bluuebunny/crossref_metadata_2025_split huggingface dataset:
msqrob2TMT: robust linear mixed models for inferring differential abundant proteins in labelled experiments with arbitrarily complex design
Authors: Vandenbulcke Stijn , Vanderaa Christophe , Crook Oliver , Martens Lennart , Clement Lieven 
Published: March 2024

AbstractLabelling strategies in mass spectrometry (MS)-based proteomics enable increased sample throughput by acquiring multiplexed samples in a single run. However, contemporary designs often require the acquisition of multiple runs, leading to a complex correlation structure. Addressing this correlation is key for correct statistical inference and reliable biomarker discovery. Therefore, we present msqrob2TMT, a set of mixed model-based workflows tailored toward differential abundance analysis for labelled MS-based proteomics data. Thanks to its increased flexibility, msqrob2TMT can model both sample-specific and feature-specific (e.g. peptide or protein) covariates, which unlocks the inference to experiments with arbitrarily complex designs as well as to correct explicitly for feature-specific properties. We benchmark our novel workflows against the state-of-the-art tools MSstatsTMT and DeqMS in a spike-in study. We show that our workflows are modular, more flexible and have improved performance by adopting robust ridge regression. We also found that reference channel normalization and imputation can have a deleterious impact on the statistical outcome. Finally, we demonstrate the significance of msqrob2TMT on a real-life mice study, showcasing the importance of effectively accounting for the hierarchical correlation structure in the data.
RNA folding kinetics control riboswitch sensitivity in vivo
Authors: Bushhouse David Z. , Fu Jiayu , Lucks Julius B. 
Published: March 2024

SUMMARYRiboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity is controlled is critical to understanding how highly conserved aptamer domains are deployed in a variety of contexts with different sensitivity demands. Here we uncover new roles by which RNA folding dynamics control riboswitch sensitivity in cells. By investigating theClostridium beijerinckii pflZTP riboswitch, we identify multiple mechanistic routes of altering expression platform sequence and structure to slow RNA folding, all of which enhance riboswitch sensitivity. Applying these methods to riboswitches with diverse aptamer architectures that regulate transcription and translation with ON and OFF logic demonstrates the generality of our findings, indicating that any riboswitch that operates in a kinetic regime can be sensitized by slowing expression platform folding. Comparison of the most sensitized versions of these switches to equilibrium aptamer:ligand dissociation constants suggests a limit to the sensitivities achievable by kinetic RNA switches. Our results add to the growing suite of knowledge and approaches that can be used to rationally program cotranscriptional RNA folding for biotechnology applications, and suggest general RNA folding principles for understanding dynamic RNA systems in other areas of biology.
Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs
Authors: Jochheim Annika , Jochheim Florian A. , Kolodyazhnaya Alexandra , Morice Étienne , Steinegger Martin , Söding Johannes 
Published: March 2024

AbstractBackgroundMetagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due to their genomic diversity caused by high mutation rates. In the standard de Bruijn graph assemblers, this genomic diversity leads to complexk-mer assembly graphs with a plethora of loops and bulges that are challenging to resolve into strains or haplotypes because variants more than thek-mer size apart cannot be phased. In contrast, overlap assemblers can phase variants as long as they are covered by a single read.ResultsHere, we present PenguiN, a software for strain resolved assembly of viral DNA and RNA genomes and bacterial 16S rRNA from shotgun metagenomics. Its exhaustive detection of all read overlaps in linear time combined with a Bayesian model to select strain-resolved extensions allow it to assemble longer viral contigs, less fragmented genomes, and more strains than existing assembly tools, on both real and simulated datasets. We show a 3-40-fold increase in complete viral genomes and a 6-fold increase in bacterial 16S rRNA genes.ConclusionPenguiN is the first overlap-based assembler for viral genome and 16S rRNA assembly from large and complex metagenomic datasets, which we hope will facilitate studying the key roles of viruses in microbial communities.
Extracellular vesicle-mediated secretion of chlorophyll biosynthetic intermediates in the cyanobacteriumLeptolyngbya boryana
Authors: Usui Kentaro , Yamamoto Haruki , Mori Hitoshi , Fujita Yuichi 
Published: March 2024

