bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solid-state NMR characterization of triacylglycerol and polysaccharides in coffee beans
Authors: Kanai Noriko , Yoshihara Naoki , Kawamura Izuru 
Published: January 2019

ABSTRACT
It is important to understand the structural characteristics of triacylglycerol (TAG), polysaccharides and trace elements in coffee beans, so that residues can be reutilized in applications including biodiesel oils. Here, we performed 1H and 13C solid-state NMR measurements on Indonesian green beans, roasted beans, and spent coffee grounds (SCGs). In the NMR spectra, there were liquid-like TAG containing linoleic acids based on observed signals of -CH=CH-CH2-CH=CH- group in an acyl chain, which play a role in decreasing TAG’s melting point. We found TAG was still abundant in the SCGs from NMR spectra. After lipids were removed from SCGs, the intensity of the TAG signal decreased considerably, with approximately 64% of the TAG was successfully extracted. We described the chemical structure of TAG in coffee beans and demonstrated that it is possible quantify the amount of extracted TAG using solid-state NMR.
ChimeraUGEM: unsupervised gene expression modeling in any given organism
Authors: Diament Alon , Weiner Iddo , Shahar Noam , Landman Shira , Feldman Yael , Atar Shimshi , Avitan Meital , Schweitzer Shira , Yacoby Iftach , Tuller Tamir 
Published: January 2019

AbstractMotivationRegulation of the amount of protein that is synthesized from genes has proved to be a serious challenge in terms of analysis and prediction, and in terms of engineering and optimization, due to the large diversity in expression machinery across species.ResultsTo address this challenge, we developed a methodology and a software tool (ChimeraUGEM) for predicting gene expression as well as adapting the coding sequence of a target gene to any host organism. We demonstrate these methods by predicting protein levels in seven organisms, in seven human tissues, and by increasing in vivo the expression of a synthetic gene up to 26-fold in the single-cell green alga Chlamydomonas reinhardtii. The underlying model is designed to capture sequence patterns and regulatory signals with minimal prior knowledge on the host organism and can be applied to a multitude of species and applications.Availability and implementationSource code (MATLAB, C) and binaries are freely available for download for non-commercial use at http://www.cs.tau.ac.il/~tamirtul/ChimeraUGEM/, and supported on macOS, Linux and Windows.Supplementary informationSupplementary data are available at Bioinformatics online.
EEG dataset and OpenBMI toolbox for three BCI paradigms: an investigation into BCI illiteracy
Authors: Lee Min-Ho , Kwon O-Yeon , Kim Yong-Jeong , Kim Hong-Kyung , Lee Young-Eun , Williamson John , Fazli Siamac , Lee Seong-Whan 
Published: January 2019

Abstract

Background
Electroencephalography (EEG)-based brain-computer interface (BCI) systems are mainly divided into three major paradigms: motor imagery (MI), event-related potential (ERP), and steady-state visually evoked potential (SSVEP). Here, we present a BCI dataset that includes the three major BCI paradigms with a large number of subjects over multiple sessions. In addition, information about the psychological and physiological conditions of BCI users was obtained using a questionnaire, and task-unrelated parameters such as resting state, artifacts, and electromyography of both arms were also recorded. We evaluated the decoding accuracies for the individual paradigms and determined performance variations across both subjects and sessions. Furthermore, we looked for more general, severe cases of BCI illiteracy than have been previously reported in the literature.

Results
Average decoding accuracies across all subjects and sessions were 71.1% (± 0.15), 96.7% (± 0.05), and 95.1% (± 0.09), and rates of BCI illiteracy were 53.7%, 11.1%, and 10.2% for MI, ERP, and SSVEP, respectively. Compared to the ERP and SSVEP paradigms, the MI paradigm exhibited large performance variations between both subjects and sessions. Furthermore, we found that 27.8% (15 out of 54) of users were universally BCI literate, i.e., they were able to proficiently perform all three paradigms. Interestingly, we found no universally illiterate BCI user, i.e., all participants were able to control at least one type of BCI system.

