bluuebunny/crossref_metadata_2025 huggingface dataset:
CNSistent integration and feature extraction from somatic copy number profiles
Authors: Streck Adam , Schwarz Roland F.
Published: December 2024

The vast majority of cancers exhibit Somatic Copy Number Alterations (SCNAs)—gains and losses of variable regions of DNA. SCNAs can shape the phenotype of cancer cells,e.g. by increasing their proliferation rates, removing tumor suppressor genes, or immortalizing cells. While many SCNAs are unique to a patient, certain recurring patterns emerge as a result of shared selectional constraints or common mutational processes. To discover such patterns in a robust way, the size of the dataset is essential, which necessitates combining SCNA profiles from different cohorts, a non-trivial task.

To achieve this, we developed CNSistent, a Python package for imputation, filtering, consistent segmentation, feature extraction, and visualization of cancer copy number profiles from heterogeneous datasets. We demonstrate the utility of CNSistent by applying it to the publicly available TCGA, PCAWG, and TRACERx cohorts. We compare different segmentation and aggregation strategies on cancer type and subtype classification tasks using deep convolutional neural networks. We demonstrate an increase in accuracy over training on individual cohorts and efficient transfer learning between cohorts. Using integrated gradients we investigate lung cancer classification results, highlightingSOX2amplifications as the dominant copy number alteration in lung squamous cell carcinoma.
Injury-induced Neuregulin-ErbB signaling from muscle mobilizes stem cells for whole-body regeneration in Acoels
Authors: Stevens Brian , Popp Riley , Valera Heather , Krueger Kyle , Petersen Christian P.
Published: December 2024

The activation of progenitor cells near wound sites is a common feature of regeneration across species, but the conserved signaling mechanisms responsible for this step in whole-body regeneration are still incompletely understood. The acoelHofstenia miamiaundergoes whole-body regeneration using Piwi+ pluripotent adult stem cells (neoblasts) that accumulate at amputation sites early in the regeneration process. The EGFR signaling pathway has broad roles in controlling proliferation, migration, differentiation, and cell survival across metazoans. Using a candidate RNAi screening approach, we identify theHofsteniaEGFRerbB4-2and Neuregulinnrg-1genes as essential for blastema formation. Structure prediction of NRG-1 and ERBB4-2 proteins supports the likelihood of these factors interacting directly. After amputation injuries,nrg-1expression is induced in body-wall muscle cells at the wound site by 6 hours and localizes to the tip of the outgrowing blastema over the next several days, whileerbB4-2is broadly expressed, including in muscle and neoblasts. Undernrg-1(RNAi)anderbB4-2(RNAi)conditions that impair blastema formation, animals still undergo the earliest responses to injury to activate expression of the Early Growth Response transcription factoregr, indicating a crucial role for EGFR signaling downstream of initial wound activation.nrg-1(RNAi)anderbB4-2(RNAi)animals possess Piwi+ and H3P+ mitotic neoblasts which hyperproliferate normally after amputation, but these cells fail to accumulate at the wound site. Therefore, muscle provides a source for Neuregulin-ErbB signaling necessary for the mobilization of proliferative progenitors to enable blastema outgrowth for whole-body regeneration inHofstenia. These results indicate a shared functional requirement for muscle signaling to enable regeneration between planarians and acoels across 550 million years of evolution.
Targeted delivery of rhodopsin’s assembled core is required for outer segment extension in mouse rod photoreceptors
Authors: Martínez-Márquez Jorge Y. , Hua Sandy , Beu Andreea M. , Stein Christopher B. , Pearring Jillian N.
Published: December 2024

Vertebrate vision in dim-light environments is initiated by rod photoreceptor cells that express the photopigment rhodopsin, a G-protein coupled receptor (GPCR). To ensure efficient light capture, rhodopsin is densely packed into hundreds of membrane discs that are tightly stacked within the rod-shaped outer segment compartment. Along with its role in eliciting the visual response, rhodopsin serves as both a building block necessary for proper outer segment formation as well as a trafficking guide for a few outer segment resident membrane proteins. An interesting aspect of rod homeostasis is that mutations that affect the localization of rhodopsin to the outer segment result in photoreceptor degeneration. In this study, we focus on determining the necessary properties of rhodopsin’s cytosolic C-terminus required for either proper outer segment trafficking and/or the capacity to extend the rudimentary outer segment in rhodopsin knockout (RhoKO) rods. We find that the well-described C-terminal QVAPA outer segment targeting motif also plays a role in endoplasmic reticulum (ER) exit and is necessary for outer segment elongation. Even minor rhodopsin mislocalization prevents efficient outer segment elongation suggesting that QVAPA-targeted delivery of rhodopsin drives outer segment extension. We identify that rhodopsin’s core, helix-8, and accessible QVAPA targeting motif are the minimal requirements to extend the rudimentary outer segment in RhoKO rods. Our findings provide useful insights into rhodopsin’s molecular features needed for outer segment delivery and subsequent elongation of this membrane-rich compartment.
Mathematical Modeling of Estrogen-Mediated Inflammation in the Gut and Immune System
Authors: Lighty Ariel M. , Islam Mohammad Aminul , Smith Brenda J. , Ford Versypt Ashlee N.
Published: December 2024

