bluuebunny/crossref_metadata_2025_split huggingface dataset:
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
Authors: Kieft Kristopher , Zhou Zhichao , Anantharaman Karthik 
Published: June 2020

Abstract
Background
Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and assessing their metabolic impacts on microbiomes.

Design
Here we present VIBRANT, the first method to utilize a hybrid machine learning and protein similarity approach that is not reliant on sequence features for automated recovery and annotation of viruses, determination of genome quality and completeness, and characterization of viral community function from metagenomic assemblies. VIBRANT uses neural networks of protein signatures and a newly developed v-score metric that circumvents traditional boundaries to maximize identification of lytic viral genomes and integrated proviruses, including highly diverse viruses. VIBRANT highlights viral auxiliary metabolic genes and metabolic pathways, thereby serving as a user-friendly platform for evaluating viral community function. VIBRANT was trained and validated on reference virus datasets as well as microbiome and virome data.

Results
VIBRANT showed superior performance in recovering higher quality viruses and concurrently reduced the false identification of non-viral genome fragments in comparison to other virus identification programs, specifically VirSorter, VirFinder, and MARVEL. When applied to 120,834 metagenome-derived viral sequences representing several human and natural environments, VIBRANT recovered an average of 94% of the viruses, whereas VirFinder, VirSorter, and MARVEL achieved less powerful performance, averaging 48%, 87%, and 71%, respectively. Similarly, VIBRANT identified more total viral sequence and proteins when applied to real metagenomes. When compared to PHASTER, Prophage Hunter, and VirSorter for the ability to extract integrated provirus regions from host scaffolds, VIBRANT performed comparably and even identified proviruses that the other programs did not. To demonstrate applications of VIBRANT, we studied viromes associated with Crohn’s disease to show that specific viral groups, namely Enterobacteriales-like viruses, as well as putative dysbiosis associated viral proteins are more abundant compared to healthy individuals, providing a possible viral link to maintenance of diseased states.

Conclusions
The ability to accurately recover viruses and explore viral impacts on microbial community metabolism will greatly advance our understanding of microbiomes, host-microbe interactions, and ecosystem dynamics.
Evaluation of drive-through pharmacy service in Queen Elizabeth Hospital Malaysia
Authors: Liew Jerry Ee Siung , Abdul Gapar Aizan Adifarhan bin , Shim Lik Ting 
Published: June 2020

AbstractBackgroundIn 2015, the drive-through pharmacy was first introduced in Queen Elizabeth Hospital (QEH), Malaysia as one of the pharmacy value-added services. Therefore, it is imperative to review the service for further amelioration to fulfil patients’ needs and expectations.ObjectiveThe aim of this study is to evaluate the drive-through pharmacy service in Queen Elizabeth Hospital, Malaysia.MethodsA cross-sectional observational study was conducted from July to December 2018. The questionnaire was developed and underwent thorough validation process which yielded a Cronbach’s alpha reliability score of 0.9130. Satisfaction was calculated by mean percentage score (0% (dissatisfied) to 100% (satisfied). All data were analysed descriptively and thematic analysis was used in analysing open-ended question.ResultsCompliance in obtaining medication was at 96.3% with a given two-week grace collection period. Insufficient quantity of medications (33.3%) was the highest near-missed medication errors occurred at the drive-through pharmacy. The mean satisfaction percentage score for all patients were 76.6% ± 8.1. A total of 69.2% (n = 83) were “very satisfied” while 30.8% (n = 37) were “satisfied” with the service. Among the reasons for satisfaction are convenience in getting medication refills (n = 74, 62%), short waiting time (n = 75, 63%) and knowledgeable dispensers (n = 87, 73%). A handful of patients were “dissatisfied” with the opening hours (n = 14, 11.7%) and the location of the drive-through pharmacy service (n = 19, 15.8%).ConclusionCompliance in medication collection is acceptable within stipulated grace period. Despite low occurrence, identification of near-missed medication errors provides useful insights for future improvement of the service. Generally, our patients are satisfied with the service. However, we need to re-evaluate on the opening hours and location of the service.
Optimized vs. Standard Automated Peritoneal Dialysis Regimens (OptiStAR): study protocol for a randomized controlled crossover trial
Authors: Bergling Karin , de Arteaga Javier , Ledesma Fabián , Öberg Carl Mikael 
Published: June 2020

