bluuebunny/crossref_metadata_2025 huggingface dataset:
Mental health outcomes following COVID-19 infection: Evidence from 11 UK longitudinal population studies
Authors: Thompson Ellen J. , Stafford Jean , Moltrecht Bettina , Huggins Charlotte F. , Kwong Alex S. F. , Shaw Richard J. , Zaninotto Paola , Patel Kishan , Silverwood Richard J. , McElroy Eoin , Pierce Matthias , Green Michael J. , Bowyer Ruth C. E. , Maddock Jane , Tilling Kate , Katikireddi S. Vittal , Ploubidis George B. , Porteous David J. , Timpson Nic , Chaturvedi Nish , Steves Claire J. , Patalay Praveetha
Published: May 2022

Background

Evidence on associations between COVID-19 illness and mental health is mixed. We examined longitudinal associations between COVID-19 and mental health while considering: 1) pre-pandemic mental health, 2) time since infection; 3) subgroup differences; and 4) confirmation of infection via self-reported test, and serology data.

Methods

Using data from 11 UK longitudinal studies, involving 54,442 participants, with 2 to 8 repeated measures of mental health and COVID-19 between April 2020 and April 2021, we standardised continuous mental health scales within each study across time. We investigated associations between COVID-19 (self-report, test-confirmed, serology-confirmed) and mental health using multilevel generalised estimating equations. We examined whether associations varied by age, sex, ethnicity, education and pre-pandemic mental health. Effect-sizes were pooled in random-effects meta-analyses.

Outcomes

Pooled estimates of the standardized difference in outcome between those with and without self-reported COVID-19 suggested associations with subsequent psychological distress (0.10 [95%CI: 0.06; 0.13], I2=42.8%), depression (0.08 [0.05; 0.10], I2=20.8%), anxiety (0.08 [0.05; 0.10], I2=0%), and lower life satisfaction (−0.06 [-0.08; -0.04], I2=29.2%). Associations did not vary by time since infection until 3+ months and were present in all age groups, with some evidence of stronger effects in those aged 50+. Self-reported COVID-19, whether suspected or test-confirmed and irrespective of serology status, was associated with poorer mental health.

Interpretation

Self-reporting COVID-19 was longitudinally associated with deterioration in mental health and life satisfaction. Our findings have important implications for mental health service provision, given the substantial prevalence of COVID-19 in the UK and worldwide.

Funding

MRC and NIHR
A Universal Day Zero Infectious Disease Testing Strategy Leveraging CRISPR-based Sample Depletion and Metagenomic Sequencing
Authors: Chan Agnes P. , Siddique Azeem , Desplat Yvain , Choi Yongwook , Ranganathan Sridhar , Choudhary Kumari Sonal , Diaz Josh , Bezney Jon , DeAscanis Dante , George Zenas , Wong Shukmei , Selleck William , Bowers Jolene , Zismann Victoria , Reining Lauren , Highlander Sarah , Hakak Yaron , Brown Keith , Armstrong Jon R. , Schork Nicholas J.
Published: May 2022

The lack of preparedness for detecting the highly infectious SARS-CoV-2 pathogen, the pathogen responsible for the COVID-19 disease, has caused enormous harm to public health and the economy. It took ∼60 days for the first reverse transcription quantitative polymerase chain reaction (RT-qPCR) tests for SARS-CoV-2 infection developed by the United States Centers for Disease Control (CDC) to be made publicly available. It then took >270 days to deploy 800,000 of these tests at a time when the estimated actual testing needs required over 6 million tests per day. Testing was therefore limited to individuals with symptoms or in close contact with confirmed positive cases. Testing strategies deployed on a population scale at ‘Day Zero’ i.e., at the time of the first reported case, would be of significant value. Next Generation Sequencing (NGS) has such Day Zero capabilities with the potential for broad and large-scale testing. However, it has limited detection sensitivity for low copy numbers of pathogens which may be present. Here we demonstrate that by using CRISPR-Cas9 to remove abundant sequences that do not contribute to pathogen detection, NGS detection sensitivity of COVID-19 is comparable to RT-qPCR. In addition, we show that this assay can be used for variant strain typing, co-infection detection, and individual human host response assessment, all in a single workflow using existing open-source analysis pipelines. This NGS workflow is pathogen agnostic, and therefore has the potential to transform how both large-scale pandemic response and focused clinical infectious disease testing are pursued in the future.

SIGNIFICANCE STATEMENT

The lack of preparedness for detecting infectious pathogens has had a devastating effect on the global economy and society. Thus, a ‘Day Zero’ testing strategy, that can be deployed at the first reported case and expanded to population scale, is required. Next generation sequencing enables Day Zero capabilities but is inadequate for detecting low levels of pathogen due to abundant sequences of little biological interest. By applying the CRISPR-Cas system to remove these sequences in vitro, we show sensitivity of pathogen detection equivalent to RT-qPCR. The workflow is pathogen agnostic, and enables detection of strain types, co-infections and human host response with a single workflow and open-source analysis tools. These results highlight the potential to transform future large-scale pandemic response.
Phenomic Network Analysis for Depression Reveals Comorbidity Architecture, Genomic Relationships, and Pleiotropic Variants
Authors: Yang Zhiyu , Jain Pritesh , Drineas Petros , Paschou Peristera
Published: May 2022

