bluuebunny/crossref_metadata_2025_split huggingface dataset:
MRI T2* imaging for assessment of liver iron overload: study of different data analysis approaches
Authors: Ibrahim El-Sayed H , Khalifa Ayman M , Eldaly Ahmed K 
Published: February 2016

Background Recently, magnetic resonance imaging (MRI) has been established as an effective technique for evaluating iron overload by measuring T2* in the liver. Purpose To investigate the effects of various factors associated with T2* calculation on the resulting measurement and to determine the analysis criterion that provides the most accurate T2* measurements. Material and Methods Both phantom and in vivo MRI experiments were conducted to study the effects of the selected region of interest (ROI) location and size, signal-averaging method, exponential-fitting model, echo truncation, iron-overload severity, and inter-/intra-observer variabilities on T2* measurements. The results were compared to reference values from the scanner processing software. Results The pixel-by-pixel calculation method provided results in better agreement with the reference values from the MRI scanner than the average or median methods. The choice of the exponential fitting model affected the results, depending on signal-to-noise ratio, number of echoes, minimum and maximum echo times, and tissue composition inside the selected ROI. The single-exponential model resulted in smaller error than the bi-exponential or exponential-plus-constant models, where the latter two models showed similar results. The relative performance of the different models and methods was not affected by the degree of iron-overload. Conclusion Various factors associated with the adopted T2* calculation method affect the resulting measurement. In this study, the pixel-by-pixel calculation method and single-exponential model provided the most accurate results based on the conducted phantom and in vivo MRI experiments.
Subclavian steal: Endovascular treatment of total occlusions of the subclavian artery using a retrograde transradial subintimal approach
Authors: Satti Sudhakar R , Golwala Sohil N , Vance Ansar Z , Tuerff Sonya N 
Published: February 2016

Introduction In symptomatic subclavian steal syndrome, endovascular treatment is the first line of therapy prior to extra-anatomic surgical bypass procedures. Subintimal recanalization has been well described in the literature for the coronary arteries, and more recently, in the lower extremities. By modifying this approach, we present a unique retrograde technique using a heavy tip microwire to perform controlled subintimal dissection. Methods We present two cases of symptomatic subclavian steal related to chronic total occlusion of the left subclavian artery and right innominate artery, respectively. Standard crossing techniques were unsuccessful. Commonly at this point, the procedures would be aborted and open surgical intervention would have to be pursued. In our cases, retrograde access was easily achieved via an ipsilateral retrograde radial artery, using controlled subintimal dissection and a heavy-tipped wire. Results We were able to easily achieve recanalization in both attempted cases of chronic total occlusion of the subclavian and innominate artery, using a retrograde radial subintimal approach. Subsequent stent-supported angioplasty resulted in complete revascularization. No major complications were encountered during the procedures; however, one patient did develop thromboembolic stroke secondary to platelet aggregation to the stent graft, 9 days post-procedure. Conclusions Endovascular treatment is considered the first-line intervention in medically refractory patients with symptomatic subclavian steal syndrome. In the setting of chronic total occlusions, a retrograde radial subintimal approach using a heavy tip wire for controlled subintimal dissection is a novel technique that may be considered when standard approaches and wires have failed.
Tachycardia burden in stroke unit is associated with functional outcome after ischemic stroke
Authors: Jeong Han-Gil , Ko Sang-Bae , Kim Chi Kyung , Kim Yerim , Jung Seunguk , Kim Tae Jung , Yoon Byung-Woo 
Published: February 2016

Background Stroke unit care is associated with decrease in mortality and improvement in neurological outcome in patients with acute stroke. Heart rate is a commonly monitored variable in the stroke unit. However, little is known about tachycardia burden in the stroke unit and its association with outcome. Aims To investigate the effects of tachycardia burden in the stroke unit on functional outcome in patients with acute ischemic stroke. Methods We collected data from 246 patients with acute ischemic stroke admitted to our stroke unit between July 2013 and June 2014. Tachycardia burden was defined as duration of heart rate over 95 per minute divided by the total monitoring time, using the heart rate data sampled every 1 min. We divided the study population into quartiles of tachycardia burden and analyzed their association with poor three-month functional outcome (modified Rankin Scale score of ≥3). Results Among included patients (age, 67.4  ±  12.8; male, 53.7%), tachycardia burden was 0.7% (median, interquartile range [0.1–5.7%]). The patients with higher tachycardia burdens were older, more likely to have higher stroke severity, cardioembolic etiology, atrial fibrillation, fever, pneumonia, higher initial glucose level, and higher white blood cell count. As compared with the lowest quartile (<0.1%), the highest quartile of tachycardia burden (≥6.0%) was significantly associated with poor outcome (adjusted odds ratio, 5.10; 95% confidence interval, 1.38–18.90; p = 0.01) after adjustment for covariates. Conclusions Patients with increased tachycardia burden during stroke unit stay have poor functional outcome. Countermeasures against worsening factors might be utilized for patients with increased tachycardia burden.
Vorapaxar monotherapy for secondary stroke prevention: A call for randomized trial
Authors: Serebruany Victor L , Kim Moo H , Hanley Daniel F 
Published: February 2016

