bluuebunny/crossref_metadata_2025 huggingface dataset:
Kitasatospora cathayae sp. nov., a novel endophytic actinomycete isolated from the leaves of Cathaya argyrophylla
Authors: Zheng Yaxi , Mo Ping , Li Jiangli , Zhou Zhibo , Huang Kerui , Luo Yushuang , Xie Peng , Wang Yun
Published: July 2024

Strain HUAS 3-15T was isolated from the leaves of Cathaya argyrophylla collected from Chenzhou, Hunan Province, PR China. The main fatty acids (>5.0 %) of the strain were anteiso-C15 : 0, C16 : 0, C18 : 1 ω9c, iso-C16 : 0, summed feature 5 (C18 : 2 ω6,9c/C18 : 0 ante), iso-C15 : 0 and anteiso-C17 : 0. MK-9(H6), MK-9(H8) and MK-9(H4) were detected as respiratory quinones. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. Galactose, glucose and ribose were also present in the cell wall. The major polar lipids consisted of diphosphatidylglycerol, phosphatidyl ethanolamine, phosphatidylinositol mannosides and unidentified phospholipids. The DNA G+C content of the genome sequence, consisting of 8 860 963 bp, is 72.4 mol%. blast analysis based on 16S rRNA gene sequences revealed that the strain belongs to the genus Kitasatospora, with 99.37, 99.03, 98.95, 98.68 and 98.67 % sequence similarity to Kitasatospora aureofaciens ATCC 10762T, Kitasatospora viridis DSM 44826T, Kitasatospora xanthocidica NBRC 13469T, Kitasatospora aburaviensis NRRL B-2218T and Kitasatospora kifunensis IFO 15206T, respectively. Phylogenetic trees based on 16S rRNA gene and whole-genome sequences demonstrated that strain HUAS 3-15T formed a well‐supported cluster with K. aureofaciens ATCC 10762T. Further genomic characterization through average nucleotide identity (ANIb/m) and digital DNA–DNA hybridization analysis between strain HUAS 3-15T and K. aureofaciens ATCC 10762T showed values of 90.62/92.55 % and 45.3 %, respectively, lower than the 95–96 % ANI threshold and 70.0 % cutoff used as guideline values for species delineation in bacteria. Furthermore, the differences between the strain and its phylogenomic neighbour in terms of physiological (e.g. sole carbon source growth) and chemotaxonomic (e.g. cellular fatty composition) characteristics further supported this conclusion. Consequently, we concluded that strain HUAS 3-15T represents a novel species of the genus Kitasatospora, for which the name Kitasatospora cathayae sp. nov. is proposed. The type strain is HUAS 3-15T (=MCCC 1K08542T=JCM 36274T).
THE USE OF COMPLEMENTARY PRACTICES BY PATIENTS UNDERGOING MEDICALLY ASSISTED REPRODUCTION: The place of Chinese medicine and related practices
Authors: Serri O. , Meunier A. , Bouet P.E. , El Hachem H. , Liu B. , May-Panloup P.
Published: July 2024

Purpose

Infertility is associated with different factors, highly intricated but sometimes ill-defined. Despite the significant recent technological and therapeutic advancements, the success rates of assisted reproductive technologies (ART) remain relatively low. In this context several women have recourse to complementary practices (CP), in the hope of improving success rates and lowering the associated strain. These methods, are quite heterogenous, and are yet to be comprehensively analyzed in the literature.

The objective of our study was to evaluate, in women consulting at our fertility center, the current interest in these CP and more specifically, the role of Traditional Chinese Medicine (TCM) and associated Mind Body Intervention (MBI).

Methods

A prospective monocentric survey study at the fertility center of the Angers University Hospital between January and May 2022.

Results

150 questionnaires were analyzed. Approximately 50% of women have recourse to CP, in the hope of improving the success rates of ART and reducing the associated stress and fatigue. The main CP used were the ones based on body manipulation, TCM and MBI. The lack of use was mainly linked to a lack of knowledge of these methods, and the vast majority of women would like to receive additional information about CP from the physicians at the center.

Conclusion

Our study shows a significant interest in CP in reproductive medicine. In view of the benefits of some of these practices, at least on the quality of life of patients, information on their value should be made available to all couples undergoing ART.
Simplifying causal gene identification in GWAS loci
Authors: Schipper Marijn , Ulirsch Jacob , Posthuma Danielle , Ripke Stephan , Heilbron Karl
Published: July 2024

Genome-wide association studies (GWAS) help to identify disease-linked genetic variants, but pinpointing the most likely causal genes in GWAS loci remains challenging. Existing GWAS gene prioritization tools are powerful but often use complex black box models trained on datasets containing unaddressed biases. Here, we use a data-driven approach to construct a truth set of causal genes in 406 GWAS loci. We train a gene prioritization tool, CALDERA, that uses a simple logistic regression model with L1 regularization and corrects for potential confounders. Using three independent benchmarking datasets of resolved GWAS loci, we compare the performance of CALDERA with three other methods (FLAMES, L2G, and cS2G). CALDERA outperforms all these methods in two out of three datasets and ranks second in the remaining dataset. We demonstrate that CALDERA prioritizes genes with expected properties, such as mutation intolerance (OR = 1.751 for pLI > 90%, P = 8.45x10-3). Overall, CALDERA provides a powerful solution for prioritizing potentially causal genes in GWAS loci and may help identify novel genetics-driven drug targets.
GRAViTy-V2: a grounded viral taxonomy application
Authors: Mayne Richard , Aiewsakun Pakorn , Turner Dann , Adriaenssens Evelien M. , Simmonds Peter
Published: July 2024

