bluuebunny/crossref_metadata_2025 huggingface dataset:
Carbon fiber reinforced polymer (CFRP) laminates: flexural strengthening method for prestressed concrete beams with anchorage loss
Authors: Gebre Abrham , Gedu Maraki , Gebre Yisihak
Published: November 2024

Post-tensioning (PT), a method of pre-stressing, involves the use of high-strength steel strands/tendons to reinforce concrete or other materials. On the contrary, carbon fiber-reinforced polymers (CFRPs) are lightweight, high-strength materials with used to strengthen concrete structures by adhering the polymer to the concrete element. Challenges with post-tensioned elements include reverse curvature of the PT strands, tendon misplacement, and frequent damage in the anchorage and dead-end zones. These difficulties frequently cause bulging of the surrounding concrete, even at lower stress levels, and can lead to concrete bursting when tension exceeds certain threshold. This study investigates into the potential of CFRP strengthening technique to improve the flexural capacity of post-tensioned concrete beams with anchorage loss. Through an experimental program, the study compares the performance of control beams to those reinforced with different layers of CFRP. The results of this study demonstrated that there was a significant increase in flexural capacity, ranging from 45.31% to 78.62% for single layers and 87.17% to 153% for double layers of CFRP sheet. Additionally, the research examines how different levels of prestressing and CFRP wraps influence crack formation and delamination patterns of carbon fiber, with promising results. It was also noted that optimal usage of CFRP fibers and tendons is found to be critical. The study suggests exploring alternative fiber types and orientations for future study.
Profit enhancement and imbalance cost reduction with solar PV-fuel cell-EV hybrid system in a wind-integrated day-ahead power market
Authors: Ravi Kumar Allu Venkata , Naresh Babu A V , Sivanagaraju S
Published: November 2024

Renewable sources’ volatility and dynamic nature lend several challenges in ensuring power system safety and steadiness. It is crucial to properly evaluate the potential system hazards that may arise in different power system conditions. In a wind-integrated deregulated electricity network, the wind farm (WF) must intimate the power-generating capacity bids to the market controller at least one day before it begins operations. The wind farm’s bid submissions are based on the estimated wind speed (EWS); nevertheless, slight differences between the real wind speed (RWS) and the EWS will result in penalties or incentives imposed by the Independent System Operator (ISO). This occurrence is known as the power market imbalance cost, and it has a direct influence on the system’s profitability. To mitigate this effect, solar PV and fuel cell storage technologies are used with the wind farm to enhance system profit by offsetting the negative effects of the imbalance cost. Here, solar PV and fuel cells are used to function in the required time i.e. operate in the charging mode when the RWS is greater than the EWS and in discharging mode when the EWS is greater than the RWS to balance the power supply in the grid as to fulfill the power bidding conditions. Furthermore, the study focuses on minimizing potential system risks, which have been assessed using several risk assessment tools such as Value-at-Risk (VaR) and Cumulative Value-at-Risk (CVaR). The work was conducted using an IEEE 14 bus test system. Initially, the solar PV-fuel cell system supplies power to meet local needs, and the remaining energy is sent to the grid to maximize the system’s profit. Electric vehicles (EVs) have also been incorporated to maximize the system economy in more quantities and to reduce the system risk further as compared to the solar PV-fuel cell operation. Three different optimization methods, i.e. AGTO (Artificial Gorilla Troops Optimizer Algorithm), ABC (Artificial Bee Colony Algorithm), and SQP (Sequential Quadratic Programming), were used in a comparative analysis to assess the effectiveness of the proposed approach. The use of AGTO in risk assessment and reduction is a major focus of this study.
Fault diagnosis of rolling bearings under variable operating conditions based on improved graph neural networks
Authors: Chang Guochao , Liu Chang , Fan Bingbing , He Feifei , Liu Tao
Published: November 2024

To address the issues of low diagnostic accuracy, insufficient generalization, and poor robustness in traditional fault diagnosis methods across different equipment and varying operating conditions. This paper proposes an improved graph neural network-based fault diagnosis method for rolling bearings to enhance model performance under complex conditions. First, the optimized wavelet transform coefficient features are used as nodes, and by exploring the correlations between features, node adjacency relationships are constructed. The associations between fault modes and feature node graphs under different conditions are studied, and a fault feature graph sample set based on subgraph structures is built, providing data for the subsequent graph neural network learning. Then, a multi-head attention mechanism (MHGAT) and multi-scale feature adaptive perception pooling (MSF-ASAP) are integrated to construct a multi-head graph attention mechanism model based on multi-scale feature adaptive perception pooling (MSM-GAT). MHGAT enhances the model’s ability to perceive global information by learning different features from multiple perspectives and dimensions, thus improving the model’s generalization. MSF-ASAP adaptively selects and aggregates multi-scale information, enabling the model to effectively extract key features across various operating conditions and resist noise interference. And this approach enhances adaptability to local information changes, thereby improving the model’s robustness under varying conditions and noisy environments. Experimental results under multiple and continuously varying conditions demonstrate that the proposed method outperforms traditional methods in terms of diagnostic accuracy and robustness. Notably, it exhibits excellent generalization when identifying unknown conditions, achieving over 95% accuracy in recognizing new conditions and maintaining over 92.5% accuracy in noisy environments.
The political economy of gender mainstreaming in energy access in Sierra Leone
Authors: Appiah Sarah , Plutshack Victoria , Agradi Mawunyo , Klug Thomas W , Nunoo Isaac , Saparapa Rajah
Published: November 2024

