bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid genomic expansion and purging associated with habitat transitions in a clade of beach crustaceans (Haustoriidae: Amphipoda)
Authors: Hancock Zachary B. , Hardin Faith O. , Murthy Archana , Hillhouse Andrew , Johnston J. Spencer
Published: August 2020

Genome sizes vary by orders of magnitude across the Tree of Life and lack any correlation with organismal complexity. Some crustacean orders, such as amphipods, have genome sizes that correlate with body size, temperature, and water depth, indicating that natural selection may constrain genome sizes due to physiological pressures. In this study, we examine the relationship between genome size, repetitive content, and environmental variables on a clade of sand-burrowing amphipods (Haustoriidae) that are distributed across the Gulf of Mexico and the North Atlantic. We uncover a 6-fold genome size variation within a clade that is less than 7 million years old. Unlike previous studies, we find no correlation between genome size and latitude, but do uncover a significant relationship between genome size and body length. Further, we find that the proportion of repetitive content predicts genome size, and that the largest genomes appear to be driven by expansions of LINE elements. Finally, we find evidence of genomic purging and body size reduction in two lineages that have independently colonized warm brackish waters, possibly indicating a strong physiological constraint of transitioning from surf-swept beaches to protected bays.

Significance Statement

The evolution of genome size has been a long-standing puzzle in biology. In this work, we find that genome sizes may be driven by different selection regimes following shifts to a new habitat. Dramatic genome size changes can occur rapidly, in only a few million years.

Data Availability Statement

Raw data sheets have been deposited on Dryad: SUBMITTED. Raw sequence reads are available at from NCBI under Bioproject SUBMITTED.
The immunodominant and neutralization linear epitopes for SARS-CoV-2
Authors: Lu Shuai , Xie Xi-xiu , Zhao Lei , Wang Bin , Zhu Jie , Yang Ting-rui , Yang Guang-wen , Ji Mei , Lv Cui-ping , Xue Jian , Dai Er-hei , Fu Xi-ming , Liu Dong-qun , zhang Lun , Hou Sheng-jie , Yu Xiao-lin , Wang Yu-ling , Gao Hui-xia , Shi Xue-han , Ke Chang-wen , Ke Bi-xia , Jiang Chun-guo , Liu Rui-tian
Published: August 2020

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becomes a tremendous threat to global health. Although vaccines against the virus are under development, the antigen epitopes on the virus and their immunogenicity are poorly understood. Here, we simulated the three-dimensional structures of SARS-CoV-2 proteins with high performance computer, predicted the B cell epitopes on spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins of SARS-CoV-2 using structure-based approaches, and then validated the epitope immunogenicity by immunizing mice. Almost all 33 predicted epitopes effectively induced antibody production, six of which were immunodominant epitopes in patients identified via the binding of epitopes with the sera from domestic and imported COVID-19 patients, and 23 were conserved within SARS-CoV-2, SARS-CoV and bat coronavirus RaTG13. We also found that the immunodominant epitopes of domestic SARS-CoV-2 were different from that of the imported, which may be caused by the mutations on S (G614D) and N proteins. Importantly, we validated that eight epitopes on S protein elicited neutralizing antibodies that blocked the cell entry of both D614 and G614 pseudo-virus of SARS-CoV-2, three and nine epitopes induced D614 or G614 neutralizing antibodies, respectively. Our present study shed light on the immunodominance, neutralization, and conserved epitopes on SARS-CoV-2 which are potently used for the diagnosis, virus classification and the vaccine design tackling inefficiency, virus mutation and different species of coronaviruses.
Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element
Authors: Schlick T. , Zhu Q. , Jain S. , Yan S.
Published: August 2020

With the rapid rate of Covid-19 infections and deaths, treatments and cures besides hand washing, social distancing, masks, isolation, and quarantines are urgently needed. The treatments and vaccines rely on the basic biophysics of the complex viral apparatus. While proteins are serving as main drug and vaccine targets, therapeutic approaches targeting the 30,000 nucleotide RNA viral genome form important complementary approaches. Indeed, the high conservation of the viral genome, its close evolutionary relationship to other viruses, and the rise of gene editing and RNA-based vaccines all argue for a focus on the RNA agent itself. One of the key steps in the viral replication cycle inside host cells is the ribosomal frameshifting required for translation of overlapping open reading frames. The frameshifting element (FSE), one of three highly conserved regions of coronaviruses, includes an RNA pseudoknot considered essential for this ribosomal switching. In this work, we apply our graph-theory-based framework for representing RNA secondary structures, “RAG” (RNA-As Graphs), to alter key structural features of the FSE of the SARS-CoV-2 virus. Specifically, using RAG machinery of genetic algorithms for inverse folding adapted for RNA structures with pseudoknots, we computationally predict minimal mutations that destroy a structurally-important stem and/or the pseudoknot of the FSE, potentially dismantling the virus against translation of the polyproteins. Additionally, our microsecond molecular dynamics simulations of mutant structures indicate relatively stable secondary structures. These findings not only advance our computational design of RNAs containing pseudoknots; they pinpoint to key residues of the SARS-CoV-2 virus as targets for anti-viral drugs and gene editing approaches.

