bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serum Immunoglobulin G4 in Discriminating Autoimmune Pancreatitis From Pancreatic Cancer
Authors: Dai Cong , Cao Qin , Jiang Min , Sun Ming-Jun 
Published: January 2018

Objective
Differentiation between autoimmune pancreatitis (AIP) and pancreatic cancer (PC) is a clinical challenge. Emerging published data on the accuracy of serum immunoglobulin G4 (IgG4) for the differential diagnosis between AIP and PC are inconsistent. The objective of our study was to perform a meta-analysis evaluating the clinical utility of serum IgG4 in the differential diagnosis between AIP and PC.

Methods
We performed a systematic literature search of multiple electronic databases. The methodological quality of each study was assessed according to the Quality Assessment of Diagnostic Accuracy Studies checklist. Random-effects model was used to summarize the diagnostic odds ratio and other measures of accuracy.

Results
Eleven studies comprising 523 AIP patients and 771 PC patients were included in the meta-analysis. The summary estimates for serum IgG4 in distinguishing AIP from PC were as follows: diagnostic odds ratio, 57.30 (95% confidence interval [CI], 23.17–141.67); sensitivity, 0.72 (95% CI, 0.68–0.76); specificity, 0.93 (95% CI, 0.91–0.94). The area under the curve of serum IgG4 in distinguishing AIP from PC was 0.9200.

Conclusions
Our meta-analysis found that serum IgG4 has high specificity and relatively low sensitivity in the differential diagnosis between AIP and PC. Therefore, serum IgG4 is useful in distinguishing AIP from PC.
Modified Primary Prophylaxis in Previously Untreated Patients With Severe Hemophilia A in Iran
Authors: Karimi Mehran , Eshghi Peyman , Safarpour Mohammad M. , Haghpanah Sezaneh , Meshksar Aidin , Zahedi Zohreh , Habibpanah Behnaz 
Published: January 2018

Background:Recently the low-dose tailoring method of primary prophylaxis has been introduced for previously untreated patients with hemophilia A.Objective:To evaluate the efficacy and safety of low-dose tailoring method of primary prophylaxis in previously untreated patients with severe hemophilia A.Materials and Methods:In this pre-post interventional study, 33 patients with severe hemophilia A who were previously untreated and affiliated to universities in the capital city and southern Iran were evaluated during 2014 to 2015. Modified primary continuous prophylaxis was used for patients with age below 3 years old, after first and before the second episodes of obvious clinical bleeding in large joints or large soft tissue hematoma or large amount of bleeding. Prophylaxis was started by 25 IU/kg once per week and increased to twice or 3 times a week according to defined bleeding events.Results:The median age at diagnosis and age of starting prophylaxis were: 4 months (at birth, 22 mo) and 12 months (1 to 35 mo), respectively. Mean annual bleeding rate of patients after prophylaxis was 1.08±2.21 episodes per year. None of the patients had inhibitors before therapy. Inhibitor was present in 5 patients (15.1%) after prophylaxis.Conclusions:It seems that modified primary continuous prophylaxis has been successful in reducing bleeding episodes in children with severe hemophilia A and in the texture of lower cost it can improve quality of life of these patients, especially in developing countries where financial resources are limited.
Arterial Vascularization of the Mandibular Condyle and Fractures of the Condyle
Authors: Toure Gaoussou 
Published: January 2018

Background:
Despite substantial displacements, fractures of the mandibular condyle rarely lead to necrosis. This illustrates the negligible role of the inferior alveolar artery in intraosseous supply to the condyle, and led to this systematization of its arterial vascularization.

Methods:
Forty-two temporomandibular joints from nonembalmed cadaveric specimens were studied following injection of latex (n = 32) or India ink (n = 10).

Results:
The intraosseous branches of the inferior alveolar artery that lead to the condyle were inconstant and often rudimentary. In this study, the arteries that consistently led to the condyle were the superficial temporal artery, the deep posterior temporal artery, and arterial branches leading to the lateral pterygoid muscle emanating directly from the maxillary artery. These arteries, along with the transverse facial artery and the masseteric artery (when they participated in condoyle vascularization), formed a quadrangle around the mandibular condyle. After India ink injection, the pterygoid muscle was the most strongly colored muscle, thus indicating substantial vascularization.

