bluuebunny/crossref_metadata_2025_split huggingface dataset:
The “Internal” Dimension of the Safe Country Concept: the Interpretation of the Safe Third Country Concept in the Dublin System by International and Internal Courts
Authors: Morgades-Gil Sílvia 
Published: February 2020

Abstract
The non-refoulement principle has been interpreted extensively as regards what kind of threats prevent removal to another country through the interpretation of the international instruments for the protection of human rights. Nevertheless, authors and institutions acknowledge that this principle does not prohibit the removal to a safe country and thus that a number of States participate in a system of shared responsibility, in which refugees and asylum seekers are transferred from one country to another in order to try to obtain (the Dublin EU system) or to benefit from international protection (resettlement). The academic literature has extensively addressed the meaning of the concept of the safe third country. This contribution is aimed at analyzing the application of this concept within a system where all States are supposed to be safe for all asylum seekers, and the principle of mutual trust and equivalence of protection applies. The paper reviews the safe country concept in the context of the Dublin system and examines when and why International, European and internal courts and other institutions have considered that one of the States participating in the system was not safe ad intra. Some final thoughts consider the impact that the analysis may have on the principle of mutual trust that is at the heart of the area of Freedom, Security and Justice.
The Interdecadal Shift of ENSO Properties in 1999/2000: A Review
Authors: Hu Zeng-Zhen , Kumar Arun , Huang Bohua , Zhu Jieshun , L’Heureux Michelle , McPhaden Michael J. , Yu Jin-Yi 
Published: February 2020

AbstractFollowing the interdecadal shift of El Niño–Southern Oscillation (ENSO) properties that occurred in 1976/77, another regime shift happened in 1999/2000 that featured a decrease of variability and an increase in ENSO frequency. Specifically, the frequency spectrum of Niño-3.4 sea surface temperature shifted from dominant variations at quasi-quadrennial (~4 yr) periods during 1979–99 to weaker fluctuations at quasi-biennial (~2 yr) periods during 2000–18. Also, the spectrum of warm water volume (WWV) index had almost no peak in 2000–18, implying a nearly white noise process. The regime shift was associated with an enhanced zonal gradient of the mean state, a westward shift in the atmosphere–ocean coupling in the tropical Pacific, and an increase in the static stability of the troposphere. This shift had several important implications. The whitening of the subsurface ocean temperature led to a breakdown of the relationship between WWV and ENSO, reducing the efficacy of WWV as a key predictor for ENSO and thus leading to a decrease in ENSO prediction skill. Another consequence of the higher ENSO frequency after 1999/2000 was that the forecasted peak of sea surface temperature anomaly often lagged that observed by several months, and the lag increased with the lead time. The ENSO regime shift may have altered ENSO influences on extratropical climate. Thus, the regime shift of ENSO in 1999/2000 as well as the model default may account for the higher false alarm and lower skill in predicting ENSO since 1999/2000.
Use and Removal of Inferior Vena Cava Filters in Patients With Acute Brain Injury
Authors: Melmed Kara , Chen Monica L. , Al-Kawaz Mais , Kirsch Hannah L. , Bauerschmidt Andrew , Kamel Hooman 
Published: February 2020