Depression is one of the most prevalent psychiatric disorders and is one of the leading causes of health ailment worldwide. It is known to be highly heritable and is frequently comorbid with other mental and physical traits. This observation motivated us to look deeper into the genetic and phenotypic connections between depression and other traits in order to identify correlations as well as potentially causal connections between them. In this study, we analyzed data from the UK biobank to systematically evaluate relationships between depression and other heritable traits both from a phenotypic and a genetic aspect. We compressed a total of 6,300 ICD codes into 412 heritable phecodes and we constructed a comorbidity network connecting depression and other disorders on over 300,000 participants of European ancestry. Additionally, we investigated the genetic correlation for each (phenotypic) connection in the resulting network. We also looked into potentially causal relationships using mendelian randomization for all pairs of significantly correlated disorders and uncovered horizontal pleiotropic genetic variants and genes contributing to disease etiologies. We found gastro-oesophageal reflux disease (GORD), body mass index, and osteoarthritis to be direct causes for depression, with GORD lying at the center of the causal network. Genes broadly expressed in various tissues, such as NEGR1, TCF4, and BTN2A1 underlie the pathways that lead not only to depression but also to other related disorders. Our work highlights the broad connections between depression and diverse traits, indicating a complex etiology and possible existence of subtypes for depression. Our findings highlight the value of cross-trait analysis in order to better understand the neurobiology of complex psychiatric disease.
The effects on clinical trial activity of direct funding and taxation policy interventions made by government: a systematic review
Authors: Crosby Sam , Rajadurai Esther , Jan Stephen , Neal Bruce , Holden Richard
Published: May 2022

Context

Governments have attempted to increase clinical trial activity in their jurisdictions using a range of methods including targeted direct funding and industry tax rebates. The effectiveness of the different approaches employed is unclear.

Objective

To systematically review the effects of direct government financing interventions and allowing companies to reduce their tax payable on clinical trial activity.

Data sources

Pub Med, Scopus, Sage, ProQuest, Google Scholar and Google were searched to the 11thof April 2022. In addition, the reference lists of all potentially eligible documents were hand searched to identify additional reports. Following feedback from co-authors, information on a small number of additional interventions were specifically sought out and included.

Data extraction

Summary information about potentially eligible reports were reviewed independently by two researchers, followed by extraction of data into a structured spreadsheet for eligible studies. The primary outcomes of interest were the number of clinical trials and the expenditure on clinical trials but data about other evaluations were also collected.

Results

There were 1694 potentially eligible reports that were reviewed. Full text assessments were done for 304, and 30 reports that provided data on 43 interventions were included – 29 that deployed targeted direct funding and 14 that provided tax rebates or exemptions. There were data describing effects on a primary outcome for 25/41 of the interventions. The most common types of interventions were direct funding to researchers via special granting mechanisms and tax offsets to companies and research organisations. All 25 of the studies for which data were available reported a positive impact on numbers and/or expenditure on clinical trials though the robustness of evaluations was limited for many. Estimates of the magnitude of effects of interventions were reported inconsistently, varied substantially, and could not be synthesised quantitatively, though targeted direct funding interventions appeared to be associated with more immediate impact on clinical trial activity.

Conclusion

There is a high likelihood that governments can increase clinical trial activity with either direct or indirect fiscal mechanisms. Direct funding may provide a more immediate and tangible return on investment than tax rebates.
The impact of communicative and critical health literacy on trust in physicians among patients with systemic lupus erythematosus: the TRUMP2-SLE project
Authors: Oguro Nao , Yajima Nobuyuki , Miyawaki Yoshia , Yoshimi Ryusuke , Shimojima Yasuhiro , Sada Ken-ei , Hayashi Keigo , Shidahara Kenta , Sakurai Natsuki , Hidekawa Chiharu , Kishida Dai , Ichikawa Takanori , Ishikawa Yuichi , Kurita Noriaki
Published: May 2022

Objectives

Accessing the Internet has increased the gap in patient health literacy (HL), impacting patient-doctor trust. We examined how trust in physicians is affected by functional HL (the ability to read and write) and by broader concepts of HL, including communicative HL (the ability to extract information from communication to use) and critical HL (the ability to analyze and use information) among patients with systemic lupus erythematosus (SLE).

Methods

This cross-sectional study enrolled 362 SLE patients at five academic centers between June 2020 and August 2021. The 14-item Functional Communicative Critical Health Literacy Scale assessed the three dimensions of HL (range: 1-4 points). Outcomes were trust in one’s physician and physicians generally using the 5-item Wake Forest Physician Trust Scale (range: 0-100 points). General linear models adjusted for age, sex, education, income, disease activity, disease duration, depression, and time using the Internet.

Results

Trust in one’s physician increased with higher functional and communicative HL (per 1-pt increase, 3.21 [95%CI 0.61, 5.81], 5.8 [95%CI 1.96, 9.63]). Trust in physicians in general increased with higher communicative HL and decreased with higher critical HL (per 1-pt increase, 7.01 [95%CI 2.27, 11.76], -6.83 [95%CI -11.67, -1.99]). Longer Internet use was associated with both higher communicative and critical HL.

