bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spin momentum-dependent orbital motion
Authors: Yan Shaohui , Li Manman , Liang Yansheng , Cai Yanan , Yao Baoli 
Published: March 2020

Abstract
We present a theoretic analysis on (azimuthal) spin momentum-dependent orbital motion experienced by particles in a circularly-polarized annular focused field. Unlike vortex phase-relevant (azimuthal) orbital momentum flow whose direction is specified by the sign of topological charge, the direction of (azimuthal) spin momentum flow is determined by the product of the field’s polarization ellipticity and radial derivative of field intensity. For an annular focused field with a definite polarization ellipticity, the intensity’s radial derivative has opposite signs on two sides of the central ring (intensity maximum), causing the spin momentum flow to reverse its direction when crossing the central ring. When placed in such a spin momentum flow, a probe particle is expected to response to this flow configuration by changing the direction of orbital motion as it traversing from one side to the other. The reversal of the particle’s orbital motion is a clear sign that spin momentum flow can affect particles’ orbital motion alone even without orbital momentum flow. More interestingly, for dielectric particles the spin momentum-dependent orbital motion tends to be ‘negative’, i.e., in the opposite direction of the spin momentum flow. This arises mainly because of spin–orbit interaction during the scattering process. For the purpose of experimental observation, we suggest the introduction of an auxiliary radially-polarized illumination to adjust the particle’s radial equilibrium position, for the radial gradient force of the circularly-polarized annular focused field tends to constrain the particle at the ring of intensity maximum.
Bias variation detection in RF amplifiers using differential OBIST
Authors: Ballot M , Stander T 
Published: March 2020

Abstract
Oscillation-based built-in self-testing with differential power detection has been shown to be a promising method for detecting degradation in radio frequency (RF) amplifiers. We demonstrate the use of the method to detect supply voltage decrease and base current variation. The efficacy of the approach is verified using simulated results of a 2.4 GHz low-noise amplifier (LNA). It is shown that these variations can be detected by using only power detection.
Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Authors: Xue Yaxin , Lanzén Anders , Jonassen Inge 
Published: March 2020

Abstract

Motivation
Technological advances in meta-transcriptomics have enabled a deeper understanding of the structure and function of microbial communities. ‘Total RNA’ meta-transcriptomics, sequencing of total reverse transcribed RNA, provides a unique opportunity to investigate both the structure and function of active microbial communities from all three domains of life simultaneously. A major step of this approach is the reconstruction of full-length taxonomic marker genes such as the small subunit ribosomal RNA. However, current tools for this purpose are mainly targeted towards analysis of amplicon and metagenomic data and thus lack the ability to handle the massive and complex datasets typically resulting from total RNA experiments.

Results
In this work, we introduce MetaRib, a new tool for reconstructing ribosomal gene sequences from total RNA meta-transcriptomic data. MetaRib is based on the popular rRNA assembly program EMIRGE, together with several improvements. We address the challenge posed by large complex datasets by integrating sub-assembly, dereplication and mapping in an iterative approach, with additional post-processing steps. We applied the method to both simulated and real-world datasets. Our results show that MetaRib can deal with larger datasets and recover more rRNA genes, which achieve around 60 times speedup and higher F1 score compared to EMIRGE in simulated datasets. In the real-world dataset, it shows similar trends but recovers more contigs compared with a previous analysis based on random sub-sampling, while enabling the comparison of individual contig abundances across samples for the first time.

Availability and implementation
The source code of MetaRib is freely available at https://github.com/yxxue/MetaRib.

Contact
yaxin.xue@uib.no or Inge.Jonassen@uib.no

Supplementary information
Supplementary data are available at Bioinformatics online.
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
Authors: Firtina Can , Kim Jeremie S , Alser Mohammed , Senol Cali Damla , Cicek A Ercument , Alkan Can , Mutlu Onur 
Published: March 2020

Abstract

Motivation
Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs. These long reads are used to construct an assembly (i.e. the subject’s genome), which is further used in downstream genome analysis. Unfortunately, third-generation sequencing technologies have high sequencing error rates and a large proportion of base pairs in these long reads is incorrectly identified. These errors propagate to the assembly and affect the accuracy of genome analysis. Assembly polishing algorithms minimize such error propagation by polishing or fixing errors in the assembly by using information from alignments between reads and the assembly (i.e. read-to-assembly alignment information). However, current assembly polishing algorithms can only polish an assembly using reads from either a certain sequencing technology or a small assembly. Such technology-dependency and assembly-size dependency require researchers to (i) run multiple polishing algorithms and (ii) use small chunks of a large genome to use all available readsets and polish large genomes, respectively.

