bluuebunny/crossref_metadata_2025 huggingface dataset:
Surgical strategy for atrial functional mitral regurgitation with atrial fibrillation
Authors: Bao Chunrong , Wei Ke , Zhao Dongfang , Zhang Junwen , Mei Ju , Ma Nan
Published: September 2024

Background

With the growing prevalence of atrial fibrillation (AF), atrial functional mitral regurgitation (AFMR) combined with AF is expected to become a common clinical issue. We have summarized various surgical treatment strategies based on the degree of mitral regurgitation (MR) alongside rhythm control therapy for patients with AFMR and AF.

Methods

This retrospective study included 145 patients with AF and MR from January 2017 to January 2023. 33 patients with AF and moderate AFMR were designated as the moderate atrial regurgitation (MAR) group. 56 patients with AF and severe AFMR were designated as the severe atrial regurgitation (SAR) group. The remaining 56 patients with AF and severe primary MR were designated as the severe primary regurgitation (SPR) group. All patients in the MAR group underwent thoracoscopic AF procedure via a unilateral approach. Patients in the SAR and SPR groups underwent mitral valvuloplasty plus the Cox Maze IV procedure (CMP IV). Descriptive characteristics and outcomes were analysed.

Results

Twenty-three patients maintained sinus rhythm (SR) following thoracoscopic AF procedure in the MAR group at average 2.6±1.1 years follow-up. The degree of regurgitation improved in 26 patients, remained unchanged in 6 patients, and worsened in 1 patient. SR maintenance benefits MR reduction (P<0.0001) compared to the non-SR patients. There was no significant difference in the rate of SR maintenance following mitral valvuloplasty plus CMP IV between SAR (43 patients, 79.6%) and SPR (49 patients, 87.5%) groups. At the last follow-up, echocardiography in the SAR group showed 47 cases with no mitral regurgitation, 4 cases with mild regurgitation, and 1 case with moderate regurgitation. The left atrial diameter in the SAR group remained larger than in the SPR group (P<0.001).

Conclusions

Rhythm control therapy is the cornerstone treatment for AFMR patients with AF. Thoracoscopic AF procedure is effective and minimally invasive for moderate AFMR patients with AF. For severe AFMR patients with AF, we recommend CMP IV plus mitral valvuloplasty for safety and effectiveness.
Resource presentation dictates genetic and phenotypic adaptation in yeast
Authors: Ahlawat Neetika , Mahilkar Anjali , Saini Supreet
Published: September 2024

Environments shape adaptive trajectories of populations, often leading to adaptive parallelism in identical, and divergence in different environments. However, how does the likelihood of these possibilities change with minute changes in the environment? In this study, we evolveSaccharomyces cerevisiaein environments which only differed in how sugar source is presented to the population. In one set of populations, carbon was presented as a mixture of glucose-galactose, and in the other, as melibiose, a glucose-galactose disaccharide. Since the two environments only differ in how the two monosaccharides are packaged, we call these environments „synonymous‟. Our results show that subtle changes in environments change the targets of selection between the two sets of evolved populations. However, despite different adaptive responses, pleiotropic effects of adaptation are largely predictable. Genome sequencing results demonstrate that small changes in the environment also strongly dictates the genetic basis of adaptation.
AQP1- A regulatory factor associated with brown adipose tissue-silencing
Authors: Cheng Chloe M , Blay Christopher J , Tsai Pei-Yin , Li Muying , Edwards Kaydine , Qu Yue , Liu Yang , Buettner Nina , Walter Claire , Snyder Mary , Costa Ines PD , Devuyst Olivier , Barrow Joeva J
Published: September 2024

The activation of non-shivering thermogenesis (NST) in brown adipose tissue (BAT) by environmental cold challenge yields strong metabolic benefit in the face of diet-induced obesity (DIO). Yet, a critical barrier to leveraging brown fat NST for therapeutic use against metabolic disease is that BAT is silenced and inactive at physiological ambient temperature conditions in humans. The mechanisms that govern this silencing process remain poorly understood. Here, we identified a putative BAT-silencing factor, aquaporin-1 (AQP1), in brown fat from wild-type (WT) mice via proteomics analysis. We generated the first BAT-specific AQP1 knockout mice (AQP1-KO) and revealed that AQP1-KO could activate NST under BAT silencing environmental conditions and that the AQP1-KO mice were significantly protected against DIO and metabolic dysfunction compared to Flox controls. We found that AQP1-KO mice on high fat diet (HFD) had reduced weight gain through reductions in fat mass, improved glucose tolerance, and increased whole body energy expenditure compared to Flox control mice. Mechanistically, we show that AQP1 ablation in mice had upregulated gene expression related to the electron transport chain (ETC) and mitochondrial translation contributing to the activation of NST under BAT environmental silenced conditions.

