bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of Quadriceps Tendon With Patellar Bone Block Anterior Cruciate Ligament Reconstruction in Adolescent Patients With a Minimum 2-Year Follow-up
Authors: Gagliardi Alexia G. , Carry Patrick M. , Parikh Harin B. , Albright Jay C. 
Published: November 2019

Background: The incidence of anterior cruciate ligament (ACL) injury in the adolescent population is increasing. The quadriceps tendon–patellar bone autograft (QPA) has been established as a reliable graft choice for ACL reconstruction in the adult population. Purpose: To investigate graft failure, ability to return to sport, patient-reported functional outcomes, joint laxity, and subsequent injury among adolescent patients >2 years after primary ACL reconstruction with the QPA. Study Design: Case series; Level of evidence, 4. Methods: Consecutive patients who underwent QPA ACL reconstruction performed by a single surgeon were identified from an existing database. Information available in the database included demographics, concomitant/subsequent injuries, surgical procedures, graft failure, return to sport, and Lachman examination collected by medical record review. Pediatric International Knee Documentation Committee (Pedi-IKDC) and Lysholm scores were collected by telephone or during a clinic visit >2 years postoperatively. Results: The final cohort included 81 of 104 consecutive adolescent patients aged 10 to 18 years (mean ± SD, 15.9 ± 1.7 years at the time of surgery) for whom follow-up information was collected at >2 years after surgery. The cumulative incidence of graft failure within the 36-month follow-up period was 1.2% (95% CI, 0.1%-11.4%). The rate of ipsilateral non-ACL injuries was similar (1.2%; 95% CI, 0.2%-7.6%). Contralateral ACL and non-ACL injuries requiring surgical intervention were documented in 9.8% (95% CI, 4.9%-19.5%). The median Pedi-IKDC score was 94 (interquartile range, 89-98). The median Lysholm score was 99.5 (interquartile range, 89.0-100.0). At 36 months after surgery, 87.9% (95% CI, 81.4%-94.9%) of individuals had returned to play. Conclusion: The quadriceps tendon–patellar autograft is a novel graft that demonstrates excellent stability and favorable patient-reported outcomes. Based on these results, the QPA is a reliable choice for primary ACL reconstruction in adolescent patients.
Outcomes of clinical ethics support near the end of life: A systematic review
Authors: Haltaufderheide Joschka , Nadolny Stephan , Gysels Marjolein , Bausewein Claudia , Vollmann Jochen , Schildmann Jan 
Published: November 2019

Background: Clinical ethics support services have been advocated in recent decades. In clinical practice, clinical ethics support services are often requested for difficult decisions near the end of life. However, their contribution to improving healthcare has been questioned and demands for evaluation have been put forward. Research indicates that there are considerable challenges associated with defining adequate outcomes for clinical ethics support services. In this systematic review, we report findings of qualitative studies and surveys, which have been conducted to evaluate clinical ethics support services near the end of life. Methods: Electronic databases and other sources were queried from 1970 to May 2018. Two authors screened studies independently. Methodological quality of studies was assessed. For each arm of the review, an individual synthesis was performed. Prospero ID: CRD42016036241. Ethical Considerations: Ethical approval is not needed as it is a systematic review of published literature. Results: In all, 2088 hits on surveys and 2786 on qualitative studies were found. After screening, nine surveys and four qualitative studies were included. Survey studies report overall positive findings using a very wide and heterogeneous range of outcomes. Negative results were reported only occasionally. However, methodological quality and conceptual justification of used outcomes was often weak and limits generalizability of results. Conclusion: Evidence points to positive outcomes of clinical ethics support services. However, methodological quality needs to be improved. Further qualitative or mixed-method research on evaluating clinical ethics support services may contribute to the development of evaluating outcomes of clinical ethics support services by means of broaden the range of appropriate (process-oriented) outcomes of (different types of) clinical ethics support services.
Are upper urinary tract stones more common in more deprived populations?
Authors: Radcliffe Robert S , Miller Steven , Williams Simon T , Stanford Richard FJ 
Published: November 2019

