bluuebunny/crossref_metadata_2025 huggingface dataset:
GuaCAMOLE: GC-bias aware estimation improves the accuracy of metagenomic species abundances
Authors: Holcik Laurenz , von Haseseler Arndt , Pflug Florian G.
Published: September 2024

GuaCAMOLE is a novel computational method which detects and removes GC bias from metagenomic sequencing data. Metagenomic sequencing measures the species composition of microbial communities, and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial communities are, however, affected by GC-content dependent biases. GuaCAMOLE works regardless of the specific amount or direction of GC-bias present in the data and requires only a single sample. The algorithm reports unbiased abundances and quantifies the amount of bias present in terms of GC-depdendent sequencing efficiencies. Experimental mock community data confirms both estimates to be accurate across a wide range of experimental protocols. In gut microbiomes of colorectal cancer patients we observe a clear bias against GC-poor species in the abundances reported by existing methods. GuaCAMOLE successfully removes this bias and corrects the abundance of clinically relevant GC-poor species such asF. nucleatum(28% GC) by up to a factor of two. GuaCAMOLE thus contributes to a better quantitative understanding of microbial communities by improving the accuracy and comparability of species abundances across experimental setups.
Medicago truncatula CORYNEregulates inflorescence meristem branching, nutrient signaling, and arbuscular mycorrhizal symbiosis
Authors: Orosz Johnathan , Lin Erica Xinlei , Lindsay Penelope , Kappes Mikayla , Bashyal Sagar , Everett Hasani , Gautam Chandan Kumar , Jackson David , Müller Lena Maria
Published: September 2024

The CLAVATA signaling pathway regulates plant development and plant-environment interactions. CLAVATA signaling consists of mobile, cell-type or environment-specific CLAVATA3/ESR-related (CLE) peptides, which are perceived by a receptor complex consisting of leucine-rich repeat receptor-like kinases such as CLAVATA1 and receptor-like proteins such as CLAVATA2, which often functions with the pseudokinase CORYNE (CRN). CLAVATA signaling has been extensively studied in various plant species for its role in meristem maintenance and in legumes for modulating root interactions with nitrogen-fixing rhizobia. Some signaling proteins involved in development and nodulation, including CLAVATA1, also regulate plant interactions with mutualistic arbuscular mycorrhizal (AM) fungi. However, our knowledge on AM symbiosis regulation by CLAVATA signaling remains limited and only a handful of genetic regulators have been identified. Here we report thatMedicago truncatula CRNcontrols inflorescence meristem branching and negatively regulates root interactions with AM fungi.MtCRNfunctions partially independently of the AM autoregulation signalMtCLE53. Transcriptomic data revealed thatcrnroots display signs of perturbed signaling related to a range of responses to biotic and abiotic factors, suggesting thatMtCRNplays various roles in plant development and interactions with the environment.
Rational inattention in neural coding for economic choice
Authors: Fine Justin M. , Moreno-Bote Rubén , Hayden Benjamin Y.
Published: September 2024

Mental operations like computing the value of an option are computationally expensive. Even before we evaluate options, we must decide how much attentional effort to invest in the evaluation process. More precise evaluation will improve choice accuracy, and thus reward yield, but the gain may not justify the cost.Rational Inattention theoriesprovide an accounting of the internal economics of attentionally effortful economic decisions. To understand this process, we examined choices and neural activity in several brain regions in six macaques making risky choices. We extended the rational inattention framework to incorporate the foraging theoretic understanding of local environmental richness or reward rate, which we predict will promote attentional effort. Consistent with this idea, we found local reward rate positively predicted choice accuracy. Supporting the hypothesis that this effect reflects variations in attentional effort, richer contexts were associated with increased baseline and evoked pupil size. Neural populations likewise showed systematic baseline coding of reward rate context. During increased reward rate contexts, ventral striatum and orbitofrontal cortex showed both an increase in value decodability and a rotation in the population geometries for value. This confluence of these results suggests a mechanism of attentional effort that operates by controlling gain through using partially distinct population codes for value. Additionally, increased reward rate accelerated value code dynamics, which have been linked to improved signal-to-noise. These results extend the theory of rational inattention to static and stationary contexts and align theories of rational inattention with specific costly, neural processes.
Derivation and validation of indices incorporating vasopressor dose and blood pressure values over time
Authors: Gervais Alain , Lamontagne François , Michaud Jean-Baptiste , Adhikari Neill KJ , Pagé Jean-Michel , Masse Marie-Hélène , Harhay Michael O , Chassé Michaël , Lamontagne Félix , Laforge Katia , Fortin Alexandra , Leclair Marc-André , Lévesque Simon , Domingue Marie-Pier , Momenzadeh Neda , Vallières Martin , Pinto Ruxandra , Morin-Lavoie Maxime , Carter Francis , Lemyre Félix Camirand
Published: September 2024

Rationale

The blood pressure value below which the benefits of vasopressors clearly outweigh their disadvantages is uncertain.

Objectives

The main objective of this analysis was to investigate the statistical properties and potential utility of indices estimating the vasopressor dose-rates as a function of blood pressure values over time.