Significance Statement

Novel strategies to combat obesity-associated metabolic dysfunction are urgently needed to curb the growing obesity epidemic. Investigation of brown adipose tissue (BAT) silencing mechanisms may reveal novel therapeutic targets that when ablated, can activate BAT to increase energy expenditure and protect subjects against the metabolic dysfunction associated with obesity. We have identified Aquaporin 1 (AQP1) as a putative BAT silencer regulatory factor and show through the generation of the first BAT-specific aquaporin-1 knockout (AQP1-KO) mouse that BAT can be activated under environmental silencing conditions. We further show that these mice are protected against diet-induced obesity, with improved glucose tolerance, and increased energy expenditure. These findings highlight AQP1 as a promising therapeutic target in the emerging research field of BAT silencers.
Cross omics risk scores of inflammation markers are associated with all-cause mortality: The Canadian Longitudinal Study on Aging
Authors: Meir Anat Yaskolka , Yun Huan , Hu Jie , Li Jun , Liu Jiaxuan , Bever Alaina , Ratanatharathorn Andrew , Song Mingyang , Heather Eliassen A. , Chibnik Lori , Koenen Karestan , Pare Guillaume , Stampfer Meir J , Liang Liming
Published: September 2024

Inflammation is a critical component of chronic diseases, aging progression, and lifespan. Omics signatures may characterize inflammation status beyond blood biomarkers. We leveraged genetics (Polygenic-Risk-Score; PRS), metabolomics (Metabolomic-Risk-Score; MRS), and epigenetics (Epigenetic-Risk-Score; ERS) to build multi-omics-multi-marker risk scores for inflammation status represented by the level of circulating C-reactive protein (CRP), interleukin 6 (IL6), and tumor necrosis factor alpha (TNFa). We found that multi-omics risk-scores generally outperformed single-omics risk scores in prediction of all-cause mortality in the Canadian Longitudinal Study on Aging. Compared with circulating inflammation biomarkers, some multi-omics risk scores had a higher HR for all cause-mortality when including both score and circulating IL6 in the same model (1-SD IL6 MRS-ERS: HR=1.77 [1.15-2.72] vs. 1-SD circulating IL6 HR=1.11 [0.75,1.66]; 1-SD IL6 PRS-MRS: HR=1.32 [1.21,1.45] vs. 1-SD circulating IL6 HR=1.31 [1.12, 1.53]; 1-SD PRS-MRS-ERS: HR=1.62 [1.04, 2.53] vs. 1-SD circulating IL6: HR=1.16 [0.77, 1.74]). In the Nurses’ Health Study (NHS), NHS II, and Health Professional Follow-up Study with available omics, 1-SD of IL6 PRS and 1-SD IL6 PRS-MRS had HR=1.13 [1.00,1.27] and HR=1.13 [1.01,1.27], among individuals >65years without mutual adjustment of the score and circulating IL6. Our study demonstrated that some multi-omics scores for inflammation markers may characterize important inflammation burden for an individual beyond those represented by blood biomarkers and improve our prediction capability for aging process and lifespan.
Leveraging the electronic health record to identify delivery of goal-concordant care
Authors: Auriemma Catherine L , Song Anne , Walsh Lake , Han Jason , Yapalater Sophia , Bain Alexander , Haines Lindsay , Scott Stefania , Whitman Casey , Taylor Stephanie P , Weissman Gary E. , Gonzales Matthew J , Weerasinghe Roshanthi , Wendt Staci J , Courtright Katherine R
Published: September 2024

Background

Goal-concordant care (GCC) is recognized as the highest quality of care and most important outcome measure for serious illness research, yet there is no agreed-upon or validated method to measure it.

Objective

Assess feasibility of measuring GCC using clinical documentation in the electronic health record (EHR).

Design

Retrospective chart review study.

Participants

Adults with ≥50% predicted six-month mortality risk admitted to three urban hospitals in a single health system. All participants had goals-of-care (GOC) discussions documented in the EHR 6 months before and 6 months after admission manually classified into one of four categories of goals: (1) comfort-focused, (2) maintain or improve function, (3) life-extension, or (4) unclear.

Main Measures

Pairs of physician-coders independently reviewed EHR notes from 6 months before through 6 months after admission to identify and classify care received between each documented GOC discussion into one of the four goals categories. Epochs between GOC discussions were then coded as goal-concordant if GOC and care received classifications were aligned, goal-discordant if they were misaligned, or uncertain if either classification was unclear or not documented. Coder inter-rater reliability was assessed using kappa statistics.

Key Results

Inter-rater reliability for classifying care received was almost perfect (95% interrater agreement; Cohen’s kappa=0.92; 95% CI, 0.86-0.99). Of 398 total epochs across 109 unique patients, 198 (50%) were goal-concordant, 112 (28%) were of uncertain concordance, and 88 (22%) were goal-discordant. Eighty (73%) patients received care of uncertain concordance during at least one epoch. Forty-eight (44%) patients received goal-discordant care during at least one epoch.

Conclusions

Clinician chart review was a feasible method for measuring GCC and can inform natural language processing and machine learning methods to improve the clinical and research utility of this method. More work is needed to understand the driving factors underlying the high rate of uncertain concordance and goal-discordant care identified among this seriously ill cohort.
Dental health of childhood cancer survivors – a report from the Swiss Childhood Cancer Survivor Study (SCCSS)
Authors: Nigg C , Matti C , Jörger P , von Bueren AO , Filippi C , Diesch-Furlanetto T , Tomášiková Z , Kuehni CE , Sommer G
Published: September 2024

Background

Cancer and its treatments can affect dental health of childhood cancer survivors. We aimed to evaluate prevalence of dental problems in survivors, compare them to their siblings, and investigate cancer-related risk factors.

