bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data
Authors: Yang Yang , Niehaus Katherine E , Walker Timothy M , Iqbal Zamin , Walker A Sarah , Wilson Daniel J , Peto Tim E A , Crook Derrick W , Smith E Grace , Zhu Tingting , Clifton David A 
Published: December 2017

Abstract

Motivation
Correct and rapid determination of Mycobacterium tuberculosis (MTB) resistance against available tuberculosis (TB) drugs is essential for the control and management of TB. Conventional molecular diagnostic test assumes that the presence of any well-studied single nucleotide polymorphisms is sufficient to cause resistance, which yields low sensitivity for resistance classification.

Summary
Given the availability of DNA sequencing data from MTB, we developed machine learning models for a cohort of 1839 UK bacterial isolates to classify MTB resistance against eight anti-TB drugs (isoniazid, rifampicin, ethambutol, pyrazinamide, ciprofloxacin, moxifloxacin, ofloxacin, streptomycin) and to classify multi-drug resistance.

Results
Compared to previous rules-based approach, the sensitivities from the best-performing models increased by 2-4% for isoniazid, rifampicin and ethambutol to 97% (P &lt; 0.01), respectively; for ciprofloxacin and multi-drug resistant TB, they increased to 96%. For moxifloxacin and ofloxacin, sensitivities increased by 12 and 15% from 83 and 81% based on existing known resistance alleles to 95% and 96% (P &lt; 0.01), respectively. Particularly, our models improved sensitivities compared to the previous rules-based approach by 15 and 24% to 84 and 87% for pyrazinamide and streptomycin (P &lt; 0.01), respectively. The best-performing models increase the area-under-the-ROC curve by 10% for pyrazinamide and streptomycin (P &lt; 0.01), and 4–8% for other drugs (P &lt; 0.01).

Availability and implementation
The details of source code are provided at http://www.robots.ox.ac.uk/~davidc/code.php.

Supplementary information
Supplementary data are available at Bioinformatics online.
Stearic Acid Supplementation in High Protein to Carbohydrate (P:C) Ratio Diet Improves Physiological and Mitochondrial Functions of Drosophila melanogaster parkin Null Mutants
Authors: Bajracharya Rijan , Bustamante Sonia , O Ballard John William 
Published: December 2017

AbstractOptimizing dietary macronutrients benefits the prevention and management of many human diseases but there is conflicting dietary advice for Parkinson’s disease (PD), and no single strategy is universally recommended. Recently, it was shown that dietary stearic acid (C18:0) improves survival and mitochondrial functions in the parkin null Drosophila model of PD. Here, we incorporate stearic acid into high protein and high carbohydrate diets and study survival, climbing ability, mitochondrial membrane potential, respiration, basal reactive oxygen species, and conduct lipidomics assays. We observed that parkin null flies showed improvement in all assays tested when stearic acid was added to the high protein diet but not to the high carbohydrate diet. When lipid proportion was examined, we observed higher levels in flies fed the high protein diet with stearic acid diet and the high carbohydrate diet. Unexpectedly, free levels of fatty acids exhibited opposite trend. Combined, these data suggest that dietary Protein: Carbohydrate ratio and stearic acid influences levels of bound fatty acids. The mechanisms that influence free and bound fatty-acid levels remain to be explored, but one possible explanation is that breakdown products can bind to membranes and improve the mitochondrial functions of parkin null flies.
The bias of the log power spectrum for discrete surveys
Authors: Repp Andrew , Szapudi István 
Published: December 2017

Abstract
A primary goal of galaxy surveys is to tighten constraints on cosmological parameters, and the power spectrum P(k) is the standard means of doing so. However, at translinear scales P(k) is blind to much of these surveys’ information – information which the log density power spectrum recovers. For discrete fields (such as the galaxy density), A* denotes the statistic analogous to the log density: A* is a ‘sufficient statistic’ in that its power spectrum (and mean) capture virtually all of a discrete survey's information. However, the power spectrum of A* is biased with respect to the corresponding log spectrum for continuous fields, and to use $P_{A^*}(k)$ to constrain the values of cosmological parameters, we require some means of predicting this bias. Here, we present a prescription for doing so; for Euclid-like surveys (with cubical cells 16h−1 Mpc across) our bias prescription's error is less than 3 per cent. This prediction will facilitate optimal utilization of the information in future galaxy surveys.
Early Antimicrobial De-escalation and Stewardship in Adult Hematopoietic Stem Cell Transplantation Recipients: Retrospective Review
Authors: Snyder Matthew , Pasikhova Yanina , Baluch Aliyah 
Published: December 2017

Abstract

Background
Antimicrobial stewardship in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients remains underutilized in North America. European guidelines advise de-escalation of broad-spectrum therapy after 72 hours in select patients with neutropenic fever of unknown origin. This is not commonplace in the United States, as current guidelines recommend broad-spectrum therapy until neutrophil engraftment. If de-escalating after at least 5 days of broad-spectrum therapy and defervescence in neutropenic allo-HSCT recipients does not predispose them to recurrent fever or infection, the practice could afford several benefits.