SIGNIFICANCE

Since the outbreak of Covid-19, numerous projects were launched to discover drugs and vaccines. Compared to protein-focused approaches, targeting the RNA genome, especially highly conserved crucial regions, can destruct the virus life cycle more fundamentally and avoid problems of viral mutations. We choose to target the small frame-shifting element (FSE) embedded in the Open Reading Frame 1a,b of SARS-CoV-2. This FSE is essential for translating overlapping reading frames and thus controlling the viral protein synthesis pathway. By applying graph-theory-based computational algorithms, we identify structurally crucial residues in the FSE as potential targets for anti-viral drugs and gene editing.
Tissue pressure and cell traction compensate to drive robust aggregate spreading
Authors: Yousafzai M. S. , Yadav V. , Amiri S. , Staddon M.F. , Tabatabai A. P. , Errami Y. , Jaspard G. , Amiri S. , Banerjee S. , Murrell M.
Published: August 2020

In liquid droplets, the balance of interfacial energies and substrate elasticity determines the shape of the droplet and the dynamics of wetting. In living cells, interfacial energies are not constant, but adapt to the mechanics of their environment. As a result, the forces driving the dynamics of wetting for cells and tissues are unclear and may be context specific. In this work, using a combination of experimental measurements and modeling, we show the surface tension of cell aggregates, as models of active liquid droplets, depends upon the size of the aggregate and the magnitude of applied load, which alters the wetting dynamics. Upon wetting rigid substrates, traction stresses are elevated at the boundary, and tension drives forward motion. By contrast, upon wetting compliant substrates, traction forces are attenuated, yet wetting occurs at a comparable rate. In this case, capillary forces at the contact line are elevated and aggregate surface tension contributes to strong outward, pressure-driven cellular flows. Thus, cell aggregates adapt to the mechanics of their environments, using pressure and traction as compensatory mechanisms to drive robust wetting.
Confinement Discerns Swarmers from Planktonic Bacteria
Authors: Chen Weijie , Mani Neha , Karani Hamid , Li Hao , Mani Sridhar , Tang Jay X.
Published: August 2020

Powered by flagella, many bacterial species exhibit collective motion on a solid surface commonly known as swarming. As a natural example of active matter, swarming is also an essential biological phenotype associated with virulence, chemotaxis, and host pathogenesis. Physical changes like cell elongation and hyper flagellation have been shown to accompany the swarming phenotype. However, less noticeable, are the contrasts of collective motion between the swarming cells and the planktonic cells of comparable cell density. Here, we show that confining bacterial movement in designed dimensions allows distinguishing bacterial swarming from collective swimming. We found that on a soft agar plate, a novel bacterial strainEnterobactersp. SM3 exhibited different motion patterns in swarming and planktonic states when confined to circular microwells of a specific range of sizes. When the confinement diameter was between 40 μm and 90 μm, swarming SM3 formed a single swirl motion pattern in the microwells whereas planktonic SM3 showed multiple swirls. Similar differential behavior is observed across a range of randomly selected gram-negative bacteria. We hypothesize that the “rafting behavior” of the swarming bacteria upon dilution might account for the motion pattern difference. We verified our conjectures via numerical simulations where swarming cells are modeled with lower repulsion and more substantial alignment force. The novel technical approach enabled us to observe swarming on a non-agar tissue surface for the first time. Our work provides the basis for characterizing bacterial swarming under more sophisticated environments, such as polymicrobial swarmer detection, andin vivoswarming exploration.
“…I can use any syringe I find”: contextual determinants of HIV risk in public injecting settings in Nigeria
Authors: Nelson Ediomo-Ubong Ekpo , Nnam Macpherson Uchenna
Published: August 2020

Purpose

The purpose of this study is to explore the contextual determinants of HIV risk among people who inject drugs (PWID) in public settings in Nigeria.

Design/methodology/approach

In-depth, individual interviews were conducted with 29 street-based PWID recruited through snowball sampling in Uyo, Nigeria. Interviews were tape-recorded, transcribed, coded and analysed hematically.

Findings

Homelessness and withdrawal pains encouraged consumption of drugs in public spaces (e.g. bunks, public parks). Conversely, the benefits of participation in street drug-use scenes, including reciprocity norms that guarantee free drugs during withdrawal and protection during overdose, fostered a preference for public injecting. Although participants recognized the need to inject with sterile syringes, scarcity of syringes compelled them to improvise with old syringes or share syringes, increasing risk for HIV transmission. HIV risk was exacerbated by unlawful and discriminatory policing practices, which deterred possession of syringes and encouraged risky behaviours such as rushing injection and sharing of equipment.

Practical implications

Contextual factors are key determinants of HIV risk for street-based PWID. Implementation of needle and syringe programmes as well as reforming legal frameworks and policing practices to support harm reduction are needed responses.

