bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individualized Molecular Analyses Guide Efforts (IMAGE): A Prospective Study of Molecular Profiling of Tissue and Blood in Metastatic Triple-Negative Breast Cancer
Authors: Parsons Heather A. , Beaver Julia A. , Cimino-Mathews Ashley , Ali Siraj M. , Axilbund Jennifer , Chu David , Connolly Roisin M. , Cochran Rory L. , Croessmann Sarah , Clark Travis A. , Gocke Christopher D. , Jeter Stacie C. , Kennedy Mark R. , Lauring Josh , Lee Justin , Lipson Doron , Miller Vincent A. , Otto Geoff A. , Rosner Gary L. , Ross Jeffrey S. , Slater Shannon , Stephens Philip J. , VanDenBerg Dustin A. , Wolff Antonio C. , Young Lauren E. , Zabransky Daniel J. , Zhang Zhe , Zorzi Jane , Stearns Vered , Park Ben H. 
Published: August 2016

Abstract
Purpose: The clinical utility of next-generation sequencing (NGS) in breast cancer has not been demonstrated. We hypothesized that we could perform NGS of a new biopsy from patients with metastatic triple-negative breast cancer (TNBC) in a clinically actionable timeframe.
Experimental Design: We planned to enroll 40 patients onto a prospective study, Individualized Molecular Analyses Guide Efforts (IMAGE), to evaluate the feasibility of obtaining a new biopsy of a metastatic site, perform NGS (FoundationOne), and convene a molecular tumor board to formulate treatment recommendations within 28 days. We collected blood at baseline and at time of restaging to assess cell-free circulating plasma tumor DNA (ptDNA).
Results: We enrolled 26 women with metastatic TNBC who had received ≥1 line of prior chemotherapy, and 20 (77%) underwent NGS of a metastatic site biopsy. Twelve (60%) evaluable patients received treatment recommendations within 28 days of consent. The study closed after 20 patients underwent NGS, based on protocol-specified interim futility analysis. Three patients went on to receive genomically directed therapies. Twenty-four of 26 patients had genetic alterations successfully detected in ptDNA. Among 5 patients, 4 mutations found in tumor tissues were not identified in blood, and 4 mutations found in blood were not found in corresponding tumors. In 9 patients, NGS of follow-up blood samples showed 100% concordance with baseline blood samples.
Conclusions: This study demonstrates challenges of performing NGS on prospective tissue biopsies in patients with metastatic TNBC within 28 days, while also highlighting the potential use of blood as a more time-efficient and less invasive method of mutational assessment. Clin Cancer Res; 23(2); 379–86. ©2016 AACR.
Prothrombin complex concentrates versus fresh frozen plasma for warfarin reversal A systematic review and meta-analysis
Authors: Chai-Adisaksopha Chatree , Hillis Christopher , Siegal Deborah M. , Movilla Ron , Heddle Nancy , Crowther Mark , Iorio Alfonso 
Published: August 2016

SummaryUrgent reversal of warfarin is required for patients who experience major bleeding or require urgent surgery. Treatment options include the combination of vitamin K and coagulation factor replacement with either prothrombin complex concentrate (PCC) or fresh frozen plasma (FFP). However, the optimal reversal strategy is unclear based on clinically relevant outcomes. We searched in MEDLINE, EMBASE and Cochrane library to December 2015. Thirteen studies (5 randomised studies and 8 observational studies) were included. PCC use was associated with a significant reduction in all-cause mortality compared to FFP (OR= 0.56, 95 % CI; 0.37–0.84, p=0.006). A higher proportion of patients receiving PCC achieved haemostasis compared to those receiving FFP, but this was not statistically significant (OR 2.00, 95 % CI; 0.85–4.68). PCC use was more likely to achieve normalisation of international normalised ratio (INR) (OR 10.80, 95 % CI; 6.12–19.07) and resulted in a shorter time to INR correction (mean difference –6.50 hours, 95 %CI; –9.75 to –3.24). Red blood cell transfusion was not statistically different between the two groups (OR 0.88, 95 % CI: 0.53–1.43). Patients receiving PCC had a lower risk of post-transfusion volume overload compared to FFP (OR 0.27, 95 % CI; 0.13–0.58). There was no statistically significant difference in the risk of thromboembolism following administration of PCC or FFP (OR 0.91, 95 % CI; 0.44–1.89). In conclusion, as compared to FFP, the use of PCC for warfarin reversal was associated with a significant reduction in all-cause mortality, more rapid INR reduction, and less volume overload without an increased risk of thromboembolic events.Supplementary Material to this article is available online at www.thrombosis-online.com.
Managing reversal of direct oral anticoagulants in emergency situations
Authors: Büller Harry R. , Falanga Anna , Hacke Werner , Hendriks Jeroen , Lobban Trudie , Merino Jose , Milojevic Ivan S. , Moya Francisco , van der Worp H. Bart , Randall Gary , Tsioufis Konstantinos , Verhamme Peter , Camm A. John , Ageno Walter 
Published: August 2016

