bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status
Authors: Jin Yuan , Zhou Jianglin , Zhou Jing , Hu Mingda , Zhang Qi , Kong Na , Ren Hongguang , Liang Long , Yue Junjie 
Published: March 2020

Abstract
Background
Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed.

Methods
We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering.

Results
We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species.

Conclusions
This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species.

Reviewer
This article was reviewed by Dr. Xianwen Ren.
Core Rehabilitation Outcome Set for Single Sided Deafness (CROSSSD) study: protocol for an international consensus on outcome measures for single sided deafness interventions using a modified Delphi survey
Authors: Katiri Roulla , Hall Deborah A. , Buggy Nora , Hogan Nicholas , Horobin Adele , van de Heyning Paul , Firszt Jill B. , Bruce Iain A. , Kitterick Pádraig T. 
Published: March 2020

Abstract
Background
Single-sided deafness (SSD) describes the presence of a unilateral severe to profound sensorineural hearing loss. SSD disrupts spatial hearing and understanding speech in background noise. It has functional, psychological and social consequences. Potential options for rehabilitation include hearing aids and auditory implants. Benefits and harms of these interventions are documented inconsistently in the literature, using a variety of outcomes ranging from tests of speech perception to quality of life questionnaires. It is therefore difficult to compare interventions when rehabilitating SSD. The Core Rehabilitation Outcome Set for Single Sided Deafness (CROSSSD) study is an international initiative that aims to develop a minimum set of core outcomes for use in future trials of SSD interventions.

Methods/design
The CROSSSD study adopts an international two-round online modified Delphi survey followed by a stakeholder consensus meeting to identify a patient-centred core outcome domain set for SSD based on what is considered critical and important for assessing whether an intervention for SSD has worked.

Discussion
The resulting core outcome domain set will act as a minimum standard for reporting in future clinical trials and could have further applications in guiding the use of outcome measures in clinical practice. Standardisation will facilitate comparison of research findings.
Diabetes mellitus and its associated risk factors in patients with human immunodeficiency virus on anti-retroviral therapy at referral hospitals of Northwest Ethiopia
Authors: Gebrie Alemu , Tesfaye Bekele , Gebru Tensae , Adane Fentahun , Abie Worku , Sisay Mekonnen 
Published: March 2020

Abstract
Background
The use of highly active anti- retroviral therapy (HAART) as well as human immunodeficiency virus (HIV) per se have been shown to be related with diabetes among patients living with HIV. There is limited evidence on the prevalence of diabetes among HIV-infected patients in developing countries like Ethiopia. Therefore, the aim of this study is to determine the prevalence of diabetes among patients living with HIV/AIDS at referral hospitals of Northwest Ethiopia.

Materials and methods
a hospital based cross-sectional study was conducted at referral hospitals of Northwest Ethiopia between February 2019 and April 2019. Using WHO stepwise approach, sociodemographic, behavioral and clinical data were collected from 407 included adult patients. Simple random sampling methods was used to select the study participants. Lipid profiles, fasting blood sugar as well as anthropometric indicators were also measured. SPSS version 25 was used for analysis of data; bivariate and multivariate binary logistic regression analysis was performed.

Result
From a total of 415 patients living with HIV deemed eligible for inclusion, 407 with complete data were included in the final analysis giving a response rate of 98%. From 407 study subjects included in the analysis, 161 (39.6%) were men. The prevalence of diabetes mellitus was found to be 8.8% (95% CI 6.05, 11.55). Multivariate logistic regression analysis revealed that age [AOR (95% CI) 1.04 (1.001,1.084), p < 0.05], educational status [AOR (95% CI) 6.27 (1.72, 22.85), p < 0.05, diploma; AOR (95% CI) 9.64 (2.57, 36.12), p < 0.05, degree and above], triglyceride level [AOR (95% CI) 1.007 (1.003, 1.010), p < 0.01] have shown statistically significant association with odds of diabetes mellitus.

