bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of Human Thrombin-Antithrombin III Complex in Plasma with an Enzyme-Linked Immunosorbent Assay
Authors: Pelzer Hermann , Schwarz Angela , Heimburger Norbert 
Published: April 2018

SummaryAn enzyme-linked immunosorbent assay (ELISA) was developed for the determination of thrombin-antithrombin III complex (TAT) in human plasma. The test system follows the sandwich principle and uses two different antibodies directed against human thrombin and human antithrombin III, respectively. The antibodies bind selectively to the corresponding antigen moieties of TAT. The assay was calibrated with definite concentrations of preformed purified TAT added to TAT-poor plasma. The lower limit of sensitivity of the assay was 0.5 μg/1. Mean coefficients of variation of 4.2% (intraassay) and 3.5% (interassay) were found for TAT concentrations between 2 and 60 μg/1. A reference range from 0.85 to 3.2 μg/1 was calculated from TAT concentration in plasma samples from 88 healthy donors (mean value ± SD: 1.45 ± 0.4 μg/I). In plasma samples from patients with pulmonary embolism (n = 17), TAT concentrations between 3 and 25 μg/1 were measured. In 15 patients with deep vein thrombosis, TAT was found up to 3 to 25 μg/1. From these data we conclude that measurement of TAT can be a sensitive parameter for specific detection of a latent activation of the clotting pathway.
Decreased Platelet Number and Function and Increased Fibrinolysis Contribute to Postoperative Bleeding in Cardiopulmonary Bypass Patients
Authors: Holloway D Scott , Summaria Louis , Sandesara Jyoti , Paul Vagher J , Alexander John C , Caprini Joseph A 
Published: April 2018

SummaryWe simultaneously evaluated platelet and fibrinolytic parameters to assess their individual and combined contributions to postoperative blood loss in cardiopulmonary (CP) bypass patients. Platelet count, platelet aggregability, hematocrit, plasminogen (PLG) concentration, alpha2-antiplasmin (AP) concentration, free protease activity (fPA), and antithrombin-III (AT-III) were measured in nine patients undergoing surgery using cardiopulmonary bypass. Chest tube drainage was used as the measure of postoperative blood loss. Hematocrit, platelet count, PT .G , AP and AT-TTT all decreased during CP bypass, with PLG and AT-III decreasing much more than dilution. During CP bypass, platelet aggregability to A DP did not change significantly from pre-bypass, but aggregability to arachidonic acid (AA) decreased significantly. Following protamine administration there was a large increase (83%) in fPA, the platelet count showed a further drop (from 61 % to 50% of pre-bypass levels) . and platelet aggregability decreased significantly (from 95% to 34% of prebypass levels for ADP, and from 55% to 11.9% for A A). Chest tube drainage during the first four postoperative hours correlated positively (p <0.05) with the combination of increase in free protease activity and decrease in platelet count. The total chest tube drainage correlated significantly with the combination of decrease in platelet count and the decrease in platelet aggregability. These combinations of changes correlated significantly with postoperative blood loss whereas the individual changes did not. These data indicate that during the early postoperative period the increased fibrinolytic activity and the decreased platelet count together contribute toward postoperative blood loss in CP bypass patients, and that during the entire first 24 hour period postoperatively the decreased platelet number and decreased platelet function are important contributors to blood loss.
Need for Quantitative Measurement Methods for Posterior Uveitis: Comparison of Dual FA/ICGA Angiography, EDI-OCT Choroidal Thickness and SUN Vitreous Haze Evaluation in Stromal Choroiditis
Authors: Fabro Filippo , Herbort Carl 
Published: April 2018

