bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying seed rain patterns in a remnant and a chronosequence of restored tallgrass prairies in north central Missouri
Authors: Wynne K. Carter , Parker-Smith Maya J. , Murdock Erica M. , Sullivan Lauren L. 
Published: July 2024

AbstractSeed rain is an influential process related to plant community diversity, composition, and regeneration. However, knowledge of seed rain patterns is limited to those observed in forests and late-assembling grasslands, which might not reflect early-assembling communities such as newly restored grasslands. Resolving this gap in our understanding provides further insight into the role of seed dispersal.Here, we measured seed rain in a remnant tallgrass prairie, which was the site of the foundational grassland seed rain study in 1978, and a nearby chronosequence of tallgrass prairie restorations. We sought to determine how the quantity, seed mass traits, timing, diversity, and composition of seed rain changed (1) long-term and (2) during community assembly. To do so, we deployed artificial turf grass seed traps into 2-year-old, 5-6-year-old, and 15-year-old restored prairies and the remnant prairie, replacing traps every two weeks from May to December 2019.We captured over twice the density and richness of seed rain in the remnant prairie in 2019 compared to 1978. We also found that seed rain patterns changed as prairies aged, with each prairie possessing a distinct community of dispersing species. Significantly more seeds, seed biomass, and species were captured in the youngest restored prairie. However, seed mass traits were similar in all prairies. Except for composition, all other seed rain metrics in the oldest restoration were eventually comparable to the remnant prairie.Synthesis and Applications: Our results revealed that grasslands, notably young prairies, produce larger quantities of seed rain than previously known (124,806 seeds m−2year−1, 97.24 g m−2year−1), and seed input in all sampled prairies far exceeded restoration broadcast seeding densities. We further found that decreases in seed rain quantity across the chronosequence did not correspond with increases in seed mass, suggesting a lack of tradeoffs between these metrics. Furthermore, tallgrass prairie restorations have not replicated the composition of seed rain seen in remnant systems. Increasing restoration seeding rates of desirable species may be needed to meet composition goals since current rates may not compete with the propagule pressure of undesirable species found in newly restored prairies.
Tempo-dependent selective enhancement of neural responses at the beat frequency can be explained by both an oscillator and an evoked model
Authors: Damsma Atser , de Roo Mitchell , Doelling Keith , Bazin Pierre-Louis , Bouwer Fleur L. 
Published: July 2024

AbstractA crucial mechanism for the brain to make sense of the auditory environment is the synchronization of neural responses to external temporal regularities, such as a musical beat. It is debated whether this synchronization and the resulting beat percept reflect phase alignment of endogenous neural oscillations to the external regularity (entrainment), or evoked responses to the rhythmic stimulus (tracking). Here, we use the tempo-dependent properties of beat processing to differentiate between the two accounts. Behaviorally, we show a shift in the perceived level of regularity towards the preferred beat rate (around 2 Hz) when listening to rhythmic patterns at different speeds. We found a similar shift in EEG data, where the hierarchical level in the rhythms at which neural synchronization was strongest depended on tempo. This selective enhancement is consistent with entrainment accounts and could indeed be mimicked by an oscillator model. However, importantly, the results were explained equally well using a model simulating evoked responses. Together, our findings demonstrate that while neural responses to rhythm are selectively enhanced at the beat rate, this enhancement need not be taken as evidence for entrainment, but can also be explained by successive evoked responses.
APP β-CTF triggers cell-autonomous synaptic toxicity independent of Aβ
Authors: Luo Mengxun , Zhou Jia , Sun Cailu , Chen Wanjia , Fu Chaoying , Si Chenfang , Zhang Yaoyang , Geng Yang , Chen Yelin 
Published: July 2024

