Miracle-dz/UniFAR-FTUs huggingface dataset:
Livestock methane emission and its perspective in the global methane cycle

Over the past three centuries, the atmospheric methane burden has grown 2.5-fold, reaching levels unprecedented in at least 650 000 years. Agricultural expansion has played a large part in this anthropogenic signal, with enterically fermented methane emitted by farmed ruminant livestock accounting for about one quarter of all anthropogenic emissions. This paper summarises the range of measurements that give confidence in estimates of the emission per animal and per unit feed intake and in their extrapolation to national and global emission inventories, while noting also some of the inherent uncertainties. Global emissions are discussed in the context of the evolving global methane cycle.
Initial Changes in the Avian Communities of Remnant Eucalypt Woodlands following a Reduction in the Abundance of Noisy Miners, Manorina melanocephala

It has been postulated that aggressive honeyeaters like the noisy miner, Manorina melanocephala, may contribute to rural tree decline by excluding small insectivorous birds from remnant patches of woodland, thereby reducing the level of predation upon defoliating insects. Previous studies provide correlational evidence that avian diversity and abundance is lower in remnant patches of woodland occupied by noisy miners than in those without noisy miners. Noisy miners were removed from three small remnant patches of woodland in north-eastern Victoria. The removal of the majority of noisy miners from a site, or even the removal of only part of a noisy miner colony from a site, resulted in a major influx of honeyeaters and other insectivorous birds to these sites in the following three months. Such major invasions were not observed on matching control sites. At two of the three removal sites, this led to an increase in both the abundance and diversity of birds on the site. At the third site, there was an increase in the diversity, but not the abundance of birds. These experiments are the first to demonstrate that noisy miners affect avian diversity and abundance by aggressive exclusion of small birds. They also showed that if domination by noisy miners is reduced, small, degraded woodland remnants can support significant populations of some small insectivorous birds and honeyeaters. Noisy miners did not reinvade the experimental sites during the following 16 months and avian diversity and abundance remained higher at the experimental sites than at the paired control sites. Long-term monitoring is needed to determine whether the small invading bird species have a lasting effect upon insect populations and tree health.
Multiple dispersals and modern human origins

Despite a massive endeavour, the problem of modern human origins not only remains unresolved, but is usually reduced to “Out of Africa” versus multiregional evolution. Not all would agree, but evidence for a single recent origin is accumulating. Here, we want to go beyond this debate and explore within the “Out of Africa” framework an issue that has not been fully addressed: the mechanism by which modern human diversity has developed. We believe there is no clear rubicon of modern Homo sapiens, and that multiple dispersals occurred from a morphologically variable population in Africa. Pre‐existing African diversity is thus crucial to the way human diversity developed outside Africa. The pattern of diversity—behavioural, linguistic, morphological and genetic—can be interpreted as the result of dispersals, colonisation, differentiation and subsequent dispersals overlaid on former population ranges. The first dispersals would have originated in Africa from where two different geographical routes were possible, one through Ethiopia/Arabia towards South Asia, and one through North Africa/Middle East towards Eurasia.
Spatio-ecological segregation of diploid and tetraploid cytotypes of Galium valdepilosum in central Europe Ekogeografická diferenciace cytotypů Galium valdepilosum ve střední Evropě

