bluuebunny/crossref_metadata_2025 huggingface dataset:
Science, patronage, and academies in early seventeenth-century Portugal: The scientific academy of the nobleman and university professor André de Almada
Authors: Carolino Luís Miguel
Published: September 2016

This paper revisits the historiography of seventeenth-century scientific academies by analyzing an informal academy established in Coimbra (Portugal) by André de Almada, a nobleman and professor of theology at the University of Coimbra. By promoting this academy and sponsoring the publication of science books, Almada stimulated research on astronomy and animated links of patronage, which included not only members of the universities but also the community of astronomers and astrologers active in Lisbon. This paper challenges the traditional view of academic societies as innovative institutions opposed to the old-fashioned universities and provides an insight into the complex relationship established between patronage, the institutional settings, and the practices of science in a country wherein science was poorly institutionalized and political power increasingly centralized.
Patient Perceptions About Prediabetes and Preferences for Diabetes Prevention
Authors: O’Brien Matthew J. , Moran Margaret R. , Tang Joyce W. , Vargas Maria C. , Talen Mary , Zimmermann Laura J. , Ackermann Ronald T. , Kandula Namratha R.
Published: September 2016

Purpose

The purpose of this study was to explore how adults with prediabetes perceive their risk of developing diabetes and examine their preferences for evidence-based treatment options to prevent diabetes.

Methods

A qualitative study was conducted in 2 large Midwest primary care practices, involving in-depth semistructured interviews with 35 adult patients with prediabetes.

Results

This ethnically diverse (77% nonwhite) sample of middle-aged primary care patients exhibited multiple diabetes risk factors. Knowledge gaps about prediabetes and its medical management were pervasive. Most patients overestimated the risk of developing diabetes and were not familiar with evidence-based treatment options for prediabetes. They suggested that receiving brief, yet specific information about these topics during the study interview motivated them to act. The majority of participants considered both intensive lifestyle intervention and metformin acceptable treatment options. Many preferred initial treatment with intensive lifestyle intervention but would take metformin if their efforts at lifestyle change failed and their primary care physician recommended it. Some participants expressed wanting to combine both treatments.

Conclusions

This qualitative study highlights potential opportunities to promote patient-centered dialogue about prediabetes in primary care settings. Providing patients specific information about the risk of developing diabetes and evidence-based treatment options to prevent or delay its onset may encourage action. Physicians’ prediabetes counseling efforts should be informed by the finding that most patients consider both intensive lifestyle intervention and metformin acceptable treatment options.
A Comparison of the Use of Clinical-Guideline–Recommended Antihypertensive Regimens in Mexican American, Non-Hispanic Black, and Non-Hispanic White Adults With Type 2 Diabetes and Hypertension in the United States
Authors: Perez Alexandra , Levin Andrea , Alam Nowrin
Published: September 2016

Purpose

The purpose of this study was to determine the use of clinical-guideline–recommended antihypertensive regimens among Mexican Americans (MAs) and non-Hispanic blacks and whites with type 2 diabetes and hypertension.

Methods

A secondary data analysis based on National Health and Nutrition Examination Survey 2003-2012 cohort data included 1857 noninstitutionalized civilian MA, black, and white adults with type 2 diabetes and hypertension. Unadjusted and adjusted 2-way analysis of variance models evaluated whether there was a difference in the use of recommended antihypertensive regimens across race/ethnic group.

Results

There was no difference in the use of recommended regimens across race/ethnic group (MAs, 79.1%; blacks, 81.7%; whites, 82.3%). Similarly, there was no difference between blood pressure goal levels and the use of recommended therapies across race/ethnicity ( P = .632). Mexican Americans were least likely and blacks most likely to be on 3 or more antihypertensive drug classes (16.8% vs 28%). Furthermore, MAs were least likely to be on recommended add-on therapies such as calcium channel blockers and diuretics.

Conclusion

Racial/ethnic medication use disparities were observed when looking at the number of antihypertensive drug classes per patient regimen, and add-on therapy use was evaluated. Along with lifestyle modifications, frequent antihypertensive regimen reassessment is necessary.
Implementing the PAINRelieveIt Randomized Controlled Trial in Hospice Care: Mechanisms for Success and Meeting PCORI Methodology Standards
Authors: Ezenwa Miriam O. , Suarez Marie L. , Carrasco Jesus D. , Hipp Theresa , Gill Anayza , Miller Jacob , Shea Robert , Shuey David , Zhao Zhongsheng , Angulo Veronica , McCurry Timothy , Martin Joanna , Yao Yingwei , Molokie Robert E. , Wang Zaijie (Jim) , Wilkie Diana J.
Published: September 2016

