bluuebunny/crossref_metadata_2025_split huggingface dataset:
The practice of the development of researchers: the “state-of-the-art”
Authors: Bromley Tony , Warnock Lorna 
Published: June 2021

PurposeIn this review paper, the authors are particularly interested in the growth in the scholarly investigation of the efficacy of developmental interventions for doctoral and early career researchers. This paper aims to provide a “State of the Art” overview of the emerging fields of research and suggest areas that command more research.Design/methodology/approachA foundation of key disseminations relating to the new discipline has become established, and it is the outputs of these that the authors look to first in their review. However, much of the work is reported in the proceedings of two specific conferences, known to the authors and does not appear in database searches, which results in a concentration of research in two specific countries, namely, the UK and Australia. Relatively little is found from database searches, however approached, but the authors also report on this work.FindingsThere is a general gap in the depth of the body of work in all areas of literature relating to research on the practice of developing researchers. We have identified specific areas as the most limited in terms of the body of published research including research governance; work life balance; engagement influence and impact training and creativity and innovation training.Research limitations/implicationsThere is much work as yet unpublished and the practice of rigorous study and publication is not yet generally embedded in this research discipline.Practical implicationsWithout the depth of rigorous and robust findings of research to provide us with evidence of good practice, the emergent discipline will struggle to have integrity in its practice. Continued growth in research in this emergent discipline is essential.Originality/valueTo the best of the authors’ knowledge, this is the first review of its kind looking at the published research in respect of the development of researchers.
Rare soil microbial taxa regulate the negative effects of land degradation drivers on soil organic matter decomposition
Authors: Wu Ying , Chen Dima , Saleem Muhammad , Wang Bing , Hu Shuijin , Delgado‐Baquerizo Manuel , Bai Yongfei 
Published: June 2021

Abstract

Land degradation drivers, including loss in vegetation and eutrophication, are expected to impact soil biodiversity and functions in drylands world‐wide. Soils contain both common and rare microbial taxa that drive multiple soil functions. Yet, little is known about how these microbial taxa influence the impacts of land degradation drivers on ecosystem functions. Obtaining this information is essential to determine whether rare taxa need to be protected, or if protecting only common taxa would be enough to sustain and protect ecosystem functions and services.

Here, we conducted an experiment to investigate the effects of N‐enrichment and vegetation loss (plant removal), which are two major land degradation drivers in semi‐arid grasslands, on the diversities of common and rare soil bacterial and fungal taxa and soil function [soil organic matter (SOM) decomposition] in a long‐term experiment.

Six years after N‐enrichment and vegetation loss, we found that N‐enrichment decreased the alpha diversities of common and rare soil bacteria and rare soil fungi, while vegetation loss only decreased the alpha diversity of rare soil fungi. Both N‐enrichment and vegetation loss altered the community composition of common and rare bacteria and fungi, except for the lack of response of common soil fungi to the vegetation loss. Moreover, both structural equation modelling and variation partitioning analyses show that land degradation drivers reduce SOM decomposition, and these were also indirectly associated with changes in the diversity of rare microbial taxa, especially that of bacteria.

Synthesis and applications. Collectively, this work shows that land degradation can have negative impacts on soil biodiversity and functions, and the rare microbial taxa indirectly regulate the impacts of land degradation on ecosystem functioning. These results indicate that the rare microbial taxa can be used as one of the ecological indicators for identifying land degradation in the semi‐arid grasslands. These findings are essential to understand the future impacts of desertification and land degradation on rare microbial taxa–function relationships in global drylands.
An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors
Authors: Dvořák Pavel , Alvarez‐Carreño Carlos , Ciordia Sergio , Paradela Alberto , de Lorenzo Víctor 
Published: June 2021

