bluuebunny/crossref_metadata_2025 huggingface dataset:
Monitoring the battleground: Antimicrobial resistance, antibiofilm patterns, and virulence factors of wound bacterial isolates from patients in hospital system
Authors: Awuor Silas O. , Mariita Richard , Omwenga Eric O. , Musila Jonathan , Musyoki Stanslaus
Published: January 2023

Extensive use of antibiotics in the treatment of bacterial infections has led to a challenge of antibiotic resistance, contributing to morbidity and mortality. Herein, evaluation of bacterial isolates from patients with wound discharge was performed and drug susceptibility patterns examined, with a goal of deciphering antibacterial resistance. A cross-sectional study was conducted between March to June 2022, in which samples were collected from patients with chronic wounds and were inoculated into appropriate media for identification and characterization. The bacterial pathogens were identified using standard microbiological methods. Shockingly, the majority of wound isolates showed positive growth in microbial analysis with high prevalence in male candidates. Further,Staphylococcus aureus28 (20.7%) was identified as the most predominant pathogen followed byKlebsiella spp. 20 (14.8%),P. aeruginosa spp. 10 (14.8%) and lastlyE. coli6 (4.4%) bacteria in the wound isolates while cotrimoxazole 13 (48.1%) followed by clindamycin 7 (25.9%) and erythromycin 7 (25.9%) were the most antibacterial resistant drugs to both Gram positive and Gram-negative bacteria. Out of the four isolates, 3 (75%) isolates were able to produce the haemolysin and protease and 2 (50%) isolates were able to produce the lipase and phospholipase. The findings herein form a clinical basis for identification of antimicrobial resistance in chronic wounds that can be applied in responsible use of antibacterial in chronic wound management and as an illumination in development of more potent antibiotics for chronic wound treatment
Genomic characterization of multidrug-resistant extended spectrum β-lactamase-producingKlebsiella pneumoniaefrom clinical samples of a tertiary hospital in South Kivu Province, eastern Democratic Republic of Congo
Authors: Irenge Leonid M. , Ambroise Jérôme , Bearzatto Bertrand , Durant Jean-François , Bonjean Maxime , Gala Jean-Luc
Published: January 2023

Multidrug-resistant (MDR) and Extended Spectrum β-Lactamase (ESBL)-producing extraintestinalK. pneumoniaeare associated with increased morbidity and mortality. This study aimed to characterize the resistance and virulence profiles of extra-intestinal MDR ESBL-producingK. pneumoniaeassociated with infections at a tertiary hospital in South-Kivu province, DRC. Whole-genome sequencing (WGS) was carried out on 37 K.pneumoniaeisolates displaying MDR, and ESBL-producing phenotype. The assembled genomes were analysed for phylogeny, virulence factors and antimicrobial resistance genes (ARG) determinants. These isolates were compared to sub-Saharan counterparts.K. pneumoniaeisolates displayed a high genetic variability with up to 16 sequence types (ST). AMR was widespread against β-lactamases (including third and fourth-generation cephalosporins, but not carbapenems), aminoglycosides, ciprofloxacin, tetracycline, erythromycin, nitrofurantoin, and cotrimoxazole. TheblaCTXM-15gene was the most common β-lactamase gene amongK. pneumoniaeisolates. No carbapenemase gene was found. ARG for aminoglycosides, quinolones, phenicols, tetracyclines, sulfonamides, nitrofurantoin were widely distributed among the isolates. Nine isolates had the colistin-resistant R256G substitution in thepmrBefflux pump gene without displaying reduced susceptibility to colistin. Despite carrying virulence genes, none had hypervirulence genes. Our results highlight the genetic diversity of MDR ESBL-producingK. pneumoniaeisolates, and underscore the importance of monitoring simultaneously the evolution of phenotypic and genotypic AMR in Bukavu and DRC, while calling for caution in administering colistin and carbapenem to patients.
Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing
Authors: Klaproth-Andrade Daniela , Hingerl Johannes , Smith Nicholas H. , Träuble Jakob , Wilhelm Mathias , Gagneur Julien
Published: January 2023

Unlike for DNA and RNA, accurate and high-throughput sequencing methods for proteins are lacking, hindering the utility of proteomics in applications where the sequences are unknown including variant calling, neoepitope identification, and metaproteomics. We introduce Spectralis, a new de novo peptide sequencing method for tandem mass spectrometry. Spectralis leverages several innovations including a new convolutional neural network layer connecting peaks in spectra spaced by amino acid masses, proposing fragment ion series classification as a pivotal task for de novo peptide sequencing, and a new peptide-spectrum confidence score. On spectra for which database search provided a ground truth, Spectralis surpassed 40% sensitivity at 90% precision, nearly doubling state-of-the-art sensitivity. Application to unidentified spectra confirmed its superiority and showcased its applicability to variant calling. Altogether, these algorithmic innovations and the substantial sensitivity increase in the high-precision range constitute an important step toward broadly applicable peptide sequencing.
A glia cell dependent mechanism at a peripheral nerve plexus critical for target-selective axon regeneration
Authors: Walker Lauren J , Guevara Camilo , Kawakami Koichi , Granato Michael
Published: January 2023

