bluuebunny/crossref_metadata_2025 huggingface dataset:
Bioinformatic-based identification of 3 immune-related genes for prognostic in breast invasive carcinoma
Authors: Cui Xiaoying , Song Shuang , Zhang Wenjuan , Wang Dawei , Fang Zhijun
Published: September 2022

Breast invasive carcinoma (BRCA) is the leading cause of cancer deaths in female worldwide. Immune cell infiltration is considered to be crucial factor for the success or failure of BRCA therapy. As we all known, early diagnosis of breast cancer can greatly improve the survival rate of patients. Hence, to screen effective biomarkers for breast cancer immunotherapy might be extremely important. In this research, we identified an immune-related, three-gene biomarkers for prognosis of BRCA. We obtained altogether 192 differentially expressed genes (DEGs) from GEO datasets (GSE22820, GSE36295) and GEPIA database, followed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. We screened 3 immune-related candidate biomarkers composing by CXCL2, CXCL9 and RBP7 that improves survival prediction outcome in BRCA. Kaplan–Meier analysis was conducted to analyze the patient survival based on 3 genes. In addition, we found that selected biomarkers were closely connected with infiltration levels of different tumor immune cells. Moreover, principal component analysis showed three biomarkers could effectively distinguish tumor samples from normal samples. In summary, these findings suggested that CXCL2, CXCL9 and RBP7 are viable prognostic and diagnostic biomarkers and provide new ideas for immunotherapy solutions of BRCA in the future.
HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph
Authors: Rubin Joshua Daniel , Vogel Nicola Alexandra , Gopalakrishnan Shyam , Sackett Peter Wad , Renaud Gabriel
Published: September 2022

Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty in assignment. We presentHaploCart, an mtDNA haplogroup classifier which usesVG’s pangenomic reference graph framework together with principles of Bayesian inference. We demonstrate that our approach significantly outperforms available tools by being more robust to lower coverage or incomplete consensus sequences and producing phylogenetically-aware confidence scores that are unbiased towards any haplogroup.HaploCartis available both as a command-line tool and through a user-friendly web interface. The program written inC++accepts as input consensus FASTA, FASTQ, or GAM files, and outputs a text file with the haplogroup assignments along with confidence estimates. Our work considerably reduces the amount of data required to obtain a confident mitochondrial haplogroup assignment.HaploCartis available as a command-line tool athttps://github.com/grenaud/vganand as a web server athttps://services.healthtech.dtu.dk/service. php?HaploCart.
Comparing Long Read Fusion Callers using Simulated Read Data
Authors: Van Twisk Daniel , Vincent Benjamin , Rubinsteyn Alex
Published: September 2022

The advent of single-molecule third generation sequencing technologies provide new possibilities for the detection of fusion transcripts in sequencing data. Here, we test three long-read fusions detection tools on simulated data, compare various tooling parameters and compare the performance between long-read and short-read fusion detection tools. We also use our fusion transcript detection pipeline to describe fusions transcripts detected in U87 and U937 glioblastoma cell lines. We find that LongGF is the most capable of the long-read fusion detection tools at identifying the most simulated fusion transcripts. While the short read fusion transcript detection tool, Arriba, had similar recall to some of the long-read tools, its precision was found to be much lower. Several fusions with ample evidence were found in U87 and U937 cell lines.
Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier
Authors: Smith Matthew Beauregard , Simpson Zack Booth , Marcotte Edward M.
Published: September 2022

We present a machine learning-based interpretive framework (whatprot) for analyzing single molecule protein sequencing data produced by fluorosequencing, a recently developed proteomics technology that determines sparse amino acid sequences for many individual peptide molecules in a highly parallelized fashion [1] [2]. Whatprot uses Hidden Markov Models (HMMs) to represent the states of each peptide undergoing the various chemical processes during fluorosequencing, and applies these in a Bayesian classifier, in combination with pre-filtering by a k-Nearest Neighbors (kNN) classifier trained on large volumes of simulated fluorosequencing data. We have found that by combining the HMM based Bayesian classifier with the kNN pre-filter, we are able to retain the benefits of both, achieving both tractable runtimes and acceptable precision and recall for identifying peptides and their parent proteins from complex mixtures, outperforming the capabilities of either classifier on its own. Whatprot’s hybrid kNN-HMM approach enables the efficient interpretation of fluorosequencing data using a full proteome reference database and should now also enable improved sequencing error rate estimates.
Diel fluctuations inin-vivoSnRK1 activity in Arabidopsis rosettes during light-dark cycles
Authors: Avidan Omri , Moraes Thiago A. , Mengin Virginie , Feil Regina , Rolland Filip , Stitt Mark , Lunn John E.
Published: September 2022