This purpose of this article is to describe how we adhere to the Patient-Centered Outcomes Research Institute’s (PCORI) methodology standards relevant to the design and implementation of our PCORI-funded study, the PAIN RelieveIt Trial. We present details of the PAIN RelieveIt Trial organized by the PCORI methodology standards and components that are relevant to our study. The PAIN RelieveIt Trial adheres to four PCORI standards and 21 subsumed components. The four standards include standards for formulating research questions, standards associated with patient centeredness, standards for data integrity and rigorous analyses, and standards for preventing and handling missing data. In the past 24 months, we screened 2,837 cancer patients and their caregivers; 874 dyads were eligible; 223.5 dyads consented and provided baseline data. Only 55 patients were lost to follow-up—a 25% attrition rate. The design and implementation of the PAIN RelieveIt Trial adhered to PCORI’s methodology standards for research rigor.
High Rate of Return to Running for Athletes After Hip Arthroscopy for the Treatment of Femoroacetabular Impingement and Capsular Plication
Authors: Levy David M. , Kuhns Benjamin D. , Frank Rachel M. , Grzybowski Jeffrey S. , Campbell Kirk A. , Brown Sara , Nho Shane J.
Published: September 2016

Background:

Femoroacetabular impingement (FAI) is most commonly diagnosed in athletes who sustain repetitive flexion loading to their hips. No studies to date have focused solely on patients’ return-to-running ability after hip arthroscopy.

Purpose:

To evaluate patients’ ability to return to running after hip arthroscopy for FAI and capsular plication.

Study Design:

Case series; Level of evidence, 4.

Methods:

Clinical data were retrospectively retrieved for 51 consecutive patients with FAI (22 men, 29 women) who had undergone hip arthroscopy for the treatment of FAI and identified themselves as recreational or competitive runners on intake forms. Two-year outcome measures included the modified Harris Hip Score (mHHS) and the Hip Outcome Score Activities of Daily Living (HOS-ADL) and Sport-Specific (HOS-SS) subscales. A postoperative return-to-running survey was used to obtain running-specific information.

Results:

Patient age and body mass index (BMI) were a mean (±SD) of 26.3 ± 7.8 years and 23.7 ± 3.3 kg/m2, respectively. Before surgery, patients had refrained from running because of pain for a mean of 8.1 ± 5.7 months. After surgery, 48 patients (94%) returned to running at a mean of 8.5 ± 4.2 months. Patients who had discontinued running for more than 8 months before surgery had a longer return-to-running time than did those who had stopped for less than 8 months (10.6 ± 4.2 vs 7.6 ± 4.1 months; P = .01). After 2 years, mean preoperative distance had decreased significantly ( P < .01) from 9.5 ± 6.5 miles per week when healthy to 6.4 ± 5.8 miles postoperatively. Despite decreased mileage, all 2-year outcomes scores improved significantly ( P < .001).

Conclusion:

Recreational and competitive runners with FAI returned to running 94% of the time at a mean of 8.5 months after hip arthroscopy. However, runners should be counseled before their surgery that they may run fewer miles than when they were pain free. Additionally, patients with a higher BMI and/or longer preoperative lull may have a longer recovery time.
Internet Dependence in an Undergraduate Population
Authors: Odacı Hatice , Çelik Çiğdem B.
Published: September 2016

This study examined the relationship between Internet dependence in university students and forms of coping with stress and self-efficacy and investigated whether Internet dependence varies according to such variables as sex roles, gender, and duration of Internet use. The study was performed with 632 university students. The Internet Addiction Test, the Coping With Stress Scale, the General Self-Efficacy Scale, the Bem Sex Role Inventory Test, and a Personal Information Form were used in the collection of data. Results revealed a significant negative correlation between Internet dependence and the seeking social support form of coping with stress. A significant negative correlation was also determined between Internet dependence and self-efficacy. In addition, university students’ Internet addiction scores varied significantly depending on sex roles.
Career counselling development
Authors: Papakota Aikaterini
Published: September 2016

Promoting the use of new technologies in the career counselling process, the Career Services Office of the Aristotle University of Thessaloniki has developed an easy-to-use career counselling guide containing multimedia applications. The purpose of this career guide, called ‘Career Counseling@Career Office of Aristotle University of Thessaloniki’, is to support students and graduates in the development of their professional skills using interactive exercises and self-presentation sample tools. It also contains, in written and/or visual form, career information, success stories of fellow students and graduates and videos with advice and tips from human resources managers, recruiters and academic staff. The sections of the electronic guide are organized as ‘stations’ that may help the student or graduate in career decision-making, planning and organizing job searches in Greece and abroad, identifying training opportunities and achieving career goals in general. This innovative application is used in combination with personal and group career counselling services. This article explains the rationale for the application in terms of its usage and the expanded functionality it offers career counsellors in higher education institutions.
Integrating entrepreneurship education across university-wide curricula
Authors: Kalimasi Perpetua Joseph , Herman Chaya
Published: September 2016

This qualitative case study explores the integration of entrepreneurship education (EE) across the curricula in two public universities in Tanzania. Based on Shapero’s model of the entrepreneurial event, the feasibility and desirability of EE in the selected universities are analysed. In-depth interviews and document analysis were used for data collection. The findings show that cross-curricula EE remains limited, largely because its implementation does not fit the pedagogical needs of some disciplines. However, the study highlights the significant role of donor support in enhancing the feasibility of fostering EE across the curricula.
Nursing’s professional respect as experienced by hospital and community nurses
Authors: Stievano Alessandro , Bellass Sue , Rocco Gennaro , Olsen Douglas , Sabatino Laura , Johnson Martin
Published: September 2016

Background:

There is growing awareness that patient care suffers when nurses are not respected. Therefore, to improve outcomes for patients, it is crucial that nurses operate in a moral work environment that involves both recognition respect, a form of respect that ought to be accorded to every single person, and appraisal respect, a recognition of the relative and contingent value of respect modulated by the relationships of the healthcare professionals in a determined context.

