bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving daytime detection of deer for surveillance and management
Authors: Logan Thomas W. , Ashton-Butt Adham , Ward Alastair I.
Published: October 2019

Maximising the detection of a target species reduces the uncertainty of survey results and can improve management outcomes. Deer (Cervidae) populations are managed worldwide due to their impacts on anthropocentric interests. In the UK, deer can only lawfully be shot during the daytime, from 1 h before sunrise to 1 h after sunset, when deer activity is at its lowest. We evaluated performance of a thermal imager relative to binoculars for their ability to detect deer during the daytime and at twilight (1 h either side of dawn and dusk). Transect surveys on Thorne Moors, UK, revealed that more roe and red deer were observed using a thermal imager than when using binoculars. More deer in much larger groups were observed at twilight than during the other daylight hours. Variation in animal detectability at different times of the day must be considered during wildlife surveys if their outputs are to be as accurate and precise as possible. The results support the continued focus of deer culling efforts during the hours of twilight. They also highlight the potential utility of thermal imagers for maximising detection probability at twilight.
Erosion of phylogenetic diversity in Neotropical bat assemblages: findings from a whole-ecosystem fragmentation experiment
Authors: Aninta Sabhrina G. , Rocha Ricardo , López-Baucells Adrià , Meyer Christoph F. J.
Published: October 2019

The traditional focus on taxonomic diversity metrics for investigating species responses to habitat loss and fragmentation has limited our understanding of how biodiversity is impacted by habitat modification. This is particularly true for taxonomic groups such as bats which exhibit species-specific responses. Here, we investigate phylogenetic alpha and beta diversity of Neotropical bat assemblages across two environmental gradients, one in habitat quality and one in habitat amount. We surveyed bats in 39 sites located across a whole-ecosystem fragmentation experiment in the Brazilian Amazon, representing a gradient of habitat quality (interior-edge-matrix, hereafter IEM) in both continuous forest and forest fragments of different sizes (1, 10, and 100 ha; forest size gradient). For each habitat category, we quantified alpha and beta phylogenetic diversity, then used linear mixed-effects models and cluster analysis to explore how forest area and IEM gradient affect phylogenetic diversity. We found that the secondary forest matrix harboured significantly lower total evolutionary history compared to the fragment interiors, especially the matrix near the 1 ha fragments, containing bat assemblages with more closely related species. Forest fragments ≥ 10 ha had levels of phylogenetic richness similar to continuous forest, suggesting that large fragments retain considerable levels of evolutionary history. The edge and matrix adjacent to large fragments tend to have closely related lineages nonetheless, suggesting phylogenetic homogenization in these IEM gradient categories. Thus, despite the high mobility of bats, fragmentation still induces considerable levels of erosion of phylogenetic diversity, suggesting that the full amount of evolutionary history might not be able to persist in present-day human-modified landscapes.
Quarantining online hate speech: technical and ethical perspectives
Authors: Ullmann Stefanie , Tomalin Marcus
Published: October 2019

In this paper we explore quarantining as a more ethical method for delimiting the spread of Hate Speech via online social media platforms. Currently, companies like Facebook, Twitter, and Google generally respondreactivelyto such material: offensive messages that have already been posted are reviewed by human moderators if complaints from users are received. The offensive posts are onlysubsequentlyremoved if the complaints are upheld; therefore, they still cause the recipients psychological harm. In addition, this approach has frequently been criticised for delimiting freedom of expression, since it requires the service providers to elaborate and implement censorship regimes. In the last few years, an emerging generation of automatic Hate Speech detection systems has started to offer new strategies for dealing with this particular kind of offensive online material. Anticipating the future efficacy of such systems, the present article advocates an approach to online Hate Speech detection that is analogous to the quarantining of malicious computer software. If a given post is automatically classified as being harmful in a reliable manner, then it can be temporarily quarantined, and the direct recipients can receive an alert, which protects them from the harmful content in the first instance. The quarantining framework is an example of more ethical online safety technology that can be extended to the handling of Hate Speech. Crucially, it provides flexible options for obtaining a more justifiable balance between freedom of expression and appropriate censorship.
Multi-hazard Groundwater Risks to Water Supply from Shallow Depths: Challenges to Achieving the Sustainable Development Goals in Bangladesh
Authors: Shamsudduha Mohammad , Joseph George , Haque Sabrina S. , Khan Mahfuzur R. , Zahid Anwar , Ahmed Kazi Matin U.
Published: October 2019

Groundwater currently provides 98% of all drinking-water supply in Bangladesh. Groundwater is found throughout Bangladesh but its quality (i.e., arsenic and salinity contamination) and quantity (i.e., water-storage depletion) vary across hydrological environments, posing unique challenges to certain geographical areas and population groups. Yet, no national-scale, multi-parameter groundwater hazard maps currently exist enabling water resources managers and policy makers to identify vulnerable areas to public health. We develop, for the first time, groundwater multi-hazard maps at the national scale of Bangladesh combining information on arsenic, salinity, and water storage. We apply geospatial techniques in ‘R’ programming language and ArcGIS environment, linking hydrological indicators for water quality and quantity to construct risk maps. A range of socioeconomic variables including access to drinking and irrigation water supplies and social vulnerability (i.e., poverty) are overlaid on these risk maps to estimate exposures. Our multi-parameter groundwater hazard maps show that a considerable proportion of land area (5–24% under extremely high to high risks) in Bangladesh is currently under combined risk of arsenic and salinity contamination, and groundwater-storage depletion. As small as 6.5 million (2.2 million poor) to 24.4 million (8.6 million poor) people are exposed to a combined risk of high arsenic, salinity, and groundwater-storage depletion. Our groundwater hazard maps reveal areas and exposure of population groups to water risks posed by arsenic and salinity contamination and depletion of water storage. These geospatial hazard maps can potentially guide policy makers in prioritizing mitigation and adaptation measures in order to achieve the United Nation’s Sustainable Development Goals across the water, agriculture, and public health sectors in Bangladesh.
Potential of dust emission resources using small wind tunnel and GIS: case study of Bakhtegan playa, Iran
Authors: Karimzadeh Siroos , Taghizadeh Mohammad Mehdi
Published: October 2019

