bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progression Risk Stratification of Asymptomatic Waldenström Macroglobulinemia
Authors: Bustoros Mark , Sklavenitis-Pistofidis Romanos , Kapoor Prashant , Liu Chia-Jen , Kastritis Efstathios , Zanwar Saurabh , Fell Geoffrey , Abeykoon Jithma P. , Hornburg Kalvis , Neuse Carl Jannes , Marinac Catherine R. , Liu David , Soiffer Jenny , Gavriatopoulou Maria , Boehner Cody , Cappuccio Joseph M. , Dumke Henry , Reyes Kaitlen , Soiffer Robert J. , Kyle Robert A. , Treon Steven P. , Castillo Jorge J. , Dimopoulos Meletios A. , Ansell Stephen M. , Trippa Lorenzo , Ghobrial Irene M. 
Published: April 2019

BACKGROUND Waldenström macroglobulinemia (WM) is preceded by asymptomatic WM (AWM), for which the risk of progression to overt disease is not well defined. METHODS We studied 439 patients with AWM, who were diagnosed and observed at Dana-Farber Cancer Institute between 1992 and 2014. RESULTS During the 23-year study period, with a median follow-up of 7.8 years, 317 patients progressed to symptomatic WM (72%). Immunoglobulin M 4,500 mg/dL or greater, bone marrow lymphoplasmacytic infiltration 70% or greater, β2-microglobulin 4.0 mg/dL or greater, and albumin 3.5 g/dL or less were all identified as independent predictors of disease progression. To assess progression risk in patients with AWM, we trained and cross-validated a proportional hazards model using bone marrow infiltration, immunoglobulin M, albumin, and beta-2 microglobulin values as continuous measures. The model divided the cohort into three distinct risk groups: a high-risk group with a median time to progression (TTP) of 1.8 years, an intermediate-risk group with a median TTP of 4.8 years, and a low-risk group with a median TTP of 9.3 years. We validated this model in two external cohorts, demonstrating robustness and generalizability. For clinical applicability, we made the model available as a Web page application ( www.awmrisk.com ). By combining two cohorts, we were powered to identify wild type MYD88 as an independent predictor of progression (hazard ratio, 2.7). CONCLUSION This classification system is positioned to inform patient monitoring and care and, for the first time to our knowledge, to identify patients with high-risk AWM who may need closer follow-up or benefit from early intervention.
Cyclo-oxygenase-2 expression is associated with mean standardised uptake value on 18F-Fluorodeoxyglucose positron emission tomography in oesophageal adenocarcinoma
Authors: Foley Kieran G , Christian Adam , Peaker James , Marshall Christopher , Spezi Emiliano , Kynaston Howard , Roberts Ashley 
Published: April 2019

Objectives:
This pilot study investigated the association of four PET image features and cyclo-oxygenase-2 (COX-2) expression in patients with oesophageal adenocarcinoma. The prognostic significance of these biomarkers was also assessed.

Methods:
50 consecutive patients [median age = 68 (range 47 – 84), males = 45) with oesophageal adenocarcinoma had PET/CT staging between January 2011 and July 2015. The maximum and mean standardised uptake values (SUVmax and SUVmean), metabolic tumour volume (MTV) and tumour lesion glycolysis (TLG) were calculated from the primary tumour. Their association with COX-2 status was assessed using Mann-Whitney U tests. Kaplan-Meier and Cox regression analysis tested their prognostic significance. A p-value &lt; 0.05 was considered statistically significant.

Results:
32 tumours (64.0%) were COX-2 positive. There was a significant association between SUVmean and COX-2 status (p = 0.019). TLG (hazard ratio (HR) 1.001, 95 % confidence intervals (CI) 1.000 – 1.002, p = 0.018) was significantly associated with overall survival on multivariable analysis.

Conclusions:
This study investigated the association between PET image features and COX-2 expression in oesophageal adenocarcinoma. The preliminary results signal that a combination of TLG (calculated as product of MTV and SUVmean) and COX-2 status may be a strong and clinically important prognostic biomarker. Our research group are planning a prospective, multi-centre study to validate these findings.