Conclusions
Our EEG dataset can be utilized for a wide range of BCI-related research questions. All methods for the data analysis in this study are supported with fully open-source scripts that can aid in every step of BCI technology. Furthermore, our results support previous but disjointed findings on the phenomenon of BCI illiteracy.
Epifauna associated with subsea pipelines in the North Sea
Authors: Lacey Nichola C , Hayes Peter 
Published: January 2019

Abstract
An increasing number of pipelines across the UK Continental Shelf are reaching the end of their economic life, resulting in a growing impetus on decommissioning. Implicit to the decommissioning process is the evaluation of the environmental impacts of the different decommissioning options, however little is known regarding the epifauna that interact with these structures. This study utilized industry-collected footage from remotely operated vehicle inspections of pipelines to assess the interactions of benthic epifauna with pipelines, and their associated structures, for the first time. Footage was analysed from across the northern and central North Sea to examine relationships between faunal community compositions and pipelines and their protective coverings. The complex habitat of concrete and Link-lok mattresses had the highest numbers of observable taxa. Differences in community composition were largely due to varying proportions of common epilithic species. There was a weak relationship between pipeline covering type and the species composition of the immediately neighbouring substrate. Depth and latitude were the strongest correlators with the observed community compositions. This study has compiled the first dataset on epifaunal associations with subsea pipelines in the North Sea.
The 2016 Morocco–Nigeria Bilateral Investment Treaty: More Practical Reality in Providing a Balanced Investment Treaty?
Authors: Ejims Okechukwu 
Published: January 2019

Abstract
The law governing international investment comprises primarily treaties between individual States and regional arrangements focusing on investment provisions that protect and promote foreign investment and the principles of customary international law that govern it. Recently, there has been rapid growth in such agreements, and growing criticism of bilateral investment treaties (BITs) due to their unbalanced content and the vague and broad investment protection standards that can be interpreted in ways that prioritise investment protection over the right of host States to regulate. In this context, the Morocco–Nigeria BIT has been applauded as a balanced and innovative example of the genre and a response to the global backlash against BITs. This article shows how this BIT has taken a bold step towards such reconciliation, by attempting to balance investor protection with series of obligations placed on the investor on human rights, and environmental and social impact assessment, effectively safeguarding the host State’s regulatory space in relation to social and environmental matters. Whether this step has resolved the issue of balancing the interests of investment protection and the preservation of the regulatory interest of the host State is unlikely, given that some substantive provisions are drafted so as not to strike a proper balance between private and public interests. The discussion also shows that many provisions remain vague and, hence, continue to grant discretion to investor–State dispute settlement (ISDS) tribunals to determine the meaning of these provisions.
Null Structures and Degenerate Dispersion Relations in Two Space Dimensions
Authors: Fu Yuqiu , Tataru Daniel 
Published: January 2019

Abstract
For a dispersive partial differential equation, the degeneracy of its dispersion relation will deteriorate dispersion of waves and strengthen nonlinear effects. Such negative effects can sometimes be mitigated by some null structure in the nonlinearity. Motivated by water-wave problems, in this paper we consider a class of nonlinear dispersive PDEs in 2D with cubic nonlinearities, whose dispersion relations are radial and have vanishing Gaussian curvature on a circle. For such a model we identify certain null structures for the cubic nonlinearity, which suffice in order to guarantee global scattering solutions for the small data problem. Our null structures in the power-type nonlinearity are weak and only eliminate the worst nonlinear interaction. Such null structures arise naturally in some water-wave problems.
Quality and effectiveness of counselling at antiretroviral therapy centres in India: capturing counsellor and beneficiary perspectives
Authors: Agarwal Reshu , Rewari Bharat Bhushan , Allam Ramesh Reddy , Chava Nalini , Rathore A S 
Published: January 2019

Abstract

Background
Ensuring the quality and effectiveness of counselling is imperative for enabling people living with HIV to cope with treatment adherence. Countrywide assessment of antiretroviral therapy (ART) centres was undertaken to assess the quality and effectiveness of counselling. The insights gained from the assessment are expected to build an improved understanding of the counselling aspect and contribute to informing decisions strengthening the counselling provided at ART centres.

