bluuebunny/crossref_metadata_2025 huggingface dataset:
COOBoostR: an extreme gradient boosting-based tool for robust tissue or cell-of-origin prediction of tumors
Authors: Yang Sungmin , Ha Kyungsik , Song Woojeung , Fujita Masashi , Kübler Kirsten , Polak Paz , de Alba Rivas Carolina Garcia , Pessina Patrizia , de Aja Julio Sainz , Rowbotham Samuel , Bhetariya Preetida , Dost Antonella , Moye Aaron L. , Hiyama Eiso , Nakagawa Hidewaki , Kim Carla F. , Kim Hong-Gee , Lee Hwajin
Published: October 2022

We here present COOBoostR (https://github.com/SWJ9385/COOBoostR), a computational method designed for the putative prediction of tissue-or cell-of-origin of various cancer types. COOBoostR leverages regional somatic mutation density information and chromatin mark features to be applied to an extreme gradient boosting-based machine-learning algorithm. COOBoostR ranks chromatin marks from various tissue and cell types which best explain the somatic mutation density landscape of any sample of interest. Through integrating either ChIP-seq based chromatin data or bulk/single cell chromatin accessibility data along with regional somatic mutation density data derived from normal cells/tissue, precancerous lesions, and cancer types, we show that COOBoostR outperforms existing random forest-based methods in prediction speed with comparable or better tissue or cell-of-origin prediction performance. In addition, our results suggest a dynamic somatic mutation accumulation at the normal tissue or cell stage which could be intertwined with the changes in open chromatin marks and enhancer sites. These results further represent chromatin marks shaping the somatic mutation landscape at the early stage of mutation accumulation, possibly even before the initiation of precancerous lesions or neoplasia.
Representation and quantification Of Module Activity from omics data with rROMA
Authors: Najm Matthieu , Cornet Matthieu , Albergante Luca , Zinovyev Andrei , Sermet-Gaudelus Isabelle , Stoven Véronique , Calzone Laurence , Martignetti Loredana
Published: October 2022

The efficiency of analyzing high-throughput data in systems biology has been demonstrated in numerous studies, where molecular data, such as transcriptomics and proteomics, offers great opportunities for understanding the complexity of biological processes.

One important aspect of data analysis in systems biology is the shift from a reductionist approach that focuses on individual components to a more integrative perspective that considers the system as a whole, where the emphasis shifted from differential expression of individual genes to determining the activity of gene sets.

Here, we present the rROMA software package for fast and accurate computation of the activity of gene sets with coordinated expression. The rROMA package incorporates significant improvements in the calculation algorithm, along with the implementation of several functions for statistical analysis and visualizing results. These additions greatly expand the package’s capabilities and offer valuable tools for data analysis and interpretation. It is an open-source package available on github at:www.github.com/sysbio-curie/rROMA.

Based on publicly available transcriptomic datasets, we applied rROMA to cystic fibrosis, highlighting biological mechanisms potentially involved in the establishment and progression of the disease and the associated genes. Results indicate that rROMA can detect disease-related active signaling pathways using transcriptomic and proteomic data. The results notably identified a significant mechanism relevant to cystic fibrosis, raised awareness of a possible bias related to cell culture, and uncovered an intriguing gene that warrants further investigation.

Contact:loredana.martignetti@curie.fr
Helicobacter pyloriFlgV forms a flagellar motor ring structure required for optimal motility
Authors: Botting Jack M. , Tachiyama Shoichi , Gibson Katherine H. , Liu Jun , Starai Vincent J. , Hoover Timothy R.
Published: October 2022

The bacteriumHelicobacter pylorihas a large flagellar motor that generates significantly higher torque than the archetypicalEscherichia colimotor. To understand howH. pylorinavigates the viscous environment of the stomach, it is essential to establish how specific motor components contribute to efficient motility. We show here that the protein FlgV, required for motility inCampylobacter jejuni, forms a novel ring associated with the MS and C rings inH. pylori. Deletion offlgVfromH. pyloriB128 or a highly motile variant ofH. pyloriG27 (G27M) resulted in reduced motility in soft agar medium. Based on comparative analyses ofin-situflagellar motor structures ofH. pyloriwild-type and ΔflgVmutants, the reduced motility of the ΔflgVmutants and the location of the FlgV ring suggest it stabilizes interactions between the MS and C rings and/or plays a role in switching the direction of flagellar rotation. Overall, these results identify a novel motor accessory likely adapted to promote flagellar function for bacterial colonization of high-load environments such as the gastric mucosa.
Conventional dendritic cells 2, the targeted antigen-presenting-cell, induces enhanced type 1 immune responses in mice immunized with CVC1302 in oil formulation
Authors: Du Luping , Qiao Xuwen , Zhang Yuanpeng , Hou Liting , Yu Xiaoming , Cheng Haiwei , Chen Jin , Zheng Qisheng , Hou Jibo , Tong Guangzhi
Published: October 2022

