bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Aspergillus oryzae before and after domestication inferred by large-scale comparative genomic analysis
Authors: Watarai Naoki , Yamamoto Nozomi , Sawada Kazunori , Yamada Takuji 
Published: November 2019

Abstract
Aspergillus oryzae is an industrially useful species, of which various strains have been identified; however, their genetic relationships remain unclear. A. oryzae was previously thought to be asexual and unable to undergo crossbreeding. However, recent studies revealed the sexual reproduction of Aspergillus flavus, a species closely related to A. oryzae. To investigate potential sexual reproduction in A. oryzae and evolutionary history among A. oryzae and A. flavus strains, we assembled 82 draft genomes of A. oryzae strains used practically. The phylogenetic tree of concatenated genes confirmed that A. oryzae was monophyletic and nested in one of the clades of A. flavus but formed several clades with different genomic structures. Our results suggest that A. oryzae strains have undergone multiple inter-genomic recombination events between A. oryzae ancestors, although sexual recombination among domesticated species did not appear to have occurred during the domestication process, at least in the past few decades. Through inter- and intra-cladal comparative analysis, we found that evolutionary pressure induced by the domestication of A. oryzae appears to selectively cause non-synonymous and gap mutations in genes involved in fermentation characteristics, as well as intra-genomic rearrangements, with the conservation of industrially useful catalytic enzyme-encoding genes.
A restoration ecology perspective on the treatment of inflammatory bowel disease
Authors: Orr Matthew R , Kocurek Kathryn M , Bakos Yong J , McDowell Ryder C 
Published: November 2019

Abstract
The human gut can be considered an ecosystem comprised of a community of microbes and nonliving components such as food metabolites and food additives. Chronic diseases are increasingly associated with disruption of this ecosystem. The science of restoration ecology was developed to restore degraded ecosystems, but its principles have not been applied widely to gut medicine, including the treatment of inflammatory bowel disease (IBD). One principle of ecological restoration is that ‘passive’ restoration, which involves removing an ecosystem disturbance, should occur before attempting additional ‘active’ interventions. We discuss evidence that poor diet is principle source of disturbance in IBD, and therefore requires better attention in its research and clinical care. Another restoration principle is that higher biodiversity may improve ecosystem behavior, but this idea has not been tested for its possible importance in donor stool during fecal microbiota transplants.
Lay summary: In patients with chronic disease the gut microbiome behaves like a disturbed ecosystem. Principles borrowed from the science of restoration ecology identify a need to better understand the influence of diet on treatment of inflammatory bowel disease and the importance of donor diversity in fecal microbiota transplants.
Immediate and late impact of reperfusion therapies in acute pulmonary embolism
Authors: Valerio Luca , Klok Frederikus A , Barco Stefano 
Published: November 2019

Abstract
Haemodynamic instability and right ventricular dysfunction are the key determinants of short-term prognosis in patients with acute pulmonary embolism (PE). Residual thrombi and persistent right ventricular dysfunction may contribute to post-PE functional impairment, and influence the risk of developing chronic thromboembolic pulmonary hypertension. Patients with haemodynamic instability at presentation (high-risk PE) require immediate primary reperfusion to relieve the obstruction in the pulmonary circulation and increase the chances of survival. Surgical removal of the thrombi or catheter-directed reperfusion strategies is alternatives in patients with contraindications to systemic thrombolysis. For haemodynamically stable patients with signs of right ventricular overload or dysfunction (intermediate-risk PE), systemic standard-dose thrombolysis is currently not recommended, because the risk of major bleeding associated with the treatment outweighs its benefits. In such cases, thrombolysis should be considered only as a rescue intervention if haemodynamic decompensation develops. Catheter-directed pharmaco-logical and pharmaco-mechanical techniques ensure swift recovery of echocardiographic and haemodynamic parameters and may be characterized by better safety profile than systemic thrombolysis. For survivors of acute PE, little is known on the effects of reperfusion therapies on the risk of chronic functional and haemodynamic impairment. In intermediate-risk PE patients, available data suggest that systemic thrombolysis may have little impact on long-term symptoms and functional limitation, echocardiographic parameters, and occurrence of chronic thromboembolic pulmonary hypertension. Ongoing and future interventional studies will clarify whether ‘safer’ reperfusion strategies may improve early clinical outcomes without increasing the risk of bleeding and contribute to reducing the burden of long-term complications after intermediate-risk PE.
Estimating tree stem diameters and volume from smartphone photogrammetric point clouds
Authors: Marzulli Maria Immacolata , Raumonen Pasi , Greco Roberto , Persia Manuela , Tartarino Patrizia 
Published: November 2019