SUCROSE-NON-FERMENTING1 (SNF1)-RELATED KINASE1 (SnRK1) is a central hub in carbon and energy signalling in plants, and is orthologous with SNF1 in yeast and the AMP-ACTIVATED PROTEIN KINASE (AMPK) in animals. Previous studies of SnRK1 relied onin-vitroactivity assays or on monitoring the expression of putative marker genes. Neither approach gives unambiguous information aboutin-vivoSnRK1 activity. We have monitoredin-vivoSnRK1 activity using Arabidopsis (Arabidopsis thaliana) reporter lines that express a chimeric polypeptide with a SNF1/SnRK1/AMPK-specific phosphorylation site. We investigated responses during an equinoctial diel cycle, and after perturbing this cycle. As expected,in vivoSnRK1 activity rose towards the end of the night and rose even further when the night was extended. Unexpectedly, although sugars rose after dawn, SnRK1 activity did not decline until about 12 hours into the light period. The sucrose signal trehalose 6-phosphate (Tre6P) has been shown to inhibit SnRK1in vitro. We introduced the SnRK1 reporter into lines that harboured an inducibleTREHALOSE-6-PHOSPHATE SYNTHASEconstruct. Elevated Tre6P decreasedin-vivoSnRK1 activity in the light period, but not at the end of the night. Reporter polypeptide phosphorylation was sometimes negatively correlated with Tre6P, but a stronger and more widespread negative correlation was observed with glucose 6-phosphate. We propose that SnRK1 operates within a network that controls carbon utilization and maintains diel sugar homeostasis, and that Tre6P, hexose phosphates and the circadian clock contribute to regulation of SnRK1 activity in a context-dependent manner, and SnRK1-signalling is further modulated by factors that act downstream of SnRK1.

One sentence summary

In vivoSnRK1 activity shows an unexpected diel response and a complex relationship with trehalose 6-phosphate and other possible metabolic regulators.
A texture statistics encoding model reveals hierarchical feature selectivity across human visual cortex
Authors: Henderson Margaret M. , Tarr Michael J. , Wehbe Leila
Published: September 2022

Mid-level visual features, such as contour and texture, provide a computational link between low- and high-level visual representations. While the detailed nature of mid-level representations in the brain is not yet fully understood, past work has suggested that a texture statistics model (P-S model; Portilla and Simoncelli, 2000) is a candidate for predicting neural responses in areas V1-V4 as well as human behavioral data. However, it is not currently known how well this model accounts for the responses of higher visual cortex regions to natural scene images. To examine this, we constructed single voxel encoding models based on P-S statistics and fit the models to fMRI data from human subjects (male and female) from the Natural Scenes Dataset (Allen et al., 2021). We demonstrate that the texture statistics encoding model can predict the held-out responses of individual voxels in early retinotopic areas as well as higher-level category-selective areas. The ability of the model to reliably predict signal in higher visual cortex voxels suggests that the representation of texture statistics features is widespread throughout the brain, potentially playing a role in higher-order processes like object recognition. Furthermore, we use variance partitioning analyses to identify which features are most uniquely predictive of brain responses, and show that the contributions of higher-order texture features increases from early areas to higher areas on the ventral and lateral surface of the brain. These results provide a key step forward in characterizing how mid-level feature representations emerge hierarchically across the visual system.

Significance Statement

Intermediate visual features, like texture, play an important role in cortical computations and may contribute to tasks like object and scene recognition. Here, we used a texture model proposed in past work to construct encoding models that predict the responses of neural populations in human visual cortex (measured with fMRI) to natural scene stimuli. We show that responses of neural populations at multiple levels of the visual system can be predicted by this model, and that the model is able to reveal an increase in the complexity of feature representations from early retinotopic cortex to higher areas of ventral and lateral visual cortex. These results support the idea that texture-like representations may play a broad underlying role in visual processing.
The FELIX Project: Deep Networks To Detect Pancreatic Neoplasms
Authors: Xia Yingda , Yu Qihang , Chu Linda , Kawamoto Satomi , Park Seyoun , Liu Fengze , Chen Jieneng , Zhu Zhuotun , Li Bowen , Zhou Zongwei , Lu Yongyi , Wang Yan , Shen Wei , Xie Lingxi , Zhou Yuyin , Wolfgang Christopher , Javed Ammar , Fouladi Daniel Fadaei , Shayesteh Shahab , Graves Jefferson , Blanco Alejandra , Zinreich Eva S. , Klauss Miriam , Mayer Philipp , Kinny-Köster Benedict , Kinzler Kenneth , Hruban Ralph H. , Vogelstein Bert , Yuille Alan L. , Fishman Elliot K.
Published: September 2022

Tens of millions of abdominal images are obtained with computed tomography (CT) in the U.S. each year but pancreatic cancers are sometimes not initially detected in these images. We here describe a suite of algorithms (named FELIX) that can recognize pancreatic lesions from CT images without human input. Using FELIX,>95% of patients with pancreatic ductal adenocarcinomas were detected at a specificity of>95% in patients without pancreatic disease. FELIX may be able to assist radiologists in identifying pancreatic cancers earlier, when surgery and other treatments offer more hope for long-term survival.
MSstatsPTM: Statistical relative quantification of post-translational modifications in bottom-up mass spectrometry-based proteomics
Authors: Kohler Devon , Tsai Tsung-Heng , Verschueren Erik , Huang Ting , Hinkle Trent , Phu Lilian , Choi Meena , Vitek Olga
Published: September 2022

