bluuebunny/crossref_metadata_2025 huggingface dataset:
Moral challenges of going to Mars under the presence of non-intelligent life scenario
Authors: Chon-Torres Octavio A.
Published: July 2019

Much is discussed what would be the ideal position in terms of our ethical treatment with respect to other forms of life, particularly those that can be discovered in other worlds, in addition to our role in terms of the expansion of terrestrial life in the universe. This represents a great philosophical challenge, but what if we should make a moral decision in the face of the inevitable situation of being forced to colonize, for example, Mars? Is there a position in which we can feel safe to act legitimately? This paper tries to force us into a mental and conceptual exercise about what can really be worth beyond the concept or the positions we may have and analyse them in light of the practicality that decision making requires in this problem.
Exposure to low Earth orbit of an extreme-tolerant cyanobacterium as a contribution to lunar astrobiology activities
Authors: Billi Daniela , Mosca Claudia , Fagliarone Claudia , Napoli Alessandro , Verseux Cyprien , Baqué Mickael , de Vera Jean-Pierre
Published: July 2019

By investigating the survival and the biomarker detectability of a rock-inhabiting cyanobacterium, Chroococcidiopsis sp. CCMEE 029, the BIOMEX space experiment might contribute to a future exploitation of the Moon as a test-bed for key astrobiology tasks such as the testing of life-detection technologies and the study of life in space. Post-flight analyses demonstrated that the mixing of dried cells with sandstone and a lunar regolith simulant provided protection against space UV radiation. During the space exposure, dried cells not mixed with minerals were killed by 2.05 × 102 kJ m−2 of UV radiation, while cells mixed with sandstone or lunar regolith survived 1.59 × 102 and 1.79 × 102 kJ m−2, respectively. No differences in survival occurred among cells mixed and not mixed with minerals and exposed to space conditions in the dark; this finding suggests that space vacuum and 0.5 Gy of ionizing radiation did not impair the cells’ presence in space. The genomic DNA of dead cells was severely damaged but still detectable with PCR amplification of a short target, thus suggesting that short sequences should be targeted in a PCR-based approach when searching for traces of life. The enhanced stability of genomic DNA of dried cells mixed with minerals and exposed to space indicates that DNA might still be detectable after prolonged periods, possibly up to millions of years in microbes shielded by minerals. Overall, the BIOMEX results contribute to future experiments regarding the exposure of cells and their biomarkers to deep space conditions in order to further test the lithopanspermia hypothesis, the biomarker stability and the microbial endurance, with implications for planetary protection and to determine if the Moon has been contaminated during past human missions.
Female ponderal index at birth and idiopathic infertility
Authors: Dupont Charlotte , Hulot Audrey , Jaffrezic Florence , Faure Céline , Czernichow Sébastien , di Clemente Nathalie , Racine Chrystele , Chavatte-Palmer Pascale , Lévy Rachel ,   Alifert group
Published: July 2019

Epidemiological studies have demonstrated an increased risk of developing non-transmittable diseases in adults subjected to adverse early developmental conditions. Metabolic and cardiovascular diseases have been the focus of most studies. Nevertheless, data from animal models also suggest early programming of fertility. In humans, it is difficult to assess the impact of the in utero environment retrospectively. Birthweight is commonly used as an indirect indicator of intrauterine development. This research is part of the ALIFERT study. We investigated a potential link between ponderal index at birth and female fertility in adulthood. Data from 51 infertile and 74 fertile women were analysed. BW was on average higher in infertile women, whereas birth length did not differ between the two groups; thus, resulting in a significantly higher ponderal index at birth in infertile women. Ponderal index at birth has been identified as a risk factor for infertility. These results suggest the importance of the intra-uterine environment, not only for long-term metabolic health but also for fertility.
The Influence of Geomagnetic Storm of 7‐8 September 2017 on the Swarm Precise Orbit Determination
Authors: Zhang Keke , Li Xingxing , Xiong Chao , Meng Xiangguang , Li Xin , Yuan Yongqiang , Zhang Xiaohong
Published: July 2019

We analyze a recent geomagnetic storm event on 7‐8 September 2017 to investigate the impact of geomagnetic storm on the precise orbit determination (POD) of Swarm constellation. The storm time performance of POD is analyzed. The quality of Swarm orbits are severely degraded during the storm main phase on 8 September and the maximum precision degradation reached over 10 cm. The enhanced thermospheric mass density at Swarm altitude during the storm enlarges the atmosphere drag for low Earth orbit satellites, which makes main contributions to the storm time degradation of Swarm orbit. This negative effect of enhanced atmosphere drag on the orbit estimation is mostly suppressed by estimating a more frequent atmosphere drag parameter. The higher‐order ionospheric effects on the POD of Swarm are also analyzed. The vertical total electron content derived from the Swarm onboard Global Positioning System receiver presents a larger enhancement on the dayside at low latitude and midlatitude during the storm main phase. This leads to an increase in the high‐order ionospheric effects, especially in the second‐order terms. No evident precision improvement is observed after correcting the high‐order ionospheric effects. The results demonstrate that during this geomagnetic storm, the enhanced thermospheric neutral density serves as a stronger error source than the enhanced ionospheric plasma density for the low Earth orbit satellite orbit determination processing.
Dawn/Dusk Asymmetry of the Martian UltraViolet Terminator Observed Through Suprathermal Electron Depletions
Authors: Steckiewicz M. , Garnier P. , Lillis R. , Toublanc D. , Leblanc F. , Mitchell D. L. , Andersson L. , Mazelle C.
Published: July 2019

