Precise control of microtubule disassembly in living cells.

Microtubules tightly regulate various cellular activities. Our understanding of microtubules is largely based on experiments using microtubule-targeting agents, which, however, are insufficient to dissect the dynamic mechanisms of specific microtubule populations, due to their slow effects on the entire pool of microtubules. To overcome this technological limitation, we have used chemo and optogenetics to disassemble specific microtubule subtypes, including tyrosinated microtubules, primary cilia, mitotic spindles, and intercellular bridges, by rapidly recruiting engineered microtubule-cleaving enzymes onto target microtubules in a reversible manner. Using this approach, we show that acute microtubule disassembly swiftly halts vesicular trafficking and lysosomal dynamics. It also immediately triggers Golgi and ER reorganization and slows the fusion/fission of mitochondria without affecting mitochondrial membrane potential. In addition, cell rigidity is increased after microtubule disruption owing to increased contractile stress fibers. Microtubule disruption furthermore prevents cell division, but does not cause cell death during interphase. Overall, the reported tools facilitate detailed analysis of how microtubules precisely regulate cellular architecture and functions.

RTL1/PEG11 imprinted in human and mouse brain mediates anxiety-like and social behaviors and regulates neuronal excitability in the locus coeruleus.

RTL1/PEG11, which has been associated with anxiety disorders, is a retrotransposon-derived imprinted gene in the placenta. However, imprinting patterns and functions of RTL1 in the brain have not been well-investigated. We found Rtl1 was paternally, but not maternally, expressed in brain stem, thalamus, and hypothalamus of mice, and imprinting status of RTL1 was maintained in human brain. Paternal Rtl1 knockout (Rtl1m+/p-) mice had higher neonatal death rates due to impaired suckling, and low body weights beginning on embryonic day 16.5. High paternal expression of Rtl1 was detected in the locus coeruleus (LC) and Rtl1m+/p- mice showed an increased delay in time of onset for action potentials and inward currents with decreased neuronal excitability of LC neurons. Importantly, Rtl1m+/p- mice exhibited behaviors associated with anxiety, depression, fear-related learning and memory, social dominance, and low locomotor activity. Taken together, our findings demonstrate RTL1 is imprinted in brain, mediates emotional and social behaviors, and regulates excitability in LC neurons.

Neuronal NLRP3 inflammasome mediates spreading depolarization-evoked trigeminovascular activation.

Spreading depolarization (SD), the underlying mechanism of migraine aura, may trigger the opening of the pannexin 1 (PANX1) pore to sustain the cortical neuroinflammatory cascades involved in the genesis of headache. Yet, the mechanism underlying SD-evoked neuroinflammation and trigeminovascular activation remains incompletely understood. We characterized the identity of inflammasome activated following SD-evoked PANX1 opening. Pharmacological inhibitors targeting PANX1 or NLRP3 as well as genetic ablation of Nlrp3 and Il1b were applied to investigate the molecular mechanism of the downstream neuroinflammatory cascades. In addition, we examined whether SD-triggered microglial activation facilitates neuronal NLRP3-mediated inflammatory cascades. Pharmacological inhibition of toll-like receptors TLR2/4, the potential receptors of the damage-associated molecular pattern HMGB1, was further employed to interrogate the neuron-microglia interplay in SD-induced neuroinflammation. We found that NLRP3 but not NLRP1 or NLRP2 inflammasome was activated following PANX1 opening after single or multiple SDs evoked by either KCl topical application or non-invasively with optogenetics. The SD-evoked NLRP3 inflammasome activation was observed exclusively in neurons but not microglia or astrocytes. Proximity ligation assay demonstrated that the assembly of the NLRP3 inflammasome occurred as early as 15 min after SD. Genetic ablation of Nlrp3 or Il1b or pharmacological inhibition of PANX1 or NLRP3 ameliorated SD-induced neuronal inflammation, middle meningeal artery dilatation, calcitonin gene-related peptide expression in trigeminal ganglion and c-Fos expression in trigeminal nucleus caudalis. Moreover, multiple SDs induced microglial activation subsequent to neuronal NLRP3 inflammasome activation, which in turn orchestrated with neurons to mediate cortical neuroinflammation, as demonstrated by decreased neuronal inflammation after pharmacological inhibition of microglia activation or blockade of the TLR2/4 receptors. To conclude, single or multiple SDs evoked activation of neuronal NLRP3 inflammasomes and its downstream inflammatory cascades to mediate cortical neuroinflammation and trigeminovascular activation. In the context of multiple SDs, the cortical inflammatory processes could be facilitated by SD-evoked microglia activation. These findings may implicate the potential role of innate immunity in migraine pathogenesis.

