bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building a syntrophicPseudomonas putidaconsortium with reciprocal substrate processing of lignocellulosic disaccharides
Authors: Burýšková Barbora , Miró-Bueno Jesús , Popelářová Barbora , Gavendová Barbora , Goñi-Moreno Ángel , Dvořák Pavel 
Published: November 2024

AbstractSynthetic microbial consortia can leverage their expanded enzymatic reach to tackle biotechnological challenges too complex for single strains, such as lignocellulose valorisation. The benefit of metabolic cooperation comes with a catch – installing stable interactions between consortium members. We constructed a syntrophic consortium ofPseudomonas putidastrains for lignocellulosic disaccharide processing. Two strains were engineered to hydrolyse and metabolise lignocellulosic sugars: one grows on xylose and hydrolyses cellobiose to produce glucose, while the other grows on glucose and cleaves xylobiose to produce xylose. This specialisation allows each strain to provide essential growth substrate to its partner, establishing a stable mutualistic interaction, which we term reciprocal substrate processing. Key enzymes fromEscherichia coli(xylose isomerase pathway) andThermobifida fusca(glycoside hydrolases) were introduced intoP. putidato broaden its carbohydrate utilisation capabilities and arranged in a way to install the strain cross-dependency. A mathematical model of the consortium assisted in predicting the effects of substrate composition, strain ratios, and protein expression levels on population dynamics. Our results demonstrated that modulating extrinsic factors such as substrate concentration can optimise growth and balance fitness disparities between the strains, but achieving this by altering intrinsic factors such as glycoside hydrolase expression levels is much more challenging. This study underscores the potential of synthetic microbial consortia to facilitate the bioconversion of lignocellulosic sugars and offers insights into overcoming the challenges of establishing synthetic microbial cooperation.
Global and selective effects of auditory attention on arousal: insights from pupil dilation
Authors: Aurélie Grandjean , Hoyer Roxane S. , Anne Mathieu , Anne Caclin , Annie Moulin , Aurélie Bidet-Caulet 
Published: November 2024

AbstractThis study investigated the interplay between attention and arousal in humans by measuring pupil dilation as a function of task engagement and stimulus relevance. Arousal in response to task-relevant and unexpected irrelevant sounds was measured in healthy young adults during the performance of an auditory detection task, the Competitive Attention Test, and in sensory matched passive conditions. Attention was manipulated using informative and uninformative visual cues. Both relevant and irrelevant sounds elicited a larger increase in pupil dilation in the active compared to the passive condition, revealing a global effect of task engagement on arousal. Additionally, in the active condition, the pupil dilation amplitude during the anticipation and detection of the task-relevant sound was greater following an informative compared to an uninformative cue, while no cue effect was found on the pupil dilation response to distracting sounds. This finding suggests that arousal can be selectively enhanced by attention for task-relevant, but not -irrelevant, events.
Development of a p62 biodegrader for autophagy targeted degradation
Authors: Thiel Zacharias , Marcellin David , Manneville Carole , Goretzki Benedikt , Egger Luca , Maher Rob , Siccardi Noémie , Sansig Gilles , Torres Laura , Probst Alexandra , Müller Catrin Swantje , George Nathalie , Vogel Markus , Sinterhauf Sabine , Lavoisier Alexandra , Choi Ji-Young , Forcellino Laurianne , Hauck Patrick , Be Celine , Villard Frédéric , Gutmann Sascha , Meyer Marc , Freuler Felix , Patoor Maude , Mitchell Gabriel , Nyfeler Beat 
Published: November 2024

