bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selenocysteine as a Substrate, an Inhibitor and a Mechanistic Probe for Bacterial and Fungal Iron‐Dependent Sulfoxide Synthases
Authors: Goncharenko Kristina V. , Flückiger Sebastian , Liao Cangsong , Lim David , Stampfli Anja R. , Seebeck Florian P. 
Published: September 2019

AbstractSulfoxide synthases are non‐heme iron enzymes that participate in the biosynthesis of thiohistidines, such as ergothioneine and ovothiol A. The sulfoxide synthase EgtB from Chloracidobacterium thermophilum (CthEgtB) catalyzes oxidative coupling between the side chains of N‐α‐trimethyl histidine (TMH) and cysteine (Cys) in a reaction that entails complete reduction of molecular oxygen, carbon–sulfur (C−S) and sulfur–oxygen (S−O) bond formation as well as carbon–hydrogen (C−H) bond cleavage. In this report, we show that CthEgtB and other bacterial sulfoxide synthases cannot efficiently accept selenocysteine (SeCys) as a substrate in place of cysteine. In contrast, the sulfoxide synthase from the filamentous fungus Chaetomium thermophilum (CthEgt1) catalyzes C−S and C−Se bond formation at almost equal efficiency. We discuss evidence suggesting that this functional difference between bacterial and fungal sulfoxide synthases emerges from different modes of oxygen activation.
Participant Engagement in Translational Genomics Research: Respect for Persons—and Then Some
Authors: Childerhose Janet E. , Finnila Candice R. , Yu Joon‐Ho , Koenig Barbara A. , McEwen Jean , Berg Stacey L. , Wilfond Benjamin S. , Appelbaum Paul S. , Brothers Kyle B. 
Published: September 2019

ABSTRACTThe expansion of both formal and informal frameworks of “engaged” research in translational research settings raises emerging and substantial normative concerns. In this article, we draw on findings from a focus group study with members of a national consortium of translational genomic research sites. The goals were to catalog informal participant engagement practices, to explore the perceived roots of these practices and the motivations of research staff members for adopting them, and to reflect on their ethical implications. We learned that participant engagement is a deliberate strategy by research staff members both to achieve instrumental research goals and to “do research differently” in response to past research injustices. While many of the participant engagement practices used in translational genomic research are not new, important insights can be gained through a closer examination of the specific contours of participant engagement in this context. These practices appear to have been shaped by the professional training of genetic counselors and by the interests and needs of participants who enroll in clinical genomics studies. The contours of this contemporary application of engaged research principles have relevance not only to clinical genomics research but also to translational research broadly, particularly for how communities of clinical researchers are interpreting the principle of respect for persons. Our findings invite normative questions about the governance of these practices and sociological questions about whether and how clinical researchers in other professions are also engaging participants in translational research settings.
Passive rewilding may (also) restore phylogenetically rich and functionally resilient forest plant communities
Authors: Morel Loïs , Barbe Lou , Jung Vincent , Clément Bernard , Schnitzler Annik , Ysnel Frédéric 
Published: September 2019

AbstractPassive rewilding is increasingly seen as a promising tool to counterbalance biodiversity losses and recover native forest ecosystems. One key question, crucial to understanding assembly processes and conservation issues underlying land‐use change, is the extent to which functional and phylogenetic diversity may recover in spontaneous recent woodlands. Here, we compared understorey plant communities of recent woodlands (which result from afforestation on agricultural lands during the 20th century) with those of ancient forests (uninterrupted for several centuries) in a hotspot of farmland abandonment in western Europe. We combined taxonomic, functional, and phylogenetic diversity metrics to detect potential differences in community composition, structure (richness, divergence), conservation importance (functional originality and specialization, evolutionary distinctiveness) and resilience (functional redundancy, response diversity). The recent and ancient forests harbored clearly distinct compositions, especially regarding the taxonomic and phylogenetic facets. Recent woodlands had higher taxonomic, functional and phylogenetic richness and a higher evolutionary distinctiveness, whereas functional divergence and phylogenetic divergence were higher in ancient forests. On another hand, we did not find any significant differences in functional specialization, originality, redundancy, or response diversity between recent and ancient forests. Our study constitutes one of the first empirical pieces of evidence that recent woodlands may spontaneously regain plant communities phylogenetically rich and functionally resilient, at least as much as those of ancient relict forests. As passive rewilding is the cheapest restoration method, we suggest that it should be a very useful tool to restore and conserve native forest biodiversity and functions, especially when forest areas are restricted and fragmented.
Ionic current in nanochannels grafted with pH‐responsive polyelectrolyte brushes modeled using augmented strong stretching theory
Authors: Sachar Harnoor Singh , Sivasankar Vishal Sankar , Etha Sai Ankit , Chen Guang , Das Siddhartha 
Published: September 2019

