bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soy protein isolates: A review of their composition, aggregation, and gelation
Authors: Zheng Li , Regenstein Joe M. , Zhou Linyi , Wang Zhongjiang 
Published: February 2022

AbstractConsidering that a series of complex issues such as environmental problems, sustainable development, animal welfare, and human health are on a global scale, the development of vegetable protein‐based meat substitutes provides a potential solution to the disparity between meat consumption demand and supply. The research and development of vegetable protein‐based meat substitutes have become a major commercial activity, and the market is expanding to meet the growing consumer demand. Soy protein isolates (SPI) are often used as a raw material for vegetable meat substitutes because of their potential to form fiber structures. Although significant initial success has been achieved, it is still a challenge to explain how the composition and aggregation of SPI influence gel properties and the mechanism(s) involved. This article reviews the latest research about SPI. The relationship between the composition, aggregation, and gelation properties of SPI is based on a through literature search. It focused on the application of SPI in heat‐ and cold‐induced gels, given the diversified market demands. The research on cold gel has helped expand the market. The methods to improve the properties of SPI gels, including physical, chemical, and biological properties, are reviewed to provide insights on its role in the properties of SPI gels. To achieve environmentally friendly and efficient ways for the food industry to use SPI gel properties, the research prospects and development trends of the gel properties of SPI are summarized. New developments and practical applications in the production technology, such as for ultrasound, microwave and high pressure, are reviewed. The potential and challenges for practical applications of cold plasma technology for SPI gel properties are also discussed. There is a need to transfer the laboratory technology to actual food production efficiently and safely.
Medium chain triglycerides (MCT): State‐of‐the‐art on chemistry, synthesis, health benefits and applications in food industry
Authors: Nimbkar Shubham , Leena M. Maria , Moses J. A. , Anandharamakrishnan C. 
Published: February 2022

AbstractMedium chain triglycerides (MCT) are esters of fatty acids with 6 to 12 carbon atom chains. Naturally, they occur in various sources; their composition and bioactivity are source and extraction process‐linked. The molecular size of MCT oil permits unique metabolic pathways and energy production rates, making MCT oil a high‐value functional food. This review details the common sources of MCT oil, presenting critical information on the various approaches for MCT oil extraction or synthesis. Apart from conventional techniques, non‐thermal processing methods that show promising prospects are analyzed. The biological effects of MCT oil are summarized, and the range of need‐driven modification approaches are elaborated. A section is devoted to highlighting the recent trends in the application of MCT oil for food, nutraceuticals, and allied applications. While much is debated about the role of MCT oil in human health and wellness, there is limited information on daily requirements, impact on specific population groups, and effects of long‐term consumption. Nonetheless, several studies have been conducted and continue to identify the most effective methods for MCT oil extraction, processing, handling, and storage. A knowledge gap exists and future research must focus on technology packages for scalability and sustainability.
Microsoft Teams desktop application forensic investigations utilizing IndexedDB storage
Authors: Paligu Furkan , Varol Cihan 
Published: February 2022

AbstractWhile the COVID‐19 virus remolded the routines of the establishments, remote collaboration and distant communication gained more popularity. As the way electronic communications are handled changes drastically, new applications and storage mechanisms are introduced. Microsoft Teams is an application offered within the scope of Microsoft Office 365 that offers services for hosting virtual meetings, team communication, and comprehensive team resource management. It is prevalently used by organizations and indicates a great potential to be a source of digital forensic investigations. This paper scrutinizes the artifacts created by Microsoft Teams in IndexedDB persistent storage. IndexedDB is a fast‐growing client‐side storage technology that is relatively new as a source for digital forensic investigations. A single‐case pretest–posttest quasi experiment was conducted to produce artifacts in Microsoft Teams IndexedDB storage. The artifacts were extracted without user credentials indicating security flaws in the application. Extracted artifacts were processed based on signature patterns and evaluated for their significance. Traditional database queries were utilized to link and present the information clustered according to their relevancy. A time‐frame analysis was constructed to display information in a suitable format for investigators. The results indicate that Microsoft Teams IndexedDB storage artifacts contain significant potential for digital investigations with extraction of complete contents of private chat messages, voice mails, and team extensions with efficient time‐frame analysis.
Grapevine virome and production of healthy plants by somatic embryogenesis
Authors: Nuzzo Floriana , Moine Amedeo , Nerva Luca , Pagliarani Chiara , Perrone Irene , Boccacci Paolo , Gribaudo Ivana , Chitarra Walter , Gambino Giorgio 
Published: February 2022

