bluuebunny/crossref_metadata_2025 huggingface dataset:
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Authors: Nurk Sergey , Walenz Brian P. , Rhie Arang , Vollger Mitchell R. , Logsdon Glennis A. , Grothe Robert , Miga Karen H. , Eichler Evan E. , Phillippy Adam M. , Koren Sergey
Published: August 2020

Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced Pacific Biosciences (PacBio) HiFi sequencing technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human genomes sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy and allele recovery compared to the current state of the art. On the effectively haploid CHM13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy of 99.999% (QV50), surpassing recent assemblies of high-coverage, ultralong Oxford Nanopore Technologies (ONT) reads in terms of both accuracy and continuity. This HiCanu assembly correctly resolves 337 out of 341 validation BACs sampled from known segmental duplications and provides the first preliminary assemblies of nine complete human centromeric regions. Although gaps and errors still remain within the most challenging regions of the genome, these results represent a significant advance toward the complete assembly of human genomes.
Phase-field modeling of multicomponent and multiphase flows in microfluidic systems: a review
Authors: Santra Somnath , Mandal Shubhadeep , Chakraborty Suman
Published: August 2020

Purpose

The purpose of this study is to perform a detailed review on the numerical modeling of multiphase and multicomponent flows in microfluidic system using phase-field method. The phase-field method is of emerging importance in numerical computation of transport phenomena involving multiple phases and/or components. This method is not only used to model interfacial phenomena typical to multiphase flows encountered in engineering and nature but also turns out to be a promising tool in modeling the dynamics of complex fluid-fluid interfaces encountered in physiological systems such as dynamics of vesicles and red blood cells). Intrinsically, a priori unknown topological evolution of interfaces offers to be the most concerning challenge toward accurate modeling of moving boundary problems. However, the numerical difficulties can be tackled simultaneously with numerical convenience and thermodynamic rigor in the paradigm of the phase field method.

Design/methodology/approach

The phase-field method replaces the macroscopically sharp interfaces separating the fluids by a diffuse transition layer where the interfacial forces are smoothly distributed. As against the moving mesh methods (Lagrangian) for the explicit tracking of interfaces, the phase-field method implicitly captures the same through the evolution of a phase-field function (Eulerian). In contrast to the deployment of an artificially smoothing function for the interface as used in the volume of a fluid or level set method, however, the phase-field method uses mixing free energy for describing the interface. This needs the consideration of an additional equation for an order parameter. The dynamic evolution of the system (equation for order parameter) can be described by Allen–Cahn or Cahn–Hilliard formulation, which couples with the Navier–Stokes equation with the aid of a forcing function that depends on the chemical potential and the gradient of the order parameter.

Findings

In this review, first, the authors discuss the broad motivation and the fundamental theoretical foundation associated with phase-field modeling from the perspective of computational microfluidics. They subsequently pinpoint the outstanding numerical challenges, including estimations of the model-free parameters. They outline some numerical examples, including electrohydrodynamic flows, to demonstrate the efficacy of the method. Finally, they pinpoint various emerging issues and futuristic perspectives connecting the phase-field method and computational microfluidics.

Originality/value

This paper gives unique perspectives to future directions of research on this topic.
Investigating risk of bridge construction project: exploring Suramadu strait-crossing cable-stayed bridge in Indonesia
Authors: Ongkowijoyo Citra S. , Gurmu Argaw , Andi Andi
Published: August 2020

Purpose

The complexities in strait-crossing cable-stayed bridge project are increasing the risks. This study aims to identify and analyze the significant and worth-considered construction risks of the first, biggest and longest spanned strait-crossing bridge project in Indonesia.

Design/methodology/approach

As many as 32 risk events were identified and determined as the risks that exist and can be represented in the Suramadu bridge project context. Data was collected through a design-based questionnaire disseminated to experts involved in the project as well as semi-formal interviews. Several quantitative methods were applied to analyze the significant risks, such as relative importance index, Spearman’s rank correlation test and Mann–Whitney U test.

Findings

The analyses reveal that “unexpected natural behavior” confirmed by both contractor and consultant parties is the most significant and crucial risk event. Another risk event found to be significant is the “delayed payment.” On the other hand, it is also found that several risks within the legal category are found to be less significant compared to other major risk events.

Research limitations/implications

The results of the present research should be interpreted in the context of several limitations. Given these possible concerns regarding the generalizability of the findings, along with the relatively low rate of participants in the current research, additional studies are needed to provide a more complete picture of stakeholder perceptions who are involved directly in the construction environment as well as to identify more construction risks specifically in the large-scale bridge project.

Practical implications

This study has provided fundamental contributions to the body of knowledge and practical implication to promote and assist decision-makers toward developing a comprehensive risk assessment of a large-scale bridge project.