Methods

In this single-center observational study, we collected blood pressure values from intensive care unit (ICU) monitors and norepinephrine dose-rates from infusion pumps corresponding to a derivation and a validation cohort. Patients included in each cohort were 18 years or older and received norepinephrine in the ICU. We defined and derived indices corresponding to vasopressor therapy above (>65 mmHg) and below (<60 mmHg) targets. We report the distribution of both indices over time from both cohorts as well as their associations with hospital mortality using logistic regression models adjusted for baseline variables.

Results

Between July 30 2020 and March 28 2022, 283 patients were included in the derivation cohort. The median ICU stay was 5 days (interquartile range [IQR] 2-10.5) and the median duration of norepinephrine therapy was 27.3 hours (IQR 13.9-54.2). The median cumulative time with a MAP below 60 mmHg was 0.9 hours (IQR 0.2-3.1), whereas the cumulative time with a MAP above 65 mmHg was 22.5 hours (IQR 10.9-40.4). Adjusting for prespecified baseline variables, the above target index was associated with hospital mortality (OR 1.6, 95% CI 1.2 –2.3) but not the below target index (OR 1.1 95% CI 0.8 – 1.5). Between May 5 2022 and December 16 2022, 83 patients were included in the validation cohort. The duration of ICU stay and the proportion of norepinephrine exposure above MAP target were consistent with the derivation cohort. The point estimates of the associations between each index and mortality were also consistent with the derivation cohort, but not statistically significant.

Conclusion

Indices of vasopressor administration as a function of blood pressure suggest that during most of vasopressor therapy episodes, patients are treated above target. The association of these indices with patient outcomes remains uncertain but could be explored in larger datasets, and future clinical trials of target MAPs may consider measurement of these indices to adjust results for treatment adherence.
Evaluation of a Mental Health Support Service for Performing Artists
Authors: Ryan Finola M , Cordeaux Claire , Davison Dermott
Published: September 2024

Background

Performing artists frequently face mental health challenges, with risk factors including performance pressure, industry competitiveness, and irregular work patterns. Barriers to seeking help encompass confidentiality concerns, fear of misunderstanding by clinicians, and scheduling conflicts due to peripatetic work.

Aims

This study aims to evaluate the accessibility, utilisation, and effectiveness of a Mental Health Support Service (MHSS) for performing artists.

Methods

A 12-month evaluation of a UK-wide MHSS for performing artists was conducted. 555 self-referred performers received 6-8 sessions of talking therapy from experienced professionals. Pre- and post-intervention mental health was assessed using PHQ-9 and GAD-7 scales. Quantitative data were analysed using paired t-tests, and qualitative feedback underwent thematic analysis.

Results

240 performers completed pre- and post-intervention scores. Significant reductions in PHQ-9 (mean decrease 6.242, p<0.0001) and GAD-7 (mean decrease 6.225, p<0.0001) scores were observed post-intervention. Qualitative feedback (n=215) revealed high satisfaction, with 88% willing to recommend the service. Key themes included appreciation for tailored support and therapist-performer compatibility. Limited data on outcomes for global majority participants and gender differences necessitate further research.

Conclusions

This evaluation of a mental health support service for performing artists reveals high satisfaction rates and willingness to recommend the service, highlighting the value of tailored interventions that address industry-specific challenges. The findings underscore the importance of developing sector-specific mental health standards and support systems, particularly for industries with high proportions of freelance workers, which could have broader implications for improving mental health support across diverse professional fields.
Identifying Proteomic Prognostic Markers for Alzheimer’s Disease with Survival Machine Learning: the Framingham Heart Study
Authors: Leng Yuanming , Ding Huitong , Ang Ting Fang Alvin , Au Rhoda , Doraiswamy P. Murali , Liu Chunyu
Published: September 2024

Background

Protein abundance levels, sensitive to both physiological changes and external interventions, are useful for assessing the Alzheimer’s disease (AD) risk and treatment efficacy. However, identifying proteomic prognostic markers for AD is challenging by their high dimensionality and inherent correlations.

Methods

Our study analyzed 1128 plasma proteins, measured by the SOMAscan platform, from 858 participants 55 years and older (mean age 63 years, 52.9% women) of the Framingham Heart Study (FHS) Offspring cohort. We conducted regression analysis and machine learning models, including LASSO-based Cox proportional hazard regression model (LASSO) and generalized boosted regression model (GBM), to identify protein prognostic markers. These markers were used to construct a weighted proteomic composite score, the AD prediction performance of which was assessed using time-dependent area under the curve (AUC). The association between the composite score and memory domain was examined in 339 (of the 858) participants with available memory scores, and in an independent group of 430 participants younger than 55 years (mean age 46, 56.7% women).

Results

Over a mean follow-up of 20 years, 132 (15.4%) participants developed AD. After adjusting for baseline age, sex, education, and APOE ε4+ status, regression models identified 309 proteins (P≤ 0.2). After applying machine learning methods, nine of these proteins were selected to develop a composite score. This score improved AD prediction beyond the factors of age, sex, education, and APOE ε4+ status across 15 to 25 years of follow-up, achieving its peak AUC of 0.84 in the LASSO model at the 22-year follow-up. It also showed a consistent negative association with memory scores in 339 participants (beta = -0.061,P= 0.046), 430 independent participants (beta = -0.060,P= 0.018), and the pooled 769 samples (beta = -0.058,P= 0.003).