AbstractIn this paper, we provide a theory to quantify the ionic current () in nanochannels grafted with pH‐responsive polyelectrolyte (PE) brushes. We consider the PE brushes to be modeled by our recently proposed augmented strong stretching theory (SST) model that improves the existing SST models by incorporating the effects of excluded volume interactions and an extended mass action law. Use of such augmented SST for this problem implies that this is the first study on computing in PE brush–grafted nanochannels accounting for the appropriate coupled configuration‐electrostatic description of the PE brushes. is obtained as functions of PE brush grafting density, medium pH and salt concentration (), and the density of polyelectrolyte chargeable sites (PECS). For large , increases linearly with (as for such , becomes independent of the PE charge and is dominated by the bulk mobility and number density of the electrolyte ions), whereas is independent of at small (where the electric double layer electrostatics and the total number of ions in the system is dominated by the hydrogen ions). We further witness an enhancement of for smaller pH and larger grafting density at low and moderate , while there is little to no effect of the PECS density on the ionic current except for weakly grafted brushes at low . We anticipate that this study will serve as a theoretical foundation for a large number of applications that are based on the brush‐induced modification of the ionic current in a nanochannel.
Detecting Amphibians in Agricultural Landscapes Using Environmental DNA Reveals the Importance of Wetland Condition
Authors: Ruso Gabrielle E. , Morrissey Christy A. , Hogan Natacha S. , Sheedy Claudia , Gallant Melanie J. , Jardine Timothy D. 
Published: September 2019

Abstract
Amphibians are declining worldwide, in part because of large-scale degradation of habitat from agriculture and pervasive pathogens. Yet a common North American amphibian, the wood frog (Lithobates sylvaticus), ranges widely and persists in agricultural landscapes. Conventional survey techniques rely on visual encounters and dip-netting efforts, but detectability limits the ability to test for the effects of environmental variables on amphibian habitat suitability. We used environmental DNA to determine the presence of wood frogs and an amphibian pathogen (ranavirus) in Prairie Pothole wetlands and investigated the effects of 32 water quality, wetland habitat, and landscape-level variables on frog presence at sites representing different degrees of agricultural intensity. Several wetland variables influenced wood frog presence, the most influential being those associated with wetland productivity (i.e., nutrients), vegetation buffer width, and proportion of the surrounding landscape that is comprised of other water bodies. Wood frog presence was positively associated with higher dissolved phosphorus (&gt;0.4 mg/L), moderate dissolved nitrogen (0.1–0.2 mg/L), lower chlorophyll a (≤15 µg/L), wider vegetation buffers (≥10 m), and more water on the landscape (≥0.25). These results highlight the effects of environmental factors at multiple scales on the presence of amphibians in this highly modified landscape—namely the importance of maintaining wetland water quality, vegetation buffers, and surrounding habitat heterogeneity. Environ Toxicol Chem 2019;38:2750–2763. © 2019 SETAC
Abstract
A graphical summary illustrating that, although detection of wood frogs did not differ between site types (grassland or cropland), a number of factors at different scales influenced detection likelihood (shown as more or fewer frogs). Positive wood frog detection was associated with greater proportion of water and wetlands on the landscape, larger vegetation buffers, higher dissolved phosphorus, a narrow range of dissolved nitrogen, and lower chlorophyll a concentrations. Water bottle image obtained from MindtheGraph.com. Chl. a = chlorophyll a; DN = dissolved nitrogen; DP = dissolved phosphorus.
BitMEX bitcoin derivatives: Price discovery, informational efficiency, and hedging effectiveness
Authors: Alexander Carol , Choi Jaehyuk , Park Heungju , Sohn Sungbin 
Published: September 2019

