bluuebunny/crossref_metadata_2025 huggingface dataset:
Recovery of high quality metagenome–assembled genomes from full–scale activated sludge microbial communities in a tropical climate using longitudinal metagenome sampling
Authors: Haryono Mindia A. S. , Law Ying Yu , Arumugam Krithika , Liew Larry C.-W. , Nguyen Thi Quynh Ngoc , Drautz-Moses Daniela I. , Schuster Stephan C. , Wuertz Stefan , Williams Rohan B. H.
Published: August 2021

Analysis of metagenome data based on the recovery of draft genomes (so called metagenome–assembled genomes, or MAG) have assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play a key role in mediating interactions between human and natural ecosystems. In this paper, we consider strategies for recovery of MAG sequence from time series metagenome surveys of full–scale activated sludge microbial communities. We generate MAG catalogues from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi–sample co–assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non–redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing the co-assembly offers clear advantages over single–sample assembly. Around 1000 MAGs were candidates for being considered high quality, based on single–copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader implications for performing genome–resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.
Serological and Molecular Investigation of Foot and Mouth Disease Virus and other animal pathogens at the Interface of Akagera National Park and Surrounding Cattle Farms between 2017 and 2020
Authors: Udahemuka Jean Claude , Aboge Gabriel , Obiero George , Angelique Ingabire , Beeton Natasha , Uwibambe Evodie , Lebea Phiyani
Published: August 2021

Background

Foot-and-Mouth Disease Virus (FMDV) is a positive-sense RNA virus of the family of the picornaviridæ and responsible for the disease with the highest economic impact, the Foot-and-Mouth Disease (FMD). FMD is endemic in Rwanda but there are gaps in knowing the seroprevalence and molecular epidemiology. This study reports the FMD seroprevalence and molecular characterization of FMDV in Eastern Rwanda. Surveillance in FMDV wild reservoirs, the African buffaloes, was also carried out revealing the presence of other pathogens and commensals.

Results

The overall seroprevalence of FMD in the study area is at 9.36% in cattle and 2.65% in goats. We detected FMDV using molecular diagnostic tools such as RT-PCR and RT-LAMP and the phylogenetic analysis of the obtained sequences revealed the presence of serotype SAT 2, lineage II. Sequencing of oropharyngeal fluids collected from African buffaloes revealed the presence of several pathogens and commensals but no FMDV was detected in buffaloes.

The plethora of pathogens identified from the buffalo gut gives an idea of the health challenges faced by cattle keepers in Eastern Rwanda due to possible cross infectivity on wildlife-domestic animals interface regions.

Conclusions

We recommend further studies to focus on sampling more African buffaloes since the number sampled was statistically insignificant to conclusively exclude the presence or absence of FMDV in Eastern Rwanda buffaloes. The use of RT-PCR alongside RT-LAMP demonstrates that the latter can be adopted in endemic areas such as Rwanda to fill in the gaps in terms of molecular diagnostics. The identification of lineage II of SAT 2 in Rwanda for the first time shows that the pools as previously established are not static over time.
Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface
Authors: Bell Emma , Lamminmäki Tiina , Alneberg Johannes , Qian Chen , Xiong Weili , Hettich Robert L. , Frutschi Manon , Bernier-Latmani Rizlan
Published: August 2021

Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic environments remain unclear. In the deep crystalline bedrock of the Fennoscandian Shield at Olkiluoto, Finland, opposing gradients of abiotic methane and ancient seawater-derived sulfate create a terrestrial sulfate-methane transition zone (SMTZ). We used chemical and isotopic data coupled to genome-resolved metaproteogenomics to demonstrate active life and, for the first time, provide direct evidence of active anaerobic oxidation of methane (AOM) in a deep terrestrial bedrock. Proteins from Methanoperedens (formerly ANME-2d) are readily identifiable despite the low abundance (≤1%) of this genus and confirm the occurrence of AOM. This finding is supported by 13C-depleted dissolved inorganic carbon. Proteins from Desulfocapsaceae and Desulfurivibrionaceae, in addition to 34S-enriched sulfate, suggest that these organisms use inorganic sulfur compounds as both electron donor and acceptor. Zerovalent sulfur in the groundwater may derive from abiotic rock interactions, or from a non-obligate syntrophy with Methanoperedens, potentially linking methane and sulfur cycles in Olkiluoto groundwater. Finally, putative episymbionts from the candidate phyla radiation (CPR) and DPANN archaea represented a significant diversity in the groundwater (26/84 genomes) with roles in sulfur and carbon cycling. Our results highlight AOM and sulfur disproportionation as active metabolisms and show that methane and sulfur fuel microbial activity in the deep terrestrial subsurface.