Determination of the high potential of dust emission is a requisite affair in the management of dusts emission and as well as avoiding its risks. Wind tunnel is among the most important approaches in the study of areas having high potential in emitting dusts. Extensive dried playas and desert areas require the making of low-cost, simple, and car-portable tunnels capable of presenting comparable data of various areas even supposing not having enough precision in the model of real wind motion. In this study, we first engaged in making a car-portable tunnel with a primarily semicircle section of 38 cm height, 50 cm diameter, and 110 cm length. A fan and key appliance with the ability to change speed were used along with a simple transformer launched with car battery. Then, concentration of the pm10 dusts was measured in the various wind speeds of 1, 2.5, 4, 5.5, and 7 m/s by the help of anemometer and digital equipments. The study of Bakhtegan playa was done, as the methodology of handling with this tunnel, in 35 positions, and zoning of the results was performed via ArcGIS software. Depending on the destructibility of the shell by wind, the areas under study were categorized as low potential (34%), medium potential (37%), and high potential (29%) in emitting dusts. The results of zoning spotted the high-potential areas on the map. The usage of small tunnels, as in the present model, may be applied in order for the low-cost and fast studies of vast areas to the purpose of playas management.
Naturally occurring radon assessment in Al-Rustumia wastewater treatment plant
Authors: Amin Sahar A. , Al-Ani Rana R.
Published: October 2019

Wastewater samples were collected from Al-Rustumia wastewater treatment plant. The methodology which was used to measure radon activity levels was long-term air measurements with passive solid-state alpha track detector CR-39. The collected samples include wastewater before and after treatment for 5 months which started from September 2017 to January 2018. The results show that the average values of radon activity level for untreated and treated wastewater samples were 0.049 Bq L−1 and 0.036 Bq L−1, respectively. Dissolved radon concentrations for the study samples were also calculated and their values were 1.270 Bq L−1 and 0.937 Bq L−1, respectively. The calculated radon surface exhalation rate for wastewater samples before treatment was 0.048 Bq m−2 h−1 and after treatment was 0.035 Bq m−2 h−1. These values are lower than the maximum acceptable radon levels as given by United States Environmental Protection Agency. As well as, the results reveal that radon activity level decreases after treatment process implementation, and there are no considerable variations with different times of the year.
Spring water quality assessment using water quality index in villages of Barwari Bala, Duhok, Kurdistan Region, Iraq
Authors: Ameen Hajar Ameen
Published: October 2019

Periodic quality assessment of drinking water sources is necessary to guarantee the quality and security of water supply to people. Accordingly, this study assessed the drinking water quality of spring water of some villages located in Barwari Bala region of Duhok Governorate, Kurdistan region, Iraq, using the water quality index (WQI). To realize this objective, 120 spring water samples were collected from ten villages during the dry and wet seasons in 2018 and were analyzed for major physicochemical characteristics, including: calcium (Ca2+), magnesium (Mg2+), sodium (Na+), potassium (K+), chloride (Cl−), sulfate (SO42−), nitrate (NO3−), pH, total dissolved solids (TDS), turbidity, total hardness (TH) and total alkalinity (TA). The results for pH, turbidity, sodium, potassium, chloride, sulfate and nitrate showed that the water samples at all the sampled springs were suitable for drinking and within permissible limits based on given standards. However, TDS, TA, calcium and magnesium exceeded the permissible limits at some sites. It was also observed that, except for SO42−, at almost all the sites, the majority of parameters were significantly greater during the wet season compared to the dry season. With reference to all the parameters, the WQI values ranged from 10.76 to 18.13 during the dry season and from 17.10 to 20.45 during the wet season, indicating that all water samples are classified as having “excellent” water quality for drinking purposes. The calculation of WQI based on specific parameters, where values were close to or exceeded the maximum acceptable limits, showed that the water quality status of all water samples was “good” quality, except for sites S6 and S8, which were classified as “poor” quality and are not considered suitable for drinking purposes without treatment. Water from almost all the sampled spring sites can be considered as suitable for drinking purposes, although some parameters exceed permissible limits. Simple filtration treatment of the sampled spring water before use is desirable for ensuring good quality and security of the water supply to people of these areas.
Donor Rules or Donors Rule? International Institutions and Political Corruption
Authors: Hafner-Burton Emilie M. , Schneider Christina J.
Published: October 2019

Political corruption is a massive barrier to economic development and good governance. International institutions have become leaders in the effort to combat the problem. A growing number of such institutions have crafted official anticorruption rules, procedures and policies designed to deter the abuse of power within their membership and within institutional practice. Despite these regulatory developments, little is known about the role these institutions play in influencing corruption or whether the growing set of governance rules now in place have any effect.
Revisiting Weertman's tombstone bed
Authors: MacAyeal Douglas R.
Published: October 2019

