bluuebunny/crossref_metadata_2025 huggingface dataset:
Benefits of a Dual-Task Training on Motor and Cognitive Functions in Community-Dwelling Older Adults
Authors: Scarmagnan Gabriella Simões , Lino Tayla Borges , Pimentel Daniel Espindola , Silva Ana Victoria Borges , da Silva Ramos Isabelly Martina , Christofoletti Gustavo
Published: October 2023

Objective

The aim of the study is to verify the effects of a 3-mo dual-task training on motor and cognitive functions in community-dwelling older adults.

Design

In this prospective, single-blinded, controlled clinical trial, a total of 40 participants were allocated to either the experimental or the control (no-exercise) group. The intervention program consisted of a combination of motor and cognitive exercises conducted twice a week on nonconsecutive days. The main outcome measures were postural stability, mobility, fear of falling, and cognitive functions. Multiple analyses of variance were used to assess the impact of the dual-task training. Effect sizes (η2p) were reported. Significance was set at 5%.

Results

Compared with the control group, participants who underwent the dual-task training showed positive outcomes in terms of postural stability (η2p = 0.298, P = 0.020), mobility (η2p = 0.285, P = 0.003), and cognitive functions (η2p = 0.536, P = 0.001). No significant differences were observed between the groups in terms of the fear of falling (P = 0.566).

Conclusions

Three-month dual-task training was beneficial for postural control, mobility, and cognitive functions in community-dwelling older adults. Based on the present findings, healthcare professionals should consider incorporating dual-task training into clinical practice.
Tenacibaculum bernardetii sp. nov., isolated from Atlantic salmon (Salmo salar L.) cultured in Chile
Authors: Avendaño-Herrera Ruben , Saldarriaga-Córdoba Mónica , Irgang Rute
Published: October 2023

Strain PVT-9aT, a novel Gram-stain-negative, aerobic, non-spore-forming, motile-by-gliding and rod-shaped bacterium, was isolated from a skin lesion of Atlantic salmon (Salmo salar L.) during a tenacibaculosis outbreak that occurred in 2016 at a Chilean fish farm. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain PVT-9aT belonged to the genus

Tenacibaculum

, being related to the closest type strains

Tenacibaculum haliotis

KCTC 52419T (98.49 % sequence similarity),

Tenacibaculum aestuariivivum

JDTF-79T (97.36 %),

Tenacibaculum insulae

JDTF-31T (97.29 %) and

Tenacibaculum ovolyticum

IFO 15947T (97.15 %). The genome size of strain PVT-9aT was 2.73 Mb with a DNA G+C content 31.09 mol%. Average nucleotide identity analysis among 30

Tenacibaculum

species rendered the most similar strains as follows:

T. haliotis

KCTC 52419T (87.91 %),

T. ovolyticum

IFO 15947T (82.47 %),

Tenacibaculum dicentrarchi

35/09T (81.08 %),

Tenacibaculum finnmarkense

gv finnmarkense TNO006T (80.91 %) and

T. finnmarkense

gv ulcerans TNO010T (80.96 %). Menaquinone MK-6 was the predominant respiratory quinone. The predominant cell fatty acids (>10 %) were iso-C15 : 0, iso-C15 : 1 G and iso-C15 : 0 3-OH. Phenotypic, chemotaxonomic and genomic data supported the assignment of strain PVT-9aT (=DSM 115155T=RGM 3472T) as representing a novel species of

Tenacibaculum

, for which the name Tenacibaculum bernardetii sp. nov. is proposed.
Wild emmer contribution in wheat domestication and adaptation to new environments
Authors: Iob Alice , Botigué Laura
Published: October 2023

Wheat is a staple crop, and its production is heavily threatened by climate change and soil erosion. Breeding programmes commonly rely on the wild progenitor, wild emmer wheat,Triticum turgidumsubsp.dicoccoides, to find markers associated with traits conferring higher resistance to biotic and abiotic stresses, albeit how its genetic diversity contributed into domestication and adaptation to agricultural systems has never been studied. We explore the population structure and the influence of wild emmer populations from both the Northern and Southern Levant during the domestication process. Additionally, we examine their potential contribution to facilitating the adaptation and dispersal of domestic landraces to new environments. We quantify the genomic proportion of wild Southern Levant ancestry in two different domestic germplasms, including landraces from Europe, Africa and Asia. We obtain direct evidence that as much as 26% of the genome has Southern Levant ancestry in the population from Europe, and up to 40% in the population from Africa and Asia. We also estimate the time since admixture of the two wild populations to produce the domestic forms, obtaining two dates, one matching the domestication in Southwest Asia (ca 9500 BP) and the other matching the dispersal towards Africa (ca 6500 BP). We also inquire about the possible adaptive role of wild emmer from the Southern Levant into domestication and dispersal and find an overrepresentation of genes associated with resistance to biotic stress and drought. Overall, our work provides more information on the origins of domestic wheat and highlights the potential of modern domestic landraces of emmer wheat in the study of the genetic basis of resilience. Modeling wheat genome evolution under different demographic scenarios is needed to confirm the observed signals of positive selection and facilitate the use of emmer landraces in future wheat breeding programmes.
Biophysical modeling of frontocentral ERP generation links circuit-level mechanisms of action-stopping to a behavioral race model
Authors: Diesburg Darcy A. , Wessel Jan R. , Jones Stephanie R.
Published: October 2023