Research question/aim:

The purpose of this study was to develop better understandings of perceptions of nursing’s professional respect in community and hospital settings in England.

Research design:

The research design was qualitative. Focus groups were chosen as the most appropriate method for eliciting discussion about nursing’s professional respect.

Participants and research context:

A total of 62 nurses who had been qualified for at least a year and were working in two localities in England participated in this study.

Methods:

Data were collected using 11 focus group sessions. The data were analysed by means of an inductive content analysis, extracting meaning units from the information retrieved and classifying the arising phenomena into conceptually meaningful categories and themes.

Ethical considerations:

To conduct the research, permission was obtained from the selected universities.

Results:

Recognition respect of human beings was perceived as ingrained in the innermost part of nurses. Regarding appraisal respect, a great importance was placed on: the interactions among healthcare professionals, the time to build trust in these relationships, the influences of the workplace characteristics and nurses’ professional autonomy and decision-making.

Conclusion:

Recognition respect of persons was embedded in the inmost part of nurses as individuals. Concerning appraisal respect, it was thought to be deeply enshrined in the inter- and intra-healthcare professional interactions. The forging of trusting relationships over time was deemed to be strongly associated with good quality interactions with other healthcare professionals.
Using the Department of Labor’s “My Next Move” to Improve Career Preparedness
Authors: Koys Daniel J.
Published: September 2016

The Department of Labor’s Occupational Information Network can help students prepare for their careers because it contains information on over 900 occupations. Occupational Information Network includes a tool called My Next Move that is designed to help people learn about those occupations. This research uses a pretest/posttest design with a treatment group and a control group to determine if an exercise based on My Next Move improves career preparedness. Results show that the exercise produces significant increases in career awareness and in perceived career preparedness skills. The positive results indicate that this tool can help students be more knowledgeable about their career options after graduation. This article can help instructors use the My Next Move exercise to help students in their job search process.
Dentigerous Cyst and Ameloblastoma of the Jaws
Authors: Barrett Andrew W. , Sneddon Kenneth J. , Tighe John V. , Gulati Aakshay , Newman Laurence , Collyer Jeremy , Norris Paul M. , Coombes Darryl M. , Shelley Michael J. , Bisase Brian S. , Liebmann Rachael D.
Published: September 2016

Aim. To determine how many ameloblastomas were misdiagnosed as dentigerous cysts (DCs) by correlating the radiological and histopathological features of a series of both entities. Methods and results. Histopathology reports and radiological imaging of 135 DCs and 43 ameloblastomas were reviewed. Any clinical or radiological feature that suggested that the diagnosis of DC was wrong—for example, absence of an unerupted tooth—prompted review of the original histology. A total of 34 cases coded as DC at diagnosis were excluded; in the remaining 101 patients, the clinicoradiological and histopathological features were consistent with DC in 96 (95.0%). Review of the histology revealed that 4 patients had actually had odontogenic keratocysts (OKCs) and one a luminal/simple unicystic ameloblastoma (UA). One other OKC and 3 other ameloblastomas (1 luminal UA, 2 solid/multicystic) had originally been diagnosed as DC; these had been identified prior to the study. Of the 9 misdiagnosed patients, 6 were ≤20 years old. Clinically, DC had been the only, or one of the differential, diagnoses in 7 patients; in the other 2, the clinical diagnosis was radicular cyst. In none of the 4 misdiagnosed ameloblastomas was the radiology compatible with a diagnosis of DC. Incorrect terminology had been used on the histopathology request form in 5 of the 34 excluded cases where the clinical diagnosis was DC, despite the cyst being periapical to an erupted carious or root-filled tooth. Conclusions. The entire clinical team must ensure that a histopathological diagnosis of DC is consistent with the clinicoradiological scenario, particularly in younger patients.
Expanding Women’s Participation in STEM
Authors: Falk Nikki A. , Rottinghaus Patrick J. , Casanova Tracy N. , Borgen Fred H. , Betz Nancy E.
Published: September 2016

Despite social cognitive and cultural barriers, women continue to consider and declare science, technology, engineering, and math (STEM) majors. Research suggests that both self-efficacy and interest are necessary to approach a career goal; however, women in STEM report lower interest and confidence compared to their male counterparts. Using integrative career profiles of 448 potential and declared STEM majors, we investigated Realistic, Investigative, Artistic, Social, Enterprising, and Conventional thresholds of self-efficacy and interest among women and men using the career and personality assessments integrative online system. Results indicated gender as a moderator for the Realistic threshold, where women have a lower threshold for approaching and declaring a STEM major compared with men. Women in this sample showed similar levels of Investigative self-efficacy and interests compared with men. This study adds to prior literature investigating people–thing orientations among men and women in STEM. These results may be utilized in broadening female participation in STEM and alleviating underrepresentation.
Relationship of Radiographic and Clinical Parameters With Hallux Valgus and Second Ray Pathology
Authors: Gribbin Caitlin K. , Ellis Scott J. , Nguyen Joseph , Williamson Emilie , Cody Elizabeth A.
Published: September 2016