Liquid chromatography coupled with bottom up mass spectrometry (LC-MS/MS)-based proteomics is increasingly used to detect changes in post-translational modifications (PTMs) in samples from different conditions. Analysis of data from such experiments faces numerous statistical challenges. These include the low abundance of modified proteoforms, the small number of observed peptides that span modification sites, and confounding between changes in the abundance of PTM and the overall changes in the protein abundance. Therefore, statistical approaches for detecting differential PTM abundance must integrate all the available information pertaining to a PTM site, and consider all the relevant sources of confounding and variation. In this manuscript we propose such a statistical framework, which is versatile, accurate, and leads to reproducible results. The framework requires an experimental design, which quantifies, for each sample, both peptides with post-translational modifications and peptides from the same proteins with no modification sites. The proposed framework supports both label-free and tandem mass tag (TMT)-based LC-MS/MS acquisitions. The statistical methodology separately summarizes the abundances of peptides with and without the modification sites, by fitting separate linear mixed effects models appropriate for the experimental design. Next, model-based inferences regarding the PTM and the protein-level abundances are combined to account for the confounding between these two sources. Evaluations on computer simulations, a spike-in experiment with known ground truth, and three biological experiments with different organisms, modification types and data acquisition types demonstrate the improved fold change estimation and detection of differential PTM abundance, as compared to currently used approaches. The proposed framework is implemented in the free and open-source R/Bioconductor package MSstatsPTM.
Where the Minor Things Are: A Pan-Eukaryotic Survey Suggests Neutral Processes May Dominate Minor Spliceosomal Intron Evolution
Authors: Larue Graham E. , Roy Scott W.
Published: September 2022

Spliceosomal introns are gene segments removed (“spliced”) from RNA transcripts by large ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second spliceosome (the minor/ U12-type) is responsible for processing a tiny minority of introns. Despite its seemingly modest role, minor splicing has persisted for roughly 1.5 billion years of eukaryotic evolution. Identifying and cataloging minor introns in > 3000 eukaryotic genomes, we report diverse evolutionary histories including surprisingly high numbers of minor introns in some fungi and green algae, repeated massive loss, as well as several general biases in the positional and genic distributions of minor introns. We estimate that ancestral minor intron densities were comparable to those of the most minor intron-rich species, suggesting a trend of long-term stasis. Finally, three findings suggest a major role for neutral processes in minor intron evolution. First, we find highly similar patterns of minor and major intron evolution, in contrast to the predictions of both functionalist and deleterious models. Second, we find that observed functional biases among minor intron-containing genes are largely explained by these genes’ greater ages. Third, we find no association of intron splicing with cell proliferation in a minor intronrich fungus, suggesting that regulatory roles are lineage-specific and thus cannot offer a general explanation for minor splicing’s persistence. These data constitute the most comprehensive view to date of modern minor introns, their evolutionary history, and the forces shaping minor splicing, and provide a foundation for future studies of these remarkable genomic elements.
The WW domain of IQGAP1 binds directly to the p110α catalytic subunit of PI 3-kinase
Authors: Bardwell A. Jane , Paul Madhuri , Yoneda Kiku C. , Andrade-Ludeña Maria D. , Nguyen Oanh T. , Fruman David A. , Bardwell Lee
Published: September 2022

IQGAP1 is a multi-domain cancer-associated protein that serves as a scaffold protein for multiple signaling pathways. Numerous binding partners have been found for the calponin homology, IQ and GAP-related domains in IQGAP1. Identification of a binding partner for its WW domain has proven elusive, however, even though a cell-penetrating peptide derived from this domain has marked anti-tumor activity. Here, usingin vitrobinding assays with human proteins and co-precipitation from human cells, we show that the WW domain of human IQGAP1 binds directly to the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K). In contrast, the WW domain does not bind to ERK1/2, MEK1/2, or the p85α regulatory subunit of PI3K when p85α is expressed alone. However, the WW domain is able to bind to the p110α/p85α heterodimer when both subunits are co-expressed, as well as to the mutationally activated p110α/p65α heterodimer. We present a model of the structure of the IQGAP1 WW domain, and experimentally identify key residues in the hydrophobic core and beta strands of the WW domain that are required for binding to p110α. These findings contribute to a more precise understanding of IQGAP1-mediated scaffolding, and of how IQGAP1-derived therapeutic peptides might inhibit tumorigenesis.
Depletion of collagen IX alpha2 interferes osteochondral homeostasis of the knee joint which ultimately causing osteoarthritis-like articular cartilage damage
Authors: Dong Rui , Xu Huihui , Wang Pinger , Fang Liang , Xiao Luwei , Lv Shuaijie , Tong Peijian , Jin Hongting
Published: September 2022