Advances in knowledge:
Mean standardised uptake value (SUVmean) on PET imaging is associated with COX-2 expression in oesophageal adenocarcinoma.
MSF: Modulated Sub-graph Finder
Authors: Farman Mariam R. , Hofacker Ivo L. , Amman Fabian 
Published: April 2019

High throughput techniques such as RNA-seq or microarray analysis have proven to be invaluable for the characterizing of global transcriptional gene activity changes due to external stimuli or diseases. Differential gene expression analysis (DGEA) is the first step in the course of data interpretation, typically producing lists of dozens to thousands of differentially expressed genes. To further guide the interpretation of these lists, different pathway analysis approaches have been developed. These tools typically rely on the classification of genes into sets of genes, such as pathways, based on the interactions between the genes and their function in a common biological process. Regardless of technical differences, these methods do not properly account for cross talk between different pathways and most of the methods rely on binary separation into differentially expressed gene and unaffected genes based on an arbitrarily set p-value cut-off. To overcome this limitation, we developed a novel approach to identify concertedly modulated sub-graphs in the global cell signaling network, based on the DGEA results of all genes tested. To this end, expression patterns of genes are integrated according to the topology of their interactions and allow potentially to read the flow of information and identify the effectors. The described software, named Modulated Sub-graph Finder (MSF) is freely available at https://github.com/Modulated-Subgraph-Finder/MSF.
Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae)
Authors: Kral Leos G. , Watson Sara 
Published: April 2019

Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.
Patient treatment pathways of multidrug-resistant tuberculosis cases in coastal South India: Road to a drug resistant tuberculosis center
Authors: Rathi Priya , Shringarpure Kalpita , Unnikrishnan Bhaskaran , Pandey Abhinav , Nair Abhirami 
Published: April 2019

Background: Delays in initiating multidrug-resistant tuberculosis (MDR TB) treatment adds risk to individual patients and the community due to disease progression, and on-going transmission. The Government of India offers free TB diagnosis and treatment, however many presumptive MDR TB patients wander within the Indian healthcare system and delay accessing the programme. To better improve access to care, it is imperative to understand the treatment pathways taken by MDR TB patients. We aimed to describe the diagnostic and treatment pathway taken by presumptive MDR TB patients registered in the Programmatic Management Drug-resistant TB Program (PMDT). Methods: We conducted a cross-sectional study of all patients registered during August 2016 – April 2017 at one PMDT center of a district in Karnataka, India. A semi-standardized questionnaire collected the number, type (private vs public sector), and dates of healthcare facilities (HCFs) visits prior to the initiation of MDR TB treatment. Delays were the number of days, expressed in medians and interquartile range (IQR), from the date of onset of illness until the date of initiation of MDR TB treatment. Results: We found that patients preferred private HCFs; however, due to lack of treatment and unaffordability they shifted to public HCFs. Median delay to register under the program was more in private HCFs (180days) in comparison with public HCFs (120 days). We also found that the diagnosis of MDR among presumptive MDR cases (detection rates) were much higher (80%) in public HCFs. Conclusion: Awareness regarding the availability of free standard diagnosis and appropriate treatment under the TB program should be increased in the general population and private practitioners. The government should involve private HCFs to provide standard diagnostics and treatment to the patients seeking a private facility.
Determinants of knowledge, attitude and practice in patients with both type 2 diabetes and chronic kidney disease in Fiji
Authors: Zibran Mohammed Alvis , Mohammadnezhad Masoud 
Published: April 2019

