bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatio-temporal individual-based network framework for West Nile virus in the USA: spreading pattern of West Nile virus
Authors: Moon Sifat A. , Cohnstaedt Lee W. , McVey D. Scott , Scoglio Caterina M. 
Published: October 2018

AbstractWest Nile virus (WNV)—a mosquito-borne arbovirus— entered the USA through New York City in 1999 and spread to the contiguous USA within three years while transitioning from epidemic outbreaks to endemic transmission. The virus is transmitted by vector competent mosquitoes and maintained in the avian populations. WNV spatial distribution is mainly determined by the movement of residential and migratory avian populations. We developed an individual-level heterogeneous network framework across the USA with the goal of understanding the long-range spatial distribution of WNV. To this end, we proposed three distance dispersal kernels model: 1) exponential—short-range dispersal, 2) power-law—long-range dispersal in all directions, and 3) power-law biased by flyway direction—long-range dispersal only along established migratory routes. To select the appropriate dispersal kernel we used the human case data and adopted a model selection framework based on approximate Bayesian computation with sequential Monte Carlo sampling (ABC-SMC). From estimated parameters, we find that the power-law biased by flyway direction kernel is the best kernel to fit WNV human case data, supporting the hypothesis of long-range WNV transmission is mainly along the migratory bird flyways. Through extensive simulation from 2014 to 2016, we proposed and tested hypothetical mitigation strategies and found that mosquito population reduction in the infected states and neighboring states is potentially cost-effective.Author summaryThe underlying pattern of West Nile virus (WNV) geographic spread across the United States is not completely clear, which is a necessary step for continental or state level mitigation strategies to reduce WNV transmission. We report a network model that explains the geographic spread of WNV in the United States. West Nile virus is a mosquito-borne pathogen that infects many avian species with different movement ranges. From our research, we found that migration patterns and routes play an essential role in the WNV spatial distribution. The virus spreads in all directions at short distances because of local birds and short-distance migratory birds. However, the virus also disperses long distances along the avian migratory routes. Our model is designed to be flexible and therefore can be used to explore spreading patterns of other infectious diseases in other geographic locations.
Antibodies against egg- and cell-grown influenza A(H3N2) viruses in adults hospitalized during the 2017-2018 season
Authors: Levine Min Z. , Martin Emily T. , Petrie Joshua G. , Lauring Adam S. , Holiday Crystal , Jefferson Stacie , Fitzsimmons William J. , Johnson Emileigh , Ferdinands Jill M. , Monto Arnold S. 
Published: October 2018

ABSTRACTBackgroundThe 2017-2018 US influenza season was severe with low vaccine effectiveness. Circulating A(H3N2) viruses from multiple genetic groups were antigenically similar to cell-grown vaccine strains. However, most influenza vaccines are egg-propagated.MethodsSerum was collected shortly after illness onset from 15 PCR confirmed A(H3N2) infected cases and 15 uninfected (controls) hospitalized adults enrolled in an influenza vaccine effectiveness study.Geometric mean titers against egg- and cell-grown A/Hong Kong/4801/2014 A(H3N2) vaccine strains and representative circulating viruses (including A/Washington/16/2017) were determined by microneutralization (MN) assays. Independent effects of strain-specific titers on susceptibility were estimated by logistic regression.ResultsMN titers against egg-A/Hong Kong were significantly higher among those who were vaccinated (MN GMT: 173 vs 41;P= 0.01). However, antibody titers to cell-grown viruses were much lower in all individuals (P>0.05) regardless of vaccination. In unadjusted models, a 2-fold increase in MN titers against egg-A/Hong Kong was not significantly protective against infection (29% reduction; p=0.09), but a similar increase in cell-A/Washington titer (3C.2a2) was protective (60% reduction; p=0.02). A similar increase in egg-A/Hong Kong titer was not significantly associated with odds of infection when adjusting for MN titers against A/Washington (15% reduction; P=0.61). A 54% reduction of odds of infection was observed with a 2-fold increase in A/Washington (not significant; P=0.07), adjusted for egg-A/Hong Kong titer.ConclusionAlthough individuals vaccinated in 2017-2018 had high antibody titers against the egg-adapted vaccine strain, antibody responses to cell-grown circulating viruses may not be sufficient to provide protection, likely due to egg-adaptation in the vaccine.
Fecal microbiota transplantation brings about bacterial strain displacement in patients with inflammatory bowel diseases
Authors: Zou Manli , Jie Zhuye , Cui Bota , Wang Honggang , Feng Qiang , Zou Yuanqiang , Zhang Xiuqing , Yang Huanming , Wang Jian , Zhang Faming , Jia Huijue 
Published: October 2018