SummaryA revised model of the aromatic binding A domain of the σ54‐dependent regulator XylR of Pseudomonas putida mt‐2 was produced based on the known 3D structures of homologous regulators PoxR, MopR and DmpR. The resulting frame was instrumental for mapping a number of mutations known to alter effector specificity, which were then reinterpreted under a dependable spatial reference. Some of these changes involved the predicted aromatic binding pocket but others occurred in distant locations, including dimerization interfaces and putative zinc binding site. The effector pocket was buried within the protein structure and accessible from the outside only through a narrow tunnel. Yet, several loop regions of the A domain could provide the flexibility required for widening such a tunnel for passage of aromatic ligands. The model was experimentally validated by treating the cells in vivo and the purified protein in vitro with benzyl bromide, which reacts with accessible nucleophilic residues on the protein surface. Structural and proteomic analyses confirmed the predicted in/out distribution of residues but also supported two additional possible scenarios of interaction of the A domain with aromatic effectors: a dynamic interaction of the fully structured yet flexible protein with the aromatic partner and/or inducer‐assisted folding of the A domain.
Allergenic components, biocides, and analysis techniques of some essential oils used in food products
Authors: Türkmenoğlu Aykut , Özmen Dilek 
Published: June 2021

AbstractNowadays, almost 300 essential oils (EOs) are commonly traded in the world market, with a prediction to be worth over $14 billion in 2024. EOs are natural preservatives for food products in order to reduce the activity of pathogenic microorganisms, therefore their use as an antioxidant or a preservative in foods has been encouraged. They are not only considered as antimicrobial or flavoring agents, but are also incorporated into food packaging materials. There are several types of EOs which have been approved as food additives by the Food and Drug Administration. Hence, it is important to use safe EO products to minimize possible adverse effect risks such as nausea, vomiting, necrosis, nephropathy, mucous membrane, and skin irritation. This review article gives information about some EOs that are used in the food industries and the types of some allergenic compounds and biocides which could make the EOs hazardous or may cause allergenic reactions in the human body. Besides, some analysis techniques of possible allergenic compounds or biocides in EOs were introduced and supported with the most relevant studies. The overall conclusion from the study is that pregnant women, patients taking drugs (e.g., diabetics) or the having a history of allergy are the most prone to be affected from EO allergenic components. As regards to biocides, organochlorine and organophosphorus types of pesticides that are carried over from the plant may be found mostly in EOs. The most common allergic reaction is skin sensitization and irritation if the EO components are oxidized during storage or transportation. Moreover, drug interactions are one of the other possible adverse effect. Hence, determination of biocides and possible allergenic component concentrations is an essential factor when they are used as a preservative or flavoring agent. The most prominent analysis techniques are gas and liquid chromatography because most of the allergens and biocides are mainly composed of volatile components.Practical ApplicationDetermining of the essential oil's content will be crucial if oils are used for food preservation or flavoring because they may have some hazardous effects, such as nausea, vomiting, necrosis and nephropathy. Therefore, after applying them to the food products, consumers (especially pregnant women) should be informed about their concentration levels and their possible adverse effects are taken into account when they are consumed over toxic limit. For this reason, we reviewed in our study that some allergenic components, biocides and toxic limits of EOs to be used in food products. In addition to this, recent analytical techniques have been explained and discussed which methods are suitable for analysis.
Development of a compound oral liquid containing herbal extracts and its effect on immunity and gastric mucosa
Authors: Pei Zejun , Lou Zaixiang , Zhang Bingjie , Wang Hongxin , Li Yaqin 
Published: June 2021

