bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broadening the positionality in migration studies: Assigned insider category
Authors: Irgil Ezgi 
Published: May 2020

Abstract
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

ABSTRACTWe 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| &gt; 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

ABSTRACT
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

Abstract
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

ABSTRACT
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

Abstract
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

AbstractThe 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

Abstract

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

Abstract

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

Abstract
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

Abstract

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

Abstract

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 &lt;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 &lt;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 &lt; 0.001), rural residence (OR = 3.126, p-value &lt; 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 (&gt;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

AbstractPhoretic 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

Abstract

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.
Huddling as an Academic Quality Improvement Initiative
Authors: Schmitt Catherine , Lancaster Rachelle J. , Janquart Susan , Nevin Mary , Brickner Shanon 
Published: May 2020

Abstract
A huddle is described as a tight group gathered together to talk privately for the purpose of reviewing performance and engaging in future planning. Although huddles are described as an effective communication tool to enhance patient safety in hospital settings, little is known about their use in academe. This article describes a quality improvement initiative involving weekly huddles of faculty teaching medical/surgical nursing and provides preliminary findings after one year.