bluuebunny/crossref_metadata_2025 huggingface dataset:
Familial Mediterranean fever gene variations could trigger VPS16-associated early-onset dystonia and diabetes mellitus: clinical identification of a family with MEFV and VPS16 genetic variation association
Authors: Inalkac Gemici Yagmur , Ekici Cemal , Batum Melike , Akbostanci Cenk , Koc Ahmet , Mavioglu Hatice
Published: July 2024

Objectives

We describe the clinical pictures of an index case with dystonia and his family resulting from VPS16 and MEFV genetic variations based on previously published data and discuss the mechanisms that may have brought out the clinical findings.

Methods

A 17-year-old male had generalized dystonia that started at age 6 years, non-febrile abdominal pain attacks and was diagnosed with type 1 diabetes at age 14 years. Meanwhile, his 13-year-old sister had the same clinical presentation. His father was diabetic and his mother was asymptomatic. There was no consanguinity between the parents. Genetic variations were detected with whole exome sequencing.

Results

VPS16 c.1513C>T/p.Arg505* (likely pathogenic), MEFV c.2080A>G p.Met694val (pathogenic) and MEFV c.1772T>C p.Ile591Thr (unknown significance) heterozygous variants were detected in his siblings. The father had VPS16 c.1513C>T/p.Arg505* and MEFV c.2080A>G p Met694val variations and the mother had MEFV c.1772T>C p.Ile591Thr variations.

Conclusions

The occurrence of these diseases in siblings but their absence in the parents suggests the idea that the coexistence of two separate variations in the VPS16 and MEFV genes determines the phenotype. In addition, the increase in MEFV variation load in this family and the fact that DM occurs at an earlier age suggest that inflammation may cause an early diabetic clinical presentation.
Friendship and the Common Good in Julius Caesar
Authors: Cavanagh Dermot
Published: July 2024

This essay proposes a new reading of Julius Caesar’s account of friendship that also illuminates Shakespeare’s broader communitarian political attitudes. It argues that the ‘quarrel’ (or reconciliation) scene between Brutus and Cassius presents a crucial turn in the play’s closely meditated account of amity. This sheds new light on Shakespeare’s response to two classical sources: Cicero’s De Amicitia and Euripides’ Iphigenia at Aulius, whose opening provides the model for this sequence. The significance of how Brutus and Cassius settle their differences, as well as their refusal to believe the enemy is always occulted within the friend, has been under-estimated. The high-minded ideals of Ciceronian amicitia seem wildly remote from the play’s exposure of how friendship works in political life. We witness it being made serviceable to ambitions and held in bad faith: Cicero acknowledges these possibilities too. Yet the neglected later sequences of Julius Caesar tell a different story about friendship that emphasizes its role in promoting commonalty and reconciliation. The tragedy lies in the loss of this potential.
Metaphors and Telescopes: The Reception of Emanuele Tesauro’s Il Cannocchiale Aristotelico in Marvell’s Poetry
Authors: Holberton Edward
Published: July 2024

This article argues that Emanuele Tesauro’s treatise on wit, Il Cannocchiale Aristotelico (1654) influenced Andrew Marvell’s Restoration satire ‘The Last Instructions to a Painter’. It highlights a number of close correspondences between the engraved allegorical frontispiece of Tesauro’s treatise and Marvell’s final envoi ‘To the King’, which ironize the poem’s claim that it only satirizes the king’s courtiers. There are also affinities between Tesauro’s and Marvell’s development of imagery drawn from a Martial epigram at another pivotal moment in the ‘The Last Instructions to a Painter’, which reveal Marvell’s keen sense of the shifting associations between poetic style, religion and Restoration politics. Marvell found in Il Cannocchiale Aristotelico, the essay argues, a discussion of the acuity of metaphor which meshed excitingly with his own previously developed practice, especially his interest in reflexive and optical imagery. The article canvasses some of the ways in which Il Cannocchiale Aristotelico may have influenced Marvell’s later poetry, particularly in the use of ‘laconic’ wit, as he adapted to the poetic and political coteries of the Restoration. But it argues that ‘The Last Instructions to a Painter’’s notoriously baroque tribute to the Scottish Catholic soldier Archibald Douglas identifies Tesauro’s theory of wit with counter-reformation aesthetics, and uses parody to negotiate an uncomfortable recognition of how Marvell’s lyric poetry might be interpreted by Restoration readers.
Human Capital Portability and Careers in Finance
Authors: Gao Janet , Wang Wenyu , Wu Yufeng
Published: July 2024

How does firm-specific human capital shape careers in the finance industry? We build a dynamic model where workers accumulate portable and nonportable (firm-specific) human capital and learn about their match quality with employers. Estimating the model using granular data on M&A advisory bankers, we show that a large fraction of bankers’ human capital is nonportable, ranging from 12% to 46% across different firm types. Bankers make a dynamic trade-off between portability and returns on human capital, leading to time-varying job preferences over their life cycle. Our results have broad implications for careers in finance and the provision of financial services.
A Policy Analysis of the Temporary Protection Statute for Venezuelans in Colombia: Normalising Exceptionality using Humanitarian Discourses
Authors: Poveda-Clavijo Juliana , Mena Rodrigo
Published: July 2024