Originality/value

The analyses of outcomes and discussion, as well as the findings of this research, have shed light on the construction risks understanding, which contributes to delivering a theoretical framework for achieving large-scale bridge project success.
Psychosocial treatment for incarcerated methamphetamine users: the Philippines experience
Authors: Hechanova Ma. Regina M. , Reyes Jennel C. , Acosta Avegale C. , Tuliao Antover P.
Published: August 2020

Purpose

The purpose of this study is to evaluate a psychosocial treatment program for prisoners incarcerated because of methamphetamine use. It compared the outcomes of prisoners who received the program while incarcerated, those who were released and received the treatment as part of community-based drug recovery program and a waitlist-control group (WC) with no treatment.

Design/methodology/approach

A quasi-experimental design was use with pre- and post-test surveys administered to three groups: a WC group, a pre-release treatment-while-incarcerated (TWI) group, and a post-release outpatient treatment group (OP). Surveys measured recovery skills, life skills and substance use disorder (SUD) symptoms were administered before and after the intervention.

Findings

Results revealed that at baseline OP and TWI had significant higher recovery skills compared to WC group. However, in terms of life skills, there was no significant difference observed among the WC, OP and TWI group at baseline. TWI had a significantly lower number of SUD symptoms compared to the WC group at baseline. As hypothesized, findings revealed significant changes in recovery and life skills among the OP and TWI group compared to the WC group. No significant change in SUD scores were observed for all groups.

Research limitations/implications

A major limitation of the study was the use of a quasi-experimental design because legal issues did not allow a randomized control trial. Future research using randomized controlled trial designs would provide more robust conclusions on the impact of the intervention. The study design was also limited to pre- and post-evaluation. Further studies are encouraged to look at longitudinal outcomes of appears on SUD symptoms and possibility of relapse.

Practical implications

Given that there were no significant differences in outcomes between OP and TWI groups, results suggest that the program may serve either as a pre- or post-release program for incarcerated drug users. However, results also suggest that completion is higher when the program is used as a pre-release program. Delivering the program prior to release also reduces challenges related to attrition including conflict in schedules and the lack of resources for transportation.

Social implications

The study suggests the value of psychosocial treatment as opposed to punitive approaches in dealing with drug use. In particular, delivering interventions prior to release can prepare participants for problems they may encounter during reintegration and prevent recidivism. In a country where drug-related killings are on the rise, the study presents an alternate and restorative justice approach.

Originality/value

The study addresses a dearth in the literature on psychosocial intervention for methamphetamine users. It also fills a vacuum in studies from developing countries such as the Philippines.
A failed success: the Barlinnie Special Unit
Authors: Wilson David , Brookes Michael
Published: August 2020

Purpose

This paper aims to explore the reasons for and the subsequent longer-term impact of the closure of the Barlinnie Special Unit (BSU).

Design/methodology/approach

The paper is both descriptive, providing an overview of the work of the BSU, and conceptual in that it argues that the limits of “prisoner rehabilitation” are observed in the closure of the BSU, which sounds a warning for other penal therapeutic communities and what it means to operate effectively.

Findings

The BSU which assisted long-term, difficult and violent prisoners moderate their prison behaviour and then to live non-offending lives, lost the confidence of government ministers and officials, as well as senior prison managers and, seemingly, the public, so closed after being in operation for 21 years. The impact of this has been that the Scottish Prison Service has not introduced, or attempted to introduce, a similar regime for managing and treating violent and disruptive prisoners.

Practical implications

There are important lessons to be learned from the BSU experience for all who manage and work in specialist, prison therapeutic units or within prison therapeutic regimes. This includes balancing the therapeutic elements of the regime, which may involve engaging in practices which are outside the norm for custodial establishments, with those establishments’ security and operational requirements, so as to not to create a disconnect between addressing offending behaviour and maintaining expected standards of wider prison conduct.

Originality/value

While there have been previous evaluations of the BSU, the longer-term impact has neither been previously considered and nor has the unit’s closure been considered from a penal philosophical perspective.
The COVID-19 pandemic and the growing need to train engineers aligned to the sustainable development goals
Authors: Anholon Rosley , Rampasso Izabela Simon , Silva Diogo A.L. , Leal Filho Walter , Quelhas Osvaldo Luiz Gonçalves
Published: August 2020

Purpose

Considering the requirements of sustainable development regarding professionals training and the challenges evidenced during Coronavirus disease (COVID-19) pandemic, this study aims to contribute to the debates regarding the need to insert sustainability into engineering education in the current context.

Design/methodology/approach

For this, the literature about sustainability in engineering education was considered, and the need for sustainability insertion in the context of the COVID-19 pandemic was debated. It is important to emphasize that this debate was based on the authors’ experience regarding sustainability research and teaching.

