bluuebunny/crossref_metadata_2025 huggingface dataset:
The structural organisation of pentraxin-3 and its interactions with heavy chains of inter-α-inhibitor regulate crosslinking of the hyaluronan matrix
Authors: Shah Anokhi , Zhang Xiaoli , Snee Matthew , Lockhart-Cairns Michael P. , Levy Colin W. , Jowitt Thomas A. , Birchenough Holly L. , Dean Louisa , Collins Richard , Dodd Rebecca J. , Roberts Abigail R. E. , Enghild Jan J. , Mantovani Alberto , Fontana Juan , Baldock Clair , Inforzato Antonio , Richter Ralf P. , Day Anthony J.
Published: August 2024

Pentraxin-3 (PTX3) is an octameric protein, comprised of eight identical protomers, that has diverse functions in reproductive biology, innate immunity and cancer. PTX3 interacts with the large polysaccharide hyaluronan (HA) to which heavy chains (HCs) of the inter-α-inhibitor (IαI) family of proteoglycans are covalently attached, playing a key role in the (non-covalent) crosslinking of HC•HA complexes. These interactions stabilise the cumulus matrix, essential for ovulation and fertilisation in mammals, and are also implicated in the formation of pathogenic matrices in the context of viral lung infections. To better understand the physiological and pathological roles of PTX3 we have analysed how its quaternary structure underpins HA crosslinking via its interactions with HCs. A combination of X-ray crystallography, cryo-electron microscopy (cryo-EM) and AlphaFold predictive modelling revealed that the C-terminal pentraxin domains of the PTX3 octamer are arranged in a central cube, with two long extensions on either side, each formed from four protomers assembled into tetrameric coiled-coil regions, essentially as described by (Nooneet al., 2022; doi:10.1073/pnas.2208144119). From crystallography and cryo-EM data, we identified a network of inter-protomer salt bridges that facilitate the assembly of the octamer. Small angle X-ray scattering (SAXS) validated our model for the octameric protein, including the analysis of two PTX3 constructs: a tetrameric ‘Half-PTX3’ and a construct missing the 24 N-terminal residues (Δ1-24-PTX3). SAXS determined a length of ∼520 Å for PTX3 and, combined with 3D variability analysis of cryo-EM data, defined the flexibility of the N-terminal extensions. Biophysical analyses revealed that the prototypical heavy chain HC1 does not interact with PTX3 at pH 7.4, consistent with our previous studies showing that, at this pH, PTX3 only associates with HC•HA complexes if they are formed in its presence. However, PTX3 binds to HC1 at acidic pH, and can also be incorporated into pre-formed HC•HA complexes under these conditions. This provides a novel mechanism for the regulation of PTX3-mediated HA crosslinking (e.g., during inflammation), likely mediated by a pH-dependent conformational change in HC1. The PTX3 octamer was found to associate simultaneously with up to eight HC1 molecules and, thus, has the potential to form a major crosslinking node within HC•HA matrices, i.e., where the physical and biochemical properties of resulting matrices could be tuned by the HC/PTX3 composition.
Distinct Proline residues in hinge-regions of SYMRK generates a phosphocode for releasing Malectin-like-Domain to allow progress of rhizobia-legume symbiosis at epidermal-cortical barrier
Authors: Chakrabarti Dipanjan , Paul Anindita , Bhattacharyya S. , Das Sagnik , Molla Firoz , Biswas Alokmoy , DasGupta Maitrayee
Published: August 2024

Symbiosis Receptor Kinase (SYMRK), a malectin-like-domain/leucine-rich-repeat receptor-like-kinase (MLD-LRR-RLK), is the upstream most component in Common-Symbiosis-Signalling-Pathway. We highlight two Proline residues that were distinctly acquired by SYMRK orthologues in its hinge-regions to evolve a signalling module for allowing progress of symbionts across transcellular barriers during rhizobia-legume symbiosis. Within the Ectodomain hinge (EctoD-hinge) all MLD-LRR-RLKs have a conserved W1xnGDPCxnW2x4C motif, where SYMRK orthologues within legumes have a distinct signature with a Proline preceding W2enabling cleavage of SYMRK-EctoD for releasing MLD. Within the kinase hinge (KD-hinge) at gatekeeper+1 position, a conserved Glutamate in MLD-LRR-RLKs is replaced by Proline in all SYMRK orthologues that enabled its dual-specific kinase activity for ensuring EctoD-cleavage. Substitution of either Proline restricted symbionts at the transcellular epidermal-cortical barrier forming infection patches in the nodule apex without affecting epidermal invasion and nodule organogenesis. This halt was entirely overcome by ectopic expression of free MLD demonstrating the released MLD to have an active role in progress of symbionts. Overall, we show that adaptations of distinct Prolines in hinge-regions of SYMRK orthologues in legumes have evolved a signalling module involving dimerization and optimal phosphorylation of SYMRK for releasing MLD as an active transducer of symbiosis signalling.
Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice
Authors: Sprockett Daniel D. , Dillard Brian A. , Landers Abigail A. , Sanders Jon G. , Moeller Andrew H.
Published: August 2024