Conclusion

These findings highlight the utility of proteomic markers in improving AD prediction and emphasize the complex pathology of AD. The composite score may aid early AD detection and efficacy monitoring, warranting further validation in diverse populations.
Morphology-based classification of sickle cell disease and β-thalassemia using a low-cost automated microscope and machine learning
Authors: Shrestha Pranav , Lohse Hendrik , Bhatla Christopher , McCartney Heather , Alzaki Alaa , Sandhu Navdeep , Oli Pradip Kumar , Li Hongquan , Prakash Manu , Amid Ali , Onell Rodrigo , Au Nicholas , Merkeley Hayley , Kapoor Videsh , Pande Rajan , Stoeber Boris
Published: September 2024

Sickle cell disease (SCD) and β-thalassemia are the most common monogenic diseases, disproportionately affecting low- and middle-income countries, where low-cost and accurate diagnostic tools are needed to reduce the global disease burden. Although the sickling test is commonly used to screen for the sickle mutation, it cannot distinguish between the asymptomatic sickle cell trait (SCT) and SCD, or identify β-thalassemia. Here, we enhanced the inexpensive sickling test using automated microscopy and morphology-based machine learning classification to detect SCD, trait conditions (SCT and β-thalassemia trait) and normal individuals with an overall area under receiver operating curve, sensitivity and specificity of 0.940 (95% confidence intervals: 0.938-0.942), 84.6% (84.2%-84.9%), and 92.3% (92.1%-92.4%), respectively. Notably, the sensitivity and specificity to detect severe disease (SCD) was over 97% and 98%, respectively, thus establishing a low-cost automated screening option for disease detection in low-resource settings. Furthermore, leveraging high-throughput microscopy, we generated an open-access dataset comprising over 300,000 images with 1.5 trillion segmented cells from 138 individuals in Canada and Nepal including individuals with sickle and/or β-thalassemia mutations, to accelerate further research.
The Effect of Firearm Laws on Pediatric Mortality in the United States
Authors: Faust Jeremy Samuel , Chen Ji , Bhat Shriya , Otugo Onyekachi , Renton Benjamin , Chen Alexander Junxiang , Lin Zhenqiu , Krumholz Harlan M.
Published: September 2024

Introduction

Firearms are the leading cause of death in US children and adolescents, but little is known about whether legal policies may be responsible.

Methods

We conducted difference-in-differences analysis on CDC WONDER data before and afterMcDonald v. Chicago, the landmark 2010 Supreme Court decision on firearms regulation. States were divided into three groups, based on legal actions taken before and since 2010, most permissive, permissive, and restricted. Firearm mortality trends before (1999-2010) and after (2010-2023) were determined and compared across the three groups for all intents and by intent (homicide and suicide). Within the most permissive state grouping, pediatric firearm mortality by 2013 urbanicity and by observed race and ethnicity were conducted. For each US state, pre-and- post 2010 all-intent pediatric firearm mortality incident rates were compared.

Results

There were 7130 excess pediatric firearms deaths in states with more permissive regulatory regimes than those with stricter frameworks, as well as higher rates of homicide and suicide. Non-Hispanic Black populations were disproportionately affected by these trends. Four states (California, Maryland, New York, and Rhode Island) had decreased pediatric firearm mortality after 2010, all of which were in the restrictive firearms law group.

Conclusion

States with more permissive firearm laws have experienced greater pediatric firearm mortality during the post-McDonald v. Chicagoera.

KEY POINTS

Question

Did states enacting permissive firearm laws after 2010—whenMcDonald v. Chicagowas decided by the United States Supreme Court—subsequently experience higher rates of pediatric firearm mortality?

Findings

Difference-in-difference analysis found that state groups that enacted more permissive firearm laws after 2010 experienced >7,100 firearm deaths in children and adolescents ages 0-17 between 2010-2023 compared to restrictive law-enacting states, of which most (77.5%) were homicides. In the permissive states groups, increases occurred in all urbanicities. The largest increase occurred in non-Hispanic Black children and adolescents. Four states had statistical decreases in pediatric firearm mortality during the study period, all of which were in states which enacted restrictive firearm policies.

Meaning

Permissive firearm laws contributed thousands of excess firearm deaths among children living in states with permissive policies. Future work should focus on determining which types of laws conferred the most harm and which the most protection.
Assessing the antimicrobial activity ofAframomum melegueta and Piper guineenseextract on pathogens of rot diseases of cucumber fruit
Authors: Akpan Patience Saturday , Umoren Eyoanwan Offon , William Ebere Ifiokobong , Ibuot Aniefon Alphonsus
Published: September 2024

