bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aquila_stLFR: diploid genome assembly based structural variant calling package for stLFR linked-reads
Authors: Liu Yichen Henry , Grubbs Griffin L , Zhang Lu , Fang Xiaodong , Dill David L , Sidow Arend , Zhou Xin 
Published: June 2021

Abstract

Motivation
Identifying structural variants (SVs) is critical in health and disease, however, detecting them remains a challenge. Several linked-read sequencing technologies, including 10X Genomics, TELL-Seq and single tube long fragment read (stLFR), have been recently developed as cost-effective approaches to reconstruct multi-megabase haplotypes (phase blocks) from sequence data of a single sample. These technologies provide an optimal sequencing platform to characterize SVs, though few computational algorithms can utilize them. Thus, we developed Aquila_stLFR, an approach that resolves SVs through haplotype-based assembly of stLFR linked-reads.

Results
Aquila_stLFR first partitions long fragment reads into two haplotype-specific blocks with the assistance of the high-quality reference genome, by taking advantage of the potential phasing ability of the linked-read itself. Each haplotype is then assembled independently, to achieve a complete diploid assembly to finally reconstruct the genome-wide SVs. We benchmarked Aquila_stLFR on a well-studied sample, NA24385, and showed Aquila_stLFR can detect medium to large size deletions (50 bp–10 kb) with high sensitivity and medium-size insertions (50 bp–1 kb) with high specificity.

Availability and implementation
Source code and documentation are available on https://github.com/maiziex/Aquila_stLFR.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
A meta-analysis on continuous versus interrupted skin closure following appendicectomy
Authors: Sharma A , Rajalingam V , Nageswaran H , Best L 
Published: June 2021

Abstract

Background
The aim of this review was to analyse RCTs comparing wound-related outcomes between continuous subcuticular and interrupted transdermal wound closures for open appendicectomies in all age groups.

Methods
A systematic literature search was conducted in April 2020 (MEDLINE, Embase, CENTRAL, Web of Science, PROSPERO, Google Scholar, WHO International Clinical Trials Registry Platform). RCTs without restrictions on study language, year, status of publication, and patient age were included. The risk of bias was assessed using the risk-of-bias tool for RCTs. Pooled risk ratios (RRs) and mean differences (MDs) for binary and continuous variables were calculated using random-effects models. A summary-of-findings table was generated to assess the level of evidence.

Results
Eleven trials were included (1781 patients analysed, 891 in continuous and 890 in interrupted groups). The overall rate of wound infection was 7.1 per cent. There was no significant difference in the risk of wound infection (11 trials, 1781 patients; RR 1.13, 95 per cent c.i. 0.77 to 1.66; P = 0.530) or wound exploration (7 trials, 1129 patients; RR 0.74, 0.41 to 1.34, P = 0.320) between the two groups. Continuous wound closure had a significantly reduced risk of wound dehiscence (6 trials, 865 patients; RR 0.16, 0.05 to 0.50; P = 0.002) and smaller wound scar (3 trials, 417 patients; MD –2.11 (95 per cent c.i. –2.57 to –1.66) mm; P &lt; 0.001). The absolute risk reduction and number needed to treat for wound dehiscence were 6.1 per cent and 16 respectively. There was no significant statistical heterogeneity for all outcomes (I2 0–15 per cent, χ2 P &gt; 0.100). Most RCTs had a high risk of bias.

Conclusion
Continuous subcuticular open appendicectomy wound closure is not associated with an increased risk of wound infection and exploration. This method of closure has a reduced risk of wound dehiscence and better cosmetic outcomes.
Prophylactic anticoagulation in sinus rhythm for stroke prevention in cardiovascular disease: contemporary meta-analysis of large randomized trials
Authors: Lander Krystle , Thakeria Priyanka , Nayyar Sachin 
Published: June 2021

Abstract

Aims
Anticoagulation with non-vitamin K oral anticoagulants (NOACs) to prevent stroke is a mainstay of atrial fibrillation (AF) management. However, multiple cardiovascular diseases (CVDs) are associated with elevated ischaemic stroke risk even in sinus rhythm. In this meta-analysis, we assess efficacy and safety of prophylactic NOAC agents for stroke prevention in patients without AF.

