bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methods to extend the shelf‐life of cottage cheese – a review
Authors: Ho Thao M , Howes Tony , Bhandari Bhesh R. 
Published: April 2016

Under typical refrigeration conditions (4–7 °C), unopened fresh cottage cheese only lasts for approximately 3 weeks unless preservatives are added. The spoilage of cottage cheese during storage is primarily due to the growth of Gram‐negative psychrotrophic bacteria, yeasts and moulds. To extend its shelf‐life, along with a strict sanitation practice throughout the manufacturing process, an appropriate preservation approach is generally applied. Many methods to preserve cottage cheese have been reported. These can be classified into three categories, namely food‐grade chemicals, heat treatment and modified atmosphere packaging. In this review, factors responsible for the spoilage of cottage cheese during storage and the methods to extend its shelf‐life are discussed.
The Puzzle of Persistently Negative Interest‐Rate–Growth Differentials: Financial Repression or Income Catch‐Up?
Authors: Escolano Julio , Shabunina Anna , Woo Jaejoon 
Published: April 2016

AbstractThe interest‐rate–growth differential (IRGD) plays a critical role in determining the sustainability of government debt. Yet it is striking that IRGDs are correlated with income levels, and are generally negative in emerging and developing economies, which contradicts standard economic theory. Negative IRGDs constitute a powerful debt‐stabilising force, driving down debt ratios or keeping them stable even in the presence of persistent primary deficits. Motivated by the puzzling facts, this paper examines the IRGDs for a large panel of advanced and non‐advanced economies by utilising a newly assembled data set. The evidence shows that large negative IRGDs in emerging and developing economies are largely due to real interest rates well below market equilibrium – stemming from financial repression and captive and distorted markets – whereas the income catch‐up process plays a relatively modest role. Therefore, the IRGD in non‐advanced economies is likely to rise with financial market development and financial global integration, perhaps even before their GDP per capita converges to advanced‐economy levels.
Evaluation of TagSeq, a reliable low‐cost alternative for RNAseq
Authors: Lohman Brian K. , Weber Jesse N. , Bolnick Daniel I. 
Published: April 2016

AbstractRNAseq is a relatively new tool for ecological genetics that offers researchers insight into changes in gene expression in response to a myriad of natural or experimental conditions. However, standard RNAseq methods (e.g., Illumina TruSeq® or NEBNext®) can be cost prohibitive, especially when study designs require large sample sizes. Consequently, RNAseq is often underused as a method, or is applied to small sample sizes that confer poor statistical power. Low cost RNAseq methods could therefore enable far greater and more powerful applications of transcriptomics in ecological genetics and beyond. Standard mRNAseq is costly partly because one sequences portions of the full length of all transcripts. Such whole‐mRNA data are redundant for estimates of relative gene expression. TagSeq is an alternative method that focuses sequencing effort on mRNAs’ 3’ end, reducing the necessary sequencing depth per sample, and thus cost. We present a revised TagSeq library construction procedure, and compare its performance against NEBNext®, the ‘gold‐standard’ whole mRNAseq method. We built both TagSeq and NEBNext® libraries from the same biological samples, each spiked with control RNAs. We found that TagSeq measured the control RNA distribution more accurately than NEBNext®, for a fraction of the cost per sample (~10%). The higher accuracy of TagSeq was particularly apparent for transcripts of moderate to low abundance. Technical replicates of TagSeq libraries are highly correlated, and were correlated with NEBNext® results. Overall, we show that our modified TagSeq protocol is an efficient alternative to traditional whole mRNAseq, offering researchers comparable data at greatly reduced cost.
Subsidies, Spillovers and WTO Rules in a Value‐chain World
Authors: Hoekman Bernard 
Published: April 2016

AbstractAs tariffs have fallen, subsidies and related policies with similar effect are being used to support local production. This raises the question of whether the existing World Trade Organization (WTO) ‘rules of the game’ are adequate. Assessing the economic effects of subsidies is complicated, given the need to consider linkages within and across supply‐chain networks. Many of the policies that affect supply‐chain operations are not considered subsidies under the WTO. There are no rules on subsidies for services or investment incentives by local governments. Conversely, some WTO rules may not be appropriate or effective given the increasing prevalence of global value chains. The widespread use of subsidies post‐2008 suggests WTO members should launch a process of deliberation to revisit the status quo set of multilateral rules on subsidies. The 2015 Nairobi WTO ministerial declaration has created the necessary window to permit interested countries to do so. A central element of this should involve a concerted effort to collect better data and to analyze how subsidies and policies with equivalent effect impact on value chains, whether negative international spillovers are created and, if so, their magnitude and incidence.
codyn: Anrpackage of community dynamics metrics
Authors: Hallett Lauren M. , Jones Sydney K. , MacDonald A. Andrew M. , Jones Matthew B. , Flynn Dan F. B. , Ripplinger Julie , Slaughter Peter , Gries Corinna , Collins Scott L. 
Published: April 2016