The inhibitory potential ofAframomum melegueta and Piper guineenseextract against the pathogens of fruit rot diseases of cucumber was assessed. Two fungal isolates isolated from rotten cucumber fruits were;Fusarium oxysporiumandPenicilliumsp. The test plant extract were prepared in concentrations of 100% and 70%. The antimicrobial potential of ethanolic extract ofPiper guineenseat 100% concentration againstFusarium oxysporiumrevealed inhibition zone of 26.6 mm while 70% concentration of same plant extract had 17.0 mm. Ethanolic plant extract ofA. meleguetaat 100% concentration showed 7.5 mm and 70% concentration of same plant extract had 6.5 mm. Aqueous plant extract of both plants showed very minimal inhibitory effect onF. oxysporiumwhich ranged from 0.00mm to 8.5mm. ForPenicilliumsp, ethanolic extract ofPiper guineenseat 100% showed inhibition of 18.0mm and at 70% concentration of same plant extract showed inhibition of 12.5mm. Ethanolic plant extract ofA. meleguetaat 100% concentration inhibited the growth ofPenicilliumsp with inhibition zone of 15.5mm and the 70% concentration of same plant extract showed 11.5mm inhibition zone. The aqueous plant extract at 100% revealed inhibition zone of 15.5 mm and 70% concentration showed no inhibition. The phytochemical screening of test plants revealed the presence of most of the phytochemicals tested in abundance with very few exception.
Postnatal Enrichment Corrects Deficits in Perineuronal Net Formation and Reversal Learning in Adult Mice Exposed to Early Adversity
Authors: Jamwal Sumit , Islam Rafiad , MacDowell Kaswan Zoe , Bowers Christian , Giuliano Lauryn , Kaffman Arie
Published: September 2024

Childhood neglect is associated with cortical thinning, hyperactivity, and deficits in cognitive flexibility that are difficult to reverse later in life. Despite being the most prevalent form of early adversity, little is currently understood about the mechanisms responsible for these neurodevelopmental abnormalities, and no animal models have yet replicated key structural and behavioral features of childhood neglect/deprivation. To address these gaps, we have recently demonstrated that mice exposed to impoverished conditions, specifically limited bedding (LB), exhibit behavioral and structural changes that resemble those observed in adolescents who have experienced severe neglect. Here, we show that LB leads to long-term deficits in reversal learning, which can be fully reversed by briefly exposing LB pups to enrichment (toys) in their home cage from postnatal days 14 to 25. Reversal learning failed to induce normal c-fos activation in the orbitofrontal cortex (OFC) of LB mice, a deficit that was normalized by early enrichment. Additionally, LB decreased the density of parvalbumin-positive cells surrounded by perineuronal nets (PV+PNN+) and increased the ratio of glutamatergic to inhibitory synapse densities in the OFC, deficits that were also reversed by enrichment. Degradation of PNN in the OFC of adult mice impaired reversal learning, reduced c-fos activation, and increased the ratio of glutamatergic to inhibitory synapse densities in the OFC to levels comparable to those observed in LB mice. Collectively, our findings suggest that postnatal deprivation and enrichment impact the formation of PV+PNN+ cells in the OFC, a developmental process that is essential for cognitive flexibility in adulthood.
Traumatic Brain Injury Exacerbates Alcohol Consumption and Neuroinflammation with Decline in Cognition and Cholinergic Activity
Authors: Gangal Himanshu , Iannucci Jaclyn , Huang Yufei , Chen Ruifeng , Purvines William , Davis W. Taylor , Rivera Arian , Johnson Giles , Xie Xueyi , Mukherjee Sanjib , Vierkant Valerie , Mims Kaley , O’Neill Katherine , Wang Xuehua , Shapiro Lee A. , Wang Jun
Published: September 2024

Traumatic brain injury (TBI) is a global health challenge, responsible for 30% of injury-related deaths and significantly contributing to disability. Annually, over 50 million TBIs occur worldwide, with most adult patients at emergency departments showing alcohol in their system. TBI is also a known risk factor for alcohol abuse, yet its interaction with alcohol consumption remains poorly understood. In this study, we demonstrate that the fluid percussion injury (FPI) model of TBI in mice significantly increases alcohol consumption and impairs cognitive function. At cellular levels, FPI markedly reduced the number and activity of striatal cholinergic interneurons (CINs) while increasing microglial cells. Notably, depleting microglial cells provided neuroprotection, mitigating cholinergic loss and enhancing cholinergic activity. These findings suggest that TBI may promote alcohol consumption and impair cognitive abilities through microglia activation and consequently reduced cholinergic function. Our research provides critical insights into the mechanisms linking TBI with increased alcohol use and cognitive deficits, potentially guiding future therapeutic strategies.
Field-crop transcriptome models are enhanced by measurements in systematically controlled environments
Authors: Hashida Yoichi , Kyogoku Daisuke , Tanaka Suguru E. , Mori Naoya , Tanabata Takanari , Watanabe Hiroyuki , Nagano Atsushi J.
Published: September 2024

Plants in the field respond to seasonal and diel changes in various environmental factors such as irradiance and temperature. We previously developed a statistical model that predicts rice gene expression from the meteorological data and identified the environmental factors regulating each gene. However, since irradiance and temperature (the two most critical environmental factors) are correlated in the field, it remains difficult to distinguish their roles in gene expression regulation. Here, we show that transcriptome dynamics in the field are predominantly regulated by irradiance, by the modelling involving diurnal transcriptome data from the 73 controlled conditions where irradiance and temperature were independently varied. The model’s prediction performance is substantially high when trained using field and controlled conditions data. Our results highlight the utility of a systematic sampling approach under controlled environments to understand the mechanism of plant environmental response and to improve transcriptome prediction under field environments.
Proteomic responses of oat (Avena sativaL.) to drought stress
Authors: Chen Caijin , Bao Mingfang , Zeng Yanxia , Wang Xuemin , Liu Wenhui
Published: September 2024

