bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine
Authors: Bogatyrev Said R. , Rolando Justin C. , Ismagilov Rustem F. 
Published: February 2020

Abstract
Background
The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively in microbiome research and enable the spatial, temporal, compositional, and functional interrogation of the gastrointestinal microbiota and its effects on the host physiology and disease phenotype. Classical, culture-based studies have documented that fecal microbial self-reinoculation (via coprophagy) affects the composition and abundance of microbes in the murine proximal gastrointestinal tract. This pervasive self-reinoculation behavior could be a particularly relevant study factor when investigating small intestine microbiota. Modern microbiome studies either do not take self-reinoculation into account, or assume that approaches such as single housing mice or housing on wire mesh floors eliminate it. These assumptions have not been rigorously tested with modern tools. Here, we used quantitative 16S rRNA gene amplicon sequencing, quantitative microbial functional gene content inference, and metabolomic analyses of bile acids to evaluate the effects of self-reinoculation on microbial loads, composition, and function in the murine upper gastrointestinal tract.

Results
In coprophagic mice, continuous self-exposure to the fecal flora had substantial quantitative and qualitative effects on the upper gastrointestinal microbiome. These differences in microbial abundance and community composition were associated with an altered profile of the small intestine bile acid pool, and, importantly, could not be inferred from analyzing large intestine or stool samples. Overall, the patterns observed in the small intestine of non-coprophagic mice (reduced total microbial load, low abundance of anaerobic microbiota, and bile acids predominantly in the conjugated form) resemble those typically seen in the human small intestine.

Conclusions
Future studies need to take self-reinoculation into account when using mouse models to evaluate gastrointestinal microbial colonization and function in relation to xenobiotic transformation and pharmacokinetics or in the context of physiological states and diseases linked to small intestine microbiome and to small intestine dysbiosis.
Formal approach to model complex adaptive computing systems
Authors: Jarrar Abdessamad , Ait Wakrime Abderrahim , Balouki Youssef 
Published: February 2020

AbstractComplex adaptive systems provide a significant number of concepts such as reaction, interaction, adaptation, and evolution. In general, these concepts are modelled employing different techniques which give an inexplicit vision on the system. Therefore, all concepts must be carefully modelled using the same approach to avoid contradiction and guarantee system homogeneity and correctness. However, developing a computing system that includes all these concepts using the same approach is not an easy task and requires a perfect understanding of the system’s behaviour. In this paper, we contribute as stepwise towards proposing an approach to model the most important concepts of complex adaptive systems while ensuring homogeneity and the correctness of models. For this aim, we present five standard agent-based models formalizing agent properties, reaction, interaction, adaptation, and evolution. These models are adapted to all cases of complex adaptive systems since they include an abstract description of these concepts. To implement our approach formally, we choose the Event-B method due to the strong assurance of bugs’ absence that it guarantees. Besides, it supports horizontal and vertical refinement which facilitates the specification process. Furthermore, the approach of this paper addresses the very abstract level of modelling which expand the use of this approach to other formal methods and tools.
The role of environmental stress and DNA methylation in the longitudinal course of bipolar disorder
Authors: Comes Ashley L. , Czamara Darina , Adorjan Kristina , Anderson-Schmidt Heike , Andlauer Till F. M. , Budde Monika , Gade Katrin , Hake Maria , Kalman Janos L. , Papiol Sergi , Reich-Erkelenz Daniela , Klöhn-Saghatolislam Farah , Schaupp Sabrina K. , Schulte Eva C. , Senner Fanny , Juckel Georg , Schmauß Max , Zimmermann Jörg , Reimer Jens , Reininghaus Eva , Anghelescu Ion-George , Konrad Carsten , Thiel Andreas , Figge Christian , von Hagen Martin , Koller Manfred , Dietrich Detlef E. , Stierl Sebastian , Scherk Harald , Witt Stephanie H. , Sivalingam Sugirthan , Degenhardt Franziska , Forstner Andreas J. , Rietschel Marcella , Nöthen Markus M. , Wiltfang Jens , Falkai Peter , Schulze Thomas G. , Heilbronner Urs 
Published: February 2020