Conclusions

Our findings suggest that rheumatologists can help patients build trust by encouraging dialogue about their health issues with their doctors and family members, rather than trying to improve their ability to discern health information.

Key messages

What is already known on this topic

Factors affecting trust in one’s physician among chronic diseases including SLE are economic status, misdiagnosis experience, and the duration of the physician-patient relationship.

In the general population, higher trust in physicians generally was associated with functional HL as patients’ external factors.

What this study adds

This is the first study to reveal an association between trust in one’s own physician and HL among patients with SLE. In addition, we were able to expand the correlates of HL by measuring broader concepts of HL dimensions, such as communicative and critical HL.

How this study may affect research, practice, or policy

This study suggests the importance of rheumatologists’ encouragement of patients to communicate, share their concerns, and resolve their misunderstandings to develop a trusting relationship. This study recommends that communictive HL (ability to obtain useful health information) should be the focus and not critical HL (ability to discern health information).
Arbuscular mycorrhizae reduce stress-induced plasticity of plant functional traits. A meta-analysis study
Authors: Globbo Florencia , Corriale María José , Gázquez Ayelén , Bordenave César Daniel , Bilenca David , Menéndez Ana
Published: May 2022

We aimed at exploring the plant functional traits whose stress-induced plasticity is altered by the presence of AM fungi, considering the direction of their changes. We also sought for a coordinated variation of plant biomass and functional traits, during plant adaptation to environmental stressors, and the role of AM status on the variation. We performed a meta-analysis across 114 articles spanning 110 plant species or cultivars. We quantified the size effect of AM symbiosis on the stress-induced plasticity of several reported and calculated functional traits, and using linear mixed model analysis (LMM). Correlation between traits plasticity and total biomass variation were also performed through LMM. The literature search and further selection yielded seven functional traits, extracted from 114 laboratory studies, including 888 observations and 110 plant species/cultivars. Evidence for significant effects of predictor variables (type of stress, AM symbiosis and/or their interaction) on plasticity were found for three of these functional traits: leaf-area ratio (LAR), root mass fraction (RMF) and root-shoot (R:S) ratio. Our results provided evidence to accept the hypothesis that AM fungal inoculation may reduce the phenotypic plasticity of important plant functional traits leaf area ratio (LAR), root mass fraction (RMF) and root-shoot (R:S) ratio, by decreasing its magnitude. We also found a weak correlation between traits plasticity and total biomass variation. Although our literature search and data collection were intensive and our results robust, the scope of our conclusions is limited by the agronomical bias of plant species targeted by the meta-analysis. Further knowledge on non-cultivable plant species and better understanding of the mechanisms ruling resources allocation in plants would allow more generalized conclusions.
Improved diagnosis of inflammatory bowel disease and prediction and monitoring of response to anti-TNF alpha treatment based on measurement of signal transduction pathway activity
Authors: Bouwman Wilbert , Verhaegh Wim , van de Stolpe Anja
Published: May 2022

Objective

Ulcerative colitis (UC) and Crohn’s disease (CD) are two subtypes of chronic inflammatory bowel disease (IBD). Differential diagnosis remains a challenge. Anti-TNFα treatment is an important treatment for IBD, yet resistance frequently occurs and cannot be predicted. Consequently, many patients receive ineffective therapy with potentially adverse effects. Novel assays are needed to improve diagnosis, and predict and monitor response to anti-TNF-α compounds.

Design

Signal transduction pathway (STP) technology was used to quantify activity of STPs (androgen and estrogen receptor, PI3K, MAPK, TGFβ, Notch, Hedgehog, Wnt, NFκB, JAK-STAT1/2, and JAK-STAT3 pathways) in colon mucosa samples of CD and UC patients, based on transcriptome analysis. Previously described STP assay technology is based on computational inference of STP activity from mRNA levels of target genes of the STP transcription factor.

Results

Results show that NFκB, JAK-STAT3, Wnt, MAPK, and androgen receptor pathways were abnormally active in CD and UC. Colon and ileum-localized CD differed with respect to STP activity, the JAK-STAT1/2 pathway being abnormally active in ileal CD. High activity of NFκB, JAK-STAT3, and TGFβ pathways was associated with resistance to anti-TNFα treatment in UC and colon-located CD, but not in ileal CD. STP activity decreased with successful treatment.