Conclusion
The prevalence of diabetes was notably high in patients living with HIV/AIDS. Factors such as increased age, educational status and higher level of serum triglyceride were found to contribute to this high prevalence of diabetes.
A comparison of three column agglutination tests for red blood cell alloantibody identification
Authors: Blomme Siska , De Maertelaere Emilie , Verhoye Eline 
Published: March 2020

AbstractObjectiveCommercial kits of column tests for pre-transfusion testing have progressively replaced conventional tube tests in most laboratories. Aim of this study was to compare three commercial test cell panels for the identification of irregular red blood cell (RBC) alloantibodies. Overall, 44 samples with a positive indirect antiglobulin test (IAT) by routine testing were used for comparison of following panels: Ortho RESOLVE®panelC (Ortho Clinical Diagnostics (OCD), Milan, Italy), ID-DiaPanel(-P) (Bio-Rad Laboratories, CA, USA) and Identisera Diana(P) (Grifols, Barcelona, Spain). Column agglutination techniques were used, with microtubes containing either microgel (Bio-Rad/Grifols) or glass bead microparticles (Ortho).ResultsAlloantibody identification was possible in 38 samples, of which identical identification was shown in 33 samples by all methods. The remaining samples showed differences between certain methods, with the gel card system being superior to the glass card system for analyzing stored samples Considering that not all samples were evaluated in all three methods, the concordance rate reached 100% between Bio-Rad and Grifols, 90.5% between Bio-Rad and OCD, 86.5% between OCD and Grifols and 90.5% between all methods. Although differences in sensitivities were seen for specific antibodies, the three methods showed comparable performance for the identification of RBC alloantibodies.
Obstacle detection in fluid flow using asymptotic analysis technique
Authors: Malek Rakia , Abdelwahed Mohamed , Chorfi Nejmeddine , Hassine Maatoug 
Published: March 2020

AbstractWe consider the geometric inverse problem of determining an immersed obstacle in a two-dimensional non-stationary Stokes fluid flow. We use the topological gradient method to solve this problem. The unknown obstacle is located and reconstructed using the leading term of the Khon–Vogelius shape function variation. We propose a simple and fast detection algorithm. The efficiency and accuracy of the proposed approach are illustrated by some numerical examples.
Rhythmic movements in sleep disorders and in epileptic seizures during sleep
Authors: Silvestri Rosalia , Walters Arthur Scott 
Published: March 2020

AbstractRhythmic movements during sleep may occur in the context of physiological sleep-related motor activity or be part of sleep-related movement disorders such as bruxism, periodic limb movement disorder, restless legs syndrome, and sleep-related rhythmic movement disorder. They may also characterize some frontal or temporal nocturnal seizures of sleep-related hypermotor epilepsy, or be considered as part of NREM parasomnias, especially sleepwalking, sexsomnia or sleep-related eating disorder, or REM-related behaviors such as REM behavior disorder or complex movements associated with pediatric narcolepsy type I.In most cases rhythmic movements, especially when complex and long in duration, are related to different levels of arousal from sleep with recurrence of ancestral motor sequences promoted by central pattern generators in the brainstem, generally activated by the arousal process.A differential diagnosis between physiological events and pathological movement disorders, and between the latter and sleep-related epilepsy is critical to provide optimal treatment and an accurate prognosis. Specific treatment options for the aforementioned disorders are beyond the scope of this article.
Quantitative imaging: systematic review of perfusion/flow phantoms
Authors: Kamphuis Marije E. , Greuter Marcel J. W. , Slart Riemer H. J. A. , Slump Cornelis H. 
Published: March 2020

Abstract
Background
We aimed at reviewing design and realisation of perfusion/flow phantoms for validating quantitative perfusion imaging (PI) applications to encourage best practices.

Methods
A systematic search was performed on the Scopus database for “perfusion”, “flow”, and “phantom”, limited to articles written in English published between January 1999 and December 2018. Information on phantom design, used PI and phantom applications was extracted.

Results
Of 463 retrieved articles, 397 were rejected after abstract screening and 32 after full-text reading. The 37 accepted articles resulted to address PI simulation in brain (n = 11), myocardial (n = 8), liver (n = 2), tumour (n = 1), finger (n = 1), and non-specific tissue (n = 14), with diverse modalities: ultrasound (n = 11), computed tomography (n = 11), magnetic resonance imaging (n = 17), and positron emission tomography (n = 2). Three phantom designs were described: basic (n = 6), aligned capillary (n = 22), and tissue-filled (n = 12). Microvasculature and tissue perfusion were combined in one compartment (n = 23) or in two separated compartments (n = 17). With the only exception of one study, inter-compartmental fluid exchange could not be controlled. Nine studies compared phantom results with human or animal perfusion data. Only one commercially available perfusion phantom was identified.

