bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic review and simulation study of ignoring clustered data in surgical trials
Authors: Dell-Kuster S , Droeser R A , Schäfer J , Gloy V , Ewald H , Schandelmaier S , Hemkens L G , Bucher H C , Young J , Rosenthal R 
Published: February 2018

Abstract

Background
Multiple surgical procedures in a single patient are relatively common and lead to dependent (clustered) data. This dependency needs to be accounted for in study design and data analysis. A systematic review was performed to assess how clustered data were handled in inguinal hernia trials. The impact of ignoring clustered data was estimated using simulations.

Methods
PubMed, Embase and the Cochrane Library were reviewed systematically for RCTs published between 2004 and 2013, including patients undergoing unilateral or bilateral inguinal hernia repair. Study characteristics determining the appropriateness of handling clustered data were extracted. Using simulations, various statistical methods accounting for clustered data were compared with an analysis ignoring clustering by assuming 100 hernias, with a varying percentage of patients having bilateral hernias.

Results
Of the 50 eligible trials including patients with bilateral hernias, 20 (40 per cent) did not provide information on how they dealt with clustered data and 18 (36 per cent) avoided clustering by assessing the outcome by patient and not by hernia. None of the remaining 12 trials (24 per cent) considered clustering in the design or analysis. In the simulations, ignoring clustering led to an increased type I error rate of up to 12 per cent and to a loss in power of up to 15 per cent, depending on whether the patient or the hernia was the randomization unit.

Conclusion
Clustering was rarely considered in inguinal hernia trials. The simulations underline the importance of considering clustering as part of the statistical analysis to avoid false-positive and false-negative results, and hence inappropriate study conclusions.
Cytologic‐histologic correlation of programmed death‐ligand 1 immunohistochemistry in lung carcinomas
Authors: Russell‐Goldman Eleanor , Kravets Sasha , Dahlberg Suzanne E. , Sholl Lynette M. , Vivero Marina 
Published: February 2018

BACKGROUNDProgrammed cell death protein 1 inhibitors increasingly are being used to treat patients with advanced lung carcinomas. Programmed death‐ligand 1 (PD‐L1) immunohistochemistry (IHC) in tumor cells (TCs) and tumor‐infiltrating immune cells (ICs) is used to select patients for programmed cell death protein 1 inhibition, but few studies have evaluated PD‐L1 IHC in cytology specimens. The objective of the current study was to compare PD‐L1 IHC in cytology cell blocks and matched surgical specimens.METHODSA total of 56 cytology specimens obtained between 2013 and 2016 with matching surgical specimens were stained with anti‐PD‐L1. Membranous positivity was scored as a percentage of the TCs and ICs by 2 pathologists. Results were compared between cytology and surgical specimens, and interobserver concordance was assessed.RESULTSThe average PD‐L1 positivity rate was 28% in TCs and 5% in ICs in surgical specimens (standard deviations of 37% and 7%, respectively), and 21% in TCs and 8% in ICs in cytology specimens (standard deviations of 33% and 15%, respectively). Interobserver concordance was high for TCs in surgical and cytology specimens (intraclass correlation coefficients of 0.96 and 0.96, respectively), and was moderate for ICs in surgical and cytology specimens (intraclass correlation coefficients of 0.47 and 0.67, respectively). There was moderate to high correlation between PD‐L1 positivity in TCs between surgical and cytology specimens (Spearman correlation coefficient [Spearman r], 0.69), particularly among fine‐needle aspiration specimens (Spearman r, 0.78), but not between PD‐L1 positivity in ICs in surgical and cytology specimens (Spearman r, 0.14), including among fine‐needle aspiration specimens (Spearman r, 0.23).CONCLUSIONSTumor PD‐L1 IHC positivity in cytology specimens appears to correlate strongly with results obtained from matching surgical specimens. PD‐L1 IHC in ICs within cytology specimens does not reflect results in matched surgical specimens and should not be used in clinical decision making. Cancer Cytopathol 2018;126:253‐63. © 2018 American Cancer Society.
Peculiarly Structured Janus Nanofibers Display Synchronous and Tuned Trifunctionality of Enhanced Luminescence, Electrical Conduction, and Superparamagnetism
Authors: Xi Xue , Ma Qianli , Dong Xiangting , Li Dan , Yu Wensheng , Wang Jinxian , Liu Guixia 
Published: February 2018