AbstractExtracellular vesicles (EVs) are derived from the outer membrane (OM) in Gram-negative bacteria and have diverse physiological functions such as toxin transport, extracellular signal transduction, nutrient acquisition, and horizontal gene transfer. EV-mediated secretion of monovinyl protochlorophyllide (MV-Pchlide), the chlorophylla(Chl) biosynthetic intermediate, was previously reported in a mutant lacking dark-operative Pchlide reductase in the cyanobacteriumLeptolyngbya boryana. This study showed a detailed characterization of EVs from the wild-type (WT) ofL. boryanagrown under photoautotrophic and dark heterotrophic conditions, focusing on the accumulation of Chl intermediates. WTL. boryanacells produce two types of EVs, low-density EVs (L-EVs) and high-density EVs (H-EVs), both under light and dark conditions. L-EVs and H-EVs showed distinct morphological features and protein compositions. L-EVs from cells grown under both light and dark conditions commonly contained carotenoids, myxol glycoside, and zeaxanthin, as major pigments. Based on the protein compositions of EVs and other cellular membrane fractions, L-EVs and H-EVs are probably derived from low-density OM and high-density OM interacting with cell walls, respectively. Fluorescence detection of pigments was applied to EVs, and the three Chl intermediates, protoporphyrin IX, demetallated Mg-protoporphyrin IX monomethyl ester, pheophorbide, and were commonly detected both L-EVs from light- and dark-grown cells, whereas L-EVs from dark-grown cells contained additional MV-Pchlide and MV-protopheophorbide. These Chl intermediates appear to transfer from the thylakoid membrane to L-EVs via an unknown transport system. Cyanobacterial EVs may play a novel function in alleviating the accumulation of Chl intermediates in cells.
Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states
Authors: Murphy Alan E , Askarova Aydan , Lenhard Boris , Skene Nathan G , Marzi Sarah J 
Published: March 2024

AbstractTo understand the complex relationship between histone mark activity and gene expression, recent advances have usedin silicopredictions based on large-scale machine learning models. However, these approaches have omitted key contributing factors like cell state, histone mark function or distal effects, that impact the relationship, limiting their findings. Moreover, downstream use of these models for new biological insight is lacking. Here, we present the most comprehensive study of this relationship to date - investigating seven histone marks, in eleven cell types, across a diverse range of cell states. We used convolutional and attention-based models to predict transcription from histone mark activity at promoters and distal regulatory elements. Our work shows that histone mark function, genomic distance and cellular states collectively influence a histone mark’s relationship with transcription. We found that no individual histone mark is consistently the strongest predictor of gene expression across all genomic and cellular contexts. This highlights the need to consider all three factors when determining the effect of histone mark activity on transcriptional state. Furthermore, we conductedin silicohistone mark perturbation assays, uncovering functional and disease related loci and highlighting frameworks for the use of chromatin deep learning models to uncover new biological insight.Graphical abstract
Exonuclease action of replicative polymerase gamma drives damage-induced mitochondrial DNA clearance
Authors: Seshadri Akshaya , Badrinarayanan Anjana 
Published: March 2024

AbstractMitochondrial DNA (mtDNA) replication is essential for mitochondrial function. This is carried out by a dedicated DNA polymerase gamma, with 5’-3’ polymerase and 3’-5’ proofreading/ exonuclease activity. Perturbations to either properties can have pathological consequences. Predominant sources for replication stress are DNA lesions, such as those induced by oxidative damage. How mtDNA lesions affect the polymerase activity and mtDNA stabilityin vivois not fully understood. To address this, we induce mtDNA-specific damage inS. cerevisiae.We observe that mtDNA damage results in significant mtDNA loss. This loss occurs independent of cell cycle progression or cell division, suggesting an active mechanism for damaged mtDNA clearance. We implicate the 3’-5’ exonuclease activity of the mtDNA polymerase in this clearance, with rates of loss being affected by cellular dNTP levels. Overall, our findings reveal context-dependent, selective regulation of two critical but opposing functions of polymerase gamma to ensure mitochondrial genome integrity.
Nest construction and its effect on post-hatching family life in the burying beetleNicrophorus vespilloides
Authors: Bladon Eleanor Kate , Kilner Rebecca Mary 
Published: March 2024