Human frontocentral event-related potentials (FC-ERPs) are ubiquitous neural correlates of cognition and control, but their generating multiscale mechanisms remain mostly unknown. We used the Human Neocortical Neurosolver(HNN)’s biophysical model of a canonical neocortical circuit under exogenous thalamic and cortical drive to simulate the cell and circuit mechanisms underpinning the P2, N2, and P3 features of the FC-ERP observed after Stop-Signals in the Stop-Signal task (SST). We demonstrate that a sequence of simulated external thalamocortical and cortico-cortical drives can produce the FC-ERP, similar to what has been shown for primary sensory cortices. We used this model of the FC-ERP to examine likely circuit-mechanisms underlying FC-ERP features that distinguish between successful and failed action-stopping. We also tested their adherence to the predictions of the horse-race model of the SST, with specific hypotheses motivated by theoretical links between the P3 and Stop process. These simulations revealed that a difference in P3 onset between successful and failed Stops is most likely due to a later arrival of thalamocortical drive in failed Stops, rather than, for example, a difference in effective strength of the input. In contrast, the same model predicted that early thalamocortical drives underpinning the P2 and N2 differed in both strength and timing across stopping accuracy conditions. Overall, this model generates novel testable predictions of the thalamocortical dynamics underlying FC-ERP generation during action-stopping. Moreover, it provides a detailed cellular and circuit-level interpretation that supports links between these macroscale signatures and predictions of the behavioral race model.

Significance statement

The frontocentral event-related potential (FC-ERP) is an easily-measurable neural correlate of cognition and control. However, the cortical dynamics that produce this signature in humans are complex, limiting the ability of researchers to make predictions about its underlying mechanisms. In this study, we used the biophysical model included in the open-source Human Neocortical Neurosolver software to simulate and evaluate the likely cellular and circuit mechanisms that underlie the FC-ERP in the Stop-Signal task. We modeled mechanisms of the FC-ERP during successful and unsuccessful stopping, generating testable predictions regarding Stop-associated computations in human frontal cortex. Moreover, the resulting model parameters provide a starting point for simulating mechanisms of the FC-ERP and other frontal scalp EEG signatures in other task conditions and contexts.
Menstrual cycle changes increased following COVID-19 mRNA vaccination: Social media validation and self-controlled case series analysis
Authors: Shetty Aishwarya N , Kattan Gonzalo Sepulveda , Javed Muhammad , Pearce Christopher , Clothier Hazel J , Buttery Jim P
Published: October 2023

Objectives

To investigate if there was an increase in menstrual abnormality related presentation post COVID-19 vaccination.

Design

BERTopic machine learning, with a guided topic modelling option was used to analyse mentions of menstrual change in relation to COVID-19 vaccination on the social media platform Reddit. Self-controlled case series (SCCS) analysis using general practice data collected via the POpulation Level Analysis and Reporting (POLAR) tool with permission from Primary Health Networks (PHNs) as the de-identified dataset owners in Victoria and New South Wales.

Setting

Globally for social media analysis. Victoria and New South Wales (NSW), Australia for POLAR

Participants

For social media analysis, people who made a Reddit post about menstrual concerns post COVID-19 vaccine. For the SCCS analysis, people who presented to a POLAR GP registered practice with a new menstrual abnormality diagnosis.

Exposures

COVID-19 vaccination with adenovirus vector [AstraZeneca’s Vaxzervria® ChadOx1-S], mRNA [Pfizer-BioNTech’s Comirnaty® BNT162b2 and Moderna’s Spikevax®] or protein-subunit [Novavax’s Nuvaxovid®]).

Outcomes and Measures

Scraped social media posts were pre-processed, analysed for positive, negative, and neutral sentiments and topic modelled. Menstrual abnormality presentations of interest were isolated from the general practice dataset aggregated by POLAR, by searching for relevant SNOMED CT codes. Similarly, relative incidence (RI) was calculated for all COVID-19 vaccine types.

Results

Social media analysis saw peaks in menstrual change posts on Reddit since the global COVID-19 vaccine rollout. The SCCS analysis demonstrates an increase in general practice presentations of menstrual abnormality diagnosis following mRNA vaccines (RI= 1.14, 95% CI: 1.07 to 1.22,P<0.001).

Conclusions and Relevance

This study demonstrates an increase in menstrual abnormality presentations following COVID-19 mRNA vaccination. Our findings validate the concerns raised on social media so people who are vaccinated or are considering future vaccines feel heard, supported, and validated. Our analysis highlights the importance of using large real-world datasets to gather reliable evidence for public health decision making.

Summary box

Section 1: What is already known on this topic?

Surveys and spontaneous surveillance systems suggested and association of menstrual cycle changes with COVID-19 vaccination.

Heavy menstrual bleeding was added to the product information for mRNA vaccines in the European Union

Section 2: What this study adds?

Our study is the first to prove an increase in menstrual abnormality related presentations post mRNA COVID-19 vaccines using routinely collected general practice data.

