bluuebunny/crossref_metadata_2025_split huggingface dataset:
H&E-stained Whole Slide Image Deep Learning Predicts SPOP Mutation State in Prostate Cancer
Authors: Schaumberg Andrew J. , Rubin Mark A. , Fuchs Thomas J. 
Published: July 2016

A quantitative model to genetically interpret the histology in whole microscopy slide images is desirable to guide downstream immuno-histochemistry, genomics, and precision medicine. We constructed a statistical model that predicts whether or not SPOP is mutated in prostate cancer, given only the digital whole slide after standard hematoxylin and eosin [H&E] staining. Using a TCGA cohort of 177 prostate cancer patients where 20 had mutant SPOP, we trained multiple ensembles of residual networks, accurately distinguishing SPOP mutant from SPOP non-mutant patients (test AUROC=0.74, p=0.0007 Fisher’s Exact Test). We further validated our full metaensemble classifier on an independent test cohort from MSK-IMPACT of 152 patients where 19 had mutant SPOP. Mutants and non-mutants were accurately distinguished despite TCGA slides being frozen sections and MSK-IMPACT slides being formalin-fixed paraffin-embedded sections (AUROC=0.86, p=0.0038). Moreover, we scanned an additional 36 MSK-IMPACT patients having mutant SPOP, trained on this expanded MSK-IMPACT cohort (test AUROC=0.75, p=0.0002), tested on the TCGA cohort (AUROC=0.64, p=0.0306), and again accurately distinguished mutants from non-mutants using the same pipeline. Importantly, our method demonstrates tractable deep learning in this “small data” setting of 20-55 positive examples and quantifies each prediction’s uncertainty with confidence intervals. To our knowledge, this is the first statistical model to predict a genetic mutation in cancer directly from the patient’s digitized H&E-stained whole microscopy slide. Moreover, this is the first time quantitative features learned from patient genetics and histology have been used for content-based image retrieval, finding similar patients for a given patient where the histology appears to share the same genetic driver of disease i.e. SPOP mutation (p=0.0241 Kost’s Method), and finding similar patients for a given patient that does not have have that driver mutation (p=0.0170 Kost’s Method).Significance StatementThis is the first pipeline predicting gene mutation probability in cancer from digitized H&E-stained microscopy slides. To predict whether or not the speckle-type POZ protein [SPOP] gene is mutated in prostate cancer, the pipeline (i) identifies diagnostically salient slide regions, (ii) identifies the salient region having the dominant tumor, and (iii) trains ensembles of binary classifiers that together predict a confidence interval of mutation probability. Through deep learning on small datasets, this enables automated histologic diagnoses based on probabilities of underlying molecular aberrations and finds histologically similar patients by learned genetic-histologic relationships.Conception, Writing: AJS, TJF. Algorithms, Learning, CBIR: AJS. Analysis: AJS, MAR, TJF. Supervision: MAR, TJF.
Bayesian model reveals latent atrophy factors with dissociable cognitive trajectories in Alzheimer’s disease
Authors: Zhang Xiuming , Mormino Elizabeth C. , Sun Nanbo , Sperling Reisa A. , Sabuncu Mert R. , Yeo B.T. Thomas ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: July 2016

