bluuebunny/crossref_metadata_2025 huggingface dataset:
Germaphobia! Does our Relationship with, and Knowledge of Biodiversity Affect our Attitudes Towards Microbes?
Authors: Robinson Jake M. , Cameron Ross , Jorgensen Anna
Published: February 2021

Germaphobia –– a pathological aversion to microorganisms –– could be contributing to an explosion in human immune-related disorders via mass sterilisation of surfaces and reduced exposure to biodiversity. Loss of biodiversity and our connectedness to nature, along with poor microbial literacy may be augmenting the negative consequences of germaphobia on ecosystem health. In this study, we created an online questionnaire to acquire data on attitudes towards, and knowledge of microbes. We collected data on nature connectedness and interactions with nature and explored the relationships between these variables. We found a significant association between attitudes towards microbes and both duration and frequency of visits to natural environments. A higher frequency of visits to nature per week, and a longer duration spent in nature per visit, significantly associated with positive attitudes towards microbes. We found no association between nature connectedness and attitudes towards microbes. We found a significant relationship between knowledge of ‘lesser known’ microbial groups (e.g., identifying that fungi, algae, protozoa, and archaea are microbes) and positive attitudes towards microbes. However, we also found that people who correctly identified viruses as being microbes expressed less positive views of microbes overall –– this could potentially be attributed to a ‘COVID-19 effect’. Our results suggest that basic microbial literacy and nature engagement may be important in reducing/preventing germaphobia. The results also suggest that a virus-centric phenomenon (e.g., COVID-19) could increase broader germaphobia. As the rise of immune-related disorders and mental health conditions have been linked to germaphobia, reduced biodiversity, and non-targeted sterilisation, our findings point to a feasible strategy to potentially help ameliorate these negative consequences. A greater emphasis on microbial literacy and promoting time spent in nature could be useful in promoting resilience in human health and more positive/constructive attitudes towards the foundations of our ecosystems – the microorganisms.
A user manual to measure gas diffusion kinetics in plants: Pneumatron construction, operation and data analysis
Authors: Trabi C.L. , Pereira L. , Guan X. , Miranda M.T. , Bittencourt P.R.L. , Oliveira R.S. , Ribeiro R.V. , Jansen S.
Published: February 2021

The Pneumatron device presented measures gas diffusion kinetics in the xylem of plants. The device provides an easy, low-cost, and powerful tool for research on plant water relations. Here, we describe in detail how to construct and operate this device to estimate xylem vulnerability to embolism, and how to analyse pneumatic data. Simple and more elaborated ways of constructing a Pneumatron are shown, either using wires, a breadboard, or a printed circuit board. The instrument is based on an open-source hardware and software system, which allows users to operate it in an automated or semi-automated way. A step-by-step manual and a troubleshooting section are provided. An excel spreadsheet and an R-script are also presented for fast and easy data analysis. This manual should help new users to avoid common mistakes, especially regarding stable measurements of the minimum and maximum amount of gas that can be discharged from xylem tissue.
Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction
Authors: Kabir Mohammad Faujul , Karami Adam , Cruz-Acuna Ricardo , Klochkova Alena , Saxena Reshu , Mu Anbin , Murray Mary Grace , Keith Kelsey , Madzo Jozef , Huang Hugh , Jelinek Jaroslav , Karakasheva Tatiana , Hamilton Kathryn E. , Muir Amanda B. , Tetreault Marie-Pier , Whelan Kelly A.
Published: February 2021

Stratified squamous epithelium of the esophagus is comprised of basal keratinocytes that execute a terminal differentiation program in overlying suprabasal and superficial cell layers. Although morphologic progression coupled with expression of specific molecular markers has been characterized along the esophageal epithelial differentiation gradient, the molecular heterogeneity within the cell types along this trajectory has yet to be classified at the level of single cell resolution. To explore the molecular characteristics of esophageal keratinocytes along the squamous differentiation continuum, we performed single cell RNA-Sequencing transcriptomic profiling of 7,972 cells from murine esophageal epithelial sheets. We identified 8 distinct cell clusters in esophageal epithelium, unveiling an unexpected level of diversity, particularly among basal cells. We further mapped the cellular pathways and lineage trajectories within basal, suprabasal, and superficial clusters as well as within the heterogeneous basal cell populations, providing a comprehensive molecular view of esophageal epithelial cells in the context of squamous differentiation. Finally, we explored the impact of tissue aging upon esophageal epithelial cell clusters and demonstrated that mitochondrial dysfunction is a feature of aging in normal esophageal epithelium. These studies provide an unparalleled molecular perspective on murine esophageal keratinocytes that will serve as a valuable resource for dissecting cell type-specific roles in esophageal biology under conditions of homeostasis, aging, and tissue pathology.
A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: effects on proteolytic cleavage and ACE2 binding
Authors: Spelios Michael G. , Capanelli Jeanne M. , Li Adam W.
Published: February 2021