Originality/value

This is one of very few qualitative studies that explore risk factors for HIV transmission among PWID in West Africa. The focus on scarcity of sterile syringes and HIV risk is unique and has important policy implications.
The UK private housebuilding sector: social media perspectives
Authors: Craig Nigel , Pilcher Nick , MacKenzie Rebecca , Boothman Chris
Published: August 2020

Purpose

The UK private housebuilding sector is the key supplier of new-build homes for customers, constituting a fifth of the entire UK construction industry. Yet, despite the high average cost of houses, and official reports advocating improvement, the sector remains blighted by criticism and a negative image of its quality. However, social media now offers customers new sources of advice and information. In this context, the purpose of this paper is to analyse social media forum posts from new-build homebuyers to reveal perceptions of the industry and illustrate the value of such data for others.

Design/methodology/approach

This paper presents and thematically analyses 147 comment posts from nine online Facebook forums under the themes of safety; standards; quality; workmanship; customer service; finance and money; advice; National House Building Council; ombudsman; and page closures.

Findings

Customers express frustration, anger, feelings of neglect and of an abdication of responsibility by the sector. Fundamentally, change is suggested at a systemic level, and it is urged this occurs through powerful and independent bodies.

Originality/value

To date, social media data has not been analysed in the context of the housebuilding sector. Yet, such data is key not only for its open and wide-reaching nature but also because it can be incorporated into government reports. It is hoped such data will be used by the new home ombudsman the UK Government hopes to establish in 2020 and help rectify many of the performance issues experienced and protect homebuyers.
Trust and knowledge contribution to agricultural cluster performance
Authors: Leonardo Sandra Bergamini , Silveira Marco Antonio Pinheiro , Martinez-Sánchez Paloma María Teresa , Romeiro Maria do Carmo
Published: August 2020

Purpose

This paper aimed to analyze the contribution of the interorganizational relationship (IOR) factors trust and knowledge resources to the relational and transactional performance of a Brazilian agricultural cluster formed by small farmers.

Design/methodology/approach

A survey was conducted using a questionnaire divided into groups of variables, each group seeking to identify one of the three constructs: trust, knowledge resources and relational and transactional performance. A theoretical framework was elaborated and later compared with survey results, which were analyzed using exploratory factor analysis (EFA) and partial least squares–structural equation modeling (PLS-SEM).

Findings

Correlations between trust and relational and transactional cluster performance varied according to actors involved, being significant between some actors and not significant between others. Knowledge resources, on the other hand, proved to be significantly relevant for cluster performance, considering both relational and transactional measures.

Research limitations/implications

It was made in a Brazilian single cluster and its conclusions cannot be generalized.

Practical implications

Farmers cannot innovate with the efficiency and effectiveness that the process demands. They need complementary capacity that apparently is not in the agricultural cluster. Research and development involve knowledge and techniques that empirical knowledge alone may not provide. And much of the formal knowledge is embedded in universities and research institutes. If there were investments by public entities in research and development to improve the culture and its by-products, this could contribute to improving the income of farmers.

Social implications

This study provided a photograph of the current scenario of a Brazilian agricultural cluster. Changes in trust and knowledge resources could affect cluster relational and transactional performance. Special attention is deserved to the important role of scientific research on agricultural clusters to strengthen the capacity of critical analysis by the researcher who, with the results in hand, makes them public, hoping that the shared information can contribute with the research of other scholars and improve the quality of life of farmers involved.

Originality/value

This study offers empirical evidence that trust and knowledge resources can contribute to a Brazilian agricultural cluster performance, which can be analyzed considering both relational and transactional measures. These findings brought new fact to Singh and Shrivastava’s (2013) research.
Robotic transformative service research: deploying social robots for consumer well-being during COVID-19 and beyond
Authors: Henkel Alexander P. , Čaić Martina , Blaurock Marah , Okan Mehmet
Published: August 2020

Purpose

Besides the direct physical health consequences, through social isolation COVID-19 affects a considerably larger share of consumers with deleterious effects for their psychological well-being. Two vulnerable consumer groups are particularly affected: older adults and children. The purpose of the underlying paper is to take a transformative research perspective on how social robots can be deployed for advancing the well-being of these vulnerable consumers and to spur robotic transformative service research (RTSR).

Design/methodology/approach

This paper follows a conceptual approach that integrates findings from various domains: service research, social robotics, social psychology and medicine.

Findings

Two key findings advanced in this paper are (1) a typology of robotic transformative service (i.e. entertainer, social enabler, mentor and friend) as a function of consumers' state of social isolation, well-being focus and robot capabilities and (2) a future research agenda for RTSR.

Practical implications

This paper guides service consumers and providers and robot developers in identifying and developing the most appropriate social robot type for advancing the well-being of vulnerable consumers in social isolation.

Originality/value

This study is the first to integrate social robotics and transformative service research by developing a typology of social robots as a guiding framework for assessing the status quo of transformative robotic service on the basis of which it advances a future research agenda for RTSR. It further complements the underdeveloped body of service research with a focus on eudaimonic consumer well-being.
Family business identity, consumer product evaluations and firm size
Authors: Shen Anyuan , Tikoo Surinder
Published: August 2020

Purpose

This study aims to examine the relationship between family business identity disclosure by firms and consumer product evaluations and the moderating impact, if any, of firm size on this relationship. Toward this end, the study seeks to develop a theoretical explanation for how consumers process family business identity information.