SummaryAnticoagulation is the cornerstone of prevention and treatment of venous thromboembolism (VTE) and stroke prevention in patients with atrial fibrillation (AF). However, the mechanisms by which anticoagulants confer therapeutic benefit also increase the risk of bleeding. As such, reversal strategies are critical. Until recently, the direct oral anticoagulants (DOACs) dabigatran, rivaroxaban, apixaban, and edoxaban lacked a specific reversal agent. This report is based on findings from the Anticoagulation Education Task Force, which brought together patient groups and professionals representing different medical specialties with an interest in patient safety and expertise in AF, VTE, stroke, anticoagulation, and reversal agents, to discuss the current status of anticoagulation reversal and fundamental changes in management of bleeding associated with DOACs occasioned by the approval of idarucizumab, a specific reversal agent for dabigatran, as well as recent clinical data on specific reversal agents for factor Xa inhibitors. Recommendations are given for when there is a definite need for a reversal agent (e.g. in cases of life-threatening bleeding, bleeding into a closed space or organ, persistent bleeding despite local haemostatic measures, and need for urgent interventions and/or interventions that carry a high risk for bleeding), when reversal agents may be helpful, and when a reversal agent is generally not needed. Key stakeholders who require 24–7/around-the-clock access to these agents vary among hospitals; however, from a practical perspective the emergency department is recommended as an appropriate location for these agents. Clearly, the advent of new agents requires standardised protocols for treating bleeding on an institutional level.
Impact of timing from blood sampling to pharmacodynamic assessment on measures of platelet reactivity in patients treated with P2Y12 receptor inhibitors
Authors: Rollini Fabiana , Franchi Francesco , Singh Kamaldeep , Cho Jung , Bhatti Mona , DeGroat Christopher , Hu Jenny , Aggarwal Niti , Alobaidi Zeina , Thano Estela , Ferrante Elisabetta , Zenni Martin M. , Bass Theodore A. , Angiolillo Dominick J. 
Published: August 2016

SummarySeveral platelet function tests (PFT) are available to assess the pharmacodynamic (PD) effects of P2Y12 inhibitors. However, there are technical variances between PFT, and P2Y12 inhibitors differ in pharmacological properties. Manufactures of PFT recommend a time-frame within which assessments needs to be executed. However, if the timing from blood sampling to processing affects PD results is unknown. We conducted a prospective study assessing the impact of timing from blood sampling to processing on PD measures using three different PFT. We studied 60 aspirin-treated patients with coronary artery disease (CAD) on maintenance P2Y12 inhibiting therapy [clopidogrel 75 mg/day (n=20), prasugrel 10 mg/day (n=20) and ticagrelor 90 mg bid (n=20)]. PD assessments (trough levels) were performed by VerifyNow P2Y12 (VN), light transmittance aggregometry (LTA) and vasodilator-stimulated phosphoprotein (VASP) at 30 minutes, 2 and 4 hours post-sampling; VASP was also performed at 24 hours. P2Y12 reaction units (PRU) by VN significantly decreased over time with all P2Y12 inhibitors (clopidogrel p<0.001; prasugrel p=0.016; ticagrelor p<0.001). PRU at 30 minutes and 2 hours were similar, but decreased at 4 hours. LTA showed consistent findings with VN. Conversely, PD measures as assessed by VASP were stable over time (p>0.1 for all P2Y12 inhibitors). In conclusion, in CAD patients on maintenance therapy with P2Y12 inhibitors, timing from blood sampling to processing significantly influences PD measures as assessed by VN and LTA, but not by VASP.
Performance of Risk-Based and Birth-Cohort Strategies for Identifying Hepatitis C Virus Infection Among People Entering Prison, Wisconsin, 2014
Authors: Stockman Lauren J. , Greer James , Holzmacher Ryan , Dittmann Beth , Hoftiezer Scott A. , Alsum Lori E. , Prieve Audrey , Westergaard Ryan P. , Guilfoyle Sheila M. , Vergeront James M. 
Published: August 2016