AbstractBitMEX is the largest unregulated bitcoin derivatives exchange, listing contracts suitable for leverage trading and hedging. Using minute‐by‐minute data, we examine its price discovery and hedging effectiveness. We find that BitMEX derivatives lead prices on major bitcoin spot exchanges. Bid–ask spreads, interexchange spreads, and relative trading volumes are important determinants of price discovery. Further analysis shows that BitMEX derivatives have positive net spillover effects, are informationally more efficient than bitcoin spot prices, and serve as effective hedges against spot price volatility. Our evidence suggests that regulators prioritize the investigation of the legitimacy of BitMEX and its contracts.
Joint analysis of multiple phenotypes using a clustering linear combination method based on hierarchical clustering
Authors: Li Xueling , Zhang Shuanglin , Sha Qiuying 
Published: September 2019

AbstractEmerging evidence suggests that a genetic variant can affect multiple phenotypes, especially in complex human diseases. Therefore, joint analysis of multiple phenotypes may offer new insights into disease etiology. Recently, many statistical methods have been developed for joint analysis of multiple phenotypes, including the clustering linear combination (CLC) method. Due to the unknown number of clusters for a given data, a simulation procedure must be used to evaluate the p‐value of the final test statistic of CLC. This makes the CLC method computationally demanding. In this paper, we use a stopping criterion to determine the number of clusters in the CLC method. We have named our method, hierarchical clustering CLC (HCLC). HCLC has an asymptotic distribution, which is very computationally efficient and makes it applicable for genome‐wide association studies. Extensive simulations together with the COPDGene data analysis have been used to assess the type I error rates and power of our proposed method. Our simulation results demonstrate that the type I error rates of HCLC are effectively controlled in different realistic settings. HCLC either outperforms all other methods or has statistical power that is very close to the most powerful method with which it has been compared.
Deacetylation of LAMP1 drives lipophagy‐dependent generation of free fatty acids by Abrus agglutinin to promote senescence in prostate cancer
Authors: Panda Prashanta Kumar , Patra Srimanta , Naik Prajna Paramita , Praharaj Prakash Priyadarshi , Mukhopadhyay Subhadip , Meher Biswa Ranjan , Gupta Piyush Kumar , Verma Rama S. , Maiti Tapas K. , Bhutia Sujit K. 
Published: September 2019

AbstractTherapy‐induced senescence in cancer cells is an irreversible antiproliferative state, which inhibits tumor growth and is therefore a potent anti‐neoplastic mechanism. In this study, low doses of Abrus agglutinin (AGG)‐induced senescence through autophagy in prostate carcinoma cells (PC3) and inhibited proliferation. The inhibition of autophagy with 3‐methyl adenine reversed AGG‐induced senescence, thus confirming that AGG‐triggered senescence required autophagy. AGG treatment also led to lipophagy‐mediated accumulation of free fatty acids (FFAs), with a concomitant decrease in the number of lipid droplets. Lalistat, a lysosomal acid lipase inhibitor, abrogated AGG‐induced lipophagy and senescence in PC3 cells, indicating that lipophagy is essential for AGG‐induced senescence. The accumulation of FFAs increased reactive oxygen species generation, a known facilitator of senescence, which was also reduced in the presence of lalistat. Furthermore, AGG upregulated silent mating type information regulator 2 homolog 1 (SIRT1), while the presence of sirtinol reduced autophagy flux and the senescent phenotype in the AGG‐treated cells. Mechanistically, AGG‐induced cytoplasmic SIRT1 deacetylated a Lys residue on the cytoplasmic domain of lysosome‐associated membrane protein 1 (LAMP1), an autolysosomal protein, resulting in lipophagy and senescence. Taken together, our findings demonstrate a novel SIRT1/LAMP1/lipophagy axis mediating AGG‐induced senescence in prostate cancer cells.
PLZF suppresses differentiation of mouse spermatogonial progenitor cells via binding of differentiation associated genes
Authors: Song Weixiang , Shi Xinglong , Xia Qin , Yuan Min , Liu Jiaxi , Hao Kunying , Qian Yinjuan , Zhao Xiaodong , Zou Kang 
Published: September 2019