Significance Statement

The deep terrestrial subsurface remains an environment in which there is limited understanding of the extant microbial metabolisms, despite its reported large contribution to the overall biomass on Earth. It is much less well studied than deep marine sediments. We show that microorganisms in the subsurface are active, and that methane and sulfur provide fuel in the oligotrophic and anoxic subsurface. We also uncover taxonomically and metabolically diverse ultra-small organisms that interact with larger host cells through surface attachment (episymbiosis). Methane and sulfur are commonly reported in terrestrial crystalline bedrock environments worldwide and the latter cover a significant proportion of the Earth’s surface. Thus, methane- and sulfur-dependent microbial metabolisms have the potential to be widespread in the terrestrial deep biosphere.
Stability Comparisons between Natural versus Engineered Archaeal Heat-Shock Proteins
Authors: Furr Mercede , Basha Sreenivasulu , Agrawal Shilpi , Alraawi Zeina , Ghosh Piyasi , Stacy Carson , Kumar T.K.S. , Ceballos Ruben Michael
Published: August 2021

Crenarchaeal group II chaperonins (a.k.a., “heat shock” proteins, HSPs) are abundantly expressed in species of the family Sulfolobaceae. HSPα and HSPβ expression is upregulated during thermal shock. HSPs are subunits of larger octadecameric complexes that function to protect intracellular proteins during thermal stress. Engineered HSPs have been constructed with the idea of protecting enzymes in industrial reactions. HSPβ-coh, a fusion protein comprised of HSPβ and type 1 cohesin from Clostridium thermocellum was used for proof-of-concept. Dockerin-endowed cellulolytic enzymes bind to the complex via cohesin-dockerin interactions. Enzymatic activity (i.e., hydrolysis of lignocellulose) is retained when the platform is used at high temperatures (e.g., 85-88°C). Moreover, enhancement persists on acid-pretreated substrates prompting the question: Are HSPs acid tolerant? In this study, HSP structural integrity is examined at different temperatures and pH. Far-UV circular dichroism and intrinsic fluorescence indicate HSPα and HSPβ retain structural integrity at neutral pH over a range of temperatures (25-90°C) while HSPβ-coh is less tolerant to thermal stress. Structural integrity is compromised for all subunits at ultra-low pH (i.e., pH 2) with HSPα showing the most susceptibility. Secondary structures of all HSPs are resilient under mildly acidic conditions (pH 4). ANS binding assays indicate a shift in tertiary structure for all subunits at ultra-low pH. Limited trypsin digestion reveals that the backbone of HSPβ-coh is the most flexible and HSPβ is the most resistant. Results suggest that HSPα and HSPβ are more resilient than HSPβ-coh under thermal challenge and that there are limits to the acid tolerance of all HSPs.
A standard knockout procedure alters expression of adjacent loci at the translational level
Authors: Egorov Artyom A. , Alexandrov Alexander I. , Urakov Valeriy N. , Makeeva Desislava S. , Edakin Roman O. , Kushchenko Artem S. , Gladyshev Vadim N. , Kulakovskiy Ivan V. , Dmitriev Sergey E.
Published: August 2021

The S. cerevisiae gene deletion collection is widely used for functional gene annotation and genetic interaction analyses. However, the standard G418-resistance cassette used to produce knockout mutants delivers strong regulatory elements into the target genetic loci. To date, its side effects on the expression of neighboring genes have never been systematically assessed. Here, using ribosome profiling data, RT-qPCR, and reporter expression, we investigated perturbations induced by the KanMX module. Our analysis revealed significant alterations in the transcription efficiency of neighboring genes and, more importantly, severe impairment of their mRNA translation, leading to changes in protein abundance. In the “head-to-head” orientation of the neighbor and the deleted gene, knockout often led to a shift of the transcription start site of the neighboring gene, introducing new uAUG codon(s) into the expanded 5’ untranslated region (5’ UTR). In the “tail-to-tail” arrangement, knockout led to activation of alternative polyadenylation signals in the neighboring gene, thus altering its 3’ UTR. These events may explain the so-called neighboring gene effect (NGE), i.e. false genetic interactions of the deleted genes. We estimate that in as much as ∼1/5 of knockout strains the expression of neighboring genes may be substantially (>2-fold) deregulated at the level of translation.
Enzyme fatigue limits the detoxification of aflatoxin by Rhodococcus species
Authors: Zaccaria Marco , Sandlin Natalie , Fu David , Domin Marek , Momeni Babak
Published: August 2021

Bacterial detoxification of mycotoxins has the potential to offer a low-cost solution to ensure that feed and food commodities contaminated by fungal growth become safe to consume. Among bacteria, Rhodococcus species are of particular interest because they can be metabolically versatile, non-pathogenic, and environment-friendly. However, the native response of Rhodococcus environmental isolates appears inadequate for current detoxification needs. By analyzing the detoxification of aflatoxin by two Rhodococcus species: R. pyridinivorans and R. erythropolis, we examine important features of the dynamics that could guide future optimization of bacterial detoxification. Our results for Rhodococcus species suggest that detoxification happens through a regulated process of secreting extracellular enzymes. We show that enzyme fatigue in the presence of the toxin determines the lifetime of the enzyme and limits the overall detoxification performance of these species. Additionally, we show that the regulation of enzyme production can be both species- and environment-dependent. Overall, our quantitative approach reveals that enzyme fatigue is a major determinant of overall detoxification and needs to be accounted for in assessing the performance of detoxification by live cells or cell-free filtrates.
Characterization of a vaccine-elicited human antibody with sequence homology to VRC01-class antibodies that binds the C1C2 gp120 domain
Authors: Gray Matthew D. , Feng Junli , Weidle Connor E. , Cohen Kristen W. , Ballweber-Fleming Lamar , MacCamy Anna J. , Huynh Crystal N. , Trichka Josephine J. , Montefiori David , Ferrari Guido , Pancera Marie , McElrath M. Juliana , Stamatatos Leonidas
Published: August 2021

