bluuebunny/crossref_metadata_2025 huggingface dataset:
The Enterococcus secretome inhibits the growth of Mycobacterium tuberculosis complex mycobacteria
Authors: Achache Wafaa , Mege Jean Louis , Fellag Mustapha , Drancourt Michel
Published: June 2023

A corrigendum of this article has been published full details can be found at https://doi.org/10.1099/acmi.0.000843

Enterococcus mundtii

, a commensal intestinal bacterium, was demonstrated to inhibit the growth of some

Mycobacterium tuberculosis

complex (MTC) species that cause tuberculosis in humans and mammals. To further explore this preliminary observation, we cross-investigated five

E. mundtii

strains and seven MTC strains representative of four MTC species using a standardized quantitative agar well diffusion assay. All five

E. mundtii

strains, calibrated at 10 MacFarland, inhibited the growth of all

M. tuberculosis

strains with various susceptibility profiles, but no inhibition was observed with lower inoculums. Further, eight

E. mundtii

freeze-dried cell-free culture supernatants (CFCS) inhibited the growth of

M. tuberculosis

, Mycobacterium africanum, Mycobacterium bovis and Mycobacterium canettii, the most susceptible MTC species (inhibition diameter 25±1 mm), proportionally to CFCS protein concentrations. The data reported here indicate that the

E. mundtii

secretome inhibited growth of all MTC species of medical interest, which broadens previously reported data. In the gut, the

E. mundtii

secretome may modulate the expression of tuberculosis, exhibiting an anti-tuberculosis effect, with some protective roles in human and animal health.
Febrile sepsis: first report of human disease due to Paenibacillus silvae
Authors: Vecchia Ilaria Dalla , Fasan Daniele , Pegoraro Manuela , Benedetti Paolo
Published: June 2023

Introduction.

Paenibacillus

species are saprophytes widely distributed in nature and rarely associated with overt human infection. Most cases have been described in people with important comorbidities and/or immunodepression. We report here what is, to the best of our knowledge, the first documented case of human disease due to

Paenibacillus silvae

, so far considered an exclusively environmental micro-organism.

Case presentation. A 57-year-old female patient was referred to our Unit after a 2 month history of remittent fever. Upon admission, a septic state and bacteraemia were revealed; P. sylvae was identified by 16S rRNA gene amplification and sequencing with matrix-assisted laser desorption/ionization-time of flight MS. The patient became afebrile after 9 days of antibiotic treatment and was completely cured after a 2 week regimen with intravenous amoxicillin-clavulanate plus oral doxycycline.

Conclusion. The patient did not report any previous episode of infection. Most of the well-known risk factors to

Paenibacillus

bacteraemia, i.e. invasive procedures, use of intravenous drugs and foreign bodies, could be excluded, although her immune system was probably impaired due to obesity and heavy smoking. We suggest that the isolation of bacteria belonging to the genus

Paenibacillus

should not be disregarded, since there is accumulating evidence that these organisms may cause disease even in immunocompetent subjects.
LEPTOSPIRAL 3-HYDROXYACYL-COA DEHYDROGENASE AS A POTENTIAL EARLY URINARY BIOMARKER OF LEPTOSPIROSIS IN A SRI LANKAN SETTING
Authors: Karunadasa A.K.U.I. , Toma Claudia , Senaratne Pavani , Kumara K.G.R.A. , Herath T.M. , Pathirage M.M.K. , Gamage Chandika D
Published: June 2023

Introduction: Leptospirosis is a globally widespread zoonotic disease. The 3-hydroxyacyl-CoA dehydrogenase (3-HADH) enzyme is of leptospiral origin, excreted in the urine of infected individuals.
Gap statement: The potential of 3-HADH as a biomarker for leptospirosis diagnosis has never been investigated in Sri Lanka. A technique capable of identifying Leptospira in a patient using urine will be valuable in regular diagnostics as well as huge epidemic scenarios, as opposed to existing serological approaches.
Aim: This study aimed to develop and evaluate an enzyme-linked immunosorbent assay (ELISA) that can detect 3-HADH enzyme in the urine of acute leptospirosis confirmed patients, thereby to assess its potential as a screening test for leptospirosis.
Method: Laboratory confirmation of acute leptospirosis was done by flaB-nested PCR for plasma samples of suspected patients. The ELISA-based determination of the presence of 3-HADH in the urine of PCR positive patients versus PCR negative patients matched with fever date was done by coating ELISA plates with supernatants of urine and using rabbit anti-3-HADH as the primary antibody.
Results: A total of 158 febrile patients were assessed, and a majority of 121 (76.6%) were males. Out of the 15 flaB nested-PCR positive patients, 12 were in the acute phase of febrile illness. According to the ROC analysis, the best cut-off was an ODav value of 0.22 for febrile patients. Sensitivity and Specificity were calculated as 83.33%, 95% CI (51.59% to 97.91%) and 83.33%, 95% CI (76.05% to 89.13%), respectively. The ODav values of PCR positive patients in the acute phase of disease (less than or equal to 7 days of fever) were significantly higher than ODav values of the same phase of PCR negative patients, as shown by independent samples Mann-Whitney U test (p<0.001, U=114.0, z= -4.946).
Conclusion: Detection of 3-HADH in urine by ELISA seems promising for screening acute leptospirosis in suspected patients.
Spartinivicinus marinus sp. nov., isolated from intertidal sediment
Authors: Liu Ji-Qing , He Xiao-Yan , Gu Tie-Ji , Wang Jia-Xuan , Liu Ning-Hua , Chen Xiu-Lan , Zhang Yu-Zhong , Song Xiao-Yan , Zhang Xi-Ying
Published: June 2023