The Venezuelan crisis has led to over three million people crossing into Colombia. One strategy to address this situation is the Temporary Protection Statute (TPS), aimed at granting migrants legal status and responsibilities without providing them refugee status. Critics argue that portraying this solution as humanitarian might undermine its role as a protective measure. Additionally, there is a lack of understanding of the TPS as a political tool and the problems it aims to tackle. Using a Post-structural Policy Analysis (PPA), this article unpacks the TPS as a political device and the driving forces behind its development. Through text analysis and qualitative semi-structured interviews, the PPA reveals how the TPS in Colombia can be seen as a multifaceted legal and political tool bridging short-term humanitarian needs (primarily protection, healthcare, and labour market access) and long-term development practices (such as integration through ensuring economic, social, and environmental rights), within a complex political landscape hindering long-term solutions. Its legal text epitomises political drivers and discourses shaping migration governance and international protection. This study also shows PPA’s effectiveness in revealing these political factors and the policy-problem-making justifying the TPS as a solution, and offers case-based insights to enhance comparative migration studies.
Crucial points about international private foundations that founders sometimes wish they had paid more attention to
Authors: Niegel Johanna
Published: July 2024

In this 20th anniversary issue of ‘Private Foundations: A World Review’, the Editor under the heading ‘Crucial points about international private foundations that founders sometimes wish they had paid more attention to’ highlights and provides an assessment of the most important issues that founders of international foundations should take into consideration before taking action: Purposes—Legal Personality—Retention of Founders Rights and International Recognition. She concludes that a bespoke founder’s role is of essence, as soon as a foundation has international connections, as an influential role of the founder may well jeopardize the integrity of a foundation.
Utility of the WHO dengue guidelines in pediatric immunological studies
Authors: Sánchez Jorge L , Salgado Doris M , Vega Martha Rocío , Castro-Trujillo Sebastián , Narváez Carlos F
Published: July 2024

Dengue is a significant health problem due to the high burden of critical infections during outbreaks. In 1997, the World Health Organization (WHO) classified dengue as dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS). It was revised in 2009 (updated in 2015), and the new guidelines recommended classifying patients as dengue without warning signs (DNS), dengue with warning signs (DWS), and severe dengue (SD). Although the utility of the revised 2009 classification for clinical studies is accepted, for immunological studies it needs to be clarified. We determined the usefulness of the 2009 classification for pediatric studies that analyze the circulating interleukin (IL)-6 and IL-8, two inflammatory cytokines. Plasma levels of IL-6 and IL-8 were evaluated in the acute and convalescent phases by flow cytometry in children with dengue classified using the 1997 and 2009 WHO guidelines. The plasma levels of IL-6 and IL-8 were elevated during the acute and decreased during convalescence, and both cytokines served as a good marker of acute dengue illness compared to convalescence. There were no differences in the plasma level of the evaluated cytokines among children with different clinical severity with any classification, except for the IL-8, which was higher in DWS than DNS. Based on the levels of IL-8, the 2009 classification identified DWS plus SD (hospital-treated children) compared to the DNS group [area under the curve (AUC): 0.7, p = 0.028]. These results support the utility of the revised 2009 (updated in 2015) classification in studies of immune markers in pediatric dengue.
Thalattosuchian crocodylomorphs from the Sinemurian (Early Jurassic) of the UK
Authors: Young Mark T , Dufeau David , Bowman Charlotte , Cowgill Thomas , Schwab Julia A , Witmer Lawrence M , Herrera Yanina , Katsamenis Orestis L , Steel Lorna , Rigby Martin , Brusatte Stephen L
Published: July 2024

Thalattosuchian crocodylomorphs were a ubiquitous component of shallow marine ecosystems during the Jurassic and Early Cretaceous. Alas, their origins remain a mystery. Here we describe three specimens from the Sinemurian (and possibly Early Pliensbachian) of the UK: a partial cranial rostrum, a series of cervical vertebrae, and two dorsal vertebrae adhered with matrix. These specimens are amongst the oldest known thalattosuchian fossils, with the partial cranial rostrum being the oldest known non-neothalattosuchian thalattosuchian. This partial cranial rostrum has a unique combination of rostral characters never seen before in any crocodylomorph, and helps to elucidate early thalattosuchian internal rostrum evolution, suggesting that the reduction in thalattosuchian paranasal sinuses was not related to either the reorganization of rostral neurovasculature seen in later diverging taxa or the increased cancellous bone microstructure. Based on our CT sample, a shift in cranial bone microstructure occurred in the Eoneustes + Metriorhynchidae subclade, one that coincided with the enlargement of the salt glands and decoupling of the external antorbital fenestra from the paranasal sinuses. Without extensive histological sampling we cannot determine whether the shift to an obligate aquatic lifestyle occurred prior to the evolution of Metriorhynchidae.
Solvability analysis for the Boussinesq model of heat transfer under the nonlinear Robin boundary condition for the temperature
Authors: Alekseev Gennady V. , Soboleva Olga V.
Published: July 2024

We consider the new boundary value problem for the generalized Boussinesq model of heat transfer under the inhomogeneous Dirichlet boundary condition for the velocity and under mixed boundary conditions for the temperature. It is assumed that the viscosity, thermal conductivity and buoyancy force in the model equations, as well as the heat exchange boundary coefficient, depend on the temperature. The mathematical apparatus for studying the inhomogeneous boundary value problem under study based on the variational method is being developed. Using this apparatus, we prove the main theorem on the global existence of a weak solution of the mentioned boundary value problem and establish sufficient conditions for the problem data ensuring the local uniqueness of the weak solution that has the additional property of smoothness with respect to temperature.

