Browse Articles

PairReg: A method for enhancing the learning of molecular structure representation in equivariant graph neural networks

The 3D structure of molecules contains a wealth of important information, but traditional 3DCNN-based methods fail to adequately address the transformations of rigid motions (rotation, translation, and mapping). Equivariant graph neural networks (EGNNs) emerge as efficient models to handle molecular 3D structures due to their unique mechanisms for capturing topological properties and equivariance to rigid motions. Historically, the optimization of EGNN models has been achieved by incorporating higher-order features to capture more complex topological properties. However, adding higher-order features incurs high computational costs. To address this issue, we explore the mechanism to mitigate the oversmoothing of equivariant graph neural networks and propose a new method (PairReg) to mitigate oversmoothing by utilizing equivariant information, such as coordinates, to enhance the model’s performance. We validate the performance of the model using the QM9 dataset and conduct ablation experiments on the rMD17 dataset. The results show that our approach enhances the model’s ability to characterize the 3D structure of molecules and offers new insights for enhancing the performance of EGNNs.

China reins in the spiralling construction costs of nuclear power — what can other countries learn?

Effects of microbial-derived long-chain polyunsaturated fatty acids from Aurantiochytrium limacinum BCC52274 and Mortierella sp. on growth and immunity in Litopenaeus vannamei post-larvae

The rapid growth of the aquaculture industry has increased the demand for feed ingredients, resulting in a shortage of fishmeal and fish oil, the latter of which serves as a source of essential fatty acids in aquaculture feed. As dietary supplementation of long-chain polyunsaturated fatty acids (LC-PUFA) improved growth and strengthened immunity in marine larvae, alternative sources for LC-PUFA are required to maintain sustainable aquaculture practice. This study explored the use of Aurantiochytrium limacinum BCC52274 (AL) and oil extracted from Mortierella sp. (ARASCO) as the source of LC-PUFA for the Pacific white shrimp Litopenaeus vannamei post-larvae (PLs) by using Artemia as a carrier. The Artemia were first enriched with combinations of AL and ARASCO with varying ratios of DHA:ARA at 100:0, 75:25, 50:50, 25:75, and 0:100, which were designated as Groups A, B, C, D, and E, respectively. The unenriched Artemia in Group R served as a control. The L. vannamei PL1 were fed with these Artemia for 18 days, revealing that the PL18 in Group A contained the highest biomass and average body weight among all feed groups. Meanwhile, other ratios of DHA:ARA supplementation were more beneficial to shrimp immunity, as the PL18 from Group D expressed the highest levels of prophenoloxidase II transcripts among all feed groups. The increasing proportion of ARA in the enriched Artemia also increased the levels of anti-inflammatory eicosanoids, including 15-deoxy-Δ12,14-prostaglandin J2, 11-hydroxyeicosatetraenoic acid (11-HETE), and 12-HETE. When these PLs were infected with white spot syndrome virus (WSSV), the PLs from Groups A, C, D, and E contained lower WSSV copy numbers compared with Group R, suggesting that the supplementation of LC-PUFAs from AL and ARASCO strengthened the immunity of these PLs against viral infection. However, the challenge with Vibrio harveyi resulted in no significant difference in the mean survival rates of PLs in all feed groups. Our results indicate that AL and ARASCO are more sustainable alternative sources of essential fatty acids that can be used strategically to enhance the growth and immunity of L. vannamei PLs.

Comparative evaluation of root canal morphology in mandibular first premolars with deep radicular grooves using direct vision, dental operating microscope, 2D radiographic visualisation and micro-computed tomography