Methods and results
A search was conducted for randomized controlled trials (RCTs) that evaluated an NOAC and control drug (placebo or antiplatelet) in non-AF patients with mixed CVD. The primary efficacy and safety outcomes were ischaemic stroke and major bleeding, respectively. Results were stratified based on primary- and mini-NOAC doses. Thirteen RCTs were identified with a total of 89 383 patients with CVD in sinus rhythm (53 778 on NOAC, 35 605 on control drug; mean age 65.5 ± 2.7 years). Over a mean follow-up of 18.3 months, 1429 (1.6%) ischaemic strokes occurred. Use of NOAC was associated with 26% reduction in stroke [odds ratio (OR) 0.74, 95% confidence interval (CI) 0.62–0.87; 1.1 vs. 1.8 events per 100 person-years], with numbers needed to treat of 153 patients to prevent one stroke. Major bleeding was increased with NOAC (OR 1.74, 95% CI 1.44–2.09; 2.1 vs. 1.0 events per 100 person-years). The weighted net clinical benefit (wNCB, composite of ischaemic stroke and bleeding) did not suggest a favourable effect with any NOAC dose (wNCB for primary-dose: −0.35; mini-dose: −0.06).

Conclusion
Current evidence does not support use of NOACs for stroke prevention in non-AF CVD population as risk of major bleeding still exceeds ischaemic stroke benefit.
The Organization of the Sinoatrial Node Microvasculature Varies Regionally to Match Local Myocyte Excitability
Authors: Grainger Nathan , Guarina Laura , Cudmore Robert H , Santana L Fernando 
Published: June 2021

Abstract
The cardiac cycle starts when an action potential is produced by pacemaking cells in the sinoatrial node. This cycle is repeated approximately 100 000 times in humans and 1 million times in mice per day, imposing a monumental metabolic demand on the heart, requiring efficient blood supply via the coronary vasculature to maintain cardiac function. Although the ventricular coronary circulation has been extensively studied, the relationship between vascularization and cellular pacemaking modalities in the sinoatrial node is poorly understood. Here, we tested the hypothesis that the organization of the sinoatrial node microvasculature varies regionally, reflecting local myocyte firing properties. We show that vessel densities are higher in the superior versus inferior sinoatrial node. Accordingly, sinoatrial node myocytes are closer to vessels in the superior versus inferior regions. Superior and inferior sinoatrial node myocytes produce stochastic subthreshold voltage fluctuations and action potentials. However, the intrinsic action potential firing rate of sinoatrial node myocytes is higher in the superior versus inferior node. Our data support a model in which the microvascular densities vary regionally within the sinoatrial node to match the electrical and Ca2+ dynamics of nearby myocytes, effectively determining the dominant pacemaking site within the node. In this model, the high vascular density in the superior sinoatrial node places myocytes with metabolically demanding, high-frequency action potentials near vessels. The lower vascularization and electrical activity of inferior sinoatrial node myocytes could limit these cells to function to support sinoatrial node periodicity with sporadic voltage fluctuations via a stochastic resonance mechanism.
Technological paradigms and the power of convergence
Authors: Pedota Mattia , Grilli Luca , Piscitello Lucia 
Published: June 2021

AbstractWith the advent of Industry 4.0, technological interdependence is becoming increasingly important in the delineation of technological development dynamics. In the present paper, we propose an extension of the theory of technological paradigms conceptualizing the role of technological interdependence in the emergence of paradigms and the coevolution of the corresponding trajectories. We corroborate our conceptual extension by means of an in-depth historical account of the genesis and evolution of the additive manufacturing paradigm. Accordingly, we elucidate how different technological paradigms may give rise to an aggregate paradigm through a process of convergence and how the aggregate paradigm may contribute to steering the direction of technological change alongside traditional science-push, demand-pull, institutional, and socioeconomic factors. Our work has two main implications: first, it shows that a technological paradigm may emerge from a process of incremental convergence and not only from radical innovations and scientific breakthroughs. Second, it shows that the dynamics of epistemological interdependence (i.e., interdependence between paradigms) matter significantly in the determination of technological development paths.
Market Court of Finland rules on reasonable compensation in a trade mark infringement case concerning cheaper foreign alcohol and a national retailing monopoly
Authors: Malvikko Max , Matikainen Teemu 
Published: June 2021

Abstract
Alko Oy v Aldar Latvia SIA, MAO:48/21, 9 February 2021
The Market Court of Finland recently determined trade mark damages in the light of complex circumstances.
Current plant diversity but not its soil legacy influences exotic plant invasion
Authors: Xue Wei , Yao Si-Mei , Huang Lin , Roiloa Sergio R , Ji Bao-Ming , Yu Fei-Hai 
Published: June 2021