AbstractNowadays, consumers have an increasing demand for health products. In this study, an oral liquid was developed using a compound extract consisting of three herbal extracts (Dendrobium nobile Lindl., Lycium barbarum, and Puerariae lobatae Radix) because the compound extract (a combination of all three extracts) was superior to every single extract in promoting the phagocytic capacity of RAW264.7 macrophages and the proliferation ability of GES‐1 cells. In this oral liquid, the dosage of the stabilizer and the sweetener was selected using a stability test and sensory quality evaluation. When 0.30% (m/v) xanthan gum and 0.20% (m/v) mogroside were added, the oral liquid had not only a good stability but also the highest sensory score for overall acceptability. The chemical composition analysis showed that the oral liquid had various functional ingredients including polysaccharides, phenols, alkaloids, and so forth. The immune‐enhancing efficacy of the oral liquid was evaluated in BALB/c mice by measuring the levels of different immune indicators. The results indicated that the oral liquid obviously enhanced nonspecific and specific immunity. A rat model with ethanol‐induced gastric ulcer was used to examine the protective effect of the oral liquid on the gastric mucosa and to explore the related mechanisms. The oral administration of the oral liquid for days significantly prevented the formation of gastric ulcer. This study provided an effective oral liquid that could enhance immunity and protect gastric mucosa.
Chronological and biological aging of the human left ventricular myocardium: Analysis of microRNAs contribution
Authors: Ramos‐Marquès Estel , García‐Mendívil Laura , Pérez‐Zabalza María , Santander‐Badules Hazel , Srinivasan Sabarathinam , Oliveros Juan Carlos , Torres‐Pérez Rafael , Cebollada Alberto , Vallejo‐Gil José María , Fresneda‐Roldán Pedro Carlos , Fañanás‐Mastral Javier , Vázquez‐Sancho Manuel , Matamala‐Adell Marta , Sorribas‐Berjón Juan Fernando , Bellido‑Morales Javier André , Mancebón‑Sierra Francisco Javier , Vaca‑Núñez Alexánder Sebastián , Ballester‐Cuenca Carlos , Jiménez‐Navarro Manuel , Villaescusa José Manuel , Garrido‐Huéscar Elisa , Segovia‐Roldán Margarita , Oliván‐Viguera Aida , Gómez‐González Carlos , Muñiz Gorka , Diez Emiliano , Ordovás Laura , Pueyo Esther 
Published: June 2021

AbstractAging is the main risk factor for cardiovascular diseases. In humans, cardiac aging remains poorly characterized. Most studies are based on chronological age (CA) and disregard biological age (BA), the actual physiological age (result of the aging rate on the organ structure and function), thus yielding potentially imperfect outcomes. Deciphering the molecular basis of ventricular aging, especially by BA, could lead to major progresses in cardiac research. We aim to describe the transcriptome dynamics of the aging left ventricle (LV) in humans according to both CA and BA and characterize the contribution of microRNAs, key transcriptional regulators. BA is measured using two CA‐associated transcriptional markers: CDKN2A expression, a cell senescence marker, and apparent age (AppAge), a highly complex transcriptional index. Bioinformatics analysis of 132 LV samples shows that CDKN2A expression and AppAge represent transcriptomic changes better than CA. Both BA markers are biologically validated in relation to an aging phenotype associated with heart dysfunction, the amount of cardiac fibrosis. BA‐based analyses uncover depleted cardiac‐specific processes, among other relevant functions, that are undetected by CA. Twenty BA‐related microRNAs are identified, and two of them highly heart‐enriched that are present in plasma. We describe a microRNA‐gene regulatory network related to cardiac processes that are partially validated in vitro and in LV samples from living donors. We prove the higher sensitivity of BA over CA to explain transcriptomic changes in the aging myocardium and report novel molecular insights into human LV biological aging. Our results can find application in future therapeutic and biomarker research.
Investor feedback: impact on analyst biases and investor critical evaluation
Authors: Barradale Nigel , Plenborg Thomas , Staehr Simone 
Published: June 2021

AbstractFinancial analysts (‘sell side’) face incentives that result in biased information for investors (‘buy side’). We examine whether a feedback channel from investors to financial analysts (comparable to the broker vote system) reduces these biases and thereby enhances information efficiency. In a controlled experiment with a monetary payment structure, 344 graduate students assume roles as analysts or investors, with the analysts making earnings recommendations for the investors in the presence of biased incentives. Under the treatment condition, the investors provide feedback to the analysts. Consistent with the monetary incentives built into the broker vote system and psychological theories, the presence of this feedback: (i) reduces bias among analysts; and (ii) enhances investors’ critical evaluation of information. Given the informational benefits of investor feedback, we highlight an unintended consequence of the European Union’s decision to abolish indirect payments to analysts from 2018 onwards.
Cytotoxicity and genotoxicity of salicylate‐ and calcium silicate‐based root canal sealers on primer human periodontal ligament fibroblasts
Authors: Erdogan Hilal , Yildirim Sibel , Cobankara Funda Kont 
Published: June 2021