Results
We introduce Apollo, a universal assembly polishing algorithm that scales well to polish an assembly of any size (i.e. both large and small genomes) using reads from all sequencing technologies (i.e. second- and third-generation). Our goal is to provide a single algorithm that uses read sets from all available sequencing technologies to improve the accuracy of assembly polishing and that can polish large genomes. Apollo (i) models an assembly as a profile hidden Markov model (pHMM), (ii) uses read-to-assembly alignment to train the pHMM with the Forward–Backward algorithm and (iii) decodes the trained model with the Viterbi algorithm to produce a polished assembly. Our experiments with real readsets demonstrate that Apollo is the only algorithm that (i) uses reads from any sequencing technology within a single run and (ii) scales well to polish large assemblies without splitting the assembly into multiple parts.

Availability and implementation
Source code is available at https://github.com/CMU-SAFARI/Apollo.

Supplementary information
Supplementary data are available at Bioinformatics online.
Fit for measure? Evaluation in community development
Authors: Ardle Oonagh Mc , Murray Una 
Published: March 2020

AbstractCommunity development is a process where people concerned with social and environmental justice act together as engaged and active citizens1 to change their collective circumstances. A concern to deliver change through these processes raises the questions: How do we know if our work is effective? What do we mean by and how do we assess outcomes? What ‘evidence’ will help us articulate and improve how we do our work? Over the past decades, there has been a growing trend globally towards evaluation to understand and improve practice. Nevertheless, there is a lack of clarity about, and application of, appropriate frameworks for community development evaluation (Motherway, 2006; CDF, 2010; Whelan et al., 2019). Drawing on current practice, this paper explores challenges, principles and methods for evaluation in community development. We argue that ‘measurement’ requires a clear understanding and agreement of community development purpose and processes, including recognition of community as within and beyond place. Drawing on international evaluation criteria and models, we conclude that community development work could learn from these, as long as communities are in central decision-making roles. We offer suggestions for principles to inform evaluation efforts in community development, suggesting that good community development processes and associated outcomes represent in themselves a theory of change.
Twitter promotion predicts citation rates of cardiovascular articles: a preliminary analysis from the ESC Journals Randomized Study
Authors: Ladeiras-Lopes Ricardo , Clarke Sarah , Vidal-Perez Rafael , Alexander Michael , Lüscher Thomas F 
Published: March 2020

Abstract

Aims
The association between the dissemination of scientific articles on Twitter and online visibility (including Altmetric score) is still controversial and the impact on citation rates has never been addressed for cardiovascular medicine journals.

Methods and Results
The ESC Journals Study randomized 696 papers published in the ESC Journals family (March 2018–May 2019) for promotion on Twitter or to a control arm (with no active tweeting from ESC channels) and aimed to assess if Twitter promotion was associated with an increase in citation rate (primary endpoint) and Altmetric score. This is a preliminary analysis of 536 articles (77% of total) published until December 2018 (therefore, papers published at least 6 months before collecting citation and Altmetrics data). In the analysis of the primary endpoint, Twitter promotion of articles was associated with a 1.43 (95% confidence interval 1.29–1.58) higher rate of citations, and this effect was independent of the type of article. Both Altmetric score and number of users tweeting were positively associated with the number of citations in both arms, with evidence of a stronger association (interaction) in the Twitter arm.