This article is part of the theme issue ‘Non-smooth variational problems with applications in mechanics’.
On hyperelastic solid with thin rigid inclusion and crack subjected to global injectivity condition
Authors: Furtsev A. I. , Rudoy E. M. , Sazhenkov S. A.
Published: July 2024

The paper investigates a problem concerning the equilibrium of a solid body containing a thin rigid inclusion and a crack. It is assumed that the body is hyperelastic, therefore, it is described within the framework of finite strain theory. One of the peculiarities of this problem is a global injectivity constraint, which prevents the body, the crack faces and the inclusion from both mutual and self penetration. First, the paper deals with the differential formulation of the problem. Next, we consider energy minimization, showing that the latter provides the weak formulation of the former. Finally, the existence of the weak solution is demonstrated through the use of the variational technique.

This article is part of the theme issue ‘Non-smooth variational problems with applications in mechanics’.
Arthrobacter horti sp. nov., isolated from mountain soil
Authors: Park Mingyeong , Kim Jaisoo
Published: July 2024

Gram-stain-positive, aerobic, rod-shaped strains, YJM1T and YJM12S, were isolated from Maebong Mountain, Dogok-dong, Gangnam-gu, Seoul, Republic of Korea. Strains YJM1T and YJM12S exhibited growth at 5–35 °C (optimum, 20–30 °C) and pH 6–9 (optimum, pH 7) and in 0–4 % (w/v) NaCl. Strains YJM1T and YJM12S showed highest 16S rRNA gene sequence similarity to the following members of the genus Arthrobacter: A. nanjingensis A33T (98.3 %/98.2 % similarity), A. woluwensis NBRC 107840T (98.2 %/98.1 %), A. humicola KV-653T (97.3 %), A. oryzae KV-651T (97.3 %), and A. globiformis NBRC 12137T (97.2 %). The strains grew well on Reasoner's 2A, nutrient, Mueller–Hinton, yeast–dextrose, and glucose–peptone–meat extract agars. The major polar lipids of strain YJM1T were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. The primary respiratory quinone of strain YJM1T was MK-9(H2), and the major fatty acids of strains YJM1T and YJM12S were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, and iso-C16 : 0. The DNA G+C content, based on the whole genome sequence of strain YJM1T, was 68.3 mol%. Average nucleotide identity values and digital DNA–DNA hybridization values between strain YJM1T and the reference strains ranged from 75.0 to 92.7 % and from 21.0 to 65.3 %, respectively. Strain YJM1T exhibited antimicrobial activity against Bacillus subtilis and Escherichia coli. Considering the chemotaxonomic, phenotypic, genotypic, and phylogenetic results, we propose the strain YJM1T represents a novel species in the genus Arthrobacter and suggest the name Arthrobacter horti sp. nov. (type strain YJM1T=KACC 23300T=JCM 36483T).
A systematic evaluation of dynamic functional connectivity methods using simulation data
Authors: Yuan Binke , Yang Junjie , Guo Xiaolin , Gao Xiaowei , Hu Zhe , Li Junjing , Liu Jiaxuan , Wang Yaling , Qu Zhiheng , Li Wanchun , Li Zhongqi , Li Wanjing , Huang Yien , Chen Jiali , Wen Hao , Li Junle , Liu Dong-Qiang , Xie Hui
Published: July 2024

Numerous dynamic functional connectivity (dFC) methods have been proposed to study time-resolved network reorganization in rest and task fMRI. However, a comprehensive comparison of their performance is lacking. In this study, we compared the efficacy of seven dFC methods (and their enhanced versions) to track transient network reconfiguration using simulation data. The seven methods include flexible least squares (FLS), dynamic conditional correlation (DCC), general linear Kalman filter (GLKF), multiplication of temporal derivatives (MTD), sliding-window functional connectivity with L1-regularization (SWFC), hidden Markov models (HMM), and hidden semi-Markov models (HSMM). Multiple datasets of non-fMRI-BOLD and fMRI-BOLD signals with predefined covariance structures, signal-to-noise ratio levels, and sojourn time distributions were simulated. We adopted inter-subject analysis to eliminate the effects of signals of non-interest, resulting in enhanced methods: ISSWFC, ISMTD, ISDCC, ISFLS, ISKF, ISHMM, and ISHSMM. Efficacy was defined as the spatiotemporal association between simulated and estimated data. We found that all enhanced dFC methods outperformed their original versions. Efficacies depend on several factors, such as considering the neurovascular effect in simulated data, the covariance structure between two time series, state sojourn distribution, and signal-to-noise ratio levels. These results highlight the importance of selecting appropriate dFC methods in fMRI study.
Exploring For Gloss: Active Exploration in Visual Material Perception
Authors: Lin Lisa P.Y. , Drewing Knut , Doerschner Katja
Published: July 2024

