bluuebunny/crossref_metadata_2025 huggingface dataset:
Network-based ranking in social systems: three challenges
Authors: Mariani Manuel S , Lü Linyuan
Published: May 2020

Ranking algorithms are pervasive in our increasingly digitized societies, with important real-world applications including recommender systems, search engines, and influencer marketing practices. From a network science perspective, network-based ranking algorithms solve fundamental problems related to the identification of vital nodes for the stability and dynamics of a complex system. Despite the ubiquitous and successful applications of these algorithms, we argue that our understanding of their performance and their applications to real-world problems face three fundamental challenges: (1) rankings might be biased by various factors; (2) their effectiveness might be limited to specific problems; and (3) agents’ decisions driven by rankings might result in potentially vicious feedback mechanisms and unhealthy systemic consequences. Methods rooted in network science and agent-based modeling can help us to understand and overcome these challenges.
The Pathfields Tool: a frailty case-finding tool using primary care IT—implications for population health management
Authors: Attwood David , Boorer James , Ellis Wendy , Earley Michelle , Denovan Jillian , Calkoen Agnies , Hart Gerard , Williams Maria , Burdett Nicholas , Lemon Mel , Hope Suzy , Chisnell Julia
Published: May 2020

Background

older people living with frailty benefit from targeted interventions which improve health and independence. However, it has been challenging within primary care to systematically identify patients living with frailty.

Study aims

Methods

primary care IT was re-programmed to create a ‘Pathfields High Risk Cohort’ (PHRC, patients felt likely to have undiagnosed frailty) and invite clinicians to opportunistically assess and diagnose frailty. Results were compared with NHS England’s current approach to frailty identification using Electronic Frailty Index (eFI) to see which approach had the highest diagnostic yield.

Results

the Pathfields Tool identified 1,348 patients in PHRC group, of whom 951 (70.5%) were clinically assessed and diagnosed:

eFI (moderate and severe) identified 683 patients of whom 598 (87.6%) were clinically assessed and diagnosed:

Extrapolated data would estimate frailty prevalence at 22.5% (1,024/4,552) (5.5% severe, 8.8% moderate, and 8.1% mild) in the practice population aged 65+.

Conclusions

the Pathfields Tool identified more patients with clinically confirmed previously undiagnosed frailty than eFI ‘moderate and severe frailty’ alone.

Sub-segmenting frailty by residential status could significantly improve the population health management of older people.
Evaluation of dosing and safety outcomes of low-dose prophylactic warfarin in children after cardiothoracic surgery
Authors: Harkin Maura , Shaddix Brittany Powers , Neely Stephen B , Peek Leigh A , Stephens Katy , Barker Philip , McMullan Lauren , Gormley Andrew , Johnson Peter N
Published: May 2020

Purpose

Prophylactic warfarin with an International Normalized Ratio (INR) goal of 1.5 to 2.0 is one antithrombotic therapy utilized in children after cardiothoracic surgery (CTS); published sources suggest a dose of 0.1 mg/kg per day to achieve this goal. However, few studies have evaluated dosing in this population. The purpose of this study was to evaluate dosing and safety outcomes in children receiving warfarin after CTS.

Methods

A descriptive, retrospective review was conducted to evaluate warfarin dosing and INR outcomes in patients 18 years of age or younger who underwent CTS and received prophylactic warfarin with an INR goal of 1.5 to 2.0 from January 2014 through December 2018. The primary objective was to determine the median initial warfarin dose. Secondary objectives included identifying the percentage of documented INR values that were outside the therapeutic range, the percentage of patients with therapeutic INRs at discharge, and the 30-day readmission rate.

Results

Twenty-six patients were included in the review. The median initial warfarin dosage was 0.07 mg/kg/d (interquartile range [IQR], 0.05-0.10 mg/kg/d). Of the total of 177 INR values collected during the entire study period, 67 (37.9%) were therapeutic, 64 (36.2%) were subtherapeutic, and 46 (26.0%) were supratherapeutic. Eighteen patients (69.2%) had at least 1 supratherapeutic INR at any point during the study period, most frequently on days 2 through 4 of therapy. At discharge, 11 patients (42.3%) had therapeutic INRs. Four patients (15.4%) were readmitted within 30 days, with bleeding documented in 2 patients during their readmission.

Conclusion

The majority of patients received an initial warfarin dose less than that specified in published recommendations but still had a supratherapeutic INR at least once during the study period. When initiating warfarin after CTS, a dosage of <0.1 mg/kg per day and frequent monitoring may be needed to achieve an INR goal of 1.5 to 2.0.
Relationship Between Vertical Glabellar Lines and the Supratrochlear and Supraorbital Arteries
Authors: Cotofana Sebastian , Alfertshofer Michael , Frank Konstantin , Bertucci Vince , Beleznay Katie , Nikolis Andreas , Sykes Jonathan , Swift Arthur , Lachman Nirusha , Schenck Thilo L
Published: May 2020

Background

Glabellar soft tissue filler injections have been shown to be associated with a high risk of causing injection-related visual compromise.

Objectives

The aim of this study was to identify the course of the superficial branch of the supratrochlear and of the deep branch of the supraorbital artery in relation to the ipsilateral vertical glabellar line and to test whether an artery is located deep to this line.