Multifunctional CD4+T helper 1 (Th1) cells, producing IFN-γ, TNF-α and IL-2, define a correlate of vaccine-mediated protection against intracellular infection. In our previous study, we found that CVC1302 in oil formulation promoted the differentiation of IFN-γ+/TNF-α+/IL-2+Th1 cells. In order to extend the application of CVC1302 in oil formulation, this study aimed to elucidate the mechanism of action in improving the Th1 immune response. Considering the signals required for the differentiation of CD4+T cells to Th1 cells, we detected the distribution of innate immune cells and the model antigen OVA-FITC in lymph node (LN), as well as the quantity of cytokines produced by the innate immune cells. The results of these experiments show that, cDC2 and OVA-FITC localized to inter-follicular region (IFR) of the draining lymph nodes, inflammatory monocytes localized to both IFR and T cell zone, which mainly infiltrate from the blood. In this inflammatory niche within LN, CD4+T cells were attracted into IFR by CXCL10, secreting by inflammatory monocytes, then activated by IL-12-secreting cDC2. Above all, CVC1302 in oil formulation, on the one hand, targeted antigen and inflammatory monocyte into the LN IFN in order to attract CD4+T cells, on the other hand, targeted cDC2 to produce IL-12 in order to promote optimal Th1 differentiation. The new finding will provide a blueprint for application of immunopotentiators in optimal formulations.

Importance

Along with the development of veterinary immunology, immunopotentiator and delivery system were not simply mixed with antigen, more and more attentions paid on the optimal compatibility in order to induce multifunctional immune responses. As reported, LPS formulated in IFA targeted antigens to the IFR of the LN, and recruited Mo into the IFR, then attracted antigen-specific CD4+T cells, which differentiated into Th1 cells under the IL-12 produced by DC-SIGN+DC(1). Herein, we further found that CVC1302 formulated with Marcol 52 induced enhanced Th1 immunity. Combined with our previous finding that CVC1302 in oil formulation induced improved humoral immunity, we concluded that CVC1302 in oil formulation provided multifunctional immunity, not only higher antibody titers to prevent pathogen infection, but also cellular immunity cytokine to prevent viral shedding.
Within-flock differences in exploratory tendency and flock performance in a highly gregarious bird
Authors: Carere Claudio , Audebrand Celine , Desigaux Florian , Pinxten Rianne , Eens Marcel , Rödel Heiko G. , d’Ettorre Patrizia
Published: October 2022

How individual differences translate into group outcomes is a timely and debated issue. Recent studies, especially in social arthropods and fish, focus on diversity of personality traits. These studies suggest that the phenotypic group assortment by personality type of an animal group, including the presence of “keystone” individuals, leads to group-level personality differences and can strongly impact both group and individual outcomes. However, little attention has been given to the variation of a given trait within a group. Theory predicts that phenotypic homogeneity rather than heterogeneity yields the optimal group performance, especially in an anti-predatory context, but the experimental support includes mainly morphological traits, e.g. body size or colouration. Here, we focus on personality and group level differences in a highly gregarious bird, the European starling (Sturnus vulgaris). We investigated how different degrees of within-flock variation in exploration affect flock outcomes in exploratory behaviour and in escape response after a frightening stimulus. First, we established consistent individual differences in exploration. Then, flocks of 4 birds were formed to obtain gradual differences in mean and in variation of exploration scores among flocks. Flocks underwent an exploration test and a perturbation test. More exploratory individuals entered the test arena earlier, tended to start flying more rapidly and also stopped flying sooner upon frightening. Flocks with a more homogeneous distribution with respect to this personality trait were significantly faster to enter the test room, but no effect on the escape response emerged. The mean exploration tendency of the flock or the maximum exploration tendency of purported ‘key’ individuals within groups did not play a notable role in explaining such differences in group performance. Our results indicate that it is not the individual that predicts/drives the flock outcome, but rather a group feature, namely phenotypic variation within the group.
OVGP1 is an oviductal fluid factor essential particularly for early embryonic development in golden hamsters
Authors: Yamatoya Kenji , Kurosawa Masaru , Hirose Michiko , Miura Yoshiki , Taka Hikari , Nakano Tomoyuki , Hasegawa Akiko , Kagami Kyosuke , Yoshitake Hiroshi , Goto Kaoru , Ueno Takashi , Fujiwara Hiroshi , Shinkai Yoichi , Kan Frederick W. K. , Ogura Atsuo , Araki Yoshihiko
Published: October 2022

The mammalian oviductal lumen is a specialized chamber that provides an environment that strictly regulates fertilization an early embryogenesis, the regulatory mechanisms to gametes/zygote are still largely unknown. In this report, we studied the oviductal regulation of early embryonic development usingOvgp1(a gene encoding an oviductal humoral factor, OVGP1)-knockout (KO) hamsters. The experimental results revealed the following: 1) FemaleOvgp1-KO hamsters fail to produce any litters at all; 2) In the oviducts from KO animal, fertilized eggs are sometimes identified, but their morphology shows abnormal features; 3) The number of implantations in the KO females is evidently low; 4) Even if implantations occur, the embryos develop abnormally and eventually become embryonic lethal; and 5)Ovgp1-KO females transferred to wild-type females produce KO egg-derived litters, but the reverse experiment does not. These results suggest that OVGP1-mediated physiological events are crucial for early embryonic developmentin vivo. This animal model shows that the fate of the fertilized egg is not only genetically determined, but that the surrounding oviductal microenvironment plays a pivotal role in normal embryonic development.