Suprathermal electron depletions are structures of the nightside ionosphere of Mars resulting from an equilibrium between electron loss and creation processes. Photoionization of oxygen and carbon dioxide by UV and EUV photons is the main ionization process of the Martian atmosphere. The observation of suprathermal electron depletions is strongly unexpected in the portion of the Martian environment where photoionization can occur. This region is delimited by the UltraViolet (UV) terminator, behind which no UV ionizing photons are detected. In this study suprathermal electron depletions are used to determine the position of the UV terminator thanks to MAVEN observations. The MAVEN spacecraft is now in its fourth year of data recording and has already covered more than one Martian year, a large range of latitude, local time, and solar zenith angle in the nightside down to 110‐km altitude. This coverage enables us to determine the approximate position of the UV terminator over one Martian year. We then investigate the variation of its position on the dawnside and duskside and depending on seasons. Our results are compared with models of the Martian atmosphere and in situ data of the atmospheric composition which all highlight an asymmetry between the duskside and the dawnside at equinox. However, models show an inversion in the position of the dusk and the dawn UV terminator at perihelion and aphelion, which cannot yet be confirmed or disproved by the data.
A Relationship Between Blue and Near‐IR Global Spectral Reflectance and the Response of Global Average Reflectance to Change in Cloud Cover Observed From EPIC
Authors: Wen Guoyong , Marshak Alexander , Song Wanjuan , Knyazikhin Yuri , Mõttus Matti , Wu Dong
Published: July 2019

We performed a detailed analysis of Earth Polychromatic Imaging Camera (EPIC) spectral data. We found that the vector composed of blue and near‐infrared (NIR) reflectance follows a counterclockwise closed‐loop trajectory from 0 to 24 UTC as Earth rotates. This nonlinear relationship was not observed by any other satellites due to limited spatial or temporal coverage of either low Earth orbit or geostationary satellites. We found that clouds play an important role in determining the nonlinear relationship in addition to the well‐known cloud‐free land‐ocean reflectance contrast in the two bands. The nonlinear relationship is the result of three factors: (1) a much larger cloud‐free land‐ocean contrast in the NIR band compared to the blue band, (2) significantly larger difference between cloudy land and cloudy ocean reflectance in the NIR band compared to the blue band, and (3) the periodic variation of fractions of clear land, clear ocean, cloudy land, and cloudy ocean in the sunlit hemisphere as Earth rotates. We found that the green vegetation contributes significantly to the NIR global average reflectance when the South and North Americas appear and disappear in the EPIC's field of view. The blue and NIR relationship can be useful for exoplanet research. Clouds impose a strong impact on global spectral reflectance, and the reflectance response to a change in cloud cover depends on whether the change is over land or over the ocean. On average, an increase of 0.1 in cloud coverage will lead to a 7% increase in spectrally integrated global average reflectance.
Genesis and Architecture of Sequences of Quaternary Coral Reef Terraces: Insights From Numerical Models
Authors: Pastier A.‐M. , Husson L. , Pedoja K. , Bézos A. , Authemayou C. , Arias‐Ruiz C. , Cahyarini S. Y.
Published: July 2019

The variety of coral reefs morphologies highlights their sensitivities to several forcings; fossil reefs stack in sequences that are accordingly diverse. In order to understand their genesis and architectures, we devised a numerical approach, accounting for Quaternary sea level oscillations, vertical land motion, initial slope, wave erosion, and reef growth. We first test our model on the subsiding sequence of Hawaii and on the uplifting sequence of Wangi‐Wangi (Sulawesi) that bears active barriers. We then construct a parametric study that we analyze based on a comprehensive yet compact description of sequences as barcodes, that depict the vertical distribution of a few geometrical characteristics (number, width, and height of the terraces and barriers). We find that geological factors suffice to explain the variety of architectures of reefal sequences at first order, regardless of additional ecosystemic processes. Vertical land motion and foundation slopes are the prime players, while reef growth rates only play a minor role. Barriers may develop both in uplift and subsidence mode, and their preservation attests for the erosional power. Last, we reappraise the genesis of sequences and find that sequences do not fingerprint discrete events of sea level oscillations but a continuous process harrowed by stochastic events: Major sea level fluctuations can be overrepresented by several terraces or conversely absent; reoccupations may yield composite terraces representing multiple events. Overall, sequences shall not be regarded as stacks of reef bodies forming during sea level highstands, which implies that the commonly assumed bijective relationship between sea level highstands and terraces shall be abandoned.
The Impact of Radiosounding Observations on Numerical Weather Prediction Analyses in the Arctic
Authors: Naakka T. , Nygård T. , Tjernström M. , Vihma T. , Pirazzini R. , Brooks I. M.
Published: July 2019