AbstractAβ is believed to play a significant role in synaptic degeneration observed in Alzheimer’s disease (AD) and is primarily investigated as a secreted peptide. However, the contribution of intracellular Aβ or other cleavage products of its precursor protein (APP) to synaptic loss remains uncertain. In this study, we conducted a systematic examination of their cell-autonomous impact using a sparse expression system. Here, these proteins/peptides were overexpressed in a single neuron, surrounded by thousands of untransfected neurons. Surprisingly, we found that APP induced dendritic spine loss only when co-expressed with BACE1. This effect was mediated by β-CTF, a β-cleavage product of APP, through an endosome-related pathway independent of Aβ. Neuronal expression of β-CTF in mouse brains resulted in defective synaptic transmission and cognitive impairments, even in the absence of amyloid plaques. These findings unveil a β-CTF-initiated mechanism driving synaptic toxicity irrespective of amyloid plaque formation and suggest a potential intervention by inhibiting the endosomal GTPase Rab5.
An off-lattice discrete model to characterise filamentous yeast colony morphology
Authors: Li Kai , Green J. Edward F. , Tronnolone Hayden , Tam Alexander K. Y. , Black Andrew J. , Gardner Jennifer M. , Sundstrom Joanna F. , Jiranek Vladimir , Binder Benjamin J. 
Published: July 2024

AbstractWe combine an off-lattice agent-based mathematical model and experimentation to explore filamentous growth of a yeast colony. Under environmental stress,Saccharomyces cerevisiaeyeast cells can transition from a bipolar (sated) to unipolar (pseudohyphal) budding mechanism, where cells elongate and bud end-to-end. This budding asymmetry yields spatially non-uniform growth, where filaments extend away from the colony centre, foraging for food. We use approximate Bayesian computation to quantify how individual cell budding mechanisms give rise to spatial patterns observed in experiments. We apply this method of parameter inference to experimental images of colonies of two strains ofS. cerevisiae, in low and high nutrient environments. The initial nutrient concentration and a forking mechanism for pseudohyphal cell proliferation are the key features driving colony morphology. Simulations run with the most likely inferred parameters produce colony morphologies that closely resemble experimental results.
Enzymatic carbon-fluorine bond cleavage by human gut microbes
Authors: Probst Silke I. , Felder Florian D. , Poltorak Victoria , Mewalal Ritesh , Blaby Ian K. , Robinson Serina L. 
Published: July 2024

AbstractFluorinated compounds are used for agrochemical, pharmaceutical, and numerous industrial applications, resulting in global contamination. In many molecules, fluorine is incorporated to enhance the half-life and improve bioavailability. Fluorinated compounds enter the human body through food, water, and xenobiotics including pharmaceuticals, exposing gut microbes to these substances. The human gut microbiota is known for its xenobiotic biotransformation capabilities, but it was not previously known whether gut microbial enzymes could break carbon-fluorine bonds, potentially altering the toxicity of these compounds.Here, through the development of a rapid, miniaturized fluoride detection assay for whole-cell screening, we discovered active gut microbial defluorinases. We biochemically characterized enzymes from diverse human gut microbial classes including Clostridia, Bacilli, and Coriobacteriia, with the capacity to hydrolyze (di)fluorinated organic acids and a fluorinated amino acid. Whole-protein alanine scanning, molecular dynamics simulations, and chimeric protein design enabled the identification of a disordered C-terminal protein segment involved in defluorination activity. Domain swapping exclusively of the C-terminus conferred defluorination activity to a non-defluorinating dehalogenase. To advance our understanding of the structural and sequence differences between defluorinating and non-defluorinating dehalogenases, we trained machine learning models which identified protein termini as important features. Models trained on 41-amino acid segments from protein C-termini alone predicted defluorination activity with 83% accuracy (compared to 95% accuracy based on full-length protein features). This work is relevant for therapeutic interventions and environmental and human health by uncovering specificity-determining signatures of fluorine biochemistry from the gut microbiome.SignificanceHumans have introduced carbon-fluorine bonds into numerous manufactured compounds, including pharmaceuticals, leading to the formation of toxic fluorinated byproducts. While the human gut microbiota is known for its ability to metabolize drugs, its encoded capacity to break the strong carbon-fluorine chemical bond was previously unknown. Here we discovered that human gut microbial enzymes are capable of cleaving carbon-fluorine bonds. We developed a 96-well colorimetric fluoride assay amenable to bacterial culture-based screening. Additionally, we trained machine learning models to predict defluorination activity and experimentally validated our findings to identify key features of defluorinating enzymes. This opens new research directions in microbiome research for the metabolism of fluorinated compounds, with implications for therapeutic development and enzyme engineering to break carbon-fluorine bonds.
Protein quality control modulates the metabolic conservation in antibiotic tolerantCampylobacter jejuni
Authors: Feng Jinsong , Li Shenmiao , Hu Yaxi , Stahl Martin , Ma Lina , Knuff-Janzen Katelyn , Wang Kaidi , Hua Marti Z. , Vallance Bruce A. , Konkel Michael E. , Finlay B. Brett , Lu Xiaonan 
Published: July 2024