AbstractHarnessing autophagy for targeted degradation is a promising extension to proteasome-based targeted protein degradation because of the capacity and versatility of lysosomes to degrade large and complex cargo, thus broadening the scope of therapeutic targets. While small-molecule degraders recruiting the autophagy machinery to targets are starting to emerge, it remains unclear which component of the autophagy lysosomal pathway is most efficacious to induce selective target degradation. Here, we describe two orthogonal induced-proximity strategies to identify and prioritize autophagy effectors that are sufficient to degrade organelles as well as soluble targets. We show that induced proximity of different effectors such as autophagy cargo receptors, ATG8-like proteins or the kinases ULK1 and TBK1 are sufficient to trigger mitophagy. In contrast, self-oligomerizing autophagy cargo receptors outperform ATG8- like effectors and autophagy-related kinases in clearing a soluble cytosolic protein. We further explore the importance of avidity for targeted degradation via autophagy and reveal that the PB1 domain of p62 fused to a LIR peptide is a minimal degron to induce the degradation of mitochondria as well as cytosolic proteins. By developing a novel and highly selective intrabody against the autophagy cargo receptor p62 into a heterobifunctional degrader, we demonstrate that recruitment of endogenous p62 is sufficient to clear mitochondria. This biodegrader, however, is unable to induce degradation of soluble cytosolic proteins due to its inhibitory effect on p62 self-oligomerization. Our study highlights the importance of avidity and suggests that autophagy cargo receptors are attractive entry points for the development of heterobifunctional degraders for complex targets such as organelles or protein aggregates.
Id1Promotes Clonal Hematopoiesis in Mice withTet2Loss of Function
Authors: Singh Shweta , Sarkar Tanmoy , Gudmundsson Kristbjorn O. , Jakubison Brad L. , Morris Holly M. , Burkett Sandra , Baktiar Karim , Pauly Gary T. , Sigano Dina M. , Schneider Joel P. , Keller Jonathan R. 
Published: November 2024

ABSTRACTHematopoietic malignancies emerge through the gradual acquisition of genetic mutations within hematopoietic stem and progenitor cells (HSPCs). Mutations that occur early in disease progression impart a selective growth advantage to HSPCs, which allows them to expand and contribute to a substantial percentage of mature blood cells. This increased expansion is termed clonal hematopoiesis (CH) and is a preleukemic phase associated with an increased risk of developing leukemia. Inhibitor of DNA binding 1 (ID1) protein is a transcriptional regulator of proliferation/differentiation of neuronal, muscle, hematopoietic and other cells, and is frequently overexpressed in cancer.Id1is expressed at low levels in normal HSCs and is induced by growth factors and other mediators of inflammatory stress and promotes HSPC proliferationin vitro and in vivo.Since chronic inflammation is associated with the progression of hematopoietic malignancies, reducingId1expression during CH may be therapeutic. Mutations inTET2are frequently observed in patients with CH, andTet2−/−mice develop CH that progress to hematopoietic malignancies.Id1is upregulated in murineTet2−/−HSPCs and in AML, CMML and MDS patient samples withTET2mutations. Genetic ablation ofId1inTet2−/−HSPCs reduces HSPC expansion/self-renewal/CH, extramedullary hematopoiesis, myeloid skewing, genetic instability and delays the onset of disease. Mechanistically, p16 expression, senescence and apoptosis were increased and proliferation decreased inTet2−/−; Id1−/−HSPCs. Thus, ID1 may represent a potential therapeutic target to reduce CH, hematopoietic hyperplasia, and delay the onset of disease.One Sentence SummaryGenetic ablation ofId1inTet2−/−mice rescues clonal hematopoiesis by increasing CDKI expression, apoptosis, senescence, and differentiation, and reducing cell growth.
Gellan gum-based nutrient medium increases the diversity of cultivated groups of soil microorganisms
Authors: Borisovna Kulikova Daria , Alekseevich Demin Konstantin , Valerievna Prazdnova Evgenia , Sergeevna Mazanko Maria , Pavlovich Kulikov Maksim 
Published: November 2024

AbstractSoil microbial communities contain a huge proportion of microorganisms that cannot be cultured on standard microbiological media and are available for study only by molecular methods such as metagenomics. Among them may be found microorganisms-producers of biologically active substances useful for medicine, biotechnology and agricultural activities of humans. Development of approaches for cultivation of such groups may open the way to the creation of fundamentally new antibiotic, antitumor drugs, phyto- and immunostimulants. We have proposed a solid oligotrophic medium for cultivation of soil microorganisms containing gellan gum, which allows to obtain cultures of more rare microorganisms compared to known media. Representatives of phylum Chloroflexota, Deinococcota, Planctomycetota, Actinomycetota, which were absent on agar media, were found in the metagenome of the community grown on this medium
Excess weight increases the risk for neurological and neuropsychiatric symptoms in post-COVID-19 condition: A systematic review and meta-analysis
Authors: Ronca Débora Barbosa , Mesquita Larissa Otaviano , Oliveira Dryelle , Figueiredo Ana Cláudia Morais Godoy , Wen Jun , Song Manshu , de Carvalho Kênia Mara Baiocchi 
Published: November 2024