The radiosounding network in the Arctic, despite being sparse, is a crucial part of the atmospheric observing system for weather prediction and reanalysis. The spatial coverage of the network was evaluated using a numerical weather prediction model, comparing radiosonde observations from Arctic land stations and expeditions in the central Arctic Ocean with operational analyses and background fields (12‐hr forecasts) from European Centre for Medium‐Range Weather Forecasts for January 2016 to September 2018. The results show that the impact of radiosonde observations on analyses has large geographical variation. In data‐sparse areas, such as the central Arctic Ocean, high‐quality radiosonde observations substantially improve the analyses, while satellite observations are not able to compensate for the large spatial gap in the radiosounding network. In areas where the network is reasonably dense, the quality of background field is more related to how radiosonde observations are utilized in the assimilation and to the quality of those observations.
A Zonal Migration of Monsoon Moisture Flux Convergence and the Strength of Madden‐Julian Oscillation Events
Authors: Hagos Samson , Zhang Chidong , Leung L. Ruby , Burleyson Casey D. , Balaguru Karthik
Published: July 2019

Understanding the variations in the strength of Madden‐Julian Oscillation (MJO) events as they propagate across the Indo‐Pacific Maritime Continent has been an unmet challenge. Moisture flux convergence estimated directly from precipitation shows a slow eastward migration of zonal moisture flux convergence between the Asian and Australian monsoon convergence centers from summer to winter. Strengths of individual MJO events vary as they propagate across this zonally and seasonally varying monsoonal moisture convergence. MJO events starting in February–April tend to be weak over the eastern Indian Ocean, but they strengthen as they propagate into the moisture convergence region over the western Pacific. During May–July, the moisture convergence pattern is reversed and MJO events weaken as they propagate into the moisture divergence region in the western Pacific. Winter MJO events are most likely to be strong over the Maritime Continent region, particularly when the Australian monsoon is strong.
Wintertime Modulation of the Local Cloud and Diagnostic Fields by the Hadley Cell Subsiding Boundary Over the Western North Pacific
Authors: Wang Xinyue , Iwabuchi Hironobu
Published: July 2019

The responses of cloud and diagnostic fields to the poleward shift of the local Hadley cell subsiding edge are examined using observational and reanalysis data from December 1982 to February 2016. Over the western North Pacific, the interannual variability of the local Hadley cell subsiding edge is marked by an anomalous rising motion, decreased large‐scale static stability, and corresponding increases of the midlevel cloud fraction over the climatological sinking zone around 35°N. The most sensitive cloud type is identified to be cumulus congestus, with cloud top pressures in the range of 440–680 hPa and optical thicknesses in the range of 23–60. This kind of cloud is estimated to be the main contributor to the net negative top‐of‐atmosphere radiation anomaly and to constrain the distribution of the anomalous precipitation associated with the local HC expansion.
Aerosol‐Mediated Glaciation of Mixed‐Phase Clouds: Steady‐State Laboratory Measurements
Authors: Desai N. , Chandrakar K. K. , Kinney G. , Cantrell W. , Shaw R. A.
Published: July 2019

What concentration of ice‐nucleating particles is required to completely glaciate a typical atmospheric supercooled liquid cloud? This seemingly esoteric question has far reaching implications, as the ratio of liquid to ice in these clouds governs, for example, their influence on Earth's radiation budget and their precipitation efficiency. Microphysical properties of steady‐state mixed‐phase clouds formed in a laboratory convection chamber are observed using digital holography. It is observed that the ratio of ice to total water content of steady‐state mixed‐phase clouds is determined by the concentration of ice‐nucleating aerosol particles. Existing theory is adapted to show such clouds result from a balance between the thermodynamic forcing (i.e., the source of excess water vapor that is condensing to liquid and ice) and the number and size of particles that become ice (i.e., the ice integral radius). The measurements quantitatively support the Korolev‐Mazin conditions for existence of mixed‐phase clouds.
Heat Flow and Near‐Seafloor Magnetic Anomalies Highlight Hydrothermal Circulation at Brothers Volcano Caldera, Southern Kermadec Arc, New Zealand
Authors: Caratori Tontini F. , Tivey M. A. , de Ronde C. E. J. , Humphris S. E.
Published: July 2019

Key Points

First systematic, integrated heat flow and magnetic study of a submarine arc volcano highlights multiscale convection cells

Deep circulation structurally controlled, with recharge through the caldera floor and discharge at the caldera walls and postcollapse cones

Shallow circulation is characterized by recharge zones in close proximity to the sites of present‐day diffuse and focused discharge
Solar Illumination Dependence of the Auroral Electrojet Intensity: Interplay Between the Solar Zenith Angle and Dipole Tilt
Authors: Ohtani S. , Gjerloev J. W. , Johnsen M. G. , Yamauchi M. , Brändström U. , Lewis A. M.
Published: July 2019