ABSTRACTAntibiotic tolerance in bacteria emerges as a phenotypic variant known as persisters and has been implicated in recurrent bacterial infections. This tolerance manifests as suppressed metabolism. We demonstrate thatCampylobacter jejunireadily forms persisters in response to both ampicillin and ciprofloxacin. Persisters induced by these two antibiotics with different mechanisms of actions experience consistent metabolic reprogramming, characterized by suppressed respiration and energy metabolism while conserving core metabolic processes. We reveal that the coordination of protein homeostasis underlies the metabolic reprogramming involved in persister formation. Mutating the caseinolytic protease geneclpP, a major component of the protein quality control system, compromises persister formationin vitroand impairs bacterial colonization in mouse. However, the deletion oflon, another component of the protein quality control system, or pre-activation ofclpPby expressing artificial disordered protein fragments does not affect the antibiotic tolerance. This suggests that specific targets of ClpP rather than the entire quality control system are critical for persister formation. Our results reveal a convergent metabolic reprogramming in persisters, highlighting the potential to limit the emergence of antibiotic tolerance by counteracting adaptive metabolism elicited by antibiotic treatment.
Local nuclear to cytoplasmic ratio regulates H3.3 incorporation via cell cycle state during zygotic genome activation
Authors: Bhatt Anusha D. , Brown Madeleine G. , Wackford Aurora B. , Shindo Yuki , Amodeo Amanda A. 
Published: July 2024

AbstractEarly embryos often have unique chromatin states prior to zygotic genome activation (ZGA). InDrosophila, ZGA occurs after 13 reductive nuclear divisions during which the nuclear to cytoplasmic (N/C) ratio grows exponentially. Previous work found that histone H3 chromatin incorporation decreases while its variant H3.3 increases leading up to ZGA. In other cell types, H3.3 is associated with sites of active transcription and heterochromatin, suggesting a link between H3.3 and ZGA. Here, we test what factors regulate H3.3 incorporation at ZGA. We find that H3 nuclear availability falls more rapidly than H3.3 leading up to ZGA. We generate H3/H3.3 chimeric proteins at the endogenous H3.3A locus and observe that chaperone binding, but not gene structure, regulates H3.3 behavior. We identify the N/C ratio as a major determinant of H3.3 incorporation. To isolate how the N/C ratio regulates H3.3 incorporation we test the roles of genomic content, zygotic transcription, and cell cycle state. We determine that cell cycle regulation, but not H3 availability or transcription, controls H3.3 incorporation. Overall, we propose that local N/C ratios control histone variant usage via cell cycle state during ZGA.
Crystal structures of lanthanum to 230 GPa
Authors: Storm C. V. , Roy C. R. , Munro K. A. , McMahon M. I. 
Published: July 2024

The structural behavior of lanthanum metal has been investigated up to 227 GPa using synchrotron x-ray diffraction. Rather than having the rhombohedral or orthorhombic structures previously reported to be stable above 80 GPa, we find that La adopts the tetragonal tI2 structure seen previously in Ce and Pr. We show that the recent claims of a rhombohedral structure arose from the misidentification of lanthanum hydride peaks. The revised pressure dependence of the atomic volume of La above 100 GPa further constrains the stoichiometry of the superconducting LaH10 superhydride, which is synthesized from La above 160 GPa.