Methods

Forty-one healthy volunteers with a mean age of 26.17 [9.6] years and a mean BMI of 23.09 [2.3] kg/m2 were analyzed. Ultrasound imaging was applied to measure the diameters, distance from skin surface, distance between the midline, distance between vertical glabella lines, and the cutaneous projection of the supratrochlear/supraorbital arteries at rest and upon frowning.

Results

The mean distance between the superficial branch of the supratrochlear artery and the ipsilateral vertical glabellar line was 10.59 [4.0] mm in males and 8.21 [4.0] mm in females, whereas it was 22.38 [5.5] mm for the supraorbital artery in males and 20.73 [5.6] mm in females. Upon frowning, a medial shift in supratrochlear arterial position of 1.63 mm in males and 1.84 mm in females and of 3.9 mm in supraorbital arterial position for both genders was observed. The mean depth of the supratrochlear artery was 3.34 [0.6] mm at rest, whereas the depth of the supraorbital artery was 3.54 [0.8] mm.

Conclusions

The hypothesis that injecting soft tissue fillers next to the vertical glabellar line is safe because the supratrochlear artery courses deep to the crease should be rejected. Additionally, the glabella and the supraorbital region should be considered as an area of mobile, rather than static, soft tissues.
GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
Authors: Schäfer Richard A , Lott Steffen C , Georg Jens , Grüning Björn A , Hess Wolfgang R , Voß Björn
Published: May 2020

Motivation

The correct prediction of bacterial sRNA homologs is a prerequisite for many downstream analyses based on comparative genomics, but it is frequently challenging due to the short length and distinct heterogeneity of such homologs. GLobal Automatic Small RNA Search go (GLASSgo) is an efficient tool for the prediction of sRNA homologs from a single input query. To make the algorithm available to a broader community, we offer a Docker container along with a free-access web service. For non-computer scientists, the web service provides a user-friendly interface. However, capabilities were lacking so far for batch processing, version control and direct interaction with compatible software applications as a workflow management system can provide.

Results

Here, we present GLASSgo 1.5.2, an updated version that is fully incorporated into the workflow management system Galaxy. The improved version contains a new feature for extracting the upstream regions, allowing the search for conserved promoter elements. Additionally, it supports the use of accession numbers instead of the outdated GI numbers, which widens the applicability of the tool.

Availability and implementation

GLASSgo is available at https://github.com/lotts/GLASSgo/ under the MIT license and is accompanied by instruction and application data. Furthermore, it can be installed into any Galaxy instance using the Galaxy ToolShed.
The cognitive consequences of the COVID-19 epidemic: collateral damage?
Authors: Ritchie Karen , Chan Dennis , Watermeyer Tam
Published: May 2020

Recovery from coronavirus disease 2019 (COVID-19) will be principally defined in terms of remission from respiratory symptoms; however, both clinical and animal studies have shown that coronaviruses may spread to the nervous system. A systematic search on previous viral epidemics revealed that while there has been relatively little research in this area, clinical studies have commonly reported neurological disorders and cognitive difficulties. Little is known with regard to their incidence, duration or underlying neural basis. The hippocampus appears to be particularly vulnerable to coronavirus infections, thus increasing the probability of post-infection memory impairment, and acceleration of neurodegenerative disorders such as Alzheimer’s disease. Future knowledge of the impact of COVID-19, from epidemiological studies and clinical practice, will be needed to develop future screening and treatment programmes to minimize the long-term cognitive consequences of COVID-19.
Altered Resting-State Functional Connectivity Between Awake and Isoflurane Anesthetized Marmosets
Authors: Hori Yuki , Schaeffer David J , Gilbert Kyle M , Hayrynen Lauren K , Cléry Justine C , Gati Joseph S , Menon Ravi S , Everling Stefan
Published: May 2020

The common marmoset (Callithrix jacchus) is a New World primate that is becoming increasingly popular as a preclinical model. To assess functional connectivity (FC) across the marmoset brain, resting-state functional MRI (RS-fMRI) is often performed under isoflurane anesthesia to avoid the effects of motion, physiological stress, and training requirements. In marmosets, however, it remains unclear how isoflurane anesthesia affects patterns of FC. Here, we investigated the effects of isoflurane on FC when delivered with either medical air or 100% pure oxygen, two canonical methods of inhalant isoflurane anesthesia delivery. The results demonstrated that when delivered with either medical air or 100% oxygen, isoflurane globally decreased FC across resting-state networks that were identified in awake marmosets. Generally, although isoflurane globally decreased FC in resting-state networks, the spatial structure of the networks was preserved. Outside of the context of RS networks, we indexed pair-wise functional connectivity between regions across the brain and found that isoflurane substantially altered interhemispheric and thalamic FC. Taken together, these findings indicate that RS-fMRI under isoflurane anesthesia is useful to evaluate the global structure of functional networks, but may obfuscate important nodes of some network components when compared to data acquired in fully awake marmosets.
Skeletal and dentoalveolar effects using tooth-borne and tooth-bone-borne RME appliances: a randomized controlled trial with 1-year follow-up
Authors: Bazargani Farhan , Lund Henrik , Magnuson Anders , Ludwig Björn
Published: May 2020

Objectives

To evaluate and compare the skeletal and dentoalveolar effects of tooth-borne (TB) and tooth-bone-borne (TBB) rapid maxillary expansion (RME).

