bluuebunny/crossref_metadata_2025 huggingface dataset:
The Global Burden of Surgical Management of Osteoporotic Fractures
Authors: Tarrant Seth M. , Balogh Zsolt J.
Published: February 2020

Osteoporosis is an epidemic in the developed world. Fracture is a major burden associated with osteoporosis. Surgical management is recommended for particular anatomical areas, whilst other fracture patterns have a less defined and controversial role for surgery. This review aims to highlight increase in the global burden of osteoporosis and subsequent fragility fractures. As health and life expectancy improves, osteoporotic fracture fixation will constitute a significant physical and economic burden. The surgical management of osteoporotic fractures involves awareness on all levels from government to the individual, from primary prevention of fracture to surgical aftercare in the community.
Epigenetic crosstalk in chronic infection with HIV-1
Authors: Lange Ulrike C , Verdikt Roxane , Ait-Ammar Amina , Van Lint Carine
Published: February 2020

Human immunodeficiency virus 1 (HIV-1) replicates through the integration of its viral DNA into the genome of human immune target cells. Chronically infected individuals thus carry a genomic burden of virus-derived sequences that persists through antiretroviral therapy. This burden consists of a small fraction of intact, but transcriptionally silenced, i.e. latent, viral genomes and a dominant fraction of defective sequences. Remarkably, all viral-derived sequences are subject to interaction with host cellular physiology at various levels. In this review, we focus on epigenetic aspects of this interaction. We provide a comprehensive overview of how epigenetic mechanisms contribute to establishment and maintenance of HIV-1 gene repression during latency. We furthermore summarize findings indicating that HIV-1 infection leads to changes in the epigenome of target and bystander immune cells. Finally, we discuss how an improved understanding of epigenetic features and mechanisms involved in HIV-1 infection could be exploited for clinical use.
Genome-wide characterization and expression analysis of the auxin response factor (ARF) gene family during melon (Cucumis melo L.) fruit development
Authors: Wu Bei , Wang Lu , Pan Gaoyang , Li Ting , Li Xin , Hao Jinghong
Published: February 2020

ARFs in plants mediate auxin signaling transduction and regulate growth process. To determine genome-wide characterization of ARFs family in melon (Cucumis melo L.), ARFs were identified via analysis of information within the melon genomic database, and bioinformatic analyses were performed using various types of software. Based on different treatment methods involving dipping with the growth regulator Fengchanji No. 2 and artificial pollination, Jingmi No. 11 melon was used as the test material, and melon plants with unpollinated ovaries served as controls. The expression of ARFs during the early development of melon was analyzed via qRT-PCR. Seventeen genes that encode ARF proteins were identified in the melon genome for the first time. The expression of these ARFs differed in different tissues. The expression levels of CmARF2, CmARF16-like, CmARF18-like2, and CmARF19-like were especially high in melon fruits. The expression of ARFs during the early development of melon fruits differed in response to the different treatments, which suggested that CmARF9, CmARF16-like, CmARF19-like, CmARF19, CmARF1, CmARF2, CmARF3, and CmARF5 may be associated with melon fruit growth during early development. Interestingly, the increase in the transverse diameter of fruits treated with growth regulators was significantly greater than that of fruits resulting from artificial pollination, while the increase in the longitudinal diameter of the fruits resulting from artificial pollination was significantly greater.
Wolbachia and Cardinium infection found in threatened unionid species: a new concern for conservation of freshwater mussels?
Authors: Mioduchowska Monika , Katarzyna Zając , Tadeusz Zając , Jerzy Sell
Published: February 2020

Endosymbiotic bacterial species that manipulate host biology, reproduction and mitochondrial genetic diversity have been identified in many metazoans, especially terrestrial arthropods. Until now, the hypothesis that Wolbachia or other bacterial endosymbiont might be absent in mollusks has remained unexplored. We present here preliminary data on bacterial communities in a freshwater mussel Unio crassus—species with doubly uniparental inheritance of mtDNA (DUI). Next generation sequencing of 16S rRNA bacterial gene fragment allowed to identify endosymbiotic Cardinium and sequences that were classified to the order Rickettsiales. Finally, we discovered Wolbachia and confirmed Cardinium infection of Unio crassus using bacterial species-specific primers. Discovering Wolbachia and Cardinium infections in Unio crassus opens new opportunities of further investigations in the second largest animal phylum on Earth, very diversified phylogenetically, widespread geographically and inhabiting many environs, including freshwater, inhabited by the most threatened molluscan species. Considering the problems caused by endosymbionts identified in arthropods, the presence of endosymbiotic factor implies possibility of their influence on taxonomy of threatened unionids, on the results of studies of genetic diversity and proper conservation planning.
Are infectious diseases risk factors for sarcoidosis or a result of reverse causation? Findings from a population-based nested case–control study
Authors: Rossides Marios , Kullberg Susanna , Askling Johan , Eklund Anders , Grunewald Johan , Di Giuseppe Daniela , Arkema Elizabeth V.
Published: February 2020

