bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Antimicrobial Efficacy Of Plasma Activated Water Is Modulated By Reactor Design And Water Composition
Authors: Rothwell Joanna G. , Alam David , Carter Dee A. , Soltani Behdad , McConchie Robyn , Zhou Renwu , Cullen Patrick J. , Mai-Prochnow Anne 
Published: July 2021

AbstractPlasma activated water (PAW) contains a cocktail of reactive oxidative species and free radicals and has demonstrated efficacy as a sanitizer for fresh produce, however there is a need for further optimization. The antimicrobial efficacy of PAW produced by a bubble spark discharge (BSD) reactor and a dielectric barrier discharge-diffuser (DBDD) reactor operating at atmospheric conditions with air, discharge frequencies of 500, 1000 and 1500 Hz, and MilliQ and tap water, was investigated with model organisms Listeria innocua and Escherichia coli. Optimal conditions were subsequently employed for pathogenic bacteria Listeria monocytogenes, E. coli and Salmonella enterica. PAW generated with the DBDD reactor reduced more than 6-log CFU of bacteria within 1 minute of treatment. The BSD-PAW, while attaining high CFU reduction was less effective, particularly for L. innocua. Analysis of physicochemical properties revealed BSD-PAW had a greater variety of reactive species than DBDD-PAW. Scavenger assays were employed to specifically sequester reactive species, including the short-lived superoxide (·O2-) radical that could not be directly measured in the PAW. This demonstrated a critical role of superoxide for the inactivation of both E. coli and L. innocua by DBDD-PAW, while in BSD-PAW it had a role in L. innocua inactivation only. Overall, this study demonstrates the potential of DBDD-PAW in fresh produce, where there is a need for sterilization while minimizing chemical inputs and residues and maintaining food quality. Highly effective PAW was generated using air as a processing gas and tap water, making this a feasible and cost-effective option.ImportanceThere is a growing demand for fresh food produced with minimal processing, however guaranteeing microbial safety in the absence of a thermal kill step is challenging. Plasma-activated water (PAW) is a promising novel antimicrobial but its use in high-risk applications like the sanitization of fresh produce requires further optimization. This study demonstrated the importance of reactor design in the production of reactive species in PAW with capacity to kill bacteria. Very effective PAW was generated using a dielectric barrier discharge-diffuser (DBDD) system, with antimicrobial activity attributed to the presence of superoxide radicals. The DBBD reactor used air as a processing gas and tap water, highlighting the potential of this approach as a cost-effective and green alternative to chemical treatment methods that are currently used in food decontamination.
Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis
Authors: Motyka Michal , Kusy Dominik , Bocek Matej , Bilkova Renata , Bocak Ladislav 
Published: July 2021

AbstractConservation efforts must be evidence-based, so rapid and economically feasible methods should be used to quantify diversity and distribution patterns. We have attempted to overcome current impediments to the gathering of biodiversity data by using integrative phylogenomic and three mtDNA fragment analyses. As a model, we sequenced the Metriorrhynchini beetle fauna, sampled from ∼700 localities in three continents. The species-rich dataset included ∼6,500 terminals, >2,300 putative species, more than a half of them unknown to science. The phylogenomic backbone enabled the integrative delimitation of robustly defined natural units that will inform future research. Using constrained mtDNA analysis, we identified the spatial structure of α-diversity, very high species-level endemism, a biodiversity hotspot in New Guinea, and high phylogenetic diversity in the Sundaland. We suggest that ∼20 person months of focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. The outcome would be a scaffold for the incorporation of further data. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.
INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants
Authors: Dong Chenyang , Simonett Shane P. , Shin Sunyoung , Stapleton Donnie S. , Schueler Kathryn L. , Churchill Gary A. , Lu Leina , Liu Xiaoxiao , Jin Fulai , Li Yan , Attie Alan D. , Keller Mark P. , Keleş Sündüz 
Published: July 2021

AbstractGenome-wide association studies have revealed many non-coding variants associated with complex traits. However, model organism studies have largely remained as an untapped resource for unveiling the effector genes of non-coding variants. We develop INFIMA,IntegrativeFine-Mapping, to pinpoint causal SNPs for Diversity Outbred (DO) mice eQTL by integrating founder mice multi-omics data including ATAC-seq, RNA-seq, footprinting, andin silicomutation analysis. We demonstrate INFIMA’s superior performance compared to alternatives with human and mouse chromatin conformation capture datasets. We apply INFIMA to identify novel effector genes for GWAS variants associated with diabetes. The results of the application are available athttp://www.statlab.wisc.edu/shiny/INFIMA/
Gene Evolutionary Trajectories inM. tuberculosisReveal Temporal Signs of Selection
Authors: Chiner-Oms Álvaro , López Mariana G. , Comas Iñaki 
Published: July 2021

