bluuebunny/crossref_metadata_2025_split huggingface dataset:
The phase transformation of CuInS2 from chalcopyrite to wurtzite
Authors: Xie Bing-Bing , Hu Bin-Bin , Jiang Li-Fang , Li Guo , Du Zu-Liang 
Published: February 2015

Abstract
In the present work, CuInS2 nanoparticles have been successfully synthesized by water-bath method with deionized water as solvent and thioglycolic acid as complexing agent at 80°C. The phase transition of CuInS2 from chalcopyrite to wurtzite was realized by adjusting the pH value of reaction solution. The emergence of Cu2S in the condition of higher pH value of reaction solution led to the formation of wurtzite CuInS2. This facile method that controls the phase structure by adjusting the solution pH value could open a new way to synthesize other I-III-VI2 ternary semiconductor compounds.
Efficacy and safety of citrate-based anticoagulation compared to heparin in patients with acute kidney injury requiring continuous renal replacement therapy: a randomized controlled trial
Authors: Stucker Fabien , Ponte Belen , Tataw James , Martin Pierre-Yves , Wozniak Hannah , Pugin Jérome , Saudan Patrick 
Published: February 2015

Abstract
Introduction
A systemic anticoagulation is often required to prevent circuit and filter clotting in ICU patients undergoing continuous renal replacement therapy (CRRT). A regional citrate-based anticoagulation (RCA) does not induce a systemic anticoagulation and prolongs the filter lifespan, but metabolic side-effects have been associated with this therapy. We conducted a randomized controlled trial with patients requiring CRRT to determine whether RCA using a balanced predilution replacement fluid is more effective than heparin in terms of renal replacement delivered dose and safety profile.

Methods
One hundred and three patients with AKI requiring CRRT were included. The patients were randomized to either CRRT with RCA or heparin anticoagulation. Primary endpoints were effective daily delivered RRT dose during the first 3 days of CRRT and filter lifespan. Secondary endpoints were 28-day and 90-day survival and severe metabolic complications and bleeding disorders.

Results
Median CRRT duration was 3.0 (2–6) days. Effective delivered daily RRT doses were 29 ± 3 and 27 ± 5 mL/kg/hr in the RCA and heparin groups, respectively (p = 0.005). Filter lifespans were 49 ± 29 versus 28 ± 23 hrs in the RCA and heparin groups (p = 0.004). Survival rates at 28 and 90 days were 80-74% in the RCA and 74-73% in the heparin group. Electrolytes and acid–base disturbances were uncommon and transient in patients treated with RCA.

Conclusions
These results show that RCA is superior to heparin-based anticoagulation in terms of delivered RRT dose and filter life span and is a safe and feasible method. This does not translate into an improvement in short term survival.

Trial registration
ClinicalTrials.gov NCT01269112. Registered 3rd January 2011.
CopywriteR: DNA copy number detection from off-target sequence data
Authors: Kuilman Thomas , Velds Arno , Kemper Kristel , Ranzani Marco , Bombardelli Lorenzo , Hoogstraat Marlous , Nevedomskaya Ekaterina , Xu Guotai , de Ruiter Julian , Lolkema Martijn P , Ylstra Bauke , Jonkers Jos , Rottenberg Sven , Wessels Lodewyk F , Adams David J , Peeper Daniel S , Krijgsman Oscar 
Published: February 2015

AbstractCurrent methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.
Influence of mesenchymal stem cells on metastasis development in mice in vivo
Authors: Meleshina Aleksandra V , Cherkasova Elena I , Shirmanova Marina V , Klementieva Natalia V , Kiseleva Ekaterina V , Snopova Ludmila В , Prodanets Natalia N , Zagaynova Elena V 
Published: February 2015

Abstract
Introduction
In recent years, mesenchymal stem cells (MSCs) have been demonstrated to play an important role in carcinogenesis. However, the effect of MSCs on tumor and metastasis development and the mechanisms underlying the interaction of cancer and stem cells are not completely understood. This study investigated the effect of MSCs on breast cancer metastasis formation by using the methods of in vivo fluorescence and luminescence imaging.