Background:In Fiji, Type 2 diabetes mellitus (T2DM) and Chronic kidney disease (CKD) are amongst the top four causes of premature mortality, disability and death. This study aims to identify the determinants of knowledge, attitude and practice (KAP) in T2DM patients with CKD in Fiji in 2018.Methods:A cross-sectional study was conducted at Sigatoka Sub-divisional Hospital (SSH) in Fiji in July-August, 2018 using a self-structured questionnaire to test KAP of 225 patients. The inclusion criteria were confirmed T2DM patients (Fijian citizens) with CKD, aged 30 years or above and attending Special Out-Patient's Department (SOPD) at SSH. Independent t-test and ANOVA was used to test differences between demographic variable and practice score while non-parametric tests were used for knowledge and attitude. Spearman correlation and multiple linear regressions were also done. All the tests were set at 5% level of significance.Results: From 249 questionnaires distributed, 225 responded thus response rate was 95%. The mean KAP level was high: knowledge, 23.3/30 (SD±3.25); attitude, 23.1/30 (SD±2.73) and practice, 7.1/10 (SD±2.04). A high level of knowledge was seen in those with university-level education (p<0.001), unemployed (p=0.05) and high average monthly income (p=0.03). Those aged 61-70 years had a 0.53-point lower attitude score (p=0.05) than other age categories, while those >70 years had a 1.78-point lower attitude score (p=0.01) than other age categories. Fijians of Indian descent (FID) had lower attitude (p=0.002) and higher practice (p=0.001) scores.Conclusion:Patients with both T2DM and CKD at SSH have high levels of KAP. The determinants of KAP have been shown and thus, this study identified high-risk groups for low KAP, which can become the focus of future public health intervention.
Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models
Authors: Baum Katharina , Rajapakse Jagath C. , Azuaje Francisco 
Published: April 2019

Background:Biological entities such as genes, promoters, mRNA, metabolites or proteins do not act alone, but in concert in their network context. Modules, i.e., groups of nodes with similar topological properties in these networks characterize important biological functions of the underlying biomolecular system. Edges in such molecular networks represent regulatory and physical interactions, and comparing them between conditions provides valuable information on differential molecular mechanisms. However, biological data is inherently noisy and network reduction techniques can propagate errors particularly to the level of edges. We aim to improve the analysis of networks of biological molecules by deriving modules together with edge relevance estimations that are based on global network characteristics. Methods: We propose to fit the networks to stochastic block models (SBM), a method that has not yet been investigated for the analysis of biomolecular networks. This procedure both delivers modules of the networks and enables the derivation of edge confidence scores. We apply it to correlation-based networks of breast cancer data originating from high-throughput measurements of diverse molecular layers such as transcriptomics, proteomics, and metabolomics. The networks were reduced by thresholding for correlation significance or by requirements on scale-freeness. Results and discussion:We find that the networks are best represented by the hierarchical version of the SBM, and many of the predicted blocks have a biological meaning according to functional annotation. The edge confidence scores are overall in concordance with the biological evidence given by the measurements. As they are based on global network connectivity characteristics and potential hierarchies within the biomolecular networks are taken into account, they could be used as additional, integrated features in network-based data comparisons. Their tight relationship to edge existence probabilities can be exploited to predict missing or spurious edges in order to improve the network representation of the underlying biological system.
Reviews
Authors: Léger Marc James , Majewska Martyna , Shevlin Linda , Smyth Ciaran , Child Danielle 
Published: April 2019

2016 in Museums, Money, and Politics, Andrea Fraser (2018) New York, San Francisco and Cambridge, MA: Westreich Wagner, CCA Wattis Institute and The MIT Press, 1000 pp., ISBN 978-0-26253-545-8, p/bk, £97.00
Bow Gamelan Ensemble: Great Noises that Fill the Air, curated by Sophia Hao, Cooper Gallery, Dundee, 27 October–15 December 2018
Syntonic State, TULCA Visual Arts Festival, Linda Shevlin, Galway, 2–18 November 2018
Beautiful World, Where Are You?: Liverpool Biennial 2018, Various Locations, 14 July–28 October 2018
Pengaruh Pencahayaan terhadap Kandungan Pigmen Tetraselmis chuii sebagai Sumber Antioksidan Alami
Authors: Ginting Nada Kristiani , Sedjati Sri , Supriyantini Endang , Ridlo Ali 
Published: April 2019

