bluuebunny/crossref_metadata_2025_split huggingface dataset:
The extended recovery ring-stage survival assay provides a superior association with patient clearance half-life and increases throughput
Authors: Davis Sage Z. , Singh Puspendra P. , Vendrely Katelyn M. , Shoue Douglas A. , Checkley Lisa A. , McDew-White Marina , Button-Simons Katrina A. , Cassady Zione , Sievert Mackenzie A.C. , Foster Gabriel J. , Nosten François H. , Anderson Timothy J.C. , Ferdig Michael T. 
Published: January 2020

Abstract
Background Tracking and understanding artemisinin resistance is key for preventing global setbacks in malaria eradication efforts. The ring-stage survival assay (RSA) is the current gold standard for in vitro artemisinin resistance phenotyping. However, the RSA has several drawbacks: it is relatively low throughput, has high variance due to microscopy readout, and correlates poorly with the current benchmark for in vivo resistance, patient clearance half-life post-artemisinin treatment. Here a modified RSA is presented, the extended Recovery Ring-stage Survival Assay (eRRSA), using 15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives, including parasite isolates with and without kelch13 mutations. Methods P. falciparum cultures were synchronized with single layer Percoll during the schizont stage of the erythrocytic cycle. Cultures were left to reinvade to early ring-stage and parasitemia was quantified using flow cytometry. Cultures were diluted to 2% hematocrit and 0.5% parasitemia in a 96-well plate to start the assay, allowing for increased throughput and decreased variability between biological replicates. Parasites were treated with 700nM of dihydroartemisinin or an equivalent amount of dimethyl sulfoxide (DMSO) for 6 h, washed three times in drug-free media, and incubated for 66 or 114 h, when samples were collected and frozen for PCR amplification. A SYBR Green-based quantitative PCR method was used to quantify the fold-change between treated and untreated samples. Results 15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives were assayed using the eRRSA. Due to the large number of pyknotic and dying parasites at 66 h post-exposure (72 h sample), parasites were grown for an additional cell cycle (114 h post-exposure, 120 h sample), which drastically improved correlation with patient clearance half-life compared to the 66 h post-exposure sample. A Spearman correlation of 0.8393 between fold change and patient clearance half-life was identified in these 15 isolates from Southeast Asia, which is the strongest correlation reported to date. Conclusions eRRSA drastically increases the efficiency and accuracy of in vitro artemisinin resistance phenotyping compared to the traditional RSA, which paves the way for extensive in vitro phenotyping of hundreds of artemisinin resistant parasites.
Personal and social patterns predict influenza vaccination decision
Authors: Shaham Adir , Chodick Gabriel , Shalev Varda , Yamin Dan 
Published: January 2020

Abstract
Background: Seasonal influenza vaccination coverage remains suboptimal in most developed countries, despite longstanding recommendations of public health organizations. The individual’s decision regarding vaccination is located at the core of non-adherence. We analyzed large-scale data to identify personal and social behavioral patterns for influenza vaccination uptake, and develop a model to predict vaccination decision of individuals in an upcoming influenza season. Methods: We analyzed primary data from the electronic medical records of a retrospective cohort of 250,000 individuals between the years 2007 and 2017, collected from 137 clinics. Individuals were randomly sampled from the database of Maccabi Healthcare Services. Maccabi’s clients are representative of the Israeli population, reflect all demographic, ethnic, and socioeconomic groups and levels. We used several machine-learning models to predict whether a patient would get vaccinated in the future. Models’ performance was evaluated based on the area under the ROC curve. Results: The vaccination decision of an individual can be explained in two dimensions, Personal and social. The personal dimension is strongly shaped by a “default” behavior, such as vaccination timing in previous seasons and general health consumption, but can also be affected by temporal factors such as respiratory illness in the prior year. In the social dimension, a patient is more likely to become vaccinated in a given season if at least one member of his family also became vaccinated in the same season. Vaccination uptake was highly assertive with age, socioeconomic score, and geographic location. An XGBoost-based predictive model achieved an ROC-AUC score of 0.91 with accuracy and recall rates of 90% on the test set. Prediction relied mainly on the patient’s individual and household vaccination status in the past, age, number of encounters with the healthcare system, number of prescribed medications, and indicators of chronic illnesses. Conclusions: Our ability to make an excellent prediction of the patient’s decision sets a major step toward personalized influenza vaccination campaigns, and will help shape the next generation of targeted vaccination efforts.
Acceptability of screening for pregnancy intention in general practice: a population survey of people of reproductive age
Authors: Hammarberg Karin , Hassard Julie , de Silva Renee , Johnson Louise 
Published: January 2020