Drought is a major abiotic factor limiting the growth and development of the oat industry, and understanding its drought tolerance mechanisms is vital to oat production. In this study, we measured the phenotypic and physiological indices of drought-resistant (Grain King [G]) and water-sensitive (XiYue [X]) oat varieties and performed comparative proteomic analysis under drought stress and normal water supply (soil water content of 75% ± 5% of field water holding capacity) conditions. The results indicated that plant height, aboveground biomass, and underground biomass of variety X were 7.9%, 9.5%, and 14.6% lower than those under normal water supply, respectively, and the difference in plant height was significant (p< 0.05), whereas the decrease in all these indicators of variety G was small. Drought stress significantly increased malondialdehyde (MDA) content, soluble sugar (SS) content, superoxide dismutase (SOD) activity, and peroxidase (POD) activity of variety G by 48.6%, 68.5%, 81.3%, and 101.7%, respectively (p< 0.05). Variety X also showed increases up to various extents, but the increases were smaller than those of variety G. Additionally, 151 and 792 differentially expressed proteins (DEPs) identified in varieties G and X, respectively. Weighted Gene Co-expression Network Analysis(WGCNA), Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genome(KEGG) analyses demonstrated that the DEPs who were highly correlated with POD and SOD activity and SS content in variety G, were majorly involved in energy metabolism, protein translation, RNA processing, amino acid metabolism, and protein folding, whereas those with high correlation with the above three physiological indicators in variety X were primarily involved in RNA processing, protein stabilization, plant photosynthesis, intracellular signal transduction, and protein folding. Overall, the study elucidated the drought resistance mechanisms of different types of oats at the protein level。
Postpartum Depression During the COVID-19 Pandemic and Associated Factors: A Cross-Sectional Study
Authors: Teruya Mariana Mie , Carrijo Gabriel Sant’Ana , Moraes Costa Gleise Aparecida , Da Silva Mariliza Henrique , Targa de Lima Júlia Ribeiro , Sacramento Veltri Costa Julia Fontanezzi , Strufaldi Rodolfo , Sobrinho Valete Cristina Ortiz
Published: September 2024

Objective

To study the prevalence of maternal depressive symptoms in the immediate postpartum period (≤ 7 days postpartum) during the COVID-19 pandemic and to identify associated factors.

Methods

We performed a cross-sectional analytical study. The study population consisted of postpartum women >18 years old enrolled at the Municipal University Hospital of São Bernardo do Campo. The Edinburgh Postnatal Depression Scale and a questionnaire on sociodemographic characteristics and clinical history were administered to 90 patients in the first week of the immediate postpartum period between June and December 2021.

Results

An Edinburgh Postnatal Depression Scale score > 10 was observed in 39 (43.3%) of the postpartum women. From a multivariate analysis, the factors associated with a score > 10 on the scale were: “having no belief/spirituality” with 83% (95% CI 1.20-2.81, p<0.006), “having had more than one pregnancy” with 50% (95% CI 0.29-0.89, p<0.02), “having a previous episode of depression” with 64% (95% CI 1.02-2.65, p<0.04), and “having a previous episode of anxiety” with 83% (95% CI 1.06-3.16, p<0.03). The other factors studied did not have statistical significance.

Conclusion

With the COVID-19 pandemic, an increase in the prevalence of depressive symptoms in the immediate postpartum period was observed. The postpartum women who scored > 10 on the EPDS had the following common associated factors: “having no belief/spirituality”, “having had more than one pregnancy”, “having a previous episode of depression”, and “having a previous episode of anxiety”. These findings indicate the need for greater attention from health professionals to these positive factors.
One Health assessment of poultry and cattle farms as reservoirs for ESBL-producingEscherichia coli
Authors: Malik Hina , Singh Randhir , Kaur Simranpreet , Parmar Neha , Tyagi Anuj , Aulakh R. S. , Gill J.P.S.
Published: September 2024

BACKGROUND

Unregulated use of antibiotics in animal food production leads to the emergence of multidrug resistant bacteria, notably extended-spectrum beta-lactamases producingEscherichia coli(ESBLE. coli). ESBLs severely limit treatment options and pose a significant threat to public health. Investigating the potential role of livestock and poultry farms in harboring ESBLE. coliis crucial, given the prevalence of ESBLE. coliin humans, animals, and the environment, following the One Health framework.

OBJECTIVES

The aim of this study was to assess and compare the potential contribution of cattle and poultry farms along with their respective human handlers to the emergence and spread of ESBLE. colifollowing One Health approach.

METHODS

Twenty cattle and twenty poultry farms were surveyed in Ludhiana, India to determine antibiotic usage, prevalent diseases in the farms. Animal faeces/poultry droppings, handler hand swabs, and stool samples were examined for the presence of ESBLE. coli. The isolates were examined for their susceptibility to 16 antibiotics and for the presence of selected antimicrobial resistance genes, including ESBL genes. Generalized linear mixed models were applied to investigate variations in the prevalence of ESBLE. coliassociated with farm animal species, farm practices, and farm biosecurity measures.