Tetraselmis chuii merupakan alga hijau yang mengandung senyawa bioaktif seperti pigmen klorofil dan karotenoid. Pigmen klorofil dapat menurunkan risiko terkena kanker dan berpotensi sebagai antioksidan. Salah satu faktor eksternal yang berpengaruh terhadap kandungan pigmen adalah cahaya. Penelitian ini bertujuan untuk mengetahui pengaruh warna pencahayaan terhadap biomassa, kandungan pigmen dan aktivitas antioksidan T. chuii. Rancangan penelitian yang digunakan adalah rancangan acak blok dengan tiga kali pengulangan. Perlakuan pencahayaan yang diberikan adalah putih, merah, dan biru. Perhitungan kepadatan dan pengukuran parameter kualitas air dilakukan setiap hari. Pemanenan dilakukan pada saat fase stasioner hari ke – 4. Kadar pigmen (klorofil a, b dan karotenoid) dilakukan secara spektrofotometri dan uji aktivitas antioksidan dilakukan dengan DPPH (1,1-difenil-2-pikrilhidrazil). Hasil penelitian menunjukkan bahwa kepadatan sel tertinggi terdapat pada perlakuan pencahayaan putih sebesar 95.800 sel/ml. Kandungan pigmen klorofil a dan klorofil b total tertinggi terdapat pada pencahayaan merah (48,28 dan 40,86 μg/ml), serta karotenoid total tertinggi terdapat pada pencahayaan biru (6,70 μg/ml). Perlakuan perbedaan pencahayaan memberikan pengaruh nyata (P<0,05) terhadap kandungan pigmen (klorofil a, dan b). Aktivitas antioksidan ekstrak T. chuii semua perlakuan tergolong sangat lemah ( IC50 lebih dari 200 ppm). Effect of Lighting on Pigments Content Tetraselmis chuii a Source of Natural Antioxidants Tetraselmis chuii is a green algae which is containing bioactive compounds such as chlorophyll and carotenoid pigments. Chlorophyll may reduce the risk of cancer and potentially as an antioxidant. This research aims to know the effect of light colour on biomass, pigment and antioxidant activity content of T. chuii. The research design used was a complete randomized design with three repetitions. The light treatments provided are white, red, and blue. Calculation of density and measurement of water quality parameters on daily basis. Harvesting is done during the stasionary phase at fourth day. Pigment levels (chlorophyll a, b and carotenoids) were performed by spectrophotometer and an antioxidant activity test was performed by DPPH (1,1-diphenyl-2-picrilhidrazil). The results showed that different colour lighting treatments had an effect (P <0.05) on pigment content (chlorophyll a, b, and carotenoid).The highest total chlorophyll content of a and chlorophyll b were found in the highest red light (48.28 and 40.86 μg/ ml) and the highest total carotenoids were in blue light (6.70 μg /ml). The highest cell desity in white lighting treatment is 95,800 cell/ml. Potential antioxidant activity of T. chuii extract for all treatments were very low (IC50 more than 200 ppm).
Kandungan Protein Spirulina platensis Pada Media Kultur Dengan Konsentrasi Nitrat (KNO3 ) Yang Berbeda
Authors: Ulya Saniyatul , Sedjati Sri , Yudiati Ervia 
Published: April 2019

