bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API
Authors: Wilson Shane , Fitzsimons Michael , Ferguson Martin , Heath Allison , Jensen Mark , Miller Josh , Murphy Mark W. , Porter James , Sahni Himanso , Staudt Louis , Tang Yajing , Wang Zhining , Yu Christine , Zhang Junjun , Ferretti Vincent , Grossman Robert L. 
Published: November 2017

Abstract
The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage and computing infrastructure and commonly used web services, software applications, and tools to create a secure, interoperable, and extensible resource for researchers. The GDC is (i) a data repository for downloading data that have been submitted to it, and also a system that (ii) applies a common set of bioinformatics pipelines to submitted data; (iii) reanalyzes existing data when new pipelines are developed; and (iv) allows users to build their own applications and systems that interoperate with the GDC using the GDC Application Programming Interface (API). We describe the GDC API and how it has been used both by the GDC itself and by third parties. Cancer Res; 77(21); e15–18. ©2017 AACR.
Interleukin-27 Exerts Its Antitumor Effects by Promoting Differentiation of Hematopoietic Stem Cells to M1 Macrophages
Authors: Chiba Yukino , Mizoguchi Izuru , Furusawa Junichi , Hasegawa Hideaki , Ohashi Mio , Xu Mingli , Owaki Toshiyuki , Yoshimoto Takayuki 
Published: November 2017

Abstract
The interleukin IL27 promotes expansion and differentiation of hematopoietic stem cells into myeloid progenitor cells. Many tumor-infiltrating myeloid cells exert immunosuppressive effects, but we hypothesized that the myeloid cells induced by IL27 would have antitumor activity. In this study, we corroborated this hypothesis as investigated in two distinct mouse transplantable tumor models. Malignant mouse cells engineered to express IL27 exhibited reduced tumor growth in vivo. Correlated with this effect was a significant increase in the number of tumor-infiltrating CD11b+ myeloid cells exhibiting a reduced immunosuppressive activity. Notably, these CD11b+ cells were characterized by an activated M1 macrophage phenotype, on the basis of increased expression of inducible nitric oxide synthase and other M1 biomarkers. In vivo depletion of these cells by administering anti–Gr-1 eradicated the antitumor effects of IL27. When admixed with parental tumors, CD11b+ cells inhibited tumor growth and directly killed the tumor in a nitric oxide-dependent manner. Mechanistically, IL27 expanded Lineage−Sca-1+c-Kit+ cells in bone marrow. Transplant experiments in Ly5.1/5.2 congenic mice revealed that IL27 directly acted on these cells and promoted their differentiation into M1 macrophages, which mobilized into tumors. Overall, our results illustrated how IL27 exerts antitumor activity by enhancing the generation of myeloid progenitor cells that can differentiate into antitumorigenic M1 macrophages.
Significance: These findings show how the interleukin IL27 exerts potent antitumor activity by enhancing the generation of myeloid progenitor cells that can differentiate into antitumorigenic M1 macrophages.Cancer Res; 78(1); 182–94. ©2017 AACR.
Truth-Conditions and Religious Language: Introduction
Authors: Gardiner Mark Q. 
Published: November 2017

AbstractIntroduction to the following set of papers: Lars Albinus, “A grammar of religious ‘truth’—pragmatic considerations on the nature of religious truth”; Terry F. Godlove, “Truth, meaning, and the study of religion”; G. Scott Davis, “Semantics and the study of religion”; Mark Q. Gardiner, “Why truth matters for the study of religion; a defense of a truth-conditional semantics”; Gabriel Levy, “Can fictional superhuman agents have mental states?”.
CO2 clearance by membrane lungs
Authors: Sun Liqun , Kaesler Andreas , Fernando Piyumindri , Thompson Alex J. , Toomasian John M. , Bartlett Robert H 
Published: November 2017

Introduction: Commercial membrane lungs are designed to transfer a specific amount of oxygen per unit of venous blood flow. Membrane lungs are much more efficient at removing CO2 than adding oxygen, but the range of CO2 transfer is rarely reported. Methods: Commercial membrane lungs were studied with the goal of evaluating CO2 removal capacity. CO2 removal was measured in 4 commercial membrane lungs under standardized conditions. Conclusion: CO2 clearance can be greater than 4 times that of oxygen at a given blood flow when the gas to blood flow ratio is elevated to 4:1 or 8:1. The CO2 clearance was less dependent on surface area and configuration than oxygen transfer. Any ECMO system can be used for selective CO2 removal.
Confusing procedures with process when appraising the impact of cognitive bias modification on emotional vulnerability
Authors: Grafton Ben , MacLeod Colin , Rudaizky Daniel , Holmes Emily A. , Salemink Elske , Fox Elaine , Notebaert Lies 
Published: November 2017