Postmenopausal osteoporosis is a chronic inflammatory disease characterized by decreased bone mass and increased bone fracture risk. Estrogen deficiency during menopause plays a major role in post-menopausal osteoporosis by influencing bone, immune, and gut cell activity. In the gut, estrogen loss decreases tight junction proteins that bind epithelial cells of the intestinal barrier together. This increases gut permeability and alters the balance of T cells, increasing inflammatory T helper (Th17) cells and decreasing anti-inflammatory regulatory T cells (Tregs). Prebiotic dietary fibers are a promising treatment modality for gut-mediated inflammation and bone loss associated with estrogen deficiency. In a previous study, we investigated the effect of butyrate (a prebiotic by-product) on Treg levels in the gut, blood, and bone starting with healthy conditions. However, a gap remains in our mechanistic understanding of how estrogen affects systemic inflammation separately and in combination with prebiotic fibers.

We developed a two-compartment dynamic model of estrogen in the gut and immune system to investigate the mechanisms of gut-mediated inflammation induced by estrogen-deficient conditions. Our initial model contains ODEs for estrogen, naive T cells, Tregs, and Th17 cells in gut and blood compartments. Estrogen is modeled using physiological mass balance equations considering its production, migration, and elimination. We integrate our estrogen model with an adapted version of our previous butyrate model, adding a population balance for Th17 cells and terms for bidirectional migration of Tregs and Th17 cells. Estrogen interactions with cells are modeled using Hill-type activation and inhibition functions. Our mathematical model predicts changes in T cell dynamics associated with changes in endogenous estrogen levels. We compare our predictions to in vivo results of estrogen, Tregs, and Th17 levels in the gut and blood after surgical menopause in mice. In the future, we will leverage this model to investigate whether the effect of prebiotic fiber treatment on estrogen-deficient bone loss is significantly affected by gut-mediated inflammation. The emphasis in this preprint is on the methods, particularly those for literature-based model parameterization.
Metabolic tuning facilitates nociceptor resilience to excitotoxicity
Authors: Yuan Lin , Chandel Navdeep S. , Julius David
Published: December 2024

The capsaicin receptor, TRPV1, mediates the detection of harmful chemical and thermal stimuli. Overactivation of TRPV1 can lead to cellular damage or death through excitotoxicity, a phenomenon associated with painful neuropathy and the paradoxical use of capsaicin as an analgesic. We exploited capsaicin-evoked death to conduct a systematic analysis of excitotoxicity through a genome-wide CRISPRi screen, thereby revealing a comprehensive network of regulatory pathways. We show that decreased expression of mitochondrial electron transport chain (ETC) components protects against capsaicin-induced toxicity by mitigating calcium imbalance and mitochondrial reactive oxygen species production via distinct pathways. Interestingly, TRPV1+sensory neurons in adult mice maintain lower expression of ETC components and can better tolerate excitotoxicity and oxidative stress compared to other sensory neuron subtypes. We further confirm the regulatory roles of the ETC in sensory neurons through gain-of-function and loss-of-function experiments. These findings implicate ETC tuning as a cellular protective strategy against sensory excitotoxicity.
The Restoration of Social Defects in Schizophrenic Mice by Plant Exposure
Authors: Li Mingxuan , Li Mingda , Zhou Kai , Zhang Xiangyu , Liu Shanshan , Wu Yuyu , Li Xinjian
Published: December 2024

Schizophrenia is a serious psychotic disorder caused by both individuals’ genetic background and their living environment. However, how the cognitive and negative symptoms can be treated is still a challenge since most anti-psychotic drugs are only effective for positive symptoms. Previous epidemic studies have demonstrated that plant exposure could decrease the risk of schizophrenia and shorten the length of psychiatric hospital admissions for patients. However, it is still unknown whether plant exposure could improve cognition-related defects in schizophrenia, with no related animal studies. In the present study, we first induced a schizophrenia mice model by giving mice long-term (2 weeks) injections of the antagonist of the NMDA receptor: MK801. We then raised the animals in environments containing plants (4 weeks) including Epipremnumaureumand rosemary, and tested their locomotive, anxious and social behaviors. We found that plant exposure did not change the locomotion behaviors of wild-type animals, but significantly reduced the schizophrenia-related social and anxious behaviors in the schizophrenic animals. In addition, we tested the expression of c-Fos in animals exposed to plants after social behavioral testing and found that the deficits in c-Fos expression in both the hippocampus and prefrontal cortex were partially rescued after plant exposure. These results indicate plant exposure will be a new tool to improve the clinical deficits of schizophrenia.
Histone H4 limits transcription of the histone locus in Drosophila
Authors: Ahmad Kami , Wooten Matt , Takushi Brittany N , Vidaurre Velinda , Chen Xin , Henikoff Steven
Published: December 2024

The expression of core histone genes is coupled to DNA replication of the genome to support chromatin packaging. In Drosophila, core histone genes are repeated in one locus as a 100-copy array and forms the Histone Locus Body; these multiple copies support varying rates of cell proliferation in different developmental stages and various tissues of the animal. We show here that the Drosophila Histone Locus Body contains a mix of active and silenced units. In the male germline reporter histone repeat units are strongly silenced, and we used this setting to test the dependence of expression on chromatin factors and histones. We find that silenced histone genes are induced in response to demand for histones, and from a selected survey we identify that only the H4 histone is required for reporter silencing. Further, histone H4 protein localizes to the Histone Locus Body and is most enriched immediately after S phase of the cell cycle. This argues for a role of histone H4 in coupling the demand for histones for chromatin packaging to histone gene expression. Binding patterns of the NPAT regulatory factor and RNA Polymerase II in K562 cells suggests that this regulatory principle also operates in human cells.