Summary statement

Deficiency an oviductal humoral factor (OVGP1) caused female infertility in the golden hamsters. The presence or absence of OVGP1 has significant physiological effects on early embryonic developmentin vivo.
Territorial aggression in male bower-building cichlidsNyassachromiscf.microcephalusis disrupted by exposure to environmental concentrations of fluoxetine
Authors: Lee Paige , Smith Alan , King Hannah , Gilbert James , Morrell Lesley , Joyce Domino
Published: October 2022

Selective serotonin reuptake inhibitors (SSRIs) are commonly prescribed drugs for treating human depression, but the role of serotonin—often called the happy chemical—is complex, associated with the regulation of appetite, anxiety, aggression, and more. With such psychoactive pharmaceuticals being increasingly detected in aquatic environments and their effects on non-target species an uncertainty, this study seeks to investigate how inhibiting the serotonin pathway with the SSRI fluoxetine affects territorial aggression, using the cichlid fishNyassachromiscf.microcephalusas a model. Males of this sand-dwelling Lake Malawi species build bowers to attract females within a lekking system, where male-male competition is intense. Being aggressive in defending against intruders would serve to maximise mating opportunities and reproductive success for the territory holding male. However, after a one-week exposure to fluoxetine at environmentally relevant concentrations, a decline in aggression was observed in the male cichlids. This implies the serotonergic system plays an important role in modulating aggression and therefore sexual selection in cichlid fishes, and that environmental pollution has the potential to disrupt these behaviours.
Natural hybridisation reduces vulnerability to climate change
Authors: Brauer Chris J. , Sandoval-Castillo Jonathan , Gates Katie , Hammer Michael , Unmack Peter J. , Bernatchez Louis , Beheregaray Luciano B.
Published: October 2022

Understanding how species can respond to climate change is a major global challenge. Species unable to track their niche via range shifts are largely reliant on genetic variation to adapt and persist. Genomic vulnerability predictions are used to identify populations that lack the necessary variation, particularly at climate relevant genes. However, hybridization as a source of novel adaptive variation is typically ignored in genomic vulnerability studies. We estimated environmental niche models and genomic vulnerability for closely related species of rainbowfish (Melanotaeniaspp.) across an elevational gradient in the Australian wet tropics. Hybrid populations between a widespread generalist and narrow range endemics exhibited reduced vulnerability to projected climates compared to pure narrow endemics. Overlaps between introgressed and adaptive genomic regions were consistent with a signal of adaptive introgression. Our findings highlight the often-underappreciated conservation value of hybrid populations and indicate that adaptive introgression may contribute to evolutionary rescue of species with narrow environmental ranges.
Contribution of genetics and lifestyle to the risk of major cardiovascular and thromboembolic complications following COVID-19
Authors: Xie Junqing , Feng Yuliang , Newby Danielle , Zheng Bang , Feng Qi , Prats-Uribe Albert , Li Chunxiao , Wareham Nicholas J , Paredes R , Prieto-Alhambra Daniel
Published: October 2022

Clinical determinants for cardiovascular and thromboembolic (CVE) complications of COVID-19 are well-understood, but the roles of genetics and lifestyle remain unknown. We performed a prospective cohort study using UK Biobank, including 25,335 participants with confirmed SARS-CoV-2 infection between March 1, 2020, and September 3, 2021. Outcomes were hospital-diagnosed atrial fibrillation (AF), coronary artery disease (CAD), ischemic stroke (ISS), and venous thromboembolism (VTE) within 90 days post-infection. Heritable risk was represented by validated polygenic risk scores (PRSs). Lifestyle was defined by a composite of nine variables. We estimated adjusted hazard ratios (aHR) and confidence intervals (CI) using Cox proportional hazards models. In the COVID-19 acute phase, PRSs linearly predicted a higher risk of AF (aHR 1.52 per standard deviation increase, 95% CI 1.39 to 1.67), CAD (1.59, 1.40 to 1.81), and VTE (1.30, 1.11 to 1.53), but not ISS (0.92, 0.64 to 1.33). A healthy lifestyle was associated with a substantially lower risk of post-COVID-19 AF (0.70, 0.53 to 0.92), CAD (0.64, 0.44 to 0.91), and ISS (0.28, 0.12 to0.64), but not VTE (0.82, 0.48 to 1.39), compared with an unhealthy lifestyle. No evidence for interactions between genetics and lifestyle was found. Our results demonstrated that population genetics and lifestyle considerably influence cardiovascular complications following COVID-19, with implications for future personalised thromboprophylaxis and healthy lifestyle campaigns to offset the elevated cardiovascular disease burden imposed by the ongoing pandemic.
Quantitative Relationship between Intracellular Metabolic Responses against Nutrient Conditions and Metabolic Inhibitions
Authors: Yamagishi Jumpei F , Hatakeyama Tetsuhiro S
Published: October 2022