SummaryIf meta-analysis is to provide valuable answers, then it is critical to ensure clarity about the questions being asked. Here, we distinguish two important questions concerning cognitive bias modification research that are not differentiated in the meta-analysis recently published by Cristea et al (2015) in this journal: (1) do the varying procedures that investigators have employed with the intention of modifying cognitive bias, on average, significantly impact emotional vulnerability?; and (2) does the process of successfully modifying cognitive bias, on average, significantly impact emotional vulnerability? We reanalyse the data from Cristea et al to address this latter question. Our new analyses demonstrate that successfully modifying cognitive bias does significantly alter emotional vulnerability. We revisit Cristea et al's conclusions in light of these findings.
Suicide prevention in low- and middle-income countries: part perceptions, partial solutions
Authors: Jacob K. S. 
Published: November 2017

SummarySuicide, a common cause of death in many low- and middle-income countries, has often been viewed through a medical/psychiatric lens. Such perspectives medicalise social and personal distress and suggest individual and medication-based treatments. This editorial argues for the need to examine suicide from a public health perspective and suggests the need for population-based social and economic interventions.
Electrooxidative Copolymerization of 3,4-Ethylenedioxithiophene and Benzene from a Mixture of Each Monomer
Authors: Tanaka Eisaku , Tateno Hiroyuki , Matsumura Yoshimasa , Nakabayashi Koji , Kawamura Izuru , Atobe Mahito 
Published: November 2017

Abstract
Electrooxidative copolymerization of 3,4-ethylenedioxithiophene (EDOT) and benzene from a mixture of the monomers with concentrations of 5 mM EDOT and 5 M benzene produced copolymer films on an anode surface. The formation of copolymer films and characterization of their electrochemical properties was confirmed using Fourier transform infrared (FTIR) spectroscopy, ultraviolet–visible absorption (UV–vis) spectroscopy, energy dispersive X-ray (EDX) spectroscopy, cyclic voltammetry (CV), and solid-state carbon-13 nuclear magnetic resonance (13C NMR) spectroscopy measurements. Furthermore, the copolymerization ratio could be controlled by selection of the oxidation potential applied for copolymerization.
Using data from a multi-hospital clinical network to explore prevalence of pediatric rickets in Kenya
Authors: Karuri Stella W. , Murithi Maureen K. , Irimu Grace , English Mike ,   Clinical Information Network authors
Published: November 2017

Background: Nutritional rickets is a public health concern in developing countries despite tropical climates and a re-emerging issue in developed countries. In this study, we reviewed pediatric admission data from the Clinical Information Network (CIN) to help determine hospital and region based prevalence of rickets in three regions of Kenya (Central Kenya, Western Kenya and Nairobi County). We also examine the association of rickets with other diagnosis, such as malnutrition and pneumonia, and study the effect of rickets on regional hospital stays. Methods: We analyzed discharge records for children aged 1 month to 5 years from county (formerly district) hospitals in the CIN, with admissions from February 1st 2014 to February 28th 2015. The strength of the association between rickets and key demographic factors, as well as with malnutrition and pneumonia, was assessed using odds ratios. The Fisher exact test was used to test the significance of the estimated odd ratios. Kaplan-Meier curves were used to analyze length of hospital stays. Results: There was a marked difference in prevalence across the three regions, with Nairobi having the highest number of cases of rickets at a proportion of 4.01%, followed by Central Region at 0.92%. Out of 9756 admissions in the Western Region, there was only one diagnosis of rickets. Malnutrition was associated with rickets; this association varied regionally. Pneumonia was found to be associated with rickets in Central Kenya. Children diagnosed with rickets had longer hospital stays, even when cases of malnutrition and pneumonia were excluded in the analysis. Conclusion: There was marked regional variation in hospital based prevalence of rickets, but in some regions it is a common clinical diagnosis suggesting the need for targeted public health interventions. Factors such as maternal and child nutrition, urbanization and cultural practices might explain these differences.
Space Reduction for a Class of Multidimensional Markov Chains: A Summary and Some Applications
Authors: He Qi-Ming , Alfa Attahiru Sule 
Published: November 2017

