bluuebunny/crossref_metadata_2025_split huggingface dataset:
Description and whole genome sequencing ofEikenella exiguasp. nov., isolated from brain abscess and blood
Authors: Stormo Kristin A. , Nygaard Randi M. , Bruvold Torbjørn S. , Dimmen Grete , Lindemann Paul Christoffer , Jordal Stina , Kommedal Øyvind 
Published: August 2019

AbstractWe herein describe the first novel species within the genus Eikenella since it was established in 1972 by the reclassification of “Bacteroides corrodens” toEikenella corrodens. From a poly-microbial brain abscess, we encountered an Eikenella isolate PXX that could not validly be namedE. corrodens. The isolate grew on blood agar with small, translucent, pitting colonies after 3 days of anaerobic incubation. By reviewing previously collected invasive isolates, we found an additional Eikenella strain EI_02 from a blood culture exhibiting the same properties as PXX. Phylogenetic analyses based on both whole genome and individual house-keeping genes confirmed that the two strains allocate in a phylogenetic cluster separate fromE. corrodens.Using specific amplification and sequencing of the EikenellanusG-gene as a method, we further detected the novel Eikenella species in six historic brain-abscesses previously reported to containE. corrodensbased on 16S metagenomics. Out of 24 Eikenella whole genome projects available in GenBank, eight cluster together with PXX and EI_02. These isolates were recovered from brain abscess (2), blood (1), bone/soft tissue (3), parotid gland (1) and unknown (1). It remains to be investigated whether the new species can be a cause of endocarditis.The average nucleotide identity (ANI) value between strain PXX and theE. corrodenstype strain ATCC 23834 was 92.1% and the corresponding genome-to-genome distance value 47.1%, both supporting the classification of PXX as a novel species. For this species we propose the nameEikenella exigua. TheE. exiguatype strain is PXXT(DSM 109756T, NCTC 14318T).
Metabolically-active obligate aerobes in anoxic (sulfidic) marine sediments
Authors: Bhattacharya Sabyasachi , Roy Chayan , Mandal Subhrangshu , Rameez Moidu Jameela , Sarkar Jagannath , Fernandes Svetlana , Mapder Tarunendu , Alam Masrure , Roy Rimi , Mondal Nibendu , Pyne Prosenjit , Haldar Prabir Kumar , Peketi Aditya , Chakraborty Ranadhir , Mazumdar Aninda , Ghosh Wriddhiman 
Published: August 2019

AbstractMetabolically-active obligate aerobes are unheard-of in tightly-anoxic environments. Present culture-independent and culture-dependent investigations revealed aerobic microbial communities along two, ~3-meter-long sediment-cores underlying the eastern Arabian Sea oxygen minimum zone, where high H2S disallows O2influx from the water-column. While genes for aerobic respiration byaa3-/cbb3-type cytochrome-coxidases and cytochrome-bdubiquinol oxidase, and aerobic oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were present across the cores, so were live aerobic, sulfur-chemolithoautotrophs and chemoorganoheterotrophs. The 8820-years-old, highly–sulfidic, methane-containing sediment-sample from 275 cmbsf of 530 mbsl yielded many such obligately-aerobic bacterial-isolates that died upon anaerobic incubation with alternative electron-acceptors/fermentative-substrates. Several metatranscriptomic reads from this sediment-sample matched aerobic-respiration-/oxidase-reaction-/transcription-/translation-/DNA-replication-/membrane-transport-/cell-division-related genes of the obligately-aerobic isolates, thereby corroborating their active aerobic metabolic-statusin situ. Metagenomic and metatranscriptomic detection of perchlorate-/chlorate-reduction genes, plus anaerobic growth of an obligately-aerobicHalothiobacillusisolate in the presence of perchlorate and perchlorate-reducing-consortia, suggested that cryptic O2produced by perchlorate-respirers could be sustaining obligately-aerobes in this environment.
High order structure in mouse courtship vocalizations
Authors: Hertz Stav , Weiner Benjamin , Perets Nisim , London Michael 
Published: August 2019

