bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting COVID-19 cases across a large university campus using complementary built environment and wastewater surveillance approaches
Authors: Hinz Aaron , Moggridge Jason A. , Ke Hanna , Hicks Alexandra M. A. , Doukhanine Evgueni , Fralick Michael , Hug Laura , MacFadden Derek , Mejbel Hebah , Nott Caroline , Raudanskis Ashley , Thampi Nisha , Wong Alex , Kassen Rees
Published: January 2024

Background

Environmental surveillance of SARS-CoV-2 via wastewater has become an invaluable tool for population-level surveillance. Built environment sampling may provide complementary spatially-refined detection for viral surveillance in congregate settings such as universities.

Methods

We conducted a prospective environmental surveillance study at the University of Ottawa between September 2021 and April 2022. Floor surface samples were collected twice weekly from six university buildings. Samples were analyzed for the presence of SARS-CoV-2 using RT-qPCR. A Poisson regression was used to model the campus-wide COVID-19 cases predicted from the fraction of floor swabs positive for SARS-CoV-2 RNA, building CO2levels, Wi-Fi usage, and SARS-CoV-2 RNA levels in regional wastewater. We used a mixed-effects Poisson regression analysis to model building-level cases using viral copies detected in floor samples as a predictor. A random intercepts logistic regression model tested whether floor samples collected in high-traffic areas were more likely to have SARS-CoV-2 present than low-traffic areas.

Results

Over the 32-week study period, we collected 554 floor swabs at six university buildings. Overall, 13% of swabs were PCR-positive for SARS-CoV-2, with positivity ranging between 4.8% and 32.7% among university buildings. Both floor swab positivity (Spearman r = 0.74, 95% CI: 0.53-0.87) and regional wastewater signal (Spearman r = 0.50, 95% CI: 0.18-0.73) were positively correlated with on-campus COVID-19 cases. In addition, built environment detection was a predictor of cases linked to individual university buildings (IRlog10(copies)+1= 17, 95% CI: 7-44). There was no significant difference in detection between floors sampled in high-traffic versus low-traffic areas (OR = 1.3, 95% CI: 0.8-2.1).

Conclusions

Detection of SARS-CoV-2 RNA on floors and viral RNA levels found in wastewater were strongly associated with the incidence of COVID-19 cases on a university campus. These data suggest a potential role for institutional built environment sampling, used together with wastewater surveillance, for predicting COVID-19 cases at both campus-wide and building level scales.
Plxnd1-mediated mechanosensing of blood flow controls the caliber of the Dorsal Aorta via the transcription factor Klf2
Authors: He Jia , Blazeski Adriana , Nilanthi Uthayanan , Menéndez Javier , Pirani Samuel C. , Levic Daniel S. , Bagnat Michel , Singh Manvendra K. , Raya José G , García-Cardeña Guillermo , Torres-Vázquez Jesús
Published: January 2024

The cardiovascular system generates and responds to mechanical forces. The heartbeat pumps blood through a network of vascular tubes, which adjust their caliber in response to the hemodynamic environment. However, how endothelial cells in the developing vascular system integrate inputs from circulatory forces into signaling pathways to define vessel caliber is poorly understood. Using vertebrate embryos andin vitro-assembled microvascular networks of human endothelial cells as models, flow and genetic manipulations, and custom software, we reveal that Plexin-D1, an endothelial Semaphorin receptor critical for angiogenic guidance, employs its mechanosensing activity to serve as a crucial positive regulator of the Dorsal Aorta’s (DA) caliber. We also uncover that the flow-responsive transcription factor KLF2 acts as a paramount mechanosensitive effector of Plexin-D1 that enlarges endothelial cells to widen the vessel. These findings illuminate the molecular and cellular mechanisms orchestrating the interplay between cardiovascular development and hemodynamic forces.

Highlights

Plexin-D1 mechanosensing of blood flow tunes the caliber of the Dorsal Aorta (DA)

The DA widens without raising endothelial cell numbers, which can change separate from the caliber

The Kruppel-like transcription factor 2 (KLF2) is a key Plexin-D1 mechano-effector during development

KLF2 increases endothelial cell size to expand the DA caliber
The effect of semantic content on the perception of audiovisual movieclips
Authors: Kesoglou Anastasia Maria , Mikellidou Kyriaki
Published: January 2024