AbstractWe employed a data-driven Bayesian model to automatically identify distinct latent factors of overlapping atrophy patterns from voxelwise structural magnetic resonance imaging (MRI) of late-onset Alzheimer’s disease (AD) dementia patients. Our approach estimated the extent to which multiple distinct atrophy patterns were expressed within each participant rather than assuming that each participant expressed a single atrophy factor. The model revealed a temporal atrophy factor (medial temporal cortex, hippocampus and amygdala), a subcortical atrophy factor (striatum, thalamus and cerebellum), and a cortical atrophy factor (frontal, parietal, lateral temporal and lateral occipital cortices). To explore the influence of each factor in early AD, atrophy factor compositions were inferred in beta-amyloid-positive (Aβ+) mild cognitively impaired (MCI) and cognitively normal (CN) participants. All three factors were associated with memory decline across the entire clinical spectrum, whereas the cortical factor was associated with executive function decline in Aβ+ MCI participants and AD dementia patients. Direct comparison between factors revealed that the temporal factor showed the strongest association with memory, while the cortical factor showed the strongest association with executive function. The subcortical factor was associated with the slowest decline for both memory and executive function compared to temporal and cortical factors. These results suggest that distinct patterns of atrophy influence decline across different cognitive domains. Quantification of this heterogeneity may enable the computation of individual-level predictions relevant for disease monitoring and customized therapies. Code from this manuscript is publicly available at link_to_be_added.
Multidrug-resistant pathogens isolated from ready-to-eat salads available at a local market in Pakistan
Authors: Ilyas Sana , Qamar Muhammad  Usman , Rasool Muhammad Hidayat , Abdulhaq Nazia , Nawaz Zeeshan 
Published: July 2016

Purpose
– The purpose of this paper is to evaluate the frequency and antimicrobial susceptibility pattern of pathogens present in ready-to-eat salads available at a local market.

Design/methodology/approach
– A 100 salad samples were collected aseptically. Each sample (25 g) was homogenized in 225 ml of sterile peptone water and was serially diluted up to 1×106. Dilutions were inoculated on nutrient agar by surface spread plate technique. Aerobic colony count (ACC) was estimated by counting the colonies. Bacterial isolates were cultured on blood and MacConkey agar and identified on the basis of their morphology, culture characteristics and confirmed by API 20E and 20NE. Antimicrobial susceptibility was determined as per CLSI 2014.

Findings
– ACC range was 1.1×103 cfu/g to 5.8×109 cfu/g. Among these the highest ACC was found in channa chat (4.9×104 to 5.8×109 cfu/g). A total of 127 microorganisms were identified; 73 were gram negative rods (GNRs) and 24 were gram positive cocci (GPC). Among GNRs; Klebsiella spp. (n=18) was the predominant whereas among GPC, Staphylococcus aureus (n=6) were the chief pathogen. Klebsiella spp. showed 100 percent resistance to ampicillin, 89-78 percent to amoxicillin/clavulanic acid and 33 percent to imipenem, however, Enterobacter spp. were resistant to ampicillin (100 percent) amoxicillin/clavulanic acid (77 percent) and imipenem (23 percent). Staphylococcus aureus showed resistance to co-amoxiclav (83 percent) and penicillin (75 percent).

Practical implications
– This study revealed that effective control measures must been implemented and respected by throughout the entire food chain and better surveillance studies should be performed at national level to reduce the spread of bacteria by fresh salads.

Originality/value
– This paper explore the high prevalence of multidrug-resistant pathogens in different salads and most of the salads were found to be unhygienic for consumption.
Consumer perceptions of free-range laying hen welfare
Authors: Pettersson Isabelle Claire , Weeks Claire Alexandra , Wilson Lorna Rachel Maven , Nicol Christine Janet 
Published: July 2016

Purpose– The purpose of this paper is to understand which factors and resources free-range egg consumers believe are important for hen welfare.Design/methodology/approach– An online survey was distributed via the mailing list of a UK free-range egg brand receiving 6,378 responses. The survey was mostly five-point Likert-scale based. The same survey was also distributed to a group of animal welfare specialists receiving 34 responses.Findings– Respondents bought free-range eggs because hens are “happier” (74.2 per cent) and “healthier” (69.0 per cent) and because they believed such eggs to taste better (57.9 per cent). They rated all the suggested factors that might contribute to hen welfare as “important” or “very important” (on average) but believed outside access and fresh air to be most important. Respondents rated the suitability of resources relating to behavioural needs high (“suitable” or “very suitable”) indoors and shelter as the most suitable outdoors. Consumers differed from welfare specialists in their views on factors contributing to hen welfare, but their views on resource suitability were similar.Research limitations/implications– The sample was biased towards free-range egg consumers who had expressed an interest in a brand marketed as high welfare.Originality/value– This is the first study to ask consumers what they consider to be important for hen welfare and how they think hen welfare can be improved. Because consumers can affect on-farm welfare through their purchasing habits assessing the degree of agreement between consumers and animal welfare specialists is important.
Food fraud and consumers’ choices in the wake of the horsemeat scandal
Authors: Agnoli Lara , Capitello Roberta , De Salvo Maria , Longo Alberto , Boeri Marco 
Published: July 2016