Taxonomic classification of viruses is essential for understanding their evolution and therefore their distribution, host interactions and pathogenic mechanisms. Classification methodologies usually rely on comparison of aligned sequence motifs in conserved genes, by genome organisation and gene complements, and at lower taxonomic ranks such as genus and species, through genome sequence identities. Building on our previous classification framework based on a novel whole-genome analysis method, we here describe Genome Relationships Applied to Viral Taxonomy Version 2 (GRAViTy-V2), which encompasses a greatly expanded range of features and numerous optimisations, packaged as an application that may be used as an alignment-free general-purpose virus classification tool. Using 28 datasets derived from the International Society on Taxonomy of Viruses 2022 taxonomy proposals, GRAViTy-V2 output was compared against human expert-curated classifications used for assignments in the 2023 round of ICTV taxonomy changes. GRAViTy-V2 produced taxonomies equivalent to manually-curated versions down to the family level and in almost all cases, to genus and species levels. However, discrepancies with our results primarily arose through various human and automated sequence annotation errors and erroneous annotations of coding sequences used in their original classification. Analysis times ranged from 1–506 min (median 3.59) on datasets with 17–1004 genomes and mean genome length of 3,000–1,000,000 bases, on a standard consumer-grade laptop. We discuss how the output from GRAViTY-V2 outputs allows for a full analysis of why taxonomic classifications were proposed, the value of the program for quality control of genetic comparisons, and how to optimise the speed of classification through proper use of GRAViTy-V2’s workflow management system.
A comprehensive analysis of the potential biological functions and prognostic values of SREBF1 for multiple cancer types including colorectal cancer
Authors: Li Dongling , Xu Fan , Cai Qinrui , Lin Ling , Zhou Xiaoya , Li Li , Chen Yao , Feng Tianlin , Gan Yuanxiu , Zhang Chenhua , Yang Fan
Published: July 2024

As an important molecule involved in lipid metabolism, Sterol Regulatory Element-Binding Protein 1 (SREBF1) plays a critical role in governing cellular lipid synthesis and uptake. However, a comprehensive understanding of the biological significance of SREBF1 in pan-cancer remains elusive. In this study, we aimed to comprehensively analyze the functional characteristics of SREBF1 in human cancers, including colorectal cancer (CRC). Our study utilized various databases and tools such as TCGA, GEO, TIMER2.0, GEPIA2.0, UALCAN, and the Human Protein Atlas to examine SREBF1 expression, genetic alterations, immune infiltration, single-cell sequencing, survival analysis, and gene enrichment. The results revealed that the expression of SREBF1 exhibited significant variations across different cancer types, and was closely associated with patient prognosis and immune infiltration. Moreover, the gene function assays indicated SREBF1 significantly affect cell growth and migration. Overall, the findings suggest that SREBF1 could serve as a potential prognostic biomarker and a novel therapeutic target in different cancer types.
Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy
Authors: Rahman Fariha , Augoustides Victoria , Tyler Emma , Daugird Timothy A. , Arthur Christian , Legant Wesley R.
Published: July 2024

The nucleus coordinates many different processes. Visualizing how these are spatially organized requires imaging protein complexes, epigenetic marks, and DNA across scales from single molecules to the whole nucleus. To accomplish this, we developed a multiplexed imaging protocol to localize 13 different nuclear targets with nanometer precision in single cells. We show that nuclear specification into active and repressive states exists along a spectrum of length scales, emerging below one micron and becoming strengthened at the nanoscale with unique organizational principles in both heterochromatin and euchromatin. HP1-α was positively correlated with DNA at the microscale but uncorrelated at the nanoscale. RNA Polymerase II, p300, and CDK9 were positively correlated at the microscale but became partitioned below 300 nm. Perturbing histone acetylation or transcription disrupted nanoscale organization but had less effect at the microscale. We envision that our imaging and analysis pipeline will be useful to reveal the organizational principles not only of the cell nucleus but also other cellular compartments.
Habitat use of rewilded horses and cattle as related to the functional and structural composition of plant communities in a European restored wetland ecosystem
Authors: Lovász Lilla , Korner-Nievergelt Fränzi , Amrhein Valentin
Published: July 2024

Rewilding initiatives in European open and semi-open lowlands increasingly involve cattle and horses for ecological restoration, especially in wetland areas of high conservation value. These large herbivores contribute to spatial heterogeneity and enhance biodiversity by shaping ecosystems through movement, grazing, and resting behaviours. However, the effect of their site-specific habitat use patterns on plant communities remains unclear.

In this study, we investigated the fine-scale spatiotemporal distribution of rewilded cattle and horses in a recently restored alluvial grassland in a French nature reserve. We explored differences in habitat use between the two species during summer and winter on a macrohabitat scale and examined structural and functional changes in vegetation traits over four years, focusing on plant height, patch cover, species richness, and light preference, nutrient-tolerance, and mowing/grazing tolerance of plants. The study site, a former agricultural area converted into a restored alluvial nature conservation site, allowed observation of ecological processes from a “zero state”.