Background:

Hallux valgus is frequently associated with additional forefoot pathologies, including hammertoes and midfoot osteoarthritis (OA). However, the pathogenesis of these concurrent pathologies remains to be elucidated. We sought to determine whether there is a relationship between demographic and radiographic parameters and the incidence of secondary pathologies in the setting of a bunion, with an emphasis on second tarsometatarsal (TMT) OA and hammertoes.

Methods:

A total of 153 patients (172 feet) who underwent reconstruction for hallux valgus were divided into 3 groups: (1) bunion only (61 patients), (2) bunion with hammertoe without second TMT joint OA (78 patients), and (3) bunion with second TMT joint OA (14 patients). Preoperative age, sex, and body mass index (BMI) as well as hallux valgus angle (HVA), intermetatarsal angle (IMA), metatarsus adductus angle (MAA), ratio of second to first metatarsal length, and Meary’s angle were recorded. One-way analysis of variance (normality demonstrated) and Kruskal-Wallis (normality not demonstrated) tests were used to assess differences in continuous variables. Post hoc tests were conducted with the Bonferroni technique. Associations between discrete variables and the study groups were analyzed using χ2 tests. Following the univariate analysis, multinomial logistic regression models were built to determine potential risk factors for hammertoe or TMT OA group placement.

Results:

Patients in the hammertoe and TMT OA groups were significantly older than patients in the bunion only group ( P < .001 for both pairwise comparisons) and had significantly higher BMIs ( P = .024 and P < .001, respectively). Patients in the TMT OA group had a significantly higher mean HVA than patients in the bunion-only group ( P = .004) and a significantly higher mean MAA relative to both other study groups ( P ≤ .001 for both comparisons). IMA, Meary’s angle, and the ratio of second to first metatarsal length did not differ significantly between groups. In the multivariate analysis, hammertoe group assignment was predicted only by age and HVA, while midfoot OA group assignment was predicted by age, HVA, BMI, and MAA.

Conclusion:

Our data show that older age and increased HVA were predictors of both second ray pathologies studied. Higher BMI and MAA were predictive only of TMT joint OA. These data may help identify patients with hallux valgus who are at greater risk for developing secondary pathologies.

Level of Evidence:

Level III, retrospective comparative series.
Mapping the Terrain
Authors: Christianson Marlys K.
Published: September 2016

My article examines how researchers use video recordings to gain insight into organizational phenomena. I conduct a literature review of articles published from 1990 to 2015 in six top-tier organizational journals: Academy of Management Journal, Administrative Science Quarterly, Journal of Management Studies, Organization Science, Organization Studies, and Strategic Management Journal. My review identifies 56 articles where video was central to the research design. My analysis demonstrates how researchers used the audible, visible, and timing affordances of video recordings to investigate organizational phenomena, including rhetoric, emotion, group interactions, and workplace studies. By exploring how researchers studied these phenomena, I show how video illuminates aspects of situated action and interaction that are difficult to evaluate using other kinds of data. My review contributes to the literature on video in organization studies by providing an overview of video-based research in these journals, highlighting the diversity of approaches used to collect and analyze video, and illustrating some of the ways that video helped to advance knowledge around organizational phenomena.
Not everyone knows what a zebroid is
Authors: Kogler Michael R
Published: September 2016

The Austrian Case C-347/14, New Media Online v. Bundeskommunikationssenat, of October 2015 gave the Court of Justice of the European Union the opportunity to clarify whether the video content of a newspaper website is covered by the European Union (EU) audiovisual media services directive (AVMSD). Advocate General Szpunar explained what was, in his view, the EU legislature’s alleged intention underlying the Directive’s definition of an audiovisual media service. The Court was not convinced by his argument and instead unambiguously concurred with the two Austrian regulatory authorities: not only films and broadcasts of long duration are governed by the AVMSD but also shorter forms of moving image material, even when these are part of a newspaper’s online offering. Assuming that this decision will significantly influence the European Commission’s plans for a ‘new’ Directive, what are the implications for a new media framework for the 21st century?
Ethnic media as communities of practice: The cultural and institutional identities
Authors: Yu Sherry S
Published: September 2016