Methods
The primary end point was rate of recurrent fever. Secondary outcomes included Clostridium difficile–associated infections, length of stay, intensive care unit (ICU) admission incidence, in-hospital mortality rate, need for re-escalation of therapy, rate of positive blood cultures for patients who had recurrent fevers, overall antimicrobial utilization from neutropenic fever onset, and pharmacoeconomic impact.

Results
A total of 120 patients were assessed in 2 groups as cohort 1 (n = 46), which received early de-escalation, and cohort 2 (n = 74), which did not. The primary end point met criteria for noninferiority, as 7 patients (15%) in cohort 1 had recurrent fever within the specified time frame compared with 14 (19%) in cohort 2 (90% CI, –0.0878 to 0.1629, P = .026). Patients in cohort 1 received significantly less gram-positive broad-spectrum antimicrobials, with trends toward lower use of broad-spectrum gram-negative agents and lower associated costs and no differences in length of stay, ICU admission incidence, need for re-escalation of therapy, rate of culture-positive bacteremia after de-escalation or discontinuation of broad-spectrum therapy, or in-hospital mortality rate.

Conclusions
De-escalating after at least 5 days of broad-spectrum therapy and defervescence did not appear to affect the rate of recurrent fever. This allowed for significant reductions in gram-positive broad-spectrum antimicrobial utilization, with trends toward lower use of broad-spectrum gram-negative agents and associated costs and no difference in clinical outcomes compared with those continuing such therapy until neutrophil engraftment.
Gram-Positive Rods on a Cerebrospinal Fluid Gram Stain
Authors: Thompson Amelia B , Wrubel David , Berkowitz Frank E 
Published: December 2017

Abstract
Cerebrospinal fluid (CSF) access device placement in the pediatric population presents challenges due to the development of infections following placement, access or revision, and/or shunt malfunctions. Here we report an unusual pediatric case of L. monocytogenes ventriculitis/VP shunt (VPS) infection and associated pseudocyst with an emphasis on the importance of VPS removal in clearing the infection due to biofilm formation.
A Mild Laryngeal Cleft Causes Severe Symptoms
Authors: Mandadi Akhila Reddy , Saeed Wajeeha , Suneja Upma , Waseem Muhammad 
Published: December 2017

Abstract
Diagnosis and treatment of laryngeal clefts (LCs) particularly type I pose a challenge. Although rare, type I LCs are becoming increasingly identified in recent years, and this is perhaps due to both an increased awareness and better diagnostic modalities. We report a young infant presenting with feeding difficulty and respiratory distress related to LC. The pertinent literature is also reviewed.
Intense 68Ga-PSMA Uptake in Diverticulum of the Sigmoid Colon
Authors: Jochumsen Mads Ryø , Bouchelouche Kirsten 
Published: December 2017

Abstract
We present a case of a diverticulum of the sigmoid colon with intense prostate-specific membrane antigen (PSMA) activity on 68Ga-PSMA PET/CT. CT scan and colonoscopy showed no signs of inflammation or malignancy. This case presents an addition to the collection of benign pitfalls when reporting PSMA PET/CT; however, a 68Ga-PSMA up-taking focus in the colon should always cause further examination, as malignant etiology must be ruled out.
Generation of Variation and Mean Fitness Increase: Necessity is the Mother of Genetic Invention
Authors: Ram Yoav , Altenberg Lee , Liberman Uri , Feldman Marcus W. 
Published: December 2017

AbstractGeneration of variation may be detrimental in well-adapted populations evolving under constant selection. In a constant environment, genetic modifiers that reduce the rate at which variation is generated by processes such as mutation and migration, succeed. However, departures from thisreduction principlehave been demonstrated. Here we analyze a general model of evolution under constant selection where the rate at which variation is generated depends on the individual. We find that if a modifier allele increases the rate at which individuals of below-average fitness generate variation, then it will increase in frequency and increase the population mean fitness. This principle applies to phenomena such as stress-induced mutagenesis and condition-dependent dispersal, and exemplifies“Necessity is the mother of genetic invention.”
Non-native Interactions Explain the Folding Rate Differences in α-Spectrin Domains and the Origin of Internal Friction Effects
Authors: da Silva Fernando Bruno , Contessoto Vinícius G. , de Oliveira Vinícius M. , Clarke Jane , Leite Vitor B. P. 
Published: December 2017

