bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Novel Long non-coding RNAs and Expression Analyses in Rectal Neuroendocrine Tumors
Authors: Padwal Mahesh Kumar , Basu Bhakti
Published: July 2021

Altered expression of long-non-coding RNAs (lncRNAs) is associated with various pathological conditions, including cancers. LncRNAs associated with rectal neuroendocrine tumors (rNETs) remain unexplored. Here, we report the identification of 418 high confidence novel lncRNAs by analyzing publicly available RNA-Seq datasets of primary rNETs and rNETs with lymph node or liver metastases. Novel lncRNAs had basic characteristics similar to the known lncRNAs and showed individual-specific expressions. Expression analysis in the normal rectal mucosa and pancreas NETs (pNETs) and small intestine NETs (siNETs) revealed high expression of two lncRNAs, namely MSTRG30689.1 and MSTRG341161.1. Functional characterization revealed that 9 lncRNAs could work as the ce-RNA and one as miRNAs precursor. Cis- and trans- analysis of the 9 PCG-associated lncRNAs revealed that these lncRNAs could regulate various important cancer-related genes. Further, an integrated regulatory mechanism for selected cancer hallmark genes such as SMAD3, ZEB1, TCF4 and ATM through lncRNAs is predicted. Taken together, our analyses reveal common and unique lncRNAs associated with rNETs and their metastatic variants, their PCG targets, and predict mechanisms of lncRNA mediated regulation of target PCGs.
Application of personalized differential expression analysis in human cancer proteome
Authors: Yachen Liu , Yalan Lin , Yujuan Wu , Zheyang Zhang , Mengsha Tong , Rongshan Yu
Published: July 2021

Owing to the recent technological advances, liquid chromatography-mass spectrometry (LC-MS)-based quantitative proteomics can measure expression of thousands of proteins from biological specimens. Currently, several studies have used the LC-MS-based proteomics to measure protein expression levels in human cancer. Identifying differentially expressed proteins (DEPs) between tumors and normal controls is a common way to investigate carcinogenesis mechanisms. However, most statistical methods used for DEPs analysis can only identify deregulated proteins at the population-level and ignore the heterogeneous differential expression of proteins in individual patients. Thus, to identify patient-specific molecular defects for personalized medicine, it is necessary to perform personalized differential analysis at the scale of a single sample. To date, there is a scarcity of systematic and easy-to-handle tool that could be used to evaluate the performance of individualized difference expression analysis algorithms in human cancer proteome. Herein, we developed a user-friendly tool kit, IDEP, to enable implementation and evaluation of personalized difference expression analysis algorithms. IDEP evaluates five rank-based tools (RankComp v1/v2, PENDA, Peng and Quantile) through classic computational and functional criteria in lung, gastric and liver cancer proteome. The results show that the within-sample relative expression orderings (REOs) of protein pairs in normal tissues were highly stable, which provided the basis for individual level DEPs analysis. Moreover, these individualized difference analysis tools could reach much higher efficiency in detecting sample-specific deregulated proteins than the group-based methods. Pathway enrichment and survival analysis results were dataset and analysis method dependent. In summary, IDEP has integrated necessary toolkits for individualized identification of DEPs and supported flexible methods evaluation analysis and visualization modules. It could provide a robust and scalable framework to extract personalized deregulation patterns and could also be used for the discovery of prognostic biomarkers for personalized medicine.
Dosage compensation in Bombyx mori is achieved by partial repression of both Z chromosomes in males
Authors: Rosin Leah F. , Chen Yang , Lei Elissa P
Published: July 2021

Interphase chromatin is organized precisely to facilitate accurate gene expression. The structure-function relationship of chromatin is epitomized in sex chromosome dosage compensation (DC), where sex-linked gene expression is balanced between males and females via sex-specific alterations to 3D chromosome structure. Studies in ZW-bearing species suggest that DC is absent or incomplete in most lineages except butterflies and moths, where male (ZZ) chZ expression is reduced by half to equal females (ZW). However, whether one chZ is inactivated (as in mammals) or both are partially repressed (as in C. elegans) is unknown. Using Oligopaints in the silkworm, Bombyx mori, we visualize autosome and chZ organization in somatic cells from both sexes for the first time. We find that B. mori interphase chromosomes are highly compact relative to Drosophila chromosomes. Importantly, we show that in B. mori males, both chZs are similar in size and shape and are more compact than autosomes or the female chZ after DC establishment, suggesting that both male chZs are partially and equally downregulated. We also find that in the early stages of DC, the female chZ repositions toward the nuclear center concomitant with increased Z-linked gene expression, revealing the first non-sequencing-based support for Ohno's hypothesis. These studies represent the first visualization of interphase genome organization and chZ structure in Lepidoptera. We uncover striking similarities between DC in B. mori and C. elegans, despite these lineages harboring evolutionarily distinct sex chromosomes (ZW/XY), suggesting convergent evolution of DC mechanisms and a possible role for holocentricity in DC evolution.
Assessing and mitigating privacy risk of sparse, noisy genotypes by local alignment to haplotype databases
Authors: Emani Prashant S. , Gürsoy Gamze , Miranker Andrew , Gerstein Mark B.
Published: July 2021