AbstractFlexible peculiarly structured [(Fe3O4/PVP)@(Tb(BA)3phen/PVP)]//[PANI/PVP] (PVP=polyvinylpyrrolidone, BA=benzoic acid, phen=1,10‐phenanthroline, and PANI=polyaniline) Janus nanofibers synchronously endowed with tuned and enhanced luminescent–magnetic–electrical trifunctionality have been prepared by electrospinning technology by using a homemade coaxis//monoaxis spinneret. It is satisfactorily found that the luminescent intensity of the peculiarly structured Janus nanofibers is higher than those of the counterpart conventional [nanofiber]//[nanofiber] Janus nanofibers and composite nanofibers owing to its peculiar nanostructure. Compared with the counterpart conventional Janus nanofibers of two independent partitions, the coaxial nanocable is used as one side of the peculiarly structured Janus nanofiber instead of nanofiber, and three independent partitions are successfully realized in the peculiarly structured Janus nanofiber, thus the interferences among various functions are further reduced, leading to the fact that excellent multifunctionalities can be obtained. The Janus nanofibers possess excellent green luminescence, superparamagnetism, and electric conductivity, and further, these performances can be, respectively, tunable by modulating the Tb(BA)3phen, Fe3O4, and PANI contents. The design philosophy and construction technique for the peculiarly structured Janus nanofibers provide guidance for fabricating other multifunctional Janus nanofibers with various performances.
Warthins tumor: Cyto histological spectrum with emphasis on diagnostic difficulties
Authors: Sood Neelam , Borah Parismrita 
Published: February 2018

Warthins tumour is characterized by the presence of epithelial proliferation in a lymphoid stroma. It has been categorized as Sieferts types: 1‐4, depending on the proportions of the 2 components. Although FNA is fairly accurate in establishing the diagnosis, the cytologic diagnosis of this tumor has potential sources of error.This retrospective study was conducted in the Department of Pathology and Lab Medicine, of a tertiary care hospital. Cytology and surgical pathology records of past 15 years were screened. A total of 1200 FNAC cases of salivary gland lesions in the past 15 years were retrieved. 36 cases with presumptive cytodiagnosis of WT were identified and histopathological correlation was done. Histopathological correlation could be done in 24 cases. 19 out of 24 cases, were confirmed as WT. The 5 cases with discordance were analyzed for potential diagnostic pitfalls. The most common discordance was in the category of papillary proliferation with minimal lymphoid infiltrate. One case proved as oncocytoma and the other was papillary oncocyticcystadenoma. The other major pitfalls, were the interpretation of atypical squamoid cells. Their presence in a lymphoid background needs consideration of cytologic diagnosis of WT, mucoepidermoid carcinoma and metastatic squamous carcinoma. FNA showed an accuracy of 79% for WT.Cytological misinterpretation can thus occur in presence of morphology other than classical Siefert type1. An awareness of these potential pitfalls should push the need for avoiding single cytologic interpretation.
Pharmacokinetics, tissue distribution, and excretion of FGF‐21 following subcutaneous administration in rats
Authors: He Yufei , Li Yazhuo , Wei Zihong , Zhang Xingyan , Gao Jing , Wang Xiaojie , Li Xiaokun , Wu Weidang , Li Wei , Yi Xiulin , Zeng Yong , Liu Changxiao 
Published: February 2018