Laboratory mice (Mus musculus domesticus) harbor gut bacterial strains that are distinct from those of wild mice1 but whose evolutionary histories are poorly understood. Understanding the divergence of laboratory-mouse gut microbiota (LGM) from wild-mouse gut microbiota (WGM) is critical, because LGM and WGM have been previously shown to differentially affect mouse immune-cell proliferation2,3, infection resistance4, cancer progression2, and ability to model drug outcomes for humans5. Here, we show that laboratory mice have retained gut bacterial symbiont lineages that diversified in parallel (co-diversified) with rodent species for > 25 million years, but that LGM strains of these ancestral symbionts have experienced accelerated accumulation of genetic load during the past ~ 120 years of captivity. Compared to closely related WGM strains, co-diversified LGM strains displayed significantly faster genome-wide rates of fixation of nonsynonymous mutations, indicating elevated genetic drift, a difference that was absent in non-co-diversified symbiont clades. Competition experiments in germ-free mice further indicated that LGM strains within co-diversified clades displayed significantly reduced fitness in vivo compared to WGM relatives to an extent not observed within non-co-diversified clades. Thus, stochastic processes (e.g., bottlenecks), not natural selection in the laboratory, have been the predominant evolutionary forces underlying divergence of co-diversified symbiont strains between laboratory and wild house mice. Our results show that gut bacterial lineages conserved in diverse rodent species have acquired novel mutational burdens in laboratory mice, providing an evolutionary rationale for restoring laboratory mice with wild gut bacterial strain diversity.
Genome-wide screen overexpressing mycobacteriophage Amelie genes identifies multiple inhibitors of mycobacterial growth
Authors: Tafoya Chelsea , Ching Brandon , Garcia Elva , Lee Alyssa , Acevedo Melissa , Bass Kelsey , Chau Elizabeth , Lin Heidi , Mamora Kaitlyn , Reeves Michael , Vaca Madyllyne , van Iderstein William , Velasco Luis , Williams Vivianna , Yonemoto Grant , Yonemoto Tyler , Heller Danielle M. , Diaz Arturo
Published: August 2024

The genome sequences of thousands of bacteriophages have been determined and functions for many of the encoded genes have been assigned based on homology to characterized sequences. However, functions have not been assigned to more than two-thirds of the identified phage genes as they have no recognizable sequence features. Recent genome-wide overexpression screens have begun to identify bacteriophage genes that encode proteins that reduce or inhibit bacterial growth. This study describes the construction of a plasmid-based overexpression library of 76 genes encoded by Cluster K1 mycobacteriophage Amelie, which is genetically similar to Cluster K phages Waterfoul and Hammy recently described in similar screens and closely related to phages that infect clinically important mycobacteria. 26 out of the 76 genes evaluated in our screen, encompassing 34% of the genome, reduced growth of the host bacteriumMycobacterium smegmatisto various degrees. More than one-third of these 26 toxic genes have no known function, and 10 of the 26 genes almost completely abolished host growth upon overexpression. Notably, while several of the toxic genes identified in Amelie shared homologs with other Cluster K phages recently screened, this study uncovered eight previously unknown gene families that exhibit cytotoxic properties, thereby broadening the repertoire of known phage-encoded growth inhibitors. This work, carried out under the HHMI-supported SEA-GENES project (Science Education Alliance Gene-function Exploration by a Network of Emerging Scientists), underscores the importance of comprehensive overexpression screens in elucidating genome-wide patterns of phage gene function and novel interactions between phages and their hosts.
ImmunoCellCycle-ID: A high-precision immunofluorescence-based method for cell cycle identification
Authors: Chen Yu-Lin , Chen Yu-Chia , Suzuki Aussie
Published: August 2024

The cell cycle is a fundamental process essential for cell proliferation, differentiation, and development. It consists of four major phases: G1, S, G2, and M. These phases collectively drive the reproductive cycle and are meticulously regulated by various proteins that play critical roles in both the prevention and progression of cancer. Traditional methods for studying these functions, such as flow cytometry, require a substantial number of cells to ensure accuracy. In this study, we have developed a user-friendly, immunofluorescence-based method for identifying cell cycle stages, providing single-cell resolution and precise identification of G1, early S, late S, early G2, late G2, and each sub-stage of the M phase using fluorescence microscopy. This method provides high-precision cell cycle identification and can serve as an alternative to, or in combination with, traditional flow cytometry to dissect detailed substages of the cell cycle in a variety of cell lines.
Quantifying anti-DUX4 therapy for facioscapulohumeral muscular dystrophy
Authors: Cowley Matthew V. , Zammit Peter S. , Banerji Christopher R. S.
Published: August 2024

Facioscapulohumeral muscular dystrophy (FSHD) is an inherited skeletal myopathy with no cure. Expression of the myotoxic transcription factor double homeobox 4 (DUX4) is believed to underlie FSHD pathogenesis and many proposed therapies target DUX4 generation or function. Which of these therapies will be the most effective is unclear. Here, by constructing a Markov-chain-based mathematical model of DUX4-mediated myotoxity in FSHD, we interrogate various anti-DUX4 FSHD therapeutic strategies. We derive an analytical function for myonuclear life expectancy in terms of the parameters ofDUX4expression and function. In a biologically relevant parameter regime, therapeutically decreasing the DUX4 protein diffusion rate is, surprisingly, predicted to be more effective at increasing myonuclear life expectancy than reducing the rate of myonuclear apoptosis caused by the expression of DUX4-target genes. We find that targeting elements ofDUX4transcription/translation, such as mRNA stability via siRNA therapy, has a limited predicted impact on DUX4-meditated toxicity when performed in isolation. However, our model predicts a super-additive effect from combining transcription/translation targeting strategies with approaches that minimise DUX4 diffusion-mediated import into neighbouring myonuclei. Importantly, we provide a computational tool to test and inform therapeutic designs, enabling pre-clinical screening of FSHD treatment approaches.
A test for microbiome-mediated rescue via host phenotypic plasticity inDaphnia
Authors: Shahmohamadloo René S. , Gabidulin Amir R. , Andrews Ellie R. , Fryxell John M. , Rudman Seth M.
Published: August 2024