ABSTRACTFecal microbiota transplantation (FMT), which is thought to have the potential to correct dysbiosis of gut microbiota, has recently been used to treat inflammatory bowel disease (IBD). To elucidate the extent and principles of microbiota engraftment in IBD patients after FMT treatment, we conducted an interventional prospective cohort study. The cohort included two categories of patients: (1) patients with moderate to severe Crohn’s disease (CD) (Harvey-Bradshaw Index ≥ 7, n = 11, and (2) patients with ulcerative colitis (UC) (Montreal classification, S2 and S3, n = 4). All patients were treated with a single FMT (via mid-gut, from healthy donors) and follow-up visits were performed at baseline, 3 days, one week, and one month after FMT (missing time points included). At each follow-up time point, fecal samples of the participants were collected along with their clinical metadata. For comparative analysis, 10 fecal samples from 10 healthy people were included to represent the diversity level of normal gut microbiota. Additionally, the metagenomic data of 25 fecal samples from 5 individuals with metabolic syndrome who underwent autologous FMT treatment were downloaded from a previous published paper to represent natural microbiota shifts during FMT. All fecal samples underwent shotgun metagenomic sequencing.We found that 3 days after FMT, 11 out of 15 recipients were in remission (3 out of 4 UC recipients; 8 out of 11 CD recipients). Generally, bacterial colonization was observed to be lower in CD recipients than in UC recipients at both species and strain levels. Furthermore, across species, different strains displayed disease-specific displacement advantages under two-disease status. Finally, most post-FMT species (> 80%) could be properly predicted (AUC > 85%) using a random forest classification model, with the gut microbiota composition and clinical parameters of pre-FMT recipients acting as the most contributive factors for prediction accuracy.
The Infectious Bronchitis Virus Coronavirus Envelope Protein Alters Golgi pH to Protect Spike Protein and Promote Release of Infectious Virus
Authors: Westerbeck Jason W. , Machamer Carolyn E. 
Published: October 2018

AbstractCoronaviruses (CoVs) are important human pathogens with significant zoonotic potential. Progress has been made toward identifying potential vaccine candidates for highly pathogenic human CoVs, including use of attenuated viruses that lack the CoV envelope (E) protein or express E mutants. However, no approved vaccines or anti-viral therapeutics exist. CoVs assemble by budding into the lumen of the early Golgi prior to exocytosis. The small CoV E protein plays roles in assembly, virion release, and pathogenesis. CoV E has a single hydrophobic domain (HD), is targeted to Golgi membranes, and has cation channel activityin vitro. The E protein from the avian infectious bronchitis virus (IBV) has dramatic effects on the secretory system, which requires residues in the HD. Mutation of the HD of IBV E during infection results in impaired growth kinetics, impaired release of infectious virions, accumulation of IBV S protein on the plasma membrane when compared IBV WT infected cells, and aberrant cleavage of IBV S on the surface of virions. We previously reported the formation of two distinct oligomeric pools of IBV E in transfected and infected cells. Disruption of the secretory pathway by IBV E correlates with a form that is likely monomeric, suggesting that the effects on the secretory pathway are independent of E ion channel activity. Here, we present evidence suggesting that the monomeric form of IBV E correlates with a rise in the pH of the Golgi lumen. We demonstrate that infection with IBV induces neutralization of Golgi luminal pH, promoting a model in which IBV E alters the secretory pathway through interaction with host cells factors, protecting IBV spike protein (S) from premature cleavage and leading to the efficient release of infectious virus from the cells.
Compressing Streams of Phylogenetic Trees
Authors: Trefzer Axel , Stamatakis Alexandros 
Published: October 2018