Methods
MSCs were isolated from bone marrow of normal donors, characterized, and genetically labeled with luciferase (luc2). The effects of MSCs on MDA-MB-231 cancer cell proliferation were evaluated in conditioned medium from MSCs. To generate lung metastases, MDA-MB-231 cells stably expressing red fluorescent protein Turbo FP650 were injected intravenously into nude mice. On day 10 after the cancer cell injection, mice were injected via the tail vein with MSCs-luc2 cells (the MET + MSCs group). Animals that received the injection of MDA-MB-231-Turbo FP650 alone (the MET group) and no injections (the intact control group) served as controls. Fluorescence and bioluminescence imaging was performed for monitoring of the metastasis formation and MSC distribution in the recipient’s body.

Results
We found that the proliferative activity of the cancer cells in the presence of MSC conditioned medium was lower than that of the cells grown in conventional culture medium. The metastasis formation in the MET + MSCs group was delayed in time as compared with the MET group. Macroscopic and histological examination of isolated lungs 8 weeks after cancer cell injection showed that the total number of metastases in animals of the MET + MSCs group was significantly lower. Using bioluminescence imaging in vivo, we found that MSCs-luc2 cells survived in the host animal for at least 7 weeks and re-migrated to the lung 6 to 7 weeks after injection. Immunohistochemical analysis revealed the presence of MSCs-luc2 in metastases and lung tissue.

Conclusions
Long-term in vivo bioluminescence imaging of intravenously injected MSCs-luc2 cells showed distribution of MSCs to the lungs and abdominal organs within the first 2 to 3 weeks and re-migration to the lungs in weeks 6 to 7. It was found that MSCs reduced the proliferative activity of cancer cells in vitro and lung metastasis formation in mice.
RETRACTED ARTICLE: Fixed point theorems for solutions of the stationary Schrödinger equation on cones
Authors: Xue Gaixian , Yuzbasi Eve 
Published: February 2015

AbstractThe main aim of this paper is to study and establish some new coincidence point and common fixed point theorems for solutions of the stationary Schrödinger equation on cones. An interesting application is to investigate the existence and uniqueness for solutions of the Dirichlet problem with respect to the Schrödinger operator on cones and the growth property of them.
Dispersion relation as a channel of plasma turbulence evolution
Authors: Comişel Horia , Narita Yasuhito , Motschmann Uwe 
Published: February 2015

Abstract
We present evidence from ion-scale plasma turbulence simulations that normal-mode waves and sideband waves co-exist when a plasma evolves from wave fields into turbulence. Ion-scale fluctuations represent normal-mode fluctuations such as Bernstein and cyclotron modes, accompanied by sideband waves having moderate frequency mismatch with the normal modes. The evolution process is studied using the method of energy partition and frequency broadening. Wave evolution into turbulence exhibits distinct stages: growth phase of normal modes, saturation, and decay. The saturation time is of the order of 1000 ion gyroperiods, which is delayed at higher values of the plasma parameter beta. We conclude that the dispersion relations play the central role in plasma turbulence evolution, serving as the energy flux channel in the spectral domain.
Prostaglandins produced during class A scavenger receptor-mediated macrophage adhesion differentially regulate cytokine production
Authors: Nikolic Dejan M , Vadali Shanthi , He Beixiang , Ware Jerry , Kelly Thomas , Post Steven R 
Published: February 2015