Findings from molecular studies suggesting that several infectious agents cause sarcoidosis are intriguing yet conflicting and likely biased due to their cross-sectional design. As done in other inflammatory diseases to overcome this issue, prospectively-collected register data could be used, but reverse causation is a threat when the onset of disease is difficult to establish. We investigated the association between infectious diseases and sarcoidosis to understand if they are etiologically related. We conducted a nested case–control study (2009–2013) using incident sarcoidosis cases from the Swedish National Patient Register (n = 4075) and matched general population controls (n = 40,688). Infectious disease was defined using inpatient/outpatient visits and/or antimicrobial dispensations starting 3 years before diagnosis/matching. Adjusted odds ratios (aOR) of sarcoidosis were estimated using conditional logistic regression and tested for robustness assuming the presence of reverse causation bias. The aOR of sarcoidosis associated with history of infectious disease was 1.19 (95% confidence interval [CI] 1.09, 1.29; 21% vs. 16% exposed cases and controls, respectively). Upper respiratory and ocular infections conferred the highest OR. Findings were similar when we altered the infection definition or varied the infection-sarcoidosis latency period (1–7 years). In bias analyses assuming one in 10 infections occurred because of preclinical sarcoidosis, the observed association was completely attenuated (aOR 1.02; 95% CI 0.90, 1.15). Our findings, likely induced by reverse causation due to preclinical sarcoidosis, do not support the hypothesis that common symptomatic infectious diseases are etiologically linked to sarcoidosis. Caution for reverse causation bias is required when the real disease onset is unknown.
The one player guessing game: a diagnosis on the relationship between equilibrium play, beliefs, and best responses
Authors: Bosch-Rosa Ciril , Meissner Thomas
Published: February 2020

Experiments involving games have two dimensions of difficulty for subjects in the laboratory. One is understanding the rules and structure of the game and the other is forming beliefs about the behavior of other players. Typically, these two dimensions cannot be disentangled as belief formation crucially depends on the understanding of the game. We present the one-player guessing game, a variation of the two-player guessing game (Grosskopf and Nagel 2008), which turns an otherwise strategic game into an individual decision-making task. The results show that a majority of subjects fail to understand the structure of the game. Moreover, subjects with a better understanding of the structure of the game form more accurate beliefs of other player’s choices, and also better-respond to these beliefs.
Current status and prospects of plant biotechnology in Kazakhstan
Authors: Zhambakin Kabyl , Zhapar Kuanysh
Published: February 2020

Biotechnological methods are becoming an integral part of biological research. This review presents some of the most significant scientific results of Kazakhstan biologists in the field of plant biotechnology over the past 10 years. One of the recent important areas of application of biotechnological methods is the conservation and study of plant genetic resources and bioremediation. Studies on the flora lead to the identification of new sources of previously unknown biologically active materials, especially among wild plants growing in Kazakhstan. In addition, various biotechnological approaches are used to increase the efficiency of breeding practices for the production of new crop varieties.
“I am Primarily Paid for Publishing…”: The Narrative Framing of Societal Responsibilities in Academic Life Science Research
Authors: Sigl Lisa , Felt Ulrike , Fochler Maximilian
Published: February 2020

Building on group discussions and interviews with life science researchers in Austria, this paper analyses the narratives that researchers use in describing what they feel responsible for, with a particular focus on how they perceive the societal responsibilities of their research. Our analysis shows that the core narratives used by the life scientists participating in this study continue to be informed by the linear model of innovation. This makes it challenging for more complex innovation models [such as responsible research and innovation (RRI)] to gain ground in how researchers make sense of and conduct their research. Furthermore, the paper shows that the life scientists were not easily able to imagine specific practices that would address broader societal concerns and thus found it hard to integrate the latter into their core responsibilities. Linked to this, researchers saw institutional reward structures (e.g. evaluations, contractual commitments) as strongly focused on scientific excellence (“I am primarily paid for publishing…”). Thus, they saw reward structures as competing with—rather than incentivising—broader notions of societal responsibility. This narrative framing of societal responsibilities is indicative of a structural marginalisation of responsibility practices and explains the claim, made by many researchers in our sample, that they cannot afford to spend time on such practices. The paper thus concludes that the core ideas of RRI stand in tension with predominant narrative and institutional infrastructures that researchers draw on to attribute meaning to their research practices. This suggests that scientific institutions (like universities, professional communities or funding institutions) still have a core role to play in providing new and context-specific narratives as well as new forms of valuing responsibility practices.
First-line endocrine therapy for postmenopausal patients with hormone receptor-positive, HER2-negative metastatic breast cancer: a systematic review and meta-analysis
Authors: Shimoi Tatsunori , Sagara Yasuaki , Hara Fumikata , Toyama Tatsuya , Iwata Hiroji
Published: February 2020

Background

In establishing the 2018 Breast Cancer Practice Guidelines of the Japan Breast Cancer Society, we explored the optimal first-line endocrine therapy for advanced postmenopausal hormone receptor-positive breast cancer.

Methods

We performed a systematic review of relevant reports from randomized-controlled studies published prior to November 2016 found using medical journal search engines. The main outcomes which we evaluated were progression-free survival (PFS), objective response rate (ORR), disease control rate (CBR), and toxicity.