Many previous studies have attempted to predict the metabolic states of cells assuming metabolic regulation is optimized through (sometimes artificial) evolution for some objective, e.g., growth rate or production of some metabolites. Conventional approaches, however, require identifying the microscopic details of individual metabolic reactions and the objective functions of cells, and their predictions sensitively depend on such details. In this study, we focus on the responses of metabolic systems to environmental perturbations, rather than their metabolic states themselves, and theoretically demonstrate a universal property of the responses independent of the systems’ details. With the help of a microeconomic theory, we show a simple relationship between intracellular metabolic responses against nutrient abundance and metabolic inhibition due to manipulation such as drug administration: these two experimentally measurable quantities show a proportional relationship with a negative coefficient. This quantitative relationship should hold in arbitrary metabolic systems as long as the law of mass conservation holds and cells are optimized for some objectives, but the true objective functions need not be known. Through numerical calculations using large-scale metabolic networks such as theE. colicore model, we confirmed that the relationship is valid from abstract to detailed models. Because the relationship provides quantitative predictions regarding metabolic responses without prior knowledge of systems, our findings have implications for experimental applications in microbiology, systems biology, metabolic engineering, and medicine, particularly for unexplored organisms or cells.
3D morphometric analysis of mouse skulls using microcomputed tomography and computer vision
Authors: Gulner Beatrice R. , Navabi Zahra S. , Kodandaramaiah Suhasa B.
Published: October 2022

Morphometric studies have provided crucial insights into the skull anatomy of commonly used wildtype (WT) laboratory mice strains such as the C57BL/6. With the increasing use of transgenic (TG) animals in neuroscience research, it is important to determine whether the results from morphometric studies performed on WT strains can be extended to TG strains derived from these WT strains. We report a new computer vision-based analysis pipeline for surveying mouse skull morphology using microcomputed tomography (μCT) scans. We applied this pipeline to study and compare eight cohorts of adult mice from two strains, including both male and female mice at two age points. We found that the overall skull morphology was generally conserved between cohorts, with only 13% of landmark distance differences reaching statistical significance. In addition, we surveyed the dorsal skull bone thickness differences between cohorts. We observed significantly thicker dorsal, parietal, and/or interparietal bones in WT, male, or older mice for 53% of thickness comparisons. This knowledge of dorsal skull bone thickness has potential implications for surgical planning through skull imaging and has applications in automating cranial microsurgeries on mice.
The protist ubiquitin ligase effector PbE3-2 targets RD21A to impede plant immunity
Authors: Li Chao , Luo Shaofeng , Feng Lu , Wang Qianqian , Cheng Jiasen , Xie Jiatao , Lin Yang , Fu Yanping , Jiang Daohong , Chen Tao
Published: October 2022

Clubroot caused by the soil-borne protist pathogenPlasmodiophora brassicaeis one of the most devastating diseases of Brassica oil and vegetable crops worldwide. Understanding the pathogen infection strategy is crucial for the development of disease control. However, the molecular mechanism by which this pathogen promotes infection remains largely unknown. Here, we identified aP. brassicae-secreted effector PbE3-2 that impedes plant immunity by ubiquitinating the immune regulator RD21A for degradation. Overexpression ofPbE3-2inArabidopsis thalianaresulted in higher susceptibility toP. brassicaeand decreases in chitin-triggered reactive oxygen species burst and expression of marker genes in salicylic acid signaling. PbE3-2 interacted with and ubiquitinated RD21Ain vitroandin vivo. Mutant plants deficient inRD21Aexhibited similar susceptibility and compromsied immune responses as inPbE3-2overexpression plants. These results suggest thatP. brassicaepromotes clubroot disease through RD21A degradation mediated by the effector PbE3-2. As PbE3-2 is widely conserved across differentP. brassicaepathotypes, the degradation of RD21A by PbE3-2 might be a prevalent infection strategy in this pathogen.
Interactome analysis identifies MSMEI_3879 as a substrate ofMycolicibacterium smegmatisClpC1
Authors: Ogbonna Emmanuel , Bheemreddy Priyanka , Schmitz Karl R.
Published: October 2022

The prevalence of drug resistantMycobacterium tuberculosisinfections has prompted extensive efforts to exploit new mycobacterial drug targets. ClpC1, the unfoldase component of the essential ClpC1P1P2 protease, has emerged as one particularly promising antibacterial target. However, efforts to identify and characterize ClpC1-targeting compounds are constrained by our limited knowledge of Clp protease function and regulation. To expand our understanding of ClpC1 physiology, we employed a co-immunoprecipitation and mass spectrometry workflow to identify proteins that interact with ClpC1 inMycolicibacterium smegmatis, a relative ofM. tuberculosis.We identify a diverse panel of interaction partners, many of which make co-immunoprecipitate with both the regulatory N-terminal domain and the ATPase core of ClpC1. Notably, our interactome analysis identifies MSMEI_3879, a truncated gene product unique toM. smegmatis, as a novel proteolytic substrate. Degradation of MSMEI_3879 by ClpC1P1P2in vitrorequires an exposed N-terminal sequence, reinforcing the idea that ClpC1 selectively recognizes disordered motifs. Fluorescent substrates incorporating MSMEI_3879 may be useful in screening for novel ClpC1-targeting antibiotics, to help address the challenge ofM. tuberculosisdrug resistance.
NanoBlot: A Simple Tool for Visualization of RNA Isoform Usage From Third Generation RNA-sequencing Data
Authors: DeMario Samuel , Xu Kevin , He Kevin , Chanfreau Guillaume
Published: October 2022