The Galium pusillum agg. (Rubiaceae), with four species native to the Czech Republic, is a taxonomically challenging complex. Of these, G. valdepilosum is particularly interesting because this relict species shows both ploidy (the incidence of diploid and tetraploid cytotypes) and habitat differentiation (occurrence on different soil types, including serpentines). With the aid of DNA flow cytometry, analysis of vegetation samples and a hydroponic cultivation experiment we addressed the cytogeographic pattern, ecological preferences of different cytotypes both across the entire range of distribution and in the contact zone and the plant’s response to serpentine edaphic stress. Ploidy distribution in G. valdepilosum is parapatric, with a narrow contact zone in southern Moravia. Neither triploids nor mixed 2x-4x populations were found, which together with the restriction of the species to isolated relict habitats, suggest the static character of the contact zone. In general, tetraploids occupied a wider range of habitats and colonized larger geographic areas. Diploids typically occurred in open low-competitive oak-pine forests on acidic soils while their tetraploid counterparts were also able to survive in open basiphilous grasslands with a comparatively higher competitive pressure. Serpentines did not play an important role in ecological sorting of the cytotypes. Cultivation experiments showed that G. valdepilosum is likely to be constitutively tolerant to serpentine chemical stress. Relative genome size and ecological data indicate that the serpentine populations from western Bohemia, traditionally referred to as G. sudeticum, differ from the type subalpine populations from the Krkonose Mts and suggest their merger with G. valdepilosum. K e y w o r d s: central Europe, contact zone, cytogeography, ecological sorting, flow cytometry, Galium sudeticum, Galium valdepilosum, ploidy distribution, polyploidy, serpentine
Reproductive Traits and Male Fertility in Plants: Empirical Approaches*

Within-population variability in plant reproductive traits can influence both male and female fitness, but research on the male function of flowers has been hindered by the difficulty of measuring male fertility. Here we evaluate studies that employ paternity analysis to examine how specific plant traits affect male reproductive success (RS) in both natural and artificial populations. These studies illustrate the risks of assuming that male RS is correlated with female RS or with components of male fitness, such as the amount of pollen produced per plant. In some studies, paternity was assigned by simple genetic exclusion using unique multilocus allozyme profiles. More powerful methods involve statistical procedures that assign paternity to the most likely father of each offspring. Lack of genetic markers is a common problem in paternity analysis, and we discuss the types of molecular markers that may soon become more widely used in small, natural populations.
Diversity and inclusion for the All of Us research program: A scoping review

The All of Us Research Program (All of Us) is a national effort to accelerate health research by exploring the relationship between lifestyle, environment, and genetics. It is set to become one of the largest research efforts in U.S. history, aiming to build a national resource of data from at least one million participants. All of Us aims to address the need for more diversity in research and set the stage for that diversity to be leveraged in precision medicine research to come. This paper describes how the program assessed demographic characteristics of participants who have enrolled in other U.S. biomedical research cohorts to better understand which groups are traditionally represented or underrepresented in biomedical research. We 1) reviewed the enrollment characteristics of national cohort studies like All of Us, and 2) surveyed the literature, focusing on key diversity categories essential to the program’s enrollment aims. Based on these efforts, All of Us emphasizes enrollment of racial and ethnic minorities, and has formally designated the following additional groups as historically underrepresented: individuals—with inadequate access to medical care; under the age of 18 or over 65; with an annual household income at or below 200% of the federal poverty level; who have a cognitive or physical disability; have less than a high school education or equivalent; are intersex; identify as a sexual or gender minority; or live in rural or non-metropolitan areas. Research accounting for wider demographic variability is critical. Only by ensuring diversity and by addressing the very barriers that limit it, can we position All of Us to better understand and tackle health disparities.
IV.—On the Literature and Nomenclature of British Fossil Crocodilia

Of all groups of fossil reptiles, there is perhaps none in greater need of critical revision than that comprising the Crocodilia. The remains of this order already discovered are so numerous, and the various descriptive accounts of them so scattered and disconnected,—so commonly has it been the custom to take advantage of each successive “find” for the manufacture of a new generic or specific name, however fragmentary the materials, and so frequently have species been imperfectly compared and characterized,—that a most intricate and perplexing synonymy has arisen, which it would require long-continued research by the profoundest of specialists to unravel. Moreover, cases are not unknown, in which type specimens have subsequently proved to be unfortunate restorations, and the occasional disregard of priority in nomenclature has also contributed to increase the confusion.
Nanomedicine and Onco-Immunotherapy: From the Bench to Bedside to Biomarkers