SARS-CoV-2 harbors a unique S1/S2 furin cleavage site within its spike protein, which can be cleaved by furin and other proprotein convertases. Proteolytic activation of SARS-CoV-2 spike protein at the S1/S2 boundary facilitates interaction with host ACE2 receptor for cell entry. To address this, high titer antibody was generated against the SARS-CoV-2-specific furin motif. Using a series of innovative ELISA-based assays, this furin site blocking antibody displayed high sensitivity and specificity for the S1/S2 furin cleavage site, and demonstrated effective blockage of both enzyme-mediated cleavage and spike-ACE2 interaction. The results suggest that immunological blocking of the furin cleavage site may afford a suitable approach to stem proteolytic activation of SARS-CoV-2 spike protein and curtail viral infectivity.
Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome
Authors: Prudence Sam , Newitt Jake , Worsley Sarah F. , Macey Michael C. , Murrell J. Colin , Lehtovirta-Morley Laura E. , Hutchings Matthew I.
Published: February 2021

Conventional methods of agricultural pest control and crop fertilisation are contributing to a crisis of biodiversity loss, biogeochemical cycle dysregulation, and ecosystem collapse. Thus, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome may contribute to this goal as microbes can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. We applied 16S rRNA gene & fungal 18S rRNA gene (ITS2 region) amplicon sequencing to profile the diversity of the bacterial, archaeal & fungal communities associated with the roots of UK elite spring bread wheat varietyTriticum aestivum var.Paragon in different soils and developmental stages. This revealed that community composition shifted significantly for all three groups across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these wereStreptomycetaceaeandBurkholderiaceae.Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. To understand which microbes are using wheat root exudates in the rhizosphere, root exudates were labelled in a13CO2DNA stable isotope probing experiment. This shows that bacterial taxa within theBurkholderiaceaefamily among other core enriched taxa, such asPseudomonadaceae,were able to use root exudates butStreptomycetaceaewere not. Overall, this work provides a better understanding of the wheat microbiome, including the endosphere community. Understanding crop microbiome formation will contribute to ecologically responsible methods for yield improvement and biocontrol in the future.
Argonaute Binding within Human Nuclear RNA and its Impact on Alternative Splicing
Authors: Chu Yongjun , Yokota Shinnichi , Liu Jing , Kilikevicius Audrius , Johnson Krystal C. , Corey David R.
Published: February 2021

Mammalian RNA interference (RNAi) is often linked to the regulation of gene expression in the cytoplasm. Synthetic RNAs, however, can also act through the RNAi pathway to regulate transcription and splicing. While nuclear regulation by synthetic RNAs can be robust, a critical unanswered question is whether endogenous functions for nuclear RNAi exist in mammalian cells. Using enhanced crosslinking immunoprecipitation (eCLIP) in combination with RNA sequencing (RNAseq) and multipleAGOknockout cell lines, we mapped AGO2 protein binding sites within nuclear RNA. The strongest AGO2 binding sites were mapped to micro RNAs (miRNAs). The most abundant miRNAs were distributed similarly between cytoplasm and nucleus, providing no evidence for mechanisms that facilitate localization of miRNAs in one compartment versus the other. Beyond miRNAs, most statistically-significant AGO2 binding was within introns. Splicing changes were confirmed by RT-PCR and were recapitulated by synthetic duplex RNAs and miRNA mimics complementary to the sites of AGO2 binding. These data support the hypothesis that miRNAs can control gene splicing. While nuclear RNAi proteins have the potential to be a natural regulatory mechanism, careful study will be necessary to identify critical RNA drivers of normal physiology and disease.
Customized de novo mutation detection for any variant calling pipeline: SynthDNM
Authors: Lian Aojie , Guevara James , Xia Kun , Sebat Jonathan
Published: February 2021

Motivation

As sequencing technologies and analysis pipelines evolve, DNM calling tools must be adapted. Therefore, a flexible approach is needed that can accurately identify de novo mutations from genome or exome sequences from a variety of datasets and variant calling pipelines.

Results

Here, we describe SynthDNM, a random-forest based classifier that can be readily adapted to new sequencing or variant-calling pipelines by applying a flexible approach to constructing simulated training examples from real data. The optimized SynthDNM classifiers predict de novo SNPs and indels with robust accuracy across multiple methods of variant calling.

Availability

SynthDNM is freely available on Github (https://github.com/james-guevara/synthdnm)

Contact

jsebat@ucsd.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
Brief stimuli cast a persistent long-term trace in visual cortex
Authors: Fritsche Matthias , Solomon Samuel G. , de Lange Floris P.
Published: February 2021

Visual processing is strongly influenced by the recent stimulus history – a phenomenon termed adaptation. Prominent theories cast adaptation as a consequence of optimized encoding of visual information, by exploiting the temporal statistics of the world. However, this would require the visual system to track the history of individual briefly experienced events, within a stream of visual input, to build up statistical representations over longer timescales. Here, using an openly available dataset from the Allen Brain Observatory, we show that neurons in the early visual cortex of the mouse indeed maintain long-term traces of individual past stimuli that persist despite the presentation of several intervening stimuli, leading to long-term and stimulus-specific adaptation over dozens of seconds. Long-term adaptation was selectively expressed in cortical, but not in thalamic neurons, which only showed short-term adaptation. Early visual cortex thus maintains concurrent stimulusspecific memory traces of past input, enabling the visual system to build up a statistical representation of the world to optimize the encoding of new information in a changing environment.