Purpose: To examine the relationship between deprivation and upper tract calculus formation, and provide a contemporary estimate of the incidence of upper urinary tract stone disease. Methods: A retrospective review of hospital episodes for patients presenting to our institution with upper urinary tract stone disease in a 3-year period between 2010 and 2014. Incidence of stone disease was calculated and stratified according to deprivation, as measured by the index of multiple deprivation (IMD) and its subdomains. Poisson regression was used to model the relationship between deprivation and stone disease. Results: The overall incidence of upper urinary tract stone disease was 115 patients/100,000 person-years (95% confidence interval (CI) 108–122 per 100,000 person-years). There is a link between the IMD (as well as a number of its subdomains) and stone disease. The rate of incident stone disease was 50.6% higher in the most deprived quintile of the IMD when compared to the least deprived ( p < 0.001). Multivariate Poisson regression found that education, skills and training deprivation was the subdomain that predicted stone disease most strongly, with the incidence rate ratio being 1.15 (95% CI 1.053–1.261) for each increase in quintile. Conclusion: This study provides a contemporary measure of the incidence of upper urinary tract stone disease derived from a population in the Midlands of England. It informs our understanding of the link between types of deprivation and stone occurrence. Level of evidence: 2b
Platelet release reaction and intracellular cGMP
Authors: Weiss A , Baenziger NL , Atkinson JP 
Published: November 2019

Abstract
Enchanced cAMP concentrations inhibit the aggregation and release reaction of isolated human platelets and platelet-rich plasma to all known inducing agents. An opposing role for cGMP in this phenomenon has been proposed by some but not by others, and the function of cGMP in this secretory process is unclear. To further elucidate the role of cGMP in the release reaction, the effect of increased concentrations of this cyclic nucleotide on 14C-serotonin release was evaluated utilizing isolated human platelets and highly purified human thrombin or commercially available bovine thrombin. Several recently described stimulators of guanylate cyclase, including sodium nitroprusside, sodium azide, nitrosoquanidines, and ascorbic acid, were found to markedly augment platelet cGMP levels. Enhanced platelet cGMP concentrations produced by these drugs or by the exogenous addition of cGMP and its analogues neither caused these cells to secrete nor modulated the thrombin-induced serotonin release reaction. The inhibition of serotonin release by increased cAMP concentrations was not counteracted by increased cGMP levels. Platelet cGMP concentrations were unaltered by thrombin. These data indicate that cGMP is not an obligatory signal or a modulator of the thrombin-induced platelet release reaction.
A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons
Authors: Listopad Stanislav A. , Norden-Krichmar Trina M. 
Published: November 2019

Abstract
Background
Researchers commonly analyze lists of differentially expressed entities (DEEs), such as differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and differentially methylated positions/regions (DMPs/DMRs), across multiple pairwise comparisons. Large biological studies can involve multiple conditions, tissues, and timepoints that result in dozens of pairwise comparisons. Manually filtering and comparing lists of DEEs across multiple pairwise comparisons, typically done by writing custom code, is a cumbersome task that can be streamlined and standardized.

Results
A-Lister is a lightweight command line and graphical user interface tool written in Python. It can be executed in a differential expression mode or generic name list mode. In differential expression mode, A-Lister accepts as input delimited text files that are output by differential expression tools such as DESeq2, edgeR, Cuffdiff, and limma. To allow for the most flexibility in input ID types, to avoid database installation requirements, and to allow for secure offline use, A-Lister does not validate or impose restrictions on entity ID names. Users can specify thresholds to filter the input file(s) by column(s) such as p-value, q-value, and fold change. Additionally, users can filter the pairwise comparisons within the input files by fold change direction (sign). Queries composed of intersection, fuzzy intersection, difference, and union set operations can also be performed on any number of pairwise comparisons. Thus, the user can filter and compare any number of pairwise comparisons within a single A-Lister differential expression command.
In generic name list mode, A-Lister accepts delimited text files containing lists of names as input. Queries composed of intersection, fuzzy intersection, difference, and union set operations can then be performed across these lists of names.