AbstractBackgroundStressful life events influence the course of affective disorders, however, the mechanisms by which they bring about phenotypic change are not entirely known.MethodsWe explored the role of DNA methylation in response to recent stressful life events in a cohort of bipolar patients from the longitudinal PsyCourse study (n = 96). Peripheral blood DNA methylomes were profiled at two time points for over 850,000 methylation sites. The association between impact ratings of stressful life events and DNA methylation was assessed, first by interrogating methylation sites in the vicinity of candidate genes previously implicated in the stress response and, second, by conducting an exploratory epigenome-wide association analysis. Third, the association between epigenetic aging and change in stress and symptom measures over time was investigated.ResultsInvestigation of methylation signatures over time revealed just over half of the CpG sites tested had an absolute difference in methylation of at least 1% over a 1-year period. Although not a single CpG site withstood correction for multiple testing, methylation at one site (cg15212455) was suggestively associated with stressful life events (p < 1.0 × 10−5). Epigenetic aging over a 1-year period was not associated with changes in stress or symptom measures.ConclusionsTo the best of our knowledge, our study is the first to investigate epigenome-wide methylation across time in bipolar patients and in relation to recent, non-traumatic stressful life events. Limited and inconclusive evidence warrants future longitudinal investigations in larger samples of well-characterized bipolar patients to give a complete picture regarding the role of DNA methylation in the course of bipolar disorder.
Habitat availability influences migration speed, refueling patterns and seasonal flyways of a fly-and-forage migrant
Authors: Hadjikyriakou Thomas G. , Nwankwo Emmanuel C. , Virani Munir Z. , Kirschel Alexander N. G. 
Published: February 2020

AbstractBackgroundDespite our understanding of the principal factors that shape bird migration strategies, there is conflicting evidence regarding the role of habitat in shaping migration routes and schedules, including day and night activity and differences between autumn and spring. For fly-and-forage migrants, we predict that habitat characteristics might guide migration speed, route selection and migrating schedules.MethodsWe use solar-powered GPS transmitters, obtaining high accuracy data, to monitor the migratory movements of Eleonora’s falcon breeding in Cyprus, which is the easternmost breeding population of the species. We tested for potential preferences in habitat characteristics along the migration routes, separately for the northern, drier part and the more vegetated southern part of the trips. We also examined the relationship between migration speed and vegetative cover during day and at night, accounting for wind support.ResultsWe found that tagged individuals repeatedly exhibited an anticlockwise loop migration pattern with spring routes being more easterly than autumn ones. We identified a preference for migration through vegetation-rich areas, where during daytime tagged individuals travel at slower migration speeds compared to vegetation-poor areas, indicating fly-and-forage activity. Birds roosted during most nights, combining refueling stopovers at selected vegetation-rich areas before or after crossing ecological barriers. Conversely, both during day and night, tagged individuals overflew unsuitable habitats more quickly.ConclusionsOur results suggest that habitat is an important factor in Eleonora’s falcon migratory strategies. Active selection of vegetation rich areas in combination with reduced migration speeds there, allows the migrating falcons to combine migration during the day with fly-and-forage refueling, while roosting most nights.
Studies on the effects of mixed light-thermal ageing on parchment by vibrational spectroscopy and micro hot table method
Authors: Cappa Federica , Paganoni Ilaria , Carsote Cristina , Badea Elena , Schreiner Manfred 
Published: February 2020