Phenotypic plasticity is a primary mechanism by which organismal phenotypes shift in response to the environment. Host-associated microbiomes often exhibit considerable shifts in response to environmental variation and these shifts could facilitate host phenotypic plasticity, adaptation, or rescue populations from extinction. However, it is unclear how much shifts in microbiome composition contribute to host phenotypic plasticity, limiting our knowledge of the underlying mechanisms of plasticity and, ultimately, the fate of populations inhabiting changing environments. In this study, we examined phenotypic responses and microbiome composition in 20 genetically distinctDaphnia magnaclones exposed to non-toxic and toxic diets containingMicrocystis, a cosmopolitan cyanobacteria and common stressor forDaphnia. Daphniaexhibited significant plasticity in survival, reproduction, and population growth rates in response toMicrocystisexposure. However, the effects ofMicrocystisexposure on theDaphniamicrobiome were limited, with the primary effect being differences in abundance observed across five bacterial families. Moreover, there was no significant correlation between the magnitude of microbiome shifts and host phenotypic plasticity. Our results suggest that microbiome composition played a negligible role in driving host phenotypic plasticity or microbiome-mediated rescue.

One sentence summary

Daphniaexhibits considerable plasticity in individual and population-level responses to a cosmopolitan stressor, yet shifts in microbiome composition are not correlated with the magnitude of this plasticity.
Cell type-specific dysregulation of gene expression due toChd8haploinsufficiency during mouse cortical development
Authors: Yim Kristina M. , Baumgartner Marybeth , Krenzer Martina , Rosales Larios María F. , Hill-Terán Guillermina , Nottoli Timothy , Muhle Rebecca A. , Noonan James P.
Published: August 2024

Disruptive variants in the chromodomain helicaseCHD8, which acts as a transcriptional regulator during neurodevelopment, are strongly associated with risk for autism spectrum disorder (ASD). Loss of CHD8 function is hypothesized to perturb gene regulatory networks in the developing brain, thereby contributing to ASD etiology. However, insight into the cell type-specific transcriptional effects of CHD8 loss of function remains limited. We used single-cell and single-nucleus RNA-sequencing to globally profile gene expression and identify dysregulated genes in the embryonic and juvenile wild type andChd8+/−mouse cortex, respectively.Chd8and other ASD risk-associated genes showed a convergent expression trajectory that was largely conserved between the mouse and human developing cortex, increasing from the progenitor zones to the cortical plate. Genes associated with risk for neurodevelopmental disorders and genes involved in neuron projection development, chromatin remodeling, signaling, and migration were dysregulated inChd8+/−embryonic day (E) 12.5 radial glia. Genes implicated in synaptic organization and activity were dysregulated inChd8+/−postnatal day (P) 25 deep- and upper-layer excitatory cortical neurons, suggesting a delay in synaptic maturation or impaired synaptogenesis due to CHD8 loss of function. Our findings reveal a complex pattern of transcriptional dysregulation inChd8+/−developing cortex, potentially with distinct biological impacts on progenitors and maturing neurons in the excitatory neuronal lineage.
Kir6.1, a component of an ATP-sensitive potassium channel, regulates natural killer cell development
Authors: Samper Natalie , Harðardóttir Lilja , Depierreux Delphine M , Song Soomin C. , Nakazawa Ayano , Gando Ivan , Nakamura Tomoe Y. , Sharkey Andrew M , Nowosad Carla R. , Feske Stefan , Colucci Francesco , Coetzee William A.
Published: August 2024

Abstract

Involved in immunity and reproduction, natural killer (NK) cells offer opportunities to develop new immunotherapies to treat infections and cancer or to alleviate pregnancy complications. Most current strategies use cytokines or antibodies to enhance NK-cell function, but none use ion channel modulators, which are widely used in clinical practice to treat hypertension, diabetes, epilepsy, and other conditions. Little is known about ion channels in NK cells. We show thatKcnj8,which codes for the Kir6.1 subunit of a certain type of ATP-sensitive potassium (KATP) channel, is highly expressed in murine splenic and uterine NK cells compared to other K+channels previously identified in NK cells.Kcnj8expression is highest in the most mature subset of splenic NK cells (CD27-CD11b+) and in NKG2A+or Ly49C/I+educated uterine NK cells. Using patch clamping, we show that a subset of NK cells expresses a current sensitive to the Kir6.1 blocker PNU-37883A.Kcnj8does not participate in NK cell degranulation in response to tumor cellsin vitroor rejection of tumor cellsin vivo. Transcriptomics show that genes previously implicated in NK cell development are amongst those differentially expressed in CD27-CD11b+NK cells deficient ofKcnj8. Indeed, we found that mice with NK-cell specificKcnj8gene ablation have fewer CD11b+CD27-and KLRG-1+NK cells in the bone barrow and spleen. These results show that the KATPsubunit Kir6.1 has a key role in NK-cell development.
Field conditions greatly modify a major growth-defense tradeoff inArabidopsis thaliana
Authors: Lundberg Derek S. , Kersten Sonja , Mehmetoğlu Ezgi , Ayutthaya Pratchaya Pramoj Na , Zhu Wangsheng , Poersch Karin , Yuan Wei , Swartz Sophia , Müller David , Bezrukov Ilja ,   HARVEST TEAM, Weigel Detlef
Published: August 2024

When plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off in the plantArabidopsis thalianais ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild plant populations maintain significant functional variation in theACD6gene, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactiveACD6alleles are resistant to diverse pathogens, yet are of smaller stature, their leaves senesce earlier, and they set fewer seeds. We hypothesized that such hyperactive alleles would not only affect the growth of microbial pathogens, but also more generally leaf microbiome assembly in the wild. To test this, we grew plants with hyperactive, standard, and defectiveACD6alleles in the same field-collected soil, both in climate-controlled conditions and outdoors. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. To our surprise, we discovered that mature field plants, in stark contrast to greenhouse plants, were unaffected by theirACD6genotype, suggesting that additional abiotic and/or microbial signals present outdoors – but not in the greenhouse – greatly modulateACD6activity.
Pyruvate kinase modulates the link between β-cell fructose metabolism and insulin secretion
Authors: Murao Naoya , Morikawa Risa , Seino Yusuke , Shimomura Kenju , Maejima Yuko , Ohno Tamio , Yokoi Norihide , Yamada Yuichiro , Suzuki Atsushi
Published: August 2024

2

Glucose triggers insulin secretion from pancreatic β-cells through intracellular glucose metabolism, ATP production, and closure of ATP-sensitive K+channels (KATPchannels). Fructose also stimulates insulin secretion, but the underlying mechanisms remain unclear. This study investigated the contribution of phospholipase C (PLC) signaling and fructose metabolism to fructose-stimulated insulin secretion (FSIS) using MIN6-K8 clonal β-cells and mouse islets.

Fructose-induced PLC activation, assessed by inositol 1-phosphate accumulation, was reduced in fructose-unresponsive β-cell models, such as diabetic mouse islets and KATPchannel-deficient β-cells, suggesting that β-cell fructose responsiveness is primarily determined by PLC signaling.

Although FSIS was dependent on KATPchannels and Ca2+influx, the ATP/ADP ratio was unexpectedly lowered by fructose, and suppression of intracellular fructose metabolism hardly affected FSIS. Metabolic flux analysis revealed that the accumulation of fructose 1-phosphate (F1P) suppressed pyruvate kinase (PK) activity, contributing to ATP depletion. Strikingly, a small-molecule PK activator, TEPP-46, antagonized F1P-mediated PK suppression, prevented the drop in the ATP/ADP ratio, and restored FSIS in MIN6-K8 cells, normal mouse islets, and fructose-unresponsive diabetic mouse islets.

These findings revealed the metabolic effects of fructose in β-cells and identified PK as a key regulator linking β-cell fructose metabolism and FSIS, thereby providing new insights into the mechanisms of insulin secretion and potential therapeutic targets for fructose-associated metabolic diseases.

1

GRAPHICAL ABSTRACT

Left: Fructose-stimulated insulin secretion (FSIS) is driven by sweet taste receptor (STR)-mediated PLC signaling in pancreatic β-cells. Meanwhile, fructose metabolism does not promote FSIS because fructose causes accumulation of fructose 1-phosphate (F1P), which suppresses pyruvate kinase M2 (PKM2), lowering the ATP/ADP ratio.

Right: A small-molecule PK activator counteracted F1P-mediated PKM2 inhibition, prevented ATP decrease, and substantially enhanced FSIS in normal and diabetic mouse β-cells. Thus, PK has been identified as a key regulator linking β-cell fructose metabolism and FSIS.
Strain-induced antiferromagnetic domain switching via the spin Jahn-Teller effect
Authors: Behr Dylan , Taran Leonid S. , Porter Daniel G. , Bombardi Alessandro , Prabhakaran Dharmalingam , Streltsov Sergey V. , Johnson Roger D.
Published: August 2024

The spin Jahn-Teller effect, where a degeneracy of magnetic ground states is spontaneously lifted by structural distortions, lends itself to exploitation by the implied magnetoelastic coupling. CoTi2O5 hosts a frustrated topology of magnetic interactions that could realize such coupling, since the observed magnetic ground state requires a spontaneous monoclinic distortion of the crystal. Using resonant elastic x-ray scattering to simultaneously probe the magnetic structure and lattice distortion of CoTi2O5, we demonstrate near complete magnetic domain switching by an applied uniaxial stress that is conjugate to the monoclinic strain. Our results, supported by density functional theory calculations, confirm that CoTi2O5 displays spin Jahn-Teller effects that can be understood in terms of modulated Heisenberg exchange interactions, and demonstrate the potential functionality of spin Jahn-Teller materials in spintronic devices sensitive to uniaxial strain.

Published by the American Physical Society
2024
Penrose limits of I-branes, twist-compactified D5-branes, and spin chains
Authors: Barbosa Marcelo , Nastase Horatiu , Nunez Carlos , Stuardo Ricardo
Published: August 2024

In this paper we consider the Penrose limit in the case of two gravity duals. One of them, consists of compactified I-branes [intersecting sets of D5-branes over (1+1) dimensions]. The second consists of D5-branes compactified on a circle. Both compactifications preserve supersymmetry. We find a match of the oscillators and masses of string modes on the resulting pp wave against a spin chain in a (2+1)-dimensional field theory in the first case, and a spin chain in a (1+1)-dimensional field theory in the second.