AbstractCurrent plant diversity can influence exotic plant invasion, but it is unclear whether there is a legacy effect of plant diversity on exotic plant invasion. As plant diversity can affect soil microbial communities and physio-chemical properties, which may cascade to impact subsequent exotic plant growth, we hypothesize that the soil legacy effect of plant diversity can influence exotic plant invasion. We conducted a plant–soil feedback experiment. In the conditioning phase, we trained soils by monocultures of 12 plant species from three functional groups (4 grasses, 3 legumes and 5 forbs) and mixtures of 8 randomly selected species with all three functional groups from this 12-species pool. In the test phase, we grew the invasive plant Bidens pilosa with a co-occurring native grass (Arthraxon hispidus), with a co-occurring native forb (Pterocypsela indica) or with both in each type of the conditioned soils. The performance of B. pilosa relative to its native competitors varied depending on the functional type of both conditioning plant species in the conditioning phase and competing plant species in the test phase. Diversity of the conditioning plants did not influence the growth difference between B. pilosa and its native competitors. However, increasing diversity of the competing plant species reduced the performance of B. pilosa relative to its native competitors. Our results suggest that current plant diversity can reduce exotic plant invasion through increasing growth inequality between invasive and native plants, but the soil legacy effect of plant diversity may have little impact on exotic plant invasion.
Hesperidin mitigates inflammation and modulates ectoenzymes activity and some cellular processes in complete Freund’s adjuvant-induced arthritic rats
Authors: Adefegha Stephen Adeniyi , Saccol Renata da Silva Pereira , Jantsch Matheus Henrique , da Silveira Karine Lanes , Leal Daniela Bitencourt Rosa 
Published: June 2021

Abstract

Objectives
This study was aimed at assessing the anti-arthritic effects of hesperidin on the inflammatory markers in serum/plasma, ectoenzymes activity in platelet, reactive oxygen species (ROS), apoptosis and cell cycle in bone marrow cells of a rat model of arthritis.

Methods
Fifty-six adult female Wistar rats (245–274 g) were grouped into eight of seven rats each: control rats given normal saline or 40 mg/kg of hesperidin or 80 mg/kg of hesperidin, 0.2 mg/kg of dexamethasone, arthritic rats given normal saline, or 40 mg/kg of hesperidin or 80 mg/kg of hesperidin, and 0.2 mg/kg of dexamethasone. Myeloperoxidase and nitrate plus nitrite levels were evaluated in the plasma and serum, respectively. The ecto-nucleoside triphosphate diphosphohydrolases, ecto-5′-nucleotidase and ecto-adenosine deaminase activities were assessed in platelets. Subsequently, the cells of the bone marrow were obtained, and the assays for ROS, apoptosis and cell cycle were evaluated using flow cytometry.

Key findings
The results showed that hesperidin mitigated inflammation, modulated adenosine nucleotides and nucleoside hydrolysing enzymes and levels, minimized ROS intracellularly, attenuated apoptotic process and activated cell cycle arrest in arthritic rat.

Conclusion
This study suggests that hesperidin could be a natural and promising anti-inflammatory compound for the management of arthritis.
Beyond the Partnership Debate: Localizing Knowledge Production in Refugee and Forced Migration Studies
Authors: Shivakoti Richa , Milner James 
Published: June 2021

AbstractThere is a growing recognition in refugee and forced migration studies that research partnerships, especially those that cross geographies of the global North and global South, are both a blessing and a potential curse. They are a blessing as they encourage new approaches to the co-creation of knowledge, build solidarity networks, and leverage support for scholars based in the global South. But they can also be a curse as they typically function within and can inadvertently reproduce deeply embedded structures of inequality. Drawing on the results of a review of forced displacement research centres based in the global South and interviews with the directors of these centres, this article encourages a shift from focusing on research partnerships to an approach that supports the localization of knowledge production in refugee and forced migration studies. This approach seeks to change the structures of knowledge production, including direct funding to researchers and research centres based in the global South, an emphasis on the transfer of power to researchers in the South, a recognition of the diverse forms and sources of knowledge produced within the field, and an appreciation for the diverse understandings of success and impact across contexts.
Prevalence of vulvovaginal candidiasis in Brazil: A systematic review
Authors: Carvalho Gabriela Corrêa , de Oliveira Rafaela Aparecida Prata , Araujo Victor Hugo Sousa , Sábio Rafael Miguel , de Carvalho Lídia Raquel , Bauab Taís Maria , Corrêa Ione , Chorilli Marlus 
Published: June 2021