Background: Few data exist regarding the rate of inferior vena cava (IVC) filter retrieval among brain-injured patients. Methods: We conducted a retrospective cohort study using inpatient claims between 2009 and 2015 from a nationally representative 5% sample of Medicare beneficiaries. We included patients aged ≥65 years who were hospitalized with acute brain injury. The primary outcome was the retrieval of IVC filter at 12 months and the secondary outcomes were the association with 30-day mortality and 12-month freedom from pulmonary embolism (PE). We used Current Procedural Terminology codes to ascertain filter placement and retrieval and International Classification of Diseases, Ninth Revision, Clinical Modification codes to ascertain venous thromboembolism (VTE) diagnoses. We used standard descriptive statistics to calculate the crude rate of filter placement. We used Cox proportional hazards analysis to examine the association between IVC filter placement and mortality and the occurrence of PE after adjustment for demographics, comorbidities, and mechanical ventilation. We used Kaplan-Meier survival statistics to calculate cumulative rates of retrieval 12 months after filter placement. Results: Among 44 641 Medicare beneficiaries, 1068 (2.4%; 95% confidence interval [CI], 2.3%-2.5) received an IVC filter, of whom 452 (42.3%; 95% CI, 39.3%-45.3) had a diagnosis of VTE. After adjusting for demographics, comorbidities, and mechanical ventilation, filter placement was not associated with a reduced risk of mortality (hazard ratio [HR], 1.0; 95% CI, 0.8-1.3) regardless of documented VTE. The occurrence of pulmonary embolism at 12 months was associated with IVC filter placement (HR, 3.19; 95% CI, 1.3-3.3) in the most adjusted model. The cumulative rate of filter retrieval at 12 months was 4.4% (95% CI, 3.1%-6.1%); there was no significant difference in retrieval rates between those with and without VTE. Conclusions: In a large cohort of Medicare beneficiaries hospitalized with acute brain injury, IVC filter placement was uncommon, but once placed, very few filters were removed. IVC filter placement was not associated with a reduced risk of mortality and did not prevent future PE.
A doublecortin-domain protein of Toxoplasma and its orthologues bind to and modify the structure and organization of tubulin polymers
Authors: Leung Jacqueline M. , Nagayasu Eiji , Hwang Yu-Chen , Liu Jun , Pierce Phillip G. , Phan Isabelle Q. , Prentice Robin A. , Murray John M. , Hu Ke 
Published: February 2020

Abstract
Background
TgDCX is a doublecortin-domain protein associated with the conoid fibers, a set of strongly curved non-tubular tubulin-polymers in Toxoplasma. TgDCX deletion impairs conoid structure and parasite invasion. TgDCX contains two tubulin-binding domains: a partial P25α and the DCX/doublecortin domain. Orthologues are found in apicomplexans and their free-living relatives Chromera and Vitrella.

Results
We report that isolated TgDCX-containing conoid fibers retain their pronounced curvature, but loss of TgDCX destabilizes the fibers. We crystallized and determined the 3D-structure of the DCX-domain, which is similar to those of human doublecortin and well-conserved among TgDCX orthologues. However, the orthologues vary widely in targeting to the conoid in Toxoplasma and in modulating microtubule organization in Xenopus cells. Several orthologues bind to microtubules in Xenopus cells, but only TgDCX generates short, strongly curved microtubule arcs. EM analysis shows microtubules decorated with TgDCX bundled into rafts, often bordered on one edge by a “C”-shaped incomplete tube. A Chromera orthologue closely mimics TgDCX targeting in Toxoplasma and binds to microtubules in Xenopus cells, but does not generate arcs or “C”-shaped tubes, and fails to rescue the defects of the TgDCX-knockout parasite.

Conclusions
These observations suggest that species-specific features of TgDCX enable it to generate strongly curved tubulin-polymers to support efficient host-cell invasion.
Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?
Authors: McGaughran Angela 
Published: February 2020

Abstract
Background
Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet-lab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of ~ 1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years.

Results
I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing.

Conclusions
Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.
Neuromyelitis optica: a pilot study of clinical presentation and status of serological biomarker AQP4 among patients admitted to a tertiary centre in NCNS, Sudan
Authors: Ibrahim Etedal Ahmed AbuElbasher , Gammer Fatima , Gassoum Alsadig 
Published: February 2020

Abstract
Background
Neuromyelitis optica (NMO) is a demyelinating disease primarily affecting the optic nerves and spinal cord. It is distinguished from other demyelinating conditions by the presence of AQP4-IgG and serum aquaporin 4 (AQP4), found mainly in the blood–brain barrier. This descriptive study was conducted from January 2015 to June 2018 at the National Center for Neurological Sciences (NCNS) in Khartoum, Sudan. All participants were Sudanese patients diagnosed with NMO. In our study the selection of cases was based on Dean Wingerchuk diagnostic criteria (2006), which states that the diagnosis of NMO should meet two absolute criteria and two supportive criteria. The absolute criteria are myelitis and optic neuritis, whereas supportive criteria include radiological findings obtained from brain and spinal cord MRI. Furthermore, AQP4-IgG levels were measured from cerebrospinal fluid (CSF) and serum using immunofluorescence. Data were collected by a pre-designed questionnaire and analyzed using SPSS version 17. A p value < 0.05 was considered statistically significant.