Abstract
Background/Purpose Quantitative methods for posterior uveitis are necessary for precise appraisal and follow-up of inflammation in practice and in clinical trials. The aim of this study was to assess fluorescein angiography (FA), indocanine green angiography (ICGA), and enhanced depth imaging optical coherence tomography choroidal thickness (EDI-OCT CT) in two stromal choroiditis entities, birdshot retinochoroiditis (BRC), and Vogt-Koyanagi-Harada disease (VKH), as well as to determine (1) disease patterns, (2) respective response to therapy, and (3) their potential utility in clinical trials in comparison to vitreous haze, the present standard outcome used in clinical trials.
Methods This retrospective study included newly diagnosed patients with BRC and VKH, seen at the Centre for Ophthalmic Specialized Care, Lausanne, Switzerland. Angiographic signs were quantified using an established dual FA/ICGA scoring system for uveitis at presentation and on follow-up. FA/ICGA score ratios were compared between diseases to determine disease patterns. EDI-OCT CT was determined using a spectral domain instrument. Vitreous haze was determined using the SUN (Standardization of Uveitis Nomenclature) method.
Results Among 1872 uveitis patients seen from 1995 to 2016, 8 newly diagnosed BRC patients (16 eyes) and 6 newly diagnosed VKH patients (12 eyes) had sufficient data for study inclusion. Patients with BRC and VKH at initial onset had mean FA scores of 16.1 ± 7.0 vs. 4.6 ± 2.1 (p < 0.0001), respectively, while mean ICGA scores were similarly high in the two diseases, 18.9 ± 3.6 (BRC) vs. 20.8 ± 7.5 (VKH). After therapy, FA and ICGA scores decreased significantly for both entities (− 60% of FA score and 55% of ICGA score in BRC vs. − 72% of FA score and − 87% for ICGA score in VKH). EDI-OCT CT decreased significantly in the two entities. Vitreous haze was almost absent in VKH and low in BRC.
Conclusion Dual FA/ICGA scoring showed the diverse disease patterns of BRC and VKH; both the retina and choroid were involved at onset in BRC, whereas VKH was a pure choroidal disease with later spillover into the retina. Dual FA/ICGA allowed for the precise measurement of inflammation at onset and upon follow-up. EDI-OCT CT responded to therapy in both diseases but was found to be of limited use in this early/subacute disease phase because it lacked sensitivity to detect subclinical recurrences and was therefore only useful for long-term follow-up. Vitreous haze was low in both entities and thus useless as an inflammatory parameter.
Cataract Surgery in High Hyperopia
Authors: Waldmann Nicolas , Gerber Nadine , Hill Warren , Goldblum David 
Published: April 2018

Abstract
Background Although cataract surgery is a well-established and standardised procedure, it can be demanding and associated with higher complication rates in high hyperopia. We present clinical data for highly hyperopic patients who underwent cataract surgery over a 12-year period (2005 – 2016) and at a single centre.
Patients and Methods Out of a total of 11 434 cataract operations, 41 highly hyperopic eyes (SN60AT ≥ 31 dpt) were included for analysis. We compared the target spherical equivalent to the final postoperative spherical equivalent for five different formulas. We also reviewed the best corrected distance visual acuity (BCDVA) before and after surgery and any complications.
Results LogMAR BCDVA increased significantly from a mean of 0.5 before to 0.37 after surgery (p = 0.02). The main reasons for the reduced final BCDVA were glaucoma, Fuchs corneal endothelial dystrophy, and age-related macular degeneration. One eye suffered a radial capsule tear and received a sulcus implanted intraocular lens (IOL). There was no statistically significant difference between formulas with respect to aberration of the final spherical equivalent.
Conclusions Patients with high hyperopia often have ocular comorbidities. Such eyes may be surgically challenging, resulting in reduced benefits from cataract surgery compared to normal eyes.
Practical reasoning and practical knowledge
Authors: Stout Rowland 
Published: April 2018

AbstractThe judgement that provides the content of intention and coincides with the conclusion of practical reasoning is a normative judgement about what to do, and not, as Anscombe and McDowell argue, a factual judgement about what one is doing. Treating the conclusion of practical reasoning as expressing a recommendation rather than a verdict undermines McDowell’s argument; the special nature of practical reasoning does not preclude its conclusions being normative. Anscombe’s and McDowell’s claim that practical self-knowledge is productive of action may be accommodated by identifying the content of practical knowledge not with the conclusion but with a premise of practical reasoning – a kind of practical reasoning that occurs within rather than before action.
The Associations Between Mental Health Status, Hypertension, and Hospital Inpatient Visits in Women in the United States
Authors: Rozario Sylvia S , Masho Saba W 
Published: April 2018