Our findings validate the concerns raised by people who menstruate and help them with their future decision to vaccinate.
Reproductive traits of the European catfish (Silurus glanis) during the early stages of invasion in the Lower Tagus River
Authors: Gkenas Christos , Ribeiro Diogo , Gago João , Dias Diogo , Verma Chandani R. , Kumkar Pradeep , Ribeiro Filipe
Published: October 2023

Freshwater ecosystems face severe challenges from biological invasions, leading to biodiversity loss, disruption of ecosystem services, and economic impacts. Human-mediated activities, such as aquarium trade and sport angling, contribute to species introductions, with potential negative consequences for native ecosystems. The European catfish (Silurus glanis) is one of the world’s largest freshwater fish and has been intentionally introduced into diverse regions, impacting native ecosystems. However, limited research exists on its reproductive traits outside its native range. This study addresses this gap by examining the reproductive characteristics of non-native European catfish populations in the Lower Tagus River in Portugal, focusing on size at maturity, spawning period, and fecundity. The observed balanced sex ratio aligns with studies of native populations. Variations in size at first maturity (TL50) among populations highlight the influence of habitat conditions, temperature, food availability, growth rate, and geographical location on this trait. The extended spawning season (March to June) in the Tagus River is consistent with native populations, but variations may occur based on environmental conditions and water temperature. Absolute fecundity ranged from 8,961 to 335,500 oocytes, showing positive relationships with body size and emphasizing the reproductive potential of European catfish in Portugal. Egg size variations, along with asynchronous egg development, contribute to the species’ reproductive strategy, favoring its invasive success. Management efforts should include monitoring, regulations on introductions, removal programs, and public awareness to mitigate their impact. Future research should focus on understanding how non-native European catfish populations adapt in various regions and continue to impact ecosystems.
Sleep consolidation potentiates skill maintenance
Authors: Solano Agustin , Lerner Gonzalo , Griffa Guillermina , Deleglise Alvaro , Caffaro Pedro , Riquelme Luis , Perez-Chada Daniel , Della-Maggiore Valeria
Published: October 2023

Contrary to its well-established role in declarative learning the impact of sleep on motor memory consolidation remains a subject of debate. Motor learning involves skill acquisition and skill maintenance, two critical aspects in achieving movement precision. Current literature suggests that whereas motor skill acquisition benefits from sleep, consolidation of skill maintenance depends solely on the passage of time. This has led to the proposal that skill maintenance may be an exception to other types of memories. Here, we address this ongoing controversy in humans through three comprehensive experiments. We found that when training occurs throughout the day consolidation of skill maintenance proceeds independently of sleep. However, when it takes place closely before bedtime so that sleep aligns with the memory stabilization window, a 30% memory enhancement emerges along with a distinct modulation of neural markers of sleep consolidation. Our findings reconcile seemingly conflicting perspectives on the active role of sleep in procedural motor learning, and offer the potential to accelerate motor recovery in rehabilitation programs through the synchronization of training sessions with sleep.
IL-27 maintains cytotoxic Ly6C+γδ T cells that arise from immature precursors
Authors: Wiesheu Robert , Edwards Sarah C. , Hedley Ann , Tosolini Marie , Fares da Silva Marcelo Gregorio Filho , Sumaria Nital , Optaczy Yasmin , Hill David G. , Hayes Alan J. , Hay Jodie , Kilbey Anna , Michie Alison M. , Graham Gerard J. , Manoharan Anand , Halsey Christina , Jones Gareth W. , Blyth Karen , Fournie Jean-Jacques , Pennington Daniel J. , Bekiaris Vasileios , Coffelt Seth B.
Published: October 2023

In mice, γδ T cells that express the co-stimulatory molecule, CD27, are committed to the IFNγ-producing lineage in the thymus, and in the periphery, these cells play a critical role in host defence and anti-tumor immunity. Unlike αβ T cells that rely on MHC-presented peptides to drive their terminal differentiation, it is unclear whether MHC-unrestricted γδ T cells undergo further functional maturation after exiting the thymus. Here, we provide evidence of phenotypic and functional diversity within peripheral IFNγ-producing γδ T cells. We found that immature CD27+Ly6C—cells convert into mature CD27+Ly6C+cells, and these mature cells control cancer progression while the immature cells cannot. The gene signatures of these two subsets were highly analogous to human immature and mature γδ T cells, indicative of conservation across species. We show that IL-27 supports the cytotoxic phenotype and function of mouse CD27+Ly6C+cells and human Vδ2+cells, while IL-27 is dispensable for mouse CD27+Ly6C—cells and human Vδ1+cells. These data reveal increased complexity within IFNγ-producing γδ T cells, comprising of immature and terminally differentiated subsets, that offer new insights into unconventional T cell biology.
Hierarchical Gaussian process models explore the dark meltome of thermal proteome profiling experiments
Authors: Le Sueur Cecile , Rattray Magnus , Savitski Mikhail
Published: October 2023

Thermal proteome profiling (TPP) is a proteome wide technology that enables unbiased detection of protein drug interactions as well as changes in post-translational state of proteins between different biological conditions. Statistical analysis of temperature range TPP (TPP-TR) datasets relies on comparing protein melting curves, describing the amount of non-denatured proteins as a function of temperature, between different conditions (e.g. presence or absence of a drug). However, state-of-the-art models are restricted to sigmoidal melting behaviours while unconventional melting curves, representing up to 50% of TPP-TR datasets, have recently been shown to carry important biological information.

We present a novel statistical framework, based on hierarchical Gaussian process models and named GPMelt, to make TPP-TR datasets analysis unbiased with respect to the melting profiles of proteins. GPMelt scales to multiple conditions, and extension of the model to deeper hierarchies (i.e. with additional sub-levels) allows to deal with complex TPP-TR protocols. Collectively, our statistical framework extends the analysis of TPP-TR datasets for both protein and peptide level melting curves, offering access to thousands of previously excluded melting curves and thus substantially increasing the coverage and the ability of TPP to uncover new biology.

