MoSBi: Automated signature mining for molecular stratification and subtyping.

The improving access to increasing amounts of biomedical data provides completely new chances for advanced patient stratification and disease subtyping strategies. This requires computational tools that produce uniformly robust results across highly heterogeneous molecular data. Unsupervised machine learning methodologies are able to discover de novo patterns in such data. Biclustering is especially suited by simultaneously identifying sample groups and corresponding feature sets across heterogeneous omics data. The performance of available biclustering algorithms heavily depends on individual parameterization and varies with their application. Here, we developed MoSBi (molecular signature identification using biclustering), an automated multialgorithm ensemble approach that integrates results utilizing an error model-supported similarity network. We systematically evaluated the performance of 11 available and established biclustering algorithms together with MoSBi. For this, we used transcriptomics, proteomics, and metabolomics data, as well as synthetic datasets covering various data properties. Profiting from multialgorithm integration, MoSBi identified robust group and disease-specific signatures across all scenarios, overcoming single algorithm specificities. Furthermore, we developed a scalable network-based visualization of bicluster communities that supports biological hypothesis generation. MoSBi is available as an R package and web service to make automated biclustering analysis accessible for application in molecular sample stratification.

RhoA rescues cardiac senescence by regulating Parkin-mediated mitophagy.

Heart failure is one of the leading causes of death worldwide. RhoA, a small GTPase, governs actin dynamics in various tissue and cell types, including cardiomyocytes; however, its involvement in cardiac function has not been fully elucidated. Here, we generated cardiomyocyte-specific RhoA conditional knockout (cKO) mice, which demonstrated a significantly shorter lifespan with left ventricular dilation and severely impaired ejection fraction. We found that the cardiac tissues of the cKO mice exhibited structural disorganization with fibrosis and also exhibited enhanced senescence compared with control mice. In addition, we show that cardiomyocyte mitochondria were structurally abnormal in the aged cKO hearts. Clearance of damaged mitochondria by mitophagy was remarkably inhibited in both cKO cardiomyocytes and RhoA-knockdown HL-1 cultured cardiomyocytes. In RhoA-depleted cardiomyocytes, we reveal that the expression of Parkin, an E3 ubiquitin ligase that plays a crucial role in mitophagy, was reduced, and expression of N-Myc, a negative regulator of Parkin, was increased. We further reveal that the RhoA-Rho kinase axis induced N-Myc phosphorylation, which led to N-Myc degradation and Parkin upregulation. Re-expression of Parkin in RhoA-depleted cardiomyocytes restored mitophagy, reduced mitochondrial damage, attenuated cardiomyocyte senescence, and rescued cardiac function both in vitro and in vivo. Finally, we found that patients with idiopathic dilated cardiomyopathy without causal mutations for dilated cardiomyopathy showed reduced cardiac expression of RhoA and Parkin. These results suggest that RhoA promotes Parkin-mediated mitophagy as an indispensable mechanism contributing to cardioprotection in the aging heart.

Characterization of Immune Cell Populations of Cutaneous Neurofibromas in Neurofibromatosis 1.

Cutaneous neurofibromas (cNFs) are characteristic of neurofibromatosis 1 (NF1), yet their immune microenvironment is incompletely known. A total of 61 cNFs from 10 patients with NF1 were immunolabeled for different types of T cells and macrophages, and the cell densities were correlated with clinical characteristics. Eight cNFs and their overlying skin were analyzed for T cell receptor CDR domain sequences, and mass spectrometry of 15 cNFs and the overlying skin was performed to study immune-related processes. Intratumoral T cells were detected in all cNFs. Tumors from individuals younger than the median age of the study participants (33 years), growing tumors, and tumors smaller than the data set median showed increased T cell density. Most samples displayed intratumoral or peritumoral aggregations of CD3-positive cells. T cell receptor sequencing demonstrated that the skin and cNFs host distinct T cell populations, whereas no dominant cNF-specific T cell clones were detected. Unique T cell clones were fewer in cNFs than in skin, and mass spectrometry suggested lower expression of proteins related to T cell-mediated immunity in cNFs than in skin. CD163-positive cells, suggestive of M2 macrophages, were abundant in cNFs. Human cNFs have substantial T cell and macrophage populations that may be tumor-specific.

