Miracle-dz/UniFAR-FTUs huggingface dataset:
Will human-induced changes in seawater chemistry alter the distribution of deep-sea scleractinian corals?

The answer to the title question is uncertain, as very few manipulative experiments have been conducted to test how deep-sea scleractinians (stony corals) react to changes in seawater chemistry. Ocean pH and calciumcarbonate saturation are decreasing due to an influx of anthropogenic CO2 to the atmosphere. Experimental evidence has shown that declining carbonate saturation inhibits the ability of marine organisms to build calcium carbonate skeletons, shells, and tests. Here we put forward a hypothesis suggesting that the global distribution of deep-sea scleractinian corals could be limited in part by the depth of the aragonite saturation horizon (ASH) in the world's oceans. Aragonite is the metastable form of calcium carbonate used by scleractinian corals to build their skeletons and the ASH is the limit between saturated and undersaturated water. The hypothesis is tested by reviewing the distribution of deep-sea, bioherm-forming scleractinian corals with respect to the depth of the ASH. Results indicate that > 95% of 410 coral locations occurred in saturated waters during pre-industrial times. Projections indicate that about 70% of these locations will be in undersaturated waters by 2099. Lab experimentation, in situ experimentation, and monitoring efforts are needed to quantify the effects of changing seawater chemistry on deep-sea coral ecosystems.
Continuous real-time breath analysis in ruminants: effect of eructation on exhaled VOC profiles

Background. The analysis of volatile organic compounds (VOCs) in breath allows non-invasive investigations of diseases. Animal studies are conducted as a model to perform research of VOCs and their relation to diseases. In large animal models ruminants were often used as experimental targets. The effect of their physiological eructation on VOC exhalation has not been examined yet and is the objective of this study. Methods. Continuous breath profiles of two young cattle, four adult goats and four adult sheep were measured through a mask, covering mouth and nose, in real-time (200 ms) by means of proton transfer reaction time of flight mass spectrometry. Each animal was analysed twelve times for 3 consecutive minutes. Results. Real-time monitoring yielded a distinction of different episodes in the breath profiles of ruminants. An algorithm to separate eructation episodes and alveolar breath was established. In the first exhalation after eructation at least 19 VOC concentrations increased (up to 36-fold) and went back to initial levels in subsequent exhalations in all investigated ruminants. Decay of concentrations was substance specific. In goats, less VOCs were affected by the eructation compared to cattle and sheep. Breath profiles without exclusion of eructation episodes showed higher variations and median values than profiles where eructation episodes were excluded. Conclusion. Real-time breath analysis of ruminants enables the discrimination and characterisation of alveolar breath and eructation episodes. This leads to a better understanding of variation in breath data and possible origins of VOCs: breath or digestion related. To avoid impairment of breath gas results and to gain further information on bacterial products from the rumen, eructation and alveolar breath data should be analysed separately.
Impact of the US Maternal Tetanus, Diphtheria, and Acellular Pertussis Vaccination Program on Preventing Pertussis in Infants <2 Months of Age: A Case-Control Evaluation

Background Infants aged <1 year are at highest risk for pertussis-related morbidity and mortality. In 2012, Tdap (tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis) vaccine was recommended for women during each pregnancy to protect infants in the first months of life; data on effectiveness of this strategy are currently limited. Methods We conducted a case-control evaluation among pertussis cases <2 months old with cough onset between 1 January 2011 and 31 December 2014 from 6 US Emerging Infection Program Network states. Controls were hospital-matched and selected by birth certificate. Mothers were interviewed to collect information on demographics, household characteristics, and healthcare providers. Provider-verified immunization history was obtained on mothers and infants. Mothers were considered vaccinated during pregnancy if Tdap was received ≥14 days before delivery; trimester was calculated using Tdap date, infant's date of birth, and gestational age. Odds ratios were calculated using multivariable conditional logistic regression; vaccine effectiveness (VE) was estimated as (1 - odds ratio) × 100%. Results A total of 240 cases and 535 controls were included; 17 (7.1%) case mothers and 90 (16.8%) control mothers received Tdap during the third trimester of pregnancy. The multivariable VE estimate for Tdap administered during the third trimester of pregnancy was 77.7% (95% confidence interval [CI], 48.3%-90.4%); VE increased to 90.5% (95% CI, 65.2%-97.4%) against hospitalized cases. Conclusions Vaccination during pregnancy is an effective way to protect infants during the early months of life. With a continuing resurgence in pertussis, efforts should focus on maximizing Tdap uptake among pregnant women.
The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