Published by the American Physical Society
2024
Dynamic Cooling on Contemporary Quantum Computers
Authors: Bassman Oftelie Lindsay , De Pasquale Antonella , Campisi Michele 
Published: July 2024

We study the problem of dynamic cooling whereby a target qubit is cooled at the expense of heating up N−1 further identical qubits by means of a global unitary operation. A standard back-of-the-envelope high-temperature estimate establishes that the target qubit temperature can be dynamically cooled by at most a factor of 1/N. Here we provide the exact expression for the minimum temperature to which the target qubit can be cooled and reveal that there is a crossover from the high initial temperature regime, where the scaling is 1/N, to a low initial temperature regime, where a much faster scaling of 1/N occurs. This slow, 1/N scaling, which was relevant for early high-temperature NMR quantum computers, is the reason dynamic cooling was dismissed as ineffectual around 20 years ago; the fact that current low-temperature quantum computers fall in the fast, 1/N scaling regime, reinstates the appeal of dynamic cooling today. We further show that the associated work cost of cooling is exponentially more advantageous in the low-temperature regime. We discuss the implementation of dynamic cooling in terms of quantum circuits and examine the effects of hardware noise. We successfully demonstrate dynamic cooling in a three-qubit system on a real quantum processor. Since the circuit size grows quickly with N, scaling dynamic cooling to larger systems on noisy devices poses a challenge. We therefore propose a suboptimal cooling algorithm, whereby relinquishing a small amount of cooling capability results in a drastically reduced circuit complexity, greatly facilitating the implementation of dynamic cooling on near-future quantum computers.

Published by the American Physical Society
2024
Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them
Authors: Dalwani Subhadra , Metz Alexander , Huschmann Franziska U. , Weiss Manfred S. , Wierenga Rik K. , Venkatesan Rajaram 
Published: July 2024

The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an α2β2 tetrameric enzyme in which the α-chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) active sites, and the β-chain provides the 3-ketoacyl-CoA thiolase (KAT) active site. Linear, medium-chain and long-chain 2E-enoyl-CoA molecules are the preferred substrates of MtTFE. Previous crystallographic binding and modeling studies identified binding sites for the acyl-CoA substrates at the three active sites, as well as the NAD binding pocket at the HAD active site. These studies also identified three additional CoA binding sites on the surface of MtTFE that are different from the active sites. It has been proposed that one of these additional sites could be of functional relevance for the substrate channeling (by surface crawling) of reaction intermediates between the three active sites. Here, 226 fragments were screened in a crystallographic fragment-binding study of MtTFE crystals, resulting in the structures of 16 MtTFE–fragment complexes. Analysis of the 121 fragment-binding events shows that the ECH active site is the `binding hotspot' for the tested fragments, with 41 binding events. The mode of binding of the fragments bound at the active sites provides additional insight into how the long-chain acyl moiety of the substrates can be accommodated at their proposed binding pockets. In addition, the 20 fragment-binding events between the active sites identify potential transient binding sites of reaction intermediates relevant to the possible channeling of substrates between these active sites. These results provide a basis for further studies to understand the functional relevance of the latter binding sites and to identify substrates for which channeling is crucial.
Familiarity analysis and time-advance experimental study of LP-NGD RC-circuit intended to operate with Unity-normalized gain
Authors: Cui Jun Yan , Silochi Hakim Epea , Wieser1 Robert , Junwen Shi , Bilal Habachi , Ngoho Samuel , Ravelo Blaise 
Published: July 2024