Author summary

Proteins interactions with other proteins, nucleic acids or metabolites, are key to all biological processes. Being able to detect these interactions is essential to understand biological systems. Thermal proteome profiling is a proteome-wide biological assay able to capture these interactions. It consists in analysing the effect of heat treatment on proteins. Indeed, proteins, under physiological conditions, are folded. This folding gets disrupted as the temperature increases. The way this unfolding happens, called the melting profile of the protein, informs on the interactions of proteins. For example, the interaction of a protein with another protein can increase (thermally stabilise) or decrease (thermally destabilise) the temperature at which this protein starts unfolding. In this work, we present a new statistical method, named GPMelt, to analyse these melting profiles. Notably, GPMelt allows to analyse any melting profiles, independently of their shapes. The proposed improvements over previously published methods allow to investigate more robustly the melting profiles of more proteins, hence increasing the ability of thermal proteome profiling assays to discover new protein interactions. We anticipate that these advancements will aid in unravelling complex biological phenomena.
Identification of potential distribution area for the sweet cherry (Prunus avium) by the MaxEnt model
Authors: Li Hongqun , Peng Xiaolong , Jiang Peng , Xing Ligang
Published: October 2023

The potential distribution of species offers important information for species management, especially for fruit trees with economic value. The sweet cherry is a tree species with higher economic value among deciduous fruit trees in north China. Herein, its potential distributions were modeled under current conditions. The performances of this model were excellent with AUCs of >0.9 for model training and testing. The key factors identified were the thermal factors (min temperature of coldest month (bio06) from -14.5 to 4.5°C, the mean temperature of warmest quarter (bio10) from 21.0 to 28.0°C), followed by water factor (the annual precipitation (bio12) from 500 to 1200 mm). Its suitable region in China mainly is located on 6 geographical regions including southwest China (eastern Sichuan, northeast and main urban areas of Chongqing, mid-western Guizhou and mid-northern Yunnan), northwest China (mid-southern Shaanxi, southern Ningxia mid-southern and eastern Gansu), northeast China (Coastal region of Liaoning), central China (most of Henan, mid-northern Hubei and central Hunan), north China (Beijing, Tianjing, mid-southern Shanxi), east China (Shanghai, Jiangsu, Shandong, central Zhejiang, central and northern Anhui and eastern Jiangxi) and south China (western Guangxi). Relative to their actual distributions, Hubei, Hunan and Anhui etc have been identified to have some potentially suitable areas for these sweet cherries. Among them, these 9 provinces or cities (Shaanxi, Beijing, Tianjing, Shanxi, Hebei, Henan, Shanghai, Jiangsu and Shandong) are main regions for its current development and utilization, followed by Sichuan, Guizhou,Yunnan, Gansu, Liaoning, Hubei, Zhejiang and Guangxi etc. The results can be adopted to identify the suitable areas for its introduction and cultivation to avoid the losses of human labor, material and financial resources due to improper decision, and to provide a scientific basis for its current introduction, cultivation and management.
Parkin R274W mutation affects muscle physiology via the PARIS-PGC-1α pathway
Authors: Sevegnani Martina , Lama Adriano , Girardi Francesco , Hess Michael W. , Castelo Maria Paulina , Pichler Irene , Biressi Stefano , Piccoli Giovanni
Published: October 2023

Recessive mutations in the Parkin gene (PRKN) are the most common cause of young-onset inherited parkinsonism. Parkin is a multifunctional E3 ubiquitin ligase that plays a variety of roles in the cell including the degradation of proteins and the maintenance of mitochondrial homeostasis, integrity, and biogenesis via the PARIS-PGC-1α pathway. In 2001 the R275W mutation in thePRKNgene was identified in two unrelated families with a multigenerational history of postural tremor, dystonia and parkinsonism. Drosophila models of Parkin R275W showed selective and progressive degeneration of dopaminergic neuronal clusters, mitochondrial abnormalities, and prominent climbing defects. In the Prkn mouse orthologue, the amino acid R274 corresponds to human R275. Here we described a muscle phenotype in R274W +/+ mice and discovered that a defective Parkin-PARIS-PGC-1α pathway may impact mitochondrial biogenesis and, eventually, myoblast proliferation and differentiation.
Enrichment of Rare and Uncommon Neanderthal Polymorphisms in Autistic Probands and Siblings
Authors: Pauly Rini , Johnson Layla , Feltus F. Alex , Casanova Emily L.
Published: October 2023

Homo sapiensand Neanderthals underwent hybridization during the Middle/Upper Paleolithic age, culminating in retention of small amounts of Neanderthal-derived DNA in the modern human genome. In the current study, we address the potential roles genic Neanderthal single nucleotide polymorphisms (SNP) may be playing in autism susceptibility using data from the Simons Foundation Powering Autism Research (SPARK) and Genotype-Tissue Expression (GTEx) databases. We have discovered that rare and uncommon variants are significantly enriched in both European- and African-American autistic probands and their unaffected siblings compared to race-matched controls. In addition, we have identified 51 SNPs (p51) significantly enriched in European-American cases of autism, 13 of which fall within autism-associated genes, as well as 1 SNP in African-American probands. In addition, SNPs within the p51 network display significant linkage disequilibrium with one another, indicating they may more often be co-inherited in autism. These results strongly suggest Neanderthal-derived DNA is playing a significant role in autism susceptibility across major populations in the United States.
Metabolic interactions of a minimal bacterial consortium drive robust nitritation at acidic pH
Authors: Ni Gaofeng , Su Zicheng , Wang Yu , Wang Zhiyao , Wu Mengxiong , Hua Zhengshuang , Hu Shihu , Yuan Zhiguo , Guo Jianhua , Greening Chris , Zheng Min
Published: October 2023