A critical step for functional recovery from peripheral nerve injury is for regenerating axons to connect with their pre-injury targets. Reestablishing pre-injury target specificity is particularly challenging for limb-innervating axons as they encounter a plexus, a network where peripheral nerves converge, axons from different nerves intermingle, and then re-sort into target-specific bundles. Here, we examine this process at a plexus located at the base of the zebrafish pectoral fin, equivalent to tetrapod forelimbs. Using live cell imaging and sparse axon labeling, we find that regenerating motor axons from three nerves coalesce into the plexus. There, they intermingle and sort into distinct branches, and then navigate to their original muscle domains with high fidelity that restores functionality. We demonstrate that this regeneration process includes selective retraction of mistargeted axons, suggesting active correction mechanisms. Moreover, we find that Schwann cells are enriched and associate with axons at the plexus, and that Schwann cell ablation during regeneration causes profound axonal mistargeting. Our data provide the first real time account of regenerating vertebrate motor axons navigating a nerve plexus and reveal a previously unappreciated role for Schwann cells to promote axon sorting at a plexus during regeneration.
The complex inhibitory mechanism of glycomimetics with human heparanase
Authors: Whitefield Cassidy , Vo Yen , Schwartz Brett D , Hepburn Caryn , Ahmed F. Hafna , Onagi Hideki , Banwell Martin G. , Nelms Keats , Malins Lara R. , Jackson Colin J
Published: January 2023

Heparanase (HPSE) is the only mammalian endo-β-glucuronidase known to catalyse the degradation of heparan sulfate. Dysfunction of HPSE activity has been linked to several disease states, resulting in HPSE becoming the target of numerous therapeutic programs, yet no drug has passed clinical trials to date. Pentosan polysulfate sodium (PPS) is a heterogeneous FDA-approved drug for the treatment of interstitial cystitis and a known HPSE inhibitor. However, due to its heterogeneity, characterisation of its mechanism of HPSE inhibition is challenging. Here we show that inhibition of HPSE by PPS is complex, involving multiple overlapping binding events, each influenced by factors such as oligosaccharide length and inhibitor-induced changes in protein secondary structure. The present work advances our molecular understanding of the inhibition of HPSE, which will aid the development of therapeutics for the treatment of a broad range of pathologies associated with enzyme dysfunction including cancer, inflammatory disease and viral infections.
Bouts of rest and physical activity in C57BL/6J mice
Authors: Pernold K. , Rullman E. , Ulfhake B.
Published: January 2023

The objective was to exploit the raw data output from a scalable home cage (type IIL IVC) monitoring (HCM) system (DVC®), to characterize pattern of undisrupted rest and physical activity (PA) of C57BL/6J mice. The system’s tracking algorithm show that mice in isolation spend 67% of the time in bouts of long rest (≥40s) and 59 % of the time was interpreted as sleep. Twenty percent is physical activity (PA), split equally between local movements and locomotion. Decomposition revealed that a day contains ∼6500 discrete bouts of short and long rest, local and locomotor movements. Mice travel ∼330m per day, mainly during the dark hours, while travelling speed is similar through the light-dark cycle. Locomotor bouts are usually <0.2m and <1% are >1m. Tracking revealed also fits of abnormal behaviour. The starting positions of the bouts showed no preference for the rear over the front of the cage floor, while there was a strong bias for the peripheral (75%) over the central floor area. The composition of bouts has a characteristic circadian pattern, however, intrusive husbandry routines increased bout fragmentation by ∼40%.

Extracting electrode activations density (EAD) from the raw data yielded results close to those obtained with the tracking algorithm, with 59% of time in long rest (<1 EAD s-1) and 20% in PA. We confirm that EAD correlates closely with movement distance (rs>0.95) and the data agreed in ∼96% of the file time. Thus, albeit EAD being less informative it may serve as a proxy for PA and rest, enabling monitoring group housed mice. The data show that a change in housing density from one to two, and up to three mice had the same effect size on EAD (∼2) with no difference between sexes. The EAD deviated significantly from this stepwise increase with 4 mice per cage, suggesting a crowdedness stress inducing sex specific adaptations.

We conclude that informative metrics on rest and PA can be automatically extracted from the raw data flow in near-real time (< 1 hrs). These metrics relay useful longitudinal information to those that use or care for the animals.
Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur)
Authors: Łazowski Krystian
Published: January 2023

Almost 80 years since the publication of the seminal work by Salvador Luria and Max Delbrück, the fluctuation assay has remained an important tool for analysing the levels of mutagenesis in microbial populations. The mutant counts originating from some average number of mutations are usually assumed to obey the Luria–Delbrück distribution. While several tools for estimating mutation rates are available, they sometimes lack accuracy or versatility under non-standard conditions. In this work we developed extensions to the Luria– Delbrück protocol to account for phenotypic lag and cellular death with either perfect or partial plating. Hence, our novel MLE MUtation Rate calculator, or mlemur, is the first tool that provides a user-friendly graphical interface allowing the researchers to model their data with consideration for partial plating, differential growth of mutants and non-mutants, phenotypic lag, cellular death, variability of the final number of cells, post-exponential-phase mutations, and the size of inoculum. Additionally, mlemur allows the users to incorporate most of these special conditions at the same time to obtain highly accurate estimates of mutation rates andpvalues, confidence intervals for an arbitrary function of data (such as fold) and perform power analysis and sample size determination for the likelihood ratio test. We assess the accuracy of point and interval estimates produced by mlemur against historical and simulated fluctuation experiments. We believe both mlemur and the analyses in this work might be of great help when evaluating fluctuation experiments and increase the awareness of the limitations of the widely-used Lea–Coulson formulation of the Luria-Delbrück distribution in the more realistic biological contexts.