SummaryNew analytical tools applied to long‐term data demonstrate that ecological communities are highly dynamic over time. We developed anrpackage,library(“codyn”), to help ecologists easily implement these metrics and gain broader insights into ecological community dynamics.library(“codyn”)provides temporal diversity indices and community stability metrics. All functions are designed to be easily implemented over multiple replicates.Temporal diversity indices include species turnover, mean rank shifts and rate of community change over time. Community stability metrics calculate overall stability and patterns of species covariance and synchrony over time, and include a null‐modelling method to test significance.Finally,library(“codyn”)contains vignettes that describe methods and reproduce figures from published papers to help users contextualize and apply functions to their own data.
Emergence of adult female Sirex nigricornis F. and Sirex noctilio F. (Hymenoptera: Siricidae) coincides with a decrease in daily minimum and maximum temperature
Authors: Hartshorn Jessica A. , Haavik Laurel J. , Allison Jeremy D. , Meeker James R. , Johnson Wood , Galligan Larry D. , Chase Kevin D. , Riggins John J. , Stephen Fred M. 
Published: April 2016

Abstract
The establishment and spread of Sirex noctilio F. (Hymenoptera: Siricidae), in northeastern North America necessitates reliable monitoring methods for this alien woodwasp pest of Pinus. The native congener, Sirex nigricornis F., is common across the eastern U.S.A. and has been studied as a proxy for S. noctilio. Predicting the emergence of S. noctilio is important for guiding monitoring efforts.
Degree‐day models have been developed to predict flight phenology of S. noctilio and S. nigricornis across eastern North America. These model parameters were tested against three years of S. nigricornis collections from two locations in Arkansas. Neither of the proposed models accurately predicted emergence.
The emergence of females for both S. noctilio and S. nigricornis was significantly negatively correlated with minimum and maximum temperature, indicating that emergence increases when minimum and maximum temperatures decrease. These results suggest that, as S. noctilio spreads south, where higher mean temperatures are present, it will emerge later in the season as the temperatures decline compared with the current northeastern population.
We propose that monitoring for the spread of S. noctilio in the southeastern U.S.A. should begin slightly before daily temperatures are expected to decline (i.e. mid‐September).
Identification of genes in longissimus dorsi muscle differentially expressed between Wannanhua and Yorkshire pigs using RNA‐sequencing
Authors: Li X.‐J. , Zhou J. , Liu L.‐Q. , Qian K. , Wang C.‐L. 
Published: April 2016

SummaryWestern commercial pig breeds have been intensively selected, resulting in a sizeable, rapid and efficient accretion of muscle but a reduction in meat quality. When compared with Western commercial pig breeds, Chinese indigenous pig breeds exhibited slower growth rates and reduced lean meat content but superior perceived meat quality. To study the factors that determine meat quality, we examined piglets of one Western commercial breed (Yorkshire) and one Chinese indigenous breed (Wannanhua) and sequenced the longissimus dorsi muscle using RNA‐sequencing (RNA‐seq). We analyzed their transcriptomes, focusing on identifying candidate genes that may influence porcine muscle growth, meat quality and adipose deposition. Gene Ontology functional enrichment and pathway enrichment analyses identified differentially expressed genes (DEGs) primarily associated with glycolytic metabolism, biological processes of muscle development and signaling pathways related to fatty acid metabolism, growth and carcass traits. This finding suggests that the DEGs may play important roles in determining meat quality traits. Quantitative real‐time reverse transcription polymerase chain reaction confirmed the differential expression of 12 selected DEG. This study identified a number of novel candidate genes for porcine meat quality and carcass traits that merit further investigation to elucidate the molecular mechanisms responsible for muscle growth and fat deposition.
Confirmatory factor analysis of the Alcohol, Smoking and Substance Involvement Screening Test (ASSIST) in community health center patients
Authors: O'Grady Kevin E. , Gryczynski Jan , Mitchell Shannon Gwin , Ondersma Steven J. , Schwartz Robert P. 
Published: April 2016

