bluuebunny/crossref_metadata_2025_split huggingface dataset:
Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes
Authors: Poulsen Casper S. , Ekstrøm Claus T. , Aarestrup Frank M. , Pamp Sünje J. 
Published: March 2019

AbstractMetagenomics is increasingly used to describe microbial communities in biological specimens. Ideally, the steps involved in the processing of the biological specimens should not change the microbiome composition in a way that it could lead to false interpretations of inferred microbial community composition. Common steps in sample preparation include sample collection, storage, DNA isolation, library preparation, and DNA sequencing. Here we assess the effect of three library preparation kits and two DNA sequencing platforms. Of the library preparation kits, one involved a polymerase chain reaction (PCR) step (Nextera), and two were PCR-free (NEXTflex and KAPA). We sequenced the libraries on Illumina HiSeq and NextSeq platforms. As example microbiomes, we assessed two pig fecal samples and two sewage samples of which aliquots were stored at different storage conditions (immediate processing and storage at −80°C). All DNA isolations were performed in duplicate, totaling 80 samples excluding controls. We found that both library preparation and sequencing platform had systematic effects on the inferred microbial community composition. The different sequencing platforms introduced more variation than library preparation and freezing the samples. The results highlight that all sample processing steps need to be considered when comparing studies. Standardization of sample processing is key to generate comparable data within a study, and comparisons of differently generated data, such as in a meta-analysis, should be performed cautiously.ImportancePrevious research has reported effects of sample storage conditions and DNA isolation procedures on metagenomics-based microbiome composition; however, the effect of library preparation and DNA sequencing in metagenomics has not been thoroughly assessed. Here, we provide evidence that library preparation and sequencing platform introduce systematic biases in the metagenomic-based characterization of microbial communities. These findings suggest that library preparation and sequencing are important parameters to keep consistent when aiming to detect small changes in microbiome community structure. Overall, we recommend that all samples in a microbiome study are processed in the same way to limit unwanted variations that could lead to false conclusions. Furthermore, if we are to obtain a more holistic insight from microbiome data generated around the world, we will need to provide more detailed sample metadata, including information about the different sample processing procedures, together with the DNA sequencing data at the public repositories.
Isolation of lactic acid bacteria capable of reducing environmental alkyl and fatty acid hydroperoxides, and the effect of their oral administration on oxidative-stressed nematodes and rats
Authors: Watanabe Akio , Yamaguchi Takuro , Murota Kaeko , Ishii Tadaaki , Terao Junji , Okada Sanae , Tanaka Naoto , Kimata Shinya , Abe Akira , Suzuki Tomonori , Uchino Masataka , Niimura Youichi 
Published: March 2019

AbstractReinforcement of hydroperoxide-eliminating activity in the intestines and colon should prevent associated diseases. We previously isolated a lactic acid bacterium,Pediococcus pentosaceusBe1, that facilitates a 2-electron reduction of hydrogen peroxide to water. In this study, we successfully isolated an alternative lactic acid bacterium,Lactobacillus plantarumP1-2, that can efficiently reduce environmental alkyl hydroperoxides and fatty acid hydroperoxides to their corresponding hydroxy derivatives through a 2-electron reduction. Each strain exhibited a wide concentration range with regard to the environmental reducing activity for each hydroperoxide. Given this, the two lactic acid bacteria were orally administered to the oxygen-sensitive short-lived nematode mutant, and this resulted in a significant expansion of its lifespan. This observation suggests thatP. pentosaceusBe1 andL. plantarumP1-2 inhibit internal oxidative stress. To determine the specific organs involved in this response, we performed a similar experiment in rats, involving induced lipid peroxidation by iron-overloading. We observed that onlyL. plantarumP1-2 inhibited colonic mucosa lipid peroxidation in rats with induced oxidative stress.
Facile assembly of an affordable miniature multicolor fluorescence microscope made of 3D-printed parts enables detection of single cells
Authors: Tristan-Landin Samuel B. , Gonzalez-Suarez Alan M. , Jimenez-Valdes Rocio J. , Garcia-Cordero Jose L. 
Published: March 2019