Johannes Weertman published his first glaciological paper in 1957 only 5 years after getting his DSc in metallurgy from the Carnegie Institute of Technology. The paper presented the very first sliding law developed quantitatively from first principles, and involved the unconventional idealization of bed roughness using cubic ‘tombstones’ of rock. Since 1957, there has been a great deal of progress in understanding glacier sliding, but few studies, if any, have preserved the original tombstone geometry that was a hallmark of this first theory. The current study presents a partial reanalysis of the sliding process over a bed with tombstone obstacles using modern numerical methods. The result confirms the enduring applicability of Weertman's model as a pedagogical tool and motivates new questions about (1) folding flow near bedrock obstacles that invert normal ice stratigraphy, (2) the presence and role of stress singularities on sharp edges of bedrock, and (3) the validity of a presumption that regelation flow can be plug-like.
A Philanthropic Approach to Supporting Emergent Disaster Response and Recovery
Authors: Schlegelmilch Jeffrey , Sury Jonathan , Brooks Jeremy , Chandler Thomas
Published: October 2019

In August 2017, Hurricane Harvey struck the US Gulf Coast and caused more than US $125 billion in damages in Texas. The loss of lives and the economic damages resulted in an outpouring of support for the recovery efforts in the form of federal assistance and private donations. The latter has supported more creative approaches to recovery. Organizations that normally would not receive funding were able to obtain resources to use in novel manners. Using the framework of Dynes typology to identify groups and their respective structures and tasks, this report from the field analyzes Hurricane Harvey and the financial support mechanisms used to support recovery efforts in Texas, what organizations were funded to do, and where they fit into Dynes typology. The authors close by noting the importance of these emerging organizations and the need to support diversity in funding disaster response and recovery efforts beyond large nonprofit organizations.
School counsellors’ resilience in Turkey: A phenomenological study
Authors: Guler Deniz , Ceyhan Esra
Published: October 2019

Resilience is a crucial personal characteristic of school counsellors to protect and maintain their wellbeing against the effects of occupational stress factors in school settings. However, there has been a lack of research investigating school counsellors’ resilience in Turkey. Therefore, this study aims to explore the resilience of school counsellors working in schools with at-risk students in terms of stress and protective factors. The study was conducted using a qualitative research method with a phenomenological approach. The data were collected through semistructured interviews from 10 school counsellors working in schools with at-risk students. The data analysis was carried out with an inductive approach using an NVivo 11 software package program. The analysis revealed a variety of findings, both positive and negative, regarding the resilience of school counsellors. In this scope, three interrelated themes emerged as ‘Occupational Stressors’, ‘Personal Factors: Strength versus Vulnerability’, and ‘Positive and Negative Results: Happiness and Satisfaction versus Helplessness and Burnout’. The results show that school counsellors working in schools with at-risk students experience a variety of occupational stresses and that their experience of happiness and satisfaction, or helplessness and burnout, depends on a level of strengths or weaknesses with reference to personal factors.
Political cultures: measuring values heterogeneity
Authors: Blaydes Lisa , Grimmer Justin
Published: October 2019

Using data from the World Values Survey, we analyze the extent to which value consensus exists within countries. To do this, we introduce a statistical model which allows us to generate country-level measures of cultural heterogeneity. Our statistical approach models each country as a mixture of subcultures that are shared across the world. Our results demonstrate that value consensus varies substantially across countries and regions.
Trust and Accountability in a Digital Age
Authors: O'Neill Onora
Published: October 2019

I have a very particular reason to be grateful to Stewart Sutherland, our late President, which is connected to some of the themes of this lecture, so want to begin by recalling a long conversation I had with him on these topics.
Protein intake per day and at each daily meal and skeletal muscle mass declines among older community dwellers in Japan
Authors: Otsuka Rei , Kato Yuki , Tange Chikako , Nishita Yukiko , Tomida Makiko , Imai Tomoko , Ando Fujiko , Shimokata Hiroshi , Arai Hidenori
Published: October 2019

Objective:

To examine associations between protein intake per day and at different meals and skeletal muscle mass declines.

Design:

Two-year prospective cohort study among older community dwellers.

Setting:

National Institute for Longevity Sciences–Longitudinal Study of Aging (NILS-LSA) in Japan.

Participants:

Older men (n 292) and women (n 363) aged 60–87 years who participated in the baseline (2006–2008) and follow-up studies (2008–2010) of NILS-LSA and did not exhibit low skeletal muscle mass at baseline. Muscle mass was assessed using dual-energy X-ray absorptiometry at baseline and follow-up. Low muscle mass was defined as skeletal muscle mass index <7·0 kg/m2 for men and <5·4 kg/m2 for women at follow-up. Daily protein intake and protein intake at each meal were calculated from 3 d dietary records at baseline and sex-stratified tertiles were determined.

Results:

Mean (sd) protein intake at breakfast, lunch and dinner was 22·7 (7·8), 26·7 (9·3) and 37·4 (10·5) g for men and 19·3 (6·3), 23·2 (7·3) and 28·5 (7·0) g for women, respectively. After adjusting for age, baseline skeletal muscle mass and other confounders in logistic modelling, greater total protein intake was associated with lower prevalence of skeletal muscle mass decline among men at follow-up (P = 0·024). Particularly, the OR (95 % CI) for high lunchtime protein intake was low (0·11 (0·02, 0·61); P = 0·01). No significant association between total protein intake and prevalence of skeletal muscle mass decline was found among women.