Author Summary

Cell proliferation in eukaryotes requires the coordination of DNA replication to duplicate the genome and synthesis of new histones to package that DNA.Drosophila melanogasterhas a single array of histone genes, where some are actively transcribed and others are silenced. Here, we present evidence that the number of activated genes responds to the demand for histones during DNA replication. We identify one histone protein as a factor that localizes to the histone gene array, and that reduced levels of this histone induce the expression of otherwise silenced histone genes. In human cells, the gene encoding this same histone is the predominant target for activating transcription proteins, and is expressed more highly than other histones. The amount of this one histone may serve to sense the demand for histones during DNA replication, so that increased levels of this histone when DNA replication is complete represses histone gene expression.
Remote Detection of Red-Edge Spectral Characteristics in Floating Aquatic Vegetation
Authors: Murakami Aoi , Komatsu Yu , Takizawa Kenji
Published: December 2024

The vegetation red-edge of terrestrial plants is a key biosignature for detecting Earth-like habitable exoplanets. Although water is essential for plants, an excess of water can limit the distribution of terrestrial vegetation. On planets with extensive water coverage and limited land, floating vegetation on the water’s surface could serve as a crucial indicator of life. This study examined the spectral reflectance of floating plants across various scales, from individual leaves to lake-wide vegetation coverage. Our comparisons between individual leaves revealed that the red-edge of floating plants was equivalent to or even more pronounced than that of terrestrial plants. Although water can reduce plant reflectance, the naturally low reflectance of water enhances the detection sensitivity for floating vegetation. Seasonal changes, such as the proliferation of floating plants in summer and their decline in winter, lead to significant variations in lake reflectance. By analyzing satellite images of lakes and marshes over a five-year period, we confirmed that these seasonal variations in reflectance reliably indicate the presence of floating vegetation. The seasonal signal showed robustness to the effects of clouds, which pose another challenge on water-rich planets. We propose that floating vegetation be considered alongside, or even in place of, terrestrial vegetation in the search for extraterrestrial life.
Molecular requirements of chromogranin B for the long-sought anion shunter of regulated secretion
Authors: Yadav Gaya P. , Annamalai Mani , Hagan D. Walker , Cui Lina , Mathews Clayton , Jiang Qiu-Xing
Published: December 2024

All eukaryotes utilize regulated secretion to release molecular signals packaged in secretory granules for local and remote signaling. An anion shunt conductance was first suggested in secretory granules of bovine chromaffin cells nearly five decades ago. Biochemical identity of this conductance remains undefined. CLC-3, an intracellular Cl-/H+exchanger, was proposed as a candidate sixteen years ago, which, however, was contested experimentally. Here, we show that chromogranin B (CHGB) makes the kernel of the long-sought anion shunter in cultured and primary neuroendocrine cells and its channel functions are essential to proper granule maturation. Intragranular pH measurements and cargo maturation assays revealed that normal granular acidification, proinsulin-insulin conversion, and dopamine-loading in neuroendocrine cells all rely on functional CHGB+ channels. Primary β-cells fromChgb-/-mice exhibited persistent granule deacidification, which suffices to uplift plasma proinsulin level, diminish glucose-induced 2nd-phase insulin secretion and dwindle monoamine content in chromaffin granules from the knockout mice. Data from targeted genetic manipulations, dominant negativity of a deletion mutant lacking channel-forming parts and tests of CLC-3/5 and ANO-1/2 all exclude CHGB-lesschannels from anion shunting in secretory granules. The highly conserved CHGB+ channels thus function in regulated secretory pathways in neuronal, endocrine, exocrine and stem cells of probably all vertebrates.

HIGHLIGHTS

Loss of CHGB channel functions impairs secretory granule acidification in neuroendocrine cells, which necessitates anion shunt conduction.

CHGBΔMIF, a mutant unable to form a functional Cl-channel, exerts negative dominance on endogenous CHGB and results in granule deacidification in cultured cells.

Neither CLC-3 & -5 nor ANO-1 & -2 participate in the CHGB-mediated granule acidification. Clcn3 knockout effects on regulated secretion can be attributed to its functions in endosomal and endolysosomal compartments.