Results

Four controlled trials comparing aromatase inhibitors (AI) and cyclin-dependent kinase (CDK)4/6 inhibitor combination therapy to AI monotherapy, and two controlled trials comparing anastrozole to fulvestrant 500 mg were analyzed. AI/CDK4/6 inhibitor combination therapy significantly improved PFS (Risk Ratio: 0.67, 95%CI 0.60–0.73), increased ORR (Risk Difference: 0.11, 95% CI 0.07–0.16), and increased CBR (Risk Difference: 0.11, 95% CI 0.07–0.15), compared with AI monotherapy. Patients who received this combination therapy had a higher grade ≥ 3 adverse event rate more than those who received AI monotherapy (Risk Difference: 43%, 95%CI: 0.39–0.47). Fulvestrant 500 mg alone significantly improved PFS (risk ratio: 0.85, 95%CI 0.72–0.98), but ORR and CBR were similar to those of anastrozole alone.

Conclusion

In the first-line treatment for advanced postmenopausal hormone receptor-positive breast cancer, a combination therapy of CDK4/6 inhibitors and AI showed significant improvement of PFS, ORR, and CBR but with significant increased toxicities compared with AI alone. Fulvestrant 500 mg monotherapy significantly prolonged PFS compared with AI monotherapy. We must wait for the results of the studies with longer follow-up period.
Hydrochemical characteristics of the groundwater in Trans-Yamuna Alluvial aquifer, Palwal District, Haryana, India
Authors: Ahmad Sarfaraz , Singh Nepal , Mazhar Syeda Nigar
Published: February 2020

Hydrochemical processes have been evaluated for the groundwater regime in Trans-Yamuna alluvial aquifer, Palwal District, Haryana. The groundwater belongs to the Na+–Mg+2 and Cl−–SO4−2 facies, and solute acquisition processes indicated that the rock weathering/evaporation is a major mechanism that characterizes the hydrochemistry. It is also indicated that dissolution and reverse ion exchange processes are playing a major role in determining the groundwater chemistry in the study area. The varied climate in Ganga plains is responsible for the importance of different hydrogeochemical processes that impact on hydrochemistry of groundwater. Groundwater quality parameters were tested for drinking and irrigation purposes. Water quality index shows that 13%, 31%, 34% and 21% fall in good, poor, very poor and unsuitable water category, respectively, for drinking purposes. On the basis of SAR and Na%, the groundwater indicated that it is safe for irrigation purposes. But high TDS of few samples suggested the salinity hazard while using it for irrigation purposes for a longer period.
Formation mechanism and height calculation of the caved zone and water-conducting fracture zone in solid backfill mining
Authors: Li Lei , Li Fengming , Zhang Yong , Yang Daming , Liu Xue
Published: February 2020

To study the heights of the caved zone and water-conducting fracture zone in backfill mining, the failure mechanism of strata during backfill mining was analyzed, and a method for determining the heights of the two zones was proposed based on key strata theory. The movement and failure regularity of the strata above the backfilling panel were revealed through numerical simulation. Considering the geologic conditions of the CT101 backfilling panel, the height of the fracture zone was determined using the proposed method along with empirical calculation, numerical simulation, and borehole detection. The results of the new calculation method were similar to in situ measurements. The traditional empirical formula, which is based on the equivalent mining height model, resulted in large errors during calculation. The findings indicate the reliability of the new method and demonstrate its significance for creating reference data for related studies.
The Fubini Product and Its Applications
Authors: Uuye Otgonbayar , Zacharias Joachim
Published: February 2020

The Fubini product of operator spaces provides a powerful tool for analysing properties of tensor products. In this paper, we apply the theory of Fubini products to the problem of computing invariant parts of dynamical systems. In particular, we study the invariant translation approximation property of discrete groups.
Respiratory viruses in the patient environment
Authors: Phan Linh T. , Sweeney Dagmar M. , Maita Dayana , Moritz Donna C. , Bleasdale Susan C. , Jones Rachael M. ,   for the CDC Prevention Epicenters Program
Published: February 2020

Objective:

To characterize the presence and magnitude of viruses in the air and on surfaces in the rooms of hospitalized patients with respiratory viral infections, and to explore the association between care activities and viral contamination.

Design:

Prospective observational study.

Setting:

Acute-care academic hospital.

Participants:

In total, 52 adult patients with a positive respiratory viral infection test within 3 days of observation participated. Healthcare workers (HCWs) were recruited in staff meetings and at the time of patient care, and 23 wore personal air-sampling devices.

Methods:

Viruses were measured in the air at a fixed location and in the personal breathing zone of HCWs. Predetermined environmental surfaces were sampled using premoistened Copan swabs at the beginning and at the end of the 3-hour observation period. Preamplification and quantitative real-time PCR methods were used to quantify viral pathogens.