Objectives. The prevalence of hepatitis C virus (HCV) infection among young adults is rising in Wisconsin. We examined the prevalence of HCV infection among male and female inmates entering two Wisconsin prisons and evaluated existing and alternate risk-based strategies for identifying HCV infection at intake. Methods. We added HCV testing to the intake procedures for all 1,239 adults prison entrants at the Wisconsin Department of Corrections (WDOC) from November 3, 2014, to January 31, 2015. We identified risk factors associated with HCV infection during the routine intake examination and calculated the sensitivity and specificity of risk-based testing strategies for identifying HCV infection. Results. The prevalence of HCV antibody among prison entrants was 12.5% (95% confidence interval [CI] 10.7, 14.4) overall and was almost two times higher at the women’s facility (21.3%, 95% CI 15.4, 27.2) than at the men’s facility (11.0%, 95% CI 0.0, 12.9) ( p<0.001). The sensitivity and specificity of the WDOC risk-based criteria were 88% (95% CI 83, 93) and 80% (95% CI 78, 83), respectively. Adding a new criterion, the 1945–1965 birth cohort, to the risk-based criteria improved the sensitivity to 92% (95% CI 88, 96) and lowered the specificity to 71% (95% CI 68, 74). Compared with entrants without these risk factors, HCV antibody prevalence was significantly higher among prison entrants who had the following risk factors: injection drug use (prevalence ratio [PR] = 9.9, 95% CI 7.4, 13.2), liver disease (PR=9.7, 95% CI 7.8, 12.0), and elevated levels of alanine transaminase (PR=3.6, 95% CI 2.7, 4.9). Conclusion. The WDOC risk criteria for HCV testing identified 88% of HCV infections among prison entrants. Including the 1945–1965 birth cohort as a criterion along with the other WDOC risk criteria increased the sensitivity of targeted testing to 92%. These findings may be informative to jurisdictions where universal HCV testing is not feasible because of resource limitations.
Epidemiology of Infectious Disease–Related Death After Release from Prison, Washington State, United States, and Queensland, Australia
Authors: Binswanger Ingrid A. , Blatchford Patrick J. , Forsyth Simon J. , Stern Marc F. , Kinner Stuart A. 
Published: August 2016

Objectives. People in prison may be at high risk for infectious diseases and have an elevated risk of death immediately after release compared with later; their risk of death is elevated for at least a decade after release. We compared rates, characteristics, and prison-related risk factors for infectious disease–related mortality among people released from prisons in Queensland, Australia, and Washington State, United States, regions with analogous available data. Methods. We analyzed data from retrospective cohort studies of people released from prison in Queensland (1997–2007, n=37,180) and Washington State (1999–2009, n=76,208) and linked identifiers from each cohort to its respective national death index. We estimated infectious disease–related mortality rates (deaths per person-years in community) and examined associations using Cox proportional hazard models. Results. The most frequent infectious disease–related underlying cause of death after release from prison was pneumonia (43%, 23/54 deaths) in the Australian cohort and viral hepatitis (40%, 69/171 deaths) in the U.S. cohort. The infectious disease–related mortality rate was significantly higher in the U.S. cohort than in the Australian cohort (51.2 vs. 26.5 deaths per 100,000 person-years; incidence rate ratio = 1.93, 95% confidence interval 1.42, 2.62). In both cohorts, increasing age was strongly associated with mortality from infectious diseases. Conclusion. Differences in the epidemiology of infectious disease–related mortality among people released from prison may reflect differences in patterns of community health service delivery in each region. These findings highlight the importance of preventing and treating hepatitis C and other infectious diseases during the transition from prison to the community.
Homicide Among American Indians/Alaska Natives, 1999–2009
Authors: Herne Mose A. , Maschino Alexandra C. , Graham-Phillips Anita L. 
Published: August 2016