Conclusion
Therefore, a social media strategy of Twitter promotion for cardiovascular medicine papers seems to be associated with increased online visibility and higher number of citations. The final analysis will include 696 papers and 2-year scientific citation rate and is estimated to be concluded in March 2021.
Bacillus subtilis RZ001 improves intestinal integrity and alleviates colitis by inhibiting the Notch signalling pathway and activating ATOH-1
Authors: Li Yanru , Zhang Tengxun , Guo Congcong , Geng Meng , Gai Sailun , Qi Wei , Li Zhongyuan , Song Yajian , Luo Xuegang , Zhang Tongcun , Wang Nan 
Published: March 2020

ABSTRACT
Intestinal mucosal barriers help the body resist many intestinal inflammatory diseases, such as inflammatory bowel disease (IBD). In this study, we identified a novel bacterium promoting the repair of intestinal mucosa and investigated the potential mechanisms underlying its activity. Culture supernatant of Bacillus subtilis RZ001 upregulated the expression of mucin 2 (MUC2) and tight junction (TJ) proteins in HT-29 cells in vitro. Oral administration of B. subtilis RZ001 may have significantly reduced symptoms such as the dextran sulfate sodium (DSS)-induced decrease in body weight, shortening of colon length and overproduction of proinflammatory factors. The number of goblet cells and levels of MUC2 and TJ proteins were significantly increased in adult mice fed with B. subtilis RZ001. B. subtilis RZ001 cells upregulated the levels of MUC2 in the intestinal organoids. Furthermore, culture supernatant of B. subtilis RZ001 could suppress the Notch signalling pathway and activate the expression of atonal homolog 1 (Atoh1). The transcription factor Atoh1 is required for intestinal secretory cell differentiation and activates transcription of MUC2 via binding to E-boxes on the MUC2 promoter. Taken together, B. subtilis strain RZ001 has the potential for treating IBD. The present study is helpful to elucidate the mechanisms of B. subtilis action.
Impact of Low Muscle Mass and Low Muscle Strength According to EWGSOP2 and EWGSOP1 in Community-Dwelling Older People
Authors: Costanzo Luisa , De Vincentis Antonio , Di Iorio Angelo , Bandinelli Stefania , Ferrucci Luigi , Antonelli Incalzi Raffaele , Pedone Claudio 
Published: March 2020

Abstract

Background
A universal definition of sarcopenia is still lacking. Since the European criteria have been recently revised, we aimed at studying prevalence of low muscle strength (LMS) and low muscle mass (LMM), as defined according to the European Working Group of Sarcopenia in Older People (EWGSOP) 2 and 1 definitions, and their individual contribution toward mortality and incident mobility disability in a cohort of community-dwelling older people.

Methods
Longitudinal analysis of 535 participants of the InCHIANTI study. LMS and LMM were defined according to the criteria indicated in the EWGSOP2 and 1. Cox and log-binomial regressions were used to examine association with mortality and 3-year mobility disability (inability to walk 400 m).

Results
We observed a lower prevalence of the combination LMM/LMS according to EWGSOP2 compared to EWGSOP1 (3.2% vs 6.2%). Using the new criteria, all sarcopenia components were associated with mortality, although the hazard ratio [HR] for the group LMM/LMS was no longer significant after adjustment for confounders (LMM: HR 2.69, 95% confidence interval [CI] 1.04–6.94; LMS: HR 3.18, 95% CI 1.44–7.01; LMM/LMS: HR 2.95, 95% CI 0.86–10.16). Using EWGSOP1, LMS alone was independently associated with mortality (HR 4.43, 95% CI 1.85–10.57). None of the sarcopenia components conferred a higher risk of mobility disability.

Conclusions
The EWGSOP2 algorithm leads to a reduction in the estimated prevalence of sarcopenia defined as combination of LMM/LMS. The finding that, independent of the adopted criteria, people with LMS and normal mass have a higher mortality risk compared to robust individuals, confirms that evaluation of muscle strength has a central role for prognosis evaluation.
CNS glycosylphosphatidylinositol deficiency results in delayed white matter development, ataxia and premature death in a novel mouse model
Authors: Lukacs Marshall , Blizzard Lauren E , Stottmann Rolf W 
Published: March 2020