Findings

The current moment unveiled companies’ financial management problems, constantly evidenced by media. In this sense, the interest of engineering students in business management may lead them to believe that companies’ survival depends only on financial aspects, neglecting environmental and social aspects. This study is characterized as a reminder to academic staff in the field of engineering to continue valuing the principles of sustainable development with their students during the COVID-19 pandemic.

Originality/value

The need to make engineering students understand the importance of social projects in the current period is emphasized. The training of professionals to consider all the sustainability aspects even during crisis moments is evidenced now and should be used as a learning lesson for the future.
The antecedents of job embeddedness and their effects on cyberloafing among employees of public universities in eastern Iran
Authors: Fakoor Saghih Amir Mohammad , Nosrati Saeid
Published: August 2020

Purpose

To perceive the reasons for misusing the internet at work, an activity known as cyberloafing, efforts were made to find a new approach to reduce this negative behavior among employees. Thus, this study aims to identify the antecedents of job embeddedness (JE) and their effects on cyberloafing among the employees of public universities in eastern Iran.

Design/methodology/approach

To this end, the antecedents of JE were first extracted by reviewing the literature in this regard. In the next step, the opinions of the expert team were taken into account to select five variables. Subsequently, the conceptual model and hypotheses were presented and tested through structural equation modeling. A 57-item questionnaire was then distributed among the employees of eastern Iranian universities, who were selected through random stratified sampling. Finally, the data collected from of 510 questionnaires were analyzed.

Findings

According to the findings, it can be argued that JE with its five antecedents of family support, work support, job flexibility, work practices and task significance is able to significantly reduce cyberloafing. Moreover, the full mediating role of JE was confirmed.

Originality/value

Cyberloafing is a term describing the actions of employees who use their internet access at work for personal purposes pretending to do legitimate work. It has been turned into a serious challenge in developing countries such as Iran. It is, therefore vital to identify its factors and antecedents to diminish the counterproductive behavior in the workplace.
Fed and ECB: which is informative in determining the DCC between bitcoin and energy commodities?
Authors: Derbali Abdelkader , Jamel Lamia , Ben Ltaifa Monia , Elnagar Ahmed K. , Lamouchi Ali
Published: August 2020

Purpose

This paper provides an important perspective to the predictive capacity of Fed and European Central Bank (ECB) meeting dates and production announcements for the dynamic conditional correlation (DCC) between Bitcoin and energy commodities returns and volatilities during the period from August 11, 2015 to March 31, 2018.

Design/methodology/approach

To assess empirically the unanticipated component of the US and ECB monetary policy, the authors pursue the Kuttner's approach and use the federal funds futures and the ECB funds futures to assess the surprise component. The authors use the approach of DCC as introduced by Engle (2002) during the period from August 11, 2015 to March 31, 2018.

Findings

The authors’ results suggest strong significant DCCs between Bitcoin and energy commodity markets if monetary policy surprises are incorporated in variance. These results confirmed the financialization of Bitcoin and commodity energy markets. Finally, the DCC between Bitcoin and energy commodity markets appears to respond considerably more in the case of Fed surprises than ECB surprises.

Originality/value

This study is a crucial topic for policymakers and portfolio risk managers.
“The image has been changed in my mind”: a case of restorative justice in a forensic mental health setting
Authors: Tapp James , Moore Estelle , Stephenson Mary , Cull Davina
Published: August 2020

Purpose

This paper aims to describe the process and outcomes of restorative justice (RJ) between a detained patient with autism and a person he harmed.

Design/methodology/approach

A single case study design was used to provide an in-depth description of a RJ referral.

Findings

Restorative outcomes that align with the theories of RJ, in particular trauma processing and emotional reconnection, were observed by RJ practitioners and reported by participants. The person harmed reported a “safer” memory of the offence.

Research limitations/implications

The absence of outcome assessments limits the findings to observational data and self-reported experiences from participants. A triangulated outcome approach is recommended.

Practical implications

RJ practices can safely be applied within a secure hospital environment. The RJ process can also be followed by a person with difficulties in social and emotional processing.

Originality/value

The RJ process provides a safe framework within which forensic mental health services can respond to the needs of victims, which are not routinely addressed in standard clinical practice, and in worst case scenarios, may even be overlooked.
The effects of regulation and supervision on the risk-taking behaviour of Islamic banks
Authors: Asutay Mehmet , Ayturk Yusuf , Aksak Ercument
Published: August 2020

Purpose

This study examines the impact of the regulatory and supervisory environment on the risk-taking behaviour of Islamic banks. The impact of the heterogeneous nature of the banking environment in the sampled countries is also considered.