Conclusions
A-Lister is a flexible tool that enables the user to rapidly narrow down large lists of DEEs to a small number of most significant entities. These entities can then be further analyzed using visualization, pathway analysis, and other bioinformatics tools.
BK Polyomavirus-specific T cell immune responses in kidney transplant recipients diagnosed with BK Polyomavirus-associated nephropathy
Authors: Bruminhent Jackrapong , Srisala Supranart , Klinmalai Chompunut , Pinsai Subencha , Watcharananan Siriorn P. , Kantachuvesiri Surasak , Hongeng Suradej , Apiwattanakul Nopporn 
Published: November 2019

AbstractBackgroundAdjustment of immunosuppression is the main therapy for BK polyomavirus (BKPyV)-associated nephropathy (BKPyVAN) after kidney transplantation (KT). Studies of BKPyV-specific T cell immune response are scarce. Here, we investigated BKPyV-specific T cell immunity in KT recipients diagnosed with BKPyVAN.MethodsAll adult KT recipients with BKPyVAN diagnosed at our institution from January 2017 to April 2018 were included. Laboratory-developed intracellular cytokine assays measuring the percentage of IFN-γ-producing CD4+and CD8+T cells, after stimulation with large-T antigen (LT) and viral capsid protein 1 (VP1), were performed both at the time of diagnosis and after adjustment of immunosuppression.ResultsWe included 12 KT recipients diagnosed with BKPyVAN (7 proven, 4 presumptive, and 1 possible). Those with presumptive BKPyVAN had a median plasma BKPyV DNA load of 5.9 log10 copies/ml (interquartile range [IQR]: 4.9–6.1). Adjusted dosing of mycophenolic acid and tacrolimus with (86%) or without (14%) adjunctive therapies were implemented after diagnosis. There was a significantly higher median percentage of IFN-γ-producing CD4+T cells to LT at a median of 3 (IQR: 1–4) months after adjustment of immunosuppression compared with at the time of diagnosis (0.004 vs. 0.015;p = 0.047). However, the difference between the median percentage of IFN-γ-producing CD4+T cells to VP1 and CD8+T cells to LT and VP1 did not reach statistical significance. Four (33%) patients achieved plasma BKPyV DNA clearance, and the remaining eight (67%) patients had persistent BKPyV DNAemia. Although eight (67%) patients developed allograft dysfunction, none required hemodialysis.ConclusionsWe observed a marginal trend of BKPyV-specific CD4+T cell recovery after adjustment of immunosuppression in KT recipients diagnosed with BKPyVAN. A further study would be benefited to confirm and better assess BKPyV-specific immune response after KT.
Knowledge and practice of immediate newborn care among midwives and nurses in public health facilities of Afar regional state, Northeast Ethiopia
Authors: Abdu Hawa , Gebrselassie Measho , Abdu Mohammed , Mare Kusse Urmale , Tadesse Woldemichael , Liben Misgan Legesse 
Published: November 2019

Abstract
Background
The care given to newborns immediately within the first few hours of birth is critical for their survival. However, their survival depends on the health professional’s knowledge and skills to deliver appropriate newborn care interventions. Therefore, this study aimed to assess the knowledge and practice of immediate newborn care among nurses and midwives in public health facilities of Afar Regional State, Northeast Ethiopia.

Methods
Institution based cross-sectional study design was employed on 357 nurses and midwives working in 48 public health facilities (45 health centers and 3 hospitals) during April 2018. Data were collected using interviewer-administered questionnaire and observation checklist. Then, data were entered into Epi-info version 7.0 and exported to SPSS version 20 for analysis. Univariable and multivariable logistic regression analyses were carried out to estimate odds ratio with 95% confidence interval. A p-value less than 0.05 was used to declare statistical significance.

Results
Overall, 53.8% [95% CI: (48.6, 59.0%)] and 62.7% [(95% CI: (57.7, 67.8%))] of the health professionals (midwives and nurses) had adequate knowledge and good practice on immediate newborn care, respectively. Working in hospital [AOR: 4.62; 95% CI (1.76, 12.10)], being a female [AOR: 0.59; 95% CI (0.39, 0.98)] and interested in providing newborn care [AOR: 0.29; 95% CI (0.13, 0.68)] were positively associated with having adequate knowledge on immediate newborn care. On the other hand, having work experience of < 5 years [AOR: 0.33; 95% CI (0.14, 0.78)], inadequate knowledge [AOR: 0.39; 95% CI (0.25, 0.64)], having work load [AOR: 2.09; 95% CI (1.17, 3.73)], being not interested to provide immediate newborn care [AOR: 0.35; 95% CI (0.16, 0.74)] and working in health center [AOR: 8.56; 95% CI (2.39, 30.63)] were negatively associated with good immediate newborn care practices.