Author Summary

Despite many recent developments in the department of fluctuation data analysis, geneticists are often limited to either a very strict classical Luria–Delbrück protocol, or possibly a modified one with relaxation of just one assumption (e.g., differential fitness of mutants and wild-type cells). In some cases, such as partial plating, researchers use historical methods whose accuracy strictly depends on the conditions of the experiment and thus are not optimal in a wide range of parameters. A novel tool for fluctuation data analysis, mlemur (MLE MUtation Rate calculator), alleviates these problems and provides new extensions that allow to account for phenotypic lag and cellular death. Additionally, we find that the failure to properly account for these additional parameters might lead to inaccurate point and interval estimates of the mutation rate. Our results underline the importance of careful examination of the fluctuation assay to ensure that the chosen statistical model reflects the biological and technical conditions of the experiment.
Compulsivity is linked to maladaptive choice variability but unaltered reinforcement learning under uncertainty
Authors: Lee Junseok K. , Rouault Marion , Wyart Valentin
Published: January 2023

Compulsivity has been associated with variable behavior under uncertainty. However, previous work has not distinguished between two main sources of behavioral variability: the stochastic selection of choice options that do not maximize expected reward (choice variability), and random noise in the reinforcement learning process that updates option values from choice outcomes (learning variability). Here we studied the relation between dimensional compulsivity and behavioral variability, using a computational model which dissociates its two sources. We found that compulsivity is associated with more frequent switches between options, triggered by increased choice variability but no change in learning variability. This effect of compulsivity on the ‘trait’ component of choice variability is observed even in conditions where this source of behavioral variability yields no cognitive benefits. These findings indicate that compulsive individuals make variable and maladaptive choices under uncertainty, but do not hold degraded representations of option values.
Metabolic engineering of anthocyanin pathway inArtemisia annuacells does not exclude the expression of artemisinin pathway
Authors: Judd Rika , Dong Yilun , Sun Xiaoyan , Zhu Yue , Li Mingzhuo , Xie De-Yu
Published: January 2023

Artemisia annuais the only medicinal crop to produce artemisinin for the treatment of malignant malaria. Unfortunately, hundreds of thousands of people still lose their life every year due to the lack of sufficient artemisinin. Artemisinin is considered to result from the spontaneous autoxidation of dihydroartemisinic acid in the presence of reactive oxygen species (ROS) in an oxidative condition of glandular trichomes (GTs),; however, whether increasing antioxidative compounds can inhibit artemisinin biosynthesis in plant cells is unknown. Anthocyanins are potent antioxidants that can remove ROS in plant cells. To date, no anthocyanins have been structurally elucidated fromA. annua. In this study, our goals were to engineer anthocyanins inA. annuacells and to understand the artemisinin biosynthesis in anthocyanin-producing cells. ArabidopsisPAP1(AtPAP1) was used to engineer four types of transgenic anthocyanin-producingA. annua(TAPA1 to 4) cells. Three wild type cell types were developed as controls. TAPA1 cells produced the highest contents of total anthocyanins. LC-MS analysis detected 17 anthocyanin or anthocyanidin compounds. Crystallization, LC/MS/MS and NMR analyses identified cyanidin, pelargonidin, one cyanin, and one pelargonin. An integrative analysis characterized that four types of TAPA cells expressed the artemisinin pathway and TAPA1 cells produced the highest artemisinin and artemisinic acid. The contents of arteannuin B were similar in seven cell types. These data showed that the engineering of anthocyanins does not eliminate the biosynthesis of artemisinin in cells. These data allow us to propose a new hypothesis that enzymes catalyze the formation of artemisinin from DHAA in non-GT cells. These findings show a new platform to increase artemisinin production via non-GT cells ofA. annua.
Bacterial muropeptides promote OXPHOS and suppress mitochondrial stress in normal and human mitochondrial disease models
Authors: Tian Dong , Cui Mingxue , Han Min
Published: January 2023

Mitochondrial dysfunction critically contributes to many major human diseases but effective therapeutic methods to combat mitochondrial dysfunction are lacking1,2. Mitochondria of animal cells are sites of interaction between gut microbial metabolites and host factors, and many such interactions may be beneficial to mitochondrial health and host physiology3, albeit that specific beneficial interactions and the underlying mechanisms remain to be uncovered. Here we report the role of muropeptides derived from bacterial cell wall peptidoglycan (PG) in promoting mitochondrial functions in mammalian models. We found that muropeptides directly bind to ATP synthase, which stabilizes the complex and promotes its activity. The benefit is seen in increased oxidative respiration and mitochondrial membrane potential, as well as decreased oxidative stress in human intestinal epithelial cells (IECs). Strikingly, we also found that muropeptide treatment can recover mitochondrial structure and functions, as well as inhibit several pathological phenotypes of mutant fibroblast cells derived from mitochondrial disease patients. In mice, we show muropeptides accumulate in mitochondria of IECs and promote small intestinal homeostasis and nutrient absorption by modulating energy metabolism. This study identifies ATP synthase as a muropeptide receptor and the corresponding physiological function in mammals, and points to a potential treatment for human mitochondrial dysfunction diseases.