Image motion contributes to the perception of visual material properties, and motion signals are generated during active exploration. However, little is known about how specific perceptual tasks influence the actions that generate these cues. In an experiment using virtual reality and real-time hand tracking, we investigated how the demands of perceptual tasks (e.g., judging gloss or lightness) shape exploratory behaviours. Participants either observed or actively explored objects varying in gloss and lightness while performing a matching task. We analysed how their exploration patterns varied based on the tasks. Using the same stimuli in both tasks, we found that participants explored objects more extensively when judging gloss than when judging lightness. These findings suggest a strategic prioritisation of relevant cues for gloss judgments, with participants using larger movements and object rotation to enhance viewing perspectives and highlight detection. Our findings show that exploration behaviours are task-dependent, with actions adapted to the demands of the perceptual task at hand.
Temperature-dependent polar lignification of a seed coat suberin layer promoting dormancy in Arabidopsis thaliana
Authors: Hyvärinen Lena , Fuchs Christelle , Utz-Pugin Anne , Gully Kay , Megies Christian , Holbein Julia , Iwasaki Mayumi , Demonsais Lara , Capitão Maria Beatriz , Barberon Marie , Franke Rochus , Nawrath Christiane , Loubéry Sylvain , Lopez-Molina Luis
Published: July 2024

The seed is a landmark plant adaptation where the embryo is sheltered by a protective seed coat to facilitate dispersion. In Arabidopsis, the seed coat, derived from ovular integuments, plays a critical role in maintaining dormancy, ensuring germination occurs during a favorable season. Dormancy is enhanced by cold temperatures during seed development by affecting seed coat permeability through changes in apoplastic barriers. However, the localization and composition of these apoplastic barriers are poorly understood. This study identifies and investigates a polar barrier in the seed coat’s outer integument (oi1) cells. We present histological, biochemical, and genetic evidence showing that cold promotes polar seed coat lignification of the outer integument 1 (oi1) cells and suberization throughout the entire oi1 cell boundary. The polar oi1 barrier is regulated by the transcription factors MYB107 and MYB9. MYB107, in particular, is crucial for the lignified polar oi1 barrier formation under cold temperatures. The absence of the oi1 barrier in mutant seeds correlates with increased permeability and reduced dormancy. Our findings elucidate how temperature-induced modifications in seed coat composition regulate dormancy, highlighting the roles of suberin and lignin in this process.

Significance statement

Our study uncovers how cold temperatures during seed development in the mother plant influence seed dormancy through apoplastic modifications in theArabidopsis thalianaseed coat. We identified a polar lignin barrier in the outer integument 1 (oi1) cells, which are also suberized. Lignification and suberization are regulated by transcription factors MYB107 and MYB9. Cold promotes lignification and suberization of oi1 cells through MYB107, thus creating a “memory” that reduces seed permeability and strengthens dormancy. Mutants defective in the oi1 barrier exhibit lower dormancy, highlighting the adaptive importance of this barrier. These findings advance our understanding of temperature-induced seed coat adaptations and their agricultural implications, particularly in the context of climate change, offering valuable insights for improving crop resilience and yield.
Predicting recoverability of collapsed food webs through perturbation and dimension reduction
Authors: Patnaik Swastik , Baruah Gaurav
Published: July 2024

Biodiversity collapse, driven by escalating environmental changes, poses significant threats to ecosystem stability and the provision of essential ecosystem services. Understanding the recoverability of collapsed food webs thus is crucial for devising effective conservation strategies. This study delves into the theoretical exploration of the recoverability of food webs from a collapsed state. Through simple tools like dimension reduction, propagation of species-specific perturbation, and dynamical simulations, we explore whether simple tri-trophic food webs can be recovered from a collapsed state. Our study examines in detail the topological features of predator-prey food webs that could either facilitate or impede their recovery. We demonstrate that the recoverability of complex food webs can be predicted by using a simple dimension-reduced model, with certain structural factors that could constrain the full recovery of collapsed food webs. Furthermore, dynamic simulations also highlighted the significance of topological features such as connectance and the number of predator links in determining recoverability. Our dimension-reduced modeling framework offers insights into the feasibility of restoring entire complex predator-prey networks through species-specific interventions. This study contributes to a deeper understanding of ecosystem resilience and aids in the development of targeted conservation strategies.
Colony demographics shape nest construction in ants
Authors: Rajendran Harikrishnan , Weinberger Roi , Fonio Ehud , Feinerman Ofer
Published: July 2024

The ant nest serves as the skeleton of the ant superorganism. Similar to a skeleton, the nest expands as the colony grows and requires repair after catastrophic events. We experimentally compared nest excavation by colonies seeded from a single mated queen and then allowed to grow for six months, to excavation triggered by a catastrophic event in colonies with fixed demographics. The areas excavated by equal group sizes differed significantly between these conditions: heterogeneous populations in naturally growing colonies as well as cohorts of young ants dig larger areas than old ant cohorts. Moreover, we find that younger ants tend to dig slanted tunnels while older ants dig straight down. This is a novel form of age polyethism, where an ant’s age dictates not only her likelihood to engage in a task but also the way she performs the task. We further present a quantitative model that predicts that under normal growth, digging is predominantly performed by the younger ants while after a catastrophe all ants dig to restore lost nest volume. The fact that the nests of naturally growing colonies exhibit slanted tunnels strengthens this prediction. Finally, our results indicate how a colony’s demographic and physical history are sketched into the current structure of its nest.
scGFT: single-cell RNA-seq data augmentation using generative Fourier transformer
Authors: Nouri Nima
Published: July 2024