Abstract

Vulvovaginal candidiasis (CVV) is a condition in which signs and symptoms are related to inflammation caused by Candida spp infection. It is the second leading cause of vaginitis in the world, representing a public health problem. The present systematic review comes with the proposal of analyze and identify the available evidence on CVV prevalence in Brazil, pointing out its variability by regions. For this, a systematic literature review was carried out with meta-analysis of cross-sectional and cohort studies, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyzes (PRISMA) guide recommendations, and was registered in the International Prospective Register of Systematic Reviews (PROSPERO 2020 CRD42020181695). The databases used for survey were LILACS, Scielo, Scopus, PUBMED, Web of Science and CINAHL. Fifteen studies were selected to estimate CVV prevalence in the Brazilian territory. South and Southeast regions have higher prevalences than the North and Northeast regions, no data were found for the Midwest region. The estimated prevalence for Brazil is 18%, however, it is suggested that this number is higher due to underreporting and the presence of asymptomatic cases. Therefore, new epidemiological studies are recommended throughout Brazil, to elucidate the profile of this disease in the country, in addition to assisting in the elaboration of an appropriate prevention plan by state.

Lay summary
Data found in the literature regarding the epidemiological profile of vulvovaginal candidiasis in Brazil are obsolete and incomplete, so the present systematic review has the proposal to analyze and identify the evidence on vulvovaginal candidiasis prevalence in Brazil. The estimated prevalence is 18%; however, this number can be higher.
Asteroseismology of RRab variable star EZ Cnc from K2 photometry and LAMOST spectroscopy
Authors: Wang Jiangtao , Fu Jian-Ning , Zong Weikai , Wang Jiaxin , Zhang Bo 
Published: June 2021

ABSTRACT
EZ Cnc, or EPIC 212182292, is a non-Blažko RRab variable star located in the field of K2 Campaign 16. Its atmospheric parameters (Teff, log g, [M/H]) and radial velocities are measured from the 55 high-quality LAMOST medium-resolution spectra. The fundamental frequency of pulsation is derived as f = 1.8323(17) d−1 from the K2 light curves. The amplitude ratios R21 = 0.5115(15), 0.490(8), R31 = 0.3249(20), 0.279(7) and Fourier phase differences φ21 = 2.7550(20), 2.764(16), φ31 = 5.7194(25), 5.719(31) are determined from the Fourier decomposition of K2 light curve and LAMOST radial velocity curve, respectively. Through the constraints of the parameters, four optimal models are obtained in a time-dependent turbulent convection model survey for EPIC 212182292. The parameters of EPIC 212182292 are derived as M = 0.48 ± 0.03 M⊙, L = 42 ± 2 L⊙, Teff = 6846 ± 50 K, log g = 2.79 ± 0.01 dex, and Z = 0.006 ± 0.002, respectively. The precisely determined parameters for RRab variable stars like EPIC 212180092 might help to better understand the period–luminosity relationship of RR Lyrae stars.
An empirical calibration of the helium abundance in H ii regions based in literature and CALIFA survey data
Authors: Valerdi M , Barrera-Ballesteros J K , Sánchez S F , Espinosa-Ponce C , Carigi L , Mejía-Narváez A 
Published: June 2021

ABSTRACT
Helium is the second most common chemical species in the Universe. The study of helium abundance has the potential to unravel the chemical evolution of and within galaxies. In this study, we provide an empirical calibration for the singly ionized helium abundance: 12 + log10(He+/H+), based on the emission line flux ratio Heλ5876/H α from Galactic and extragalactic H ii regions compiled from the literature. Based on this calibrator, we explore for the first time the helium abundance in a large sample of H ii regions located in galaxies representative of the nearby Universe from the CALIFA survey. Furthermore, this calibrator allows us to explore the variations of the helium abundance with respect to the oxygen abundance. The observed trends are in agreement with a change in the chemical enrichment with mass/oxygen abundance similar to the one observed due to the inside-out model in a MW-galaxy (highlighting the connection between resolved and global trends in galaxies). Our calibrator provides an empirical proxy to estimate the helium abundance at kpc scales as well as to constrain chemical evolutionary models.
Does concentration drive the scatter in the stellar-to-halo mass relation of galaxy clusters?
Authors: Zu Ying , Shan Huanyuan , Zhang Jun , Singh Sukhdeep , Shao Zhiwei , Chen Xiaokai , Yao Ji , Golden-Marx Jesse B , Cui Weiguang , Jullo Eric , Kneib Jean-Paul , Zhang Pengjie , Yang Xiaohu 
Published: June 2021