Single nucleotide polymorphisms (SNPs) from omics data carry a high risk of reidentification for individuals and their relatives. While the ability of thousands of SNPs (especially rare ones) to identify individuals has been repeatedly demonstrated, the ready availability of small sets of noisy genotypes – such as from environmental DNA samples or functional genomics data – motivated us to quantify their informativeness. Here, we present a computational tool suite, PLIGHT (“Privacy Leakage by Inference across Genotypic HMM Trajectories”), that employs population-genetics-based Hidden Markov Models of recombination and mutation to find piecewise alignment of small, noisy query SNP sets to a reference haplotype database. We explore cases where query individuals are either known to be in a database, or not, and consider a variety of queries, including simulated genotype “mosaics” (composites from 2 source individuals) and genotypes from swabs of coffee cups from a known individual. Using PLIGHT on a database with ~5,000 haplotypes, we find for common, noise-free SNPs that only ten are sufficient to identify individuals, ~20 can identify both components in two-individual simulated mosaics, and 20-30 can identify first-order relatives (parents, children, and siblings). Using noisy coffee-cup-derived SNPs, PLIGHT identifies an individual (within the database) using ~30 SNPs. Moreover, even when the individual is not in the database, local genotype matches allow for some phenotypic information leakage based on coarse-grained GWAS SNP imputation and polygenic risk scores. Overall, PLIGHT maximizes the identifying information content of sparse SNP sets through exact or partial matches to databases. Finally, by quantifying such privacy attacks, PLIGHT helps determine the value of selectively sanitizing released SNPs without explicit assumptions about underlying population membership or allele frequencies. To make this practical, we provide a sanitization tool to remove the most identifying SNPs from a query set.
Empirical prediction of variant-associated cryptic-donors with 87% sensitivity and 95% specificity
Authors: Dawes Ruebena , Joshi Himanshu , Cooper Sandra T.
Published: July 2021

Predicting which cryptic-donors may be activated by a genetic variant is notoriously difficult. Through analysis of 5,145 cryptic-donors activated by 4,811 variants (versus 86,963 decoy-donors not used; any GT or GC), we define an empirical method predicting cryptic-donor activation with 87% sensitivity and 95% specificity. Strength (according to four algorithms) and proximity to the authentic-donor appear important determinants of cryptic-donor activation. However, other factors such as auxiliary splicing elements, which are difficult to identify, play an important role and are likely responsible for current prediction inaccuracies. We find that the most frequent mis-splicing events at each exon-intron junction, mined from 40,233 RNA-sequencing samples, predict with remarkable accuracy which cryptic-donor will be activated in rare disease. Aggregate RNA-Sequencing splice-junction data provides an accurate, evidence-based method to predict variant-activated cryptic-donors in genetic disorders, assisting pathology consideration of possible consequences of a variant for the encoded protein and RNA diagnostic testing strategies.
CLARA: A web portal for interactive exploration of the cardiovascular cellular landscape in health and disease
Authors: Dona Malathi S.I. , Hsu Ian , Rathnayake Thushara S. , Farrugia Gabriella E. , Gaynor Taylah L. , Kharbanda Malvika , Skelly Daniel A. , Pinto Alexander R.
Published: July 2021

Mammalian cardiovascular tissues are comprised of complex and diverse collections of cells. Recent advances in single-cell profiling technologies have accelerated our understanding of tissue cellularity and the molecular networks that orchestrate cardiovascular development, maintain homeostasis, and are disrupted in pathological states. Despite the rapid development and application of these technologies, many cardiac single-cell functional genomics datasets remain inaccessible for most cardiovascular biologists. Access to custom visual representations of the data, including querying changes in cellular phenotypes and interactions in diverse contexts, remains unavailable in publicly accessible data portals. Visualizing data is also challenging for scientists without expertise in processing single-cell genomic data. Here we present CLARA—CardiovascuLAR Atlas—a web portal facilitating exploration of the cardiovascular cellular landscape. Using mouse and human single-cell transcriptomic datasets, CLARA enables scientists unfamiliar with single-cell-omic data analysis approaches to examine gene expression patterns and the cell population dynamics of cardiac cells in a range of contexts. The web-application also enables investigation of intercellular interactions that form the cardiac cellular niche. CLARA is designed for ease-of-use and we anticipate that the portal will aid deeper exploration of cardiovascular cellular landscapes in the context of development, homeostasis and disease. CLARA is freely available at https://clara.baker.edu.au.
Botrytis cinerea BcPTP1 is a late infection phase, cysteine rich protein cytotoxic effector
Authors: Zhu Wenjun , Yu Mengxue , Xu Ran , Bi Kai , Xiong Chao , Liu Zhiguo , Sharon Amir , Jiang Daohong , Wu Mingde , Gu Qiongnan , Gong Ling , Chen Weidong , Wei Wei
Published: July 2021