Methods

As part of the population-based Swiss Childhood Cancer Survivors Study, we sent questionnaires inquiring about dental problems to survivors aged 5-19 years and their siblings. We retrieved cancer-relevant information from the Swiss Childhood Cancer Registry and used logistic regressions to compare dental problems between survivors and siblings and to investigate cancer-related risk factors.

Results

We included 735 survivors and 144 siblings. Almost half of survivors and siblings reported at least one dental problem. Compared to siblings, survivors had a greater risk for hypo- or microdontia (OR 1.7; 95%CI 0.9-3.2) and enamel hypoplasia (2.2; 0.8-6.0), but similar risk for cavities or cavity-related tooth loss (0.8; 0.6-1.3). Chemotherapy was associated with enamel hypoplasia (3.0; 1.2-10.4), cavities or cavity-related tooth loss (1.5; 1.0-2.3), and gum problems during (23.0; 9.4-76.2) and after (4.6; 2.0-13.5) treatment. Hematopoietic stem cell transplantation (HSCT) was related to hypo- or microdontia (5.4; 2.6-10.7), cavities or cavity-related tooth loss (2.1; 1.2-3.6), and gum problems during treatment (2.0; 1.2-3.6). For hypo- or microdontia and cavities, associations with treatment were driven by patients diagnosed <5 years.

Conclusion

Childhood cancer patients treated with chemotherapy or HSCT, especially at a young age, were at higher risk for dental problems. Regular dental check-ups guided by healthcare teams and dental hygiene habits can mitigate risks and promote survivor’s long-term dental health.
Assessment of effectiveness of ‘Nilee Vyema brochure’ on knowledge of breastfeeding, kangaroo mother care and hygiene practice among mothers in central Tanzania. A quasi experiment study protocol
Authors: Ngeze Shimwe Amos , Ntwenya Julius , Mongi Richard
Published: September 2024

Background

Prematurity is a challenge affecting child health worldwide and mothers who are the sole care providers of preterm infants post discharge must possess the necessary knowledge to be able to properly care for their preterm infant at home.

Objective

The main objective of this study will be to assess the effectiveness ofNILEE VYEMAbrochure on knowledge of breastfeeding, kangaroo care and hygiene among mothers with preterm infants in central Tanzania. A sample of 112 mothers with preterm infants will be recruited from two randomly selected regional hospitals in central Tanzania in 2024. A quasi pre-test post-test experimental design will be used and theNilee Vyemabrochure will be adapted from several literatures. Both the control group and intervention group will be given the pretest questionnaire to assess baseline knowledge. The control group will receive routine education lecture based on breastfeeding, kangaroo mother care and hygiene topics while the intervention group will receive both routine education in conjunction with theNilee Vyemabrochure. Interventional sessions will include lectures on breastfeeding, kangaroo mother care and hygiene to influence the knowledge and skills of these mothers in caring for their preterm. After the intervention, both groups will be given the pretest questionnaire which will assess end-line knowledge.

Analysis

Data will be analyzed using SPSS (version 20) for descriptive statistics to describe the characteristics of the study samples and inferential statistics to test the effectiveness of the brochure before and after intervention. Furthermore, chi-square test will be used to describe the relationship between categorical variables at p < 0.05.
An integrative analysis of cell-specific transcriptomics and nuclear proteomics of sleep-deprived mouse cerebral cortex
Authors: Jha Pawan K. , Valekunja Utham K. , Reddy Akhilesh B.
Published: September 2024

Sleep regulation follows a homeostatic pattern. The mammalian cerebral cortex is the repository of homeostatic sleep drive and neurons and astrocytes of the cortex are principal responders of sleep need. The molecular mechanisms by which these two cell types respond to sleep loss are not yet clearly understood. By combining cell-type specific transcriptomics and nuclear proteomics we investigated how sleep loss affects the cellular composition and molecular profiles of these two cell types in a focused approach. The results indicate that sleep deprivation regulates gene expression and nuclear protein abundance in a cell-type-specific manner. Our integrated multi-omics analysis suggests that this distinction arises because neurons and astrocytes employ different gene regulatory strategies under accumulated sleep pressure. These findings provide a comprehensive view of the effects of sleep deprivation on gene regulation in neurons and astrocytes.
Hyperexcitability precedes CA3 hippocampal neurodegeneration in a dox-regulatable TDP-43 mouse model of ALS-FTD
Authors: Rodemer William , Ra Irene , Jia Elizabeth , Gujral Jaskeerat , Zhang Bin , Hoxha Kevt’her , Xing Bo , Mehta Sanya , Farag Madona , Porta Silvia , Jensen Frances E. , Talos Delia M. , Lee Virginia M.-Y.
Published: September 2024

