bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing and assuring interoperability of a genomics file format
Authors: Niu Yi Nian , Roberts Eric G. , Denisko Danielle , Hoffman Michael M.
Published: January 2022

Background

Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, and only rarely do the creators of these tools robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results.

Methods

We sought (1) to assess the interoperability of a wide range of bioinformatics software using a shared genomics file format and (2) to provide a simple, reproducible method for enhancing inter-operability. As a focus, we selected the popular Browser Extensible Data (BED) file format for genomic interval data. Based on the file format’s original documentation, we created a formal specification. We developed a new verification system, Acidbio (https://github.com/hoffmangroup/acidbio), which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases—potentially unexpected inputs that exemplify the limits of the format. To analyze the performance of existing software, we tested the input validation of 80 Bioconda packages that parsed the BED format. We also used a fuzzing approach to automatically perform additional testing.

Results

Of 80 software packages examined, 75 achieved less than 70% correctness on our test suite. We categorized multiple root causes for the poor performance of different types of software. Fuzzing detected other errors that the manually designed test suite could not. We also created a badge system that developers can use to indicate more precisely which BED variants their software accepts and to advertise the software’s performance on the test suite.

Discussion

Acidbio makes it easy to assess interoperability of software using the BED format, and therefore to identify areas for improvement in individual software packages. Applying our approach to other file formats would increase the reliability of bioinformatics software and data.
Digenic genotypes: the interface of inbreeding, linkage, and linkage disequilibrium
Authors: Smith Reginald D.
Published: January 2022

Many traits in populations are well understood as being Mendelian effects at single loci or additive polygenic effects across numerous loci. However, there are important phenomena and traits that are intermediate between these two extremes and are known as oligogenic traits. Here we investigate digenic, or two-locus, traits and how their frequencies in populations are affected by non-random mating, specifically inbreeding, linkage disequilibrium, and selection. These effects are examined both separately and in combination to demonstrate how many digenic traits, especially double homozygous ones, can show significant, sometimes unexpected, changes in population frequency with inbreeding, linkage, and linkage disequilibrium. The effects of selection on deleterious digenic traits are also detailed. These results are applied to both digenic traits of medical significance as well as measuring inbreeding in natural populations.
Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR
Authors: Perez Verdaguer Mireia , Zhang Tian , Paulo Joao A. , Wallace Callen , Watkins Simon C. , Gygi Steven P. , Sorkin Alexander
Published: January 2022

Ligand binding to the EGF receptor (EGFR) triggers multiple signal transduction processes and promotes endocytosis of the receptor. The mechanisms of EGFR endocytosis and its crosstalk with signaling are poorly understood. Here, we combined peroxidase-catalyzed proximity labeling, isobaric peptide tagging and quantitative mass-spectrometry to define the dynamics of the proximity proteome of ligand-activated EGFR. Using this approach, we identified a network of signaling proteins, which remain associated with the receptor during its internalization and trafficking through the endosomal system. We showed that Trk-fused gene (TFG), a protein known to function at the endoplasmic reticulum exit sites, was enriched in the proximity proteome of EGFR in early/sorting endosomes and localized in these endosomes, and demonstrated that TFG regulates endosomal sorting of EGFR. This study provides a comprehensive resource of time-dependent nanoscale environment of EGFR, thus opening avenues to discovering new regulatory mechanisms of signaling and intracellular trafficking of receptor tyrosine kinases.
Comprehensive analysis of disease pathology in immunocompetent and immunocompromised hamster models of SARS-CoV-2 infection
Authors: Ramasamy Santhamani , Kolloli Afsal , Kumar Ranjeet , Husain Seema , Soteropoulos Patricia , Chang Theresa L. , Subbian Selvakumar
Published: January 2022

The pathogenesis of SARS-CoV-2 in the context of a specific immunological niche is not fully understood. Here, we used a golden Syrian hamster model to systematically evaluate the kinetics of host response to SARS-CoV-2 infection, following disease pathology, viral loads, antibody responses, and inflammatory cytokine expression in multiple organs. The kinetics of SARS-CoV-2 pathogenesis and genomewide lung transcriptome was also compared between immunocompetent and immunocompromised hamsters. We observed that the body weight loss was proportional to the SARS-CoV-2 infectious dose and lasted for a short time only in immunocompetent hamsters. Body weight loss was more prominent and prolonged in infected immunocompromised hamsters. While the kinetics of viral replication and peak live viral loads were not significantly different at low and high infectious doses (LD and HD), the HD-infected immunocompetent animals developed severe lung disease pathology. The immunocompetent animals cleared the live virus in all tested tissues by 12 days post-infection and generated a robust serum antibody response. In contrast, immunocompromised hamsters mounted an inadequate SARS-CoV-2 neutralizing antibody response, and the virus was detected in the pulmonary and multiple extrapulmonary organs until 16 days post-infection. These hamsters also had prolonged moderate inflammation with severe bronchiolar-alveolar hyperplasia/metaplasia. Consistent with the difference in disease presentation, distinct changes in the expression of inflammation and immune cell response pathways and network genes were seen in the lungs of infected immunocompetent and immunocompromised animals. This study highlights the interplay between the kinetics of viral replication and the dynamics of SARS-CoV-2 pathogenesis at organ-level niches and maps how COVID-19 symptoms vary in different immune contexts. Together, our data suggest that the histopathological manifestations caused by progressive SARS-CoV-2 infection may be a better predictor of COVID-19 severity than individual measures of viral load, antibody response, and cytokine storm at the systemic or local (lungs) levels in the immunocompetent and immunocompromised hosts.
Now I can see: how brand interactions influence channel loyalty and purchase intention in optical physical stores
Authors: Bilro Ricardo Godinho , Dias Fernando
Published: January 2022

Purpose

This study aims to analyse the effect of brand interactions such as personal interaction, problem-solving, reliability and store physical appearance on channel loyalty and purchase intention in optical physical stores.