Botrytis cinerea is a broad-host-range necrotrophic phytopathogen responsible for serious crops diseases. To facilitate infection, B. cinerea secretes a large number of effectors that induce plant cell death. In screening secretome data of B. cinerea during infection stage, we identified a phytotoxic protein (BcPTP1) that can also induce immune resistance in plants. BcPTP1 is a small (90 aa), cysteine rich protein without any known domains. Transiently expression of BcPTP1 in leaves caused chlorosis that intensifies with time and eventually lead to cell death. Point mutations in eight of the 10 cysteine residues of BcPTP1 abolished the toxic effect, however residual toxic activity remained after heating the peptide, suggesting contribution of unknown epitopes to protein phytotoxic effect. The transcript level of the bcptp1 gene was low during the first 36 h after inoculation and increased sharply upon transition to the late infection stage, suggesting a role of BcPTP1 in lesion spreading. While statistically insignificant, deletion of the bcptp1 gene led to slightly smaller lesions on bean leaves. Further analyses indicated that BcPTP1 is internalized into plant cells after secreting into the apoplast and its phytotoxic effect is negatively regulated by the receptor-like kinases BAK1 and SOBIR1. Collectively, our findings show that BcPTP1 is a virulence factor that toxifies the host cells and facilitates lesion spreading during the late infection stage.
Development and application of a tender X-ray ptychographic coherent diffraction imaging system on BL27SU at SPring-8
Authors: Abe Masaki , Kaneko Fusae , Ishiguro Nozomu , Kudo Togo , Matsumoto Takahiro , Hatsui Takaki , Tamenori Yusuke , Kishimoto Hiroyuki , Takahashi Yukio
Published: July 2021

Ptychographic coherent diffraction imaging (CDI) allows the visualization of both the structure and chemical state of materials on the nanoscale, and has been developed for use in the soft and hard X-ray regions. In this study, a ptychographic CDI system with pinhole or Fresnel zone-plate optics for use in the tender X-ray region (2–5 keV) was developed on beamline BL27SU at SPring-8, in which high-precision pinholes optimized for the tender energy range were used to obtain diffraction intensity patterns with a low background, and a temperature stabilization system was developed to reduce the drift of the sample position. A ptychography measurement of a 200 nm thick tantalum test chart was performed at an incident X-ray energy of 2.500 keV, and the phase image of the test chart was successfully reconstructed with approximately 50 nm resolution. As an application to practical materials, a sulfur polymer material was measured in the range of 2.465 to 2.500 keV including the sulfur K absorption edge, and the phase and absorption images were successfully reconstructed and the nanoscale absorption/phase spectra were derived from images at multiple energies. In 3 GeV synchrotron radiation facilities with a low-emittance storage ring, the use of the present system will allow the visualization on the nanoscale of the chemical states of various light elements that play important roles in materials science, biology and environmental science.
Unraveling the mechanism to develop health consciousness from organic food: a cross-comparison of Brazilian and Spanish millennials
Authors: Japutra Arnold , Vidal-Branco Murilo , Higueras-Castillo Elena , Molinillo Sebastian
Published: July 2021

Purpose

The aim of this study is to analyze the drivers of health consciousness related to millennials’ organic food consumption and the impact of health consciousness on millennials’ willingness to pay premium through a cross-cultural study.

Design/methodology/approach

A comparative analysis was conducted in two countries (Brazil vs Spain). Based on the stimuli-organism-response framework, the authors present a conceptual model to investigate the relationship between cognitive and affective stimuli (i.e. natural content, value for money, sensorial appeal, price fairness, trend, emotional appeal and food safety concern) and customers’ health consciousness with the mediating effect of food safety concern and their impact on the customers’ response (i.e. willingness to pay premium). A survey and a structural equation approach are applied.

Findings

The results show that cognitive and affective stimuli and food safety concern improve millennials’ health consciousness and, consequently, their willingness to pay a premium price for organic food. The results present a high validity correlation of constructs with significant differences between the two countries.

Originality/value

The originality of this study lies in the comparison of drivers of health consciousness and their impact on organic food consumption among millennials from two countries (developed vs developing). This work contributes to the study of organic food consumption with an analysis of the impact of seven drivers on health consciousness and its relationship with willingness to pay premium in a cross-comparison of Brazilian and Spanish millennials.
Research shows role of pre-hire and post-hire outcomes in effectiveness of social media recruitment
Authors: Smith David
Published: July 2021

Purpose

The authors were motivated to carry out their study by the increasing popularity of social media as a recruitment tool. They focused on the recruitment managers as previous studies have concentrated on the experiences of the candidates.

Design/methodology/approach

The authors wanted to test two hypotheses. The first one was split into two parts – Hypothesis 1A was that: “Recruiters intentions to adopt SMR are significantly related to pre-hire ROs.” And Hypothesis 1B was that: “Recruiters intentions to adopt SMR are significantly related to post-hire ROs.” Their second hypothesis was that: “CS (credibility and satisfaction) will mediate the relationship between SMR intention and ROs”. They surveyed 240 recruitment managers in the manufacturing and services sector, in Gujarat, India.

Findings

The results confirmed both of the hypotheses. Firstly, the responses showed that recruiters intended to use social media as it provides pre-hire benefits. Similarly, results showed SMR is more compatible, less complex and ensures better trialability and observability. Secondly, the research showed SMR intentions are significantly related to post-hire ROs. The study proved that SMR was “cost-effective, attracts better talents and retains them”.