In 2017, the Economic Community of West African States launched its Policy for Gender Mainstreaming in Energy Access with each member state tasked to create a National Action Plan (NAP). This study explores the case of Sierra Leone to understand how stakeholders have influenced the NAP process, and what that might mean for implementation. Using the Actors, Objectives, Context framework with interview data from key gender and energy actors, we find elements that make Sierra Leone’s NAP unique, such as addressing systematic barriers, explicitly promoting solar energy and heavily relying on civil society for implementation. The study finds that a policy focus on gender reflects both a push from international donor organisations and the national efforts of civil society. Sierra Leone’s NAP reflects the tension between the high priority of gender politics at the national and international level and more immediate interest from the Ministry of Energy and government actors on economic development. It affirms the uneasy co-existence of the liberal and liberating view of women in international development with some evidence that the liberal view prevails. Still, despite the government’s focus on economic development, poor engagement with the private sector and cultural barriers are likely to hamper the inclusion of women into the energy industry.
Introduction: The Governance Model
Authors: He Xin
Published: November 2024

The introduction of this book challenges the conventional wisdom of the judicial independence and rights-based approaches to understanding the Chinese court system. Instead, the book proposes a governance model that views the courts as agents of the state, with two primary functions—policy implementation and legitimacy enhancement. Through an exploration of the different policies that the courts are responsible for enforcing, and the approaches they use to enhance their legitimacy and that of the state, the book sheds new light on the evolution of the Chinese court system. This governance model is distinct from the dualism and order-maintenance theses which have been used to understand the Chinese legal system in the past.
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases
Authors: Choi Hwisoo , Kim Hyeonkyu , Chung Hoebin , Lee Dong-Sung , Kim Junil
Published: November 2024

Recent advancements in single-cell technologies, including single-cell RNA sequencing (scRNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), have greatly improved our insight into the epigenomic landscapes across various biological contexts and diseases. This paper reviews key computational tools and machine learning approaches that integrate scRNA-seq and scATAC-seq data to facilitate the alignment of transcriptomic data with chromatin accessibility profiles. Applying these integrated single-cell technologies in neurodegenerative diseases, such as Alzheimer’s disease and Parkinson's disease, reveals how changes in chromatin accessibility and gene expression can illuminate pathogenic mechanisms and identify potential therapeutic targets. Despite facing challenges like data sparsity and computational demands, ongoing enhancements in scATAC-seq and scRNA-seq technologies, along with better analytical methods, continue to expand their applications. These advancements promise to revolutionize our approach to medical research and clinical diagnostics, offering a comprehensive view of cellular function and disease pathology.
ADTGP: correcting single-cell antibody sequencing data using Gaussian process regression
Authors: Liu Alex C H , Chan Steven M
Published: November 2024

We present ADTGP, an R package that uses Gaussian process regression to correct droplet-specific technical noise in single-cell protein sequencing data. ADTGP improves the interpretability of the data by modeling the distribution of protein expression, conditioned on equal isotype control counts across cells. ADTGP is written in R and needs only the protein raw counts, isotype control raw counts, and a design matrix to run.

Availability and implementation

ADTGP can be installed from https://github.com/northNomad/ADTGP. It depends on Stan and the R package ‘cmdstanr’.
Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell
Authors: van den Broek Remco L , Bello Xabier , Küpper Rebecca V , van Westen Gerard J P , Jespers Willem , Gutiérrez-de-Terán Hugo
Published: November 2024

Memprot.GPCR-ModSim leverages our previous web-based protocol, which was limited to class-A G protein-coupled receptors, to become the first one-stop web server for the modelling and simulation of any membrane protein system. Motivated by the exponential growth of experimental structures and the breakthrough of deep-learning-based structural modelling, the server accepts as input either a membrane-protein sequence, in which case it reports the associated AlphaFold model, or a 3D (experimental, modelled) structure, including quaternary complexes with associated proteins and/or ligands of any kind. In both cases, the molecular dynamics (MD) protocol produces a membrane-embedded, solvated, and equilibrated system, ready to be used as a starting point for further MD simulations, including ligand-binding free energy calculations.