Objectives The objective of this study was to evaluate the effectiveness of clinically applicable diagnostic methods such as Direct Vision (DV), Dental Operating Microscope (DOM), and two-dimensional (2D) radiographs in detecting canal orifices and root canal configurations in mandibular first premolars with deep radicular grooves. The study also aimed to compare these methods with micro-computed tomography (micro-CT) to better understand their diagnostic capabilities and to assess the applicability of the Ahmed et al. (2017) classification system across different imaging modalities. Methods A total of 133 mandibular first premolars with deep radicular grooves were scanned using micro-CT. After scanning, two examiners, blinded to micro-CT results, accessed and examined the root canal orifices of the study samples under DV, and DOM. Further evaluation of the root canal configurations was undertaken using exploration and 2D radiographic images. A second round of relocation of canals was undertaken if the radiographic view showed the presence of a missed canal. The data were then compared with the original reconstructed micro-CT images. Descriptive statistical analysis, Kappa and chi-square tests were performed to compare between methods and examiners, and the p-value was set at 0.05. Results Except for three teeth, all samples exhibited multiple canals. Micro-CT data revealed a wide range of root canal configurations, with the most common being 1MFP1-2 (19.54%), followed by 1MFP1-2-3 (15.78%), 1MFP1-2-3-2 (5.26%), and both 1MFP1-2-4 and 1MFP1-2-1 configurations, each at 4.51%. For both examiners, using the DOM resulted in detection of more canal orifices compared to DV (p < 0.001). A number of root canal configuration types including 1MFP1-2 and 1MFP1-2-1 was identified using exploration and radiographic imaging. Both examiners identified additional canals in the relocation phase. A significant difference was found when the radiographic method is compared with micro-CT results (p < 0.001), in which the latter method showed more complex root canal configuration types. Conclusions Mandibular first premolars with deep proximal grooves exhibit considerable variability and complexity in their root canal systems. The use of a dental operating microscope (DOM) significantly improves the detection of canal orifices compared to direct vision. The most frequently observed root canal configuration was 1MFP1-2. A high percentage of additional canals may be missed due to atypical locations of bifurcations along the root. While micro-CT imaging is not applicable in clinical settings, it remains a valuable reference tool in studies for enhancing our understanding of root canal morphology and guiding the development of clinically feasible diagnostic strategies.

Clinical and molecular characterization of hepatic glycogen storage disease in Saudi Arabia

Background and objectives The paucity of data on glycogen storage diseases (GSDs) from Arabs prompted us to report on hepatic GSD to characterize its clinical and molecular features and outcomes among Saudi children and to evaluate genotype‒phenotype correlations. Methods We retrospectively reviewed the charts of 65 children (37 females) with genetically confirmed hepatic GSD who presented between 2008 and 2020 and were followed up for a median duration of 9 years (range: 0.4–21 years). Results The most common hepatic GSD in our cohort was GSD Ia (37%), followed by GSD III (20%), GSD Ib (12.3%), and GSDVI (10.8%). Twenty-seven variants were identified (8 novel and 4 from the common ancestor, i.e., “founder in nature”). The most common founder variant is P.(Arg83Cys) in the G6PC1 gene (20% of the 65 GSD patients), clustering in Aseer Province. Six patients underwent liver transplantation (due to difficulty controlling hypoglycemia in 5 GSD Ia patients and severe portal hypertension in one GSD IV patient). One patient with GSD type 1b developed hepatic adenoma at the age of 17 years. A patient with GSD IXc developed portal hypertension at the age of 5 years, and one patient with GSD IXa developed cirrhosis. Renal complications developed in 18 patients. An echocardiogram was performed in 16 patients and revealed mild–moderate asymptomatic left ventricular hypertrophy in 5 patients. The majority of the hepatic GSD cases in our cohort manifested a severe phenotype (hepatomegaly, hypoglycemia, ± systemic involvement); only the 7 GSD VI patients manifested a mild phenotype (hepatomegaly without hypoglycemia). No “genotype‒phenotype correlations” could be observed when the two common G6PC1 gene variants [p.(Arg83Cys) versus p.(Gln20Arg)] were compared. Conclusion With the exception of GSD VI, all the hepatic GSD subtypes in Saudi Arabia are associated with a severe phenotype. Identification of the predominant gene variants and their geographic distribution in any population is likely to facilitate rapid molecular analysis by future targeting of that specific mutation.