Conclusions
A significant number of nurses and midwives had inadequate knowledge and poor practice on immediate newborn care. Therefore, providing a comprehensive newborn care training and creating an opportunity for nurses and midwives working at health centers to share experience from those hired in hospitals are very crucial to improve their knowledge and skills on newborn care.
A regional systems intervention for suicide prevention in the Netherlands (SUPREMOCOL): study protocol with a stepped wedge trial design
Authors: Hofstra Emma , Elfeddali Iman , Metz Margot , Bakker Marjan , de Jong Jacobus J. , van Nieuwenhuizen Chijs , van der Feltz-Cornelis Christina M. 
Published: November 2019

AbstractBackgroundIn the Netherlands, suicide rates showed a sharp incline and this pertains particularly to the province of Noord-Brabant, one of the southern provinces in the Netherlands. This calls for a regional suicide prevention effort.Methods/designStudy protocol. A regional suicide prevention systems intervention is implemented and evaluated by a stepped wedge trial design in five specialist mental health institutions and their adherent chain partners. Our system intervention is called SUPREMOCOL, which stands for Suicide Prevention by Monitoring and Collaborative Care, and focuses on four pillars: 1) recognition of people at risk for suicide by the development and implementation of a monitoring system with decision aid, 2) swift access to specialist care of people at risk, 3) positioning nurse care managers for collaborative care case management, and 4) 12 months telephone follow up. Eligible patients are persons attempting suicide or expressing suicidal ideation. Primary outcome is number of completed suicides, as reported by Statistics Netherlands and regional Public Health Institutes. Secondary outcome is number of attempted suicides, as reported by the regional ambulance transport and police. Suicidal ideation of persons registered in the monitoring system will, be assessed by the PHQ-9 and SIDAS questionnaires at baseline and 3, 6, 9 and 12 months after registration, and used as exploratory process measure. The impact of the intervention will be evaluated by means of the RE-AIM dimensions reach, efficacy, adoption, implementation, and maintenance. Intervention integrity will be assessed and taken into account in the analysis.DiscussionThe present manuscript presents the design and development of the SUPREMOCOL study. The ultimate goal is to lower the completed suicides rate by 20%, compared to the control period and compared to other provinces in the Netherlands. Moreover, our goal is to provide specialist mental health institutions and chain partners with a sustainable and adoptable intervention for suicide prevention.Trial registrationNetherlands Trial Register under registration numberNL6935(5 April 2018). This is the first version of the study protocol (September 2019).
Density of outdoor advertising of consumable products in NYC by neighborhood poverty level
Authors: Adjoian Tamar , Dannefer Rachel , Farley Shannon M. 
Published: November 2019

Abstract

Background
To determine if outdoor advertising density for non-alcoholic drinks, food, tobacco products, and alcohol, is associated with neighborhood poverty or other Census-level characteristics in New York City (NYC).

Methods
From June – July of 2015, photographs were taken of all street-level, stationary outdoor advertising (posters, stickers, decals, etc.) for consumable products in a sample of 953 NYC retail-dense street segments. Density of product images was analyzed by neighborhood poverty level and other characteristics using multivariate negative-binomial regression.

Results
A total of 16,305 discrete advertisements displaying 50,673 product images were photographed. Total product image prevalence relative to retail density was not significantly higher in high- vs. low-poverty neighborhoods, as hypothesized (OR: 1.31; 95% CI: 0.98, 1.77). However, total product image prevalence was higher in neighborhoods with a higher percentage of Black residents (OR: 1.08; 95% CI: 1.04, 1.12), and for sugary drinks in areas with a higher percentage of adults with <HS diploma (OR: 1.32; 95% CI: 1.11, 1.58).