Abstract
The damaging effects of mixed light-thermal ageing on parchment were studied by exposing mock-ups to artificial light (162 W/m2 irradiance) at controlled temperature and relative humidity (52 °C, 30% RH) for up to 748 h, with testing being made during this time incrementally. The physical–chemical changes (deterioration) resulting from these conditions were analysed by applying FTIR-ATR and Raman spectroscopy, colorimetric measurements and MHT. The deterioration found includes the formation of collagen-destabilised intermediate states which then progressively convert to disorganised structures, e.g. pregelatinised collagen and gelatin. The process is characterized by molecular changes of collagen associated with its photo-oxidation. These are shown by changes in the position and intensity of the main FTIR absorption bands of collagen, namely those of Amide I, Amide II, and Amide III, as well as by the occurrence and the increase of a shoulder at 1740 cm−1. The shrinking activity of the collagen fibres in the parchment mock-ups was measured by the micro-hot-table (MHT) method, which revealed the presence of multiple collagen populations with distinct thermal stabilities and confirmed the deterioration pattern suggested by the molecular changes.
Model studies of plus and double box shaped skirted footings resting on sand
Authors: Gnananandarao Tammineni , Dutta Rakesh Kumar , Khatri Vishwas Nandkishor 
Published: February 2020

AbstractThe paper presents the investigation on the model unskirted/skirted footings (plus and the double box) on sand. Skirt depth, sand relative density, footing interface condition and skirted footing type were varied parameters. Skirt depth (Ds) varied in this investigation was from 0.25 B to 1.5 B (B, footing width). The results show that the footing geometry and the skirt increased the bearing capacity and improved the overall behaviour. The results further revealed that the lowest percentage improvement for the square shaped footing with Ds/B = 0.25 was 26.08% at a relative density of 60%, whereas the highest improvement for the double box shaped footing with Ds/B = 1.50 was 364.12% at a relative density of 30%. The settlement reduction factors with the use of skirt from this investigation ranged from 0.16 to 1.0 and depended on the pressure applied and the depth ratio of the skirt. Finally, for the settlement reduction factor, an empirical equation was developed. This expression can be used to calculate the settlement of the plus and double box shaped skirted footings on sand.
Gaps in the structuring of organizations in the graduate employment context in Uganda
Authors: Ntale Peter Dithan , Ssempebwa Jude , Musisi Badiru , Musoke Genza Gyaviira , Joseph Kimoga , Mugimu C. B. , Muhammed Ngoma , Ntayi Joseph 
Published: February 2020

AbstractThe complexity of global challenges requires that organizations collaborate with one another. To do this, stakeholders need flexible structures that are designed in a way that allows organizations to collaborate. However, it is not known whether Uganda’s organizations are structured in a way that allows them to collaborate with one another, casting doubt as to whether they can manage the complexity of global challenges such as graduate unemployment. Informed by Hage and Aiken (1967), we studied the structures of selected organizations in Uganda and found out that their major components, i.e., centralization and formalization, are designed in a way that may not allow collaboration to occur. We found out that the organizational structures were exclusive in decision-making, had high power distance (HPD), jobs were strictly codified, and organizations enforced stringent rule observation. These gaps make it difficult for people interaction and involvement and deny them of their freedom to relate with one another, making it difficult for a collaboration between different agencies to occur. To enhance organizational collaboration, it is recommended that organizations should be restructured to become more inclusive, interactive, and democratic since organizations structured in this way have shown collaboration success and greater achievement of society needs.
Genetic diversity and spread of glyphosate-resistant flaxleaf fleabane
Authors: Minati Mohammed Hussein , Preston Christopher , Malone Jenna 
Published: February 2020

Abstract
Background
Continual application of herbicides for flaxleaf fleabane control readily results in the evolution of herbicide resistance. Flaxleaf fleabane has evolved resistance to different modes of action herbicides in many countries. Due to the comprehensive geographical distribution of flaxleaf fleabane in Australia, it was classified as a cosmopolitan weed and it therefore has no specific climatic requirement.