The present study investigates the dependence of the local auroral electrojet (AEJ) intensity on solar illumination by statistically examining northward geomagnetic disturbances in the auroral zone in terms of the solar zenith angle χ. It is found that on the dayside, both westward and eastward electrojets (WEJ and EEJ) are more intense for smaller χ, suggesting that the solar extreme ultraviolet‐induced conductance is the dominant factor for the AEJ intensity. On the nightside, in contrast, the χ dependence of the AEJ intensity, if sorted solely by the magnetic local time, apparently depends on the station longitude and hemisphere. However, if additionally sorted by the dipole tilt angle ψ, a consistent pattern emerges. That is, although χ and ψ are correlated, the solar zenith angle and dipole tilt angle have physically different effects on the AEJ intensity. The nightside AEJ, especially the WEJ, tends to be more intense for smaller |ψ|. Moreover, whereas the WEJ is statistically more intense when the ionosphere is dark, the EEJ is more intense when it is sunlit. The preference of the WEJ for the dark ionosphere prevails widely in magnetic local time from premidnight to dawn, and therefore, it cannot be attributed to the previously proposed processes of the preferred monoenergetic or broadband auroral precipitation in the dark ionosphere. Instead, it may be explained, at least morphologically, in terms of the conductance enhancement due to the diffuse auroral precipitation, which is also prevalent from premidnight to dawn and is more intense in the dark hemisphere.
Characteristics of Relativistic Microburst Intensity From SAMPEX Observations
Authors: Douma E. , Rodger C. J. , Blum L. W. , O'Brien T. P. , Clilverd M. A. , Blake J. B.
Published: July 2019

Relativistic electron microbursts are an important electron loss process from the radiation belts into the atmosphere. These precipitation events have been shown to significantly impact the radiation belt fluxes and atmospheric chemistry. In this study we address a lack of knowledge about the relativistic microburst intensity using measurements of 21,746 microbursts from the Solar Anomalous Magnetospheric Particle Explorer (SAMPEX). We find that the relativistic microburst intensity increases as we move inward in L, with a higher proportion of low‐intensity microbursts (<2,250 [MeV cm2 sr s]−1) in the 03–11 magnetic local time region. The mean microburst intensity increases by a factor of 1.7 as the geomagnetic activity level increases and the proportion of high‐intensity relativistic microbursts (>2,250 [MeV cm2 sr s]−1) in the 03–11 magnetic local time region increases as geomagnetic activity increases, consistent with changes in the whistler mode chorus wave activity. Comparisons between relativistic microburst properties and trapped fluxes suggest that the microburst intensities are not limited by the trapped flux present alongside the scattering processes. However, microburst activity appears to correspond to the changing trapped flux; more microbursts occur when the trapped fluxes are enhancing, suggesting that microbursts are linked to processes causing the increased trapped fluxes. Finally, modeling of the impact of a published microburst spectra on a flux tube shows that microbursts are capable of depleting <500‐keV electrons within 1 hr and depleting higher‐energy electrons in 1–23 hr.
Ionospheric Peaked Structures and Their Local Time, Seasonal, and Solar Activity Dependence Based on Global Ionosphere Maps
Authors: Tsai T. C. , Jhuang H. K. , Lee L. C. , Ho Y. Y.
Published: July 2019

The total electron content (TEC) data from Global Ionosphere Maps are used to obtain the tidal modes through two‐dimensional Fourier transform in both universal time and LT (local time) frames. In the LT frame, a north‐south TEC asymmetry is observed along the longitude, where there is a large displacement of the geomagnetic equator from the geographic equator. The phases of tidal modes lead to a constructive or destructive interference of contributing tidal modes, producing different zonal waves and longitudinal peaked structures at different local time (tLT). The summation of all nonmigrating zonal waves in the low‐latitude region (geomagnetic latitude < 30°) produces a peaked structure with two to four major peaks at most local hours. The amplitude of this peaked structure in June solstice is smaller than those in other seasons. During solar maximum (minimum), the amplitude of peaked structure has a value ~20 (~12) TECu with two to four (one to three) peaks. The locations of peaked structures formed by the nonmigrating tides in 2006 (solar minimum) and in 2014 (solar maximum) are similar. The Weddell Sea Anomaly is found to have a density enhancement in the region from 135°E to 90°W and from 40°S to 80°S with an amplitude ~19.85 (~5.07) TECu during March equinox (December solstice) of solar maximum (minimum).
Environmental Forcings on the Remotely Sensed Phytoplankton Bloom Phenology in the Central Ross Sea Polynya
Authors: Park Jinku , Kim Jeong‐Hoon , Kim Hyun‐cheol , Hwang Jihyun , Jo Young‐Heon , Lee Sang Heon
Published: July 2019