Design/methodology/approach

The hypotheses are tested through quantitative research based on a questionnaire with a sample of 414 respondents. Researchers conduct multiple regressions to analyse the data.

Findings

The findings reveal that channel loyalty and purchase intention are positively influenced differently. Person-to-person interactions play a vital role in both constructs (dependent variables). This study also offers relevant managerial implications and future research avenues.

Originality/value

Despite the relevance of purchase intention in the literature, almost no studies have been published about the intention to buy glasses in the optical physical stores, a relevant contribution this paper offers to the literature. The finding that the store’s physical aspect did not prove to be influential for channel loyalty is also an innovative and relevant contribution of this research.
Examining our own relationships to racism as the foundation of decolonising systemic practices. ‘No time like the present’
Authors: Chin Jasmine , Hughes Gillian , Miller Ashley
Published: January 2022

Racist discourses embedded in our social structures can have a profoundly negative impact on people's emotional well‐being. This paper calls for a re‐focusing within systemic therapy on anti‐colonial and social justice approaches specifically on addressing racism. We propose that if we are to make this shift in our practice, we need to first engage in processes of self‐reflexivity about the impact of racism on ourselves and our personal relationships. We draw on Paolo Freire's idea of ‘conscientisation’, or consciousness raising – a form of self‐reflexivity through the lens of power, and on the work of McKenzie‐Mavinga, who highlights the importance of therapists developing their awareness and understanding of how racism operates in their lives. We illustrate these ideas through an exploration of how we have approached this work within a long‐standing peer supervision group.
Clinical feasibility of transfer to combined therapy with peritoneal dialysis and hemodialysis for patients on peritoneal dialysis: A prospective multicenter study in Japan
Authors: Maruyama Yukio , Yokoyama Keitaro , Higuchi Chieko , Sanaka Tsutomu , Tanaka Yoshihide , Sakai Ken , Kanno Yoshihiko , Ryuzaki Munekazu , Sakurada Tsutomu , Hosoya Tatsuo , Nakayama Masaaki ,   for the EARTH (Evaluation of the Adequacy of Renal replacement THerapy) study group
Published: January 2022

Introduction

Although combined therapy with peritoneal dialysis (PD) and hemodialysis (HD) is widespread in Japan, its clinical utility has been reported only in retrospective or before‐and‐after test lacking a control group.

Methods

We conducted a prospective, multicenter, observational cohort study of 176 incident PD patients and compared patient survival and changes in clinical parameters between patients on different dialysis modalities.

Results

During a median follow‐up of 41 months, 47 patients transferred to combined therapy and 35 patients transferred directly to HD. Patients transferred to combined therapy had a significantly better survival than those transferred directly to HD. However, we could not establish this difference in a multivariate analysis because only six patients died among these groups. The decreases in urea nitrogen and serum creatinine were more prominent among patients directly transferred to HD.

Conclusion

This is the first report revealing clinical feasibility of transfer to combined therapy for PD patients.
Performance Targets and Ex Post Incentive Plan Adjustments†
Authors: Hyun Jeong‐Hoon , MatĚjka Michal , (Seung Hwan) Oh Peter , Ahn Tae Sik
Published: January 2022

Performance evaluations are typically based on a formula that specifies in advance all performance measures, their relative incentive weights, and targets to be met. However, beginning‐of‐year performance targets can become outdated due to unforeseen events that call for ex post adjustments to formula‐based incentive plans to restore incentives. We discuss three types of ex post incentive plan adjustments—end‐of‐year subjective performance evaluation, changes in next‐year relative incentive weights, and changes in next‐year performance targets—and empirically examine the extent to which they are used to discourage failure to meet a target by a wide margin. Specifically, we use 2004–2015 data on formula‐based bonus plans, subjective performance evaluations, and performance in Korean state‐owned enterprises. Consistent with our predictions, we find that very low performance relative to target is associated with (i) low subjective evaluations and (ii) an increase in next‐year incentive weights, conditions that render areas with poor performance more important in future evaluations. These findings are more pronounced on performance dimensions of high importance and less pronounced when very low performance is due to an adverse uncontrollable shock. Finally, we find evidence that ex post incentive plan adjustments are associated with future performance improvements. Combined, our findings suggest that ex post incentive plan adjustments can be used to strengthen incentives when performance targets get outdated.
Anatomical position of the palmar/plantar nerves at the metacarpal/metatarsal distal level in horses: An in vivo study by means of ultrasonography
Authors: Maia Beatriz Tofani , Vendruscolo Cynthia do Prado , de Souza Anderson Fernando , Zoppa André Luis do Valle De
Published: January 2022