The broad relationship between the immune system and cancer is opening a new hallmark to explore for nanomedicine. Here, all the common and synergy points between both areas are reviewed and described, and the recent approaches which show the progress from the bench to the beside to biomarkers developed in nanomedicine and onco-immunotherapy.
Occurrence of severe rotavirus gastroenteritis in children younger than three years of age before and after the introduction of rotavirus vaccine: a prospective observational study in four pediatric clinics in Shibata City, Niigata Prefecture, Japan

ABSTRACT In Japan, rotavirus (RV) vaccines have already been introduced but not used for universal vaccination as of 2018. Therefore, we identified cases of severe rotavirus gastroenteritis (RVGE) in children younger than three years of age and investigated the occurrence of infection before and after the introduction of RV vaccines. An ecological study through prospective surveillance was conducted in four pediatric clinics in Shibata City, Niigata Prefecture, Japan, during the 2011 to 2018 RVGE epidemic seasons. We divided the study period into three eras: pre-vaccine introduction era (2011), low-mid coverage transitional era (2012 to 2014, RV vaccine coverage rate: 32.9–56.5%), and high coverage plateau era (2015 to 2018, 67.7–81.7%). In this study, the incidence rate of severe RVGE was significantly lower in the plateau era than in the pre-vaccine introduction and transitional eras. Furthermore, the hospitalization rate due to RVGE in Shibata City was lower in the plateau era than in the pre-vaccination introduction and transitional eras. The number of hospitalizations due to RVGE in subjects who required or did not require intravenous rehydration at the pediatric clinics significantly decreased with the increase in vaccine coverage rates by more than 70% in the plateau era.
A Preliminary Prototype High-Speed Feedback Control of an Artificial Cochlear Sensory Epithelium Mimicking Function of Outer Hair Cells

A novel feedback control technique for the local oscillation amplitude in an artificial cochlear sensory epithelium that mimics the functions of the outer hair cells in the cochlea is successfully developed and can be implemented with a control time on the order of hundreds of milliseconds. The prototype artificial cochlear sensory epithelium was improved from that developed in our previous study to enable the instantaneous determination of the local resonance position based on the electrical output from a bimorph piezoelectric membrane. The device contains local patterned electrodes deposited with micro electro mechanical system (MEMS) technology that is used to detect the electrical output and oscillate the device by applying local electrical stimuli. The main feature of the present feedback control system is the principle that the resonance position is recognized by simultaneously measuring the local electrical outputs of all of the electrodes and comparing their magnitudes, which drastically reduces the feedback control time. In this way, it takes 0.8 s to control the local oscillation of the device, representing the speed of control with the order of one hundred times relative to that in the previous study using the mechanical automatic stage to scan the oscillation amplitude at each electrode. Furthermore, the intrinsic difficulties in the experiment such as the electrical measurement against the electromagnetic noise, adhesion of materials, and fatigue failure mechanism of the oscillation system are also shown and discussed in detail based on the many scientific aspects. The basic knowledge of the MEMS fabrication and the experimental measurement would provide useful suggestions for future research. The proposed preliminary prototype high-speed feedback control can aid in the future development of fully implantable cochlear implants with a wider dynamic range.
Reconstruction of Compressed-sensing MR Imaging Using Deep Residual Learning in the Image Domain

Purpose: A deep residual learning convolutional neural network (DRL-CNN) was applied to improve image quality and speed up the reconstruction of compressed sensing magnetic resonance imaging. The reconstruction performances of the proposed method was compared with iterative reconstruction methods. Methods: The proposed method adopted a DRL-CNN to learn the residual component between the input and output images (i.e., aliasing artifacts) for image reconstruction. The CNN-based reconstruction was compared with iterative reconstruction methods. To clarify the reconstruction performance of the proposed method, reconstruction experiments using 1D-, 2D-random under-sampling and sampling patterns that mix random and non-random under-sampling were executed. The peak-signal-to-noise ratio (PSNR) and the structural similarity index (SSIM) were examined for various numbers of training images, sampling rates, and numbers of training epochs. Results: The experimental results demonstrated that reconstruction time is drastically reduced to 0.022 s per image compared with that for conventional iterative reconstruction. The PSNR and SSIM were improved as the coherence of the sampling pattern increases. These results indicate that a deep CNN can learn coherent artifacts and is effective especially for cases where the randomness of k-space sampling is rather low. Simulation studies showed that variable density non-random under-sampling was a promising sampling pattern in 1D-random under-sampling of 2D image acquisition. Conclusion: A DRL-CNN can recognize and predict aliasing artifacts with low incoherence. It was demonstrated that reconstruction time is significantly reduced and the improvement in the PSNR and SSIM is higher in 1D-random under-sampling than in 2D. The requirement of incoherence for aliasing artifacts is different from that for iterative reconstruction.
Molecular Basis of Effector Recognition by Plant NB‐LRR Proteins