Availability and implementation

Memprot.GPCR-ModSim web server is publicly available at https://memprot.gpcr-modsim.org/. The standalone modules for 3D modelling (PyModSim) or membrane embedding and MD equilibration (PyMemDyn) are available under CC BY-NC 4.0 license terms at the GitHub repository https://github.com/GPCR-ModSim/.
Effects of left ventrolateral prefrontal stimulation on forming and maintaining deep and shallow episodic traces
Authors: Peng Nan , Wu Wei , Della Sala Sergio , Hoffman Paul
Published: November 2024

The levels-of-processing framework, proposing that deep encoding enhances retention, plays a crucial role in episodic memory research. Neuroimaging evidence highlights that increased activity of the left ventrolateral prefrontal cortex during deep encoding predicts subsequent memory success. However, cognitive mechanisms underlying this region’s involvement in establishing and consolidating deep and shallow traces remain unclear. In this preregistered study, we investigated whether repetitive transcranial magnetic stimulation over the left ventrolateral prefrontal cortex versus the vertex differentially modulates the formation and maintenance of deep and shallow traces. Trains of 20 Hz online repetitive transcranial magnetic stimulation were delivered over the left ventrolateral prefrontal cortex or vertex during tasks involving pleasantness (deep) and alphabetical order (shallow) judgments of words. Following encoding, two recognition tests assessed immediate and 24-h delayed recognition of words. Compared to the vertex control, ventrolateral prefrontal stimulation selectively disrupted the formation of episodic memory under deep encoding conditions, evidenced by increased response time at encoding and reduced immediate recognition in the deep but not shallow condition. Notably, forgetting rates across the 24-h delay were similar for disrupted deep, intact deep, and shallow items, implying that the rate of trace decay is independent of the strength of trace formation. The constant trace decay indicates that distinct mechanisms are involved in establishing and maintaining episodic traces.
Developmental encoding of natural sounds in the mouse auditory cortex
Authors: Zucca Stefano , La Rosa Chiara , Fellin Tommaso , Peretto Paolo , Bovetti Serena
Published: November 2024

Mice communicate through high-frequency ultrasonic vocalizations, which are crucial for social interactions such as courtship and aggression. Although ultrasonic vocalization representation has been found in adult brain areas along the auditory pathway, including the auditory cortex, no evidence is available on the neuronal representation of ultrasonic vocalizations early in life. Using in vivo two-photon calcium imaging, we analyzed auditory cortex layer 2/3 neuronal responses to USVs, pure tones (4 to 90 kHz), and high-frequency modulated sweeps from postnatal day 12 (P12) to P21. We found that ACx neurons are tuned to respond to ultrasonic vocalization syllables as early as P12 to P13, with an increasing number of responsive cells as the mouse age. By P14, while pure tone responses showed a frequency preference, no syllable preference was observed. Additionally, at P14, USVs, pure tones, and modulated sweeps activate clusters of largely nonoverlapping responsive neurons. Finally, we show that while cell correlation decreases with increasing processing of peripheral auditory stimuli, neurons responding to the same stimulus maintain highly correlated spontaneous activity after circuits have attained mature organization, forming neuronal subnetworks sharing similar functional properties.
Acute coronary syndrome as the initial manifestation of infective endocarditis in an apparently normal native valve: a case report
Authors: Lozano Pineda Felipe , Navarro Navajas Alberto , Senior Juan Manuel
Published: November 2024

Background

Acute coronary syndrome is a rare complication of infectious endocarditis. We present the case of a patient with a bicuspid aortic valve who presented an acute ST elevation myocardial infarction (STEMI) of the inferior wall secondary to vegetation that generated obstruction of the ostium of the right coronary artery (RCA).

Case summary

A 54-year-old patient with only a history of smoking was admitted for chest pain. An acute STEMI in the inferior wall was documented; he underwent an emergent coronary angiography, which showed a mass that obstructed the ostium of the RCA that did not allow its channelling. An angiotomography of the aorta was performed, where dissection was ruled out and the presence of a mass in the right coronary sinus that protruded towards the ostium of the coronary artery was confirmed. In the extension studies, a bicuspid aortic valve and thrombosis in the right brachial artery and in the infrarenal abdominal aorta were documented.

Discussion

The case was taken to a medical meeting and given the embolic and mechanical compromise; it was decided to perform surgery where a mass that invaded the proximal segment of the RCA was resected. The histopathological study documented findings of vegetation; the cultures were positive for Staphylococcus epidermidis, and he finally received antibiotic and anticoagulation treatment.
The ecomorphological radiation of phyllostomid bats
Authors: Santana Sharlene E , Sadier Alexa , Mello Marco A R
Published: November 2024

Neotropical leaf-nosed bats (family Phyllostomidae) underwent an impressive adaptive radiation characterized primarily by the diversification of dietary strategies in tandem with functional morphological diversification of their craniodental and sensory systems. In this perspective, we integrate information from extensive research across multiple fields to outline the interplay between extrinsic and intrinsic drivers of the phyllostomid adaptive radiation and the resulting ecomorphological diversity of the clade. We begin by exploring the relationship between phyllostomids and their environments, focusing on the ecogeographical drivers of their radiation. Then, we detail current knowledge about the role of genes and development in enabling morphological diversification of the group. Finally, we describe the breathtaking ecomorphological diversification of phyllostomids, trying to unveil functional connections underlying their diverse dietary niches.
Evaluating the impact of redox potential on the growth capacity of anaerobic gut fungi
Authors: England Emma E , Pratt Carrie J , Elshahed Mostafa S , Youssef Noha H
Published: November 2024