Design/methodology/approach

A qualitative pre-study was conducted to obtain preliminary evidence that consumers’ perceptions of family businesses originate from both family- and business-based category beliefs. A product evaluation experiment, involving young adult subjects, was used to test the research hypotheses, and the experiment data were analyzed using MANOVA.

Findings

The key finding was that the effect of family business identity disclosure on consumer product evaluations is moderated by firm size.

Practical implications

This research has implications for businesses seeking to promote their family business identity in branding communications.

Originality/value

This research provides a theoretical account of why consumers might hold different perceptions of family business brands. The interactive effect of firm size and family business identity information disclosure on consumer product evaluations contributes new insight to family business branding.
Effectiveness of a brief versus a comprehensive social marketing program
Authors: Durl James , Dietrich Timo , Kubacki Krzysztof
Published: August 2020

Purpose

Gamified and engaging school-based alcohol social marketing programs have demonstrated effectiveness; however, wide-scale dissemination of these programs is limited by their resource-intensive character. The purpose of this paper is to address this limitation, a brief alcohol social marketing pilot program was derived from a comprehensive alcohol social marketing program to compare effectiveness.

Design/methodology/approach

A sample of 115 14–16-year-old adolescents from six secondary schools participated in the brief alcohol social marketing pilot program. Program effectiveness was assessed using repeated measure analysis on adolescents’ knowledge, attitudes, social norms, self-efficacy and intentions to binge drink. Results were compared with the comprehensive social marketing program and a control group.

Findings

The brief pilot program produced statistically significant outcomes for the same measures as the comprehensive program across attitudinal variables, descriptive norms and opportunistic self-efficacy.

Research limitations/implications

Converting existing social marketing programs into brief alternates is more cost-effective and, in this case, demonstrated better outcome effects. However, findings are limited as in-depth comparisons were hindered by changes to content across program modes. No process for converting comprehensive programs into brief alternates was identified prior to this study, and therefore a number of considerations for program alteration were derived from program facilitator experiences.

Originality/value

The findings provide initial evidence that a brief version of an existing comprehensive program can be an effective alternate to more resource-intensive programs under more cost-effective circumstances for program developers and facilitators.
Stakeholders’ consensus on organizational technology acceptance; using thematic analysis and SEM
Authors: Sarkeshikian Ali , Zakery Amir , Shafia Mohammad Ali , Aliahmadi Alireza
Published: August 2020

Purpose

Much research has been conducted on technology acceptance (TA), which is mainly about the acceptance by one user. As more than one person should be involved in business-to-business TA decision-making, it is suggested that different processes for making a consensus among different stakeholders should be considered. The purpose of this study is to demonstrate a model for essential activities and characteristics of advocators for accelerating the stakeholders’ consensus in the technology acceptance (SCTA).

Design/methodology/approach

The conceptual model of this research is presented using a thematic analysis of the interviews with the relevant experts and existing literature. Furthermore, the structural equation model was applied for analyzing empirically how advocators’ characteristics and activities affect consensus. In total, 248 respondents completed the questionnaires. Experts’ opinions, Krippendorff’s alpha index, Cronbach’s alpha coefficient and goodness of fit indices were applied to verify the reliability of the results.

Findings

Results show that “being leader” and “being influential” are two main characteristics for the advocators’ team that significantly affect SCTA. Reducing perceived “risk” for each stakeholder, developing a “common understanding” among them and demonstrating “resource readiness” are also the main tasks of advocators leading to SCTA.

Originality/value

The role of advocators in SCTA has been neglected. The main contribution of this study is identifying the required advocators’ activities and characteristics for achieving SCTA.
Ownership structure and auditor selection
Authors: Hall Curtis M. , Hoffman Benjamin W. , Liu Zenghui
Published: August 2020

Purpose

This paper aims to investigate the effect that ownership structure (public vs private) has on the demand for high-quality auditors, specifically in the US banking industry.

Design/methodology/approach

The authors predict that public banks are more likely to hire a high-quality auditor than private banks and pay a higher audit fee premium for that high-quality auditor (due to higher agency costs, more demand for financial information and higher litigation risk). The authors analyze 2008–2014 banking data from the Federal Reserve using probit and OLS regression analysis to examine if there is a higher probability that public banks choose higher quality auditors and pay higher audit fees when they do so.

Findings

The results show that private banks are less likely to hire Big 4 auditors and industry-expert auditors than public banks. The authors also find that both private and public banks pay higher audit fees for Big 4 and industry-expert auditors, and that public banks pay a higher premium for Big 4 auditors and industry experts than private banks.

Research limitations/implications

The findings may not be fully generalizable to other types of firms, as banking is a heavily regulated and complex industry. However, inferences from this study may be generalizable to other similar industries such as insurance or health care.

Practical implications

The results of this paper imply that public and private banks have differing priorities when hiring their financial statement auditor. This may be of interest to investors and auditing regulators.

Social implications

The findings of this paper underscore the value of hiring an industry-expert auditor in an industry that is highly complex and regulated. This may be of interest to managers and policymakers.