PrimaryChgb-/-β-cells exhibit persistent granule deacidification, presenting a unifying mechanism for disparate mouse phenotypes: hyperproinsulinemia, near abrogation of 2ndphase insulin release after glucose challenge and diminution of monoamine contents in chromaffin granules.
A reference metagenome sequence of the lichenCladonia rangiformis
Authors: Heuberger Matthias , Wehrkamp Carlotta Marie , Pfammatter Alina , Poretti Manuel , Graf Johannes Peter , Herger Aline , Isaksson Jonatan , Schlagenhauf Edith , Honegger Rosmarie , Wicker Thomas , Sotiropoulos Alexandros G.
Published: December 2024

● Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont ofCladonia rangiformis.

● Using long read sequences from an entire symbiotic complex, plus short read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species.

● We constructed chromosome-scale assemblies of theC. rangiformisfungus and its trebouxioid green algal photobiontAsterochloris mediterranea. The genome of the fungus comprises ∼22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found thatA. mediterraneacentromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil.

● Our study revealed that the thalli ofC. rangiformishave a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria.
sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing
Authors: Dehghannasiri Roozbeh , Kokot Marek , Starr Alexander L. , Maziarz Jamie , Gordon Tal , Tan Serena Y. , Wang Peter L. , Voskoboynik Ayelet , Musser Jacob M. , Deorowicz Sebastian , Salzman Julia
Published: December 2024

Typical high-throughput single-cell RNA-sequencing (scRNA-seq) analyses are primarily conducted by (pseudo)alignment, through the lens of annotated gene models, and aimed at detecting differential gene expression. This misses diversity generated by other mechanisms that diversify the transcriptome such as splicing and V(D)J recombination, and is blind to sequences missing from imperfect reference genomes. Here, we present sc-SPLASH, a highly efficient pipeline that extends our SPLASH framework for statistics-first, reference-free discovery to barcoded scRNA-seq (10x Chromium) and spatial transcriptomics (10x Visium); we also provide its optimized module for preprocessing andk-mer counting in barcoded data, BKC, as a standalone tool. sc-SPLASH rediscovers known biology including V(D)J recombination and cell-type-specific alternative splicing in human and trans-splicing in tunicate (Ciona) and when applied to spatial datasets, detects sequence variation including tumor-specific somatic mutation. In sponge (Spongilla) and tunicate (Ciona), we uncover secreted repeat proteins expressed in immune-type cells and regulated during development; the sponge genes were absent from the reference assembly. sc-SPLASH provides a powerful alternative tool for exploring transcriptomes that is applicable to the breadth of life’s diversity.
High-Throughput Free Amino Acid Quantification from Maize Tissues
Authors: Ansaf Huda , Yobi Abou , Angelovici Ruthie
Published: December 2024

Amino acids in maize can exist in both a free and protein-bound state. While most amino acids are part of a protein backbone, a small percentage of them remain free and play important biological roles, serving as signaling molecules, nitrogen transporters, osmolytes, and precursors for multiple primary and secondary metabolites. Their levels vary widely especially in maize leaves, depending on the developmental stage and in response to environmental conditions. Therefore, accurate and reliable quantification of free amino acids (FAAs) is vital in any effort aimed at studying their response to developmental and environmental cues. In this protocol, we describe a robust, high-throughput method that quantifies the 20 proteogenic amino acids (i.e., those that can be incorporated into proteins) that are found in the free form in maize tissue. This method consists of three major parts: first, aqueous extraction of FAAs from maize tissue; second, separation, detection, and quantification of all 20 proteogenic amino acids using ultraperformance liquid chromatography-tandem mass spectrometry; and third, data analysis and processing using the MassLynx data analysis software, TargetLynx.
Plasma characterization and modulation techniques for 1.3 GHz, 9-cell superconducting rf cavity cleaning
Authors: Zhu Tongtong , Bao Xinghai , He Yuan , Xue Zongheng , Qiu Yubo , Li Chunlong , Xue Wentian , Jiang Tiancai , Chu Qingwei , Guo Hao , Huang Shichun , Yang Ziqin , Yue Weiming , Chen Jinfang , Xu Mengxin , Zhang Shenghu , Zhang Kun , Zhao Hongwei , Tan Teng , Wu Andong
Published: December 2024

Plasma cleaning is extensively employed in superconducting radio-frequency (SRF) accelerators to mitigate field emissions induced by hydrocarbon contaminants. This study explores the plasma physical characteristics and modulation techniques in a commonly utilized 1.3 GHz 9-cell tesla-shaped SRF cavity through the integration of optical emission spectroscopy and a plasma fluid model. Investigations of argon and neon plasma demonstrate that argon generates a higher electron density due to its lower ionization energy, while neon plasma exhibits higher electron temperature and potential that promotes the decomposition of oxygen and the rate of surface chemical reactions. Furthermore, the research reveals that the electron density, temperature, and electric potential of the neon plasma within the cavity exhibit a centrally symmetric distribution, with maximum values of 1×1015  m−3, 0.53 eV, and 24.5 V, respectively. Subsequently, the effects of power, gas pressure, and frequency on the physical properties of the plasma are systematically analyzed. Among these, the 640 nm spectral line was selected as a qualitative indicator of glow intensity and plasma state changes within the cavity due to its strongest peak intensity. Findings indicate that increasing power and gas pressure enhance electron density and 640 nm spectral line intensity while reducing electron temperature. Additionally, comparative analysis of plasma properties in cells 1-9 reveals that most cells exhibit higher electron temperature and electron density at frequency II. (Frequency I serves as the transfer mode for plasma transfer, while frequency II acts as the stable mode for plasma stabilization.) Consequently, plasma cleaning of the 1.3 GHz 9-cell cavity using neon gas at this frequency is anticipated to yield superior cleaning outcomes. These findings enhance our understanding and control of plasma behavior within the SRF cavity and provide valuable insights for optimizing plasma cleaning processes.