Conclusion

We believe that measuring mucosal STP activity provides clinically relevant information to improve differential diagnosis of IBD and prediction of resistance to anti-TNFα treatment in patients with colon-localized IBD, and provides new targets for treatment and overcoming anti-TNFα resistance.
In vitro and in vivo gene introduction in the cloudy catshark (Scyliorhinus torazame), a cartilaginous fish
Authors: Fujimori Chika , Umatani Chie , Chimura Misaki , Ijiri Shigeho , Bando Hisanori , Hyodo Susumu , Kanda Shinji
Published: May 2022

Cartilaginous fishes have various unique physiological features such as cartilaginous skeletons and a urea-based osmoregulation strategy for adaptation to their marine environment. Also, because they are considered a sister group of bony vertebrates, understanding their unique features is important from an evolutionary perspective. However, experimental approaches are limited in cartilaginous fishes. Particularly, genetic engineering, which can analyze gene functions as well as cellular behavior, has not been effectively utilized in cartilaginous fishes. This is partly because their reproductive strategy involves internal fertilization, which results in difficulty in microinjection into fertilized eggs at the early developmental stage. Trials of gene transfer have also been limited both in in vitro cultured cells and in vivo. Here, to identify efficient gene transfer methods in cartilaginous fishes, we examined the effects of various methods both in vitro and in vivo using the cloudy catshark, a candidate model cartilaginous fish species. In all methods, green fluorescent protein (GFP) expression was used to evaluate exogenous gene introduction. First, we established a primary cell culture containing fibroblast-like and epithelial-like cells from cloudy catshark embryos. Using these primary cultured cells, we attempted gene transfection by lipofection, polyethylenimine (PEI), adenovirus, baculovirus and electroporation. Among the methods tested, lipofection, electroporation and baculovirus infection enabled the successful introduction of exogenous genes into primary cultured cells, allowing us to study physiological mechanisms at a single-cell level in culture conditions close to those in a living cartilaginous fish. We also attempted in vivo transfection into cloudy catshark embryos by electroporation and baculovirus infection. Although baculovirus-injected groups did not show GFP fluorescence, electroporation successfully introduced GFP into various tissues including muscle cells. Furthermore, we succeeded in GFP introduction into adult testis by electroporation. The in vitro and in vivo gene introduction methods that worked in this study may identify paths for future genetic manipulation including knockout experiments and cellular linage analysis in cartilaginous fishes.
Improved SpCas9 and LbCas12a genome editing systems in Brassica oleracea and Brassica napus
Authors: Lawrenson Tom , Chhetry Monika , Clarke Martha , Hundleby Penny , Harwood Wendy
Published: May 2022

We report highly efficient genome editing in Brassica species. We compare the efficiency of targeted mutagenesis using four Streptococcus pyogenes Cas9 (SpCas9) systems in Brassica oleracea and Brassica napus over 3 target genes and five guides to identify two which show a striking improvement to our first published system (Lawrenson et al., 2015). Targeted mutagenesis occurred in up to 100% of T0 plants with the improved systems, compared to 20% in the original system. This is the only reported comparison of SpCas9 systems we are aware of in Brassica species.

Secondly, we report the first successful use of Lachnospiraceae bacterium Cas12a (LbCas12a) in Brassica oleracea. We test three LbCas12a coding sequences and two guide architectures against one target gene using four guides. From this we identify the best performing combination of our novel, multi-intron coding sequence and a ribozyme flanked guide expression cassette. In this case 68% of T0 plants contained targeted mutations. Heritability of LbCas12a mutations is shown. We show that our two useful and novel LbCas12a coding sequences have utility in Brassica species.
Juxtaposition of Bub1 and Cdc20 on phosphorylated Mad1 during catalytic mitotic checkpoint complex assembly
Authors: Fischer Elyse S. , Yu Conny W.H. , Hevler Johannes F. , McLaughlin Stephen H. , Maslen Sarah L. , Heck Albert J.R. , Freund Stefan M.V. , Barford David
Published: May 2022

In response to improper kinetochore-microtubule attachments in mitosis, the spindle assembly checkpoint (SAC) assembles the mitotic checkpoint complex (MCC) to inhibit the anaphase- promoting complex/cyclosome, thereby delaying entry into anaphase. The MCC is a complex of Mad2, Cdc20 and BubR1:Bub3. Its assembly is catalysed by unattached kinetochores on a catalytic Mad1:Mad2 platform. Mad1-bound closed-Mad2 (C-Mad2) recruits open-Mad2 (O- Mad2) through self-dimerization. This interaction, combined with Mps1 kinase-mediated phosphorylation of Bub1 and Mad1, accelerates MCC assembly, in a process that requires conversion of O-Mad2 to C-Mad2 and concomitant binding of Cdc20. How Mad1 phosphorylation catalyses MCC assembly is poorly understood. In this study we characterized Mps1 phosphorylation of Mad1 and obtained structural insights into a phosphorylation-specific Mad1:Cdc20 interaction. This interaction, together with the Mps1-phosphorylation dependent association of Bub1 and Mad1, generates a tripartite assembly of Bub1 and Cdc20 onto the C- terminal domain of Mad1 (Mad1CTD). We additionally identified a folded state of the Mad1:Mad2 complex that suggests how the Cdc20:Mad1CTDinteraction brings the Mad2- interacting motif (MIM) of Cdc20 (Cdc20MIM) into close proximity with O-Mad2. We also show that Cdc20MIMis sufficient to catalyse Mad2 conversion and its entrapment by the Mad2 safety- belt. Thus, Mps1-dependent formation of the MCC-assembly scaffold functions to position and orient Cdc20MIMnear O-Mad2, thereby catalysing formation of C-Mad2:Cdc20.
The L1 Cell Adhesion Molecule Constrains Dendritic Spine Density through Ankyrin Binding in Pyramidal Neurons of the Mouse Cerebral Cortex
Authors: Murphy Kelsey E. , Wade Sarah D. , Sperringer Justin E. , Mohan Vishwa , Duncan Bryce W. , Pak Yubin , Lutz David , Schachner Melitta , Maness Patricia F.
Published: May 2022