Design/methodology/approach

A dynamic panel data analysis with system GMM estimators was used with a sample consisting of 120 Islamic banks from 21 countries for the period 2000-2013.

Findings

The results demonstrate that main regulation and supervision proxies have significant negative effects on risk levels of Islamic banks, which implies that further restricted regulatory and supervisory environment can lower risk levels of Islamic banks. In addition, the Islamic banks operating under the dual banking system seem to prefer to take a lower risk. Furthermore, the results identify that a stable political environment encourages Islamic banks to take higher risks in their operations.

Originality/value

In addition to examining the common factors, the empirical analysis in this study is extended to the investigation of the effects of several political indicators on risk-taking behaviour of Islamic banks, which should be considered as an important contribution.
Will the real “Mrs Smith” please stand up: a critical examination of the role of vignettes in integrated service development and delivery
Authors: George Thomas , Toze Michael , Ray Mo , Clayton Owen
Published: August 2020

Purpose

To explore the use of fictitious vignettes representing older people and the extent to which they serve as an effective resource in developing service provision and transforming health and social care.

Design/methodology/approach

Based on a critical review of research and academic discourse.

Findings

Fictitious vignettes or case studies of older adults, such as “Mrs Smith”, may be a useful means to promote communication with and between health and social care colleagues about current services and transforming or re-organising service provision. However, we argue that while there may be a role for vignettes, care should be taken in their use. The potential to “homogenise” older people into the “typical” patient personified by Mrs Smith may do very little to challenge age- based stereotypes and assumptions. Moreover, vignettes cannot match the potential value and importance of older men and women directly participating in the evaluation and development of services.

Practical implications

This article argues that changing the way services are organised and delivered must be underpinned by critical reflection of the assumptions which underpin attitudes towards old age, including our tendency to define older people by chronological age and to homogenise “the elderly” into a single group. The value of participatory methods which meaningfully involve older citizens in both evaluating and planning services could contribute significantly to innovation in service development.

Social implications

This paper highlights the critical importance of challenging age-based stereotypes and ageist policy and practice. Recognising old age as being characterised by diversity and difference could challenge the tendency to see old age, especially advanced old age, as an inevitable problem.

Originality/value

This article offers a critical perspective on the use of vignettes.
Public and patient involvement in research on ageing and dementia
Authors: Ashton Julian , Aldus Clare F. , Richmond Peter , Allen Helen
Published: August 2020

Purpose

This paper aims to assess the current state, and various methods, of public and patient involvement, particularly but not exclusively in research on ageing and dementia.

Design/methodology/approach

Interviews were carried out with a researcher, who has had a leading role in research on dementia; a public contributor with extensive relevant experience; and a member of the research design service with responsibility for patient and public involvement.

Findings

All those involved in the research can benefit considerably from public and patient involvement and it can make a significant difference to the course of a project. The importance of choosing an appropriate method of involvement is discussed and planning for it in both financial terms and time allowed. Examples are given of successful studies.

Research limitations/implications

Those who took part in the interviews were chosen for their record in furthering public and patient involvement in research. There is no attempt to compare their views with those of the wider research community.

Practical implications

The various ways in which patients and the public are involved in relevant research is a guide to those designing projects and those who may want to explore opportunities for involvement.

Social implications

Social implications include being able to influence research projects, contributors of all ages find they are valued.

Originality/value

The format of the paper is original, eliciting material from three viewpoints on research and involvement.
Leadership qualities and style: a panacea for job productivity and effective service delivery among library staff in academic libraries in South South, Nigeria
Authors: Akparobore Daniel , Omosekejimi Ademola Ferdinand
Published: August 2020

Purpose

The purpose of this study is to examine leadership qualities and style as panacea for job productivity and effective service delivery among library staff members in academic libraries in Nigeria. This study will help to ascertain the leadership style that is mostly adopted by university library management staff members in university libraries in South South, Nigeria, ascertain the type of leadership style that can be adopted by library management to attain productivity and effective service delivery among staff members in university libraries in South South, Nigeria and identify the leadership qualities that allows for productivity and effectiveness of staff members in university libraries in South South, Nigeria among others.

Design/methodology/approach

A descriptive survey research design was adopted for this study. The target population for this study comprises 672 library staff members from 23 university libraries across the South South region of Nigeria. Total enumeration sampling technique was used to sample the entire population. The instrument used for data collection was a structured questionnaire. A total of 672 copies of the questionnaire were administered and total of 623 were duly completed and found useable, therefore there was 93% response rate. The data collected for this study was analyzed using simple percentage/frequency counts and weighed mean.