Abstract
Inflammation is associated with modification of the extracellular environment, changes in cytokine expression, and the accumulation of immune cells. Such modifications create ligands that support SR-A-mediated macrophage adhesion and retention. This may be particularly important in settings, such as atherosclerosis and diabetes, as modified lipoproteins and gluc-collagen are ligands for SR-A. SR-A-mediated adhesion requires the PLA2-dependent generation of AA and its metabolism by 12/15 LOX. In contrast, the inhibition of the COX-dependent conversion of AA to PG had no effect on SR-A-mediated adhesion. In this study, macrophages were isolated from SR-A+/+ and SR-A−/− mice and plated on gluc-collagen to test the hypothesis that COX-derived PGs are produced during SR-A-mediated adhesion and regulate macrophage function. SR-A-mediated binding to gluc-collagen induced a rapid but transient increase in PG production, which required the activation of PLA2 and Src kinase but not PI3K. SR-A+/+ macrophages cultured on gluc-collagen for 24 h secreted a similar amount of TNF-α and 2.5-fold more IL-10 than SR-A−/− macrophages. The inhibition of COX substantially increased TNF-α production but reduced IL-10 levels in SR-A+/+ macrophages. These effects of COX inhibition were reversed by exogenous PGE2 and mimicked by specific antagonism of the EP4 receptor. Thus, in addition to the enhancement of macrophage adhesion, SR-A binding to gluc-collagen stimulates PG production, which in turn, differentially regulates the expression of inflammatory cytokines.
mTOR and metabolic regulation of conventional and regulatory T cells
Authors: Liu Chaohong , Chapman Nicole M , Karmaus Peer W F , Zeng Hu , Chi Hongbo 
Published: February 2015

Abstract
mTOR signaling links bioenergetic and biosynthetic metabolism to immune responses. mTOR is activated by diverse upstream stimuli, including immune signals, growth factors, and nutrients. Recent studies highlight crucial roles of mTOR signaling in immune functions mediated by conventional T cells and Tregs. In this review, we discuss the regulation of mTOR signaling in T cells and the functional impacts of mTOR and metabolic pathways on T cell-mediated immune responses, with a particular focus on the differentiation and function of Tregs.
Neutrophils and inflammatory metabolism in antimicrobial functions of the mucosa
Authors: Campbell Eric L , Colgan Sean P 
Published: February 2015

Abstract
In this mini-review, we will discuss recent findings that implicate neutrophil infiltration and function in establishing a metabolic environment to facilitate efficient pathogen clearance. For decades, neutrophils have been regarded as short lived, nonspecific granulocytes, equipped with toxic antimicrobial factors and a respiratory burst generating ROS. Recent findings demonstrate the importance of HIF signaling in leukocytes and surrounding tissues during inflammation. Here, we will review the potential mechanisms and outcomes of HIF stabilization within the intestinal mucosa.
Functional analysis of NK cell subsets activated by 721.221 and K562 HLA-null cells
Authors: Lisovsky Irene , Isitman Gamze , Bruneau Julie , Bernard Nicole F 
Published: February 2015

Abstract
HLA-null cell lines [721.221 (henceforth, 721) and K562] are often used to study NK cell activation. NK cells are innate immune lymphocytes that express a variety of stochastically expressed inhibitory and activating receptors. Although it is known that 721 and K562 have divergent origins, they have been used interchangeably to stimulate NK cells in many studies. We hypothesized that the differences between 721 and K562 cells may result in differential NK cell-activation patterns. In this report, we assessed all possible combinations of CD107a expression and IFN-γ and CCL4 secretion in total NK and 3DL1+/− NK cell populations induced by these 2 cell lines. 721 activates a significantly higher frequency of NK cells and 3DL1+ NK cells than K562. The NK cell functional subsets that are stimulated to a higher degree by 721 than K562 include those secreting IFN-γ and/or CCL4. On the other hand, the functional subsets that include CD107 expression contribute to a higher proportion of the total NK cell response following stimulation with K562 than 721. These results have implications for the selection of HLA-null cell lines to use as NK cell stimuli in investigations of their role in infectious diseases, cancer, and transplantation.
Neutrophils in host defense: new insights from zebrafish
Authors: Harvie Elizabeth A , Huttenlocher Anna 
Published: February 2015

Abstract
Neutrophils are highly motile phagocytic cells that play a critical role in the immune response to infection. Zebrafish (Danio rerio) are increasingly used to study neutrophil function and host-pathogen interactions. The generation of transgenic zebrafish lines with fluorescently labeled leukocytes has made it possible to visualize the neutrophil response to infection in real time by use of optically transparent zebrafish larvae. In addition, the genetic tractability of zebrafish has allowed for the generation of models of inherited neutrophil disorders. In this review, we discuss several zebrafish models of infectious disease, both in the context of immunocompetent, as well as neutrophil-deficient hosts and how these models have shed light on neutrophil behavior during infection.
Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells
Authors: Joshi Anagha , Pooley Christopher , Freeman Tom C , Lennartsson Andreas , Babina Magda , Schmidl Christian , Geijtenbeek Teunis , Michoel Tom , Severin Jessica , Itoh Masayoshi , Lassmann Timo , Kawaji Hideya , Hayashizaki Yoshihide , Carninci Piero , Forrest Alistair R R , Rehli Michael , Hume David A 
Published: February 2015