Materials and methods

Fifty-two consecutive patients who met the eligibility criteria were recruited and allocated to either the TB group, mean age 9.3 years [standard deviation (SD) 1.3], or the TBB group, mean age 9.5 years (SD 1.2). Cone-beam computed tomography (CBCT) records and plaster models were taken before (T0), directly after (T1), and 1 year after expansion (T2). Dentoalveolar and skeletal measurements were made on the CBCT images. The dental expansion was also measured on the plaster models.

Randomization

Participants were randomly allocated in blocks of different sizes using the concealed allocation principle in a 1:1 ratio. The randomization list was also stratified by sex to ensure homogeneity between groups.

Blinding

Due to clinical limitations, only the outcomes assessors were blinded to the groups to which the patients were allocated.

Results

Skeletal expansion in the midpalatal suture and at the level of the nasal cavity was significantly higher in the TBB group. However, the magnitude of the expansion in the midpalatal suture was around 1 mm [95 per cent confidence interval (CI) 0.5–1.7, P = 0.001] more and perhaps not clinically significant. The magnitude of the expansion at the level of the nasal cavity was almost two times higher in the TBB group (95 per cent CI 0.7–2.6, P = 0.001). The dental expansion, alveolar bending, tipping of the molars, and stability 1 year post-expansion did not show any statistically significant differences between the groups. The actual direct cost of the treatment for the TBB group was approximately €300 higher than TB group.

Limitations

Double blinding was not possible due to the clinical limitations.

Conclusions

In young preadolescents with constricted maxilla and no signs of upper airway obstruction, it seems that conventional TB RME achieves the same clinical results with good stability 1 year post-expansion at lower cost.

Trial registration

The trial was not registered.
Trade wars: What do they mean? Why are they happening now? What are the costs?
Authors: Mattoo Aaditya , Staiger Robert W
Published: May 2020

How should economists interpret current trade wars and the recent US trade actions that have initiated them? In this paper, we offer an interpretation of current US trade actions that are at once more charitable and less forgiving than that typically offered by economic commentators. More charitable, because we argue that it is possible to see a logic to these actions: the United States is initiating a change from ‘rules-based’ to ‘power-based’ tariff bargaining and is selecting countries with which it runs bilateral trade deficits as the most suitable targets of its bargaining tariffs. Less forgiving, because the main costs of these trade tactics cannot be avoided even if they happen to ‘work’ and deliver lower tariffs. Rather, we show that the main costs will arise from the use of the tactics themselves and from the damage done by those tactics to the rules-based multilateral trading system and the longer-term interests of the United States and the rest of the world. JEL codes: F02, F13
Measuring family caregivers’ experience of interprofessional care for patients and families: development of the Japanese version of the Caregivers’ Experience Instrument
Authors: Nakayama Gen , Masumoto Shoichi , Haruta Junji , Maeno Tetsuhiro
Published: May 2020

Background

Improving individuals’ experience of care is now a critical goal of health care systems. Although a number of instruments have been developed to measure experience of care, few instruments measure family caregivers’ experience of interprofessional care for patients and families.

Objective

To develop the Japanese version of the Caregivers’ Experience Instrument (J-IEXPAC CAREGIVERS) and to investigate its validity in assessing quality of integrated care for both patients with chronic conditions and their family caregivers, from the caregivers’ perspective, in Japan.

Methods

We used a cross-sectional questionnaire survey to test the validity and internal consistency of J-IEXPAC CAREGIVERS. Four hundred family caregivers were recruited in three municipalities. We evaluated the feasibility, structural validity, internal consistency and hypothesis testing for construct validity of the scale.

Results

A total of 274 (68.5%) questionnaires were analysed. Confirmatory factor analysis showed acceptable model fit for the hypothesized two-factor model according to fit indices, as identified for the original version: attention for the patient and attention for the caregiver. Cronbach’s alpha for score in J-IEXPAC CAREGIVERS with 12 items was high (0.92). Spearman’s rank correlation coefficient between overall caregiver satisfaction and J-IEXPAC CAREGIVERS score was 0.71. Family caregivers who experienced home-visit services had significantly (P = 0.001) higher total scores than those who did not.

Conclusions

This pilot study showed that the J-IEXPAC CAREGIVERS is valid and reliable. This scale can be useful for evaluating quality of integrated care, with focus on family caregivers and patients with chronic conditions in Japan.
Do Big Five Personality Traits Moderate the Effects of Stressful Life Events on Health Trajectories? Evidence From the Health and Retirement Study
Authors: Mitchell Lauren L , Zmora Rachel , Finlay Jessica M , Jutkowitz Eric , Gaugler Joseph E
Published: May 2020

Objectives

Theory suggests that individuals with higher neuroticism have more severe negative reactions to stress, though empirical work examining the interaction between neuroticism and stressors has yielded mixed results. The present study investigated whether neuroticism and other Big Five traits moderated the effects of recent stressful life events on older adults’ health outcomes.

Method

Data were drawn from the subset of Health and Retirement Study participants who completed a Big Five personality measure (N = 14,418). We used latent growth curve models to estimate trajectories of change in depressive symptoms, self-rated physical health, and C-reactive protein levels over the course of 10 years (up to six waves). We included Big Five traits and stressful life events as covariates to test their effects on each of these three health outcomes. We examined stressful life events within domains of family, work/finances, home, and health, as well as a total count across all event types.