AbstractFluorescence microscopy is one of the workhorses of biomedical research and laboratory diagnosis; however, their cost, size, maintenance, and fragility has prevented their adoption in developing countries or low-resource settings. Although significant advances have decreased their size, cost and accessibility, their designs and assembly remain rather complex. Here, inspired on the simple mechanism from a nut and a bolt we report the construction of a portable fluorescence microscope that operates in bright field mode and in three fluorescence channels: UV, green, and red. It is assembled in under 10 min from only six 3D printed parts and basic electronic components that can be readily purchased in most locations or online for US $85. Adapting a microcomputer and a touch LCD screen, the microscope can capture time-lapse images and videos. We characterized its resolution and illumination conditions and benchmarked its performance against a high-end fluorescence microscope by tracking a biological process in single cells. We also demonstrate its application to image cells inside a microfluidic device in bright-field and fluorescence mode. Our microscope fits in a CO2 chamber and can be operated in time-lapse mode. Our portable microscope is ideal in applications where space is at a premium, such as lab-on-a-chips or space missions, and can find applications in clinical research, diagnostics, telemedicine and in educational settings.
Knowledge and awareness of cervical cancer in Southwestern Ethiopia is lacking: a descriptive analysis
Authors: Saleem Atif , Bekele Alemayehu , Fitzpatrick Megan B. , Mahmoud Eiman A. , Lin Athena W. , Velasco H. Eduardo , Rashed Mona M. 
Published: March 2019

AbstractPurposeCervical cancer remains the second most common cancer and cancer-related death among women in Ethiopia. This is the first study, to our knowledge, describing the demographic, and clinicopathologic characteristics of cervical cancer cases in a mainly rural, Southwestern Ethiopian population with a low literacy rate to provide data on the cervical cancer burden and help guide future prevention and intervention efforts.MethodsA descriptive analysis of 154 cervical cancer cases at the Jimma University Teaching Hospital in Southwestern Ethiopia from January 2008 – December 2010 was performed. Demographic and clinical characteristics were obtained from patient questionnaires and cervical punch biopsies were histologically examined.ResultsOf the 154 participants with a histopathologic diagnosis of cervical cancer, 95.36% had not heard of cervical cancer and 89.6% were locally advanced at the time of diagnosis. Moreover, 86.4% of participants were illiterate, and 62% lived in a rural area.ConclusionA majority of the 154 women with cervical cancer studied at the Jimma University Teaching Hospital in Southwestern Ethiopia were illiterate, had not heard of cervical cancer and had advanced disease at the time of diagnosis. Given the low rates of literacy and knowledge regarding cervical cancer in this population which has been shown to correlate with a decreased odds of undergoing screening, future interventions to address the cervical cancer burden here must include an effective educational component.
Efficiency of protein synthesis inhibition depends on tRNA and codon compositions
Authors: Rudorf Sophia 
Published: March 2019

AbstractRegulation and maintenance of protein synthesis are vital to all organisms and are thus key targets of attack and defense at the cellular level. Here, we mathematically analyze protein synthesis for its sensitivity to the inhibition of elongation factor EF-Tu and/or ribosomes in dependence of the system’s tRNA and codon compositions. We find that protein synthesis reacts ultrasensitively to a decrease in the elongation factor’s concentration for systems with an imbalance between codon usages and tRNA concentrations. For well-balanced tRNA/codon compositions, protein synthesis is impeded more effectively by the inhibition of ribosomes instead of EF-Tu. Our predictions are supported by re-evaluated experimental data as well as by independent computer simulations. Not only does the described ultrasensitivity render EF-Tu a distinguished target of protein synthesis inhibiting antibiotics. It may also enable persister cell formation mediated by toxin-antitoxin systems. The strong impact of the tRNA/codon composition provides a basis for tissue-specificities of disorders caused by mutations of human mitochondrial EF-Tu as well as for the potential use of EF-Tu targeting drugs for tissue-specific treatments.Author SummaryWe predict and analyze the response of differently composed protein synthesis systems to the inhibition of elongation factor EF-Tu and/or ribosomes. The study reveals a strong interdependency of a protein synthesis system’s composition and its susceptibility to inhibition. This interdependency defines a generic mechanism that provides a common basis for a variety of seemingly unrelated phenomena including, for example, persister cell formation and tissue-specificity of certain mitochondrial diseases. The described mechanism applies to simple artificial translation systems as well as to complex protein synthesis in vivo.
Quantification of biomolecular dynamics inside real and synthetic nuclear pore complexes using time-resolved atomic force microscopy
Authors: Stanley George J. , Akpinar Bernice , Shen Qi , Ellis Fisher Patrick D. , Lusk C. Patrick , Lin Chenxiang , Hoogenboom Bart W. 
Published: March 2019