As one of the branched chains of Type IX collagen (Col9), Collagen IX alpha2 (Col9α2) has been reported to be associated with several orthopedic conditions. To probe the relationship between Col9α2 and knee osteoarthritis (KOA), we performed a systematic analysis of Col9α2-deficient (Col9α-/-) mice using whole-mount skeletal staining, Micro-CT (μCT), biomechanics, histomorphometry, immunohistochemistry (IHC), immunofluorescence (IF) and Enzyme-linked immunosorbent (Elisa). Although whole-mount skeletal staining displayed no difference in bone length and ossification between Col9α-/- mice and wild-type (Col9α2+/+) mice at mid-gestation and adult stages, the knee joint exhibited dramatic discrepancies. Specifically, the subchondral bone (SCB) in the knee joint of Col9α-/- mice became sparse and deformed in the early stage, with altered bone morphometric parameters, reduced load-bearing capacity, dysfunctional bone homeostasis (decreased osteogenesis capacity and elevated bone resorption capacity), diminished cartilage proteoglycans and disrupted cartilage extracellular matrix (ECM) anabolism and catabolism compared with the Col9α2+/+ mice. In the late stage, the cartilage degeneration in Col9α2-/- mice were particularly pronounced compared to Col9α2+/+ mice, as evidenced by severe cartilage destruction and a marked reduction in cartilage thickness and area. Overall, Col9α2 is essential for maintaining osteochondral homeostasis in the knee joint of mice, and the absence of this gene is accompanied by distinct sclerosis of the SCB and a reduction in load-bearing capacity; in the late stage, in the lack of SCB stress inhibition, excessive load is consistently exerted on the cartilage, ultimately leading to osteoarthritic-like articular cartilage damage. Hence, Col9α2 may serve as a potential candidate biomarker associated with KOA.
Digestive exophagy of Bacterial Biofilms by an Amoeba Predator is Mediated by Specific Biofilm Recognition
Authors: Zanditenas Eva , Trebicz-Geffen Meirav , Domínguez-García Laura , Romero Diego , Kolodkin-Gal Ilana , Ankri Serge
Published: September 2022

The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites are released from the cysts to colonize the large intestine, where they primarily feed on bacterial cells. In these scenarios, bacterial cells form aggregates or structured communities too large for phagocytosis. Our results show that E. histolytica can degrade pre-established biofilms of Bacillus subtilis and Escherichia coli in a dose- and time-dependent manner. Surprisingly, trophozoites incubated with B. subtilis biofilm exhibit a unique transcriptome signature compared to those incubated with planktonic cells or without bacteria. Biofilm-induced genes include cysteine proteases (CPs), and the general inhibition of CPs by E64D or by the use of specific small-RNA (sRNA)-based RNA interference impairs the degradation of biofilms by E. histolytica. The degradation of B. subtilis extracellular matrix (ECM) protein TasA by CPs is associated with partial biofilm digestion and activation of the stress response in the interacting B. subtilis cells. The interaction with B. subtilis biofilms was also associated with lower levels of oxidoreductases. Oxidoreductase downregulation can be a readout of the embedding of E. histolytica trophozoites within the biofilm-produced extracellular matrix, reducing their exposure to oxidative stress (OS). Our results indicate that parasites may digest biofilms by a controlled mechanism of digestive exophagy as secretion of digestive enzymes as a conserved mechanism for biofilm degradation allows phagocytic digestion of biofilm cells. Furthermore, the partially digested biofilms can serve as an unexpected shield protecting parasites from oxidative environments and thereby may regulate the persistence and virulence of the parasite.
Crypt-top and crypt-bottom colonic epithelial cell population microRNA expression demonstrates cell type-specificity and correlation with endoscopic activity in ulcerative colitis
Authors: Inciuraite Ruta , Ramonaite Rima , Kupcinskas Juozas , Dalgediene Indre , Kulokiene Ugne , Kiudelis Vytautas , Varkalaite Greta , Zvirbliene Aurelija , Jonaitis Laimas Virginijus , Kiudelis Gediminas , Franke Andre , Schreiber Stefan , Juzenas Simonas , Skieceviciene Jurgita
Published: September 2022

Background and Aims

Colonic epithelial barrier loss and dysfunction are one of the early events in ulcerative colitis (UC) and microRNAs (miRNAs) participate in its regulation. However, cell type-specific profile of miRNAs during inflammation in UC is still unknown. Thus, we aimed to perform miRNA profiling on colon tissue and epithelial cell levels in active and quiescent UC.

Methods

Small RNA-sequencing in colon tissue, crypt-bottom (CD44+), and crypt-top (CD66a+) colonic epithelial cell populations from two independent cohorts of UC patients (active and quiescent, n=74), and healthy individuals (n=50) was performed. Data analysis encompassed differential expression, weighted gene co-expression network (WGCNA), correlation, gene-set enrichment analyses (GSEA).

Results

In colon tissue of active and quiescent UC, differentially expressed miRNAs were shown to be potentially involved in intestinal barrier integrity regulation. Consecutive analysis of crypt-bottom and crypt-top colonic epithelial cells revealed distinct miRNA expression patterns in response to UC-caused inflammation. GSEA indicated that differentially expressed epithelial miRNAs are commonly involved in inflammation- and intestinal barrier integrity-related processes (such as signalling of interleukin-4 and interleukin-13), while miRNA differences between cell populations might reflect their function, i.e., crypt-bottom cell miRNA target genes involved in regulation of cell differentiation. Finally, pro-inflammatory miRNA co-expression module correlating with endoscopic UC activity was defined not only in both epithelial cell populations, but also in the colon tissue.