AbstractRecent experimental and computational studies have shown the influence of internal friction in protein folding dynamics. However, uncertainty remains over its molecular origin. α-spectrin experimental results indicate that R15 domain folds three orders of magnitude faster than its homologous R16 and R17. Such anomalous observations are usually attributed to the influence of internal friction on protein folding rates. To study this phenomenon, we carried out molecular dynamics simulations with structure-based Cα models, in which the folding process of α-spectrin domains was investigated by adding non-native interactions. The simulations take into account the hydrophobic and the electrostatic contributions separately. The folding time results have shown a qualitative agreement with experimental data. We have also investigated mutations in R16 and R17, and the simulation folding time results correlate with the observed experimental ones. We suggest that the origin of the internal friction emerges from a cooperativity effect of these non-native interactions.
Assessment of the effectiveness of green practices in the management of two supply chains
Authors: Sellitto Miguel Afonso 
Published: December 2017

PurposeThe purpose of this paper is to introduce and test a model for numerical evaluation of the effectiveness of green practices implemented in two industrial supply chains (SCs). Two real case applications were made: footwear and metal-mechanics industry.Design/methodology/approachThe research method is quali-quantitative modeling. By literature review, a model based on three constructs was proposed (green strategy, green innovation, and green operations), organized in 16 categorical indicators, prioritized with analytic hierarchy process. Three practitioners of each focal companies assessed the indicators fulfilling scales (very good to very bad).FindingsThe overall performance reached 51 and 57 percent, respectively of the maximum possible. The indicators that most jeopardized the performance were complexity management and communication, barriers to green supply chain management, green products, and green market (first case) and innovation in processes, and green market (second case).Research limitations/implicationsThe model cannot be generalized or extended to other SCs. Further refinement and testing are required.Practical implicationsManagers and practitioners can improve the eco-efficiency of SC, focusing on the green practices that should be prioritized in greening strategies for the entire chain.Social implicationsImprovement of eco-efficiency is positively correlated with corporate social responsibility.Originality/valueThe model can produce a numerical overall value that represents the level or degree of implementation of green practices in the context of a SC management.
Building excellence through the Agile Reengineering Performance Model (ARPM)
Authors: Petrillo Antonella , Di Bona Gianpaolo , Forcina Antonio , Silvestri Alessandro 
Published: December 2017

PurposeThe purpose of this paper is to build a theoretic and practical framework, based on agile project management, to support the decision-making process in order to help companies in optimizing the reengineering production processes and improve management costs.Design/methodology/approachThis paper seeks to propose an agile Reengineering Performance Model (ARPM) for managing projects of reengineering of processes and applies it in a real case study concerning a water bottling plant.FindingsThe proposed model should serve as a valuable tool to facilitate a successful business process reengineering design in the project management and intends to assist companies as they operate projects of transferring and optimizing production lines. Thanks to the use of ARPM tools, it is easy to modify the evolution of the project, with the possibility of extending or enhancing the application if necessary.Research limitations/implicationsThe main limits of the ARPM model are: it requires close collaboration among team; it is rather intense for developers; and it is necessary flexibility to change course as needed and to ensure delivery of the right product.Practical implicationsThe main implications of the authors’ work for research and business are to propose a structured methodological approach, rigorous but simple, suitable to implement in any companies.Originality/valueThe novelty of the approach is to apply the agile approach not for software development but in a manufacturing company.
ERP benefits capability framework: orchestration theory perspective
Authors: Badewi Amgad , Shehab Essam , Zeng Jing , Mohamad Mostafa 
Published: December 2017

PurposeThe purpose of this paper is to answer two research questions: what are the ERP resources and organizational complementary resources (OCRs) required to achieve each group of benefits? And on the basis of its resources, when should an organization invest more in ERP resources and/or OCRs so that the potential value of its ERP is realised?Design/methodology/approachStudying 12 organizations in different countries and validating the results with 8 consultants.FindingsERP benefits realization capability framework is developed; it shows that each group of benefits requires ERP resources (classified into features, attached technologies and information technology department competences) and OCRs (classified into practices, attitudes, culture, skills and organizational characteristics) and that leaping ahead to gain innovation benefits before being mature enough in realising a firm’s planning and automation capabilities could be a waste of time and effort.Research limitations/implicationsIt is qualitative study. It needs to be backed by quantitative studies to test the results.Practical implicationsAlthough the “P” in ERP stands for planning, many academics and practitioners still believe that ERP applies to automation only. This research spotlights that the ability to invest in ERP can increase the innovation and planning capabilities of the organization only if it is extended and grown at the right time and if it is supported by OCRs. It is not cost effective to push an organization to achieve all the benefits at the same time; rather, it is clear that an organization would not be able to enjoy a higher level of benefits until it achieves a significant number of lower-level benefits. Thus, investing in higher-level benefit assets directly after an ERP implementation, when there are no organizational capabilities available to use these assets, could be inefficient. Moreover, it could be stressful to users when they see plenty of new ERP resources without the ability to use them. Although it could be of slight benefit to introduce, for example, business intelligence to employees in the “stabilizing period” (Badewiet al., 2013), from the financial perspective, it is a waste of money since the benefits would not be realised as expected. Therefore, orchestrating ERP assets with the development of organizational capabilities is important for achieving the greatest effectiveness and efficiency of the resources available to the organization. This research can be used as a benchmark for designing the various blueprints required to achieve different groups of benefits from ERP investments.Originality/valueThis research addresses two novel questions:RQ1: what are the ERP resources and OCRs required to achieve the different kinds of ERP benefits?RQ2: when, and on what basis, should an organization deploy more resources to leverage the ERP business value?
Creative collaboration: student creative works in the institutional repository
Authors: Sliger Krause Rose , Langhurst Eickholt Andrea , Otto Justin L. 
Published: December 2017