In an increasingly multicultural, multiethnic, and multilingual media environment, ethnic media are an important part of the public sphere, and the process in which ethnic discourse is produced deserves attention. This article advances Husband’s work on ethnic media as communities of practice by exploring ethnic media of young diaspora. Just as ethnic communities are heterogeneous across ethnic groups, depending on immigration history, demographics, and communication infrastructure, among other factors, ethnic media as communities of practice are never homogeneous and lineal practices. The case of Korean media in Vancouver and Los Angeles, one of the most rapidly growing ethnic media sectors in North America, suggests two new identities – cultural identity and institutional identity – in addition to the journalists’ subjective identities, which Husband discussed. These two identities that are specific to Korean media confirm diversity within communities of practice and suggest the variations to be considered in the broader discussion of ethnic media as communities of practice.
Graphing trillions of triangles
Authors: Burkhardt Paul
Published: September 2016

The increasing size of Big Data is often heralded but how data are transformed and represented is also profoundly important to knowledge discovery, and this is exemplified in Big Graph analytics. Much attention has been placed on the scale of the input graph but the product of a graph algorithm can be many times larger than the input. This is true for many graph problems, such as listing all triangles in a graph. Enabling scalable graph exploration for Big Graphs requires new approaches to algorithms, architectures, and visual analytics. A brief tutorial is given to aid the argument for thoughtful representation of data in the context of graph analysis. Then a new algebraic method to reduce the arithmetic operations in counting and listing triangles in graphs is introduced. Additionally, a scalable triangle listing algorithm in the MapReduce model will be presented followed by a description of the experiments with that algorithm that led to the current largest and fastest triangle listing benchmarks to date. Finally, a method for identifying triangles in new visual graph exploration technologies is proposed.
HiGame: Improving elderly well-being through horticultural interaction
Authors: Wu Yi-Sin , Chang Teng-Wen , Datta Sambit
Published: September 2016

Family support is the key to the well-being problems of elderly. Unlike health problem, mental problem often depends on the social network of elderly. How to enhance elderly well-being problems will become how to increase the interaction between elderly and their family. Horticultural interaction proves to be an effective but smooth impact on improving well-being problems of elderly. By designing a horticultural interaction game for motivating or invoking the communication between elderly and their family members, the prototype is developed based on the framework of behavior setting and semi-fixed features. Three groups of games, physical games, virtual games, and spatial interaction games, are analyzed and 14 cases are studied and evaluated for the features required. Particularly, spatial interaction games with both physical and virtual games are brought into scope, and HiGame (Horticultural Interaction Game, hi game) is developed. Five scenarios using sensor network and mobile interface are unleashed and tested in an experiment with two sets of elderly family participants. HiGame has connection to both physical and virtual spaces for elderly and their family. Elderly interact with distant family through physical watering, weeding, and fertilizing. And distant family use virtual game to support elderly. The interaction process can be further enhanced with the following: (1) separating the tasks for elderly and family ends individually and then cooperating together might enforce the intergenerational interaction and reflection on cooperation in the gaming process; (2) the connection among each scenario can be further developed into a different process, such as competition of different members for helping the elderly to complete certain task might motivate the game experience further.
Renal Transplantation and Outcome
Authors: Manfredini Roberto , Gallerani Massimo , De Giorgi Alfredo , Tiseo Ruana , Lamberti Nicola , Manfredini Fabio , Forcellini Silvia , Storari Alda , La Manna Gaetano , Fabbian Fabio
Published: September 2016

Emergency surgery represents an independent risk factor for death and postoperative complications. The aim of this study was to investigate the literature data regarding outcome of daytime or nighttime renal transplantation surgery. Relevant papers, focused on renal transplantation surgery, time of the day, and complications, were searched across the PubMed database. We used the following search terms: “renal”, “transplantation”, “surgery”, “daytime”, “nighttime”, and “outcome”. A total of five papers, including 6,991 adult patients were evaluated. All patients received renal transplantation from deceased donor. Daytime or nighttime surgery do not seem to negatively impact on graft survival in renal transplantation. However, two out five studies reported higher odds of complications after nighttime operation. Since it is not possible to predict the availability of a deceased donor, nighttime surgery remains a valid option when necessary, maybe deserving a higher level of caution to reduce or avoid complications.
A distributed algorithm for maximizing utility of data collection in a crowd sensing system
Authors: Chen Qinghua , Weng Zhengqiu , Han Yang , Zhu Yanmin
Published: September 2016

Mobile crowd sensing harnesses the data sensing capability of individual smartphones, underpinning a variety of valuable knowledge discovery, environment monitoring, and decision-making applications. It is a central issue for a mobile crowd sensing system to maximize the utility of sensing data collection at a given cost of resource consumption at each smartphone. However, it is particularly challenging. On the one hand, the utility of sensing data from a smartphone is usually dependent on its context which is random and varies over time. On the other hand, because of the marginal effect, the sensing decision of a smartphone is also dependent on decisions of other smartphones. Little work has explored the utility maximization problem of sensing data collection. This article proposes a distributed algorithm for maximizing the utility of sensing data collection when the smartphone cost is constrained. The design of the algorithm is inspired by stochastic network optimization technique and distributed correlated scheduling. It does not require any prior knowledge of smartphone contexts in the future, and hence sensing decisions can be made by individual smartphone. Rigorous theoretical analysis shows that the proposed algorithm can achieve a time average utility that is within O(1/ V) of the theoretical optimum.
Making quality improvement simple: The Model for Improvement
Authors: Raymond Mareeni , Dawda Paresh
Published: September 2016