ABSTRACT
Concentration is one of the key dark matter halo properties that could drive the scatter in the stellar-to-halo mass relation of massive clusters. We derive robust photometric stellar masses for a sample of brightest central galaxies (BCGs) in SDSS redmapper clusters at 0.17 &lt; z &lt; 0.3, and split the clusters into two equal-halo mass subsamples by their BCG stellar mass $M_*^{\mathrm{BCG}}$. The weak lensing profiles ΔΣ of the two cluster subsamples exhibit different slopes on scales below $1\, h^{-1}\, {\mathrm{Mpc}}$. To interpret such discrepancy, we perform a comprehensive Bayesian modelling of the two ΔΣ profiles by including different levels of miscentring effects between the two subsamples as informed by X-ray observations. We find that the two subsamples have the same average halo mass of $1.74\times 10^{14}\, h^{-1}\, \mathrm{M}_{\odot }$, but the concentration of the low-$M_*^{\mathrm{BCG}}$ clusters is $5.87_{-0.60}^{+0.77}$, ∼1.5σ smaller than that of their high-$M_*^{\mathrm{BCG}}$ counterparts ($6.95_{-0.66}^{+0.78}$). Furthermore, both cluster weak lensing and cluster-galaxy cross-correlations indicate that the large-scale bias of the low-$M_*^{\mathrm{BCG}}$, low-concentration clusters are ${\sim}10{{\ \rm per\ cent}}$ higher than that of the high-$M_*^{\mathrm{BCG}}$, high-concentration systems, hence possible evidence of the cluster assembly bias effect. Our results reveal a remarkable physical connection between the stellar mass within $20{-}30\, h^{-1}\, {\mathrm{kpc}}$, the dark matter mass within ${\sim}200\, h^{-1}\, {\mathrm{kpc}}$, and the cosmic overdensity on scales above $10\, h^{-1}\, {\mathrm{Mpc}}$, enabling a key observational test of theories of co-evolution between massive clusters and their central galaxies.
Feasibility and Morbidity of Magnetic Resonance Imaging-Guided Stereotactic Laser Ablation of Deep Cerebral Cavernous Malformations: A Report of 4 Cases
Authors: Malcolm James G , Douglas J Miller , Greven Alex , Rich Christopher , Dawoud Reem A , Hu Ranliang , Reisner Andrew , Barrow Daniel L , Gross Robert E , Willie Jon T 
Published: June 2021

Abstract

BACKGROUND
Magnetic resonance imaging (MRI)-guided laser interstitial thermal therapy (MRgLITT) has been used successfully to treat epileptogenic cortical cerebral cavernous malformations (CCM). It is unclear whether MRgLITT would be as feasible or safe for deep CCMs

OBJECTIVE
To describe our experience with MRgLITT for symptomatic deep CCMs

METHODS
Patients’ records were reviewed retrospectively. MRgLITT was carried out using a commercially available system in an interventional MRI suite with efforts to protect adjacent brain structures. Immediate postoperative imaging was used to judge ablation adequacy. Delayed postoperative MRI was used to measure lesion volume changes during follow-up.

RESULTS
Four patients with CCM in the thalamus, putamen, midbrain, or subthalamus presented with persistent and disabling neurological symptoms. A total of 2 patients presented with disabling headaches and sensory disturbances and 2 with recurrent symptomatic hemorrhages, of which 1 had familial CCM. Patients were considered by vascular neurosurgeons to be poor candidates for open surgery or had refused it. Multiple trajectories were used in most cases. Adverse events included device malfunction with leakage of saline causing transient mass effect in one patient, and asymptomatic tract hemorrhage in another. One patient suffered an expected mild but persistent exacerbation of baseline deficits. All patients showed improvement from a previously aggressive clinical course with lesion volume decreased by 20% to 73% in follow-up.

CONCLUSION
MRgLITT is feasible in the treatment of symptomatic deep CCM but may carry a high risk of complications without the benefit of definitive resection. We recommend cautious patient selection, low laser power settings, and conservative temperature monitoring in surrounding brain parenchyma.