AbstractMany complex motor behaviors can be decomposed into sequences of simple individual elements. Mouse ultrasonic vocalizations (USVs) are naturally divided into distinct syllables and thus are useful for studying the neural control of complex sequences production. However, little is known about the rules governing their temporal order. We recorded USVs during male-female courtship (460,000 USVs grouped into 44,000 sequences) and classified them using three popular algorithms. Modeling the sequences as Markov processes revealed a significant temporal structure which was dependent on the specific classification algorithm. To quantify how syllable misclassification obscures the true underlying sequence structure, we used information theory. We developed the Syntax Information Score and ranked the syllable classifications of the three algorithms. Finally, we derived a novel algorithm (Syntax Information Maximization) that utilized sequence statistics to improve the classification of individual USVs with respect to the underlying sequence structure.
Immortalization of human zone I hepatocytes from biliary atresia with CDK4R24C, cyclin D1, and TERT for cytochrome P450 induction testing
Authors: Nishiwaki Manami , Toyoda Masashi , Oishi Yoshie , Ishida Seiichi , Horiuchi Shin-ichiro , Makino Hatsune , Kimura Tohru , Ohno Shin-ichi , Ohkura Takashi , Enosawa Shin , Akutsu Hidenori , Nakazawa Atsuko , Kasahara Mureo , Kiyono Tohru , Umezawa Akihiro 
Published: August 2019

AbstractBackgroundHepatocytes are an important tool for in vitro toxicology testing. In addition to primary cultures, a limited number of immortalized cell lines have been developed. We here describe a new cell line, designated as HepaMN, which has been established from a liver associated with biliary atresia.MethodsHepatocytes were isolated from a liver of 4-year-old girl with biliary atresia and immortalized by inoculation with CSII-CMV-TERT, CSII-CMV-Tet-Off, CSII-TRE-Tight-cyclin D1 and CSII-TRE-Tight-CDK4R24C (mutant CDK4: an INK4a-resistant form of CDK4) lentiviruses at the multiplicity of infection of 3 to 10.ResultsHepaMN cells exhibited morphological homogeneity, displaying hepatocyte-like phenotypes. Phenotypic studies in vivo and in vitro revealed that HepaMN cells showed polarized and functional hepatocyte features along with a canalicular cell phenotype under defined conditions, and constitutively expressed albumin and carbamoyl phosphate synthetase I in addition to epithelial markers. Since HepaMN cells are immortal and subcloned, kinetics and expression profiles were independent of population doublings.ConclusionsHepaMN cells showed increased CYP3A4 expression after exposure to rifampicin, implying that their close resemblance to normal human hepatocytes makes them suitable for research applications including drug metabolism studies.
Diagnostic value of galactomannan in bronchoalveolar lavage fluid for chronic respiratory disease with pulmonary aspergillosis
Authors: Lai Guangbin , Zeng Chao , Mo Jianming , Song Wei-dong , Xu Ping 
Published: August 2019

ABSTRACTObjectiveTo explore the diagnostic value of the bronchoalveolar lavage fluid galactomannan (BALF GM) test for chronic respiratory disease with pulmonary aspergillosis, and establish the optimal cut-off value.MethodsA total of 180 chronic respiratory disease patients seen at the Respiratory Medicine Department of Peking University Shenzhen Hospital from September 2017 to September 2018 were analyzed. According to the diagnostic criteria, we divided the patients into the case group (n = 70, comprising 5, 20, and 45 proven, probable, and possible cases, respectively) and the control group (n = 110). Bronchoalveolar lavage fluid was collected, and the BALF GM test results were analyzed.ResultsA non-parametric rank-sum test showed that the mean rank of the case group was 140.80, which was higher than that of the control group (58.49). The Z-value was 10.335 (P = 0.000), indicating that the general distribution of BALF GM differed between the two groups. A BALF GM cut-off value of 0.485 showed the highest diagnostic efficacy for pulmonary aspergillosis. The sensitivity, specificity, positive predictive value, and negative predictive value were 92.9%, 100%, 92.8%, and 100%, respectively. As the cut-off value increased, the specificity and sensitivity of the BALF GM test increased and decreased, respectively.ConclusionsThe BALF GM test can be used confirm the diagnosis of patients with pulmonary aspergillosis and chronic respiratory disease. The optimum BALF GM cut-off value was 0.485. Antifungal therapy is important for treating pulmonary aspergillus infection in patients with chronic respiratory disease.
Design concepts of low-frequency electromagnetic devices based on a data-driven approach
Authors: Ghorbanian Vahid , Mohammadi Mohammad Hossain , Lowther David 
Published: August 2019