Background and ObjectivesTo investigate the factor structure of the Alcohol, Smoking, and Substance Involvement Screening Test (ASSIST).MethodsSecondary analysis on an adult primary care sample (N = 2,599).Results and DiscussionFactor analysis of the tobacco, alcohol, and cannabis items did not yield an acceptable oblique, three‐factor solution, due in part to floor effects and limited variability. A short form comprises three items (past‐3‐month frequency of use, urge to use, and whether others have expressed concern for use), that showed good psychometrics.Scientific SignificanceSupports the need for further investigation of the ASSIST factor structure and a short form. (Am J Addict 2016;25:259–263)
Definition, aims, and implementation of GA2LEN Urticaria Centers of Reference and Excellence
Authors: Maurer M. , Metz M. , Bindslev‐Jensen C. , Bousquet J. , Canonica G. W. , Church M. K. , Godse K. V. , Grattan C. E. , Hide M. , Kocatürk E. , Magerl M. , Makris M. , Meshkova R. , Saini S. S. , Sussman G. , Toubi E. , Zhao Z. , Zuberbier T. , Gimenez‐Arnau A. 
Published: April 2016

AbstractBackgroundGA²LEN, the Global Allergy and Asthma European Network, has recently launched a program for the development, interaction, and accreditation of centers of reference and excellence in special areas of allergy embedded in its overall quality management of allergy centers of excellence. The first area chosen is urticaria. Urticaria is a common and debilitating condition and can be a challenge for both patients and treating physicians, especially when chronic. Centers of reference and excellence in urticaria (UCAREs) can help to improve the management of hard‐to‐treat conditions such as urticaria.AimsHere, we describe the aims, the requirements and deliverables, the application process, and the audit and accreditation protocol for GA²LEN UCAREs.ResultsThe main aims of GA²LEN UCAREs are to provide excellence in urticaria management, to increase the knowledge of urticaria by research and education, and to promote the awareness of urticaria by advocacy activities. To become a certified GA²LEN UCARE, urticaria centers have to apply and fulfill 32 requirements, defined by specific deliverables that are assessed during an audit visit.Discussion and ConclusionThe GA²LEN UCARE program will result in a strong network of urticaria specialists, promote urticaria research, and harmonize and improve urticaria management globally.
Hepatic resection of non‐colorectal non‐endocrine liver metastases
Authors: Gandy Robert C. , Bergamin Paul A. , Haghighi Koroush S. 
Published: April 2016

BackgroundHepatic resection is standard treatment for liver metastases from colorectal and neuroendocrine cancers as well as primary biliary and hepatic carcinomas. The role of hepatic resection in patients with non‐colorectal non‐endocrine liver metastases (NCNELM) is less defined. Overall survival in this group of patients is poor with few patients surviving beyond two years, even with modern chemotherapy.MethodsA prospective database of all liver resections performed by a single surgeon (KSH) from January 2007 to December 2014 was maintained. Patient demographics, surgical and pathological data were collected prospectively; survival data were updated retrospectively. Patients were grouped according to pathology and analysis was performed using SPSS (version 21).ResultsA total of 48 patients underwent hepatic resection for NCNELM, of which 18 were major resections. Pathologies encountered included sarcoma in 8/48, both breast and ovarian in 6/48 each and renal cell carcinoma and melanoma, each representing 5/48. A result of 38/48 patients undertook chemotherapy prior to surgery. R0 margin was achieved in 96%. Seven patients suffered complications from surgery and one peri‐operative mortality. Overall survival at 1, 3 and 5 years was 93%, 83% and 61%, respectively. Forty‐four percent of patients developed disease recurrence, 29% at distant sites.ConclusionHepatic resection can be achieved safely for NCNELM. Patient selection is key, along with a standardized surgical and anaesthetic technique. Patients should be rigorously investigated to exclude disseminated disease and multidisciplinary discussion must take place prior to surgery. Patients with NCNELM should not routinely be excluded from liver resection and selected patients may benefit from resection.
Plasma interleukin‐10 predicts short‐term mortality of acute‐on‐chronic hepatitis B liver failure
Authors: Wang N. , Fan Y.‐C. , Xia H. H.‐X. , Sun Y.‐Y. , Wang K. 
Published: April 2016