Significance Statement

In the natural world, previous sensory input is predictive of current input over multi-second timescales. The visual system could exploit these predictabilities by adapting current visual processing to the long-term history of visual input. However, it is unclear whether the visual system can track the history of individual briefly experienced images, within a stream of input, to build up statistical representations over such long timescales. Here, we show that neurons in early visual cortex of the mouse brain exhibit remarkably long-term adaptation to brief stimuli, persisting over dozens of seconds, and despite the presentation of several intervening stimuli. The visual cortex thus maintains long-term traces of individual briefly experienced past images, enabling the formation of statistical representations over extended timescales.
Structures of the germline-specific Deadhead and thioredoxin T proteins fromDrosophila melanogasterreveal unique features among thioredoxins
Authors: Freier Regina , Aragón Eric , Bagiński Błażej , Pluta Radoslaw , Martin-Malpartida Pau , Ruiz Lidia , Condeminas Miriam , Gonzalez Cayetano , Macias Maria J.
Published: February 2021

Thioredoxins (Trxs) are ubiquitous enzymes that regulate the redox state in cells. InDrosophila, there are two germline-specific Trxs, Deadhead (Dhd) and thioredoxin T (TrxT), that belong to the lethal(3)malignant brain tumor signature genes and to the `survival network' of genes that mediate the cellular response to DNA damage. Dhd is a maternal protein required for early embryogenesis that promotes protamine–histone exchange in fertilized eggs and midblastula transition. TrxT is testis-specific and associates with the lampbrush loops of the Y chromosome. Here, the first structures of Dhd and TrxT are presented, unveiling new features of these two thioredoxins. Dhd has positively charged patches on its surface, in contrast to the negatively charged surfaces commonly found in most Trxs. This distinctive charge distribution helps to define initial encounter complexes with DNA/RNA that will lead to final specific interactions with cofactors to promote chromatin remodeling. TrxT contains a C-terminal extension, which is mostly unstructured and highly flexible, that wraps the conserved core through a closed conformation. It is believed that these new structures can guide future work aimed at understanding embryo development and redox homeostasis inDrosophila. Moreover, due to their restricted presence in Schizophora (a section of the true flies), these structures can help in the design of small-molecular binders to modulate native redox homeostasis, thereby providing new applications for the control of plagues that cause human diseases and/or bring about economic losses by damaging crop production.
CSR disclosure and firm performance: evidence from an emerging market
Authors: P. Fahad , Busru Showkat Ahmad
Published: February 2021

Purpose

This study aims to investigate the effect of corporate social responsibility (CSR) disclosure on firm performance, considering both firm profitability and firm value in an emerging market, India.

Design/methodology/approach

The study examines the effect of CSR disclosure on firm performance using panel regressions for the final sample that consists of 386 companies listed in the BSE 500 index, India. It covers all major players in the capital market for ten years from 2007–2016.

Findings

The result shows a trend toward the negative effect of CSR disclosure on firm profitability and firm value in India; this negative effect is mainly influenced by environmental disclosure score and social disclosure score. An adverse effect of firm profitability and firm value on CSR disclosure is also observed to underline the inverse relationship.

Practical implications

The study provides implications to consumers, investors, managers and policymakers. Firstly, consumers have to be more aware of CSR initiatives of companies, and they should support those companies to do more. Secondly, investors can use the ESG disclosure score as a signal for the level of CSR activities, which negatively affects firm performance. Thirdly, managers have to consider CSR more seriously and spend CSR amount wisely after proper research and not just to meet the mandatory limit. In addition, managers have to take necessary actions to make the public aware of the CSR activities of the company to gain an advantage in the future. Finally, policymakers have to give more emphasis on the promotion of CSR activities to reach the ultimate consumers who lie in the remote areas of the country, and more awareness has to be given to them regarding CSR activities.

Originality/value

The findings contribute to the literature by providing insights on CSR disclosure and firm performance relationship in India, an emerging market with increasing international attention where such studies are scant and less clear, especially after the amendments in the Companies Act, 2013. Furthermore, the measurement of CSR disclosure using environmental, social and governance (ESG) score is novel in the Indian context.
Constraint absorption in emerging economies: the role of business groups
Authors: Ahmed Mueen , Pratap Sankalp
Published: February 2021

Purpose

The purpose of this paper is to highlight the motivation for firms in emerging economies to engage in constraint absorption. It illustrates the mechanisms that enable business group (BG) affiliated firms to manage interdependencies vis-à-vis standalone firms in emerging economies.