AbstractThrough the effort required to construct them, the microenvironmental conditions they impose on the family and their indirect influence on post-hatching care, nests play a key role in influencing family life. We combined experimental evolution with cross-fostering experiments on laboratory populations ofNicrophorus vespilloidesto investigate three ways in which the nest can contribute more broadly to parental investment. We used replicate populations ofN. vespilloidesthat had evolved for 42 generations under contrasting regimes of care. Populations were either able to supply post-hatching care (“Full Care”) or prevented from supplying any post-hatching care (“No Care”). Research on these populations has previously shown that the No Care populations evolved to build rounder nests, more rapidly, by Generation 14. Here we found: 1) larvae raised by Full Care parents on nests prepared by parents from the No Care population did not attain a higher mass by the end of larval development than larvae in other treatments. However, we did discover that: 2) cross-fostering nests between families consistently reduced larval mass – and to a similar extent whether nests were cross-fostered between or within the populations. We suggest that cross-fostering disrupted the chemical environment on and around the nest since we found no evidence that 3) nests mediate interactions between males and females. The duration of paternal care was consistently shorter than the duration of maternal care, and even shorter for males from the No Care populations than males from the Full Care populations. Nevertheless, the duration of male care did not predict variation in duration of female care. In short, although the nest is the substrate for burying beetle family life, we found little evidence that it had evolved divergently in our experimental populations to influence parental investment.
VISION — an open-source software for automated multi-dimensional image analysis of cellular biophysics
Authors: Weber Florian , Iskrak Sofiia , Ragaller Franziska , Schlegel Jan , Plochberger Birgit , Sezgin Erdinc , Andronico Luca A. 
Published: March 2024

AbstractEnvironment-sensitive probes are frequently used in spectral/multi-channel microscopy to study alterations in cell homeostasis. However, the few open-source packages available for processing of spectral images are limited in scope. Here, we present VISION, a stand-alone software based on Phyton for spectral analysis with improved applicability. In addition to classical intensity-based analysis, our software can batch-process multidimensional images with an advanced single-cell segmentation capability and apply user-defined mathematical operations on spectra to calculate biophysical and metabolic parameters of single cells. VISION allows for 3D and temporal mapping of properties such as membrane fluidity and mitochondrial potential. We demonstrate the broad applicability of VISION by applying it to study the effect of various drugs on cellular biophysical properties; the correlation between membrane fluidity and mitochondrial potential; protein distribution in cell-cell contacts; and properties of nanodomains in cell-derived vesicles. Together with the code, we provide a graphical user interface for facile adoption. We anticipate that VISION will find a broad range of applications in different fields of biology, spanning from molecular and tissue biology to immunology and biophysics.Summary statementVISION, an open-source software, enables high throughput and correlative analysis of cellular biophysical properties.
Correlation between the exchange bias effect and antisite disorder in
Sr2−xLaxCoNbO6