Conclusions

miRNA expression patterns are colon epithelial cell population- and UC state-specific and correlate with endoscopic UC activity. Irrespective of the UC stage deregulated epithelial miRNAs are potentially involved in regulation of intestinal barrier integrity.
Involvement of superior colliculus in complex figure detection of mice
Authors: Cazemier J. Leonie , Tran T. K. Loan , Hsu Ann T. Y. , Husić Medina , Kirchberger Lisa , Self Matthew W. , Roelfsema Pieter R. , Heimel J. Alexander
Published: September 2022

Object detection is an essential function of the visual system. Although the visual cortex plays an important role in object detection, the superior colliculus can support detection when the visual cortex is ablated or silenced. Moreover, it has been shown that superficial layers of mouse SC (sSC) encode visual features of complex objects, and that this code is not inherited from the primary visual cortex. This suggests that mouse sSC may provide a significant contribution to complex object vision. Here, we use optogenetics to show that mouse sSC is causally involved in figure detection based on differences in figure contrast, orientation and phase. Additionally, our neural recordings show that in mouse sSC, image elements that belong to a figure elicit stronger activity than those same elements when they are part of the background. The discriminability of this neural code is higher for correct trials than incorrect trials. Our results provide new insight into the behavioral relevance of the visual processing that takes place in sSC.
VOCAL SIMILARITY AND DIFFERENCES IN FOUR SPECIES OF THE GENUSANTHUS: ACOUSTIC FEATURE ANALYSIS OF SOME COMMON CALLS
Authors: Dragonetti Marco
Published: September 2022

Birds of the same genus often share similar call repertoires, the aim of this paper is to find species-specific and common acoustic features across species. This can be a useful tool for identification purposes and for studying intra-interspecific communication. Similar flight call (tsip) in two closely related species (Anthus pratensis, Anthus spinoletta) were studied to find characteristics, that allows to discriminate the two species with acoustic means. Three different call types (tsip, softandalarm) of four species of the genus Anthus (A. pratensis, A. spinoletta, A. petrosus, A. cervinus) were also studied to find whether these common call types show different degrees of similarity. Discriminant function analysis correctly classified 98.4% ofA. pratensisandA. spinolettaflight calls. Three acoustic parameters showed the highest discrimination power: the frequency modulations, the maximum frequency value and the minimum frequency value of the peak frequency contour. Using these three values I proposed a simpler procedure for recognizing these two species, that allowed a correct classification of 96% of calls.The three call types of the fourAnthusspecies were studied using cross correlation among spectrogram contours.Alarmcalls of the four species showed stronger similarity, while the other call types were more distinctive, withsoftcall seeming to have a lower similarity between species and hence a higher distinctive power. These results suggest the hypothesis thatalarmcall is similar, because it retains features of a common ancestor easing heterospecific communication, while the other calls showed decreasing similarity and more species-specific features.
Cryo-EM structure of the Agrobacterium tumefaciens type IV secretion system-associated T-pilus reveals stoichiometric protein-phospholipid assembly
Authors: Kreida Stefan , Narita Akihiro , Johnson Matthew D , Tocheva Elitza I , Das Anath , Ghosal Debnath , Jensen Grant J.
Published: September 2022

Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease by the horizontal transfer of oncogenic DNA that is integrated into the host’s genome. The conjugation is mediated by the conjugative VirB/D4 type 4 secretion system (T4SS). A. tumefaciens T4SS assembles an extracellular filament, the T-pilus, that is involved in the formation of a mating pair between A. tumefaciens and the recipient plant cell by a not fully understood mechanism. Here, we present a 3 Å cryo-EM structure of the T-pilus, solved by helical reconstruction. Our structure reveals that the T-pilus comprises the major pilin protein VirB2 and phosphatidylglycerol (PG) phospholipid at a 1:1 stoichiometric ratio with 5-start helical symmetry. We further show that PG-headgroups and the positively charged Arg 91 residues of VirB2 protomers form extensive electrostatic interactions in the lumen of the T-pilus. Mutagenesis of Arg 91 destabilized the VirB2 protein and completely abolished pilus formation. While our T-pilus structure shows architectural similarity with previously published conjugative pili structures, positively charged sidechains protrude into the lumen and the lumen is narrower, raising questions whether the T-pilus is a conduit for ssDNA transfer. We also show that the VirB2 subunits in T-pilus filament are not cyclic, as previously thought.
Perceived concern and risk of getting infected with monkeypox among MSM: Evidence and perspectives from the Netherlands, July 2022
Authors: Wang Haoyi , de Paulo Kennedy J.I. d’Abreu , Gültzow Thomas , Zimmermann Hanne M.L. , Jonas Kai. J.
Published: September 2022