Published by the American Physical Society
2024
Search for Baryon-Number-Violating Processes in
B−
Decays to the
Ξ¯c0Λ¯c−
Final State
Authors: Gu T. , Savinov V. , Adachi I. , Aihara H. , Asner D. M. , Atmacan H. , Aushev T. , Ayad R. , Banerjee Sw. , Belous K. , Bennett J. , Bessner M. , Bhardwaj V. , Bhuyan B. , Biswas D. , Bobrov A. , Bodrov D. , Borah J. , Bozek A. , Bračko M. , Branchini P. , Browder T. E. , Budano A. , Campajola M. , Červenkov D. , Chang M.-C. , Chang P. , Cheon B. G. , Chilikin K. , Cho K. , Choi S.-K. , Choi Y. , Choudhury S. , Das S. , De Nardo G. , De Pietro G. , Dhamija R. , Di Capua F. , Dingfelder J. , Doležal Z. , Dong T. V. , Dubey S. , Ecker P. , Ferber T. , Ferlewicz D. , Fulsom B. G. , Gaur V. , Giri A. , Goldenzweig P. , Graziani E. , Guan Y. , Gudkova K. , Hadjivasiliou C. , Hayasaka K. , Hayashii H. , Hedges M. T. , Herrmann D. , Hou W.-S. , Hsu C.-L. , Ipsita N. , Ishikawa A. , Itoh R. , Iwasaki M. , Jacobs W. W. , Jia S. , Jin Y. , Joo K. K. , Kawasaki T. , Kiesling C. , Kim C. H. , Kim D. Y. , Kim K.-H. , Kim Y. J. , Kodyš P. , Korobov A. , Korpar S. , Kovalenko E. , Križan P. , Krokovny P. , Kuhr T. , Kumara K. , Kumita T. , Kwon Y.-J. , Lai Y.-T. , Lee S. C. , Levit D. , Li L. K. , Li Y. B. , Li Gioi L. , Liventsev D. , Masuda M. , Matsuda T. , Maurya S. K. , Meier F. , Merola M. , Metzner F. , Miyabayashi K. , Mizuk R. , Mohanty G. B. , Mussa R. , Nakamura I. , Nakao M. , Natkaniec Z. , Natochii A. , Nayak L. , Nayak M. , Niiyama M. , Nishida S. , Ogawa S. , Pakhlova G. , Pardi S. , Park H. , Park J. , Park S.-H. , Passeri A. , Patra S. , Paul S. , Pedlar T. K. , Pestotnik R. , Piilonen L. E. , Podobnik T. , Prencipe E. , Prim M. T. , Röhrken M. , Russo G. , Sandilya S. , Santelj L. , Schnell G. , Schwanda C. , Seino Y. , Senyo K. , Sevior M. E. , Shan W. , Sharma C. , Shiu J.-G. , Solovieva E. , Starič M. , Takizawa M. , Tamponi U. , Tanida K. , Tenchini F. , Tiwary R. , Trabelsi K. , Uchida M. , Unno Y. , Uno S. , Usov Y. , Vahsen S. E. , Varvell K. E. , Vinokurova A. , Wang E. , Wang M.-Z. , Wang X. L. , Watanuki S. , Won E. , Xu X. , Yabsley B. D. , Yan W. , Yang S. B. , Yuan L. , Zhang Z. P. , Zhilich V. , Zhukova V. ,   Belle Collaboration
Published: August 2024

We report the results of the first search for B− decays to the Ξ¯c0Λ¯c− final state using 711  fb−1 of data collected at the ϒ(4S) resonance with the Belle detector at the KEKB asymmetric-energy e+e− collider. The results are interpreted in terms of both direct baryon-number-violating B− decay and Ξc0−Ξ¯c0 oscillations which follow the standard model decay B−→Ξc0Λ¯c−. We observe no evidence for baryon number violation and set the 95% confidence-level upper limits on the ratio of baryon-number-violating and standard model branching fractions B(B−→Ξ¯c0Λ¯c−)/B(B−→Ξc0Λ¯c−) to be <2.7% and on the effective angular frequency of mixing ω in Ξc0−Ξ¯c0 oscillations to be <0.76  ps−1 (equivalent to τmix>1.3  ps).

Published by the American Physical Society
2024
Noisy Circumnutations Facilitate Self-Organized Shade Avoidance in Sunflowers
Authors: Nguyen Chantal , Dromi Imri , Kempinski Ahron , Gall Gabriella E. C. , Peleg Orit , Meroz Yasmine
Published: August 2024

Circumnutations are widespread in plants and typically associated with exploratory movements; however, a quantitative understanding of their role remains elusive. In this study we report, for the first time, the role of noisy circumnutations in facilitating an optimal growth pattern within a crowded group of mutually shading plants. We revisit the problem of self-organization observed for sunflowers, mediated by shade response interactions. Our analysis reveals that circumnutation movements conform to a bounded random walk characterized by a remarkably broad distribution of velocities, covering 3 orders of magnitude. In motile animal systems such wide distributions of movement velocities are frequently identified with enhancement of behavioral processes, suggesting that circumnutations may serve as a source of functional noise. To test our hypothesis, we developed a Langevin-type parsimonious model of interacting growing disks, informed by experiments, successfully capturing the characteristic dynamics of individual and multiple interacting plants. Employing our simulation framework we examine the role of circumnutations in the system, and find that the observed breadth of the velocity distribution represents a sharp transition in the force-noise ratio, conferring advantageous effects by facilitating exploration of potential configurations, leading to an optimized arrangement with minimal shading. These findings represent the first report of functional noise in plant movements and establish a theoretical foundation for investigating how plants navigate their environment by employing computational processes such as task-oriented processes, optimization, and active sensing. Since plants move by growing, space and time are coupled, and dynamics of self-organization lead to emergent 3D patterns. As such, this system provides conceptual insight for other interacting growth-driven systems such as fungal hyphae, neurons and self-growing robots, as well as active matter systems where agents interact with past trajectories of their counterparts, such as stigmergy in social insects. This foundational insight has implications in statistical physics, ecological dynamics, agriculture, and even swarm robotics.