In our first article, ‘An introduction to quality improvement’, we discussed the philosophy and principles of quality improvement and suggested that a structured and systematic approach to quality improvement is necessary. In this article we discuss the Model for Improvement as a simple and effective framework to achieve this objective.
Melissa officinalis L: A Review Study With an Antioxidant Prospective
Authors: Miraj Sepide , Rafieian-Kopaei  , Kiani Sara
Published: September 2016

Melissa officinalis is a plant cultivated in some parts of Iran. The leaves of lemon balm, Melissa officinalis L (Lamiaceae), are used in Iranian folk medicine for their digestive, carminative, antispasmodic, sedative, analgesic, tonic, and diuretic properties, as well as for functional gastrointestinal disorders. This review article was aimed not only to introduce Melissa officinalis (its growth condition, its chemical compounds, and its traditional usages) but also to overview its antioxidant properties in detail. This review was carried out by searching studies in PubMed, Medline, Web of Science, and IranMedex databases up to 2016. The search terms used were “ Melissa officinalis L,” “antioxidant properties,” oxidative stress,” “oxidative damage”, “ROS.” Articles whose full texts were not available were excluded from the study. In this study, firstly, traditional usage of this herb was reviewed, including antimicrobial activity (antiparasitic, antibacterial, antiviral, etc), antispasmodic, and insomnia properties. Then, its antioxidant properties were overviewed. Various studies have shown that Melissa officinalis L possesses high amount of antioxidant activity through its chemical compounds including high amount of flavonoids, rosmaric acid, gallic acid, phenolic contents. Many studies confirmed the antioxidative effects of Melissa officinalis; thus, its effect in preventing and treating oxidative stress-related diseases might be reliable.
Drop a Pebble in the Water
Authors: Black Kate , Warhurst Russell
Published: September 2016

This article responds to Stoten’s (2016) article in Management Teaching Review on the use of PebblePad+ (PP+) to support learning, teaching, and assessment. We examined the realities of efforts to engender curriculum change using PP+ on a large undergraduate thesis course within a U.K. business school. We analyzed 2,143 emails between the 123 supervising-faculty and the professors leading the course. Field notes supplemented these data. We have demonstrated that while 18 supervising-faculty asserted the value of the use of PP+ (14.6%), the majority of faculty (54.5%) expressed concerns about using this technology, with eight supervisors failing to use the technology at all. We propose that these latter reactions resulted from a lack of self-efficacy with technology, a perceived task–technology mismatch, and perhaps, most significant, a threatened sense-of-self as “expert” in the eyes of their students and peers. We offer three key recommendations for readers who are considering technology-mediated change.
IL1RAP antibodies block IL-1–induced expansion of candidate CML stem cells and mediate cell killing in xenograft models
Authors: Ågerstam Helena , Hansen Nils , von Palffy Sofia , Sandén Carl , Reckzeh Kristian , Karlsson Christine , Lilljebjörn Henrik , Landberg Niklas , Askmyr Maria , Högberg Carl , Rissler Marianne , Porkka Kimmo , Wadenvik Hans , Mustjoki Satu , Richter Johan , Järås Marcus , Fioretos Thoas
Published: September 2016

Key Points

IL-1 activates signaling and promotes proliferation of primitive CML cells. IL1RAP antibodies block IL-1–induced effects and mediate cell killing in chronic and blast phase CML in vivo models.
NBLDA: negative binomial linear discriminant analysis for RNA-Seq data
Authors: Dong Kai , Zhao Hongyu , Tong Tiejun , Wan Xiang
Published: September 2016

Background

RNA-sequencing (RNA-Seq) has become a powerful technology to characterize gene expression profiles because it is more accurate and comprehensive than microarrays. Although statistical methods that have been developed for microarray data can be applied to RNA-Seq data, they are not ideal due to the discrete nature of RNA-Seq data. The Poisson distribution and negative binomial distribution are commonly used to model count data. Recently, Witten (Annals Appl Stat 5:2493–2518, 2011) proposed a Poisson linear discriminant analysis for RNA-Seq data. The Poisson assumption may not be as appropriate as the negative binomial distribution when biological replicates are available and in the presence of overdispersion (i.e., when the variance is larger than or equal to the mean). However, it is more complicated to model negative binomial variables because they involve a dispersion parameter that needs to be estimated.

Results

In this paper, we propose a negative binomial linear discriminant analysis for RNA-Seq data. By Bayes’ rule, we construct the classifier by fitting a negative binomial model, and propose some plug-in rules to estimate the unknown parameters in the classifier. The relationship between the negative binomial classifier and the Poisson classifier is explored, with a numerical investigation of the impact of dispersion on the discriminant score. Simulation results show the superiority of our proposed method. We also analyze two real RNA-Seq data sets to demonstrate the advantages of our method in real-world applications.