The neurovascular bundle of the equine distal cannon can dynamically vary with limb position, and this can affect the performance of low 4‐ or 6‐point block. This study aims to identify and describe the anatomical position and variations of the lateral and medial palmar/plantar nerve at the metacarpal/metatarsal distal level in horses by ultrasonography. Eight mares underwent ultrasound examination on the lateral and medial palmar/plantar sides of the metacarpus/metatarsus. Images were obtained for measurements of the cross‐sectional area of the nerve, distances between the nerve and the skin surface, branch of the suspensory ligament (SL), deep digital flexor tendon (DDFT) and superficial digital flexor tendon (SDFT) with limbs supported and elevated. The distance to the skin for forelimbs was higher on the lateral side when the limb was elevated (p < 0.001). The comparisons between supported and elevated limbs on the same side showed longer distances to the skin with the limb supported on the medial side (p < 0.001). Hindlimbs showed longer distances to the skin with the limb supported on the medial face (p = 0.027). The anatomical position of palmar/plantar nerves was similar between the lateral and medial sides of the limb, generally being in contact with the dorsal edge of DDFT. The strategy of elevating the limb during the injection of the low 4‐ or 6‐point block can lead to a higher risk of puncture of the digital sheath.
Comparison of Indian and Nepalese media on “Nepal's New Political Map”
Authors: Aryal Saroj K. , Bharti Simant S.
Published: January 2022

A newly revised political map was published by the Nepalese government on May 20, 2020, which includes, as part of Nepali territory, the disputed areas of Lipulekh, Kalapani, and Limpiyadhura. The long‐existing border dispute between India and Nepal gets heated up again. Nepal considered the updated political map as a retaliation toward India and India considered it as a breach of the friendship line between the two countries. During this period, the media from both sides were engaged and the narrative that we find contradicts each other in many ways. This review article conducts a media analysis and present the different narratives that we found during these period.
Rabbit antithymocyte globulin dose and early subclinical and clinical rejections in kidney transplantation
Authors: Mehta Rajil B. , Shimko Kristen , Zhang Xingyu , Puttarajappa Chethan , Wu Christine , Sharma Akhil , Molinari Michele , Tevar Amit D. , Hariharan Sundaram , Sood Puneet
Published: January 2022

Antithymocyte globulin (ATG) is a commonly used induction agent in kidney transplant recipients. However, the optimal dosing has not been well defined. Our protocol aims for a 5–6 mg/kg cumulative dose. It is unclear if a dose lower than 5 mg/kg is associated with more rejection.

We performed a retrospective cohort study of patients who received a kidney transplant at our center between January 1, 2013 and December 31, 2016. Primary outcome was biopsy proven acute rejection (clinical and subclinical) in the first 6 months after kidney transplant. CMV viremia in high risk (D+/R−) recipients and BK viremia was compared as a secondary endpoint.

Of the 543 patients, the Low Dose (LD) group (n = 56) received <5 mg/kg ATG and Regular Dose (RD) group (n = 487) received ≧5 mg/kg. Patients in RD were more sensitized (higher PRA and CPRA). LD received a dose of 4 ± 1.1 mg/kg ATG whereas RD received 5.6 ± .3 mg/kg ATG (P < .001). TCMR (Banff 1A or greater) was present in 34% of patients in LD versus 22% in RD (P = .04) (OR 2.1; 95%CI 1.12–3.81; P = .019). There was no difference in the incidence of CMV or BK viremia.

ATG doses lower than 5 mg/kg may be associated with a heightened risk of rejection despite a low degree of sensitization.
An observational study of the Covid‐19 situation following the first pan‐European mass sports event
Authors: Cuschieri Sarah , Grech Stephan , Cuschieri Andrea
Published: January 2022

Background

All events in Europe, including EURO2020 football championship, were postponed due to Covid‐19 in 2020. Instead, Euro2020 took place in 2021, as mitigation measures were relaxed, cross‐country mobility increased and the Delta variant was spreading across Europe. This study explored the possibility of an increased Covid‐19 spread across Europe following EURO2020 matches.

Methods

Covid‐19 data on cases, vaccination and delta variant for participating countries, host cities/regions and neighbouring countries, for May till July 2021, were obtained from European Centre for Disease Prevention and Control, Our World in Data, Johns Hopkins COVID‐19 Dashboard and the UK Government website. EURO2020 data were obtained from the Union of European Football Associations official website.

Results

A general increase in Covid‐19 positivity trend in Europe was observed following a week of EURO2020 matches across most countries and host cities. A similar trend was observed for the Delta variant sample positivity rate. The increased incidence was mostly among the young generation (<49 years). A decline in positive cases was observed on a national level for most countries following the Finals match.

Conclusion

The EURO2020 was an anticipated mass sports event, and it was the first‐time spectators were allowed to enter stadiums in Europe. Stadiums instituted several mitigations to safeguard the spectators although reports of transmission were still present. The major challenges were the gatherings outside the stadiums that might have contributed to these observations. Targeted restrictions might be required during mass sport events especially in the presence of highly transmissible variant(s) and low vaccination rates among the young generation.
Property and inequality: Housing dynamics in a nineteenth‐century city
Authors: Rodger Richard
Published: January 2022

The internal structure of the city is analysed through the ownership, tenancy, and management of residential property using assessed rents to reflect current market value. The analysis reveals the interactions of agents, institutions, and trusts, and explores ownership in terms of gender, absenteeism, occupational categories, portfolio sizes, and values. Rents are used to develop both an index of housing affordability according to occupations, and an index of dissimilarity in rental variations within and between streets to provide a nuanced and more realistic understanding of the internal dynamics of an entire city—Edinburgh. While empirical material underpinning the analysis is place‐specific, the underlying urban processes and relationships are generalizable, and provide a comprehensive overview of residential property relationships.
Investing for retirement: Terminal wealth constraints or a desired wealth target?
Authors: Donnelly Catherine , Khemka Gaurav , Lim William
Published: January 2022