Broadly HIV-1 neutralizing VRC01-class antibodies bind the CD4-binding site of the HIV-1 envelope (Env) and contain VH1-2*02-derived heavy chains paired with light chains expressing five amino acid long CDRL3s. Their unmutated forms do not recognize Env or neutralize HIV-1. The lack of elicitation of VRC01-class antibodies in human clinical trials could potentially be due to the absence of activation of the corresponding naïve B cells by the vaccine Env immunogens. To address this point directly, we examined Env-specific BCR sequences from participants in the HVTN 100 clinical trial. Of all the sequences analyzed only one displayed sequence homology to VRC01-class antibodies, but the corresponding antibody (FH1) recognized the C1C2 gp120 domain. For FH1 to switch epitope recognition to the CD4-binding site, alterations in both the CDRH3 and CDRL3 were necessary. Our findings support the use of specifically designed immunogens to activate VRC01-class B cells in future human vaccine trials.
Acquisition of cell identity in the brown alga Ectocarpus: which of time, cell shape or position matters most?
Authors: Billoud Bernard , Saint-Marcoux Denis , Chenivesse Sabine , Duchêne Carole , Noûs Camille , Langdale Jane A. , Charrier Bénédicte
Published: August 2021

During development, cells undergo simultaneous changes of different types that together depict cell “identity”. In the multicellular brown alga Ectocarpus sp., while ageing, cells change shape and relative position within the filament. Understanding how these factors act and interact to specify cell identity requires markers of cell identity and the ability to genetically separate age, shape and position. Here we used laser capture microdissection (LCM) to isolate specific cell types from young sporophytes of Ectocarpus, and performed differential RNA-seq analysis. Transcriptome profiles of cell types in the wild-type strain provided signatures of the five cell types that can be identified by shape and position. In two mutants, where the relationship between cell shape, position and age are altered, transcriptome signatures revealed that little differential expression could be identified when only shape was perturbed. More generally, although the two mutants are characterised by opposite morphological phenotypes, their transcriptomes were remarkably similar. We concluded that despite the robustness of cell differentiation during WT development, neither the shape nor the position of the cell could serve as a faithful gauge for tracking differentiation.
Multiple knockout mutants reveal a high redundancy of phytotoxic compounds that determine necrotrophic pathogenesis of Botrytis cinerea
Authors: Leisen Thomas , Werner Janina , Pattar Patrick , Ymeri Edita , Sommer Frederik , Schroda Michael , Scheuring David , Hahn Matthias
Published: August 2021

Botrytis cinerea is a major pathogen of more than 1400 plant species. During infection, the kills host cells during infection and spreads through necrotic tissue, which is believed to be supported by induction of programmed plant cell death. To comprehensively evaluate the contributions of most of the currently known plant cell death inducing proteins (CDIPs) and metabolites for necrotrophic infection, an optimized CRISPR/Cas protocol was established which allowed serial marker-free mutagenesis to generate Botrytis mutants lacking up to 12 different CDIPs. Infection analysis revealed a decrease in virulence with increasing numbers of knockouts, and differences in the effects of knockouts on different host plants. The on planta secretomes obtained from these mutants revealed substantial remaining necrotic activity after infiltration into leaves. Our study has addressed for the first time the functional redundancy of virulence factors of a fungal pathogen, and demonstrates that B. cinerea releases a highly redundant cocktail of proteins and metabolites to achieve necrotrophic infection of a wide variety of host plants.
Bifurcating Neurons In The Anterior Thalamic Nuclei
Authors: Pei Y , Tasananukorn S , Wolff M , Dalrymple-Alford JC
Published: August 2021

The anterior thalamic nuclei (ATN) form a nodal point within a distributed memory network. The conventional view of ATN function describes segregated efferents to different terminal regions. By contrast, we found that bifurcating neurons are common within the anteromedial nucleus (AM) of the ATN. A substantial proportion of AM neurons (∼36% within a region of interest) showed collateral projections when one of two retrograde neurotracers, Cholera Toxin Subunit B (CTB) conjugated to either Alexa Fluor® 488 or 594, was placed in the medial prefrontal cortex (mPFC) or dorsal subiculum (dSub). A marked degree of collateralization (∼20% AM neurons) was also found when neurotracers were placed in mPFC and caudal retrosplenial cortex (cRSC); about 10% showed collaterals when the cRSC was paired with either dSub or vHF; the fewest (6%) was found for mPFC paired with the ventral hippocampal formation (vHF). A generally similar range of percentages of bifurcating neurons was found in the adjacent nucleus reuniens (Re). Evidence that AM neurons project simultaneously to many distantly-located structures provides a new perspective on ATN function. These neurons would facilitate direct coordination among key neural structures to support memory and may explain the strong association between the ATN and diencephalic amnesia.
Chemistry, Taxonomy and Ecology of the potentially chimpanzee-dispersedVepris tevasp.nov. (Rutaceae) of coastal thicket in the Congo Republic
Authors: Langat Moses , Kami Teva , Cheek Martin
Published: August 2021