Design/methodology/approach

The propositions outlined in this study are rooted in the theoretical lens of resource dependence theory (RDT). The authors integrate RDT with the resource-based view and institutional theory to explain the effect of BG affiliation on the relationship between the two types of interdependence (i.e. mutual dependence and power imbalance) and the likelihood of constraint absorption.

Findings

This paper theorizes that BG affiliation influences the relationship between mutual dependence/power imbalance and the likelihood of constraint absorption. However, if both the firms in a dyad are affiliated to a BG, the likelihood of constraint absorption is likely to be low owing to a process called “co-optation” even if mutual dependence or power imbalance between the firms is high.

Originality/value

This paper highlights how BG affiliated firms are better at managing contingencies in the external environment vis-à-vis standalone firms. This paper also advises managers that the type of organizational form is an important factor to be considered while engaging in constraint absorption in an emerging economy.
Prioritising the mobilisation of emergency medical services: patient making at the healthcare gateway
Authors: Allen Davina
Published: February 2021

Purpose

The purpose of this paper is to analyse the socio-material practices through which organisational understanding of patients is accomplished in order to prioritise calls and mobilise emergency medical services at the gateway of the healthcare system.

Design/methodology/approach

The methodology of this paper is an ethnographic study of the co-ordination of collective action in an emergency services control room in the Welsh NHS, with data generation and analysis informed by Translational Mobilisation Theory.

Findings

Mobilisation of emergency medical services entails the translation of callers' undifferentiated problems into response priority categories, which are used by dispatch operators to mobilise crews. A central actor in these processes is the computerised Medical Priority Dispatch System. While designed to enable non-clinically qualified call handlers to triage calls in a standardised way, the system constrains caller–call handler interaction, which negatively impacts the categorisation process. Analysis of these interactional difficulties and associated mitigation strategies highlights opportunities for intervening to support co-ordination at this healthcare boundary.

Originality/value

Orthodox approaches to improving interface management are founded on a conceptualisation of “patients” as immutable actors in care transfer processes. Translational Mobilisation Theory brings into view the multiple versions of the “patient” produced by healthcare systems and offers a framework for analysing the mechanisms of action necessary to create organisational understandings of patients at boundary crossings. While the ambulance control centre is a singular case, the paper illustrates the value of attending to these processes in interface organisation.
Integrated thinking, orchestration of the six capitals and value creation
Authors: Herath Roshan , Senaratne Samanthi , Gunarathne Nuwan
Published: February 2021

Purpose

This paper aims to explore how the integrated thinking of a chief executive officer (CEO) impacts the management’s orchestration of the six capitals to create value in an organization.

Design/methodology/approach

Following a case study approach, data was gathered on two business organizations in Sri Lanka through interviews, focus group discussions and documentary analyzes. Thematic and cross-case analyzes were used in analyzing the data based on an analytical framework that was developed using systems and resource orchestration theories.

Findings

The study finds that the integrated thinking perspective of the CEO determines which capitals to embrace in the pursuit of value creation by an organization. A broader perspective on the integrated thinking of the CEO can lead to a sustainable perspective for value creation focusing on integrated corporate responsibility. On the contrary, a constrained perspective of integrated thinking can lead to a business case perspective for value creation that focuses mainly on the key areas of responsibility extended for operational efficiency. These different perspectives result in differences in value creation in organizations over time.

Practical implications

The capitals embraced in the integrated thinking perspective of a CEO should be translated into objectives, strategies and performance measurement and implemented at every level of the company to create value. This perspective of a CEO can be institutionalized through the adoption of accredited management systems. To foster value creation, managers should use a variety of information technology platforms and internal networks.

Originality/value

This is one of the first studies that explore how the perception of integrated thinking of the CEO impacts value creation in an organization through a combination of resource orchestration and systems thinking theory lenses.
Parametric study on tensile and flexural properties of ULTEM 1010 specimens fabricated via FDM
Authors: Pandelidi Chrysoula , Maconachie Tobias , Bateman Stuart , Kelbassa Ingomar , Piegert Sebastian , Leary Martin , Brandt Milan
Published: February 2021

Purpose

Fused deposition modelling (FDM) is increasingly being explored as a commercial fabrication method due to its ability to produce net or near-net shape parts directly from a computer-aided design model. Other benefits of technology compared to conventional manufacturing include lower cost for short runs, reduced product lead times and rapid product design. High-performance polymers such as polyetherimide, have the potential for FDM fabrication and their high-temperature capabilities provide the potential of expanding the applications of FDM parts in automotive and aerospace industries. However, their relatively high glass transition temperature (215 °C) causes challenges during manufacturing due to the requirement of high-temperature build chambers and controlled cooling rates. The purpose of this study is to investigate the mechanical properties of ULTEM 1010, an unfilled polyetherimide grade.

Design/methodology/approach

In this research, mechanical properties were evaluated through tensile and flexural tests. Analysis of variance was used to determine the significance of process parameters to the mechanical properties of the specimens, their main effects and interactions. The fractured surfaces were analysed by scanning electron microscopy and optical microscopy and porosity was assessed by X-ray microcomputed tomography.