Our results suggest that cattle and horses exhibit similar habitat use with seasonal variations, potentially indicating partially shared feeding niches. The mixed-species grazing prevented vegetation overgrowth by keeping plant cover and vegetation height under control, yet without causing destructive impacts. The two herbivore species induced a clear increase in grazing-tolerant plants and slight changes in the abundance of light-preferring and nutrient-tolerant species.

Synthesis: Overall, we found that the varying spatiotemporal distribution of rewilded horses and cattle likely induces changes in plant community on the patch scale but results in vegetation stability on the landscape scale, which is known to facilitate ecosystem functioning. Our study therefore informs managers of conservation initiatives, proposing rewilding with year-round grazing horses and cattle a promising strategy for ecological restoration and natural habitat maintenance in wetland areas.
CDK4/6 and SHP2 mediate BRAF/MEK inhibitor resistance in Class 2 and 3 BRAF mutant cancers
Authors: Rose April A. N. , Maxwell Jennifer , Rousselle Emmanuelle , Riaud Melody , Elkholi Islam E. , Mukonoweshuro Chantel , Biondini Marco , Cianfarano Erica , Soria-Bretones Isabel , Tobin Chantal , McGuire Meghan , King Ian , Zhang Tong , Pugh Trevor J. , Saeed Kamil Zaid , Shepherd Frances A. , Leighl Natasha , Abdul Razak Albiruni , Hansen Aaron , Saibil Sam , Bedard Philippe , Siegel Peter M. , Siu Lillian L. , Cescon David W. , Spreafico Anna
Published: July 2024

Class 2 and 3 non-V600EBRAFmutations are oncogenic drivers in many cancer types. Currently, there are no established targeted therapies with proven efficacy for cancers with non-V600EBRAFmutations. We developed the investigator-initiated, Phase II BEAVER clinical trial (NCT03839342) to evaluate the efficacy of BRAF and MEK inhibitors in patients with non-V600EBRAFmutations. The best objective response rate was 14% (3/21). By analyzing genomic data from patient tumors, circulating tumor DNA (ctDNA), patient-derived xenograft (PDX) models generated from enrolled patients, and functional genomics of Class 2 & 3BRAFmutant cell lines, we discovered MAPK-dependent and independent mechanisms of intrinsic and acquired resistance to BRAF/MEK inhibition. These included the acquisition of new mutations inNRAS, MAP2K1, RAF1,andRBin ctDNA at the time of disease progression. We observed an enrichment for alterations in genes that regulate cell cycle progression amongst non-responders and increased expression of genes mediating cell cycle progression in tumors Class 2BRAFmutant cell lines with acquired resistance to BRAF/MEK inhibitors. In Class 3 BRAF mutant cancers specifically,PTPN11(SHP2) was an essential gene. CDK4/6 and SHP2 were found to mediate intrinsic resistance to BRAF/MEK inhibition in Class 2 & 3 BRAF mutant tumors. Therapeutic strategies combining CDK4/6 or SHP2 inhibitors with BRAF/MEK inhibitors were more effective than BRAF/MEK inhibitors alonein vitroandin vivo, highlighting the need to explore therapeutic targets outside of the MAPK pathway in these hard-to-treat Class 2 & 3BRAFmutant cancers.
Protein surface chemistry encodes an adaptive tolerance to desiccation
Authors: Romero-Pérez Paulette Sofía , Moran Haley M. , Horani Azeem , Truong Alexander , Manriquez-Sandoval Edgar , Ramirez John F. , Martinez Alec , Gollub Edith , Hunter Kara , Lotthammer Jeffrey M. , Emenecker Ryan J. , Liu Hui , Iwasa Janet H. , Boothby Thomas C. , Holehouse Alex S. , Fried Stephen D. , Sukenik Shahar
Published: July 2024

Cellular desiccation - the loss of nearly all water from the cell - is a recurring stress in an increasing number of ecosystems that can drive protein unfolding and aggregation. For cells to survive, at least some of the proteome must resume function upon rehydration. Which proteins tolerate desiccation, and the molecular determinants that underlie this tolerance, are largely unknown. Here, we apply quantitative and structural proteomic mass spectrometry to show that certain proteins possess an innate capacity to tolerate rehydration following extreme water loss. Structural analysis points to protein surface chemistry as a key determinant for desiccation tolerance, which we test by showing that rational surface mutants can convert a desiccation sensitive protein into a tolerant one. Desiccation tolerance also has strong overlap with cellular function, with highly tolerant proteins responsible for production of small molecule building blocks, and intolerant proteins involved in energy-consuming processes such as ribosome biogenesis. As a result, the rehydrated proteome is preferentially enriched with metabolite and small molecule producers and depleted of some of the cell’s heaviest consumers. We propose this functional bias enables cells to kickstart their metabolism and promote cell survival following desiccation and rehydration.