Neuronal hyperexcitability is a hallmark of amyotrophic lateral sclerosis (ALS) but its relationship with the TDP-43 aggregates that comprise the predominant pathology in over 90% of ALS cases remains unclear. Emerging evidence in tissue and slice culture models indicate that TDP-43 pathology induces neuronal hyperexcitability suggesting it may be responsible for the excitotoxicity long believed to be a major driver of ALS neuron death. Here, we characterized hyperexcitability and neurodegeneration in the hippocampus of doxycycline-regulatable rNLS8 mice (NEFH-tTA x tetO-hTDP-43ΔNLS), followed by treatment with AAV encoded DREADDs and anti-seizure medications to measure the effect on behavioral function and neurodegeneration. We found that approximately half of the CA3 neurons in the dorsal hippocampus are lost between 4 and 6 weeks after TDP-43ΔNLS induction. Neurodegeneration was preceded by selective hyperexcitability in the mossy fiber – CA3 circuit, leading us to hypothesize that glutamate excitotoxicity may be a significant contributor to neurodegeneration in this model. Interestingly, hippocampal injection of AAV encoded inhibitory DREADDs (hM4Di) and daily activation with CNO ligand rescued anxiety deficits on elevated zero maze (EZM) but did not reduce neurodegeneration. Therapeutic doses of the anti-seizure medications, valproic acid and levetiracetam, did not improve behavior or prevent neurodegeneration. These results highlight the complexity of TDP-43 - induced alterations to neuronal excitability and suggest that whereas targeting hyperexcitability can meliorate some behavioral deficits, it may not be sufficient to halt or slow neurodegeneration in TDP-43-related proteinopathies.

Significance Statement

Cytoplasmic aggregates of TAR DNA Binding Protein 43 (TDP-43) are the predominant pathology in over 90% of Amyotrophic lateral sclerosis (ALS) and the majority of frontotemporal lobar degeneration (FTLD-TDP) cases. Understanding how TDP-43 pathology promotes neurodegeneration may lead to therapeutic strategies to slow disease progression in humans. Recent reports in mouse and cell culture models suggest loss-of-normal TDP-43 function may drive neuronal hyperexcitability, a key physiological hallmark of ALS and possible contributor to neurodegeneration. In this study, we identified region-specific hyperexcitability that precedes neurodegeneration in the inducible rNLS8 TDP-43 mouse model. Suppressing hyperexcitability with chemogenetics improved behavioral function but did not reduce hippocampal neuron loss. Anti-seizure medications had no beneficial effects suggesting directly targeting hyperexcitability may not be therapeutically effective.
BrainScale: Enabling Scalable Online Learning in Spiking Neural Networks
Authors: Wang Chaoming , Dong Xingsi , Jiang Jiedong , Ji Zilong , Liu Xiao , Wu Si
Published: September 2024

Spiking neural networks (SNNs) have been recognized as a key approach for studying brain functions and realizing neuromorphic intelligence. However, a critical obstacle hindering their widespread application is the lack of a scalable online learning algorithm capable of supporting large-scale training of complex brain dynamics over behavioral timescales. Existing training algorithms are either limited to offline learning [46], impeding behavioral task training; constrained by high memory complexity [8, 6], hindering network scaling; or use oversimplified models [82] that fail to capture the intricate brain dynamics. Here, we introduceBrainScale, which achieves scalable online learning in SNNs across three levels. First,BrainScaleaccommodates the complex brain dynamics by supporting a wide spectrum of SNNs through a streamlined abstraction of synaptic interactions. Second, leveraging the inherent properties of SNNs,BrainScalesimplifies the full gradient computation, realizing an online learning algorithm with linear memory complexity. Finally,BrainScaleprovides a program compiler that enables automatic derivation and execution of online learning computations for any user-defined model. Comprehensive evaluations demonstrate that compared to existing methods,BrainScalenot only enables unprecedented complex and large-scale SNN training over behavioral timescales, but also generates more biologically realistic neural activity and synaptic connectivity in brain simulation models, as well as achieves comparable or even superior performance in neuromorphic tasks. These results highlight the potential ofBrainScale-powered SNN online learning for widespread applications in brain simulation and neuromorphic computing.
Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition
Authors: Zelasko Susan , Swaney Mary-Hannah , Suh Won Se , Sandstrom Shelby , Carlson Caitlin , Cagnazzo Julian , Golfinos Athena , Fossen Jen , Andes David , Kalan Lindsay R. , Safdar Nasia , Currie Cameron R.
Published: September 2024

The oral microbiome has been understudied as a reservoir for clinical pathogens, including drug-resistant strains. Understanding how alterations in microbiome functioning render this site vulnerable to colonization is essential, as multidrug-resistant organisms (MDRO) carriage is a major risk factor for developing serious infections. To advance our knowledge of oral MDRO carriage and protection against pathogen colonization conferred by native microbiota, we examined microbiomes from individuals colonized by MDROs (n=33) and non-colonized age-matched controls (n=30). Shotgun metagenomic analyses of oral swabs from study participants revealed significant differences in microbial communities with depletion ofStreptococcusspp. among those colonized by multidrug-resistant gram-negative bacilli (RGNB), compared to non-carriers. We utilized metagenomic sequencing to characterize the oral resistome and find antimicrobial resistance genes are present in higher abundance among RNGB carriers versus non-carriers. High-throughput co-culture screening revealed oral bacteria isolated from MDRO non-carriers demonstrate greater inhibition of gram-negative pathogens, compared to isolates from carriers. Moreover, biosynthetic gene clusters from streptococci are found in higher abundance from non-carrier microbiomes, compared to RGNB carrier microbiomes. Bioactivity-guided fractionation of extracts fromStreptococcusisolate SID2657 demonstrated evidence of strongE. coliandA. baumanniiinhibition in a murine model of infection. Together, this provides evidence that oral microbiota shape this dynamic microbial community and may serve as an untapped source for much-needed antimicrobial small-molecules.
Stimulating the regenerative capacity of the human retina with proneural transcription factors in 3D cultures
Authors: Wohlschlegel Juliette , Kierney Faith , Arakelian Kayla L. , Luxardi Guillaume , Suvarnpradip Naran , Hoffer Dawn , Rieke Fred , Moshiri Ala , Reh Thomas A.
Published: September 2024