Our brain is skilled with the ability to perceive and process multimodal stimuli. This process known as crossmodal perceptual integration, has been in the research spotlight for a long time, providing evidence for the integration of information coming from different modalities. Prior research mostly utilized pictures and focused on the semantic content of a single sound or word. The present study aims to investigate crossmodal perceptual integration in realistic conditions using short movieclips (1500ms) and auditory meaningful three-word sentences to evaluate target detection in terms of accuracy and response times. Two experimental tasks were developed using PsychoPy, where participants had to indicate whether a target (noun for Experiment 1, verb for Experiment 2) was present or absent. In trials without a target, target-related information was always present, either through one of the two senses (vision or audition; incongruent condition) or through both senses (congruent condition). We observed superior performance when the target was absent generally (Mexp1=93.9%, SDexp1=0.04, Mexp2=84.2%, SDexp2=0.182) compared to when it was present (Mexp1=82.3%, SDexp1=0.143, Mexp2=73.7%, SDexp2=0.184). Moreover, superior performance was noted in incongruent target-related movieclips, which significantly decreased during congruent target-related movieclips. In Experiment 1, we observed that in the audio condition when the target-related word was a noun, participant performance was superior compared to when it was a verb (M=99.4% vs. M=86.7%; tincVerb vs. incNoun=-8.428, p=.001). In Experiment 2, the judgment scores were similarly high in incongruent movieclips and significantly lower in congruent ones regardless of whether the target-related information presented was a verb or noun. The present results provide evidence regarding the role of complexity of semantics, and especially the diverse role verbs and nouns could play in crossmodal perceptual integration in more realistic situations. Our findings can enrich the content of learning techniques, as well as the design of AI models, by taking advantage of the supporting role of semantic audiovisual information, while taking into consideration the potential confusion that the complexity of semantic information can induce to perception experience.
Interferon-γas a Potential Inhibitor of SARS-CoV-2 ORF6 Accessory Protein
Authors: Krachmarova Elena , Petkov Peicho , Lilkova Elena , Stoynova Dayana , Malinova Kristina , Hristova Rossitsa , Gospodinov Anastas , Ilieva Nevena , Nacheva Genoveva , Litov Leandar
Published: January 2024

ORF6 protein of the SARS-CoV-2 virus plays a crucial role in blocking the innate immune response of the infected cells by inhibiting interferon pathways. Additionally, it binds and immobilises the RAE1 protein onto the cytoplasmic membranes, thereby blocking the transport of mRNA from the nucleus to the cytoplasm. In all these cases the host cell proteins are tethered by the flexible C-terminus of ORF6. A possible strategy to inhibit the biological activity of ORF6 is to bind its C-terminus with suitable ligands. Our in silico experiments suggest that hIFNγbinds the ORF6 protein with high affinity, thus impairing its interactions with RAE1 and, consequently, its activity in viral invasion. The here reported in vitro studies reveal a shift of the localization of RAE1 in ORF6 overexpressing cells upon treatment with hIFNγfrom predominantly cytoplasmic to mainly nuclear, resulting in restoration of the export of mRNA from the nucleus. We also explored the expression of GFP in transfected with ORF6 cells by means of fluorescence microscopy and qRT-PCR, finding that treatment with hIFNγunblocks the mRNA trafficking and reinstates the GFP expression level. The ability of the cytokine to block ORF6 is also reflected in minimising its negative effects on DNA replication by reducing accumulated RNA-DNA hybrids. Our results, therefore, suggest hIFNγas a promising inhibitor of the most toxic SARS-CoV-2 protein.
Wnt7a is Required for Regeneration of Dystrophic Skeletal Muscle
Authors: Gurriaran-Rodriguez Uxia , Kodippili Kasun , Datzkiw David , Javandoost Ehsan , Xiao Fan , Rejas Maria Teresa , Rudnicki Michael A.
Published: January 2024

Intramuscular injection of Wnt7a has been shown to accelerate and augment skeletal muscle regeneration and to ameliorate dystrophic progression inmdxmuscle, a model for Duchenne muscular dystrophy (DMD). However, loss-of-function studies to investigate the requirement for Wnt7a in muscle regeneration has not been evaluated. Here, we assessed muscle regeneration and function in wild type (WT) andmdxmice where Wnt7a was specifically deleted in muscle using a conditionalWnt7afloxed allele and aMyf5-Credriver. We found that both WT andmdxmice with deletion of Wnt7a in muscle, exhibited marked deficiencies in muscle regeneration at 21 d following cardiotoxin (CTX) induced injury. Unlike WT, deletion of Wnt7a inmdxresulted in a marked decrease in specific force generation prior to CTX injury. However, both WT andmdxmuscle lacking Wnt7a displayed decreased specific force generation following CTX injection. Notably the regeneration deficit observed inmdxmice lacking Wnt7a in muscle was rescued by a single tail vein injection of an extracellular vesicle preparation containing Wnt7a (Wnt7a-EVs). Therefore, we conclude that the regenerative capacity of muscle inmdxmice is due to the upregulation of endogenous Wnt7a following injury, and that systemic delivery of Wnt7a-EVs represents a therapeutic strategy for treating DMD.
Diverse Database and Machine Learning Model to Narrow the Generalization Gap in RNA Structure Prediction
Authors: de Lajarte Albéric A. , Martin des Taillades Yves J. , Kalicki Colin , Fuchs Wightman Federico , Aruda Justin , Salazar Dragui , Allan Matthew F. , L’Esperance-Kerckhoff Casper , Kashi Alex , Jossinet Fabrice , Rouskin Silvi
Published: January 2024