AbstractOver the past decades, atomic force microscopy (AFM) has emerged as an increasingly powerful tool to study the dynamics of biomolecules at nanometre length scales. However, the more stochastic the nature of such biomolecular dynamics, the harder it becomes to distinguish them from AFM measurement noise. Rapid, stochastic dynamics are inherent to biological systems comprising intrinsically disordered proteins. One role of such proteins is in the formation of the transport barrier of the nuclear pore complex (NPC): the selective gateway for macromolecular traffic entering or exiting the nucleus. Here, we use AFM to observe the dynamics of intrinsically disordered proteins from two systems: the transport barrier of native NPCs, and the transport barrier of a mimetic NPC made using a DNA origami scaffold. Analysing data recorded with 50-200 ms temporal resolution, we highlight the importance of drift correction and appropriate baseline measurements in such experiments. In addition, we describe an auto-correlation analysis to quantify time scales of observed dynamics and to assess their veracity — an analysis protocol that lends itself to the quantification of stochastic fluctuations in other biomolecular systems. The results reveal the surprisingly slow rate of stochastic, collective transitions inside mimetic NPCs, highlighting the importance of FG-nup cohesive interactions.
A new hybrid analytical model based on winding function theory for analysis of surface mounted permanent magnet motors
Authors: Faiz Jawad , Rezaee-Alam Farhad 
Published: March 2019

Purpose
The purpose of this paper is to present an improved winding function theory (IWFT) for performance analysis of surface mounted permanent magnet (SMPM) motors, which can precisely and simultaneously consider the impacts of stator slotting, the winding distribution, the magnetic flux density within PMs because of the armature reaction, the PM magnetization angle and the magnetic saturation,.

Design/methodology/approach
To obtain this improved analytical model, the conformal mappings (CMs) are introduced to calculate the relative complex permeance of slotted air-gap, which is used to obtain the function of slotted air-gap length. The equivalent magnetizing current model is used to extract the equivalent winding function for each PM pole. For retaining the basic assumption of WFT, the magnetic saturation is also considered by a proper increase in the air-gap length in the front of the stator teeth.

Findings
A new hybrid analytical model (HAM) based on WFT is presented in this paper, which can simultaneously and accurately consider the effects of slotting, the magnetic saturation, the variation of PM operating point and the winding distribution. In fact, IWFT removes all the drawbacks of the conventional WFT. Moreover, IWFT is more user-friendly and faster than other analytical and numerical techniques.

Practical implications
The obtained HAM can be used for design, optimization and fault diagnosis in electric machines.

Originality/value
This paper presents a new HAM for accurate modeling the SMPM motors, which includes different considerations of electromagnetic modeling. This new HAM can also be used for modeling the other electric motors.
The influences of contract structure, contracting process, and service complexity on supplier performance
Authors: Zou Wenting , Brax Saara A. , Vuori Mervi , Rajala Risto 
Published: March 2019

PurposeTo build a more comprehensive understanding of factors affecting the success of service contracting, the purpose of this paper is to investigate the influences of service complexity, contract structure and contracting process on the buyer-perceived supplier performance in business-to-business (B2B) services.Design/methodology/approachA research model is developed based on transaction cost economics and the research on service contracting. The model is tested by the survey data collected. Professional focus groups on LinkedIn are used to generate the list of potential respondents. The sample consists of 177 purchasing professionals from 25 countries.FindingsThe results indicate that three major contract dimensions and follow-up management practices positively influence buyer-perceived supplier performance. Furthermore, service complexity amplifies the effects of incentives designed in the contract and the buyer’s follow-up contract management on perceived supplier performance.Research limitations/implicationsThe sample consists of respondents from 25 countries and provides good geographic coverage. However, the results should be generalized with caution because not all countries were represented equally.Practical implicationsThe study suggests a framework and guidelines for purchasing managers to improve the design and management of service contracts to secure good performance from their supplier.Originality/valueThis paper contributes to understanding the performance-enhancing aspects of designing and monitoring service contracts in B2B contexts. It also adds to the knowledge of the role of service complexity in successful B2B service purchasing.
Policy implementation under stress
Authors: Fjeldstad Odd-Helge , Ali Merima , Katera Lucas 
Published: March 2019

Purpose
Inter-organisational cooperation in revenue collection has received limited attention in the tax administration literature. Recent experiences from Tanzania offer a unique opportunity to examine opportunities and challenges facing such cooperation between central and local government agencies in a developing country context. The administration of property taxes (PT) in Tanzania has been oscillating between decentralised and centralised collection regimes. This paper aims to examine how inter-organisational cooperation affected implementation of the reforms.

Design/methodology/approach
The study draws on data from a variety of sources of information collected during a series of fieldworks over the past decade. Semi-structured interviews were conducted with a wide range of stakeholders, including senior managers and operational staff of the national and municipal tax administrations. The interviews focused on the background and objectives of the property tax reforms, working relations between the central and local government revenue administrations, technical and administrative challenges and innovations, and changes over time with respect to revenue enhancement and implementation of the reforms. Relevant tax legislation and regulations, budget speeches and reports were reviewed.

Findings
Two lessons of broader relevance for policy implementation and PT administration are highlighted. First, institutional trust matters. Top-down reform processes, ambiguity related to the rationale behind the reforms and lack of consultations on their respective roles and expectations have acted as barriers to constructive working relationships between the local and central government revenue agencies. Second, administrative constraints, reflected in poor preparation, outdated property registers and valuation rolls and inadequate incentives for the involved agencies to cooperate hampered the implementation of the reforms.