We investigated the interannual variability of the phytoplankton bloom in the central Ross Sea Polynya derived from the annual phenology metrics of the bloom based on ocean color satellite measurements obtained between 2002 and 2017. The phenology metrics determined by the adjusted Gaussian fitting method include the bloom amplitude (BA), bloom initiation timing (BIT), and bloom peak timing (BPT). We found the following results for three phenology metrics. The BA tended to increase since 2002, probably related to the formation of open water area by the atmospheric circulation changes on the synoptic scale over the Ross Sea. The significant sea ice loss trend due to the changing winds over the entire southern coast of the Ross Sea was found. Continuous winds in widened open water can move surface water masses more easily along the wind direction, transferring water masses or chlorophyll pigments themselves accordingly. This process has led to the recent intense bloom in the central Ross Sea Polynya. The interannual variability of the BIT is a function of the sea surface temperature in November and wind speed in October, implying that there is a strong association between ice drift and melting, which can be primarily related to the onset of the polynya expansion. Although there was no direct factor to the BPT, it was somewhat related to the BIT and BA. In other words, the environmental factors forming the BIT and BA might have indirectly influenced the BPT, suggesting that early polynya and large biomass could lead to promoting the bloom decay.
Open Data in Science
Authors: Murray-Rust Peter
Published: July 2019

Open Data (OD) is an emerging term in the process of defining how scientific data may be published and re-used without price or permission barriers. Scientists generally see published data as belonging to the scientific community, but many publishers claim copyright over data and will not allow its re-use without permission. This is a major impediment to the progress of scholarship in the digital age. This article reviews the need for Open Data, shows examples of why Open Data are valuable and summarizes some early initiatives in formalizing the right of access to and re-use of scientific data.
Multifunctional Hybrid Silica Particles for Multicolor Imaging and Multiplex Tasking
Authors: koo Sang Man , Kim Hae Sung , Jung Chan Yoon , Kim Ha Young , Hah Hoe Jin
Published: July 2019

Multifunctional submicron particles have recently emerged as great promises for biological applications such as bio-labeling, medical diagnostics, and drug delivery. These particles are non-toxic and have size comparable to biomolecules, becoming very suitable for biomedical applications. The particle structures can be engineered to perform multicolor imaging, as well as multiplex tasking such as site-selective binding, detection, and separation. In addition, these particles can load a large amount of fluorescent dye for signal amplification. Several synthetic techniques have been developed for a variety of submicron particles, including core-shell synthesis, layer-by-layer techniques, multi-block polymer emulsifications, and surface modifications. Silica particles are one of the most extensively studied particles as they can be easily modified with organic functionalities. However, these silica particles usually have only a single type of functional group. Therefore, multiple sequential modification steps have to be employed in order to attach multitasking components such as imaging components, drugs and targeting moieties. For wider biological applications, the development of a simple and efficient preparation method for particles with various types of functionalities is of great importance. Herein, a "ONE-POT"; synthesis of multifunctional hybrid silica (MHS) particles of uniform size and morphology with homogeneously distributed multiple functional moieties is reported. The MHS particles can be tagged with various multitasking components for detection, selective binding, and separation using different functionalities, in an easier and more flexible way than those particles with a single functional group. Moreover, each functional moiety can be further modified with additional organic or inorganic groups. We demonstrate here following abilities of MHS particles: 1) expansion of surface functionality through the reaction with organic or inorganic compounds; 2) multicolor imaging by surface-conjugation with multiple dyes; 3) controlled assembly of 3-dimensional aggregates from two different types of MHS particles; 4) multiplex tasking through dye-tagging and selective binding to a patterned surface.
A review of journal policies for sharing research data
Authors: Piwowar Heather , Chapman Wendy
Published: July 2019

*Background:*

Sharing data is a tenet of science, yet commonplace in only a few subdisciplines. Recognizing that a data sharing culture is unlikely to be achieved without policy guidance, some funders and journals have begun to request and require that investigators share their primary datasets with other researchers. The purpose of this study is to understand the current state of data sharing policies within journals, the features of journals which are associated with the strength of their data sharing policies, and whether the strength of data sharing policies impact the observed prevalence of data sharing. *Methods:* We investigated these relationships with respect to gene expression microarray data in the journals that most often publish studies about this type of data. We measured data sharing prevalence as the proportion of papers with submission links from NCBI's Gene Expression Omnibus (GEO) database. We conducted univariate and linear multivariate regressions to understand the relationship between the strength of data sharing policy and journal impact factor, journal subdiscipline, journal publisher (academic societies vs. commercial), and publishing model (open vs. closed access).

*Results:*

Of the 70 journal policies, 18 (26%) made no mention of sharing publication-related data within their Instruction to Author statements. Of the 42 (60%) policies with a data sharing policy applicable to microarrays, we classified 18 (26% of 70) as moderately strong and 24 (34% of 70) as strong.Existence of a data sharing policy was associated with the type of journal publisher: half of all commercial publishers had a policy compared to 82% of journals published by academic society. All four of the open-access journals had a data sharing policy. Policy strength was associated with impact factor: the journals with no data sharing policy, a weak policy, and a strong policy had respective median impact factors of 3.6, 4.5, and 6.0. Policy strength was positively associated with measured data sharing submission into the GEO database: the journals with no data sharing policy, a weak policy, and a strong policy had median data sharing prevalence of 11%, 19%, and 29% respectively.*Conclusion:* This review and analysis begins to quantify the relationship between journal policies and data sharing outcomes and thereby contributes to assessing the incentives and initiatives designed to facilitate widespread, responsible, effective data sharing.
Overnight weight loss: relationship with sleep structure and heart rate variability
Authors: Moraes Walter , Poyares Dalva , Guilleminault Christian , Rosa Agostinho , Mello Marco Tulio , Rueda Adriana , Tufik Sergio
Published: July 2019

Background:

Weight loss can be caused by a loss of body mass due to metabolism and by water loss as unsensible water loss, sweating, or excretion in feces and urine. Although weight loss during sleep is a well-known phenomenon, it has not yet been studied in relation to sleep structure or autonomic tonus during sleep. Our study is proposed to be a first step in assessing the relationship between overnight weight loss, sleep structure, and HRV (heart rate variability) parameters.