Highlights

Bacterial muropeptides bind and stabilize ATP synthase complex and enhance its activity

Muropeptides enhance mitochondrial OXPHOS in human IECs

Muropeptides recover mitochondrial structure and functions in mitochondrial disease cells

Muropeptides promote small intestinal epithelial homeostasis and nutrient uptake in mice
Low dimensional criticality embedded in high dimensional awake brain dynamics
Authors: Fontenele Antonio J. , Sooter J. Samuel , Norman V. Kindler , Gautam Shree Hari , Shew Woodrow L.
Published: January 2023

Whether cortical neurons operate in a strongly or weakly correlated dynamical regime determines fundamental information processing capabilities and has fueled decades of debate. Here we offer a resolution of this debate; we show that two important dynamical regimes, typically considered incompatible, can coexist in the same local cortical circuit by separating them into two different subspaces. In awake mouse motor cortex, we find a low-dimensional subspace with large fluctuations consistent with criticality – a dynamical regime with moderate correlations and multi-scale information capacity and transmission. Orthogonal to this critical subspace, we find a high-dimensional subspace containing a desynchronized dynamical regime, which may optimize input discrimination. The critical subspace is apparent only at long timescales, which explains discrepancies among some previous studies. Using a computational model, we show that the emergence of a low-dimensional critical subspace at large timescale agrees with established theory of critical dynamics. Our results suggest that cortex leverages its high dimensionality to multiplex dynamical regimes across different subspaces.

Teaser

Temporal coarse-graining reveals a low-dimensional critical subspace coexistent with a desynchronized subspace in awake cortex.
Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in earlyDrosophilaembryos
Authors: Syed Sahla , Duan Yifei , Lim Bomyi
Published: January 2023

It is well known that enhancers regulate the spatiotemporal expression of their target genes by recruiting transcription factors (TFs) to the cognate binding sites in the region. However, the role of multiple binding sites for the same TFs and their specific spatial arrangement in determining the overall competency of the enhancer has yet to be fully understood. In this study, we utilized the MS2-MCP live imaging technique to quantitatively analyze the regulatory logic of thesnaildistal enhancer in earlyDrosophilaembryos. Through systematic modulation of Dorsal and Twist binding motifs in this enhancer, we found that a mutation in any one of these binding sites causes a drastic reduction in transcriptional amplitude, resulting in a reduction in total mRNA production of the target gene. We provide evidence of synergy, such that multiple binding sites with moderate affinities cooperatively recruit more TFs to drive stronger transcriptional activity than a single site. Moreover, a Hidden Markov-based stochastic model of transcription reveals that embryos with mutated binding sites have a higher probability of returning to the inactive promoter state. We propose that TF-DNA binding regulates spatial and temporal gene expression and drives robust pattern formation by modulating transcriptional kinetics and tuning bursting rates.
Dihydroxy-Metabolites of Dihomo-gamma-linolenic Acid Drive Ferroptosis-Mediated Neurodegeneration
Authors: Sarparast Morteza , Pourmand Elham , Hinman Jennifer , Vonarx Derek , Reason Tommy , Zhang Fan , Paithankar Shreya , Chen Bin , Borhan Babak , Watts Jennifer L. , Alan Jamie , Lee Kin Sing Stephen
Published: January 2023

Even after decades of research, the mechanism of neurodegeneration remains understudied, hindering the discovery of effective treatments for neurodegenerative diseases. Recent reports suggest that ferroptosis could be a novel therapeutic target for neurodegenerative diseases. While polyunsaturated fatty acid (PUFA) plays an important role in neurodegeneration and ferroptosis, how PUFAs may trigger these processes remains largely unknown. PUFA metabolites from cytochrome P450 and epoxide hydrolase metabolic pathways may modulate neurodegeneration. Here, we test the hypothesis that specific PUFAs regulate neurodegeneration through the action of their downstream metabolites by affecting ferroptosis. We find that the PUFA, dihomo gamma linolenic acid (DGLA), specifically induces ferroptosis-mediated neurodegeneration in dopaminergic neurons. Using synthetic chemical probes, targeted metabolomics, and genetic mutants, we show that DGLA triggers neurodegeneration upon conversion to dihydroxyeicosadienoic acid through the action of CYP-EH, representing a new class of lipid metabolite that induces neurodegeneration via ferroptosis.
Impaired migration and premature differentiation underlie the neurological phenotype associated with PCDH12 loss of function
Authors: Rakotomamonjy Jennifer , Rylaarsdam Lauren , Fares-Taie Lucas , McDermott Sean , Davies Devin , Yang George , Fagbemi Fikayo , Epstein Maya , Guemez-Gamboa Alicia
Published: January 2023