PurposeThis paper aims to propose a data-driven approach to determine the design guidelines for low-frequency electromagnetic devices.Design/methodology/approachTwo different devices, a core-type single-phase transformer and a motor-drive system, are used to show the usefulness and generalizability of the proposed approach. Using a finite element solver, a large database of design possibilities is created by varying design parameters, i.e. the geometrical and control parameters of the systems. Design rules are then extracted by performing a statistical analysis and exploring optimal and sub-optimal designs considering various targets such as efficiency, torque ripple and power factor.FindingsIt is demonstrated that the correlation of the design parameters influences the way the data-driven approach must be made. Also, guidelines for defining new design constraints, which can lead to a more efficient optimization routine, are introduced for both case studies.Originality/valueUsing the proposed approach, new design guidelines, which are generally not obtainable by the classical design methods, are introduced. Also, the proposed approach can potentially deal with different parameter–objective correlations, as well as different number of connected systems. This approach is applicable regardless of the device type.
Role of gender on the performance of Indian microfinance institutions
Authors: Ghosh Chandralekha , Guha Samapti 
Published: August 2019

PurposeMicrofinance institutions (MFIs) are known for their contribution to the women empowerment and poverty alleviation but it is not clear about the role of gender on the performance of this industry. It is important to explore the representation of both the gender in three levels, namely, decision-making, day-to-day management and implementation of the micro-financial services. This study aims to examine the impact of female board members, female managers and female field officers on the financial and social performance of the MFIs.Design/methodology/approachThe authors have used random effect panel data analysis. The study covers 104 MFIs operating in India. The time period of the analysis is from 2010 to 2014.FindingsThe study has shown that as the number of female directors within the board increase there is an increase in cost per borrower. This is an indication that more female clients are being targeted. The increase in number of female managers leads to an increase in the number of active borrowers. The increase in the number of female staff members leads to an increase of operational self-sufficiency and yield of the gross portfolio.Research limitations/implicationsThe present study has faced a lot of limitation due to the non-availability of the secondary data on the governance system of the microfinance industry. The study could not be undertaken for an extended period because of the unavailability of data for a long period.Practical implicationsThis study has highlighted the role of gender in case of performance of microfinance institutions. The gender diversity at the field level has shown to enhance the financial performance of the MFIs. So, the MFIs should try to bring gender diversity at the operation level.Social implicationsThis study has shown that an increase of woman directors at the board level increase female clients of MFIs. The increase of female managers also enhances number of female clients. So, the gender diversity at the managerial level and director level help MFIs to meet their social performance by reaching to more number of needy female clients.Originality/valueThe gender diversity at the three levels, namely, board level, managerial level and field operation level has not been analyzed in the Indian context. In India MFIs mainly target the female clients so in this context having gender diversity at the three levels of operation of the MFIs, which can improve both the financial and social performance of the MFIs.
Justification of TPM pillars for enhancing the performance of manufacturing industry of Northern India
Authors: Singh Jagdeep , Singh Harwinder 
Published: August 2019

Purpose
The purpose of this paper is to assess TPM pillars for manufacturing performance improvement in the manufacturing organizations of Northern India and to identify critical and non-critical components based on failure history, to minimize machine downtime, maximize component/machine availability and to identify failure modes, their causes and effects of these failures on machines or components in the case company under study.