The current monkeypox epidemic is most prevalent among men-who-have-sex-with-men (MSM). PrEP users and MSM with HIV (MSMHIV) are considered having the highest risk for monkeypox infection in the Netherlands and being targeted for monkeypox vaccination. Next to the epidemiological evidence, perceived concern/risk are also important in decision making about health behaviour uptake, e.g., vaccination uptake. It is thus relevant to examine which subpopulations among MSM consider themselves most at risk and most concerned about monkeypox. This study aimed to investigate this to complement and to help determining if the current measures to curb the epidemic are successfully targeted or not in the Netherlands. We conducted an online survey among 394 Dutch MSM. We first calculated the prevalence and standardised prevalence ratio (SPR) of high perceived concern/risk of monkeypox by the PrEP-use and HIV status. We then conducted two multivariable logistic regression analyses to investigate the perceived concern/risk of monkeypox and their potential socio-demographic/behavioural/health/psycho-social determinants. Among the included MSM, 52% showed high perceived concern and 30% showed high perceived risk of monkeypox. PrEP users (SPR=0.83) showed a significantly lower chance of perceived concern; and MSMHIV (SPR=2.09) were found to have a significant higher chance of perceiving high risk of monkeypox. In the multivariable logistic analyses, non-PrEP users (aOR=2.55) were more likely to perceive high concern, while MSM who were retired (aOR=0.23) and who had chemsex recently (aOR=0.63) were less likely to perceive high concern. MSMHIV (aOR=4.29) and MSM who had an unknown/undisclosed HIV status (aOR=6.07), who had attended private sex parties (aOR=2.10), and who knew people who have/had monkeypox (aOR=2.10) were more likely to perceive high risk of monkeypox. We found that a higher perceived risk (aOR=2.97) and a higher concern (aOR=3.13) of monkeypox were correlated with each other, more results see Table 2. In sum, only one-third of Dutch MSM considered themselves at a high risk of a monkeypox infection, and only half of them showed a high concern. We identified a potential discrepancy between the “actual risk” and the perceived risk and concern of monkeypox among MSM in this early stage of the monkeypox epidemic in the Netherlands, especially among PrEP users and MSMHIV. More refined public health communication strategies may be needed to improve the understanding and knowledge of the “actual risk” of monkeypox infections among these MSM sub-populations to encourage and facilitate an improved health behaviour uptake.
Impact of mindfulness-based stress reduction intervention on the performance of construction professionals
Authors: Leung Mei-Yung , Ahmed Khursheed , Famakin Ibukun Oluwadara
Published: September 2022

Purpose

Construction professionals (CPs) are often exposed to various challenges and pressures at work including urgent deadlines, high demands, uncertainty in tasks, and complex problems, which may induce stress and affect performance directly. Mindfulness-based stress reduction (MBSR) training has been used for several years to reduce stress among various types of people, such as nurses, teachers, and family caregivers, but its application to CPs with highly dynamic environment remains uncertain. This study aimed to investigate the impact of MBSR training on the performance of CPs via an intervention study involving two groups (MBSR and control).

Design/methodology/approach

Participants in both groups were assessed using a questionnaire survey and a semi-structured interview at the pre- and post-intervention stage. Multiple research methods were used to derive quantitative and qualitative analyses, including factor analysis, independent t-test, Pearson correlation, and contextual analysis.

Findings

The findings overall confirm that MBSR has a direct effect on CPs, improving their mindfulness characteristics and enhancing performance by reducing their stress.

Practical implications

A number of practical recommendations are made such as (1) arranging standard eight-week MBSR training for CPs; (2) giving special leave for attending the full mindfulness training; (3) establishing a suitable environment in the office for meditation;(4) allowing CPs an opportunity to pause at difficult moments to create space to respond instead of simply reacting; and (5) expressing love and kindness through gratitude, recognition, and regular feedback.

Originality/value

This research can be considered as valid evidence to convince construction organizations conducting MBSR to the CPs, which is indeed not too remote to enhance their performance as well as the holistic construction performance.
Do more concentrated supplier portfolios benefit firm innovation? The moderating roles of financial slack and growth opportunities
Authors: Chen Meng , Liu Hefu , Tang Xinlin
Published: September 2022

Purpose

Firms are increasingly depending on supplier portfolios in the quest for firm innovation. However, whether concentrated supplier portfolios are beneficial to innovation remains highly disputed. This study aims to investigate the effect of supplier portfolio concentration on firm innovation and the contingencies that shape this effect.

Design/methodology/approach

The authors build on the knowledge search view to theorize a U-shaped effect of supplier portfolio concentration on firm innovation and further propose that the U-shaped effect is contingent on financial slack and growth opportunities. The authors collected panel data from 1,320 manufacturing firms in China. The negative binomial regression analyses were performed to test the hypotheses.

Findings

Supplier portfolio concentration has a U-shaped effect on firm innovation. This U-shaped effect is weakened and flipped by financial slack but strengthened by growth opportunities.

Originality/value

The findings extend current understandings of the influence of supplier portfolio on firm innovation by clarifying the U-shaped effect of supplier portfolio concentration on innovation and the circumstances under which supplier portfolio concentration is more effective for firm innovation.
University instructors' burnout: antecedents and consequences
Authors: Siyum Berihu Asgele
Published: September 2022

Purpose

The purpose of this study was to examine the antecedents and consequences of burnout among the Ethiopian Civil Service University and Kotebe Metropolitan University instructors in Ethiopia.

Design/methodology/approach

The study employed purely quantitative research and then used a cross-sectional survey design. Therefore, questionnaires adopted from the Maslach Burnout Inventory were collected from 158 university instructors.

Findings

The antecedents of burnout were a job, organizational and individual characteristics, whereas the consequences of burnout were job satisfaction, affective commitment and turnover intention. Work experience, educational status, job characteristics, organizational support and reward and recognition were reported as primary sources of burnout among instructors. Therefore, all the identified antecedents were correlated with burnout. Besides, turnover intention and affective commitment were the major consequences of burnout. Burnout partially mediated the relationship between the antecedents and consequences. Therefore, the antecedents directly impact burnout, but they also indirectly affect the consequences through burnout.