Findings

A range of mean tensile and flexural strengths, 60–94 MPa and 62–151 MPa, respectively, were obtained highlighting the dependence of performance on process parameters and their interactions. The specimens were found to fracture in a brittle manner. The porosity of tensile samples was measured between 0.18% and 1.09% and that of flexural samples between 0.14% and 1.24% depending on the process parameters. The percentage porosity was found to not directly correlate with mechanical performance, rather the location of those pores in the sample.

Originality/value

This analysis quantifies the significance of the effect of each of the examined process parameters has on the mechanical performance of FDM-fabricated specimens. Further, it provides a better understanding of the effect process parameters and their interactions have on the mechanical properties and porosity of FDM-fabricated polyetherimide specimens. Additionally, the fracture surface of the tested specimens is qualitatively assessed.
Cannot give you because of living on the top of a castle: CEOs, corporate philanthropy and firm age
Authors: Cha Wonsuk , Rew Dongjun
Published: February 2021

Purpose

This study aims to investigate the role of firm age in the relationship between CEO characteristics (measured by founder status and civic engagement) and the level of corporate philanthropy which is one of the important components of corporate social responsibility (CSR) practices (Carroll, 1991).

Design/methodology/approach

Drawing from upper echelons theory, this study argues that firm age functions as a barrier that limits the relationship between CEO characteristics and the level of corporate philanthropy. Moderated regression analysis (MRA) was used to analyze data from 146 publicly traded US firms between 2010 and 2017.

Findings

This study verified that there is a significantly positive relationship between CEO civic engagement and the level of corporate philanthropy although the relationship between CEO founder status and the level of corporate philanthropy was not found to be significant. Specifically, the relationship between CEO characteristics and the level of corporate philanthropy was weaker as firms get older. Overall, the results indicate that the organizational inertia of older firms can restrict the effect of CEO characteristics on corporate philanthropy.

Research limitations/implications

This study provides new insight into the underlying mechanisms between CEOs and firm age. This study also suggests that CEOs interpret corporate philanthropy as an important part of their civic engagement which broadly supports business legitimacy for their firm.

Practical implications

This study provides lessons for executive selection and succession decisions toward CSR strategies. Specifically, this study provides a practical foundation of how executives’ civic engagement can be related to corporate philanthropy as an important dimension of CSR practices. Furthermore, this study suggests that shareholders pay more attention to the ultimate decision-maker, the CEO, in an organization as his or her background characteristics can reflect a firm’s social responsibility initiatives, including corporate philanthropy.

Originality/value

This study contributes to on-going scholarly work in the field of strategic leadership and corporate philanthropy literature. In addition, this study provides empirical evidence to the nature of scholarly conversations regarding the role of firm age in shaping the relationship between CEO characteristics and corporate philanthropy.
Recent changes in mountain birch forest structure and understory vegetation depend on the seasonal timing of reindeer grazing
Authors: Stark Sari , Ylänne Henni , Kumpula Jouko
Published: February 2021

Subarctic forest‐tundra ecotones dominated by mountain birch (Betula pubescens ssp. czerepanovii) are an important habitat for semi‐domestic reindeer Rangifer tarandus. The seasonal timing of reindeer grazing may direct vegetation trajectories in these systems, because in the summer ranges, mountain birches are subjected to browsing, while in the winter ranges, reindeer feed on understorey vegetation and arboreal lichens but leave the mountain birches intact.

Based on earlier research, we predicted that (a) summer browsing dampens ongoing vegetation ‘shrubification’ in semi‐dry and dry mountain birch forests and (b) ‘shrubification’ is accompanied by a decline in lichens. We tested these predictions through re‐analysing forest structure and understorey vegetation after 12 years in areas where winter and summer ranges had been separated since the 1980s. We also tested how changes in lichen abundances align with changes in shrub abundances through correlation analyses.

The number of tall mountain birch seedlings had increased twice as fast in winter than summer ranges, while big mountain birches had increased in summer ranges. The dominant evergreen dwarf shrub mountain crowberry (Empetrum nigrum ssp. hermaphroditum) had increased to a greater extent in winter ranges in a semidry habitat, and to a greater extent in summer ranges in a dry habitat. Deciduous dwarf shrub and graminoid biomass had increased similarly in summer and winter ranges.

We found no evidence to support that increasing shrub abundances had contributed to a decline in lichens; instead, the lichen cover increased with increasing number of mountain birch seedlings.