Originality/value

Due to data restrictions, the emphasis of prior literature on the banking industry has been on public banks. This study is the first to analyze the differences between public and private banks’ demand for audit services.
Stakeholder perceptions of drivers for, and barriers to, the incorporation of sustainability in PPP infrastructure projects in Nigeria
Authors: Babatunde Solomon Olusola , Ekundayo Damilola , Udeaja Chika , Abubakar Uthman Olawande
Published: August 2020

Purpose

Although several studies have been undertaken on sustainability within infrastructure projects, limited attention has paid to the drivers for, and the barriers to, the incorporation of sustainability in public–private partnership (PPP) infrastructure projects through empirical study, particularly in Nigeria. Therefore, this study aims to identify and examine the drivers that promote sustainability in Nigerian PPP infrastructure projects and assess the barriers to the full integration of sustainability practices into current Nigerian PPP infrastructure projects.

Design/methodology/approach

Primary data were collected using a questionnaire survey. The questionnaire survey was targeted on four different stakeholders’ organizations. They were public sector authorities, concessionaires, consultants and banks already undertaking PPP infrastructure projects in Lagos State, Nigeria. The obtained data were analyzed using frequency, percentage, mean score, standard deviation and the Kruskal–Wallis test.

Findings

The study identified 17 drivers that promote the incorporation of sustainability in PPP infrastructure projects. The analysis of the total ranking of the drivers in Nigeria revealed the top five ranked drivers to be: consideration of long-term performance; contractual arrangements; incentives for new market penetration; award criteria; and selection criteria, respectively. The study further identified 11 barriers to sustainability integration in PPP infrastructure projects and the top five ranked barriers in Nigeria are as follows: comprehensive sustainability procurement guidelines; no enabling environment; education needs; uncertain economic environment; and a lack of clear government policy, respectively. The results of the Kruskal–Wallis test conducted on both the 17 identified drivers for, and the 11 barriers to, the incorporation of sustainability in Nigerian PPP infrastructure projects revealed that there is no significant statistical difference in both rankings from the perceptions of the aforementioned four different respondents’ groups.

Research limitations/implications

The study provides empirical insights on the knowledge and awareness of drivers which could lead to a greater uptake in sustainability measures by the stakeholders in Nigerian PPP projects; it also identified barriers to overcome.

Originality/value

The importance of the incorporation of sustainability in public procurement cannot be over-emphasized. It is anticipated that the study will be of great value to PPP stakeholders involved in sustainability decision-making processes when delivering sustainable PPP projects.
Final analysis of a phase II study of nivolumab in combination with ipilimumab for unresectable chemotherapy‐naive advanced melanoma
Authors: Namikawa Kenjiro , Kiyohara Yoshio , Takenouchi Tatsuya , Uhara Hisashi , Uchi Hiroshi , Yoshikawa Shusuke , Takatsuka Sumiko , Koga Hiroshi , Wada Naoko , Minami Hironobu , Hatsumichi Masahiro , Namba Yoshinobu , Yamazaki Naoya
Published: August 2020

Nivolumab plus ipilimumab combination is currently one of the preferred regimens for advanced melanoma in recently updated clinical practice guidelines. However, the evidence on the efficacy of the combination for acral or mucosal subtypes remains less robust. This is the final analysis of a multicenter, open‐label, uncontrolled phase II study that investigated the long‐term efficacy and safety in treatment‐naive Japanese patients with advanced melanoma, including acral or mucosal subtypes, and subsequent therapy after discontinuation of the investigational agents. Patients received four doses of nivolumab (1 mg/kg i.v.) in combination with ipilimumab (3 mg/kg i.v.) at 3‐week intervals, followed by doses of nivolumab (3 mg/kg i.v.) at 2‐week intervals. The median follow‐up period was 20.8 months (range, 5.2–35.0). The centrally and locally assessed objective response rates were both 43.3% (13/30; 95% confidence interval [CI], 25.5–62.6). Median progression‐free survival was not reached (95% CI, 3.02–not reached), and median overall survival was also not reached (95% CI, 19.52–not reached). The 30‐month progression‐free survival and overall survival rates were 50.3% and 54.2%, respectively. No new safety concerns were detected. After discontinuation of the investigational agents, 83.3% of patients received some form of subsequent therapy including 43.3% of patients who received nivolumab monotherapy and 26.7% of patients who received radiotherapy. Of the four patients who discontinued the investigational agents because of immune‐related adverse events, two received subsequent therapy (nivolumab and ipilimumab, respectively) and the other two showed long‐term treatment‐free survival (659 and 590 days, respectively). Long‐term survival with nivolumab plus ipilimumab was observed in Japanese patients with melanoma including acral and mucosal subtypes, which is consistent with the CheckMate 067 study. Many patients continued to receive some form of treatment safely after stopping treatment with nivolumab plus ipilimumab.
Skin microbiota in health and disease: From sequencing to biology
Authors: Ederveen Thomas H. A. , Smits Jos P. H. , Boekhorst Jos , Schalkwijk Joost , van den Bogaard Ellen H. , Zeeuwen Patrick L. J. M.
Published: August 2020