Originality/value

The study suggested social media sites like Facebook could maximize the number of applicants and be more effective than traditional advertising in targeting passive job seekers. Second, it showed managers could optimize their SM post-hire outcomes to improve talent retention. Third, the results suggested that SMR could attract dream candidates by providing credible information. Finally, HR departments needed to understand social media complements rather than replaces traditional recruitment methods.
Effects of air mattress pressure on sleep quality and physiological responses: comparison of shoulder and hip pressure relief
Authors: Baek Yoon Jeong , Kim Seung-Hyun , Kim Sayup , Yoo Eui-Sang , Lee Joo-Young
Published: July 2021

Purpose

The purpose of the present study was to evaluate the effect of air mattress pressure on sleep quality.

Design/methodology/approach

Ten young healthy males participated in all hard surface [AH], shoulder soft [SS] and shoulder and hip soft mattress [SHS] conditions. The surface pressure for SS and SHS were set at their preferred levels.

Findings

The results showed that sleep efficiencies were over 95% for all the three conditions; there were no significant differences in individual sleep variables among the three conditions, but overall sleep quality was better for SS than AH (p = 0.065); heart rates during sleep was greater for AH than the other two conditions (p < 0.1); and a stronger relationship between clothing and bed microclimate humidity were found for SS and SHS than that for AH.

Research limitations/implications

These results indicated that the both pressure relief air mattresses that were set at their own preferred levels provided high quality sleep with no marked differences.

Practical implications

Air pressure relief mattresses can improve sleep quality of healthy individuals during sleep at night. The results can be used to understand appropriate pressure distribution on surface mattress according to body region, and also to develop algorithms to provide optimum sleep using mattresses with surface pressure control by body region.

Originality/value

The present study found that the shoulder and/or hip pressure relief air mattresses that were set at their own preferred levels provided high quality sleep with no marked differences.
The transformational leadership role in achieving organizational resilience through adaptive cultures: the case of Dubai service sector
Authors: Madi Odeh Rana B.S. , Obeidat Bader Yousef , Jaradat Mais Osama , Masa'deh Ra'ed , Alshurideh Muhammad Turki
Published: July 2021

Purpose

This empirical research draws on the existing theory of transformational leadership, adaptive culture and organizational resilience, and investigates the effect of the elected TQM leadership style “transformational leadership” through the mediating effect of adaptive culture on organizational resilience, that is the key of survival during crises like the recent COVID-19 pandemic, which has severely impacted the business globally.

Design/methodology/approach

This study exploited a cross-sectional online questionnaire of a random sample of Dubai service firms, with the unit of analysis being at the firm level. In total, 379 usable responses were received. Regression analysis was conducted to test hypotheses.

Findings

The overall findings of this study supported that transformational leadership is positively associated with both adaptive culture and firm's resilience and significantly impacts them. Adaptive culture was found partially mediating the effect of transformational leadership on organizational resilience.

Practical implications

The research findings provide important insights to practitioners (managers and leaders) to better improve their transformational qualities, as these qualities are expected to improve the organizational adaptive cultures and capacity of resilience.

Originality/value

To the best of the authors' knowledge, this is one of the first studies to examine the transformational leadership effect on organizational adaptive culture and firm's resilience. This investigation expands the boundaries of leadership style theory into new arenas, attempting to partially address the identified knowledge gap in this vein.
Bonded design in the virtual environment: the transition of a participatory design methodology
Authors: Nesset Valerie , Davis Elisabeth C. , Stewart-Robertson Owen , Bible J. Brice
Published: July 2021

Purpose

This paper examines how bonded design (BD), a participatory design methodology, was influenced by the transition to working in a virtual environment necessitated by the coronavirus disease 2019 (COVID-19) pandemic.

Design/methodology/approach

Abiding by the participatory design tenets of creativity, learning-by-doing and mutual learning, the BD methodology was created for the specific purpose of fostering meaningful communication and interaction between two disparate groups. Previous iterations of BD are discussed, including its naissance with intergenerational teams, its adaptation to provide a framework for a university-wide initiative, the Faculty Information Technology (IT) Liaison Program that brought together faculty members and IT professional staff, and its current use in helping public librarians to develop with older adults, targeted library programming and services.

Findings

Analysis of the findings from the assessment of the BD methodology in different physical contexts demonstrates that the flexibility in the makeup and order of design techniques (discussion, evaluation, brainstorming, prototyping, consensus-building) makes BD potentially adaptable to online spaces. Recommendations for implementing the BD methodology online are outlined. It is argued that BD’s adaptability makes it an ideal method for creating meaningful and productive collaborations within both physical and virtual environments.

Originality/value

The proposed iteration of the BD methodology responds to a need for innovative practices to foster collaborative work in a virtual environment. BD is a unique, inclusive and cost-effective methodology to encourage meaningful interaction and communication between disparate groups in physical or online contexts.
Do reputational signals matter for nonprofit organizations? An experimental study
Authors: Shahid Subhan , Becker Annika , Kundi Yasir Mansoor
Published: July 2021

Purpose

This paper aims to untangle the underlying mechanisms through which reputational signals promote stakeholders' intentions to donate in nonprofit organizations via stakeholder trust.