Retinal diseases often lead to degeneration of specific retinal cell types with currently limited therapeutic options to replace the lost neurons. Previous studies have reported that overexpression of ASCL1 or combinations of proneural factors in Müller glia (MG) induces regeneration of functional neurons in the adult mouse retina. Recently, we applied the same strategy in dissociated cultures of fetal human MG and although we stimulated neurogenesis from MG, our effect in 2D cultures was modest and our analysis of newborn neurons was limited. In this study, we aimed to improve our MG reprogramming strategy in a more intact retinal environment. For this purpose, we used an in vitro culture system of human fetal retinal tissue and adult human postmortem retina. To stimulate reprogramming, we used lentiviral vectors to deliver constructs with a glial-specific promoter (HES1) driving ASCL1 alone or in combination with additional developmental transcription factors such as ATOH1 and NEUROD1. Combining IHC, scRNA-seq and electrophysiology, we show for the first time that human MG can generate new neurons even in adults. This work constitutes a key step towards a future clinical application of this regenerative medicine approach for retinal degenerative disorders.
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions
Authors: Zdimal Amanda M. , Dio Giacomo Di , Liu Wanxiang , Aftab Tanya , Collins Taryn , Colin Remy , Shrivastava Abhishek
Published: September 2024

The bacterial Type 9 Secretion System (T9SS) is essential for the development of periodontal diseases and Bacteroidetes gliding motility. T9SS-driven motile bacteria, abundant within the human oral microbiota, transport non-motile oral microbes and bacteriophages as cargo, shaping the spatial structure of polymicrobial communities. However, the physical rules governing the dispersal of T9SS-driven bacterial swarms are barely understood. Here, we collected time-lapse images, under anaerobic conditions, of developing swarms of a T9SS-driven microbe common to the human oral microbiota. Tracking of swarms revealed that small peripheral flares emerging from a colony develop structures that resemble fireworks displaying a chrysanthemum effect and flower-like patterns that convert to wave-like patterns and which further evolve into scattered microcolonies. Particle-image velocimetry showed density-dependent phase transitions and initial vorticity within these emerging patterns. Numerical simulations demonstrate that these patterns arise due to changes in swarm speed and alignment strength. Our data reveal a strategy used by an anaerobic swarming bacterium to control swarm behavior, resulting in scattered microcolonies distant from the mother colony, thus reducing competition for resources among colony members. This might ensure species survival even if conditions change drastically in one location of the human oral cavity.
Modeling protein-small molecule conformational ensembles with ChemNet
Authors: Anishchenko Ivan , Kipnis Yakov , Kalvet Indrek , Zhou Guangfeng , Krishna Rohith , Pellock Samuel J. , Lauko Anna , Lee Gyu Rie , An Linna , Dauparas Justas , DiMaio Frank , Baker David
Published: September 2024

Modeling the conformational heterogeneity of protein-small molecule systems is an outstanding challenge. We reasoned that while residue level descriptions of biomolecules are efficient for de novo structure prediction, for probing heterogeneity of interactions with small molecules in the folded state an entirely atomic level description could have advantages in speed and generality. We developed a graph neural network called ChemNet trained to recapitulate correct atomic positions from partially corrupted input structures from the Cambridge Structural Database and the Protein Data Bank; the nodes of the graph are the atoms in the system. ChemNet accurately generates structures of diverse organic small molecules given knowledge of their atom composition and bonding, and given a description of the larger protein context, and builds up structures of small molecules and protein side chains for protein-small molecule docking. Because ChemNet is rapid and stochastic, ensembles of predictions can be readily generated to map conformational heterogeneity. In enzyme design efforts described here and elsewhere, we find that using ChemNet to assess the accuracy and pre-organization of the designed active sites results in higher success rates and higher activities; we obtain a preorganized retroaldolase with akcat/KMof 11000 M-1min- 1, considerably higher than any pre-deep learning design for this reaction. We anticipate that ChemNet will be widely useful for rapidly generating conformational ensembles of small molecule and small molecule-protein systems, and for designing higher activity preorganized enzymes.
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads
Authors: Han Seong Woo , Jewell San , Thomas-Tikhonenko Andrei , Barash Yoseph
Published: September 2024

Mapping transcriptomic variations using either short- or long-read RNA sequencing is a staple of genomic research. Long reads are able to capture entire isoforms and overcome repetitive regions, whereas short reads still provide improved coverage and error rates. Yet, open questions remain, such as how to quantitatively compare the technologies, can we combine them, and what is the benefit of such a combined view? We tackle these questions by first creating a pipeline to assess matched long- and short-read data using a variety of transcriptome statistics. We find that across data sets, algorithms, and technologies, matched short-read data detects ∼30% more splice junctions, such that ∼10%–30% of the splice junctions included at ≥20% by short reads are missed by long reads. In contrast, long reads detect many more intron-retention events and can detect full isoforms, pointing to the benefit of combining the technologies. We introduce MAJIQ-L, an extension of the MAJIQ software, to enable a unified view of transcriptome variations from both technologies and demonstrate its benefits. Our software can be used to assess any future long-read technology or algorithm and can be combined with short-read data for improved transcriptome analysis.
Ferri-ionic coupling in
CuInP2S6
nanoflakes: Polarization states and controllable negative capacitance
Authors: Morozovska Anna N. , Kalinin Sergei V. , Eliseev Eugene A. , Kopyl Svitlana , Vysochanskii Yulian M. , Evans Dean R.
Published: September 2024