Results
A total of 31 patients were enrolled in this study [6 male (19.4%) and 25 female (80.6%)]. The mean age was 38 ± 12.8 years. Motor and visual difficulties were the initial symptoms and occurred in 21 (67.7%) and 10 (32.3%) patients, respectively. Fundoscopy confirmed optic atrophy in 22 (71.0%) patients. The course of the disease revealed one relapse in 21 patients (67.7%). Seropositive AQP4-IgG were seen in 23 patients (79.31%). There was a significant correlation between AQP4 and response to treatment (p ≤ 0.038). The correlation between serum AQP4-IgG, showed that, complete improvement was detected in 2 patients (6.9%) one of them was positive and the other was negative, 20 (69.0%) patients presented with some disability, among them 18 (62.1%) were positive and 2 (6.9%) were negative, while 7 patients showed no improvement (24.1%) 4 out of them were positive (13.8%) and 3 were negative (10.3%).

Conclusion
At the initial presentation of NMO, longitudinal myelitis was observed more frequently than optic neuritis. More than two third of the patients showed strong seropositivity for serum AQP4. Most seropositive patients showed a good response to treatment but with residual disabilities.
Nerylneryl diphosphate is the precursor of serrulatane, viscidane and cembrane-type diterpenoids in Eremophila species
Authors: Gericke Oliver , Hansen Nikolaj Lervad , Pedersen Gustav Blichfeldt , Kjaerulff Louise , Luo Dan , Staerk Dan , Møller Birger Lindberg , Pateraki Irini , Heskes Allison Maree 
Published: February 2020

Abstract
Background
Eremophila R.Br. (Scrophulariaceae) is a diverse genus of plants with species distributed across semi-arid and arid Australia. It is an ecologically important genus that also holds cultural significance for many Indigenous Australians who traditionally use several species as sources of medicines. Structurally unusual diterpenoids, particularly serrulatane and viscidane-types, feature prominently in the chemical profile of many species and recent studies indicate that these compounds are responsible for much of the reported bioactivity. We have investigated the biosynthesis of diterpenoids in three species: Eremophila lucida, Eremophila drummondii and Eremophila denticulata subsp. trisulcata.

Results
In all studied species diterpenoids were localised to the leaf surface and associated with the occurrence of glandular trichomes. Trichome-enriched transcriptome databases were generated and mined for candidate terpene synthases (TPS). Four TPSs with diterpene biosynthesis activity were identified: ElTPS31 and ElTPS3 from E. lucida were found to produce (3Z,7Z,11Z)-cembratrien-15-ol and 5-hydroxyviscidane, respectively, and EdTPS22 and EdtTPS4, from E. drummondii and E. denticulata subsp. trisulcata, respectively, were found to produce 8,9-dihydroserrulat-14-ene which readily aromatized to serrulat-14-ene. In all cases, the identified TPSs used the cisoid substrate, nerylneryl diphosphate (NNPP), to form the observed products. Subsequently, cis-prenyl transferases (CPTs) capable of making NNPP were identified in each species.

Conclusions
We have elucidated two biosynthetic steps towards three of the major diterpene backbones found in this genus. Serrulatane and viscidane-type diterpenoids are promising candidates for new drug leads. The identification of an enzymatic route to their synthesis opens up the possibility of biotechnological production, making accessible a ready source of scaffolds for further modification and bioactivity testing.
Peripheral arterial disease and its correlates in patients with type 2 diabetes mellitus in a teaching hospital in northern Nigeria: a cross-sectional study
Authors: Agboghoroma Orighomisan Freda , Akemokwe Fatai Momodu , Puepet Fabian H. 
Published: February 2020

Abstract
Background
Peripheral arterial disease (PAD) is a risk factor for diabetic foot ulcer, limb amputation as well as coronary heart disease. It is more common in patients with diabetes mellitus (DM) and co-exists with peripheral neuropathy. Prevalence of PAD in type 2 DM patients in northern Nigeria is largely unknown. We investigated the occurrence and factors associated with PAD among patients with type 2 DM in a tertiary hospital in northern Nigeria.