Integrating single-cell RNA sequencing (scRNA-seq) with artificial intelligence (AI) ushers in a new frontier for advanced therapeutic discoveries. However, for this synergy to achieve its full potential, extensive datasets are required to effectively train the AI component. This demand is particularly challenging when delving into rare diseases and uncommon cell types. Generative models designed to address data scarcity often face similar limitations due to their reliance on pre-training, inadvertently perpetuating a cycle of data inadequacy. To overcome this obstacle, we introduce scGFT (single-cell Generative Fourier Transformer), a train-free, cell-centric generative model adept at synthesizing single cells that exhibit natural gene expression profiles present within authentic datasets. Using both simulated and experimental data, we demonstrate the mathematical rigor of scGFT and validate its ability to synthesize cells that preserve the intrinsic characteristics delineated in scRNA-seq data. By streamlining single-cell data augmentation, scGFT offers a scalable solution to overcome data scarcity and holds the potential to advance AI-driven precision medicine.
Identification of a Monovalent Pseudo-Natural Product Degrader Class Supercharging Degradation of IDO1 by its native E3 KLHDC3
Authors: Hennes Elisabeth , Lucas Belén , Scholes Natalie S. , Cheng Xiu-Fen , Scott Daniel C. , Bischoff Matthias , Reich Katharina , Gasper Raphael , Lucas María , Xu Teng Teng , Pulvermacher Lisa-Marie , Dötsch Lara , Imrichova Hana , Brause Alexandra , Naredla Kesava Reddy , Sievers Sonja , Kumar Kamal , Janning Petra , Gersch Malte , Murray Peter J. , Schulman Brenda A. , Winter Georg E. , Ziegler Slava , Waldmann Herbert
Published: July 2024

Targeted protein degradation (TPD) modulates protein function beyond inhibition of enzyme activity or protein-protein interactions. Most degrader drugs function by directly mediating proximity between a neosubstrate and hijacked E3 ligase. Here, we identified pseudo-natural products derived from (-)-myrtanol, termed iDegs that inhibit and induce degradation of the immunomodulatory enzyme indoleamine-2,3-dioxygenase 1 (IDO1) by a distinct mechanism. iDegs boost IDO1 ubiquitination and degradation by the cullin-RING E3 ligase CRL2KLHDC3, which we identified to natively mediate ubiquitin-mediated degradation of IDO1. Therefore, iDegs increase IDO1 turnover using the native proteolytic pathway. In contrast to clinically explored IDO1 inhibitors, iDegs reduce formation of kynurenine by both inhibition and induced degradation of the enzyme and, thus, would also modulate non-enzymatic functions of IDO1. This unique mechanism of action may open up new therapeutic opportunities for the treatment of cancer beyond classical inhibition of IDO1.
A dynamic redox switch turns TRC40 into a chaperone protecting human cells against ATP-depleting, oxidative stress
Authors: Dempsey Bianca , Dubrall Risai , Chan Olivia , Lapacz Kim Jasmin , Riemer Jan , Jakob Ursula , Ulrich Kathrin
Published: July 2024

Oxidative stress represents a major challenge for cellular proteostasis. The accumulation of reactive oxygen species, such as hydrogen peroxide, impairs the fidelity of protein biosynthesis and causes non-specific oxidative protein modifications and aggregation. This situation is further aggravated by the oxidative stress-mediated drop in cellular ATP levels, which reduces the activity of ATP-dependent chaperones and proteases. We now demonstrate that to cope with oxidative unfolding stress, human cells rely on the moonlighting function of TRC40, which turns from an ATP-dependent targeting factor into an ATP-independent chaperone upon oxidation. Controlled by a highly conserved redox switch, oxidized TRC40 forms chaperone-active tetramers and high-molecular complexes which prevent the aggregation of unfolding proteins. Acute oxidative stress leads to the reversible formation of distinct TRC40 foci, associated with the canonical chaperones Hsp70 and Hsp110, suggesting a role of these stress-induced structures in recovering and sorting aberrant proteins. Consistently, we discovered that TRC40 is essential upon ATP-depleting, oxidative stress conditions to counteract the accumulation of mis- and unfolded proteins, which are rapidly cleared in an TRC40-dependent manner. Our data reveal that TRC40 is an integral part of protein quality control and support its role as a triaging factor in cellular proteostasis.
Transcriptomic analysis of meiotic genes during the mitosis-to-meiosis transition inDrosophilafemales
Authors: Vallés Ana Maria , Rubin Thomas , Macaisne Nicolas , Toe Laurine Dal , Molla-Herman Anahi , Antoniewski Christophe , Huynh Jean-René
Published: July 2024