Teaser

Proteins can resist extreme dryness by tuning the amino acids on their surfaces.
Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation
Authors: Blumer L. Moritz , Burskaia Valentina , Artiushin Ilia , Saha Jaysmita , Camacho Garcia Julia , Campuzano Jimenez Francisco , Hooft Van Der Huysdynen Alexander , Elkin Joel , Fischer Bettina , Van Houtte Natalie , Zhou Chenxi , Gresham Sophie , Malinsky Milan , Linderoth Tyler , Sawasawa Wilson , Vernaz Grégoire , Bista Iliana , Hickey Aaron , Kucka Marek , Louzada Sandra , Zatha Richard , Yang Fengtang , Rusuwa Bosco , Santos M. Emilia , Chan Y. Frank , Joyce Domino A. , Böhne Astrid , Miska Eric A , Ngochera Maxon , Turner George F. , Durbin Richard , Svardal Hannes
Published: July 2024

Chromosomal inversions contribute to adaptive speciation by linking co-adapted alleles. Querying 1,375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large inversions segregating in the benthic subradiation that each suppress recombination over more than half a chromosome. Two inversions were transferred from deepwater pelagic Diplotaxodon via admixture, while the others established early in the deep benthic clade. Introgression of haplotypes from lineages inside and outside the Malawi radiation coincided with bursts of species diversification. Inversions show evidence for transient sex linkage and a striking excess of protein changing substitutions points towards selection on neuro-sensory, physiological and reproductive genes. We conclude that repeated interplay between depth adaptation and sex-specific selection on large inversions has been central to the evolution of this iconic system.
pH-dependent direct sulfhydrylation pathway is required for the pathogenesis ofMycobacterium tuberculosis
Authors: Nain Vaibhav Kumar , Barik Vishawjeet , Pandey Manitosh , Pareek Mohit , Sharma Taruna , Pal Rahul , Tyagi Shaifali , Bajpai Manish , Dwivedi Prabhanjan , Panda Bhishma Narayan , Kumar Yashwant , Asthana Shailendra , Pandey Amit Kumar
Published: July 2024

Methionine is essential for the survival ofMycobacterium tuberculosis(M. tuberculosis) inside the host. However, the transsulfuration pathway, a major contributor of methionine, is dispensable for the growth ofM. tuberculosissuggesting redundancy in the methionine biosynthesis pathway. Orthologues of MetZTBin other bacterial species are known to operate a redundant single-step methionine biosynthesis pathway calleddirect sulfhydrylation.In this study, we demonstrate that genetic disruption of themetZ-mediated direct sulfhydrylation pathway inM. tuberculosishinders growth at low pH, an effect mitigated by methionine supplementation. Computational analyses, includingin-silicomolecular docking and molecular dynamics (MD) simulations, reveal enhanced binding of the MetZ substrate, O-succinyl homoserine (OSH), to the active site of MetZ at acidic pH. Intriguingly, despite increased intracellular ATP levels, a relative decrease in the frequency of Bedaquiline (BDQ)-induced persisters is observed inmetZ-deficient strain, suggesting a role of direct sulfhydrylation pathway in modulating BDQ sensitivity. Finally, we demonstrated that the absence ofmetZimpedes the ability ofM. tuberculosisto grow inside the host.
Proteomic analysis reveals the dominant effect of ipomoeassin F on the synthesis of membrane and secretory proteins in triple-negative breast cancer cells
Authors: Sicairos Brihget , Zhou Jianhong , Hu Zhijian , Zhang Qingyang , Shi Wei Q , Du Yuchun
Published: July 2024

Ipomoeassin F (Ipom-F) is a natural compound with embedded carbohydrates that exhibits a potent cytotoxic effect on triple-negative breast cancer (TNBC) cells. The mechanism behind this selective potency remains unclear. To elucidate this mechanism, we analyzed the proteome profiles of the TNBC MDA-MB-231 cells after exposure to Ipom-F at different time points and increasing doses using a quantitative proteomic method. Our proteomic data demonstrate that the major effect of Ipom-F on MDA-MB-231 cells is the inhibition of membrane and secreted protein expression. Our proteomic data are consistent with the recently uncovered molecular mechanism of action of Ipom-F, which binds to Sec61-α and inhibits the co-translational import of proteins into the endoplasmic reticulum. We have defined a subset of membrane and secreted proteins particularly sensitive to Ipom-F. Analysis of the expression of these Ipom-F-sensitive proteins in cancer cell lines and breast cancer tissues demonstrates that some of these proteins are upregulated in TNBC cells. Thus, it is likely that TNBC cells may have adapted to the elevated levels of some proteins identified as sensitive to Ipom-F in this study; inhibition of the expression of these proteins leads to a crisis in proliferation and/or survival for the cells.
Modulation of Electrostatic Interactions as a Mechanism of Cryptic Adaptation ofColwelliato High Hydrostatic Pressure
Authors: Makhatadze George I.
Published: July 2024