Conclusions:
Although there is a lack of consensus in the literature regarding the constancy and proportions of the arteries participating in vascularization of the condyle, the superficial temporal artery, the maxillary arterial branches leading to the lateral pterygoid muscle, and the deep posterior temporal artery were constant in this study. This study shows the important role of the lateral pterygoid in the vascularization of the condyle. In case of a fracture with substantial displacement, the vascularization emanating from the superficial temporal artery and the lower alveolar artery is ruptured or compromised.
Preoperative and Postoperative Assessment of Rectus Abdominis Muscle Size and Function following DIEP Flap Surgery
Authors: Seal Shane K. F. , Hewitt Mark K. , Martin Michael L. , Brasher Penelope M. A. , Macadam Sheina A. 
Published: January 2018

Background:
Prospective evaluation of rectus abdominis muscle function after deep inferior epigastric artery perforator (DIEP) flap breast reconstruction is limited. Elimination of muscle harvest with this procedure is theoretically associated with preservation of rectus abdominis function and minimization of abdominal wall morbidity. In this study, the authors evaluate the change in rectus abdominis muscle size and function after DIEP flap surgery.

Methods:
Patients undergoing unilateral DIEP flap surgery were recruited prospectively. Using computed tomography, the change in preoperative to postoperative rectus abdominis muscle size was compared between the operative side rectus abdominis muscle and the contralateral, nonoperative control rectus abdominis. Postoperative muscle integrity and contractility were evaluated using ultrasound by comparing the change in rectus abdominis muscle dimensions between contractile and relaxed states. The BREAST-Q was used to score patients' subjective satisfaction. Clinical and radiographic hernia rates were also calculated.

Results:
Analysis of 26 paired rectus abdominis muscles revealed no significant change in muscle size from preoperative to postoperative values. Furthermore, dimensional change from contractile to relaxed states postoperatively was similar for paired operative and nonoperative rectus abdominis muscles. BREAST-Q scores indicated a high degree of satisfaction in abdominal well-being, breast satisfaction, and surgical experience domains. There were no clinical or radiographic abdominal wall hernias noted.

Conclusions:
The DIEP flap is an effective surgical procedure with minimal abdominal wall morbidity that is associated with no measurable loss in rectus abdominis size and contractile function postoperatively. Patients are highly satisfied with their abdominal function postoperatively using this technique.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
HIV Care Continuum Disparities Among Black Bisexual Men and the Mediating Effect of Psychosocial Comorbidities
Authors: Friedman M. Reuel , Sang Jordan M. , Bukowski Leigh A. , Matthews Derrick D. , Eaton Lisa A. , Raymond H. Fisher , Stall Ron 
Published: January 2018

Introduction:
Differences across the HIV care continuum between men who have sex with men and women (MSMW) and men who have sex with men only (MSMO) are emerging in recent literature but have not been comprehensively documented among black MSM. Although MSMW have lower HIV prevalence than MSMO, they are more likely to be HIV-positive unaware and be virally unsuppressed. Explanatory factors for these differences have not previously been assessed.

Methods:
Between 2014 and 2016, we surveyed sexually active black MSM 18 years or older at Black Gay Pride events in 6 U.S. cities (n = 3881), 1229 of whom either self-reported HIV-positive status or tested HIV-positive onsite. We compared HIV-positive MSMW (n = 196) with HIV-positive MSMO (n = 1033) by HIV-positive unaware status, HIV care uptake, and viral load suppression. We conducted multivariable logistic regressions and built a structural equation model assessing mediating effects of psychosocial comorbidities (violence victimization, depression, and polydrug use) on the relationship between MSMW status and unsuppressed virus.

Results:
MSMW were more likely than MSMO to be HIV-positive unaware [adjusted odds ratio (aOR) = 2.17; 95% confidence interval (CI): 1.58 to 3.00]. Among those who were HIV-positive aware (n = 720), MSMW were more likely to report never receiving HIV care (aOR = 2.74; 95% CI: 1.05 to 7.16) and to report detectable viral loads (aOR = 2.34; 95% CI: 1.31 to 4.19). Psychosocial comorbidities significantly mediated (P = 0.01) the relationship between MSMW status and unsuppressed virus.

Discussion:
Black MSMW were less likely than black MSMO to uptake biomedical care and secondary prevention. Biobehavioral intervention development specific to HIV-positive black MSMW will be most successful if psychosocial comorbidities are also addressed.
Prognostic Factors Change Over Time After Hepatectomy for Colorectal Liver Metastases
Authors: Margonis Georgios Antonios , Buettner Stefan , Andreatos Nikolaos , Wagner Doris , Sasaki Kazunari , Barbon Carlotta , Beer Andrea , Kamphues Carsten , Løes Inger Marie , He Jin , Pawlik Timothy M. , Kaczirek Klaus , Poultsides George , Lønning Per Eystein , Cameron John L. , Mischinger Hans Joerg , Aucejo Federico N. , Kreis Martin E. , Wolfgang Christopher L. , Weiss Matthew J. 
Published: January 2018

Objective:
To evaluate the changing impact of genetic and clinicopathologic factors on conditional overall survival (CS) over time in patients with resectable colorectal liver metastasis.

Background:
CS estimates account for the changing likelihood of survival over time and may reveal the changing impact of prognostic factors as time accrues from the date of surgery.