Does an improved HDI trigger tourism outflows for China? New evidence from the ARDL cointegration approach

Extant studies have predominantly focused on understanding the effects of inbound tourism on economic growth. At the same time, it ignores the key factors that promote outbound tourism in a country. Outbound tourism not only plays a crucial role in the sustainable development of the host country but also helps foster an understanding of cross-cultural similarities and differences, promoting goodwill towards the home country. It also provides an opportunity to experience the cuisine, weather, and working habits of different geographical locations. Therefore, this study aims to investigate the relationship between the Human Development Index and tourism outflows in the context of China. We use data from the period 1995–2020 to estimate the relationship between the Human Development Index (HDI) and tourism outflows. The short-run and long-run Autoregressive Distributed Lag (ARDL) results indicate that improving China’s Human Development Index (HDI) has a positive impact on tourism outflows. More precisely, a 1 unit increase in the HDI index will increase tourism outflow by 5.25%. Furthermore, the results of individual HDI show that life expectancy, per capita income, and education considerably promote China’s tourism outflows. Policy prescriptions are outlined regarding the spillover effects of China’s human development on the tourism-led economic growth of recipient countries.

Comprehensive analysis of molecular characteristic and clinical prognosis of CD8+ T cell related genes in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive, life-threatening interstitial lung disease whose pathogenesis remains unclear. There is evidence showing the possible role of CD8+ T cells in the pathogenesis of IPF and the correlation with the clinical symptoms of IPF. In order to further explore the role of CD8+ T cells in IPF, we screened CD8+ T cell related genes (CRG) that are associated with IPF prognosis, and established the molecular typing characteristics of IPF. Subsequently, CXCR4, GPR56 and PAK1 were screened as independent prognostic factors. Expression profiles and multivariate analysis coefficients were used to establish and validate prognostic features of IPF. Immuno-infiltration characteristics of the established feature were also analyzed. Subsequent in vitro experiments verified the abnormal expressions of three independent prognostic factors in TGF-β1 treated IPF model at protein and mRNA levels. Our findings shed new light on the important role of CD8+ T cells in the pathogenesis of IPF and provide potential targets for predicting prognosis and possible future clinical applications.

An instrumented approach to quantify wrist and finger flexor spasticity: A study protocol

Spasticity in the upper limb is a common condition observed in individuals with Cerebral Palsy, post-stroke or following traumatic brain injury. Affected patients present with significant functional and care challenges. Advances in both conservative and surgical treatments necessitate improved assessment tools. This study aims to develop and validate an instrumented measurement procedure combining 3D motion analysis, surface electromyography (sEMG), and musculoskeletal modeling to assess wrist and finger spasticity and function. The goal is to create a preoperative assessment tool for surgical strategy determination and a postoperative outcome measurement. We hypothesize that this combination of technologies will offer superior assessment accuracy compared to traditional methods and provide predictive insights into therapeutical outcomes.

Expression of Concern: Atm inhibition decreases lens opacity in a rat model of galactose-induced cataract

Effect of tillage system on epigeal and foliar insect predation in an organic cropping system in Pennsylvania, USA

Organic growers rely largely on cultural and biological control to manage pest populations and often use soil disturbance with inversion tillage to manage pests and weeds, incorporate crop residues and fertility amendments, and create seedbeds. Reduced-tillage systems are often associated with greater populations of insect generalist predators, as tillage can directly and indirectly disrupt predators and their activity. We investigated the in-season and legacy effects of soil disturbance in three organic feed grain and one forage production systems that varied in frequency and intensity of disturbance on epigeal predation rates on larval waxworms, Galleria mellonella L., and foliar predation rates on eggs of the western bean cutworm, Striacosta albicosta Smith, and European corn borer, Ostrinia nubilalis (Hübner), by arthropod natural enemies. The experimental site included three annual feed grain production systems comprised of a corn, Zea mays L., soybean, Glycine max (L.) Merr., and wheat Triticum aestivum L. sequence and one forage production system represented by a biculture of alfalfa, Medicago sativa L. and orchardgrass, Dactylis glomerata L. We also measured damage to corn ears from naturally occurring lepidopteran pests and corn yield. The epigeal predation rate on sentinel waxworms in the system managed predominantly with reduced tillage (64 ± 6.4%) was significantly greater than in the systems managed predominantly with inversion tillage (44 ± 5.5%) or with a shallow high-speed disk (48 ± 5.1%). There was no effect of intensity or frequency of soil disturbance on foliar predation or foliar predator community composition in corn. Damage to corn ears from lepidopteran pests was greater in the system managed predominantly with a shallow high-speed disk (51 ± 4.4% damaged ears) compared to systems predominantly managed with inversion tillage (35 ± 4.3%) or no-till planting (31 ± 1.4%). There was no difference in corn yield across systems, but corn yield variability was greatest in the reduced tillage system. We suggest that the occasional use of inversion tillage with a moldboard plow may not have lasting detrimental effects on foliar or epigeal predation rates on arthropod pests in annual organic grain production systems.