Conclusions:

High total protein intake, particularly at lunchtime, is associated with retention of skeletal muscle mass in men.
3‐D Modeling of Vertical Gravity Gradients and the Delimitation of Tectonic Boundaries: The Caribbean Oceanic Domain as a Case Study
Authors: Gómez‐García Ángela María , Meeßen Christian , Scheck‐Wenderoth Magdalena , Monsalve Gaspar , Bott Judith , Bernhardt Anne , Bernal Gladys
Published: October 2019

Geophysical data acquisition in oceanic domains is challenging, implying measurements with low and/or nonhomogeneous spatial resolution. The evolution of satellite gravimetry and altimetry techniques allows testing 3‐D density models of the lithosphere, taking advantage of the high spatial resolution and homogeneous coverage of satellites. However, it is not trivial to discretise the source of the gravity field at different depths. Here, we propose a new method for inferring tectonic boundaries at the crustal level. As a novelty, instead of modeling the gravity anomalies and assuming a flat Earth approximation, we model the vertical gravity gradients (VGG) in spherical coordinates, which are especially sensitive to density contrasts in the upper layers of the Earth. To validate the methodology, the complex oceanic domain of the Caribbean region is studied, which includes different crustal domains with a tectonic history since Late Jurassic time. After defining a lithospheric starting model constrained by up‐to‐date geophysical data sets, we tested several a‐priory density distributions and selected the model with the minimum misfits with respect to the VGG calculated from the EIGEN‐6C4 data set. Additionally, the density of the crystalline crust was inferred by inverting the VGG field. Our methodology enabled us not only to refine, confirm, and/or propose tectonic boundaries in the study area but also to identify a new anomalous buoyant body, located in the South Lesser Antilles subduction zone, and high‐density bodies along the Greater, Lesser, and Leeward Antilles forearcs.
Magnetic Pore Fabrics: The Role of Shape and Distribution Anisotropy in Defining the Magnetic Anisotropy of Ferrofluid‐Impregnated Samples
Authors: Biedermann Andrea R.
Published: October 2019

Pore fabrics define physical properties of a rock, such as permeability and elasticity, both of which are important to many geological, hydrological, and environmental applications. Minerals and hence pores are often preferentially aligned, leading to anisotropy of physical properties and preferred flow directions. Preferred flow paths are defined by the shape and arrangement of pores, and a characterization of this pore fabric forms the basis for prediction of fluid flow directions. Magnetic pore fabrics (MPFs), that is, magnetic anisotropy measurements on ferrofluid‐impregnated samples, are a promising and fast way to characterize the pore fabric of connected pores in 3‐D, while analyzing a large number of pores with sizes down to 10 nm, without the need for any a priori knowledge about fabric orientation. Empirical relationships suggest that the MPF is related to the pore shape and orientation and approximates permeability anisotropy. This study uses models including shape and distribution anisotropy to better understand and quantify MPFs, using simple pore shapes and pore assemblies measured in previous studies. The results obtained in this study show that (1) shape anisotropy reliably predicts the MPF of single pores, (2) both shape and distribution anisotropy are needed to predict MPFs of pore assemblies, and (3) the anisotropy parameters P, L, and F are affected by the intrinsic susceptibility of the ferrofluid in addition to pore geometry. These findings can help explain some of the variability in empirical relationships and are an important step toward a quantitative understanding and application of MPFs in geological and environmental studies.
Author Correction: Blunting neuroinflammation with resolvin D1 prevents early pathology in a rat model of Parkinson’s disease
Authors: Krashia Paraskevi , Cordella Alberto , Nobili Annalisa , La Barbera Livia , Federici Mauro , Leuti Alessandro , Campanelli Federica , Natale Giuseppina , Marino Gioia , Calabrese Valeria , Vedele Francescangelo , Ghiglieri Veronica , Picconi Barbara , Di Lazzaro Giulia , Schirinzi Tommaso , Sancesario Giulia , Casadei Nicolas , Riess Olaf , Bernardini Sergio , Pisani Antonio , Calabresi Paolo , Viscomi Maria Teresa , Serhan Charles Nicholas , Chiurchiù Valerio , D’Amelio Marcello , Mercuri Nicola Biagio
Published: October 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
IRF2 is a master regulator of human keratinocyte stem cell fate
Authors: Mercado Nicolas , Schutzius Gabi , Kolter Christian , Estoppey David , Bergling Sebastian , Roma Guglielmo , Gubser Keller Caroline , Nigsch Florian , Salathe Adrian , Terranova Remi , Reece-Hoyes John , Alford John , Russ Carsten , Knehr Judith , Hoepfner Dominic , Aebi Alexandra , Ruffner Heinz , Beck Tanner C. , Jagannathan Sajjeev , Olson Calla M. , Sheppard Hadley E. , Elsarrag Selma Z. , Bouwmeester Tewis , Frederiksen Mathias , Lohmann Felix , Lin Charles Y. , Kirkland Susan
Published: October 2019

Resident adult epithelial stem cells maintain tissue homeostasis by balancing self-renewal and differentiation. The stem cell potential of human epidermal keratinocytes is retained in vitro but lost over time suggesting extrinsic and intrinsic regulation. Transcription factor-controlled regulatory circuitries govern cell identity, are sufficient to induce pluripotency and transdifferentiate cells. We investigate whether transcriptional circuitry also governs phenotypic changes within a given cell type by comparing human primary keratinocytes with intrinsically high versus low stem cell potential. Using integrated chromatin and transcriptional profiling, we implicate IRF2 as antagonistic to stemness and show that it binds and regulates active cis-regulatory elements at interferon response and antigen presentation genes. CRISPR-KD of IRF2 in keratinocytes with low stem cell potential increases self-renewal, migration and epidermis formation. These data demonstrate that transcription factor regulatory circuitries, in addition to maintaining cell identity, control plasticity within cell types and offer potential for therapeutic modulation of cell function.
Detecting changes at the leading edge of an interface between oceanic water layers
Authors: Tang Qunshu , Tong Vincent C. H. , Hobbs Richard W. , Morales Maqueda Miguel Ángel
Published: October 2019

