bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catalyzing Interdisciplinary Research and Training: Initial Outcomes and Evolution of the Affinity Research Collaboratives Model
Authors: Ravid Katya , Seta Francesca , Center David , Waters Gloria , Coleman David 
Published: April 2017

Team science has been recognized as critical to solving increasingly complex biomedical problems and advancing discoveries in the prevention, diagnosis, and treatment of human disease. In 2009, the Evans Center for Interdisciplinary Biomedical Research (ECIBR) was established in the Department of Medicine at Boston University School of Medicine as a new organizational paradigm to promote interdisciplinary team science. The ECIBR is made up of affinity research collaboratives (ARCs), consisting of investigators from different departments and disciplines who come together to study biomedical problems that are relevant to human disease and not under interdisciplinary investigation at the university. Importantly, research areas are identified by investigators according to their shared interests. ARC proposals are evaluated by a peer review process, and collaboratives are funded annually for up to three years.
Initial outcomes of the first 12 ARCs show the value of this model in fostering successful biomedical collaborations that lead to publications, extramural grants, research networking, and training. The most successful ARCs have been developed into more sustainable organizational entities, including centers, research cores, translational research projects, and training programs.
To further expand team science at Boston University, the Interdisciplinary Biomedical Research Office was established in 2015 to more fully engage the entire university, not just the medical campus, in interdisciplinary research using the ARC mechanism. This approach to promoting team science may be useful to other academic organizations seeking to expand interdisciplinary research at their institutions.
Absence of Ulnar Artery Inflow Detected by Allen’s Test Prior to Radial Forearm Free Flap
Authors: Taylor Benjamin A. , Alzahrani Faisal , Levi Eric , Taylor S. Mark , Rigby Matthew H. , Trites Jonathan , Hart Robert D. 
Published: April 2017

Summary:
Radial forearm free flaps are commonly used for soft-tissue reconstruction after resection of head and neck cancer. It is perfused by the radial artery, leaving the ulnar artery for perfusion of the hand and digits. The absence of distal ulnar artery and associated superficial palmar arch, however, has not been reported in cadaveric dissection. We report a case of unilateral ulnar artery flow absence, detected by Allen’s test, during preoperative preparation for a radial forearm free flap. Based on the simplicity, safety, and ease, we recommend Allen’s test to be performed preoperatively on every patient for whom such a flap is a consideration.
A Pilot Randomized Trial on Safety and Efficacy of a Novel Topical Combined Inhibitor of Janus Kinase 1/3 and Spleen Tyrosine Kinase for GVHD-Associated Ocular Surface Disease
Authors: Kheirkhah Ahmad , Di Zazzo Antonio , Satitpitakul Vannarut , Fernandez Merle , Magilavy Daniel , Dana Reza 
Published: April 2017

Purpose:
Janus kinase (JAK) and spleen tyrosine kinase (SYK) play critical functions in T-cell activation and in inflammation. Because of their antiinflammatory effects, JAK and SYK inhibitors have recently been evaluated in several immunopathogenic disorders. This pilot study was designed to assess the safety and efficacy of a topical combined JAK/SYK inhibitor, R348, ophthalmic solution for treatment of ocular surface disease in graft-versus-host disease (GVHD).

Methods:
This phase 2, double-masked, randomized, pilot trial included 30 patients with ocular surface disease due to GVHD who were randomized to receive topical 0.5% R348, 0.2% R348, or vehicle, twice daily for 12 weeks. Before and after treatment, a comprehensive ophthalmic evaluation was performed, which included Ocular Surface Disease Index (OSDI) questionnaire, Ocular Comfort Index questionnaire, corneal fluorescein staining, conjunctival lissamine green staining, and Schirmer test with anesthesia. Changes in these parameters were compared between the 3 groups.

Results:
The mean decrease in total corneal fluorescein staining at 12 weeks after treatment was higher in the 0.5% R348 group (−6.0 ± 3.9, NEI scoring) compared with the vehicle (−2.1 ± 2.6, P = 0.045) or the 0.2% R348 group (−4.1 ± 3.6, P = 0.34). However, there were no significant differences among the groups in terms of treatment-induced changes in OSDI, Ocular Comfort Index, conjunctival lissamine green staining, or Schirmer scores. R348 eye drops were well tolerated.