Unexpected danger lurks in this giant fault in the Yukon

Synthesis, physical properties, and root canal sealing of experimental MTA- and salicylate-based root canal sealers

Objectives To develop and evaluate the physical properties and sealing ability within the root canal of three experimental sealers based on MTA and a salicylate resin. Materials and methods The experimental sealers were composed of two pastes. The base paste was prepared using 1,3-butyleneglycol disalicylate and bismuth oxide. Three different catalytic pastes were formulated, creating three groups: [MTA] n,n,dihydroxyethyl-p-toluidine (DPT), titanium dioxide (TiO2), and mineral trioxide aggregate (MTA); [MTA-HA] DPT + TiO2 + MTA + hydroxyapatite (HA); and [MTA-DCPD] DPT + TiO2 + MTA + dibasic calcium phosphate dihydrate (DCPD). MTA Fillapex (Angelus) was used as the commercial reference (control). The sealers were manipulated at a 1:1 ratio (base paste:catalyst). Tests for working time and setting time, flow, and film thickness were conducted following ISO 6876:2012 standards. Single-rooted human teeth root canals were utilized for evaluating root canal filling using micro-computed tomography, push-out bond strength testing, and sealer penetration into dentinal tubules using confocal microscopy. Failure patterns in the push-out test were classified as adhesive, cohesive, or mixed. Sealer micromorphology was analyzed via scanning electron microscopy. Data were analyzed statistically (α = 0.05). Results MTA Fillapex showed the longest working and setting times, highest flow, the lowest film thickness, and better penetration into dentinal tubules. There was no difference in void among evaluated sealers. Overall, MTA-DCPD sealer showed the lowest bond strength values for cervical and apical thirds. Micromorphological analysis revealed similar crystallographic properties among all sealers. Conclusions The sealers tested showed reduced working and setting times, with flow and film thickness according to ISO 6876:2012. Their void volume and bond strength were similar to MTA Fillapex, except for MTA-DCPD. Clinical Relevance: The experimental root canal sealers demonstrated suitable physical properties and good adaptation within the root canal.

Experience of clinical incivility and stress in nursing students: A mixed-method study

Nursing students often experience uncivil words or actions during clinical practice which can lead to significant stress. The purpose of our study was to quantitatively investigate the degree of clinical incivility and stress experienced by students and the statistical relationship between them and qualitatively explore students’ personal experiences of clinical incivility and stress. Our study was conducted from April 25 to May 27, 2023, using a mixed-method design. Phase One, the quantitative component, used a non-experimental, descriptive, cross-sectional study design with a 10-minute self-administered online survey. Phase Two, the qualitative component, used an in-person focus group to collect data on participants’ personal experiences of clinical incivility and stress. A total of 159 junior and senior pre-licensure nursing students attending a clinical practicum of a Bachelor of Science in Nursing (BSN) program in South Korea completed the quantitative online survey. Subsequently, 20 students voluntarily attended focus group sessions. To analyze the online survey data the study sample was divided into a clinical incivility group and a non-clinical incivility group. A group comparative analysis using chi-square and t-test was conducted. To analyze the qualitative focus group data, Colaizzi’s method to identify significant themes was used. Prevalence of clinical incivility experience in the students was 79.9% (n = 123 out of 159). Clinical incivility was significantly positively correlated with the students’ reported stress level (r = .317, p < .001); students who experienced greater clinical incivility reported higher levels of stress. Additionally, higher levels of clinical incivility were linked to lower levels of satisfaction with clinical practice and the clinical site. Analysis of the focus group data revealed four main themes regarding the students’ experiences: 1) Being defenselessly exposed to verbal or nonverbal abuse, 2) Not being treated as a student nurse, 3) Experiencing a combination of negative feelings, and 4) Taking incivility for granted in the clinical site. Major perpetrators of clinical incivility among nursing students were nurses at the clinical sites. To prevent and manage clinical incivility, nursing schools and clinical agencies must collaborate to establish incivility monitoring, communication, and evidence-based policies and intervention programs.