Many physical phenomena in the ocean involve interactions between water masses of different temperatures and salinities at boundaries. Of particular interest is the characterisation of finescale structure at the marginal interaction zones of these boundaries, where the structure is either destroyed by mixing or formed by stratification. Using high-resolution seismic reflection imaging, we present observations of temporal changes at the leading edge of an interface between sub-thermocline layers in the Panama Basin. By studying time-lapse images of a seismic reflector between two water boundaries with subtle differences, we provide empirical constraints on how stratified layers evolve. The leading edge of this reflector, which is characterised by a gradual lateral decrease in vertical temperature contrast ($$|\Delta T|$$
∣
Δ
T
∣
), increases in length over ~3 days coupled with an increase in $$|\Delta T|$$
∣
Δ
T
∣
. A critical mixing state, in which turbulent diffusion is gradually replaced by double-diffusion as the dominant mixing process, is thus revealed.
Author Correction: Ras hyperactivation versus overexpression: Lessons from Ras dynamics in Candida albicans
Authors: Pratyusha Vavilala A. , Victoria Guiliana Soraya , Khan Mohammad Firoz , Haokip Dominic T. , Yadav Bhawna , Pal Nibedita , Sethi Subhash Chandra , Jain Priyanka , Singh Sneh Lata , Sen Sobhan , Komath Sneha Sudha
Published: October 2019

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
A new species in the major malaria vector complex sheds light on reticulated species evolution
Authors: Barrón Maite G. , Paupy Christophe , Rahola Nil , Akone-Ella Ousman , Ngangue Marc F. , Wilson-Bahun Theodel A. , Pombi Marco , Kengne Pierre , Costantini Carlo , Simard Frédéric , González Josefa , Ayala Diego
Published: October 2019

Complexes of closely related species provide key insights into the rapid and independent evolution of adaptive traits. Here, we described and studiedAnopheles fontenilleisp.n., a new species in theAnopheles gambiaecomplex that we recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of theAn.gambiaecomplex, revealing important introgression events with other members of the complex. Particularly, we detected recent introgression, withAnopheles gambiaeandAnopheles coluzzii, of genes directly involved in vectorial capacity. Moreover, genome analysis of the new species allowed us to clarify the evolutionary history of the 3La inversion. Overall,An.fontenilleisp.n. analysis improved our understanding of the relationship between species within theAn.gambiaecomplex, and provided insight into the evolution of vectorial capacity traits that are relevant for the successful control of malaria in Africa.
Experimental challenge with bovine respiratory syncytial virus in dairy calves: bronchial lymph node transcriptome response
Authors: Johnston Dayle , Earley Bernadette , McCabe Matthew S. , Lemon Ken , Duffy Catherine , McMenamy Michael , Cosby S. Louise , Kim JaeWoo , Blackshields Gordon , Taylor Jeremy F. , Waters Sinead M.
Published: October 2019

Bovine Respiratory Disease (BRD) is the leading cause of mortality in calves. The objective of this study was to examine the response of the host’s bronchial lymph node transcriptome to Bovine Respiratory Syncytial Virus (BRSV) in a controlled viral challenge. Holstein-Friesian calves were either inoculated with virus (103.5 TCID50/ml × 15 ml) (n = 12) or mock challenged with phosphate buffered saline (n = 6). Clinical signs were scored daily and blood was collected for haematology counts, until euthanasia at day 7 post-challenge. RNA was extracted and sequenced (75 bp paired-end) from bronchial lymph nodes. Sequence reads were aligned to the UMD3.1 bovine reference genome and differential gene expression analysis was performed using EdgeR. There was a clear separation between BRSV challenged and control calves based on gene expression changes, despite an observed mild clinical manifestation of the disease. Therefore, measuring host gene expression levels may be beneficial for the diagnosis of subclinical BRD. There were 934 differentially expressed genes (DEG) (p < 0.05, FDR <0.1, fold change >2) between the BRSV challenged and control calves. Over-represented gene ontology terms, pathways and molecular functions, among the DEG, were associated with immune responses. The top enriched pathways included interferon signaling, granzyme B signaling and pathogen pattern recognition receptors, which are responsible for the cytotoxic responses necessary to eliminate the virus.
The link between yeast cell wall porosity and plasma membrane permeability after PEF treatment
Authors: Stirke Arunas , Celiesiute-Germaniene Raimonda , Zimkus Aurelijus , Zurauskiene Nerija , Simonis Povilas , Dervinis Aldas , Ramanavicius Arunas , Balevicius Saulius
Published: October 2019