SummaryBackgroundInterleukin (IL)‐10 is a pleiotropic cytokine with anti‐inflammatory and immunosuppressive properties in liver failure. Biomarkers are urgently needed to predict prognosis of acute‐on‐chronic hepatitis B liver failure (ACHBLF).AimTo investigate the potential diagnostic value of plasma IL‐10 as a biomarker for predicting the mortality of ACHBLF.MethodsThis prospective study consisted of 115 newly diagnosed ACHBLF patients from May 2009 to October 2013 as a training cohort and 54 ACHBLF patients from November 2013 to March 2015 as a validating cohort. Plasma IL‐10 level was measured using enzyme‐linked immunosorbent assay.ResultsIn the training cohort, the plasma IL‐10 level of nonsurvivals [median (centile25; centile75): 12.38 (8.76; 15.52) pg/mL] was significantly higher than that in survivals [6.55 (5.43; 7.65) pg/mL, P < 0.001]. Plasma IL‐10 (hazard ratio = 1.205, 95% confidence interval: 1.145–1.267, P < 0.001) was identified as an independent risk factor for mortality of ACHBLF patients. Furthermore, plasma IL‐10 showed higher area under the curve of receiver operating characteristic (AUROC) than model for end‐stage liver diseases (MELD) for predicting 1‐month (0.887 vs. 0.779, P < 0.05), 2‐month (0.878 vs. 0.779, P < 0.05) and 3‐month (0.917 vs. 0.776, P < 0.001) mortality. However, we did not find significant differences in AUROC between IL‐10 and IL‐10 plus MELD for 1‐, 2‐ and 3‐month mortality. ACHBLF patients with plasma IL‐10 > 9.6 pg/mL showed poor survival time than patients with plasma IL‐10 ≤ 9.6 pg/mL at the end of 1 month in the training and validation cohorts.ConclusionsPlasma IL‐10 performed better than MELD in predicting the prognosis of acute‐on‐chronic hepatitis B liver failure. Furthermore, plasma IL‐10 > 9.6 pg/mL predicts a poor 1‐month mortality.
Pharmacodynamics, pharmacokinetics, and safety of ticagrelor in Chinese patients with stable coronary artery disease
Authors: Li Haiyan , Guo Jingchuan , Carlson Glenn F. , Teng Renli 
Published: April 2016

AimThe aim of the study was to assess ticagrelor's effects on inhibition of platelet aggregation (IPA), P2Y12 reaction units (PRU, measure of platelet P2Y12 receptor blockade), pharmacokinetic (PK) parameters and safety in Chinese patients with stable coronary artery disease (CAD).MethodsThis was an open label, single centre, randomized study. Thirty‐six patients on low dose aspirin (75–100 mg day–1) received ticagrelor 45, 60 or 90 mg (single dose, days 1 and 7; twice daily, days 3–6). IPA (final extent), PRU and ticagrelor and AR‐C124910XX plasma concentrations were determined.ResultsOn day 1, peak IPA >80% occurred 2–6 h post‐dose (all doses). PRU was markedly reduced at 1 h vs. baseline (all doses). With ticagrelor 45 and 90 mg twice daily, maximum IPA (mean, SD) was 91% (13%), and 99% (3%), and maximum PRU reduction from baseline (mean, SD) was 82% (17%) and 92% (9%), respectively. Approximate dose‐proportional increases (mean [%CV]; 45 vs. 90 mg twice daily) in ticagrelor Cmax (616 [37] vs. 1273 [43] ng ml–1) and AUC (3882 [42] vs. 8206 [51] ng ml–1 h) and AR‐C124910XX parameters were seen. Pharmacodynamic and PK differences between 45 and 60 mg were small. No safety issues were identified.ConclusionsIn Chinese patients with CAD, ticagrelor (45, 60 and 90 mg) markedly reduced platelet aggregation. The IPA and PRU magnitude increased generally with increasing doses. However, the mean pharmacodynamic differences between 45 and 60 mg doses were small. Following single and multiple doses, the mean Cmax and AUC values of ticagrelor and AR‐C124910XX increased approximately dose proportionally between 45 and 90 mg doses.
PD-1 blockade: a therapeutic option for treatment of metastatic Merkel cell carcinoma
Authors: Winkler J.K. , Bender C. , Kratochwil C. , Enk A. , Hassel J.C. 
Published: April 2016