Objective. We determined estimates of homicide among American Indians/Alaska Natives (AI/ANs) compared with non-Hispanic white people to characterize disparities and improve AI/AN classification in incidence and mortality reporting. Methods. We linked 1999–2009 death certificate data with Indian Health Service (IHS) patient registration data to examine death rates from homicide among AI/AN and non-Hispanic white people. Our analysis focused primarily on residents of IHS Contract Health Service Delivery Area counties and excluded Hispanic people to avoid underestimation of incidence and mortality in AI/ANs and for consistency in our comparisons. We used age-adjusted death rates per 100,000 population and stratified our analyses by sex, age, and IHS region. Results. Death rates per 100,000 population from homicide were four times higher among AI/ANs (rate = 12.1) than among white people (rate = 2.8). Homicide rates for AI/ANs were highest in the Southwest (25.6 and 6.9 for males and females, respectively) and in Alaska (17.7 and 10.3 for males and females, respectively). Disparities between AI/ANs and non-Hispanic white people were highest in the Northern Plains region among men (rate ratio [RR] = 9.8, 95% confidence interval [CI] 8.5, 11.3) and among those aged 25–44 years (RR=9.0, 95% CI 7.5, 10.7) and 0–24 years (RR=7.4, 95% CI 6.1, 8.9). Conclusion. Death rates from homicide among AI/ANs were higher than previously reported and varied by sex, age, and region. Violence prevention efforts involving a range of stakeholders are needed at the community level to address this important public health issue.
Intracluster Correlation Coefficients of Household Economic and Agricultural Outcomes in Mozambique
Authors: Geyer Judy , Davis Mikal , Narayan Tulika 
Published: August 2016

Background: This article offers important statistics to evaluators planning future evaluations in southeast Africa. There are little to no published statistics describing the variance of southeast African agricultural and household indicators. Objective: We seek to publish the standard deviations, intracluster correlation coefficients (ICCs), and R2s from outcomes and covariates used in a 2014 quasi-experimental evaluation of the Millennium Challenge Corporation’s Mozambique Farmer Income Support Project (FISP) and thus guide researchers in their calculation of design effects relevant to future evaluations in the region. Method: We summarize data from a roughly 168-item farmer survey conducted in 1,227 households during June–July 2014 in coconut-farming regions of the Zambezia province in Mozambique. We report descriptive statistics, estimates of ICC, and R2s obtained from linear regression models with cluster random effects. We consider three different cluster definitions. Results: We report ICCs for a range of different specifications. For the FISP evaluation, the average design effect for education outcomes is 1.16. Average design effects for wealth measures based on consumption are 1.23. For agricultural-related outcomes, 1.05 is the average design effects for income measures, 1.47 for knowledge, and 1.64 for sales of specific crops. Conclusion: We offer a detailed picture of the variance structure of agricultural and other outcomes in Mozambique. Our results indicate that the design effect associated with these outcomes is less than the rule-of-thumb design effect (2.0) used in nutrition studies which are commonly cited in the studies of this region.
A generic framework for ontology-based information retrieval and image retrieval in web data
Authors: Vijayarajan V. , Dinakaran M. , Tejaswin Priyam , Lohani Mayank 
Published: August 2016

AbstractIn the internet era, search engines play a vital role in information retrieval from web pages. Search engines arrange the retrieved results using various ranking algorithms. Additionally, retrieval is based on statistical searching techniques or content-based information extraction methods. It is still difficult for the user to understand the abstract details of every web page unless the user opens it separately to view the web content. This key point provided the motivation to propose and display an ontology-based object-attribute-value (O-A-V) information extraction system as a web model that acts as a user dictionary to refine the search keywords in the query for subsequent attempts. This first model is evaluated using various natural language processing (NLP) queries given as English sentences. Additionally, image search engines, such as Google Images, use content-based image information extraction and retrieval of web pages against the user query. To minimize the semantic gap between the image retrieval results and the expected user results, the domain ontology is built using image descriptions. The second proposed model initially examines natural language user queries using an NLP parser algorithm that will identify the subject-predicate-object (S-P-O) for the query. S-P-O extraction is an extended idea from the ontology-based O-A-V web model. Using this S-P-O extraction and considering the complex nature of writing SPARQL protocol and RDF query language (SPARQL) from the user point of view, the SPARQL auto query generation module is proposed, and it will auto generate the SPARQL query. Then, the query is deployed on the ontology, and images are retrieved based on the auto-generated SPARQL query. With the proposed methodology above, this paper seeks answers to following two questions. First, how to combine the use of domain ontology and semantics to improve information retrieval and user experience? Second, does this new unified framework improve the standard information retrieval systems? To answer these questions, a document retrieval system and an image retrieval system were built to test our proposed framework. The web document retrieval was tested against three key-words/bag-of-words models and a semantic ontology model. Image retrieval was tested on IAPR TC-12 benchmark dataset. The precision, recall and accuracy results were then compared against standard information retrieval systems using TREC_EVAL. The results indicated improvements over the standard systems. A controlled experiment was performed by test subjects querying the retrieval system in the absence and presence of our proposed framework. The queries were measured using two metrics, time and click-count. Comparisons were made on the retrieval performed with and without our proposed framework. The results were encouraging.
Multi-disciplinary management of complex pressure sore reconstruction: 5-year review of experience in a spinal injuries centre
Authors: Thomson CH , Choudry M , White C , Mecci M , Siddiqui H 
Published: August 2016