Abstract
Background: Optimal parental preconception health benefits reproductive outcomes . However, preconception health promotion is not routinely offered in primary health care settings to people of reproductive age. The aim was to gauge the planned preconception health behaviours and attitudes towards being asked about pregnancy intention by a general practitioner (GP) among people of reproductive age in Australia. Method: The research was conducted on a single wave of Australia’s first and only probability-based online panel, Life in Australia™. Members of the Life in Australia™ panel are Australian residents aged 18 years or over. All active members between the ages of 18 and 45 years were eligible to participate. Eligible panel members were invited to complete a survey about fertility and childbearing. Data were collected from 18 February to 4 March 2019. Results: In all 965 female and male members of Life in Australia™ aged between 18 and 45 years were invited to complete the survey. Of these, 716 (74.2%) agreed. Most respondents indicated that if they were planning to have a child they would try to optimise their preconception health by adopting a healthier diet (80%), seeing a GP for a health check-up (78%), reducing alcohol consumption (78% of those consuming alcohol), getting fitter (73%), and stopping smoking (70% of smokers). Three in four (74%) stated that they would not mind if their GP asked them about their pregnancy intentions. Conclusion: Findings suggests that routinely asking people of reproductive age about their pregnancy intentions and advising those who are planning pregnancy about what they can do to ensure optimal preconception health would be acceptable to most people and may improve reproductive outcomes.
Effects of Low Versus Standard Pressure Pneumoperitoneum on Renal Syndecan-1 Shedding and VEGF Receptor-2 Expression in Living-donor Nephrectomy: A Randomized Controlled Study
Authors: Aditianingsih Dita , Mochtar Chaidir Arif , Lydia Aida , Siregar Nuryati Chairani , Margyaningsih Nur Ita , Madjid Amir Sjarifuddin , Suwarto Suhendro 
Published: January 2020