A Gram-stain-negative, aerobic, flagellated, and long rod-shaped bacterium, designated strain SM1973T, was isolated from an intertidal sediment sample collected from the coast of Qingdao, PR China. Strain SM1973T grew at 15–37 °C and with 0–5.5 % NaCl. It reduced nitrate to nitrite and hydrolysed aesculin but did not hydrolyse casein and gelatin. The strain showed the highest 16S rRNA gene sequence similarity (98.2 %) to the type strain of

Spartinivicinus ruber

. The phylogenetic trees based on the 16S rRNA genes and single-copy orthologous clusters showed that strain SM1973T clustered with

S. ruber

, forming a separate lineage within the family

Zooshikellaceae

. The major cellular fatty acids were summed feature 3 (C16 : 1
ω7с and/or C16 : 1
ω6с) and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The main respiratory quinone was ubiquinone-9. The genomic DNA G+C content of strain SM1973T was 40.4 mol%. Based on the polyphasic evidence presented in this paper, strain SM1973T is considered to represent a novel species within the genus

Spartinivicinus

, for which the name Spartinivicinus marinus sp. nov. is proposed. The type strain is SM1973T (=MCCC 1K04833T=KCTC 72846T).
Leisingera thetidis sp. nov., isolated from coastal water
Authors: Kim Min-Ju , Guan Yong , Choe Hanna , Li Zhun , Chung Namhyun , Kang Yoon-Ho , Lee Mi-Kyung
Published: June 2023

A Gram-strain-negative, strictly aerobic, rod-shaped, catalase-positive, oxidase-positive and pinkish beige colony-forming bacterial strain designated as BMJM1T was isolated from a marine sample collected from coastal water near Tongyeong, Republic of Korea. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that BMJM1T represents a member of the genus

Leisingera

as it is closely related to

Leisingera daeponensis

KCTC 12794T (98.27%),

Leisingera caerulea

DSM 24564T (97.98%),

Leisingera aquaemixtae

KCTC 32538T (97.91%),

Leisingera methylohalidivorans

DSM 14336T (97.26%) and

Leisingera aquimarina

DSM 24565T (97.25%). Optimal growth occurred at 25–30°C, pH 7.0 and with 2% NaCl. Digital DNA–DNA hybridisation (dDDH) and average nucleotide identity (ANI) values between strain BMJM1T and the closely related species of the genus

Leisingera

were below 40 and 90%, respectively, which are far below the thresholds to delineate a novel species. The predominant fatty acids (>10%) are summed feature 8 (C18:1ω7c and/or C18:1ω6c) (68.4%) and C14:1iso E (11.6%). The major polar lipids were phosphatidylethanolamine and phospholipid. The major isoprenoid quinone was ubiquinone-10. The DNA G+C content was 64.0%. On the basis of the results of the polyphasic taxonomic characterisation, BMJM1T represents a novel species of the genus

Leisingera

, for which the name is Leisingera thetidis sp. nov. is proposed, with that type strain BMJM1T (= KCTC 92110T = GDMCC 1.2992T).
Different stages of the infection cycle are enriched for Campylobacter strains with distinct phenotypes and levels of fluoroquinolone resistance
Authors: Carney Gillian , Weimer Bart C. , Clyne Marguerite , Ó Cróinín Tadhg
Published: June 2023

Campylobacter

species are the leading cause of bacterial diarrhoea worldwide and consumption of contaminated chicken meat is the most common route of infection. Chickens can be infected with multiple strains of

Campylobacter

and during the infection cycle this pathogen must survive a wide variety of environments. Numerous studies have reported a high degree of genetic variability in this pathogen that can use antigenic and phase variation to alter the expression of key phenotypes. In this study the phenotypic profile of isolates from freshly slaughtered chickens, chicken products in the supermarket and stool samples from infected patients were compared to identify phenotypic changes during the passage of the bacteria through the infection cycle. Isolates from different stages of the infection cycle had altered phenotypic profiles with isolates from human stool samples showing a lower ability to form a biofilm and an increased ability to associate with epithelial cells in vitro. Resistance to fluoroquinolones was found in all cohorts but at a much higher occurrence (94%) in isolates from supermarket chicken. Isolates displaying high levels of resistance to fluoroquinolones also were more likely to display a higher tolerance to growth in the presence of oxygen. In conclusion, isolates with specific phenotypes appear to be overly represented at different stages of the infection cycle suggesting that environmental stresses may be enriched for strains with these phenotypes.
Ancient DNA in Lycoptera Fossils: Key Discoveries for Evolution and Methodological Reassessment
Authors: Zhao Wan-Qian , Guo Zhan-Yong , Tian Zeng-Yuan , Su Tong-Fu , Cao Gang-Qiang , Qi Zi-Xin , Qin Tian-Cang , Zhou Wei , Yang Jin-Yu , Chen Ming-Jie , Zhang Xin-Ge , Zhou Chun-Yan , Zhu Chuan-Jia , Tang Meng-Fei , Wu Di , Song Mei-Rong , Guo Yu-Qi , Qiu Li-You , Liang Fei , Li Mei-Jun , Geng Jun-Hui , Zhao Li-Juan , Zhang Shu-Jie
Published: June 2023