Methods:
CS analysis was performed in 1099 patients of an international, multi-institutional cohort. Three-year CS (CS3) estimates at the “xth” year after surgery were calculated as follows: CS3 = CS (x + 3)/CS (x). The standardized difference (d) between CS3 rates was used to estimate the changing prognostic power of selected variables over time. A d < 0.1 indicated very small differences between groups, 0.1 ≤ d < 0.3 indicated small differences, 0.3 ≤ d < 0.5 indicated moderate differences, and d ≥ 0.5 indicated strong differences.

Results:
According to OS estimates calculated at the time of surgery, the presence of BRAF and KRAS mutations, R1 margin status, resected extrahepatic disease, patient age, primary tumor lymph node metastasis, tumor number, and carcinoembryonic antigen levels independently predicted worse survival. However, when temporal changes in the prognostic impact of these variables were considered using CS3 estimates, BRAF mutation dominated prognosis during the first year (d = 0.48), whereas surgeon-related variables (ie, surgical margin and resected extrahepatic disease) determined prognosis thereafter (d ≥ 0.5). Traditional clinicopathologic factors affected survival constantly, but only to a moderate degree (0.3 ≤ d < 0.5).

Conclusions:
The impact of genetic, surgery-related, and clinicopathologic factors on OS and CS3 changed dramatically over time. Specifically, BRAF mutation status dominated prognosis in the first year, whereas positive surgical margins and resected extrahepatic disease determined prognosis thereafter.
Laparoscopic Surgery’s 100 Most Influential Manuscripts: A Bibliometric Analysis
Authors: Mellor Katie L. , Powell Arfon G.M.T. , Lewis Wyn G. 
Published: January 2018

Purpose:
Bibliometric analysis of the 100 most cited manuscripts in laparoscopic surgery.

Materials and Methods:
Web of Science database was used to identify all English language full manuscripts with search terms “laparoscop*” and “surg*.” The 100 most cited publications were analyzed by; topic, journal, author, year, and institution.

Results:
In total, 71,524 eligible papers were returned with a median citation of 585.76. The 2 most cited papers received 1635 citations each. Nelson and colleagues, compared laparoscopic with open colectomy for malignancy, and Clavien and colleagues, classified postoperative morbidity by severity. Annals of Surgery published the largest number of papers (n=22), and received most citations (n=12,356). The United States (n=55) and 2004 (n=13) had the highest number of publications. The most ubiquitous topic was cancer treatment (n=35), followed by surgical technique (n=24), and comparison of laparoscopic with open surgery (n=22).

Conclusions:
The most cited topic compared laparoscopic surgical techniques and comparisons thereof with open surgery.
Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package
Authors: Mermelstein Daniel J. , Charles Lin , Gard Nelson , Rachael Kretsch , McCammon J. Andrew , Walker Ross C. 
Published: January 2018

AbstractAlchemical free energy calculations (AFE) based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability, and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907-atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER.
Nonlinear averaging of thermal experience predicts population growth rates in a thermally variable environment
Authors: Bernhardt Joey R. , Sunday Jennifer M. , Thompson Patrick L. , O’Connor Mary I. 
Published: January 2018

AbstractAs thermal regimes change worldwide, projections of future population and species persistence often require estimates of how population growth rates depend on temperature. These projections rarely account for how temporal variation in temperature can systematically modify growth rates relative to projections based on constant temperatures. Here, we tested the hypothesis that population growth rates in fluctuating thermal environments differ from growth rates in constant conditions, and that the differing thermal performance curves (TPCs) can be predicted quantitatively. With experimental populations of the green alga Tetraselmis tetrahele, we show that nonlinear averaging techniques accurately predicted increased as well as decreased population growth rates in fluctuating thermal regimes relative to constant thermal regimes. We extrapolate from these results to project critical temperatures for population growth and persistence of 89 phytoplankton species in naturally variable thermal environments. These results advance our ability to predict population dynamics in the context of global change.
Characterizing functional consequences of DNA copy number alterations in breast and ovarian tumors by spaceMap
Authors: Conley Christopher J. , Ozbek Umut , Wang Pei , Peng Jie 
Published: January 2018