Understanding macromolecular structures of proteins and nucleic acids is critical for discerning their functions and biological roles. Advanced techniques—crystallography, NMR, and CryoEM—have facilitated the determination of over 180,000 protein structures, all cataloged in the Protein Data Bank (PDB). This comprehensive repository has been pivotal in developing deep learning algorithms for predicting protein structures directly from sequences. In contrast, RNA structure prediction has lagged, and suffers from a scarcity of structural data. Here, we present the secondary structure models of 1098 pri-miRNAs and 1456 human mRNA regions determined through chemical probing. We develop a novel deep learning architecture, inspired from the Evoformer model of Alphafold and traditional architectures for secondary structure prediction. This new model, eFold, was trained on our newly generated database and over 300,000 secondary structures across multiple sources. We benchmark eFold on two new test sets of long and diverse RNA structures and show that our dataset and new architecture contribute to increasing the prediction performance, compared to similar state-of-the-art methods. All together, our results reveal that merely expanding the database size is insufficient for generalization across families, whereas incorporating a greater diversity and complexity of RNAs structures allows for enhanced model performance.
Herpes Simplex Virus-1 targets the 2’-3’cGAMP importer SLC19A1 as an antiviral countermeasure
Authors: Szemere Zsuzsa K. , Murphy Eain A.
Published: January 2024

To establish a successful infection, herpes simplex virus-1 (HSV-1), a virus with high seropositivity in the human population, must undermine host innate and intrinsic immune defense mechanisms, including the stimulator of interferon genes (STING) pathway. Recently it was discovered that not onlyde novoproduced intracellular 2’-3’cGAMP, but also extracellular 2’-3’cGAMP activates the STING pathway by being transported across the cell membrane via the folate transporter, SLC19A1, the first identified extracellular antiporter of this signaling molecule. We hypothesized that the import of exogenous 2’-3’cGAMP functions to establish an antiviral state like that seen with the paracrine antiviral activities of interferon. Further, to establish a successful infection, HSV-1 must undermine this induction of the STING pathway by inhibiting the biological functions of SLC19A1. Herein, we report that treatment of the monocytic cell line, THP-1 cells, epithelial cells (ARPE-19) and SH-SY5Y neuronal cell line with exogenous 2’-3’cGAMP induces interferon production and establishes an antiviral state. Using either pharmaceutical inhibition or genetic knockout of SLC19A1 blocks the 2’-3’cGAMP-induced antiviral state. Additionally, HSV-1 infection results in the reduction of SLC19A1 transcription, translation, and importantly, the rapid removal of SLC19A1 from the cell surface of infected cells. Our data indicate SLC19A1 functions as a newly identified antiviral mediator for extracellular 2’-3’cGAMP which is undermined by HSV-1. This work presents novel and important findings about how HSV-1 manipulates the host’s immune environment for viral replication and discovers details about an antiviral mechanism which information could aid in the development of better antiviral drugs in the future.

Importance

HSV-1 has evolved multiple mechanisms to neutralize of the host’s innate and intrinsic defense pathways, such as the STING pathway. Here, we identified an antiviral response in which extracellular 2’-3’cGAMP triggers IFN production via its transporter SLC19A1. Moreover, we report that HSV-1 blocks the functions of this transporter thereby impeding the antiviral response, suggesting exogenous 2’-3’cGAMP can act as an immunomodulatory molecule in uninfected cells to activate the STING pathway, and priming an antiviral state, similar to that seen in interferon responses. The details of this mechanism highlight important details about HSV-1 infections. This work presents novel findings about how HSV-1 manipulates the host’s immune environment for viral replication and reveals details about a novel antiviral mechanism. These findings expand our understanding of how viral infections undermine host responses and may help in the development of better broad based antiviral drugs in the future.
The diverse viromes of Australian lizards are shaped by host taxonomy and habitat
Authors: Mahar Jackie E. , Wille Michelle , Harvey Erin , Moritz Craig C. , Holmes Edward C.
Published: January 2024

Lizards inhabit diverse ecologies and evolutionary histories and hence represent a promising group to explore how hosts shape virome structure and virus evolution. Yet little is known about the viromes of these animals. In Australia, squamates (lizards and snakes) comprise the most diverse order of vertebrates, and Australia hosts the highest diversity of lizards globally, with the greatest breadth of habitat use. We used meta-transcriptomic sequencing to determine the virome of nine co-distributed, tropical lizard species from three taxonomic families in Australia and analyzed these data to identify host traits associated with viral abundance and diversity. We show that lizards carry a large diversity of viruses, identifying more than 30 novel, highly divergent vertebrate-associated viruses. These viruses were from nine viral families, including several that contain well known pathogens, such as theFlaviviridae,Picornaviridae,Bornaviridae, IridoviridaeandRhabdoviridae. Members of theFlaviviridaewere particularly abundant across species sampled here, largely belonging to the genusHepacivirus: 14 novelHepaciviruseswere identified, broadening the known diversity of this group and better defining its evolution by uncovering new reptilian clades. The evolutionary histories of the viruses studied here frequently aligned with the biogeographic and phylogenetic histories of the hosts, indicating that exogenous viruses may help infer host evolutionary history if sampling is strategic and sampling density high enough. Notably, analysis of alpha and beta diversity revealed that virome composition and richness was shaped by host taxonomy, habitat and range size. In sum, we identified a diverse range of reptile viruses that broadly contributes to our understanding of virus-host ecology and evolution.
Superspreading of SARS-CoV-2: a systematic review and meta-analysis of event attack rates and individual transmission patterns
Authors: McKee Clifton D. , Yu Emma X. , Garcia Andrés , Jackson Jules , Koyuncu Aybüke , Rose Sophie , Azman Andrew S. , Lobner Katie , Sacks Emma , Van Kerkhove Maria D. , Gurley Emily S.
Published: January 2024