Research limitations/implications

This study has a narrow geographical scope and is limited to a cross-sectional design. Therefore, a longitudinal study representing a large number of universities using mixed research is required to generalize about instructors' burnout in Ethiopia.

Practical implications

This study helps to familiarize scholars, universities and researchers with instructors' burnout in Ethiopia. More specifically, the results of this study help the Ethiopian Civil Service University and Kotebe Metropolitan University to recognize the antecedents and consequences of burnout among their instructors and help them take corrective measures to address the problems of their employees as well as to improve efficiency and quality of education to the community through eliminating the antecedents.

Originality/value

This study gives a better understanding of burnout and becomes good literature on the magnitude and relationship of the antecedents and consequences of burnout among university instructors in Ethiopia. Thus, it provides a conceptual basement for research on university instructors' burnout in Ethiopia.
A robust analysis of trade policy: the chicken and softwood lumber wars
Authors: Smith Nathaniel Webb
Published: September 2022

Purpose

The paper extends the robust political economy framework to analyze the impact of tariffs on the entrepreneurial market process. It proposes that the unintended consequences of using trade policy to bolster a nation's economy will inevitably prevent an economy from allocating its resources to their highest-valued use. The study aims to expand the robust political economy literature to international trade.

Design/methodology/approach

The paper develops a robust analysis of trade policy and illustrates it with two case studies of trade wars: The Chicken War (1963) and the US–Canada softwood lumber disputes (1982-present).

Findings

The paper provides theoretical insights into how the entrepreneurial market process is distorted by trade barriers. The case studies show that the theoretical insights have real-world implications that should not be ignored when planning trade policy.

Originality/value

This paper applies a robust political economy framework to international trade.
Disability coaching in a pandemic
Authors: Doyle Nancy , Bradley Emily
Published: September 2022

Purpose

An applied study using convenience data was conducted to compare the experiences of neurodivergent adults undergoing workplace coaching before and during the pandemic.

Design/methodology/approach

The naturally occurring opportunity permitted a comparison of face-to-face and remote coaching in three cohorts, pre-pandemic (100% face-to-face), forced-remote (100% remote) and choice (remote or face-to-face; 85% selected remote). A total of 409 participants self-reported performance before and 12 weeks after completing an average of 11-h coaching.

Findings

Significant differences between before and after scores for performance, with large effect sizes, were reported for all three cohorts across six dependent variables: memory, time management, organisational skills, stress management, understanding neurodiversity and concentration. There was no significant difference between the cohorts in terms of the magnitude of the effect. There were significant differences between the cohorts in terms of which topics were chosen as foci for the coaching, with executive functions related topics becoming less popular in the choice cohort.

Research limitations/implications

The authors abductively reasoned the results to suggest a positive relationship between personalised environments and cognitive demands for this client group. They call for further, theoretically grounded research exploring the role of coaching and environment in understanding the work performance of neurodivergent adults at work.

Originality/value

The study contributes to the emerging knowledge on the different experiences of in-person and video-mediated coaching. The focus on neurodivergent employees, which are heretofore less well researched within the workplace, provides essential data to support practitioners in maximising opportunity for a marginalised group.
Housing demand of urban fringe residents and underlying causes: example of Ankara, Türkiye
Authors: Hayrullahoğlu Gizem , Aliefendioğlu Tanrıvermiş Yeşim
Published: September 2022

Purpose

This study aims to explore the housing demand of urban fringe residents in southwest Ankara. Two subquestions were developed: What are the respondents’ perceptions of Ankara city center and which characteristics do they prioritize for living in the urban fringe? Data were collected through a face-to-face household survey, and a hedonic regression model was developed based on responses.

Design/methodology/approach

Increasing housing demand, lifestyle change and faulty housing policies in Ankara have triggered urban sprawl along fringe areas, which causes several urban problems. Considering that urban sprawl is related to housing demand, it is essential to examine the structure of housing demand and the preference to live near the urban fringe.

Findings

According to the survey results, security, crime, noise pollution, traffic congestion and parking problems that reduce the welfare of Ankara city center encouraged expansion toward the rural–urban fringe, in addition to low-quality or traditional housing attributes. The urban core became unattractive to the respondents for being insecure, chaotic and down-market. The hedonic model showed that seven variables, all related to housing characteristics, best explain the housing demand in the area. Socioeconomic status and lifestyle were found to be associated with the desire to live on the urban fringe, also indicating the snob effect.

Originality/value

The authors propose taking domain-specific housing demand patterns in the spatial planning assumptions and housing policies into consideration for a well-governed urban development in Ankara. Making the city center more appealing through rehabilitation should be preferable rather than limiting demand on the urban fringe with a strict intervention in housing supply.
Salinity‐driven ecology and diversity changes of heterocytous cyanobacteria in Australian freshwater and coastal‐marine microbial mats
Authors: Campbell Matthew A. , Bauersachs Thorsten , Schwark Lorenz , Proemse Bernadette C. , Eberhard Rolan S. , Coolen Marco J. L. , Grice Kliti
Published: September 2022