Background and Purpose Vorapaxar, a novel platelet thrombin protease-activated receptor 1 blocker, is currently approved for post-myocardial infarction and peripheral artery disease indications on top of clopidogrel or/and aspirin. We sought to summarize the conflicting stroke data after vorapaxar for justifying a secondary stroke prevention trial. Methods Analyses of the stroke data after vorapaxar yielded from thrombin-receptor antagonist vorapaxar in acute coronary syndromes (TRACER) and TRA2P clinical trials, and affiliated Food and Drug Administration (FDA) reviews. Results The stroke data are mixed, with catastrophic 2.5 excess of intracranial bleeding risks (HR = 2.52; 95% CI = 1.46–4.36, p < 0.0001); trend to worsened second stroke rates (13.0% vs. 11.7%; HR = 1.03; 95% CI = 0.85–1.25, p = NS), but a hint towards less primary ischemic strokes in vorapaxar indicated population (HR = 0.57; 95% CI = 0.43 to 0.75; p < 0.001). These conflicting data are not solely attributed to vorapaxar, but rather reflect unreasonably aggressive triple antiplatelet strategies utilized frequently in TRA2P and dominant in TRACER. Overall, the FDA-confirmed evidence advocates future vorapaxar secondary stroke prevention trial due to being first-in-class agent, unique pharmakynetics, and exhibiting very mild “comfort zone” antiplatelet profile. The three arm trial testing head-to-head monotherapy with vorapaxar (Zontivity®), versus clopidogrel (Plavix®), and versus extended-released dipyridamole with very low dose aspirin (Aggrenox®) is warranted. Conclusions Vorapaxar may be superior to currently recommended antiplatelet strategies and should be tested as a monotherapy in a randomized outcome-driven secondary stroke prevention trial.
Case-Based Reasoning for Insulin Bolus Advice
Authors: Pesl Peter , Herrero Pau , Reddy Monika , Oliver Nick , Johnston Desmond G. , Toumazou Christofer , Georgiou Pantelis 
Published: February 2016

Background: Insulin bolus calculators assist people with Type 1 diabetes (T1D) to calculate the amount of insulin required for meals to achieve optimal glucose levels but lack adaptability and personalization. We have proposed enhancing bolus calculators by the means of case-based reasoning (CBR), an established problem-solving methodology, by individualizing and optimizing insulin therapy for various meal situations. CBR learns from experiences of past similar meals, which are described in cases through a set of parameters (eg, time of meal, alcohol, exercise). This work discusses the selection, representation and effect of case parameters used for a CBR-based Advanced Bolus Calculator for Diabetes (ABC4D). Methods: We analyzed the usage and effect of selected parameters during a pilot study (n = 10), where participants used ABC4D for 6 weeks. Retrospectively, we evaluated the effect of glucose rate of change before the meal on the glycemic excursion. Feedback from study participants about the choice of parameters was obtained through a nonvalidated questionnaire. Results: Exercise and alcohol were the most frequently used parameters, which was congruent with the feedback from study participants, who found these parameters most useful. Furthermore, cases including either exercise or alcohol as parameter showed a trend in reduction of insulin at the end of the study. A significant difference ( P < .01) was found in glycemic outcomes for meals where glucose rate of change was rising compared to stable rate of change. Conclusions: Results from the 6-week study indicate the potential benefit of including parameters exercise, alcohol and glucose-rate of change for insulin dosing decision support.
Medication therapy management by pharmacists in a kidney transplant ambulatory clinic
Authors: Lee Puay Hoon , Fan Petrina Yuen Wai , Kee Terence Yi Shern 
Published: February 2016