Conclusions:
This pilot study indicates that 0.5% R348 JAK/SYK inhibitor ophthalmic solution is well tolerated and may have some therapeutic efficacy in treating ocular GVHD. Larger trials are required to derive more definitive data.
Uncertainty quantification and optimal decisions
Authors: Farmer C. L. 
Published: April 2017

A mathematical model can be analysed to construct policies for action that are close to optimal for the model. If the model is accurate, such policies will be close to optimal when implemented in the real world. In this paper, the different aspects of an ideal workflow are reviewed: modelling, forecasting, evaluating forecasts, data assimilation and constructing control policies for decision-making. The example of the oil industry is used to motivate the discussion, and other examples, such as weather forecasting and precision agriculture, are used to argue that the same mathematical ideas apply in different contexts. Particular emphasis is placed on (i) uncertainty quantification in forecasting and (ii) how decisions are optimized and made robust to uncertainty in models and judgements. This necessitates full use of the relevant data and by balancing costs and benefits into the long term may suggest policies quite different from those relevant to the short term.
Quantification of cancer cell migration with an integrated experimental-computational pipeline
Authors: Juarez Edwin F. , Garri Carolina , Ghaffarizadeh Ahmadreza , Macklin Paul , Kani Kian 
Published: April 2017

AbstractWe describe an integrated experimental-computational pipeline for quantifying cell migrationin vitro.This pipeline is robust to image noise, open source, and user friendly. The experimental component uses the Oris cell migration assay (Platypus Technologies) to create migration regions. The computational component of the pipeline creates masks in Matlab (MathWorks) to cell-covered regions, uses a genetic algorithm to automatically select the migration region, and outputs a metric to quantify the migration of cells. In this work we demonstrate the utility of our pipeline by quantifying the effects of a drug (Taxol) and of the secreted Anterior Gradient 2 (sAGR2) protein in the migration of MDA-MB-231 cells (a breast cancer cell line). In particular, we show that blocking sAGR2 reduces migration of MDA-MB-231 cells.
Escalation of Memory Length in Finite Populations
Authors: Harrington Kyle , Pollack Jordan 
Published: April 2017

AbstractThe escalation of complexity is a commonly cited benefit of coevolutionary systems, but computational simulations generally fail to demonstrate this capacity to a satisfactory degree. We draw on a macroevolutionary theory of escalation to develop a set of criteria for coevolutionary systems to exhibit escalation of strategic complexity. By expanding on a previously developed model of the evolution of memory length for cooperative strategies by Kristian Lindgren, we resolve previously observed limitations to the escalation of memory length. We present long-term coevolutionary simulations showing that larger population sizes tend to support greater escalation of complexity than smaller population sizes. Additionally, escalation is sensitive to perturbation during transitions of complexity. In whole, a long-standing counter-argument to the ubiquitous nature of coevolution is resolved, suggesting that the escalation of coevolutionary arms races can be harnessed by computational simulations.
Parameter estimation in mathematical models of viral infections using R
Authors: Nguyen Van Kinh , Hernandez-Vargas Esteban A. 
Published: April 2017

AbstractIn recent years, mathematical modeling approaches have played a central role to understand and to quantify mechanisms in different viral infectious diseases. In this approach, biological-based hypotheses are expressed via mathematical relations and then tested based on empirical data. The simulation results can be used to either identify underlying mechanisms, provide predictions on infection outcomes, or evaluate the efficacy of a treatment.Conducting parameter estimation for mathematical models is not an easy task. Here we detail an approach to conduct parameter estimation and to evaluate the results using the free software R. The method is applicable to influenza virus dynamics at different complexity levels, widening experimentalists capabilities in understanding their data. The parameter estimation approach presented here can be also applied to other viral infections or biological applications.
High-resolution single-cell sequencing of malaria parasites
Authors: Trevino Simon G. , Nkhoma Standwell C. , Nair Shalini , Daniel Benjamin J. , Moncada Karla , Khoswe Stanley , Banda Rachel L. , Nosten François , Cheeseman Ian H. 
Published: April 2017