The effect of a bone-preserving board game program on the knowledge, attitudes and preventive behaviors of osteoporosis in older adults.

Osteoporosis predisposes to fractures, which affect the quality of life and can be life-threatening. However, the knowledge, attitudes and preventive behaviors of osteoporosis in older adults are insufficient. The aim of this paper was to develop and test the effect of a bone-preserving board game program among older adults. A convenience sample of 85 older adults recruited from two community activity centers in southern Taiwan were assigned to either an experimental group or a control group. The experimental group played a bone-preserving board game for 4 weeks, and the control group participated in routine community center activities. The generalized estimating equation showed significantly larger improvements in knowledge, attitudes, and preventive behaviors in the experimental group than in the control group. Board games designed for older adults can support public health education and help prevent osteoporosis. Our results provide a reference for educators, clinical practitioners and researchers.

Investigation of New Psychoactive Substances (NPS), Other Illicit Drugs, and Drug-Related Compounds in a Taiwanese Wastewater Sample Using High-Resolution Mass-Spectrometry-Based Targeted and Suspect Screening.

The proliferation of new psychoactive substances (NPSs) in recent years has posed a significant challenge to public health. Traditional monitoring methods have proven insufficient in tracking these constantly evolving substances, leading to the development of alternative approaches such as wastewater-based epidemiology (WBE). The present study aims to utilize high-resolution mass spectrometry (HRMS)-based targeted and suspect screening to profile NPS, other illicit drugs, and drug-related compounds in a Taiwanese wastewater sample. For the targeted analysis, 8 out 18 standards of illicit drugs have been identified. The suspect screening approach based on approximately 3600 substances in the SWGDRUG library can further identify 92 compounds, including opiate analgesics, synthetic cathinones, phenylalkylamines derivatives, phenethylamine derivatives, tryptamine derivatives, steroids, and ephedrine-related compounds. Additionally, the presence of 5-methoxy-2-aminoindane (MEAI) in the wastewater indicates that drug dealers have recently sold this potential NPS to evade drug regulations. This study firstly reports the HRMS-based comprehensive profile of NPS, other illicit drugs, and drug-related compounds in Taiwan, which could be applied as biomarkers for estimating the consumption of drugs.

The efficacy of a mindfulness-based exercise program in older residents of a long-term care facility in Taiwan.

Older people living in long-term care facilities remain largely inactive, and therefore promoting exercise in this population is necessary. This study evaluated the efficacy of a mindfulness-based exercise program in older residents of a long-term care facility in Taiwan. A convenience sample of 72 older residents of a long-term care facility were recruited and assigned to either an experimental group or a control group. The experimental group (n = 36) participated in an 8-week mindfulness-based exercise program, and the control group (n = 36) received routine care. The generalized estimating equation showed significantly larger improvements in a fear of falling, exercise self-efficacy, dynamic balance, and muscle strength in the experimental group than in the control group from baseline to the end of the intervention and 3 months after the end of the intervention. This study provides a reference for how to improve exercise practice in older people living in long-term care facilities.

Fluid intelligence is associated with cortical volume and white matter tract integrity within multiple-demand system across adult lifespan.