Continuing a survey of the chemistry of species of the largely continental African genusVepris, we investigate a species previously referred to asVeprissp. 1 of Congo. From the leaves ofVeprissp. 1 we report six compounds. The compounds were three furoquinoline alkaloids, kokusaginine(1), maculine(2), and flindersiamine(3), two acridone alkaloids, arborinine(4)and 1-hydroxy-3-methoxy-10-methylacridone(5), and the triterpenoid, ß-amyrin(6). Compounds1-4are commonly isolated from otherVeprisspecies, compound5has been reported before once, from MalagasyVepris pilosa, while this is the first report of ß-amyrin fromVepris. This combination of compounds has never before been reported from any species ofVepris. We test the hypothesis thatVeprissp.1 is new to science and formally describe it asVepris teva, unique in the genus in that the trifoliolate leaves are subsessile, with the median petiolule far exceeding the petiole in length. Similar fleshy-leathery 4-locular syncarpous fruits are otherwise only known in the genus inVepris glaberrima(formerly the monotypic genusOriciopsisEngl.), a potential sister species, but requiring further investigation to confirm this phylogenetic position. We briefly characterise the unusual and poorly documented Atlantic coast equatorial ecosystem, whereVepris tevais restricted to evergreen thicket on white sand, unusual in a genus usually confine to evergreen forest. This endemic-rich ecosystem with a unique amphibian as well as plants, extends along the coastline from the mouth of the Congo River to southern Rio Muni, a distance of about 1000 km, traversing five countries. We map and illustrateVepris tevaand assess its extinction risk as Endangered (EN B1ab(iii)+B2ab(iii)) using the IUCN standard. Only three locations are known, and threats include port and oil refinery construction and associated activities, with only one protected location, the Jane Goodall Institute’s Tchimpounga Reserve. Initial evidence indicates that the seeds ofVepris tevaare dispersed by chimpanzees, previously unreported in the genus
Primate-specific ZNF808 is essential for pancreatic development in humans
Authors: De Franco Elisa , Owens Nick D L , Montaser Hossam , Wakeling Matthew N , Saarimäki-Vire Jonna , Ibrahim Hazem , Triantou Athina , Balboa Diego , Caswell Richard C , Johnson Matthew B , Ellard Sian , Wright Caroline F ,   Pancreatic Agenesis Gene Discovery Consortium, Flanagan Sarah E , Otonkoski Timo , Hattersley Andrew T , Imbeault Michael
Published: August 2021

Identifying genes linked to extreme phenotypes in humans has the potential to highlight new biological processes fundamental for human development. Here we report the identification of homozygous loss of function variants in the primate-specific gene ZNF808 as a cause of pancreatic agenesis. ZNF808 is a member of the KRAB zinc finger protein (KZFPs) family, a large and rapidly evolving group of epigenetic silencers that target transposable elements. We show that loss of ZNF808 in vitro results in aberrant activation of many transposable elements it normally represses during early pancreas development. This results in inappropriate specification of cell fate with induction of genes associated with liver endoderm and a loss of pancreatic identity. We show that ZNF808 and its transposable element targets play a critical role in cell fate specification during human pancreatic development. This is the first report of loss of a primate-specific gene causing a congenital developmental disease and highlights the essential role of ZNF808 for pancreatic development in humans.
Variational inference using approximate likelihood under the coalescent with recombination
Authors: Liu Xinhao , Ogilvie Huw A. , Nakhleh Luay
Published: August 2021

Coalescent methods are proven and powerful tools for population genetics, phylogenetics, epidemiology, and other fields. A promising avenue for the analysis of large genomic alignments, which are increasingly common, is coalescent hidden Markov model (coalHMM) methods, but these methods have lacked general usability and flexibility. We introduce a novel method for automatically learning a coalHMM and inferring the posterior distributions of evolutionary parameters using black-box variational inference, with the transition rates between local genealogies derived empirically by simulation. This derivation enables our method to work directly with three or four taxa and through a divide-and-conquer approach with more taxa. Using a simulated data set resembling a human–chimp–gorilla scenario, we show that our method has comparable or better accuracy to previous coalHMM methods. Both species divergence times and population sizes were accurately inferred. The method also infers local genealogies, and we report on their accuracy. Furthermore, we discuss a potential direction for scaling the method to larger data sets through a divide-and-conquer approach. This accuracy means our method is useful now, and by deriving transition rates by simulation, it is flexible enough to enable future implementations of various population models.
Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
Authors: Tock Andrew J. , Holland Daniel M. , Jiang Wei , Osman Kim , Sanchez-Moran Eugenio , Higgins James D. , Edwards Keith J. , Uauy Cristobal , Franklin F. Chris H. , Henderson Ian R.
Published: August 2021