We investigate how well different investment strategies can give pre‐retirees more certainty about their income in retirement, whilst allowing them to benefit from taking investment risk. Under an expected utility‐maximizing framework, we find that a loss aversion utility function gives a high degree of certainty about its desired wealth target and is robust to different market models. Imposing terminal wealth constraints does not improve the certainty of achieving the desired target enough to counterbalance the increased chance of obtaining a lower income. The power utility function is not robust to different market models and becomes too risk‐averse with wealth constraints.
Conservation of vaccine antigen sequences encoded by sequenced strains ofStreptococcus equisubsp.equi
Authors: Frosth Sara , Morris Ellen Ruth A. , Wilson Hayley , Frykberg Lars , Jacobsson Karin , Parkhill Julian , Flock Jan‐Ingmar , Wood Tim , Guss Bengt , Aanensen David M. , Boyle Ashley G. , Riihimäki Miia , Cohen Noah D. , Waller Andrew S.
Published: January 2022

Background

Streptococcus equisubspeciesequi(S equi) is the cause of Strangles, one of the most prevalent diseases of horses worldwide. Variation within the immunodominant SeM protein has been documented, but a new eight‐component fusion protein vaccine, Strangvac, does not contain liveS equior SeM and conservation of the antigens it contains have not been reported.

Objective

To define the diversity of the eight Strangvac antigens across a diverseS equipopulation.

Study design

Genomic description.

Methods

Antigen sequences from the genomes of 759S equiisolates from 19 countries, recovered between 1955 and 2018, were analysed. Predicted amino acid sequences in the antigen fragments of SEQ0256(Eq5), SEQ0402(Eq8), SEQ0721(EAG), SEQ0855(SclF), SEQ0935(CNE), SEQ0999(IdeE), SEQ1817(SclI) and SEQ2101(SclC) in Strangvac and SeM were extracted from the 759 assembled genomes and compared.

Results

The predicted amino acid sequences of SclC, SclI and IdeE were identical across all 759 genomes. CNE was truncated in the genome of five (0.7%) isolates. SclF was absent from one genome and another encoded a single amino acid substitution. EAG was truncated in two genomes. Eq5 was truncated in four genomes and 123 genomes encoded a single amino acid substitution. Eq8 was truncated in three genomes, one genome encoded four amino acid substitutions and 398 genomes encoded a single amino acid substitution at the final amino acid of the Eq8 antigen fragment. Therefore, at least 1579 (99.9%) of 1580 amino acids in Strangvac were identical in 743 (97.9%) genomes, and all genomes encoded identical amino acid sequences for at least six of the eight Strangvac antigens.

Main limitations

Three hundred and seven (40.4%) isolates in this study were recovered from horses in the UK.

Conclusions

The predicted amino acid sequences of antigens in Strangvac were highly conserved across this collection ofS equi.
A comprehensive and comparative proteomic analysis of horse serum proteins in colitis
Authors: Minamijima Yohei , Tozaki Teruaki , Kuroda Taisuke , Urayama Shuntaro , Nomura Motoi , Yamamoto Kazuo
Published: January 2022

Background

Equine colitis is a diarrhoeal disease caused by inflammation of the large bowel and can potentially be life‐threatening due to its rapid progression. Pathogenesis is multifactorial and pathophysiology is highly complicated, therefore, reliable diagnostic biomarkers are needed in the veterinary field.

Objective

Serum is one of the most commonly used diagnostic tools in equine clinical investigation. To discover diagnostic or prognostic protein markers for colitis in horse serum, comprehensive and comparative proteomic analysis was conducted using liquid chromatography‐tandem mass spectrometry (LC‐MS/MS).

Study design

Case‐control study.

Methods

Serum samples were collected from 36 healthy Thoroughbreds and 12 Thoroughbreds with colitis. Serum from each horse suffering from colitis was collected daily until death or recovery. Collected sera were digested with trypsin. Peptides obtained from serum proteins were measured by Q‐Exactive HF Orbitrap mass spectrometer. The identification and quantification of peptides were performed using Proteome Discoverer version 2.2.

Results

On day 1 of treatment, eight proteins in the colitis group were upregulated (P < .05, more than a twofold change) compared with the healthy group. Among the eight proteins, biliverdin reductase B was significantly upregulated (P < .05) in the non‐survivor group (n = 5) compared with the survivor group (n = 7). On the last day of the treatment, haemoglobin subunit alpha, clusterin, glyceraldehyde‐3‐phosphate dehydrogenase, lipopolysaccharide‐binding protein, and biliverdin reductase B showed significant increases (P < .05) in the non‐survivor group.

Main limitations

The number of the identified proteins is limited due to the existence of abundant proteins.