SARS-CoV-2 superspreading occurs when transmission is highly efficient and/or an individual infects many others, contributing to rapid spread. To better quantify heterogeneity in SARS-CoV-2 transmission, particularly superspreading, we performed a systematic review of transmission events with data on secondary attack rates or contact tracing of individual index cases published before September 2021, prior to emergence of variants of concern and widespread vaccination. We reviewed 592 distinct events and 9,883 index cases from 491 papers. Meta-analysis of secondary attack rates identified substantial heterogeneity across 12 chosen event types/settings, with the highest transmission (25–35%) in co-living situations including households, nursing homes, and other congregate housing. Among index cases, 67% produced zero secondary cases and only 3% (287) infected >5 secondary cases (“superspreaders”). Index case demographic data was limited, with only 55% of individuals reporting age, sex, symptoms, real-time PCR cycle threshold values, or total contacts. With the data available, we identified a higher percentage of superspreaders among symptomatic individuals, individuals aged 49–64 years, and individuals with over 100 total contacts. Addressing gaps in reporting on transmission events and contact tracing in the literature is needed to properly explain heterogeneity in transmission and facilitate control efforts for SARS-CoV-2 and other infections.
Probing a neural unreliability account of auditory sensory processing atypicalities in Rett Syndrome
Authors: Brima Tufikameni , Beker Shlomit , Prinsloo Kevin D. , Butler John S. , Djukic Aleksandra , Freedman Edward G. , Molholm Sophie , Foxe John J.
Published: January 2024

Background

In the search for objective tools to quantify neural function in Rett Syndrome (RTT), which are crucial in the evaluation of therapeutic efficacy in clinical trials, recordings of sensory-perceptual functioning using event-related potential (ERP) approaches have emerged as potentially powerful tools. Considerable work points to highly anomalous auditory evoked potentials (AEPs) in RTT. However, an assumption of the typical signal-averaging method used to derive these measures is “stationarity” of the underlying responses – i.e. neural responses to each input are highly stereotyped. An alternate possibility is that responses to repeated stimuli are highly variable in RTT. If so, this will significantly impact the validity of assumptions about underlying neural dysfunction, and likely lead to overestimation of underlying neuropathology. To assess this possibility, analyses at the single-trial level assessing signal-to-noise ratios (SNR), inter-trial variability (ITV) and inter-trial phase coherence (ITPC) are necessary.

Methods

AEPs were recorded to simple 100Hz tones from 18 RTT and 27 age-matched controls (Ages: 6-22 years). We applied standard AEP averaging, as well as measures of neuronal reliability at the single-trial level (i.e. SNR, ITV, ITPC). To separate signal-carrying components from non-neural noise sources, we also applied a denoising source separation (DSS) algorithm and then repeated the reliability measures.

Results

Substantially increased ITV, lower SNRs, and reduced ITPC were observed in auditory responses of RTT participants, supporting a “neural unreliability” account. Application of the DSS technique made it clear that non-neural noise sources contribute to overestimation of the extent of processing deficits in RTT. Post-DSS, ITV measures were substantially reduced, so much so that pre-DSS ITV differences between RTT and TD populations were no longer detected. In the case of SNR and ITPC, DSS substantially improved these estimates in the RTT population, but robust differences between RTT and TD were still fully evident.

Conclusions

To accurately represent the degree of neural dysfunction in RTT using the ERP technique, a consideration of response reliability at the single-trial level is highly advised. Non-neural sources of noise lead to overestimation of the degree of pathological processing in RTT, and denoising source separation techniques during signal processing substantially ameliorate this issue.
Mdivi-1 affects neuronal activity by inhibition of Complex I and respiratory supercomplex assembly
Authors: Marx Nico , Ritter Nadine , Disse Paul , Seebohm Guiscard , Busch Karin B.
Published: January 2024

Several human diseases, including cancer and neurodegeneration, are associated with excessive mitochondrial fragmentation. In this context, mitochondrial division inhibitor (Mdivi-1) has been tested as a therapeutic to block the fission-related protein dynamin-like protein-1 (Drp1). Recent studies suggest that Mdivi-1 interferes with mitochondrial bioenergetics. Here we show that the molecular mechanism of Mdivi-1 is based on inhibition of complex I at the IQ site. This leads to the destabilization of complex I, impairs the assembly of N- and Q-respirasomes and is associated with increased ROS production. The result is a reduced efficiency of ATP generation. Second, the calcium homeostasis of cells is impaired, which severely affects the electrical activity of neurons. Given the results presented here, a potential therapeutic application of Mdivi-1 is challenging because of its impact on synaptic activity. Similar to the Complex I inhibitor rotenone, Mdivi-1 may lead to neurodegenerative effects in the long term.