AbstractSingle-cell genomics is a powerful tool for determining the genetic structure of complex communities of unicellular organisms. Patients infected with the malaria-causing parasite,Plasmodium falciparum, often carry multiple, genetically distinct parasites. Little is known about the diversity and relatedness of these lineages. We have developed an improved single-cell genomics protocol to reconstruct individual haplotypes from infections, a necessary step in uncovering parasite ecology within the host. This approach captures singly-infected red blood cells (iRBCs) by fluorescence-activated cell sorting (FACS) prior to whole genome amplification (WGA) and whole genome sequencing (WGS). Here, we demonstrate that parasites in late cell cycle stages, which contain increased DNA content, are far superior templates for generating high quality genomic data. Targeting of these cells routinely generates near-complete capture of the 23MbP. falciparumgenome (mean breadth of coverage 90.7%) at high efficiency. We used this approach to analyze the genomes of 48 individual cells from a polyclonal malaria infection sampled in Chikhwawa, Malawi. This comprehensive dataset enabled high-resolution estimation of the clonality and the relatedness of parasite haplotypes within the infection, long-standing problems in malaria biology.
Transcription factor Rv0081 fromMycobacterium tuberculosis: purification, crystallization and initial crystallographic analysis
Authors: Dong Shishang , Ding Zhenzhen , Wang Yu , Yang Yan , Mao Yonghong , Wang Ying 
Published: April 2017

Because of its high infectivity and pathogenicity,Mycobacterium tuberculosisis a serious threat to human health. While the transcription-regulatory system ofM. tuberculosisremains incompletely understood, Rv0081, an essential regulatory hub, is known to mediate the initial response to hypoxia in the long-term survival ofM. tuberculosis. Here, the production, crystallization and initial X-ray crystallographic analysis of Rv0081 are reported. The crystals of Rv0081 belonged to space groupP62, with unit-cell parametersa= 67.48,b = 67.48,c = 40.84 Å, γ = 120°. The Matthews coefficient is 2.09 Å3 Da−1, assuming the presence of one molecule in the asymmetric unit, with a corresponding solvent content of 41.27%. Phasing of the native crystal form of Rv0081 was performed by molecular replacement. Currently, the structure has been refined to 2.00 Å resolution with anRworkof 25.99% and anRfreeof 30.88%.
Comparing the factors that influence the adoption of CPFR by retailers and suppliers
Authors: Fu Hsin-Pin 
Published: April 2017

Purpose
The purpose of this paper is to compare the factors that influenced the adoption of a Collaborative Planning, Forecasting, and Replenishment (CPFR) model by a retailer that is a lifestyle accessories chain, and a supplier that is a food manufacturer.

Design/methodology/approach
The study started with the construction of a questionnaire based on the factors of the theoretical framework of a Technology-Organization-Environment that were discovered through a literature review and distribution of the questionnaire to experts. The fuzzy analytical hierarchy process method was used to determine the weights (importance) of these factors.

Findings
The study found that among the top ten factors, two are the same for both the retailer and the supplier – “partner trust and communication,” and “support of top managers” – while the other factors differ. In addition, it was found that the supplier pays more attention to the environmental issues, while the retailer focuses on organizational issues when introducing a CPFR model.

Practical implications
This study offers five practical implications for the successful adoption of a CPFR model: first, top management support and trusting relationship building are important factors for both the retailer and the supplier; second, adoption of CPFR is a management issue, rather than a technological issue; third, retailers lead more successfully; fourth, a careful selection of collaborative partners is essential; and finally, an innovative model should be constructed.

Originality/value
The results can serve as a reference to help enterprises to better allocate their resources, according to the weights of the important adoption factors when they are formulating their strategies for the adoption of CPFR. Decisions based upon this guideline can increase the success rate of CPFR adoptions and can ensure better allocation of resources.
Estimation of salt intake of normotensive subjects of Jaipur City
Authors: Dhemla Sonal , Varma Kanika 
Published: April 2017

Purpose
There has been a dramatic increase in hypertension in developing countries along with changes in food consumption patterns contributing to higher levels of sodium. Evidence shows that a high level of sodium intake is a major cause of high blood pressure and other heart diseases along with other associated diseases. Therefore, it is important to determine current consumption levels of sodium in a population to facilitate the development and implementation of any specific salt reduction program.