A novel function for L1 cell adhesion molecule and its interaction with Ankyrin, an actin-spectrin adaptor protein, was identified in constraining dendritic spine density on pyramidal neurons in the mouse neocortex. In an L1-null mouse mutant increased spine density was observed on apical but not basal dendrites of pyramidal neurons in diverse cortical areas (prefrontal cortex layer 2/3, motor cortex layer 5, visual cortex layer 4).The Ankyrin binding motif (FIGQY) in L1’s cytoplasmic domain was critical for spine formation, as demonstrated by increased spine density in the prefrontal cortex of a mouse mutant (L1YH) harboring a tyrosine to histidine mutation in this motif, which disrupts L1-Ankyrin association. This mutation is a known variant in the human L1 syndrome. In both mutants mature mushroom spines rather than immature spines were predominant. L1 was detected in spines and dendrites of wild-type prefrontal cortical neurons by immmunostaining. L1 coimmunoprecipitated with Ankyrin B (220 kDa) from cortical lysates of wild-type but not L1YH mice. Spine pruning assays in cortical neuron cultures from wild-type and L1YH mutant mice showed that the L1-Ankyrin interaction mediated spine retraction in response to the class 3 Semaphorins, Sema3F and to a lesser extent Sema3B. These ligands also induce spine pruning through other L1 family adhesion molecules, NrCAM and Close Homolog of L1 (CHL1), respectively. This study provides insight into the molecular mechanism of spine regulation and underscore the potential for this adhesion molecule to regulate cognitive and other L1-related functions that are abnormal in the L1 syndrome.
MFGE8 links absorption of dietary fatty acids with catabolism of enterocyte lipid stores through HNF4γ-dependent transcription of CES enzymes
Authors: Datta Ritwik , Gholampour Mohammad A , Yang Christopher D , Volk Regan , Lin Sinan , Podolsky Michael J , Arnold Thomas , Rieder Florian , Zaro Balyn W. , Verzi Michael , Lehner Richard , Abumrad Nada , Lizama Carlos O , Atabai Kamran
Published: May 2022

Enterocytes modulate the extent of postprandial lipemia, a potent risk factor for developing atherosclerotic disease, by storing dietary fats in cytoplasmic lipid droplets (cLDs). We have previously demonstrated that the integrin ligand MFGE8 links absorption of dietary fats with activation of triglyceride (TG) hydrolases that catabolize cLDs for chylomicron production. The hydrolase(s) responsible for mobilization of TG from diet-derived cLDs is unknown though recent evidence indicates that this process is independent of the canonical pathway of TG hydrolysis mediated by ATGL. Here we identify CES1D as the key hydrolase downstream of the MFGE8-αvβ5 integrin pathway that regulates catabolism of diet-drive cLDs. Mfge8 KO enterocytes have reduced CES1D transcript and protein levels and reduced protein levels of the transcription factor HNF4γ. Mice KO for Ces1d or Hnf4γ have decreased enterocyte TG hydrolase activity coupled with retention of TG in cLDs. Mechanistically, MFGE8-dependent fatty acid uptake through CD36 leads to stabilization of HNF4γ protein levels; HNF4γ then increases Ces1d transcription. Our work identifies a regulatory network by which MFGE8 and αvβ5 regulate the severity of postprandial lipemia by linking dietary fat absorption with protein stabilization of a transcription factor that increases expression of enterocyte TG hydrolases that catabolize diet-derived cLDs.
Integration of multi-omics data shows downregulation of mismatch repair, purin, and tublin pathways in AR-negative triple-negative chemotherapy-resistant breast tumors
Authors: Tang Xiaojia , Thompson Kevin J. , Kalari Krishna R. , Sinnwell Jason P. , Suman Vera J. , Vedell Peter T. , McLaughlin Sarah A. , Northfelt Donald W. , Aspitia Alvaro Moreno , Gray Richard J. , Carter Jodi , Weinshilboum Richard , Wang Liewei , Boughey Judy C. , Goetz Matthew P.
Published: May 2022

Triple negative breast cancer (TNBC) patients who fail to achieve a pathological complete response to neoadjuvant chemotherapy (NAC) will likely experience recurrence of the disease within 3-4 years. Prognostic assessment of early recurrence could facilitate clinical decisions and impact disease survival. This study investigated pre- and post-NAC multi-omics data from both an in-house and a public clinical study to identify biomarkers of NAC response. We observed significant transcriptional differences associated with response in the residual disease (post-NAC biopsies), which did not exist in the pre-NAC biopsies. We further refined the post-NAC transcriptional changes to a 17-gene signature and machine learning models were applied to evaluate the signature’s diagnostic potential (area under the curve ≥ 0.8). Interestingly, the signature was enriched with down-regulated immune genes and several of these genes demonstrated prognostic potential in basal TNBC tumors. Our 17-gene signature provides additional insight into TNBC recurrence, which warrants further investigation.
A high-throughput test of anxiety for zebrafish (Danio rerio) larvae: the larval diving response (LDR)
Authors: Fontana Barbara D. , Parker Matthew O.
Published: May 2022

Background

Zebrafish are used in anxiety research as the species’ naturalistic diving response to a new environment is a reliable and validated marker for anxiety-like behavior. One of the benefits of using zebrafish is the potential for high throughput drug screens in fish at the larval stage. However, at present, tests of anxiety in larvae and adults often measure different endpoints.