Conclusion
We provided insights into contemporary phantom approaches to PI, which can be used for ground truth evaluation of quantitative PI applications. Investigators are recommended to verify and validate whether assumptions underlying PI phantom modelling are justified for their intended phantom application.
Nutritional and antioxidant significance of selenium-enriched mushrooms
Authors: Kora Aruna Jyothi 
Published: March 2020

Abstract
Background
The element selenium (Se) acts as a double-edged sword for humans and animals by being a nutrient at trace level and a toxin at elevated concentrations. It is needed for the biosynthesis of selenoenzymes and selenoproteins which mediate an array of activities such as antioxidant defense, detoxification, immunomodulation, carcinogenesis prevention, thyroid functioning, and sperm motility and maturation. Because of their culinary, nutritional, and health benefits, the demand for mushroom cultivation is increasing in India. The mushrooms are enriched with proteins, phenolics, antioxidants, vitamins, and microelements. Most of the edible and cultivated mushrooms show an array of biological properties. However, they are Se deficient, and it mandates the cultivation of Se-fortified edible mushrooms.

Aim of work
This review focuses on Se forms, distribution, dietary importance, mushroom cultivation, need of Se-enriched mushrooms, enrichment methods, nutritional and antioxidant significance, and anticancer activity of Se-biofortified mushrooms.

Methodology and results
Se-enriched mushrooms are produced by cultivation on substrates enriched with either inorganic or organic forms of Se and Se-hyperaccumulated agricultural residues. Edible mushrooms accumulate Se from substrate into selenoproteins and selenoenzymes as selenomethionine and selenocysteine, the organic and most bioavailable forms of Se. Without affecting the biological efficiency, the enrichment process enhances the total protein and total phenolic content and bioaccessibility of trace elements. The antioxidant action was higher for Se-fortified mushrooms in terms of total phenolics, total antioxidant, 1, 1-diphenyl-dipicrylhydrazyl (DPPH) scavenging, metal chelating, and lipid peroxidation inhibition activities in comparison with unfortified mushrooms. Also, Se-enriched mushrooms are known to retard chemically induced mammary tumors and proliferation of lung cancer cell lines.

Conclusions
Se-biofortified mushrooms act as potential functional food, nutraceutical, and diet supplements. Dietary intake of Se-fortified mushrooms aids in treatment and prevention of various conditions such as HIV infection, cancer, aging, cardiovascular, neurodegenerative and immunological diseases. The cultivation of Se-enriched mushrooms leads to sustainable empowerment of marginal, landless farmers; rural women; unemployed youth; and self-help groups. However, the technology development for Se enrichment is needed for commercial scale production. Other studies on volatile Se compound release during cultivation, safe disposal of spent compost, and Se leaching into ground water are warranted. The impact of cooking and traditional preservation methods on Se availability from mushroom meal to humans has to be evaluated.
Once versus twice daily antihypertensive medications for the control of nocturnal blood pressure: a comparative study
Authors: Youssef Ghada , Nagy Sherif , El-gengehe Ahmed , Abdel Hamid Magdy , Abdel Aal Amr 
Published: March 2020

Abstract
Background
Blood pressure (BP) shows short-term variability within the 24 h, which can only be assessed with 24-h ambulatory blood pressure monitoring (ABPM). It is of utmost importance to control BP throughout the night to reduce incidence of hypertension complications. The purpose of this study is to evaluate the effect of timing and frequency of antihypertensive medications on the average nighttime and 24-h blood pressure control.