Results

Big Five traits and stressful life events were independently related to depressive symptoms and self-rated health. There were no significant interactions between Big Five traits and stressful life events. C-reactive protein levels were unrelated to Big Five traits and stressful life events.

Discussion

Findings suggest that personality and stressful life events are important predictors of health outcomes. However, we found little evidence that personality moderates the effect of major stressful events across a 2-year time frame. Any heightened reactivity related to high neuroticism may be time-limited to the months immediately after a major stressful event.
Deformation of a spherical, viscoelastic, and incompressible Earth for a point load with periodic time change
Authors: Tang He , Dong Jie , Zhang Lan , Sun Wenke
Published: May 2020

Planetary-scale mass redistributions occur on Earth for certain spatiotemporal periods, and these surface mass changes excite the global periodic loading deformations of a viscoelastic Earth. However, the characteristics of periodic viscoelastic deformations have not been well investigated even in a simple earth model. In this study, we derive the semi-analytical Green's functions (fully analytical Love numbers) for long-standing point sources with given periods using a modified asymptotic scheme in a homogeneous Maxwell spherical earth model. Here, the asymptotic scheme is needed in order to obtain accurate semi-analytical time-dependent Green's functions. The amplitudes and phases of the Green's functions may be biased if only the series summations of the Love numbers are used because the influence of viscoelasticity is degree-dependent. We compare the viscoelastic and elastic periodic Green's functions with different material viscosities and loading periods and investigate the amplitude increase percentage and phase delay of the periodic displacement and geoid change. For example, our analysis revealed that the viscosity increases the amplitude by 40–120 per cent and delays the phase approximately −100° to 60° for the displacement and geoid change when bearing a 10-yr loading period, assuming a viscosity of 1018 Pa s and a shear modulus 4 × 1010 Pa.
Alexandrov–Bakelman–Pucci-Type Estimate for Plurisubharmonic Functions
Authors: Dinew Sławomir , Dinew Żywomir
Published: May 2020

We prove an optimal Alexandrov–Bakelman–Pucci-type estimate for plurisubharmonic functions without assuming their continuity. This generalizes a result of Wang. As a corollary, we generalize an estimate from [15]. We also address a problem posed in [29].
Injuries on the Youth Soccer (Football) Field: Do Additional Referees Reduce Risk? Randomized Crossover Trial
Authors: Schwebel David C , Long D Leann , McClure Leslie A
Published: May 2020

Objective

Youth soccer injury can be prevented through various means, but few studies consider the role of referees. Following previous research suggesting children take fewer risks when supervised intensely, this randomized crossover trial evaluated whether risky play and injuries decrease under supervision from three referees instead of one referee.

Methods

Youth soccer clubs serving a metropolitan U.S. area participated. Boys’ and girls’ clubs at under age 10 (U10) and under age 11 (U11) levels were randomly assigned such that when the same clubs played each other twice in the same season, they played once with one referee and once with three referees. A total of 98 games were videotaped and subsequently coded to obtain four outcomes: collisions between players, aggressive fouls (involving physical player-to-player contact) called by the referee(s) on the field, aggressive fouls judged by trained coders, and injuries requiring adult attention or play stoppage.

Results

Poisson mixed model results suggest players in the 98 games committed fewer aggressive fouls, as identified independently by referees (rate ratio [RR] 0.58; 95% confidence interval [CI] 0.35–0.96) and by researchers (RR 0.67; 95% CI 0.50–0.90), when there were three referees versus one referee. Collisions (RR 0.98; 95% CI 0.86–1.12) and injury rates (RR 1.15; 95% CI 0.60–2.19) were similar across conditions.

Conclusion

When the same youth soccer clubs played with three referees rather than one, they committed fewer aggressive fouls. More intense supervision created better rule adherence. Injury rates were unchanged with increased supervision. Results raise questions concerning whether financial investment in additional referees on youth soccer fields yields safety benefits.
Types of Assays for SARS-CoV-2 Testing: A Review
Authors: Smithgall Marie C , Dowlatshahi Mitra , Spitalnik Steven L , Hod Eldad A , Rai Alex J
Published: May 2020

Clinical laboratory testing routinely provides actionable results, which help direct patient care in the inpatient and outpatient settings. Since December 2019, a novel coronavirus (SARS-CoV-2) has been causing disease (COVID-19 [coronavirus disease 2019]) in patients, beginning in China and now extending worldwide. In this context of a novel viral pandemic, clinical laboratories have developed multiple novel assays for SARS-CoV-2 diagnosis and for managing patients afflicted with this illness. These include molecular and serologic-based tests, some with point-of-care testing capabilities. Herein, we present an overview of the types of testing available for managing patients with COVID-19, as well as for screening of potential plasma donors who have recovered from COVID-19.
An epistemic interpretation of the posterior likelihood ratio distribution
Authors: Meester Ronald , Slooten Klaas
Published: May 2020