PurposeThe purpose of this paper is to develop a familiarity analysis of resistive-capacitive (RC) network active circuit operating with unfamiliar low-pass (LP) type negative group delay (NGD) behavior. The design method of NGD circuit is validated by simulation with commercial tool and experimental measurement.Design/methodology/approachThe present research work methodology is structured in three main parts. The familiarity theory of RC-network LP-NGD circuit is developed. The LP-NGD circuit parameters are expressed in function of the targeted time-advance. Then, the feasibility study is based on the theory, simulation and measurement result comparisons.FindingsThe RC-network based LP-NGD proof of concept is validated with −1 and −0.5 ms targeted time-advances after design, simulation, test and characterized. The LP-NGD circuit unity gain prototype presents NGD cut-off frequencies of about 269 and 569 Hz for the targeted time-advances, −1 and −0.5 ms, respectively. Bi-exponential and arbitrary waveform signals were tested to verify the targeted time-advance.Research limitations/implicationsThe performance of the unfamiliar LP-NGD topology developed in the present study is limited by the parasitic elements of constituting lumped components.Practical implicationsThe NGD circuit enables to naturally reduce the undesired delay effect from the electronic and communication systems. The NGD circuit can be exploited to reduce the delay induced by electronic devices and system.Social implicationsAs social impacts of the NGD circuit application, the NGD function is one of prominent solutions to improve the technology performances of future electronic device in term of communication aspect and the transportation system.Originality/valueThe originality of the paper concerns the theoretical approach of the RC-network parameters in function of the targeted time-advance and the input signal bandwidth. In addition, the experimental results are also particularly original.
Tackling inventory losses of small accessories in engineering manufacturing: a case study of Euro Manufacturing
Authors: Shaikh Abdul Rehman , Mirani Manzoor Ali , Ali Saqib 
Published: July 2024

Learning outcomes
After completion of the case study, the students will be able to understand ABC analysis and develop a systematic approach using PDCA, analyze processes, technology, employee training and supplier relationships when analyzing shrink and developing solutions, evaluate how technology improves production inventory control and visibility and recognize the importance of fostering a culture of employee accountability and ownership to minimize inventory loss and improve overall operational efficiency.

Case overview/synopsis
On June 2, 2023, sitting in his office in Karachi, Pakistan, Khan Aamir, the manager of store and inventory at Euro Manufacturing, found himself immersed in a cloud of confusion. The incessant loss of inventory items, particularly the nut bolts and small accessories, had become a perplexing challenge. To address these losses and provide a cycle count report to the director of supply chain, Aamir, manager of store and inventory, was given the responsibility to take action. He was looking for a comprehensive approach to address the current problems and prevent further losses in the future. This case study examines the various reasons for the losses, including theft, inadequate inventory control methods, human error and problems with suppliers. It highlights the importance of established procedures, the use of technology (such as barcode scanning, radio-frequency identification tagging and inventory management software) and the cultivation of a culture of accountability among employees.

Complexity academic level
This case study is developed for class discussion in the course of operations management or supply chain management. This case study is suitable for use with undergrad students. This case study can be taught in a module on operations management or supply chain management, as part of a broader course in business management or industrial engineering.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS: 9: Operations and logistics.
Research on the construction and application of a smart library services maturity evaluation system based on CMM
Authors: Bai Zhongxian , Yu Lvna , Zhao Lei , Wang Weijia 
Published: July 2024

Purpose
Smart libraries are the result of the application of smart technologies in the era of digital intelligence. The establishment and improvement of its service evaluation system serve as indicators for evaluating the growth of smart libraries.

Design/methodology/approach
This study introduces and improves the capability maturity model (CMM), creatively constructs a service maturity model specifically designed for smart libraries and combines the Delphi method with the analytic hierarchy process (AHP) to establish a service maturity evaluation system for smart libraries while calculating indicator weights. Finally, two representative smart libraries are selected as case studies, and an empirical application is conducted using the fuzzy comprehensive evaluation method.

Findings
The empirical study shows that the developed smart libraries service maturity evaluation system holds significant theoretical and practical value in evaluating smart libraries.

Originality/value
Enhances the CMM and creatively constructs a service maturity model for smart libraries. Combines the Delphi method with AHP to establish a service maturity evaluation system while calculating indicator weights. Uses a fuzzy comprehensive evaluation method to evaluate two representative smart libraries. Demonstrates that the smart library services maturity evaluation system holds significant theoretical and practical value.