Design/methodology/approach
The study was conducted among 60 subjects (25-45 years) residing in Jaipur City. Subjects’ sodium consumption levels were assessed via assessment of 24-h urinary sodium excretion levels, the “gold standard” method advocated by WHO/PAHO (2010) and 24-h dietary recall for three days including one holiday.

Findings
The findings of the study indicated that the subjects were found to be consuming higher levels of sodium (males, 5,792 mg/d; females, 5,911 mg/d) than recommended by WHO, i.e. less than 2,300 mg/d. Completeness of urine was confirmed by fat-free mass determined by electrical bio-impedance (47.6 ± 7.6 kg) and determined by using 24-h urinary excretion of creatinine (33.7 ± 10.1 kg). Two variables were found to be significantly correlated (r = 0.52, p = 0.00). Assuming that the sodium eliminated in the urine comes from the salt only, this excretion would correspond with a dietary salt intake of 14.71 and 15.01 g/d in males and females, respectively. Dietary sodium intake was reported to be 4,133 ± 1,111 mg/day and 3,953 ± 945 mg/d in males and females, respectively. A non-significant difference was found between the two variables. Urinary sodium excretion correlated non-significantly with systolic and diastolic blood pressure figures (r = 0.09 and r = −0.02, respectively).

Research limitations/implications
The limitations of this study included the small sample size. Purposive sampling was adopted due to difficulty in obtaining urine sample and required willingness of the respondent. This may give fair robust estimate.

Originality/value
The present results will help provide new data about the baseline salt intake in young and middle-aged population of Jaipur City and will further help the concerned agencies to plan meaningful strategies to reduce salt intake, and it must involve public education and awareness to change the consumption pattern.
Optimization of olive pomace enzymatic hydrolysis for fermentable sugar production
Authors: Abo Chameh Ghassan , Kheder Fadi , Karabet Francois 
Published: April 2017

PurposeThe purpose of this paper was to find out the appropriate enzymatic hydrolysis conditions of alkali pretreated olive pomace (OP) which enable maximum yield of reducing sugar.Design/methodology/approachThe commercial enzymatic preparation (Viscozyme®L) was used for the hydrolysis of OP. The effects of pretreatment, time, temperature, pH, enzyme quantity and substrate loading on the hydrolysis yield were investigated.FindingsThis study showed that enzymatic hydrolysis of OP using Viscozyme®L can be successfully performed at 50°C. Alkaline pretreatment step of OP prior the enzymatic hydrolysis was indispensable. The hydrolysis yield of alkaline pretreated OP was 2.6 times higher than the hydrolysis yield of untreated OP. Highest hydrolysis yield (33.5 ± 1.5 per cent) was achieved after 24 h using 1 per cent (w/v) OP load in the presence of 100 μl Viscozyme®L at 50°C and pH 5.5 with mixing rate of 100 rpm (p= 0.05).Originality/valueReaction time, temperature, pH value and enzyme quantity were found to have a significant effect on enzymatic hydrolysis yield of alkali pretreated of OP. Although high-solid loadings of OP lowered the hydrolysis yield, it produced higher concentration of reducing sugars, which may render the OP conversion process more economically feasible.
Quality characteristics and overall acceptability of steamed and boiled blue whiting fish (Micromesistius poutassou) cracker
Authors: Omoba Olufunmilayo Sade , Azeez Hafsat Idowu 
Published: April 2017

Purpose
This paper focuses on the quality characteristics of steamed and boiled blue whiting fish (Micromesistius poutassou) cracker, with the aim of encouraging and promoting the use of this small pelagic inexpensive, readily available fish in food production and reducing post-harvest losses of the fish.