AbstractBayesian Markov-Chain Monte Carlo (MCMC) methods for phylogenetic tree inference, that is, inference of the evolutionary history of distinct species using their molecular sequence data, typically generate large sets of phylogenetic trees. The trees generated by the MCMC procedure are samples of the posterior probability distribution that MCMC methods approximate. Thus, they generate a stream of correlated binary trees that need to be stored. Here, we adapt state-of-the art algorithms for binary tree compression to phylogenetic tree data streams and extend them to also store the required meta-data. On a phylogenetic tree stream containing 1, 000 trees with 500 leaves including branch length values, we achieve a compression rate of 5.4 compared to the uncompressed tree files and of 1.8 compared to bzip2-compressed tree files. For compressing the same trees, but without branch length values, our compression method is approximately an order of magnitude better than bzip2. A prototype implementation is available at https://github.com/axeltref/tree-compression.git.
Evidence for Bias of Genetic Ancestry in Resting State Functional MRI
Authors: Altmann Andre , Mourao-Miranda Janaina 
Published: October 2018

ABSTRACTResting state functional magnetic resonance imaging (rs-fMRI) is a popular imaging modality for mapping the functional connectivity of the brain. Rs-fMRI is, just like other neuroimaging modalities, subject to a series of technical and subject level biases that change the inferred connectivity pattern. In this work we predicted genetic ancestry from rs-fMRI connectivity data at very high performance (area under the ROC curve of 0.93). Thereby, we demonstrated that genetic ancestry is encoded in the functional connectivity pattern of the brain at rest. Consequently, genetic ancestry constitutes a bias that should be accounted for in the analysis of rs-fMRI data.
Treatment Outcome of Diabetic Ketoacidosis Among Patients Atending General Hospital in North-West Ethiopia: Hospital Based Study
Authors: Abegaz Tadesse Melaku , Mekonnen Gizework Alemnew , Gebreyohannes Eyob Alemayehu , Gelaye Kasssahun Alemu 
Published: October 2018

AbstractBackgroundDiabetic ketoacidosis is an acute life-threatening complication of diabetes mellitus. There was limited data on level of in-hospital mortality, hospital stay and factors associated with length of hospital stay among diabetic patients admitted to diabetic ketoacidosis at Debretabor General Hospital.ObjectiveThe aim of the study was to determine the length of hospital stay and in-hospital mortality of diabetic ketoacidosis patients and to assess determinants of long hospital stay among diabetic patients admitted with Diabetic ketoacidosis at Debretabor General Hospital.MethodA retrospective study was conducted at Debretabor General Hospital from June 1to 30, 2018. Participants included in the study were all diabetic patients with diabetic ketoacidosis admitted to the hospital from August 2010 to May 31, 2018 whose medical records contained complete pertinent data. The primary outcome was to determine the length of hospital stay and in-hospital mortality of diabetic ketoacidosis patients. All the statistical data was carried out using Statistical Package for Social Sciences (SPSS). Descriptive statistics was presented using means with standard deviation and percentages.ResultA total of 387 patients’ medical records contained pertinent complete information included in this study. Mean age of the patients was 33.30± 14.96 years. The majority of patients were females 244 (63.0%). The mean length of hospital stay was 4.64(±2.802) days. About twenty percent 79(20.41%) patients had long hospital stay (>7days). The majority 370 (95.60%) of patients improved and discharged and 17 (4.40%) patients died in the hospital. patients who had mild DKA; AOR: 0.16 [0.03-0.78] and patients between the age of 35-44years, AOR: 0.125[0.017-0.92] had reduced length of hospital stay. further, patients with DKA precipitated by infection were 4.59 times more likely to have long hospital stay than patients with DKA precipitated by unknown causes; AOR 4.59[1.08-19.42].ConclusionsIn the current study, the mean length of hospital stay was around five days. About twenty percent patients had long hospital stay. Nearly ninety five percent of patientsimproved and discharged. The presence of infection, frequent rebound hyperglycemia and severity of DKA were the major determinants of long hospital stay.
Balancing selection at a premature stop mutation in themyostatingene underlies a recessive leg weakness syndrome in pigs
Authors: Matika Oswald , Robledo Diego , Pong-Wong Ricardo , Bishop Stephen C. , Riggio Valentina , Finlayson Heather , Lowe Natalie R. , Hoste Annabelle E. , Walling Grant A. , Archibald Alan L. , Woolliams John A. , Houston Ross D. 
Published: October 2018