Often the expression of a likelihood ratio involves model parameters θ. This fact prompted many researchers to argue that a likelihood ratio should be accompanied by a confidence interval, as one would do when estimating θ itself. We first argue against this, based on our view of the likelihood ratio as a function of our knowledge of the model parameters, rather than being a function of the parameters themselves. There is, however, another interval that can be constructed, and which has been introduced in the literature. This is the interval obtained upon sampling from the so-called ‘posterior likelihood ratio distribution’, after removing, say, the most extreme 5% of a sample from this distribution. Although this construction appears in the literature, its interpretation remained unclear, as explicitly acknowledged in the literature. In this article we provide an interpretation: the posterior likelihood ratio distribution tells us which likelihood ratios we can expect if we were to obtain more information. As such, it can play a role in decision making procedures, for instance about the question whether or not it is worthwhile to try to obtain more data. The posterior likelihood ratio distribution has no relevance for the evidential value of the current data with our current knowledge. We illustrate all this with a number of examples.
Broadening the positionality in migration studies: Assigned insider category
Authors: Irgil Ezgi
Published: May 2020

This article contributes to the debates on positionality in migration studies by introducing assigned insider as a new category. I define it as a position when both the interviewees and the researcher are of the same local origin in which the researcher is considered ‘an insider of the host community’ and the interview questions are about a migrant group. I developed this category based on interviews with host community members during my field study in Bursa, Turkey, where I was born and raised. Previous studies focused on the researcher being an insider from a migrant community or being an outsider conducting research on a migrant community different from his/her own. Assigned insider has two elements that require it to be considered differently: same local origin operates as an overriding feature that goes beyond ethnicity and the interviewees being from the host community involves different ethical aspects than that from a migrant community. I argue that these reflect on the researcher during the interviews through active and passive discontent manifestations of the interviewees. While the former emphasises the direct confrontations of the interviewees that lead them to ‘correct’ the researcher, the latter manifests itself through non-verbal ways, which can result in refraining from answering questions.
Behaviour of the Mg ii 2798 Å line over the full range of AGN variability
Authors: Homan David , MacLeod Chelsea L , Lawrence Andy , Ross Nicholas P , Bruce Alastair
Published: May 2020

We investigate the responsiveness of the 2798 Å Mg ii broad emission line in active galactic nuclei (AGNs) on time-scales of several years. Our study is based on a sample of extremely variable AGNs as well as a broad population sample. The observed response of the line in previous studies has been mixed. By focusing on extreme variability (|Δg| > 1), we find that Mg ii clearly does respond to the continuum. However, the degree of responsiveness varies strikingly from one object to another: We see cases of Mg ii changing by as much as the continuum, more than the continuum, or very little at all. In 74 per cent of the highly variable sample, the behaviour of Mg ii corresponds with that of H β, with 30 per cent of the objects showing large variations in both lines. We do not detect any change in the line width that would correspond to broad-line region ‘breathing’, in accordance with results from the literature. Some of the objects in our highly variable sample show a clear asymmetry in the Mg ii profile. This skewness can be both to the blue and the red of the line centre. Results from our broad population sample show that highly variable quasars have lower Eddington ratios. This result holds for the variability of the continuum, but the correlation is significantly reduced for the variability of the Mg ii line. For the first time, we present an overview of the value of the intrinsic Baldwin effect for Mg ii in a large sample.
On testing CDM and geometry-driven Milky Way rotation curve models with Gaia DR2
Authors: Crosta Mariateresa , Giammaria Marco , Lattanzi Mario G , Poggio Eloisa
Published: May 2020

Flat rotation curves (RCs) in disc galaxies provide the main observational support to the hypothesis of surrounding dark matter (DM). Despite of the difficulty in identifying the DM contribution to the total mass density in our Galaxy, stellar kinematics, as tracer of gravitational potential, is the most reliable observable for gauging different matter components. From the Gaia second data release catalogue, we extracted parallaxes, proper motions, and line-of-sight velocities of unprecedented accuracy for a carefully selected sample of disc stars. This is the angular momentum supported population of the Milky Way (MW) that better traces its observed RC. We fitted such data to both a classical, i.e. including a DM halo, velocity profile model, and a general relativistic one derived from a stationary axisymmetric galaxy-scale metric. The general relativistic MW RC results statistically indistinguishable from its state-of-the-art DM analogue. This supports the ansatz that a weak gravitational contribution due to the off-diagonal term of the metric, by explaining the observed flatness of MW’s RC, could fill the gap in a baryons-only MW, thus rendering the Newtonian-origin DM a general relativity-like effect. In the context of Local Cosmology, our findings are suggestive of the Galaxy’s phase space as the exterior gravitational field in equilibrium far from a Kerr-like inner source, possibly with no need for extra matter to account for the disc kinematics.
PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences
Authors: Boskova Veronika , Stadler Tanja
Published: May 2020