Results:

Overall, 43% of stationary and 22% of personal air samples were positive for virus. Positive stationary air samples were associated with ≥5 HCW encounters during the observation period (odds ratio [OR], 5.3; 95% confidence interval [CI], 1.2–37.8). Viruses were frequently detected on all of the surfaces sampled. Virus concentrations on the IV pole hanger and telephone were positively correlated with the number of contacts made by HCWs on those surfaces. The distributions of influenza, rhinoviruses, and other viruses in the environment were similar.

Conclusions:

Healthcare workers are at risk of contracting respiratory virus infections when delivering routine care for patients infected with the viruses, and they are at risk of disseminating virus because they touch virus-contaminated fomites.
Urbanization, Citizenship, and Economic Growth in the Long Run
Authors: Goldstone Jack A.
Published: February 2020

Maarten Prak argues that urban citizen associations remained vigorous in the West from the Middle Ages through the Industrial Revolution, and that their support for commercial activity helped bring about that Revolution. That is half correct. During the two thousand years from 300 BC to 1750 AD, numerous societies had similar peaks of urbanization, commercial activity, and per capita income (often approaching, but never exceeding, a “peak pre-industrial income” level of roughly $1,900 in 1990 international dollars.) Vigorous urban societies produced repeated episodes of comparably high incomes, not ever-escalating levels of GDP/capita. What produced the breakthrough of the Industrial Revolution was a particular manifestation of urban citizenship that occurred only in Great Britain – the victory of Parliament over royal authority creating exceptional religious and intellectual freedom and institutionalized pluralism. This was not common to urbanized, commercial societies except in rare periods; only in Britain did urban associations and culture blend with scientific culture, producing a broad surge of scientific and technical activity that overcame the prior limits on organic societies.
The mobilities of care in later life: exploring the relationship between caring and mobility in the lives of older people
Authors: Croucher Karen , Gilroy Rose , Bevan Mark , Attuyer Katia
Published: February 2020

There has been a renewed call for a revaluing of informal caring in order to counter the way that caring is undervalued, taken for granted and invisible. Travel is one area where a detailed critique of this issue has emerged with the concept of ‘mobility of care’, however, this concept has only been applied in relation to younger age groups, and our understanding of mobilities of care in later life remains underdeveloped. By ‘mobilities of care’ we mean journeys made for the purpose of giving and receiving informal care and support. This paper draws on the mobility narratives of 99 older people (aged 55 and above) living in three locations in the North of England who participated in a two-year qualitative longitudinal study that explored the inter-play between mobility, wellbeing and life transitions. We focused on the experience of managing life transitions rather than assume that chronology per se determines wellbeing. Narratives of ageing emphasise the importance of getting out and about, and being socially connected active citizens. Our study demonstrates that for many older people getting out and about is not for leisure or utility purposes but to give support and care. As such, these journeys have a particular significance in the lives of older people and in the construction of roles, meaning and identity in later life.
Improved Semi-Bit Differential Acquisition Method for Navigation Bit Sign Transition and Code Doppler Compensation in Weak Signal Environment
Authors: Nezhadshahbodaghi M. , Mosavi M. R. , Rahemi N.
Published: February 2020

The presence of code Doppler and navigation bit sign transitions means that the acquisition of global positioning system (GPS) signals is difficult in weak signal environments where the output signal-to-noise ratio (SNR) is significantly reduced. Post-correlation techniques are typically utilised to solve these problems. Despite the advantages of these techniques, the post-correlation techniques suffer from problems caused by the code Doppler and the navigation bit sign transitions. We present an improved semi-bit differential acquisition method which can improve the code Doppler and the bit sign transition issues in the post-correlation techniques. In order to overcome the phenomenon of navigation bit sign transitions, the proposed method utilises the properties of the navigation bit. Since each navigation bit takes as long as 20 ms, there would be 10 ms correlations duration integration time between the received signal and the local coarse/acquisition (C/A) code in which the navigation bit sign transitions will not occur. Consequently, this problem can be cancelled by performing 10 ms correlations in even and odd units separately. Compensation of the code Doppler is also accomplished by shifting the code phase of the correlation results. To validate the performance of our suggested method, simulations are performed based on three data sets. The results show that the quantity of required input SNR to detect at least four satellites in the proposed method is − 48·3 dB, compared with − 20 dB and − 9 dB, respectively, in traditional differential and non-coherent methods.
The Populist Pope?: Politics, Religion, and Pope Francis
Authors: McCormick William
Published: February 2020

While religion and democracy have been intertwined since World War II, scholars have made little of the connections between religion and populism, largely conceptualizing religion as a tool of populism. In this paper, however, I argue that Pope Francis' deployment of Catholicism resists such instrumentalization by populist politics, and offers resources for political ills underlying populism. I show that Francis' focus on the people allows him to capitalize on populist currents in global politics, while also reforming those currents into something more constructive than populism. I further explore how his political theology and institutional autonomy render his thought and example relatively impervious to appropriation by political actors.
Ion‐Scale Flux Rope Observed inside a Hot Flow Anomaly
Authors: Bai Shi‐Chen , Shi Quanqi , Liu Terry Z. , Zhang Hui , Yue Chao , Sun Wei‐Jie , Tian Anmin , Degeling Alexander W. , Bortnik Jacob , Rae I. Jonathan , Wang Mengmeng
Published: February 2020