Findings

Finding from the study revealed that the leadership style mostly adopted and practiced by the staff members at the management level in academic libraries in South South, Nigeria is the autocratic type of leadership. Also, Almost all library staff members in academic libraries in South South, Nigeria upholds the view that democratic type of leadership, if practiced by staff members at the management level in academic libraries will allow for maximum job productivity and effectiveness among library staff members, that commitment and passion for their job, excellent communication skills, good decision-making skill, delegation of authority/subordinate empowerment among others are qualities a good leader.

Originality/value

This submission is a work by the researcher and to the best of the researcher's knowledge contains no materials previously published or written by another person.
Co-creation in tourism: a systematic mapping study
Authors: Mohammadi Fatemeh , Yazdani Hamid Reza , Jami Pour Mona , Soltani Morteza
Published: August 2020

Purpose

The purpose of this study is to organize and analyze the existing literature on co-creation in tourism to identify the state-of-the-art studies and the research gap in this field.

Design/methodology/approach

As the research questions seek to provide an overview of the studies in the available literature, the systematic mapping study (SMS) has been selected as the research method. A suitable mapping study method for analyzing and structuring a broad research field concerning methods, designs and research focuses on the existing publications. In total, 137 articles published during 2006–2019 in reliable academic databases such as Science Direct, Emerald, Scopus, Wiley, ProQuest, Sage, Web of Science and Taylor and Francis were selected and analyzed.

Findings

The results show a rising trend of published articles in tourism, with the maximum number published in 2019 and the minimum number in 2006. Also, analysis of input articles revealed that most of the studies focused on the antecedents and prerequisites for co-creation and paid less attention to the co-creation context. Other findings show that in the field of tourism, the hospitality sector, especially hotels have paid special attention to co-creation. The majority of papers were the empirical type with quantitative design. Furthermore, most studies used the survey method, while the case study and other methods were the next choices.

Originality/value

This study addresses a major research gap by summarizing the literature related to value co-creation with a specific focus on tourism using the SMS method that provides an overview of the studies in this field. Categorizing papers through SMS helps researchers to review the status of studies in a visual summary to identify gaps and directions for future research.
Single administration of avelumab induced a complete response in thyroid transcription factor 1‐positive combined Merkel cell carcinoma
Authors: Kanemaru Hisashi , Fukushima Satoshi , Mizukami Yukari , Sawamura Soichiro , Nakamura Kayo , Honda Noritoshi , Makino Katsunari , Kajihara Ikko , Aoi Jun , Makino Takamitsu , Kawasaki Takeshi , Kudou Erina , Jhono Masayoshi , Ito Takaaki , Arima Nobuyuki , Ihn Hironobu
Published: August 2020

Merkel cell carcinoma (MCC) is an aggressive neoplasm and patients with metastasis have poor survival outcomes. Recently, avelumab, an anti‐programmed death ligand 1 (PD‐L1) immune checkpoint inhibitor, was approved for first‐line treatment in patients with metastatic MCC. While the administration interval of avelumab is every 2 weeks, the durable effect of a single administration of avelumab is unknown. Additionally, the effect of avelumab in pure MCC or combined MCC concurrent with non‐MCC histology has not been fully elucidated. Herein, we report a case of combined MCC concurrent with squamous cell carcinoma; the patient had a complete response after a single administration of avelumab. Although the levels of avelumab were outside the detection limit within 12 weeks, a remarkable efficacy remained for more than 28 weeks after administration. Immunohistochemical analyses revealed that the expression of PD‐L1 and Merkel cell polyomavirus large T antigen was almost negative or only partial in the primary tumor lesion of this patient. Conversely, thyroid transcription factor 1 (TTF‐1) expression was positive in the primary MCC lesion, which is consistent with a previous report that combined MCC is positive for TTF‐1 expression. In conclusion, this case study presents a rare case of TTF‐1‐positive combined MCC showing complete response after a single administration of avelumab.
Biological Flora of the British Isles: Lathraea clandestina
Authors: Atkinson Mark D. , Atkinson Elaine
Published: August 2020

This account presents information on all aspects of the biology of Lathraea clandestina L. (Purple Toothwort) that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the Biological Flora of the British Isles: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, floral and seed characters, hervbivores and disease, history and conservation.

Lathraea clandestina is a holoparasitic perennial herb essentially devoid of chlorophyll which can parasitize a wide range of host plants. These include ferns, herbs and trees although it is most frequent on Populus spp., Salix spp. and Alnus glutinosa. It usually flowers between April and June. It is pollinated principally by long‐tongued bumblebees (Bombus spp.). The flowers arise directly from a subterranean stem and have specialised features to reduce nectar theft particularly by ants and birds. Seeds are explosively ejected and can spread up to 8 m. For most of the year, plants are not visible.