New Method

Here, for the first time, we have adapted the novel tank diving response test for examining diving behavior in zebrafish larvae to assess anxiety-like behaviors at very early-stages (7 days-post-fertilization [dpf]).

Comparison with Existing Methods

Current methods to examine anxiety in larvae can show low reliability, and measure different endpoints as in adults, thus calling into question their translational relevance.

Results

We found that 7dpf zebrafish spent more time at the bottom of a small novel tank. We validated this as anxiety-like behaviors with diazepam reducing, and caffeine increasing the time spent in the bottom of the novel environment.

Conclusions

This new automated and high-throughput screening tool has the potential use for screening of anxiogenic and anxiolytic compounds, and for studies aiming to understand the mechanisms underlying affective disorders.
xia2.multiplex: a multi-crystal data-analysis pipeline
Authors: Gildea Richard J. , Beilsten-Edmands James , Axford Danny , Horrell Sam , Aller Pierre , Sandy James , Sanchez-Weatherby Juan , Owen C. David , Lukacik Petra , Strain-Damerell Claire , Owen Robin L. , Walsh Martin A. , Winter Graeme
Published: May 2022

In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals; for example, small-wedge data collections from micro-crystals, in situ room-temperature data collections and data collection from membrane proteins in lipidic mesophases. Whilst the indexing and integration of individual data sets may be relatively straightforward with existing software, merging multiple data sets from small wedges presents new challenges. The identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. Furthermore, the presence of non-isomorphous or poor-quality data sets may reduce the overall quality of the final merged data set. To facilitate and help to optimize the scaling and merging of multiple data sets, a new program, xia2.multiplex, has been developed which takes data sets individually integrated with DIALS and performs symmetry analysis, scaling and merging of multi-crystal data sets. xia2.multiplex also performs analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferential orientation. After the description of a number of use cases, the benefit of xia2.multiplex is demonstrated within a wider autoprocessing framework in facilitating a multi-crystal experiment collected as part of in situ room-temperature fragment-screening experiments on the SARS-CoV-2 main protease.
Contact-consistent visual object pose estimation for contact-rich robotic manipulation tasks
Authors: Tian Zhonglai , Cheng Hongtai , Du Zhenjun , Jiang Zongbei , Wang Yeping
Published: May 2022

Purpose

The purpose of this paper is to estimate the contact-consistent object poses during contact-rich manipulation tasks based only on visual sensors.

Design/methodology/approach

The method follows a four-step procedure. Initially, the raw object poses are retrieved using the available object pose estimation method and filtered using Kalman filter with nominal model; second, a group of particles are randomly generated for each pose and evaluated the corresponding object contact state using the contact simulation software. A probability guided particle averaging method is proposed to balance the accuracy and safety issues; third, the independently estimated contact states are fused in a hidden Markov model to remove the abnormal contact state observations; finally, the object poses are refined by averaging the contact state consistent particles.

Findings

The experiments are performed to evaluate the effectiveness of the proposed methods. The results show that the method can achieve smooth and accurate pose estimation results and the estimated contact states are consistent with ground truth.

Originality/value

This paper proposes a method to obtain contact-consistent poses and contact states of objects using only visual sensors. The method tries to recover the true contact state from inaccurate visual information by fusing contact simulations results and contact consistency assumptions. The method can be used to extract pose and contact information from object manipulation tasks by just observing the demonstration, which can provide a new way for the robot to learn complex manipulation tasks.
Corporate governance and risk disclosure: evidence from integrated reporting adopters
Authors: Raimo Nicola , NIcolò Giuseppe , Tartaglia Polcini Paolo , Vitolla Filippo
Published: May 2022

Purpose

This study aims to examine the impact of corporate governance attributes, in the form of board characteristics, on risk disclosures provided through integrated reporting (IR).

Design/methodology/approach

Drawing upon an agency theory perspective, this study examines the effect of the main corporate governance board characteristics (size, gender diversity, independence and meeting frequency) on the level of risk disclosure provided by a sample of 95 IR adopters from 24 countries for 2018.

Findings

The results suggest that firms are slow to realise IR’s potential to produce innovations in risk disclosure mechanisms. In addition, certain board characteristics, such as gender diversity, independence of directors and meeting frequency, are positive drivers of the risk disclosure provided via IR.