Purpose
– In 2012, the European food industry was hit by a food fraud: horsemeat was found in pre-prepared foods, without any declaration on the package. This is commonly referred to as the “horsemeat scandal”. The purpose of this paper is to investigate consumers’ preferences across Europe for a selected ready meal, ready to heat (RTH) fresh lasagne, to consider whether the effects of potential food frauds on consumers’ choices can be mitigated by introducing enhanced standards of RTH products.

Design/methodology/approach
– An online survey was administered to 4,598 consumers of RTH lasagne in six European countries (Republic of Ireland, France, Italy, Spain, Germany and Norway), applying discrete choice experiments to estimate consumers’ willingness to pay for enhanced food safety standards and highlight differences between countries.

Findings
– Many similarities across countries emerged, as well as some differences. Consumers in Europe are highly concerned with the authenticity of the meat in ready meals and strongly prefer to know that ingredients are nationally sourced. Strong regional differences in price premiums exist for enhanced food safety standards.

Originality/value
– This research adds relevant insights in the analysis of consumers’ reaction to food fraud, providing practical guidelines on the most appropriate practices that producers should adopt and on the information to reduce food risk perception among consumers. This would prove beneficial for the food processing industry and the European Union. The survey is based on a representative sample of European consumers making this the largest cross-country study of this kind.
Origin based agro-food products: how to communicate their experiential value online?
Authors: Iaia Lea , Maizza Amedeo , Fait Monica , Scorrano Paola 
Published: July 2016

Purpose– The purpose of this paper is to investigate the experiential dimension of certain Italian agrofood products’ websites, which are seen as exemplifying best practices in the terms of the representation of the brand-land relationship, including their link with the territory of origin in the sense of terroir.Design/methodology/approach– The study was conducted after the conception and experimentation of a model (called SObER), the fruit of detailed studies of experiential marketing (Schmitt, 1999a, b). The model was tested using the user-based focus group technique (Mich, 2007) and verified with reference to certain consortia brands considered to reflect best practices in communication of the brand-land connection.Findings– The analysis made it possible to identify the key elements for expressing both the experiential dimension and the brand-land relationship of traditional agrofood products, ensuring their effective online communication.Research limitations/implications– Although the research uses a benchmarking technique, it focuses on specific case studies; thus, the outcomes can be generalised by means of an extension of the analysis.Originality/value– The value of the analysis carried out lies in the creation of a model aimed at the assessment of agrofood products and, more generally, their link with the territory of origin in the online context. In addition, the marketing literature on the experiential dimension applied to website tools is still limited. For this reason, this work may stimulate future in-depth analysis with reference to the proposed model.
Citizens’ perception of modern pig production in Germany: a mixed-method research approach
Authors: Weible Daniela , Christoph-Schulz Inken , Salamon Petra , Zander Katrin 
Published: July 2016