We report an earthward moving ion‐scale flux rope embedded within the trailing edge of a hot flow anomaly (HFA) observed by the Magnetospheric Multiscale satellite constellation on 17 December 2016 upstream of Earth's quasi‐parallel bow shock. The driver of the HFA, a tangential discontinuity, was observed by the Wind spacecraft without flux rope signatures around it in the solar wind. This suggests that the earthward moving flux rope was generated inside the HFA. This ion‐scale flux rope is not a force free structure and expands due to a strong magnetic pressure gradient force. Solar wind ions are decelerated inside the flux rope by the static electric field likely caused by the charge separation of solar wind particles. Our observations imply that magnetic reconnection may have occurred inside the HFA. Reconnection and flux ropes may play a role in particle acceleration/heating inside foreshock transients.
Venus: A Thick Basal Magma Ocean May Exist Today
Authors: O'Rourke J. G.
Published: February 2020

Basal magma oceans develop in Earth and Venus after accretion as their mantles solidify from the middle outward. Fractional crystallization of the basal mantle is buffered by the core and radiogenic and latent heat in the magma ocean. Previous studies showed that Earth's basal magma ocean would have solidified after two or three billion years. Venus has a relatively hot interior that cools slowly in the absence of plate tectonics, which reduces heat flow through the solid mantle. Consequentially, the basal magma ocean could remain as thick as ~200–400 km today. Vigorous convection of liquid silicates could power a global magnetic field until recently while a core‐hosted dynamo is suppressed. The basal magma ocean may be a hidden reservoir of potassium and other incompatible elements. A high tidal Love number could reveal a basal magma ocean and would definitively establish that the core is at least partially liquid.
Three dimensional Gravity Local Inversion Across the Area Struck by the 2016–2017 Seismic Events in Central Italy
Authors: Mancinelli Paolo , Pauselli Cristina , Fournier Dominique , Fedi Maurizio , Minelli Giorgio , Barchi Massimiliano R.
Published: February 2020

In this work, the crustal volume struck by the 2016–2017 seismic sequence in Central and Northern Apennines is investigated using constrained 3‐D inversion of the gravity anomalies. In order to focus on the area comprising the two mainshocks of the sequence, we perform a regional field removal on the data as a preprocessing step. This residual data set is then inverted into a 3‐D density contrast model. We perform a series of inversions to test different geological scenarios and parameters, with increasing complexity in the reference geometries. We first test a model comprising turbidites, carbonates and evaporites, and basement and then introduce a low‐density layer at the top of the basement. The geometries are obtained in agreement with the available geological and geophysical information in the area. We found that the density distribution with depth is compatible with previous models. Moreover, results support the hypothesis based on borehole evidence of a low‐density upper basement across the entire area, possibly consisting of low‐grade metamorphic rocks (phyllites). Finally, we compare our modeling results to the spatial distribution at depth of major seismic events between August and November 2016. These events appear to be concentrated within the denser units at both shallow and deep locations, while the deeper events often occur in a region of major density contrast corresponding to the top of the basement.
Chemo‐mechanical Alterations Induced From CO2 Injection in Carbonate‐Cemented Sandstone: An Experimental Study at 71 °C and 29 MPa
Authors: Wu Z. , Luhmann A. J. , Rinehart A. J. , Mozley P. S. , Dewers T. A. , Heath J. E. , Majumdar B. S.
Published: February 2020

Carbon capture, utilization, and storage may lead to mechanical degradation of the subsurface reservoir from fluid‐rock interaction, which could lead to wellbore instability or reservoir compaction. To better understand potential relationship between mechanical degradation with various carbonate cement textures and compositions in sandstone reservoirs, six flow‐through experiments were conducted. Formation water (TDS = 5,390 mg/L) enriched with CO2 flowed through two types of Pennsylvanian Morrow B Sandstone: an ankerite‐siderite‐cemented sandstone (disseminated cement texture) and a calcite‐cemented sandstone (poikilotopic cement texture). The experiments produced little change in permeability in the ankerite‐siderite‐cemented sandstone, but permeability increased up to more than 1 order of magnitude in the calcite‐cemented sandstone. Ultrasonic measurements and cylinder‐splitting tests (also known as Brazilian tests) suggested negligible mechanical degradation of the ankerite‐siderite‐cemented sandstone. Variable changes, with significant mechanical degradation in the static moduli, were observed in the calcite‐cemented sandstone. Thus, dissolution of the disseminated ankerite‐siderite cement (0.28–0.30%) had minimal impact on modifying the flow network and the mechanical integrity of the sandstone, whereas dissolution of the poikilotopic calcite cement (0.89–1.13%, quantified with fluid chemistry and visualized with X‐ray microcomputed tomography) impacted the mechanical strength of the sandstone by disconnecting framework grains. With the high water‐to‐rock mass ratios (7.3–8.2) and number of pore volumes (147–675) employed in these experiments, potential risks are most relevant to regions near injection wells. Ultimately, the chemo‐mechanical effects induced by CO2 injection are strongly influenced by the cement texture and composition and the burial history of the reservoir rock.
Features of Slope Intrusion Mesoscale Eddies in the Northern South China Sea
Authors: Su Danyi , Lin Pengfei , Mao Huabin , Wu Jiaxue , Liu Hailong , Cui Yongsheng , Qiu Chunhua
Published: February 2020