Methods:

Twenty-five healthy volunteers received a 487 kcal meal and 200 ml water before experiment. Volunteers were weighed before and after polysomnography. Absolute and relative weight indices were calculated. Time and frequency domain analysis of heart rate variability was assessed during stages 2, 4, and REM. Nonparametric linear regression analysis was performed between night weight loss parameters, polysomnographic, and HRV ariables.

Results:

HF correlated positively with weight loss during stage 4. Slow wave sleep duration correlated positively with weight loss and weight loss rate. The duration of Stage 2 correlated negatively with absolute and relative weight loss.

Conclusions:

Weight loss during sleep is dependent upon sleep stage duration and sleep autonomic tonus. Slow-wave sleep and sleep parasympathetic tonus may be important for weight homeostasis.
Identification of the prebiotic translation apparatus within the contemporary ribosome
Authors: Agmon Ilana , Davidovich Chen , Bashan Anat , Yonath Ada
Published: July 2019

A structural element that could have existed independently in the prebiotic era was identified at the active site of the contemporary ribosome. It is suggested to have functioned as a proto-ribosome catalyzing peptide bond formation and non-coded elongation in the same manner that contemporary ribosomes exert positional catalysis, namely by accommodating the reactants in stereochemistry favourable for inline nucleophilic attack. This simple apparatus is a dimer of self-folding RNA units that could have assembled spontaneously into a symmetrical pocket-like structure, sufficiently efficient to be preserved throughout evolution as the active site of modern ribosomes, thus presenting a conceivable starting point for translation.Here we discuss the proto-ribosome emergence hypothesis and show that the tendency for dimerization, a prerequisite for obtaining the catalytic centre, is linked to the fold of its two components, indicating functional selection at the molecular level in the prebiotic era and supporting the existence of dimeric proto-ribosome.
Plant functional constraints on foliar N:P ratios in a tropical forest landscape
Authors: Sierra Carlos
Published: July 2019

Although large scale analyses of foliar N:P ratios suggest and overall pattern of P limitation in tropical forests, analyses within the biome are less indicative of a consistent pattern of nutrient limitation. High tree species diversity and soil heterogeneity are important factors driving the variability of foliar chemistry in the tropics; however, this variability could be reduced at the level of the functional characteristics of the species present at a site. In this study it is hypothesized that foliar N:P ratios would be more constrained when the species are grouped according to functional characteristics, and would reveal patterns of nutrient limitation. The study was conducted in a tropical forest landscape of the Porce region in Colombia, which consists of patches of primary and secondary forests of different ages. The functional groupings revealed consistent patterns of conservative N cycling in species present at young secondary sites, as well as conservative P cycling of the species present later in succession and in primary forests. Although the observed data have limitations in terms of capturing the overall variability for each functional group, the classification used here provided support for the proposed hypotheses. It is concluded that functional composition, rather than taxonomic composition, can potentially improve our understanding of nutrient cycling in tropical forests.
Survey of the diagenesis process and effect these process on reservoir quality of the Kangan formation in South Pars Field
Authors: Hosseinyar Gholamreza , Rahimpour-Bonab Hossein , Asadi Esksndar Ashkan , Asgharian Rostami Masoud
Published: July 2019

Kangan and Upper Dalan formations are forming reservoir sequence of the South Pars field. Litology of the kangan formation is carbonate and (limestone and dolomite with anhydrite intervals), so digenetic processes were very active in this formation and these processes have changeed the reservoir quality. Importances of the digenetic process are including dissolution, calcite cements, dolomitization, anhydritization, physical and chemical compaction and fracturing.
Inhibition of Acid Phosphatase Enzyme Activity in the Presence of Noncrystalline Calcium Phosphate and Nanocrystalline Calcium Apatite: a Preliminary Study
Authors: Pekounov Yassen
Published: July 2019

Background

Our bones are remodelled repeatedly throughout life. New and “healthy” bone tissue replaces the old one. It has been shown that the bone degrading cells, the osteoclasts, prefer old and fatigued bone. The young bone mineral, i.e. calcium apatite, is less crystalline than the mature one. Is it possible that the osteoclasts distinguish between relatively old and new bone via its mineral crystallinity?Methodology/Principal FindingsAcid phosphatase is an enzyme abundantly expressed by the osteoclasts during resorption and therefore used as a marker of the cells’ activity. This study explores whether its enzymatic activity would be decreased in the presence of biomimetically prepared noncrystalline calcium phosphate and nanocrystalline bone-like calcium apatite. The results showed that both biomimetic samples decreased significantly the enzyme activity while commercially available calcium phosphate samples (hydroxyapatite and brushite) did not. Consistent with our hypothesis the noncrystalline calcium phosphate had the greater inhibition effect.