Results
The study enrolled 199 hypertensive patients with controlled office blood pressure; 135 (67.8%) patients were on once daily antihypertensive medication (group 1) while 64 (32.2%) patients were on twice daily doses (group 2). The mean office SBP was 128.7 ± 7.8 mmHg in group 1 vs 129.6 ± 6.6 mmHg in group 2, (p = 0.421). ABPM readings for both groups were as follows: mean daytime SBP was 125.4 ± 11.6 mmHg vs 130.1 ± 12.9, p = 0.011; mean nighttime SBP was 117.0 ± 12.4 mmHg vs 123.1 ± 13.9 mmHg, p = 0.002, and mean 24-h SBP was 122.7 ± 10.6 mmHg vs 127.5 ± 12.0, p = 0.005. The prevalence of non-dipping was 68.9% in group 1 vs 70.3% in group 2 patients, p = 0.8 (the mean dipping ratio was 0.93 ± 0.08 in group 1 vs 0.95 ± 0.07 in group 2, p = 0.198). The prevalence of masked hypertension was higher in group 2 (28.1% vs 43.8%, p = 0.029).

Conclusion
Taking an extra antihypertensive pill at night did not show a decrease in the nighttime or the average 24H blood pressure in hypertensive patients with controlled office BP. On the contrary, patients who used twice daily antihypertensive medications seem to have higher nighttime and 24-h SBP, although the dipping ratio was comparable in both groups.
Implications of the 21-gene recurrence score assay (Oncotype DX) on adjuvant treatment decisions in ER-positive early-stage breast cancer patients: experience of Kuwait Cancer Control Center
Authors: Fayaz Salah , Eissa Heba El-Sayed , Demian Gerges Attia 
Published: March 2020

Abstract
Background
The Oncotype DX is a quantitative assay of the expression of 16 tumor-related genes and 5 reference genes that predicts the potential of adjuvant chemotherapy benefit in estrogen receptor (ER)-positive early breast cancer patients. The study aims to evaluate the impact of Oncotype DX as a tool for adjuvant treatment decision of ER-positive, HER2-negative, N0/N1 early-stage breast cancer patients and to determine which clinicopathological criteria derived the greatest advantage.

Results
A hundred patients at a median age of 50 years were included. TNM stage distribution was 34, 63, and 3 patients for stages I, II, and IIIA respectively. Fifty-four patients had luminal A and 46 had luminal B tumors. The recurrence score (RS) results were low, intermediate, and high risk in 54, 34, and 12 patients respectively. Before the test results, adjuvant chemoendocrine therapy (CET) was recommended for 46 patients while 54 were advised for endocrine therapy (ET). After getting the test results, 25 patients received CET (1, 12, and12 patients in the low-, intermediate-, and high-risk groups respectively) and 75 received ET. Treatment change was documented in 37 patients (8 patients from ET to CET and 29 from CET to ET; p = 0.001, McNemar test). Treatment change was significant among patients ≤ 50 years, luminal B tumors, stage II and IIIA disease, and node-positive disease.

Conclusion
Oncotype DX testing resulted in significant changes in the adjuvant treatment decisions in ER-positive, HER2-negative early breast cancer particularly in the case of young, luminal B, N1, and stage II–IIIA disease.
Opportunity Costs of Receiving Palliative Chemotherapy for Metastatic Pancreatic Ductal Adenocarcinoma
Authors: Bange Erin M. , Doucette Abigail , Gabriel Peter E. , Porterfield Florence , Harrigan James J. , Wang Robin , Wojcieszynski Andrzej P. , Boursi Ben , Mooney Bethany I. , Reiss Kim A. , Mamtani Ronac 
Published: March 2020

PURPOSE: The median overall survival (OS) for metastatic pancreatic ductal adenocarcinoma (mPDAC) is < 1 year. Factors that contribute to quality of life during treatment are critical to quantify. One factor—time spent obtaining clinical services—is understudied. We quantified total outpatient time among patients with mPDAC receiving palliative systemic chemotherapy. METHODS: We conducted a retrospective analysis using four patient-level time measures calculated from the medical record of patients with mPDAC receiving 5-fluorouracil infusion, leucovorin, oxaliplatin, and irinotecan; gemcitabine/nab-paclitaxel; or gemcitabine within the University of Pennsylvania Health System between January 1, 2011 and January 15, 2019. These included the total number of health care encounter days (any day with at least one visit) and total visit time. Total visit time represented the time spent receiving care (care time) plus time spent commuting and waiting for care (noncare time). We performed descriptive statistics on these outpatient time metrics and compared the number of encounter days to OS. RESULTS: A total of 362 patients were identified (median age, 65 years; 52% male; 78% white; 62% received gemcitabine plus nab-paclitaxel). Median OS was 230.5 days (7.6 months), with 79% of patients deceased at the end of follow-up. On average, patients had 22 health care encounter days, accounting for 10% of their total days survived. Median visit time was 4.6 hours, of which 2.5 hours was spent commuting or waiting for care. CONCLUSION: On average, patients receiving palliative chemotherapy for mPDAC spend 10% of survival time on outpatient health care. More than half of this time is spent commuting and waiting for care. These findings provide an important snapshot of the patient experience during ambulatory care, and efforts to enhance efficiency of care delivery may be warranted.
Terahertz-frequency dielectric anisotropy in three-dimensional polymethacrylates fabricated by stereolithography
Authors: Park S. , Li Y. , Fullager D. B. , Schöche S. , Herzinger C. M. , Lee S. , Hofmann T. 
Published: March 2020