Summary
The immune system is extremely important in the development and progression of Merkel cell carcinoma (MCC). Immune checkpoint blockade has recently been shown to enable efficacious treatment of a variety of tumours. We report the use of an anti-programmed death receptor 1 (PD-1) antibody for treatment of a patient with metastatic MCC. An 80-year-old patient with metastatic MCC received off-label treatment with the anti-PD-1 antibody pembrolizumab after the disease had progressed during therapy with oral etoposide. A positron emission tomography (PET) computed tomography scan performed after three cycles of pembrolizumab revealed responses to therapy with reduced size of the adrenal gland metastases and less PET activity in the adrenal gland and lymph node metastases. Treatment was resumed owing to disease progression after a treatment-free interval of &gt; 4 months. During subsequent months of treatment, the size of the metastases stabilized and uptake of nuclide by all tumour sites once again decreased. These results reveal the potential efficacy of an anti-PD-1 antibody for treatment of metastatic MCC. Thus, they contribute to currently limited data on the use of anti-PD-1 antibodies for the treatment of MCC. Moreover, this is the first report of successful resumption of treatment of metastatic MCC with an anti-PD-1 antibody. Results from ongoing trials will contribute to determination of the relevance of PD-1 blockade in metastatic MCC.
Patient–physician communication and health‐related quality of life of patients with localised prostate cancer undergoing radical prostatectomy – a longitudinal multilevel analysis
Authors: Ernstmann Nicole , Weissbach Lothar , Herden Jan , Winter Nicola , Ansmann Lena 
Published: April 2016

ObjectivesTo examine whether patient–physician communication is associated with health‐related quality of life (HRQoL) in a sample of patients with localised prostate cancer undergoing radical prostatectomy (RP).Patients and methodsHAROW (Hormonal therapy, Active Surveillance, Radiation, Operation, Watchful Waiting) is a prospective, observational study designed to collect data of the different treatment options for newly diagnosed patients with localised prostate cancer under real‐life conditions. At 6‐months intervals, clinical data (D'Amico risk categories, Charlson comorbidity index), aspects of patient–provider communication (standardised psychosocial‐care instrument for patients’ assessment of communication; Cologne Patient Questionnaire), and HRQoL (European Organization for Research and Treatment of Cancer Quality of Life Questionnaire) were assessed. Data were analysed by longitudinal multilevel analysis.ResultsCompleted questionnaires for 1772 patients undergoing a RP were analysed over a 3‐year follow‐up period. Patients rated the patient‐provider communication generally high with slight variations over the course of treatment (3.2–3.8). The HRQoL of the patients varied substantial over time and between the reported subscales (global HRQoL 71.1–77.2; physical functioning 89.1–92.1; role functioning 81.0–88.1; emotional functioning 74.4–84.0; cognitive functioning 84.3–87.7; social functioning (77.7–84.0). The longitudinal multilevel models showed significant associations between patient–provider communication in terms of devotion, support and shared decision‐making, and functional aspects of HRQoL.ConclusionPatient–provider communication is a valuable resource to support patients with prostate cancer coping with the disease and to improve their HRQoL. Future interventions should be designed especially for urologists to enhance their awareness for the importance of communication and the relationship with their patients with prostate cancer for treatment outcomes.
Fruit selection by Andean forest birds: influence of fruit functional traits and their temporal variation
Authors: Blendinger Pedro G. , Martín Eduardo , Osinaga Acosta Oriana , Ruggera Román A. , Aráoz Ezequiel 
Published: April 2016

AbstractFruit selection, i.e., the consumption of fruits disproportionately to their availability, results from the interaction between diet preferences and ecological factors that modify them. We assessed the importance of functional fruit traits to explain fruit selection by birds in Andean subtropical forests, taking into account temporal variation in trait distribution in the assembly of available fruits. During 2 yr, we measured the abundance of ripe fruits and their consumption by birds in a 6‐ha plot during 11 bimonthly samplings, and we used 17 phenological, morphological, and nutritional traits to characterize fruits selected by four bird species. Fruit selection was pervasive year‐round, highly variable over time and across bird species. Fruit species were selected over time periods shorter than their ripening phenology, and the selection of fruits with particular traits was specific to the fruit‐eating species. Maximization in pulp reward per consumed fruit seems to be the main driving force behind fruit selection, indicating that birds select fruits with traits that directly affect net energy gain. Our results can be interpreted in a framework of a hierarchy of foraging decisions, under which the spatiotemporal context of the fruiting environment modifies the relative intake rates of a particular fruit, while the ability to discriminate fruit contents becomes increasingly important on a smaller dimension. We show that fruit‐selection properties are contingent on specific fruit traits and particular spatiotemporal conditions, which modify the structure of mutualistic interactions.