AbstractBackground/purpose: Excess weight has been identified as a potential risk factor for the development of post-COVID-19 condition (PCC). This review investigates whether excess weight increases the risk of neurological and neuropsychiatric symptoms associated with PCC.Methods: Studies published up to July 2023 were searched independently across eight electronic databases to evaluate the risk of developing neurological and neuropsychiatric symptoms more than 12 weeks post-infection between exposure and controls groups (excess weightvs.normal weight; obesityvs.non-obesity). Meta-analyses were conducted under a random-effects model.Results:Of the 10,122 abstracts screened, 18 studies (n= 139,091 adults) met the inclusion criteria and reported PCC symptoms according to nutritional status. These studies included 79,050 individuals with excess weightvs57,926 normal-weight individuals and 30,694 individuals with obesityvs107,612 non-obese individuals. The presence of excess weight in PCC significantly increased the risk of depression (RR = 1.21; 95% CI: 1.03–1.42), headache (RR = 1.21; 95% CI: 1.09–1.35), memory issues (RR = 1.43; 95% CI: 1.24–1.65), sleep disturbance (RR = 1.31; 95% CI: 1.16–1.48), and vertigo (RR = 1.21; 95% CI: 1.04– 1.41). Obesity significantly increased the risk of headache (RR = 1.41; 95% CI: 1.34– 1.49), smell disorder (RR = 1.15; 95% CI: 1.09–1.21), taste disorder (RR = 1.21; 95% CI: 1.07–1.36), and vertigo (RR = 1.44; 95% CI: 1.35–1.53).Conclusions:Excess weight or obesity increases the risk of experiencing neuro-symptoms related to PCC. Individuals with these conditions urgently need enhanced personalized care management in current post-pandemic context.
Nano3P-seq: charting the coding and non-coding transcriptome at single molecule resolution
Authors: Begik Oguzhan , Pryszcz Leszek P , Niazi Adnan Muhammad , Valen Eivind , Novoa Eva Maria 
Published: November 2024

AbstractRNA polyadenylation is crucial for RNA maturation, stability and function, with polyA tail lengths significantly influencing mRNA translation, efficiency and decay. Here, we provide a step-by-step protocol to perform Nanopore 3’ end-capture sequencing (Nano3P-seq), a nanopore-based cDNA sequencing method to simultaneously capture RNA abundances, tail composition and tail length estimates at single-molecule resolution. Taking advantage of a template switching-based protocol, Nano3P-seq can sequence any RNA molecule from its 3’ end, regardless of its polyadenylation status, without the need for PCR amplification or RNA adapter ligation. We provide an updated Nano3P-seq protocol that is compatible with R10.4 flowcells, as well as compatible software for polyA tail length and content prediction, which we termPolyTailor. We demonstrate thatPolyTailorprovides accurate estimates of transcript abundances, tail lengths and content information, while capturing both coding and non-coding RNA biotypes, including mRNAs, snRNAs, and rRNAs. This method can be applied to any RNA sample of interest (e.g. poly(A)-selected, ribodepleted, total RNA), and can be completed in one day. The Nano3P-seq protocol can be performed by researchers with moderate experience in molecular biology techniques and nanopore sequencing library preparation, and basic knowledge of linux bash syntax and R programming. This protocol makes Nano3P-seq accessible and easy to implement by future users aiming to study the tail dynamics and heterogeneity of both coding and non-coding transcriptome in a comprehensive and reproducible manner.Key PapersBeğik O, Diensthuber G, Liu H, Delgado-Tejedor A, Kontur C, Niazi AM, Valen E, Giraldez AJ, Beaudoin JD, Mattick JS, Novoa EM. Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing.Nature Methods20, 75–85 (2023).https://doi.org/10.1038/s41592-022-01714-wDelgado-Tejedor A, Medina M, Begik O, Cozzuto L, Lopez J, Blanco B, Ponomarenko J, Novoa EM. Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites.NatComm15, 10054 (2024).https://doi.org/10.1038/s41467-024-54368-x
Investigation of pion-nucleon contributions to nucleon matrix elements
Authors: Alexandrou Constantia , Koutsou Giannis , Li Yan , Petschlies Marcus , Pittler Ferenc 
Published: November 2024