Methods
Assessment of counselling at 357 ART centres entailed interviews with counsellors and beneficiaries using a structured questionnaire administered by trained technical experts. Two counsellors and five beneficiaries at each ART centre were interviewed to assess both the quality and effectiveness of counselling. Beneficiaries were selected from different risk groups to understand their varied concerns and experiences.

Results
During the assessment, 618 counsellors were interviewed (45% women); also, 1785 beneficiaries were interviewed, consisting of 892 (49.9%) men, 857 (48.1%) women and 36 (2.0%) transgender. Counsellors were found to be relatively well informed on topics pertaining to pre-ART, ART preparedness and positive healthy living, and the psychosocial support extended to patients. Counsellors surveyed were not aware of critical areas such as counselling of pregnant women (44.5%) , drug adherence (44.8%) and the use of information, education and communication material during counselling, and pill count. The majority of beneficiaries reported being informed on issues pertaining to retention; however, 30–40% of beneficiaries were not informed regarding the critical elements of adherence such as counselling on ART side effects (68.5%), pill count (62.8%) and information on access to social benefit schemes (25.7%). Factors such as client volume, the training of the counsellors and adequate space for counselling affected the quality of counselling.

Conclusion
With concerted efforts in bridging the gaps in knowledge, infrastructure and information needs, India’s national AIDS control programme (NACP) can enhance the counselling services at ART centres and improve the quality of services for patient retention.
Populism, Hindu Nationalism, and Foreign Policy in India: The Politics of Representing “the People”
Authors: Wojczewski Thorsten 
Published: January 2019

AbstractThere is today a growing sense of a global rise of populism. Right-wing populist leaders and parties claim to represent the people and pit them against a “corrupt” elite and “dangerous” Others. However, the international dimensions of populism remain largely unexplored in the populism and international relations (IR) literature. By analyzing the relationship between foreign policy and populism, this article seeks to show how the phenomenon of populism can be integrated into IR theory and how IR scholarship can inform debates on populism. The article argues that poststructuralist IR, with its focus on foreign policy as a boundary-drawing practice that demarcates the Self from the Other, allows us to study how populist actors can use foreign policy as a site for the reproduction of their claim to represent the people. To grasp this, the article identifies different discursive strategies through which the people/elite antagonism can be constructed and interacts with other antagonisms such as the inside/outside divide of nationalism. It illustrates its arguments with a case study on India's foreign policy discourse under the Hindu nationalist Narendra Modi, who has promised to purify India from a corrupt elite and pursue an “India first” policy.
Model-Based Screening for Robust Estimation in the Presence of Deviations from Linearity in Small Domain Models
Authors: Gershunskaya Julie , Savitsky Terrance D 
Published: January 2019

AbstractSmall domain estimation models, like the Fay-Herriot (FH), often assume a normally distributed latent process centered on a linear mean function. The linearity assumption may be violated for domains that express idiosyncratic phenomena not captured by the predictors. The direct sample estimate for such domain will be viewed as an outlier by FH when, in fact, it reflects an underlying true value. The model interpretation is also confounded by the variances of direct sample estimates because, while typically treated as fixed and known, they are estimates and thus contain noise. In this article, we construct a joint model for the direct estimates and their variances with nonparametric mixtures of normal distributions with the goal to improve robustness in estimation quality for these idiosyncratic domains. We devise a model-based screening tool to nominate domains where the model may not accurately account for deviations from the linearity assumption. We replace the modeled values for nominated domains with the direct estimate which we show robustify our models. The US Bureau of Labor Statistics’ Current Employment Statistics (CES) survey publishes monthly employment estimates for domains defined by industry and geography. Model estimation is performed for smaller domains to improve the reliability of the direct estimator. We compare fit performances for our candidate models under data constructed to be similar to the CES and conduct a simulation study to assess the robustness of our candidate models in the presence of deviations from linearity. We apply our model-based screening method and quantify its ability to improve the quality of published estimates.
Military Relics: Soldiers and Sailors at Home in Thomas Hardy’s The Trumpet-Major
Authors: Hunt Aeron 
Published: January 2019