High-quality ancient DNA (aDNA) is crucial for advancements in molecular paleontology. However, current research is often limited to fossil samples less than 1 million years old (Ma) due to DNA degradation and contamination by environmental DNA (eDNA). To overcome these limitations, we used nanoparticle affinity beads to successfully extract DNA from Lycoptera davidi fossils dating back to the Early Cretaceous period, approximately 120 Ma. Utilizing high-throughput sequencing technology, we obtained 1,258,901 DNA sequences. To ensure the accuracy and authenticity of these sequences, we established the rigorous “mega screen method.” This approach allowed us to identify 243 originalin situDNA (oriDNA) fragments likely belonging to the Lycoptera genome. These fragments have an average length of over 100 base pairs and show no signs of “deamination”. Additionally, we discovered 10 transposase coding sequences, which provide insights into a unique self-renewal mechanism within the Lycoptera genome. The update of protein-coding sequences was responsible for the significant divergence of ray-finned fishes in the Cretaceous. Surprisingly, we identified numerous hominid aDNA fragments from the fossil extracts. These fragments, probably from the environmental source during later epochs, had been deposited in the voids that formed after the fossil rocks developed. Notably, these fragments also exhibited no signs of “deamination”. This study provides invaluable data to further our understanding of fish evolution. Also, the non-remain DNA evidence offers crucial clues for anthropologists in their quest for undocumented human-like skeletons in various locations. It also shows the potential for transforming the field of molecular paleontology via studying aDNA in exceptional old rocks.
Contralateral delay activity and alpha lateralization reflect retinotopic and screen-centered reference frames in visual memory
Authors: Mössing Wanja A. , Schroeder Svea C. Y. , Biel Anna Lena , Busch Niko A.
Published: June 2023

The visual system represents objects in a lateralized manner, with contralateral cortical hemispheres responsible for left and right visual hemifields. This organization extends to visual short-term memory (VSTM), as evidenced by electrophysiological indices of VSTM maintenance: contralateral delay activity (CDA) and alpha-band lateralization. However, it remains unclear if VSTM represents object locations in gaze-centered (retinotopic) or screen-centered (spatiotopic) coordinates, especially after eye movements. In two experiments, participants encoded the colors of target objects and made a lateral saccade during the maintenance interval, thereby shifting the object’s location on the retina. A non-lateralized probe stimulus was then presented at the new fixation for a change detection task. The CDA maintained lateralization towards the target’s original retinotopic location, unaffected by subsequent saccades, and did not invert polarity even when a saccade brought that location into the opposite hemifield. We also found conventional alpha lateralization towards the target’s location before a saccade. After a saccade, however, alpha was lateralized towards the screen center regardless of the target’s original location, even in a control condition without any memory requirements. This suggest that post-saccadic alpha-band lateralization reflects attentional processes unrelated to memory, while pre- and post-saccade CDA reflect VSTM maintenance in a retinotopic reference frame.
Development and Optimisation of in vitro Sonodynamic Therapy for Glioblastoma
Authors: Keenlyside Andrew , Marples Theodore , Gao Zifan , Hu Hong , Nicely Lynden Guy , Nogales Joaquina , Li Han , Landgraf Lisa , Solth Anna , Melzer Andreas , Hossain-Ibrahim Kismet , Huang Zhihong , Banerjee Sourav , Joseph James
Published: June 2023

Background

Sonodynamic therapy (SDT) is currently on critical path for glioblastoma therapeutics. However, the molecular mechanisms underlying the therapeutic functions of SDT remain enigmatic due to the lack of intricately optimised instrumentation capable of modulating SDT delivery in vitro. We established and validated an automated in vitro SDT system and assessed its SDT efficacy.

Methods

An automated in vitro SDT system was established and validated to allow the application and mapping of focused ultrasound fields under varied acoustic exposure conditions and setup configurations. Ultrasound field simulations were performed to assess the acoustic energy exposure. Systematic in vitro investigations were performed to optimise ultrasound frequency, intensity, plate base material, thermal effect, and the integration of live cells.

Results

In the presence of 5-ALA, focused ultrasound induces apoptotic cell death in primary patient-derived glioma cells with concurrent upregulation of intracellular reactive oxygen species. Intriguingly, primary glioma stem neurospheres also exhibit remarkably reduced 3D growth upon SDT exposure. Further, ultrasound field simulations performed established acoustic field distribution and the impact of acoustic standing waves within the well-plates.