Anaerobic gut fungi (AGF, Neocallimastigomycota) inhabit the alimentary tract of herbivores. Although strict anaerobes, studies have suggested their capacity to retain viability after various durations of air exposure. It is currently unclear whether AGF can actively grow, and not merely survive, in redox potentials (Eh) higher than those encountered in the herbivorous gut. We evaluated the growth of two AGF strains (Orpinomyces joyonii and Testudinimyces gracilis) at various Eh levels, achieved by manipulating the concentrations of reductant (cysteine hydrochloride) in culture media. Both strains exhibited robust and sustainable growth at negative Eh (−50 mV or below). However, growth in the absence of cysteine hydrochloride (Eh value around +50 mV) was possible only for O. joyonii and only for one subcultivation. The capacity to grow at +50 mV was further confirmed in four additional taxa (Pecoramyces ruminatium, Anaeromyces mucronatus, Aklioshbmyces papillarum, and Piromyces communis), while two (Aestipascuomyces dupliciliberans and Capellomyces foraminis) failed to grow under these conditions. Our results establish the ability of AGF to grow at redox potential values higher than those encountered in their natural habitats. Such capability could contribute to efficient AGF dispersal and horizontal transmission between hosts, and could have important implications for industrial applications of AGF.
Chromosome-level reference genome for the Jonah crab, Cancer borealis
Authors: Polinski Jennifer M , O’Donnell Timothy P , Bodnar Andrea G
Published: November 2024

The Jonah crab, Cancer borealis, is integral to marine ecosystems and supports a rapidly growing commercial fishery in the northwest Atlantic Ocean. This species also has a long history as a model for neuroscience that has expanded our understanding of central pattern generators, neuromodulation, synaptic plasticity, and the connectivity of neural circuits. Here, we present a highly contiguous reference genome for the Jonah crab that will provide an essential resource to advance fisheries, conservation, and biomedical research. Using a combination of PacBio long-read sequencing and Omni-C scaffolding, we generated a final genome assembly spanning 691 Mb covering 51 chromosome-length scaffolds and 106 additional contigs. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis indicated a high-quality assembly with a completeness score of 90.8%. Repeat annotation identified 1,649 repeat families making up 48.27% of the Jonah crab genome. Gene model predictions annotated 24,830 protein coding genes with a 92.3% BUSCO score. Gene family evolution analysis revealed the expansion of gene families associated with nervous system function, and targeted analysis revealed an extensive repertoire of neural genes. The Jonah crab genome will not only provide a resource for neuroscience research but will also serve as a foundation to investigate adaptation to stress and population structure to support sustainable fisheries management during this time of rapidly changing environmental conditions in the northwest Atlantic Ocean.
Detection and annotation of unique regions in mammalian genomes
Authors: Vieira Mourato Beatriz , Haubold Bernhard
Published: November 2024

Long unique genomic regions have been reported to be highly enriched for developmental genes in mice and humans. In this paper, we identify unique genomic regions using an efficient method based on fast string matching. We quantify the resource consumption and accuracy of this method before applying it to the genomes of 18 mammals. We annotate their unique regions (URs) of at least 10 kb and find that they are strongly enriched for developmental genes across the board. We then investigated the subset of URs that lack annotations, which we call “anonymous.” The longest anonymous UR in the Tasmanian devil spanned 83 kb and contained the gene encoding inositol polyphosphate-5-phosphatase A, which is an essential part of intracellular signaling. This discovery of an essential gene in a UR implies that URs might be given priority when annotating mammalian genomes. Our documented pipeline for annotating URs in any mammalian genome is available from the repository github.com/evolbioinf/auger; the additional data for this study are available from the dataverse at doi.org/10.17617/3.4IKQAG.
Measuring hospital inpatient Procedure Access Inequality in the United States
Authors: Bergman Alon , David Guy , Nathan Ashwin , Giri Jay , Ryan Michael , Chikermane Soumya , Thompson Christin , Clancy Seth , Gunnarsson Candace
Published: November 2024

Geographic disparities in access to inpatient procedures are a significant issue within the US healthcare system. This study introduces the Procedure Access Inequality (PAI) index, a standardized metric to quantify these disparities while adjusting for disease prevalence. Using data from the Healthcare Cost and Utilization Project State Inpatient Databases, we analyzed inpatient procedure data from 18 states between 2016 and 2019. The PAI index reveals notable variability in access inequality across different procedures, with minimally invasive and newer procedures exhibiting higher inequality. Key findings indicate that procedures such as skin grafts and minimally invasive gastrectomy have the highest PAI scores, while cesarean sections and percutaneous coronary interventions have the lowest. The study highlights that higher inequality is associated with greater market concentration and in particular, fewer hospitals offering these procedures. These findings emphasize the need for targeted policy interventions to address procedural access disparities to promote more equitable healthcare delivery across the United States.
Development of a Rapid, Culture-Free, Universal Microbial Identification System Using Internal Transcribed Spacer Targeting Primers
Authors: Asthana Vishwaratn , Nieves Erika Martínez , Bugga Pallavi , Smith Clara , Dunn Tim , Narayanasamy Satish , Dickson Robert P , VanEpps J Scott
Published: November 2024