Protocadherins (PCDHs) are cell adhesion molecules that regulate many essential neurodevelopmental processes related to neuronal maturation, dendritic arbor formation, axon pathfinding, and synaptic plasticity. Bi-allelic loss-of-function variants inPCDH12are associated with several neurodevelopmental disorders (NDDs) such as diencephalic-mesencephalic dysplasia syndrome, cerebral palsy, cerebellar ataxia, and microcephaly. Despite the highly deleterious outcome resulting from loss of PCDH12, little is known about its role during brain development and disease. Here, we show that PCDH12 loss severely impairs cerebral organoid development with reduced proliferative areas and disrupted laminar organization. 2D models further show that neural progenitor cells lacking PCDH12 prematurely exit cell cycle and differentiate earlier when compared to wildtype. Furthermore, we show that PCDH12 regulates neuronal migration through a mechanism requiring ADAM10-mediated ectodomain shedding and membrane recruitment of cytoskeleton regulators. Our data demonstrate a critical and broad involvement of PCDH12 in cortical development, revealing the pathogenic mechanisms underlying PCDH12-related NDDs.
Omicron Spike Protein Is Vulnerable to Reduction
Authors: Yao Zhong , Geng Betty , Marcon Edyta , Pu Shuye , Tang Hua , Merluza John , Bello Alexander , Snider Jamie , Lu Ping , Wood Heidi , Stagljar Igor
Published: January 2023

SARS-CoV-2 virus spike (S) protein is an envelope protein responsible for binding to the ACE2 receptor, driving subsequent entry into host cells. The existence of multiple disulfide bonds in the S protein makes it potentially susceptible to reductive cleavage. Using a tri-part split luciferase-based binding assay, we evaluated the impacts of chemical reduction on S proteins from different virus variants and found that those from the Omicron family are highly vulnerable to reduction. Through manipulation of different Omicron mutations, we found that alterations in the receptor binding module (RBM) are the major determinants of this vulnerability. Specifically we discovered that Omicron mutations facilitate the cleavage of C480-C488 and C379-C432 disulfides, which consequently impairs binding activity and protein stability. The vulnerability of Omicron S proteins suggests a mechanism that can be harnessed to treat specific SARS-CoV-2 strains.
Case report: olaparib use in metastatic lung adenocarcinoma withBRCA2pathogenic variant
Authors: Soon Jian Hao Jonathan , Hoai Chan Sock , Weng Daniel Tan Shao , Ngeow Joanne , Chiang Jianbang
Published: January 2023

Poly (ADP-ribose) polymerase (PARP) inhibitors have been approved in malignancies associated with germlineBRCA1orBRCA2pathogenic variants, such as breast, ovarian, prostate, and pancreatic cancer. In malignancies not associated with germlineBRCA1orBRCA2pathogenic variants, the therapeutic relevance of PARP inhibitors is less clear. Non-small-cell lung cancer (NSCLC) is known to demonstrate somatic alterations inBRCA1orBRCA2gene. The current report is on a gentleman with metastatic lung adenocarcinoma with a somaticBRCA2pathogenic variant, who was effectively treated with olaparib. Furthermore, we discuss the existing data for use of PARP inhibitors in NSCLC. This study highlights the utility of next-generation sequencing in identifying gene mutations and demonstrates how such information can be used to select targeted therapies in patients with actionable molecular alterations.
Homology-Directed Repair by CRISPR–Cas9 Mutagenesis inXenopusUsing Long Single-Stranded Donor DNA Templates via Simple Microinjection of Embryos
Authors: Nakayama Takuya , Grainger Robert M. , Cha Sang-Wook
Published: January 2023

We describe a step-by-step procedure to perform homology-directed repair (HDR)-mediated precise gene editing inXenopusembryos using long single-stranded DNA (lssDNA) as a donor template for HDR in conjunction with the CRISPR–Cas9 system. A key advantage of this method is that it relies on simple microinjection of fertilizedXenopuseggs, resulting in high yield of healthy founder embryos. These embryos are screened for those animals carrying the precisely mutated locus to then generate homozygous and/or heterozygous mutant lines in the F1generation. Therefore, we can avoid the more challenging “oocyte host transfer” technique, which is particularly difficult forXenopus tropicalis, that is required for an alternate HDR approach. Several key points of this protocol are (1) to use efficiently active single-guide RNAs for targeting, (2) to use properly designed lssDNAs, and (3) to use 5′-end phosphorothioate-modification to obtain higher-efficiency HDR.
Long-Term Brain Organotypic Cultures of the Turquoise KillifishNothobranchius furzeri
Authors: Bagnoli Sara , Brogi Letizia , Fronte Baldassare , Bibbiani Carlo , Terzibasi Tozzini Eva , Cellerino Alessandro
Published: January 2023

Organotypic culture is a well-established method for culturing ex vivo tissue samples. The advantages of culturing tissue slices for prolonged time periods ex vivo are numerous and consist primarily of the maintenance of the overall in vivo architecture of the isolated sample, the lack of the ematoencephalic barrier, and the ease of pharmacological treatments and interventions that can be conducted under controlled conditions as in in vitro systems such as cell cultures. Given the extremely short life span ofNothobranchius furzeriand the emergence of aging signs only after a few months of life, it is of particular interest to establish this protocol forN. furzerias a potential method to study brain aging ex vivo.
RNA In Situ Hybridization of Whole-Mount Mosquito Olfactory Tissues
Authors: Herre Margaret
Published: January 2023

This protocol presents a method for RNA in situ hybridization of whole-mounted preparations of mosquito antennae and maxillary palps. It can be adapted for other peripheral appendages such as the legs or proboscis.
Data reduction for X-ray serial crystallography using machine learning
Authors: Rahmani Vahid , Nawaz Shah , Pennicard David , Setty Shabarish Pala Ramakantha , Graafsma Heinz
Published: January 2023