Abstract
Thomas Hardy’s 1880 text The Trumpet-Major, a historical novel set during the period of the Napoleonic invasion scares, is notable for its generic inconsistency and the strangeness of its plot and characters. This essay analyses the novel’s array of soldiers, sailors, members of the yeomanry focused on civil defence, and military veterans, arguing that Hardy’s novel’s formal strangeness grows in part out of its preoccupation with these examples of military figures at home – roles that, I suggest, focused a contemporary anxiety about social connectedness and the continuities and consistencies of life stories and identities. In highlighting the disquiet that these military figures register in the novel as well as outside it, in wider discussions of army reform and policies toward veterans and members of the military, I suggest that in Victorian accounts and in the ruptures registered in Hardy’s text we may find new insights into the languages of social connection – and their failures – that continue to vex us today.
Occupational exposure to foreigners and attitudes towards equal opportunities
Authors: Pecoraro Marco , Ruedin Didier 
Published: January 2019

Abstract
We examine the relationship between attitudes to foreigners and the share of foreigners at the occupational level. Using a question on equal opportunities for foreigners from the Swiss Household Panel, ordered probit regression models show a negative association between the share of foreigners in one’s occupation and positive attitudes to foreigners: workers seem to react to competition with foreigners. When we add the occupational unemployment rate, objective pressures in the labour market appear as relevant as contact at the occupational level. Further controlling for occupational heterogeneity establishes that both factors—particularly objective pressures—are probably accounted for by sorting on job quality. We also show that the association between the occupational share of foreigners and attitudes decreases for workers with better job prospects. This implies that workers welcome foreigners to overcome labour market shortages.
Stochastic Variational Inference for Bayesian Phylogenetics: A Case of CAT Model
Authors: Dang Tung , Kishino Hirohisa 
Published: January 2019

AbstractThe pattern of molecular evolution varies among gene sites and genes in a genome. By taking into account the complex heterogeneity of evolutionary processes among sites in a genome, Bayesian infinite mixture models of genomic evolution enable robust phylogenetic inference. With large modern data sets, however, the computational burden of Markov chain Monte Carlo sampling techniques becomes prohibitive. Here, we have developed a variational Bayesian procedure to speed up the widely used PhyloBayes MPI program, which deals with the heterogeneity of amino acid profiles. Rather than sampling from the posterior distribution, the procedure approximates the (unknown) posterior distribution using a manageable distribution called the variational distribution. The parameters in the variational distribution are estimated by minimizing Kullback–Leibler divergence. To examine performance, we analyzed three empirical data sets consisting of mitochondrial, plastid-encoded, and nuclear proteins. Our variational method accurately approximated the Bayesian inference of phylogenetic tree, mixture proportions, and the amino acid propensity of each component of the mixture while using orders of magnitude less computational time.
Genome editing in large animals: current status and future prospects
Authors: Zhao Jianguo , Lai Liangxue , Ji Weizhi , Zhou Qi 
Published: January 2019

AbstractLarge animals (non-human primates, livestock and dogs) are playing important roles in biomedical research, and large livestock animals serve as important sources of meat and milk. The recently developed programmable DNA nucleases have revolutionized the generation of gene-modified large animals that are used for biological and biomedical research. In this review, we briefly introduce the recent advances in nuclease-meditated gene editing tools, and we outline these editing tools’ applications in human disease modeling, regenerative medicine and agriculture. Additionally, we provide perspectives regarding the challenges and prospects of the new genome editing technology.
What Mentors Tell Us About Acknowledging Effort and Sustaining Academic Research Mentoring: A Qualitative Study
Authors: Mancuso Carol A. , Berman Jessica R. , Robbins Laura , Paget Stephen A. 
Published: January 2019

Introduction:
Continuing education is necessary to foster new and effective research mentoring skills. We asked faculty about their research mentoring practices and what would support their skills and abilities as ongoing and effective research mentors.