AbstractAs one of the fibroblast growth factor (FGF) superfamily, FGF‐21 has been extensively investigated for its functions and roles since its discovery. It has been demonstrated to be one of the key regulators for glucose and lipid metabolism, and exhibits beneficial effects on cardiovascular disease. However, studies focusing on its pharmacokinetic behavior in vivo as a novel therapeutic agent have not been reported. In the present study, rapid and sensitive analytical approaches including radioactivity assay and assay after precipitation/separation by high performance liquid chromatography (HPLC) were established to determine the content of FGF‐21 tagged with 125I in plasma, tissue, and excrement. The results indicated that FGF‐21 were quickly absorbed into systematic circulation and slowly eliminated; Cmax and exposure increased in a dose‐dependent manner, exhibiting a typical linear pharmacokinetic pattern. Tissue distribution also confirmed that the kidney is the primary organ for FGF‐21 to be distributed, even though radioactivity of FGF‐21 was recovered in all tissues examined. In addition, the results also supported that urinary excretion was the critical route for FGF‐21 to be eliminated. The study fully clarifies the pharmacokinetic behavior of FGF‐21 and can provide valuable information and support further safety and toxicology development.
Pre‐outbreak forest conditions mediate the effects of spruce beetle outbreaks on fuels in subalpine forests of Colorado
Authors: Mietkiewicz Nathan , Kulakowski Dominik , Veblen Thomas T. 
Published: February 2018

AbstractOver the past 30 years, forest disturbances have increased in size, intensity, and frequency globally, and are predicted to continue increasing due to climate change, potentially relaxing the constraints of vegetation properties on disturbance regimes. However, the consequences of the potentially declining importance of vegetation in determining future disturbance regimes are not well understood. Historically, bark beetles preferentially attack older trees and stands in later stages of development. However, as climate warming intensifies outbreaks by promoting growth of beetle populations and compromising tree defenses, smaller diameter trees and stands in early stages of development now are being affected by outbreaks. To date, no study has considered how stand age and other pre‐outbreak forest conditions mediate the effects of outbreaks on surface and aerial fuel arrangements. We collected fuels data across a chronosequence of post‐outbreak sites affected by spruce beetle (SB) between the 1940s and the 2010s, stratified by young (<130 yr) and old (>130 yr) post‐fire stands. Canopy and surface fuel loads were calculated for each tree and stand, and available crown fuel load, crown bulk density, and canopy bulk densities were estimated. Canopy bulk density and density of live canopy individuals were reduced in all stands affected by SB, though foliage loss was proportionally greater in old stands as compared to young stands. Fine surface fuel loads in young stands were three times greater shortly (<30 yr) following outbreak as compared to young stands not affected by outbreak, after which the abundance of fine surface fuels decreased to below endemic (i.e., non‐outbreak) levels. In both young and old stands, the net effect of SB outbreaks during the 20th and 21st centuries reduced total canopy fuels and increased stand‐scale spatial heterogeneity of canopy fuels following outbreak. Importantly, the decrease in canopy fuels following outbreaks was greater in young post‐fire stands than in older stands, suggesting that SB outbreaks may more substantially reduce risk of active crown fire when they affect stands in earlier stages of development. The current study shows that the effects of SB outbreaks on forest structure and on fuel profiles are strongly contingent on pre‐outbreak conditions as determined by pre‐outbreak disturbance history.
Estimating abundance of an open population with anN‐mixture model using auxiliary data on animal movements
Authors: Ketz Alison C. , Johnson Therese L. , Monello Ryan J. , Mack John A. , George Janet L. , Kraft Benjamin R. , Wild Margaret A. , Hooten Mevin B. , Hobbs N. Thompson 
Published: February 2018

AbstractAccurate assessment of abundance forms a central challenge in population ecology and wildlife management. Many statistical techniques have been developed to estimate population sizes because populations change over time and space and to correct for the bias resulting from animals that are present in a study area but not observed. The mobility of individuals makes it difficult to design sampling procedures that account for movement into and out of areas with fixed jurisdictional boundaries. Aerial surveys are the gold standard used to obtain data of large mobile species in geographic regions with harsh terrain, but these surveys can be prohibitively expensive and dangerous. Estimating abundance with ground‐based census methods have practical advantages, but it can be difficult to simultaneously account for temporary emigration and observer error to avoid biased results. Contemporary research in population ecology increasingly relies on telemetry observations of the states and locations of individuals to gain insight on vital rates, animal movements, and population abundance. Analytical models that use observations of movements to improve estimates of abundance have not been developed. Here we build upon existing multi‐state mark–recapture methods using a hierarchicalN‐mixture model with multiple sources of data, including telemetry data on locations of individuals, to improve estimates of population sizes. We used a state‐space approach to model animal movements to approximate the number of marked animals present within the study area at any observation period, thereby accounting for a frequently changing number of marked individuals. We illustrate the approach using data on a population of elk (Cervus elaphus nelsoni) in Northern Colorado, USA. We demonstrate substantial improvement compared to existing abundance estimation methods and corroborate our results from the ground based surveys with estimates from aerial surveys during the same seasons. We develop a hierarchical Bayesian N‐mixture model using multiple sources of data on abundance, movement and survival to estimate the population size of a mobile species that uses remote conservation areas. The model improves accuracy of inference relative to previous methods for estimating abundance of open populations.
Axl and MerTK receptor tyrosine kinases maintain human macrophage efferocytic capacity in the presence of viral triggers
Authors: Grabiec Aleksander M , Goenka Anu , Fife Mark E , Fujimori Toshifumi , Hussell Tracy 
Published: February 2018