Conclusions

Measuring the changes of these proteins together may enable a potential prognosis or early diagnosis of horses suffering from colitis.
Induction and generalization of nocebo effects on itch
Authors: Weng Lingling , van Laarhoven Antoinette I. M. , Peerdeman Kaya J. , Evers Andrea W. M.
Published: January 2022

Nocebo effects, that is, negative treatment outcomes due to negative expectancies, can increase itch. Moreover, indirect evidence has shown that nocebo hyperknesis can generalize to another itch modality. Knowledge on response generalization can help to prevent and decrease negative effects. The aims of this study were to investigate (1) the efficacy of inducing nocebo effects on cowhage‐evoked itch via verbal suggestions and (2) whether these effects can generalize to (2a) mechanically evoked touch and (2b) mechanically evoked itch. Forty‐four healthy participants watched a video suggesting that a nocebo solution increases cowhage‐evoked itch and that a control solution does not affect itch. Subsequently, cowhage, mechanical itch, and mechanical touch stimuli were applied. Nocebo effects were measured as the difference in both mean and peak of the outcomes itch and urge to scratch between nocebo and control trials. Main analyses revealed significant nocebo effects on mean and peak itch for all stimuli. For urge to scratch, a significant nocebo effect was only observed for mechanical touch (peak). As mechanical stimuli did not induce pure sensations as planned, posthoc sensitivity analyses were run for mechanical stimuli that individually induced either touch or itch at baseline. These analyses showed similar results for generalization to mechanical itch, but generalization to mechanical touch was non‐significant. This study showed that merely verbal suggestion can induce nocebo effects on cowhage‐evoked itch and that these effects can generalize to another itch modality. Future studies may examine how to prevent negative experiences from generalizing to subsequent encounters.
Secondary Ion Mass Spectrometry Reference Materials for Lithium in Carbonaceous Matrices
Authors: Teichert Zebadiah , Bose Maitrayee , Williams Peter , Hervig Richard L. , Williams Lynda B.
Published: January 2022

Secondary ion mass spectrometry techniques are used to study trace elements in organic samples where matrix compositions vary spatially. This study was conducted to develop calibrations for lithium content and lithium isotope measurements in kerogen. Known concentrations of Li ions (6Li and 7Li) were implanted into organic polymers, with a range of H/C and O/C ratios similar to kerogen, along with glassy carbon (SPI Glas‐22) and silicate glass (NIST SRM 612). Results show that Li content calibration factors (K*) are similar for carbonaceous samples when analysed using a 5 kV secondary ion accelerating voltage. Using a 9 kV secondary ion accelerating voltage, K* factors are negatively correlated with the sample O content, changing ~ 30% between 0 and 15 oxygen atomic %. Thus, to avoid the matrix effect related to O content, using a 5 kV secondary ion accelerating voltage is best for quantification of Li contents based on 7Li+/12C+ ratios. Under these analytical conditions, Li ppm (atomic) = (132 (± 8) × 7Li+/12C+) × 12C atom fraction of the sample measured. Lithium isotope ratio measurements of SPI Glas‐22 and NIST SRM 612 are within uncertainty; however, the organic polymer samples as a group show a 10‰ higher δ7Li than NIST SRM 612.
Antioxidant activity assessment of Yingjisha sweet almond oil
Authors: Zhao Wei , Wang Liwen , Yang Fan , Zhang Ning , Fan Jiahuan , Qin Shini , Shao Tong , Xu Xianao , Yan Shiyin , Guo Hongxing , Li Jianying , Zhao Hui
Published: January 2022

Sweet almond is one of the main cash crops in Yingjisha, Xinjiang Autonomous Region, China. The composition of sweet almond oil (SAO) was analysed by gas chromatography‐mass spectrometry (GC‐MS). SAO’s antioxidant activities were investigated by measuring its scavenging ability with 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH), 2,2′‐Azino‐bis (3‐ethylbenzothiazoline‐6‐sulfonic acid) (ABTS), hydroxyl radical scavenging assay and 6‐hydroxy‐2,5,7,8‐tetramethylchroman‐2‐carboxylic acid (Trolox) equivalent antioxidant capacity (TEAC) assay. Furthermore, in vivo antioxidant capacity was assessed using Saccharomyces cerevisiae model stimulated by hydrogen peroxide (H2O2) and carbon tetrachloride (CCl4). The results showed that SAO was mainly composed of methyl oleate (21.28%), methyl stearate (18.55%) and methyl palmitate (14.1%). In vitro antioxidant test results showed that compared with the scavenging three free radicals capacity of 1 mmol L−1 Trolox, the SAO needed to reach 5 mg mL−1, 20 mg mL−1 and less than 20 mg mL−1, respectively. In vivo experiments showed that SAO rescued the survival and inhibited intracellular oxidation and lipid peroxidation of Saccharomyces cerevisiae exposed to H2O2 and CCl4. Additionally, our results showed that the catalase encoded by the Gsh1 gene may be involved in the mechanism of action of SAO against intracellular oxidation. These findings suggest that SAO possesses antioxidant capacities, and it is recommended to develop dietary antioxidants based on SAO.
Effect of the structure and potential allergenicity of glycated tropomyosin, the shrimp allergen
Authors: Lv Liangtao , Ahmed Ishfaq , Qu Xin , Ju Guangxiu , Yang Ni , Guo Yuman , Li Zhenxing
Published: January 2022