The role of various interactions in determining the pressure adaptation of the proteome in piezophilic organisms remains to be established. It is clear that the adaptation is not limited to one or two proteins, but has a more general evolution of the characteristics of the entire proteome, the so-called cryptic evolution. Using the synergy between bioinformatics, computer simulations, and some experimental evidence, we probed the physico-chemical mechanisms of cryptic evolution of the proteome of psychrophilic strains of model organism,Colwellia, to adapt to life at various pressures, from the surface of the Arctic ice to the depth of the Mariana Trench. From the bioinformatics analysis of proteomes of several strains of Colwellia, we have identified the modulation of interactions between charged residues as a possible driver of evolutionary adaptation to high hydrostatic pressure. The computational modeling suggests that these interactions have different roles in modulating the function-stability relationship for different protein families. For several classes of proteins, the modulation of interactions between charges evolved to lead to an increase in stability with pressure, while for others, just the opposite is observed. The latter trend appears to benefit enzyme activity by countering structural rigidification due to the high pressure.
Quantitative assessment and spatial distribution ofPlasmopara viticolaoospores in vineyard soil
Authors: Poeydebat Charlotte , Courchinoux Eva , Demeaux Isabelle , Rodriguez Marie , Chataigner Alexandre , Lelièvre Mélanie , Goutouly Jean-Pascal , Rossi Jean-Pierre , Raynal Marc , Delière Laurent , Delmotte François
Published: July 2024

Grapevine downy mildew, caused by the oomycetePlasmopara viticola, is one of the most devastating diseases of grapevine worldwide. While primary inoculum plays a decisive role in disease epidemics, we still know very little about the abundance and the distribution of oospores, which are the overwintering forms of the pathogen resulting from sexual reproduction. In this study, we used ddPCR to describe the spatial distribution ofP. viticolainoculum in a vineyard soil at the onset of the growing season. We foundP. viticolaoospores in all soil samples except one. The distribution of primary inoculum at the field scale was not random but characterized by 25 m-diameter patches of concentrically increasing oospore concentration. There was a positive coregionalization between soil inoculum and soil moisture spatial distributions, possibly mediated by disease incidence. The results indicated that oospores accumulated 5 times more in the ridge of soil below the vine stocks than in the inter-row. We conducted a leaf disc bioassay to assess soil infectious potential on a subset of samples collected in the field. Soil infectious potential estimated through infected leaf-disc area was positively correlated with our DNA-based quantification of oospores. Overall, the quantitative and spatially explicit survey of primary inoculum reservoir gained from these molecular and biological methods will contribute to the design of management strategies aimed at preventing primary inoculum accumulation in the vineyard from one season to the next.
Long-lived searches of vectorlike lepton and its accompanying scalar at colliders
Authors: Cao Qing-Hong , Guo Jinhui , Liu Jia , Luo Yan , Wang Xiao-Ping
Published: July 2024

Recently, the vectorlike leptons (VLLs) as a simple extension to the standard model (SM) have attracted widespread attention both in theory and experiments. The present collider searches mainly focus on the studies of their prompt decays, which prefer a relatively large coupling. In this paper, we concentrate on searches for long-lived signatures of the singlet VLLs F or their accompanying scalar particles ϕ both in the hadronic and electronic colliders. The long-lived signatures are naturally induced from small chiral mass mixing between VLLs and SM leptons. Two specific models distinguished by whether the VLLs couple to scalar particles are introduced to realize the aforementioned features. For the long-lived VLLs case, we find that with the kink track method the sensitivities at future HL-LHC with s=14  TeV can reach the regions for VLL mass mF∈[200,1100]  GeV and the mass mixing parameter θL∈[10−10,3×10−8]. For the long-lived accompanying scalar particle case, by fixing VLLs or scalar mass, or the mass ratio between VLL and the accompanying scalar, we explore the projected sensitivities through the time delay and displaced vertex strategies, which can probe the regions for mF∈[200,1200]  GeV and coupling yθL∈[10−11,10−6]. Furthermore, we also explore the long-lived accompanying scalars at the future CEPC provided that the VLLs can couple to the SM first-generation leptons. We find that CEPC has good performances for mϕ<120  GeV and mF<1200  GeV. These long-lived searches are complementary to previous studies, which opens the door toward the smaller coupling regions.

Published by the American Physical Society
2024
Quantization of skyrmions using instantons
Authors: Cork Josh , Halcrow Chris
Published: July 2024

We provide a step-by-step method to construct skyrmions from instanton ADHM data, including when the exact ADHM data is unknown. The configurations look like clusters of smaller skyrmions, and can be used to build manifolds of skyrmions with or without symmetries. Nuclei are described by quantum states on these manifolds. We describe the construction and quantization procedure generally, then apply the methods in detail to the 8-skyrmion which describes the Beryllium-8 nucleus.

Published by the American Physical Society
2024
Evaluation of a new teaching-learning sequence on the particulate nature of matter using crystal structures
Authors: Budimaier Florian , Hopf Martin
Published: July 2024

Although there has been extensive research on students’ understanding of the particulate nature of matter (PNM), there is still a lack of research on contexts that can be used to teach this challenging topic. In a previous design-based research study, the authors developed a teaching-learning sequence (TLS) on the PNM in the context of crystal structures based on 40 student interviews using the method of probing acceptance. Data suggested that salt and snow crystals form an effective context for learning the concept of emergence and therefore gaining a better understanding of the PNM. To test whether the TLS also promotes students’ use of the PNM in a realistic classroom setting, a proof of principle study was conducted. In six eighth-grade classes in Vienna, students’ use of the PNM was assessed with a pretest before they were taught the TLS during four lessons. After the intervention, students were given a post-test. Open-ended questions were coded using evaluative qualitative content analysis so that quantitative analysis could be applied. T-tests comparing the means of students’ scores on both tests show significant improvements in students’ use of the PNM in the post-test. The context of crystal structures seems to be helpful to students, as most of them use the PNM when asked about crystal formation. In addition, in the post-test, students more often accepted the idea of empty space between particles and associated particle motion with temperature. However, when asked about phase changes, most students remained in a continuous conception of matter.