Some mesoscale eddies intrude over the continental slope in the northern South China Sea, supporting cross‐shelf matter transport. We investigated the characteristics, the intruding tracks and formation mechanisms, of slope intrusion mesoscale eddies using satellite altimeter data and model outputs. In total, 36 and 22 slope intrusion anticyclonic and cyclonic eddies (SAEs/SCEs) are found, respectively. Slope intrusion eddies have longer lifetimes (~58 days), smaller size (~110 km), and greater eddy kinetic energy and vorticity compared to ordinary eddies but are more unstable and more easily deformed during their life cycles. The statistical results show that more slope intrusion eddies are generated during winter than other seasons. It is found that slope intrusion eddies mainly propagate westward/northwestward, and southwestward along the continental slope and shelf. Eddy intrusions occur mainly near the Dongsha Islands, east of Hainan, and north of the Xisha Islands. SAEs continue to propagate onshore after arrival at the continental slope, while SCEs dissipate more quickly. Using mooring data, we found that eddy‐ambient flow interaction could cause the differences between SAEs and SCEs around the Dongsha Islands. Energy conversion was analyzed in these three regions using numerical products. During intrusion, eddies lose eddy kinetic energy and ambient flows gain energy.
Vertical Turbulent Cooling of the Mixed Layer in the Atlantic ITCZ and Trade Wind Regions
Authors: Foltz Gregory R. , Hummels Rebecca , Dengler Marcus , Perez Renellys C. , Araujo Moacyr
Published: February 2020

The causes of the seasonal cycle of vertical turbulent cooling at the base of the mixed layer are assessed using observations from moored buoys in the tropical Atlantic Intertropical Convergence Zone (ITCZ) (4°N, 23°W) and trade wind (15°N, 38°W) regions together with mixing parameterizations and a one‐dimensional model. At 4°N the parameterized turbulent cooling rates during 2017–2018 and 2019 agree with indirect estimates from the climatological mooring heat budget residual: both show mean cooling of 25–30 W m
during November–July, when winds are weakest and the mixed layer is thinnest, and 0–10 W m
during August–October. Mixing during November–July is driven by variability on multiple time scales, including subdiurnal, near‐inertial, and intraseasonal. Shear associated with tropical instability waves (TIWs) is found to generate mixing and monthly mean cooling of 15–30 W m
during May–July in 2017 and 2019. At 15°N the seasonal cycle of turbulent cooling is out of phase compared to 4°N, with largest cooling of up to 60 W m
during boreal fall. However, the relationships between wind speed, mixed layer depth, and turbulent mixing are similar: weaker mean winds and a thinner mixed layer in the fall are associated with stronger mixing and turbulent cooling of SST. These results emphasize the importance of seasonal modulations of mixed layer depth at both locations and shear from TIWs at 4°N.
Does the Mass Balance of the Reactive Tracers Resazurin and Resorufin Close at the Microbial Scale?
Authors: Dallan Eleonora , Regier Peter , Marion Andrea , González‐Pinzón Ricardo
Published: February 2020

Resazurin (Raz) is a phenoxazine dye that can be reduced irreversibly to the daughter compound resorufin (Rru) by aerobic respiration. Previous hydrologic studies using the Raz‐Rru reactive tracer system to quantify water‐sediment interactions and metabolic activity have reported that dilution‐corrected masses of Raz and Rru recovered are smaller than the mass of Raz injected. This lack of mass balance closure has been reported as a nonideality of this tracer system and, to date, it is still unclear what drives incomplete recovery. We used controlled laboratory experiments varying the initial concentrations of Raz, the duration of the experiments, and the type of microbial communities present to quantify mass balances of Raz and Rru under conditions that removed other suspected causes of incomplete recovery in field experiments, i.e., sorption to sediments and photodecay. We used the summation of Raz and Rru concentrations over time to assess mass recovery and variability and found mass recoveries in the range of 85.6–110.4%, with a maximum standard deviation of 7.5%. In three of the four experiments, no strong temporal trend in mass recovery is present. In an experiment with Bacillus subtilis bacteria, lower recovery and evidence of a temporal trend in recovery only occurred after 13 hr past the complete transformation of Raz (i.e., beyond the duration of most field experiments). These results suggest that the lack of mass recovery in field studies is likely associated with physical or chemical mechanisms rather than biological interactions with the Raz‐Rru tracer system.
Active sulfur cycling in the terrestrial deep subsurface
Authors: Bell Emma , Lamminmäki Tiina , Alneberg Johannes , Andersson Anders F , Qian Chen , Xiong Weili , Hettich Robert L , Frutschi Manon , Bernier-Latmani Rizlan
Published: February 2020