Design/methodology/approach

The authors apply a moderated mediation model using an experimental design with N = 248 business and public management students of France.

Findings

The results indicate that both a formal reputational signal (third-party certificate) and an informal reputational signal (self-proclaiming to be social entrepreneurial) affect stakeholder trust and intentions to donate. Stakeholder trust partially mediated the relationship between the formal signal and intentions to donate, and the mediation effect was stronger when an informal signal was present (vs. not present).

Practical implications

Trust is central to the exchange of nonprofit organizations and their external stakeholders. To enhance trust and supportive behavior toward nonprofit organizations, these organizations may consider using formal and informal reputational signaling within their marketing strategies.

Originality/value

This research highlights the pivotal role of formal and informal reputational signals for the enhancing stakeholders' trust and donation behavior in a nonprofit context.
Development and post-dicing wet release of MEMS magnetometer: an approach
Authors: Aditi  , Das Supriyo , Gopal Ram
Published: July 2021

Purpose

Si-based micro electro mechanical systems (MEMS) magnetometer does not require specialized magnetic materials avoiding magnetic hysteresis, ease in fabrication and low power consumption. It can be fabricated using the same processes used for gyroscope and accelerometer fabrication. The paper reports the dicing mechanism for the released MEMS xylophone magnetic sensor fabricated using wafer bonding technology and its characterization in ambient pressure and under vacuum conditions. The purpose of this paper is to dice the wafer bonded Si-magnetometer in a cost-effective way without the use of laser dicing and test it for Lorentz force transduction.

Design/methodology/approach

A xylophone bar MEMS magnetometer using Lorentz force transduction is developed. The fabricated MEMS-based xylophone bars in literature are approximately 500 µm. The present work shows the released structure (L = 592 µm) fabricated by anodic bonding technique using conducting Si as the structural layer and tested for Lorentz force transduction. The microstructures fabricated at the wafer level are released. Dicing these released structures using conventional diamond blade dicing may damage the structures and reduce the yield. To avoid the problem, positive photoresist S1813 was filled before dicing. The dicing of the wafer, filled with photoresist and later removal of photoresist post dicing, is proposed.

Findings

The devices realized are stiction free and straight. The dynamic measurements are done using laser Doppler vibrometer to verify the released structure and test its functionality for Lorentz force transduction. The magnetic field is applied using a permanent magnet and Helmholtz coil. Two sensors with quality factors 70 and 238 are tested with resonant frequency 112.38 kHz and 114.38 kHz, respectively. The sensor D2, with Q as 238, shows a mechanical sensitivity of 500 pm/Gauss and theoretical Brownian noise-limited resolution of 53 nT/vHz.

Originality/value

The methodology and the study will help develop Lorentz force–based MEMS magnetometers such that stiction-free structures are released using wet etch after the mechanical dicing.
Mechanical and durability properties of adobe blocks filled with date palm wastes
Authors: Zaidi Amine , Izemmouren Ouarda , Taallah Bachir , Guettala Abdelhamid
Published: July 2021

Purpose

Earthen construction does not meet today’s requirements due to certain limitations such as low water resistance and its high vulnerability to cracking damage. The purpose of this study is to improve the mechanical properties and low durability of adobe blocks by incorporating date palm wastes as a natural reinforcement and lime as a stabilizer.

Design/methodology/approach

Soil from the region of Biskra in Algeria was mixed with sand and lime in suitable ratios. Then, date palm wastes were added to the previous mixture at different ratios (0.3%, 0.6% and 0.9%) by dry mix weight to manufacture adobes. Cubical and cylindrical specimens were prepared and tested in a laboratory to investigate the curing time, mechanical and durability characteristics of the formulated blocks. In addition, X-ray diffraction and scanning electron microscopy (SEM) tests were used to identify the materials.

Findings

It has been observed that the addition of lime to the soil is very beneficial for its stabilization, in particular for an optimum of 12%. The presence of date palm waste in the mixture (soil + lime) generated a significant improvement in tensile strength reaching a rate of about 67%. The same observation was made for the tests of resistance to dry abrasion, resistance to erosion, attack by external sulphate and wetting/drying. However, for cases of compressive strength, water absorption and swelling an unfavorable effect was recorded.

Originality/value

Based on the above-mentioned findings, this paper presents a novel solution to increase the durability of adobe materials using date palm wastes with oven curing at 65°C for about nine days. Adopting such an approach would certainly encourage building durable mud housing on a large scale. This can contribute to solving the acute housing shortage, particularly in poor countries.
Soil acidification mediates changes in soil bacterial community assembly processes in response to agricultural intensification
Authors: Zhou Xingang , Khashi u Rahman Muhammad , Liu Junjie , Wu Fengzhi
Published: July 2021