(x=0, 0.2)
Authors: Kumar Ajay , Schwarz B. , Dhaka R. S. 
Published: March 2024

We unravel the effect of La substitution and hence antisite disorders on the exchange bias (EB) mechanism in Sr2−xLaxCoNbO6 (x=0, 0.2) double-perovskite samples using the detailed analysis of the field cooled magnetization isotherms (M−H) and training effect. The field dependence of the freezing temperature deviates from both Gabay-Toulouse and de Almeida-Thouless lines and the analysis suggests that the x=0 sample follows a different universality class with moderate anisotropy in the frozen spins. Interestingly, we find that the EB effect is significantly suppressed in the x=0.2 sample due to increase [decrease] in the size of ferromagnetic (FM) [cluster glass (CG)] domain, which reduces the effective disordered interface responsible for the EB. The changes in fraction of FM, antiferromagnetic, and CG-like interactions with the La substitution and applied magnetic field are found to be crucial in governing the EB effect in these samples. Furthermore, the training effect measurements show the unequal shift in the left and right branches of the M−H loops and their different evolution with the field cycles (n). The analysis reveals that the rotatable spins relax approximately one order of magnitude faster than the frozen spins at the disordered interface. We find a possible correlation between the observed EB effect and the antisite disorders in these samples.

Published by the American Physical Society
2024
Sensitivity of polarizations and spin correlations of
Z
boson to anomalous neutral triple gauge couplings at lepton collider with polarized beams
Authors: Subba Amir , Singh Ritesh K. 
Published: March 2024

We investigate the effects of anomalous neutral triple gauge couplings in ZZ and Zγ production processes, followed by the leptonic decay of the Z boson, at a lepton collider with center-of-mass energy s=250  GeV and polarized beams. We use an effective Lagrangian formalism to parametrize the anomalous couplings in terms of dimension-8 operators cB˜W, cBW, cWW, and cBB, and study the sensitivity of observables such as cross section, polarization, and spin correlation as functions of these couplings. We perform a Bayesian statistical analysis using Markov Chain Monte Carlo methods to determine simultaneous limits on the anomalous couplings, taking into account various luminosities L∈{0.1  ab−1,0.3  ab−1,1  ab−1,3  ab−1,10  ab−1} and systematic uncertainties. We find that polarization and spin correlation observables significantly enhance the sensitivity to anomalous couplings, providing stringent constraints on these couplings.

Published by the American Physical Society
2024
An analytical solution and stability analysis of asymmetric non-actuator guided projectiles
Authors: Taban Mahmoud , Novinzadeh Alireza Basohbat 
Published: March 2024

Purpose
One of the challenges encountered in the design of guided projectiles is their prohibitive cost. To diminish it, an appropriate avenue many researchers have explored is the use of the non-actuator method for guiding the projectile to the target. In this method, biologically inspired by the flying concept of the single-winged seed, for instance, that of maple and ash trees, the projectile undergoes a helical motion to scan the region and meet the target in the descent phase. Indeed, the projectile is a decelerator device based on the autorotation flight while it attempts to resemble the seed’s motion using two wings of different spans. There exists a wealth of studies on the stability of the decelerators (e.g. the mono-wing, samara and pararotor), but all of them have assumed the body (exclusive of the wing) to be symmetric and paid no particular attention to the scanning quality of the region. In practice, however, the non-actuator-guided projectiles are asymmetric owing to the presence of detection sensors. This paper aims to present an analytical solution for stability analysis of asymmetric decelerators and apprise the effects of design parameters to improve the scanning quality.

Design/methodology/approach
The approach of this study is to develop a theoretical model consisting of Euler equations and apply a set of non-dimensionalized equations to reduce the number of involved parameters. The obtained governing equations are readily applicable to other decelerator devices, such as the mono-wing, samara and pararotor.

Findings
The results show that the stability of the body can be preserved under certain conditions. Moreover, pertinent conclusions are outlined on the sensitivity of flight behavior to the variation of design parameters.