AbstractMotivationWe propose a novel conditional graphical model — spaceMap — to construct gene regulatory networks from multiple types of high dimensional omic profiles. A motivating application is to characterize the perturbation of DNA copy number alterations (CNA) on downstream protein levels in tumors. Through a penalized multivariate regression framework, spaceMap jointly models high dimensional protein levels as responses and high dimensional CNA as predictors. In this setup, spaceMap infers an undirected network among proteins together with a directed network encoding how CNA perturb the protein network. spaceMap can be applied to learn other types of regulatory relationships from high dimensional molecular pro-files, especially those exhibiting hub structures.ResultsSimulation studies show spaceMap has greater power in detecting regulatory relationships over competing methods. Additionally, spaceMap includes a network analysis toolkit for biological interpretation of inferred networks. We applied spaceMap to the CNA, gene expression and proteomics data sets from CPTAC-TCGA breast (n=77) and ovarian (n=174) cancer studies. Each cancer exhibited disruption of ‘ion transmembrane transport’ and ‘regulation from RNA polymerase II promoter’ by CNA events unique to each cancer. Moreover, using protein levels as a response yields a more functionally-enriched network than using RNA expressions in both cancer types. The network results also help to pinpoint crucial cancer genes and provide insights on the functional consequences of important CNA in breast and ovarian cancers.AvailabilityThe R package spaceMap — including vignettes and documentation — is hosted at https://topherconley.github.io/spacemap
An origin of the immunogenicity of in vitro transcribed RNA
Authors: Mu Xin , Greenwald Emily , Ahmad Sadeem , Hur Sun 
Published: January 2018

ABSTRACTThe emergence of RNA-based therapeutics demands robust and economical methods to produce RNA with few byproducts from aberrant activity. While in vitro transcription using the bacteriophage T7 RNA polymerase is one such popular method, its transcripts are known to display an immune-stimulatory activity that is often undesirable and uncontrollable. We here showed that the immune-stimulatory activity of T7 transcript is contributed by its aberrant activity to initiate transcription from a promoter-less DNA end. This activity results in the production of an antisense RNA that is fully complementary to the intended sense RNA product, and consequently a long double-stranded RNA (dsRNA) that can robustly stimulate a cytosolic pattern recognition receptor, MDA5. This promoter-independent transcriptional activity of the T7 RNA polymerase was observed for a wide range of DNA sequences and lengths, but can be suppressed by altering the transcription reaction with modified nucleotides or by reducing the Mg concentration. The current work thus not only offers a previously unappreciated mechanism by which T7 transcripts stimulate the innate immune system, but also shows that the immune-stimulatory activity can be readily regulated.
Feasibility of particle swarm optimization and multiple regression for the prediction of an environmental issue of mine blasting
Authors: Eskandar Hajar , Heydari Elham , Hasanipanah Mahdi , Jalil Masir Mehrshad , Mahmodi Derakhsh Ali 
Published: January 2018

PurposeBlasting is an economical method for rock breakage in open-pit mines. Backbreak is an undesirable phenomenon induced by blasting operations and has several unsuitable effects such as equipment instability and decreased performance of the blasting. Therefore, accurate estimation of backbreak is required for minimizing the environmental problems. The primary purpose of this paper is to propose a novel predictive model for estimating the backbreak at Shur River Dam region, Iran, using particle swarm optimization (PSO).Design/methodology/approachFor this work, a total of 84 blasting events were considered and five effective factors on backbreak including spacing, burden, stemming, rock mass rating and specific charge were measured. To evaluate the accuracy of the proposed PSO model, multiple regression (MR) model was also developed, and the results of two predictive models were compared with actual field data.FindingsBased on two statistical metrics [i.e. coefficient of determination (R2) and root mean square error (RMSE)], it was found that the proposed PSO model (withR2= 0.960 and RMSE = 0.08) can predict backbreak better than MR (withR2= 0.873 and RMSE = 0.14).Originality/valueThe analysis indicated that the specific charge is the most effective parameter on backbreak among all independent parameters used in this study.
Improved plant growth simulation and genetic hybrid algorithm (PGSA-GA) and its structural optimization
Authors: Shi Kairong , Ruan Zhijian , Jiang Zhengrong , Lin Quanpan , Wang Long 
Published: January 2018

Purpose
The purpose of this paper is to propose a new hybrid algorithm, named improved plant growth simulation algorithm and genetic hybrid algorithm (PGSA-GA), for solving structural optimization problems.

Design/methodology/approach
PGSA-GA is based on PGSA and three improved strategies, namely, elitist strategy of morphactin concentration calculation, strategy of intelligent variable step size and strategy of initial growth point selection based on GA. After a detailed formulation and explanation of its implementation, PGSA-GA is verified using the examples of typical truss and single-layer lattice shell.

Findings
Improved PGSA-GA was implemented and optimization was carried out for two typical optimization problems; then, a comparison was made between the PGSA-GA and other methods. The results show that the method proposed in the paper has the advantages of high efficiency and rapid convergence, which enable it to be used for the optimization of various types of steel structures.

Originality/value
Through the examples of typical truss and single-layer lattice shell, it shows that the optimization efficiency and effect of PGSA-GA are better than those of other algorithms and methods, such as GA, secondary optimization method, etc. The results show that PGSA-GA is quite suitable for structural optimization.