Originality/value

To the best of the authors’ knowledge, this is the first study that investigates the impact of corporate governance mechanisms on risk disclosure provided via IR. Connecting corporate governance mechanisms to IR risk disclosure practices can contribute to enhancing the practical and theoretical understanding of the role that the board of directors may play in stimulating transparency and accountability about risks via an alternative communication tool, IR, to the benefit of both investors and other stakeholders.
Artificial intelligence application in university libraries of Pakistan: SWOT analysis and implications
Authors: Ali Muhammad Yousuf , Naeem Salman Bin , Bhatti Rubina , Richardson Joanna
Published: May 2022

Purpose

The purpose of this study Artificial intelligence (AI) is one of the important emerging trends in information technology and is slowly being implemented in libraries. The researchers have presented a brief strengths, weaknesses, opportunities and threats (SWOT) analysis of the application of AI in Pakistani university libraries.

Design/methodology/approach

This study uses an ethnographic approach for data retrieval. Five chief librarians were interviewed by phone, during which they were asked to identify one key strength, weakness, opportunity and threat in terms of introducing AI technologies. The researchers have used a standard SWOT matrix to report the respondents’ comments.

Findings

AI is already slowly being introduced into Pakistani university libraries. While commenting on ways in which AI could help their libraries deliver more innovative services and better meet user needs, respondents expressed concern about the investment required in funding, time and staff.

Research limitations/implications

Further study is indicated to identify existing AI implementations in Pakistani university libraries and to assess relevant library users’ perspectives. This study is limited to brief, qualitative data; its main purpose is to validate the use of a SWOT analysis.

Practical implications

Given that AI-based tools are already being used in libraries to some degree regardless of location, now is an opportune time to develop strategies for implementing AI technologies more widely. A SWOT analysis can be used to identify and categorize challenges and risks specific to AI in a logical way to support strategic decision-making.

Originality/value

To date, no SWOT analysis has been conducted in the context of AI applications in libraries, let alone specifically university libraries in Pakistan.
Challenging experiences differentiation: a theoretical framework of its implications for work units
Authors: Carvalho Sheldon , Carvalho Fallan Kirby , Carvalho Charles
Published: May 2022

Purpose

Previous research has provided substantial attention to how individual-level challenging experiences lead to individual- and organization-related outcomes. This paper aims to expand existing challenging experiences theory and research by proposing a theoretical framework that addresses how challenging experiences differentiation relates to work unit effectiveness.

Design/methodology/approach

The authors integrate the literature on challenging experiences with that of work unit identification and citizenship behavior to shed light on the intervening mechanisms through which challenging experiences differentiation relates to work unit effectiveness.

Findings

The authors’ theoretical framework proposes that challenging experiences differentiation diminishes work unit effectiveness through the mediating roles of variation in work unit identification and variation in citizenship behavior among unit members.

Originality/value

By linking challenging experiences differentiation and work unit effectiveness, the authors’ framework highlights the importance of studying challenging experiences at the unit level of analysis.
Peer-to-peer accommodation amid COVID-19: the effects of Airbnb cleanliness information on guests’ trust and behavioral intentions
Authors: Godovykh Maksim , Back Robin M. , Bufquin Diego , Baker Carissa , Park Jeong-Yeol
Published: May 2022

Purpose

This study aims to explore the influence of different types of cleanliness information provided on the Airbnb platform (hosts’ sanitation labels, Airbnb cleaning protocol and previous guests’ reviews) on guests’ trust and behavioral intentions.

Design/methodology/approach

This study uses an online scenario-based experimental design. A two-step approach was applied to discover the proposed relationships by assessing the measurement model fit and validity of the constructs with confirmatory factor analysis and testing study hypotheses with structural equation modeling.

Findings

The results demonstrate that three types of cleanliness information (i.e. provided by Airbnb’s hosts, platform and customer reviews) had statistically significant effects on customers’ trust and behavioral intentions.

Practical implications

The research results provide practical recommendations for Airbnb hosts and peer-to-peer accommodation platforms on using several types of textual and visual cleanliness information to influence guests’ attitudes and behavioral intentions.

Originality/value

This study advances knowledge by introducing new factors affecting guests’ trust and behavioral intentions in peer-to-peer accommodation settings and differentiating the effects of different sources of cleanliness information and different types of guests’ trust.
High-performance work system and knowledge hoarding: the mediating role of competitive climate and the moderating role of high-performance work system psychological contract breach
Authors: Tran Huy Phuong
Published: May 2022

Purpose

High-performance work system (HPWS) has been verified as a promoter of both organizational and individual outcomes. However, this research takes the conflicting view of HPWS to examine the impact of HPWS perception on knowledge hoarding. In addition, competitive climate is proposed to mediate the relationship while HPWS psychological contract breach is hypothesized to moderate the HPWS-knowledge hoarding linkage.

Design/methodology/approach

A quantitative research design is adopted with data collected from 367 MBA and PhD students in Vietnam. Partial least square structural equation modeling is used to test the hypotheses.

Findings

The perception of HPWS increase knowledge hoarding with competitive climate acting as a partial mediator. HPWS psychological contract breach intensifies the relationship.

Research limitations/implications

The research provides additional evidences to support the dark-side view of HPWS on employees' outcomes. The adoption and implementation of HPWS should be clearly announced to reduce perceptions of mismatch between expectation and reality.