RT-PCR and Northern blots have long been used to study RNA isoforms usage for single genes. Recently, advancements in long read sequencing have yielded unprecedented information about the usage and abundance of these RNA isoforms. However, visualization of long-read sequencing data remains challenging due to the high information density. To alleviate these issues we have developed NanoBlot, a simple, open-source, command line tool, which generates Northern blot and RT-PCR-like images from third generation sequencing data. NanoBlot accepts processed bam files. Plotting is based around ggplot2 and is easily customizable. Advantages of NanoBlots include: designing probes to visualize isoforms which would be impossible with traditional RT-PCR or Northern blots, excluding reads from the Nanoblots based on the presence or absence of a specified region and, multiplexing plots with multiple colors. We present examples of NanoBlots compared to actual northern blot data. In addition to traditional gel-like images, NanoBlot also outputs other visualizations such as violin plots. The use of Nanoblot should provide a simple answer to the challenge of visualization of long-read RNA sequencing data.
Sensitivity to direction and velocity of fast frequency chirps in the inferior colliculus of awake rabbit
Authors: Mitchell Paul W. , Henry Kenneth S. , Carney Laurel H.
Published: October 2022

Neurons in the mammalian inferior colliculus (IC) are sensitive to the velocity (speed and direction) of fast frequency chirps contained in Schroeder-phase harmonic complexes (SCHR). However, IC neurons are also sensitive to stimulus periodicity, a prominent feature of SCHR stimuli. Here, to disentangle velocity sensitivity from periodicity tuning, we introduced a novel stimulus consisting of aperiodic random chirps. Extracellular, single-unit recordings were made in the IC of Dutch-belted rabbits in response to both SCHR and aperiodic chirps. Rate-velocity functions were constructed from aperiodic-chirp responses and compared to SCHR rate profiles, revealing interactions between stimulus periodicity and neural velocity sensitivity. A generalized linear model analysis demonstrated that periodicity tuning influences SCHR response rates more strongly than velocity sensitivity. Principal component analysis of rate-velocity functions revealed that neurons were more often sensitive to the direction of lower-velocity chirps and were less often sensitive to the direction of higher-velocity chirps. Overall, these results demonstrate that sensitivity to chirp velocity is common in the IC. Harmonic sounds with complex phase spectra, such as speech and music, contain chirps, and velocity sensitivity would shape IC responses to these sounds.

Highlights

IC neurons had diverse sensitivity to chirp velocity (speed and direction) of periodic and aperiodic-chirp stimuli.

Both velocity and periodicity sensitivity were necessary to predict neural responses to Schroeder-phase harmonic complexes.

Neurons were more commonly sensitive to the direction of chirps at lower-speeds (e.g., < 2 kHz/ms) than higher-speeds (e.g., > 2 kHz/ms) in the tested range.

The chirp speeds for which IC neurons were most sensitive are present in common harmonic sounds with realistic phase spectra, such as speech and music.
Performance evaluation of new fluorescent-based lateral flow immunoassay for quantification of HbA1c in diabetic patients
Authors: Younes Nadin , Al Ghwairi Mahmoud M. , Majdalawieh Amin F. , Al-Dweik Nader , Nasrallah Gheyath K.
Published: October 2022

Background

Rapid and constant HbA1c level monitoring is essential in slowing the progression of Type 2 diabetes. This need becomes challenging in low resources countries where the social burden of the disease is overwhelming. Recently, fluorescent-based lateral flow immunoassays (LFIAs) gained wide attention for small or non-laboratory settings and population surveillance.

Aim

This study aim to evaluate the performance of novel fluorescence-based LFIA Finecare™ HbA1c Rapid Quantitative Test for quantitative measurement of HbA1c along with its reader (Model No. FS-113).

Methods

We conducted a retrospective study using 147 samples (fingerstick and venepuncture whole blood samples) analysed by Finecare™ HbA1c Rapid Quantitative Test. For validating Finecare™ measurements, results were compared with results of the reference assay: Roche Cobas Pro c 503.

Results

Finecare™ showed 92.7% sensitivity and 94.7% specificity compared to the Roche Cobas Pro c 503 using fingerstick whole blood samples. On the other hand, Finecare™ showed 98.7% sensitivity and 100% specificity compared to the Roche Cobas Pro c 503 using venepuncture blood samples. Cohen’s Kappa statistic denoted excellent agreement with Roche Cobas Pro c 503, with values being 0.84 (95% CI: 0.72-0.97) and 0.97 (95% CI: 0.92-1.00) using fingerstick whole blood samples and venous blood, respectively. In addition, a strong correlation was observed between Finecare™/Roche Cobas Pro c 503 (r>0.9,p<0.0001) with fingerstick and venous blood samples. Most importantly, Finecare™ showed a significant difference between the normal, pre-diabetic, and diabetic samples (p<0.001).

