner Horst , Brenn Günter , Poedts Stefaan , Foysi Holger , Khodachenko Maxim L , Zaqarashvili Teimuraz V 
Published: May 2020

ABSTRACT
A new class of one-dimensional solar wind models is developed within the general polytropic, single-fluid hydrodynamic framework. The particular case of quasi-adiabatic radial expansion with a localized heating source is considered. We consider analytical solutions with continuous Mach number over the entire radial domain while allowing for jumps in the flow velocity, density, and temperature, provided that there exists an external source of energy in the vicinity of the critical point that supports such jumps in physical quantities. This is substantially distinct from both the standard Parker solar wind model and the original nozzle solutions, where such discontinuous solutions are not permissible. We obtain novel sample analytic solutions of the governing equations corresponding to both slow and fast winds.