Serial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large-scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the `bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.
Crystal structure of caesium dimethyl-N-benzoylamidophosphate monohydrate
Authors: Kariaka Nataliia S. , Dyakonenko Viktoriya V. , Shishkina Svitlana V. , Sliva Tatiana Yu. , Amirkhanov Vladimir M.
Published: January 2023

The caesium salt of dimethyl-N-benzoylamidophosphate, namely, aqua[dimethyl (N-benzoylamido-κO)phosphonato-κO]caesium, [Cs(C9H11NO4P)(H2O)] or CsL·H2O, is reported. The compound crystallizes in the monoclinic crystal system in the P21/c space group and forms a mono-periodic polymeric structure due to the bridging function of the dimethyl-N-benzoylamidophosphate anions towards the caesium cations.
Synthesis, characterization, and crystal structures of N,N′-bis(2-dialkylaminophenyl)thioureas
Authors: Lee Kyounghoon
Published: January 2023

N,N′-Bis[2-(dimethylamino)phenyl]thiourea, C17H22N4S (1), and N,N′-bis[2-(diethylamino)phenyl]thiourea, C21H30N4S (2), were prepared by the treatment of 1,1′-thiocarbonyldiimidazole and 2 equivalents of 2-amino-N,N′-dialkylaniline. Both compounds exhibit intramolecular hydrogen bonds between the N—H(thiourea) and NR
2 (R = Me, Et) groups. The other N—H bonds face the sulfur atoms of S=C bonds in an adjacent molecule, which forms an intermolecular interaction in the packed structure. The structural details match the spectroscopic data acquired from NMR and IR spectroscopy.
4-(Allyloxy)benzohydrazide
Authors: Khan Sultana Shakila , Howlader Md. Belayet Hossain , Miyatake Ryuta , Sheikh Md. Chanmiya , Zangrando Ennio
Published: January 2023

The non-H atoms of the title compound, C10H12N2O2, are approximately coplanar with the exception of those at the ends: the terminal allyl carbon atom and terminal hydrazide nitrogen atom are displaced from the mean plane by 0.67 (2) and 0.20 (2) Å, respectively. In the crystal, the molecules are linked by N—H...O and N—H...N hydrogen bonds, which give rise a two-dimensional network propagating in the (001) plane.
5,8-Dihydroxy-2,2-dimethyl-12-(3-methylbut-2-enyl)pyrano[3,2-b]xanthen-6-one (brasixanthone B)
Authors: Binti Seruji Nurr Maria Ulfa , Rosli Mohd Mustaqim , Jong Vivien Yi Mian , Karunakaran Thiruventhan , Lizazman Mas Atikah , Marlina Anita , Binti Halid Yanti Yana
Published: January 2023

The title compound (trivial name brasixanthone B), C23H22O5, isolated from Calophyllum gracilentum, is characterized by a xanthone skeleton of three fused six-membered rings plus an additional fused pyrano ring and one 3-methylbut-2-enyl side chain. The core xanthone moiety is almost planar, with a maximum deviation 0.057 (4) Å from the mean plane. In the molecule, an intramolecular O—H...O hydrogen bond forms an S(6) ring motif. The crystal structure features intermolecular O—H...O and C—H...O interactions.
(S)-2-[(S)-2,2,2-Trifluoro-1-hydroxyethyl]-1-tetralone
Authors: Motaln Klemen , Cotman Andrej Emanuel , Lozinšek Matic
Published: January 2023

The crystal structure of the title compound, C12H11F3O2, was elucidated by low-temperature single-crystal X-ray diffraction. The enantiopure compound crystallizes in the Sohncke space group P21 and features one molecule in the asymmetric unit. The structure displays intermolecular O—H...O hydrogen bonding, which links the molecules into infinite chains propagating parallel to [010]. The absolute configuration was established from anomalous dispersion.
1H-Benzo[g]pteridine-2,4-dione
Authors: Uppu Rao M. , Fronczek Frank R.
Published: January 2023

The structure of the title compound, C10H6N4O2, reported by Smalley et al. [(2021). Cryst. Growth Des.
22, 524–534] from powder diffraction data and 15N NMR spectroscopy, is confirmed using low-temperature data from a twinned crystal. The tautomer in the solid state is alloxazine (1H-benzo[g]pteridine-2,4-dione) rather than isoalloxazine (10H-benzo[g]pteridine-2,4-dione). In the extended structure, the molecules form hydrogen-bonded chains propagating in the [0\overline{1}1] direction through alternating centrosymmetric R
2
2(8) rings with pairwise N—H...O interactions and centrosymmetric R
2
2(8) rings with pairwise N—H...N interactions. The crystal chosen for data collection was found to be a non-merohedral twin (180° rotation about [001]) in a 0.446 (4):0.554 (6) domain ratio.
‘Be a game changer and keep the ball rolling’: exploring linkages between football clubs, charitable foundations and doing good
Authors: Hyndman Noel , Liguori Mariannunziata
Published: January 2023

Purpose

There has been limited research on why football clubs contribute to charity. This paper examines how football clubs and their charitable conduits report information when discussing their connectedness. In addition, it explores reasons why, and the extent to which, football clubs support altruism via such charitable vehicles.