Abstract
Background
Laparoscopic nephrectomy is a preferred technique for living kidney donation. However, positive-pressure pneumoperitoneum may have an unfavorable effect on the remaining kidney and other distant organs due to inflamed vascular endothelium and renal tubular cell injury in response to increased systemic inflammation. Early detection of vascular endothelial and renal tubular response is needed to prevent further kidney injury due to increased intraabdominal pressure induced by pneumoperitoneum. Transperitoneal laparoscopic living donor nephrectomy represented a human model of mild increasing intraabdominal pressure. This study aimed to assess the effect of increased intraabdominal pressure on vascular endothelium and renal tubular cells by comparing the effects of low and standard pressure pneumoperitoneum on vascular endothelial growth factor receptor-2 (VEGFR-2) expression and the shedding of syndecan-1 as the early markers to a systemic inflammation.
Methods
We conducted a prospective randomized study on 44 patients undergoing laparoscopic donor nephrectomy. Subjects were assigned to standard (12 mmHg) or low pressure (8 mmHg) groups. Baseline, intraoperative, and postoperative plasma interleukin-6, syndecan-1, and sVEGFR-2 were quantified by ELISA. Syndecan-1 and VEGFR-2 expression were assessed immunohistochemically in renal cortex tissue. Renal tubule and peritubular capillary ultrastructures were examined using electron microscopy. Perioperative hemodynamic changes, end-tidal CO2, serum creatinine, blood urea nitrogen, and urinary KIM-1 were recorded.
Results
The low pressure group showed lower intra- and postoperative heart rate, intraoperative plasma IL-6, sVEGFR-2 levels and plasma syndecan-1 than standard pressure group. Proximal tubule syndecan-1 expression was higher in the low pressure group. Proximal-distal tubules and peritubular capillary endothelium VEGFR-2 expression were lower in low pressure group. The low pressure group showed renal tubule and peritubular capillary ultrastructure with intact cell membranes, clear cell boundaries, and intact brush borders, while standard pressure group showed swollen nuclei, tenuous cell membrane, distant boundaries, vacuolizations, and detached brush borders.
Conclusion
The low pressure pneumoperitoneum attenuated the inflammatory response and resulted in reduction of syndecan-1 shedding and VEGFR-2 expression as the renal tubular and vascular endothelial proinflammatory markers to injury due to a systemic inflammation in laparoscopic nephrectomy.
Trial registration
ClinicalTrial.gov NCT:03219398, July 17th 2017.
Keywords: pneumoperitoneum, renal resistive index, interleukin-6, syndecan-1, sVEGFR-2, laparoscopic nephrectomy
The effects of combined magnesium and zinc supplementation on metabolic status in patients with type 2 diabetes mellitus and coronary heart disease
Authors: Hamedifard Zahra , Farrokhian Alireza , Reiner Željko , Bahmani Fereshteh , Taghizadeh Mohsen , Ghotbi Maryam , Asemi Zatollah 
Published: January 2020

Abstract
Background: The present research aimed to analyze the impacts of magnesium and zinc supplement on the metabolic level in the patients suffering from CHD (coronary heart disease) and T2DM (type 2 diabetes mellitus). Methods: According to the research design, a randomized, double-blind, placebo-controlled trial has been implemented on 55 women suffering from CHD and T2DM. Therefore, the participants have been randomly divided into 2 groups for taking placebo (n = 28) or 250 mg magnesium oxide plus 220 mg zinc sulfate (n =27) or for 12 weeks. Results: Magnesium and zinc considerably declined the levels of fasting plasma glucose (FPG) (β -9.44 mg/dL, 95% CI, -18.30, -0.57; P = 0.03) and levels of insulin (β -1.37 µIU/mL, 95% CI, -2.57, -0.18; P = 0.02). Moreover, levels of HDL-cholesterol have been remarkably enhanced (β 2.09 mg/dL, 95% CI, 0.05, 4.13; P = 0.04) in comparison to the placebo. There have been an association between magnesium and zinc intake and a considerable decrease of C-reactive protein (CRP) (β -0.85 mg/L, 95% CI, -1.26, -0.45; P < 0.001), a considerable enhancement in the total nitrite (β 5.13 µmol/L, 95% CI, 1.85, 8.41; P = 0.003), and total anti-oxidant capacities (TAC) (β 43.44 mmol/L, 95% CI, 3.39, 83.50; P=0.03) in comparison to the placebo. Furthermore, magnesium and zinc remarkably reduced the Beck Depression Inventory index (BDI) (β -1.66; 95% CI, -3.32, -0.009; P = 0.04) and Beck Anxiety Inventory (BAI) (β -1.30; 95% CI, -2.43, -0.16; P=0.02) in comparison to the placebo. Conclusions: In patients with T2DM and CVD the 12-week intake of magnesium and zinc affected FPG, HDL-cholesterol, CRP, insulin, NO, TAC levels, and BDI and BAI score usefully. Trial registration: Current Controlled Trials http://www.irct.ir: IRCT20130211012438N31 at 11 May 2019 of registration. This study retrospectively registered.
Evaluation of the national implementation of the VA Diffusion of Excellence Initiative on Advance Care Planning via Group Visits: Protocol for a quality improvement evaluation
Authors: Matthieu Monica M. , Ounpraseuth Songthip T. , Painter Jacob , Waliski Angie , Williams James “Silas” , Hu Bo , Smith Robin , Garner Kimberly K. 
Published: January 2020