Published by the American Physical Society
2024
An efficient illumination compensation method for reverse time migration
Authors: Zhou Yang
Published: August 2024

By directly solving the full two‐way wave equation, reverse time migration has superiority over other imaging algorithms in handling steeply dipping structures and other complicated geological models. Moreover, by incorporating the asymptotic inversion operator into reverse time migration imaging condition, the imaging algorithm is able to give a quantitative estimation of parameter perturbation in high‐frequency approximation sense. However, because conventional asymptotic inversion only accounts for geometrical spreading, uneven illumination due to irregular acquisition geometry and inhomogeneous subsurface at each image point is neglected. The omit of illumination compensation significantly affects the imaging quality. Wave‐equation‐based illumination compensation methods have been extensively studied in the past. However, the traditional wave‐equation‐based illumination compensation methods usually require high computational cost and huge storage. In this paper, we propose an efficient wave‐equation‐based illumination compensation method. Under high‐frequency approximation, we first define a Jacobian determinant to measure the regularity of subsurface illumination, and then illumination compensation operators are proposed based on the Jacobian. Through boundary integration, we further express the illumination compensation operators through extrapolated wavefields; the explicit computation of asymptotic Green's functions is thus avoided, and an efficient illumination compensation implementation for reverse time migration is achieved. Numerical results with both synthetic and field data validate the effectiveness and efficiency of the presented method.
Unravelling the genomic and environmental diversity of the ubiquitous Solirubrobacter
Authors: Jara‐Servin Angélica , Mejia Gerardo , Romero Miguel F. , Peimbert Mariana , Alcaraz Luis David
Published: August 2024

Solirubrobacter, though widespread in soils and rhizospheres, has been relatively unexplored despite its ubiquity. Previously acknowledged as a common soil bacterium, our research explores its phylogenomics, pangenomics, environmental diversity, and interactions within bacterial communities. By analysing seven genomic sequences, we have identified a pangenome consisting of 19,645 protein families, of which 2644 are shared across all studied genomes, forming the core genome. Interestingly, despite the non‐motility of reported isolates, we discovered genes for flagellin and a partial flagellum assembly pathway. Examining the 16S ribosomal RNA genes of Solirubrobacter revealed substantial diversity, with 3166 operational taxonomic units identified in Mexican soils. Co‐occurrence network analysis further demonstrated its significant integration within bacterial communities. Through phylogenomic scrutiny, we conclusively excluded the NCBI's GCA_009993245.1 genome from being classified as a Solirubrobacter. Our research into the metagenomic diversity of Solirubrobacter across various environments confirmed its presence in rhizospheres and certain soils, underscoring its adaptability. The geographical ubiquity of Solirubrobacter in rhizospheres raises intriguing questions regarding its potential interactions with plant hosts and the biotic and abiotic factors influencing its presence in soil. Given its ecological significance and genetic diversity, Solirubrobacter warrants further investigation as a potentially crucial yet underappreciated keystone species.
The Changing Face of Allotments: Findings from a Comprehensive Birmingham Study
Authors: Bloomfield Jon , Draycott David
Published: August 2024

Interest in allotments is growing across the country, yet relatively little is known about them. Who are the current plot‐holders; what do they grow and the volumes of crops harvested; what are the wider health and social benefits gained from being a plot‐holder; how are allotments responding to an era of local government austerity?

To explore these issues, we undertook a survey of allotment tenants and site secretaries across Birmingham's 113 sites in the most substantial study of plot‐holders undertaken in recent years. This article highlights the key findings and the potential implications for policy makers, local councillors and national politicians. It also indicates the need for similar studies elsewhere in the country to confirm or modify the picture suggested from this initial study.
Do Celebrities Make Policy?
Authors: Street John
Published: August 2024

Do celebrities exercise power over policy making? It can seem that they do, at least in the way the media reports their political activities. We need to think only of the coverage of the footballer Marcus Rashford's seemingly successful campaign to get the Johnson administration to change its policy on free school meals. But are such accounts to be trusted? This is a question whose answer has implications for how we understand and judge contemporary democracy. Celebrities, after all, are unelected and unaccountable. This article asks, therefore, whether it is plausible to claim that stars of popular culture are to be counted amongst the politically powerful.
The effectiveness of the Mediterranean Diet for primary and secondary prevention of cardiovascular disease: An umbrella review
Authors: Hareer Laima W. , Lau Yan Ying , Mole Frances , Reidlinger Dianne P. , O'Neill Hayley M. , Mayr Hannah L. , Greenwood Hannah , Albarqouni Loai
Published: August 2024

Aims

This study aimed to review meta‐analyses of randomised controlled trials that evaluated the effectiveness of the Mediterranean Diet for the primary and secondary prevention of cardiovascular disease.

Methods

Five databases (Medline, Embase, Cochrane, CINAHL and ProQuest) were searched from inception to November 2022. Inclusion criteria were: (i) systematic review of randomised controlled studies with metanalysis; (ii) adults ≥18 years from the general population with (secondary prevention) and without (primary prevention) established cardiovascular disease; (iii) Mediterranean Diet compared with another dietary intervention or usual care. Review selection and quality assessment using AMSTAR‐2 were completed in duplicate. GRADE was extracted from each review, and results were synthesised narratively.