Abstract
The glycosylphosphatidylinositol (GPI) anchor is a post-translational modification added to approximately 150 different proteins to facilitate proper membrane anchoring and trafficking to lipid rafts. Biosynthesis and remodeling of the GPI anchor requires the activity of over 20 distinct genes. Defects in the biosynthesis of GPI anchors in humans lead to inherited glycosylphosphatidylinositol deficiency (IGD). IGD patients display a wide range of phenotypes though the central nervous system (CNS) appears to be the most commonly affected tissue. A full understanding of the etiology of these phenotypes has been hampered by the lack of animal models due to embryonic lethality of GPI biosynthesis gene null mutants. Here we model IGD by genetically ablating GPI production in the CNS with a conditional mouse allele of phosphatidylinositol glycan anchor biosynthesis, class A (Piga) and Nestin-Cre. We find that the mutants do not have structural brain defects but do not survive past weaning. The mutants show progressive decline with severe ataxia consistent with defects in cerebellar development. We show that the mutants have reduced myelination and defective Purkinje cell development. Surprisingly, we found that Piga was expressed in a fairly restricted pattern in the early postnatal brain consistent with the defects we observed in our model. Thus, we have generated a novel mouse model of the neurological defects of IGD which demonstrates a critical role for GPI biosynthesis in cerebellar and white matter development.
Transition Without Transformation: The Legacy of Sudan’s Comprehensive Peace Agreement
Authors: Carolan Gene 
Published: March 2020

Abstract
In recent years, the transitional justice framework has expanded to include a broader notion of transformative justice, which strives for socio-political reform in addition to legal accountability. Over the course of two civil wars, Sudan has grappled with various attempts at transition and transformation with mixed results. Though the 2005 Comprehensive Peace Agreement brought an end to decades of North–South conflict, South Sudan’s subsequent descent into civil war has been characterised by a flawed transition and a lack of any immediate transformative potential.
This paper analyses the Comprehensive Peace Agreement’s transitional mechanisms. In doing so, it explores how certain mechanisms frame the ‘meta-conflict’ about what the conflict is about, and how this can cut off a range of conflict resolution opportunities. It concludes by considering the legacy of the Comprehensive Peace Agreement in contemporary Sudan and South Sudan, and how it might inform the prospective transitions in both countries.
Generalized Cesàro Operators: Geometry of Spectra and Quasi-Nilpotency
Authors: Limani Adem , Malman Bartosz 
Published: March 2020

Abstract
For the class of Hardy spaces and standard weighted Bergman spaces of the unit disk, we prove that the spectrum of a generalized Cesàro operator $T_g$ is unchanged if the symbol $g$ is perturbed to $g+h$ by an analytic function $h$ inducing a quasi-nilpotent operator $T_h$, that is, spectrum of $T_h$ equals $\{0\}$. We also show that any $T_g$ operator that can be approximated in the operator norm by an operator $T_h$ with bounded symbol $h$ is quasi-nilpotent. In the converse direction, we establish an equivalent condition for the function $g \in \textbf{BMOA}$ to be in the $\textbf{BMOA}$ norm closure of $H^{\infty }$. This condition turns out to be equivalent to quasi-nilpotency of the operator $T_g$ on the Hardy spaces. This raises the question whether similar statement is true in the context of Bergman spaces and the Bloch space. Furthermore, we provide some general geometric properties of the spectrum of $T_{g}$ operators.
A Fruitful Endeavor: Scent Cues and Echolocation Behavior Used by Carollia castanea to Find Fruit
Authors: Leiser-Miller L B , Kaliszewska Z A , Lauterbur M E , Mann Brianna , Riffell J A , Santana S E 
Published: March 2020

Synopsis
Frugivores have evolved sensory and behavioral adaptations that allow them to find ripe fruit effectively, but the relative importance of different senses in varying foraging scenarios is still poorly understood. Within Neotropical ecosystems, short-tailed fruit bats (Carollia: Phyllostomidae) are abundant nocturnal frugivores that rely primarily on Piper fruits as a food resource. Previous research has demonstrated that Carollia employs olfaction and echolocation to locate Piper fruit, but it is unknown how their sensory use and foraging decisions are influenced by the complex diversity of chemical cues that fruiting plants produce. Using free-ranging C. castanea and their preferred food, Piper sancti-felicis, we conducted behavioral experiments to test two main hypotheses: (1) foraging decisions in C. castanea are primarily driven by ripe fruit scent and secondarily by vegetation scent, and (2) C. castanea re-weights their sensory inputs to account for available environmental cues, with bats relying more heavily on echolocation in the absence of adequate scent cues. Our results suggest that C. castanea requires olfactory information and relies almost exclusively on ripe fruit scent to make foraging attempts. Piper sancti-felicis ripe fruit scent is chemically distinct from vegetation scent; it is dominated by 2-heptanol, which is absent from vegetation scent, and has a greater abundance of β-caryophyllene, β-ocimene, γ-elemene, and α-cubebene. Although variation in echolocation call parameters was independent of scent cue presence, bats emitted longer and more frequent echolocation calls in trials where fruit scent was absent. Altogether, these results highlight the adaptations and plasticity of the sensory system in neotropical fruit bats.
Assessment of medicine use among outpatients at healthcare facilities in Ethiopia using the WHO’s prescribing indicators with a focus on antibiotics: a systematic review and meta-analysis
Authors: Teni Fitsum Sebsibe , Wubishet Befikadu Legesse , Yimenu Dawit Kumilachew 
Published: March 2020