Conclusions

The optimised in vitro SDT system and associated ultrasound field simulations establish the basis for further understanding of SDT and its therapeutic potentials in cancer.
Measuring stimulus-related redundant and synergistic functional connectivity with single cell resolution in auditory cortex
Authors: Koçillari Loren , Celotto Marco , Francis Nikolas A. , Mukherjee Shoutik , Babadi Behtash , Kanold Patrick O. , Panzeri Stefano
Published: June 2023

Measures of functional connectivity have played a central role in advancing our understanding of how information is communicated within the brain. Traditionally, these studies have focused on identifying redundant functional connectivity, which involves determining when activity is similar across different sites. However, recent research has highlighted the potential importance of also identifying synergistic connectivity—that is, connectivity that gives rise to information not contained in either site alone. Here, we measured redundant and synergistic functional connectivity with individual-neuron resolution in the primary auditory cortex of the mouse during a perceptual task. Specifically, we identified pairs of neurons that exhibited directed functional connectivity between them, as measured using Granger Causality. We then used Partial Information Decomposition to quantify the amount of redundant and synergystic information carried by these neurons about auditory stimuli. Our findings revealed that functionally connected pairs carry proportionally more redundancy and less synergy than unconnected pairs, suggesting that their functional connectivity is primarily redundant in nature. Furthermore, we observe that the proportion of redundancy is higher for correct than for incorrect behavioral choices, supporting the notion that redundant connectivity is beneficial for behavior.
Quantifying and correcting bias in transcriptional parameter inference from single-cell data
Authors: Grima Ramon , Esmenjaud Pierre-Marie
Published: June 2023

The snapshot distribution of mRNA counts per cell can be measured using single molecule FISH or single-cell RNA sequencing. These distributions are often fit to the steady-state distribution of the two-state telegraph model to estimate the three transcriptional parameters for a gene of interest: mRNA synthesis rate, the switching on rate (the on state being the active transcriptional state) and the switching off rate. This model assumes no extrinsic noise, i.e. parameters do not vary between cells, and thus estimated parameters are to be understood as approximating the average values in a population. The accuracy of this approximation is currently unclear. Here we develop a theory that explains the size and sign of estimation bias when inferring parameters from single-cell data using the standard telegraph model. We find specific bias signatures depending on the source of extrinsic noise (which parameter is most variable across cells) and the mode of transcriptional activity. If gene expression is not bursty then the population averages of all three parameters are overestimated if extrinsic noise is in the synthesis rate; underestimation occurs if extrinsic noise is in the switching on rate; both underestimation and overestimation can occur if extrinsic noise is in the switching off rate. We find that some estimated parameters tend to infinity as the size of extrinsic noise approaches a critical threshold. In contrast when gene expression is bursty, we find that in all cases, the mean burst size (ratio of the synthesis rate to the switching off rate) is overestimated while the mean burst frequency (the switching on rate) is underestimated. We estimate the size of extrinsic noise from the covariance matrix of sequencing data and use this together with our theory to correct published estimates of transcriptional parameters for mammalian genes.
Systematic Characterization of LSD metabolites inC. elegansby ultra-high performance liquid chromatography coupled with high-resolution tandem mass spectrometry
Authors: Silveira Christiane Martins de Vasconcellos , dos Santos Vanessa Farelo , Ornelas Isis Moraes , Carrilho Beatriz de Sá , Ventura Matheus Antônio Vieira de Castro , Pereira Henrique Marcelo Gualberto , Rehen Stevens Kastrup , Junqueira Magno
Published: June 2023

Psychedelic compounds have gained renewed interest for their potential therapeutic applications, but their metabolism and effects on complex biological systems remain poorly understood. Here, we present a systematic characterization of LSD metabolites in the model organismCaenorhabditis elegansusing state-of-the-art analytical techniques. By employing ultra-high performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMS/MS), we identified and quantified a range of LSD metabolites, shedding light on their metabolic pathways and offering insights into their pharmacokinetics. Our study demonstrates the suitability ofC. elegansas a valuable model system for investigating the metabolism of psychedelic compounds and provides a foundation for further research on the therapeutic potential of LSD. These findings contribute to the growing body of knowledge in the field and highlight the importance of advanced analytical methodologies in elucidating the effects of psychedelic substances on biological systems.
State-dependent dynamics of cuttlefish mantle activity
Authors: Cohen-Bodénès Sophie , Neri Peter
Published: June 2023

Cuttlefish skin is a powerful rendering device, capable of producing extraordinary changes in visual appearance over a broad range of temporal scales. This unique ability is typically associated with camouflage, however cuttlefish often produce skin patterns that do not appear connected with the surrounding environment, such as fast large-scale fluctuations with wave-like characteristics. Little is known about the functional significance of these dynamic patterns. In this study, we develop novel tools for analyzing pattern dynamics, and we demonstrate their utility for detecting changes in feeding state that occur without concomitant changes in sensory stimulation. Under these conditions, we find that the dynamic properties of specific pattern components differ for different feeding states, despite no measurable change in the overall expression of those components. These dynamic changes are therefore not detectable by conventional analyses focusing on pattern expression, requiring analytical tools specifically targeted to pattern dynamics.
A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types
Authors: Tibi Muhammad , Biton Stav , Hochgerner Hannah , Lin Zhige , Givon Shachar , Ophir Osnat , Shay Tal , Mueller Thomas , Segev Ronen , Zeisel Amit
Published: June 2023