Results

Eighteen meta‐analyses of 238 randomised controlled trials were included, with an 8% overlap of primary studies. Compared to usual care, the Mediterranean Diet was associated with reduced cardiovascular disease mortality (n = 4 reviews, GRADE low certainty; risk ratio range: 0.35 [95% confidence interval: 0.15–0.82] to 0.90 [95% confidence interval: 0.72–1.11]). Non‐fatal myocardial infarctions were reduced (n = 4 reviews, risk ratio range: 0.47 [95% confidence interval: 0.28–0.79] to 0.60 [95% confidence interval: 0.44–0.82]) when compared with another active intervention. The methodological quality of most reviews (n = 16/18; 84%) was low or critically low and strength of evidence was generally weak.

Conclusions

This review showed that the Mediterranean Diet can reduce fatal cardiovascular disease outcome risk by 10%–67% and non‐fatal cardiovascular disease outcome risk by 21%–70%. This preventive effect was more significant in studies that included populations with established cardiovascular disease. Better quality reviews are needed.
Seven new Rhopalomyia gall midges (Diptera: Cecidomyiidae) from Australia broaden the scope of the genus
Authors: Adair Robin J. , Kolesik Peter , Bronstein Omri , Dorchin Netta
Published: August 2024

Seven new species of Rhopalomyia Rübsaamen, 1892 are described from eastern Australia feeding on a diverse range of plant genera and families. All induce galls on flower or growth buds: Rhopalomyia cassiniae Adair & Kolesik, sp. nov. on Cassinia subtropica (Asteraceae), Rhopalomyia digitata Adair & Kolesik, sp. nov. on Podolobium ilicifolium (Fabaceae), Rhopalomyia glebosa Adair & Kolesik, sp. nov. on Parsonsia straminea (Apocynaceae), Rhopalomyia inconspicua Adair & Kolesik, sp. nov. on Kunzea sp. (Myrtaceae), Rhopalomyia ozothamniae Adair & Kolesik, sp. nov. on Ozothamnus ferrugineus (Asteraceae), Rhopalomyia pultenicola Adair & Kolesik, sp. nov. on Pultenaea forsythiana (Fabaceae) and Rhopalomyia stypheliae Adair & Kolesik, sp. nov. on Syphelia triflora (Ericaceae). The scope of Rhopalomyia is broadened to contain species with a partially setulose gonostyle and a four‐segmented palp, a decision supported by a phylogenetic analysis based on the barcoding section of the mitochondrial COI gene. Apocynaceae, Ericaceae, Fabaceae and Myrtaceae are recorded as hosts of Rhopalomyia for the first time.
New insect family for Australia: Chrysostylops australiensis Benda & Straka, gen. et sp. nov. (Strepsiptera: Stylopidae) described from Chrysocolletes aureus Leijs & Hogendoorn, 2021 (Hymenoptera: Colletidae)
Authors: Benda Daniel , Parslow Ben A. , Leijs Remko , Straka Jakub
Published: August 2024

A new genus and species of Strepsiptera, Chrysostylops australiensis Benda & Straka, gen. et sp. nov., is described. It represents the first record of the family Stylopidae from Australia. It was parasitising the bee species Chrysocolletes aureus Leijs & Hogendoorn, 2021 (Neopasiphaeinae). The diagnosis and description of the genus and species are provided based on the characters of the female cephalothorax. Diagnostic characters are discussed. The male and first instar larvae of C. australiensis are unknown. We removed Hylecthrini Ulrich, 1930 reinst. stat. from synonymy based on the specific sculpture on the female cephalothorax. The tribe is specialised for bees of the family Colletidae.
Subjective sleep may mediate the associations between tomorrow anticipations and next‐day affect
Authors: Lee Soomi
Published: August 2024

This study investigated whether stress and positive anticipations about tomorrow are associated with emotional experiences the following day, mediated by the preceding night's sleep. Data were from 141 full‐time nurses, utilizing a 14‐day ecological momentary assessment combined with actigraphy sleep monitoring. Each evening, participants rated the anticipated pleasantness or stressfulness of the following day. Each morning, participants reported on their previous night's sleep. Additionally, participants reported their momentary positive affect (PA) and negative affect (NA) three times per day, with daily averages computed. Multilevel mediation models, adjusted for sociodemographics, work shift, workday, and previous day's affect, revealed that days following more stress anticipations were associated with reduced PA and increased NA. Conversely, days following more pleasantness anticipations were associated with increased PA and decreased NA. These within‐person associations were mediated by self‐reported time‐in‐bed, sufficiency, and quality, such that less stressful and more pleasant anticipations were associated with better sleep, and better sleep was subsequently associated with increased PA and decreased NA. No mediation was found by the actigraphy sleep parameters. Findings suggest that emotional states may covary not only with present stimuli but also with anticipation of future events and subjective sleep recovery in the context of those anticipations.
Narrative Matters: When does the history of ADHD not begin?
Authors: Smith Matthew
Published: August 2024

This commentary discusses the history of ADHD and how it can inform contemporary debates about the disorder. It critiques retrospective histories of ADHD, which propose earlier origins for the disorder than match the historical evidence. It concludes by indicating when ADHD did emerge as a distinctive disorder and why it did so.
Applying current European periodontitis clinical practice guidelines is not feasible even for the richest countries in the world
Authors: Raittio Eero , Grytten Jostein , Lopez Rodrigo , Blich Carl Christian , Vettore Mario Vianna , Baelum Vibeke
Published: August 2024