Microbial minimal generation times range from a few minutes to several weeks. They are evolutionarily determined by variables such as environment stability, nutrient availability, and community diversity. Selection for fast growth adaptively imprints genomes, resulting in gene amplification, adapted chromosomal organization, and biased codon usage. We found that these growth-related traits in 214 species of bacteria and archaea are highly correlated, suggesting they all result from growth optimization. While modeling their association with maximal growth rates in view of synthetic biology applications, we observed that codon usage biases are better correlates of growth rates than any other trait, including rRNA copy number. Systematic deviations to our model reveal two distinct evolutionary processes. First, genome organization shows more evolutionary inertia than growth rates. This results in over-representation of growth-related traits in fast degrading genomes. Second, selection for these traits depends on optimal growth temperature: for similar generation times purifying selection is stronger in psychrophiles, intermediate in mesophiles, and lower in thermophiles. Using this information, we created a predictor of maximal growth rate adapted to small genome fragments. We applied it to three metagenomic environmental samples to show that a transiently rich environment, as the human gut, selects for fast-growers, that a toxic environment, as the acid mine biofilm, selects for low growth rates, whereas a diverse environment, like the soil, shows all ranges of growth rates. We also demonstrate that microbial colonizers of babies gut grow faster than stabilized human adults gut communities. In conclusion, we show that one can predict maximal growth rates from sequence data alone, and we propose that such information can be used to facilitate the manipulation of generation times. Our predictor allows inferring growth rates in the vast majority of uncultivable prokaryotes and paves the way to the understanding of community dynamics from metagenomic data.
Interference fracturing: Nonuniform distributions of perforation clusters that promote simultaneous growth of multiple hydraulic fractures

© 2015 Society of Petroleum Engineers. One of the important hurdles in horizontal-well stimulation is the generation of hydraulic fractures (HFs) from all perforation clusters within a given stage, despite the challenges posed by stress shadowing and reservoir variability. In this paper, we use a newly developed, fully coupled, parallel-planar 3D HF model to investigate the potential to minimize the negative impact of stress shadowing and thereby to promote more-uniform fracture growth across an array of HFs by adjusting the location of the perforation clusters. In this model, the HFs are assumed to evolve in an array of parallel planes with full 3D stress coupling while the constant fluid influx into the wellbore is dynamically partitioned to each fracture so that the wellbore pressure is the same throughout the array. The model confirms the phenomenon of inner-fracture suppression because of stress shadowing when the perforation clusters are uniformly distributed. Indeed, the localization of the fracture growth to the outer fractures is so dominant that the total fractured area generated by uniform arrays is largely independent of the number of perforation clusters. However, numerical experiments indicate that certain nonuniform cluster spacings promote a profound improvement in the even development of fracture growth. Identifying this effect relies on this new model's ability to capture the full hydrodynamical coupling between the simultaneously evolving HFs in their transition from radial to Perkins-Kern-Nordgren (PKN)-like geometries (Perkins and Kern 1961; Nordgren 1972).
Housing privatization and the return of the state: changing governance in China

ABSTRACT Housing privatization seems to suggest a process of state retreat. However, this is not always the case in China. This paper examines an estate that is mixed with work-unit housing and municipal public housing to understand its changing governance. It is intriguing to observe that the state has had to return to this neighborhood to strengthen its administration following housing privatization, because the attempt to transfer responsibility to commercial property management failed. The neighborhood governance, however, has transformed from one based on work-units to a government-funded administrative agency. The return of the state has been achieved through professional social workers, and it is struggling to operate, leading to the alienation and disempowerment of former state work-unit residents. The side effect of this approach to governance is that, through encouraging market provision and commercial operation which is not fully working, reciprocal activities are restrained. Since housing privatization, the neighborhood has deteriorated from a brand-new estate into an ‘old and dilapidated neighborhood’ in less than 25 years.
Department of Finance Understanding the Relationship between Founder-ceos and Firm Performance Understanding the Relationship between Founder-ceos and Firm Performance

While previous empirical literature has examined the effect of founder-CEOs on Þrm performance , it has largely ignored the effect of Þrm performance on founder-CEO status. In this paper, we use instrumental variables methods to better understand the relationship between founder-CEOs and performance. Using the proportion of the Þrm's founders that are dead and the number of people who founded the company as instruments for founder-CEO status, we Þnd strong evidence that founder-CEO status is endogenous in performance regressions. This implies that the direct effect of founder-CEOs on Þrm performance cannot be estimated correctly without accounting for the endogeneity of founder-CEO status. Perhaps surprisingly, we Þnd that performance is negatively related to the likelihood that founders retain the CEO title. This result appears to be driven primarily by founder departures after periods of good performance, rather than by an entrenchment effect that allows founders to remain as CEOs following poor performance. After factoring out the effect of performance on founder-CEO status, we Þnd a residual positive correlation between founder-CEO status and Þrm performance. This Þnding suggests that there is a positive causal link from founder-CEOs to Þrm performance.
Effects of Calcination Holding Time on Properties of Wide Band Gap Willemite Semiconductor Nanoparticles by the Polymer Thermal Treatment Method