The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. We investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.
Refined spatial temporal epigenomic profiling reveals intrinsic connection between PRDM9-mediated H3K4me3 and the fate of double-stranded breaks
Authors: Chen Yao , Lyu Ruitu , Rong Bowen , Zheng Yuxuan , Lin Zhen , Dai Ruofei , Zhang Xi , Xie Nannan , Wang Siqing , Tang Fuchou , Lan Fei , Tong Ming-Han
Published: February 2020

Meiotic recombination is initiated by the formation of double-strand breaks (DSBs), which are repaired as either crossovers (COs) or noncrossovers (NCOs). In most mammals, PRDM9-mediated H3K4me3 controls the nonrandom distribution of DSBs; however, both the timing and mechanism of DSB fate control remain largely undetermined. Here, we generated comprehensive epigenomic profiles of synchronized mouse spermatogenic cells during meiotic prophase I, revealing spatiotemporal and functional relationships between epigenetic factors and meiotic recombination. We find that PRDM9-mediated H3K4me3 at DSB hotspots, coinciding with H3K27ac and H3K36me3, is intimately connected with the fate of the DSB. Our data suggest that the fate decision is likely made at the time of DSB formation: earlier formed DSBs occupy more open chromatins and are much more competent to proceed to a CO fate. Our work highlights an intrinsic connection between PRDM9-mediated H3K4me3 and the fate decision of DSBs, and provides new insight into the control of CO homeostasis.
Nanocatalytic activity of clean-surfaced, faceted nanocrystalline gold enhances remyelination in animal models of multiple sclerosis
Authors: Robinson Andrew P. , Zhang Joanne Zhongyan , Titus Haley E. , Karl Molly , Merzliakov Mikhail , Dorfman Adam R. , Karlik Stephen , Stewart Michael G. , Watt Richard K. , Facer Benjin D. , Facer Jon D. , Christian Noah D. , Ho Karen S. , Hotchkin Michael T. , Mortenson Mark G. , Miller Robert H. , Miller Stephen D.
Published: February 2020

Development of pharmacotherapies that promote remyelination is a high priority for multiple sclerosis (MS), due to their potential for neuroprotection and restoration of function through repair of demyelinated lesions. A novel preparation of clean-surfaced, faceted gold nanocrystals demonstrated robust remyelinating activity in response to demyelinating agents in both chronic cuprizone and acute lysolecithin rodent animal models. Furthermore, oral delivery of gold nanocrystals improved motor functions of cuprizone-treated mice in both open field and kinematic gait studies. Gold nanocrystal treatment of oligodendrocyte precursor cells in culture resulted in oligodendrocyte maturation and expression of myelin differentiation markers. Additional in vitro data demonstrated that these gold nanocrystals act via a novel energy metabolism pathway involving the enhancement of key indicators of aerobic glycolysis. In response to gold nanocrystals, co-cultured central nervous system cells exhibited elevated levels of the redox coenzyme nicotine adenine dinucleotide (NAD+), elevated total intracellular ATP levels, and elevated extracellular lactate levels, along with upregulation of myelin-synthesis related genes, collectively resulting in functional myelin generation. Based on these preclinical studies, clean-surfaced, faceted gold nanocrystals represent a novel remyelinating therapeutic for multiple sclerosis.
HemoSYS: A Toolkit for Image-based Systems Biology of Tumor Hemodynamics
Authors: Senarathna Janaka , Prasad Ayush , Bhargava Akanksha , Gil Stacy , Thakor Nitish V. , Pathak Arvind P.
Published: February 2020

Abnormal tumor hemodynamics are a critical determinant of a tumor’s microenvironment (TME), and profoundly affect drug delivery, therapeutic efficacy and the emergence of drug and radio-resistance. Since multiple hemodynamic variables can simultaneously exhibit transient and spatiotemporally heterogeneous behavior, there is an exigent need for analysis tools that employ multiple variables to characterize the anomalous hemodynamics within the TME. To address this, we developed a new toolkit called HemoSYS for quantifying the hemodynamic landscape within angiogenic microenvironments. It employs multivariable time-series data such as in vivo tumor blood flow (BF), blood volume (BV) and intravascular oxygen saturation (Hbsat) acquired concurrently using a wide-field multicontrast optical imaging system. The HemoSYS toolkit consists of propagation, clustering, coupling, perturbation and Fourier analysis modules. We demonstrate the utility of each module for characterizing the in vivo hemodynamic landscape of an orthotropic breast cancer model. With HemoSYS, we successfully described: (i) the propagation dynamics of acute hypoxia; (ii) the initiation and dissolution of distinct hemodynamic niches; (iii) tumor blood flow regulation via local vasomotion; (iv) the hemodynamic response to a systemic perturbation with carbogen gas; and (v) frequency domain analysis of hemodynamic heterogeneity in the TME. HemoSYS (freely downloadable via the internet) enables vascular phenotyping from multicontrast in vivo optical imaging data. Its modular design also enables characterization of non-tumor hemodynamics (e.g. brain), other preclinical disease models (e.g. stroke), vascular-targeted therapeutics, and hemodynamic data from other imaging modalities (e.g. MRI).
Genome-wide screening of lipoproteins in Actinobacillus pleuropneumoniae identifies three antigens that confer protection against virulent challenge
Authors: Cao Yurou , Gao Lulu , Zhang Li , Zhou Lixiang , Yang Jihong , Deng Lingfu , Zhao Jin , Qi Chao , Liu Jinlin
Published: February 2020