Spirulina platensis merupakan mikroalga hijau biru yang mengandung nutrisi protein tinggi sehingga banyak digunakan sebagai pakan alami. Pertumbuhan dan kandungan protein mikroalga dipengaruhi oleh beberapa faktor, salah satunya adalah pemberian makronutrien pada media kultur mikroalga. Penelitian ini bertujuan untuk melihat pengaruh pertumbuhan dan kandungan protein pada mikroalga S. platensis dengan pemberian konsentrasi nitrat yang berbeda. Rancangan penelitian yang digunakan adalah rancangan acak blok dengan tiga kali pengulangan. Perlakuan konsentrasi nitrat berbeda yang diberikan adalah 50 ppm, 100 ppm, dan 150 ppm. Perhitungan kepadatan dan pengukuran parameter kualitas air dilakukan setiap hari. Pemanenan dilakukan pada hari ke – empat. Kadar prorein dianalisis dengan menggunakan metode Kjedahl. Hasil penelitian pertumbuhan S. platensis menunjukkan nilai kepadatan sel S. platensis tertinggi pada hari ke – empat berada pada perlakuan C dengan konsentrasi nitrat 150 ppm (169,58 . 103 sel/mm3). Hasil analisis ANOVA menunjukkan bahwa konsentrasi nitrat berpengaruh terhadap pertumbuhan S. platensis (p < 0,05) namun perbedaan konsentrasi nitrat tidak berpengaruh pada kadar protein (p ≥ 0,05). Berdasarkan hasil penelitian dapat disimpulkan bahwa konsentrasi nitrat yang ditambahkan pada media kultur S. platensis berpengaruh terhadap pertumbuhan S. platensis namun tidak berpengaruh pada kandungan proteinnya. Protein Content of Spirulina platensis in Different Culture Media with Nitrate (KNO3) Concentration Spirulina platensis is green-blue microalgae that contain high protein nutrient and could be used as natural food. Growth and protein content of microalgae are influenced by several factors and one of those is giving macronutrient to microalgae’s culture medium. The purpose of this research is to compare the growth and protein content of the S. platensis with different nitrate consentrations.The research design used was a completely randomized block design with three repetitions. The different nitrate concentration treatments were 50 ppm, 100 ppm and 150 ppm. Determination of density and water quality measurement parameters was done on daily basis. Spirulina platensis was harvested done on fourth day of culture. Protein levels were analyzed by Kjedahl method. The result of the S. platensis growth that the highest density on day fourth in C treatment with 150 ppm nitrate consentration (169,58 . 103 sel/mm3). The result of ANOVA analysis show that the concentration of nitrate affected on S. platensis growth (p < 0,05) but the difference of nitrate concentration wasn’t affected in protein analysis (p ≥ 0,05). Based on the result of this research, it can be concluded that the concentration of nitrate added to the S. platensis culture medium effectively and improved the growth of S. platensis but had no effect on the protein content.
Analisis Sebaran Klorofil-A dan Suhu Permukaan Laut sebagai Fishing Ground Potensial (Ikan Pelagis Kecil) di Perairan Kendal, Jawa Tengah
Authors: Agung Andita , Zainuri Muhammad , Wirasatriya Anindya , Maslukah Lilik , Subardjo Petrus , Suryosaputro Agus Anugroho Dwi , Handoyo Gentur 
Published: April 2019

Perairan Kendal merupakan salah satu kabupaten di Jawa Tengah dengan luas wilayah ± 1.002,23 dan mengalami perkembangan pesat terutama di bidang perikanan. Perairan Kendal adalah salah satu wilayah penyebaran ikan demersal dan pelagis yang cukup potensial di perairan Utara Jawa Tengah. Tujuan penelitian ini untuk memprediksi zonasi fishing ground ikan pelagis kecil di Perairan Kendal berdasarkan parameter klorofil-a dan suhu permukaan laut. Penelitian ini menggunakan metode kuantitatif, penentuan lokasi pengambilan sampel menggunakan metode purposive sampling. Berdasarkan hasil penelitian diketahui bahwa perairan Kendal memiliki nilai konsentrasi klorofil-a berkisar antara 0.34 – 4.86 mg/ konsentrasi tertinggi di Timur Laut muara sungai Bodri dan di ikuti dengan hasil tangkapan ikan paling banyak yaitu 53 kg. Konsentrasi suhu permukaan laut berkisar 30,5 - 31ᵒC. Perbedaan nilai konsentrasi klorofil-a dan suhu permukaan laut dipengaruhi oleh angin yang berhembus di perairan sehingga diduga mengakibatkan terjadinya proses mixing. Analysis of Chlorophyll-A Distribution and Potential Sea Surface As Fishing Ground Temperature in Kendal Coastal, Central JavaThe waters of Kendal is one district in Central Java with an area of ± 1.002.23 and experienced rapid development, especially in the field of fisheries. The waters of Kendal is one of the potential demersal and pelagic fish distribution areas in the waters of North Central Java. The purpose of this study was to predict the potential fishing ground of small pelagic fish in Kendal Waters based on the parameters of chlorophyll-a and sea surface temperature. This research uses quantitative method while determining the location of sampling using purposive sampling method. Based on the research results it can be seen that the waters of Kendal has a value of chlorophyll-a concentration ranging from 0.34 - 4.86 mg/ with the highest concentration that is in the Northeast estuary Bodri river and followed by the catch of most fish that is 53 kg. Concentrations of sea surface temperature range from 30.5 - 31ᵒC. Differences in the value of a-chlorophyll concentration and sea-surface temperatures across the waters are influenced by winds that blow in the waters resulting in a mixing process.