Controversial ‘arsenic life’ paper retracted after 15 years — but authors fight back

Protein-primed homopolymer synthesis by an antiviral reverse transcriptase

Genetic diversity and evolutionary insights of Dali tea (Camellia taliensis) in the Lancang River Basin: Implications for tea breeding and resource conservation

Dali tea (Camellia taliensis), serving as a primitive wild species within the section Thea, represents a crucial genetic source for the domestication of Pu-erh tea (C. sinensis var. assamica) due to its strong stress tolerance and unique biochemical composition. It is of key value for the conservation of tea genetic resources and breeding innovation. Utilizing the SLAF-seq (Specific-Locus Amplified Fragment Sequencing) technique, this study systematically analyzed the genetic diversity and evolutionary relationships among five geographic populations (16 C. taliensis and 4 C. sinensis var. assamica accessions) within the Lancang River basin. Results revealed significant genetic differentiation among the C. taliensis populations. Pronounced genetic isolation was observed between the Lincang Daxueshan and Dali Nanjian populations. Localized gene introgression occurred between wild C. taliensis (Nanjian population) and C. sinensis var. assamica.The wild Lincang Daxueshan population formed a monophyletic clade at the base of the phylogenetic tree, exhibiting strong genetic isolation and high differentiation levels (Fst = 0.364) but low genetic diversity. In contrast, the cultivated population (Banna Germplasm Repository) displayed a mixed genetic background, with wild genetic components constituting only 50%−60%. The Lincang Daxueshan wild population showed a low minor allele frequency (MAF = 0.204) and a mild inbreeding coefficient (Fis = 0.09), indicating a potential risk of genetic erosion. Conversely, the Banna Germplasm Repository population exhibited the highest genetic diversity (Shannon Index = 0.318), highlighting the effectiveness of ex situ conservation and its potential as a vital gene donor for tea breeding. This study underscores the unique status of the upper Lancang River basin in Yunnan as a core conservation area for C. taliensis genetic diversity. We propose strategies of “delineating priority zones for in situ conservation” and “facilitating inter-population germplasm exchange,” providing a molecular basis for conserving wild tea resources and breeding for stress resistance. Employing high-density SNP markers, we obtained 5,182,931 loci with an average sequencing depth of 19.30x. This enabled quantification of gene flow between wild and cultivated populations (Nm = 0.18) and clarified the contribution of introgressive domestication to the genetic makeup of cultivated tea. These findings provide a theoretical foundation for understanding interspecific interaction mechanisms in tea plant evolution and hold significant implications for promoting regional ecological conservation and biodiversity maintenance.

Apparent differences between human and chimp proteomes are reduced when considering human population: Human specific variants are enriched in disordered and compositionally biased regions

Humans exhibit significant differences from other primates in anatomy, physiology, behavior, and culture, despite having similar genomes. Understanding the genetic basis of these unique human traits has long been a goal of science and philosophy. Previous studies, including the comparison of the reference genomes, showed a high degree of sequence identity between the proteomes of humans and chimpanzees (Pan troglodytes), suggesting that differences may lie in gene regulation rather than protein function. To pinpoint human-specific protein mutations with possible relevance for human-specific traits, we went further in the study of human-chimp proteome differences by taking into account human genetic variation data from the Genome Aggregation Database (gnomAD) at protein-coding genes. We additionally included 11 primate genomes to identify human-specific amino acids. Results showed that human-specific positions were dramatically reduced when considering population diversity. Our analysis identified 6210 human-specific amino acid substitutions across 4475 proteins. Interestingly, these residues are enriched on disordered and compositionally biased regions, suggesting a role in protein regulation instead of a catalytic or structural one. Accordingly, the set of proteins holding them was significantly enriched in proteins with disordered regions and with protein binding functions. We found that a subset of these residues is not only different in humans but also conserved across non-human primates, further supporting their potential importance in making us different from other primates.