Methods
This was a cross- sectional analytic study. We recruited 200 patients with type 2 DM consecutively from the diabetes clinic of the Jos University Teaching Hospital. Ankle brachial index was assessed for each participant. Clinical information, anthropometric indices and blood samples were collected for assay. Data was analysed using CDC Epi-Info and logistic regression analysis was used to determine independent correlates of PAD.
RESULTS:PAD was present in 38.5%(n = 77) of subjects and it was associated with the female sex, age ≥ 50 years, Body mass index (BMI) ≥ 25 kg/m2 and low HDL cholesterol levels. However, on multiple logistic regression, a BMI ≥ 25 kg/m2 and a low HDL cholesterol level were independent correlates of PAD(adjusted OR = 2.13,95% CI = 1.04–4.36 and adjusted OR = 2.31, 95% CI = 1.04–5.15, respectively).

Conclusion
PAD is present in more than a third of patients with type 2 DM in a tertiary hospital in northern Nigeria. A BMI of ≥25 kg/m2 and low HDL cholesterol levels were independent correlates of PAD.
SLC5A2 mutations, including two novel mutations, responsible for renal glucosuria in Chinese families
Authors: Yu Lei , Wu Meng , Hou Ping , Zhang Hong 
Published: February 2020

Abstract
Background
Familial renal glucosuria (FRG) is characterized by persistent glucosuria without other impairments of tubular function in the presence of normal serum glucose. SGLT2, which is almost exclusively expressed in the kidney, accounts for most of the glucose reabsorption. Recently, some studies have confirmed that SLC5A2 mutations are responsible for the pathogenesis of familial renal glucosuria, but FRG cases are still rare. Furthermore, there are a few reports about splice-site mutations in previous studies, but the effect of these variants at the mRNA level has hardly been verified.

Methods
Ten patients were recruited in our renal division because of persistent glucosuria, and clinical data of the patients and their family members were recorded as much as possible. The entire coding region and adjacent intronic segments of SLC5A2 were sequenced in FRG patients and their relatives. Permanent growing lymphoblastoid cell lines from FRG patients were established to better preserve genetic information.

Results
A total of nine different mutations were identified: IVS1-16C > A, c.305C > T/p.(A102V), c.395G > A/p.(R132H), c.736C > T/p.(P246S), c.886(−10_-31)delGCAAGCGGGCAGCTGAACGCCC, c.1152_1163delGGTCATGCTGGC/p.(Val385_Ala388del), c.1222G > T/p.(D408Y), c.1496G > A/p.(R499H) and c.1540C > T/p.(P514S); two novel mutations in SLC5A2, c.1222G > T/p.(D408Y) and c.1496G > A/p.(R499H), were identified in the Chinese FRG pedigrees. Ten individuals with heterozygous or compound heterozygous variants had glucosuria in the range of 3.1 to 37.6 g/d.

Conclusion
We screened ten additional Chinese FRG pedigrees for mutations in the SLC5A2 gene and found nine mutations, including two novel mutations. Most variants were private, but IVS1-16C > A and c.886(−10_-31) del may be high frequency splice-site mutations that could be preferentially screened when variants cannot be found in the SLC5A2 exon. Furthermore, we successfully established a permanent growing lymphoblastoid cell line from patients with FRG, which could facilitate further studies of the SLC5A2 gene. The current study provides a valuable clue for further research on the molecular mechanism of SGLT2.
Comparison of frequency-domain and continuous-wave near-infrared spectroscopy devices during the immediate transition
Authors: van Essen Tanja , Goos Tom G. , van Ballegooijen Liza , Pichler Gerhard , Urlesberger Berndt , Reiss Irwin K. M. , de Jonge Rogier C. J. 
Published: February 2020

Abstract
Background
Non-invasive monitoring of cerebral tissue oxygen saturation (rcSO2) during transition is of growing interest. Different near-infrared spectroscopy (NIRS) techniques have been developed to measure rcSO2. We compared rcSO2 values during the immediate transition in preterm neonates measured with frequency-domain NIRS (FD-NIRS) with those measured with continuous-wave NIRS (CW-NIRS) devices in prospective observational studies.