In this paper, we present examples of a class of Markov chains that occur frequently, but whose associated matrices are a challenge to construct efficiently. These are Markov chains that arise as a result of several identical Markov chains running in parallel. Specifically for the cases considered, both the infinitesimal generator matrix for the continuous case, and more so the transition probability matrix for the discrete equivalent, are complex to construct effectively and efficiently. We summarize the algorithms for constructing the associated matrices and present examples of applications, ranging from special queueing problems to reliability issues and order statistics. MATLAB subroutines are provided in an online supplement for the implementation of the algorithms. The online supplement is available at https://doi.org/10.1287/ijoc.2017.0759 .
Computing the Maximum Volume Inscribed Ellipsoid of a Polytopic Projection
Authors: Zhen Jianzhe , den Hertog Dick 
Published: November 2017

We introduce a novel scheme based on a blending of Fourier-Motzkin elimination (FME) and adjustable robust optimization techniques to compute the maximum volume inscribed ellipsoid (MVE) in a polytopic projection. It is well-known that deriving an explicit description of a projected polytope is NP-hard. Our approach does not require an explicit description of the projection, and can easily be generalized to find a maximally sized convex body of a polytopic projection. Our obtained MVE is an inner approximation of the projected polytope, and its center is a centralized relative interior point of the projection. Since FME may produce many redundant constraints, we apply an LP-based procedure to keep the description of the projected polytopes at its minimal size. Furthermore, we propose an upper bounding scheme to evaluate the quality of the inner approximations. We test our approach on a simple polytope and a color tube design problem, and observe that as more auxiliary variables are eliminated, our inner approximations and upper bounds converge to optimal solutions. The online supplement is available at https://doi.org/10.1287/ijoc.2017.0763 .
β-11-Keto-boswellic acid derived amides: synthesis and cytotoxicity
Authors: Wolfram Ratna Kancana , Barthel-Niesen Anja , Schäfer Renate , Heller Lucie , Al-Harrasi Ahmed , Csuk René 
Published: November 2017

The aim of this study was to prepare 11-keto-β-boswellic acid derivatives modified at C-24 and to evaluate their in vitro cytotoxicity. Acetyl-11-keto-β-boswellic acid (AKBA) was isolated from frankincense and transformed into 11-keto-β-boswellic acid (KBA). Both compounds served as starting materials for the synthesis of several amides or hydrazides. The derivatives were fully characterized, and their cytotoxicity was evaluated in vitro using sulforhodamine B (SRB) assays employing two human tumor cell lines (A2780 and MCF7) as well as nonmalignant mouse fibroblasts (NIH 3T3). Nearly all of the compounds were more cytotoxic than their parent compounds. The highest cytotoxicity was observed for (3 α, 4 β) 3-acetyloxy-N-(3- aminopropyl)-11-oxo-urs-12-en-24-amide (15) and (3 α, 4 β) 3-acetyloxy-N-[4-(3-aminopropyl)piperazin-1-yl]- propyl-11-oxo-urs-12-en-24-amide (16) and the ovarian carcinoma cell line A2780. These compounds showed EC50 = 1.0-1.7 µM while being significantly less toxic for the mouse fibroblasts NIH 3T3 (EC50 = 9.3-16.3µM). Thus, compounds 15 and 16 have good antitumor effects and may serve as starting points for developing potential and selective antitumor agents
Pengaruh Konsentrasi Doping Nitrogen (N) pada Material Fotokatalis Seng Oksida (ZnO) Terhadap Degradasi Limbah Zat Pewarna Tekstil
Authors: Sutanto Heri , Hidayanto Eko , Irwanto Muhammad , Romadhon Agus , Wahyono Yoyon 
Published: November 2017