AbstractMethods for the three-dimensional (3D) reconstruction of forest trees have been suggested for data from active and passive sensors. Laser scanner technologies have become popular in the last few years, despite their high costs. Since the improvements in photogrammetric algorithms (e.g. structure from motion—SfM), photographs have become a new low-cost source of 3D point clouds. In this study, we use images captured by a smartphone camera to calculate dense point clouds of a forest plot using SfM. Eighteen point clouds were produced by changing the densification parameters (Image scale, Point density, Minimum number of matches) in order to investigate their influence on the quality of the point clouds produced. In order to estimate diameter at breast height (d.b.h.) and stem volumes, we developed an automatic method that extracts the stems from the point cloud and then models them with cylinders. The results show that Image scale is the most influential parameter in terms of identifying and extracting trees from the point clouds. The best performance with cylinder modelling from point clouds compared to field data had an RMSE of 1.9 cm and 0.094 m3, for d.b.h. and volume, respectively. Thus, for forest management and planning purposes, it is possible to use our photogrammetric and modelling methods to measure d.b.h., stem volume and possibly other forest inventory metrics, rapidly and without felling trees. The proposed methodology significantly reduces working time in the field, using ‘non-professional’ instruments and automating estimates of dendrometric parameters.
Effect of Helicobacter pylori-eradication therapy on hepatic steatosis in patients with non-alcoholic fatty liver disease: a randomized–controlled pilot study
Authors: Maharshi Vikas , Gupta Pooja , Kumar Vijay L , Upadhyay Ashish Datt , Das Prasenjit , Yadav Rajni , Nayak Baibaswata , Kumar Ramesh , Shalimar  
Published: November 2019

AbstractBackgroundHelicobacter pylori infection has been associated with insulin resistance and non-alcoholic fatty liver disease (NAFLD). This study was done to evaluate the effect of H. pylori-eradication therapy (HPET) in patients with NAFLD compared to standard management therapy (SMT).MethodsEighty NAFLD patients with H. pylori co-infection were randomized into SMT (diet and exercise, n = 36) and HPET (SMT plus amoxicillin, clarithromycin, and pantoprazole, n = 44) groups. The controlled attenuation parameter (CAP), anthropometric parameters, liver enzymes, lipid profile, and glycemic parameters including homeostasis model assessment-insulin resistance (HOMA-IR) were measured and compared between two groups at the baseline and 24 weeks.ResultsSixty-four participants (SMT group [n = 28] and HPET group [n = 36]) were included in a modified intention-to-treat analysis. Both the SMT group and the HPET group had a significant reduction in CAP scores at 24 weeks (P = 0.002 and P &lt; 0.001, respectively), but the change between the groups was insignificant (P = 0.213). Successful eradication of H. pylori occurred in 68% of the HPET group and led to greater improvement in HOMA-IR at 24 weeks compared to SMT or non-responder patients (P = 0.007). The liver enzymes reduced significantly at 24 weeks in both groups, but the changes between the groups were similar. The lipid parameters remained unchanged within the groups and between the groups at 24 weeks. A significant increase in the levels of reduced glutathione was noted in the HPET group, but the change between the two groups was not statistically different.ConclusionsHPET was found to be comparable to SMT alone in reducing hepatic steatosis and liver enzymes at 24 weeks in NAFLD patients. However, successful eradication of H. pylori led to greater improvement in HOMA-IR (Trial registration CTRI/2017/05/008608).
Becoming a Selfish Clan: Recombination Associated to Reverse-Transcription in LTR Retrotransposons
Authors: Drost Hajk-Georg , Sanchez Diego H 
Published: November 2019