Purpose– The wide divergence of the people’s expectations and agricultural reality results in conflicts between the agricultural sector and the general public. Contemporary animal husbandry systems are being increasingly critically addressed by media; however, there is no information about peoples’ perceptions and attitudes concentrating precisely on specific animal husbandry systems. The purpose of this paper is to explore citizens’ perceptions, expectations and main points of criticism in regard to intensive pig production in Germany, and to identify and describe distinct population groups reflecting different attitudes.Design/methodology/approach– A mixed method approach combining qualitative focus groups with a quantitative online survey has been employed. Focus groups capture a wide variety of opinions and concerns in an exploratory manner. Based on these findings, the quantitative survey (n=1,500 citizens) allowed the identification and characterisation of population groups with identical attitudes regarding pig husbandry.Findings– Qualitative research uncovered a huge range of criticism on pig husbandry, e.g. lack of space, frequency and prophylactic use of medications as well as a lack of care. A relationship was seen between the lack of space, widespread use of medications and behavioural disorders. Consumer preferences for buying cheap meat were believed to be part of the problem since this behaviour fosters the development of larger farms. Quantitative research confirmed the generally critical perception and identified three population groups. Only one third of the population was really concerned about animal husbandry. Younger people and people with better knowledge of agriculture were stronger opponents of intensive pig husbandry.Practical implications– Results indicate that increasing people’s knowledge may have an adverse effect on their acceptance of modern farming systems. More communication and better information strategies will probably not improve societal acceptance by itself. Instead, agricultural production systems need to be improved to meet better consumers’ expectations whereas communicating these improvements to consumers and the general public in a well-targeted manner will be required as well.Originality/value– When considering options for enhancing public acceptance of modern animal husbandry, a combination of different strategies by different stakeholders is needed. The agricultural sector should improve its communication with the general public and rethink its production practices against the background of public expectations. The government and its agencies urgently need to improve monitoring of the compliance of actual production practices with existing laws and to enforce them. Additionally, adjustments of current regulations of animal husbandry in light of public expectations should be considered.
Online monitoring of priority and dangerous pollutants in natural and urban waters
Authors: Capodaglio Andrea G , Callegari Arianna , Molognoni Daniele 
Published: July 2016

Purpose
– Advancements in real-time water monitoring technologies permit rapid detection of water quality, and threats from waste loads. Water Framework Directive mandating the establishment of Member States’ water resources monitoring, presence of hazardous contaminants in effluents, and perception of vulnerability of water distribution system to attacks, have spurred technical and economic interests. The paper aims to discuss these issues.

Design/methodology/approach
– As alternative to traditional analyzers, chemosensors, operate according to physical principles, without sample collection (online), and are capable of supplying parameter values continuously and in real-time. Their low selectivity and stability issues have been overcome by technological developments. This review paper contains a comprehensive survey of existing and expected online monitoring technologies for measurement/detection of pollutants in water.

Findings
– The state-of-the-art in online water monitoring is presented. Application examples are reported. Monitoring costs will become a lesser part of a water utility budget due to the fact that automation and technological simplification will abate human cost factors, and reduce the complexity of laboratory procedures.

Originality/value
– An overview of applicable instrumentation, and forthcoming developments, is given. Technological development in this field is very rapid, and astonishing advances are anticipated in several areas (fingerprinting, optochemical sensors, biosensors, molecular techniques). Online monitoring is becoming an ever-important tool not only for compliance control or plant management purposes, but also as a useful approach to pollution control and reduction, minimizing the environmental impact of discharges.
Design of a risk assessment methodology for the introduction of invasive species from ship ballast waters
Authors: Bouda Abderrahmane , Bachari Nour El Islam , Bahmed Lylia , Boubenia Ryad 
Published: July 2016

Purpose
– Ballast water of merchant ship is a source of introduction of invasive species around the globe. The purpose of this paper is to present a quantitative risk assessment applied to a model port, the Port of Arzew in Algeria, and based on an analysis of this port’s shipping traffic.

Design/methodology/approach
– The risk assessment for introduction of invasive species is interpreted in the form of a probabilistic process, with a combination of two probabilities. The first probability is related to the ability of a species to arrive to the destination (recipient port), depending on the quantity of water ballast discharged and the duration of voyage. The second one is based on the species ability to survive in their new environment, which depends on the environmental similarity between donor port and Arzew port.

Findings
– This assessment’s outcome consists on a classification of scenarios regarding their acceptability. Consequently, it helped to classify donor ports according to a risk scale, from low risk to high-risk donor ports.