AbstractThe aim of this study was to evaluate the biocompatibility of epoxy‐resin‐based AHPlus, salicylate‐based MTA‐Fillapex and calcium silicate‐based iRootSP root canal sealers. Cytotoxicity was assessed by XTT test. The extracts from sealers of different setting times were serially diluted. Cell viability was calculated as the percentage of the control group (100%). The optimal concentration of each sealer was used at genotoxicity test, and micronuclei formations were detected. Statistical analyses were done by using Kruskal–Wallis and Dunn post hoc test with Bonferroni correction. AHPlus and MTA‐Fillapex showed the lowest percentage of cell viability at higher concentrations (1:1, 1:2, 1:4), especially at first 12 h. iRootSP showed higher viability at all concentrations and times than AHPlus and MTA‐Fillapex. At genotoxicity assay, AHPlus increased the number of micronuclei. MTA‐Fillapex slightly induced micronucleus formation (not significant) and iRootSP was not increased. In conclusion, calcium silicate‐based iRootSP had lowest cytotoxic and genotoxic potential and can be considered as a highly biocompatible material.
Single‐marker and haplotype‐based genome‐wide association studies for the number of teats in two heavy pig breeds
Authors: Bovo S. , Ballan M. , Schiavo G. , Ribani A. , Tinarelli S. , Utzeri V. J. , Dall'Olio S. , Gallo M. , Fontanesi L. 
Published: June 2021

SummaryThe number of teats is a reproductive‐related trait of great economic relevance as it affects the mothering ability of the sows and thus the number of properly weaned piglets. Moreover, genetic improvement of this trait is fundamental to parallelly help the selection for increased litter size. We present the results of single‐marker and haplotypes‐based genome‐wide association studies for the number of teats in two large cohorts of heavy pig breeds (Italian Large White and Italian Landrace) including 3990 animals genotyped with the 70K GGP Porcine BeadChip and other 1927 animals genotyped with the Illumina PorcineSNP60 BeadChip. In the Italian Large White population, genome scans identified three genome regions (SSC7, SSC10, and SSC12) that confirmed the involvement of the VRTN gene (as we previously reported) and highlighted additional loci known to affect teat counts, including the FRMD4A and HOXB1 gene regions. A different picture emerged in the Italian Landrace population, with a total of 12 genome regions in eight chromosomes (SSC3, SSC6, SSC8, SSC11, SSC13, SSC14, SSC15, and SSC16) mainly detected via the haplotype‐based genome scan. The most relevant QTL was close to the ARL4C gene on SSC15. Markers in the VRTN gene region were not significant in the Italian Landrace breed. The use of both single‐marker and haplotype‐based genome‐wide association analyses can be helpful to exploit and dissect the genome of the pigs of different populations. Overall, the obtained results supported the polygenic nature of the investigated trait and better elucidated its genetic architecture in Italian heavy pigs.
The role of decidual natural killer cell‐derived soluble factors in early pregnancy
Authors: Zhang Xueling , Li Yuye , Huang Chunyu , Liu Su , Chen Xian , Yu Shuyi , Diao Lianghui , Zeng Yong 
Published: June 2021

AbstractDecidual natural killer cells (dNK), the predominant decidual lymphocytes in early pregnancy, are primarily identified based on their CD56bright CD16− phenotype and play an important role in maintaining immune tolerance at the maternal–fetal interface. dNK dysfunction reportedly leads to pathological pregnancy. Indeed, various dNK‐derived soluble factors are involved in a series of key processes related to pregnancy outcomes. In this review, we summarize the roles of these dNK‐derived factors in immune tolerance and embryonic development to improve the current understanding regarding the physiological and pathological mechanisms that occur during pregnancy, while potentially informing the development of effective therapeutics.
A prospective study comparing rectal water contrast‐transvaginal ultrasonography with sonovaginography for the diagnosis of deep posterior endometriosis
Authors: Barra Fabio , Leone Roberti Maggiore Umberto , Evangelisti Giulio , Scala Carolina , Alessandri Franco , Vellone Valerio Gaetano , Stabilini Cesare , Ferrero Simone 
Published: June 2021