Synthesis and application. The vegetation trajectories of dry and semi‐dry subarctic mountain birch forests depend greatly on whether the area is used as a winter or a summer range for the reindeer. The recent changes in vegetation are likely to lead to improved summer forage availability for the reindeer, while the opposite may be true for the winter forage availability.
Low CyaA expression and anti‐cooperative binding of cAMP to CRP frames the scope of the cognate regulon of Pseudomonas putida
Authors: Arce‐Rodríguez Alejandro , Nikel Pablo I. , Calles Belén , Chavarría Max , Platero Raúl , Krell Tino , de Lorenzo Victor
Published: February 2021

Although the soil bacterium Pseudomonas putida KT2440 bears a bona fide adenylate cyclase gene (cyaA), intracellular concentrations of 3′,5′‐cyclic adenosine monophosphate (cAMP) are barely detectable. By using reporter technology and direct quantification of cAMP under various conditions, we show that such low levels of the molecule stem from the stringent regulation of its synthesis, efflux and degradation. Poor production of cAMP was the result of inefficient translation of cyaA mRNA. Moreover, deletion of the cAMP‐phosphodiesterase pde gene led to intracellular accumulation of the cyclic nucleotide, exposing an additional cause of cAMP drain in vivo. But even such low levels of the signal sustained activation of promoters dependent on the cAMP‐receptor protein (CRP). Genetic and biochemical evidence indicated that the phenomenon ultimately rose from the unusual binding parameters of cAMP to CRP. This included an ultratight cAMP‐CrpP. putida affinity (KD of 45.0 ± 3.4 nM) and an atypical 1:1 effector/dimer stoichiometry that obeyed an infrequent anti‐cooperative binding mechanism. It thus seems that keeping the same regulatory parts and their relational logic but changing the interaction parameters enables genetic devices to take over entirely different domains of the functional landscape.
The sensory and physical properties of Shortbread biscuits cooked using different sucrose granule size fractions
Authors: Tyuftin Andrey A. , Richardson Aislinn M. , O’ Sullivan Maurice G. , Kilcawley Kieran N. , Gallagher Eimear , Kerry Joseph P.
Published: February 2021

A rich sugar diet has negative health implications so it is necessary to reduce sugar where possible. The objective of this study was to determine if different sugar size fractions could increase the sweetness intensity of Shortbread biscuits and therefore, permit sugar reduction. For this, the unground commercial sugar (Control, 102 to 378 µm) and two of its sieved separates, (Coarse (C), 228 to 377 µm and Fine (F), 124 to 179 µm) were investigated in biscuit formulation with the following content: Control 100% or 50%; (C), 100 or 50% and (F), 100 or 50% or its initial content. Biscuits were tested using sensory (hedonic and intensity), physical (dimensions, fracture properties, color), and compositional analyses. Trends showed that samples containing C‐sugar with its 50% content were more preferable than samples containing the Control and F‐ sugar fractions at the same level without impact upon acceptability of the final product in all three sugar fraction sizes. As sweetness intensity scores correlated directly with flavor liking scores, these findings promote the use of this sugar fraction in the formulation of low‐sugar baked biscuits. Sugar particle size manipulation could be used as a viable, cheap, technological approach to reduce sugar in baked goods and therefore promote consumer acceptable and commercially available baked biscuits products.

Practical Application

In order to reduce sucrose content in products one of the approaches might be via the utilization of small sugar particles which has been shown to increase the intensity of sweetness in chocolate brownies, which has been previously shown by Richardson et al. in 2018. This study investigates the use of a clean label approach in sugar reduction of short bread biscuits. This approach involves decreasing the sugar particles size and demonstrates how reducing the content to half of its initial content formulation will affect the sensory perception and physical properties.
Effect of cyclooxygenase inhibitor use on immunotherapy efficacy in non‐small cell lung cancer
Authors: Kanai Osamu , Ito Takanori , Saito Zentaro , Yamamoto Yuki , Fujita Kohei , Okamura Misato , Hashimoto Masayuki , Nakatani Koichi , Sawai Satoru , Mio Tadashi
Published: February 2021

Background

A synergistic effect of cyclooxygenase inhibitors (COX‐I) and immune checkpoint inhibitors (ICIs) has been suggested. However, the impact of COX‐I on the efficacy of ICIs is unclear. Here, we aimed to evaluate the relationship between COX‐I use and the efficacy of ICI in patients with non‐small cell lung cancer (NSCLC).

Methods

We retrospectively reviewed NSCLC patients who received ICI monotherapy. We defined COX‐I use as regular use of COX‐I other than low‐dose aspirin during the initiation of ICIs to the first evaluation of efficacy. The efficacy of ICIs was evaluated with response rate (RR), disease control rate (DCR), progression free survival (PFS), and overall survival (OS). Differences in baseline characteristics by COX‐I use were controlled by using an inverse probability of treatment weighting (IPW) adjusted analysis.

Results

A total of 198 patients with NSCLC received ICIs; 128, 50, and 20 patients received nivolumab, pembrolizumab, and atezolizumab, respectively; there were 65 (32.8%) COX‐I users. While there was no significant difference in RR (15.4% vs. 13.5%; p = 0.828), DCR (41.5% vs. 49.6%; p = 0.294), PFS (median, 2.69 vs. 3.68 months; 95% confidence intervals [CI], 1.77–5.19 vs. 2.20–4.60 months; p = 0.630), COX‐I users had significantly shorter OS than non‐COX‐I users (median, 6.08 vs. 16.10 months; 95% CI: 3.78–11.66 vs. 9.49–19.68 months; p = 0.003). On IPW adjusted analysis, there was no significant difference in OS (median, 7.85 vs. 15.11 months; 95% CI: 5.03–14.92 vs. 9.49–19.32 months; p = 0.081).