We investigate contributions of excited states to nucleon matrix elements computed in lattice QCD by employing, in addition to the standard nucleon interpolating operator, pion-nucleon (π−N) operators. We solve a generalized eigenvalue problem (GEVP) to obtain an optimal interpolating operator that minimizes overlap with the π−N states. We derive a variant of the standard application of the GEVP method, which allows for constructing 3-point correlation functions using the optimized interpolating operator without requiring the computationally demanding combination that includes π−N operators in both sink and source. We extract nucleon matrix elements using two twisted mass fermion ensembles, one ensemble generated using pion mass of 346 MeV and one ensemble tuned to reproduce the physical value of the pion mass. Especially, we determine the isoscalar and isovector scalar, pseudoscalar, vector, axial, and tensor matrix elements. We include results obtained using a range of kinematic setups, including momentum in the sink. Our results using this variational approach are compared with previous results obtained using the same ensembles and multistate fits without GEVP improvement. We find that for the physical mass point ensemble, the improvement, in terms of suppression of excited states using this method, is most significant for the case of the matrix elements of the isovector axial and pseudoscalar currents.

Published by the American Physical Society
2024
Equivalence of gauge-invariant models for massive integer-spin fields
Authors: Fegebank Arcadia John , Kuzenko Sergei M. 
Published: November 2024

There are several approaches to formulate gauge-invariant models for massive integer-spin fields in d dimensions including the following: (i) in terms of symmetric tensor fields ϕμ1…μk, with k=s,s−1,…,0, restricted to be double traceless for k≥4; and (ii) in terms of a quartet of symmetric tensor fields ψμ1…μk, of rank k=s,s−1,s−2,s−3. We demonstrate that these formulations in Minkowski space Md are equivalent to the gauge-invariant theory for a massive integer-spin field proposed in 1989 by Pashnev. We also make use of the Klishevich-Zinoviev theory in Md to derive a unique generalization of the Singh-Hagen model for a massive integer-spin field in d>4 dimensions.

Published by the American Physical Society
2024
High-Coherence Kerr-Cat Qubit in 2D Architecture
Authors: Hajr Ahmed , Qing Bingcheng , Wang Ke , Koolstra Gerwin , Pedramrazi Zahra , Kang Ziqi , Chen Larry , Nguyen Long B. , Jünger Christian , Goss Noah , Huang Irwin , Bhandari Bibek , Frattini Nicholas E. , Puri Shruti , Dressel Justin , Jordan Andrew N. , Santiago David I. , Siddiqi Irfan 
Published: November 2024

The Kerr-cat qubit is a bosonic qubit in which multiphoton Schrödinger cat states are stabilized by applying a two-photon drive to an oscillator with a Kerr nonlinearity. The suppressed bit-flip rate with increasing cat size makes this qubit a promising candidate to implement quantum error correction codes tailored for noise-biased qubits. However, achieving strong light-matter interactions necessary for stabilizing and controlling this qubit has traditionally required strong microwave drives that heat the qubit and degrade its performance. In contrast, increasing the coupling to the drive port removes the need for strong drives at the expense of large Purcell decay. By integrating an effective band-block filter on chip, we overcome this trade-off and realize a Kerr-cat qubit in a scalable 2D superconducting circuit with high coherence. This filter provides 30 dB of isolation at the qubit frequency with negligible attenuation at the frequencies required for stabilization and readout. We experimentally demonstrate quantum nondemolition readout fidelity of 99.6% for a cat with eight photons. Also, to have high-fidelity universal control over this qubit, we combine fast Rabi oscillations with a new demonstration of the X(π/2) gate through phase modulation of the stabilization drive. Finally, the lifetime in this architecture is examined as a function of the cat size of up to ten photons in the oscillator, achieving a bit-flip time higher than 1 ms and only a linear increase in the phase-flip rate, in good agreement with the theoretical analysis of the circuit. Our qubit shows promise as a building block for fault-tolerant quantum processors with a small footprint.