The hexaploid bread wheat genome comprises over 16 gigabases of sequence across 21 chromosomes. Meiotic crossovers are highly polarized along the chromosomes, with elevation in the gene-dense distal regions and suppression in the Gypsy retrotransposon-dense centromere-proximal regions. We profiled the genomic landscapes of the meiotic recombinase DMC1 and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes. Distal ChIP-seq enrichment is consistent with spatiotemporally biased cytological immunolocalization of DMC1 and ASY1 close to the telomeres during meiotic prophase I. DMC1 and ASY1 ChIP-seq peaks show significant overlap with genes and transposable elements in the Mariner and Mutator superfamilies. However, DMC1 and ASY1 ChIP-seq peaks were detected along the length of each chromosome, including in low-crossover regions. At the fine scale, crossover elevation at DMC1 and ASY1 peaks and genes correlates with enrichment of the Polycomb histone modification H3K27me3. This indicates a role for facultative heterochromatin, coincident with high DMC1 and ASY1, in promoting crossovers in wheat and is reflected in distalized H3K27me3 enrichment observed via ChIP-seq and immunocytology. Genes with elevated crossover rates and high DMC1 and ASY1 ChIP-seq signals are overrepresented for defense-response and immunity annotations, have higher sequence polymorphism, and exhibit signatures of selection. Our findings are consistent with meiotic recombination promoting genetic diversity, shaping host–pathogen co-evolution, and accelerating adaptation by increasing the efficiency of selection.
The High Energy Density Scientific Instrument at the European XFEL
Authors: Zastrau Ulf , Appel Karen , Baehtz Carsten , Baehr Oliver , Batchelor Lewis , Berghäuser Andreas , Banjafar Mohammadreza , Brambrink Erik , Cerantola Valerio , Cowan Thomas E. , Damker Horst , Dietrich Steffen , Di Dio Cafiso Samuele , Dreyer Jörn , Engel Hans-Olaf , Feldmann Thomas , Findeisen Stefan , Foese Manon , Fulla-Marsa Daniel , Göde Sebastian , Hassan Mohammed , Hauser Jens , Herrmannsdörfer Thomas , Höppner Hauke , Kaa Johannes , Kaever Peter , Knöfel Klaus , Konôpková Zuzana , Laso García Alejandro , Liermann Hanns-Peter , Mainberger Jona , Makita Mikako , Martens Eike-Christian , McBride Emma E. , Möller Dominik , Nakatsutsumi Motoaki , Pelka Alexander , Plueckthun Christian , Prescher Clemens , Preston Thomas R. , Röper Michael , Schmidt Andreas , Seidel Wolfgang , Schwinkendorf Jan-Patrick , Schoelmerich Markus O. , Schramm Ulrich , Schropp Andreas , Strohm Cornelius , Sukharnikov Konstantin , Talkovski Peter , Thorpe Ian , Toncian Monika , Toncian Toma , Wollenweber Lennart , Yamamoto Shingo , Tschentscher Thomas
Published: August 2021

The European XFEL delivers up to 27000 intense (>1012 photons) pulses per second, of ultrashort (≤50 fs) and transversely coherent X-ray radiation, at a maximum repetition rate of 4.5 MHz. Its unique X-ray beam parameters enable groundbreaking experiments in matter at extreme conditions at the High Energy Density (HED) scientific instrument. The performance of the HED instrument during its first two years of operation, its scientific remit, as well as ongoing installations towards full operation are presented. Scientific goals of HED include the investigation of extreme states of matter created by intense laser pulses, diamond anvil cells, or pulsed magnets, and ultrafast X-ray methods that allow their diagnosis using self-amplified spontaneous emission between 5 and 25 keV, coupled with X-ray monochromators and optional seeded beam operation. The HED instrument provides two target chambers, X-ray spectrometers for emission and scattering, X-ray detectors, and a timing tool to correct for residual timing jitter between laser and X-ray pulses.
High-resolution fast-tomography brain-imaging beamline at the Taiwan Photon Source
Authors: Chen Hsiang Hsin , Yang Shun-Min , Yang Kai-En , Chiu Ching-Yu , Chang Chia-Ju , Wang Ya-Sian , Lee Tsung-Tse , Huang Yu-Fen , Chen Yi-Yun , Petibois Cyril , Chang Shih-Hung , Cai Xiaoqing , Low Chian-Ming , Tan Francis Chee Kuan , Teo Alvin , Tok Eng Soon , Lim Jae-Hong , Je Jun-Ho , Kohmura Yoshiki , Ishikawa Tetsuya , Margaritondo Giorgio , Hwu Yeukuang
Published: August 2021

The new Brain Imaging Beamline (BIB) of the Taiwan Photon Source (TPS) has been commissioned and opened to users. The BIB and in particular its endstation are designed to take advantage of bright unmonochromatized synchrotron X-rays and target fast 3D imaging, ∼1 ms exposure time plus very high ∼0.3 µm spatial resolution. A critical step in achieving the planned performances was the solution to the X-ray induced damaging problems of the detection system. High-energy photons were identified as their principal cause and were solved by combining tailored filters/attenuators and a high-energy cut-off mirror. This enabled the tomography acquisition throughput to reach >1 mm3 min−1, a critical performance for large-animal brain mapping and a vital mission of the beamline.
Development of healthier gluten-free chicken products coated with different cereal sources
Authors: Uyarcan Müge , Yayla Emine , Akgül Deniz , İşseven Damla
Published: August 2021

Purpose

According to the dietary needs of celiac people and very limited variety of commercially available foodstuff, the demand for gluten-free products is increasing every day. Keeping this in view, the present study aims to develop healthier gluten-free chicken products by using different cereal sources and to determine the effect of substitution of wheat flour with gluten-free flours on quality of chicken products.