Conclusions/Significance

The in vitro data suggest that the bone-resorbing cells’ activity could be regulated by the degree of crystallinity of the bone mineral. These findings imply that changes in the properties of biogenic inorganic materials induce specific interactions with biomolecules, which in turn should define the cell’s behaviour. These results would support an interesting mechanism of cell regulation if confirmed in vivo.
Do not log-transform count data
Authors: O'Hara Robert , Kotze Johan
Published: July 2019

1. Ecological count data (e.g., number of individuals or species) are often log-transformed to satisfy parametric test assumptions.2. Apart from the fact that generalized linear models are better suited in dealing with count data, a log-transformation of counts has the additional quandary in how to deal with zero observations. With just one zero observation (if this observation represents a sampling unit), the whole dataset needs to be fudged by adding a value (usually 1) before transformation. 3. Simulating data from a negative binomial distribution, we compared the outcome of fitting models that were transformed in various ways (log, square-root) with results from fitting models using Poisson and negative binomial models to untransformed count data. 4. We found that the transformations performed poorly, except when the dispersion was small and the mean counts were large.  The Poisson and negative binomial models consistently performed well, with little bias.
The origin of vertebrates and their symmetry, segmentation, chord and tubular nervous system
Authors: Ermolenko Alexander , Perepada Elena
Published: July 2019

Development of vertebrata begins with formation of a multicellular organism by ordered repeated division of a reproductive cell and nondisjunction of the new formed cells, which have kept connection by means of the extracellular matrix. Further there is a consecutive formation of organisms due to aggregation of similar structures: blastaea; segmentella, supersegmentella. Supersegmentella gave development to tunicates, hemichordates, chordates like lancelet and to predecessors of vertebrata. Segmentation of organisms is determined by aggregation of supergastraeas into one integrated. Symmetry is determined by structure-forming quality of extracellular matrix. Symmetry of primary organisms was radial; then radial-bilateral, and the first plane of symmetry divided the organism into dorsal and ventral sides. With the arrangement of supergastraeas in a line radial-two-plane symmetry consistently formed. Radial-three-plane symmetry formed by association of two segmentellas by posterior edges. The third plane of symmetry divided the organism into anterior and posterior antimeres. From extracellular matrix originated mesogloea, and then a chord; endodermic embolies gave development to the primary gut; ectodermic embolies after the concentration there earlier diffusely located nervous cells transformed first into a trench, and then into a tubular nervous system; the condensed nervous fabric of aboral poles gave development to the central nervous system. The glandulocytes of supergastraeas became starting material for all glands of the organism.
Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro
Authors: Tollervey David , Houseley Jonathan
Published: July 2019

Trans-splicing, the in vivo joining of two RNA molecules, is well characterized in several groups of simple organisms but was long thought absent from fungi, plants and mammals. However, recent bioinformatic analyses of expressed sequence tag (EST) databases suggested widespread trans-splicing in mammals^1-2^. Splicing, including the characterised trans-splicing systems, involves conserved sequences at the splice junctions. Our analysis of a yeast non-coding RNA revealed that around 30% of the products of reverse transcription lacked an internal region of 117 nt, suggesting that the RNA was spliced. The junction sequences lacked canonical splice-sites but were flanked by direct repeats, and further analyses indicated that the apparent splicing actually arose because reverse transcriptase can switch templates during transcription^3^. Many newly identified, apparently trans-spliced, RNAs lacked canonical splice sites but were flanked by short regions of homology, leading us to question their authenticity. Here we report that all reported categories of non-canonical splicing could be replicated using an in vitro reverse transcription system with highly purified RNA substrates. We observed the reproducible occurrence of ostensible trans-splicing, exon shuffling and sense-antisense fusions. The latter generate apparent antisense non-coding RNAs, which are also reported to be abundant in humans^4^. Different reverse transcriptases can generate different products of template switching, providing a simple diagnostic. Many reported examples of splicing in the absence of canonical splicing signals may be artefacts of cDNA preparation.
Effects of diamagnetic levitation on bacterial growth in liquid
Authors: Hill Richard , Larkin Oliver , Anthony Paul , Davey Michael , Eaves Laurence , Rees Catherine , Dijkstra Camelia
Published: July 2019