An investigation of the yeast cell resealing process was performed by studying the absorption of the tetraphenylphosphonium (TPP+) ion by the yeast Saccharomyces cerevisiae. It was shown that the main barrier for the uptake of such TPP+ ions is the cell wall. An increased rate of TPP+ absorption after treatment of such cells with a pulsed electric field (PEF) was observed only in intact cells, but not in spheroplasts. The investigation of the uptake of TPP+ in PEF treated cells exposed to TPP+ for different time intervals also showed the dependence of the absorption rate on the PEF strength. The modelling of the TPP+ uptake recovery has also shown that the characteristic decay time of the non-equilibrium (PEF induced) pores was approximately a few tens of seconds and this did not depend on the PEF strength. A further investigation of such cell membrane recovery process using a florescent SYTOX Green nucleic acid stain dye also showed that such membrane resealing takes place over a time that is like that occurring in the cell wall. It was thus concluded that the similar characteristic lifetimes of the non-equilibrium pores in the cell wall and membrane after exposure  to  PEF indicate a strong coupling between these parts of the cell.
Adipocyte PU.1 knockout promotes insulin sensitivity in HFD-fed obese mice
Authors: Lackey Denise E. , Reis Felipe C. G. , Isaac Roi , Zapata Rizaldy C. , El Ouarrat Dalila , Lee Yun Sok , Bandyopadhyay Gautam , Ofrecio Jachelle M. , Oh Da Young , Osborn Olivia
Published: October 2019

Insulin resistance is a key feature of obesity and type 2 diabetes. PU.1 is a master transcription factor predominantly expressed in macrophages but after HFD feeding PU.1 expression is also significantly increased in adipocytes. We generated adipocyte specific PU.1 knockout mice using adiponectin cre to investigate the role of PU.1 in adipocyte biology, insulin and glucose homeostasis. In HFD-fed obese mice systemic glucose tolerance and insulin sensitivity were improved in PU.1 AKO mice and clamp studies indicated improvements in both adipose and liver insulin sensitivity. At the level of adipose tissue, macrophage infiltration and inflammation was decreased and glucose uptake was increased in PU.1 AKO mice compared with controls. While PU.1 deletion in adipocytes did not affect the gene expression of PPARg itself, we observed increased expression of PPARg target genes in eWAT from HFD fed PU.1 AKO mice compared with controls. Furthermore, we observed decreased phosphorylation at serine 273 in PU.1 AKO mice compared with fl/fl controls, indicating that PPARg is more active when PU.1 expression is reduced in adipocytes. Therefore, in obesity the increased expression of PU.1 in adipocytes modifies the adipocyte PPARg cistrome resulting in impaired glucose tolerance and insulin sensitivity.
A docking-based structural analysis of geldanamycin-derived inhibitor binding to human or Leishmania Hsp90
Authors: Palma Luana Carneiro , Ferreira Luiz Felipe Gomes Rebello , Petersen Antonio Luis de Oliveira Almeida , Dias Beatriz Rocha Simões , Menezes Juliana Perrone Bezerra de , Moreira Diogo Rodrigo de Magalhães , Hernandes Marcelo Zaldini , Veras Patricia Sampaio Tavares
Published: October 2019

Leishmaniasis is a neglected disease that affects millions of individuals around the world. Regardless of clinical form, treatment is based primarily on the use of pentavalent antimonials. However, such treatments are prolonged and present intense side effects, which lead to patient abandonment in many cases. The search for chemotherapeutic alternatives has become a priority. Heat Shock Protein 90 (Hsp90) inhibitors have recently come under investigation due to antiparasitic activity in Plasmodium sp., Trypanosoma sp. and Leishmania sp. Some of these inhibitors, such as geldanamycin and its analogs, 17-AAG and 17-DMAG, bind directly to Hsp90, thereby inhibiting its activity. Previous studies have demonstrated that different parasite species are more susceptible to some of these inhibitors than host cells. We hypothesized that this increased susceptibility may be due to differences in binding of Hsp90 inhibitors to Leishmania protein compared to host protein. Based on the results of the in silico approach used in the present study, we propose that geldanamycin, 17-AAG and 17-DMAG present an increased tendency to bind to the N-terminal domain of Leishmania amazonensis Hsp83 in comparison to human Hsp90. This could be partially explained by differences in intermolecular interactions between each of these inhibitors and Hsp83 or Hsp90. The present findings demonstrate potential for the use of these inhibitors in the context of anti-Leishmania therapy.
Functional analysis and development of a CRISPR/Cas9 allelic series for a CPR5 ortholog necessary for proper growth of soybean trichomes
Authors: Campbell Benjamin W. , Hoyle Jacob W. , Bucciarelli Bruna , Stec Adrian O. , Samac Deborah A. , Parrott Wayne A. , Stupar Robert M.
Published: October 2019

Developments in genomic and genome editing technologies have facilitated the mapping, cloning, and validation of genetic variants underlying trait variation. This study combined bulked-segregant analysis, array comparative genomic hybridization, and CRISPR/Cas9 methodologies to identify a CPR5 ortholog essential for proper trichome growth in soybean (Glycine max). A fast neutron mutant line exhibited short trichomes with smaller trichome nuclei compared to its parent line. A fast neutron-induced deletion was identified within an interval on chromosome 6 that co-segregated with the trichome phenotype. The deletion encompassed six gene models including an ortholog of Arabidopsis thaliana CPR5. CRISPR/Cas9 was used to mutate the CPR5 ortholog, resulting in five plants harboring a total of four different putative knockout alleles and two in-frame alleles. Phenotypic analysis of the mutants validated the candidate gene, and included intermediate phenotypes that co-segregated with the in-frame alleles. These findings demonstrate that the CPR5 ortholog is essential for proper growth and development of soybean trichomes, similar to observations in A. thaliana. Furthermore, this work demonstrates the value of using CRISPR/Cas9 to generate an allelic series and intermediate phenotypes for functional analysis of candidate genes and/or the development of novel traits.
Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations
Authors: Maruyama Kei , Imai Hirotatsu , Kawamura Momoko , Ishino Sonoko , Ishino Yoshizumi , Ito Kosuke , Uchiumi Toshio
Published: October 2019