Design/methodology/approach

Buckwheat, chickpea and rice flours were used as gluten-free flours for the production of chicken products. The physical (yield parameters, crust colour), chemical (proximate composition, caloric value, pH) and sensorial properties of coated chicken products were measured. Duncan's multiple range test and principles component analysis were performed.

Findings

Gluten-free flours were significantly effective on yield parameters, colour, moisture, protein, lipid and caloric value of the samples (p < 0.05). The results showed that gluten-free chicken products had better pickup, lighter appearance, higher cooking yield and moisture, lower cooking loss, oil absorption, lipid and caloric values compared to commercial wheat flour coated control. Regarding the overall impression rank sums, the panellists were more preferred gluten-free products than control group. The samples coated with chickpea flour were best rated by the panellists. The results of the study suggested that the use of chickpea coating flour could be best nutritionally and sensorially suitable option for producing gluten-free chicken product.

Originality/value

This study offers potential healthy alternatives to increase the variety of gluten-free products that celiac people desperately need today.
Factors influencing green purchasing inconsistency of Ecuadorian millennials
Authors: Carrión Bósquez Nelson Geovany , Arias-Bolzmann Leopoldo Gabriel
Published: August 2021

Purpose

This study aimed to identify whether attitudes and subjective norms influence green purchase intentions of university millennials, based on the Theory of Planned Behavior. It also analyzed whether purchase intentions resulted in actual purchases and the factors that influenced green purchasing inconsistencies.

Design/methodology/approach

This was a cross-sectional quantitative study with 710 millennial participants, who were university students of the four most populated cities of Ecuador; however, only 126 (18%) participants were found to frequently consume organic products during the last months. The results were tested by the Cronbach's alpha coefficient to determine the instrument's internal consistency. Subsequently, an exploratory factor analysis was developed to verify if the questions were grouped into their corresponding constructs. Finally, the proposed research model's validity was verified through a confirmatory factor analysis and structural equation modeling. SPSS 20 and AMOS 24 were used for the abovementioned statistical analyses.

Findings

Attitudes and subjective norms influence green purchase intentions. Although university millennials have high purchase intentions, the majority (82%) did not result in actual purchases. It was determined that consumption habit is the main factor influencing green purchasing inconsistencies.

Originality/value

This is the first study to measure green purchasing inconsistencies in developing countries in South America (Ecuador), exposing that purchase intention is not the best predictor of actual purchases in developing economies. It also provides answers to previous studies that suggested determining levels of inconsistency and attitude-behavior gaps.
Green supply chain management pressures, practices and performance: a critical literature review
Authors: Choudhary Kailash , Sangwan Kuldip Singh
Published: August 2021

Purpose

The concept of green supply chain management (GSCM) is evolving rapidly due to the environmental concerns and gaining popularity in the research community. This study critically analyze the literature of GSCM pressure, practice and performance for manufacturing enterprises based on the results of bibliometric, network and frequency analyses.

Design/methodology/approach

Scopus database is used for literature search. Bibliometric network and frequency analysis are used to critically review the evolution of identified constructs and measures of GSCM pressure, practice and performance.

Findings

This study has identified that the selected topic is in growing stage through the collaborative effort of the worldwide researchers. This study also shows the diffusion of influence in developing countries and there are enormous opportunities of research in these regions. The study finds evaluation of GSCM constructs and measures with time and shift in focus areas by the researchers. The study suggests more focus on the measurement of informative pressures, reverse logistics practices and negative impact on economic performance due to the adoption of GSCM practices. There is a need of simultaneous analysis of GSCM pressures, practices and performance to identify the cascading effect in different regions and industrial sectors and developed a conceptual framework to identify this effect. This study also observes the need of more quantitative measures-based case studies and suggests the use of life cycle assessment for the quantification of environmental performance.

Originality/value

This study for the first time has analyzed a specific topic of GSCM pressure, practice and performance through bibliometric and network analyses. This study critically reviews the constructs and measures of GSCM pressure, practice and performance and identified the future research directions.
The hindrance of cloud computing acceptance within the financial sectors in Germany
Authors: Stewart Harrison
Published: August 2021

Purpose

The purpose of this study is to develop a model called “IaaS adoption” to identify the various challenges and precise implications that hinder the adoption of infrastructure as a service (IaaS) in Germany.

Design/methodology/approach

The model was validated by an online survey of 208 bank employees.

Findings

The study found that the nine-five-circle factors (data security, risk and trust) and other factors proved to be statistically significant challenges for IaaS acceptance among banks in Germany.