Research limitations/implications
– The phenomenon of invasion of aquatic species is a complex process. Factors such as adaptation and tolerance of species, the attendance or absence of predators, were not taken into account in this study.

Practical implications
– This study could be used by the maritime administration as a decision-making tool regarding the issue of exemptions under the IMO International Convention on the Management of Ballast Water and Sediments 2004.

Originality/value
– This is one of the first known studies in Algeria and dealing with ballast water management. The results of this assessment provide useful information to policy makers, in order to develop a national strategy to reduce the impact of shipping pollution on the marine environment.
Optimization of biological transesterification of waste cooking oil in different solvents using response surface methodology
Authors: Balasubramanian Bharathiraja , Ramanujam Praveen Kumar , Ravi Kumar Ranjith , Muninathan Chakravarthy , Dhinakaran Yogendran 
Published: July 2016

Purpose
– The purpose of this paper is to speak about the production of biodiesel from waste cooking oil which serves as an alternate fuel in the absence of conventional fuels such as diesel and petrol. Though much research work was carried out using non-edible crops such as Jatropha and Pongamia, cooking oil utilized in bulk quantity is discarded as a waste. This is reused again as it contains more of esters that when combined with an alcohol in presence of an enzyme as a catalyst yields triglycerides (biodiesel).

Design/methodology/approach
– The lipase producing strain Rhizopus oryzae and pure enzyme lipase is immobilized and treated with waste cooking oil for the production of FAME. Reaction parameters such as temperature, time, oil to acyl acceptor ratio and enzyme concentration were considered for purified lipase and in the case of Rhizopus oryzae, pH, olive oil concentration and rpm were considered for optimization studies. The response generated through each run were evaluated and analyzed through the central composited design of response surface methodology and thus the optimized reaction conditions were determined.

Findings
– A high conversion (94.01 percent) was obtained for methanol when compared to methyl acetate (91.11 percent) and ethyl acetate (90.06 percent) through lipase catalyzed reaction at oil to solvent ratio of 1:3, enzyme concentration of 10 percent at 30°C after 24 h. Similarly, for methanol a high conversion (83.76 percent) was obtained at an optimum pH of 5.5, olive oil concentration 25 g/L and 150 rpm using Rhizopus oryzae when compared to methyl acetate (81.09 percent) and ethyl acetate (80.49 percent).

Originality/value
– This research work implies that the acyl acceptors methyl acetate and ethyl acetate which are novel solvents for biodiesel production can also be used to obtain high yields as compared with methanol under optimized conditions.
Perceptions, attitudes and behaviours toward urban surface water quality in Accra, Ghana
Authors: Abraham Ernest Mensah , Martin Adrienne , Cofie Olufunke , Raschid-Sally Liqa 
Published: July 2016

Purpose
– The purpose of this paper is to explore people’s perceptions, stated attitudes, and observed and reported behaviour to water and other environmental quality.

Design/methodology/approach
– The study adopted a mixed method approach. It employed a cross-sectional survey design. Ten communities were selected in Accra and its surrounding communities to indicate various levels of infrastructure provision and environmental quality. Four separate focus group discussions (FGDs) were carried out in each community, with a mixed group of older and young adult men and women, a group of men only, a group of women only, and a group of young adults only. Following the FGDs, further information was obtained through structured household questionnaire survey involving 443 respondents.

Findings
– Different ideas were employed to explain people’s perceptions of water quality. There were common ideas such as on health, history of water use, perceptions which affect water use, and management of community activities which affect water sources. These ideas which emerged from the focus groups helped participants to assign meaning to their environment. Reported behaviour was influenced by the ability to pay for services, their availability and the influence of shared community norms. Although citizen participation in water and environmental management decision making was very limited, community collective action can be harnessed to enhance water and other environmental management.

Originality/value
– Adopted an interdisciplinary approach that enabled explanations to phenomenon to emerge from the perspectives of the society rather than views being suggested to them. Thus, resulting in evidence-based issues for intervention.