Published by the American Physical Society
2024
Ring solids and supersolids in spherical shell-shaped dipolar Bose-Einstein condensates
Authors: Sánchez-Baena J. , Bombín R. , Boronat J.
Published: July 2024

We study the interplay between the anisotropy of the dipole-dipole interaction and confinement in a curved geometry by means of the extended Gross-Pitaevskii equation, which allows us to characterize the ground state of a dipolar Bose gas under the confinement of a bubble trapping potential. We do so in terms of the scattering length a and the number of particles. We observe the emergence of a wide variety of dipolar solids, consisting on arrangements of different number of droplets along a ring over the equator of the spherical shell confinement. We also show that the transition between the different phases of the system can be engineered by varying a, the number of particles or the radius of the trap, parameters, which can be experimentally tuned. Finally, we show the importance of working in microgravity conditions as gravity unstabilizes the observed dipolar solids.

Published by the American Physical Society
2024
Double-edge scan wavefront metrology and its application in crystal diffraction wavefront measurements
Authors: Liu Fang , Li Ming , Diao Qianshun , Li Zhe , Shen Zhibang , Li Fan , Hong Zhen , Lian Hongkai , Yue Shuaipeng , Hou Qingyan , Zhang Changrui , Zhang Dongni , Li Congcong , Yang Fugui , Yang Junliang
Published: July 2024

Achieving diffraction-limited performance in fourth-generation synchrotron radiation sources demands monochromator crystals that can preserve the wavefront across an unprecedented extensive range. There is an urgent need for techniques of absolute crystal diffraction wavefront measurement. At the Beijing Synchrotron Radiation Facility (BSRF), a novel edge scan wavefront metrology technique has been developed. This technique employs a double-edge tracking method, making diffraction-limited level absolute crystal diffraction wavefront measurement a reality. The results demonstrate an equivalent diffraction surface slope error below 70 nrad (corresponding to a wavefront phase error of 4.57% λ) r.m.s. within a nearly 6 mm range for a flat crystal in the crystal surface coordinate. The double-edge structure contributes to exceptional measurement precision for slope error reproducibility, achieving levels below 15 nrad (phase error reproducibility < λ/100) even at a first-generation synchrotron radiation source. Currently, the measurement termed double-edge scan (DES) has already been regarded as a critical feedback mechanism in the fabrication of next-generation crystals.
Exploring serial crystallography for drug discovery
Authors: Dunge A. , Phan C. , Uwangue O. , Bjelcic M. , Gunnarsson J. , Wehlander G. , Käck H. , Brändén G.
Published: July 2024

Structure-based drug design is highly dependent on the availability of structures of the protein of interest in complex with lead compounds. Ideally, this information can be used to guide the chemical optimization of a compound into a pharmaceutical drug candidate. A limitation of the main structural method used today – conventional X-ray crystallography – is that it only provides structural information about the protein complex in its frozen state. Serial crystallography is a relatively new approach that offers the possibility to study protein structures at room temperature (RT). Here, we explore the use of serial crystallography to determine the structures of the pharmaceutical target, soluble epoxide hydrolase. We introduce a new method to screen for optimal microcrystallization conditions suitable for use in serial crystallography and present a number of RT ligand-bound structures of our target protein. From a comparison between the RT structural data and previously published cryo-temperature structures, we describe an example of a temperature-dependent difference in the ligand-binding mode and observe that flexible loops are better resolved at RT. Finally, we discuss the current limitations and potential future advances of serial crystallography for use within pharmaceutical drug discovery.
The crystal structure of olanzapine form III
Authors: Anyfanti Goulielmina , Husanu Elena , Andrusenko Iryna , Marchetti Danilo , Gemmi Mauro
Published: July 2024

The antipsychotic drug olanzapine is well known for its complex polymorphism. Although widely investigated, the crystal structure of one of its anhydrous polymorphs, form III, is still unknown. Its appearance, always in concomitance with forms II and I, and the impossibility of isolating it from that mixture, have prevented its structure determination so far. The scenario has changed with the emerging field of 3D electron diffraction (3D ED) and its great advantages in the characterization of polyphasic mixtures of nanosized crystals. In this study, we show how the application of 3D ED allows the ab initio structure determination and dynamical refinement of this elusive crystal structure that remained unknown for more than 20 years. Olanzapine form III is monoclinic and shows a similar but shifted packing with respect to form II. It is remarkably different from the lowest-energy structures predicted by the energy-minimization algorithms of crystal structure prediction.
Crystallographic fragment screen of the c-di-AMP-synthesizing enzyme CdaA from Bacillus subtilis
Authors: Garbers Tim , Neumann Piotr , Wollenhaupt Jan , Dickmanns Achim , Weiss Manfred S. , Ficner Ralf
Published: July 2024