Germline cells produce gametes, which are specialized cells essential for sexual reproduction. Germline cells first amplify through several rounds of mitosis before switching to the meiotic program, which requires specific sets of proteins for DNA recombination, chromosome pairing and segregation. Surprisingly, we previously found that some proteins of the synaptonemal complex, a prophase I meiotic structure, are already expressed and required in the mitotic region ofDrosophilafemales. Here, to assess if additional meiotic genes were expressed earlier than expected, we isolated mitotic and meiotic cell populations to compare their RNA content. Our transcriptomic analysis reveals that all known meiosis I genes are already expressed in the mitotic region, however, only some of them are translated. As a case study, we focused onmei-W68, theDrosophilahomologue ofSpo11, to assess its expression at both the mRNA and protein levels, and used different mutant alleles to assay for a pre-meiotic function. We could not detect any functional role for Mei-W68 during homologous chromosome pairing in dividing germ cells. Our study paves the way for further functional analysis of meiotic genes expressed in the mitotic region.

Article Summary

Germline cells, crucial for sexual reproduction, were thought to switch to meiosis only after several rounds of mitosis. Surprisingly, a few meiotic proteins were found active in the mitotic phase of female flies. Here, we discovered that all known meiosis genes were expressed during mitosis, but only some produced proteins. This study suggests that genes related to reproduction are active earlier than expected, prompting further exploration into their functions during early cell division.
Simplest Model of Nervous System. IV. General Solution
Authors: Sinitskiy Anton V.
Published: July 2024

In this paper, we extend our previous work on a simplified model of the nervous system by solving the general optimization problem for the evolutionary cost of the nervous system. This optimization takes into account constraints on the scales of membrane potential kinetics and sensory response function to ensure finite, biologically plausible solutions. Our analysis reduces the variational problem to a system of two integro-differential equations, which we solve asymptotically using series expansions. This study confirms the emergence of sharp finite neuronal spikes and robust sensory and motor response functions as evolutionarily optimal solutions. We note that, in principle, alternative evolutionary solutions with different biophysical interpretations might exist for this optimization problem. This work provides a rigorous mathematical framework bridging evolutionary optimization with the fundamental properties of nervous systems.
A rapid method to determine the genetic lineage ofEscherichia coliusing open reading frame composition in the shallow sequencing
Authors: Yagi Nobuyoshi , Uechi Ayumi , Hirai Itaru
Published: July 2024

Determining the genetic background of bacterial isolates and evaluating the genetic relatedness among these isolates in a short time period are important to identify the spreading route(s) in cases of healthcare-associated infections and outbreaks caused by antimicrobial-resistant bacteria. Previously, we proposed a shallow sequencing (Shall-seq) procedure to determine the genetic backgrounds of clinical isolates using the minimum amount of sequence data. However, it took a longer time, such as longer than 10 h, to determine the genetic background of one clinical isolate. In this study, we developed a search procedure using open reading frame (ORF) composition to select the reference genome sequence with the highest matching ratio (>90%), the indicator genome sequence (IGS), for the examined bacterial isolate. Consequently, IGSs were selected for 28 (96.6%) of the examined 29 isolates and selection was performed within 30 min for each bacterial isolate. More importantly, the comparison of IGSs indicated that the IGSs, determined by ORF composition, of the examined bacterial isolates were closely related to the genome sequences determined using the Shall-seq procedure. Taken together, these results suggest that our newly developed search procedure can quickly determine the genetic background of bacterial isolates.
Proxiaml Temporary Occlusion using Balloon Guide Catheter for Mechanical Thrombectomy (PROTECT-MT): Study protocol for a multicenter randomized trial
Authors: Zhou Yu , Zhang Lei , Zhang Yongwei , Li Zifu , Xing Pengfei , Shen Hongjian , Zhu Xuan , Goyal Mayank , Liu Jianmin , Yang Pengfei ,   PROTECT-MT investigators
Published: July 2024

Background and Rationale

Uncertainty exists over balloon guide catheter(BGC) usage for Mechanical Thrombectomy(MT) in patients with acute ischemic stroke acute ischemic stroke due to anterior circulation large vessel occlusion.

Objective

To determine the effectiveness of balloon guide catheter(BGC) as compared to conventional guide catheter on functional outcome in patients with acute ischemic stroke and treated with MT.

Design

Proximal TEmporary oCclusion using balloon guide caTheter for Mechanical Thrombectomy (PROTECT-MT) is an investigator-initiated, multicenter, prospective, open label trial with blinded outcome assessment (PROBE design) assessing the effectiveness and safety of BGC in acute ischemic stroke. An estimated 1074 patients meet the inclusion criteria would be randomized (1:1) to receive either MT with BGC(intervention) or MT with conventional guide catheter(control). The primary outcome is an ordinal shift analysis of scores on the modified Rankin scale (mRS) at 90 days.

Progress

Recruitment started on February 7, 2023. At a meeting of the independent Data and Safety Monitoring Board in November 2023 to review primary outcome data available for 169 patients, they recommended suspension of recruitment due to safety concerns, which was implemented by the Trial Steering Committee (TSC) with 329 randomized patients. The TSC stopped recruitment due to the safety concerns persisted on further review of the data on April 18, 2024.