AbstractBACKGROUNDPoor mental health status is more prevalent in women and may be related to poor hypertension outcomes and increased hospital inpatient visits. This study aims to find the association between mental health status and hypertension in women and the combined effect of mental health status and hypertension on hospital inpatient visits in women in the United States.METHODSThe household component of 2014 Medical Expenditure Panel Surveys (MEPS) was analyzed (N = 9,137). Kessler (K6) scale for mental health status (poor, good/excellent), hypertension (yes, no), and hospital inpatient visits (yes, no) were examined. A combined effect variable for mental health status and hypertension was created. Multiple logistic regression analysis was conducted and adjusted odds ratios (AORs) with corresponding 95% confidence intervals (CIs) were calculated.RESULTSAfter adjusting for confounders, women who reported poor mental health had significantly higher odds of hypertension compared to women who reported good/excellent mental health (AOR = 1.39, 95% CI = 1.16, 1.68). Further, women who reported hypertension coupled with poor mental health had higher odds of having hospital inpatient visits compared to women who reported no hypertension coupled with good/excellent mental health in the adjusted analysis (AOR = 3.03, 95% CI = 1.96, 4.69).CONCLUSIONSThere is a significant association between mental health status and hypertension in women. Further, poor mental health status coupled with hypertension leads to increase hospital inpatient visits for women. It is important that health professionals focus on utilizing available screening tools to assess mental health status of women for early detection and to manage the disorder.
Dissecting newly transcribed and old RNA using GRAND-SLAM
Authors: Jürges Christopher , Dölken Lars , Erhard Florian 
Published: April 2018

Abstract
Summary: Global quantification of total RNA is used to investigate steady state levels of gene expression. However, being able to differentiate pre-existing RNA (that has been synthesized prior to a defined point in time) and newly transcribed RNA can provide invaluable information e.g. to estimate RNA half-lives or identify fast and complex regulatory processes. Recently, new techniques based on metabolic labeling and RNA-seq have emerged that allow to quantify new and old RNA: Nucleoside analogs are incorporated into newly transcribed RNA and are made detectable as point mutations in mapped reads. However, relatively infrequent incorporation events and significant sequencing error rates make the differentiation between old and new RNA a highly challenging task. We developed a statistical approach termed GRAND-SLAM that, for the first time, allows to estimate the proportion of old and new RNA in such an experiment. Uncertainty in the estimates is quantified in a Bayesian framework. Simulation experiments show our approach to be unbiased and highly accurate. Furthermore, we analyze how uncertainty in the proportion translates into uncertainty in estimating RNA half-lives and give guidelines for planning experiments. Finally, we demonstrate that our estimates of RNA half-lives compare favorably to other experimental approaches and that biological processes affecting RNA half-lives can be investigated with greater power than offered by any other method. GRAND-SLAM is freely available for non-commercial use at http://software.erhard-lab.de; R scripts to generate all figures are available at zenodo (doi: 10.5281/zenodo.1162340).
Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping
Authors: Raimondi Daniele , Orlando Gabriele , Moreau Yves , Vranken Wim F 
Published: April 2018

Abstract

Motivation
Evolutionary information is crucial for the annotation of proteins in bioinformatics. The amount of retrieved homologs often correlates with the quality of predicted protein annotations related to structure or function. With a growing amount of sequences available, fast and reliable methods for homology detection are essential, as they have a direct impact on predicted protein annotations.

Results
We developed a discriminative, alignment-free algorithm for homology detection with quasi-linear complexity, enabling theoretically much faster homology searches. To reach this goal, we convert the protein sequence into numeric biophysical representations. These are shrunk to a fixed length using a novel vector quantization method which uses a Discrete Cosine Transform compression. We then compute, for each compressed representation, similarity scores between proteins with the Dynamic Time Warping algorithm and we feed them into a Random Forest. The WARP performances are comparable with state of the art methods.

Availability and implementation
The method is available at http://ibsquare.be/warp.