Microbial communities efficiently mediate aerobic ammonia oxidation even at acidic pH. However, little is known about the adaptations and interactions that allow these communities to withstand challenges such as acidic stress, reactive nitrogen species, and resource deprivation under such conditions. Here we combined metagenomic analysis and biogeochemical measurements to infer the composition, metabolic interactions, and stress adaptation mechanisms of microbial consortia in three acidic nitritation bioreactors, operating at pH 5 to 2. This resulted in the recovery of 70 high-quality and mostly novel metagenome-assembled genomes (MAGs). The dominant ammonia oxidiser across all three bioreactors was a novel proteobacterium, herein named Candidatus (Ca.) Nitrosoglobus kelleri, that we enriched to a relative abundance of 55%. Also present were several heterotrophic bacteria that are predicted to engage in metabolically cross-feeding with theNitrosoglobus. Particularly abundant were mycobacteria, including the novel actinobacteriumCa. Mycobacterium cookii, which are predicted to use organic carbon, hydrogen, carbon monoxide, sulfide and possibly nitrite as energy sources to drive aerobic respiration and denitrification. Remarkably, we observed efficient conversion of ammonia to nitrate even at pH 2, by a minimalistic community comprising theNitrosoglobusandMycobacteriumas its only core members. Genomic analysis suggests these bacteria each use multiple strategies to maintain intracellular pH homeostasis, detoxify reactive nitrogen species, and scavenge nutrients at this pH. Altogether, these findings reveal that minimal communities can drive a key biogeochemical process even at acidic pH, and have implications for understanding nitrogen cycling and enhancing wastewater treatment.
Cilostazol may be a better therapeutic agent for acute ischemic stroke because of its efficacy in preventing post-stroke depression
Authors: Zhang Yuling , Yang Ganggang , Wang Rui , Wang Xin , Tan Xiying , Tang Chaozhi
Published: October 2023

Post-stroke depression (PSD) has more than 1/3 complications in ischemic stroke (IS) patients, but there is still no specific drug that can effectively prevent the occurrence of PSD. Cilostazol, commonly used in the treatment of IS, has been found to rescue cognition impairment in recent years, but whether it has the efficacy in preventing PSD remains uncertain. In this study, a total of 431 acute ischemic stroke (AIS) patients treated with and without cilostazol during 2021-2022 were recruited and followed up for 6 months. At the end of follow-up, we found that AIS patients of cilostazol-treated group had significantly lower National Institutes of Health Stroke Scale (NIHSS) and 24-item Hamilton’s Depression Scale (HAMDS) scores than patients of cilostazol-free group (p<0.05), the total incidence of depression was 15.47% in patients of cilostazol-treated group and 36.02% in patients of cilostazol-free group, including 8.84% and 16.67% mild depression (p<0.05), 6.08% and 12.90% moderate depression (p<0.05), 0.55% and 6.45% major depression (p<0.01), respectively. In addition, the plasma levels of high-sensitive C-reactive protein (Hs-CRP), homocysteine (HCY), tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) and neutrophil/lymphocyte ratio (NLR) in AIS patients of cilostazol-treated group were all lower than those in patients of cilostazol-free group (p<0.05). These results suggest that cilostazol is a better therapeutic agent for AIS because it may prevent PSD by decreasing the levels of inflammation in patients.
The mitochondrial mRNA stabilizing protein, SLIRP, regulates skeletal muscle mitochondrial structure and respiration by exercise-recoverable mechanisms
Authors: Pham Tang Cam Phung , Raun Steffen Henning , Havula Essi , Henriquez-Olguín Carlos , Rubalcava-Gracia Diana , Frank Emma , Fritzen Andreas Mæchel , Jannig Paulo R. , Andersen Nicoline Resen , Kruse Rikke , Ali Mona Sadek , Halling Jens Frey , Ringholm Stine , Needham Elise J. , Hansen Solvejg , Lemminger Anders Krogh , Schjerling Peter , Petersen Maria Houborg , de Almeida Martin Eisemann , Jensen Thomas Elbenhardt , Kiens Bente , Hostrup Morten , Larsen Steen , Ørtenblad Niels , Højlund Kurt , Kjær Michael , Ruas Jorge L. , Trifunovic Aleksandra , Wojtaszewski Jørgen Frank Pind , Nielsen Joachim , Qvortrup Klaus , Pilegaard Henriette , Richter Erik Arne , Sylow Lykke
Published: October 2023

Summary and graphical abstract

Decline in mitochondrial function associates with decreased muscle mass and strength in multiple conditions, including sarcopenia and type 2 diabetes. Optimal treatment could include improving mitochondrial function, however, there are limited and equivocal data regarding the molecular cues controlling muscle mitochondrial plasticity. Here we uncover the mitochondrial-mRNA-stabilizing protein SLIRP, in complex with LRPPRC, as a PGC-1α target that regulates mitochondrial structure, respiration, and mitochondrially-encoded-mRNA pools in skeletal muscle. Exercise training effectively counteracted mitochondrial defects induced by loss of LRPPRC/SLIRP, despite sustained low mitochondrially-encoded-mRNA pools, via increased mitoribosome translation capacity. In humans, exercise training robustly increased muscle SLIRP and LRPPRC protein content across exercise modalities and sexes, yet this increase was less prominent in subjects with type 2 diabetes. Our work identifies a mechanism of post-transcriptional mitochondrial regulation in skeletal muscle through mitochondrial mRNA stabilization. It emphasizes exercise as an effective approach to alleviate mitochondrial defects by possibly increasing mitoribosome capacity.