Discussion

PROTECT-MT is the largest RCT assessing the effectiveness of BGC versus conventional guide catheter on functional outcome in large vessel occlusion patients treated with MT, it will provide further randomized evidence on the role of BGC in AIS patients treated with MT.
Post-proline cleaving enzymes also show specificity to reduced cysteine
Authors: Kalaninová Zuzana , Portašiková Jasmína Mária , Jirečková Barbora , Polák Marek , Nováková Jana , Kavan Daniel , Novák Petr , Man Petr
Published: July 2024

In proteomics, post-proline cleaving enzymes (PPCEs) likeAspergillus nigerprolyl endopeptidase and neprosin complement proteolytic tools because proline is a stop site for many proteases. However, our systematic analysis of cleavage preferences showed that both PPCEs also display specificity to reduced cysteine. Post-cysteine cleavage was blocked by Cys alkylation, explaining why this activity has remained undetected. Our findings redefine their applicability and how we study and interpret their cleavage mechanism.
Stabilization Mechanism of Initiator Transfer RNA in the Small Ribosomal Subunit from Coarse-Grained Molecular Simulations
Authors: Mori Yoshiharu , Tanaka Shigenori
Published: July 2024

Proteins play a variety of roles in biological phenomena in cells. Proteins are synthesized by a ribosome, which is a large molecular complex composed of proteins and nucleic acids. Among many molecules involved in the process of protein synthesis, transfer RNA (tRNA) is one of the essential molecules. In this study, coarse-grained molecular dynamics simulations were performed to understand how the tRNA molecule is stabilized in the ribosome, and the free energy along the dissociation path of the tRNA was calculated. We found that some ribosomal proteins, which are components of the ribosome, are involved in the stabilization of the tRNA. The positively charged amino acid residues in the C-terminal region of the ribosomal proteins are particularly important for the stabilization. These findings contribute to our understanding of the molecular evolution of protein synthesis in terms of the ribosome, which is a universal component of life.

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Global Phylogeography and Microdiversity of the Marine Diazotrophic CyanobacteriaTrichodesmiumand UCYN-A
Authors: Nguyen Angie , Ustick Lucas J. , Larkin Alyse A. , Martiny Adam C.
Published: July 2024

Cyanobacterial diazotrophs, specifically the generaTrichodesmiumand UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution ofTrichodesmiumand UCYN-A using the nitrogenase gene (nifH) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera.Trichodesmiumexhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution.Trichodesmiumclades were primarily influenced by temperature and nutrient availability, and particularly frequent in regions of phosphorus stress. In contrast UCYN-A was found in regions of iron stress. UCYN-A clades demonstrated a more homogeneous distributions, with a single sequencing variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations ofTrichodesmiumand UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. This study underscores the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing cyanobacteria.
Oxford Nanopore’s 2024 sequencing technology forListeria monocytogenesoutbreak detection and source attribution: progress and clone-specific challenges
Authors: Biggel Michael , Cernela Nicole , Horlbog Jule Anna , Stephan Roger
Published: July 2024

Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chromosomes and plasmids. Limited accuracy has hindered its use for investigating pathogen transmission, but recent technology updates have brought significant improvements. To evaluate its readiness for outbreak detection, we selected 78Listeria monocytogenesisolates from diverse lineages or known epidemiological clusters for sequencing with ONT’s V14 Rapid Barcoding Kit and R10.4.1 flow cells. The most accurate of several tested workflows generated assemblies with a median of one error (SNP or indel) per assembly. For 66 isolates, cgMLST profiles from ONT-only assemblies were identical to those generated from Illumina data. Eight assemblies were of lower quality with more than 20 erroneous sites each, primarily caused by methylations at the GAAGAC motif (5′-GAAG6mAC-3 / 3′-GT4mCTTC-5′). This led to inaccurate clustering, failing to group isolates from a persistence-associated clone that carried the responsible restriction-modification system. Out of 50 methylation motifs detected among the 78 isolates, only the GAAGAC motif was linked to substantially increased error rates. Our study shows that mostL. monocytogenesgenomes assembled from ONT-only data are suitable for high-resolution genotyping, but further improvements of chemistries or basecallers are required for reliable routine use in outbreak and food safety investigations.
A Kruppel-like factor establishes cellular heterogeneity during schistosome tegumental maintenance
Authors: Zhao Lu , Wendt George R , Collins James J
Published: July 2024

Schistosomes are blood-dwelling parasitic flatworms that rely on a syncytial surface coat, known as the tegument, for long-term survival and immune evasion in the blood of their human hosts. Previous studies have shown that cells within the tegumental syncytium are perpetually turned over and renewed by somatic stem cells called neoblasts. Yet, little is known about this renewal process on a molecular level. Here, we characterized a Kruppel-like factor 4 (klf4) using a combination of bulk and single cell RNAseq approaches and demonstrate thatklf4is essential for the maintenance of a specific tegumental lineage, resulting in the loss of a subpopulation of molecularly-unique tegument cells. Thus,klf4is critical for maintaining the balance between different tegumental progenitor pools, thereby fine-tuning the molecular composition of the mature tegument. Understanding these distinct tegumental cell populations is expected to provide insights into parasite defense mechanisms and suggest new avenues for therapeutics.
Nitration of a ribosomal pentapeptide generates a noncanonical precursor for nonribosomal peptide synthesis
Authors: Padva Leo , Zimmer Lukas , Gullick Jemma , Zhao Yongwei , Sasi Vishnu Mini , Schittenhelm Ralf B. , Jackson Colin J. , Cryle Max , Crüsemann Max
Published: July 2024