Next-generation sequencing of pathogen quasispecies within a host yields data sets of tens to hundreds of unique sequences. However, the full data set often contains thousands of sequences, because many of those unique sequences have multiple identical copies. Data sets of this size represent a computational challenge for currently available Bayesian phylogenetic and phylodynamic methods. Through simulations, we explore how large data sets with duplicate sequences affect the speed and accuracy of phylogenetic and phylodynamic analysis within BEAST 2. We show that using unique sequences only leads to biases, and using a random subset of sequences yields imprecise parameter estimates. To overcome these shortcomings, we introduce PIQMEE, a BEAST 2 add-on that produces reliable parameter estimates from full data sets with increased computational efficiency as compared with the currently available methods within BEAST 2. The principle behind PIQMEE is to resolve the tree structure of the unique sequences only, while simultaneously estimating the branching times of the duplicate sequences. Distinguishing between unique and duplicate sequences allows our method to perform well even for very large data sets. Although the classic method converges poorly for data sets of 6,000 sequences when allowed to run for 7 days, our method converges in slightly more than 1 day. In fact, PIQMEE can handle data sets of around 21,000 sequences with 20 unique sequences in 14 days. Finally, we apply the method to a real, within-host HIV sequencing data set with several thousand sequences per patient.
Disappearing apple snails (Caenogastropoda: Ampullariidae) of Thailand: a comprehensive update of their taxonomic status and distribution
Authors: Ng Ting Hui , Annate Supunya , Jeratthitikul Ekgachai , Sutcharit Chirasak , Limpanont Yanin , Panha Somsak
Published: May 2020

Ampullariidae include the largest of all freshwater snails and are of ecological, evolutionary and anthropogenic importance in Southeast Asia (SEA). Native ampullariids belonging to the genus Pila face various threats but are understudied, with their species taxonomy being confused and data on their distributions being scarce. We provide a comprehensive update on the nomenclature, status and distribution of Pila species in Thailand, based on DNA barcoding and geometric morphometric analysis of recently collected material. We confirm that at least five Pila species are extant in Thailand: Pila virescens, P. celebensis, P. turbinis, P. gracilis and P. pesmei. Pila celebensis, which has distinctive egg masses among all the known Southeast Asian Pila, appears to be sister to a clade comprising other SEA and some African Pila. Our results suggest that Pila may have dispersed into SEA on at least two separate occasions. Two singletons collected from northern and eastern Thailand may constitute separate species, but this requires further study. Intraspecific diversity of the mitochondrial cytochrome c oxidase subunit I gene was relatively high for P. celebensis, P. gracilis and P. pesmei (maximum uncorrected p-distances varied from 7% to 9%), and may include cryptic species. Conversely, P. virescens showed low intraspecific p-distances (c. 0%) among clades collected from different localities. This strongly suggests that introductions by humans may be the major cause of this pattern, and our own observations—we found that this species is being cultured and is commonly sold in markets for human consumption—are consistent with this. Pila turbinis was the rarest species, with live snails being collected from only two localities. Throughout Thailand, invasive confamilial Pomacea species appear to be replacing native Pila species, particularly in the Chao Phraya basin. While Thai Pila exhibit surprisingly high genetic diversity, with cryptic species likely being present, widespread invasive snails pose a major threat to their survival and urgent conservation action is needed.
The conformational landscape of transcription intermediates involved in the regulation of the ZMP-sensing riboswitch from Thermosinus carboxydivorans
Authors: Binas Oliver , Schamber Tatjana , Schwalbe Harald
Published: May 2020

Recently, prokaryotic riboswitches have been identified that regulate transcription in response to change of the concentration of secondary messengers. The ZMP (5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR))-sensing riboswitch from Thermosinus carboxydivorans is a transcriptional ON-switch that is involved in purine and carbon-1 metabolic cycles. Its aptamer domain includes the pfl motif, which features a pseudoknot, impeding rho-independent terminator formation upon stabilization by ZMP interaction. We herein investigate the conformational landscape of transcriptional intermediates including the expression platform of this riboswitch and characterize the formation and unfolding of the important pseudoknot structure in the context of increasing length of RNA transcripts. NMR spectroscopic data show that even surprisingly short pre-terminator stems are able to disrupt ligand binding and thus metabolite sensing. We further show that the pseudoknot structure, a prerequisite for ligand binding, is preformed in transcription intermediates up to a certain length. Our results describe the conformational changes of 13 transcription intermediates of increasing length to delineate the change in structure as mRNA is elongated during transcription. We thus determine the length of the key transcription intermediate to which addition of a single nucleotide leads to a drastic drop in ZMP affinity.
Two-step mechanism for selective incorporation of lncRNA into a chromatin modifier
Authors: Müller Marisa , Schauer Tamas , Krause Silke , Villa Raffaella , Thomae Andreas W , Becker Peter B
Published: May 2020

The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we developed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity for U-/A-rich sequences and tandem stem-loop structures and binds many RNAs beyond roX in vitro. The selectivity of the helicase for physiological substrates is further enhanced by the core DCC. Unwinding of roX2 by MLE induces a highly selective RNA binding surface in the unstructured C-terminus of the MSL2 subunit and triggers-specific association of MLE and roX2 with the core DCC. The exquisite selectivity of roX2 incorporation into the DCC thus originates from intimate cooperation between the helicase and the core DCC involving two distinct RNA selection principles and their mutual refinement.
Evidence of an intestinal phosphate transporter alternative to type IIb sodium-dependent phosphate transporter in rats with chronic kidney disease
Authors: Ichida Yasuhiro , Ohtomo Shuichi , Yamamoto Tessai , Murao Naoaki , Tsuboi Yoshinori , Kawabe Yoshiki , Segawa Hiroko , Horiba Naoshi , Miyamoto Ken-ichi , Floege Jürgen
Published: May 2020

Background

Phosphate is absorbed in the small intestine via passive flow and active transport.NaPi-IIb, a type II sodium-dependent phosphate transporter, is considered to mediate active phosphate transport in rodents. To study the regulation of intestinal phosphate transport in chronic kidney disease (CKD), we analyzed the expression levels of NaPi-IIb, pituitary-specific transcription factor 1 (PiT-1) and PiT-2 and the kinetics of intestinal phosphate transport using two CKD models.