BACKGROUND: Fluid intelligence (Gf) is the innate ability of an individual to respond to complex and unexpected situations. Although some studies have considered that the multiple-demand (MD) system of the brain was the biological foundation for Gf, further characterization of their relationships in the context of aging is limited. The present study hypothesized that the structural metrics of the MD system, including cortical thickness, cortical volumes, and white matter (WM) tract integrity, was the brain correlates for Gf across the adult life span. Partial correlation analysis was performed to investigate whether the MD system could still explain Gf independent of the age effect. Moreover, the partial correlations between Gf and left/right structural metrics within the MD regions were compared to test whether the correlations displayed distinct lateralization. METHODS: The participants were recruited from the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) databank, comprising the images of 603 healthy participants aged 18-88 years acquired on a 3-T system. The MRI data included high-resolution T1-weighted and diffusion-weighted images, from which gray matter and WM structural metrics of the MD system were analyzed, respectively. The structural metrics of gray matter were quantified in terms of cortical volume/thickness of five pairs of cortical regions, and those of WM were quantified in terms of the mean axial diffusivity (DA), radial diffusivity (DR), mean diffusivity (DM), and generalized fractional anisotropy (GFA) on five pairs of tracts. Partial correlation controlling for age and sex effects, was performed to investigate the associations of Gf scores with the mean DA, DR, DM and GFA of all tracts in the MD system, those of left and right hemispheric tracts, and those of each tract. Fisher's exact test was used to compare the partial correlations between left and right MD regions. RESULTS: The linear relationship between cortical volumes and Gf was evident across all levels of the MD system even after controlling for age and sex. For the WM integrity, diffusion indices including DA, DR, DM and GFA displayed linear relationships with Gf scores at various levels of the MD system. Among the 10 WM tracts connecting the MD regions, bilateral superior longitudinal fasciculus I and bilateral frontal aslant tracts exhibited the strongest and significant associations. Our results did not show significant inter-hemispheric differences in the associations between structural metrics of the MD system and Gf. CONCLUSION: Our results demonstrate significant associations between Gf and both cortical volumes and tract integrity of the MD system across the adult lifespan in a population-based cohort. We found that the association remained significant in the entire adult lifespan despite simultaneous decline of Gf and the MD system. Our results suggest that the MD system might be a structural underpinning of Gf and support the fronto-parietal model of cognitive aging. However, we did not find hemispheric differences in the Gf-MD correlations, not supporting the hemi-aging hypothesis.

Diminution of context association memory structure in subjects with subjective cognitive decline.

Alzheimer's disease (AD) progresses insidiously from the preclinical stage to dementia. While people with subjective cognitive decline (SCD) have normal cognitive performance, some may be in the preclinical stage of AD. Neurofibrillary tangles appear first in the transentorhinal cortex, followed by the entorhinal cortex in the clinically silent stage of AD. We expected the earliest changes in subjects with SCD to occur in medial temporal subfields other than the hippocampal proper. These selective structural changes would affect specific memory subcomponents. We used the Family Picture subtest of the Wechsler Memory Scale-III, which was modified to separately compute character, activity, and location subscores for episodic memory subcomponents. We recruited 43 subjects with SCD, 44 subjects with amnesic mild cognitive impairment, and 34 normal controls. MRI was used to assess cortical thickness, subcortical gray matter volume, and fractional anisotropy. The results demonstrated that SCD subjects showed significant cortical atrophy in their bilateral parahippocampus and perirhinal and the left entorhinal cortices but not in their hippocampal regions. SCD subjects also exhibited significantly decreased mean fractional anisotropy in their bilateral uncinate fasciculi. The diminution of cortical thickness over the mesial temporal subfields corresponded to brain areas with early tangle deposition, and early degradation of the uncinate fasciculus was in accordance with the retrogenesis hypothesis. The parahippocampus and perirhinal cortex contribute mainly to context association memory while the entorhinal cortex, along with the uncinate fasciculus, contributes to content-related contextual memory. We proposed that context association and related memory structures are vulnerable in the SCD stage.

Clinicopathological features and cancer transcriptomic profiling of poorly cohesive gastric carcinoma subtypes.