Abstract
Background
It has been estimated that automated peritoneal dialysis (APD) is currently the fastest growing renal replacement therapy in the world. However, in light of the growing number of diabetic patients on peritoneal dialysis (PD), the unwanted glucose absorption during APD remains problematic. Recent results, using an extended 3-pore model of APD, indicated that large reductions in glucose absorption are possible by using optimized bi-modal treatment regimens, having “UF cycles” using a higher glucose concentration, and “Clearance cycles” using a low concentration or, preferentially, no glucose. The present study is designed to test the theoretical prediction of a lower glucose absorption using these novel regimes.

Methods
This study is a randomized single-center, open-label, prospective study. Prevalent PD patients between 18 and 75 years old without known catheter problems or recent peritonitis are eligible for inclusion. Patients are allocated to a first treatment session of either standard APD (6 × 2 L 1.36% over 9 h) or optimized APD (7 × 2 L 2.27% + 5 × 2 L 0.1% over 8 h). A second treatment session using the other treatment will be performed in a crossover fashion. Samples of the dialysis fluid will be taken before and after the treatment, and the volume of the dialysate before and after the treatment will be carefully assessed. The primary endpoint is difference in glucose absorption between the optimized and standard treatment. Secondary endpoints are ultrafiltration, sodium removal, Kt/V urea, and Kt/V Creatinine. The study will be closed when a total of 20 patients have successfully completed the interventions or terminated according to interim analysis. A Monte Carlo power analysis shows that the study has 80% power to detect a difference of 10 g (in line with that of theoretical results) in glucose absorption between the two treatments in 10 patients.

Discussion
The present study is the first clinical investigation of optimized bi-modal treatments proposed by recent theoretical studies.

Trial registration
ClinicalTrials.gov identifier: NCT04017572. Registration date: July 12, 2019, retrospectively registered.
The impacts of pill contraceptive low-dose on plasma levels of nitric oxide, homocysteine, and lipid profiles in the exposed vs. non exposed women: as the risk factor for cardiovascular diseases
Authors: Momeni Zahra , Dehghani Ali , Fallahzadeh Hossein , Koohgardi Moslem , Dafei Maryam , Hekmatimoghaddam Seyed Hossein , Mohammadi Masoud 
Published: June 2020

Abstract
Background
Consuming oral contraceptive pills is one of the methods for preventing pregnancy worldwide. As using the pills has always caused the greatest concern for the likelihood of developing cardiovascular diseases and also given the limited conducted studies in this regard, this study was carried out to determine the impacts of low dose birth control pills on plasma levels of nitric oxide, homocysteine, and lipid profiles in the exposed vs. non exposed women as the risk factors for cardiovascular diseases.

Methods
This was a combined cohort study conducted on 100 women, having the age range 20–35 years and normal menstrual cycles, referred to the health care centers in Yazd, Iran. The demographic data were obtained through face to face interviews performed by the researcher. Anthropometric indexes were measured and biochemical factors were determined by testing blood samples. Then, using SPSS 16 and statistical independent t-test and Chi- square, the data were analyzed.

Results
The mean ± standard deviations of plasma levels of homocysteine, nitric oxide, cholesterol, triglyceride, Low Density Lipoprotein, and High Density Lipoprotein levels in the group consumed low dose contraceptive pills were 3.84 ± 2.35 μmol/l, 181.36 ± 90.44 μM, 180.7 ± 38.28 mg/dl, 129.82 ± 47.92 mg/ dl, 101.42 ± 30.66 mg/dl, and 56.46 ± 8.42 mg/dl, There were significant statistical differences between those consuming the pills and those not consuming the pills regarding cholesterol (P < 0.05).