Lathraea clandestina is native to Belgium, throughout much of western France as far north as Brittany, Andorra, the Pyrenees in France and Spain, northern Spain and in Italy where it has a very disjunct distribution. It has been widely introduced in Britain and Ireland and is extensively naturalised. It has been introduced and naturalised also in The Netherlands, Switzerland and Germany. It is very commonly a riparian plant and can spread downstream.

As a parasite dwelling underground for most of the year, L. clandestina draws solutes from the xylem of the host root using hydathode glands on the inner surface of the scales. Consequently a stream of liquid is exuded which affects surrounding vegetation. Lathraea clandestina still exhibits vestiges of some of the enzyme activity associated with photosynthesis and has a very limited ability to assimilate inorganic nitrogen and carbon. Its chloroplast genome is less reduced than in many other holoparasitic plants.
From evidence to implementation
Authors: Papageorghiou Aris T
Published: August 2020

Deputy Editor‐in‐Chief Dr Aris T Papageorghiou discusses the latest thinking in women's health and highlights articles from this issue in an audio podcast available at: https://soundcloud.com/bjog/sept-editorial-2020
Bacterial but not fungal challenge up‐regulates the transcription of Coleoptericin genes in Tenebrio molitor
Authors: Jang Ho Am , Park Ki Beom , Kim Bo Bae , Ali Mohammadie Kojour Maryam , Bae Young Min , Baliarsingh Snigdha , Lee Yong Seok , Han Yeon Soo , Jo Yong Hun
Published: August 2020

Antimicrobial peptides (AMPs) are effector candidates that elicit humoral immunity in invertebrates. AMPs facilitate bacterial clearance by either physically disrupting the microbial membranes or the intracellular targets. In the Coleopteran pest, Tenebrio molitor, transcriptional regulation of AMPs has been studied in the context of innate immune signaling cascades and antimicrobial immunity. Here, we report the transcriptional response of three AMP genes, Coleoptericin A, B, and C (TmCole A, B and C) in T. molitor in response to bacterial (Escherichia coli, Staphylococcus aureus), and fungal (Candida albicans) challenges. These genes were expressed essentially in the gut and hemocytes followed by the integument tissue of the T. molitor larva. Further, these genes were highly expressed in the late‐larval, pupal, and early adult stages. Furthermore, while all of these transcripts were highly upregulated in the fat body and Malpighian tubules after bacterial challenge, TmCole B and TmCole C were induced in the gut after E. coli challenge. Fungal stimulation was not required for the upregulation of the transcription of Coleoptericin genes in T. molitor.
Overwintering stages of Callosobruchus chinensis (L.) in the field
Authors: Chiluwal Kashinath , Roh Gwang Hyun , Park Chung Gyoo
Published: August 2020

Adzuki bean beetle, Callosobruchus chinensis, is a worldwide oligophagous and a field‐to‐storage pest of legumes including adzuki beans (Vigna angularis). Its over‐wintering stage is yet to be confirmed. A series of experiments was carried out at Jinju, in the southern part of the Republic of Korea, to elucidate the overwintering stages. Top‐ and sub‐soil samplings followed by pod and seed samplings from left over plants from adzuki bean fields in the winter of 2015, and an outdoor overwintering test (during Nov 2018 to Jun 2019) by exposing bean seeds harboring different stages (eggs, larvae, pupae, pharates and adults) of laboratory reared C. chinensis to the winter environment were carried out. None of the C. chinensis stages was detected from the top‐ and sub‐soil samples. When the pods and seeds from left over plants were sampled, only a few live pupae were obtained. In the outdoor test with laboratory reared C. chinensis, all the stages (larvae, pupae, and adults), except eggs, were detected on every other weekly samples of infested adzuki bean seeds throughout the winter. These results showed that the overwintering stages of C. chinensis in Jinju, southern Korea, are larvae, pupae, pharates and adults.
In silico identification and expression analyses of Defensin genes in the mealworm beetle Tenebrio molitor
Authors: Jang Ho Am , Park Ki Beom , Kim Bo Bae , Ali Mohammadie Kojour Maryam , Bae Young Min , Baliarsingh Snigdha , Lee Yong Seok , Han Yeon Soo , Jo Yong Hun
Published: August 2020