Abstract Figure
Neural manifolds carry reactivation of phonetic representations during semantic processing
Authors: Orepic Pavo , Truccolo Wilson , Halgren Eric , Cash Sydney S. , Giraud Anne-Lise , Proix Timothée
Published: October 2023

Traditional models of speech perception posit that neural activity encodes speech through a hierarchy of cognitive processes, from low-level representations of acoustic and phonetic features to high-level semantic encoding. Yet it remains unknown how neural representations are transformed across levels of the speech hierarchy. Here, we analyzed unique microelectrode array recordings of neuronal spiking activity from the human left anterior superior temporal gyrus, a brain region at the interface between phonetic and semantic speech processing, during a semantic categorization task and natural speech perception. We identified distinct neural manifolds for semantic and phonetic features, with a functional separation of the corresponding low-dimensional trajectories. Moreover, phonetic and semantic representations were encoded concurrently and reflected in power increases in the beta and low-gamma local field potentials, suggesting top-down predictive and bottom-up cumulative processes. Our results are the first to demonstrate mechanisms for hierarchical speech transformations that are specific to neuronal population dynamics.
Root phosphatase activity is coordinated with the root conservation gradient across a phosphorus gradient in a lowland tropical forest
Authors: Guilbeault-Mayers Xavier , Laliberté Etienne
Published: October 2023

Soil phosphorus (P) is a growth-limiting nutrient in tropical ecosystems, driving diverse P-acquisition strategies among plants. Particularly, mining for inorganic P through phosphomonoesterase (PME) activity is essential, given the substantial proportion of organic P in soils. Yet the relationship between PME activity and other P-acquisition root traits remains unclear.

We measured root PME activity and commonly-measured root traits, including root diameter, specific root length (SRL), root tissue density (RTD), and nitrogen concentration ([N]) in 18 co-occurring trees across soils with varying P availability to better understand trees response to P supply.

Root [N] and RTD were inversely related, and that axis was related to soil P supply. Indeed, both traits correlated positively and negatively to PME activity, which responded strongly to P supply. Conversely, root diameter was inversely related to SRL, but this axis was not related to P supply.

Suggesting that limiting similarity influenced variation along the diameter-SRL axis, explaining high local trait diversity. Meanwhile, environmental filtering tended to impact trait values along the root [N]-RTD axis. Overall, P availability indicator traits like PME activity and root hairs only tended to be associated with these axes, highlighting limitations of these axes in describing convergent adaptations at local sites.
The Evolution of Heteroresistance via Small Colony Variants inEscherichia coliFollowing Long Term Exposure to Bacteriostatic Antibiotics
Authors: Gil-Gil Teresa , Berryhill Brandon A. , Manuel Joshua A. , Smith Andrew P. , McCall Ingrid C. , Baquero Fernando , Levin Bruce R.
Published: October 2023

Traditionally, bacteriostatic antibiotics are agents able to arrest bacterial growth. Despite being traditionally viewed as unable to kill bacterial cells, when they are used clinically the outcome of these drugs is frequently as effective as when a bactericidal drug is used. We explore the dynamics ofEscherichia coliafter exposure to two ribosome-targeting bacteriostatic antibiotics, chloramphenicol and azithromycin, for thirty days. The results of our experiments provide evidence that bacteria exposed to these drugs replicate, evolve, and generate a sub-population of small colony variants (SCVs) which are resistant to multiple drugs. These SCVs contribute to the evolution of heteroresistance and rapidly revert to a susceptible state once the antibiotic is removed. Stated another way, exposure to bacteriostatic drugs selects for the evolution of heteroresistance in populations previously lacking this trait. More generally, our results question the definition of bacteriostasis as populations exposed to bacteriostatic drugs are replicating despite the lack of net growth.
A virally encoded high resolution screen of cytomegalovirus host dependencies
Authors: Finkel Yaara , Nachshon Aharon , Aharon Einav , Arazi Tamar , Simonovsky Elena , Dobesova Martina , Gluck Avi , Fisher Tal , Stanton Richard J. , Schwartz Michal , Stern-Ginossar Noam
Published: October 2023

Genetic screens have transformed our ability to interrogate cellular factor requirements in infection, yet current approaches are limited in their sensitivity, biased towards early stages of infection and provide only simplistic phenotypic information which is often based on infected cell survival. Here, by engineering human cytomegalovirus to express sgRNA libraries directly from the viral genome, we developed a sensitive, versatile, viral centric approach that allows profiling of different stages along viral infection in a pooled format. Using this approach, which we termed VECOS (Virus Encoded CRISPR-based direct readOut Screening system), we identified hundreds of novel host dependency and restriction factors and quantified their direct effects on viral genome replication, viral particle secretion and infectiousness of secreted particles, providing a multi-dimensional perspective on viral-host interactions. These high resolution measurements reveal that perturbations that alter late stages in HCMV life cycle mostly regulate HCMV particle quality rather than quantity, defining correct virion assembly as a critical stage that is heavily reliant on viral-host interactions. Overall, VECOS facilitates systematic high resolution dissection of human proteins’ role along the infection cycle, providing a roadmap for in-depth dissection of host–herpesvirus interactions.
Hydroponics: A Novel Approach to CulturingAphanomyces euteiches
Authors: Done Ethan
Published: October 2023