ABSTRACTBalancing selection provides a plausible explanation for the maintenance of deleterious alleles at moderate frequency in livestock, including lethal recessives exhibiting heterozygous advantage in carriers. In the current study, a leg weakness syndrome causing mortality of piglets in a commercial line showed monogenic recessive inheritance, and a region on chromosome 15 associated with the syndrome was identified by homozygosity mapping. Whole genome resequencing of cases and controls identified a mutation coding for a premature stop codon within exon 3 of the porcineMyostatin (MSTN)gene, similar to those causing a double-muscling phenotype observed in several mammalian species. TheMSTNmutation was in Hardy-Weinberg equilibrium in the population at birth, but significantly distorted amongst animals still in the herd at 110 kg, due to an absence of homozygous mutant genotypes. In heterozygous form, theMSTNmutation was associated with a major increase in muscle depth and decrease in fat depth, suggesting that the deleterious allele was maintained at moderate frequency due to heterozygous advantage. Knockout of the porcineMSTNby gene editing has previously been linked to problems of low piglet survival and lameness. ThisMSTNmutation is an example of putative balancing selection in livestock, providing a plausible explanation for the lack of disrupting MSTN mutations in pigs despite many generations of selection for lean growth.
Experimental study of a pitching and plunging wing
Authors: Gkiolas Dimitris , Yiasemides Demetri , Mathioulakis Demetri 
Published: October 2018

Purpose
The complex flow behavior over an oscillating aerodynamic body, e.g. a helicopter rotor blade, a rotating wind turbine blade or the wing of a maneuvering airplane involves combinations of pitching and plunging motions. As the parameters of the problem (Re, St and phase difference between these two motions) vary, a quasi-steady analysis fails to provide realistic results for the aerodynamic response of the moving body, whereas this study aims to provide reliable experimental data.

Design/methodology/approach
In the present study, a pitching and plunging mechanism was designed and built in a subsonic closed-circuit wind tunnel as well as a rectangular aluminum wing of a 2:1 aspect-ratio with a NACA64-418 airfoil, used in wind turbine blades. To measure the pressure distribution along the wing chord, a number of fast responding transducers were embedded into the mid span wing surface. Simultaneous pressure measurements were conducted along the wing chord for the Reynolds number of 0.85 × 106 for both steady and unsteady cases (pitching and plunging). A flow visualization technique was used to detect the flow separation line under steady conditions.

Findings
Elevated pressure fluctuations coincide with the flow separation line having been detected through surface flow visualization and flattened pressure distributions appear downstream of the flow separation line. Closed hysteresis loops of the lift coefficient versus angle of attack were measured for combined pitching and plunging motions.

Practical implications
The experimental data can be used for improvement of unsteady fluid mechanics problem solvers.

Originality/value
In the present study, a new installation was built allowing the aerodynamic study of oscillating wings performing pitching and plunging motions with prescribed frequencies and phase lags between the two motions. The experimental data can be used for improvement of computational fluid dynamics codes in case that the examined aerodynamic body is oscillating.
A BIM–LCA integration technique to embodied carbon estimation applied on wall systems in Brazil
Authors: Crippa Julianna , Boeing Letícia Cavassin , Caparelli Ana Paula Angonese , da Costa Marienne do Rocio de Mello Maron , Scheer Sergio , Araujo Aline Medeiros Ferreira , Bem Diogo 
Published: October 2018