Defensins are a major family of antimicrobial peptides that serve as the innate immune defense of both vertebrates and invertebrates. Due to their antimicrobial, chemotactic, and regulatory activities, Defensins have been exploited for their therapeutic potential. Insect Defensins are cysteine‐rich and contain an N‐terminal loop, α‐helix, and antiparallel β‐sheet, forming a “cysteine‐stabilized alpha beta (CSαβ)” or “loop–helix‐sheet” structure. In this study, we identified the full‐length open reading frame (ORF) sequences of Defensin (TmDef) and Defensin‐like (TmDef‐like) genes from the mealworm beetle Tenebrio molitor using in silico methods. TmDef and TmDef‐like genes encode the peptides of 72 and 71 amino acid residues, respectively. TmDefensin is comprised of a Defensin domain and the TmDefensin‐like is comprised of a signal peptide of 21 amino acid residues. Phylogenetic analysis revealed close similarities of TmDefensin with the Defensin of Acalolepta luxuriosa of the longhorn beetle family. The expression of TmDef mRNA was found to be greater than that of TmDef‐like mRNA and was mostly expressed in the pupal and adult stages. Tissue distribution showed high expression of TmDef‐like mRNA in larval hemocytes, gut, integument, and fat body, while in adults, the expression was high in gut and hemocytes. Following bacterial and fungal stimulation in vivo, TmDef was upregulated at 24 h post‐infection in whole body, fat body, and hemocytes of the larvae. Even TmDef‐like mRNA was upregulated in the gut and hemocytes at 12 and 9 h post‐infection respectively. These results suggest that TmDef and TmDef‐like genes play important roles in protecting T. molitor from microbial contact.
Acceptability of bread made with hemp (Cannabis sativa subsp. sativa) flour evaluated fresh and following a partial bake method
Authors: Hayward Lydia , McSweeney Matthew B.
Published: August 2020

With an increasing demand for gluten‐free foods, there has been an interest in the utilization of nonconventional ingredients to improve the nutritional quality, sensory attributes, and functionality of gluten‐free products. Hemp (Cannabis sativa subsp. Sativa) is one of these ingredients that have yet to be thoroughly evaluated. The primary objective of this study was to determine the acceptability and consumers’ sensory perceptions of gluten‐free bread (GFB) made with hemp flour. The secondary objective was to assess if the acceptability of the bread changes after 45 days of frozen storage following a partial bake method. The first trial (n = 89) instructed participants to assess six fresh bread samples of varying hemp percentages (0%, 5%, 10%, 15%, 20%, and 25%), using check‐all‐that‐apply questionnaire and a 9‐point hedonic scale. This procedure was repeated for the second trial (n = 81), which used partially baked bread samples of the same composition. Overall, as the percentage of hemp flour increased, the overall liking of the GFB decreased. The 5% hemp incorporation in the fresh bread and the 15% hemp incorporation or less in the partially baked bread did not significantly differ from the control bread (fresh and partially baked, respectively). Attributes found to drive the liking of bread were smooth (only for the frozen bread), porous, moist, and soft, whereas the attributes that led to disliking were yeasty and dense. In future research, partial baking methods should be varied to assess the optimal freezing and baking ratio that are specific for hemp‐based breads.

Practical Application

The gluten‐free bread (GFB) made with 5% hemp incorporation was not significantly different from the control and was acceptable to consumers. The partially baking method is a suitable method to be used with GFBs incorporated with hemp as it did not affect the consumer acceptability. Additionally, hemp flour incorporation in partially baked GFB was acceptable up to 15%. Consumers prefer GFB with hemp that possesses smooth, porous, moist, and soft attributes.
Serotyping and antibiotic resistance of Listeria monocytogenes isolated from raw water buffalo milk and milk products
Authors: Terzi Gulel Goknur , Gucukoglu Ali , Cadirci Ozgur , Saka Erdem , Alisarli Mustafa
Published: August 2020

This study was aimed to investigate the presence of Listeria monocytogenes in raw water buffalo milk and milk products, besides determining its serotype and the extent of its resistance against various antibiotics. A total of 188 samples of raw water buffalo milk and milk products were collected from Samsun Province, Turkey between November 2012 and May 2013. The classical culture technique was used to isolate and identify L. monocytogenes, as described in EN ISO 11290‐1. The isolates were confirmed as L. monocytogenes by using PCR with (hylA) primers specific for the hemolysin gene. The antimicrobial susceptibility test was achieved by using the VITEK 2 compact system and VITEK 2 AST‐P640 card. L. monocytogenes was found in 7 (3.7%) of the 188 samples. Four of them were obtained from cheese and three from milk samples. Whereas, L. monocytogenes was not detected in any of the clotted cream samples. A total of 13 isolates were confirmed by PCR as L. monocytogenes. Among these isolates, one was 1/2c (or 3c) (7.6%), three were 4b (or 4d, 4e) (23%), four were 1/2b (or 3b) (30.7%), and the other five isolates were serotype 1/2a (or 3a) (38.4%). The highest antimicrobial resistance was recorded against fosfomycine (100%) followed by oxacillin (92%), penicillin (84%), and erythromycin (69%). However, no resistance was determined against ciprofloxacin, gentamicin, and tigecycline.