Published by the American Physical Society
2024
Reducing heat load density with asymmetric and inclined double-crystal monochromators: principles and requirements revisited
Authors: Huang XianRong , Assoufid Lahsen , Macrander Albert T. 
Published: November 2024

Asymmetric double-crystal monochromators (aDCMs) and inclined DCMs (iDCMs) can significantly expand the X-ray beam footprint and consequently reduce the heat load density and gradient. Based on rigorous dynamical theory calculations, the major principles and properties of aDCMs and iDCMs are presented to guide their design and development, particularly for fourth-generation synchrotrons. In addition to the large beam footprint, aDCMs have very large bandwidths (up to ∼10 eV) and angular acceptance, but the narrow angular acceptance of the second crystal requires precise control of the relative orientations and strains. Based on Fourier coupled-wave diffraction theory calculations, it is rigorously proved that the iDCM has almost the same properties as the conventional symmetric DCM, including the efficiency, angular acceptance, bandwidth, tuning energy range and sensitivity to misalignment. The exception is that, for the extremely inclined geometry that can achieve very large footprint expansion, the iDCM has (beneficially) a larger bandwidth and wider angular acceptance. Inclined diffraction has the `rho-kick effect' that can be cancelled by the second reflection of the iDCM (even with misalignment), except that inhomogeneous strains may cause non-uniform rho-kick angles. At present, fabrication/mounting-induced strains pose low risk since they can be controlled to <0.5 µrad over large areas. The only uncertain challenge is the thermally induced strains, yet it is estimated that these strains are naturally lowered by the large footprint and may be further mitigated by optimized cryogenic cooling to the 1–2 µrad level. Overall, aDCMs and iDCMs have more stringent requirements than normal DCMs, but they are feasible schemes in practice.
Haar wavelet analysis of axisymmetric vibration of 2-D functionally graded porous thin annular plate resting on the Winkler foundation
Authors: Kumar Yajuvindra , Pandit Sapna 
Published: November 2024

Purpose In this paper, free axisymmetric vibration analysis of a two-directional functionally graded porous thin annular plate resting on the Winkler foundation is presented utilizing the classical plate theory (CPT). The mechanical properties are considered to be varying in the radial-thickness plane.Design/methodology/approach Based on the CPT, the governing differential equation of motion is derived. The highest-order derivative of displacement is approximated by Haar wavelets and successive lower-order derivatives are obtained by integration. The integration coefficients are calculated using boundary conditions. The fundamental frequency for clamped-clamped, clamped-simply supported, simply supported-clamped and simply supported-simply supported boundary conditions is obtained.Findings The effects of the porosity coefficient, the coefficient of radial variation, the exponent of power law, the foundation parameter, the aspect ratio and boundary conditions are investigated on fundamental frequency. A convergence study is conducted to validate the present analysis. The accuracy and reliability of the Haar wavelets are shown by comparing frequencies with those available in the literature. Three-dimensional mode shapes in the fundamental mode for all four boundary conditions are presented.Originality/value Based on the Haar wavelet method, a free axisymmetric vibration model of a porous thin annular plate is solved in which 2-D variation of mechanical properties is considered.
Job crafting agility: a conceptual proposition for rethinking behaviour in organizations
Authors: Dhanpat Nelesh 
Published: November 2024

PurposeThis research proposes a new construct towards the job crafting theory, termed job crafting agility. The study provides the potential contributions of job crafting agility in the context of rethinking behaviours in organizations during times of disruption and change.Design/methodology/approachA conceptual analysis is followed to present the construct of job crafting agility, based on a review of job crafting and agility literature.FindingsThe research proposes job-crafting agility as a dynamic and proactive process of balancing job demands and resources in response to changing or fluctuating circumstances. The study provides four propositions on job-crafting agility. This research contributes to the existing literature by proposing a new construct, job-crafting agility that can help organizations and employees adapt to changing circumstances during disruption and change. It highlights the unique components of job-crafting agility and its theoretical foundations and distinguishes the new construct from other forms of job crafting.Research limitations/implicationsThe construct of job crafting agility is new and requires further empirical validation. It presents several propositions as recommendations for future studies.Practical implicationsThe paper provides practical implications for organizations and managers on promoting job crafting agility among employees. It emphasizes the importance of creating a work environment that encourages flexibility, experimentation and learning to enable employees to adjust to changing circumstances effectively.Originality/valueThis research makes a novel contribution by introducing and defining job crafting agility, and advances job crafting theory by exploring how job crafting agility can foster resilience and positive organizational outcomes amid continual change and disruption.