Originality/value
This paper contributes to the literature on inter-organisational cooperation in revenue collection through a detailed case study of property tax reforms in a developing country context. It also contributes to the literature on policy implementation by identifying political and administrative factors challenging the reform process. In line with this literature, the study shows that policy implementation is not necessarily a coherent process. Instead, it is frequently fragmented and disrupted by changes in policy formulation and access to adequate resources.
China–Pakistan economic corridor and maritime security collaboration
Authors: Chang Yen-Chiang , Khan Mehran Idris 
Published: March 2019

Purpose
This study aims to explore why marine development and maritime security in Pakistan are significant and what the Chinese concerns are. Therefore, the objective of this research is to analyse a growing Pak–China bilateral interests, particularly at Gwadar, to achieve the geostrategic objectives of China–Pakistan Economic Corridor (CPEC).

Design/methodology/approach
The study adopts a qualitative means to discuss the significance of China’s ambitions towards the CPEC project concerning strategic deep-sea management and maritime regulations in the region, with a particular focus on the Gwadar Port.

Findings
The paper concludes that the Gwadar Port is a critical element for maritime security in the whole region. The study also provides an analysis of national and international, security and legal challenges associated with CPEC.

Originality/value
Most of the potential outcomes have already been discussed in public, though a limited academic discussion is available on the legal aspects. It is particularly so with regard to the development and capacity building in the maritime sector of Pakistan under this project. This study aims to explore why marine development and maritime security in Pakistan is significant and what the Chinese concerns are.
Clinical and radiological outcomes of infantile hemangioma treated with oral propranolol: A long‐term follow‐up study
Authors: Yu Zhang , Cai Ren , Chang Lei , Qiu Yajing , Chen Xuanfeng , Chen Qianyi , Ma Gang , Jin Yunbo , Lin Xiaoxi 
Published: March 2019

AbstractInfantile hemangiomas (IH) undergo rapid growth during early infancy followed by gradual involution. After involution, a part of IH remain as residual lesions. Since 2008, oral propranolol has been widely used in the treatment of IH. However, long‐term outcome of IH treated with propranolol remains unknown. This study aimed to investigate the sequelae of IH treated with propranolol. In this study, propranolol was given at a dose of 2 mg/kg per day at the age of 3.8 ± 2.5 months and follow‐up visits were arranged to continue at least through the age of 4 years. Types of sequela were recorded and classified as four degrees (“none”, “minimal”, “significant” and “severe” at last visit), then subsequent therapy was evaluated with the help of magnetic resonance imaging (MRI). A total of 73 patients with complete follow up were enrolled in the study. The most common types of sequela were telangiectasia, fibrofatty tissue and erythema. Significant and severe sequelae were observed in 72.4% of treated IH; superficial IH led to more but not significantly significant and severe sequelae than mixed IH (P > 0.05). Despite propranolol treatment, surgery was still needed in 37.5% of IH at a mean age of 70.3 months, and for the main reason of surgery, fibrofatty or hemangioma residua, MRI was useful for us to choose an appropriate surgical procedure.
Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species
Authors: Mizuno Carolina M. , Prajapati Bina , Lucas‐Staat Soizick , Sime‐Ngando Telesphore , Forterre Patrick , Bamford Dennis H. , Prangishvili David , Krupovic Mart , Oksanen Hanna M. 
Published: March 2019

SummaryThe diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non‐contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV‐4. Differently from HRTV‐4, HFTV1 encodes host‐derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.
Private Actions and Preferences for Coordinated Groundwater Conservation in Colorado's Republican River Basin
Authors: Shepler Ryan , Suter Jordan F. , Manning Dale T. , Goemans Chris 
Published: March 2019

AbstractConservation of groundwater resources is critical for maintaining the future productivity of irrigated land in the Ogallala Aquifer Region and beyond. This research explores motivations and behavior related to groundwater conservation among agricultural producers in the Colorado portion of the Republican River Basin, which is part of the Ogallala Aquifer. The empirical modeling uses data from a recently conducted survey to analyze how a common set of producer, farm, and resource characteristics influence groundwater values, concern for future groundwater availability, private conservation actions, and support for coordinated conservation efforts. We find two factors, producer age and land owner status, are consistently correlated with the key conservation‐related outcomes we evaluate. More generally, the results suggest considerable similarities in the characteristics that drive private conservation actions and support for coordinated conservation. This knowledge could be used to better target and incentivize future groundwater conservation efforts in the region. Editor's note: This paper is part of the featured series on Optimizing Ogallala Aquifer Water Use to Sustain Food Systems. See the February 2019 issue for the introduction and background to the series.