Abstract
Background Traditionally system leaders, service line managers, researchers, and program evaluators, hire specifically dedicated implementation staff to ensure that a healthcare quality improvement effort can “go to scale”. However, little is known about the impact of hiring dedicated staff and whether funded positions, amid a host of other delivered implementation strategies, is the main difference among sites with and without funding used to execute the program, on implementation effectiveness and cost outcomes. Methods/Design In this mixed methods program evaluation, we will determine the impact of funding staff positions to implement, sustain, and spread a program, Advance Care Planning (ACP) via Group Visits (ACP-GV), nationally across the entire United States Department of Veterans Affairs (VA) healthcare system. In ACP-GV, Veterans, their families, and trained clinical staff with expertise in ACP meet in a group setting to engage in discussions about ACP and the benefits to Veterans and their trusted others of having an Advance Directive (AD) in place. To determine the impact of the ACP-GV National Program, we will use a propensity score matched control design to compare ACP-GV and non-ACP-GV sites on the proportion of ACP discussions in VHA facilities. To account for variation in funding status, we will document and compare funded and unfunded sites on the effectiveness of implementation strategies (individual and combinations) used by sites in the National Program on ACP discussion and AD completion rates across the VHA. In order to determine the fiscal impact of the National Program and to help inform future dissemination across VHA, we will use a budget impact analysis. Finally, we will purposively select, recruit, and interview key stakeholders, who are clinicians and clinical managers in the VHA who offer ACP discussions to Veterans, to identify the characteristics of high-performing (e.g., high rates or sustainers) and innovative sites (e.g., unique local program design or implementation of ACP) to inform sustainability and further spread. Discussion As an observational evaluation, this protocol will contribute to our understanding of implementation science and practice by examining the natural variation in implementation and spread of ACP-GV with or without funded staff positions.
Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes
Authors: Liu Benwen , Hu Yu Xin , Hu Zheng Yu , Liu Guo Xiang , Zhu Huan 
Published: January 2020

Abstract
Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.
Management of complex renal cysts in Canada: Results of a survey study
Authors: Couture Félix , Finelli Antonio , Tétu Amélie , Bhindi Bimal , Breault Rodney H. , Kapoor Anil , Kassouf Wassim , Lavallée Luke , Tanguay Simon , Violette Philippe D. , Richard Patrick O. 
Published: January 2020

Abstract
Background Bosniak III and IV cysts have a high risk of malignancy and have traditionally been managed surgically. However, growing evidence suggests that many can be managed by active surveillance. The main objective of this study was to characterize the use of surveillance in the management of complex renal cysts. Methods A web-based survey was sent to all registered, active members of the Canadian Urological Association (N=583) in October 2018. Results The survey response rate was 24.7%. Management of Bosniak III cysts varied considerably. A large proportion of respondents (33.1%) offered active surveillance in >50% of cases. Only 13.7% of respondents reported never or rarely (<5% of cases) offering surveillance. In contrast, for Bosniak IV cysts, 60.1% of urologists never or rarely offered surveillance, while only 10.1% offer it in >50% of cases. A significantly greater proportion of academic urologists, compared to non-academic urologists, viewed surveillance as a management option for patients with a Bosniak III or IV cyst. The most commonly reported barriers to a greater adoption of surveillance were concerns regarding its oncologic safety, the lack of data to support surveillance in this population, and the lack of triggers for discontinuation of active surveillance and intervention. Conclusions Despite active surveillance being included as a management option in guidelines, many Canadian urologists are reluctant to offer surveillance to patients with Bosniak III or IV cysts. Practice patterns are heterogeneous among those offering surveillance. High-quality studies are required to better define the benefits and risks of cystic renal mass surveillance.
Long term outcomes of Burch colposuspension and transobturator tape and single incision needleless (DynaMesh®- SIS minor) for the surgical treatment of female stress urinary incontinence patients who underwent combined pelvic reconstructive surgery or hysterectomy
Authors: Akdemir Yesim , Dincer Fadime , Buyukuysal Cagatay , Ozmen Ulku , Harma Muge , Harma Mehmet Ibrahim 
Published: January 2020