RESULTS

Our findings revealed a higher prevalence of ESBLE. coliin poultry farms (53.75%) than in cattle farms (40.72%) and overall lower prevalence (12%) in human handlers. Of the total isolates, 86.52% were multidrug resistant, and 93.91% showed a high multiple antibiotic resistance (MAR) index (>0.2). Isolates from poultry farms exhibited a higher level of resistance with 97% of isolates exhibiting multidrug resistance, 100% isolates with MAR index of more than 0.2, and 90.70% carrying theblaCTXMgene.

CONCLUSION

Our findings highlight cattle and poultry farms as potential reservoirs for multidrug-resistant and ESBLE. coli, contributing to the rising environmental burden of antibiotic resistance genes. This emphasizes the urgency of limiting antibiotic use in animal farming, especially in poultry production, to address the escalating problem of antibiotic resistance and protect both animal and human health.
PHluorin-conjugated secondary nanobodies as a tool for measuring synaptic vesicle exo- and endocytosis
Authors: Georgiev Svilen V. , Rizzoli Silvio O.
Published: September 2024

Neuronal communication relies on synaptic vesicle recycling, which has long been investigated by live imaging approaches. Synapto-pHluorins, genetically encoded reporters that incorporate a pH-sensitive variant of GFP within the lumen of the synaptic vesicle, have been especially popular. However, they require genetic manipulation, implying that a tool combining their excellent reporter properties with the ease of use of classical immunolabeling would be desirable. We introduce this tool here, relying on primary antibodies against the luminal domain of synaptotagmin 1, decorated with secondary single-domain antibodies (nanobodies) carrying a pHluorin moiety. The application of the antibodies and nanobodies to cultured neurons results in labeling their recycling vesicles, without the need for any additional manipulations. The labeled vesicles respond to stimulation, in the expected fashion, and the pHluorin signals enable the quantification of both exo- and endocytosis. We conclude that pHluorin-conjugated secondary nanobodies are a convenient tool for the analysis of vesicle recycling.
PointTree: Automatic and accurate reconstruction of long-range axonal projections of single-neuron
Authors: Cai Lin , Fan Taiyu , Qu Xuzhong , Zhang Ying , Gou Xianyu , Ding Quanwei , Feng Weihua , Cao Tingting , Lv Xiaohua , Liu Xiuli , Huang Qing , Quan Tingwei , Zeng Shaoqun
Published: September 2024

Single-neuron axonal projections reveal the route map of neuron output and provide a key cue for understanding how information flows across the brain. Reconstruction of single-neuron axonal projections requires intensive manual operations in tens of terabytes of brain imaging data, and is highly time-consuming and labor-intensive. The main issue lies in the need for precise reconstruction algorithms to avoid reconstruction errors, yet current methods struggle with densely distributed axons, focusing mainly on skeleton extraction. To overcome this, we introduce a point assignment-based method that uses cylindrical point sets to accurately represent axons and a minimal information flow tree model to suppress the snowball effect of reconstruction errors. Our method successfully reconstructs single-neuron axonal projections across hundreds of GBs images with an average of 80% F1-score, while current methods only provide less than 40% F1-score reconstructions from a few hundred MBs images. This huge improvement is helpful for high-throughput mapping of neuron projections.
Mesenchymal-epithelial transition reduces proliferation but increases immune evasion in tumor spheroids
Authors: Dimari Gina , Hu Yueyuan , Frenzel Annika , Fuchs Anke , Wurm Alexander , Fischer-Friedrich Elisabeth
Published: September 2024

Mesenchymal-epithelial transition (MET) has been associated with secondary tumor outgrowth during metastasis but the underlying mechanism remains elusive. Using MET-inducible mesenchymal breast cancer cells, we investigated whether MET benefits tumor outgrowth by enhancing proliferation. We found that crowding inhibition of proliferation is present before and after MET, but mesenchymal cells gain a proliferative advantage through more effective escape from crowded cell islands. In 3D culture, proliferation is reduced upon MET with differential effects of focal-adhesion-signalling and actomyosin activity. In particular, inhibition of Src-signalling leads to increased growth after MET. Finally, in co-culture experiments, MET-induced tumor spheroids evade immune cell attack to a larger extent, likely due to more confined epithelial spheroid shape and changes in immunomodulatory molecules. Our data suggest that, contrary to previous assumptions in the field, MET might promote secondary tumor outgrowth not through a proliferation boost but through increased survival rate in the presence of immune cells.
Examination of low-intensity focused ultrasound parameters for human neuromodulation
Authors: Ennasr Areej , Isaac Gabriel , Strohman Andrew , Legon Wynn
Published: September 2024

Background

Low-intensity focused ultrasound (LIFU) is a promising form of non-invasive neuromodulation characterized by a rich parameter space that includes intensity, duration, duty cycle and pulsing strategy. The effect and interaction of these parameters to affect human brain activity is poorly understood. A better understanding of how parameters interact is critical to advance LIFU as a potential therapeutic.

Objective/Hypothesis

To determine how different parameters, including intensity, duration, and duty cycle interact to produce neuromodulation effects in the human brain. Further, this study assesses the effect of pulsing versus continuous ultrasound. We hypothesize that higher duty cycles will confer excitation. Increasing intensity or duration will increase the magnitude of effect. Pulsing LIFU will not be more effective than continuous wave ultrasound.