AbstractGenetic differences between differentMycobacterium tuberculosiscomplex (MTBC) strains determine their ability to transmit within different host populations, their latency times, and their drug-resistance profiles. Said differences usually emerge throughde novomutations and are maintained or discarded by the balance of evolutionary forces. Using a dataset of ~5,000 strains representing global MTBC diversity, we determined the past and present selective forces that have shaped the current variability observed in the pathogen population. We identified regions that have evolved under changing types of selection since the time of the MTBC common ancestor. Our approach highlighted striking differences in the genome regions relevant for host-pathogen interaction and, in particular, suggested an adaptive role for the sensor protein of two-component systems. In addition, we applied our approach to successfully identify potential determinants of resistance to drugs administered as second-line tuberculosis treatments.
Potato juice, a starch industry waste, as a cost-effective medium for the biosynthesis of bacterial cellulose
Authors: Ciecholewska-Juśko Daria , Broda Michał , Żywicka Anna , Styburski Daniel , Sobolewski Peter , Gorący Krzysztof , Migdał Paweł , Junka Adam , Fijałkowski Karol 
Published: July 2021

ABSTRACTThe unique properties of bacterial cellulose (BC) make it of great interest for numerous branches of industry. Nevertheless, the high cost of the dedicated, microbiological medium used for BC production significantly hinders possibility of widespread use. Searching for an alternative, we turned our attention to potato tuber juice (PJ), a major waste product of the potato starch industry. We verified the possibility of using PJ as a cost-effective, ecological-friendly medium that yielded BC with properties equivalent to those from conventional commercial Hestrin-Schramm medium. The BC yield from PJ medium (>4 g/L) was comparable, despite the lack of any pre-treatment. Likewise, the macro- and microstructure, physicochemical parameters, and chemical composition showed no significant differences between PJ and control BC. Importantly, BC obtained from PJ was not cytotoxic against fibroblast cell line L929 in vitro and did not contain any hard-to-remove impurities. These are very important aspects from an application standpoint, particularly in biomedicine. Therefore, we conclude that using PJ for BC biosynthesis is a path towards significant valorization of an environmentally problematic waste product of the starch industry and can help ultimately lower BC production costs.HighlightsPotato juice (PJ) was used as a culture medium for cellulose-synthesizing bacteria.PJ was suitable as source of nutrients and did not required any pre-treatment.Yield of BC from PJ was equivalent to that obtained from conventional HS.PJ-BC did not differ from conventionally produced HS-BC in terms of its properties.PJ-BC can be used in the same applications as commercially produced BC.Graphical abstract
Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heteromorphic invasive populations ofLudwigia grandiflora subsp. hexapetala
Authors: Portillo Lemus Luis O. , Harang Marilyne , Bozec Michel , Haury Jacques , Stoeckel Solenn , Barloy Dominique 
Published: July 2021

AbstractBreeding system influences local population genetic structure, effective size, offspring fitness and functional variation. Determining the respective importance of self- and cross-fertilization in hermaphroditic flowering plants is thus important to understand their ecology and evolution. The worldwide invasive species,Ludwigia grandiflora subsp. hexapetala(Lgh) presents two floral morphs: one self-compatible short-styled morph (S-morph) and one self-incompatible long-styled morph (L-morph). In this study, we identified the breeding systems of western European experimental and natural populations of Lgh by comparing structural characteristics of pollen and style, by studying self- and cross-pollen tube elongations and the viability of the resulting seeds and seedlings in both floral morphs. Our results showed no differences in pollen shape and stigma surfaces no matter the floral morph. In the self-incompatible L-morph flowers, self-pollen tubes were stopped tardily, in the ovarian area, and were unable to fertilize the ovules. This first formal identification of a late-acting, prezygotic self-incompatible system (LSI) inLudwigiagenus contributes a case of LSI in an additional family within the Myrtales order. In the self-compatible S-morph flowers, self-pollen always succeeded to self-fertilize the ovules that nearly all developed into viable seedlings. However, cross-pollen tubes always elongated faster than self-pollen tubes in both morphs. S-morph individuals may thus advantage preferential allogamy over selfing when cross-pollen is available despite its self-compatibility. As expected in late-acting self-incompatible systems, L-morph flowers authorised 0.2‰ of selfed seeds during the uppermost flowering season, that increased to 1‰ at the end of the flowering season. Such delayed selfing resulted in a significant quantity of viable floating seeds. They may contribute to the local regeneration, seed bank and propagation of the L-morph, which may contribute to explain its invasion success worldwide. Management plans of Lgh would gain to consider the breeding systems we identified.
Large-scale identification of viral quorum sensing systems reveals density-dependent sporulation-hijacking mechanisms in bacteriophages
Authors: Bernard Charles , Li Yanyan , Lopez Philippe , Bapteste Eric 
Published: July 2021