The indiscriminate administration of broad-spectrum antibiotics is a primary contributor to the increasing prevalence of antibiotic resistance. Unfortunately, culture, the gold standard for bacterial identification is a time intensive process. Due to this extended diagnostic period, broad-spectrum antibiotics are generally prescribed to prevent poor outcomes. To overcome the deficits of culture-based methods, we have developed a rapid universal bacterial identification system. The platform uses a unique universal polymerase chain reaction primer set that targets the internal transcribed spacer regions between conserved bacterial genes, creating a distinguishable amplicon signature for every bacterial species. Bioinformatic simulation demonstrates that nearly every bacteria in a set of 45 commonly isolated pathogenic species can be uniquely identified using this approach. We experimentally confirmed these predictions on a representative set of pathogenic bacterial species. We further showed that the system can determine the corresponding concentration of each pathogen. Finally, we validated performance in clinical urinary tract infection samples.
Resistance profiles of carbapenemase-producing Enterobacterales in a large centre in England: are we already losing cefiderocol?
Authors: Baltas Ioannis , Patel Trupti , Soares Ana Lima
Published: November 2024

Background

Carbapenemase-producing Enterobacterales (CPE) pose difficult therapeutic challenges. We aimed to characterize antimicrobial resistance profiles of CPE in our centre.

Methods

All non-duplicate CPE isolates between 1 August 2020 and 31 August 2023 in a large teaching trust in England were retrospectively studied. Cefiderocol antimicrobial susceptibility testing (AST) was performed using disc diffusion, ceftazidime/avibactam using disc diffusion and gradient diffusion, and ceftazidime/avibactam aztreonam synergy using the double disc diffusion method. EUCAST version 14.0 breakpoints were used.

Results

A total of 158 CPE from 136 patients were isolated. Most patients were colonized with CPE, but only 16.9% had active infections. Thirty-day all-cause mortality was 10.3%, increasing to 13% for patients with infections and to 18.2% for bacteraemias. OXA-48 was the most prevalent carbapenemase (48.1%), followed by NDM (38%). All isolates exhibited MDR profiles, with high levels of resistance to meropenem (41.1%). Resistance to cefiderocol was found in 69.7% of NDM-producing isolates, with a further 18.2% in the area of technical uncertainty. Ceftazidime/avibactam and aztreonam synergy was seen in 87.5% of isolates, whereas colistin and fosfomycin susceptibility remained high (98.1% and 97.2%, respectively). All OXA-48-producing isolates were susceptible to ceftazidime/avibactam, and 15.3% were resistant to cefiderocol. No patients had been exposed to cefiderocol beforehand, whereas three had been exposed to ceftazidime/avibactam. The most common risk factor for CPE isolation was travel and receiving healthcare abroad, especially in Asia.

Conclusions

We found high rates of resistance to cefiderocol in CPE isolates without prior cefiderocol exposure. Our results prohibit empirical use of cefiderocol for the treatment of CPE infections in our setting.
Addressing underestimation of waterborne disease risks due to fecal indicator bacteria bound in aggregates
Authors: Angelescu Dan E , Abi-Saab David , Ganaye Raphael , Wanless David , Wong Joyce
Published: November 2024

Aims

This study aims to identify and address significant limitations in current culture-based regulatory methods used for monitoring microbiological water quality. Specifically, these methods’ inability to distinguish between planktonic forms and aggregates containing higher bacterial loads and associated pathogens may lead to a severe underestimation of exposure risks, with critical public health implications.

Methods and results

We employed a novel methodology combining size fractionation with ALERT (Automatic Lab-in-a-vial E.coli Remote Tracking), an automated rapid method for comprehensive quantification of culturable fecal indicator bacteria (FIB). Our findings reveal a substantial and widespread presence of aggregate-bound indicator bacteria across various water matrices and geographical locations. Comprehensive bacterial counts consistently exceeded those obtained by traditional methods by significant multiples, such as an average of 3.4× at the Seine River 2024 Olympic venue, and occasionally up to 100× in irrigation canals and wastewater plant effluent. These results, supported by microscopic and molecular analyses, underscore a systematic bias in global water safety regulatory frameworks.

Conclusions

Our research demonstrates the inadequacy of traditional culture-based techniques in assessing microbiological risks posed by aggregate-bound FIB and associated pathogens, particularly in water matrices affected by FIB-rich fecal particles from recent sewer overflows or sediment, which can carry higher infectious risks. Incorporating comprehensive FIB analysis techniques, including molecular methods and rapid culture-based approaches as shown in this study, offers a promising and effective solution to these risk assessment limitations.
Pediococcus pentosaceus RC007 and Saccharomyces boulardii RC009 as antibiotic alternatives for gut health in post-weaning pigs
Authors: Parada Julián , Magnoli Alejandra , Poloni Valeria , Corti Isgro Maite , Rosales Cavaglieri Lorenzo , Luna María Julieta , Carranza Alicia , Cavaglieri Lilia
Published: November 2024

Aims

The aim of the present study was to evaluate a novel probiotic Pediococcus pentosaceus RC007 used alone and convined with Saccharomyces cerevisiae var. boulardii RC009, as in-feed additives to substitute the nontherapeutic use of antibiotics, and evaluate the different structural characteristics of intestinal bacterial populations between groups, correlated with pig production performance.