Graphical abstract

Mdivi-1 inhibits respiratory complex I at the IQ-site

Inhibition destabilizes complex I and reduces supercomplex formation

Mitochondrial ATP levels decrease

Ca2+metabolism is affected

Neuronal activity is compromised
Tracking exocytic vesicle movements reveals the spatial control of secretion in epithelial cells
Authors: Richens Jennifer H. , Dmitrieva Mariia , Zenner Helen L. , Muschalik Nadine , Butler Richard , Glashauser Jade , Camelo Carolina , Luschnig Stefan , Munro Sean , Rittscher Jens , St Johnston Daniel
Published: January 2024

Understanding how specific secretory cargoes are targeted to distinct domains of the plasma membrane in epithelial cells requires analysing the trafficking of post-Golgi vesicles to their sites of secretion. We used the RUSH (retention using selective hooks) system to synchronously release an apical cargo, Cadherin 99C (Cad99C), and a basolateral cargo, the ECM protein Nidogen, from the endoplasmic reticulum and follow their movements to the plasma membrane. We also developed an interactive vesicle tracking framework, MSP-tracker and viewer, that exploits developments in computer vision and deep learning to determine vesicle trajectories in a noisy environment without the need for extensive training data. MSP-tracker outperformed other tracking software in detecting and tracking post-Golgi vesicles, revealing that Cad99c vesicles predominantly move apically with a mean speed of 1.1µm/sec. This is reduced to 0.85 µm/sec by a dominant slow dynein mutant, demonstrating that dynein transports Cad99C vesicles to the apical cortex. Furthermore, both the dynein mutant and microtubule depolymerisation cause lateral Cad99C secretion. Thus, microtubule organisation plays a central role in targeting apical secretion, suggesting thatDrosophiladoes not have distinct apical versus basolateral vesicle fusion machinery. Nidogen vesicles undergo planar-polarised transport to the leading edge of follicle cells as they migrate over the ECM, whereas most Collagen is secreted at trailing edges. The follicle cells therefore bias secretion of different ECM components to opposite sides of the cell, revealing that the secretory pathway is more spatially organised than previously thought.
Spatial Lipidomics Maps Brain Alterations Associated with Mild Traumatic Brain Injury
Authors: Leontyev Dmitry , Pulliam Alexis N. , Ma Xin , Gaul David A. , LaPlaca Michelle C. , Fernandez Facundo M.
Published: January 2024

Traumatic brain injury (TBI) is a global public health problem with 50-60 million incidents per year, most of which are considered mild (mTBI) and many of these repetitive (rmTBI). Despite their massive implications, the pathologies of mTBI and rmTBI are not fully understood, with a paucity of information on brain lipid dysregulation following mild injury event(s). To gain more insight on mTBI and rmTBI pathology, a non-targeted spatial lipidomics workflow utilizing ultrahigh resolution mass spectrometry imaging was developed to map brain region-specific lipid alterations in rats following injury. Discriminant multivariate models were created for regions of interest including the hippocampus, cortex, and corpus callosum to pinpoint lipid species that differentiated between injured and sham animals. A multivariate model focused on the hippocampus region differentiated injured brain tissues with an area under the curve of 0.994 using only four lipid species. Lipid classes that were consistently discriminant included polyunsaturated fatty acid-containing phosphatidylcholines (PC), lysophosphatidylcholines (LPC), LPC-plasmalogens (LPC-P) and PC potassium adducts. Many of the polyunsaturated fatty acid-containing PC and LPC-P selected have never been previously reported as altered in mTBI. The observed lipid alterations indicate that neuroinflammation, oxidative stress and disrupted sodium-potassium pumps are important pathologies that could serve to explain cognitive deficits associated with rmTBI. Therapeutics which target or attenuate these pathologies may be beneficial to limit persistent damage following a mild brain injury event.
Yellow and oxidation-resistant derivatives of a monomeric superfolder GFP
Authors: Valbuena Fernando M. , Krahn Adam H. , Tokamov Sherzod A. , Greene Annie C. , Fehon Richard G. , Glick Benjamin S.
Published: January 2024

Fluorescent proteins (FPs) are essential tools in biology. The utility of FPs depends on their brightness, photostability, efficient folding, monomeric state, and compatibility with different cellular environments. Despite the proliferation of available FPs, derivatives of the originally identifiedAequorea victoriaGFP often show superior behavior as fusion tags. We recently generated msGFP2, an optimized monomeric superfolder variant ofA. victoriaGFP. Here, we describe two derivatives of msGFP2. The monomeric variant msYFP2 is a yellow superfolder FP with high photostability. The monomeric variant moxGFP2 lacks cysteines but retains significant folding stability, so it works well in the lumen of the secretory pathway. These new FPs are useful for common imaging applications.
CDK-4 regulates nucleolar size and metabolism at the cost of late-life fitness inC. elegans
Authors: Webster Rachel , Quintana Maria , Kafri Ran , Derry W Brent
Published: January 2024

An outstanding question in biology concerns mechanisms of size control in organs, cells, and organelles. Size impacts metabolic efficiency, surface area-to-volume ratio, and environmental adaptation, which are all required for optimal function. Cyclin-dependent kinase 4 (CDK4), traditionally recognized for its role in cell cycle progression, has gained increasing support for cell cycle-independent roles. Previously, we described a mechanism of cell size control involving a CDK4 and p38 MAPK circuitry that dictates target cell size. In this study, we target the CDK4/6 ortholog CDK-4 in the nematode wormCaenorhabditis elegansto describe functional consequences of changing biological sizein vivo. Our data suggest that CDK-4 regulates nucleolar size and anabolic metabolism independent from cell cycle progression. When size and metabolism are increased, we report enhanced thermotolerance early in life but accelerated aging and reduced longevity late in life, suggesting a novel function of CDK-4 in somatic maintenance and organism health.
The Protection Motivation Theory as an explanatory model for Intention to use Alcohol Protective Behavioral Strategies among Young Adults
Authors: González-Ponce Bella M. , Carmona-Márquez José , Pilatti Angelina , Díaz-Batanero Carmen , Fernández-Calderón Fermín
Published: January 2024

Aims

This study aimed to prospectively examine the explanatory value of the Protection Motivation Theory (PMT) for the intention to use MD PBS, and to explore its invariance across genders

Method

A targeted sampling procedure was used to recruit 339 young adults in the community (Meanage= 21.1;SD= 2.21; female = 50.7%) who completed baseline and 2-month follow-up measures of the constructs of the PMT and for intentions to use each of the five MD PBS.