Abstract THE EFFECT OF NITROGEN (N) DOPING IN PHOTOCATALYST MATERIAL OF ZINC OXIDE (ZnO) ON DEGRADATION OF WASTE OF TEXTILES DYE. The textile industry produces 50% of the wasted dye and liquid waste which can cause damage to the river ecosystem. The results of synthesis and characterization of N-ZnO photocatalysts and its ability to degrade waste water of batik dye by identifying of the effect of nitrogen (N) doping on ZnO were reported in this paper. Synthesis of N-ZnO material was performed using sol-gel method at room temperature, then the solution was deposited on a glass substrate at 450oC with a spray coating method. N-ZnO was prepared by N doping with different percentages of 0, 3, 5, 7 and 9%, respectively. Degradation of dye waste was performed under UV radiation for 12 hours. The synthesis results show that thin layers have wurtzite polycrystalline structure with dominant orientation field (002). The addition of N doping causes the value of the energy band gap of ZnO to be smaller. The test results of photocatalysts show that the addition of doping N on ZnO does not have a significant influence on the percentage of degradation waste batik dye under UV light. The best ability of N-ZnO photocatalytic was obtained in 5% of N doping, and the degradation percentage, COD and BOD were 11.83%, 6.12% and 6.40% respectively. Keywords: degradation; N doped; ZnO photocatalyst; batik dye waste Abstrak Industri tekstil menghasilkan 50% zat warna yang terbuang dan menjadi limbah dalam bentuk cair yang dapat mengakibatkan rusaknya ekosistem sungai. Pada paper ini dilaporkan hasil sintesis dan karakterisasi fotokatalis N-ZnO serta uji kemampuan fotokatalitiknya dalam mendegradasi limbah cair zat pewarna batik dengan mengidentifikasi pengaruh doping Nitrogen (N) pada ZnO. Sintesis material N-ZnO menggunakan metode sol-gel pada temperatur kamar, kemudian larutan dideposisi di atas substrat kaca pada temperatur 450oC dengan metode spray coating. Material N-ZnO dibuat dengan persentase doping N yang berbeda yaitu 0, 3, 5, 7, dan 9%. Degradasi limbah zat warna dilakukan dibawah radiasi sinar UV selama 12 jam. Hasil sintesis menunjukkan bahwa lapisan tipis mempunyai struktur polikristal wurtzite dengan bidang orientasi dominan (002). Penambahan doping N secara umum menyebabkan terjadinya pengecilan nilai celah pita energi ZnO. Hasil uji fotokatalitik menunjukkan bahwa penambahan doping N pada ZnO tidak memberikan pengaruh yang signifikan terhadap persentase degradasi limbah cair pewarna batik dibawah cahaya UV. Diperoleh kemampuan uji fotokatalitik N-ZnO terbaik pada doping N sebesar 5% dengan nilai % degradasi sebesar 11,83%, COD 6,12% dan BOD 6,40%. Kata kunci: degradasi; doping N; fotokatalis ZnO; limbah pewarna batik .
Primary adrenal insufficiency in adult population: a Portuguese Multicentre Study by the Adrenal Tumours Study Group
Authors: Ferreira Lia , Silva João , Garrido Susana , Bello Carlos , Oliveira Diana , Simões Hélder , Paiva Isabel , Guimarães Joana , Ferreira Marta , Pereira Teresa , Bettencourt-Silva Rita , Martins Ana Filipa , Silva Tiago , Fernandes Vera , Pereira Maria Lopes , _ _ 
Published: November 2017

Introduction
Primary adrenal insufficiency (PAI) is a rare but severe and potentially life-threatening condition. No previous studies have characterized Portuguese patients with PAI.

Aims
To characterize the clinical presentation, diagnostic workup, treatment and follow‐up of Portuguese patients with confirmed PAI.

Methods
This multicentre retrospective study examined PAI patients in 12 Portuguese hospitals.

Results
We investigated 278 patients with PAI (55.8% were females), with a mean age of 33.6 ± 19.3 years at diagnosis. The most frequent presenting clinical features were asthenia (60.1%), mucocutaneous hyperpigmentation (55.0%) and weight loss (43.2%); 29.1% of the patients presented with adrenal crisis. Diagnosis was established by high plasma ACTH and low serum cortisol in most patients (43.9%). The most common aetiology of PAI was autoimmune adrenalitis (61.0%). There were 38 idiopathic cases. Autoimmune comorbidities were found in 70% of the patients, the most frequent being autoimmune thyroiditis (60.7%) and type 1 diabetes mellitus (17.3%). Seventy-nine percent were treated with hydrocortisone (mean dose 26.3 ± 8.3 mg/day) mostly in three (57.5%) or two (37.4%) daily doses. The remaining patients were treated with prednisolone (10.1%), dexamethasone (6.2%) and methylprednisolone (0.7%); 66.2% were also on fludrocortisone (median dose of 100 µg/day). Since diagnosis, 33.5% of patients were hospitalized for disease decompensation. In the last appointment, 17.2% of patients had complaints (7.6% asthenia and 6.5% depression) and 9.7% had electrolyte disturbances.

Conclusion
This is the first multicentre Portuguese study regarding PAI. The results emphasize the need for standardization in diagnostic tests and etiological investigation and provide a framework for improving treatment.
Epidemiology of Pediatric Zika Virus Infections
Authors: Griffin Isabel , Zhang Guoyan , Fernandez Danielle , Cordero Christina , Logue Teresa , White Stephen L. , Llau Anthoni , Thomas Lakisha , Moore Emily , Noya-Chaveco Pedro , Etienne Marie , Rojas Mercedes , Goldberg Cynthia , Rodriguez Genevie , Mejia-Echeverry Alvaro , Rico Edhelene , Gillis Leah D. , Cone Marshall , Jean Reynald , Rivera Lillian 
Published: November 2017

BACKGROUND AND OBJECTIVE:
In July 2016, local transmission of Zika virus (ZIKV) was announced in Miami-Dade County, Florida. In this report, we describe the epidemiology of pediatric ZIKV infections in locally acquired and travel-associated cases.