Methods and results

The in vivo study was conducted on post-weaning pigs, from 21 to 56 days old. Three dietary treatments were included: T1—basal diet (BD—control group); T2—BD with P. pentosaceus RC007; and T3—BD with a mix of P. pentosaceus RC007 and S. boulardii RC009. The weight gain increase of pigs consuming non-therapeutic antibiotics was similar to those that did not consume antibiotics during the study (P = 0.0234), but had better health indicators. The use of a probiotic combination increased carcass weight and significantly reduced the lumbar fat thickness. In terms of taxonomic composition, there was a tendency to modify the abundance of Proteobacteria, Cyanobacteria, Enterobacteriaceae, and Lactobacillaceae in pigs that consumed the additives. The genus Butyricicoccus, Collinsella, and Ruminococcus tended to be more abundant in the microbiota of pigs at T3.

Conclusions

For the first time, the results of the present study indicate that P. pentosaceus RC007 and S. boulardii RC009, a probiotic combination, could be a good substitute for antibiotics in improving pig production performance, while also contributing to a healthier gut microbiota, especially with the reduced abundance of Proteobacteria and Cyanobacteria.
Variation of six local poplar clones in growth and eco-physiological traits in two types of arid valleys
Authors: Mao Liang , Liu Jie , Xiang Xiang , Tian Feifei , Yang Linkai , Wan Xueqin , Yang Hanbo , He Fang , Chen Gang , Chen Lianghua
Published: November 2024

Six clones of native poplars were used in a field trial to investigate variations in survival, growth, and adaptation to arid-warm and arid-hot valleys. In the arid-hot valley, clone Y1-2 exhibited the highest survival rate and growth condition, surpassing other clones, while clones B7-4 and P3-6 demonstrated superior survival and growth performance in the arid-warm valley. Clone B7-4 displayed the highest soluble sugar content in leaves across both habitats. SOD and APX activities, along with MDA content in leaves, were higher in the arid-hot valley for all clones compared to the arid-warm valley. Long-term water use efficiency, as indicated by δ13C in leaves, was significantly higher for all clones in the arid-hot valley, particularly for H1-6, T3-2, and P3-6. Increases in upper epidermis thickness were observed in clones E1, B7-4, and P3-6, while Y1-2 exhibited a higher palisade parenchyma thickness (PT) in the arid-hot valley compared to the arid-warm valley. Vein densities were higher in leaves of clones E-1, B7-4, Y1-2, and P3-6 in both valleys compared to other clones, with B7-4 showing a significant increase in mean vein width in the arid-hot valley. In conclusion, the superior growth performance of clone B7-4 in the arid-warm valley may be attributed to its stronger osmotic adjustment and higher capacity to maintain water transportation through venation. The exceptional performance of clone Y1-2 in the arid-hot valley may be associated with its compact arrangement of PT, as well as its stronger capacity for hydraulic transport and antioxidant resistance in leaves.
Mesenteroaxial gastric volvulus in an elderly patient 5 years after Nissen fundoplication and hiatal hernia repair
Authors: Gill Harpreet , Guan Angel , Nguyen Alexandra , Kim So Un , Bhat Gunjan , Malkoc Aldin , Patel Sunal
Published: November 2024

Gastric volvulus is a rare and potentially life-threatening condition that usually presents acutely and requires immediate intervention via either endoscopic or surgical detorsion. Most often, it presents secondary to a hiatal hernia, with herniation and torsion of the stomach through the hiatus. Only a small subset of patients present with gastric volvulus after Nissen fundoplication for hiatal hernia repair. We report the case of an elderly patient with a previous hiatal hernia repair with Nissen fundoplication who presented with an intra-abdominal gastric volvulus that developed over the course of several months. The combination of her surgical history and volvulus etiology made her disease rare. She was treated with laparoscopic surgery and gastropexy with gastrostomy tube placement, which led to the resolution of the upper gastrointestinal symptoms.
Nuclear transfer leads to aberrant cell cycle regulation and translation, as determined by gene expression, and selection of mitochondrial DNA in porcine blastocysts
Authors: Penn Alexander , Andreas Eryk , Okada Takashi , St John Justin C
Published: November 2024