Originality/value

This study is among the first to investigate the association between HPWS and knowledge hoarding. In addition, the mediating role of competitive climate represents a novelty in HPWS research. Finally, the concept of HPWS psychological contract breach has been introduced to the literature.
The effect of virtual reality technology and education on sustainable behavior: a comparative quasi-experimental study
Authors: Ronaghi Mohammad Hossein
Published: May 2022

Purpose

Sustainability is one of the global challenges, individuals and businesses need to change their behavior and consumption patterns to move towards sustainable development. This is not possible without planning for education and related knowledge transfer. On the other hand, disruptive technologies such as virtual reality (VR) have revolutionized the field of education. The purpose of this study is to evaluate the effect of holding traditional training courses and VR-based training courses on sustainable behavior.

Design/methodology/approach

It is a quasi-experimental study, in which pretest-posttest design and control group are used. The statistical population includes students of one of the Iranian universities. A total of 105 students were randomly divided into two experimental groups and one control group (35 students in each group). Experimental group 1 underwent a training course using VR and Experimental group 2 received a traditional training course. At first, a pre-test was performed and after completing the eight-session period (two 1-h sessions per week), the post-test was conducted again for the groups.

Findings

The results of analysis of variance test show that there was a significant difference between the mean scores of sustainable behaviors in the post-test phase in the two experimental groups and the control group. Using Tukey’s test, it was found that the scores of sustainable behavior were different among three groups in pairs. That is, holding a training course as well as using VR has been effective on sustainable behavior. Environmental policymakers and planners can use technologies such as VR to teach environmental issues to create a culture of sustainability and sustainable development, in addition to training and educational courses.

Originality/value

Contribution of this study shows that the use of VR can be effective in learning sustainable behavior. Also, holding training courses is a way to change the consumption pattern and behavior of people to maintain the environment and sustainability.
The contest for materiality. What counts as CSR?
Authors: Raith Dirk
Published: May 2022

Purpose

The paper aims to show that materiality in the EU's non-financial reporting directive (NFRD) is an ambiguous concept, that its meaning is contested and that this contest for materiality is a contest for the meaning of Corporate Social Responsibility (CSR). Thus, the paper shall highlight a new aspect of materiality as a core principle in non-financial reporting.

Design/methodology/approach

The paper combines a historical analysis of the EU's CSR policies, an in-depth textual analysis of the EU's 2014 NFRD and associated documents, of non-financial reporting frameworks and exemplary adoptions of the NFRD in national laws.

Findings

The paper identifies two conflicting views of materiality in the NFRD. It shows that these “additive” and “cumulative” views correspond to the approaches taken by the Global Reporting Initiative (GRI) and International Integrated Reporting Council (IIRC) frameworks and by different national adoptions of the NFRD. The paper concludes that this contest for materiality is a contest for CSR – focusing either on business risks or impacts, shareholders or stakeholders, the business case or the social case for such a responsibility.

Research limitations/implications

The paper is mainly based on an in-depth analysis of the European debate on materiality in non-financial reporting. Some of the paper's descriptive results are thus limited to this particular case. However, the main conceptual findings are backed up by an analysis of internationally established reporting frameworks and scholarly debates on the issue.

Practical implications

The paper reveals the practical implications of the contesting “additive” and “cumulative“ understandings of materiality present in the NFRD. The paper thus further underpins the preference for a “double materiality” perspective in the revision of the NFRD and the EC's 2021 CSRD proposal.

Originality/value

The paper makes an original contribution in its explication of different understandings of materiality in non-financial reporting and how these eventually represent different, competing perspectives on the nature of the NFRD and of CSR.
Manager perceptions of decision-making for evaluation indicators: a centralized data envelopment analysis based approach
Authors: Abedian Mansour , Amindoust Atefeh , Maddahi Reza , Jouzdani Javid
Published: May 2022

Purpose

This paper aims to propose an integrated centralized data envelopment analysis (CDEA)-balanced scorecard (BSC) model to provide a selective approach to determine the most efficient indicators for evaluating the four perspectives of the BSC.

Design/methodology/approach

An integer linear programming model based on the efficiency concept of the CDEA method is presented to select the best indicators for evaluating four perspectives of the BSC. The basis for selecting indicators in this method is to maximize the overall performance of each BSC perspective. The modeling is performed on a real case. The considered model is solved using a general algebraic modeling system software for the data set of the real case.

Findings

A real-world case is solved using the proposed method. The integration of the CDEA and the BSC seems to be advantageous because it sheds more light on the complexity and tradeoffs inherent in actual performance measurement. It is important to note that there cannot be a unique and universal model of performance measurement applicable in every situation, in every organization and at any time.

Research limitations/implications

The data set of a single organization in the manufacturing industry is used to show the performance of the proposed mathematical model; therefore, generalization of the results should be done cautiously. This framework is based on the Iranian community and experts’ viewpoints; therefore, different results may be obtained if it is applied elsewhere, and the importance of perspectives and their indicators might show different results in other populations and other countries. In addition, because the data is collected in a specific period of time, the results cannot be extended to other periods of time.

Originality/value

The main contribution of this paper lies in the adaption of a new integrated CDEA-BSC model to performance measurement in the industrial sector that technology improves the ultimate results of performance measurement and provides wider opportunities for decision-makers. This paper aids managers and decision-makers to control the efficient indicators in perspectives.