Microbiota live in a closely regulated interaction with their environment, and vice versa. The presence and absence of microbial entities is greatly influenced by features of the niche in which they thrive. Characteristic of this phenomenon is that different human skin sites harbor niche‐specific communities of microbes. Microbial diversity is considerable, and the current challenge lies in determining which microbes and (corresponding) functionality are of importance to a given ecological niche. Furthermore, as there is increasing evidence of microbial involvement in health and disease, the need arises to fundamentally understand microbiome processes for application in health care, nutrition and personal care products (e.g. diet, cosmetics, probiotics). This review provides a current overview of state‐of‐the‐art sequencing‐based techniques and corresponding data analysis methodology for profiling of complex microbial communities. Furthermore, we also summarize the existing knowledge regarding cutaneous microbiota and their human host for a wide range of skin diseases.
National Food Consumption Patterns: Converging Trends and the Implications for Health
Authors: Le Thai H. , Disegna Marta , Lloyd Tim
Published: August 2020

Worldwide, obesity almost tripled between 1975 and 2016 and is now prevalent in both rich and poor countries. Using annual food availability data produced by the Food and Agriculture Organisation of the United Nations (FAO) covering half a century in 118 countries, this article explores the diets that are central to the problem of obesity, identifying groups of countries with similar consumption patterns. Applying algorithms from the fuzzy clustering literature, five distinct consumption patterns are revealed whose dietary composition broadly corresponds to diets that we label ‘Western’, ‘Traditional’, ‘Mediterranean’, ‘Tropical’ and ‘Vegetarian’. Despite differences in dietary characteristics, all five share two common themes: rising total calories and declining healthiness, both of which are linked to the substitution of plant‐based foods with food derived from animals. That the evidence points to a convergence on the ‘Western’ diet, the most obesogenic and least healthy of all the diets we consider, is a cause for concern. The key message is that in a future where people are predicted to live longer – but not necessarily healthier – lives, recent efforts to address the challenge are prescient, and as the results in the article imply, need to be heeded globally.
Physicochemical evaluation and Fourier transform infrared spectroscopy characterization of quality protein maize starch subjected to different modifications
Authors: Awolu Olugbenga Olufemi , Odoro Joshua Wisdom , Adeloye Jumoke Bukola , Lawal Oluranti Mopelola
Published: August 2020

Quality protein maize (QPM) is a biofortified maize rich in lysine and tryptophan, essential amino acids required in human nutrition. This research therefore characterizes native and modified starches from QPM by evaluating the physicochemical properties, Fourier transform infrared spectra (FTIR), and pasting properties. The native QPM starch was modified by oxidation, acetylation, pregelatinization, and acid thinning techniques. The starch yield of native QPM was 43.80%, while that of modified starches were from 88.22 to 98.34%. The moisture content of the native and modified starches was from 4.56 to 9.20 g/100g. Modifications significantly (P ≤ 0.05) reduced the lipid, protein, and amylose contents of the QPM. While the native starch had 0.72 g/cm3 bulk density, modified starches were between 0.59 and 0.88 g/cm3; chemical modification reduced the bulk density and physical modification increased it. In addition, all the modifications except oxidation significantly (P ≤ 0.05) increased water absorption capacity. The oil absorption of the starch samples was increased by modification techniques used with the exception of physical modification. Chemical modification reduced the viscosity of QPM starch while physical modification increased it. The reducing sugar content of the starch was reduced by both the physical and chemical starch modification techniques. Acetylated sample exhibited the highest swelling power while acid‐thinned sample had the least. The major functional groups identified via FTIR were OH, C‐H, C=H, and C≡H. Modifications did not affect the functional groups as all the native and modified starches (except oxidized sample) all have similar spectrum and bands stretch.

Practical Application

The study contributes to existing knowledge on valorization of modified starch from quality protein maize. Profiling the chemical attributes of modified starches is especially valuable in novel food processing techniques.
Bacillus subtilis as a host for mosquitocidal toxins production
Authors: Ursino Emanuela , Albertini Alessandra M. , Fiorentino Giulia , Gabrieli Paolo , Scoffone Viola Camilla , Pellegrini Angelica , Gasperi Giuliano , Di Cosimo Alessandro , Barbieri Giulia
Published: August 2020

Aedes albopictus transmits several arboviral infections. In the absence of vaccines, control of mosquito populations is the only strategy to prevent vector‐borne diseases. As part of the search for novel, biological and environmentally friendly strategies for vector control, the isolation of new bacterial species with mosquitocidal activity represents a promising approach. However, new bacterial isolates may be difficult to grow and genetically manipulate. To overcome these limits, here we set up a system allowing the expression of mosquitocidal bacterial toxins in the well‐known genetic background of Bacillus subtilis. As a proof of this concept, the ability of B. subtilis to express individual or combinations of toxins of Bacillus thuringiensis israelensis (Bti) was studied. Different expression systems in which toxin gene expression was driven by IPTG‐inducible, auto‐inducible or toxin gene‐specific promoters were developed. The larvicidal activity of the resulting B. subtilis strains against second‐instar Ae. albopictus larvae allowed studying the activity of individual toxins or the synergistic interaction among Cry and Cyt toxins. The expression systems here presented lay the foundation for a better improved system to be used in the future to characterize the larvicidal activity of toxin genes from new environmental isolates.
Anti‐cyclic citrullinated peptide but not rheumatoid factor is associated with ultrasound‐detected bone erosion among rheumatoid arthritis patients with at least moderate disease activity
Authors: Tan York Kiat , Li HuiHua , Allen John Carson , Thumboo Julian
Published: August 2020

Aim

To investigate anti‐cyclic citrullinated peptide (anti‐CCP) and rheumatoid factor (RF) in relation to ultrasound‐detected joint inflammation and bone erosion in patients with rheumatoid arthritis (RA) as previous studies have mainly utilized radiographic damage as imaging outcomes.