AbstractPromyelocytic leukaemia zinc finger (PLZF) is a key factor in inhibiting differentiation of spermatogonial progenitor cells (SPCs), but the underlying mechanisms are still largely unknown. In this study, the regulation of PLZF on Kit, Stra8, Sohlh2, and Dmrt1 (SPCs differentiation related genes) was investigated. We found some PLZF potential binding sites existed in the promoters of Kit, Stra8, Sohlh2, and Dmrt1. Additionally, the expressions of KIT, STRA8, SOHLH2, and DMRT1 were upregulated when PLZF was knockdown in SPCs. Furthermore, chromatin immunoprecipitation quantitative polymerase chain reaction revealed PLZF directly bound to the promoters of Kit, Stra8, Sohlh2, and Dmrt1. Besides, dual luciferase assay verified PLZF repressed those gene expressions. Collectively, our finding indicate that PLZF binds to the promoter regions of Kit, Stra8, Sohlh2, and Dmrt1 to regulate SPCs differentiation, which facilitate us to further understand the regulatory mechanism of PLZF in SPCs fates.
Hydrodynamics of the bladderwort feeding strike
Authors: Berg Otto , Brown Matthew D. , Schwaner M. Janneke , Hall Maxwell R. , Müller Ulrike K. 
Published: September 2019

AbstractThe aquatic bladderwort Utricularia gibba captures zooplankton in mechanically triggered underwater traps. With characteristic dimensions <1 mm, the trapping structures are among the smallest known that work by suction—a mechanism that would not be effective in the creeping‐flow regime. To understand the adaptations that make suction feeding possible on this small scale, we have measured internal flow speeds during artificially triggered feeding strikes in the absence of prey. These data are compared with complementary analytical models of the suction event: an inviscid model of the jet development in time and a steady‐state model incorporating friction. The initial dynamics are well described by a time‐dependent Bernoulli equation in which the action of the trap door is represented by a step increase in driving pressure. According to this model, the observed maximum flow speed (5.2 m/s) depends only on the pressure difference, whereas the initial acceleration (3 × 104 m/s2) is determined by pressure difference and channel length. Because the terminal speed is achieved quickly (~0.2 ms) and the channel is short, the remainder of the suction event (~2.0 ms) is effectively an undeveloped viscous steady state. The steady‐state model predicts that only 17% of power is lost to friction. The energy efficiency and steady‐state fluid speed decrease rapidly with decreasing channel diameter, setting a lower limit on practical bladderwort size.
Estuarine fish assemblages present a species‐specific difference in the multixenobiotics resistance activity
Authors: Macêdo Anderson Kelvin Saraiva , da Silva Jicaury Roberta Pereira , dos Santos Helio Batista , Thomé Ralph Gruppi , Vendel Ana Lúcia , Amado Enelise Marcelle 
Published: September 2019

AbstractWe investigated the activity of the multixenobiotic resistance (MXR) phenotype, a biological defense system in aquatic organisms, in the fish assemblages of two tropical estuaries with different degrees of environmental impacts, the Paraiba River and Mamanguape River Estuaries. The aim of this work was to compare the activity of the MXR phenotype of different fishes to test the hypothesis that each species has an inherent activity level and to use this activity as a bioindicator of aquatic contamination. We assessed the MXR activity of the gills, using rhodamine B (RB) accumulation assay. The results demonstrated a species‐specific difference in the MXR activity of fishes caught in the same estuarine zone. Also, the pelagic species Eucinostomus melanopterus, Eucinostomus argenteus, and Lutjanus jocu had higher RB accumulation, while the demersal species Sphoeroides testudineus and Sphoeroides greeleyi had the lowest RB accumulation, suggesting that the ecological characteristic of fish in the water column exerts an influence on MXR activity. Besides, we demonstrated the potential of using the gill MXR activity of the key estuarine species, the Brazilian silversides Atherinella brasiliensis, as a tool for biomonitoring estuaries.
Greater neurodegeneration and behavioral deficits after single closed head traumatic brain injury in adolescent versus adult male mice
Authors: Guilhaume‐Correa Fernanda , Cansler Shelby M. , Shalosky Emily M. , Goodman Michael D. , Evanson Nathan K. 
Published: September 2019