Crystallographic fragment screening has become a pivotal technique in structure-based drug design, particularly for bacterial targets with a crucial role in infectious disease mechanisms. The enzyme CdaA, which synthesizes an essential second messenger cyclic di-AMP (c-di-AMP) in many pathogenic bacteria, has emerged as a promising candidate for the development of novel antibiotics. To identify crystals suitable for fragment screening, CdaA enzymes from Streptococcus pneumoniae, Bacillus subtilis and Enterococcus faecium were purified and crystallized. Crystals of B. subtilis CdaA, which diffracted to the highest resolution of 1.1 Å, were used to perform the screening of 96 fragments, yielding data sets with resolutions spanning from 1.08 to 1.87 Å. A total of 24 structural hits across eight different sites were identified. Four fragments bind to regions that are highly conserved among pathogenic bacteria, specifically the active site (three fragments) and the dimerization interface (one fragment). The coordinates of the three active-site fragments were used to perform an in silico drug-repurposing screen using the OpenEye suite and the DrugBank database. This screen identified tenofovir, an approved drug, that is predicted to interact with the ATP-binding region of CdaA. Its inhibitory potential against pathogenic E. faecium CdaA has been confirmed by ITC measurements. These findings not only demonstrate the feasibility of this approach for identifying lead compounds for the design of novel antibacterial agents, but also pave the way for further fragment-based lead-optimization efforts targeting CdaA.
Unveiling shadows: exploring the dark side of digital transformation in Abu Dhabi
Authors: Badri Masood , Alkhaili Mugheer , Aldhaheri Hamad , Yang Guang , Albahar Muna , Yaageib Saad , Alrashdi Asma
Published: July 2024

Purpose

This research aims to investigate the negative aspects of digital transformation (DT) impacting various segments of society in the Emirate of Abu Dhabi, one of the seven Emirates comprising the United Arab Emirates. Specifically, it focuses on perceptions of participants to well-being: social connections and activities, physical health, mental health, the impact on the younger generation, and security/cybercrime.

Design/methodology/approach

Using data from the 3rd Abu Dhabi Quality of Life Survey, which is an annual large-scale survey, this study employs analysis of variance and regression analysis to explore the associations between the perceived negative impact of DT and various well-being indicators.

Findings

The study reveals that the perceived negative impact of digital transformation on the younger generation is of the highest concern, followed by concerns about mental health and social relationships. Results also show significant variations among different demographic categories. Among the perceived negative impacts, mental health, social trust, and happiness emerge as the most affected well-being indicators.

Originality/value

The originality and value of this study lie in its large social survey sample of over 80,000 participants. The findings suggest that the negative effects of DT are not uniformly experienced across different segments of the population. The study highlights the need for further research on the adverse effects of DT and recommends that policymakers develop targeted strategies to address the specific needs of different community segments, particularly vulnerable groups. Additionally, it emphasizes the importance of adaptive policies for younger age groups to prepare them for a digital future.
Organizational justice and employee acceptance of management decisions: the mediating role of perceived organizational adaptation to hindering external conditions
Authors: Burdziej Stanisław , Haffer Rafał , Moszyńska Anna , Karwacki Arkadiusz
Published: July 2024

Purpose

Previous research has demonstrated that the experience of fair treatment (organizational justice) motivates workers to accept their leaders’ decisions, even when these decisions are viewed as unfavorable. We aim at extending these findings by testing for mediating effects of the perceived impact of the COVID-19 pandemic on the organization as a particular example of a hindering external condition. We expected that employees’ perception of management response to the pandemic would partly mediate the effect of organizational fairness on employee compliance.

Design/methodology/approach

In Study 1 we surveyed a nationally representative (N = 1,001) sample of employees. In Study 2 we used a representative sample (N = 250) of those workers who were laid off during the pandemic.

Findings

We show that an organization’s perceived ability to adapt to the pandemic partly mediated the relationship between organizational justice and acceptance of management decisions. Employees who were treated fairly were more ready to accept management decisions and viewed their organization as better prepared for hindering external conditions such as COVID-19. Their perceptions of organization’s ability to adapt partly mediated the effect of organizational justice on decision acceptance.

Originality/value

Our study is among the first to identify a link between organizational fairness and organizational adaptation. We show that employees perceive fair organizations as better prepared for external shocks.
A systematic review of the literature on the use of information technologies in supply chain management
Authors: Al-Talib Moayad , Al-Saad Walid , Alzoubi Anan , Anosike Anthony I.
Published: July 2024

Purpose

The purpose of this study is to explore the opportunities provided by information technologies (IT) to improve supply chain processes. It aims to conduct a systematic literature review (SLR) to identify research areas that require further exploration to leverage IT and enhance supply chain performance.

Design/methodology/approach

This study employs a systematic literature review methodology to analyse a set of 177 publications, including journal papers, conference papers, periodicals, theses, and books published between 2013 and 2023. Thematic synthesis was chosen as the most appropriate approach to amalgamate the findings obtained from the systematic literature review conducted in the study. This method involves interpreting thematic information and facilitating the development of a comprehensive understanding of the literature being reviewed.