Clinical practice guidelines aim to enhance the quality, equality and consistency of care but often demand more time than is available, rendering adherence impractical and exceeding feasible resources. The 2017 introduction of a new periodontal classification system by the American Academy of Periodontology (AAP) and the European Federation of Periodontology (EFP) sought to refine clinical and epidemiological practices by serving as the basis for clinical practice guidelines and epidemiological investigations around the world. Following this classification, the EFP recommends supportive periodontal care visits every 3–12 months for all periodontitis cases. Given that in Norway, approximately 72% of the adult population are identified as periodontitis cases under the current AAP/EFP case definition, this poses a significant demand on healthcare resources. We calculated that between 60% and 70% of all estimated available working hours available for adult dental care provided by dentists and dental hygienists in Norway in 2017 would be spent on supportive periodontal care visits alone if the recommendations were to be met. This situation calls for a reevaluation of disease definitions and clinical practice guidelines to ensure they are practical, financially feasible and patient‐outcome relevant.
Unveiling the shield: Troglitazone's impact on epilepsy‐induced nerve injury through ferroptosis inhibition
Authors: Wang Zhi‐Bin , Liu Jun‐Yan , Jiang Shi‐Long , Zhuo Wei , Xie Pan , Dai Wen‐Ting , Mao Xiao‐Yuan , Liu Zhao‐Qian
Published: August 2024

Background

Epilepsy is a widespread central nervous system disorder with an estimated 50 million people affected globally. It is characterized by a bimodal incidence peak among infants and the elderly and is influenced by a variety of risk factors, including a significant genetic component. Despite the use of anti‐epileptic drugs (AEDs), drug‐refractory epilepsy develops in about one‐third of patients, highlighting the need for alternative therapeutic approaches.

Aims

The primary aim of this study was to evaluate the neuroprotective effects of troglitazone (TGZ) in epilepsy and to explore the potential mechanisms underlying its action.

Methods

We employed both in vitro and in vivo models to assess TGZ's effects. The in vitro model involved glutamate‐induced toxicity in HT22 mouse hippocampal neurons, while the in vivo model used kainic acid (KA) to induce epilepsy in mice. A range of methods, including Hoechst/PI staining, CCK‐8 assay, flow cytometry, RT‐PCR analysis, Nissl staining, scanning electron microscopy, and RNA sequencing, were utilized to assess various parameters such as cellular damage, viability, lipid‐ROS levels, mitochondrial membrane potential, mRNA expression, seizure grade, and mitochondrial morphology.

Results

Our results indicate that TGZ, at doses of 5 or 20 mg/kg/day, significantly reduces KA‐induced seizures and neuronal damage in mice by inhibiting the process of ferroptosis. Furthermore, TGZ was found to prevent changes in mitochondrial morphology. In the glutamate‐induced HT22 cell damage model, 2.5 μM TGZ effectively suppressed neuronal ferroptosis, as shown by a reduction in lipid‐ROS accumulation, a decrease in mitochondrial membrane potential, and an increase in PTGS2 expression. The anti‐ferroptotic effect of TGZ was confirmed in an erastin‐induced HT22 cell damage model as well. Additionally, TGZ reversed the upregulation of Plaur expression in HT22 cells treated with glutamate or erastin. The downregulation of Plaur expression was found to alleviate seizures and reduce neuronal damage in the mouse hippocampus.

Conclusion

This study demonstrates that troglitazone has significant therapeutic potential in the treatment of epilepsy by reducing epileptic seizures and the associated brain damage through the inhibition of neuronal ferroptosis. The downregulation of Plaur expression plays a crucial role in TGZ's anti‐ferroptotic effect, offering a promising avenue for the development of new epilepsy treatments.
Comparative Analysis of Fistula Development After Parotid Gland Surgery: Lateral Parotidectomy Versus Extracapsular Dissection Technique
Authors: Sadok Nadia , Bastian Tobias , Voss Noemi , Stähr Kerstin , Arweiler‐Harbeck Diana , Lang Stephan , Meyer Moritz
Published: August 2024

Purpose

The primary objective of this study was to explore the potential disparity in postoperative fistula occurrence rates between patients who undergo (partial) lateral parotidectomy and those who undergo the extracapsular dissection technique for the management of benign parotid gland tumours.

Methods

A consecutive series of 363 patients treated with (partial) lateral parotidectomy and extracapsular dissection technique for benign parotid gland tumours at one tertiary centre between 2018 and 2022 were included. To evaluate the impact of the surgical technique and possible other risk factors (tumour location, tumour size, Body Mass Index, age, smoking, diabetes mellitus, arterial hypertension) for the development of fistulas, multivariate logistic regression analyses using backward lection were applied to estimate odds ratios (ORs) and 95%‐confidence intervals (CIs).

Results

In 363 patients, 21 patients (5.8%) developed a fistula. Patients who underwent (partial) lateral parotidectomy had three times higher chance of developing a fistula compared to patients who were operated using the extracapsular dissection technique (ORadjusted = 2.6, 4.1% vs. 12.5%, p = 0.044). In the multivariate analyses, no other risk factors for the development of fistulas were statistically significant in this cohort. The incidence of facial nerve paralysis was not significantly different between the extracapsular dissection and lateral parotidectomy group (5/73 = 6.8% vs. 11/290 = 3.8%, p = 0.333).

Conclusion

Fistulas occur more often in patients treated by means of a (partial) lateral parotidectomy approach compared to patients treated using the extracapsular dissection technique. Therefore, surgeons should be vigilant about postoperative fistula risks in lateral parotidectomy and consider preventive measures.