AbstractIntroductionPreoperative assessment of deep endometriotic (DE) nodules is necessary to inform patients about the possible treatments and provide informed consent in case of surgery. This study aims to investigate the diagnostic performance of rectal water‐contrast transvaginal ultrasonography (RWC‐TVS) and sonovaginography (SVG) in women with suspicion of posterior DE.Material and methodsThis prospective comparative study (NCT04296760) enrolled women with clinical suspicion of DE at our institution (Piazza della Vittoria 14 SRL, Genoa, Italy). Exclusion criteria were previous diagnosis of DE by imaging techniques or laparoscopy. All patients underwent RWC‐TVS and SVG, independently performed by two gynecological sonologists blinded to the other technique's results. Patients underwent laparoscopic surgery within the following three months; imaging findings were compared with surgical and histological results.ResultsIn 208 of 281 (74.0%) patients included, posterior DE was surgically confirmed in rectosigmoid (n = 88), vagina (n = 21), rectovaginal septum (n = 34) and uterosacral ligaments (n = 156). RWC‐TVS and SVG demonstrated similar sensitivity (SE; 93.8% vs 89.4%; p = 0.210) and specificity (SP; 86.3% vs 79.4%; p = 0.481) in diagnosing posterior DE. Specifically, both examinations had similar accuracy in detecting nodules of uterosacral ligaments (p = 0.779), vagina (p = 0.688) and rectovaginal septum (p = 0.824). RWC‐TVS had higher SE (95.2% vs 82.0%; p = 0.003) and similar SP (99.5% vs 98.5%; p = 0.500) in diagnosing rectosigmoid endometriosis and estimated better infiltration of intestinal submucosa (p = 0.039), and distance between these nodules and anal verge (p < 0.001); only RWC‐TVS allowed the estimation of bowel lumen stenosis. A similar proportion of discomfort was experienced during both examinations (p = 0.191), although a statistically higher mean visual analog score was reported during RWC‐TVS (p < 0.001).ConclusionsAlthough RWC‐TVS and SVG have similar accuracy in the diagnosis of DE, RWC‐TVS performed better in assessment of the characteristics of rectosigmoid endometriosis.
Biallelic mutations in KATNAL2 cause male infertility due to oligo‐astheno‐teratozoospermia
Authors: Wei Xiaoli , Liu Wensheng , Zhu Xingshen , Li Youzhu , Zhang Xiaoya , Chen Jing , Isachenko Vladimir , Sha Yanwei , Lu Zhongxian 
Published: June 2021

AbstractOligo‐astheno‐teratozoospermia (OAT) is a common cause of male infertility, and most of idiopathic OAT patients are thought to be caused by genetic defects. Here, we recruited 38 primary infertile patients with the OAT phenotype and 40 adult men with proven fertility for genetic analysis and identified biallelic mutations of KATNAL2 by whole‐exome sequencing in two cases. F013/II:1, from a consanguineous family, carried the KATNAL2 c.328C > T:p.Arg110X homozygous mutations. The other carried c.55A > G: p.Lys19Glu and c.169C > T: p Arg57Trp biallelic mutations. None of the KATNAL2 variants were found in the 40 adult men with proven fertility. The spermatozoa from patients with KATNAL2 biallelic mutations exhibited conspicuous defects in maturation, head morphology, and the structure of mitochondrial sheaths and flagella. KATNAL2 was mainly expressed in the pericentriolar material and mitochondrial sheath of the spermatozoa from control subjects, but it was undetectable in the spermatozoa from the patients. Furthermore, Katnal2 null male mice were infertile and displayed an OAT phenotype. Our results proved that the biallelic mutations in KATNAL2 cause male infertility and OAT in humans for the first time, to our knowledge, which could enrich the genetic defect spectrum of OAT and be beneficial for its accurate genetic screening and clinical diagnosis.