Design/methodology/approach
The blue whiting fish cracker was developed using boiling and steaming methods. Minced blue whiting fish meat was mixed with cassava starch in the ratio of 50:50, and other ingredients were incorporated. The dough obtained was divided into two and stuffed into two different muslin cloths. One of the stuffed dough was steamed (100°C for 15 min), whereas the other was boiled in water for 90 min. The boiled and steamed doughs were cooled at 4°C for 12 h, sliced at 2 mm thickness and oven dried at 50°C for 12 h to obtain non-expanded blue whiting fish crackers. The non-expanded blue whiting fish crackers were fried in vegetable oil to obtain expanded blue whiting fish crackers. The quality characteristics of the expanded crackers were determined using standard methods, and data obtained were subjected to analysis of variance; the mean scores were compared using Turkey’s (HSD) test. The sensory evaluation was done using 25 untrained panellists, and results were analysed statistically.

Findings
The study revealed the steamed fish cracker has significantly higher nutritional composition in terms of the proximate, mineral, fatty acid and amino acid compositions. Potassium was the most predominant mineral in the crackers, and copper was the least predominant mineral. The saturated fatty acid contents were 43.2 per cent (steamed) and 48.6 per cent (boiled), whereas the unsaturated fatty acid contents were 55.5 (steamed) and 48.5 per cent (boiled). The n6/n3 ratio obtained for steamed and boiled fish cracker was 4.0. The steamed fish cracker had a higher L* value, whereas the Brown index (100 − L*) of the steamed fish cracker was lower (33.4) than that of the boiled fish cracker. The linear expansion was higher for the boiled blue whiting fish crackers (41.8 per cent). The boiled blue whiting fish cracker had higher expanded starch structure than the steamed blue whiting fish cracker. The aroma and taste were highly correlated with overall acceptability.

Originality/value
The paper reports the quality characteristics and overall acceptability of steamed and boiled blue whiting fish crackers.
Data collaboratives as “bazaars”?
Authors: Susha Iryna , Janssen Marijn , Verhulst Stefaan 
Published: April 2017

Purpose
In “data collaboratives”, private and public organizations coordinate their activities to leverage data to address a societal challenge. This paper aims to focus on analyzing challenges and coordination mechanisms of data collaboratives.

Design/methodology/approach
This study uses coordination theory to identify and discuss the coordination problems and coordination mechanisms associated with data collaboratives. The authors also use a taxonomy of data collaborative forms from a previous empirical study to discuss how different forms of data collaboratives may require different coordination mechanisms.

Findings
The study analyzed data collaboratives from the perspective of organizational and task levels. At the organizational level, the authors argue that data collaboratives present an example of the bazaar form of coordination. At the task level, the authors identified five coordination problems and discussed potential coordination mechanisms to address them, such as coordination by negotiation, by third party, by standardization, to name a few.

Research limitations/implications
This study is one of the first few to systematically analyze the phenomenon of “data collaboratives”.

Practical implications
This study can help practitioners better understand the coordination challenges they may face when initiating a data collaborative and to develop successful data collaboratives by using coordination mechanisms to mitigate these challenges.

Originality/value
Data collaboratives are a novel form of data-driven initiatives which have seen rapid experimentation lately. This study draws attention to this concept in the academic literature and highlights some of the complexities of organizing data collaboratives in practice.
Open data driven public accountability
Authors: Lourenço Rui Pedro , Piotrowski Suzanne , Ingrams Alex 
Published: April 2017

Purpose
This paper aims to analyse extant literature on open data, distinguish and categorize the strands of public accountability research and use the results to provide better clarity in the concept of open data-driven public accountability.

Design/methodology/approach
Systematic review of 135 open data articles and 155 accountability articles from the e-government reference library. A multi-stage analysis results in 12 articles which are categorized using Bovens’ (2007) accountability theory of information, discussion and consequences. Conceptual development, using the literature analysis, forms the final section of the paper.

Findings
Research demonstrates that a range of open data topics has been advanced. However, just 12 articles exist that simultaneously address open data and accountability theory. Of the total 155 public accountability articles, the preponderant focus is on the information (N = 25) and discussion (N = 7) stages of the accountability process. Just one article focuses on the complete accountability process. To address this problem, the characterization of open (government) data-driven public accountability establishes conceptual crispness and clarity.

Originality/value
Public accountability theory on open government has become overshadowed by social and economic value perspectives. This paper clarifies and advances the open data-driven public accountability perspective. It takes stock of public accountability research, delimits the key issues and questions and highlights the next steps needed for developing scholarship.