Conclusion
Consuming Low Dose contraceptive pills can increase the plasma levels of cholesterol, triglyceride, and Low Density Lipoprotein levels; i.e. this condition is called dyslipidemia. On the other hand, there were no changes in the levels of homocysteine and nitric oxide in the healthy women consuming the pills; therefore, the pills may not develop cardiovascular diseases in healthy women. Accordingly, it is recommended that the health care providers prescribe the pills for the women with cautions.
Sea as a color palette: the ecology and evolution of fluorescence
Authors: Macel Marie-Lyne , Ristoratore Filomena , Locascio Annamaria , Spagnuolo Antonietta , Sordino Paolo , D’Aniello Salvatore 
Published: June 2020

AbstractFluorescence and luminescence are widespread optical phenomena exhibited by organisms living in terrestrial and aquatic environments. While many underlying mechanistic features have been identified and characterized at the molecular and cellular levels, much less is known about the ecology and evolution of these forms of bioluminescence. In this review, we summarize recent findings in the evolutionary history and ecological functions of fluorescent proteins (FP) and pigments. Evidence for green fluorescent protein (GFP) orthologs in cephalochordates and non-GFP fluorescent proteins in vertebrates suggests unexplored evolutionary scenarios that favor multiple independent origins of fluorescence across metazoan lineages. Several context-dependent behavioral and physiological roles have been attributed to fluorescent proteins, ranging from communication and predation to UV protection. However, rigorous functional and mechanistic studies are needed to shed light on the ecological functions and control mechanisms of fluorescence.
The effect of differences in group composition on knowledge transfer, group achievement, and learners’ affective responses during reciprocal concept mapping with the Kit-Build Approach
Authors: Sadita Lia , Hirashima Tsukasa , Hayashi Yusuke , Furtado Pedro G. F. , Junus Kasiyah , Santoso Harry Budi 
Published: June 2020

AbstractCollaborative learning requires a structured and open environment where individuals can actively exchange and elaborate their ideas to achieve a high-quality problem-solving solution. The use of concept map has been extensively implemented to facilitate idea generation and maintain shared focus during discussion. This study employs the Reciprocal Kit-Build (RKB) approach as a designed activity to support collaborative concept mapping. Though previous studies show the RKB is promising to promote productive discussion and achieve high-quality group products, they have not investigated how individual knowledge differences may potentially influence the effectiveness of collaboration. This study aims to identify the effect of group composition on learning effectiveness at the level of interaction between individual and group and at the level of the group as a whole. At the interaction level, we investigate the amount of knowledge transfer from shared and unshared individual knowledge to group solutions, while at the group level, the quality of collaborative maps is evaluated. Moreover, we explore the affective responses of learners during designated activities. A single group design is applied to illustrate the learning activities in a practical classroom settings where all students receive the same treatment. Our findings show that the transfer of individual shared and unshared knowledge is considerably high in all group conditions. Group composition does not significantly affect knowledge transfer and final group-outcome products; however, it may induce learners to experience different affective states. The results are essential for practitioners who intend to apply the RKB in their classroom to determine the appropriate group settings.
Synaptic loss and amyloid beta alterations in the rodent hippocampus induced by streptozotocin injection into the cisterna magna
Authors: Ahn Yujin , Seo Jincheol , Park Junghyung , Won Jinyoung , Yeo Hyeon-Gu , Kim Keonwoo , Jeon Chang-Yeop , Huh Jae-Won , Lee Sang-Rae , Lee Dong-Seok , Lee Youngjeon 
Published: June 2020

AbstractTo date, researchers have developed various animal models of Alzheimer’s disease (AD) to investigate its mechanisms and to identify potential therapeutic treatments. A widely recognized model that mimics the pathology of human sporadic AD involves intracerebroventricular (ICV) injection with streptozotocin (STZ). However, ICV injections are an invasive approach, which creates limitations in generalizing the results. In this study, we produced a rodent model of AD using STZ (3 mg/kg) injection via the cisterna magna (CM) once every week for 4 weeks, and analyzed at 4 weeks and 16 weeks after final injection. In the CM-STZ rodent model of AD, we observed increase in extracellular amyloid-beta (Aβ) deposition and decrease and abnormal morphology of post-synaptic protein, PSD95 in 16 weeks STZ-injected group. The model developed using our less-invasive method induced features of AD-like pathology, including significantly increased extracellular amyloid-beta deposition, and decreased synaptic protein in the hippocampus. These findings supporting the success of this alternative approach, and thus, we suggest this is a promising, less invasive model for use in future AD research.
Role of early postoperative ultrasonography in prediction of AV fistula failure in hemodialysis patients
Authors: Abd-Elmageed Mohamed Kamel , Elsayed Basma Fathy , Elkholy Mohamed Ramadan 
Published: June 2020