Aphanomyces euteichesis a soil-borne, economically impactful pathogen that afflicts pulse crops. Isolating it from environmental soil samples is made difficult by other microorganisms naturally present in field soil, particularlyRhizopus, that outcompete it on selective media. However, by isolating and culturingA. euteichesfrom pea plants grown in a hydroponics apparatus inoculated with field soil, this can be ameliorated to allow for enhanced observation and culturing ofA. euteichesin media. This experiment tested and validated a method of hydroponic growth forA. euteiches, and confirmed that it yieldedA. euteichesisolates using universal CPN60 sequencing.
Cytosolic heme metabolism by alternative localization of heme oxygenase 1 in plant cells
Authors: Chen Yingxi , Nishimura Kohji , Tokizawa Mutsutomo , Yamamoto Yoshiharu Y. , Oka Yoshito , Matsushita Tomonao , Hanada Kousuke , Shirai Kazumasa , Mano Shoji , Shimizu Takayuki , Masuda Tatsuru
Published: October 2023

Heme, an organometallic molecule, is widely engaged in oxygen transport, electron delivery, enzymatic reactions, and signal transduction. Additionally, heme serves as a precursor to phytochromobilin, the chromophore of plant phytochrome. Heme oxygenase (HO) initiates the first committed step in heme metabolism. Our transcription start site-sequencing (TSS-seq) revealed thatHO1inArabidopsis thalianaandOryza sativa(rice) has two TSSs, producing long (HO1L) and short (HO1S) transcripts, with or without an intact N-terminal plastid transit peptide.HO1LandHO1Sproducts localize in plastids and the cytosol, respectively. In Arabidopsis,HO1Lis prevalent in light-exposed shoots, whileHO1Sis clearly detected in roots and etiolated seedlings. During de-etiolation and early development,HO1Lratio gradually rises andHO1Sratio decreases. Light perception via phytochrome and cryptochrome elevatesHO1Lratio and reduceHO1Sratio through the functioning of HY5 and HYH transcription factors, and the suppression of DET1, E3 ubiquitin ligase COP1, and PIFs transcription factors. As expected,HO1Lproduct was able to complement theHO1-deficient mutantgun2(hy1), but surprisingly,HO1Sexpression could also restore the short hypocotyl phenotype and high pigment content, and make the mutant recover from thegunphenotype. This indicates the formation of functional holo-phytochrome within these lines. Our work highlights the presence of a cytosolic pathway for heme metabolism, especially during etiolation and early development. Furthermore, it supports the hypothesis that a mobile heme signal is involved in the mediation of retrograde signaling from the chloroplast.

Significance Statement

In this research, through both TSS-seq and CAGE-seq, we discovered that theHO1(GUN2orHY1) gene in both Arabidopsis and rice has two TSSs, generatingHO1LandHO1Stranscripts. We reveal that theHO1TSS regulation pathway is the same as the light signaling pathway. Significantly, our study identifies that a cytosolic heme metabolism pathway is existent in plant cells.
Cobalamin production in phototrophic and mixotrophic cultures of nine duckweed species (Lemnaceae)
Authors: Linda Klamann , Rhishika Dutta , Lusine Ghazaryan , Michal Sela-Adler , Inna Khozin-Goldberg , Osnat Gillor
Published: October 2023

To feed the rapidly increasing world population, food production will have to double while the amount of water and arable land remain unchanged. Therefore, we must transition to environmentally sustainable, but just as nutritious diets by 2050. This will require drastic reduction in animal-based foods and increasing plant-based foods. Plant- based diets are more sustainable and healthier, with but one exception, plants are low in cobalamin (vitamin B12). Only a few plant and fungi species contain cobalamin, and some of the cobalamin forms present in algae and mushrooms are not available to humans. Recently, the smallest known plant, the edible duckweedWolffia globosaMankai, was shown to contain high concentrations of bioavailable cobalamin. We hypothesized that the production of bioavailable cobalamin is not unique toW. globosaMankai but is common to other duckweed species. We also hypothesized that cobalamin production depends on the conditions under which the duckweed is grown. To test our hypotheses, we cultivated nine duckweed species under mixotrophic and phototrophic conditions, then measured the concentration and identified the bioavailability of cobalamin using biological and analytical methods. Our results showed that all duckweed species tested produce bioavailable cobalamin while pseudocobalamin (the non-available form of cobalamin) was not detected. We also found that mixotrophic conditions enhanced duckweed growth but reduced cobalamin concentrations. Our results establish duckweed species as a novel source of plant-derived bioavailable cobalamin and highlight the effect of growth conditions on production. More research is needed to identify the bacteria responsible for the production of cobalamin in duckweed and to optimize the conditions for cobalamin production.
Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types
Authors: Xu Peng , Zhang Bin
Published: October 2023