METHODS:
All children aged 1 to 17 years tested for ZIKV between October 1, 2015, and March 29, 2017, were included. SAS 9.4 was used to analyze age, sex, race and/or ethnicity, origin of exposure, onset date, affiliation with a household cluster, clinical symptoms, hospitalizations, viremia, viruria, and antibody detection in specimens.

RESULTS:
Among 478 confirmed ZIKV cases in Miami-Dade County, 33 (6.9%) occurred in children (1–17 years). Twenty-seven (82.3%) cases were travel-associated. The median age of a pediatric Zika case patient was 11 years. Seventeen (51.5%) case patients were boys, and 23 (69.9%) were Hispanic. Among 31 symptomatic cases, all reported having rash, 25 (80.6%) reported fever, 9 (29.0%) reported conjunctivitis, and 7 (22.6%) reported arthralgia. Sixteen (48.5%) cases reported 2 of 4 and 8 (24.2%) reported 3 of 4 main symptoms.

CONCLUSIONS:
This report found that the majority of children identified during the 2016 ZIKV outbreak only presented with 2 of the 4 main symptoms. In addition, pediatric ZIKV cases were frequently associated with symptomatic household members.
Does Oxidative Stress Change During Orthotopic Liver Transplantation?
Authors: Tsikas Dimitrios 
Published: November 2017

In clinical ischemia/reperfusion injury, damage resulting from oxidative and nitrosative stress is generally considered crucial for graft functioning. Yet, there is increasing evidence that modern clinical transplantation including orthotopic liver transplantation (OLT) is not associated with elevation of oxidative and nitrosative stress upon organ reoxygenation. We measured two currently used biomarkers of oxidative stress, i.e., 15(S)-8-iso-prostaglandin F2a (15(S)-8-iso-PGF2a) and cis-epoxyoctadecanoic acid (cis-EpOA), in human plasma during the entire time duration of OLT in eight patients suffering from end-stage liver disease. No considerable concentration changes of 15(S)-8-iso-PGF2a and cis-EpOA were observed, indicating lack of oxidative stress. Previously, we found in the same patients that nitrosative stress, measured as 3-nitrotyrosine and 3-nitrotyrosinoalbumin. Yet, as 15(S)-8-iso-PGF2a, cis-EpOA and 3-nitrotyrosine are produced both by chemical and enzymatic reactions, the current concepts of oxidative and nitrosative stress require reconsideration.
Atributos físicos do neossolo regolítico distrófico sob pastagem submetido à colheita mecanizada da forragem e pastejo animal
Authors: Nascimento V. N. , Almeida G. L. P. , Batista P. H. D. , Coutinho A. S. 
Published: November 2017

O pastejo de bovinos e a utilização de máquinas em várias operações de preparo, semeadura, tratos culturais, colheita, entre outros, nos solos brasileiros tem sido apontada como a principal causa da compactação. Esse efeito reduz o crescimento e o desenvolvimento radicular, aumenta a perda de nitrogênio por desnitrificação e a erosão do solo pela menor infiltração de água. Diante disso, objetivou-se determinar e avaliar os atributos físicos e a velocidade de infiltração básica de água em um Neossolo Regolítico sob pastagem com diferentes formas de manejo (área sob pastejo extensivo e colheita mecanizada de forragem). O estudo foi conduzido na Fazenda Roçadinho, município de Capoeiras, Agreste de Pernambuco, sob pastagem com capim Búffel (Cenchrus ciliares L.) em pastejo contínuo de bovinos, com lotação média de 2 unidades animais (vacas leiteiras com peso vivo médio de 450 kg), e sob cultivo da mesma forrageira, ambos estabelecidos há mais de 5 anos, com colheita mecanizada da forragem, com a colhedora acoplada ao reboque do trator e com engate para carreta. O delineamento experimental utilizado foi inteiramente casualizado, aplicando-se o teste F a 5% de significância. O pastejo contínuo ocasionou maior resistência à penetração e densidade e menor porosidade do solo em comparação à área onde é realizada a colheita mecanizada de forragem, assim como uma menor velocidade de
infiltração básica do solo. O pisoteio animal causa maior compactação do solo quando comparado à colheita mecanizada de forragem, portanto, a área de pastejo extensivo apresenta maior resistência à penetração e densidade, e obtém menor porosidade total e velocidade de infiltração da água na camada superficial do solo.