Practical Application

This study showed that some samples of raw buffalo milk and the milk products were contaminated with Listeria monocytogenes. The serotype with the highest prevalence was determined as L. monocytogenes 1/2a. This study also demonstrated that most of the L. monocytogenes isolates had developed multiresistance to many frequently used medical antimicrobial agents.
Characterization of the sensory, chemical, and microbial quality of microwave‐assisted, thermally pasteurized fried rice during storage
Authors: Montero María Laura , Sablani Shyam , Tang Juming , Ross Carolyn F.
Published: August 2020

Companies producing ready‐to‐eat (RTE) meals are looking for processing alternatives that allow them to gain presence in the supermarket chill section. Microwave‐assisted pasteurization systems (MAPS) offer the potential to produce safe, high‐quality foods. This research examined sensory, physical, chemical, and microbial changes in fried rice processed with MAPS and stored at 7 °C over a 6‐week storage period. Additional fried rice samples (cooked but not MAPS‐processed) were stored at –31 °C and were used as the control. Randomly selected trays of each type of rice were analyzed at 1, 4, and 6 weeks of storage. Aroma, appearance, taste/flavor, texture, mouthfeel, and aftertaste were evaluated by a semitrained sensory panel with rate‐all‐that‐apply questions. The type of rice treatment (MAPS or control) significantly influenced sensory attributes (P < 0.05), with firm texture attribute of the egg being more intense in the MAPS‐rice compared to the control. In addition, storage time affected the sensory modalities of both rice samples, including aroma, appearance, and taste/flavor (P < 0.05). No spoilage‐associated sensory attributes were detected in the MAPS‐rice during storage. At each examination point, various physical, chemical, and microbial analyses were conducted for the MAPS‐ and control rice. From the physical and chemical perspective, the MAPS‐rice did not present relevant changes over the period tested. Microbial growth was the main cause of spoilage of the MAPS‐rice; however, MAPS was able to extend the regular 5‐day shelf life of a chilled fried rice meal to 6 weeks, demonstrating the potential of this technology for the RTE industry.

Practical Application

The findings of this study indicate that, by applying microwave technology to RTE fried rice, the shelf life can be extended from 5 to 7 days up to 42 days (6 weeks) when stored at 7 °C. This temperature closely mimics that of consumers’ refrigerators in the United States. This study also shows the potential of working with a semitrained panel and RATA questions when characterizing sensory changes during storage.
Tocilizumab for severe COVID‐19 pneumonia: Case series of 5 Australian patients
Authors: West Timothy A. , Malik Sameer , Nalpantidis Anastasios , Tran Tuan , Cannon Christine , Bhonagiri Deepak , Chan Kevin , Cheong Elaine , Wan Sai Cheong Jenny , Cheung Winston , Choudhury Faisal , Ernest David , Farah Claude S. , Fernando Shelanah , Kanapathipillai Rupa , Kol Mark , Murfin Brendan , Naqvi Haider , Shah Asim , Wagh Atul , Ojaimi Samar , Frankum Bradley , Riminton Sean , Keat Karuna
Published: August 2020

Aim

To describe the first Australian cases of severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV2) disease (COVID‐19) pneumonia treated with the interleukin‐6 receptor antagonist tocilizumab.

Methods

Retrospective, open‐label, real‐world, uncontrolled, single‐arm case series conducted in 2 tertiary hospitals in NSW, Australia and 1 tertiary hospital in Victoria, Australia. Five adult male patients aged between 46 and 74 years with type 1 respiratory failure due to COVID‐19 pneumonia requiring intensive care unit (ICU) admission and biochemical evidence of systemic hyperinflammation (C‐reactive protein greater than 100 mg/L; ferritin greater than 700 μg/L) were administered variable‐dose tocilizumab.

Results

At between 13 and 26 days follow‐up, all patients are alive and have been discharged from ICU. Two patients have been discharged home. Two patients avoided endotracheal intubation. Oxygen therapy has been ceased in three patients. Four adverse events potentially associated with tocilizumab therapy occurred in three patients: ventilator‐associated pneumonia, bacteremia associated with central venous catheterization, myositis and hepatitis. All patients received broad‐spectrum antibiotics, 4 received corticosteroids and 2 received both lopinavir/ritonavir and hydroxychloroquine. The time from first tocilizumab administration to improvement in ventilation, defined as a 25% reduction in fraction of inspired oxygen required to maintain peripheral oxygen saturation greater than 92%, ranged from 7 hours to 4.6 days.

Conclusions

Tocilizumab use was associated with favorable clinical outcome in our patients. We recommend tocilizumab be included in randomized controlled trials of treatment for patients with severe COVID‐19 pneumonia, and be considered for compassionate use in such patients pending the results of these trials.