Originality/value
The analytical solution and sensitivity analysis presented here can efficiently reduce the design cost of the asymmetric decelerator.
Multidimensional poverty analysis of women, children and households in Nigeria: the first order dominance approach
Authors: Okogun Oluwanishola , Hiwatari Masato 
Published: March 2024

PurposeThis study examines the dynamics of multidimensional poverty in Nigeria from 2003 to 2018, focusing on women and children, to understand the reality of poverty in Nigeria, where poverty reduction has been stagnant.Design/methodology/approachThis study employed the first-order dominance (FOD) methodology to conduct a multidimensional analysis of poverty among households, women and children in Nigeria, using data from the Demographic and Health Surveys (DHS) conducted in 2003, 2008, 2013 and 2018. We examined how the relative position of multidimensional poverty in each zone has changed for approximately 20 years.FindingsThe results indicated that the north-south poverty gap in Nigeria persisted as of 2018 and, regarding within the north and south, changes in the relative pecking order of poverty between the zones have occurred considerably over the past two decades. Different trends were also observed for child and female poverty, suggesting the influence of the unique dimensions of poverty and cultural differences.Originality/valueThis study is the first poverty analysis to apply the FOD approach to children and women in Nigeria, the country with the highest poverty, over a relatively long period of 2003–2018.
The Zomato dilemma: a realistic growth trajectory and share price fair valuation?
Authors: Tuyon Jasman , Huang Chia-Hsing , Swanepoel Danielle 
Published: March 2024

Learning outcomes
This case study is related to start-up post-listing investment analysis. Through this case study, students will be able to perform the business analysis guided by the Venture Evaluation Metric tool, perform financial analysis using the discounted cash flow methods and perform investment analysis recommendation with justifications from the business and financial analysis performed above.

Case overview/synopsis
This case study sets out the study of a scalable start-up, Zomato, which is a successfully listed start-up firm in India. Despite the start-up development success in the pre-listing, the firm has exhibited a continuous unprofitable finance performance in the post-listing and has further experienced a volatile share price performance, both of which have puzzled existing and potential investors. In addition, some analysts are in the opinions that the firm share price valuation have been inflated with overvaluation since in the initial public offering stage and remain traded with overvaluation in the market. Notably, considering the negative indicators mentioned above, investors are concerned about long-term sustainability of the firm business and financial performance. In the context of post-listing investment, the following questions are material to investors: What is the realistic growth trajectory for Zomato in the medium term? What is Zomato’s share fair value in the medium term? Can one see opportunities or risks ahead of investing in Zomato’s shares? What will be the investment strategy for new investors?

Complexity academic level
This case study is suited to bachelor’s and master’s level in business schools studying entrepreneurial finance analysis.

Supplementary material
Teaching notes are available for educators only.

Subject code
CSS 1: Accounting and finance.
Food insecurity: addressing a challenging social problem with supply chains and service ecosystems
Authors: García-Dastugue Sebastián Javier , García-Contreras Rogelio , Stauss Kimberly , Milford Thomas , Leuschner Rudolf 
Published: March 2024

PurposeExtant literature in supply chain management tends to address a portion of the product flow to make food accessible to clients in need. The authors present a broader view of food insecurity and present nuances relevant to appreciate the complexities of dealing with this social problem.Design/methodology/approachThe authors conducted an inductive study to reveal the deep meaning of the context as managers of nonprofit organizations (NPO) define and address food insecurity. The focus was on a delimited geographic area for capturing interactions among NPOs which have not been described previously.FindingsThis study describes the role of supply chains collaborating in unexpected ways in the not-for-profit context, leading to interesting insights for the conceptual development of service ecosystems. This is relevant because the solution for the food insecure stems from the orchestration of assistance provided by the many supply chains for social assistance.Research limitations/implicationsThe authors introduce two concepts: customer sharing and customer release. Customer sharing enables these supply chains behave like an ecosystem with no focal organization. Customer release is the opposite to customer retention, when the food insecure stops needing assistance.Social implicationsThe authors describe the use of customer-centric measures of success such improved health measured. The solution to food insecurity for an individual is likely to be the result of the orchestration of assistance provided by several supply chains.Originality/valueThe authors started asking who the client is and how the NPOs define food insecurity, leading to discussing contrasts between food access and utilization, between hunger relief and nourishment, between assistance and solution of the problem, and between supply chains and ecosystems.