Agricultural intensification is known to alter the assembly of soil microbial communities, which regulate several critical ecosystem processes. However, the underlying ecological processes driving changes in microbial community assembly, particularly at the regional scale, remain poorly understood. Using 16S rDNA sequencing, we characterized soil bacterial community assembly in three land‐use types with increasing land‐use intensity: open fields cultivated with main crops (CF) or vegetables (VF), and greenhouses cultivated with vegetables (VG). Compared with CF, VF and VG altered bacterial community composition and decreased spatial turnover rates of edaphic variables and bacterial communities. Bacterial community assembly was primarily governed by deterministic processes; however, bacterial communities in VF and VG were phylogenetically less clustered and more influenced by variable selection and less by dispersal limitation. Soil pH was the most important edaphic variable mediating the changes in bacterial community assembly processes induced by agricultural intensification. Specifically, decreasing soil pH led to stochastic assembly of bacterial community. Soil pH was lower in more intensively managed lands, especially in case of VG (pH range: 5.86–7.42). Overall, agricultural intensification altered soil bacterial community assembly processes, which was associated with soil acidification. These findings may have implications for improving soil quality and agroecosystem sustainability.
Reactivity of flavanols: Their fate in physical food processing and recent advances in their analysis by depolymerization
Authors: Liu Xuwei , Le Bourvellec Carine , Guyot Sylvain , Renard Catherine M. G. C.
Published: July 2021

Flavanols, a subgroup of polyphenols, are secondary metabolites with antioxidant properties naturally produced in various plants (e.g., green tea, cocoa, grapes, and apples); they are a major polyphenol class in human foods and beverages, and have recognized effect on maintaining human health. Therefore, it is necessary to evaluate their changes (i.e., oxidation, polymerization, degradation, and epimerization) during various physical processing (i.e., heating, drying, mechanical shearing, high‐pressure, ultrasound, and radiation) to improve the nutritional value of food products. However, the roles of flavanols, in particular for their polymerized forms, are often underestimated, for a large part because of analytical challenges: they are difficult to extract quantitatively, and their quantification demands chemical reactions. This review examines the existing data on the effects of different physical processing techniques on the content of flavanols and highlights the changes in epimerization and degree of polymerization, as well as some of the latest acidolysis methods for proanthocyanidin characterization and quantification. More and more evidence show that physical processing can affect content but also modify the structure of flavanols by promoting a series of internal reactions. The most important reactivity of flavanols in processing includes oxidative coupling and rearrangements, chain cleavage, structural rearrangements (e.g., polymerization, degradation, and epimerization), and addition to other macromolecules, that is, proteins and polysaccharides. Some acidolysis methods for the analysis of polymeric proanthocyanidins have been updated, which has contributed to complete analysis of proanthocyanidin structures in particular regarding their proportion of A‐type proanthocyanidins and their degree of polymerization in various plants. However, future research is also needed to better extract and characterize high‐polymer proanthocyanidins, whether in their native or modified forms.
Effects of digested flours from four different sweet potato (Ipomoea batatas L.) root varieties on the composition and metabolic activity of human colonic microbiota in vitro
Authors: de Albuquerque Thatyane Mariano Rodrigues , Magnani Marciane , Lima Marcos dos Santos , Castellano Lúcio Roberto Cançado , de Souza Evandro Leite
Published: July 2021

This study evaluated the effects of flours from four different sweet potato root (SPR) varieties, being two with white peel and two with purple peel, on the composition and metabolic activity of human colonic microbiota in vitro. The capability of these SPR flours (20 g/L) to cause alterations in relative abundance of different bacterial groups found as part of human colonic microbiota, as well as in lactic acid and short‐chain fatty acid production was evaluated during 48 hr of an in vitro colonic fermentation. The SPR flours were submitted to a simulated gastrointestinal digestion prior to use in experiments. The four SPR flours increased the relative abundance of Lactobacillus/Enterococcus (range: 0.49–4.48%) and Bifidobacterium (range: 0.32–3.27%) and decreased the relative abundance of Bacteroides/Prevotella (range: 0.29–7.49%), Clostridium histolyticum (range: 0.15–2.08%), and Eubacterium rectale/Clostridium coccoides (range: 0.28–3.86%) during the 48 hr of colonic fermentation. The four SPRF flours had positive prebiotic indexes (> 0.38) after 24 and 48 hr of colonic fermentation, reinforcing the occurrence of selective stimulatory effects on colonic microbiota. An increased metabolic activity of human colonic microbiota was caused by tested SPR flours, which was evidenced by decreased pH (range: 3.20–3.83) and increased lactic acid and short chain fatty acid production during the 48 hr of colonic fermentation. The four examined SPR flours were capable of causing positive alterations in composition and driving the metabolic activity of human colonic microbiota during in vitro colonic fermentation, which should be linked to their prebiotic properties.