Conclusion

Finecare™ is a reliable assay and can be easily implemented for long-term monitoring of HbA1c in diabetic patients, particularly in none or small laboratory settings.
Investigation of physical properties of Si crystallites in W/Si multilayers
Authors: Chkhalo N. I. , Garakhin S. A. , Kumar N. , Nikolaev K. V. , Polkovnikov V. N. , Rogachev A. , Svechnikov M. V. , Tatarsky D. A. , Yakunin S. N.
Published: October 2022

The structural inhomogeneities of silicon films embedded within W/Si multilayer mirrors were studied by X-ray reflection, grazing-incidence small-angle X-ray scattering (GISAXS) and X-ray photoelectron spectroscopy (XPS). In the diffuse scattering spectra, evidence of laterally and vertically ordered in-layer inhomogeneities was consistently observed. In particular, specific substructures resonant in nature (named here `ridges') were detected. The properties of the ridges were similar to the roughness determined by quasi-Bragg peaks of scattering, which required a high interlayer correlation of particles. The XPS showed the nanocrystalline nature of the Si particles in the amorphous matrix. The geometric characteristics and in-layer and inter-layer correlations of the nanoparticles were determined. In GISAXS imaging, the unusual splitting of the waists between the Bragg sheets into filament structures was observed, whose physical nature cannot yet be explained.
Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8
Authors: Preussner Marco , Santos Karine F. , Alles Jonathan , Heroven Christina , Heyd Florian , Wahl Markus C. , Weber Gert
Published: October 2022

Small nuclear ribonucleoprotein complexes (snRNPs) represent the main subunits of the spliceosome. While the assembly of the snRNP core particles has been well characterized, comparably little is known of the incorporation of snRNP-specific proteins and the mechanisms of snRNP recycling. U5 snRNP assembly in yeast requires binding of the the Aar2 protein to Prp8p as a placeholder to preclude premature assembly of the SNRNP200 helicase, but the role of the human AAR2 homolog has not yet been investigated in detail. Here, a crystal structure of human AAR2 in complex with the RNase H-like domain of the U5-specific PRPF8 (PRP8F RH) is reported, revealing a significantly different interaction between the two proteins compared with that in yeast. Based on the structure of the AAR2–PRPF8 RH complex, the importance of the interacting regions and residues was probed and AAR2 variants were designed that failed to stably bind PRPF8 in vitro. Protein-interaction studies of AAR2 with U5 proteins using size-exclusion chromatography reveal similarities and marked differences in the interaction patterns compared with yeast Aar2p and imply phosphorylation-dependent regulation of AAR2 reminiscent of that in yeast. It is found that in vitro AAR2 seems to lock PRPF8 RH in a conformation that is only compatible with the first transesterification step of the splicing reaction and blocks a conformational switch to the step 2-like, Mg2+-coordinated conformation that is likely during U5 snRNP biogenesis. These findings extend the picture of AAR2 PRP8 interaction from yeast to humans and indicate a function for AAR2 in the spliceosomal assembly process beyond its role as an SNRNP200 placeholder in yeast.
The antibacterial activity and biochemical composition of Adansonia Digitata edible parts
Authors: El Yahyaoui Ouafae , Bouabid Bahia , Ait Ouaaziz Nabil , El Bakkali Mohamed , El Harche Hanae , Lrhorfi Lalla Aicha , Nakari Kamal , Bengueddour Rachid
Published: October 2022

Purpose

Within the framework of the valorization of natural resources, a characterization of the biochemical composition of the edible parts of Adansonia Digitata is applied. The antibacterial effect against bacteria is also realized and compared to some synthetic antibiotics.

Design/methodology/approach

The biochemical characterization is carried out according to the norms of the French Association of Normalization, methods of Association of Official Analytical Chemists (AOAC International) and gas chromatography (GC). The antibacterial activity is tested by disk diffusion on a solid medium. Parametric tests are used to compare the differences between groups and heat maps to show the expression of the mean inhibitions according to the studied parameters. Multivariate logistic modeling is applied to study the effect of extracts and antibiotics on bacteria.

Findings

Biochemical characterization showed a variable importance of proteins, fibers and total sugars, with the presence of highly desired fatty acids such as palmitic, oleic, stearic, linoleic and a-linolenic acids. This gives the tested parts important energy values, especially in the seeds very rich in fatty acids. Methanol proved to be a better extraction solvent than dichloromethane. Antibacterial activity showed that pulp and leaves extracted with methanol had quite similar inhibitory activities against Enterococcus faecalis ATCC29212 and that this effect was better than some antibiotics. Multivariate analysis showed that the leaves had a similar effect to antibiotics, and a significant effect against Staphylococcus aureus ATCC29213.