SummaryGrapevine (Vitis spp.) is a widespread fruit tree hosting many viral entities that interact with the plant modifying its responses to the environment. The production of virus‐free plants is becoming increasingly crucial for the use of grapevine as a model species in different studies. Using high‐throughput RNA sequencing, the viromes of seven mother plants grown in a germplasm collection vineyard were sequenced. In addition to the viruses and viroids already detected in grapevine, we identified 13 putative new mycoviruses. The different spread among grapevine tissues collected in vineyard, greenhouse and in vitro conditions suggested a clear distinction between viruses/viroids and mycoviruses that can successfully be exploited for their identification. Mycoviruses were absent in in vitro cultures, while plant viruses and viroids were particularly accumulated in these plantlets. Somatic embryogenesis applied to the seven mother plants was effective in the elimination of the complete virome, including mycoviruses. However, different sanitization efficiencies for viroids and grapevine pinot gris virus were observed among genotypes. The absence of mycoviruses in in vitro plantlets, associated with the absence of all viral entities in somaclones, suggested that this regeneration technique is also effective to eradicate endophytic/epiphytic fungi, resulting in gnotobiotic or pseudo‐gnotobiotic plants.
COVID‐19 and children: medical impact and collateral damage
Authors: Brüssow Harald 
Published: February 2022

SummaryChildren mostly experience mild SARS‐CoV‐2 infections, but the extent of paediatric COVID‐19 disease differs between geographical regions and the distinct pandemic waves. Not all infections in children are mild, some children even show a strong inflammatory reaction resulting in a multisystem inflammatory syndrome. The assessments of paediatric vaccination depend on the efficacy of protection conferred by vaccination, the risk of adverse reactions and whether children contribute to herd immunity against COVID‐19. Children were also the target of consequential public health actions such as school closure which caused substantial harm to children (educational deficits, sociopsychological problems) and working parents. It is, therefore, important to understand the transmission dynamics of SARS‐CoV‐2 infections by children to assess the efficacy of school closures and paediatric vaccination. The societal restrictions to contain the COVID‐19 pandemic had additional negative effects on children’s health, such as missed routine vaccinations, nutritional deprivation and lesser mother–child medical care in developing countries causing increased child mortality as a collateral damage. In this complex epidemiological context, it is important to have an evidence‐based approach to public health approaches. The present review summaries pertinent published data on the role of children in the pandemic, whether they are drivers or followers of the infection chains and whether they are (after elderlies) major sufferers or mere bystanders of the COVID‐19 pandemic.
“Escalibur”—A practical pipeline for the de novo analysis of nucleotide variation in nonmodel eukaryotes
Authors: Korhonen Pasi K. , Shaban Babak , Faux Noel G. , Kinkar Liina , Chang Bill C. H. , Wang Daxi , Yang Bicheng , Young Neil D. , Gasser Robin B. 
Published: February 2022

AbstractThe revolution in genomics has enabled large‐scale population genetic investigations of a wide range of organisms, but there has been a relatively limited focus on improving analytical pipelines. To efficiently analyse large data sets, highly integrated and automated software pipelines, which are easy to use, efficient, reliable, reproducible and run in multiple computational environments, are required. A number of software workflows have been developed to handle and process such data sets for population genetic analyses, but effective, specialized pipelines for genetic and statistical analyses of nonmodel organisms are lacking. For most species, resources for variomes (sets of genetic variations found in populations of species) are not available, and/or genome assemblies are often incomplete and fragmented, complicating the selection of the most suitable reference genome when multiple assemblies are available. Additionally, the biological samples used often contain extraneous DNA from sources other than the species under investigation (e.g., microbial contamination), which needs to be removed prior to genetic analyses. For these reasons, we established a new pipeline, called Escalibur, which includes: functionalities, such as data trimming and mapping; selection of a suitable reference genome; removal of contaminating read data; recalibration of base calls; and variant‐calling. Escalibur uses a proven gatk variant caller and workflow description language (WDL), and is, therefore, a highly efficient and scalable pipeline for the genome‐wide identification of nucleotide variation in eukaryotes. This pipeline is available at https://gitlab.unimelb.edu.au/bioscience/escalibur (version 0.3‐beta) and is essentially applicable to any prokaryote or eukaryote.
Chromosomal‐level genome of a sheet‐web spider provides insight into the composition and evolution of venom
Authors: Zhu Bingyue , Jin Pengyu , Hou Zhonge , Li Jianlong , Wei Shujun , Li Shuqiang 
Published: February 2022