AbstractObjectivesTo summarize studies on prescribing medicine to general outpatients through the WHO/International Network for Rational Use of Drugs (INRUD) prescribing indicators with a focus on antibiotic prescription.MethodsA systematic review and random-effects meta-analysis of studies on the WHO prescribing indicators with a focus on the percentage of encounters with antibiotics prescribed (PEAP) was performed. The databases PubMed, Web of Science, EMBASE and Global Index Medicus were searched.ResultsTwenty-six studies with a total of over 34 000 prescription encounters were included in the systematic review, showing a mean of two medicines per encounter. In each meta-analysis, a range of 19 to 25 studies was included. The percentages of medicines prescribed with an international non-proprietary name (INN) and from the essential medicines list (EML) were 91% and 96% of the total number of medicines, respectively, while 19% of encounters contained injections. Studies with over 25 000 prescription encounters reported an average PEAP of 58% and PEAP showed an increasing trend over the years included in this review. Multivariable meta-regression showed that PEAP increased with the average number of medicines per encounter (estimate = 0.83, P value = 0.0005). The number of medicines, study design and year of prescription explained over 40% of the variation in PEAP across studies.ConclusionsPatterns of medicine use within and close to the WHO reference values were reported for the number of medicines, INN prescribing, prescription of injections and compliance with the EML, on average. Prescription of antibiotics requires attention as amounts much higher than the reference values were prescribed, which were even higher with polypharmacy and increasing over the years included in this review.
Evaluation of the CERTUS Environmental Listeria Species Detection Kit for the Detection of Listeria Species on Environmental Surfaces: AOAC Performance Tested MethodSM 101802
Authors: Bodner John , Toribo Mike , Carruthers Erin , Weber Michael , Urquhart Holly , Perera Nevin , Illingworth Simon , Miller Dean , Yamaki Kiyoshi , Bastin Benjamin , Bird Patrick , Klass Nicole , Agin James , Goins David 
Published: March 2020

Abstract

Background
CERTUS Environmental Listeria species Detection Kit (CERTUS EL Detection Kit) is a real-time, bio-contained assay designed to accurately detect Listeria species (L. grayi, L. innocua, L. ivanovii, L. marthii, L. monocytogenes, L. seeligeri, and L. welshimeri) from environmental surface matrixes using an antibody-coupled magnetic microparticle with a Surface Enhanced Raman Spectroscopy (SERS) nanoparticle technology test system paired with proprietary CERTUS EL Selective Growth Media and CERTUS Detection Unit.

Objective
The method was evaluated for AOAC®Performance Tested MethodSM certification.

Methods
Inclusivity and exclusivity, matrix studies, product consistency and stability were conducted to evaluate the CERTUS EL Detection Kit.

Results
In the matrix studies, stainless steel, ceramic tile, plastic (polystyrene) and sealed concrete environmental surfaces (4 × 4” test areas) were tested. No statistically significant differences were found by Probability of Detection analysis (POD) in any of the matrixes when results were compared to the U.S. Food and Drug Administration cultural microbiology reference method for Listeria. The CERTUS EL Detection Kit correctly identified all 50 target Listeria isolates and correctly excluded all 30 non-target strains that were analyzed. Probability of Detection analysis of CERTUS EL Detection Kit robustness, product consistency (lot-to-lot) and stability studies demonstrated no statistically significant differences, and no variation was observed between instruments.

Conclusions
The data collected in these studies demonstrate that the CERTUS EL Detection Kit is a reliable method for the rapid and specific detection of Listeria from stainless steel, ceramic tile, plastic (polystyrene) and sealed concrete environmental surfaces.