AbstractThe requirement to remove apoptotic cells is equally important in homeostasis and inflammatory disease. In particular, during viral infections large quantities of infected cells undergo apoptosis and need to be efficiently cleared by phagocytes to prevent secondary necrosis. Although specific roles of several apoptotic cell sensors, such as the TAM (Tyro3, Axl, MerTK) receptor family, have been characterized in mouse models, little is known about their regulation and involvement in apoptotic cell uptake (efferocytosis) by human macrophages under inflammatory conditions. We show that whereas pro‐inflammatory stimuli consistently downregulated MerTK expression in human monocyte‐derived macrophages (MDMs), stimuli indicative of a viral infection, interferon‐α (IFN‐α) and the TLR3 ligand poly(I:C), specifically induced Axl expression and promoted binding of the bridging molecule Gas6. Axl induction by IFN‐α and poly(I:C) was associated with higher MDM efferocytic capacity compared to cells treated with other pro‐inflammatory stimuli, such as LPS and IFN‐γ. While MerTK blocking antibody uniformly suppressed apoptotic cell uptake by MDMs, Axl blocking antibody significantly reduced efferocytosis by poly(I:C)‐stimulated MDMs, but not by resting MDMs. Our observations demonstrate that Axl induction during viral infections contributes to maintaining macrophage capacity to engulf apoptotic cells, which may have important consequences for resolution of anti‐viral immune responses.
Preoperative sarcopenia and post‐operative accelerated muscle loss negatively impact survival after resection of pancreatic cancer
Authors: Choi Moon Hyung , Yoon Seung Bae , Lee Kyungjin , Song Meiying , Lee In Seok , Lee Myung Ah , Hong Tae Ho , Choi Myung‐Gyu 
Published: February 2018

AbstractBackgroundSarcopenia and post‐operative accelerated muscle loss leading to cachexia are commonly observed in patients with pancreatic cancer. This study aimed to assess the influence of body compositions and post‐operative muscle change on survival of patients with surgically treated pancreatic cancer.MethodsWe analysed data of patients diagnosed with pancreatic adenocarcinoma who underwent surgery from 2008 to 2015. Skeletal muscle areas, muscle attenuation, and visceral and subcutaneous adipose tissue areas were measured from two sets of computed tomography images at L3 vertebral levels. In addition, muscle change was calculated from images obtained before and after cancer resection. We set our own cut‐off values of various body compositions based on sex‐specific tertiles.ResultsA total of 180 patients were analysed. Patients with perioperative sarcopenia (n = 60) showed poorer overall survival than those without perioperative sarcopenia (P = 0.031). Fifty (28.6%) patients with accelerated muscle loss after surgery (>10%/60 days) had poorer survival compared with the others (P = 0.029). Sarcopenia (hazard ratio, 1.79: 95% confidence interval, 1.20–2.65] and post‐operative muscle change (%/60 days) (hazard ratio, 0.94: 95% confidence interval, 0.92–0.96) were identified as significant predictors of survival on multivariable analyses.ConclusionsPreoperative sarcopenia identified on CT scan was associated with poor overall survival in patients with pancreatic cancer following surgery. Accelerated muscle loss after surgery also negatively impacted survival in pancreatic cancer patients.
Immunotherapy synergizes with debridement and antibiotic therapy in a murine 1‐stage exchange model of MRSA implant‐associated osteomyelitis
Authors: Yokogawa Noriaki , Ishikawa Masahiro , Nishitani Kohei , Beck Christopher A. , Tsuchiya Hiroyuki , Mesfin Addisu , Kates Stephen L. , Daiss John L. , Xie Chao , Schwarz Edward M. 
Published: February 2018