AbstractSpiders are the most abundant venomous predators in the world. Previous research related to spider venom has mostly relied on transcriptomes and proteomes, with only a few high‐quality genomes available. This is far from consistent with the species diversity of spiders. In this study, we constructed a high‐quality chromosome‐level genome assembly of Hylyphantes graminicola, which contained 13 chromosomes, with a genome length of 931.68 Mb and scaffold N50 of 77.07 Mb. Integrating genome, transcriptome, and proteome profiling, we identified a total of 59 coding genes among nine toxin gene families. Among them, Group 7 allergen (ALL7) protein was reported in spider venom for the first time. Its coding genes had a predicted signal peptide and maintained high expression levels in the venom, suggesting that ALL7 plays an important role in venom and maybe is a type of newly discovered venom toxin in the spider. By implementing comparative genomics, we found a similar gene number of main toxin gene families in spiders and the scorpion genome with conservative evolutionary rates, indicating that these toxin genes could be an ancient (~400 million years) and a conserved "basic toolkit" for spiders and scorpions to perform primary defence functions. Obtaining high‐quality chromosome‐level genomes from spiders not only facilitates venom research and toxin resource application, but also can improve comparative genomic analysis in other important traits, like the evolution of silk or behaviour.
The uniform AUC: Dealing with the representativeness effect in presence–absence models
Authors: Jiménez‐Valverde Alberto 
Published: February 2022

Abstract

Species distribution models use occurrence data of the focus species together with environmental variables to estimate a habitat suitability score. Typically, the discrimination capacity of the models, that is, how good the instances of presence and absence are correctly classified, is assessed with statistics such as the area under the receiver operating characteristic curve (AUC). However, the value of any discrimination statistic depends on the distribution of the suitability scores in the evaluation dataset, the so‐called representativeness effect. For example, the same well‐calibrated model evaluated with two datasets, one set with mostly intermediate predicted values (around 0.5) and another set in which most cases have extreme predicted values (close to 0 and close to 1), will yield low (towards 0.5) and high (towards 1) AUC values, respectively. Thus, discrimination values are entirely context dependent and cannot be directly compare between datasets because they are not intrinsic measures of a model’s performance.

In this contribution, I propose a methodology based on stratified bootstrapping with an inverse probability weighting that makes the distribution of the suitability values uniform and harmonizes the AUC so that the so‐called uAUC can now be compared between different datasets. I run simulations considering a range of sample sizes and different initial distributions of the suitability values to validate the method. I apply the method to an empirical exercise, and implement it in the R package vandalico.

Although I mainly focused on the AUC, the harmonization procedure can be applied to any other discrimination measure that is prevalence independent in a strict mathematical sense, such as the sensitivity star (Se*). To provide accurate estimations, it is important to have a high‐quality evaluation dataset, that is, a dataset that covers the whole spectrum of suitability values and a minimum sample size of at least 150 cases.

Further research is needed to develop a method to estimate reliable confidence intervals. I expect the harmonization methodology proposed here to be of interest in other research areas (besides ecology) that deal with discrimination/classification problems.
Passive acoustic tracking of the three‐dimensional movements and acoustic behaviour of toothed whales in close proximity to static nets
Authors: Macaulay Jamie , Kingston Al , Coram Alex , Oswald Michael , Swift René , Gillespie Doug , Northridge Simon 
Published: February 2022

Abstract

Entanglement in net fisheries (static and drift) is the largest known cause of direct anthropogenic mortality to many small cetacean species, including harbour porpoise (Phocoena phocoena), in UK waters. Despite this, little is known about the behaviour of small cetaceans in proximity to nets.

We have developed a passive acoustic monitoring (PAM) system for tracking the fine‐scale three‐dimensional (3D) movements of echolocating cetaceans around actively fishing nets by localising their acoustic clicks. The system consists of two compact four‐channel acoustic recorders with sample‐synchronised sensor packages that use 3D motion tracking technology to accurately log orientation, depth, water temperature and ambient light level. Two recorders were used in tandem, with each one attached to and floating above the net floatline. The system can be deployed during normal fishing operations by a trained researcher or experienced fisheries observer. Recordings were analysed in PAMGuard software and the 3D positions of echolocating animals in the vicinity of the system were calculated using an acoustic particle filter‐based localisation method.

We present findings from four deployments in UK waters (each 1–2 days in duration) in which 12 distinct harbour porpoise encounters yielded a sufficient number of detected clicks to track their movements around the net. The tracks show a variety of behaviours, including multiple instances of animals actively foraging in close proximity to the fishing net.