Willemite is a wide band gap semiconductor used in modern day technology for optoelectronics application. In this study, a new simple technique with less energy consumption is proposed. Willemite nanoparticles (NPs) were produced via a water–based solution consisting of a metallic precursor, polyvinylpyrrolidone (PVP), and underwent a calcination process at 900 °C for several holding times between 1–4 h. The FT–IR and Raman spectra indicated the presence of metal oxide bands as well as the effective removal of PVP. The degree of the crystallization and formation of the NPs were determined by XRD. The mean crystallite size of the NPs was between 18.23–27.40 nm. The morphology, particle shape and size distribution were viewed with HR-TEM and FESEM analysis. The willemite NPs aggregate from the smaller to larger particles with an increase in calcination holding time from 1–4 h with the sizes ranging between 19.74–29.71 nm. The energy values obtained from the experimental band gap decreased with increasing the holding time over the range of 5.39 eV at 1 h to at 5.27 at 4 h. These values match well with band gap obtained from the Mott and Davis model for direct transition. The findings in this study are very promising and can justify the use of these novel materials as a potential candidate for green luminescent optoelectronic applications.
Prevention of hepatocyte allograft rejection in rats by transferring adenoviral early region 3 genes into donor cells

Hepatocyte transplantation is being evaluated as an alternative to liver transplantation for metabolic support during liver failure and for definitive treatment of inherited liver diseases. However, as with liver transplantation, transplantation of allogeneic hepatocytes requires prolonged immunosuppression with its associated untoward effects. Therefore, we explored strategies for the genetic modification of donor hepatocytes that could eliminate allograft rejection, obviating the need for immunosuppression. Products of early region 3 (AdE3) of the adenoviral genome are known to protect infected cells from immune recognition and destruction. In the present study we showed that immortalized rat hepatocytes that had been stably transduced with AdE3 before transplantation into fully MHC‐mismatched rats are protected from allograft rejection. Quantitative real‐time PCR analysis showed that a similar number of engrafted AdE3‐transfected hepatocytes had survived in syngeneic and allogeneic recipients. AdE3 expression did not reduce expression of MHC class I on the surfaces of donor hepatocytes. Consistent with this, the in vivo cytotoxic cell–mediated alloresponse was attenuated but not abolished in recipients of AdE3‐transfected allogeneic hepatocytes. In contrast, graft survival correlated with a marked reduction in cell‐surface localization of Fas receptor in the transplanted cells and inhibition of Fas‐mediated apoptosis, which are related to the antiapoptotic functions of the AdE3 proteins. CONCLUSION:AdE3 gene products prevent hepatocyte allograft rejection mainly by protecting the cells from the effector limb of the host immune response and could be used as a tool to facilitate allogeneic hepatocyte transplantation. (HEPATOLOGY 2007;45:755–766.)
Patterns of mitochondrial membrane remodeling parallel functional adaptations to thermal stress

ABSTRACT The effect of temperature on mitochondrial performance is thought to be partly due to its effect on mitochondrial membranes. Numerous studies have shown that thermal acclimation and adaptation can alter the amount of inner-mitochondrial membrane (IMM), but little is known about the capacity of organisms to modulate mitochondrial membrane composition. Using northern and southern subspecies of Atlantic killifish (Fundulus heteroclitus) that are locally adapted to different environmental temperatures, we assessed whether thermal acclimation altered liver mitochondrial respiratory capacity or the composition and amount of IMM. We measured changes in phospholipid headgroups and headgroup-specific fatty acid (FA) remodeling, and used respirometry to assess mitochondrial respiratory capacity. Acclimation to 5°C and 33°C altered mitochondrial respiratory capacity in both subspecies. Northern F. heteroclitus exhibited greater mitochondrial respiratory capacity across acclimation temperatures, consistent with previously observed subspecies differences in whole-organism aerobic metabolism. Mitochondrial phospholipids were altered following thermal acclimation, and the direction of these changes was largely consistent between subspecies. These effects were primarily driven by remodeling of specific phospholipid classes and were associated with shifts in metabolic phenotypes. There were also differences in membrane composition between subspecies that were driven largely by differences in phospholipid classes. Changes in respiratory capacity between subspecies and with acclimation were largely but not completely accounted for by alterations in the amount of IMM. Taken together, these results support a role for changes in liver mitochondrial function in the ectothermic response to thermal stress during both acclimation and adaptation, and implicate lipid remodeling as a mechanism contributing to these changes. Summary: Mitochondrial performance and mitochondrial membrane composition are consistent with thermal acclimation and local adaptation effects on whole-organism thermal tolerance and aerobic metabolism in a eurythermal ectotherm.
Field investigation of preferential fissure flow paths with hydrochemical analysis of small-scale sprinkling experiments