Introduction: Pharmacists play an essential role as part of the multidisciplinary transplant team in providing comprehensive pharmaceutical care for kidney transplant recipients. Methods: A prospective, observational, single-centre study evaluated the clinical pharmacy service in a kidney transplant ambulatory clinic. At each visit, pharmacists reviewed and optimised the medication regimens of transplant recipients, which include the medication therapy management of immunosuppression, infective and non-infective complications commonly seen post-transplantation. Pharmacists also performed medication reconciliation and provided medication education during each visit. Any drug-related problems or discrepancies identified were communicated to the physicians in the clinic. Results: Between September 2013 and March 2015, a total of 3581 cases were reviewed. Pharmacists identified 663 drug-related problems involving 319 recipients. Most of the pharmacists’ clinical recommendations (93%) were accepted by physicians. The common drug-related problems identified were ‘inappropriate dosage regimen’ (38%), ‘omission of drug therapy’ (28%) and ‘monitoring parameters recommendation’ (9%). Common drug classes involved were immunosuppressive agents (25%), anti-infectives (14%) and anti-hypertensive agents (12%). During medication reconciliation, pharmacists identified 180 medication discrepancies. Common medication discrepancies identified include ‘incorrect dose’ (68%), ‘incorrect duration’ (17%) and ‘incorrect drug’ (13%). All drug-related problems and medication discrepancies were resolved or addressed at the same clinic visit. Conclusions: Pharmacists play a pivotal role in the provision of medication therapy management to ensure safe and effective use of medications in kidney transplant recipients with complex medication regimens. This was achieved through identification and resolution of drug-related problems from medication review and medication discrepancies from medication reconciliation.
Clinical and laboratory variability in a cohort of patients diagnosed with type 1 VWD in the United States
Authors: Flood Veronica H. , Christopherson Pamela A. , Gill Joan Cox , Friedman Kenneth D. , Haberichter Sandra L. , Bellissimo Daniel B. , Udani Rupa A. , Dasgupta Mahua , Hoffmann Raymond G. , Ragni Margaret V. , Shapiro Amy D. , Lusher Jeanne M. , Lentz Steven R. , Abshire Thomas C. , Leissinger Cindy , Hoots W. Keith , Manco-Johnson Marilyn J. , Gruppo Ralph A. , Boggio Lisa N. , Montgomery Kate T. , Goodeve Anne C. , James Paula D. , Lillicrap David , Peake Ian R. , Montgomery Robert R. 
Published: February 2016

Key Points
Type 1 VWD in the United States is highly variable, including patients with very low VWF levels as well as those with mild or minimal VWF deficiency. The frequency of sequence variants in the VWF gene increases with decreasing VWF level, but BS does not vary by VWF level.
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments
Authors: Daily Jeff 
Published: February 2016

Abstract
Background
Sequence alignment algorithms are a key component of many bioinformatics applications.
Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations.

Results
A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar’s ‘striped’ approach. Rognes’s SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail’s prefix scan implementation is generally the fastest, faster even than Farrar’s ‘striped’ approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail
under the Battelle BSD-style license.

Conclusions
Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.
Development of a Quantitative PCR Assay for Detection of Human Insulin-Like Growth Factor Receptor and Insulin Receptor Isoforms
Authors: Flannery Clare A. , Rowzee Anne M. , Choe Gina H. , Saleh Farrah L. , Radford Caitlin C. , Taylor Hugh S. , Wood Teresa L. 
Published: February 2016

Abstract
The biological activity of insulin and the insulin-like growth factor (IGF) ligands, IGF-I and IGF-II, is based in part on the relative abundance and distribution of their target receptors: the insulin receptor (IR) splice variants A (IR-A) and B (IR-B) and IGF 1 receptor (IGF-1R). However, the relative quantity of all three receptors in human tissues has never been measured together on the same scale. Due to the high homology between insulin receptor (IR)-A and IR-B proteins and lack of antibodies that discern the two IR splice variants, their mRNA sequence is the most reliable means of distinguishing between the receptors. Hence, highly specific primers for IR-A, IR-B, and IGF-1R mRNA were designed to accurately detect all three receptors by quantitative RT-PCR and enable direct quantification of relative receptor expression levels. A standard concentration curve of cDNA from each receptor was performed. Assay specificity was tested using competition assays and postamplification analysis by gel electrophoresis and cloning. Forward and reverse primer concentrations were optimized to ensure equal efficiencies across primer pairs. This assay enables a specific molecular signature of IGF/insulin signaling receptors to be assayed in different tissues, cell types, or cancers.
Angioinvasive rhinocerebral mucormycosis with complete unilateral thrombosis of internal carotid artery—case report and review of literature
Authors: Patil Aruna , Mohanty Himansu Shekhar , Kumar Sharath , Nandikoor Shrivalli , Meganathan Prabhu 
Published: February 2016

Abstract
Angioinvasive rhinocerebral mucormycosis is an acute fulminant infection caused by fungi of the order Mucorales that targets uncontrolled diabetics and other immunosupressed individuals. Early imaging features of angioinvasiveness include the presence of thrombosed vessels, especially in the orbital regions and the “black turbinate” sign representing devitalized paranasal sinus mucosa. Intracranial extension carries a grave prognosis, with death reported in 90% of cases. This case report highlights the early and key imaging features of angioinvasive rhinocerebral mucormycosis and a rare complication of complete internal carotid artery thrombosis.
Cytokine-release kinetics of platelet-rich plasma according to various activation protocols
Authors: Roh Y. H. , Kim W. , Park K. U. , Oh J. H. 
Published: February 2016