Practical Application

The four examined sweet potato root flours (SPRF) caused beneficial alterations in composition besides of driving the metabolic activity of human colonic microbiota in vitro. These results characterize the examined SPRF as candidates for use as prebiotic ingredients by food industry for formulation of value‐added functional foods or dietary supplements.
Does Susceptibility to the Numerosity Heuristic Impact Juror Assessments of Auditors' Liability?*
Authors: Joe Jennifer R. , Luippold Benjamin L. , Sanderson Kerri‐Ann
Published: July 2021

We provide evidence that regulatory guidance aimed at improving audit efficiency and effectiveness—allowing auditor reliance on a multi‐location client's competent and objective internal audit function (IAF)—can unintentionally increase auditors' litigation risk. Our research is important in demonstrating how client characteristics and juror cognitive processing, such as the number of client locations and jurors' susceptibility to the numerosity heuristic, factors beyond auditors' control, can exacerbate their litigation exposure. Consistent with theoretical predictions, we find that susceptibility to the numerosity heuristic contributes to jurors assessing an increased likelihood of misstatement on multi‐location compared to single‐location audits. Furthermore, these assessments of higher misstatement risk on multi‐location audits lead jurors to perceive that auditor reliance on the client's IAF in multi‐location audits is less appropriate (i.e., not normal). Accordingly, jurors judge that auditors are more negligent when they rely on the IAF during multi‐location audits than when they do not, but IAF reliance does not impact auditor negligence on single‐location audits. Our results suggest auditor reluctance to use a qualified IAF, despite client pressure and regulatory allowance, can provide potential benefits to firms in terms of reduced litigation exposure. Thus, we demonstrate the legal regime can undermine the objectives of regulators' guidance to enhance audit efficiency and corporate governance.
Associations between naloxone prescribing and opioid overdose among patients with acute and chronic pain conditions
Authors: Qeadan Fares , Madden Erin Fanning
Published: July 2021

Aims

To assess whether naloxone prescribing in clinical contexts targeted pain patients most at risk for opioid overdose.

Design

A retrospective cohort study using data from the Health Facts Database.

Setting

Over 600 United States healthcare facilities.

Participants

Three patient groups were followed for 2 years during 2009 to 2017: individuals with shoulder or long bone fractures (n = 252 424), chronic pain syndrome (CPS) (n = 76 141), or non‐traumatic low back pain (n = 792 956) who received an opioid prescription. Groups were chosen based on previous work.

Measurements

The outcome was opioid overdose identified by International Classification of Diseases codes (ICDs) and the primary predictor was number of naloxone prescriptions identified by National Drug Codes (NDCs).

Findings

Opioid overdoses occurred among 0.16% of fracture patients (average follow‐up time to overdose [AFU] = 240 days), 1.28% of CPS patients (AFU = 244 days), and 0.30% low back pain patients (AFU = 264 days). A total of 58 083 bone fracture patients received naloxone prescriptions, and naloxone prescription was associated with subsequent opioid overdose (hazard ratio [HR] = 1.87, 95% CI = 1.68–2.09), and number of subsequent overdoses (incidence rate ratio [IRR] = 1.89, 95% CI = 1.69–2.12). A total of 19 529 CPS patients received naloxone prescriptions, and naloxone prescription was associated with subsequent opioid overdose (HR = 1.69, 95% CI = 1.61–1.78) and number of subsequent overdoses (IRR = 1.74, 95% CI = 1.67–1.83). A total of 110 608 low back pain patients received naloxone prescriptions, and naloxone prescription was associated with subsequent opioid overdose (HR = 1.33, 95% CI = 1.27–1.40) and number of subsequent overdoses (IRR = 1.35, 95% CI = 1.29–1.41).

Conclusions

Receiving a naloxone prescription appears to be associated with increased risk of subsequent opioid overdose among patients with acute and chronic pain, suggesting prescribers often identify patients most in need of naloxone.
An Assessment of Abenomics: Evolution and Achievements
Authors: Ito Takatoshi
Published: July 2021

This paper evaluates the first two arrows of Abenomics. The first arrow, aggressive monetary policy, was successful in lifting the Japanese economy out of deflation, although the 2% inflation target was not achieved. The real economy and financial markets recovered strongly. Unconventional monetary policy was successful through the channels of the yen and stock prices. The second arrow, “flexible” fiscal policy, can be interpreted as an enhanced counter‐cyclical policy, that is, to stimulate when needed, but tighten when possible. The first fiscal supplementary budget of February 2013 was a powerful boost to the economy. For fiscal consolidation, the consumption tax rate was hiked from 5% to 10% in two installments in April 2014 and October 2019. This helped to shrink the deficits. With strong macroeconomic performances, Shinzo Abe established a record as the longest‐serving prime minister in Japanese history.
Antibody response after one and two jabs of the BNT162b2 vaccine in nursing home residents: The CONsort‐19 study
Authors: Blain Hubert , Tuaillon Edouard , Gamon Lucie , Pisoni Amandine , Miot Stéphanie , Rolland Yves , Picot Marie‐Christine , Bousquet Jean
Published: July 2021

Background

The humoral immune response following COVID‐19 vaccination in nursing home residents is poorly known. A longitudinal study compared levels of IgG antibodies against the spike protein (S‐RBD IgG) (S‐RDB protein IgG) after one and two BNT162b2/Pfizer jabs in residents with and without prior COVID‐19.

Methods

In 22 French nursing homes, COVID‐19 was diagnosed with real‐time reverse‐transcriptase polymerase chain reaction (RT‐PCR) for SARS‐CoV‐2. Blood S‐RDB‐protein IgG and nucleocapsid (N) IgG protein (N‐protein IgG) were measured 21–24 days after the first jab (1,004 residents) and 6 weeks after the second (820 residents).