Methods

N = 18 healthy human volunteers underwent 20 different parameter combinations that included a fully parametrized set of two intensities (ISPPA: 6 & 24 W/cm2), five duty cycles (1, 10, 30, 50, 70%) and two durations (100, 500 msec) with a constant pulse repetition frequency of 1 kHz delivered concurrently with transcranial magnetic stimulation (TMS) to the primary motor cortex (M1). Four of these parameter combinations were also delivered continuously, matched on the number of cycles. Motor-evoked potential (MEP) amplitude was the primary outcome measure. All parameter combinations were collected time-locked to MEP generation.

Results

There was no evidence of excitation from any parameter combination. 3 of the 24 parameter sets resulted in inhibition. The parameter set that resulted in the greatest inhibition (∼ 30%) was an intensity of 6W/cm2with a duty cycle of 30% and a duration of 500 msec. A three-way ANOVA revealed an interaction of intensity and duty cycle. The analysis of continuous versus pulsed ultrasound revealed a 3-way interaction of intensity, pulsing, and the number of cycles such that under the 6W/cm2condition higher cycles of pulsed ultrasound resulted in inhibition whereas lower number of cycles using continuous LIFU resulted in inhibition.

Conclusions

LIFU to M1 in humans, in the range employed, either conferred inhibition or had no effect. Significant excitation was not observed. In general, lower intensity looks to be more efficacious for inhibition that depends on duration. Finally, pulsed ultrasound looks to be more effective for inhibition as compared to continuous wave after controlling for total energy delivered.
Apurinic/apyrimidinic endodeoxyribonuclease 2 (APEX2/APE2) is required for efficient expression ofTERTin human embryonic stem cells
Authors: Stern Josh L. , Rizzardi Lindsay F. , Gassman Natalie R.
Published: September 2024

Human stem cells rely on enhanced DNA repair mechanisms to safeguard their ability to replenish somatic tissues. Telomerase counteracts telomere shortening and is a component of the stem cell DNA repair system that is regulated by ATM and ATR kinases. Here, we report that the DNA repair enzyme APEX2, but not its close paralog APEX1, is required for efficient telomerase reverse transcriptase (TERT) gene expression in human embryonic stem cells (hESC) and a melanoma cell line. We also observed that APEX2 knockdown significantly diminished telomerase enzyme activity. While APEX1 is known to regulate certain transcription factors, APEX2 has not been reported to influence gene expression. To gain insight into how APEX2 influences gene expression, we conducted RNA-seq following APEX2 knockdown in hESC. These results indicated that a number of genes, in addition toTERT, relied on APEX2 for efficient expression. Genes affected by APEX2 knockdown were significantly enriched for specific repetitive DNA families. These include mammalian-wide interspersed repeats (MIRs) andAluelements. Chromatin immunoprecipitation experiments demonstrated the highest APEX2 binding near MIR sequences inTERTintron 2. Surprisingly, binding was low in theTERTproximal promoter, a region known to controlTERTtranscription. MIR and other repetitive DNA regions are common sites of DNA damage, suggesting that APEX2 recruitment and repair ofTERTMIR sequences may play a role in influencingTERTexpression. This new role for APEX2 in promoting efficient gene expression deepens our understanding of an emerging cancer therapeutic target. Further, as theTERTgene plays critical roles in stem cell maintenance, organismal development and aging, as well as in short telomere disorders and cancer, our observations provide insight into new strategies to modulate the expression of this important enzyme.
Constraining long-lived particles from Higgs boson decays at the LHC with displaced vertices and jets
Authors: Wang Zeren Simon
Published: September 2024

Long-lived particles (LLPs) originating from decays of Standard-Model-like or beyond-the-Standard-Model Higgs bosons are often featured with signatures of displaced vertices (DVs) and jets at colliders. In this work, we show that a recent ATLAS search for DVs plus jets, with its recast implementation, can efficiently place bounds on such hadronically or semileptonically decaying LLPs. In particular, we find the search is uniquely sensitive to LLP proper decay lengths of about 1–100 mm, probing complementary regions in the parameter space of the relevant models compared to other prompt and LLP searches.

Published by the American Physical Society
2024
Influence of device configuration and noise on a machine learning predictor for the selection of nanoparticle small-angle X-ray scattering models
Authors: Monge Nicolas , Amini Massih-Reza , Deschamps Alexis
Published: September 2024

Small-angle X-ray scattering (SAXS) is a widely used method for nanoparticle characterization. A common approach to analysing nanoparticles in solution by SAXS involves fitting the curve using a parametric model that relates real-space parameters, such as nanoparticle size and electron density, to intensity values in reciprocal space. Selecting the optimal model is a crucial step in terms of analysis quality and can be time-consuming and complex. Several studies have proposed effective methods, based on machine learning, to automate the model selection step. Deploying these methods in software intended for both researchers and industry raises several issues. The diversity of SAXS instrumentation requires assessment of the robustness of these methods on data from various machine configurations, involving significant variations in the q-space ranges and highly variable signal-to-noise ratios (SNR) from one data set to another. In the case of laboratory instrumentation, data acquisition can be time-consuming and there is no universal criterion for defining an optimal acquisition time. This paper presents an approach that revisits the nanoparticle model selection method proposed by Monge et al. [Acta Cryst. (2024), A80, 202–212], evaluating and enhancing its robustness on data from device configurations not seen during training, by expanding the data set used for training. The influence of SNR on predictor robustness is then assessed, improved, and used to propose a stopping criterion for optimizing the trade-off between exposure time and data quality.
Effective utilization of waste plastics and ammonia as biodiesel to assess performance and emission
Authors: Ramar Kumarasubramanian , Subbiah Ganesan
Published: September 2024

Purpose

This study aims to examine the environmental effects of plastic waste on the atmosphere and its implications for disaster waste management. It focuses on using ammonia, pyrolyzed plastic oil and the effectiveness of alumina nanoparticles as a catalyst.