We consider nanoflakes of van der Waals ferrielectric CuInP2S6 covered by an ionic surface charge and reveal the appearance of polar states with a relatively large polarization of approximately 5 µC/cm2 and stored free charge of around 10 µC/cm2, which can mimic “midgap” states associated with a surface-field-induced transfer of Cu and/or In ions in the van der Waals gap. The change in the ionic screening degree and mismatch strains induce a broad range of the transitions between paraelectric phase, antiferroelectric, ferrielectric, and ferri-ionic states in CuInP2S6 nanoflakes. The states’ stability and/or metastability is determined by the minimum of the system free energy consisting of electrostatic energy, elastic energy, and a Landau-type four-well potential of the ferrielectric dipole polarization. The possibility of governing the transitions by strain and ionic screening can be useful for controlling the tunneling barrier in thin-film devices based on CuInP2S6 nanoflakes. Additionally, we predict that the CuInP2S6 nanoflakes reveal features of the controllable negative capacitance effect, which make them attractive for advanced electronic devices, such as nanocapacitors and gate oxide nanomaterials with reduced heat generation.

Published by the American Physical Society
2024
Stability and dynamics of magnetic skyrmions in FM/AFM heterostructures
Authors: Cheenikundil Rajgowrav , Lu Zhiwei , Pereiro Manuel , Delin Anna , Thonig Danny
Published: September 2024

Magnetic skyrmions have garnered attention for their potential roles in spintronic applications, such as information carriers in computation, data storage, and nano-oscillators due to their small size, topological stability, and the requirement of small electric currents to manipulate them. Two key challenges in harnessing skyrmions are the stabilization requirement through a strong out-of-plane field, and the skyrmion Hall effect (SkHE). Here, we present a systematic model study of skyrmions in ferromagnetic/antiferromagnetic (FM/AFM) multilayer structures by employing both atomistic Monte Carlo and atomistic spin dynamics simulations. We demonstrate that skyrmions stabilized by exchange bias have superior stability to field-stabilized skyrmions due to the formation of a magnetic imprint within the AFM layer. Additionally, stacking two skyrmion hosting FM layers between two AFM layers suppresses the SkHE and enables the transport of AFM-coupled skyrmions with high velocity in the order of a few km/s. This proposed multilayer configuration could serve as a pathway to overcome existing limitations in the development of skyrmion-based devices, and the insights obtained through this study contribute significantly to the broader understanding of topological spin textures in magnetic materials.

Published by the American Physical Society
2024
Predicting possible molecular states of nucleons with
Ξc
,
Ξc*
, and
Ξc′
Authors: Huo Jin-Yu , Sheng Li-Cheng , Chen Rui , Liu Xiang
Published: September 2024

In the framework of a one-boson-exchange model, we carry out a comprehensive investigation of the ΞcN/ΛcΣ/Ξc′N/ΣcΛ/Ξc*N/Σc*Λ/ΣcΣ/Σc*Σ interactions. We consider the

S

−

D

-wave mixing effects and the coupled-channel effects to derive the relevant effective potentials. Our results can predict several possible charm-strange deuteronlike Ξc(′,*)N hexaquarks, the Ξc′N molecules with I(IP)=0(0+), 0(1+), 1(1+), the Ξc*N molecules with 0(1+), 0(2+), 1(2+), and the coupled ΞcN/Ξc′N/Ξc*N/ΣcΣ/Σc*Σ molecule with 0(1+). We expect the experiments to search for our predictions of the Ξc(′,*)N bound states.

Published by the American Physical Society
2024
Testing the equivalence between the planar Gross-Neveu and Thirring models at
N=1
Authors: Martins Everlyn , Gomes Y. M. P. , Pinto Marcus Benghi , Ramos Rudnei O.
Published: September 2024

It is known that the Fierz identities predict that the Gross-Neveu and Thirring models should be equivalent when describing systems composed of a single fermionic flavor, N=1. Here, we consider the planar version of both models within the framework of the optimized perturbation theory at the two-loop level, in order to verify if the predicted equivalence emerges explicitly when different temperature and density regimes are considered. At vanishing densities, our results indicate that both models indeed describe exactly the same thermodynamics, provided that N=1. However, at finite chemical potentials we find that the N=1 Fierz equivalence no longer holds. After examining the relevant thermodynamic potentials, we have identified the contributions which lead to this puzzling discrepancy. Finally, we discuss different frameworks in which this (so far open) problem could be further understood and eventually circumvented.

Published by the American Physical Society
2024
Odd-derivative couplings in heterotic theory
Authors: Garousi Mohammad R.
Published: September 2024

In this paper, our focus is on exploring the gauge-invariant basis for bosonic couplings within the framework of heterotic string theories, specifically examining three-, five-, and seven-derivative terms. We thoroughly analyze the invariance of these couplings under T-duality transformations and make a notable observation: the T-duality constraint enforces the vanishing of these couplings. We speculate that this result likely holds true for all higher odd-derivative couplings as well. This is unlike the result in type I superstring theory, where, for example, the couplings of five Yang-Mills field strengths are nonzero. The vanishing of couplings is consistent with the O(d,d+16) symmetry of the cosmological reduction of the effective action.