Pathogens attack plants in attempts to assimilate nutrients from them. These pathogens include bacteria, viruses, nematodes, fungi, and oomycetes. All current plant species have been successful in surmounting pathogen attack. Nonetheless, the struggle between plant pathogens and their hosts continues. This co-evolutionary battle has equipped plants with sophisticated defense mechanisms and cognate pathogens with a corresponding arsenal of counterstrategies to overcome them (Chisholm et al. 2006; Bent and Mackey 2007). Plants rely on passive and induced defense mechanisms to resist pathogen infection (Jones and Dangl 2006). Examples of passive defenses are physical and biochemical barriers such as trichomes, epidermal wax layers, the cell wall, and the production of antimicrobial compounds (Heath 2000; Chisholm et al. 2006). Adapted pathogens able to breach these passive defense barriers are confrontedwith induced defense responses that are orchestrated by amultilayered innate immune system (Segonzac and Zipfel, 2011). The first layer of the induced immune system uses membranelocalized pattern recognition receptors (PRRs) that sense microbe-associated molecular patterns (MAMPs) or pathogen-associated molecular patterns (PAMPs). Recognition of these conserved and essential molecules by PRRs initiates PAMP-triggered immunity (PTI). Specialized pathogens evolved strategies to overcome PTI by the production of effector proteins. To counteract the virulence activities of effectors, resistant plants have evolved resistance (R) proteins. R proteins represent the key component of the second layer of the induced immune system. On effector recognition by an R protein, defense responses are initiated that often culminate into a hypersensitive response (HR), concomitant with a localized cell death response around the infection site (Heath 2000; Thomma et al. 2011). Effectors recognized by R proteins are called avirulence (Avr) factors, and the resistance reaction initiated is known as effector-triggered immunity (ETI) (Jones and Dangl 2006; Dodds and Rathjen 2010). This specific recognition phenomenon was first described by Flor in 1942 as the gene-for-gene hypothesis (Flor 1971). In those days, the gene pairs involved were unknown, but nowadays numerous Avr genes have been cloned, and in 1992 the first R gene was isolated: theHm1 from maize that confers race-specific resistance to the fungus Cochliobolus carbonum (Johal and Briggs 1992). At the present time,>70 R genes have been cloned from both monocot and dicot plant species conferring resistance to a wide variety of pathogens (Martin et al. 2003; Liu et al. 2007).
CHAPTER 5 GENETIC IDENTIFICATION OF FISH HARVESTED FROM OFFSHORE AQUACULTURE: AN EXAMPLE INVOLVING RED DRUM, SCIAENOPS OCELLATUS, FROM THE NORTHERN GULF OF MEXICO