Conclusions

We have developed a new classifier using the negative binomial model for RNA-seq data classification. Our simulation results show that our proposed classifier has a better performance than existing works. The proposed classifier can serve as an effective tool for classifying RNA-seq data. Based on the comparison results, we have provided some guidelines for scientists to decide which method should be used in the discriminant analysis of RNA-Seq data. R code is available at http://www.comp.hkbu.edu.hk/~xwan/NBLDA.Ror https://github.com/yangchadam/NBLDA
Tissue enrichment analysis for C. elegans genomics
Authors: Angeles-Albores David , N. Lee Raymond Y. , Chan Juancarlos , Sternberg Paul W.
Published: September 2016

Background

Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze these datasets is to associate ontologies (hierarchical, descriptive vocabularies with controlled relations between terms) with genes and to look for enrichment of specific terms. Although Gene Ontology (GO) is available forCaenorhabditis elegans, it does not include anatomical information.

Results

We have developed a tool for identifying enrichment ofC. eleganstissues among gene sets and generated a website GUI where users can access this tool. Since a common drawback to ontology enrichment analyses is its verbosity, we developed a very simple filtering algorithm to reduce the ontology size by an order of magnitude. We adjusted these filters and validated our tool using a set of 30 gold standards from Expression Cluster data in WormBase. We show our tool can even discriminate between embryonic and larval tissues and can even identify tissues down to the single-cell level. We used our tool to identify multiple neuronal tissues that are down-regulated due to pathogen infection inC. elegans.

Conclusions

Our Tissue Enrichment Analysis (TEA) can be found within WormBase, and can be downloaded using Python’s standard pip installer. It tests a slimmed-downC. eleganstissue ontology for enrichment of specific terms and provides users with a text and graphic representation of the results.
A haplotype-based normalization technique for the analysis and detection of allele specific expression
Authors: Hodgkinson Alan , Grenier Jean-Christophe , Gbeha Elias , Awadalla Philip
Published: September 2016

Background

Allele specific expression (ASE) has become an important phenotype, being utilized for the detection of cis-regulatory variation, nonsense mediated decay and imprinting in the personal genome, and has been used to both identify disease loci and consider the penetrance of damaging alleles. The detection of ASE using high throughput technologies relies on aligning short-read sequencing data, a process that has inherent biases, and there is still a need to develop fast and accurate methods to detect ASE given the unprecedented growth of sequencing information in big data projects.

Results

Here, we present a new approach to normalize RNA sequencing data in order to call ASE events with high precision in a short time-frame. Using simulated datasets we find that our approach dramatically improves reference allele quantification at heterozygous sites versus default mapping methods and also performs well compared to existing techniques for ASE detection, such as filtering methods and mapping to parental genomes, without the need for complex and time consuming manipulation. Finally, by sequencing the exomes and transcriptomes of 96 well-phenotyped individuals of the CARTaGENE cohort, we characterise the levels of ASE across individuals and find a significant association between the proportion of sites undergoing ASE within the genome and smoking.

Conclusions

The correct treatment and analysis of RNA sequencing data is vital to control for mapping biases and detect genuine ASE signals. By normalising RNA sequencing information after mapping, we show that this approach can be used to identify biologically relevant signals in personal genomes.
Riemann solvers and Alfven waves in black hole magnetospheres
Authors: Punsly Brian , Balsara Dinshaw , Kim Jinho , Garain Sudip
Published: September 2016

In the magnetosphere of a rotating black hole, an inner Alfven critical surface (IACS) must be crossed by inflowing plasma. Inside the IACS, Alfven waves are inward directed toward the black hole. The majority of the proper volume of the active region of spacetime (the ergosphere) is inside of the IACS. The charge and the totally transverse momentum flux (the momentum flux transverse to both the wave normal and the unperturbed magnetic field) are both determined exclusively by the Alfven polarization. Thus, it is important for numerical simulations of black hole magnetospheres to minimize the dissipation of Alfven waves. Elements of the dissipated wave emerge in adjacent cells regardless of the IACS, there is no mechanism to prevent Alfvenic information from crossing outward. Thus, numerical dissipation can affect how simulated magnetospheres attain the substantial Goldreich-Julian charge density associated with the rotating magnetic field. In order to help minimize dissipation of Alfven waves in relativistic numerical simulations we have formulated a one-dimensional Riemann solver, called HLLI, which incorporates the Alfven discontinuity and the contact discontinuity. We have also formulated a multidimensional Riemann solver, called MuSIC, that enables low dissipation propagation of Alfven waves in multiple dimensions. The importance of higher order schemes in lowering the numerical dissipation of Alfven waves is also catalogued.
Neoadjuvant Therapy Followed by Resection Versus Upfront Resection for Resectable Pancreatic Cancer: A Propensity Score Matched Analysis
Authors: Mokdad Ali A. , Minter Rebecca M. , Zhu Hong , Augustine Mathew M. , Porembka Matthew R. , Wang Sam C. , Yopp Adam C. , Mansour John C. , Choti Michael A. , Polanco Patricio M.
Published: September 2016

Purpose

To compare overall survival between patients who received neoadjuvant therapy (NAT) followed by resection and those who received upfront resection (UR)—as well as a subgroup of UR patients who also received adjuvant therapy—for early-stage resectable pancreatic adenocarcinoma.