Objectives This study was conducted to evaluate the cytokine-release kinetics of platelet-rich plasma (PRP) according to different activation protocols. Methods Two manual preparation procedures (single-spin (SS) at 900 g for five minutes; double-spin (DS) at 900 g for five minutes and then 1500 g for 15 minutes) were performed for each of 14 healthy subjects. Both preparations were tested for platelet activation by one of three activation protocols: no activation, activation with calcium (Ca) only, or calcium with a low dose (50 IU per 1 ml PRP) of thrombin. Each preparation was divided into four aliquots and incubated for one hour, 24 hours, 72 hours, and seven days. The cytokine-release kinetics were evaluated by assessing PDGF, TGF, VEGF, FGF, IL-1, and MMP-9 concentrations with bead-based sandwich immunoassay. Results The concentration of cytokine released from PRP varied over time and was influenced by various activation protocols. Ca-only activation had a significant effect on the DS PRPs (where the VEGF, FGF, and IL-1 concentrations were sustained) while Ca/thrombin activation had effects on both SS and DS PRPs (where the PDGF and VEGF concentrations were sustained and the TGF and FGF concentrations were short). The IL-1 content showed a significant increase with Ca-only or Ca/thrombin activation while these activations did not increase the MMP-9 concentration. Conclusion The SS and DS methods differed in their effect on cytokine release, and this effect varied among the cytokines analysed. In addition, low dose of thrombin/calcium activation increased the overall cytokine release of the PRP preparations over seven days, relative to that with a calcium-only supplement or non-activation. Cite this article: Professor J. H. Oh. Cytokine-release kinetics of platelet-rich plasma according to various activation protocols. Bone Joint Res 2016;5:37–45. doi: 10.1302/2046-3758.52.2000540
Mitigation of mercury contamination through the acceleration of vegetation succession
Authors: EKYASTUTI WIWIK , FARIDAH ENY , SUMARDI SUMARDI , SETIADI YADI 
Published: February 2016

Ekyastuti W, Faridah E, Sumardi, Setiadi Y. 2016. Mitigation of mercury contamination through the acceleration of vegetation succession. Biodiversitas 17: 84-89. The success of the restoration of the tailings ex-gold mining through the succession isÂ highly dependent on the ability of plants to grow and adapt to the troubled land. Restoration through natural succession takes a very longÂ time. Therefore, human intervention is required to accelerate the succession. The purpose of this research was to improve theÂ effectiveness of mitigation of mercury contamination through the acceleration of vegetation succession. This research has been carriedÂ out in a greenhouse using an experiment with a completely randomized design. There are 8 treatment consists of four indigenous species (Dillenia excelsa, Melastoma affine, Cinnamomum porrectum and Casuarina junghuhniana)Â grown alone (one species) and collective (more than one species) in the tailing media with a mercury content of 20 ppm. The results showed that the planting collectively have a mutually supportive interaction, so that increased the plant growth. In addition, collective planting two or four different species of plants, and the D. excelsa itself could decrease the concentration of mercury in the tailing. The acceleration of vegetation succession through the right choice of plants species and planting collectively, capable to increasing the potential of mitigation of mercury contamination in the tailings.
On double stage minimax-shrinkage estimator for generalized Rayleigh model
Authors: Salman Abbas Najim , Ameen Maymona 
Published: February 2016

<p>This paper is concerned with minimax shrinkage estimator using double stage shrinkage technique for lowering the mean squared error, intended for estimate the shape parameter (a) of Generalized Rayleigh distribution in a region (R) around available prior knowledge (a<sub>0</sub>) about the actual value (a) as initial estimate in case when the scale parameter (l) is known .</p><p>In situation where the experimentations are time consuming or very costly, a double stage procedure can be used to reduce the expected sample size needed to obtain the estimator.</p><p>The proposed estimator is shown to have smaller mean squared error for certain choice of the shrinkage weight factor y(<strong>×</strong>) and suitable region R.</p><p>Expressions for Bias, Mean squared error (MSE), Expected sample size [E (n/a, R)], Expected sample size proportion [E(n/a,R)/n], probability for avoiding the second sample and percentage of overall sample saved for the proposed estimator are derived.</p><p>Numerical results and conclusions for the expressions mentioned above were displayed when the consider estimator are testimator of level of significanceD.</p><p>Comparisons with the minimax estimator and with the most recent studies were made to shown the effectiveness of the proposed estimator.</p>