We show that a relatively inexpensive PAM system, which is practical to deploy from active fishing vessels, is capable of providing highly detailed data on harbour porpoise behaviour around nets. As harbour porpoises are the one of the most difficult species to localise, this methodology is likely to be suitable for elucidating the behaviour of many other toothed whale species in a variety of situations.
Reduced calibration between subjective and objective measures of episodic future thinking in alcohol use disorder
Authors: Noël Xavier , Saeremans Mélanie , Kornreich Charles , Chatard Armand , Jaafari Nemet , D’Argembeau Arnaud 
Published: February 2022

AbstractBackgroundA reduced capacity to mentally simulate future scenarios could be of clinical importance in alcohol use disorder (AUD). However, little is known about the mechanisms underlying episodic future thinking (EFT) impairment in AUD.MethodsWe tested patients with severe AUD using two measures of EFT: the individual's own subjective experience of their imaginings (phenomenology) and the objective number of details included in imagined events, as assessed by an independent observer (examination). The comparison between the two measures allowed us to investigate the extent to which the subjective and objective characteristics of EFT are calibrated in healthy and AUD participants matched for age, education, and gender. The possible impact of cognitive functioning and disturbed mood on EFT measures was also investigated.ResultsIn terms of objective details of EFT, patients with AUD (n = 40) generated fewer episodic components and more non‐episodic components than control participants (n = 40), even when controlling for cognitive functioning. However, self‐ratings of phenomenological characteristics indicated that participants with AUD perceived imagined future events at a similar level of detail as control participants. Additionally, there was a significant correlation between objective and subjective measures in healthy individuals but not in the AUD group. A higher depression score in the AUD group was not associated with the EFT measures.ConclusionsThese results suggest a distorted self‐assessment of the richness of imagined future events in individuals with AUD. We discuss these apparent limitations in metacognitive abilities and verbal descriptions of imagined events among individuals with AUD and their clinical implications.
Time to leave? The interaction of temporal focus and turnover intentions in explaining voluntary turnover behaviour
Authors: Peltokorpi Vesa , Allen David G. , Shipp Abbie J. 
Published: February 2022

AbstractAlthough turnover intentions are the strongest predictors of voluntary turnover behaviours, many employees who express intentions to leave do not. To explain why some employees translate turnover intentions into behaviour and others do not, this study examines the moderating effect of temporal focus (i.e. the degree to which one thinks about the past, present and future) between turnover intentions and voluntary turnover, using the lens of theory of planned behaviour. Data were collected from 683 full‐time employees in a range of organisations at three points in time. Results show that past temporal focus conditions the positive relationship between turnover intention and turnover, such that the relationship is stronger when past temporal focus is high. Future temporal focus has an opposite moderating effect, such that the relationship between turnover intention and turnover is weaker when future temporal focus is high. Results show no significant moderating effect of current temporal focus. Overall, temporal focus helps explain why some employees leave and others stay by conditioning the likelihood of translating turnover intentions into quitting. We speculate that a dominant, unspoken paradigm in turnover research is an assumption that individuals are current focused, yet our results suggest scholars should explicitly examine this assumption.
Systematic review: non‐endoscopic surveillance for colorectal neoplasia in individuals with Lynch syndrome
Authors: van Liere Elsa L. S. A. , de Boer Nanne K. H. , Dekker Evelien , van Leerdam Monique E. , de Meij Tim G. J. , Ramsoekh Dewkoemar 
Published: February 2022

SummaryBackgroundIndividuals with Lynch syndrome are at high risk for colorectal cancer (CRC). Regular colonoscopies have proven to decrease CRC incidence and mortality. However, colonoscopy is burdensome and interval CRCs still occur. Hence, an accurate, less‐invasive screening method that guides the timing of colonoscopy would be of important value.AimTo outline the performance of non‐endoscopic screening modalities for Lynch‐associated CRC and adenomas.MethodsSystematic literature search in MEDLINE and EMBASE to identify studies investigating imaging techniques and biomarkers for detection of CRC and adenomas in Lynch syndrome. The QUADAS‐2 tool was used for the quality assessment of included studies.ResultsSeven of 1332 screened articles fulfilled the inclusion criteria. Two studies evaluated either CT colonography or MR colonography; both techniques were unable to detect CRC and (advanced) adenomas <10 mm. The other five studies evaluated plasma methylated‐SEPTIN9, faecal immunochemical test (FIT), faecal tumour DNA markers (BAT‐26, hMLH1, p53, D9S171, APC, D9S162, IFNA and DCC) and faecal microbiome as screening modalities. Sensitivity for CRC varied from 33% (BAT‐26) to 70% (methylated‐SEPTIN9) to 91% (hMLH1). High specificity (94–100%) for CRC and/or adenomas was observed for methylated‐SEPTIN9, FIT and BAT‐26. Desulfovibrio was enriched in the stool of patients having adenomas. However, all these studies were characterised by small populations, high/unclear risk of bias and/or low prevalence of adenomas.ConclusionsImaging techniques are unsuitable for colon surveillance in Lynch syndrome, whereas biomarkers are understudied. Having outlined biomarker research in Lynch‐associated and sporadic CRC/adenomas, we believe that these non‐invasive markers may hold potential (whether or not combined) for this population. As they could be of great value, (pre‐)clinical studies in this field should be prioritised.