Conclusions

There was no additional or negative impact of COX‐I use on the efficacy of ICIs in NSCLC.
GPSeqClus: An R package for sequential clustering of animal location data for model building, model application and field site investigations
Authors: Clapp Justin G. , Holbrook Joseph D. , Thompson Daniel J.
Published: February 2021

Evaluating the concentration of animal locations, in space and time, provides insight regarding animal activity and behaviour. Most commonly collected via global positioning system technology, these concentrations are identified using rule sets resulting in location ‘clusters’. Cluster algorithms provide a framework for modelling and predicting behavioural states when paired with field data to evaluate habitat characteristics and validate results.

We provide a sequential clustering algorithm package (GPSeqClus) to process location datasets based on user‐defined parameters. GPSeqClus also calculates an array of movement attributes commonly applied as covariates to develop cluster‐based models. Our package maps locations and clusters, with additional functions to assess specific clusters for site investigations and to export GPS Exchange format (.gpx) files for navigation. We highlight the ability of GPSeqClus to modify existing cluster attributes or to append additional attributes, and the flexibility to accommodate archived or near real‐time (satellite‐driven) datasets.

Although spatio‐temporal clustering is widely used in animal ecology, clustering routines are commonly applied to assess carnivore movement patterns to predict denning or feeding locations, evaluate prey composition and estimate kill rates and handling times. We demonstrate the applicability of GPSeqClus by constructing clusters using mountain lion Puma concolor location data.

Our package provides an efficient data processing routine to build, characterize, visualize and navigate to clusters. Attributes provided within GPSeqClus can be used when developing predictive cluster models, or can be applied to other modelling procedures to advance understandings of animal behaviour.
High abundance and large proportion of medium and large duikers in an intact and unhunted afrotropical protected area: Insights into monitoring methods
Authors: Breuer Thomas , Breuer‐Ndoundou Hockemba Mireille , Opepa Cisquet Kiebou , Yoga Sarah , Mavinga Franck Barrel
Published: February 2021

Unsustainable hunting of bushmeat has dramatic impacts on ecological processes and people's livelihoods. Unfortunately, there is often a strong controversy regarding the sustainability of duiker hunting due to their continued presence in bushmeat markets, on the one hand, and the predictions of sustainable harvest models for duiker abundance, on the other. This apparent contradiction is largely due to biased low abundance estimates from dung surveys. We present results from a 52.4 km line transect dung survey using site decay rates to estimate duiker densities. In addition, camera trapping (14,995 camera trap‐days) was used to provide detection rates and a baseline for the ratio of blue to red duikers as an index of hunting pressure from Nouabalé‐Ndoki National Park, with almost zero levels of hunting. Dung surveys revealed high overall duiker densities (totalling 107.4 duikers per km2) and quick dung decay rate. Camera trapping revealed high‐duiker detection rates and a high ratio of red to blue duikers. Pristine protected areas and no‐hunting zones continue to act as source habitats for high recruitment of harvested species. We discuss future options for monitoring duikers and applying the ratio of red to blue duikers as an index of the level of duiker hunting.
How Does Minority Political Representation Affect School District Administration and Student Outcomes?
Authors: Kogan Vladimir , Lavertu Stéphane , Peskowitz Zachary
Published: February 2021

We employ a regression discontinuity design leveraging close school board elections to investigate how the racial and ethnic composition of California school boards affects school district administration and student achievement. We find some evidence that increases in minority representation lead to cumulative achievement gains of approximately 0.1 standard deviations among minority students by the sixth post‐election year. These gains do not come at the expense of white students' academic performance, which also appears to improve. Turning to the policy mechanisms that may explain these effects, we find that an increase in minority representation leads to greater capital funding and a larger proportion of district principals who are non‐white. We find no significant effects of minority representation on school segregation, the reclassification of English language learners, or teacher staffing.
The impact of peripheral arterial disease on left ventricular assist device implantation: A propensity‐matched analysis of the nationwide inpatient sample database
Authors: Ullah Waqas , Zahid Salman , Thalambedu Nishant , Khan Maria , Massey Howard , Haas Donald , Tchantchaleishvili Vakhtang , Rame Eduardo
Published: February 2021