Conclusions
Product images were abundant throughout NYC’s retail-dense areas, with marginally greater prevalence by some Census-level demographics, irrespective of the content displayed.
Inhibitory effects of berberine on proinflammatory M1 macrophage polarization through interfering with the interaction between TLR4 and MyD88
Authors: Gong Jing , Li Jingbin , Dong Hui , Chen Guang , Qin Xin , Hu Meilin , Yuan Fen , Fang Ke , Wang Dingkun , Jiang Shujun , Zhao Yan , Huang Wenya , Huang Zhaoyi , Lu Fuer 
Published: November 2019

Abstract
Backgrounds
Inflammation is recognized as the key pathological mechanism of type 2 diabetes. The hypoglyceamic effects of berberine (BBR) are related to the inhibition of the inflammatory response, but the mechanism is not completely clear.

Methods
The inflammatory polarization of Raw264.7 cells and primary peritoneal macrophages were induced by LPS, and then effects and underlying mechanisms of BBR were explored. An inflammatory model was established by LPS treatment at different concentrations for different treatment time. An ELISA assay was used to detect the secretions of TNF-α. RT-PCR was applied to detect M1 inflammatory factors. The F4/80+ ratio and CD11c+ ratio of primary peritoneal macrophages were determined by flow cytometry. The expressions of p-AMPK and TLR4 were detected by Western blot. The cytoplasmic and nuclear distributions of NFκB p65 were observed by confocal microscopy. The binding of TLR4 to MyD88 was tested by CoIP, and the affinity of BBR for TLR4 was assessed by molecular docking.

Results
Upon exposure to LPS, the secretion of TNF-α and transcription of inflammatory factors in macrophages increased, cell morphology changed and protrusions appeared gradually, the proportion of F4/80+CD11c+ M1 macrophages increased, and the nuclear distribution of NFκB p65 increased. BBR pretreatment partially inhibited the changes mentioned above. However, the expression of TLR4 and p-AMPK did not change significantly after LPS intervention for 3 h. Meanwhile, CoIP showed that the interaction between TLR4 and MyD88 increased, and BBR inhibited the binding. Molecular docking suggested that BBR might interact with TLR4.

Conclusions
Inflammatory changes were induced in macrophages after LPS stimulation for 3 h, and BBR pretreatment inhibited inflammatory polarization. BBR might interact with TLR4 and disturb TLR4/MyD88/NFκB signalling pathway, and it might be the mechanism by which BBR attenuated inflammation in the early phase.
Antibacterial activities, proposed mode of action and cytotoxicity of leaf extracts from Triumfetta welwitschii against Pseudomonas aeruginosa
Authors: Mombeshora Molly , Mukanganyama Stanley 
Published: November 2019

Abstract
Background
Pseudomonas aeruginosa has become a main cause of Gram-negative infection, particularly in patients with compromised immunity. High rates of resistance to antibiotics are associated with nosocomial infections caused by P. aeruginosa strains. The search for novel antimicrobials has been necessitated by the emergence of antimicrobial resistance in some bacteria Plant-based antimicrobials has great potential to combat microbial infections using a variety of mechanisms. Triumfetta welwitschii plant roots are traditionally used to treat symptoms of diarrhoea and fever, suggesting that it possess antimicrobial and immunomodulatory effects. Since research investigating antimicrobial properties of the roots of Triumfetta welwitschii has been explored, there is need to investigate the antimicrobial activity of its leaf extracts in order to probe their prospective use as new antimicrobial agents that can be used to combat nosocomial infections. The objective of this study was to evaluate the antibacterial activities, the mode of action and cytotoxicity of T. welwitschii leaf extracts.

Method
Extracts of T. welwitschii leaves were obtained using eight different solvents, the serial exhaustive extraction method and the cold maceration technique. In vitro antibacterial activity evaluation of the extracts was done on eight bacterial isolates using the broth microdilution method. The mode of action for the most potent extracts was investigated using the rhodamine 6G efflux assay and the propidium iodide-based membrane damage assay. Toxicity of the extracts was evaluated using the haemolytic and MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assays.

Results
The results showed that acetone, ethanol and dichlorometane: methanol extracts had the most potent antibacterial activities against Pseudomonas aeruginosa (ATCC 27853). All three extracts caused membrane disruption of P. aeruginosa as shown by nucleic acid leakage. All three extracts were unable to inhibit efflux pumps.

Conclusion
The presence of antibacterial activities and low toxicity shown by the extracts indicates that the plant may be a source of effective antibacterial against some bacterial infections caused by P. aeruginosa. The disruption of membrane integrity is one possible mode of action of antibacterial activity of the potent extracts.