Method

In this cross‐sectional study, patients were grouped based on their Disease Activity Score at 28 joints (DAS28 < 3.2, DAS28 ≥ 3.2). Ultrasound variables (power Doppler and gray scale joint inflammation graded 0‐3 semi‐quantitatively; bone erosion graded Yes = 1/No = 0 dichotomously) were correlated with antibodies levels using Pearson correlation. Simple linear regression was used to characterize relationships between variables. Receiver operating characteristic (ROC) analysis was performed to determine statistically optimal cut‐off values for identifying patient subgroups with ultrasound erosion scores >25th, >50th and >75th percentiles.

Results

One thousand and eighty joints and 1800 joint recesses from 36 peripheral joint sites were scanned in 30 adult RA patients (mean disease duration, 70.3 months; 93.3% female; 93.3% anti‐CCP positive; 93.3% RF positive). In the DAS28 < 3.2 group, no significant correlations were found between antibody levels and ultrasound variables. In the DAS28 ≥ 3.2 group, anti‐CCP levels correlated significantly (r = 0.46, P = .048) and were predictive (P = .048) of ultrasound erosion scores. Area under the ROC curve based on cut‐off anti‐CCP level of ≥95.2 to identify patients with ultrasound erosion scores >7 (75th percentile) was 0.72 (sensitivity = 83.3%, specificity = 53.8%).

Conclusion

The association of anti‐CCP and RF with joint damage appears to differ in RA. Among patients with at least moderate disease activity (DAS28 ≥ 3.2), anti‐CCP—but not RF—is associated with joint damage, being moderately correlated with ultrasound‐detected bone erosion.
Whole‐genome sequencing reveals breed‐differential CNVs between Tongcheng and Large White pigs
Authors: Wu Q. , Zhou Y. , Wang Y. , Zhang Y. , Shen Y. , Su Q. , Gao G. , Xu H. , Zhou X. , Liu B.
Published: August 2020

Large phenotypic differences have been observed between Tongcheng and Large White pigs. However, little is known about their genetic basis. This study performed a genome‐wide comparison of CNVs between Tongcheng and Large White pigs using genome sequencing data. By combining the advantages of three different strategies (read depth, paired‐end mapping and split read), we detected in total 18 687 CNVs that covered approximately 3.5% of the pig genome length for Tongcheng and Large White pigs. We identified 1864 breed‐stratified CNVs (top 10%) by performing VST statistics. Functional enrichment analyses for genes located in breed‐stratified CNVs were found to be involved in pigmentation, behavior, immune system and reproductive processes, which coincide with phenotypic differences between the two breeds. Using a systematic analysis of the genome and transcriptome data, we further identified four novel breed‐differential CNVs on the functional genes (disease‐resistant, DCUN1D2 and SPARCL1; lipid metabolism, PLEKHA2 and SLCO1A2). Subsequent PCR validation confirmed their accurate breakpoint positions in 33 Tongcheng pigs and 33 Large White pigs. This study provides essential information on differential CNVs for further research on the genetic basis of phenotypic differences between Tongcheng and Large White pigs.
RPRD1B is a potentially molecular target for diagnosis and prevention of human papillomavirus E6/E7 infection‐induced cervical cancer: A case‐control study
Authors: Wen Na , Bian Lihua , Gon Jing , Meng Yuanguang
Published: August 2020

Background

The objective of the study is to investigate the biomarkers for diagnosis and prevention of human papillomavirus (HPV) infection‐induced cervical cancer.

Methods

Cervical cancer tissues were collected from patients with cervical cancer, while noncancer tissues were collected from patients diagnosed with cervical lesions or uterine fibroids at the Chinese PLA General Hospital 301 and 309, China from December 2017 to June 2018. The cancer tissues were collected from the site of lesion, while the noncancer tissues were collected from similar anatomical locations. Quantitative real‐time PCR, Western blot (WB), and immunohistochemistry (IHC) were used to detect the mRNA and protein levels of HPV E6/E7, RPRD1B (regulation of nuclear pre‐mRNA domain containing 1B), cyclin D1, and transcription factor 4 (TCF4) between cervical cancer tissues and noncancer tissues. The correlation of HPV E6/E7, RPRD1B, cyclin D1, and TCF4 expressions was analyzed.