Left ventricular assist device (LVAD) candidacy screening includes evaluation for peripheral arterial disease (PAD). However, given current evidence, the impact of PAD on post‐LVAD complications remains unknown. The National Inpatient Sample (NIS) database (2002‐2017) was utilized to identify all LVAD cases. The in‐hospital safety endpoints included major cardiovascular adverse events and its components. A propensity‐matched analysis was used to obtain adjusted odds ratios (aOR). A subgroup analysis of patients with diabetes mellitus (DM) with PAD was also performed. A total of 27 424 patients with LVAD implantation (PAD: 516 [1.8%] and no‐PAD 26 908 [98.2%]) were included. There were significant intergroup differences in the demographics and baseline comorbidities. A weighted sample of 1053 (no‐PAD 537, PAD 516) propensity‐matched population was selected. The adjusted odds for in‐hospital mortality (aOR 1.7; 95% CI, 1.2‐2.44, P = .004) were found to be significantly higher for LVAD‐patients with PAD. There was no significant difference in the adjusted odds of MACE (aOR 1.16, 95% CI 0.87‐1.5), postprocedure bleeding (aOR 0.88, 95% CI 0.62‐1.26, P = .54) and risk of pneumonia (aOR 0.67, 95% CI 0.44‐1.15, P = .63) between the two groups. A selected cohort of DM‐only population (7339) consistently showed a higher adjusted mortality rate in PAD patients with LVAD implantation (aOR 2.3, 95% CI 1.2‐4.47, P = .01). The rate of MACE (P = .17), myocardial infarction (P = .12), stroke (P = .60), postprocedural (0.10), and major bleeding (P = .51) remained identical between patients with PAD and those with no‐PAD. PAD confers an increased risk of in‐hospital all‐cause mortality in patients undergoing LVAD implantation. This risk increases further in patients with a concomitant diagnosis of DM.
Biocompatibility performance evaluation of high flux hydrophilic CO3Ap/HAP/PSF composite membranes for hemodialysis application
Authors: Zaman Shafiq Uz , Saif‐ur‐Rehman  , Zaman Muhammad Khaliq U , Arshad Amber , Rafiq Sikander , Muhammad Nawshad , Saqib Sidra , Jamal Muddasar , Wajeeh Salman , Imtiaz Sania , Sadiq Muhammad Tahseen
Published: February 2021

Carbonate apatite/hydroxyapatite (CO3Ap/HAP) additive was obtained by calcination of wasted chicken bones at 900°C. Intermolecular attraction exists between CO3Ap/HAP additive and blended polysulfone (PSF) polymer. Electron dispersive X‐ray (EDX) and FTIR analysis were carried out to check the elemental composition and bonding chemistry of prepared additive. The instantaneous demixing process generated consistent finger‐like networks in CO3Ap/HAP/PSF‐based composite membranes while sponge‐like structure was shown by PSF as revealed by SEM images. The increase in weight % of additive loading is also confirmed by EDX analysis. Furthermore, the interaction mechanism of CO3Ap/HAP additive with polysulfone medium was analyzed by FTIR exploration. The water absorption experiment defined a 93% expansion in hydrophilic performance. Change in porosity occurs with additive loading and pure water permeation flux improved up to 11 times. Approximately, antifouling results revealed that 87% of water flux was recovered after treating with a protein solution, whereas a 30% improvement in antifouling capability in case of bovine serum albumin solution occurred. In vitro cytotoxicity, and clotting times study was carried out to evaluate virulent behavior and anticoagulation activity of formulated membranes.
Elevated sputum IL‐36 levels are associated with neutrophil‐related inflammation in COPD patients
Authors: Li Wei , Meng Xiaoli , Hao Yuqiu , Chen Mo , Jia Yuxi , Gao Peng
Published: February 2021

Background

Interleukin (IL)‐36, including IL‐36α, IL‐36β, and IL‐36γ in the IL‐1 family, are agonists of their receptors. IL‐36 expression is associated with inflammation, including lung infection in humans. However, there is no information on its role in the inflammation of different types of chronic obstructive pulmonary disease (COPD).

Objective

This study focused on the sputum IL‐36α, IL‐36β, and IL‐36γ levels in stable COPD patients and their relationship with lung function and other cytokines in different inflammatory types of COPD patients.

Methods

Sputum specimens were collected from 73 stable COPD patients and 20 age‐ and gender‐matched healthy controls. The levels of sputum IL‐36α, IL‐36β, and IL‐36γ and other cytokines were quantified and sputum cells were characterized. The potential relationship between the levels of sputum IL‐36α, IL‐36β, or IL‐36γ and lung functional measures, inflammatory cells, and cytokines was analyzed.

Results

In comparison with the healthy controls, sputum IL‐36α and IL‐36γ levels significantly increased in COPD (106.8 pg/mL vs. 76.9 pg/mL P =.001, 397.9 pg/mL vs. 359.5 pg/mL P =.006). The sputum IL‐36α and IL‐36γ levels were significantly higher in the neutrophilic and mixed granulocytic types than that in the eosinophilic and paucigranulocytic types of COPD patients. The sputum IL‐36α levels were positively correlated with sputum IL‐36γ levels and the numbers of sputum neutrophils, and the sputum IL‐36γ levels were positively correlated with the numbers of sputum lymphocytes in COPD patients.

Conclusions

Elevated levels of sputum IL‐36α and IL‐36γ were detected in COPD patients and may provide insights into the inflammatory pathways in neutrophilic COPD.