Abstract
Background
Doppler ultrasonography (US) is the main imaging modality of hemodialysis AV fistula as it is safe non-invasive accurate modality. This study is to measure the arteriovenous (AV) fistula blood flow during early postoperative period (7–14 days) and assess its predictive role in AV fistula failure in hemodialysis patients. Color Doppler ultrasonography (CDU) was used to estimate the blood flow in the AV fistula of 100 patients at (7–14 days) after the fistula creation. The performance of fistula blood flow during early postoperative periods for predicting fistula failure was evaluated, and optimal cutoff value was determined.

Results
During the follow-up period (6 months), we classified the fistulas as 82 mature, and 18 failed. The blood flow was considerably lower in the failure group than that in the mature group at the early postoperative period (P value = 0.001). The areas under the curves (AUC) were 0.952, and the cutoff value was 200.5 ml/min. The sensitivity of CDU in prediction of fistula failure is 99% with negative predictive value 94% and accuracy 97%, and with specificity 89% and positive predictive value 98%.

Conclusion
Measuring blood flow of the AV fistula at the early postoperative period probably has a predictive role in the AV fistula failure. There is risk of failure if the blood flow less than 200 ml/min at (day 7–14)
Ready, set, go!: exploring use of a readiness process to implement pharmacy services
Authors: Livet Melanie , Yannayon Mary , Richard Chloe , Sorge Lindsay , Scanlon Paul 
Published: June 2020

Abstract
Background
Readiness is an essential precursor of successful implementation; however, its conceptualization and application has proved elusive. R = MC2 operationalizes readiness for use in practice. The purpose of this study was to (1) describe the application of R = MC2 to assess and build readiness in nine healthcare sites responsible for implementing medication management services and (2) gain insights into the sites’ experience.

Methods
This mixed methods exploratory study used data collected as part of a process evaluation. Understanding application of the readiness process (Aim 1) involved examining team members’ involvement (who?), readiness challenges and readiness building strategies (what?), strategy execution (how much?), and resulting changes (for what purpose?). To understand the sites’ experience with the R = MC2 system (Aim 2), interviews were conducted with six of the sites to identify facilitators, barriers, and lessons learned. Data sources included a document review (e.g., sites’ action plans), survey results, and interview data.

Results
Sites included primary care and specialty clinics, pharmacies within health systems, and community pharmacies. Teams consisted of 4–11 members, including a lead pharmacist. The teams’ readiness activities clustered into five broad categories of readiness building strategies (e.g., building the operational infrastructure for service integration). Of the 34 strategies identified across sites, 68% were still in progress after 4 months. Engaging in the readiness process resulted in a number of outputs (e.g., data management systems) and benefits (e.g., an opportunity to ensure alignment of priorities and fit of the intervention). Based on the interviews, facilitators of the readiness process included assistance from a coach, internal support, and access to the readiness tools. Competing priorities and lack of resources, timely decision-making, and the timing of the readiness process were cited as barriers. The importance of service fit, stakeholder engagement, access to a structured approach, and rightsizing the readiness process emerged as lessons learned.