Teleost fish form the largest group of vertebrates, making them critically important for the study on the mechanisms of brain evolution. In fact, teleosts show a tremendous variety of adaptive behaviors similar to birds and mammals, however, the neural basis mediating these behaviors remains elusive. We performed a systematic comparative survey of the goldfish telencephalon; the seat of plastic behavior, learning and memory in vertebrates. We delineated and mapped goldfish telencephalon cell types using single-cell RNA-seq and spatial transcriptomics, resulting inde novomolecular neuroanatomy parcellation. Glial cells were highly conserved across 450 million years of evolution separating mouse and goldfish, while neurons showed diversity and modularity in gene expression. Specifically, somatostatin (SST) interneurons, famously interspersed in the mammalian isocortex for local inhibitory input, were curiously aggregated in a single goldfish telencephalon nucleus, but molecularly conserved. Cerebral nuclei including the striatum, a hub for motivated behavior in amniotes, had molecularly and spatially conserved goldfish homologues. We further suggest different elements of a hippocampal

formation across the goldfish pallium. Together, our atlas provides new insights to organization and evolution of vertebrate forebrains and may serve as a resource for the functional study underlying cognition in teleost fish.

Teaser

Detailed mapping of goldfish forebrain cells unwraps how 450 million years of evolution may have impacted brain function
Comparative 3D genome analysis between neural retina and RPE reveals differentialcis-regulatory interactions at retinal disease loci
Authors: D’haene Eva , Soriano Victor López , Martínez-García Pedro Manuel , Kalayanamontri Soraya , Dueñas Rey Alfredo , Sousa-Ortega Ana , Naranjo Silvia , Van de Sompele Stijn , Vantomme Lies , Mahieu Quinten , Vergult Sarah , Neto Ana Bastos , Gómez-Skarmeta José Luis , Martínez-Morales Juan R. , Bauwens Miriam , Tena Juan J. , De Baere Elfride
Published: June 2023

Vision depends on the functional interplay between the photoreceptor cells of the neural retina and the supporting cells of the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases (IRD) display highly specific spatiotemporal expression within these interconnected retinal components through the local recruitment ofcis-regulatory elements (CREs) in 3D nuclear space.

To understand the role of differential chromatin architecture in establishing tissue-specific expression patterns at IRD loci in the human neural retina and the RPE, we mapped genome-wide chromatin interactions by applyingin situHi-C and H3K4me3 HiChIP to human adult post-mortem donor retinas. A comparative 3D genome analysis between neural retina and RPE/choroid revealed that almost 60% of 290 known IRD genes were marked by differential 3D genome structure and/orcis-regulatory interactions. One of these genes wasABCA4, which is implicated in the most common autosomal recessive IRD. We zoomed in on tissue-specific chromatin interactions at theABCA4locus using high-resolution UMI-4C assays. Upon integration with bulk and single-cell epigenomic datasets andin vivoenhancer assays in zebrafish, we revealed tissue-specific CREs interacting withABCA4.

In summary, through extensive comparative 3D genome mapping, based on genome-wide (Hi-C), promoter-centric (HiChIP) and locus-specific (UMI-4C) assays of human neural retina and RPE, we have shown that gene regulation at key IRD loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes of IRD genes, but also delineate the search space for non-coding genomic variation underlying unsolved IRD.

Abstract Figure
Compensatory mutations are associated with increasedin vitrogrowth in resistant clinical samples ofMycobacterium tuberculosis
Authors: Brunner Viktoria , Fowler Philip W
Published: June 2023

Mutations inMycobacterium tuberculosisassociated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness ofM. tuberculosispopulations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations (CMs) in other regions of the affected protein. CMs are of particular interest clinically since they could lock in resistance mutations, encouraging the spread of resistant strains worldwide. Here, we report the statistical inference of a comprehensive set of CMs in the RNA polymerase ofM. tuberculosis, using over 70,000M. tuberculosisgenomes that were collated as part of the CRyPTIC project. The unprecedented size of this data set gave the statistical tests to investigate the association of putative CMs with resistance-conferring mutations much more power. Overall, we propose 51 high-confidence CMs by means of statistical association testing and suggest hypotheses for how they exert their compensatory mechanism by mapping them onto the protein structure. In addition, we were able to show an association of CMs with higherin vitrogrowth densities, and hence presumably with higher fitness, in resistant samples in the more virulentM. tuberculosisLineages 2 and 3. In Lineage 2, our results even suggest the association of CM presence with significantly higherin vitrogrowth than for wild-type samples, although this association is confounded with lineage and sub-lineage affiliation. Our findings emphasise the integral role of CMs and lineage affiliation in resistance spread and increases the urgency for antibiotic stewardship, which implies accurate, cheap and widely accessible diagnostics forM. tuberculosisinfections to not only improve patient outcomes but also to prevent the spread of resistant strains.
Pangenome genotyped structural variation improves molecular phenotype mapping in cattle
Authors: Leonard Alexander S. , Mapel Xena M. , Pausch Hubert
Published: June 2023