Gastric poorly cohesive carcinoma (PCC) manifests with a diffuse pattern and diverse tumor cell morphologies, often indicating a more unfavorable prognosis. Recent consensus has reclassified PCC based on the proportion of signet-ring cells (SRCs) in tumors for research purposes. The two most distinct subtypes, poorly cohesive carcinoma not otherwise specified (PCC-NOS) and signet-ring cell carcinoma (SRCC), are characterized by less than 10% and more than 90% SRCs, respectively. However, research comparing the clinicopathological and transcriptomic differences between these subtypes remains limited. In this study, we conducted a comparative analysis of clinicopathological features in 55 advanced-stage PCCs, consisting of 43 PCC-NOS and 12 SRCC cases. Subsequently, 12 PCC-NOS and 5 SRCC cases were randomly selected for initial cancer-related gene expression profiling and pathway enrichment analysis using the GeoMx digital spatial profiler, followed by validation in a separate validation group comprising 16 PCC-NOS and 6 SRCC cases. These transcriptomic findings were then correlated with tumor morphology and clinicopathological data. PCC-NOS cases exhibited larger tumor size, a higher prevalence of pathological N3 disease, and a worse 1-year progression-free survival rate compared to SRCC cases. Clustering of PCC-NOS and SRCC was successfully achieved using the GeoMx Cancer Transcriptome Atlas. Among all studied genes, only MMP7 showed differential expression, with its overexpression significantly associated with the PCC-NOS subtype, increased perineural invasion, and earlier disease progression. Pathway analysis revealed significantly enriched pathways in PCC-NOS related to vesicle-mediated transport, adaptive immune systems, oncogenic signaling, and extracellular matrix organization, while SRCC displayed significant enrichment in pathways associated with respiratory electron transport and the cell cycle. In conclusion, this study compares and correlates clinicopathological features and transcriptomic data between PCC-NOS and SRCC at advanced stages, employing the latest consensus classification and a novel platform for analysis.

Study on Anti-Inflammatory Effects of and Muscle Recovery Associated with Transdermal Delivery of Chaenomeles speciosa Extracts Using Supersonic Atomizer on Rat Model.

Repetitive motion or exercise is associated with oxidative stress and muscle inflammation, which can lead to declining grip strength and muscle damage. Oleanolic acid and ursolic acid have anti-inflammatory and antioxidant properties and can be extracted from Chaenomeles speciosa through ultrasonic sonication. We investigated the association between grip strength declines and muscle damage induced by lambda carrageenan (LC) injection and exercise exposure in rats. We also assessed the reparative effects of transdermal pretreatment and post-treatment with C. speciosa extracts (CSEs) by using a supersonic atomizer. The half-maximal inhibitory concentration (IC50) of CSEs for cells was 10.5 mg/mL. CSEs significantly reduced the generation of reactive oxygen species and inflammatory factors (interleukin [IL]-6 and IL-1ß) in in vitro cell tests. Rats subjected to LC injection and 6 weeks of exercise exhibited significantly increased inflammatory cytokine levels (IL-1ß, TNF-α, and IL-6). Hematoxylin and eosin staining revealed inflammatory cell infiltration and evident muscle damage in the gastrocnemius muscle, which exhibited splitting and the appearance of the endomysium and perimysium. The treated rats' grip strength significantly declined. Following treatment with CSEs, the damaged muscles exhibited decreased IL-1ß, TNF-α, and IL-6 levels and normal morphologies. Moreover, grip strength significantly recovered. Pretreatment with CSEs yielded an immediate and significant increase in grip strength, with an increase of 180% and 165% occurring in the rats exposed to LC injection and exercise within the initial 12 h period, respectively, compared with the control group. Pretreatment with CSEs delivered transdermally using a supersonic atomizer may have applications in sports medicine and training or competitions.

A bovine whey protein extract can induce the generation of regulatory T cells and shows potential to alleviate asthma symptoms in a murine asthma model.

The number of people with asthma has dramatically increased over the past few decades and the cost of care is more than $11·3 billion per year. The use of steroids is the major treatment to control asthma symptoms, but the side effects are often devastating. Seeking new drugs or new strategies to reduce the dose of steroid taken has always been an important task. A bovine whey protein extract (WPE), which is enriched in transforming growth factor-ß (TGF-ß), has been demonstrated to have the potential for reducing symptoms associated with mild-to-moderate T-helper cell type 1-mediated psoriasis in human subjects. However, whether WPE also has potential for inhibiting T-helper cell type 2 (Th2)-mediated disease remains unclear. In the present study, using a murine asthma model, we found that sensitised mice fed WPE daily, before they were challenged, resulted in reducing airway inflammation, serum ovalbumin-specific IgE, Th2-related cytokine production and airway hyperresponsiveness. Increase in the regulatory T cell (Treg) population in vitro and in vivo was observed when treated with WPE. According to the results from the TGF-ß-blocking antibody study, we suggest that TGF-ß is the main component that endows WPE with the potential to reduce the generation of Treg. Thus, the present data suggest that WPE has the potential to alleviate the symptoms of asthma by inducing the generation of Treg. Therefore, regular administration of WPE might be potentially beneficial for patients with asthma.