The aim is to elucidate whether the structural changes of shrimp tropomyosin (TM) following ribose treatment affected its potential allergenicity. The structural changes of glycated TM were analysed by fluorescence, ultraviolet spectrum (UV), circular dichroism (CD) and liquid chromatography‐tandem mass spectrometry (LC‐MS/MS), and the changes in allergenicity were investigated by enzyme‐linked immunosorbent assay (ELISA) and RBL‐2H3 cell model. The result indicated that ribose could cause the conformational structural changes of TM. Moreover, the phenylalanine, isoleucine and DL‐methionine residues were altered by ribose by LC‐MS/MS analysis. These modified amino acids also appeared in the shrimp allergic epitopes region. Furthermore, the glycated TM (4000 mmol L−1 ribose) could significantly decrease the IgE‐binding capacity and inhibit the release of cytokines and mediators from RBL‐2H3 cells. These findings suggest that ribose‐induced glycation could damage the allergic epitope of TM, decreasing the potential allergenicity and could be considered for alleviating TM‐induced food allergy.
What is in a name? Effects of game‐framing on perceptions of hiring organizations
Authors: McChesney Jenna , Campbell Chelsi , Wang Jet , Foster Lori
Published: January 2022

This Open Science Framework preregistered experiment examines the effects of game‐framing, the labeling of a selection test as a game without changing its content, on prospective applicants’ attitudes toward a fictitious hiring organization. Participants (N = 277) were asked to view a screenshot of a hypothetical organization's hiring assessment, which was labeled as either an online test or game. Aligned with signaling theory, game‐framing resulted in higher ratings of organizational innovation and increased organizational attraction. Surprisingly, openness to experience and propensity to innovate did not moderate this relationship. Implications of these findings for organizations using gamified and game‐based assessments are discussed along with directions for future research.
Hepatocellular carcinoma (HCC) is changing its face: analysis of the temporal trends in aetiology and clinical patterns of HCC in South Australia
Authors: Chandran Vidhyaleha , Rajandran Arvinf , Loo Kee Fong , Bate John , Wigg Alan , Chinnaratha Mohamed A.
Published: January 2022

Background

The epidemiology of chronic liver disease is changing with the introduction of potent antiviral therapies for chronic hepatitis C virus (HCV) and the increasing prevalence of non‐alcoholic steatohepatitis (NASH).

Aim

To establish the impact of this change on the rates and clinical patterns of hepatocellular carcinoma (HCC) in South Australia (SA).

Methods

Newly diagnosed HCC patients from January 2014 until December 2019 from four tertiary centres in SA were included. The overall age‐standardised incidence rates (ASIR) of HCC were calculated using 2016 SA population as the standard. To assess the trends, Join‐Point regression models were used to calculate the average annual percentage change (AAPC). Forecasting of overall and aetiology‐specific HCC from 2020 to 2024 was performed using linear regression.

Results

There were 626 new cases of HCC in SA (males 80%; median age 64 years) during the study period. There was a significant increase in NASH‐related HCC (AAPC: +7.0%; P < 0.05) from 2014 to 2019. However, there were no significant differences in the ASIR for overall HCC (AAPC: −4.1%), HCV‐related HCC (AAPC: −8.0%) and stage of HCC diagnosis (AAPC: +3.0%; P > 0.05). Forecasting analysis projected the decline and increase in the incidence of HCV and NASH‐related HCC, respectively, over the next few years.

Conclusion

Overall ASIR of HCC has plateaued in SA. However, NASH‐related HCC has increased significantly and is expected to continue to increase in the near future. Further research and intervention is required to reduce NASH‐related HCC, a major contributor to the current and future burden of HCC.
Preventive and therapeutic aspects of fermented foods
Authors: Baruah Rwivoo , Ray Mousumi , Halami Prakash M.
Published: January 2022

In recent times, the status of some fermented foods which are considered as functional foods that confer health benefits in certain disease conditions has grown rapidly. The health benefits of fermented foods are due to the presence of probiotic microbes and the bioactive compounds formed during fermentation. Microbes involved and metabolites produced by them are highly species specific and contribute to the authenticity of the fermented foods. Several studies pertaining to the effect of fermented foods on various disease conditions have been conducted in recent years using both animal models and clinical trials on humans. This review focuses on the impact of fermented foods on conditions such as diabetes, cardiovascular disease, obesity, gastrointestinal disorder, cancer and neurodegenerative disorders.
Piscine mycobacteriosis in the ornamental fish trade in Trinidad and Tobago
Authors: Phillips Savage Ayanna Carla N. , Blake Lemar , Suepaul Rod , McHugh O’Shane , Rodgers Ray , Thomas Calvern , Oura Christopher , Soto Esteban
Published: January 2022

The freshwater ornamental fish trade represents a major contributor to the livelihoods of many producers in Trinidad and Tobago, with stocks destined for local, regional and international markets. A review of clinical cases presented to the Aquatic Animal Health Unit at the University of the West Indies, School of Veterinary Medicine for the period September 2010 to December 2012 suggested that piscine mycobacteriosis may be widespread throughout the local ornamental fish industry. Thus, to determine the prevalence of mycobacteriosis in ornamental fish sold in pet stores, a total of 122 specimens were sourced from 24 retail suppliers across Trinidad. Fish were killed and internal organs were examined for lesions suggestive of granulomas. All wet‐mount slides were acid‐fast stained, regardless of the presence or absence of observed granuloma‐like lesions. Histological analysis was performed on one randomly selected whole specimen from each facility. Mycobacterium sp. was identified using real‐time PCR detecting the 16S rRNA gene in tissue samples. Associations between parasitism, facility biosecurity and presence of positive animals were determined. The prevalence of Mycobacterium sp. infection was 61 ± 7% (74/122), with positive specimens being acquired from 54.2% (13/24) of facilities examined. Further, 100% of facilities did not employ optimum biosecurity measures.
Hymen and virginity: What every paediatrician should know
Authors: Moussaoui Dehlia , Abdulcadir Jasmine , Yaron Michal
Published: January 2022