ABSTRACTCommunication between viruses supported by quorum sensing systems (QSSs) were found to optimize the fitness of temperate bacteriophages of Bacilli by guiding the transition from the host-destructive lytic cycle to the host-protective lysogenic cycle in a density-dependent manner. All known phage-encoded QSSs consist of a communication propeptide and a cognate intracellular receptor that regulates the expression of adjacent target genes upon recognition of the matured peptide, a signature known as RRNPP and found in chromosomes, plasmids and phages of Firmicutes bacteria. Recently, we have introduced the RRNPP_detector software to detect novel genetic systems matching the RRNPP signature, which unearthed many novel phage-encoded candidate QSSs. Here, by looking at the adjacent genes likely regulated by these viral candidate QSSs, we identified an unsuspected clustering of viral QSSs with viral genes whose bacterial homologs are key regulators of the last-resort bacterial sporulation initiation pathway (rap, spo0E or abrB). Consistently, we found evidence in published data that certain of these QSSs encoded by prophages (phage genomes inserted within a bacterial genome) dynamically manipulate the timing of sporulation in the host. Because these viral QSSs are genetically diverse and are found associated with different sporulation regulators, this suggests a convergent evolution in bacteriophages of density-dependent sporulation-hijacking mechanisms.SIGNIFICANCECommunication between viruses supported by quorum sensing systems (QSSs) is a brand new research area that has transformed our views of viral adaptation and virus-host co-evolution. The viral QSSs discovered so far were found to guide the lysis-lysogeny decision in temperate bacteriophages as a function of phage density. Here, we identified that quorum sensing-mediated communication between phages can not only guide the regulation of viral processes but also the manipulation of the bacterial sporulation pathway. Our finding introduces the new view that not only bacteria decide when it is time to sporulate, some bacteriophages are also key stakeholders in this dynamical decision-making process. Considering that spores are the transmissive form of many pathogens, these new insights have important applied implications.
Reciprocal regulation of Shh trafficking and H2O2 levels via a noncanonical BOC-Rac1 pathway
Authors: Thauvin Marion , Amblard Irène , Rampon Christine , Mourton Aurélien , Queguiner Isabelle , Li Chenge , Gautier Arnaud , Joliot Alain , Volovitch Michel , Vriz Sophie 
Published: July 2021

SummaryAmong molecules that bridge environment, cell metabolism, and cell signaling, H2O2 recently appeared as an emerging but central player. Its level depends on cell metabolism and environment and was recently shown to play key roles during embryogenesis, contrasting with its long-established role in disease progression. We decided to explore whether the secreted morphogen Sonic hedgehog (Shh), known to be essential in a variety of biological processes ranging from embryonic development to adult tissue homeostasis and cancers, was part of these interactions. Here, we report that H2O2 levels control key steps of Shh delivery and that physiological in vivo modulation of H2O2 levels changes Shh distribution and tissue patterning. A feedback loop exists in which Shh trafficking controls H2O2 synthesis via a non-canonical BOC-Rac1 pathway, leading to cytoneme growth. Our findings reveal that Shh directly impacts its own distribution, thus providing a molecular explanation for the robustness of morphogenesis to both environmental insults and individual variability.
The transformation of education during the corona pandemic: exploring the perspective of the private university students in Bangladesh
Authors: Shahriar Shamsul Huq Bin , Arafat Sayed , Sultana Nayeema , Akter Silvia , Khan Md. Mahfuzur Rahman , Nur J.M. Ekram Hossain , Khan Syful Islam 
Published: July 2021

PurposeIn 2020, the education system was preliminary halted by the COVID-19 crisis and went through radical improvisation, and online-based distance learning was the only plausible initiative to continue educational activities ensuring health guidelines properly. However, in reality, such desperate measure in case of a lower-middle-income developing nation lacking proper structural capabilities raised some issues and concerns for both pupils and mentors, and this study aims to explore the practice of online-based distance learning in private universities of Bangladesh and the challenges associated with it.Design/methodology/approachThis exploratory research is qualitative in nature. A total number of 89 undergraduate level university students from different private universities were divided into two main clusters and interviewed in depth.FindingsThe findings of this paper revealed that common developing country syndromes like improper technological infrastructure development, limitation to devices or internet accessibility and financial hindrances can disrupt the harmony of the online learning experience. Also, the lack of tech literacy has created a huge tension and psychological inertia among both the teachers and the students.Social implicationsThe coronavirus pandemic event, with its dreadful influence, is creating immense mental pressures for students to cope well with the online learning system. Comprehending the underlying challenges affiliated with online-based distance learning and enabling faculties or respected personnel with training and development programs to handle impediments better way, this learning initiative can ensure the best outcomes.Originality/valueThe significance of this study lies in comprehending the feasibility of online-based education regarding lower-middle-income developing nation context and the realism of such learning process's acceptability considering its actual effectiveness.
Aircraft air data system fault detection and reconstruction scheme design
Authors: Kilic Ugur , Unal Gulay 
Published: July 2021