Peptide natural products possess a fascinating array of complex structures and diverse functions. Central to this is a repertoire of modified amino acid building blocks, which stem from fundamentally different biosynthesis pathways for peptides of nonribosomal and ribosomal origins. Given these origins, integration of nonribosomal and ribosomal pathways have previously been thought unlikely. Now, we demonstrate that ribosomal biosynthesis generates a key noncanonical 3-nitrotyrosine building block for the nonribosomal synthesis of rufomycin. In this pathway, a biarylitide-type ribosomal peptide is nitrated by a modified cytochrome P450 crosslinking enzyme, with the nitrated residue liberated by the actions of a dedicated protease found within the rufomycin gene cluster before being incorporated into rufomycin by the rufomycin nonribosomal peptide synthetase. This resolves the enigmatic origins of 3-nitrotyrosine within rufomycin biosynthesis and demonstrates unexpected integration of ribosomal peptide synthesis as a mechanism for the generation of noncanonical building blocks within nonribosomal synthesis pathways.
Psychological capital: a literature review and research trends
Authors: Nguyen Thanh D. , Cao Thi H. , Nguyen Tuan M. , Nguyen Tuan T.
Published: July 2024

Purpose

This literature review aims to explore the various aspects of psychological capital (PsyCap), including its theoretical foundations, measurement methods, and the factors directly associated with PsyCap.

Design/methodology/approach

The approach employed in this study is scientific document synthesis, with a specific emphasis on scholarly articles published between 2001 and 2023. The selection of articles is limited to those published in internationally renowned journals that are indexed by reputable databases, including ISI (WoS) and SJR (Scopus).

Findings

Psychological capital is closely linked to other concepts at different levels. Scholars are investigating various factors associated with PsyCap, including health, project success, service marketing, banking services. It is important to note that different research areas have varying conceptualizations and scales when it comes to PsyCap.

Originality/value

This literature review of related studies reveals a growing global interest among researchers in the concept of positive psychological capital. The research results have shown significant interest in the items related to PsyCap, and and the factors directly associated with it, including antecedents, mediators, moderators, and outcomes.
Psychological need profiles during online shopping: exploring associations with word-of-mouth and loyalty
Authors: Ling Tianye , Zhao Rui , Jang Hyungshim
Published: July 2024

Purpose

Drawing on self-determination theory, a person-centered approach was used to investigate how the satisfaction and frustration of the basic psychological needs of autonomy and competence produce adaptive vs maladaptive consumer behavior during the online shopping experience.

Design/methodology/approach

We collected questionnaire data from 1,399 respondents engaged in online shopping, including 65% females with an average age of 29.9. Latent profile analysis tested the hypotheses, using Mplus 8.3.

Findings

The online shopping experience sometimes satisfies and sometimes frustrates consumers’ basic psychological needs for autonomy and competence. This research used latent profile analysis to identify two profiles of the online shopping experience: “satisfied-dominant” and “moderately satisfied/frustrated.” Online shoppers who experienced only need satisfaction showed adaptive consumer behavior in terms of positive word-of-mouth and high loyalty, while online shoppers who experienced both moderate need satisfaction and frustration showed maladaptive consumer behavior.

Originality/value

An online shopping experience of need satisfaction vs frustration explains consumers’ adaptive vs maladaptive behavior. Specifically, when online shoppers experience only autonomy and competence need satisfaction, they engage in positive word-of-mouth and show high loyalty.
Support for housing recovery of home-based survivors: disaster case management after the 2011 Great East Japan Earthquake and tsunami
Authors: Uto Akihiro , Maly Elizabeth
Published: July 2024

Purpose

After the Great East Japan Earthquake (GEJE), the need for disaster case management (DCM) was highlighted through the efforts of the Sendai Bar Association, which investigated the situation of survivors. This paper provides an overview of DCM in Japan since the GEJE, including key findings from investigations and legal consultations conducted by the Sendai Bar Association and the first author, who took part in the surveys with survivors in Ishinomaki City, clarifying the large number of homebound survivors and their needs.

Design/methodology/approach

In recent years there has been growing attention to the importance of DCM for supporting life and housing recovery of disaster survivors. Along with the expansion of DCM activities over several decades in Japan, the need for DCM was increasingly recognized after the 2011 GEJE and tsunami, especially for home-based survivors left out of government-provided disaster recovery support programs. As one-on-one advice to support individual recovery needs, the focus of DCM in Japan is legal advice to help survivors effectively navigate support policies.

Findings

Since the GEJE, there has been growing support for DCM in Japan, including from practitioners, scholars, and regional and national governments. However, although DCM can be an effective way to support housing recovery, even 12 years after the GEJE, there are still survivors in need of additional support.

Originality/value

Drawing on a detailed case study and action research of the first author, this paper contributes to the still limited international literature on DCM in Japan.