Cancer is a complex disease with diverse molecular mechanisms that affect patient prognosis. Network-based approaches are effective in revealing a holistic picture of cancer prognosis and gene interactions. However, a comprehensive landscape of coexpression networks and prognostic gene modules across multiple cancer types remains elusive. In this study, we performed a systematic analysis of coexpression networks in 32 cancer types. Our analysis identified 4749 prognostic modules that play a vital role in regulating cancer progression. Integrative epigenomic analyses revealed that these modules were regulated by interactions between gene expression and methylation. Coregulated genes of network modules were enriched in chromosome cytobands and preferentially localized in open chromatin regions. The preserved network modules formed 330 module clusters that resided in chromosome hot spots. The cancer-type-specific prognostic modules participated in unique essential biological processes in different cancer types. Overall, our study provides rich resources of prevalent gene networks and underlying multiscale regulatory mechanisms driving cancer prognosis, which lay a foundation for biomarker discovery and therapeutic target development.
Project ECHO-AIDD: recommendations for care of adults with intellectual and developmental disabilities
Authors: Mendoza Olivia , Thakur Anupam , Niel Ullanda , Thomson Kendra , Lunsky Yona , Bobbette Nicole
Published: October 2023

Purpose

This study aims to describe patients presented in an interprofessional, virtual education program focused on the mental health of adults with intellectual and developmental disabilities (IDD), as well as present interprofessional recommendations for care.

Design/methodology/approach

In this retrospective chart review, descriptive statistics were used to describe patients. Content analysis was used to analyze interprofessional recommendations. The authors used the H.E.L.P. (health, environment, lived experience and psychiatric disorder) framework to conceptualize and analyze the interprofessional recommendations.

Findings

Themes related to the needs of adults with IDD are presented according to the H.E.L.P. framework. Taking a team-based approach to care, as well as ensuring care provider knowledge of health and social histories, may help better tailor care.

Originality/value

This project draws on knowledge presented in a national interprofessional and intersectoral educational initiative, the first in Canada to focus on this population.
IndiGrid: Creating India's First Power Transmission InvIT (A)1
Authors: Agarwalla Sobhesh Kumar , Pandey Ajay
Published: October 2023

The case describes the structure of Infrastructure Investment Trusts (InvITs) created and launched in Indian markets in 2017. Besides introducing InvITs and their potential role in relaxing the financing constraint created by the lack of an active corporate debt market in India, the case can help in analysing why the market is discounting the IndiGrid unit price relative to its issue price. It also offers an opportunity to value IndiGrid's Patran acquisition.
Customer perception of corporate social responsibility and its impact on customer engagement: critical significance of corporate reputation
Authors: Parray Zahoor Ahmad , Iqbal Junaid , Mushtaq Rashid
Published: October 2023

Purpose

The primary goal of this research is to examine how corporate social responsibility (CSR) affects customer engagement (CE) and how corporate reputation (CR) serves as a mediator of this relationship.

Design/methodology/approach

The data for this paper were gathered from the customers who were actively engaging with the banks. A total of 445 questionnaires were circulated among the respondents, 397 were selected after removing the faulty ones, which estimates around 90% of the total questionnaire distributed. Customers were asked to record their perceptions regarding CSR, CR and CE. The data were collected from both the regions of Jammu and Kashmir simultaneously.

Findings

The findings reinforced the hypothesized associations, indicating that CR successfully and positively mediates the association between CSR and CE.

Practical implications

The outcomes of this study will assist top managers in the organization in understanding the significant impact of CSR and CR, as well as how they both positively impact the CE.

Originality/value

This research introduces a fresh dimension by exploring the influence of cognitive biases in shaping the relationship between CSR efforts, reputation-building and customer engagement. Through this innovative approach, the study establishes a more intricate and comprehensive link between theories, shedding light on the underlying mechanisms that drive these dynamics within the realm of corporate behavior and consumer perceptions.
The contextual information requirements for collection and use of occupant feedback in BIM-enabled FM
Authors: Artan Deniz , Tekce Isilay , Yilmaz Neziha , Ergen Esin
Published: October 2023

Purpose

Occupant feedback is crucial for healthy, comfortable and productive offices. Existing facility management (FM) systems are limited in effective use of occupant feedback, as they fail to collect the vital contextual information (e.g. related building element, space) associated with the feedback. The purpose of this study is to formalise the contextual information requirements for structured collection of occupant feedback for rapid diagnosis and resolution of problems and integrating occupant feedback with building information modelling (BIM) for making use of its visualisation and analysis capabilities, and eventually for effective use of occupant feedback in FM operations.

Design/methodology/approach

A mixed-methods approach was conducted in four steps: (1) identifying occupant feedback types (e.g. echo in meeting room) in office buildings, (2) examining the current practice in collecting and processing occupant feedback via use cases, (3) determining the contextual information requirements via expert interviews and (4) validation of the information requirements via a BIM-integrated prototype.

Findings

The findings present the contextual information requirements for 107 occupant feedback types grouped under thermal comfort, indoor air quality, acoustic comfort, visual comfort, building design and facility services.

Practical implications

Feedback-specific contextual information items enable structured data collection and help to avoid missing data and minimise the time lost in manual data entry and recursive interaction with the occupants during FM operations.

Originality/value

The contextual information requirements determined are expected to enhance occupant satisfaction and FM performance in office buildings by better use of the occupant feedback and integration into BIM-enabled FM and can be extended to other building types in future studies by using the proposed methodology.