PurposeAiming to simplify the extraction of embodied carbon data using a building information modeling (BIM) software, the purpose of this paper is to present a framework that integrates BIM and life cycle assessment (LCA), which are useful to the architecture, engineer and construction (AEC) industry. As a further purpose, this study also tests four different wall systems.Design/methodology/approachThe study applies design science research and it presents a framework that integrates BIM and LCA. For analysis and validation, a case study features four different wall systems costs based on the Brazilian context. In the proposed framework, SimaPro8 accomplishes the LCA, while ArchiCAD 19 the modeling.FindingsThe first analysis covers embodied carbon and the second covers the total cost of each m² of wall. The proposed framework performs well, and it is effective in the Brazilian context. Concerning the walls, the wood frame system is the most sustainable option within this analysis and the most financially feasible option in Brazil.Originality/valueThe present study contributes to embodied carbon data analysis, ensuring that the best choice of elements and components is being used in the building project. This BIM–LCA integrated solution is valuable not only to the AEC industry and to professionals, but also to future researchers. This analysis is of great value to new ventures, since the society shows a great concern about reducing GHGs emissions.
Towards better understanding of determinants logistical factors in SMEs for cloud ERP adoption in developing economies
Authors: AL-Shboul Moh’d Anwer 
Published: October 2018

PurposeThe purpose of this paper is to investigate the main determinants logistical factors that have an impact on the adoption of cloud enterprise resource planning (ERP) among small- and medium-sized enterprises (SMEs) in developing economies. By adopting the diffusion of innovation, technological, organizational and environmental model as a theoretical framework, the 14 factors examined in this study are as follows: relative advantage (RA), compatibility, complexity, value creation, technology readiness (TR), security concerns, technical barriers, top management support (TMS), enterprise readiness (ER), enterprise size (ES), enterprise status, competitive advantage, government support and infrastructure/telecommunication.Design/methodology/approachData were collected from 131 respondents’ senior executives and IT managers in SMEs in developing economies (Jordan, Lebanon, King Saudi Arabia, Bahrain, Qatar, Emirates, Egypt, Oman, Kuwait and Turkey). A web-based survey questionnaire was used for data collection process. The research framework and the derived hypotheses were tested by logistic regression analysis.FindingsThe findings indicate that compatibility, TR, technical barriers, TMS, ER, ES and competitive pressure have a significant effect on the adoption of cloud ERP. This conclusion can be utilized in enhancing the strategies for approaching ERP cloud by pinpointing the reasons why some SMEs choose to adopt this technology, while others still do not go forward with this.Originality/valueThis study provides an overview and empirically shows the main determinants logistical factors that might face SMEs in the developing economies. The findings also help SMEs consider their information technologies investments when they think to adopt cloud ERP.
Organizational learning and change: can they coexist?
Authors: Watad Mahmoud 
Published: October 2018

Purpose
The purpose of this paper is to explore the dynamics of IT-enabled change and organizational learning. This research defines organizational learning in general terms as the capacity of acquiring, transferring and creating knowledge within an organization.

Design/methodology/approach
This research design represents a common form of ex-post facto analysis, in which the exploration of relationships between variables is the main focus. The questionnaire used in the first phase was self-administered in a report format, wherein managers were asked to describe the organizational context and problems; the IT intervention or managers’ response to the problems; and the benefits that resulted from the introduction of IT. In the follow-up phase, the interviews used a similar version of the survey, focusing on the same themes.

Findings
This paper contends that IT-enabled change such as process redesign and productivity improvements do not take place simultaneously with an organization’s attempts to increase its knowledge base or its capacity to acquire knowledge. Organizations alter processes and re-engineer their operations to improve productivity, not to enhance their knowledge-acquiring and decision-making capacities. It seems that the attention structure of managers may be limited and, therefore, they cannot focus on improving both ends simultaneously. This may suggest that when an organization alters its processes, it may overlook its ability to acquire knowledge and its learning capacity at least for the short term.

Originality/value
The findings of this study can serve as important insights regarding managers’ work practices. Findings support a pragmatic view where managers are concerned with showing immediate gains through the introduction of IT which implies a lack of long-term planning. The findings also can serve as an important lesson to managers in that when they alter organizational processes, they should not overlook the issues of organizational learning and knowledge creation. The findings highlight the complexity of organizations and the conflicting objectives which organizations may attempt to achieve when engaging in change efforts such as the adoption of new technologies.