Results

The results of regression analyses revealed that the coping appraisal components (response efficacy and self-efficacy) had greater explanatory power for intention to use PBS than the threat appraisal components (perceived vulnerability and perceived severity). Perceived vulnerability to alcohol consequences was not prospectively associated with any specific behavioral intention or with the total MD PBS score. In contrast, perceived severity was prospectively associated with the intention to use three out of five PBS and the total MD score. Regression coefficients showed gender invariance for all six models.

Conclusions

Our findings suggest that interventions aimed at promoting motivation to use alcohol PBS among young adults could benefit the most from including components that promote self- efficacy to use PBS and the perceived usefulness of PBS for reducing alcohol-related consequences.

Short Summary

This study has shown that the coping appraisal components of Protection Motivation Theory have greater explanatory value than threat appraisal components for motivation to use Alcohol Protective Behavioral Strategies related to manner of drinking among young adults who use alcohol. Likewise, the results of this model were invariant across genders.
Cortical representational geometry of diverse tasks reveals subject-specific and subject-invariant cognitive structures
Authors: Nakai Tomoya , Kubo Rieko , Nishimoto Shinji
Published: January 2024

The variability in brain function forms the basis for our uniqueness. Prior studies indicate smaller individual differences and larger inter-subject correlation (ISC) in sensorimotor areas than in the association cortex. These studies, deriving information from brain activity, leave individual differences in cognitive structures based on task similarity relations unexplored. This study quantitatively evaluates these differences by integrating ISC, representational similarity analysis, and vertex-wise encoding models using functional magnetic resonance imaging across 25 cognitive tasks. ISC based on cognitive structures enables subject identification with 100% accuracy using at least 14 tasks. ISC is larger in the fronto-parietal association and higher-order visual cortices, suggesting subject-invariant cognitive structures in these regions. Principal component analysis reveals different cognitive structure configurations within these regions. This study provides new evidence of individual variability and similarity in abstract cognitive structures.
Functional brain adaptations during speech processing in 4-month-old bilingual infants
Authors: Blanco Borja , Molnar Monika , Arrieta Irene , Caballero-Gaudes César , Carreiras Manuel
Published: January 2024

Language learning is influenced by both neural development and environmental experiences. This work investigates the influence of early bilingual experience on the neural mechanisms underlying speech processing in 4-month-old infants. We study how an early environmental factor such as bilingualism interacts with neural development by comparing monolingual and bilingual infants’ brain responses to speech. We used functional near-infrared spectroscopy (fNIRS) to measure 4-month-old Spanish-Basque bilingual and Spanish monolingual infants’ brain responses while they listened to forward (FW) and backward (BW) speech stimuli in Spanish. We reveal distinct neural signatures associated with bilingual adaptations, including increased engagement of bilateral inferior frontal and temporal regions during speech processing in bilingual infants, as opposed to left hemispheric specialization observed in monolingual infants. This study provides compelling evidence of bilingualism-induced brain adaptations during speech processing in infants as young as four months. These findings emphasize the role of early language experience in shaping neural plasticity during infancy suggesting that bilingual exposure at this young age profoundly influences the neural mechanisms underlying speech processing.

Research Highlights

This research sheds light on the intricate relationship between language learning, neural maturation, and environmental factors in early infancy.

Bilingual infants exhibit unique functional brain adaptations during speech processing as early as 4 months of age.

This study underscores the critical role of language experience in shaping the developing brain.

These findings have implications for our understanding of language acquisition and neuroplasticity in infants growing up in bilingual environments.
Employing quasidegenerate optical modes for chiral sensing
Authors: Almousa S. F. , Weiss T. , Muljarov E. A.
Published: January 2024

Chiral molecules cannot be superposed with their own mirror image. This yields two enantiomers of opposite handedness that are made out of the same building blocks, but interact differently with their environment. Hence, chiral sensing is of utmost importance for biology, chemistry, and life sciences. However, the impact of the handedness and chirality is very weak in most sensing schemes. Nevertheless, it has been demonstrated recently that chirality may result in strong coupling between resonant states with high quality factors. This is achieved by spectrally overlapping two quasibound states in the continuum in a periodic array of nanostructures. We demonstrate that this requires neither quasibound states in the continuum nor periodic arrays, which is exemplified for three achiral systems: a sphere with equal permittivity and permeability, a single core-shell structure, and a dielectric metasurface. For such achiral systems, we have shown previously that isolated resonant states exhibit a quadratic energy shift in the Pasteur parameter. However, for quasidegenerate states, we observe, using the rigorous resonant-state expansion and full-wave simulations, a linear energy shift and linear splitting in the presence of a chiral medium or molecule. Thus, the splitting is more sensitive to low concentrations of chiral molecules, which paves the way for novel chiral sensing schemes.