Expression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so the genomic variation is often called from short read alignments which are unable to comprehensively resolve structural variation. Here we build a pangenome from 16 HiFi haplotype-resolved assemblies to identify small and structural variation and genotype them with PanGenie in 307 short read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-called small variation, and confidently genotype close to 21M small and 43k structural variants in the larger population. We validate 85% of these structural variants (with MAF>0.1) directly with a subset of 25 short read samples that also have medium coverage HiFi reads. We then conduct e/sQTL mapping with this comprehensive variant set in a subset of 117 cattle that have testis transcriptome data and find 92 structural variants as causal candidates for eQTL and 73 for sQTL. We find that roughly half of top associated structural variants affecting expression or splicing are transposable elements, such as SV-eQTLs forSTN1andMYH7and SV-sQTLs forCEP89andASAH2. Extensive linkage disequilibrium between small and structural variation results in only 28 additional eQTL and 17 sQTL discovered when including SVs, although many top associated SVs are compelling candidates.
Large-scale phylogenomics uncovers a complex evolutionary history and extensive ancestral gene flow in an African primate radiation
Authors: Jensen Axel , Swift Frances , de Vries Dorien , Beck Robin , Kuderna Lukas F.K. , Knauf Sascha , Chuma Idrissa S. , Keyyu Julius D. , Kitchener Andrew C. , Farh Kyle , Rogers Jeffrey , Marques-Bonet Tomas , Detwiler Kate M. , Roos Christian , Guschanski Katerina
Published: June 2023

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as a potential facilitator of adaptive radiations. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world’s largest primate radiations, we show that rampant gene flow characterizes their evolutionary history, and identify ancient hybridization across deeply divergent lineages differing in ecology, morphology and karyotypes. Lineages experiencing gene flow tend to be more species-rich than non-admixed lineages. Mitochondrial transfers between distant lineages were likely facilitated by co-introgression of co-adapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. This study provides important insights into the prevalence, role and outcomes of ancestral hybridization in a large mammalian radiation.
Converting Organic Municipal Solid Waste into Volatile Fatty Acids and Biogas: Experimental Pilot and Batch Studies with Statistical Analysis
Authors: Borhany Hojjat
Published: June 2023

Background

Italy can augment its profit from biorefinery products by altering the operation of digesters or different designs to obtain more precious bio-products like volatile fatty acids (VFAs) than biogas from organic municipal solid waste. In this context, recognizing the process stability and outputs through operational interventions and its technical and economic feasibility is a critical issue. Hence, the present study is an anaerobic digester in Treviso in northern Italy.

Objectives

This research compares the novel line, consisting of pretreatment, acidogenic fermentation, and anaerobic digestion, with single-step anaerobic digestion regarding financial profit and surplus energy. Therefore, a mass flow model was created and refined based on the outputs from the experimental and numerical studies. These studies examine the influence of hydraulic retention time (HRT), pretreatment, biochar addition, and fine-tuned feedstock/inoculum (FS/IN) ratio on bio-products and operational parameters.

Methods

VFA concentration, VFA weight ratio distribution (VWRD), and biogas yield were quantified by gas chromatography. Then, attest was conducted to analyze the significance of dissimilar HRTs in changing the VFA content. Further, a feasible biochar dosage was identified for an assumed FS/IN ratio with an adequate long HRT using the First-Order (FO) rate model. Accordingly, the parameters for a mass flow model were adopted for 70,000 population equivalents to determine the payback period and surplus energy for two scenarios. We also explored the effectiveness of amendments in improving the process kinetics.

Results

Both HRTs were identical concerning the VFA/SCOD (0.88 kg/kg) and VWRD: mainly acetic acid (40%), butyric acid (24%), and caproic acid (17%). However, a significantly higher mean VFA content was confirmed for HRT 4.5d than the quantity for HRT 3d (30.77 vs 27.66, g-SCOD/L) using attest (t =- 2.68, df=8,P=.03, CI=95%). In this research, 83% of the fermented volatile solids were converted into biogas to obtain a specific methane production of 0.133 (/kg−VS). While biochar addition improved only the maximum methane content by 20% (86% v/v), the feedstock/inoculum ratio of 0.3 (volatile solid basis) with thermal plus fermentative pretreatment improved the hydrolysis rate substantially (0.57 vs 0.07, 1/d). Furthermore, the biochar dosage of 0.12 (g-biochar/g-VS) with HRT 20d was identified as a feasible solution. Principally, our novel line payback period would be almost 2 years with surplus energy of +2251 (MJ/d) compared to 45 years and +21567 (MJ/d) for single-step anaerobic digestion.