Translation elongation factor EF1A delivers aminoacyl-tRNA to the ribosome in a GTP-bound form, and is released from the ribosome in a GDP-bound form. This association/dissociation cycle proceeds efficiently via a marked conformational change in EF1A. EF1A function is dependent on the ribosomal “stalk” protein of the ribosomal large subunit, although the precise mechanism of action of the stalk on EF1A remains unclear. Here, we clarify the binding mode of archaeal stalk aP1 to GTP-bound aEF1A associated with aPelota. Intriguingly, the C-terminal domain (CTD) of aP1 binds to aEF1A•GTP with a similar affinity to aEF1A•GDP. We have also determined the crystal structure of the aP1-CTD•aEF1A•GTP•aPelota complex at 3.0 Å resolution. The structure shows that aP1-CTD binds to a space between domains 1 and 3 of aEF1A. Biochemical analyses show that this binding is crucial for protein synthesis. Comparison of the structures of aP1-CTD•aEF1A•GTP and aP1-CTD•aEF1A•GDP demonstrates that the binding mode of aP1 changes markedly upon a conformational switch between the GTP- and GDP-bound forms of aEF1A. Taking into account biochemical data, we infer that aP1 employs its structural flexibility to bind to aEF1A before and after GTP hydrolysis for efficient protein synthesis.
Characterization of biological variation of peripheral blood immune cytome in an Indian cohort
Authors: Kanodia Parna , Kaur Gurvinder , Coshic Poonam , Chatterjee Kabita , Neeman Teresa , George Anna , Rath Satyajit , Bal Vineeta , Prabhu Savit B.
Published: October 2019

Immune parameters show characteristic normal baseline levels and variance in the population. We characterised the degree of inter-individual and within-individual variation over one-year time period in 33 immune cell subsets by flow cytometry in peripheral blood mononuclear cells from 43 healthy young adult volunteers. Our analysis revealed that immune subsets that showed low variability between individuals also showed low short-term fluctuations within-individuals, as well as concordance in siblings. However, when baseline levels and degree of fluctuation were considered together, individuals failed to cluster into discreet groups. Together, the data reveal complex inter-relationships between immune subsets in individuals, and provide insights into the observed heterogeneity between individuals and between multiple immune subsets.
Hypoxia-inducible factor-1α is the therapeutic target of the SGLT2 inhibitor for diabetic nephropathy
Authors: Bessho Ryoichi , Takiyama Yumi , Takiyama Takao , Kitsunai Hiroya , Takeda Yasutaka , Sakagami Hidemitsu , Ota Tsuguhito
Published: October 2019

Previous studies have demonstrated intrarenal hypoxia in patients with diabetes. Hypoxia-inducible factor (HIF)-1 plays an important role in hypoxia-induced tubulointerstitial fibrosis. Recent clinical trials have confirmed the renoprotective action of SGLT2 inhibitors in diabetic nephropathy. We explored the effects of an SGLT2 inhibitor, luseogliflozin on HIF-1α expression in human renal proximal tubular epithelial cells (HRPTECs). Luseogliflozin significantly inhibited hypoxia-induced HIF-1α protein expression in HRPTECs. In addition, luseogliflozin inhibited hypoxia-induced the expression of the HIF-1α target genes PAI-1, VEGF, GLUT1, HK2 and PKM. Although luseogliflozin increased phosphorylated-AMP-activated protein kinase α (p-AMPKα) levels, the AMPK activator AICAR did not changed hypoxia-induced HIF-1α expression. Luseogliflozin suppressed the oxygen consumption rate in HRPTECs, and subsequently decreased hypoxia-sensitive dye, pimonidazole staining under hypoxia, suggesting that luseogliflozin promoted the degradation of HIF-1α protein by redistribution of intracellular oxygen. To confirm the inhibitory effect of luseogliflozin on hypoxia-induced HIF-1α protein in vivo, we treated male diabetic db/db mice with luseogliflozin for 8 to 16 weeks. Luseogliflozin attenuated cortical tubular HIF-1α expression, tubular injury and interstitial fibronectin in db/db mice. Together, luseogliflozin inhibits hypoxia-induced HIF-1α accumulation by suppressing mitochondrial oxygen consumption. The SGLT2 inhibitors may protect diabetic kidneys by therapeutically targeting HIF-1α protein.
Optical Coherence Tomography Angiography Evaluation of Retinal Microvasculature Before and After Carotid Angioplasty and Stenting
Authors: Lee Chia-Wei , Cheng Hui-Chen , Chang Feng-Chi , Wang An-Guor
Published: October 2019