Methods

CKD was induced in rats via adenine orThy1 antibody injection. Phosphate uptake by intestinal brush border membrane vesicles (BBMV) and the messenger RNA (mRNA) expression of NaPi-IIb, PiT-1 and PiT-2 were analyzed. The protein expression level of NaPi-IIb was measured by mass spectrometry (e.g. liquid chromatography tandem mass spectrometry).

Results

In normal rats, phosphate uptake into BBMV consisted of a single saturable component and its Michaelis constant (Km) was comparable to that of NaPi-IIb. The maximum velocity (Vmax) correlated with mRNA and protein levels of NaPi-IIb. In the CKD models, intestinal phosphate uptake consisted of two saturable components. The Vmax of the higher-affinity transport, which is thought to be responsible for NaPi-IIb, significantly decreased and the decrease correlated with reduced NaPi-IIb expression. The Km of the lower-affinity transport was comparable to that of PiT-1 and -2. PiT-1 mRNA expression was much higher than that of PiT-2, suggesting that PiT-1 was mostly responsible for phosphate transport.

Conclusions

This study suggests that the contribution of NaPi-IIb to intestinal phosphate absorption dramatically decreases in rats with CKD and that a low-affinity alternative to NaPi-IIb, in particular PiT-1, is upregulated in a compensatory manner in CKD.
Long-Term Outcome of Surgical Management in Symptomatic Pediatric Vertebral Hemangiomas Presenting With Myelopathy
Authors: Singh Pankaj K , Chandra Sarat P , Agrawal Mohit , Sawarkar Dattaraj , Kumar Rajender , Kumar Amandeep , Verma Satish , Kale Shashank S
Published: May 2020

BACKGROUND

Vertebral hemangiomas are benign, highly vascular lesions of the vertebra, rarely seen in the pediatric age group.

OBJECTIVE

To analyze the long-term (>3 yr) outcome of patients of pediatric vertebral hemangioma presenting with myelopathy and to describe our surgical strategy to treat such cases.

METHODS

All patients up to 18 yr of age with a symptomatic vertebral hemangioma treated at our hospital from May 2003 to August 2016, with at least 3-yr follow-up were included. Functional clinical outcomes were measured using American Spinal Injury Association (ASIA) score.

RESULTS

There were 7 male and 7 female patients. All hemangiomas were located in the thoracic spine with single-level involvement. Upper thoracic spine involvement was more common (12 cases: 85.71%) than lower thoracic spine involvement (2 cases: 14.29%). All patients had features of myelopathy. The mean age was 14.57 yr, ranging from 10 to 18 yr. The mean follow-up was 62.21 mo, ranging from 36 to 90 mo. All patients had improvement in motor strength of both lower limbs postoperatively. Local pain, which was present in 1 patient, resolved, and the bladder symptoms present in 5 patients also resolved.

CONCLUSION

Our experience in treating symptomatic pediatric vertebral hemangiomas, along with the long-term follow-up data, suggests that good postoperative results can be achieved with minimal complications in carefully selected patients.
Surveying brain tumor heterogeneity by single-cell RNA-sequencing of multi-sector biopsies
Authors: Yu Kai , Hu Yuqiong , Wu Fan , Guo Qiufang , Qian Zenghui , Hu Waner , Chen Jing , Wang Kuanyu , Fan Xiaoying , Wu Xinglong , Rasko John EJ , Fan Xiaolong , Iavarone Antonio , Jiang Tao , Tang Fuchou , Su Xiao-Dong
Published: May 2020

Brain tumors are among the most challenging human tumors for which the mechanisms driving progression and heterogeneity remain poorly understood. We combined single-cell RNA-seq with multi-sector biopsies to sample and analyze single-cell expression profiles of gliomas from 13 Chinese patients. After classifying individual cells, we generated a spatial and temporal landscape of glioma that revealed the patterns of invasion between the different sub-regions of gliomas. We also used single-cell inferred copy number variations and pseudotime trajectories to inform on the crucial branches that dominate tumor progression. The dynamic cell components of the multi-region biopsy analysis allowed us to spatially deconvolute with unprecedented accuracy the transcriptomic features of the core and those of the periphery of glioma at single-cell level. Through this rich and geographically detailed dataset, we were also able to characterize and construct the chemokine and chemokine receptor interactions that exist among different tumor and non-tumor cells. This study provides the first spatial-level analysis of the cellular states that characterize human gliomas. It also presents an initial molecular map of the cross-talks between glioma cells and the surrounding microenvironment with single-cell resolution.
Modified Facet Joint Fusion for Lumbar Degenerative Disease: Case Series of a Fusion Technique, Clinical Outcomes, and Fusion Rate in 491 Patients
Authors: Ren Zhinan , Li Zheng , Li Shugang , Xu Derong , Chen Xin
Published: May 2020

BACKGROUND

Controversy still exists regarding the optimal fusion technique for the treatment of unstable lumbar spondylolisthesis.

OBJECTIVE

To evaluate the safety and efficacy of modified facet joint fusion (MFF).