A total of 31 nuclear-encoded microsatellites and an ~ 370 base pair fragment from the ‘control’ region of mitochondrial (mt)DNA were employed to resolve potential forensic issues relating to legal sale of red drum (Sciaenops ocellatus) harvested from offshore aquaculture operations in the northern Gulf of Mexico. Exclusion analyses demonstrated that only 16 microsatellites (13 if mtDNA was employed) were necessary to exclude a sample of 101 ‘wild’ red drum from Biloxi Bay, Mississippi, as having been produced by broodfish in a hatchery near Corpus Christi, Texas; the probability of incorrectly assigning a ‘wild’ fish as having been produced by the broodfish ranged from 2.58 x 10 –19 to 1.33 x 10 –27 . Probabilities that the most common, hatchery-produced ‘composite’ genotype would occur in the sample from Biloxi Bay ranged from 1.38 x 10 –27 to 2.98 x 10 –42 . All probability values were several orders of magnitude smaller than the reciprocal of the total number of adult red drum (10 6 –10 7 ) estimated to occur in the northern Gulf of Mexico. Comparison of results with and without mtDNA indicated that it would be more cost effective to first sequence individuals for the mtDNA fragment and then determine the number of individuals that needed to be assayed for microsatellite genotypes. The study demonstrated that unequivocally distinguishing red drum spawned from broodstock obtained offshore of Corpus Christi, Texas, from the ‘wild’ stock in Biloxi Bay, Mississippi, is fairly straightforward, given (i) a sufficient number of polymorphic (variable), independent genetic markers, (ii) the genotypes of the broodfish, and (iii) a survey of allelic variation at the genetic markers among representatives of the ‘wild’ stock. The three ‘requirements’ essentially would be the same for any offshore aquaculture operation where legal sale of the cultured species could be an issue.
An illustrated key to the fiddler crabs (Crustacea, Decapoda, Ocypodidae) from the Atlantic coast of Brazil

Abstract Fiddler crabs are one of the most notable animal groups in Brazilian estuarine environments, due to their high density and characteristic waving of males. An illustrated key to the ten species recorded as far in the country is provided using only clearly visible characters of males. Furthermore, additional recognition characters, information about geographic distribution and biology of each species are presented. Most examined crabs were collected in Guaratuba Bay, southern Brazil.
Involvement of protein kinase Cα (PKCα) in the early action of angiotensin II type 2 (AT2) effects on neurite outgrowth in NG108-15 cells : AT2-receptor inhibits PKCα and p21ras activity

The aim of the present study was to investigate whether protein kinase C (PKC) isoforms may be among the putative candidates implicated in the primary effects of the Ang II type 2 (AT2) receptor. Western blot analyses revealed the presence of PKCα,e, ι, and ζ in NG108–15 cells. After a 3-d treatment with 3 nm Go6976, a specific inhibitor of classical PKC isoforms, cells were characterized by the presence of one elongated process similar to that observed after treatment with Ang II or with CGP42112, a selective AT2 receptor agonist. Similar findings were observed in cells expressing a dominant-negative mutant of PKCα (K368A). Inhibition of PKCα in NG108–15 cells also decreased cell number and proliferation. In conditions of acute stimulation, Ang II induced a time-dependent and transient inhibition of PKCα activity, as well as a decrease in PKCα levels associated with the membrane. Treatment of cells with Go6976 was also found to inhibit p21ras (between 1–10 min) but stimulated Rap1 activity (1–5 min) in a.
Effects of Restoration Thinning on Presettlement Pinus ponderosa in Northern Arizona

In the 100 years following the arrival of Euro‐American settlers in northern Arizona, Pinus ponderosa (ponderosa pine) forests changed from open, low‐density stands to closed, high‐density stands. The increase in tree density has been detrimental to the vigor of old‐growth trees that established before settlement (presettlement trees). In this study, we examined whether the vigor of presettlement trees could be improved by restoring the original stand structure by thinning the ponderosa pines that established after settlement (postsettlement trees). The restoration treatment caused the following changes in the presettlement trees and their environment in the first year following thinning: an increase in volumetric soil water content between May and August, an increase in predawn xylem water potential in July and August, a decrease in midday xylem water potential in June and August, an increase in net photosynthetic rate in August, an increase in foliar nitrogen concentration in July and August, and an increase in bud and needle size. The results show that the thinning restoration treatment improved the condition of presettlement ponderosa pines by increasing canopy growth and the uptake of water, nitrogen, and carbon.