Conclusions

This research elaborated on the advantage of the refined novel line over the single-step anaerobic digestion and confirmed its financial and technical feasibility. Further, changing HRT and other amendments significantly raised the VFA concentration and the process kinetics and stability.
A systematic study of the interplay between guest molecule structure and intermolecular interactions in crystalline sponges
Authors: Carroll Robert C. , Harrowven David C. , Pearce James E. , Coles Simon J.
Published: June 2023

Utilization of the crystalline sponge {[(ZnI2)3(tpt)2·x(solvent)]n} method has enabled characterization of a novel family of synthetic organic oils. The systematic structural differences and diversity of functional groups offered by 13 related molecular adsorbates provide a detailed quantitative understanding of the relationship between the guest structure, its conformation, and the type of intermolecular interactions adopted with neighbouring guests and the host framework. This analysis is extended to assess the connection of these factors to the resulting quality indicators for a particular molecular structure elucidation.
Organizing construction logistics outsourcing: a logistics strategy perspective
Authors: Haglund Petter , Janné Mats
Published: June 2023

Purpose

The construction industry shows an increased interest in how to manage logistics within construction projects. Often construction logistics is outsourced to a logistics service provider (LSP). However, construction logistics is normally approached either as a strategic decision or as an operational issue and rarely as a tactical concern. The purpose of this study is to explore how to organize the logistics outsourcing decision at strategic, tactical and operational levels.

Design/methodology/approach

This study is performed as a single-case study within a construction corporation, containing (amongst others) a building contractor (BC) and a construction equipment rental company (CERC) offering logistics services.

Findings

The study shows that to procure construction logistics service successfully, BCs need logistics capabilities at strategic and tactical levels to maintain an alignment between the use of logistics services and operational characteristics. Simultaneously, CERC’s need to design their service offerings to correspond to the needs of the BC.

Research limitations/implications

This study builds on a single-case study of a Swedish construction corporation. Further research is needed to better understand current logistics outsourcing and development practices and how these can be improved to foster better logistics management at the project level.

Practical implications

BCs find suggestions of different logistics organization structures and suitable outsourcing arrangements. CERCs and LSPs can use the findings to understand their customers’ needs and adapt service offerings.

Originality/value

To the best of the authors’ knowledge, this study is one of the first studies of how two companies within a corporation can work together to develop construction logistics service offerings.
Girls’ and young women’s leader identity development: a scoping review
Authors: Dixon Sakina , Niewoehner-Green Jera Elizondo , Smulowitz Stacy , Smith Deborah N. , Rutstein-Riley Amy , Thomas Trenae M.
Published: June 2023

Purpose

This scoping review aims to examine peer-reviewed literature related to girls’ (age 0–18) and young women’s (age 19–30) leader identity development.

Design/methodology/approach

This study uses a scoping review. A research librarian was consulted at the start of the project. Two sets of search terms (one for each age group) were identified and then used to find publications via our selected databases. The search results were uploaded to Covidence and evaluated using the determined inclusion and exclusion criteria. The final sample of articles for the review was analyzed using exploratory coding methods.

Findings

From the analysis, four domains were identified that influence girls’ and young women’s leader identity development: relationships, personal characteristics, meaningful engagement and social identities.

Originality/value

To the best of the authors’ knowledge, this is the first study to solely explore girls’ and young women’s leader identity development. The factors and domains identified provide useful guidance for future research and practice. The findings reveal considerations about leader identity that can inform the creation of effective leadership development initiatives for girls early in their lifespan. These interventions could provide girls with a strong leadership foundation that could drastically alter their leadership trajectories in adulthood. Previous research has conveyed the advantages of having more women participate in leadership. Thus, this potential not only benefits girls and women but organizations and society at large.
Financial inclusion and poverty: evidence from developing economies
Authors: Nyarko Eunice Stella , Amoateng Kofi , Aboagye Anthony Qabitoo Quame
Published: June 2023

Purpose

This paper examines the impact of financial inclusion on poverty through access to mobile money in developing economies.

Design/methodology/approach

The authors employ the principal component analysis to construct an index of financial inclusion using demand and supply indicators, including mobile accounts. The authors use the two-step system GMM estimator for the analysis because of its efficiency and robustness in addressing heteroscedasticity and autocorrelation.

Findings

The main finding is that financial inclusion generally increased and significantly reduces poverty in the sample period. Furthermore, income inequality worsens poverty.

Research limitations/implications

This study has few limitations. First, the empirical analysis of the study is restricted to macroeconomic factors only because of limited Household Finance Survey data set and time availability. Second, the study is limited to developing countries and the results cannot be generalized.

Practical implications

Financial inclusion is a significant policy tool for poverty reduction. There is the need to enhance strategies that further improve financial inclusion by expanding and improving the use of mobile money accounts.

Social implications

The paper sheds light on how developing countries can harness financial inclusion to reduce poverty.

Originality/value

The paper differs from the previous studies in two ways. Firstly, mobile money account is included in the computation of financial inclusion index over the sample period. It also determines the impact of financial inclusion on poverty for short-run and long-run periods.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-11-2021-0690
A rare case of signet ring cell carcinoma with diffuse cutaneous systemic sclerosis: A case report
Authors: Sano Yuriko , Yoshida Kosuke , Hibi Erina , Sekiya Atsushi , Watanabe Yuriko , Shibata Daijiro
Published: June 2023