The unsaturated zone largely controls groundwater recharge by buffering precipitation while at the same time providing preferential flow paths for infiltration. The importance of preferential flow on landslide hydrology is recognised in the literature; however, its monitoring and quantification remain difficult. This paper presents a combined hydrological and hydrochemical analysis of small-scale sprinkling experiments. It aims at showing the potential of such experiments for studying the spatial differences in dominant hydrological processes within a landslide. This methodology was tested in the highly heterogeneous black marls of the Super-Sauze landslide. The tests were performed in three areas characterised by different displacement rates, surface morphology and local hydrological conditions. Special attention was paid to testing the potential of small-scale sprinkling experiments for identifying and characterising preferential flow patterns and dominant hydrological processes.
Effects of sodium chloride on heat resistance, oxidative susceptibility, motility, biofilm and plaque formation of Burkholderia pseudomallei

Burkholderia pseudomallei is an environmental saprophyte and the causative agent of melioidosis, a severe infectious disease prevalent in tropical areas, including southeast Asia and northern Australia. In Thailand, the highest incidence of melioidosis is in the northeast region, where saline soil and water are abundant. We hypothesized that B. pseudomallei develops an ability to thrive in saline conditions and gains a selective ecological advantage over other soil‐dwelling microorganisms. However, little is known about how an elevated NaCl concentration affects survival and adaptive changes in this pathogen. In this study, we examined the adaptive changes in six isolates of B. pseudomallei after growth in Luria‐Bertani medium containing different concentrations of NaCl at 37°C for 6 hr. The bacteria were then investigated for resistance to heat at 50°C and killing by hydrogen peroxide (H2O2). In addition, flagellar production, biofilm formation, and the plaque formation efficiency of B. pseudomallei after culture in saline conditions were observed. In response to exposure to 150 and 300 mmol L−1 NaCl, all B. pseudomallei isolates showed significantly increased thermal tolerance, oxidative resistance, and plaque‐forming efficiency. However, NaCl exposure notably decreased the number of B. pseudomallei flagella. Taken together, these results provide insight into the adaptations of B. pseudomallei that might be crucial for survival and persistence in the host and/or endemic environments with high salinity.
Expression profiles of circular RNAs in sheep skeletal muscle

Objective Circular RNAs (circRNAs) are a newfound class of non-coding RNA in animals and plants. Recent studies have revealed that circRNAs play important roles in cell proliferation, differentiation, autophagy and apoptosis during development. However, there are few reports about muscle development-related circRNAs in livestock. Methods RNA sequencing analysis was employed to identify and annotate circRNAs from longissimus dorsi of sheep. Reverse transcription followed by real-time quantitative (q) polymerase chain reaction (PCR) analysis verified the presence of these circRNAs. Targetscan7.0 and miRanda were used to analyse the interaction of circRNA-microRNA (miRNA). To investigate the function of circRNAs, an experiment was conducted to perform enrichment analysis hosting genes of circRNAs using gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathways. Results About 75.5 million sequences were obtained from RNA libraries of sheep skeletal muscle. These sequences were mapped to 729 genes in the sheep reference genome. We identified 886 circRNAs, including numerous circular intronic RNAs and exonic circRNAs. Reverse transcription PCR (RT-PCR) and DNA sequencing analysis confirmed the presence of several circRNAs. Real-Time RT-PCR analysis exhibited resistance of sheep circRNAs to RNase R digestion. We found that many circRNAs interacted with muscle-specific miRNAs involved in growth and development of muscle, especially circ776. The GO and KEGG enrichment analysis showed that hosting genes of circRNAs was involved in muscle cell development and signaling pathway. Conclusion The study provides comprehensive expression profiles of circRNAs in sheep skeletal muscle. Our study offers a large number of circRNAs to facilitate a better understanding of their roles in muscle growth. Meanwhile, we suggested that circ776 could be analyzed in future study.