Design/methodology/approach

The research explores different combinations of conventional diesel and nano Al2O3 derived from pyrolyzed plastic oil (ranging from P10 to P40). Critical performance metrics evaluated include brake mean effective pressure (BMEP), brake specific fuel consumption, brake thermal efficiency and emissions of CO2, CO and NOx. The study specifically investigates the impact of adding 50 ppm of Al2O3 nanoparticles to these blends.

Findings

The findings indicate that using blended fuels with nanoadditives significantly lowers pollution. Specifically, the P30 blend with 50 ppm of Al2O3 nanoparticles greatly reduced CO emissions. Additionally, the same blend reduced NOx emissions and CO2 emissions. The P30 mix showed improved BMEP and brake thermal efficiency due to its density, calorific value and viscosity (6.3 bar). The P30 blend exhibited higher thermal efficiency due to decreased heat loss, whereas conventional diesel demonstrated the best mechanical efficiency due to its longer ignition delay.

Originality/value

This study highlights the potential of using Al2O3 nanoparticles and pyrolyzed plastic oil to reduce emissions and enhance the performance of internal combustion engines. It underscores the environmental benefits and implications for disaster waste management by converting plastic waste into useful resources and reducing air pollution.
Social class and lunch: differences in midday meal format in Santiago, Chile
Authors: Giacoman Claudia , Ayala Arancibia Pamela , Joustra Camila
Published: September 2024

Purpose

The social sciences have extensively studied meals; nonetheless, a few have investigated the menu format, with all the data originating from European countries. Within this framework, the novelty of this research is that it analyses the relationship between social class and lunch structure among adults in a Global South city: Santiago, Chile.

Design/methodology/approach

The study worked with data from the Survey of Commensality in Adults (>18) of the Metropolitan Region, which used a questionnaire and a self-administered eating event diary. The analysis unit was lunches (n = 3,595). The dependent variable was the structure of the lunches (single course, starter with a main course, a main course with dessert or a full-course menu with starter, main course and dessert). The independent variable was the individual’s social class (either the working, intermediate or service class).

Findings

The data showed that lunches are mostly semi- or fully structured (only 44.5% of the lunches reported by the participants contained a single course). The odds of eating a single course were lower in the service class than the working one and the odds of eating a full-course meal were higher in the service class than the working one.

Originality/value

The results provide new quantitative evidence from a representative sample of a Global South city about the relevance of social class as a differentiating factor in food, specifically regarding the existence of simpler meals among the lower classes.
Role of star–nonstar exchange, psychological empowerment and task complexity in shaping nonstar performance
Authors: Xue Xianfang , Wang Bei , Ali Ahsan
Published: September 2024

Purpose

This study aims to examine how star–nonstar exchange (SNE) influences nonstars’ performance using social information processing theory.

Design/methodology/approach

A time-lagged survey approach is utilized to collect data from 531 nonstars in China. Structural equation modeling and process macro models are applied to test the moderated mediation model of this study.

Findings

Results reveal that SNE has a positive effect on nonstars’ performance through their psychological empowerment, with task complexity moderating the relationship between psychological empowerment and innovative performance. However, no moderating effect was found for routine performance.

Originality/value

Although previous research has delved into how leader–member exchange and team–member exchange influence employee performance. This study uniquely concentrates on how the exchange relationship between star performers and nonstars influences nonstars’ performance – a dimension that has generally been overlooked in existing literature. Findings are important for understanding SNE influence on nonstars’ performance while managing task complexity.
CEO self-transcendent values influence top managers’ socially responsible behaviors: from a social learning perspective
Authors: Jia Yingya , Yin Ziqi , Wang Xiaoyu , Fang Manci
Published: September 2024

Purpose

This study aims to explore the impact of chief executive officers’ (CEOs) values on the socially responsible behaviors (SRBs) of top management teams. Drawing from the social learning framework, it examines the mechanisms through which CEOs’ values shape SRBs within organizational leadership.

Design/methodology/approach

Using the hierarchical regression model, this study assesses direct effects, while the Monte Carlo method is used to evaluate indirect effects. The analysis is based on time-lagged data collected from 122 CEOs and 287 corresponding top managers from small- and medium-sized enterprises in China.

Findings

The results indicate a positive correlation between CEOs’ self-transcendent values and their own SRBs (i.e. doing-good and avoiding harm behavior). This, in turn, promotes top managers’ SRBs.

Originality/value

By highlighting the micro-foundations of corporate social responsibility, this study enriches the understanding of SRBs enhancement in management teams. It reveals the significance of CEO self-transcendent values as a precursor to SRBs and elucidates the learning processes involved.