Design/methodology/approach

Case studies of four major football teams (Manchester City/Manchester United in England and AC Milan/Inter Milan in Italy) are discussed, with formal reports of the clubs and their associated charitable conduits being analysed.

Findings

Boundaries between the clubs and their charitable conduits are frequently blurred. Evidence suggests that acknowledging the co-existence of different factors may help to understand what is reported by these organisations and address some of the caveats in terms of autonomy and probity of their activities and reporting practices.

Research limitations/implications

The research uses case studies of four major ‘powerhouses’ of the game and their associated charitable spinoffs. While this is innovative and novel, expanding the research to investigate more clubs and their charitable endeavours would allow greater generalisations.

Practical implications

The study provides material that can be used to reflect on the very topical subject of ‘sportswashing’. This has the potential to input to deliberations relating to the future governance of the game.

Originality/value

The paper explores relationships between businesses and charities/nonprofits in a sector so far little investigated from a charitable accountability perspective. It suggests that motives for engaging in charitable activity and highlighting such engagement may extend beyond normal altruism or warm-glow emotions.
Factors related to corporate social responsibility implementation: the case of mobile operators in the Kingdom of Bahrain
Authors: Al-Alawi Adel Ismail , BinZaiman Fatima Abdulrahman , Elnaggar Nehal F.
Published: January 2023

Purpose

This paper aims to examine the factors affecting the implementation of corporate social responsibility (CSR) sustainably in mobile operators in the kingdom of Bahrain.

Design/methodology/approach

The research relies on the existing literature as a secondary data source. The primary data was collected through questionnaires distributed to three leading mobile operators in the Kingdom of Bahrain. The research's population numbered 1,689, and the sample size was 313; the simple random sampling method was used for data collection with a response rate of 87.2% out of a total sample size of 273 respondents. In addition, the responses were analyzed using statistical package for the social sciences (SPSS) software version 24.0; specifically, Spearman's rank correlation was used to test the hypotheses. The research design was quantitative, so a nonparametric procedure was applied to test the hypotheses.

Findings

The research produced positive relationships between the independent variables (economic, legal, ethical, philanthropic and environmental responsibilities) and the dependent variable: CSR implementation by Bahrain mobile operators; therefore, the five proposed hypotheses were accepted; furthermore, the highest positive correlation coefficient was 0.735 for environmental responsibility, and the lowest correlation coefficient was 0.533 for economic responsibility.

Research limitations/implications

The research produced positive relationships between the independent variables (economic responsibility, legal responsibility, ethical responsibility, philanthropic responsibility and environmental responsibility) and the dependent variable: CSR implementation by Bahrain mobile operators; therefore, the five proposed hypotheses were accepted; furthermore, the highest positive correlation coefficient was 0.735 for environmental responsibility, and the lowest correlation coefficient was 0.533 for economic responsibility.

Social implications

The outcomes of the research mainly suggest that mobile operators assign employees who have been working with the company for more than 7 years to implement CSR; due to their engagement to implement CSR as a sustainable practice more than others with less than 3 years or 3-6 years in Bahrain mobile operators. Besides, the research provides a starting point by which other researchers could investigate CSR in other sectors in the Kingdom of Bahrain.

Originality/value

The research provided a framework for Bahrain mobile operators to assist them in enhancing the implementation of CSR in a sustainable manner, which are economic, legal, ethical, philanthropic and environmental responsibilities.
Evaluation of the integration of industrialization and information-based entropy AHP–cross-efficiency DEA model
Authors: Zhu Jianhua , Wan Luxin , Zhao Huijuan , Yu Longzhen , Xiao Siyu
Published: January 2023

Purpose

The purpose of this paper is to provide scientific guidance for the integration of industrialization and information (TIOII). In recent years, TIOII has promoted the development of intelligent manufacturing in China. However, many enterprises blindly invest in TIOII, which affects their normal production and operation.

Design/methodology/approach

This study establishes an efficiency evaluation model for TIOII. In this paper, entropy analytic hierarchy process (AHP) constraint cone and cross-efficiency are added based on traditional data envelopment analysis (DEA) model, and entropy AHP–cross-efficiency DEA model is proposed. Then, statistical analysis is carried out on the integration efficiency of enterprises in Guangzhou using cross-sectional data, and the traditional DEA model and entropy AHP–cross-efficiency DEA model are used to analyze the integration efficiency of enterprises.

Findings

The data show that the efficiency of enterprise integration is at a medium level in Guangzhou. The efficiency of enterprise integration has no significant relationship with enterprise size and production type but has a low negative correlation with the development level of enterprise integration. In addition, the improved DEA model can better reflect the real integration efficiency of enterprises and obtain complete ranking results.

Originality/value

By adding the entropy AHP constraint cone and cross-efficiency, the traditional DEA model is improved. The improved DEA model can better reflect the real efficiency of TIOII and obtain complete ranking results.
Design and dimensioning of a test bench for investigating the relationship between critical temperature and axial mechanical stress of GdBaCuO tape conductors
Authors: Liebrich Johannes , Kreischer Christian
Published: January 2023

Purpose

Superconductors offer several advantages compared with conventional conductors. However, it is not clear at this stage whether these types of conductors provide the same durability. For this reason, tape conductors under mechanical forces need to be studied in detail. The purpose of this paper is to investigate the relationship between critical temperature and axial mechanical stress of GdBaCuO tape conductors.