Methods:
Twenty-two experienced mentors were interviewed and asked about perceived areas for improvement, and challenges and facilitators to continued research mentoring. Responses were analyzed with qualitative techniques using semistructured interviews, grounded theory, and a constant comparative analytic strategy.

Results:
The average time since the completion of the doctoral degree was 26 years. Twenty-one participants believed that more comprehensive institutional acknowledgment for their efforts would enhance research mentoring. This specifically included acknowledging their time spent and service (ie, effort) in multiple in-person and behind-the-scenes tasks. These research mentoring efforts were largely viewed as overlooked by the traditional focus on the achievement of tangible outcomes. Participants thought that a formal plan to organize research mentoring (such as a mentor's charter, and continuing education tailored to both novice and experienced research mentors) was needed to promote evolution of skills and documentation of time and service. Possible methods to support research mentors were suggested and included financial support for travel to national meetings, assistance in developing new projects, and consideration of mentoring activities in the process for academic promotion.

Discussion:
Research mentors wanted their achievements, time spent, and service (ie, effort) to be acknowledged by the institution. A formal written mentoring charter and corresponding continuing education could facilitate acknowledging achievements, time, and service and thus help to sustain academic research mentoring.
A Case Report of Complete Blockage of a Baerveldt Glaucoma Implant Following Insertion of a 3-0 Supramid Suture
Authors: Lee Richard M.H. , Bouremel Yann , Eames Ian , Brocchini Steve , Khaw Peng Tee 
Published: January 2019

Purpose:
The aim of this study was to present a case of a Baerveldt glaucoma implant lumen being completely occluded with a 3-0 Supramid stent suture.

Patient and Methods:
The patient underwent Baerveldt glaucoma implant surgery with placement of an intraluminal 3-0 Supramid stent suture that acts to restrict flow across the device and reduce the risk of postoperative hypotony. Following suturing of the implant to the sclera, the device was flow tested. No flow was observed through the device tube and a significant ballooning of the tube diameter occurred with increased pressure on the device. The device was explanted from the eye and replaced with a different implant without further postoperative complication. The explanted device was assessed using custom microfluidic equipment in an in vitro environment.

Results:
This phenomenon occurred despite using several different batches of the 3-0 Supramid stent suture and the device had to be removed and replaced with another device without complication. In vitro microfluidic assessment of the device demonstrated no flow across the device tube despite over 150 mm Hg of pressure being exerted on the device.

Conclusions:
We hypothesize that the blockage occurred at the junction between the device tube and plate and that the ballooning phenomenon observed was due to a defect in the tube wall. This case highlights the importance of flow testing all glaucoma drainage devices before insertion given the variation in manufacturing conditions to avoid the risk of intraoperative complications.
Consideration of sexually transmitted infections in the differential diagnosis: Case studies
Authors: O'Byrne Patrick , MacPherson Paul , Kitson Cynthia , Bourgault Andree 
Published: January 2019

ABSTRACT

Background and Purpose:
The rates of many sexually transmitted infections (STIs) have increased in recent years. Many health care professionals miss these potential diagnoses in clinical practice.

Methods:
Two case studies are presented, one an adult female with dysuria; the other an adult male with a rash. Appropriate differential diagnoses and relevant history, examination, and investigation details are discussed.

Conclusions:
Not all dysuria signifies a urinary tract infection. Although most rashes are not syphilis or HIV, it is important to rule out these etiologies for rashes in adults without a previous history of similar dermatologic conditions.

Implications for Practice:
Due to increased rates of many STI and HIV, it is important for nurse practitioners who work in primary care to consider these infections in patients who present with dysuria and rashes. Similarly, nurse practitioners who work in STI clinic settings should consider non-STI diagnoses in their work. In both cases, a perspective that includes both STI and non-STI etiologies is essential.