Published by the American Physical Society
2024
Dumbbell shapes in the superasymmetric fission of heavy nuclei
Authors: Ivanyuk F. A. , Carjan N.
Published: December 2024

We have calculated the fission fragments' mass distributions for several isotopes of heavy and superheavy nuclei from uranium to flerovium within an improved scission point model. For all considered nuclei, in addition to the standard mass-asymmetric fission mode we have found the mass super-asymmetric mode with the mass of heavy fragments equal 190. For the actinide nuclei, the probability of superasymmetric fission is by six orders of magnitude smaller than for standard asymmetric fission. For the superheavy nuclei this probability is only by two orders of magnitude smaller. In all cases, the superasymmetric scission shapes are dumbbells with the heavy fragment close to a sphere. We have estimated the stability of the light fragment concerning the variation of the neck and found out that sequential ternary fission is not favored energetically. The calculations were carried out with nuclear shape described by generalized Cassinian ovals with six deformation parameters, α, α1, α2, α3, α4, and α5. The configuration at the moment of the neck rupture was defined by fixing α=0.98. This value corresponds to a neck radius rneck≈1.5 fm.

Published by the American Physical Society
2024
Breaking local quantum speed limits with steering
Authors: Centrone Federico , Gessner Manuel
Published: December 2024

We show how quantum correlations allow us to break the local speed limits of physical processes using only local measurements and classical communication between two parties that share an entangled state. Inequalities that bound the minimal time of evolution of a quantum state by energy fluctuations can be violated in the presence of steering by conditioning on the measurement outcomes of a remote system. Our results open up pathways for studying how quantum correlations influence the dynamical properties of states and observables.

Published by the American Physical Society
2024
Saturation and Recurrence of Quantum Complexity in Random Local Quantum Dynamics
Authors: Oszmaniec Michał , Kotowski Marcin , Horodecki Michał , Hunter-Jones Nicholas
Published: December 2024

Quantum complexity is a measure of the minimal number of elementary operations required to approximately prepare a given state or unitary channel. Recently, this concept has found applications beyond quantum computing—in studying the dynamics of quantum many-body systems and the long-time properties of anti–de Sitter black holes. In this context, Brown and Susskind [] conjectured that the complexity of a chaotic quantum system grows linearly in time up to times exponential in the system size, saturating at a maximal value, and remaining maximally complex until undergoing recurrences at doubly exponential times. In this work, we prove the saturation and recurrence of complexity in two models of chaotic time evolutions based on (i) random local quantum circuits and (ii) stochastic local Hamiltonian evolution. Our results advance an understanding of the long-time behavior of chaotic quantum systems and could shed light on the physics of black-hole interiors. From a technical perspective, our results are based on establishing new quantitative connections between the Haar measure and high-degree approximate designs, as well as the fact that random quantum circuits of sufficiently high depth converge to approximate designs.

Published by the American Physical Society
2024
Crystal structure of di-μ-acetato-κ4
O:O′-bis{(acetato-κ2
O,O′)tetraaqua[1-(pyridin-2-ylmethylidene-κN)-2-(pyridin-2-yl-κN)hydrazine-κN
1]lanthanum(III)} dinitrate hemihydrate
Authors: Ndiaye-Gueye Mbossé , Traoré Bocar , Thiam Ibrahima Elhadji , Diouf Ousmane , Wenger Emmanuel , Sall Abdou Salam , Lecomte Claude , Gaye Mohamed
Published: December 2024

In the binuclear title complex, [La2(C2H3O2)4(C11H10N4)(H2O)4](NO3)2·0.5H2O, the two lanthanum ions are nine coordinate in a distorted trigonal–prismatic geometry. Each LaIII ion is bonded to three N atoms of the Schiff base, 1-(pyridin-2-yl)-2-(pyridin-2-ylmethylene)hydrazine and is coordinated by one acetate group, which acts in η
2-bidentate mode and two acetate groups that act in μ
2-mode between the two LaIII ions. Two η
1-water molecules complete the coordination sphere. All bond lengths in the coordination environment of the LaIII ion are slightly larger than those observed in the isostructural NdIII and SmIII complexes. The LaIII...LaIII distance is 4.6696 (6) Å. In the crystal, extensive O—H...O hydrogen-bonding interactions involving the coordinated water molecules and the non-coordinating nitrate anions, as well as the oxygen atoms of the acetate groups, generate an overall three-dimensional supramolecular network.
3-Iodoaniline
Authors: Slamang Ferhan , Hosten Eric Cyriel , Betz Richard
Published: December 2024