Results

In 735 residents without prior COVID‐19, 41.7% remained seronegative for S‐RDB‐protein IgG after the first jab vs. 2.1% of the 270 RT‐PCR‐positive residents (p < 0.001). After the second jab, 3% of the 586 residents without prior COVID‐19 remained seronegative. However, 26.5% had low S‐RDB‐protein IgG levels (50–1050 UA/ml) vs. 6.4% of the 222 residents with prior COVID‐19. Residents with an older infection (first wave), or with N‐protein IgG at the time of vaccination, had the highest S‐RDB‐protein IgG levels. Residents with a prior COVID‐19 infection had higher S‐RDB‐protein IgG levels after one jab than those without after two jabs.

Interpretation

A single vaccine jab is sufficient to reach a high humoral immune response in residents with prior COVID‐19. Most residents without prior COVID‐19 are seropositive for S‐RDB‐protein IgG after the second jab, but around 30% have low levels. Whether residents with no or low post‐vaccine S‐RDB protein IgG are at higher risk of symptomatic COVID‐19 requires further analysis.
The relationship of serum testosterone levels with the clinical course and prognosis of COVID‐19 disease in male patients: A prospective study
Authors: Cinislioglu Ahmet Emre , Cinislioglu Nazan , Demirdogen Saban Oguz , Sam Emre , Akkas Fatih , Altay Mehmet Sefa , Utlu Mustafa , Sen Irem Akin , Yildirim Fatih , Kartal Seyfi , Aydin Hasan Riza , Karabulut Ibrahim , Ozbey Isa
Published: July 2021

Background

A potential role of testosterone among sex hormones has been hypothesized in identifying sex‐related differences in the clinical consequences of severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection. Due to the high global prevalence of hypogonadism, the relationship between hypogonadism and SARS‐CoV‐2 infection outcomes deserves an in‐depth study.

Objective

The present study aimed to investigate the relationship of serum testosterone with other laboratory parameters on the prognosis of coronavirus disease‐19 (COVID‐19) in male patients with COVID‐19 diagnosis.

Materials and methods

This prospective cohort study included 358 male patients diagnosed with COVID‐19 and 92 COVID‐19 negative patients admitted to the urology outpatient clinics as a control group. The COVID‐19 patients were divided into groups according to prognosis (mild‐moderate and severe group), lung involvement in chest computed tomography (<50% and >50%), intensive care unit needs, and survival.

Results

The measured serum total testosterone level of the COVID‐19 patients group was found to be significantly lower than that of the control group (median, 140 ng/dl; range, 0.21–328, 322 ng/dl; range, median, 125–674, p < 0.001, respectively). The serum TT levels were statistically significantly lower in severe COVID‐19 patients compared to mild‐moderate COVID‐19 patients (median, 85.1 ng/dl; range, 0.21–532, median, 315 ng/dl; range, 0.88–486, p < 0.001, respectively), in COVID‐19 patients in need of intensive care compared to COVID‐19 patients who did not need intensive care (median, 64.0 ng/dl; range, 0.21–337, median, 286 ng/dl; range, 0.88–532 p < 0.001, respectively), and in COVID‐19 patients who died compared to survivors (median, 82.9 ng/dl; range, 2.63–165, median, 166 ng/dl; range, 0.21–532, p < 0.001, respectively).

Discussion and conclusion

Our data are compatible with low TT levels playing a role on the pathogenesis of the disease in Covid‐19 patients with poor prognosis and a mortal course and may guide clinicians in determining the clinical course of the disease.
Methodological considerations in measuring specific force in human single skinned muscle fibres
Authors: Kalakoutis Michaeljohn , Di Giulio Irene , Douiri Abdel , Ochala Julien , Harridge Stephen D. R. , Woledge Roger C.
Published: July 2021

Chemically skinned fibres allow the study of human muscle contractile function in vitro. A particularly important parameter is specific force (SF), that is, maximal isometric force divided by cross‐sectional area, representing contractile quality. Although SF varies substantially between studies, the magnitude and cause of this variability remains puzzling. Here, we aimed to summarize and explore the cause of variability in SF between studies. A systematic search was conducted in Medline, Embase and Web of Science databases in June 2020, yielding 137 data sets from 61 publications which studied healthy, young adults. Five‐fold differences in mean SF data were observed. Adjustments to the reported data for key methodological differences allowed between‐study comparisons to be made. However, adjustment for fibre shape, swelling and sarcomere length failed to significantly reduce SF variance (I2 = 96%). Interestingly, grouping papers based on shared authorship did reveal consistency within research groups. In addition, lower SF was found to be associated with higher phosphocreatine concentrations in the fibre activating solution and with Triton X‐100 being used as a skinning agent. Although the analysis showed variance across the literature, the ratio of SF in single fibres containing myosin heavy chain isoforms IIA or I was found to be consistent across research groups. In conclusion, whilst the skinned fibre technique is reliable for studying in vitro force generation of single fibres, the composition of the solution used to activate fibres, which differs between research groups, is likely to heavily influence SF values.