AbstractTransposable elements (TEs) are parasitic DNA bits capable of mobilization and mutagenesis, typically suppressed by host’s epigenetic silencing. Since the selfish DNA concept, it is appreciated that genomes are also molded by arms-races against natural TE inhabitants. However, our understanding of evolutionary processes shaping TEs adaptive populations is scarce. Here, we review the events of recombination associated to reverse-transcription in LTR retrotransposons, a process shuffling their genetic variants during replicative mobilization. Current evidence may suggest that recombinogenic retrotransposons could beneficially exploit host suppression, where clan behavior facilitates their speciation and diversification. Novel refinements to retrotransposons life-cycle and evolution models thus emerge.
Alteration of Fungal Microbiota After 5-ASA Treatment in UC Patients
Authors: Jun Xu , Ning Chen , Yang Song , Zhe Wu , Na Wu , Yifan Zhang , Xinhua Ren , Yulan Liu 
Published: November 2019

Abstract
The effect of treatment regimens on fungal microbiota is unclear in ulcerative colitis (UC) patients. Here, we aimed to clarify the effect of 5-aminosalicylic acid (5-ASA) treatment on gut fungal microbiota in UC patients. Fifty-seven UC patients, including 20 treatment-naïve and 37 5-ASA-treated, were recruited into an exploration study. We compared the gut fungal profiles of these 2 groups of patients using ITS1-2 rDNA sequencing. Ten out of 20 treatment-naïve UC patients were followed up and enrolled for a validation study and underwent a 5-ASA treatment. We assessed the longitudinal differences of fungal microbiota in these patients before and after 5-ASA treatment. Results acquired from the validation study were accordant to those from the exploration study. Ascomycota was the dominant phylum in both noninflamed and inflamed mucosae. At the phylum level, Ascomycota decreased in inflamed mucosae before 5-ASA treatment. At the genus level, pathogens such as Scytalidium, Morchella, and Paecilomyces increased, and Humicola and Wickerhamomyces decreased in inflamed mucosae. After 5-ASA treatment, Ascomycota and Wickerhamomyces increased and Scytalidium, Fusarium, Morchella, and Paecilomyces decreased in both noninflamed and inflamed mucosae. Additionally, the balanced bacteria–fungi correlation was interrupted in inflamed mucosae, and 5-ASA treatment altered group-specific fungal microbiota and restored bacteria–fungi correlation in UC patients. Our results demonstrated that fungal diversity and composition were altered and the bacteria–fungi correlation was restored in inflamed mucosae after 5-ASA treatment.
Is mode of transport to work associated with mortality in the working-age population? Repeated census-cohort studies in New Zealand, 1996, 2001 and 2006
Authors: Shaw Caroline , Blakely Tony , Atkinson June , Woodward Alistair 
Published: November 2019

Abstract

Background
Increasing active transport is proposed as a means to address both health and environmental issues. However, the associations between specific modes, such as cycling, walking and public transport, and health outcomes remain unclear. We examined the association between mode of travel to work and mortality.

Methods
Cohort studies of the entire New Zealand working population were created using 1996, 2001 and 2006 censuses linked to mortality data. Mode of travel to work was that reported on census day, and causes of death examined were ischaemic heart disease and injury. Main analyses were Poisson regression models adjusted for socio-demographics. Sensitivity analyses included: additional adjustment for smoking in the 1996 and 2006 cohorts, and bias analysis about non-differential misclassification of cycling vs car use.

Results
Walking (5%) and cycling (3%) to work were uncommon. Compared with people reporting using motor vehicles to travel to work, those cycling had a reduced all-cause mortality (ACM) in the socio-demographic adjusted models RR 0.87 (0.77–0.98). Those walking (0.97, 0.90–1.04) and taking public transport (0.96, 0.88–1.05) had no substantive difference in ACM. No mode of transport was associated with detectable statistically significant reductions in cause-specific mortality. Sensitivity analyses found weaker associations when adjusting for smoking and stronger associations correcting for likely non-differential misclassification of cycling.