The title compound, C6H6IN, is the meta-iodinated derivative of aniline. The asymmetric unit contains two molecules. The structure was refined as a two-component inversion twin with a volume ratio of 55.6:44.4. In the crystal, cooperative hydrogen bonds of the N–H...N type connect the molecules into infinite chains propagating along the a-axis direction. Dispersive I...I contacts extend these chains to sheets perpendicular to the crystallographic c axis.
Towards a new rural and urban intersection, “R-Urban”: the Beykoz district case in Istanbul
Authors: Turgut Hulya , Keskin Ozge , Girgin Dilara
Published: December 2024

Purpose

Urbanization is among current global challenges along with climate change, population growth and depletion of natural resources. Rural areas have been transformed due to urbanization pressures, which leads to a change in the relationship between rural and urban spaces, blurring the boundaries between rural and urban areas. Due to the lack of a clear distinction, a new form of rural–urban relationship has emerged. The convergence and even disappearance of borders has paved the way for a rural–urban dichotomy and re-questioning the relationship between cities and nature. In the case of Istanbul, this transformation, especially since 1980, has been reshaping rural–urban relations. Thus, the present article aimed to rethink this new pattern described as “R-Urban”, a hybrid intersection as a field of experience.

Design/methodology/approach

R-Urban creates an ambiguous and dynamic hybrid space where urban and rural operate within flexible and layered spatial boundaries. In the article, initially, a conceptual framework is presented based on the analysis of existing conceptual framework of rural–urban relationships, with transactional and dialectical perspectives. Secondly, fieldwork was investigated with representational tools such as mapping, photography and collages to determine the current status based on quantitative and qualitative data. Then, the rural–urban situation of Istanbul was conceptualized, with a focus on Beykoz neighborhood, a peripheral development with blurred rural and urban borders.

Findings

Beykoz, as an R-Urban space, has a significant potential regenerating the relations between nature, humans and space and production to practices to ensure ecological resilience. The article demonstrated that the coexistence of different lifestyles paved the way for cultural diversity and the development of social relations. This diversity allowed innovative and sustainable practices while increasing social cooperation and solidarity in the region.

Practical implications

To improve urban resilience, especially in Istanbul against future poly-crises, effective use of resources, healthy social environment, production-consumption network and symbiotic rural-urban relationships could be developed.

Social implications

Strengthening the socio-cultural, economic and ecological systems could lead to dynamic interactions that would reduce vulnerabilities in rural–urban intersections that would regenerate and renew the city and reconsider adaptation capabilities.

Originality/value

The present article rethinks this new pattern described as “R-Urban”, a hybrid intersection as a field of experience, highlighting the potential of these rural–urban intersections for future urban resilience and adaptation capabilities.
Harm reduction design: doing health and safety differently
Authors: Campbell Nancy D.
Published: December 2024

Purpose

This paper aims to document a novel course titled Harm Reduction Design Studio. The course introduced the harm reduction problem space to design students for designing objects, social worlds, infrastructures and ecologies that shape human and nonhuman social interactions within them.

Design/methodology/approach

Extending tenets drawn from social movements for harm reduction from the focus on drugs and habits begins the reparative work of undoing past harms, living well in the present and reducing future harms. This course introduces history, theory and practice of harm reduction in relation to health, well-being, social connection and safety.

Findings

The course was piloted from August to December 2024 in the Department of Science and Technology Studies at Rensselaer Polytechnic Institute in Troy, New York, USA.

Social implications

Society-wide implications for mainstreaming harm reduction are far-reaching. For instance, the U.S. National Science Foundation has recently called for ways to “incorporate ethical, social, safety, and security considerations” into research design to mitigate potential harms of scientific research and amplify societal benefits. This course prepares students to think upfront about incorporating harm reduction into the design of technological artifacts.

Originality/value

This course presents a replicable model for bringing harm reduction and design pedagogy together in the shared spirit of encouraging the readership of Drugs, Habits and Social Policy to widen participation in design practice.
Understanding what, how and when green logistics practices influence carbon-neutral supply chain performance
Authors: Tetteh Francis Kamewor , Mensah John , Owusu Kwateng Kwame
Published: December 2024

Purpose

Integrating green (sustainable) practices in logistics management play a crucial role in accelerating the transition to a circular economy, realizing its sustainability potential and position in the net zero emission target by 2050. Over the past decade, this integration has attracted significant attention in both academic and industrial discourse. Despite the increasing recognition of the benefits of green logistics practices (GLPs), only a few firms have implemented green-oriented or sustainable logistics practices; hence, a comprehensive understanding of what could drive its implementation as well as how and when firms can benefit from GLPs is of key importance for theory, policy and practice. Drawing on dual theoretical lenses, this study investigated how supply chain ethical leadership (SCEL) could stimulate green logistics practices by building green core competencies (GCC) under varying conditions of corporate green culture (CGC).

Design/methodology/approach

An integrated model motivated by social learning and contingency theories was tested using responses from 208 managers of logistics firms in Ghana. SPSS 23 and covariance-based structural equation modeling (CB-SEM) were used for data analyses.