Nuclear transfer technologies, such as metaphase II spindle transfer (MII-ST), are being developed to overcome poor oocyte quality and prevent children from acquiring severe mitochondrial DNA (mtDNA) disease. However, it is unclear whether these technologies perturb gene expression, and mtDNA carryover can be reduced to minimal levels. Using our pig model, we isolated individual karyoplasts with limited mtDNA carryover (306 ± 49 copies) from mature oocytes. First, we reintroduced the spindle into its original cytoplast (autologous), fertilized and cultured the resultant embryos to the hatching blastocyst stage of development. Following RNA-seq, 64 genes were differentially expressed at false discovery rate < 0.05 and 1327 genes at P< 0.05. Pathways associated with cell cycle and epigenetic regulation and genes associated with nuclear–mitochondrial interactions were upregulated whilst protein translation pathways were downregulated. We then transferred karyoplasts to third-party cytoplasts (heterologous) and undertook mtDNA next-generation sequencing of two-cell to hatching blastocyst stage preimplantation embryos. Nine of twenty embryos possessed two mitochondrial genomes. Our outcomes show that autologous nuclear transfer alone significantly changes hatching blastocyst gene expression; very low levels of mtDNA carryover can be preferentially replicated during early development; and nuclear and mitochondrial synchrony has not been re-established.
A thematic analysis of shared decision-making in consultations with patients with a presumed brain tumor and neurosurgeons
Authors: Bras Iris J M , Joosen Margot C W , Rutten Geert-Jan M , van Vugt Ingrid J M , Sitskoorn Margriet M , Boele Florien W , Hoogendoorn Petra , Gehring Karin
Published: November 2024

Background

Patients with brain tumors, family members, and healthcare professionals face complex healthcare decisions that can significantly impact everyday life. Engaging in shared decision-making (SDM) can help ensure treatment decisions align with patients’ preferences and goals. Little is known about the decision-making process in neurosurgical consultations. This study aims to qualitatively explore and describe the SDM process during neurosurgical consultations for patients with a presumed brain tumor.

Methods

The first consultation between patients with presumed glioma or meningioma and their neurosurgeons was audio-recorded and transcribed. Decision-making models were used as sensitization concepts, with coding carried out inductively. We employed a reflexive thematic analysis to develop themes and subthemes until saturation was beginning to emerge.

Results

Analyzing eleven consultations, we developed three main themes and twelve subthemes. The results depict decision-making guided by neurosurgeons (theme 1), with varying degrees of engagement from patients and family members (theme 2) and personalization of the decision-making process based on the medical situation and everyday life priorities (theme 3). The consultations lacked specific attention to the everyday life priorities of the patients.

Conclusions

The decision-making processes seemed to focus primarily on medically informing patients with a presumed brain tumor, in line with informed decision-making. However, less emphasis was placed on learning more about the patient’s everyday life and preferences to integrate into the decision-making process, which is key to SDM. Incorporating patient goals may lead to greater personalization and decisions that align with both the patient’s medical situation and their goals.
Coping with an awake brain tumor resection in patients and their primary contacts: A qualitative study
Authors: Kranenburg Leonieke W , van Ark Tom , van Haren Mathijs M J , Schouten Joost W , Busschbach Jan J , Klimek Markus
Published: November 2024

Background

The diagnosis and awake removal of a brain tumor is a major life event. A better understanding of the needs of this group of patients and their primary contacts in the perioperative trajectory can further improve care.

Methods

Adult patients who underwent an awake craniotomy (AC) in the Erasmus MC, the Netherlands and their primary contacts were interviewed 1–2 weeks prior to surgery and 2–4 weeks after surgery. Semi-structured interviews on the impact of the diagnosis on their lives and coping mechanisms with the AC procedure were conducted. Interview transcripts were analyzed in accordance with the principles of grounded theory.

Results

Twenty-one patients and 19 primary contacts were interviewed at least once during this period. Analyses and coding of the transcripts resulted in a conceptual model, distinguishing coping with the disease and coping with specific procedures of AC. In general, participants tended to rely on their pre-existing ways of coping. Situation-specific coping mostly refers to perceiving control, and related to that, trust in the medical team.

Conclusions

Patients with a brain tumor and their primary contacts perceive coping with the AC procedure as a part of coping with the disease. Although the procedure may be perceived as stressful, at the same time it offers hope and prospect. In coping with the specifics of the AC procedure, we found that feeling in control and as an extension of that, trust in the AC team were key aspects.
Population Genomics Reveals Demographic History and Climate Adaptation in Japanese Arabidopsis halleri
Authors: Suda Ryo A , Kubota Shosei , Kumar Vinod , Castric Vincent , Krämer Ute , Morinaga Shin-Ichi , Tsuchimatsu Takashi
Published: November 2024

Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge (∼50, 000 years ago). The ecological niche modeling predicted the geographic or distribution range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.
The advancements of organoids push the boundaries of glioblastoma research
Authors: Cui Gang , Xue Song , Wang Xiaoshan , Song Wei
Published: November 2024

Glioblastoma (GBM) is a malignant tumor of the nervous system, which is difficult to treat due to its strong invasiveness, rapid progression, and poor prognosis. To understand the complex biological behavior of glioblasts and the interaction between tumors and hosts, a new in vitro platform based on human cells is required, which can summarize the complex cellular structure and cell diversity of the human brain, as well as the biological behavior of GBM. Organoids are 3D self-organizing tissues, partially similar to source tissues, which can simulate the structure and physiological functions of organs or tissues in vitro. In this review, we underline the widespread application of different types of GBOs models in GBM pathogenesis, including cells derived, tumor tissues derived, and other co-culture models, as well as their application and shortcomings in the treatment of GBM.
Mobile health applications for individuals with psoriatic arthritis
Authors: Awad Rami , Pham Tammy , Stratton Jackie , Leibowitz Evan , Solomon Daniel H
Published: November 2024

Objectives

Mobile health applications (apps) hold promise as tools for symptom tracking and management of chronic rheumatic diseases such as PsA. Apps for PsA have not been systematically evaluated. We conducted a comprehensive review of apps designed for patients with PsA.