Assessing the Resilience of Machine Learning Classification Algorithms on SARS-CoV-2 Genome Sequences Generated with Long-Read Specific Errors.

The emergence of third-generation single-molecule sequencing (TGS) technology has revolutionized the generation of long reads, which are essential for genome assembly and have been widely employed in sequencing the SARS-CoV-2 virus during the COVID-19 pandemic. Although long-read sequencing has been crucial in understanding the evolution and transmission of the virus, the high error rate associated with these reads can lead to inadequate genome assembly and downstream biological interpretation. In this study, we evaluate the accuracy and robustness of machine learning (ML) models using six different embedding techniques on SARS-CoV-2 error-incorporated genome sequences. Our analysis includes two types of error-incorporated genome sequences: those generated using simulation tools to emulate error profiles of long-read sequencing platforms and those generated by introducing random errors. We show that the spaced k-mers embedding method achieves high accuracy in classifying error-free SARS-CoV-2 genome sequences, and the spaced k-mers and weighted k-mers embedding methods are highly accurate in predicting error-incorporated sequences. The fixed-length vectors generated by these methods contribute to the high accuracy achieved. Our study provides valuable insights for researchers to effectively evaluate ML models and gain a better understanding of the approach for accurate identification of critical SARS-CoV-2 genome sequences.

Benchmarking machine learning robustness in Covid-19 genome sequence classification.

The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome-millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional approaches to understanding the diversity, dynamics, and evolution of viruses, is nonetheless a rich resource for machine learning (ML) approaches as alternatives for extracting such important information from these data. It is of hence utmost importance to design a framework for testing and benchmarking the robustness of these ML models. This paper makes the first effort (to our knowledge) to benchmark the robustness of ML models by simulating biological sequences with errors. In this paper, we introduce several ways to perturb SARS-CoV-2 genome sequences to mimic the error profiles of common sequencing platforms such as Illumina and PacBio. We show from experiments on a wide array of ML models that some simulation-based approaches with different perturbation budgets are more robust (and accurate) than others for specific embedding methods to certain noise simulations on the input sequences. Our benchmarking framework may assist researchers in properly assessing different ML models and help them understand the behavior of the SARS-CoV-2 virus or avoid possible future pandemics.

Comparing the effectiveness of board game-based and drill-based education programs in improving Taiwanese nurses' fire safety knowledge, attitudes, and behavior: A quasi-experimental study.

BACKGROUND: Fire education is currently dominated by drill-based programs, however only a limited number of participants may take part in fire drills. This gap could be addressed by the development of innovative board game-based educational programs. OBJECTIVE: This study sought to compare the effectiveness of board game-based and drill-based fire safety education programs in improving nurses' fire safety knowledge, attitudes, and behavior. METHODS: In this quasi-experimental study, 122 nurses were purposively sampled from a hospital in southern Taiwan. The participants were divided into two groups based on their willingness. Sixty-two nurses in the game-based group took part in an hour-long educational board game for fire safety; and 60 in the drill-based group took part in an hour-long fire drill organized by the hospital. The participants' pre- (T0) and post-intervention (T1) questionnaire scores on fire safety knowledge, attitudes, and behavior were recorded. The statistical methods included descriptive statistics and t-tests. RESULTS: After the interventions, both groups had improved safety knowledge, attitudes, and behavior. However, from T0 to T1, only fire safety knowledge was significantly higher in the game-based group than in the drill-based group, and there were no significant differences in fire safety attitudes and behavior between the two groups. CONCLUSIONS: A board game-based fire education program is similar to a tabletop exercise, and drill-based programs more accurately reflect actual circumstances. Both methods can be applied based on the educational objectives and actual educational settings. The results of this study may function as a reference for designing clinical, educational, and academic interventions for fire safety in healthcare settings.