Published by the American Physical Society
2024
Robust macroscopic Schrödinger's cat on a nucleus
Authors: Gupta Pragati , Vaartjes Arjen , Yu Xi , Morello Andrea , Sanders Barry C.
Published: January 2024

We propose a scheme to generate spin cat states, i.e., superpositions of maximally separated quasiclassical states on a single high-dimensional nuclear spin in a solid-state device. We exploit a strong quadrupolar nonlinearity to drive the nucleus significantly faster than usual gate sequences, achieving collapses and revivals two orders of magnitude faster than the dephasing timescale. Furthermore, these states are engineered without entanglement with an ancilla, hence, are robust against error propagation. With our multitone control, we can realize arbitrary high-spin rotations within an experimentally feasible regime, as well as transform a spin coherent state to a spin cat state using only phase modulation, opening the possibility of storing and manipulating high-fidelity cat states.

Published by the American Physical Society
2024
Unified topological characterization of electronic states in spin textures from noncommutative
K
-theory
Authors: Lux Fabian R. , Ghosh Sumit , Prass Pascal , Prodan Emil , Mokrousov Yuriy
Published: January 2024

The nontrivial topology of spin systems such as skyrmions in real space can promote complex electronic states. Here, we provide a general viewpoint at the emergence of topological spectral gaps in spin systems based on the methods of noncommutative K-theory. By realizing that the structure of the observable algebra of spin textures is determined by the algebraic properties of the noncommutative torus, we arrive at a unified understanding of topological electronic states which we predict to arise in various noncollinear setups. The power of our approach lies in an ability to categorize emergent topological states algebraically without referring to smooth real- or reciprocal-space quantities. This opens a way towards an educated design of topological phases in aperiodic, disordered, or nonsmooth textures of spins and charges containing topological defects.

Published by the American Physical Society
2024
Local enhancement in transient absorption spectroscopy by gating the resonance in the time domain
Authors: He Yu , Ott Christian , Pfeifer Thomas , Gaarde Mette B.
Published: January 2024

The concept of resonant perfect absorption, enabled by the combined action of pulse propagation and an auxiliary gate pulse, was recently proposed and demonstrated in a group of two-level systems [Y. He , ]. Here we exploit this method in a more realistic scenario by solving the coupled time-dependent Schrödinger equation and the Maxwell wave equation in helium. Through emptying the population of the 1s2p excited state after its excitation, we explore the evolution of the spectral profile with time delay and propagation distance and link the observations to the controlled interference between the original field and the gated new field. We find that resonant absorption for higher-lying states can also be strongly enhanced, in spite of the congestion of multiple resonances and the presence of complex laser-induced couplings. Our results show that interferometric control of absorption using intense laser fields can be applied selectively in both the temporal and spatial domains.

Published by the American Physical Society
2024
Observing quantum matter-wave diffraction in the energetic
He2+-He
collisions
Authors: Siddiki Md Abul Kalam Azad , Mukherjee Jibak , Kumar Kamal , Tőkési Károly , Misra Deepankar , Agueny Hicham
Published: January 2024

We present an experiment combined with numerical simulations to study single and double electron capture processes induced during the collisions between the He target and the He2+ projectile in the energy range 2–20 keV/u. According to our experimental observations, measuring the angular distribution of the scattered projectile He2+ reveals a clear oscillatory structure. The latter records an imprint of the collision dynamics, specifically, a signature of the matter-wave scattering and the internal electronic structure of the collisional system He2+-He. We found that this feature is sensitive to the incident projectile's energy and the nature of the involved process. With the help of four-body semiclassical close coupling and classical trajectory Monte Carlo methods, we show that the observed structure is of a quantum nature. This is further supported by a simple mathematical model based on Fraunhofer-type diffraction of light, to which the oscillations are attributed. Our findings thus provide insights into the role of quantum phenomena in characterizing collision dynamics.

Published by the American Physical Society
2024
Quantum Sensing in Tweezer Arrays: Optical Magnetometry on an Individual-Atom Sensor Grid
Authors: Schäffner Dominik , Schreiber Tobias , Lenz Fabian , Schlosser Malte , Birkl Gerhard
Published: January 2024

We implement a scalable platform for quantum sensing comprising hundreds of sites capable of holding individual laser-cooled atoms and demonstrate the applicability of this single-quantum-system sensor array to magnetic field mapping on a two-dimensional grid. With each atom being confined in an optical tweezer within an area of 0.5μm2 at mutual separations of 7.0(2)μm, we obtain micrometer-scale spatial resolution and highly parallelized operation. An additional steerable optical tweezer allows rearrangement of atoms within the grid and enables single-atom scanning microscopy with submicron resolution. This individual-atom sensor platform finds an immediate application in mapping an externally applied dc gradient magnetic field. In a Ramsey-type measurement, we obtain a field resolution of 98(29) nT. We estimate the sensitivity to be 25μT/Hz.