Conclusions
These findings provide valuable insights into the application of a readiness process. If readiness is to be integrated into routine practice as part of any implementation effort, it is critical to gain a better understanding of its application and value.
Analysis of the impact of social network sites and eWOM marketing, considering the reinforcing dimensions of the concept of luxury, on tendency toward luxury brand
Authors: MajlesiRad Zahra , Haji pour Shoushtari Abdol Hamid 
Published: June 2020

AbstractThis study, with regard to new ways of marketing in today’s digital world, has tried to analyze and evaluate the impact of marketing through social network sites as the most effective electronic word-of-mouth marketing strategy on tendency toward luxury brand or in other words, on purchase intent trigger toward this type of brand. It also outlines that “communication” policy plays a significant role on establishment of strong relationship with customers among luxury marketing mix strategies. The research has been done among users of social network sites that live in the north of Tehran (district nos. 1, 2 and 3). They are considered as social classes A and B, and there is high demand of purchasing luxury brands among them. The impact of structural factors of these sites, as well as demographic factors, with regard to the dimensions that reinforce the concept of “luxury” was studied on the tendency of people toward luxury brands. This study is considered as applied research, and the data collection method is survey-descriptive. The validity of the questionnaire was investigated by exploratory factor analysis through performing principal component analysis. Then the data analysis was conducted by structural equations modeling technique and also Spearman correlation test. At last, most of the hypotheses were confirmed and the results showed a significant impact of social network sites marketing on tendency to luxury brand. The research offers implications for developing effective marketing strategy through social network sites and helps luxury brand managers to build strong customer–brand relationship.
Toward a better understanding of low-frequency electrical relaxation — An enhanced pore space characterization
Authors: Kruschwitz Sabine , Halisch Matthias , Dlugosch Raphael , Prinz Carsten 
Published: June 2020

The relaxation phenomena observed in the electrical low-frequency range (approximately 1 MHz–10 kHz) of natural porous media such as sandstones are often assumed to be directly related to the dominant (modal) pore throat sizes measured, for instance, with mercury intrusion porosimetry. Attempts to establish a universally valid relationship between pore size and peak spectral induced polarization (SIP) relaxation time have failed, considering sandstones from very different origins and featuring great variations in textural and chemical compositions as well as in geometric pore space properties. In addition working with characteristic relaxation times determined in Cole-Cole or Debye decomposition fits to build the relationship have not been successful. In particular, samples with narrow pore throats are often characterized by long SIP relaxation times corresponding to long “characteristic length scales” in these media, assuming that the diffusion coefficients along the electrical double layer were constant. Based on these observations, three different types of SIP relaxation can be distinguished. We have developed a new way of assessing complex pore spaces of very different sandstones in a multimethodical approach to combine the benefits of mercury intrusion porosimetry, micro-computed tomography, and nuclear magnetic resonance. In this way, we achieve much deeper insight into the pore space due to the different resolutions and sensitivities of the applied methods to pore constrictions (throats) and wide pores (pore bodies). We experimentally quantify pore aspect ratios and volume distributions within the two pore regions. We clearly observe systematic differences between three SIP relaxation types identified previously, and we can attribute the SIP peak relaxation times to measured characteristic length scales within our materials. We highlight selected results for a total of nine sandstones. It seems that SIP relaxation behavior depends on the size difference of the narrow pore throats to the wide pore bodies, which increases from SIP type 1 to type 3.
Referral of patients with emotionally unstable personality disorder for specialist psychological therapy: why, when and how?
Authors: Roughley Matthew , Maguire Amy , Wood Grace , Lee Tennyson 
Published: June 2020

SummaryAlthough we commonly work with patients with emotionally unstable personality disorder (EUPD) in community mental health teams (CMHTs), only some enter evidence-based psychological therapies. Many patients are not considered ready to engage in specialist treatments and remain in CMHTs without any clear focus or structure to their treatment, which is unsatisfactory for patients, clinicians and services. We present a fictional case and synthesise available literature and lived experience to explore readiness and ways to promote it. We highlight relevant issues for trainees to consider in practice. Patients with EUPD who have not received specialist treatment can be considered in terms of the transtheoretical model's stages of change. Identifying a patient's stage can help guide how to increase readiness for referral and decide when to refer. Interventions available to all healthcare professionals which may promote readiness include: psychoeducation, personal formulations, crisis planning, goal-setting, peer support, distress tolerance skills, motivational interviewing and mindfulness.