Findings

Both SCEL and GCC significantly influenced GLPs. The findings also showed that GLPs significantly enhanced carbon-neutral supply chain performance (CNSCP). The results further showed that GCC mediates the SCEL–GLPs link. We also found that the effect of SCEL on GLPs was amplified at a high level of CGC.

Practical implications

This study offers fresh insight into how managers can leverage SCEL to support GLP and when they can also combine green competence and green culture to achieve enhanced benefits in the form of carbon-neutral SCP. This further implies that building ethical leadership and competencies alone may not be sufficient to drive superior emission reduction and subsequent sustainability; rather, cultivating a green-oriented culture that values sustainable logistics is crucial to fully realize the potential of ethical leadership and competencies in enabling the implementation of GLPs and subsequently enhancing carbon-neutral SCP.

Originality/value

The novelty of the present study lies in the integration of social learning and contingency theories to unearth the mechanism and conditional roles of green competence and green culture in optimizing the SCEL–GLPs–GLP relationship. The study is also among the few attempts to shed light on how firms can leverage GLPs to enhance carbon-neutral supply chain performance, which is rare.
Conv-DMSA: an efficient imputation model for multivariate time series through diagonal mask self-attention
Authors: Zhang Hao , Ding Weilong , Yu Qi , Liu Zijian
Published: December 2024

Purpose

The proposed model aims to tackle the data quality issues in multivariate time series caused by missing values. It preserves data set integrity by accurately imputing missing data, ensuring reliable analysis outcomes.

Design/methodology/approach

The Conv-DMSA model employs a combination of self-attention mechanisms and convolutional networks to handle the complexities of multivariate time series data. The convolutional network is adept at learning features across uneven time intervals through an imputation feature map, while the Diagonal Mask Self-Attention (DMSA) block is specifically designed to capture time dependencies and feature correlations. This dual approach allows the model to effectively address the temporal imbalance, feature correlation and time dependency challenges that are often overlooked in traditional imputation models.

Findings

Extensive experiments conducted on two public data sets and a real project data set have demonstrated the adaptability and effectiveness of the Conv-DMSA model for imputing missing data. The model outperforms baseline methods by significantly reducing the Root Mean Square Error (RMSE) metric, showcasing its superior performance. Specifically, Conv-DMSA has been found to reduce RMSE by 37.2% to 63.87% compared to other models, indicating its enhanced accuracy and efficiency in handling missing data in multivariate time series.

Originality/value

The Conv-DMSA model introduces a unique combination of convolutional networks and self-attention mechanisms to the field of missing data imputation. Its innovative use of a diagonal mask within the self-attention block allows for a more nuanced understanding of the data’s temporal and relational aspects. This novel approach not only addresses the existing shortcomings of conventional imputation methods but also sets a new standard for handling missing data in complex, multivariate time series data sets. The model’s superior performance and its capacity to adapt to varying levels of missing data make it a significant contribution to the field.
Leveraging the experiencescape for destination attractiveness: empirical insights from casino resorts
Authors: Ji Chunli , Liu Shuang , Ho Hong-Wai , Sthapit Erose , Garrod Brian
Published: December 2024

Purpose

The experiencescape is a relatively new concept, and research using it remains scarce. This study contributes to the understanding of the experiencescape and its role in tourism consumption by constructing a novel conceptual model of the experiencescape elements of a casino resort visit and their effects on its attractiveness.

Design/methodology/approach

Partial least squares structural equation modelling was employed, using data collected from 491 casino resort visitors in Macao, to establish a link between the experiencescape and visitors’ perceived overall attractiveness of the casino resort through the mediating effect of arousal.

Findings

The findings establish the relationship between experiencescapes and the perceived overall attractiveness of integrated casino resorts through the mediating effect of arousal.

Practical implications

Casino resort executives are advised to orchestrate various experience elements from the perspective of the experiencescape to trigger positive tourism experiences. Specifically, all factors related to tangible, gaming and non-gaming and social experiential stimuli need to be continually reviewed, improved and innovated.

Originality/value

This study presents novel insights into the role of emotions in an integrated casino resort context. It identifies a set of strategies through which managers can increase the attractiveness of their resorts by stimulating customers’ emotions.
Asset specificity, inter-firm ecosystem, firm adaptability and supply chain integration
Authors: Nakayima Farida , Namagembe Sheila , Kabagambe Levi , Ntayi Joseph , Muhwezi Moses
Published: December 2024

Purpose

This study investigates the effect of asset specificity, inter-firm ecosystem and firm adaptability on supply chain integration. The study also investigates the mediation effect of firm adaptability on the relationship between asset specificity and supply chain integration and inter-firm ecosystem and supply chain integration.

Design/methodology/approach

This research applied a quantitative research methodology to investigate the interdependencies between study variables. A disproportionate stratified simple random sampling technique was used to select the firms that participated in the study. As a result, 103 food processing firms were selected from a total population of 345 firms located in Kampala district.