Originality/value

This important activity and the attractive nutritional value of this plant could justify its extensive use in the traditional pharmacopoeia.
The impact of corporate governance and firm-specific characteristics on dividend policy: an emerging market case
Authors: Farooq Muhammad , Al-Jabri Qadri , Khan Muhammad Tahir , Ali Ansari Muhamamad Akbar , Tariq Rehan Bin
Published: October 2022

Purpose

The present study aims to investigate the impact of corporate governance proxies by ownership structure and firm-specific characteristics, i.e. firm size, leverage, growth opportunities, previous year dividend, firm risk, profitability, and liquidity on dividend behavior of the Pakistan Stock Exchange (PSX) listed firms.

Design/methodology/approach

Final sample of the study consists of 140 PSX-listed firms. The study covers a period of six years, starting from 2015 to 2020. Dividend payout dummy, dividend payout ratio, and dividend yield were used to assess the dividend behavior of the sample firms. The appropriate regression procedures (logistic, probit, ordinary least square (OLS), and fixed effect regression) are used to test the study hypothesis. To check the robustness of the result, a system GMM estimation technique is also used in the present study.

Findings

The study reveals that institutional ownership, foreign ownership, and individual ownership have a significant positive whereas managerial ownership has a significant negative impact on the dividend decision of sample firms. Among firm-specific characteristics, it was found that liquidity, profitability, and the previous year's dividend were significantly positive, while growth opportunities were significantly inversely associated with dividend payout decisions of PSX-listed firms.

Practical implications

This study sheds light on the relationship between dividend policy, ownership structure, and firm-specific factors in the context of an emerging market like Pakistan. The study's findings have important implications for managers, minority shareholders, lawmakers, and investors looking for guidance on the dividend policy of publicly-traded non-financial firms.

Originality/value

The literature lacks studies that together analyze the ownership characteristics and firm-specific variables on dividend decisions, particularly in the context of developing economies. The current study aims to fill this gap.
The corporate risk-taking and performance of politically connected firms: evidence from Malaysia
Authors: Chin Alice , Lye Ooi Chin , Najaf Khakan
Published: October 2022

Purpose

One of the significant components of a firm's overall sustainability is establishing and nurturing governance. This study attempts to understand how politically connected firms maintain sustainability measures in terms of risk-taking strategies. This paper has two purposes. The first purpose is to provide empirical evidence on the politically connected (PC) firms' corporate risk-taking and performance. The second purpose is to investigate the moderating impact of PC firms' risk on corporate performance.

Design/methodology/approach

To conduct the analysis to test our hypothesis efficiently, data has been collected from Bloomberg and annual reports of all Malaysian PC and non-PC companies. The final sample comprises 561 firms over the investigation period 2010–2019. The methodology entails Ordinary Least Squares (OLS) regressions of the impact of the PC firms on corporate risk-taking and performance. The authors also conduct t-tests of the equality of means of corporate risk-taking and performance between PC and non-PC companies.

Findings

The authors’ results show that politically connected firms undertake significant less corporate risk and relish higher financial performance than their counterparts. It implicatively insinuates that the presence of a politician on the board enables the management to mitigate the risk-taking, which makes the firms more profitable. The authors’ results corroborate network theory, suggesting that political ties alleviate the agency issue and safeguard the shareholders' interest.

Research limitations/implications

The study's results were important as they highlighted the sustainable development of PC and non-PC companies, offering insights to researchers, policymakers, regulators, financial report users, investors, environmental unions, employees, clients and society.

Originality/value

This paper is novel since it is unique in evaluating sustainable practice in PC and non-PC firms.
Data mining analytics investigation on TikTok users' behaviors: social media app development
Authors: Liao Shu-hsien , Widowati Retno , Lee Ching-Yu
Published: October 2022

Purpose

TikTok, a social media application (app), was originally positioned as a short music video community suitable for young users, and the app is user-generated content (UGC) short video of vertical music. Users can make their own creative videos. Following the rhythm of the music, users can shoot various video content, personal talents, life records, performances, dances, plot interpretations, etc. However, what are the profiles and preferences of TikTok users, whereby the social media app is mainly developed by UGC? What is the impact of TikTok on the development of social media? In addition, what is UGC's social media model for user interactions in social networks? The purpose of this paper is to address and study these proposed issues.

Design/methodology/approach

All questionnaire items are designed as nominal and ordinal scales (not Likert scale). The obtained data from questionnaires are put into the relational database (N = 2,011). This empirical study takes Taiwan TikTok users as the research object, implements data mining analytics to generate user profiles through clustering analysis and further uses association rules’ analysis to analyze social media apps in social network interaction and social apps’ development by proposing two patterns and several meaningful rules.

Findings

This study finds that social media apps is a valuable practical research topic on online social media development. In addition, besides the TikTok, the authors eagerly await subsequent research to provide more valuable findings of social media apps in both theory and practice.

Originality/value

This study presents the research evidences that social media apps such as TikTok will be able to transcend the current development pattern of social media and make good use of the media and technology innovation of apps in social development and social informatics.
“One of these things is not like the others”: the role of authentic leadership in cross-cultural leadership development
Authors: Lewis Clif P. , Aldossari Maryam
Published: October 2022

Purpose

The purpose of this research is to explore a possible relationship between the presence of authentic organisational leadership and the leadership development experience.