Originality/value

The adoption of cloud technology and its advantages is still a critical issue for the conventional banking sectors in Germany.
From accident to hospital: measuring inequality in pre-hospital emergency services in a city in the North of Iran
Authors: Omidi Mohaddese , Zohrevandi Behzad , Homaie Rad Enayatollah
Published: August 2021

Purpose

As a human right, people need to arrive early at the hospitals when they are injured in traffic accidents. Both the mean and equality of the time of arriving at the hospital are important. This study aimed to investigate inequality in arrival time of emergent traffic accident patients to the hospital in 2018–2019 in a city in the North of Iran.

Design/methodology/approach

The authors extracted the data from the Guilan province trauma system databank in Poursina Hospital in Rasht in 2018 and 2019. The Gini coefficient was used to calculate inequality, and a regression model was estimated for determining the reason for inequality in time to receive hospital services.

Findings

The study showed that patients’ arrival time from the time of the accident to the time of arrival to the hospital was 64.48 ± 47.63 min (minimum of 9 min and maximum 462 min). Gini coefficient was 0.31 (p <0.001), which does not show high inequality. Regression results showed that the transfer time of patients by car was 40 min longer (p-value <0.001) than ambulances (p = 0.036). In children, the transfer time was 42 min less (p = 0.003). Other variables did not explain the inequality (p > 0.05).

Originality/value

According to the time of arrival of patients and Gini index, in Rasht, inequality in providing services is not in a bad condition. This indicates that the emergency department does not systematically transport people to the hospital late.
Mediating effect of organisational innovation in the prediction of change-oriented leadership on organisational performance
Authors: AlAnazi Amer Ahmad , Kura Kabiru Maitama , Suleiman Ebi Shahrin , Abubakar Ramatu Abdulkareem
Published: August 2021

Purpose

To address this question, this study aims to drew from resource-based view to examine the mediating role organisational innovation in the relationship between change-oriented leadership and organisational performance.

Design/methodology/approach

Given that the unit of analysis is an organisation, 219 principal officers, including Presidents/Rectors, Vice Presidents/Vice-Rectors, Registrars and Deans, were invited to complete the survey on behalf of their universities.

Findings

Results of the partial least squares structural equation modelling confirmed the positive relationship between change-oriented leadership and university performance. The results provide evidence that organisational innovation directly facilitates university performance. As expected, the relationship between change-oriented leadership and university performance was found to be mediated by organisational innovation.

Practical implications

Overall, this study successfully modelled organisational innovation as an underlying mechanism behind the change-oriented leadership – university performance relationship, thereby by testing resource-based theory in Saudi Arabian context. From a practical perspective, results suggest that to improve their performance is imperative for executive leaders in Saudi universities to focus on several specific work design strategies, obtaining feedback about their change-oriented leadership style from followers.

Originality/value

Whilst there has been a considerable amount of research emphasising the importance of change-oriented leadership, there has been little research linking this fundamental aspect of leadership to organisational performance. Yet an understanding of the possible mechanisms behind this linkage has not received attention.
Empirical evaluation of code smells in open-source software (OSS) using Best Worst Method (BWM) and TOPSIS approach
Authors: Tandon Stuti , Kumar Vijay , Singh V.B.
Published: August 2021

Purpose

Code smells indicate deep software issues. They have been studied by researchers with different perspectives. The need to study code smells was felt from the perspective of software industry. The authors aim to evaluate the code smells on the basis of their scope of impact on widely used open-source software (OSS) projects.

Design/methodology/approach

The authors have proposed a methodology to identify and rank the smells in the source code of 16 versions of Apache Tomcat Software. Further, the authors have analyzed the categorized smells by calculating the weight of the smells using constant weights as well as Best Worst Method (BWM). Consequently, the authors have used Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) to determine the rank of versions using constant weights as well as BWM.

Findings

Version 1 of Apache Tomcat has least smell, and version 8 is reported to contain the maximum code smells. Notable differences in both the cases during the trend analysis are reported by the study. The findings also show that increase is observed in the number of code smells with the release of newer versions. This increment is observed till version 8, followed by a subtle marked depreciation in the number of code smells in further releases.

Originality/value

The focus is to analyze smells and rank several versions of Apache Tomcat, one of the most widely used software for code smell study. This study will act as a significant one for the researchers as it prioritizes the versions and will help in narrowing down the options of the software used to study code smell.
On inference and design under progressive type-I interval censoring scheme for inverse Gaussian lifetime model
Authors: Roy Soumya , Pradhan Biswabrata , Purakayastha Annesha
Published: August 2021

Purpose

This article considers Inverse Gaussian distribution as the basic lifetime model for the test units. The unknown model parameters are estimated using the method of moments, the method of maximum likelihood and Bayesian methods. As part of maximum likelihood analysis, this article employs an expectation-maximization algorithm to simplify numerical computation. Subsequently, Bayesian estimates are obtained using the Metropolis–Hastings algorithm. This article then presents the design of optimal censoring schemes using a design criterion that deals with the precision of a particular system lifetime quantile. The optimal censoring schemes are obtained after taking into account budget constraints.

Design/methodology/approach

This article first presents classical and Bayesian statistical inference for Progressive Type-I Interval censored data. Subsequently, this article considers the design of optimal Progressive Type-I Interval censoring schemes after incorporating budget constraints.