Patients and Methods

Adult patients with resected, clinical stage I or II adenocarcinoma of the head of the pancreas were identified in the National Cancer Database from 2006 to 2012. Patients who underwent NAT followed by curative-intent resection were matched by propensity score with patients whose tumors were resected upfront. Overall survival was compared by using a Cox proportional hazards regression model. Early postoperative and oncologic outcomes were evaluated.

Results

We identified 15,237 patients with clinical stage I or II resected pancreatic head adenocarcinoma. From the NAT group, 2,005 patients (95%) were matched with 6,015 patients who underwent UR. The NAT group was associated with improved survival compared with UR (median survival, 26 months v 21 months, respectively; stratified log-rank P < .01; hazard ratio, 0.72; 95% CI, 0.68 to 0.78). Patients in the UR group had higher pathologic T stage (pT3 and T4: 86% v 73%; P < .01), higher positive lymph nodes (73% v 48%; P < .01), and higher positive resection margin (24% v 17%; P < .01). Compared with a subset of UR patients who received adjuvant therapy, NAT patients had a better survival (adjusted hazard ratio, 0.83; 95% CI, 0.73 to 0.89).

Conclusion

NAT followed by resection has a significant survival benefit compared with UR in early-stage, resected pancreatic head adenocarcinoma. These findings support the use of NAT, particularly as a patient selection tool, in the management of resectable pancreatic adenocarcinoma.
Ghrelin Octanoylation Is Completely Stabilized in Biological Samples by Alkyl Fluorophosphonates
Authors: McGovern-Gooch Kayleigh R. , Rodrigues Trevor , Darling Joseph E. , Sieburg Michelle A. , Abizaid Alfonso , Hougland James L.
Published: September 2016

Ghrelin is a peptide hormone involved in multiple physiological processes related to energy homeostasis. This hormone features a unique posttranslational serine octanoylation modification catalyzed by the enzyme ghrelin O-acyltransferase, with serine octanoylation essential for ghrelin to bind and activate its cognate receptor. Ghrelin deacylation rapidly occurs in circulation, with both ghrelin and desacyl ghrelin playing important roles in biological signaling. Understanding the regulation and physiological impact of ghrelin signaling requires the ability to rapidly protect ghrelin from deacylation in biological samples such as blood serum or cell lysates to preserve the relative concentrations of ghrelin and desacyl ghrelin. In in vitro ghrelin O-acyltransferase activity assays using insect microsomal protein fractions and mammalian cell lysate and blood serum, we demonstrate that alkyl fluorophosphonate treatment provides rapid, complete, and long-lasting protection of ghrelin acylation against serine ester hydrolysis without interference in enzyme assay or ELISA analysis. Our results support alkyl fluorophosphonate treatment as a general tool for stabilizing ghrelin and improving measurement of ghrelin and desacyl ghrelin concentrations in biochemical and clinical investigations and suggest current estimates for active ghrelin concentration and the ghrelin to desacyl ghrelin ratio in circulation may underestimate in vivo conditions.
Systematic Quality Assessment of Published Antishivering Protocols
Authors: Choi Ko-Eun , Park Bomi , Moheet Asma M. , Rosen Amanda , Lahiri Shouri , Rosengart Axel
Published: September 2016

Shivering is a common side effect of targeted temperature modulation and general anesthesia. Antishivering strategies often employ a stepwise approach involving both pharmacological and physical interventions. However, approaches to treat shivering are often empiric and vary widely across care environments. We evaluated the quality of published antishivering protocols and guidelines with respect to methodological rigor, reliability, and consistency of recommendations.

Using 4 medical databases, we identified 4027 publications that addressed shivering therapy, and excluded 3354 due to lack of relevance. After applying predefined eligibility criteria with respect to minimal protocol standards, 18 protocols/guidelines remained. Each was assessed using a modified Appraisal of Guidelines for Research and Evaluation II (mAGREE II) instrument containing 23 quality items within 6 domains (maximal score 23). Among 18 protocols/guidelines, only 3 incorporated systematically reviewed recommendations, whereas 15 merely targeted practice standardization. Fifteen of 18 protocols/guidelines addressed shivering during therapeutic cooling in which skin counterwarming and meperidine were most commonly cited. However, their mAGREE II scores were within the lowest tertile (1 to 7 points) and the median for all 18 protocols was 5. The quality domains most commonly absent were stakeholder involvement, rigor of development, and editorial independence. Three of 18 protocols/guidelines addressed postanesthetic antishivering. Of these, the American Society of Anesthesiologists guidelines recommending forced-air warming and meperidine received the highest mAGREE II score (14 points), whereas the remaining 2 recommendations had low scores (<5 points).

Current published antishivering protocols/guidelines lack methodological rigor, reliability, and strength, and even the highest scoring of the 18 protocols/guidelines fulfilled only 60% of quality items. To be consistent with evidence-based protocol/guideline development processes, future antishivering treatment algorithms should increase methodological rigor and transparency.