ABSTRACTMethicillin‐resistant Staphylococcus aureus (MRSA) reinfection following revision surgery remains a major orthopaedic problem. Toward the development of immunotherapy with anti‐glucosaminidase monoclonal antibodies (anti‐Gmd), we aimed to: (i) develop a murine 1‐stage exchange model of bioluminescent MRSA (USA300LAC::lux) contaminated femoral implants; and (ii) utilize this model to demonstrate the synergistic effects of combination vancomycin and anti‐Gmd therapy on reinfection and bone healing. Following an infection surgery, the original plate and two screws were removed on day 7, and exchanged with sterile implants. Mice were randomized to five groups: (i) no infection control; (ii) infected placebo; (iii) anti‐Gmd; (iv) vancomycin; and (v) combination therapy. Bioluminescent imaging (BLI) was performed on days 0, 1, 3, 5, 7, 8, 10, 12, and 14. Mice were euthanized on day 14 (day 7 post‐revision), and efficacy was assessed via colony forming units (CFU) on explanted hardware, micro‐CT, and histology. As monotherapies, anti‐Gmd inhibited Staphylococcus abscess communities, and vancomycin reduced CFU on the implants. However, only combination therapy prevented increased BLI post‐revision surgery, with a significant 6.5‐fold reduction on day 10 (p < 0.05 vs. placebo), and achieved sterile implant levels by day 12. Synergistic effects were also apparent from reduced osteolysis and increased new bone formation around the screws only observed following combination therapy. Taken together, we find that: (i) this murine femoral plate 1‐stage revision model can efficiently evaluate therapies to prevent reinfection; and (ii) immunotherapy plays a distinct role from antibiotics to reduce reinfection following revision surgery, such that synergy to achieve osseointegration is possible. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:1590–1598, 2018.
Characterization of Biosurfactant Produced by a Novel Strain ofPseudomonas aeruginosa, Isolate ADMT1
Authors: Tiwary Meenakshi , Dubey Ashok K. 
Published: February 2018

AbstractSeveral biosurfactant‐producing bacterial strains were isolated from petroleum‐contaminated soil. The isolate ADMT1, identified as a new strain ofPseudomonas aeruginosa, was selected for further studies on the basis of oil displacement test and emulsification index (E24). The optimal parameters for production, determined by employing Box–Behnken design, were temperature 36.5 °C and pH 7. The environmental isolate ADMT1 produced significant amount of biosurfactant (1.7 g L−1in 72 h) in minimal salt medium (MSM) using dextrose as the sole carbon source. The E24 value and critical micelle concentration (CMC) of the biosurfactant was 100% and 150 mg L−1, respectively. At CMC, the surface tension of water was reduced to 28.4 mN m−1. The biosurfactant exhibited hemolytic activity and antibacterial activity against 8 reference strains of pathogenic bacteria, including 2 methicillin‐resistantStaphylococcus aureusstrains (MRSA ATCC 562 and MRSA ATCC 43300), with minimum inhibitory concentration (MIC) of 0.4 and 0.2 mg mL−1, respectively. The structure of biosurfactant was characterized by FTIR,1H, and13C NMR spectroscopy. 7 di‐rhamnolipid (RL) congeners were identified in the biosurfactant by ultraperformance liquid chromatography–mass spectrometry analysis. The major congeners, which constituted 67% of the RL mixture, included Rha‐Rha‐C10‐C10, Rha‐Rha‐C12‐C10, and Rha‐Rha‐C12:1‐C10. The minor congeners were Rha‐Rha‐C10‐C8, Rha‐Rha‐C10:1‐C10, Rha‐Rha‐C10‐C14:1, and Rha‐Rha‐C10‐C14. The congener Rha‐Rha‐C10‐C14is being reported for the first time from any species ofPseudomonas. The high surface activity and E24 value make the ADMT1‐RL a potential candidate for its use in detergents, environmental bioremediation, and as an emulsifier in the food industry.