Results
The high percentage of polymorphisms in the samples of the susceptible population (79.8%, 75%) suggests that susceptible populations of flaxleaf fleabane, even within one site, originated from a number of parents. However, the percentage of polymorphism in the resistant populations (51.5%, 66.8%) suggests that resistant populations of flaxleaf fleabane within one site could have originated from fewer parents. In addition, any site containing resistant and susceptible populations of flaxleaf fleabane may have been populated by a large number of parents, evidenced by the relatively high percentage of polymorphisms detected by amplified fragment length polymorphism (AFLP) analysis (86.5%). Despite the large geographic distances between collection locations, populations from across states clustered in several groups showing a close genetic relationship among these populations over these large distances. These high levels of genetic diversity within and between populations confirmed in the sequencing of enolpyruvylshikimate-3-phosphate above support the results of AFLP studies and gave the author more confidence to report the genetic diversity seen within and between population studies.

Conclusion
To prevent further resistance spread, flaxleaf fleabane management in infested areas should focus on decreasing seed movement from resistant sites as well as reducing the selection pressure for resistance to glyphosate by adopting alternative management strategies.
Method validation for bifenthrin emulsifiable concentrate and uncertainty calculation using gas chromatographic approach
Authors: Nazir Arif , Iqbal Javaid , Iqbal Munawar , Abbas Mazhar , Nisar Numrah 
Published: February 2020

Abstract
Background
Bifenthrin is the third-generation synthetic pyrethroid insecticide having an effective control on the pest of cotton, vegetable, and fruits. This study is focused on the validation of the test procedure for the quantitative determination of bifenthrin contents in the emulsifiable concentrate and measurement of uncertainty. The purpose of this validation procedure is to demonstrate that it is suitable for the intended use. This was determined by gas chromatography with a flame ionization detector (FID). The estimation was carried out on Shimadzu GC equipped with TRB-5 (95% dimethyl, 5% diphenyl polysiloxane) column using a nitrogen carrier gas.

Results
Different parameters of validation (precision, accuracy, linearity, specificity, selectivity, and robustness) were executed. All steps of method validation were performed, and its uncertainty is determined. The method is simple, selective, accurate, precise, cost-effective, and suitable. The validation parameters are based on harmonized guidelines on the validation of the analytical test method.

Conclusions
Pesticide formulation bodies can use this method for the qualitative and quantitative determination of bifenthrin different formulations. These data verify that the method is validated, and all results are in an acceptable limit. The method is developed on GC. Moreover, the analysis time is also short as compared to that of HPLC. The developed method is simple reliable and has a realistic approach.
Comparing the broadband acoustic frequency response of single, clustered, and arrays of marine air guns
Authors: Landrø Martin , Langhammer Jan 
Published: February 2020

Field data acquired from a seismic vessel by a seabed hydrophone is used to analyze the broadband response (10 Hz to 62.5 kHz) for various source configurations: single air guns, clustered air guns, and a full array consisting of 30 air guns. The various parts of the acoustic signal are analyzed in detail, and it is found that a high-frequency signal arriving prior to the main peak of a single air-gun signal most likely is caused by small vapor cavities collapsing at or close to the surface of the gun. This is confirmed by high-speed photographs taken when a small air gun is fired in a water tank. When the full array is used, a second type of cavitation signal is observed: ghost cavitation caused by acoustic stimulation by the negative pressure that is backscattered from the free surface. As this ghost signal from 30 different guns arrives at a specific location in the water, cavities might be formed, and they create a high-frequency acoustic signal.
Experimental study on the bifurcation of a density oscillator depending on density difference
Authors: Ito H. , Itasaka T. , Takeda N. , Kitahata H. 
Published: February 2020

Abstract
Hydrodynamic instabilities often cause spatio-temporal pattern formations and transitions between them. We investigate a model experimental system, a density oscillator, where the bifurcation from a resting state to an oscillatory state is triggered by the increase in the density difference of the two fluids. Our results show that the oscillation amplitude increases from zero and the period decreases above a critical density difference. The detailed data close to the bifurcation point provide a critical exponent consistent with the supercritical Hopf bifurcation.
Multiple lineages enable robust development of the neuropil-glia architecture in adult Drosophila
Authors: Kato Kentaro , Orihara-Ono Minako , Awasaki Takeshi 
Published: February 2020