AbstractTraumatic brain injury (TBI) is a major public health concern affecting 2.8 million people per year in the United States, of whom about 1 million are children under 19 years old. Animal models of TBI have been developed and used in multiple ages of animals, but direct comparisons of adult and adolescent populations are rare. The current studies were undertaken to directly compare outcomes between adult and adolescent male mice, using a closed head, single‐impact model of TBI. Six‐week‐old adolescent and 9‐week‐old adult male mice were subjected to mild–moderate TBI. Histological measures for neurodegeneration, gliosis, and microglial neuroinflammation, and behavioral tests of locomotion and memory were performed. Adolescent TBI mice have increased mortality (Χ2 = 20.72, p < 0.001) compared to adults. There is also evidence of hippocampal neurodegeneration in adolescents that is not present in adults. Hippocampal neurodegeneration correlates with histologic activation of microglia, but not with increased astrogliosis. Adults and adolescents have similar locomotion deficits after TBI that recover by 16 days postinjury. Adolescents have memory deficits as evidenced by impaired novel object recognition between 3–4 and 4–16 days postinjury (F1,26 = 5.23, p = 0.031) while adults do not. In conclusion, adults and adolescents within a close age range (6–9 weeks) respond to TBI differently. Adolescents are more severely affected by mortality, neurodegeneration, and inflammation in the hippocampus compared to adults. Adolescents, but not adults, have worse memory performance after TBI that lasts at least 16 days postinjury.
All‐trans retinoic acid exposure increases connexin 43 expression in cumulus cells and improves embryo development in bovine oocytes
Authors: Read Casey C. , Dyce Paul W. 
Published: September 2019

AbstractIn developing follicles, cellular coupling within cumulus–oocyte complexes (COCs) creates a functional syncytium allowing for the passage of small molecules. In many species, intercellular coupling between granulosa cells results from the expression of connexin 43 (CX43 or Gja1) and the formation of gap junctional plaques. Previously, our lab has shown that oocytes with a higher developmental potential had higher CX43 expression in their cumulus cells compared with developmentally incompetent oocytes. All‐trans retinoic acid (ATRA) has been shown to increase CX43 expression in several different cell types. In this study we investigated the effect of ATRA treatment, during maturation, on CX43 expression and localization in cumulus cells and the developmental competence of bovine oocytes. COCs and granulosa cells exposed to ATRA during maturation had significantly higher CX43 expression and increased gap junctional coupling, respectively. In addition, there was a significant increase in the maturation, cleavage, and blastocyst rates in ATRA treated COCs. Data from these studies suggest that not only can CX43 be used as a biomarker for oocyte health, it can also potentially be manipulated using ATRA to increase the number of oocytes achieving developmental competence.
Accuracy of Water Delivery in Enteral Nutrition Pumps
Authors: Bertagnolli Erin J. , Patterson Mindy A. , Utech Anne , Walker Renee N. 
Published: September 2019

AbstractBackgroundAdequate delivery of both enteral formula and water in patients receiving enteral nutrition (EN) is critical. Pump accuracy has been identified as a factor impeding enteral formula delivery; however, rarely is enteral water delivery investigated. The purpose of this study was to explore accuracy of delivering 1 L of water by EN pumps using different flush volumes and hang heights.MethodsThree EN pumps were used in vitro to flush 1 L of water at 50 mL every hour for 20 hours (50 mL, 20 times per day) and 500 mL every 4 hours for 8 hours (500 mL, 2 times per day) at 0 in. and 18 in. (or 45.72 cm) hang heights. Fifteen runs were conducted at each volume and hang height per pump. Actual delivered enteral water, remaining volume in enteral feeding bags, and volume reported per pump were recorded.ResultsHang height of 18 in. delivered a mean 3.91% (95% CI, 3.25–4.57) more water than bags hung at 0 in. (P < .0005). When delivering water in 500 mL increments, 1.57% (95% CI, 0.92–2.23) more water was delivered than when delivered in 50 mL increments (P < .005).ConclusionAppropriate hang height recommendations improve enteral water delivery in patients receiving EN. The most accurate setting was 500 mL at 18 in., resulting in accurate water delivery in 97.8% of runs, whereas 50 mL at 0 in. delivered accurately 17.8% of the time. Appropriate bag hang height and water delivery volume is critical to maintain hydration status of patients receiving EN.