Published by the American Physical Society
2024
Dose increment in ultrashort particle irradiations via coherent stopping power
Authors: Curcio Alessandro , Gatti Giancarlo , Volpe Luca , Chiadroni Enrica , Migliorati Mauro , Mostacci Andrea , Palumbo Luigi , Petrarca Massimo
Published: September 2024

We present a relativistic self-consistent theory of the coherent stopping power (CSP) of ultradense charged particle beams propagating in a dense matter. CSP corresponds to a collective inelastic collision which adds to the ordinary stopping power of individual particles. Unlike the latter, which depends only on the particles' energy, CSP depends upon many more parameters such as the total charge of the ensemble and its charge density and shape. This paves the way for a broad variety of novel methods to tailor particle absorption and penetration in a dense matter. CSP losses can be explained both by collective excitations of single or multiple molecules and by the emission of coherent Cherenkov radiation. Here we demonstrate that the former mechanism is more relevant than the latter. We find that the coherent energy absorption of subpicosecond particle bunches in water occurs exciting a broad Debye process in the GHz range and an intermolecular stretching vibration mode in the THz region. We generalize the Bethe-Bloch stopping power formula to coherent effects including self-forces, dielectric screening, and absorption by the dense matter. For the sake of a self-consistent dynamical theory including phase space evolution, we have also generalized the Fermi-Eyges theory of particle diffusion to the presence of forces. Nonlinear dynamics is demonstrated, inducing nonlinear dose release, beam self-focusing, and self-enhancement of coherent losses. Given the advent of ultraintense particle sources and their use for biomedical and other relevant applications, our results may be of paramount importance for contemporary and future developments of science and technology.

Published by the American Physical Society
2024
Quantum Many-Body Spin Ratchets
Authors: Zadnik Lenart , Ljubotina Marko , Krajnik Žiga , Ilievski Enej , Prosen Tomaž
Published: September 2024

Introducing a class of SU(2) invariant quantum unitary circuits generating chiral transport, we examine the role of broken space-reflection and time-reversal symmetries on spin-transport properties. Upon adjusting parameters of local unitary gates, the dynamics can be either chaotic or integrable. The latter corresponds to a generalization of the space-time discretized (Trotterized) higher-spin quantum Heisenberg chain. We demonstrate that breaking of space-reflection symmetry results in a drift in the dynamical spin susceptibility. Remarkably, we find a universal drift velocity given by a simple formula, which, at zero average magnetization, depends only on the values of SU(2) Casimir invariants associated with local spins. In the integrable case, the drift velocity formula is confirmed analytically based on the exact solution of thermodynamic Bethe ansatz equations. Finally, by inspecting the large fluctuations of the time-integrated current between two halves of the system in stationary maximum-entropy states, we demonstrate violation of the Gallavotti-Cohen symmetry, implying that such states cannot be regarded as equilibrium ones. We show that the scaled cumulant generating function of the time-integrated current instead obeys a generalized fluctuation relation.

Published by the American Physical Society
2024
Unpacking synergistic dynamics between corporate governance and CSR – the role of stakeholder salience
Authors: Ledi Klenam Korbla , Ameza-Xemalordzo Enya Besa , Mensah Henry Kofi
Published: September 2024

Purpose

This study delves into the mediating role of corporate social responsibility (CSR) in the relationship between corporate governance and firm performance while simultaneously considering stakeholder salience as a crucial boundary condition that modulates both the influence of corporate governance on CSR adoption and the impact of CSR on firm performance.

Design/methodology/approach

A quantitative approach was adopted, utilising a survey questionnaire to gather data from 315 manufacturing firms. The collected data were analysed using partial least squares and structural equation modelling was used to test the hypotheses.

Findings

The study demonstrated a direct positive relationship between corporate governance and firm performance as well as an indirect positive effect mediated by corporate social responsibility. Furthermore, the study uncovered a robust positive correlation between corporate governance and CSR, strengthened by a high level of stakeholder salience.

Practical implications

Firms should consider CSR initiatives not only as ethical endeavours but also as strategic tools for enhancing performance in conjunction with sound governance practices.

Originality/value

The study goes beyond individual impacts of CSR and corporate governance on firm performance to dissect and analyse the dynamics of corporate governance and CSR interaction and how they synergistically stimulate firm performance. The study also acknowledges the complex and dynamic nature of stakeholder relationships by recognising that the effectiveness of corporate governance and CSR may be contingent on the perceived importance of stakeholders, thereby providing fresh insights into the corporate management puzzle.
Using machine learning to forecast clean energy, commodities, green bonds and ESG index prices: How important is financial stress?
Authors: Soltani Hayet , Taleb Jamila , Ben Hamadou Fatma , Boujelbène-Abbes Mouna
Published: September 2024

Purpose

This study investigates clean energy, commodities, green bonds and environmental, social and governance (ESG) index prices forecasting and assesses the predictive performance of various factors on these asset prices, used for the development of a robust forecasting support decision model using machine learning (ML) techniques. More specifically, we explore the impact of the financial stress on forecasting price.