N2‐fixing heterocytous cyanobacteria are considered to play a minor role in sustaining coastal microbial mat communities developing under normal marine to hypersaline conditions. Here, we investigated microbial mats growing under different salinities from freshwater mats of Giblin River (Tasmania) to metahaline and hypersaline mats of Shark Bay (Western Australia). Analyses of genetic (rRNA and mRNA) and biological markers (heterocyte glycolipids) revealed an unexpectedly large diversity of heterocytous cyanobacteria in all the studied microbial mat communities. It was observed that the taxonomic distribution as well as abundance of cyanobacteria is strongly affected by salinity. Low salinity favoured the presence of heterocytous cyanobacteria in freshwater mats, while mats thriving in higher salinities mainly supported the growth unicellular and filamentous non‐heterocytous genera. However, even though mRNA transcripts derived from heterocytous cyanobacteria were lower in Shark Bay (<6%) microbial mats, functional analyses revealed that these diazotrophs were transcribing a substantial proportion of the genes involved in biofilm formation and nitrogen fixation. Overall, our data reveal an unexpectedly high diversity of heterocytous cyanobacteria (e.g. Calothrix, Scytonema, Nodularia, Gloeotrichia, Stigonema, Fischerella and Chlorogloeopsis) that had yet to be described in metahaline and hypersaline microbial mats from Shark Bay and that they play a vital role in sustaining the ecosystem functioning of coastal‐marine microbial mat systems.
Sarcopenia measurements and clinical outcomes in Crohn's disease surgical patients
Authors: Hong Jason T. , James Simon , Tran Anthony , Kutaiba Numan
Published: September 2022

Background

Patients with Crohn's disease (CD) have a high likelihood of being sarcopenic. Several studies have shown a positive correlation between sarcopenia measured as skeletal muscle index (SMI) and poor surgical outcomes in patients with CD. Our primary aim was to correlate SMI with the psoas muscle index (PMI), an easier measurement of sarcopenia. Secondary aim was to correlate SMI and PMI with clinical outcomes in a cohort of CD patients requiring surgery.

Methods

A retrospective cohort study of CD patients who underwent surgery at a public health service from January 2010 to December 2019. Using computed tomography and magnetic resonance enterography studies, skeletal muscle area was measured at the third lumbar vertebra level. SMI and PMI were calculated and correlated. Correlation between SMI and PMI with surgical outcomes was performed.

Results

Seventy‐six patients were included. Median length of stay (LOS) was 6 days (IQR, 5 to 9). Eleven patients (14.5%) required ICU admission, nine patients (11.8%) required TPN and thirteen patients (17.1%) had complications. The prevalence of sarcopenia was 63.2% based on the SMI threshold of 52.4 and 38.5 cm2/m2 for men and women, respectively. A positive correlation between SMI and PMI was found (r = 0.72, P < 0.0001). Sarcopenia status based on reported thresholds for SMI and for PMI showed no significant correlation with outcomes (LOS, ICU admission and complications).

Conclusions

SMI and PMI show good correlation but there is insufficient evidence to suggest that sarcopenia status using either measurement has a significant impact on predicting clinical outcomes.
A systematic review of paediatric neurogenic lower urinary tract dysfunction guidelines using the Appraisal of Guidelines and Research Evaluation (AGREE) II instrument
Authors: Yadav Priyank , Alsabban Abdulrahman , de Los Reyes Thomas , Varghese Abby , Ming Jessica M. , Milford Karen , Yang Stephen S. , Silangcruz Jan M. , Dos Santos Joana , Bagli Darius J. , Rickard Mandy , Lorenzo Armando J. , Church Paige , Chua Michael E.
Published: September 2022

Objective

To examine and critique current international clinical practice guidelines (CPGs) on management of paediatric neurogenic lower urinary tract dysfunction (NLUTD) and assess the applicability of these guidelines to clinical practice.

Materials and Methods

We conducted a systematic review of all CPGs on NLUTD published in English from the year 2010 to 2022. Six reviewers independently used the Appraisal of Guidelines and Research Evaluation (AGREE) II instrument to appraise all eligible CPGs. This instrument is comprised of 23 items organised into six quality domains. The scores for each item and domain were tabulated for each reviewer and interrater reliability was assessed for each domain using the intraclass correlation coefficient (ICC).

Results

Six CPGs were appraised and these included: National Institute for Health and Care Excellence (NICE), European Society for Paediatric Urology, International Children's Continence Society, Irish, Spina Bifida Association (SBA), and International Brazilian Journal of Urology guidelines. They had high mean standardised scores in the domain on ‘scope and purpose’ and ‘clarity of presentation’ but had low scores in the domain of ‘applicability’. The top three CPGs based on overall score were the NICE, Irish and SBA guidelines and the reviewers had high degree of interrater reliability (ICC 0.912, P < 0.001). The mean scores in various domains for the top three guidelines were 95.8 (scope and purpose), 87.5 (stakeholder involvement), 69.1 (rigour of development), 94.0 (clarity of presentation), 68.4 (applicability), and 59.7 (editorial independence). The diagnostic and treatment recommendations of the top three guidelines were presented.

Conclusion

The existing CPGs on paediatric NLUTD provide high‐quality evidence based recommendations. The NICE, Irish and SBA guidelines were the top three CPGs identified. They scored high on most domains except applicability and editorial independence. These domains need to be considered for future updates to improve the utility.