Design/methodology/approach

The paper investigates the influence of axial mechanical stresses on the critical temperature of superconductors. For these investigations, a multi-physical test rig was developed, which makes it possible to perform these types of investigations. With the presented measurement methodology, the influence of mechanical stresses on the tape conductor can be determined.

Findings

The investigations show a correlation between the critical temperature and the acting mechanical stresses. The analytically presented approach to describe the transition temperature is valid for the investigated samples. In addition, it is determined that the effects are not reversible, and therefore, permanent damage to the tape conductor is observed.

Originality/value

The presented investigations make it possible to create more accurate models of GdBaCuO tape conductors. This enables to extend the superconducting state space, which so far depends on three critical quantities, by the quantity of the axial stress.
Glasgow climate pact and the global clean energy index constituent stocks
Authors: Pandey Dharen Kumar , Kumar Rahul , Kumari Vineeta
Published: January 2023

Purpose

This study examined the impact of the Glasgow Climate Pact on the abnormal returns of global clean energy stocks. Further, this study examines which country-specific and firm-specific variables drive the cumulative abnormal returns (CARs) of clean energy stocks.

Design/methodology/approach

The authors used the event study method and cross-sectional multivariate regression model. The clean energy stocks in this study are limited to 81 constituent firms of the S&P Global Clean Energy Index across 17 nations. The final sample includes 80 firms and the sample period ranges from January 26, 2021, to December 07, 2021.

Findings

The study finds that the Glasgow Climate Pact negatively affects the stock returns of clean energy firms. Moreover, the climate change performance index (CCPI) positively impacts cumulative abnormal returns (CARs), signifying that clean energy investors react positively to firms in nations with good CCPI scores. The environmental, social and governance (ESG) measure for the shorter window (−1, +1) exhibited a negative relationship with CARs. The firm-specific variables (BTM, stock liquidity, size and past returns) exhibit a negative relationship with CARs in different event windows.

Research limitations/implications

The authors use the CCPI as a proxy for the stringency of environmental policies in any nation. The authors extend the existing literature by employing firm-specific variables and supporting previous findings. Their findings have policy implications for clean energy investors, policymakers and other market participants.

Practical implications

Climate risks impact the global financial market, so the findings have implications for global regulatory bodies. Currently, there are bankruptcy cases due to climate risks. Because financial markets must play a critical role in shifting the economy toward a green one, regulators can use the cross-sectional drivers of this study to shape policy. It is also critical for regulators to reduce stock price volatility in the event of the implementation of environmental regulations and improve environmental disclosures by publicly traded companies. Furthermore, governments are interested in researching the effects of environmental regulations to protect stakeholders' interests. These regulations significantly impact emerging markets because they lack the same solid institutional frameworks as developed markets.

Originality/value

The authors provide evidence that firms with better ESG scores and larger firm sizes have experienced fewer abnormal returns, as these firms have stable financial and non-financial fundamentals. This timely study on the ongoing regulatory shift in environmental policy will help investors, policymakers, firms and other stakeholders make relevant decisions.
Developing maqasid index for Islamic CSR: the case of Ummah’s Endowment Fund in Indonesia
Authors: Ascarya Ascarya , Masrifah Atika Rukminastiti
Published: January 2023

Purpose

This study aims to develop the maqasid index (MI) for Islamic corporate social responsibility (CSR), namely, Dana Abadi Umat (DAU) (Ummah’s Endowment Fund) or MI-DAU in Indonesia.

Design/methodology/approach

Modeling and weighting are based on Delphi and analytic network process (ANP) methods, called Delphi–ANP additive weighting. The Delphi method was applied to design and validate the factors of the MI-DAU model, and the ANP method was applied to generate and validate weights for these factors. Finally, the MI-DAU is calculated, based on the planned budget and actual allocation of DAU returns, called the maslahah fund, using additive weighting.

Findings

Delphi and ANP show significant and robust results. The priority order and weights of maqasid Shariah are safeguard the faith (0.32), safeguard the intellect (0.219), safeguard the life (0.204), safeguard the wealth (0.171) and safeguard the lineage (0.104). Meanwhile, the priority order and weights of the main activities are education (0.190), Ummah’s economy (0.167), Hajj service (0.155), Da’wah (0.124), health care (0.118), social-religious (0.097), worship facilities (0.085) and disaster emergency response (0.065). Finally, the results of MI-DAU show a high index in 2019 and 2020 of 71.89 and 69.51, respectively, generated from allocation ratio of 90.63% and 85.98%, respectively.

Research limitations/implications

Maqasid Shariah used in this study follows Al-Ghazali, where it could also follow maqasid Shariah of Abu Zahrah or Al-Najjar. Moreover, the MI-DAU score uses additive calculations, where it can also use Pentagon calculation.

Practical implications

The improved framework and method used to design MI-DAU in this study could be applied to design more scientific MI for other Islamic financial institutions.

Originality/value

The novelty of this study is in the improved method used to design the MI model, including its factors, using Delphi, and to assign weights of all factors using ANP, where both provide validation for more robust MI model.