Ameliorative Effects of Cumin Extract-Encapsulated Chitosan Nanoparticles on Skeletal Muscle Atrophy and Grip Strength in Streptozotocin-Induced Diabetic Rats.

Skeletal muscle atrophy is a disorder characterized by reductions in muscle size and strength. Cumin extract (CE) possesses anti-inflammatory, antioxidant, and hypoglycemic properties. Its pharmaceutical applications are hindered by its low water solubility and by its cytotoxicity when administered at high doses. In this study, we have developed a simplified water distillation method using a rotary evaporator to isolate the active components in cumin seeds. The anti-inflammatory effects of CE and its potential to ameliorate skeletal muscle atrophy in rats with streptozotocin (STZ)-induced diabetes were evaluated. The half-maximal inhibitory concentration (IC50) of CE for cells was 80 µM. By encapsulating CE in chitosan nanoparticles (CECNs), an encapsulation efficacy of 87.1% was achieved with a slow release of 90% of CE after 24 h of culturing, resulting in CECNs with significantly reduced cytotoxicity (IC50, 1.2 mM). Both CE and CECNs significantly reduced the inflammatory response in interleukin (IL)-6 and IL-1ß assays. STZ-induced diabetic rats exhibited sustained high blood glucose levels (>16.5 mmol/L), small and damaged pancreatic ß islets, and skeletal muscle atrophy. CE and CECN treatments ameliorated skeletal muscle atrophy, recovered muscle fiber striated appearance, increased grip strength, and decreased IL-6 level. Furthermore, CE and CECNs led to a reduction of damage to the pancreas, restoring its morphological phenotype, increasing serum insulin levels, and lowering blood glucose levels in STZ-induced diabetic rats. Taken together, treatment with CECNs over a 6-week period yielded positive ameliorative effects in STZ-induced rats of muscle atrophy.

Validation of neuroimaging-based brain age gap as a mediator between modifiable risk factors and cognition.

Neuroimaging-based brain age gap (BAG) is presumably a mediator linking modifiable risk factors to cognitive changes, but this has not been verified yet. To address this hypothesis, modality-specific brain age models were constructed and applied to a population-based cohort (N = 326) to estimate their BAG. Structural equation modeling was employed to investigate the mediation effect of BAG between modifiable risk factors (assessed by 2 cardiovascular risk scores) and cognitive functioning (examined by 4 cognitive assessments). The association between higher burden of modifiable risk factors and poorer cognitive functioning can be significantly mediated by a larger BAG (multimodal: p = 0.014, 40.8% mediation proportion; white matter-based: p = 0.023, 15.7% mediation proportion), which indicated an older brain. Subgroup analysis further revealed a steeper slope (p = 0.019) of association between cognitive functioning and multimodal BAG in the group of higher modifiable risks. The results confirm that BAG can serve as a mediating indicator linking risk loadings to cognitive functioning, implicating its potential in the management of cognitive aging and dementia.

Improved Linear Convergence of Training CNNs With Generalizability Guarantees: A One-Hidden-Layer Case.

We analyze the learning problem of one-hidden-layer nonoverlapping convolutional neural networks with the rectified linear unit (ReLU) activation function from the perspective of model estimation. The training outputs are assumed to be generated by the neural network with the unknown ground-truth parameters plus some additive noise, and the objective is to estimate the model parameters by minimizing a nonconvex squared loss function of the training data. Assuming that the training set contains a finite number of samples generated from the Gaussian distribution, we prove that the accelerated gradient descent (GD) algorithm with a proper initialization converges to the ground-truth parameters (up to the noise level) with a linear rate even though the learning problem is nonconvex. Moreover, the convergence rate is proved to be faster than the vanilla GD. The initialization can be achieved by the existing tensor initialization method. In contrast to the existing works that assume an infinite number of samples, we theoretically establish the sample complexity of the required number of training samples. Although the neural network considered here is not deep, this is the first work to show that accelerated GD algorithms can find the global optimizer of the nonconvex learning problem of neural networks. This is also the first work that characterizes the sample complexity of gradient-based methods in learning convolutional neural networks with the nonsmooth ReLU activation function. This work also provides the tightest bound so far of the estimation error with respect to the output noise.

Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design.

Designing novel protein sequences for a desired 3D topological fold is a fundamental yet nontrivial task in protein engineering. Challenges exist due to the complex sequence-fold relationship, as well as the difficulties to capture the diversity of the sequences (therefore structures and functions) within a fold. To overcome these challenges, we propose Fold2Seq, a novel transformer-based generative framework for designing protein sequences conditioned on a specific target fold. To model the complex sequence-structure relationship, Fold2Seq jointly learns a sequence embedding using a transformer and a fold embedding from the density of secondary structural elements in 3D voxels. On test sets with single, high-resolution and complete structure inputs for individual folds, our experiments demonstrate improved or comparable performance of Fold2Seq in terms of speed, coverage, and reliability for sequence design, when compared to existing state-of-the-art methods that include data-driven deep generative models and physics-based RosettaDesign. The unique advantages of fold-based Fold2Seq, in comparison to a structure-based deep model and RosettaDesign, become more evident on three additional real-world challenges originating from low-quality, incomplete, or ambiguous input structures. Source code and data are available at https://github.com/IBM/fold2seq.

F1 ATP synthase ß subunit is a putative receptor involved in white spot syndrome virus infection in shrimp by binding with viral envelope proteins VP51B and VP150.

White spot syndrome virus (WSSV) is highly virulent toward shrimp, and F1 ATP synthase ß subunit (ATPsyn-ß) has been suggested to be involved in WSSV infection. Therefore, in this study, interactions between Penaeus monodon ATPsyn-ß (PmATPsyn-ß) and WSSV structural proteins were characterized. Based on the results of yeast two-hybrid, co-immunoprecipitation, and protein pull-down assays, WSSV VP51B and VP150 were identified as being able to interact with PmATPsyn-ß. Membrane topology assay results indicated that VP51B and VP150 are envelope proteins with large portions exposed outside the WSSV virion. Cellular localization assay results demonstrated that VP51B and VP150 co-localize with PmATPsyn-ß on the membranes of transfected cells. Enzyme-linked immunosorbent assay (ELISA) and competitive ELISA results demonstrated that VP51B and VP150 bound to PmATPsyn-ß in a dose-dependent manner, which could be competitively inhibited by the addition of WSSV virions. In vivo neutralization assay results further showed that both recombinant VP51B and VP150 could delay mortality in shrimp challenged with WSSV.

Altered mismatch response of inferior parietal lobule in amnestic mild cognitive impairment: A magnetoencephalographic study.

BACKGROUND: Mismatch negativity (MMN) reflects the functional integrity of sensory memory function. With the advantages of independence of individual's focused attention and behavioral cooperation, this neurophysiological signal is particularly suitable for investigating elderly with cognitive decline such as amnestic mild cognitive impairment (aMCI). However, the existing results remain substantially inconsistent whether these patients show deficits of MMN. In order to reconcile the previous disputes, the present study used magnetoencephalography combined with distributed source imaging methods to determine the source-level magnetic mismatch negativity (MMNm) in aMCI. METHODS: A total of 26 healthy controls (HC) and 26 patients with aMCI underwent an auditory oddball paradigm during the MEG recordings. MMNm amplitudes and latencies in the bilateral superior temporal gyrus, inferior frontal gyrus, and inferior parietal lobule (IPL) were compared between HC and aMCI groups. The correlations of MMNm responses with performance of auditory/verbal memory tests were examined. Finally, MMNm and its combination with verbal/auditory memory tests were submitted to receiver operating characteristic (ROC) curve analysis. RESULTS: Compared to HC, patients with aMCI showed significantly delayed MMNm latencies in the IPL. Among the patients with aMCI, longer MMNm latencies of left IPL were associated with lower scores of Chinese Version Verbal Learning Test (CVVLT). The ROC curve analysis revealed that the combination of MMNm latencies of left IPL and CVVLT scores yielded a moderate accuracy in the discrimination of aMCI from HC at an individual level. CONCLUSIONS: Our data suggest dysfunctional MMNm in patients with aMCI, particularly in the IPL.