Conclusions
This large cohort study supports an association between cycling to work and reduced ACM, but found no association for walking or public-transport use and imprecise cause-specific mortality patterns.
Thermophotovoltaic applications in waste heat recovery systems: example of GaSb cell
Authors: Utlu Zafer 
Published: November 2019

Abstract
In this study, it is aimed at evaluating real data in high temperature GaSb cell thermophotovoltaic (TPV) systems. The TPV systems are considered as an alternative energy source in terms of efficient use of waste heat, cost and efficiency. The TPV system can be defined as a system that converts waste heat energy emitted from heat sources into electrical energy at high temperature. In this context, efficiency and parameters of TPV GaSb cells have been determined in laboratory conditions. The conversion of the high temperature applied to the cell to electrical energy has been investigated by selecting the GaSb photovoltaic cell as the cell type. According to the analysis have been done so far, TPV high-temperature real graphics have been obtained using GaSb cell. The temperature parameters used are, namely, cell temperature and source temperature. With these graphs, energy efficiency, fill factor, effect of open-circuit voltage and short-circuit current values have been determined. While the efficiency value of the GaSb TPV cell systems was calculated, the radiation source temperature values have been taken in increments of 300 K between 1300 and 3100 K. In this analysis, the optimum energy conversion efficiency values of GaSb solar cell structure have been detected to be 21.57%. Opinions about the feasibility, efficiency and development of thermophotovoltaic energy conversion systems are stated, and suggestions are presented.
Longitudinal Analysis of Group A Streptococcus emm Types and emm Clusters in a High-Prevalence Setting: Relationship between Past and Future Infections
Authors: Campbell Patricia Therese , Tong Steven Y C , Geard Nicholas , Davies Mark R , Worthing Kate A , Lacey Jake A , Smeesters Pierre R , Batzloff Michael R , Kado Joseph , Jenney Adam W J , Mcvernon Jodie , Steer Andrew C 
Published: November 2019

Abstract
Group A Streptococcus is a pathogen of global importance, but despite the ubiquity of group A Streptococcus infections, the relationship between infection, colonization, and immunity is still not completely understood. The M protein, encoded by the emm gene, is a major virulence factor and vaccine candidate and forms the basis of a number of classification systems. Longitudinal patterns of emm types collected from 457 Fijian schoolchildren over a 10-month period were analyzed. No evidence of tissue tropism was observed, and there was no apparent selective pressure or constraint of emm types. Patterns of emm type acquisition suggest limited, if any, modification of future infection based on infection history. Where impetigo is the dominant mode of transmission, circulating emm types either may not be constrained by ecological niches or population immunity to the M protein, or they may require several infections over a longer period of time to induce such immunity.
Affine screening operators, affine Laumon spaces and conjectures concerning non-stationary Ruijsenaars functions
Authors: Shiraishi Jun’ichi 
Published: November 2019

AbstractBased on the screened vertex operators associated with the affine screening operators, we introduce the formal power series $f^{\widehat{\mathfrak gl}_N}(x,p|s,\kappa|q,t)$ which we call the non-stationary Ruijsenaars function. We identify it with the generating function for the Euler characteristics of the affine Laumon spaces. When the parameters $s$ and $\kappa$ are suitably chosen, the limit $t\rightarrow q$ of $f^{\widehat{\mathfrak gl}_N}(x,p|s,\kappa|q,q/t)$ gives us the dominant integrable characters of $\widehat{\mathfrak sl}_N$ multiplied by $1/(p^N;p^N)_\infty$ (i.e. the $\widehat{\mathfrak gl}_1$ character). Several conjectures are presented for $f^{\widehat{\mathfrak gl}_N}(x,p|s,\kappa|q,t)$, including the bispectral and the Poincaré dualities, and the evaluation formula. The main conjecture asserts that (i) one can normalize $f^{\widehat{\mathfrak gl}_N}(x,p|s,\kappa|q,t)$ in such a way that the limit $\kappa\rightarrow 1$ exists, and (ii) the limit $f^{{\rm st.}\,\widehat{\mathfrak gl}_N}(x,p|s|q,t)$ gives us the eigenfunction of the elliptic Ruijsenaars operator. The non-stationary affine $q$-difference Toda operator ${\mathcal T}^{\widehat{\mathfrak gl}_N}(\kappa)$ is introduced, which comes as an outcome of the study of the Poincaré duality conjecture in the affine Toda limit $t\rightarrow 0$. The main conjecture is examined also in the limiting cases of the affine $q$-difference Toda ($t\rightarrow 0$), and the elliptic Calogero–Sutherland ($q,t\rightarrow 1$) equations.
DETECTING BID-RIGGING CARTELS WITH DESCRIPTIVE STATISTICS
Authors: Imhof David 
Published: November 2019