METHODS

A total of 491 patients with unstable lumbar spondylolisthesis who underwent MFF were retrospectively reviewed. Computed tomography was used to evaluate the fusion rate of MFF at 6- and 12-mo follow-up postoperatively. Clinical outcomes included visual analog scale pain scores for low back pain (VAS-LBP) and leg pain (VAS-LP), Japanese Orthopedic Association scores (JOA), and Oswestry Disability Index (ODI), all of which were obtained preoperatively and postoperatively at 1-, 3-, 6-, and 12-mo follow-up times. The clinical outcomes were determined to be excellent, good, fair, or poor according to the MacNab classification at the last follow-up time.

RESULTS

Of the 491 patients, the fusion rates at the 6-mo and 1-yr follow-up were 56.8% and 96.1%, respectively. Between baseline and 1-yr follow-up time, VAS-LP and VAS-LBP improved from 5.6 ± 0.9 to 0.4 ± 0.5 and 5.1 ± 1.2 to 1.5 ± 0.9, respectively (P < .001). JOA improved from 9.0 ± 2.0 to 27.7 ± 1.0, and ODI decreased from 64.0 ± 2.0 to 19 ± 1.0 (P < .001). At the final evaluation, 93.6% patients showed excellent or good results, and 3.2% showed fair results. There were no MFF technique-related complications.

CONCLUSION

MFF technique achieved satisfactory clinical outcomes and fusion rate and appears to be a promising alternative fusion technique for the treatment of unstable lumbar spondylolisthesis.
Treatment Outcomes of Childhood Tuberculosis in Three Districts of Balochistan, Pakistan: Findings from a Retrospective Cohort Study
Authors: Abdullah Abid , Ahmad Nafees , Atif Muhammad , Khan Shereen , Wahid Abdul , Ahmad Izaz , Khan Asad
Published: May 2020

Background

This study aimed to evaluate treatment outcomes and factors associated unsuccessful outcomes among pediatric tuberculosis (TB) patients (age ≤14 years).

Methods

This was a retrospective cohort study conducted at three districts (Quetta, Zhob and Killa Abdullah) of Balochistan, Pakistan. All childhood TB patients enrolled for treatment at Bolan Medical Complex Hospital (BMCH) Quetta and District Headquarter Hospitals of Zhob and Killa Abdullah from 1 January 2016 to 31 December 2018 were included in the study and followed until their treatment outcomes were reported. Data were collected through a purpose developed standardized data collection form and analyzed by using SPSS 20. A p-value <0.05 was considered statistically significant.

Results

Out of 5152 TB patients enrolled at the study sites, 2184 (42.4%) were children. Among them, 1941 childhood TB patients had complete medical record were included in the study. Majority of the study participants were <5 years old (66.6%) and had pulmonary TB (PTB; 65%). A total of 45 (2.3%) patients were cured, 1680 (86.6%) completed treatment, 195 (10%) lost to follow-up, 15 (0.8%) died, 5 (0.3%) failed treatment and 1 (0.1%) was not evaluated for outcomes. In multivariate binary logistic regression analysis, treatment at BMCH Quetta (OR = 25.671, p-value < 0.001), rural residence (OR = 3.126, p-value < 0.001) and extra-PTB (OR = 1.619, p-value = 0.004) emerged as risk factors for unsuccessful outcomes.

Conclusion

The study sites collectively reached the World Health Organization’s target of treatment success (>85%). Lost to follow-up was the major reason for unsuccessful outcomes. Special attention to patients with identified risk factors for unsuccessful outcomes may improve outcomes further.
Phoretic copulation in Aculeata (Insecta: Hymenoptera): a review
Authors: Vivallo Felipe
Published: May 2020

Phoretic copulation is a type of reproductive strategy in which a winged male carries a wingless female during mating through a complex system of genital-locking structures present in both sexes. During flight, the female is suspended from the genitalia of the male and stays in that position during much of the copulation. This kind of mating allows, in addition to the transfer of gametes, the dispersal of females in the environment. Phoretic copulation evolved several times within Hymenoptera, but in groups not closely related phylogenetically and through morphological changes specific to each group. This paper presents a review of phoretic mating in the clade Aculeata, Hymenoptera, especially considering the biomechanical aspects that allow this mating strategy.
A 15-Year Trend Study of Internationally Educated Nurses’ NCLEX-RN Performance
Authors: Montegrico James
Published: May 2020

AIM

The aim of the study was to describe trends in internationally educated nurses’ (IEN) National Council Licensure Examination-Registered Nurses (NCLEX®-RN) performance from 2003 to 2017 and to determine the odds of passing the exam based on country of nursing education.

BACKGROUND

IEN comprise 5.6 percent of US nurses; more than half come from the Philippines. There is a lack of research on IEN NCLEX-RN performance.

METHOD

Correlational research was used to determine the performance and likelihood of passing the NCLEX-RN based on country of nursing education using secondary data analysis. Odds ratios were estimated to express the odds of passing.

RESULTS

IEN NCLEX-RN applications and pass rates are decreasing. The odds of passing the NCLEX-RN among Philippine-educated nurses are lower compared to all other IEN. The odds of passing the Canadian NCLEX-RN are higher for all IEN.

CONCLUSION

The low NCLEX-RN pass rate of IEN reflects differences in nursing education and practice across countries.