Supplementary information
Supplementary data are available at Bioinformatics online.
A highly sensitive trap vector system for isolating reporter cells and identification of responsive genes
Authors: Ishikawa Kosuke , Kobayashi Yuta , Wakabayashi Yutaro , Watanabe Shinya , Semba Kentaro 
Published: April 2018

Abstract
We devised a versatile vector system for efficient isolation of reporter cells responding to a certain condition of interest. This system combines nontoxic GAL4-UAS and piggyBac transposon systems, allowing application to mammalian cells and improved expression of a fluorescent reporter protein for cell sorting. Case studies under conditions of c-MYC gene induction or endoplasmic reticulum (ER) stress with thapsigargin on mouse or human cell lines confirmed easy and efficient isolation of responsive reporter cells. Sequence analyses of the integrated loci of the thapsigargin-responsive clones identified responsive genes including BiP and OSBPL9. OSBPL9 is a novel ER stress-responsive gene and we confirmed that endogenous mRNA expression of OSBPL9 is upregulated by thapsigargin, and is repressed by IRE1α inhibitors, 4μ8C and toyocamycin, but not significantly by a PERK inhibitor, GSK2656157. These results demonstrate that this approach can be used to discover novel genes regulated by any stimuli without the need for microarray analysis, and that it can concomitantly produce reporter cells without identification of stimuli-responsive promoter/enhancer elements. Therefore, this system has a variety of benefits for basic and clinical research.
Ascending aortic aneurysm repair 44 years after Starr–Edwards caged-ball aortic valve replacement
Authors: Hatton Gabrielle E , Tanaka Akiko , Estrera Anthony L 
Published: April 2018

Abstract
We report a case of ascending aortic aneurysm repair and redo aortic valve replacement with a bioprosthesis 44 years after aortic valve replacement with a Starr–Edwards metal caged-ball prosthesis. The patient presented with a moderately stenotic caged-ball valve and a 50-mm ascending aortic aneurysm on a routine follow-up transthoracic echocardiography. We replaced the valve with a bioprosthesis at the time of aortic repair as the patient wished to stop anticoagulation therapy. Intraoperatively, we found that the cloth covering of the cage was nearly completely destroyed.
Two-scale method for the Monge–Ampère equation: pointwise error estimates
Authors: Nochetto R H , Ntogkas D , Zhang W 
Published: April 2018

Abstract
In this paper we continue the analysis of the two-scale method for the Monge–Ampère equation for dimension d ≥ 2 introduced in the study by Nochetto et al. (2017, Two-scale method for the Monge–Ampère equation: convergence to the viscosity solution. Math. Comput., in press). We prove continuous dependence of discrete solutions on data that in turn hinges on a discrete version of the Alexandroff estimate. They are both instrumental to prove pointwise error estimates for classical solutions with Hölder and Sobolev regularity. We also derive convergence rates for viscosity solutions with bounded Hessians which may be piecewise smooth or degenerate.
A visual analytics approach for pattern-recognition in patient-generated data
Authors: Feller Daniel J , Burgermaster Marissa , Levine Matthew E , Smaldone Arlene , Davidson Patricia G , Albers David J , Mamykina Lena 
Published: April 2018

AbstractObjectiveTo develop and test a visual analytics tool to help clinicians identify systematic and clinically meaningful patterns in patient-generated data (PGD) while decreasing perceived information overload.MethodsParticipatory design was used to develop Glucolyzer, an interactive tool featuring hierarchical clustering and a heatmap visualization to help registered dietitians (RDs) identify associative patterns between blood glucose levels and per-meal macronutrient composition for individuals with type 2 diabetes (T2DM). Ten RDs participated in a within-subjects experiment to compare Glucolyzer to a static logbook format. For each representation, participants had 25 minutes to examine 1 month of diabetes self-monitoring data captured by an individual with T2DM and identify clinically meaningful patterns. We compared the quality and accuracy of the observations generated using each representation.ResultsParticipants generated 50% more observations when using Glucolyzer (98) than when using the logbook format (64) without any loss in accuracy (69% accuracy vs 62%, respectively, p = .17). Participants identified more observations that included ingredients other than carbohydrates using Glucolyzer (36% vs 16%, p = .027). Fewer RDs reported feelings of information overload using Glucolyzer compared to the logbook format. Study participants displayed variable acceptance of hierarchical clustering.ConclusionsVisual analytics have the potential to mitigate provider concerns about the volume of self-monitoring data. Glucolyzer helped dietitians identify meaningful patterns in self-monitoring data without incurring perceived information overload. Future studies should assess whether similar tools can support clinicians in personalizing behavioral interventions that improve patient outcomes.
Post-chemoradiation volumetric response predicts survival in newly diagnosed glioblastoma treated with radiation, temozolomide, and bevacizumab or placebo
Authors: Ellingson Benjamin M , Abrey Lauren E , Garcia Josep , Chinot Olivier , Wick Wolfgang , Saran Frank , Nishikawa Ryo , Henriksson Roger , Mason Warren P , Harris Robert J , Leu Kevin , Woodworth Davis C , Mehta Arnav , Raymond Catalina , Chakhoyan Ararat , Pope Whitney B , Cloughesy Timothy F 
Published: April 2018