Findings

The findings reveal that the direct relationship between asset specificity and supply chain integration and inter-firm ecosystem and supply chain integration was found positive but insignificant. Both asset specificity and inter-firm ecosystem are associated positively with firm adaptability. A partial mediation was established between asset specificity and SCI while a full mediation effect was found in inter-firm ecosystem and SCI.

Research limitations/implications

The study used perceptual measures to obtain responses on the various constructs investigated and how these constructs relate. To avoid biasing the results, key suppliers and customers were not involved due to multi-level relationships that they maintain with various firms.

Originality/value

This study contributes to existing studies by applying two theories. First, the study applies the Transaction Cost Theory to study the effect of asset specificity on supply chain integration. Secondly, the Complexity Adaptive System Theory was applied to examine the influence of firm adaptability and inter-firm ecosystem on supply chain integration. Few studies have focused on the effect of inter-firm ecosystem in the supply chain; yet, SCI involves network of various player making supply chains complex This study is among the few studies that have focused on adaptability in the food processing sector in a developing country like Uganda.
The Role of Boundary Spanning in Building Trust: A Place‐Based Study on Engaging Hardly Reached Groups in Community Healthcare Settings
Authors: Bianchi Lara , Kelemen Mihaela , Shivji Alysha Kate , Tallant Jonathan , Timmons Stephen
Published: December 2024

This paper investigates the impact of boundary spanning activities on building trust as a means of tackling health inequalities in hardly reached communities. Lack of trust has been identified as a barrier to engagement with healthcare services, resulting in poorer health outcomes. Engaging with hardly reached communities is challenging due to the social and symbolic boundaries prevalent in community healthcare settings. Drawing on empirical data from a recent year‐long collaborative research project with communities from seven economically deprived areas in the City of Nottingham, we identify two boundary spanning activities that facilitate the development of trust: communication across boundaries and intergroup relationship building. By cross fertilising sociological accounts on trust with insights derived from philosophy, the study finds that for hardly reached communities, trusting relevant individuals is more potent and widespread than the trust they have in healthcare institutions. By developing individual trust, hardly reached communities are more likely to consequently perceive the existence of institutional goodwill and competence. This counter‐intuitive finding invites us to regard trust as context specific and relational rather than as a binary choice between trusting individuals or institutions and to situate cross boundary activities focused on trust development within the power asymmetries in which they unfold.
Conjoining Bion’s Reading of C. G. Jung’s Memories, Dreams, Reflections with his Clinical Seminars in Rio de Janeiro and São Paulo
Authors: Aguayo Joseph
Published: December 2024

This author read W. R. Bion’s (1974) unpublished, personally annotated copy of C. G. Jung’s Memories, Dreams, Reflections (MDR). The interest here is to conjoin Bion’s reading of Jung with his own contemporaneous work. After setting out a context for Jung and Bion’s meeting one another in 1935, we look at Bion’s subsequent psychoanalytic development over the decades until 1974, particularly in the area of clinical intuition. The author takes up Bion’s clinical seminars in Rio de Janeiro and São Paulo in 1974. He maintains that direct correlations can be made between Bion’s marginal comments in MDR and material that he directly lectured on in his 1974 clinical seminars. Bion’s interest here centred on the development of clinical intuition, dreams and precocious intellectual development. Even though he never mentioned Jung by name in 1974, it seems that Jung was clearly to the back of his mind as he lectured to his Brazilian colleagues in 1974. The fields of psychoanalysis and analytical psychology can be further enhanced by exploring how Bion and Jung’s ideas converge as well as diverge.
A Study on Gastrointestinal Tract of Bardhoka Autochthonous Sheep Breed in Kosovo
Authors: Duro Sokol , Jashari Tefik , Gündemir Ozan , Pérez William
Published: December 2024

The Bardhoka sheep breed, also known as Dukagjini white sheep (Ovis aries), is considered to be a medium‐sized sheep that is a typical grazing ruminant. The aim of this study was to investigate and measure the parameters of the gastrointestinal tract (GIT) of Bardhoka sheep to determine the morphometry, volume, ratio and surface areas of its different parts. The GIT of eight adult healthy Bardhoka sheep with an average body mass (BM) of 57.63 kg, aged from one to three years, was evaluated immediately after slaughter. Descriptive statistics, including mean values, standard deviations, coefficients of variation and correlations, were calculated using SPSS (version 22). Detailed measurements of the forestomach and intestines were described. The full and empty average weight of the GIT was approximately 23.92% and 5.64% of BM, respectively. The weight of the rumenoreticulum tissue, after removing the content, was about 2.02% of BM. The percentages of the small and large intestines, full and empty, were about 12.28% and 21.55%, and 14.25% and 24.31% of the GIT, respectively. These percentages were 2.94%, 1.24%, 3.45% and 1.37% of the BM, respectively. The allometry ratio of the total intestinal length, small intestine and large intestine to the average BM was 0.68, 0.53 and 0.15, respectively. The length ratio between the small and large intestines was 1:3.54, while the full weight ratio between the two segments of the intestine was 1:1.15 in favour of the large intestine. In conclusion, this study detailed the morphometry parameters of all GIT parts of Bardhoka sheep. This study can serve as a basis for comparative studies and as a database for other similar research.