Methods

The iOS and Android app stores were searched using the term ‘arthritis’ and individual app descriptions were reviewed for ‘psoriatic arthritis’. Apps were downloaded and rated using the Mobile Application Rating Scale (MARS). Additionally, the apps were evaluated to determine functionality, use of symptom scales and potential for integration within clinical care.

Results

The search was conducted in spring 2024 and 130 apps were found that mentioned ‘arthritis’. Seven had specific mentions of PsA in their description. We found several other relevant apps by following recommendations in the app stores. In total, 10 apps for patients with PsA were identified. MARS scores suggest they were moderate to excellent in quality. The functionality of the 10 apps differed: 7 allowed for symptom tracking, 3 allowed for data export to health records, 2 allowed for medication tracking and 1 contained a patient community platform. The symptom tracking capabilities varied widely and we could find only one published study of any of the apps.

Conclusions

We analysed apps for PsA to identify potential unmet needs and found that there are few publicly available apps, their functionality varies tremendously and testing of these apps is almost non-existent. There appears to be room for improvement of apps for PsA.
Attention Deficit Hyperactivity Disorder Among Youth at Clinical High Risk of Psychosis
Authors: Braun Amy , Liu Lu , Bearden Carrie E , Cadenhead Kristin S , Cornblatt Barbara A , Keshavan Matcheri , Mathalon Daniel H , Perkins Diana O , Stone William S , Tsuang Ming T , Walker Elaine F , Woods Scott W , Cannon Tyrone D , Addington Jean
Published: November 2024

Background

Attention Deficit Hyperactivity Disorder (ADHD) affects a significant proportion of the population and is associated with numerous adverse outcomes including lower educational attainment, occupational challenges, increased substance use, and various mental health issues including psychosis. This study examined the demographic, clinical, cognitive, social cognitive, and functional differences between youth at clinical high-risk (CHR) for psychosis with and without comorbid ADHD.

Method

Data were drawn from the North American Prodrome Longitudinal Studies (NAPLS2 and NAPLS3), which included 764 and 710 CHR individuals, respectively. After applying exclusion criteria, the sample consisted of 271 CHR participants with ADHD and 1118 without ADHD. All data were examined cross-sectionally.

Results

Compared with the non-ADHD group, the ADHD group was younger, had more difficulties with role functioning, premorbid functioning, and social cognition, were more likely to have a comorbid learning disorder, and reported less depression symptoms. There were no significant differences between the groups on positive or negative psychotic symptoms, transition rates, adverse events, or other comorbid disorders including substance use and depression.

Discussion

Comorbid ADHD is likely not a significant predictor of transition to psychosis among CHR youth; however, those CHR with ADHD may experience symptoms at a younger age than those without and present with a distinct clinical profile.
Enhanced detection and molecular modeling of adaptive mutations in SARS-CoV-2 coding and non-coding regions using the c/µ test
Authors: Paradis Nicholas J , Wu Chun
Published: November 2024

Accurately identifying mutations under beneficial selection in viral genomes is crucial for understanding their molecular evolution and pathogenicity. Traditional methods like the Ka/Ks test, which assesses non-synonymous (Ka) versus synonymous (Ks) substitution rates, assume that synonymous substitutions at synonymous sites are neutral and thus is equal to the mutation rate (µ). Yet, evidence suggests that synonymous sites in translated regions (TRs) and untranslated regions (UTRs) can be under strong beneficial selection (Ks > µ) and strongly conserved (Ks ≈ 0), leading to false predictions of adaptive mutations from codon-by-codon Ka/Ks analysis. Our previous work used a relative substitution rate test (c/µ, c: substitution rate in UTR/TR, and µ: mutation rate) to identify adaptive mutations in SARS-CoV-2 genome without the neutrality assumption of the synonymous sites. This study refines the c/µ test by optimizing µ value, leading to a smaller set of nucleotide and amino acid sites under beneficial selection in both UTR (11 sites with c/µ > 3) and TR (69 nonsynonymous sites: c/µ > 3 and Ka/Ks > 2.5; 107 synonymous sites: Ks/µ > 3). Encouragingly, the top two mutations in UTR and 70% of the top nonsynonymous mutations in TR had reported or predicted effects in the literature. Molecular modeling of top adaptive mutations for some critical proteins (S, NSP11, and NSP5) was carried out to elucidate the possible molecular mechanism of their adaptivity.