The aim of the study was to evaluate the influence of carotid angioplasty and stenting (CAS) on retinal microvasculature using optical coherence tomography angiography (OCTA) in patients with severe carotid stenosis. 20 patients with severe carotid stenosis underwent comprehensive ophthalmic examinations and OCTA before and one month after CAS. Automated algorithms were used to quantify vessel density in the macular superficial vascular complex (SVC), deep vascular complex (DVC), and radial peripapillary capillary (RPC) around the optic disc. Eyes on the operated side constituted the ipsilateral eye group, and the other eye constituted the fellow eye group. In the ipsilateral eye group, the vessel density in the DVC increased significantly after stent implantation (P = 0.010), but the vessel density change in the SVC was not statistically different (P = 0.999). In the fellow eye group, the vessel density in the SVC (P = 0.028) and DVC (P = 0.034) were significantly increased after stent implantation. The vessel density in the RPC did not significantly change in the ipsilateral (P = 0.363) or fellow (P = 0.878) eye groups. This study shows that unilateral CAS for severe carotid stenosis increases macular vessel densities in both eyes.
Author Correction: Multimodal imaging analyses in patients with genetic and sporadic forms of small vessel disease
Authors: Kim Ko Woon , Kwon Hunki , Kim Young-Eun , Yoon Cindy W. , Kim Yeo Jin , Kim Yong Bum , Lee Jong Min , Yoon Won Tae , Kim Hee Jin , Lee Jin San , Jang Young Kyoung , Kim Yeshin , Jang Hyemin , Ki Chang-Seok , Youn Young Chul , Shin Byoung-Soo , Bang Oh Young , Kim Gyeong-Moon , Chung Chin-Sang , Kim Seung Joo , Na Duk L. , Duering Marco , Cho Hanna , Seo Sang Won
Published: October 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Reprogramming Escherichia coli for the production of prenylated indole diketopiperazine alkaloids
Authors: Dubois Pavlina , Correia Isabelle , Le Chevalier Fabien , Dubois Steven , Jacques Isabelle , Canu Nicolas , Moutiez Mireille , Thai Robert , Gondry Muriel , Lequin Olivier , Belin Pascal
Published: October 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Endogenous intronic antisense long non-coding RNA, MGAT3-AS1, and kidney transplantation
Authors: Nagarajah Subagini , Xia Shengqiang , Rasmussen Marianne , Tepel Martin
Published: October 2019

β-1,4-mannosylglycoprotein 4-β-N-acetylglucosaminyltransferase (MGAT3) is a key molecule for the innate immune system. We tested the hypothesis that intronic antisense long non-coding RNA, MGAT3-AS1, can predict delayed allograft function after kidney transplantation. We prospectively assessed kidney function and MGAT3-AS1 in 129 incident deceased donor kidney transplant recipients before and after transplantation. MGAT3-AS1 levels were measured in mononuclear cells using qRT-PCR. Delayed graft function was defined by at least one dialysis session within 7 days of transplantation. Delayed graft function occurred in 22 out of 129 transplant recipients (17%). Median MGAT3-AS1 after transplantation was significantly lower in patients with delayed graft function compared to patients with immediate graft function (6.5 × 10−6, IQR 3.0 × 10−6 to 8.4 × 10−6; vs. 8.3 × 10−6, IQR 5.0 × 10−6 to 12.8 × 10−6; p < 0.05). The median preoperative MGAT3-AS1 was significantly lower in kidney recipients with delayed graft function (5.1 × 10−6, IQR, 2.4 × 10−6 to 6.8 × 10−6) compared to recipients with immediate graft function (8.9 × 10−6, IQR, 6.8 × 10−6 to 13.4 × 10−6; p < 0.05). Receiver-operator characteristics showed that preoperative MGAT3-AS1 predicted delayed graft function (area under curve, 0.83; 95% CI, 0.65 to 1.00; p < 0.01). We observed a positive predictive value of 0.57, and a negative predictive value of 0.95. Long non-coding RNA, MGAT3-AS1, indicates short-term outcome in patients with deceased donor kidney transplantation.
A novel ratiometric fluorescent probe for highly sensitive and selective detection of peroxynitrite and its application for tracing endogenous peroxynitrite in live cells
Authors: Li Zilu , Yu Chen , Chen Yanan , Liu Caiyun , Jia Pan , Zhu Hanchuang , Zhang Xue , Sheng Wenlong , Zhu Baocun
Published: October 2019

A novel, highly sensitive and selective ratiometric fluorescent probe was developed to trace endogenous peroxynitrite in live cells.
A folic acid modified polystyrene nanosphere surface for circulating tumor cell capture
Authors: Chen Changchong , Wang Zhili , Zhao Yuewu , Cao Yi , Ding Pi , Liu Hui , Su Na , Pei Renjun
Published: October 2019

A polystyrene nanosphere (PSNP) substrate was developed to capture CTCs from blood samples, and the captured target cells were proliferated using an in situ culture strategy.
Ultrafine cobalt nitride nanoparticles supported on carbon nanotubes as efficient electrocatalyst for rechargeable zinc–air batteries
Authors: Xu Ruizhi , Luo Fang , Li Min , Yang Zehui
Published: October 2019

Ultrafine (5 nm) cobalt nitride nanoparticles supported on carbon nanotubes (CoN/CNT) are reported as air electrodes for rechargeable zinc–air batteries (ZABs).
Designing antiferromagnetically coupled mono-, di- and tri-bridged copper(ii)-based catecholase models by varying the ‘Auxiliary Parts’ of the ligand and anionic co-ligand
Authors: Dasgupta Sanchari , Chakraborty Prateeti , Kundu Priyanka , Kara Hulya , Aullón Gabriel , Zangrando Ennio , Das Debasis
Published: October 2019

The role of the auxiliary part of ligands towards the architecture of copper(ii)-based catecholase models were unveiled with the help of DFT study.
Regioselective [2 + 2] cycloaddition reaction within a pair of polymorphic co-crystals based upon halogen bonding interactions
Authors: Bosch Eric , Kruse Samantha J. , Reinheimer Eric W. , Rath Nigam P. , Groeneman Ryan H.
Published: October 2019

A pair of photoreactive polymorphic co-crystals that undergo a regioselective solid-state [2 + 2] cycloaddition reaction that yields exclusively the head-to-tail photoproduct is reported.