Methods
We compared rcSO2 values measured with an FD-NIRS device during the first 15 min after birth in neonates with a gestational age ≥ 30 weeks but < 37 weeks born at the Erasmus MC- Sophia Children’s Hospital, Rotterdam, the Netherlands, with similar values measured with a CW-NIRS device in neonates born at the Medical University of Graz, Austria. Mixed models were used to adjust for repeated rcSO2 measurements, with fixed effects for time (non-linear), device, respiratory support and the interaction of device and respiratory support with time. Additionally, parameters such as total haemoglobin concentration and oxygenated and deoxygenated haemoglobin concentrations measured by FD-NIRS were analysed.

Results
Thirty-eight FD-NIRS measurements were compared with 58 CW-NIRS measurements. The FD-NIRS rcSO2 values were consistently higher than the CW-NIRS rcSO2 values in the first 12 min, irrespective of respiratory support. After adjustment for respiratory support, the time-dependent trend in rcSO2 differed significantly between techniques (p < 0.01).

Conclusion
As cerebral saturation measured with the FD-NIRS device differed significantly from that measured with the CW-NIRS device, differences in absolute values need to be interpreted with care. Although FD-NIRS devices have technical advantages over CW-NIRS devices, FD-NIRS devices may overestimate true cerebral oxygenation and their benefits might not outweigh the usability of the more clinically viable CW-NIRS devices.
Acute respiratory infection and its associated factors among children under-five years attending pediatrics ward at University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia: institution-based cross-sectional study
Authors: Dagne Henok , Andualem Zewudu , Dagnew Baye , Taddese Asefa Adimasu 
Published: February 2020

AbstractBackgroundAcute respiratory infection is manifested by cough accompanied by short rapid breathing which may be associated with death especially when there are other co-morbidities. From an estimated 5.4 million children under –five years that died in 2017—roughly half of those deaths occurred in sub-Saharan Africa and acute respiratory infection contributed to the highest number of deaths. The current study aimed at evaluating the prevalence of, and risk factors associated with, acute respiratory infection hospitalization in under-five years children hospitalized at the University of Gondar Comprehensive Specialized Hospital.MethodAn institution-based cross-sectional study was carried out from May 01/2019 to July 10/2019. After the selection of participants using simple random sampling, face to face interview was performed using a semi-structured pre-tested questionnaire. Data were also extracted from medical registration charts. We used EPI Info 7 for data entry and exported into SPSS 21 for analysis. Results were presented by simple frequency, percentage and mean for descriptive variables. Binary logistic regression analysis was used to test the association of covariates and outcome variable. Variables with ap < 0.2 during the bivariable binary logistic regression analysis were included in the multivariable logistic regression analysis. Variables withp < 0.05 were considered as significantly associated with acute respiratory infection. This study is reported following the Strengthening the Reporting of Observational Studies in Epidemiology guideline.ResultsFour hundred and twenty-two under-five years’ children attending the Pediatrics ward were included in this study. The prevalence of acute respiratory infection among under-five years’ children in this study was 27.3%. Children aged below 12 months (AOR:3.39, 95% CI: 1.19, 9.65), maternal age of 16 to 27 years (AOR: 1.95, 95% CI: 1.03, 3.70), maternal age of 28 to 33 years (AOR: 2.73, 95% CI: 1.40, 5.34), lack of maternal awareness of handwashing (AOR: 2.79, 95% CI: 1.15, 6.76), rural residence (AOR:2.27, 95% CI: 1.18, 4.39), and lack of meningitis (AOR: 0.22, 95% CI: 0.08, 0.55), were significantly associated with acute respiratory infection.ConclusionAcute respiratory infection was common among children under-five years. Child and maternal age, residence and maternal hand hygiene information were significant factors identified to be associated with an acute respiratory infection.