Abstract
The paper shows that descriptive statistics, used as screens, capture the effect of bid rigging in the distribution of the bids. The bid-rigging cartel studied in this paper negatively affected the variance of the bids as illustrated by the coefficient of variance and the kurtosis statistic. Furthermore, it cleverly manipulated the differences between bids to secure that the designated bidder from the cartel won the contract. Such cover-bidding mechanism produced asymmetry in the distribution of the bids illustrated by the relative distance, the skewness statistic, and the percentage difference between the first and second lowest bids. The descriptive statistics capture the change in the statistical pattern of the distribution of the bids between periods of collusion and competition. Moreover, the bid rotation screen shows that the behavior of firms changed radically between the cartel and post-cartel periods. Finally, the paper discusses policy implications for competition agencies wishing to set up a detection method for screening procurement markets.
Discrimination and Career Satisfaction: Perceptions from US Forest Service Scientists
Authors: Kern Christel C , Kenefic Laura S , Dockry Michael J , Cobo-Lewis Alan 
Published: November 2019

AbstractResearch, largely focused on academia, has shown demographic differences in perceptions and experiences of workplace culture in science fields, including natural resources. Less is known about experiences of those working for government institutions. This study examined relationships between demographic characteristics (gender, scientific discipline, years as a scientist), experiences of discrimination or harassment, and perceptions of career success and satisfaction as reported in a survey by 100 research scientists in the US Forest Service: a hierarchical federal agency with explicit goals for workforce diversification. Approximately half the survey respondents, and more women than men, indicated that they had experienced work-related discrimination or harassment. Survey respondents identified gender as the most common basis of discrimination. Although most felt successful and satisfied in their careers, this perception was lower among those who had experienced discrimination or harassment. These findings highlight challenges of workforce diversification, especially in hierarchical institutions where organizational structure favors conformity.
The 21 cm bispectrum during reionization: a tracer of the ionization topology
Authors: Hutter Anne , Watkinson Catherine A , Seiler Jacob , Dayal Pratika , Sinha Manodeep , Croton Darren J 
Published: November 2019

ABSTRACT
We compute the bispectra of the 21cm signal during the epoch of reionization for three different reionization scenarios that are based on a dark matter N-body simulation combined with a self-consistent, semi-numerical model of galaxy evolution and reionization. Our reionization scenarios differ in their trends of ionizing escape fractions (fesc) with the underlying galaxy properties and cover the physically plausible range, i.e. fesc effectively decreasing, being constant, or increasing with halo mass. We find the 21 cm bispectrum to be sensitive to the resulting ionization topologies that significantly differ in their size distribution of ionized and neutral regions throughout reionization. From squeezed to stretched triangles, the 21 cm bispectra features a change of sign from negative to positive values, with ionized and neutral regions representing below-average and above-average concentrations contributing negatively and positively, respectively. The position of the change of sign provides a tracer of the size distribution of the ionized and neutral regions, and allows us to identify three major regimes that the 21 cm bispectrum undergoes during reionization. In particular the regime during the early stages of reionization, where the 21 cm bispectrum tracks the peak of the size distribution of the ionized regions, provides exciting prospects for pinning down reionization with the forthcoming Square Kilometre Array.