Abstract
Background Women with SUI often require combined pelvic reconstructive surgery because of sharing risk factors of pelvic relaxation. The aim of this study was to evaluate the efficacy of Burch colposuspension, the transobturator tape (TOT), and single incision needleless (DynaMesh®- SIS minor) procedures in patients with SUI who also underwent combined pelvic reconstructive surgery or hysterectomy. Methods We carried out a prospective cohort study that included 142 patients who underwent Burch colposuspension (n:43), TOT(n:40), or SIS(n:39) procedures combined pelvic reconstructive surgery or hysterectomy between January 2010 and July 2018. During clinical follow-up, objective cure, subjective cure, failure and surgical success rates were analyzed. Quality of life and symptom severity were assessed by IIQ-7, UDI-6, OAB-V8, SSI, SSQ-8 and PGI-I. Primary outcome was surgical success which was defined when any of the objective cure, subjective cure or improvement has achieved and secondary outcomes were; intraoperative bladder injury, sling extrusion, de novo urgency, voiding dysfunction, length of hospital stay, and outcomes of patient reported quality of life questionnaires. Results Surgical success rate were higher in Burch group than SIS group and also higher in TOT group than SIS group (88,4% vs 61,5% and 87,5% vs 61,5% respectively, p=0,003) Urinary incontinence complaints were higher and quality of life were lower in in SIS group when compared with Burch group. No difference was seen in between Burch and TOT groups, and TOT and SIS groups in terms of IIQ-7, UDI-6, OAB-V8, SSI, and SSQ-8 scores. Conclusions Both Burch and TOT were safe and effective procedures in patients with SUI who required additional pelvic surgeries. Although surgical outcome of SIS procedure in SUI patients that had concomitant pelvic surgeries in our study was not promising, the data are not clear and further randomized studies are needed to clarify these observations.
The Expression of Ptch1 and Ptch2 in the Stenotic Tissue of Congenital Ureteropelvic Junction Obstruction in Children
Authors: Yang Yanfang , han wenwen , Zhang Weiping , Sun Ning 
Published: January 2020

Abstract
Objective Ptch1 and Ptch2 are expressed in tubular epithelium and stromal cells adjacent to the UPJ. They mediated inhibition of smoothened, a transmembrane protein expressed on the cell surface. If the pathway was disturbed, UPJO might be onset. The aim of this study was to determine the expression of Ptch1 (P1) and Ptch2 (P2) in stenotic segments in children with congenital ureteropelvic junction obstruction (UPJO) versus in normal control subjects. Materials and methods Stenotic segments of ureter tissues were obtained from 20 UPJO patients. Extrinsic stenosis, such as vessel and ureteral polyp, were excluded. The control ureter specimens were obtained from 10 patients with Wilm’s tumor, and the tissues were confirmed histologically to be unaffected. Immunofluorescence, Western blot and real-time PCR were used to investigate the expression of P1 and P2. Statistical methods were used to find the differences between the two groups Results P1 and P2 were identified that located in the cytoplasm of smooth muscle in two groups through Immunohistochemistry. However, there were no statistical differences between the two groups in P1 and P2 with immunohistochemistry (P=0.31 and P=0.3, respectively). Meanwhile there were no statistical differences with Western blot (P=0.75 and P=0.9, respectively) and real-time PCR (P=0.52 and P=0.45, respectively). But we found that in the immunofluorescence P1 were diffused in controls and mainly surrounding the nucleuses of smooth muscle cells in UPJO. Conclusions The expression of P1 and P2 between the two group had no statistically significant. P1 mainly surrounding the nucleuses of smooth muscle cells in UPJO. The P1 pathway might be disturbed by the abnormal distribution of P1 rather than the quantity.