Findings

A real dataset is analyzed to demonstrate the methods developed in this article. The adequacy of the lifetime model is ensured using a simulation-based goodness-of-fit test. Furthermore, the performance of various estimators is studied using a detailed simulation experiment. It is observed that the maximum likelihood estimator relatively outperforms the method of moment estimator. Furthermore, the posterior median fares better among Bayesian estimators even in the absence of any subjective information. Furthermore, it is observed that the budget constraints have real implications on the optimal design of censoring schemes.

Originality/value

The proposed methodology may be used for analyzing any Progressive Type-I Interval Censored data for any lifetime model. The methodology adopted to obtain the optimal censoring schemes may be particularly useful for reliability engineers in real-life applications.
How the peer-to-peer market for tourist accommodation has responded to COVID-19
Authors: Benítez-Aurioles Beatriz
Published: August 2021

Purpose

This study aims to analyze the COVID-19 pandemic’s impact on the peer-to-peer (p2p) market for tourist accommodation.

Design/methodology/approach

Using monthly panel data from Airbnb listings in 22 cities worldwide, the authors run a differences-in-differences analysis comparing the period of February–October 2020 to the previous year.

Findings

Besides a decline in accommodation supply, the pandemic made prices and demand fall in all cities significantly, after controlling for room characteristics, host traits, booking policies and individual fixed effects. There is also evidence of an alteration of the influence on prices of certain variables such as superhost and instant booking.

Research limitations/implications

The main limitations are related to the reference spatial and temporal environment. Besides, the samples are limited to listings that stayed before and after the pandemic; therefore, it is possible that the real effect on review growth and/or prices is actually more negative.

Practical implications

The analysis performed shows a scenario that represents an opportunity for public managers to test more imaginative regulations that overcome the limitations of those implemented so far. Likewise, hosts who aspire to make their accommodations profitable must adapt to the conditions imposed by the economic environment of the cities in which they operate.

Originality/value

This is the first study to econometrically estimate the impact of COVID-19 on prices in the p2p market for tourist accommodation in a set of cities worldwide.
Design and analysis of magnetorheological damper based ankle-foot prosthesis prototype
Authors: Negi Sachin , Sagar Ujjwal , Nautiyal Vijay Kumar , Sharma Neeraj
Published: August 2021

Purpose

This paper aims to design and analyze a controlled magnetorheological damper-based ankle-foot prosthesis prototype.

Design/methodology/approach

The ankle-foot prostheses prototype is proposed using the lightweight three dimensional (3 D)-printed parts, MR damper and digital servomotor. Initially, the computer-aided design (CAD) model of the prosthetic foot, leaf spring, retention spring and the various connecting parts required to connect the pylon and damper actuator assemblies are designed using CAD software. Later, the fused deposition modeling 3 D printer-based technique prints a prosthetic foot and other connecting parts using Acrylonitrile Butadiene Styrene filament. The prototype consists of two control parts: the first part controls the MR actuator that absorbs the impacts during walking. The second part is the control of the electric actuator intended to generate the dorsiflexion and plantar flexion movements. Finally, the prototype is tested on a transtibial amputee under the supervision of a prosthetist.

Findings

The ANalysis SYStems software-based analysis has shown that the prosthetic foot has a factor of safety values between 4.7 and 8.7 for heel strike, mid-swing and toe-off; hence, it is safe from mechanical failure. The designed MR damper-based ankle-foot prosthesis prototype is tested on an amputee for a level-ground walk; he felt comfortable compared to his passive prosthesis.

Originality/value

The design of an MR damper-based prosthesis prototype offers a better dynamic range for locomotion than passive prostheses. It reduces the injuries and provides relief to the transtibial amputees.
A new mechanism for purchasing through personal interactions: fairness, trust and social influence in online group buying
Authors: Hung Shiu-Wan , Cheng Min-Jhih , Lee Chia-Jung
Published: August 2021

Purpose

The purpose of this article was to explore the influence of individual perception and social climate on consumer-initiated group-buying purchase decisions. An extended cross-level research model was used to explain how a new mechanism for purchasing through personal interactions could work.

Design/methodology/approach

This study utilised a questionnaire survey for data gathering. The subjects of the investigation were group-buying initiators. Hierarchical linear modelling (HLM) was used to experimentally examine the research hypotheses.

Findings

The empirical results of the study indicate that the social influence of critical mass can effectively promote positive attitudes and intentions towards consumer-initiated online group buying. An individuals' perception of an initiator's fairness influences their trust in the initiator. In addition, trust in the initiator can positively and significantly influence buyers' attitudes and intentions to online group buying.

Originality/value

Most previous studies on online group-buying focus on how social media influences group-buying behaviours. This study extends social media research by introducing an extended cross-level model to provide a comprehensive investigation into online-shopping. It is a preliminary attempt to systematically verify relationships at the individual and aggregate levels. The decision to group buying requires a relationship of trust to be formed before any transaction takes place, thereby increasing the intention to make a purchase. As a result, group buying is perceived as positive when interpersonal communication is very efficient, or when social influence is high.