Findings

The literature review reveals that certain information technologies, such as the Internet of Things (IoT), Big Data, artificial intelligence (AI), Blockchain, information and communications technology (ICT) and information sharing, offer significant potential for improving supply chain processes. However, the application of these technologies in the field of supply chain is currently under-researched. The findings highlight the need for further exploration of these technologies and their impact on supply chain redesign and enhancement.

Originality/value

This study contributes to the existing body of knowledge by providing a systematic overview of the potential benefits of IT in the context of supply chains. It emphasises the under-researched nature of specific technologies and their potential to support organisations in improving their supply chain processes. The originality of this study lies in its comprehensive analysis of relevant literature and its identification of research gaps that need to be addressed in future studies.
Analysis of load carrying capacity of bridges strengthened by extracorporeal prestressing after five years of operation: a case study
Authors: Wan Lijun , Qiao Jiaqi , Sun Quansheng
Published: July 2024

Purpose

The application of reinforcing old bridges by adding external prestressed steel bundles is becoming more and more widespread. However, the long-term safety performance test of the strengthening method is rarely carried out. In this paper, the bearing capacity of a 420 m prestressed concrete (PC) continuous girder bridge after five years of strengthening is analyzed.

Design/methodology/approach

The bridge model of the bridge structure and strengthening scheme is established by the finite element software of the bridge. The theoretical load-bearing capacity of the bridge under the latest standard load grade is obtained by finite element analysis. The actual bearing capacity of the bridge is obtained by field test. Through the comparative analysis of theory and practice, the health state of the bridge after five years of reinforced operation is judged. The damage to the overall stiffness and external prestressing of the bridge is also analyzed.

Findings

The results of deflection and strain show that the stiffness and strength of the secondary side span and the middle span decrease slightly, and the maximum reduction of bearing capacity is 4.5%. The static stiffness of the whole bridge decreases as a result of cracks, and the maximum decrease is 21%. In the past five years, the relaxation loss of the external prestressing of the bridge is 3.31–3.97%, which is the main reason for the decrease in bearing capacity.

Originality/value

Through the joint analysis of the bridge stiffness and the loss of external prestressing, the strengthening condition of the bridge after five years of operation is effectively analyzed. The strengthening effect of the external prestressed steel beam strengthening method is analyzed, which can provide a reference for similar bridge strengthening.
Give me credit! Microcredit for sustainable development and ethical finance in Rione Sanità, Naples
Authors: Gatto Andrea , Mosca Rosa , Elia Gianluigi , Piscopo Paolo
Published: July 2024

Purpose

The purpose of microcredit is to offer small loans to people who are not covered by traditional financial channels. It can facilitate entrepreneurship, boosting local socio-economic development and improving environmental and political factors.

Design/methodology/approach

This paper aims to analyse microcredit in Italy, focusing on a project based in Rione Sanità, Naples. Rione Sanità is one of the poorest areas of Southern Italy, displaying high rates of criminality and unemployment, especially among youth, women, migrants and the vulnerable. The district is renowned for its fine and ancient handicrafts, food, trade and historical heritage – potential drivers for boosting tourism in the area. Qualitative methodologies were used to collect primary data through field visits and interviews with project bankers, local businesses, artisans, associations and religious representatives, project volunteers, as well as participation at local meetings. These data were corroborated by budget analysis based on the project's accounting.

Findings

The study shows encouraging results for the project and policy prospects. Despite the tiny starting numbers, there emerges a significant potential for microcredit to spread in the district, as in Southern Italy, providing an effective strategy to combat unemployment, usury and criminality, yielding community development and favoring broad societal challenges.

Originality/value

With this evidence, the paper attempts to shed some light and verify the potential of microfinance projects as a driver of sustainable development and ethical finance in poor areas of developed countries.
Implications of green knowledge sharing, organizational green culture and green training and development for organizational environmental citizenship behavior in the hotel sector
Authors: Andoh Raphael Papa Kweku , Owusu Nester Kumiwaa , Hayford Cecilia , Ansong Linda Obeng , Ansong Abraham
Published: July 2024

Purpose

The purpose of this study was to investigate the implications of green knowledge sharing (GKS), organizational green culture (OGC) and green training and development (GTD) for organizational environmental citizenship behavior (OECB) in the hotel sector in Ghana.

Design/methodology/approach

Using self-administered survey procedures, 415 operational-level employees in hotel facilities provided the data and was analyzed through partial least square structural equation modeling. Bootstrapping was conducted using 10,000 subsamples and Importance-Performance Map Analysis (IPMA) performed.

Findings

It was established that GKS influences both OECB and OGC. OGC also influenced OECB and played a mediating role in the influence of GKS on OECB. Similarly, GTD played a positive moderating role in the link GKS has on OECB. Finally, it was revealed via IPMA that OECB’s most important antecedent is GKS.

Practical implications

Due to the roles of GKS and GTD in promoting OGC and OECB, organizations should motivate their employees to share green knowledge and also invest more in GTD. Gamification and sponsoring employees to attend GTD programs are examples of actions to be taken in this regard.

Originality/value

This study explores antecedents of OECB which is overlooked in the literature in general and specifically, hospitality industry-focused green studies. Using IPMA, it also determines the most important antecedent of OECB which most studies focused on the hospitality industry do not go further to do.