Abstract

Background
In the current study we used contrast-enhanced T1 subtraction maps to test whether early changes in enhancing tumor volume are prognostic for overall survival (OS) in newly diagnosed glioblastoma (GBM) patients treated with chemoradiation with or without bevacizumab (BV).

Methods
Seven hundred ninety-eight patients (404 BV and 394 placebo) with newly diagnosed GBM in the AVAglio trial (NCT00943826) had baseline MRI scans available, while 337 BV-treated and 269 placebo-treated patients had >4 MRI scans for response evaluation. The volume of contrast-enhancing tumor was quantified and used for subsequent analyses.

Results
A decrease in tumor volume during chemoradiation was associated with a longer OS in the placebo group (hazard ratio [HR] = 1.578, P < 0.0001) but not BV-treated group (HR = 1.135, P = 0.4889). Results showed a higher OS in patients on the placebo arm with a sustained decrease in tumor volume using a post-chemoradiation baseline (HR = 1.692, P = 0.0005), and a trend toward longer OS was seen in BV-treated patients (HR = 1.264, P = 0.0724). Multivariable Cox regression confirmed that sustained response or stable disease was prognostic for OS (HR = 0.7509, P = 0.0127) when accounting for age (P = 0.0002), KPS (P = 0.1516), postsurgical tumor volume (P < 0.0001), O6-methylguanine-DNA methyltransferase status (P < 0.0001), and treatment type (P = 0.7637) using the post-chemoradiation baseline.

Conclusions
The post-chemoradiation timepoint is a better baseline for evaluating efficacy in newly diagnosed GBM. Early progression during the maintenance phase is consequential in predicting OS, supporting the use of progression-free survival rates as a meaningful surrogate for GBM.
Successful Treatment of Cerebral Toxoplasmosis Using Pyrimethamine Oral Solution Compounded From Inexpensive Bulk Powder
Authors: Hodgson Hayley A , Sim Taeyong , Gonzalez Hemil , Aziz Mariam , Rhee Yoona , Lewis Paul O , Jhobalia Neel , Shields Beth , Wang Sheila K 
Published: April 2018

AbstractA price increase of pyrimethamine tablets in the United States has made the life-saving drug difficult to acquire for hospitalized patients who need it most. We report the successful use of a pyrimethamine oral suspension compounded from an economical bulk powder in a patient with acute toxoplasmic encephalitis.
The impact of free access to swimming pools on children’s participation in swimming. A comparative regression discontinuity study
Authors: Higgerson J , Halliday E , Ortiz-Nunez A , Barr B 
Published: April 2018

Abstract

Objective
Investigating the extent to which providing children with free swimming access during school holidays increased participation in swimming and whether this effect differed according to the socioeconomic deprivation of the neighbourhoods in which children lived.

Setting
A highly disadvantaged local authority (LA) in North West England.

Intervention
Provision of children with free swimming during the summer holidays.

Outcome measures
Number of children swimming, and the number of swims, per 100 population in 2014.

Design
Comparative regression discontinuity investigating the extent to which participation rates amongst children aged 5–15 were greater in the intervention LA compared to a similar control LA. We estimated the differential effect of the intervention across five groups, defined by quintiles of area deprivation.

Results
Free swimming during the summer holidays was associated with an additional 6% of children swimming (95% CI: 4–9%) and an additional 33 swims per 100 children per year (95% CI: 21–44). The effects were greatest in areas with intermediate levels of deprivation (quintiles 3 and 4) within this deprived LA.

Conclusion
Providing free facilities for children in disadvantaged areas is likely to increase swimming participation and may help reduce inequalities in physical activity.