Purpose
The purpose of this paper is to describe the music performance collection preserved in Eastern Washington University’s institutional repository (IR). This collection of recordings of student music performances is the result of an ongoing collaboration between the university?s library and music department, which serves to provide discoverability, preservation and access to a collection of student creative works, which had heretofore been a hidden collection.

Design/methodology/approach
This collection of student creative work was identified as a suitable project for the Eastern Washington University’s IR while it was still in the planning stages because it was identified as an existing need that the new IR could address. Much of the groundwork for the collaboration between the library and music department was completed prior to IR implementation. Thus, the library was ready to begin work on this collection once the IR was operational.

Findings
The student music performance collection has been a successful project for the IR, which benefits the music department by making student performances discoverable and accessible, and benefits the library by providing the opportunity to demonstrate that the then-new IR could support the university’s student-centered focus on teaching and learning.

Originality/value
While there is a growing body of literature on IRs emphasizing student work, there is little literature on music or other creative works’ collections in IRs, much less on creative works by students. This paper adds to the limited body of literature on student creative works in the IR by describing the development, implementation and lessons learned from the successful music performances collection.
Creating capacity for digital projects
Authors: Newman Jess , Bonefas Suzanne , Trenthem Wendy 
Published: December 2017

Purpose
This paper offers a case study in creating capacity for digital initiatives at Rhodes College in Memphis, Tennessee through an exploration of the Crossroads to Freedom program, a decade-long digital public history initiative. At present, digital scholarship and preservation work falls under the purview of information services (IS), a merged information technology (IT) and library division and home to the digital preservation and scholarship (DPS) team. DPS is a multidisciplinary group of undergraduate students, IS staff and various internal and external partners.

Design/methodology/approach
By exploring the evolution of digital projects at a small, liberal arts college, this paper will introduce readers to one dynamic path to cultivating capacity and support for digital initiatives within the confines of limited staffing and monetary resources.

Findings
Topics and strategies include working effectively with community partners, leveraging existing strengths, building and sustaining a community of practice (CoP), integrating undergraduates as full staff members and navigating cultural change within the library and higher education more broadly.

Originality/value
This paper demonstrates a decade of successful innovation and adaptation to the changing landscape of digital initiatives and the library’s role in higher education that is rooted in community-centric commitment to social justice. Discussion of these strategies and theoretical frameworks should prove helpful to institutions looking to reimagine traditional approaches to digital archives and scholarship programs.
Culturally varied relationality in buyer-supplier negotiations: a multi-session simulation
Authors: Cheng Junjun , Huang Yimin , Su Yong 
Published: December 2017

PurposeThe purpose of this paper is to empirically examine the role of relationality in buyer–supplier negotiations and how it varies across cultural settings.Design/methodology/approachUsing a multisession simulation design, this study recruited research participants (n = 82) from diverse cultural backgrounds to play the role of either buyer or supplier for two negotiation tasks. Regression analyses were used to test the relationships among relational constructs as well as the moderating role of relational culture.FindingsResults show that negotiators’ relational self-construal enhances their relational commitment to the ongoing negotiations, which leads to a higher level of relational capital accumulated at the end of negotiations. The impact of relational self-construal on relational commitment and that of relational commitment on counterparts’ relational capital are stronger for negotiators from a high (as opposed to low) relational cultural background. Furthermore, intercultural negotiation context, when compared with intracultural context, weakens the impact of relational commitment on relational capital.Originality/valueThis research is among the first to empirically examine the culturally varied relationality in negotiations. The findings offer important theoretical and practical implications regarding how relationality, when interacting with cultural factors, has varying impacts on business negotiations.