Results

Twenty patients with cervical cancer and 27 controls without cervical cancer were included in this study. The mRNA expression of HPV E6/E7and RPRD1B was significantly higher in patients with cervical cancer than controls, while cyclin D1 mRNA expression was significantly lower in patients with cervical carcinoma in situ stage, compared with controls. RPRD1B protein expression was significantly higher in patients compared to controls when analyzed by IHC. TCF4 was significantly lower in clinical stage I and Ib of cervical cancer when analyzed by WB. The mRNA and protein expressions of RPRD1B and cyclin D1 were significantly different between patients younger than 50 years old, compared to patients 50 years and older.

Conclusions

HPV E6/E7 expression was associated with RPRD1B level in cervical cancer. The expression of RPRD1B and cyclin D1 in patients with cervical cancer might be affected by age.
People Haven't Had Enough of Experts: Technocratic Attitudes among Citizens in Nine European Democracies
Authors: Bertsou Eri , Caramani Daniele
Published: August 2020

Political representation theory postulates that technocracy and populism mount a twofold challenge to party democracy, while also standing at odds with each other in the vision of representation they advocate. Can these relationships be observed empirically at the level of citizen preferences, and what does this mean for alternative forms of representation? The article investigates technocratic attitudes among citizens following three dimensions—expertise, elitism, and anti‐politics—and, using latent class analysis, identifies citizen groups that follow a technocratic, populist, and party‐democratic profile in nine European democracies. Results show that technocratic attitudes are pervasive and can be meaningfully distinguished from populist attitudes, though important overlaps remain. We investigate differences in demographics and political attitudes among citizen profiles that are relevant to political behavior and conclude by highlighting the role that citizens’ increasing demands for expertise play in driving preferences for alternative types of governance
Paediatric supraventricular tachycardia patients potentially more at risk of developing psychological difficulties compared to healthy peers
Authors: Tester Matthew A. , Riehm Kira E. , Perry Frances , Franciosi Sonia , Escudero Carolina A. , Maghrabi Khadijah , Sneddon Penny , Sanatani Shubhayan
Published: August 2020

Aim

Assess executive and socio‐emotional/behavioural functioning in paediatric supraventricular tachycardia (SVT) patients.

Methods

SVT patients aged 7‐17 who had not undergone catheter ablation were included. Parents completed the Child Behaviour Checklist (CBCL/6‐18) and the Behavior Rating Inventory of Executive Functioning (BRIEF). Participants age 11‐17 years completed the Youth Self‐Report (YSR/11‐18) and the BRIEF Self‐Report (BRIEF‐SR). One‐sample z test was used to compare questionnaire results to the average t‐score range (M = 50, SD = 10).

Results

Thirty (18 female) children/adolescents participated (M = 12.6 years old, SD = 3.2 years) with a mean SVT onset age of 7 years (SD = 4.3 years). BRIEF and BRIEF‐SR results suggested no difference in executive functioning from average. Mean t‐scores of CBCL/6‐18 and YSR/11‐18 subscales Anxious/Depressed, Withdrawn/Depressed, Somatic Complaints, Thought Problems, Diagnostic and Statistical Manual of Mental Disorders (DSM) Affective Problems, DSM Anxiety Problems and DSM Somatic Problems were significantly elevated compared to average. YSR/11‐18 subscales Social Problems, Attention Problems, Internalizing Problems, DSM ADHD Problems and DSM Oppositional Defiant Problems had elevated mean t‐scores compared to average. Effect sizes were small to medium (0.2 ≤ d ≤ 0.8).

Conclusion

Paediatric patients with SVT potentially have a greater risk of developing behaviour, especially internalizing, problems compared to similarly aged children/adolescents without SVT.
Children breathe their own air: Reflections on children’s geographies, the urban political ecology of air pollution, and ongoing participatory action research with undergraduates near an east London primary school
Authors: Gustafson Seth
Published: August 2020

The health effects of urban air pollution are particularly acute for children. This paper details a research project with undergraduates drawing on UPE and children’s geography that attempts to address the uneven burdens of air pollution in an east London neighbourhood.
Fat depot‐specific effects of body fat distribution and adipocyte size on intramuscular fat accumulation in Wagyu cattle
Authors: Yamada Tomoya , Kamiya Mituru , Higuchi Mikito
Published: August 2020

Ectopic fats have been recognized as a new risk factor for metabolic syndrome. In obese humans, ectopic fat accumulations are affected by body fat distribution. Intramuscular adipose tissue is categorized as one of the ectopic fats. Japanese black cattle (Wagyu) are characterized by the ability to accumulate high amounts of intramuscular adipose tissue. In Japan, the marbling level is indicated by the beef marbling standard number (BMS No.), which reflects the intramuscular fat content of longissimus muscle. We hypothesized that the intramuscular fat accumulation is affected by the body fat distribution in Wagyu cattle. In this study, we showed that the BMS No. was not correlated with the subcutaneous and visceral adipocyte diameter. In contrast, the BMS No. was positively correlated with intramuscular adipocyte diameter. These results indicate that the intramuscular adipocyte diameter of Wagyu is hypertrophied with an increase in the intramuscular fat accumulation. In addition, we showed that the BMS No. was positively correlated with the subcutaneous fat percentage. In contrast, the BMS No. was negatively correlated with the visceral fat percentage. These results indicate that highly marbled Wagyu cattle have a higher percentage of subcutaneous fat and a lower percentage of visceral fat.