The anisotropic optical dielectric functions of slanted columnar layers fabricated using polymethacrylate based stereolithography are reported for the terahertz-frequency domain using generalized spectroscopic ellipsometry. The slanted columnar layers are composed of spatially coherent columnar structures with a diameter of 100 µm and a length of 700 µm that are tilted by 45° with respect to the surface normal of the substrates. A simple biaxial (orthorhombic) layer homogenization approach is used to analyze the terahertz ellipsometric data obtained at three different sample azimuthal orientations. The permittivity along the major polarizability directions varies by almost 25%. Our results demonstrate that stereolithography allows tailoring of the polarizability and anisotropy of the host material, and provides a flexible alternative metamaterials fabrication method for the terahertz spectral range.
High-power passively mode-locked cryogenic Yb:YLF laser
Authors: Demirbas Umit , Thesinga Jelto , Cankaya Huseyin , Kellert Martin , Kärtner Franz X. , Pergament Mikhail 
Published: March 2020

We report, to the best of our knowledge, the first mode-locked operation of Yb:YLF gain media at cryogenic temperatures. A saturable Bragg reflector was used for initiating and sustaining mode locking. Once aligned, the system was self-starting and quite robust. Using output couplers in the 10–40% range, 3–5 ps long pulses with an average power as high as 28 W were achieved. The repetition rate was 46.45 MHz, and the corresponding pulse energy and peak power were as high as 602 nJ and 126.5 kW, respectively. The central wavelength of the mode-locked pulses could be tuned in the 1013.5–1019 nm range using an intracavity birefringent filter. The achieved output power performance is two to three orders of magnitude higher than previous room-temperature Yb:YLF systems.
Gemeinschaft „sub unica Veritatis auctoritate“
Authors: Herms Eilert 
Published: March 2020

Zusammenfassung
Das gegenwärtige Pontifikat betreibt den Ökumenismus pragmatisch und mit ethischem Schwerpunkt. Gleichwohl bleibt die Klärung der Frage nach den fundamentaltheologischen (offenbarungstheoretischen) und dogmatischen (ekklesiologischen) Fundamenten von Kirchenordnung und Kirchenrecht für die begründete Erklärung von sichtbarer Einheit unabdingbar. Differenzen bestehen hier nicht nur zwischen reformatorischer und römisch-katholischer Theologie, sondern auch innerhalb der letzteren. Sie reichen – das zeigt die systematische Analyse von drei jüngeren römisch-katholischen Veröffentlichungen zum Thema – von unterschiedlichen Vorstellungen über die methodische Fortsetzung des Bemühens um Erreichung eines „differenzierten Konsensen“ über Einzelfragen bis zu einer (jetzt auch römisch-katholischen!) grundsätzlichen Infragestellung der „Konsenspapierökumene“ zugunsten einer Klärung des „Grunddissens“ zwischen katholischer und evangelischer Christentumsauffassung und Denkform im ganzen. Keine der Positionen hat ein angemessenes Verständnis von Ansatz und Pointe reformatorischer Theologie erreicht. Dringend ist also, dass evangelische Theologie deutlicher als bisher zeigt: Das reformatorische Verständnis von Offenbarung und Glaube hat präzise Konsequenzen für das reformatorische Verständnis der sichtbaren Kirche (von Kirchenordnung und Kirchenrecht).