Published by the American Physical Society
2024
Refinement of X-ray and electron diffraction crystal structures using analytical Fourier transforms of Slater-type atomic wavefunctions in Olex2
Authors: Kleemiss Florian , Peyerimhoff Norbert , Bodensteiner Michael
Published: January 2024

An implementation of Slater-type spherical scattering factors for X-ray and electron diffraction for elements in the range Z = 1–103 is presented within the software Olex2. Both high- and low-angle Fourier behaviour of atomic electron density and electrostatic potential can thus be addressed, in contrast to the limited flexibility of the four Gaussian plus constant descriptions which are currently the most widely used method for calculating atomic scattering factors during refinement. The implementation presented here accommodates the increasing complexity of the electronic structure of heavier elements by using complete atomic wavefunctions without any interpolation between precalculated tables or intermediate fitting functions. Atomic wavefunctions for singly charged ions are implemented and made accessible, and these show drastic changes in electron diffraction scattering factors compared with the neutral atom. A comparison between the two different spherical models of neutral atoms is presented as an example for four different kinds of X-ray and two electron diffraction structures, and comparisons of refinement results using the existing diffraction data are discussed. A systematic but slight improvement in R values and residual densities can be observed when using the new scattering factors, and this is discussed relative to effects on the atomic displacement parameters and atomic positions, which are prominent near the heavier elements in a structure.
JUAMI, the joint undertaking for an African materials institute: building materials science research collaborations and capabilities between continents
Authors: Billinge Simon J. L.
Published: January 2024

JUAMI, the joint undertaking for an African materials institute, is a project to build collaborations and materials research capabilities between PhD researchers in Africa, the United States, and the world. Focusing on research-active universities in the East African countries of Kenya, Ethiopia, Tanzania and Uganda, the effort has run a series of schools focused on materials for sustainable energy and materials for sustainable development. These bring together early-career researchers from Africa, the US, and beyond, for two weeks in a close-knit environment. The program includes lectures on cutting-edge research from internationally renowned speakers, highly interactive tutorial lectures on the science behind the research, also from internationally known researchers, and hands-on practicals and team-building exercises that culminate in group proposals from self-formed student teams. The schools have benefited more than 300 early-career students and led to proposals that have received funding and have led to research collaborations and educational non-profits. JUAMI continues and has an ongoing community of alumni who share resources and expertise, and is open to like-minded people who want to join and develop contacts and collaborations internationally.
A triclinic polymorph of miconazole
Authors: Kaspiaruk Hanna , Chęcińska Lilianna
Published: January 2024

The crystal structure of the new triclinic polymorph of miconazole {MIC; C18H14Cl4N2O; systematic name: (RS)-1-[2-(2,4-dichlorobenzyloxy)-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole} is reported and compared with the monoclinic form of solvent-free miconazole previously reported [Kaspiaruk & Chęcińska (2022). Acta Cryst. C78, 343–350]. A comparison shows a different orientation of imidazole and one dichlorophenyl ring between polymorphic molecules. In the crystal structure of the title compound, only weak halogen bonds and C—H...π(arene) interactions are found. Hirshfeld surface analysis and energy framework calculations complement the comparison of the two polymorphic forms of the miconazole drug.
Crystal structure and Hirshfeld surface analysis of (2E)-1-phenyl-3-(1H-pyrrol-2-yl)propen-1-one
Authors: Safarova Ayten S. , Khalilov Ali N. , Akkurt Mehmet , Maharramov Abel M. , Bhattarai Ajaya , Naghiyev Farid N. , Mamedov İbrahim G.
Published: January 2024

The title compound, C13H11NO, adopts an E configuration about the C=C double bond. The pyrrole ring is inclined to the phenyl ring at an angle of 44.94 (8)°. In the crystal, molecules are linked by N—H...O hydrogen bonds, forming ribbons parallel to (020) in zigzag C(7) chains along the a axis. These ribbons are connected via C—H...π interactions, forming a three-dimensional network. No significant π–π interactions are observed.
(S)-(+)-1-(4-Bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine and bis{(S)-(+)-1-(4-bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine-κN}dichloridopalladium(II)
Authors: Anzaldo Bertin , Moreno Morales Gloria E. , Villamizar C. Claudia P. , Mendoza Ángel , Hernández Téllez Guadalupe
Published: January 2024

The (S)-(+)-1-(4-bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine ligand, C16H16BrNO, (I), was synthesized through the reaction of 4-methoxyanisaldehyde with (S)-(−)-1-(4-bromophenyl)ethylamine. It crystallizes in the orthorhombic space group P212121 belonging to the Sohncke group, featuring a single molecule in the asymmetric unit. The refinement converged successfully, achieving an R factor of 0.0508. The PdII complex bis{(S)-(+)-1-(4-bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine-κN}dichloridopalladium(II), [PdCl2(C16H16BrNO)2], (II), crystallizes in the monoclinic space group P21 belonging to the Sohncke group, with two molecules in the asymmetric unit. The central atom is tetracoordinated by two N atoms and two Cl atoms, resulting in a square-planar configuration. The imine moieties exhibit a trans configuration around the PdII centre, with average Cl—Pd—N angles of approximately 89.95 and 90°. The average distances within the palladium complex for the two molecules are ∼2.031 Å for Pd—N and ∼2.309 Å for Pd—Cl.