Systemic sclerosis, an autoimmune disease characterized by fibrosis and vasculopathy of the skin and other multiple organs has been associated with an increased risk of malignancy. We present the case of a 74‐year‐old woman who had diffused cutaneous systemic sclerosis and uterine cervical cancer. The patient was initially diagnosed with stage IIB squamous cell carcinoma and concurrent chemoradiotherapy was planned. However, cisplatin could not be administered due to acute renal failure, so the patient was treated solely with radiotherapy. However, complications of systemic sclerosis progressed rapidly, and the patient died 63 days later from pulmonary edema. An autopsy later revealed that uterine cervix had primary signet ring cell carcinoma. We suspected that this patient had a combination of signet ring cell carcinoma and squamous cell carcinoma, with squamous cell carcinoma disappearing after radiotherapy. This case highlighted the importance of systemic management for cancers associated with systemic sclerosis.
Temporal and Spatial Variability of Soil-Vegetation Variables in the West Region of Santa Catarina State
Authors: Ramos-da-Silva Renato
Published: June 2023

The western region of the state of Santa Catarina (SC) has suffered several episodes of drought, thus impacting vegetation, agricultural production and water availability. This study aimed to evaluate the spatial and temporal variability of soil-vegetation parameters in the region. Monthly data of evapotranspiration, precipitation, radiation, air and soil moisture and temperature were obtained from the NASA-funded Famine Early Warning Systems Network (FEWS NET) project, Land Data Assimilation System (FLDAS). The study focused on the western region of SC. Evapotranspiration anomalies showed that the years 2015 and 2020 had the lowest values in the last years (i.e. 1990 and 2022). Precipitation had greater variability in recent years, having months of high rainfall combined with periods of severe drought. An evaluation for the Xanxerê city region showed that the year 2020 presented records of low precipitation, evapotranspiration, soil moisture and NDVI, compared to the entire time series. Spatial correlation of the evapotranspiration controlling variables showed that precipitation, air temperature and humidity, and short-wave radiation presented variable correlations in different regions of SC. Soil moisture, however, had the highest positive correlation in the entire territory, showing that this is the main controlling variable of local evapotranspiration and therefore an indicator of the importance of vegetation transpiration in the latent heat fluxes. Equivalent water thickness obtained from the GRACE satellite show that after a maximum occurred in December 2015 its magnitudes steadily decreased, reaching very low groundwater values in 2022. This trend represents a 3.3 mm decrease per year. These results show that the region is undergoing a change in these soil-vegetation parameters that needs to be better monitored and understood.
Modeling the Surface Pressure Spectrum on Rough Walls in Pressure Gradients
Authors: Fritsch Daniel J. , Vishwanathan Vidya , Roy Christopher J. , Todd Lowe K. , Devenport William J.
Published: June 2023

Models for surface pressure spectra beneath rough wall boundary layers are assessed, with particular emphasis on prediction from steady, Reynolds-averaged Navier–Stokes (RANS) data. RANS roughness boundary conditions are shown to have qualitatively good trends between roughness function and roughness Reynolds number, but model-to-model discrepancies remain and the universality of an equivalent sandgrain roughness height for turbulence models is doubtful. Existing empirical models for the surface pressure spectrum show good agreement in some spectral regions and a newly proposed model shows good matching across the spectrum in a variety of pressure gradient conditions. Adjustments are made to existing TNO analytical models to incorporate rough wall effects, including changes to the velocity spectrum model and the inclusion of a wall-shift, shown to be independent of local Reynolds number, pressure gradient, or turbulence model. The mathematical character of the rough wall spectrum has been revealed, but challenges remain to implement both flow and spectral modeling without a priori knowledge of the flow.
Boundary Control Design of Three-Dimensional Vibrating Marine Riser System With Barrier Term
Authors: Wan Min , Zhou Li , Yin Yanxia , Wang Guorong
Published: June 2023

In this paper, a boundary control with barrier term is proposed for a typical three-dimensional flexible riser system by integrating backstepping technique with barrier Lyapunov functions. The proposed boundary control does not depend on the exact value of interference and can effectively restrain the vibration of the riser and constrain the angle between the riser and the platform. The proposed control has a small amount of calculation and strong robustness, and can effectively restrain the riser vibration when the environmental disturbance changes. In addition, based on the proposed boundary control method, the stability of the closed-loop system in space and time is proved by Lyapunov stability theorem when the initial conditions are satisfied. Numerical simulation shows the effectiveness and superiority of the controller.
Data Fusion and Pattern Classification in Dynamical Systems Via Symbolic Time Series Analysis
Authors: Chen Xiangyi , Ray Asok
Published: June 2023

Symbolic time series analysis (STSA) plays an important role in the investigation of continuously evolving dynamical systems, where the capability to interpret the joint effects of multiple sensor signals is essential for adequate representation of the embedded knowledge. This technical brief develops and validates, by simulation, an STSA-based algorithm to make timely decisions on dynamical systems for information fusion and pattern classification from ensembles of multisensor time series data. In this context, one of the most commonly used methods has been neural networks (NN) in their various configurations; however, these NN-based methods may require large-volume data and prolonged computational time for training. An alternative feasible method is the STSA-based probabilistic finite state automata (PFSA), which has been shown in recent literature to require significantly less training data and to be much faster than NN for training and, to some extent, for testing. This technical brief reports a modification of the current PFSA methods to accommodate (possibly heterogeneous and not necessarily tightly synchronized) multisensor data fusion and (supervised learning-based) pattern classification in real-time. Efficacy of the proposed method is demonstrated by fusion of time series of position and velocity sensor data, generated from a simulation model of the forced Duffing equation.