Paediatricians may face the notion of ‘virginity’ in various situations while caring for children and adolescents, but are often poorly prepared to address this sensitive topic. Virginity is a social construct. Despite medical evidence that there is no scientifically reliable way to determine virginity, misconceptions about the hymen and its supposed association with sexual history persist and lead to unethical practices like virginity testing, certificate of virginity or hymenoplasty, which can be detrimental to the health and well‐being of females of all ages. The paediatrician has a crucial role in providing evidence‐based information and promoting positive sexual education to children, adolescents and parents. Improving knowledge can help counter misconceptions and reduce harms to girls and women.
Corporate governance, firm dynamics, and wage inequality
Authors: Chao Chi‐Chur , Wang Leonard F. S.
Published: January 2022

This paper investigates the distributive and welfare effects of corporate governance with firm competition. In the short run, where the number of manufacturing firms is given, a better corporate governance can raise both of the skilled and unskilled wage rates, but the skilled‐unskilled wage gap will be widened in the economy. Nonetheless, in the long run, a better corporate governance causes manufacturing firms to exit, which in turn reallocates some capital to the agricultural sector. This benefits unskilled workers and raises their wages, while reducing the skilled wage rate via the firm‐exit effect. The exit of manufacturing firms mitigates the issue of excessive entry of firms, which can improve social efficiency in the long run. As a result, the optimal level of corporate governance is higher in the long run.
Limitation by vapour pressure deficit shapes different intra‐annual growth patterns of diffuse‐ and ring‐porous temperate broadleaves
Authors: Tumajer Jan , Scharnweber Tobias , Smiljanic Marko , Wilmking Martin
Published: January 2022

Understanding the effects of temperature and moisture on radial growth is vital for assessing the impacts of climate change on carbon and water cycles. However, studies observing growth at sub‐daily temporal scales remain scarce.

We analysed sub‐daily growth dynamics and its climatic drivers recorded by point dendrometers for 35 trees of three temperate broadleaved species during the years 2015–2020. We isolated irreversible growth driven by cambial activity from the dendrometer records. Next, we compared the intra‐annual growth patterns among species and delimited their climatic optima.

The growth of all species peaked at air temperatures between 12 and 16°C and vapour pressure deficit (VPD) below 0.1 kPa.Acer pseudoplatanusandFagus sylvatica, both diffuse‐porous, sustained growth under suboptimal VPD. Ring‐porousQuercus roburexperienced a steep decline of growth rates with reduced air humidity. This resulted in multiple irregular growth peaks ofQ. roburduring the year. By contrast, the growth patterns of the diffuse‐porous species were always right‐skewed unimodal with a peak in June between day of the year 150–170.

Intra‐annual growth patterns are shaped more by VPD than temperature. The different sensitivity of radial growth to VPD is responsible for unimodal growth patterns in both diffuse‐porous species and multimodal growth pattern inQ. robur.
Targeted protein degradation: from small molecules to complex organelles—a Keystone Symposia report
Authors: Cable Jennifer , Weber‐Ban Eilika , Clausen Tim , Walters Kylie J. , Sharon Michal , Finley Daniel J. , Gu Yangnan , Hanna John , Feng Yue , Martens Sascha , Simonsen Anne , Hansen Malene , Zhang Hong , Goodwin Jonathan M. , Reggio Alessio , Chang Chunmei , Ge Liang , Schulman Brenda A. , Deshaies Raymond J. , Dikic Ivan , Harper J. Wade , Wertz Ingrid E. , Thomä Nicolas H. , Słabicki Mikołaj , Frydman Judith , Jakob Ursula , David Della C. , Bennett Eric J. , Bertozzi Carolyn R. , Sardana Richa , Eapen Vinay V. , Carra Serena
Published: January 2022

Targeted protein degradation is critical for proper cellular function and development. Protein degradation pathways, such as the ubiquitin proteasomes system, autophagy, and endosome–lysosome pathway, must be tightly regulated to ensure proper elimination of misfolded and aggregated proteins and regulate changing protein levels during cellular differentiation, while ensuring that normal proteins remain unscathed. Protein degradation pathways have also garnered interest as a means to selectively eliminate target proteins that may be difficult to inhibit via other mechanisms. On June 7 and 8, 2021, several experts in protein degradation pathways met virtually for the Keystone eSymposium “Targeting protein degradation: from small molecules to complex organelles.” The event brought together researchers working in different protein degradation pathways in an effort to begin to develop a holistic, integrated vision of protein degradation that incorporates all the major pathways to understand how changes in them can lead to disease pathology and, alternatively, how they can be leveraged for novel therapeutics.
ACE2 and TMPRSS2 immunolocalization and oral manifestations of COVID‐19
Authors: Park Gi Cheol , Bang Soo‐Young , Lee Hyoun Wook , Choi Kyung Un , Kim Ji Min , Shin Sung‐Chan , Cheon Yong‐il , Sung Eui‐Suk , Lee Minhyung , Lee Jin‐Choon , Kim Hyung‐Sik , Lee Byung‐Joo
Published: January 2022

Objectives

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) entry into the host cells depends on the expression of angiotensin‐converting enzyme 2 (ACE2) and transmembrane protease serine 2 (TMPRSS2). We investigated the distribution of ACE2‐ and TMPRSS2‐expressing cells in various oral tissues to identify the underlying mechanism of oral manifestations in patients with coronavirus disease 2019.