Design/methodology/approach

We utilize feature selection techniques to evaluate the predictive efficacy of various factors on asset prices. Moreover, we have developed a forecasting model for these asset prices by assessing the accuracy of two ML models: specifically, the deep learning long short-term memory (LSTM) neural networks and the extreme gradient boosting (XGBoost) model. To check the robustness of the study results, the authors referred to bootstrap linear regression as an alternative traditional method for forecasting green asset prices.

Findings

The results highlight the significance of financial stress in enhancing price forecast accuracy, with the financial stress index (FSI) and panic index (PI) emerging as primary determinants. In terms of the forecasting model's accuracy, our analysis reveals that the LSTM outperformed the XGBoost model, establishing itself as the most efficient algorithm among the two tested.

Practical implications

This research enhances comprehension, which is valuable for both investors and policymakers seeking improved price forecasting through the utilization of a predictive model.

Originality/value

To the authors' best knowledge, this marks the inaugural attempt to construct a multivariate forecasting model. Indeed, the development of a robust forecasting model utilizing ML techniques provides practical value as a decision support tool for shaping investment strategies.
Leadership internal communication and employee creativity; role of symmetrical communication, employee advocacy and proactive personality
Authors: Khalid Jamshed , Mi Chuanmin , Ashraf Muhammad Umair , Islam Md Shamimul
Published: September 2024

Purpose

This study aims to examine the relationship between managerial supportive communication, CEO relational communication and symmetrical internal communication. It specifically investigates the mediating role of symmetrical internal communication and employee advocacy, as well as the moderating influence of proactive personality on the link between employee advocacy and employee creativity.

Design/methodology/approach

A survey was conducted involving 290 full-time employees, and a Partial Least Square Structural Equation Modeling (PLS-SEM) statistical approach was used to assess the proposed relationships.

Findings

Both managerial supportive communication and CEO relational communication were found to be positively associated with symmetrical internal communication. Furthermore, results indicated that symmetrical internal communication and employee advocacy acted as strong mediators in the hypothesized relationships. Notably, the study also found that the impact of employee advocacy on employee creativity was significantly amplified in cases where employees exhibited a higher degree of proactive personality.

Practical implications

By emphasizing managerial supportive communication, enhancing CEO relational communication and promoting symmetrical internal communication and employee advocacy, organizations can create an environment conducive to innovation and creativity among employees. Additionally, recognizing the buffering effect of proactive personality on employee advocacy's impact on creativity enables organizations to better tailor their strategies for fostering creativity.

Originality/value

This research presents a novel contribution to the field by exploring the less-explored relationships between these critical communication factors and employee creativity. It uncovers the mediating and moderating mechanisms, shedding new light on how internal communication dynamics influence creativity. This unique approach provides an original perspective on the role of communication in promoting creativity at workplace.
Fire messaging: a qualitative exploration of how adults teach children about fire
Authors: Horsley Faye , Birrell Emily , Gouldthorp Grace , Kohli Danisha , McLackland Faith , Taylor Ellie
Published: September 2024

Purpose

Research indicates that children’s early experience of fire can influence what and how they learn about fire. In turn, early fire-learning can influence how people come to use it later in life, including whether they engage in maladaptive use, i.e. firesetting. Little is known about the underlying mechanisms of fire-learning, which was the basis for this study. The research question was: “how do adults educate children about fire in the UK/ Ireland”? The purpose of this study was to explore the child fire education process from an adult perspective.

Design/methodology/approach

Semi-structured interviews was conducted with 21 fire-educators who had regular contact with children. Data was analysed using abbreviated grounded theory. Steps were taken to ensure reliability and validity, including a Cohen’s Kappa calculation, indicating an agreement level of 0.9 between two raters.

Findings

Four core themes were identified: the fire narrative, enabling growth, risk management, and communication, from which the fire-learning process model (F-LPM) was formed.

Research limitations/implications

The main limitation is the nature of the sample, in that it was diverse and self-selecting.

Practical implications

The findings are discussed, including how they offer support for social learning theory (SLT) perspectives on fire-learning.

Social implications

The social construction of fire (i.e. the way fire is viewed by society as a whole in the UK/ Ireland) is discussed in depth, and cultural variability is highlighted. Suggestions are made for how the societal view of fire and, consequently, how adults convey this to young people, could be better balanced.

Originality/value

To the best of the authors’ knowledge, this is the first study in the UK/ Ireland to consider how adults educate young people about fire from a concurrent perspective. This is important given that research indicates early experiences of fire can impact how people later go on to use it (including maladaptive use in the form of firesetting).
War Captivity as a Contact Zone: The Case of British Prisoners of War on Parole in Napoleonic France
Authors: DUCHÉ ELODIE
Published: September 2024

The existing scholarship on Napoleonic captivity tends to focus on French prisoners of war held in Britain at the time. This article seeks to help redress this gap by drawing upon a range of English and French sources to investigate how British captives on parole experienced displacement in Napoleonic France during up to eleven years of their lives, between 1803 and 1814. The multifaceted relations that prisoners developed with residents and fellow captives offer important nuances for our understanding of Franco‐British relations during the period. They also provide an insight into how war captivity formed a ‘contact zone’ amidst the conflict. Through this case study, the article highlights that the notion of ‘contact zone’ can provide a helpful framework to further conceptualise histories of prisoner of war experience, even beyond the Napoleonic Wars.