Design/methodology/approach

This study uses a qualitative exploratory hybrid research design which draws on data from multiple sources. Data were collected by means of semi-structured interviews, document analysis and non-participant observations across two case study organisations in Saudi Arabia.

Findings

The authors' findings suggest that the presence of authentic leadership (AL) within an organisation is a significant factor in the leadership development experience. This study also highlights the key importance of advancing leadership development theory that is holistic and comprehensive.

Research limitations/implications

The study was conducted as case studies within a specific social context. Findings cannot be generalised but offer valuable direction for future research.

Originality/value

The research advances leadership development theory by highlighting the inadequacy of the person-focussed perspective and offering exploratory evidence for the role of social context, organisational leadership and organisational artefacts in the leadership development process.
Police stress: the role of occupational culture and officer characteristics
Authors: Paoline III Eugene A. , Gau Jacinta M.
Published: October 2022

Purpose

The purpose of the current study was to augment the police culture and stress literature by empirically examining the impact of features of the internal and external work environment, as well as officer characteristics, on police officer stress.

Design/methodology/approach

The current empirical inquiry utilized survey data collected from street-level officers in a mid-sized urban police department in a southern region of the United States (n = 349).

Findings

This study revealed that perceived danger, suspicion of citizens and cynicism toward the public increased police occupational stress, while support from supervisors mitigated it. In addition, Black and Latinx officers reported significantly less stress than their White counterparts.

Research limitations/implications

While this study demonstrates that patrol officers' perceptions of the external and internal work environments (and race/ethnicity) matter in terms of occupational stress, it is not without limitations. One limitation related to the generalizability of the findings, as results are gleaned from a single large agency serving a metropolitan jurisdiction in the Southeast. Second, this study focused on cultural attitudes and stress, although exact connections to behaviors are more speculative. Finally, the survey took place prior to the onset of the COVID-19 pandemic and the killing of George Floyd (and others), which radically shook police–community relationships nationwide.

Practical implications

Police administrators should be cognizant of the importance that views of them have for patrol officer stress levels. Moreover, police trainers and supervisors concerned with occupational stress of their subordinates should work toward altering assignments and socialization patterns so that officers are exposed to a variety of patrol areas, in avoiding prolonged assignments of high social distress.

Originality/value

The study augmented the police culture and stress literature by empirically uncovering the individual-level sources of patrol officers' job-related stress. This study builds off of Paoline and Gau's (2018) research using data collected some 15 years ago by examining a more contemporary, post–Ferguson, context.
Tone complexity and the cost of debt retrospective data from the USA
Authors: Bendriouch Fatimazahra , Jabbouri Imad , Satt Harit , Jariri Zineb , M'hamdi Mohamed
Published: October 2022

Purpose

This paper explores the impact of tone complexity on the cost of debt in the USA.

Design/methodology/approach

A sampling from 692 publicly nonfinancial-traded companies in the USA is employed over the period between 2010 and 2018. Generalized methods of moments (GMM) model is implemented to examine the impact of tone complexity on the cost of debt and its implications upon creditors and users.

Findings

The findings show that high-tone complexity is associated with a greater cost of debt. The use of a more complex tone in a company's annual reports has been shown to influence creditors' perceptions of risk.

Originality/value

This research pursues innovation by examining how creditors can use the tone complexity of annual report to assess the level of information asymmetry and estimate the required rate of return accordingly.
Training value, employee internal states and training transfer: examining the web of relationships
Authors: Andoh Raphael Papa Kweku , Owusu Emmanuel Afreh , Annan-Prah Elizabeth Cornelia , Boampong Georgina Nyantakyiwaa
Published: October 2022

Purpose

This study aims to examine the web of relationships among training value, employee internal states (psychological empowerment, employee engagement and motivation to transfer) and training transfer.

Design/methodology/approach

Data is obtained from different categories of employees a few months after attending different training programs organized by their organization. Structural equation modeling is used to analyze the data. Bias-corrected and accelerated (BCa) confidence intervals are used to determine the significance of the hypothesized paths.

Findings

This study finds that training value relates to motivation to transfer, psychological empowerment and employee engagement. Motivation to transfer also relates to training transfer and employee engagement. Again, psychological empowerment relates to motivation to transfer, employee engagement and training transfer. Concerning the mediated relationship, psychological empowerment and motivation to transfer fully mediate the relationship between training value and training transfer.

Practical implications

Internal states must be the focus of human resource department (HRD) scholars in their quest to discover training transfer improvement mechanisms. HRD practitioners and organizations generally should also prioritize the enhancement of the internal states of employees to aid training transfer.

Originality/value

In this study, training transfer facilitating factors particularly employee internal states are explored by examining the web of relationships comprising training value, motivation to transfer, psychological empowerment, employee engagement and training transfer in a pentagonal model using a homogeneous sample with a common understanding of training transfer due to the similarities in their training as well as job conditions.