Design/methodology/approach
In this paper, TPM pillars in the paint manufacturing plant have been elaborated to ascertain the tangible and intangible benefits accrued as a result of successful TPM implementation. The approach has been directed toward justification of TPM implementation for its support to competitive manufacturing in the context of Indian manufacturing industries.

Findings
Findings suggest that maintenance planning is more effective than small improvements for achieving benefits from TPM pillars. Moreover, results indicated that critical components show average reliability and failure probability of about 50 percent.

Originality/value
The present study encompasses systematic identification of maintenance-related losses, setting up of targets regarding maintenance performance improvements and developing guidelines for achieving enhanced manufacturing system performance through strategic TPM implementation in the manufacturing plant, which can also be important to all concerned with maintenance in various manufacturing enterprises.
Contract amendments: for better or for worse?
Authors: Malatesta Deanna , Smith Craig 
Published: August 2019

PurposePublic management researchers have successfully leveraged theory to advance the understanding of contracts and the different governance structures that underpin contract relationships. Yet there is still much to learn about the implications for different governance structures. Applying insights from property rights, the purpose of this paper is to examine the substance of initial government contracts and their subsequent amendments in order to determine whether allocation of decision rights leads to better or worse contract amendments.Design/methodology/approachThe authors evaluate the text of initial contracts and their subsequent amendments in 258 government–business relationships and focus on the implications of assigning key decision rights to the party with most relevant knowledge expertise.FindingsTwo primary findings are presented. First, initial contracts where knowledge expertise and the associated decision rights are co-located (i.e. integrated) are likely to be associated withex postadjustments that benefit both parties to the contract. Second, the authors find that this initial finding is likely a result of government integration as opposed to supplier integration.Originality/valueGiven that we know most professional service contracts require some form of contract amendment over time, this research helps us understand why some amendments will reinforce the collaborative (Pareto enhancing) nature of the relationship, while others may be more one sided (rent seeking). Unlike other theoretical approaches (e.g. transaction cost theory), property rights theory provides guidance for such decision making.
Cutting-edge technology and nocturnal headaches in adolescent smart phone users in Chiang Mai, Thailand
Authors: Chongchitpaisan Wanna , Wiwatanadate Phongtape , Tanprawate Surat , Narkpongphun Assawin , Siripon Nipapon 
Published: August 2019

Purpose
Nocturnal headaches among adolescents were reported to be increased with the development of modern technology. The purpose of this paper is to investigate the smartphone electromagnetic radiation related to nocturnal headaches among high school students.

Design/methodology/approach
The time series study of all 12,969 records from 145 high school students Chiang Mai Province was selected from the population in the first phase by setting criteria. The samples completed a headache diary utilizing a smartphone application. The smartphone output power (SOP) was measured and recorded by the smartphone application and transmitted by e-mail to a researcher. The smartphone use, sleep quality, anxiety and depression also were assessed. Data were analyzed using Generalized Estimating Equation adjusting for demographic data, smartphone use, and sleep quality and otherwise.

Findings
The resulted showed the prevalence of repeated headaches to be 13.4 percent, nocturnal headache only 5.3 percent and the strongest effect of day time SOP at a 1.80–1.99×10−5 mW range on nocturnal headaches (ORadj5.18; 95% CI: 3.44–7.81). Meanwhile, Lag_6 of daily SOP exposure produced a nocturnal headache effect in a reverse dose-response manner. Furthermore, the nocturnal headache also had the strongest association with age, internet use and device brand (ORadj2.33; 95% CI: 1.08–5.05, ORadj2.14; 95% CI: 1.07–4.2 and ORadj1.68; 95% CI: 1.1–2.4).

Originality/value
The electromagnetic radiation from a smartphone is the environmental variables influences on headache. The results suggested that there should be limited times for smartphone use and older age to start using a smartphone to prevent headache attacks at night.
A unified simulation for effects of gellan polymer concentrations on large strain elastic behaviors of gellan gels
Authors: Ding Xie-Fei , Zhan Lin , Xi Hui-Feng , Xiao Heng 
Published: August 2019

Purpose
A direct and unified approach is proposed toward simultaneously simulating large strain elastic behaviors of gellan gels with different gellan polymer concentrations. The purpose of this paper is to construct an elastic potential with certain parameters of direct physical meanings, based on well-designed invariants of Hencky’s logarithmic strain.