Purpose
The purpose of this study is to detect and reconstruct a fault in pitot probe and static ports, which are components of the air data system in commercial aircrafts, without false alarm and no need for pitot-static measurements. In this way, flight crew will be prevented from flying according to incorrect data and aircraft accidents that may occur will be prevented.

Design/methodology/approach
Real flight data collected from a local airline was used to design the relevant system. Correlation analysis was performed to select the data related to the airspeed and altitude. Fault detection and reconstruction were carried out by using adaptive neural fuzzy inference system and artificial neural networks, which are machine learning methods. MATLAB software was used for all the calculations.

Findings
No false alarm was detected when the fault test following the fault modeling was carried out at 0–2 s range by filtering the residual signal. When the fault was detected, fault reconstruction process was initiated so that system output could be achieved according to estimated sensor data.

Practical implications
The presented alternative analytical redundant airspeed and altitude calculation scheme could be used when the pitot-static system contains any fault condition.

Originality/value
Instead of using the methods based on hardware redundancy, the authors designed a new system within the scope of this study. Fault situations that may occur in pitot probes and static ports are modeled and different fault scenarios that can be encountered in all flight phases have been examined.
Consumer perception on halal meat logistics
Authors: Tieman Marco , Che Ghazali Maznah , van der Vorst Jack G.A.J. 
Published: July 2021

PurposeThe purpose of this paper is to investigate the preferred minimum level of segregation for halal meat in supermarket, transport, storage and terminals; the responsibility of halal logistics; and the willingness to pay for halal logistics in a Muslim and non‐Muslim country.Design/methodology/approachThis is a comparative study involving Muslim consumers in Malaysia and The Netherlands. Cross‐sectional data were collected through a survey with 251 Muslims in Malaysia and 250 Muslims in The Netherlands. Data were analysed by means of nonparametric tests.FindingsThere is a preferred higher level of segregation in a Muslim country than a non‐Muslim country. A Muslim country has a higher willingness to pay for a halal logistics system as compared to a non‐Muslim country. Furthermore, there lies a heavy responsibility with the manufacturer to extend halal assurance towards supply chain management.Research limitations/implicationsThe study confirms there is a need for a different level of segregation and therefore different halal logistics standard in a Muslim country and a non‐Muslim country. However, during the survey in The Netherlands significant rejections were received from especially first generation Muslims due to the lack of understanding of the Dutch language. Similar surveys need to be conducted in other countries in order to be able to generalise over the various Islamic schools of thought, localfatwasand local customs.Practical implicationsHalal logistics is important to the Muslim consumer and critical for the trust in a halal certified brand, which requires extending halal integrity from point of production to the point of consumer purchase.Originality/valueThis study is a preliminary one investigating the consumer perception on halal logistics. The study indicates the level of segregation required for a halal meat supply chain in a Muslim and non‐Muslim country.
Modeling of a simplified hybrid algorithm for short-term load forecasting in a power system network
Authors: Mayilsamy Kathiresh , A, Maideen Abdhulkader Jeylani , Akbarali Mahaboob Subahani , Sathiyanarayanan Haripranesh 
Published: July 2021

Purpose
The purpose of this paper is to develop a hybrid algorithm, which is a blend of auto-regressive integral moving average (ARIMA) and multilayer perceptron (MLP) for addressing the non-linearity of the load time series.

Design/methodology/approach
Short-term load forecasting is a complex process as the nature of the load-time series data is highly nonlinear. So, only ARIMA-based load forecasting will not provide accurate results. Hence, ARIMA is combined with MLP, a deep learning approach that models the resultant data from ARIMA and processes them further for Modelling the non-linearity.

Findings
The proposed hybrid approach detects the residuals of the ARIMA, a linear statistical technique and models these residuals with MLP neural network. As the non-linearity of the load time series is approximated in this error modeling process, the proposed approach produces accurate forecasting results of the hourly loads.

Originality/value
The effectiveness of the proposed approach is tested in the laboratory with the real load data of a metropolitan city from South India. The performance of the proposed hybrid approach is compared with the conventional methods based on the metrics such as mean absolute percentage error and root mean square error. The comparative results show that the proposed prediction strategy outperforms the other hybrid methods in terms of accuracy.