INTRODUCTION In our regional spinal injuries unit, complex pressure ulcer reconstruction is facilitated by a monthly multidisciplinary team clinic. This study reviews a series of the more complex of these patients who underwent surgery as a joint case between plastics and other surgical specialties, aiming to provide descriptive data as well as share the experience of treating these complex wounds. MATERIALS AND METHODS Patients operated on as a joint case from 2010 to 2014 were identified through a locally held database and hospital records were then retrospectively reviewed for perioperative variables. Descriptive statistics were collected. RESULTS 12 patients underwent 15 procedures as a joint collaboration between plastic surgery and other surgical specialties: one with spinal surgery, 12 with orthopaedic and two with both orthopaedic and urology involvement. Ischial and trochanteric wounds accounted for 88% of cases with five Girdlestone procedures being performed and 12 requiring soft-tissue flap reconstruction. Mean operative time was 3.8hours. Four patients required high-dependency care and 13 patients received long-term antibiotics. Only three minor complications (20%) were seen with postoperative wound dehiscence. DISCUSSION The multidisciplinary team clinic allows careful assessment and selection of patients appropriate for surgical reconstruction and to help match expectations and limitations imposed by surgery, which are likely to influence their current lifestyle in this largely independent patient group. Collaboration with other specialties gives the best surgical outcome both for the present episode as well as leaving avenues open for potential future reconstruction.
Blood pressure and lipid profiles in adolescents with hypertensive parents
Authors: Fitriany Julia , Ramayati Rafita , Supriatmo Supriatmo , Rusdidjas Rusdidjas , Rina Oke , Siregar Rosmayanti 
Published: August 2016

problem of increasing prevalence and causes high morbidityand mortality. It is found primarily in young males, with afamilial history of hypertension and/or cardiovascular disease.Examination of lipid profiles has been used to detect the risk ofhypertension in adolescents.Objective To compare blood pressure and lipid profiles inadolescents with and without a parental history of hypertension.Methods This cross-sectional study was conducted from January toFebruary 2012 on students from a senior high school in the TobaSamosir District, North Sumatera. Sixty-eight adolescents wereincluded, aged 15 to 18 years. Group I comprised 34 adolescentswith hypertensive parents, and group II comprised 34 adolescentswith normotensive parents. Subjects were selected based onquestionnaires. Subjects’ blood pressures were measured at rest.Three measurements were made in intervals of 10-15 minutes,then averaged for both systolic and diastolic blood pressures. Lipidprofiles were measured using the CardioCheck cholesterol testafter subjects had fasted for 12 hours.Results The median systolic blood pressures (SBP) in groupsI and II were 110 mmHg (range 93.3-123.3) and 106.7 mmHg(range 96.7-123.3), respectively, (P=0.584). The median diastolicblood pressures (DBP) were 73.3 mmHg (range 66.7-83.3) and71.7 mmHg (range 63.3-80.0), respectively, (P=0.953). Totalcholesterol and low-density lipoprotein cholesterol (LDL-C) levelsin group I were significantly higher than those levels in group II[median total cholesterol: 162.0 (range 158-170) vs. 159.0 (range150-170), respectively; (P=0.001); and mean LDL-C: 103.5 (SD3.72) vs. 99.1 (SD 4.63), respectively; (P=0.001). Multivariateanalysis revealed a correlation of moderate strength betweenparental history of hypertension and increased LDL-C (P<0.001)in adolescents.Conclusion Adolescents with and without familial historyof hypertension have no significant median blood pressuredifferences. However, adolescents with hypertensive parents have afsignificantlyhigher median total cholesterol and mean LDL-C.Furthermore, we find a correlation between parental history ofhypertension and increased LDL-C in adolescents.