Design/methodology/approach
For each given value of the concentration, the values of the parameters incorporated may be determined in the sense of achieving accurate agreement with large strain uniaxial extension and compression data. By means of a new interpolating technique, each parameter as a function of the concentration is then obtained from a given set of parameter values for certain concentration values.

Findings
Then, the effects of gellan polymer concentrations on large strain elastic behaviors of gellan gels are studied in demonstrating how each parameter relies on the concentration. Plane-strain (simple shear) responses are also presented for gellan gels with different polymer concentrations.

Originality/value
A direct, unified approach was proposed toward achieving a simultaneous simulation of large elastic strain behaviors of gellan gels for different gellan polymer concentrations. Each parameter incorporated in the proposed elastic potential will be derived as a function of the polymer concentration in an explicit form, in the very sense of simultaneously simulating large strain data for different concentrations.
The scaling of fine root nitrogen versus phosphorus in terrestrial plants: A global synthesis
Authors: Wang Zhiqiang , Yu Kailiang , Lv Shiqi , Niklas Karl J. , Mipam Tserang Donko , Crowther Thomas W. , Umaña María N. , Zhao Qi , Huang Heng , Reich Peter B. 
Published: August 2019

AbstractLeaves and roots may differ in nitrogen (N), phosphorus (P) and N:P stoichiometry, which can influence plant growth and ecosystem functioning. As compared to leaves, however, relatively little is known about the N versus P scaling relationship and N:P stoichiometry in root systems, particularly in fine roots.We used a global dataset comprising 1,890 observations for a total of 763 terrestrial plant species in 123 families (spanning 433 sites world‐wide) to examine live fine root N and P concentrations and stoichiometry, and to determine the scaling of N versus P within and across different plant groups and ecosystems.The global geometric mean values of fine root N and P concentrations and N:P ratios were 10.84 mg/g, 0.94 mg/g and 11.55, respectively. Fine root N and P concentrations and N:P ratios varied both within and across plant groups and ecosystems. A 0.82‐power law described the scaling of fine root N with respect to P across the entire dataset and for major plant phylogenetic and functional groups; however, the numerical value of the N versus P scaling exponent declined from the tropics to higher latitudes and varied significantly at different local sites. Soil nutrient account for much of the variation observed in the scaling of fine root N versus P concentration at different local sites.This study advances our knowledge about limiting resource allocation strategies in below‐ground organs and has important implications for modelling plant growth at local, regional and global levels.A freePlain Language Summarycan be found within the Supporting Information of this article.
Bayesian data integration and variable selection for pan‐cancer survival prediction using protein expression data
Authors: Maity Arnab Kumar , Bhattacharya Anirban , Mallick Bani K. , Baladandayuthapani Veerabhadran 
Published: August 2019

AbstractAccurate prognostic prediction using molecular information is a challenging area of research, which is essential to develop precision medicine. In this paper, we develop translational models to identify major actionable proteins that are associated with clinical outcomes, like the survival time of patients. There are considerable statistical and computational challenges due to the large dimension of the problems. Furthermore, data are available for different tumor types; hence data integration for various tumors is desirable. Having censored survival outcomes escalates one more level of complexity in the inferential procedure. We develop Bayesian hierarchical survival models, which accommodate all the challenges mentioned here. We use the hierarchical Bayesian accelerated failure time model for survival regression. Furthermore, we assume sparse horseshoe prior distribution for the regression coefficients to identify the major proteomic drivers. We borrow strength across tumor groups by introducing a correlation structure among the prior distributions. The proposed methods have been used to analyze data from the recently curated “The Cancer Proteome Atlas” (TCPA), which contains reverse‐phase protein arrays–based high‐quality protein expression data as well as detailed clinical annotation, including survival times. Our simulation and the TCPA data analysis illustrate the efficacy of the proposed integrative model, which links different tumors with the correlated prior structures.