ABSTRACT
Neural remodeling is essential for the development of a functional nervous system and has been extensively studied in the metamorphosis of Drosophila. Despite the crucial roles of glial cells in brain functions, including learning and behavior, little is known of how adult glial cells develop in the context of neural remodeling. Here, we show that the architecture of neuropil-glia in the adult Drosophila brain, which is composed of astrocyte-like glia (ALG) and ensheathing glia (EG), robustly develops from two different populations in the larva: the larval EG and glial cell missing-positive (gcm+) cells. Whereas gcm+ cells proliferate and generate adult ALG and EG, larval EG dedifferentiate, proliferate and redifferentiate into the same glial subtypes. Each glial lineage occupies a certain brain area complementary to the other, and together they form the adult neuropil-glia architecture. Both lineages require the FGF receptor Heartless to proliferate, and the homeoprotein Prospero to differentiate into ALG. Lineage-specific inhibition of gliogenesis revealed that each lineage compensates for deficiency in the proliferation of the other. Together, the lineages ensure the robust development of adult neuropil-glia, thereby ensuring a functional brain.
Villin controls the formation and enlargement of punctate actin foci in pollen tubes
Authors: Zhao Wanying , Qu Xiaolu , Zhuang Yuhui , Wang Ludi , Bosch Maurice , Franklin-Tong Vernonica E. , Xue Yongbiao , Huang Shanjin 
Published: February 2020

ABSTRACT
Self-incompatibility (SI) in the poppy Papaver rhoeas triggers dramatic alterations in actin within pollen tubes. However, how these actin alterations are mechanistically achieved remains largely unexplored. Here, we used treatment with the Ca2+ ionophore A23187 to mimic the SI-induced elevation in cytosolic Ca2+ and trigger formation of the distinctive F-actin foci. Live-cell imaging revealed that this remodeling involves F-actin fragmentation and depolymerization, accompanied by the rapid formation of punctate actin foci and subsequent increase in their size. We established that actin foci are generated and enlarged from crosslinking of fragmented actin filament structures. Moreover, we show that villins associate with actin structures and are involved in this actin reorganization process. Notably, we demonstrate that Arabidopsis VILLIN5 promotes actin depolymerization and formation of actin foci by fragmenting actin filaments, and controlling the enlargement of actin foci via bundling of actin filaments. Our study thus uncovers important novel insights about the molecular players and mechanisms involved in forming the distinctive actin foci in pollen tubes.
Mechanisms of malignancy in glioblastoma cells are linked to mitochondrial Ca2+ uniporter upregulation and higher intracellular Ca2+ levels
Authors: Li Xiaoyun , Spelat Renza , Bartolini Anna , Cesselli Daniela , Ius Tamara , Skrap Miran , Caponnetto Federica , Manini Ivana , Yang Yili , Torre Vincent 
Published: February 2020

ABSTRACT
Glioblastoma (GBM) is one of the most malignant brain tumours and, despite advances in treatment modalities, it remains largely incurable. Ca2+ regulation and dynamics play crucial roles in different aspects of cancer, but they have never been investigated in detail in GBM. Here, we report that spontaneous Ca2+ waves in GBM cells cause unusual intracellular Ca2+ ([Ca2+]i) elevations (&gt;1 μM), often propagating through tumour microtubes (TMs) connecting adjacent cells. This unusual [Ca2+]i elevation is not associated with the induction of cell death and is concomitant with overexpression of mitochondrial Ca2+ uniporter (MCU). We show that MCU silencing decreases proliferation and alters [Ca2+]i dynamics in U87 GBM cells, while MCU overexpression increases [Ca2+]i elevation in human astrocytes (HAs). These results suggest that changes in the expression level of MCU, a protein involved in intracellular Ca2+ regulation, influences GBM cell proliferation, contributing to GBM malignancy.
This article has an associated First Person interview with the first author of the paper.