Surgical workspace in porcine thoracoscopy with two-lung ventilation

In neonatal and pediatric thoracoscopy, two-lung ventilation is often used due to the size constraints of double-lumen tubes or selective bronchial blockers. Reducing the volume of both lungs to create surgical workspace requires moderation in the application of capnothorax insufflation pressures, and requires experienced anesthesiologists to manage ventilation. This balance was investigated in anesthetized pigs in the left decubitus position with a capnothorax, using volume-guaranteed intermittent positive pressure ventilation. End-expiratory computed tomography scans were obtained in 10 pigs (median weight 21.5 kg, range 17.8 to 26.3 kg) during incremental CO2 insufflation pressures of 0, 3, 5, 6, 8 and 10 mmHg. Capnothorax, right lung and left lung volumes were measured. At an insufflation pressure of 10 mmHg, peak ventilation pressures had a median of 35 cmH2O. Insufflation pressures ≥ 6 mmHg had profound cardiorespiratory effects, requiring inotropic support. Capnothorax volume reached a median of 1503 (IQR 1465–1596) ml at 10 mmHg, at which diaphragmatic displacement contributed 79.5% to capnothorax volume, with smaller contributions from lung volume (16.1%) and thoracic expansion (4.4%). Thoracoscopic workspace during two-lung ventilation originates mainly from diaphragmatic displacement. In a porcine model the marked cardiorespiratory consequences of insufflation emphasized the need to minimize insufflation pressures.

Iterative learning control of neuronal firing based on FHN and HR models

Neuronal firing patterns are fundamental to neural information processing and functional regulation, with abnormal firing closely linked to a range of neurological disorders. However, existing neuromodulation techniques largely rely on open-loop stimulation strategies, which lack adaptability and fail to provide precise control over neuronal dynamics. To address this limitation, this study introduces a novel iterative learning control (ILC) framework based on proportional-integral (PI) control for closed-loop modulation of neuronal firing patterns. The proposed method is developed and validated using two representative neuron models: the FitzHugh–Nagumo (FHN) and Hindmarsh–Rose (HR) models. A dynamical analysis of these models is conducted, followed by the design and implementation of a PI-based ILC strategy. Numerical simulations demonstrate that the proposed control method significantly outperforms conventional PI control, achieving lower tracking errors, enhanced control accuracy, and improved system stability. Additionally, the ILC approach exhibits strong adaptability to different neuronal dynamics, highlighting its potential for precise and robust regulation in complex neural systems. These findings offer a theoretical basis for advancing closed-loop neuromodulation technologies, with promising implications for applications in neurorehabilitation and the treatment of neurological disorders.

Evaluating the short-term effects of dance on motor and non-motor outcomes in people living with Parkinson’s: A crossover study

Purpose To investigate the short-term effects of a single dance class on motor and non-motor outcomes in people living with Parkinson’s. Methods A crossover design was used. Nineteen people participated. All participants took part in both dance and lecture control conditions seven days apart in a counterbalanced order. Outcomes of gait, balance, functional mobility, and aspects of cognition were measured before and after each condition. A visual analogue scale evaluated self-perceived changes in fatigue, energy, depression, anxiety, concentration, and movement. Statistical analyses were performed using 2x2 repeated-measures ANOVAs with time (pre vs. post) and condition (dance vs. lecture) as factors. Results Results showed functional mobility (measured by the Timed Up and Go) improved to a greater extent after dance compared to the lecture. Significant improvements after both dance and lecture sessions were demonstrated for other outcomes measuring balance, cognition, and anxiety, indicating either both conditions had a comparable impact or practice effects may have influenced results. Conclusions Further research is needed to confirm the presence and strength of the short-term effect of dance on functional mobility, to assess the impact of dancing on aspects of cognition and anxiety, and to hone the approach to studying the short-term effects of dance.