Abstract
The generation of myeloid cells from their progenitors is regulated at the level of transcription by combinatorial control of key transcription factors influencing cell-fate choice. To unravel the global dynamics of this process at the transcript level, we generated transcription profiles for 91 human cell types of myeloid origin by use of CAGE profiling. The CAGE sequencing of these samples has allowed us to investigate diverse aspects of transcription control during myelopoiesis, such as identification of novel transcription factors, miRNAs, and noncoding RNAs specific to the myeloid lineage. We further reconstructed a transcription regulatory network by clustering coexpressed transcripts and associating them with enriched cis-regulatory motifs. With the use of the bidirectional expression as a proxy for enhancers, we predicted over 2000 novel enhancers, including an enhancer 38 kb downstream of IRF8 and an intronic enhancer in the KIT gene locus. Finally, we highlighted relevance of these data to dissect transcription dynamics during progressive maturation of granulocyte precursors. A multifaceted analysis of the myeloid transcriptome is made available (http://www.myeloidome.roslin.ed.ac.uk). This high-quality dataset provides a powerful resource to study transcriptional regulation during myelopoiesis and to infer the likely functions of unannotated genes in human innate immunity.
Five-Year Survival Rates for Treatment-Naive Patients With Advanced Melanoma Who Received Ipilimumab Plus Dacarbazine in a Phase III Trial
Authors: Maio Michele , Grob Jean-Jacques , Aamdal Steinar , Bondarenko Igor , Robert Caroline , Thomas Luc , Garbe Claus , Chiarion-Sileni Vanna , Testori Alessandro , Chen Tai-Tsang , Tschaika Marina , Wolchok Jedd D. 
Published: February 2015

Purpose There is evidence from nonrandomized studies that a proportion of ipilimumab-treated patients with advanced melanoma experience long-term survival. To demonstrate a long-term survival benefit with ipilimumab, we evaluated the 5-year survival rates of patients treated in a randomized, controlled phase III trial. Patients and Methods A milestone survival analysis was conducted to capture the 5-year survival rate of treatment-naive patients with advanced melanoma who received ipilimumab in a phase III trial. Patients were randomly assigned 1:1 to receive ipilimumab at 10 mg/kg plus dacarbazine (n = 250) or placebo plus dacarbazine (n = 252) at weeks 1, 4, 7, and 10 followed by dacarbazine alone every 3 weeks through week 22. Eligible patients could receive maintenance ipilimumab or placebo every 12 weeks beginning at week 24. A safety analysis was conducted on patients who survived at least 5 years and continued to receive ipilimumab as maintenance therapy. Results The 5-year survival rate was 18.2% (95% CI, 13.6% to 23.4%) for patients treated with ipilimumab plus dacarbazine versus 8.8% (95% CI, 5.7% to 12.8%) for patients treated with placebo plus dacarbazine (P = .002). A plateau in the survival curve began at approximately 3 years. In patients who survived at least 5 years and continued to receive ipilimumab, grade 3 or 4 immune-related adverse events were observed exclusively in the skin. Conclusion The additional survival benefit of ipilimumab plus dacarbazine is maintained with twice as many patients alive at 5 years compared with those who initially received placebo plus dacarbazine. These results demonstrate a durable survival benefit with ipilimumab in advanced melanoma.
Psychosocial Telephone Counseling for Survivors of Cervical Cancer: Results of a Randomized Biobehavioral Trial
Authors: Wenzel Lari , Osann Kathryn , Hsieh Susie , Tucker Jo A. , Monk Bradley J. , Nelson Edward L. 
Published: February 2015