Subjects

We analyzed the expression patterns of ACE2 and TMPRSS2 in the oral mucosa (tongue, palate, and buccal mucosa), trigeminal ganglion, vessels, and salivary glands of 9 Sprague‐Dawley rats using immunohistochemistry and immunofluorescence.

Results

ACE2 and TMPRSS2 were strongly expressed in the intermediate layer of the squamous epithelia of tongue papillae and buccal mucosa. ACE2‐ and TMPRSS2‐positive cells were observed in the taste buds of the tongue. Additionally, ACE2 and TMPRSS2 were co‐expressed in the ductal epithelium and acinar cells of salivary glands. Furthermore, both ACE2 and TMPRSS2 were stained in the neuronal cell body of trigeminal ganglia, but not in Schwann cells. Moreover, ACE2 and TMPRSS2 were expressed in capillaries, but not in venules/arterioles.

Conclusions

SARS‐CoV‐2 can spread the suprabasal area of squamous epithelia of the oral mucosa, invades taste bud, trigeminal nerve, parotid gland, and microvessel, resulting in oral manifestations.
Autoimmune disorders in oral lichen planus: A systematic review and meta‐analysis
Authors: De Porras‐Carrique Teresa , Ramos‐García Pablo , Aguilar‐Diosdado Manuel , Warnakulasuriya Saman , González‐Moles Miguel Ángel
Published: January 2022

Objectives

The association of OLP with other autoimmune processes points to the possibility that OLP‐affected patients are actually developing an autoimmune status that predisposes them to autoaggression against different targets. This systematic review and meta‐analysis aim to evaluate the current evidence on the prevalence of autoimmune disorders in patients with OLP and their magnitude of association.

Methods

We searched PubMed, Embase, Web of Science, Scopus databases for the studies published before May 2021, with no limitation in regards to their publication date or language. We evaluated the quality of studies, carried out meta‐analyses and performed heterogeneity, subgroups, meta‐regression, and small‐study effects analyses.

Results

Inclusion criteria were met by 153 studies (23,327 patients). Our results indicate the existence of high prevalence and a frequent association between OLP and some autoimmune disorders, especially in regards to thyroid disease (PP = 7.96%, 95% CI = 6.32–9.75; OR = 1.99, 95% CI = 1.60–2.49, p < 0.001) and diabetes mellitus (PP = 9.41%,95% CI = 8.16–10.74; OR = 1.64, 95% CI = 1.34–2.00, p < 0.001).

Conclusions

Our study demonstrates the existence of a comorbidity between autoimmune thyroid diseases as well as between diabetes mellitus and OLP respectively. Quality of evidence should be upgraded on other autoimmune diseases (fibromyalgia, gastrointestinal disorders, rheumatic diseases, Sjogren's syndrome, lupus erythematosus, and dermatological diseases) for which the current data do not allow us to know whether they are really associated with OLP.
Comparing oyster population structure and disease prevalence between a disease‐resistant and transplanted wild population in Barnegat Bay, NJ (U.S.A.)
Authors: Thompson Christine M. , Evert Steve , Baez Jessica A.
Published: January 2022

Restoration efforts for the Eastern oyster, Crassostrea virginica, in Barnegat Bay are limited by natural habitat, shell resources, and recruitment. A pilot study was performed to compare two oyster restoration approaches direct‐planted at a subtidal site. The first approach used a disease‐resistant oyster strain remote set on whelk shell and the second approach used dredged oysters from a nearby wild population. Population size structure, mortality, and disease prevalence were monitored for both types for 3 years. Disease prevalence was significantly higher in the transplanted oysters resulting in reduced size and survivorship. This study highlights challenges restoring oysters with substrate limitations and proposes suggestions for future work in this location and similar areas.
Futuristic restoration as a policy tool for environmental justice objectives
Authors: Pape Timothy
Published: January 2022

The United Nations Decade on Ecosystem Restoration promises to educate society on the many ways ecological restoration projects can benefit humankind. One avenue of possibilities for restoration ecology lies with concerns of environmental justice. The concept of futuristic restoration, which posits a paradigm of ecological restoration that is future‐oriented, aligns well with calls for policymakers to address the circumstances, processes, and systems within which environmental inequalities are typically produced. This article offers three policy arenas where futuristic restoration can be employed in order to further environmental justice goals: (1) Land conservation prioritization; (2) Urban development plans; and (3) Mine remediation projects. The temporal dimension of sustainability and how it pertains to restoration projects will also be addressed.
Spectral analysis of Markov switching GARCH models with statistical inference
Authors: Cavicchioli Maddalena
Published: January 2022

We derive matrix expressions in closed form for the autocovariance function and the spectral density of Markov switching GARCH models and their powers. For this, we apply the Riesz–Fischer theorem which defines the spectral representation as the Fourier transform of the autocovariance function. Under suitable assumptions, we prove that the sample estimator of the spectral density is consistent and asymptotically normally distributed. Further statistical implications in terms of order identification and parameter estimation are discussed. A simulation study confirms the validity of the asymptotic properties. These methods are also well suited for financial market applications, and in particular for the analysis of time series in the frequency domain, as shown in some proposed real‐world examples.