Actinobacillus pleuropneumoniaeis an important veterinary pathogen that causes porcine pleuropneumonia. Lipoproteins of bacterial pathogens play pleiotropic roles in the infection process. In addition, many bacterial lipoproteins are antigenic and immunoprotective. Therefore, characterization of lipoproteins is a promising strategy for identification of novel vaccine candidates or diagnostic markers. We cloned 58 lipoproteins fromA.pleuropneumoniaeJL03 (serovar 3) and expressed them inEscherichia coli. Five proteins with strong positive signals in western blotting analysis were used to immunize mice. These proteins elicited significant antibody responses, and three of them (APJL_0922, APJL_1380 and APJL_1976) generated efficient immunoprotection in mice against lethal heterologous challenge withA.pleuropneumoniae4074 (serovar 1), both in the active and passive immunization assays. Then immunogenicity of these three lipoproteins (APJL_0922, APJL_1380 and APJL_1976) were further tested in pigs. Results showed that these proteins elicited considerable humoral immune responses and effective protective immunity against virulentA.pleuropneumoniaechallenge. Our findings suggest that these three novel lipoproteins could be potential subunit vaccine candidates.
A secreted protein of 15 kDa plays an important role in Phytophthora palmivora development and pathogenicity
Authors: Pettongkhao Sittiporn , Navet Natasha , Schornack Sebastian , Tian Miaoying , Churngchow Nunta
Published: February 2020

Phytophthora palmivorais a destructive oomycete plant pathogen with a wide host range. So far, little is known about the factors governing its infection structure development and pathogenicity. From the culture filtrate of aP. palmivorastrain isolated from papaya, we identified a secreted glycoprotein of 15 kDa, designated as Ppal15kDa, using liquid chromatography tandem mass spectrometry. Two gene variants,Ppal15kDaAandPpal15kDaBwere amplified from aP. palmivorapapaya isolate. Transient expression of both variants inNicotiana benthamianaby agroinfiltration enhancedP. palmivorainfection. SixPpal15kDamutants with diverse mutations were generated via CRISPR/Cas9-mediated gene editing. All mutants were compromised in infectivity onN. benthamianaand papaya. Two mutants with allPpal15kDacopies mutated almost completely lost pathogenicity. The pathogenicity of the other four containing at least one wild-type copy ofPpal15kDawas compromised at varying levels. The mutants were also affected in development as they produced smaller sporangia, shorter germ tubes, and fewer appressoria. The affected levels in development corresponded to the levels of reduction in pathogenicity, suggesting that Ppal15kDa plays an important role in normal development ofP. palmivorainfection structures. Consistent with its role in infection structure development and pathogenicity,Ppal15kDawas found to be highly induced during appressorium formation. In addition, Ppal15kDa homologs are broadly present inPhytophthoraspp., but none were characterized. Altogether, this study identified a novel component involved in development and pathogenicity ofP. palmivoraand possibly otherPhytophthoraspp. known to contain a Ppal15kDa homolog.
Discoidin Domain Receptors, DDR1b and DDR2, Promote Tumour Growth within Collagen but DDR1b Suppresses Experimental Lung Metastasis in HT1080 Xenografts
Authors: Wasinski Benjamin , Sohail Anjum , Bonfil R. Daniel , Kim Seongho , Saliganan Allen , Polin Lisa , Bouhamdan Mohamad , Kim Hyeong-Reh C. , Prunotto Marco , Fridman Rafael
Published: February 2020

The Discoidin Domain Receptors (DDRs) constitute a unique set of receptor tyrosine kinases that signal in response to collagen. Using an inducible expression system in human HT1080 fibrosarcoma cells, we investigated the role of DDR1b and DDR2 on primary tumour growth and experimental lung metastases. Neither DDR1b nor DDR2 expression altered tumour growth at the primary site. However, implantation of DDR1b- or DDR2-expressing HT1080 cells with collagen I significantly accelerated tumour growth rate, an effect that could not be observed with collagen I in the absence of DDR induction. Interestingly, DDR1b, but not DDR2, completely hindered the ability of HT1080 cells to form lung colonies after intravenous inoculation, suggesting a differential role for DDR1b in primary tumour growth and lung colonization. Analyses of tumour extracts revealed specific alterations in Hippo pathway core components, as a function of DDR and collagen expression, that were associated with stimulation of tumour growth by DDRs and collagen I. Collectively, these findings identified divergent effects of DDRs on primary tumour growth and experimental lung metastasis in the HT1080 xenograft model and highlight the critical role of fibrillar collagen and DDRs in supporting the growth of tumours thriving within a collagen-rich stroma.