Purpose Survivors of cervical cancer experience quality-of-life (QOL) disruptions that persist years after treatment. This study examines the effect of a psychosocial telephone counseling (PTC) intervention on QOL domains and associations with biomarkers. Patients and Methods We conducted a randomized clinical trial in survivors of cervical cancer, who were ≥ 9 and less than 30 months from diagnosis (n = 204), to compare PTC to usual care (UC). PTC included five weekly sessions and a 1-month booster. Patient-reported outcomes (PROs) and biospecimens were collected at baseline and 4 and 9 months after enrollment. Changes in PROs over time and associations with longitudinal change in cytokines as categorical variables were analyzed using multivariable analysis of variance for repeated measures. Results Participant mean age was 43 years; 40% of women were Hispanic, and 51% were non-Hispanic white. Adjusting for age and baseline scores, participants receiving PTC had significantly improved depression and improved gynecologic and cancer-specific concerns at 4 months compared with UC participants (all P < .05); significant differences in gynecologic and cancer-specific concerns (P < .05) were sustained at 9 months. Longitudinal change in overall QOL and anxiety did not reach statistical significance. Participants with decreasing interleukin (IL) -4, IL-5, IL-10, and IL-13 had significantly greater improvement in QOL than those with increasing cytokine levels. Conclusion This trial confirms that PTC benefits mood and QOL cancer-specific and gynecologic concerns for a multiethnic underserved population of survivors of cancer. The improvement in PROs with decreases in T-helper type 2 and counter-regulatory cytokines supports a potential biobehavioral pathway relevant to cancer survivorship.
Prognostic Significance of NPM1 Mutations in the Absence of FLT3–Internal Tandem Duplication in Older Patients With Acute Myeloid Leukemia: A SWOG and UK National Cancer Research Institute/Medical Research Council Report
Authors: Ostronoff Fabiana , Othus Megan , Lazenby Michelle , Estey Elihu , Appelbaum Frederick R. , Evans Anna , Godwin John , Gilkes Amanda , Kopecky Kenneth J. , Burnett Alan , List Alan F. , Fang Min , Oehler Vivian G. , Petersdorf Stephen H. , Pogosova-Agadjanyan Era L. , Radich Jerald P. , Willman Cheryl L. , Meshinchi Soheil , Stirewalt Derek L. 
Published: February 2015

Purpose Younger patients with acute myeloid leukemia (AML) harboring NPM1 mutations without FLT3–internal tandem duplications (ITDs; NPM1-positive/FLT3-ITD–negative genotype) are classified as better risk; however, it remains uncertain whether this favorable classification can be applied to older patients with AML with this genotype. Therefore, we examined the impact of age on the prognostic significance of NPM1-positive/FLT3-ITD–negative status in older patients with AML. Patients and Methods Patients with AML age ≥ 55 years treated with intensive chemotherapy as part of Southwest Oncology Gorup (SWOG) and UK National Cancer Research Institute/Medical Research Council (NCRI/MRC) trials were evaluated. A comprehensive analysis first examined 156 patients treated in SWOG trials. Validation analyses then examined 1,258 patients treated in MRC/NCRI trials. Univariable and multivariable analyses were used to determine the impact of age on the prognostic significance of NPM1 mutations, FLT3-ITDs, and the NPM1-positive/FLT3-ITD–negative genotype. Results Patients with AML age 55 to 65 years with NPM1-positive/FLT3-ITD–negative genotype treated in SWOG trials had a significantly improved 2-year overall survival (OS) as compared with those without this genotype (70% v 32%; P < .001). Moreover, patients age 55 to 65 years with NPM1-positive/FLT3-ITD–negative genotype had a significantly improved 2-year OS as compared with those age > 65 years with this genotype (70% v 27%; P < .001); any potential survival benefit of this genotype in patients age > 65 years was marginal (27% v 16%; P = .33). In multivariable analysis, NPM1-positive/FLT3-ITD–negative genotype remained independently associated with an improved OS in patients age 55 to 65 years (P = .002) but not in those age > 65 years (P = .82). These results were confirmed in validation analyses examining the NCRI/MRC patients. Conclusion NPM1-positive/FLT3-ITD–negative genotype remains a relatively favorable prognostic factor for patients with AML age 55 to 65 years but not in those age > 65 years.