Diamagnetic levitation is a technique that uses a strong, spatially-varying magnetic field to levitate diamagnetic materials, such as water and biological cells. This technique has the potential to simulate aspects of weightlessness, on the Earth. In common with all ground-based techniques to simulate weightlessness, however, there are effects introduced by diamagnetic levitation that are not present in space. Since there have been few studies that systematically investigate these differences, diamagnetic levitation is not yet being fully exploited. For the first time, we critically assess the effect of diamagnetic levitation on a bacterial culture in liquid. We used a superconducting magnet to levitate growing bacterial cultures for up to 18 hours, in a series of experiments to determine the effect of diamagnetic levitation on all phases of the bacterial growth cycle. We find that diamagnetic levitation increases the rate of population growth in a liquid culture. The speed of sedimentation of the bacterial cells to the bottom of the container is considerably reduced. Further experiments and microarray gene analysis show that the growth enhancement is due to greater oxygen availability in the magnetically levitated sample. We demonstrate that the magnetic field that levitates the cells also induces convective stirring in the liquid, an effect not present in microgravity. We present a simple theoretical model, showing how the paramagnetic force on dissolved oxygen can cause the liquid to become unstable to convection when the consumption of oxygen by the bacteria generates an oxygen concentration gradient. We propose that this convection enhances oxygen availability by transporting oxygen around the sample. Since convection is absent in space, these results are of significant importance and timeliness to researchers considering using diamagnetic levitation to explore weightless effects on living organisms and a broad range of other topics in the physical and life sciences.
Differential expression analysis for sequence count data
Authors: Anders Simon , Huber Wolfgang
Published: July 2019

*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

Results:

We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. *Availability:* A free open-source R software package, DESeq, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq.
Clinical validity assessment of a breast cancer risk model combining genetic and clinical information
Authors: Mealiffe Matthew , Stokowski Renee , Rhees Brian , Prentice Ross , Pettinger Mary , Hinds David
Published: July 2019

Background:

The extent to which common genetic variation can assist in breast cancer (BCa) risk assessment is unclear. We assessed the addition of risk information from a panel of BCa-associated single nucleotide polymorphisms (SNPs) on risk stratification offered by the Gail Model.Methods: We selected 7 validated SNPs from the literature and genotyped them among white women in a nested case-control study within the Women’s Health Initiative Clinical Trial. To model SNP risk, previously published odds ratios were combined multiplicatively. To produce a combined clinical/genetic risk, Gail Model risk estimates were multiplied by combined SNP odds ratios. We assessed classification performance using reclassification tables and receiver operating characteristic (ROC) curves. Results: The SNP risk score was well calibrated and nearly independent of Gail risk, and the combined predictor was more predictive than either Gail risk or SNP risk alone. In ROC curve analysis, the combined score had an area under the curve (AUC) of 0.594 compared to 0.557 for Gail risk alone. For reclassification with 5-year risk thresholds at 1.5% and 2%, the net reclassification index (NRI) was 0.085 (Z = 4.3, P = 1.0 × 10^-5^). Focusing on women with Gail 5-year risk of 1.5-2% results in an NRI of 0.195 (Z = 3.8, P = 8.6 × 10^−5^).

Conclusions:

Combining clinical risk factors and validated common genetic risk factors results in improvement in classification of BCa risks in white, postmenopausal women. This may have implications for informing primary prevention and/or screening strategies. Future research should assess the clinical utility of such strategies.
Evolution of 11[beta]-Hydroxysteroid Dehydrogenase-Type 1 and 11[beta]-Hydroxysteroid Dehydrogenase-type 3
Authors: Baker Michael
Published: July 2019

A key regulator of glucocorticoid action is 11[beta]-hydroxysteroid dehydrogenase type-1 (11[beta]-HSD1), which catalyzes the conversion of cortisone to cortisol, the biologically active glucocorticoid. 11[beta]-HSD1 is a paralog of 11[beta]-HSD3, whose physiological function remains unclear. As reported here, 11[beta]-HSD3 has orthologs in sea urchin, amphioxus and Ciona, while 11[beta]-HSD1 first appears in sharks. Thus, 11[beta]HSD3 arose before the evolution of glucocorticoid signaling, suggesting different ancestral function(s) for 11[beta]-HSD3. Four perplexing findings arise from this evolutionary analysis: 1) 11[beta]-HSD1 is not present in a ray-finned fish genome, 2) zebrafish and fathead minnow contain two isoforms of 11[beta]-HSD3; 3) neither rat nor mouse contain 11[beta]-HSD3 and 4) amphioxus contains sixteen 11[beta]-HSD3 paralogs.
Snca and Bdnf gene expression in the VTA and raphe nuclei of midbrain in chronically victorious and defeated male mice
Authors: Kudryavtseva Natalia N. , Bondar Natalia P. , Boyarskikh Ul'yana A. , Filipenko Maxim L.
Published: July 2019

The study aimed to analyze the mRNA levels of Snca and Bdnf genes in the ventral tegmental area (VTA) and raphe nuclei of the midbrain in male mice that had each won or defeated 20 encounters in daily agonistic interactions. Groups of animals that had the same winning and losing track record followed by a no-fight period for 14 days were also studied. Snca mRNA levels were increased in the raphe nuclei in the losers and in the VTA of the winners. After fighting deprivation Snca mRNA levels were decreased to the control level in both groups. Snca mRNA levels were similar to the control level in the VTA of the losers and in the raphe nuclei of the winners. However Snca gene expression was increased in these areas after no-fight period in the winners and losers in comparison with respective mRNA levels in the undeprived animals. Significant positive correlations were found between the mRNA levels of Snca and Bdnf genes in the raphe nuclei. It was concluded, that social experience affects Snca gene expression depending on brain areas and functional activity of monoaminergic systems in chronically victorious or defeated mice.