Emerging Enterovirus A71 Subgenogroup B5 Causing Severe Hand, Foot, and Mouth Disease, Vietnam, 2023.

We report on a 2023 outbreak of severe hand, foot, and mouth disease in southern Vietnam caused by an emerging lineage of enterovirus A71 subgenogroup B5. Affected children were significantly older than those reported during previous outbreaks. The virus should be closely monitored to assess its potential for global dispersal.

Late-onset sensory-motor axonal neuropathy, a novel SLC12A6-related phenotype.

We describe five families from different regions in Norway with a late-onset autosomal-dominant hereditary polyneuropathy sharing a heterozygous variant in the SLC12A6 gene. Mutations in the same gene have previously been described in infants with autosomal-recessive hereditary motor and sensory neuropathy with corpus callosum agenesis and mental retardation (Andermann syndrome), and in a few case reports describing dominantly acting de novo mutations, most of them with onset in childhood. The phenotypes in our families demonstrated heterogeneity. Some of our patients only had subtle to moderate symptoms and some individuals even no complaints. None had CNS manifestations. Clinical and neurophysiological evaluations revealed a predominant sensory axonal polyneuropathy with slight to moderate motor components. In all 10 patients the identical SLC12A6 missense variant, NM_001365088.1 c.1655G>A p.(Gly552Asp), was identified. For functional characterization, the mutant potassium chloride cotransporter 3 was modelled in Xenopus oocytes. This revealed a significant reduction in potassium influx for the p.(Gly552Asp) substitution. Our findings further expand the spectrum of SLC12A6 disease, from biallelic hereditary motor and sensory neuropathy with corpus callosum agenesis and mental retardation and monoallelic early-onset hereditary motor and sensory neuropathy caused by de novo mutations, to late-onset autosomal-dominant axonal neuropathy with predominant sensory deficits.

Spatiotemporal Evolution of SARS-CoV-2 Alpha and Delta Variants during Large Nationwide Outbreak of COVID-19, Vietnam, 2021.

We analyzed 1,303 SARS-CoV-2 whole-genome sequences from Vietnam, and found the Alpha and Delta variants were responsible for a large nationwide outbreak of COVID-19 in 2021. The Delta variant was confined to the AY.57 lineage and caused >1.7 million infections and >32,000 deaths. Viral transmission was strongly affected by nonpharmaceutical interventions.

Characterization of Expanded Gamma Delta T Cells from Atypical X-SCID Patient Reveals Preserved Function and IL2RG-Mediated Signaling.

Abnormally high γδ T cell numbers among individuals with atypical SCID have been reported but detailed immunophenotyping and functional characterization of these expanded γδ T cells are limited. We have previously reported atypical SCID phenotype caused by hypomorphic IL2RG (NM_000206.3) c.172C > T;p.(Pro58Ser) variant. Here, we have further investigated the index patient's abnormally large γδ T cell population in terms of function and phenotype by studying IL2RG cell surface expression, STAT tyrosine phosphorylation and blast formation in response to interleukin stimulation, immunophenotyping, TCRvγ sequencing, and target cell killing. In contrast to his âºß T cells, the patient's γδ T cells showed normal IL2RG cell surface expression and normal or enhanced IL2RG-mediated signaling. Vδ2 + population was proportionally increased with a preponderance of memory phenotypes and high overall tendency towards perforin expression. The patient's γδ T cells showed enhanced cytotoxicity towards A549 cancer cells. His TCRvγ repertoire was versatile but sequencing of IL2RG revealed a novel c.534C > A; p.(Phe178Leu) somatic missense variant restricted to γδ T cells. Over time this variant became predominant in γδ T cells, though initially present only in part of them. IL2RG-Pro58Ser/Phe178Leu variant showed higher cell surface expression compared to IL2RG-Pro58Ser variant in stable HEK293 cell lines, suggesting that somatic p.(Phe178Leu) variant may at least partially rescue the pathogenic effect of germline p.(Pro58Ser) variant. In conclusion, our report indicates that expansion of γδ T cells associated with atypical SCID needs further studying and cannot exclusively be deemed as a homeostatic response to low numbers of conventional T cells.

New metrics of dietary carbohydrate quality.

PURPOSE OF REVIEW: The aim of this study was to introduce novel metrics of dietary carbohydrates quality relevant for products and diets. RECENT FINDINGS: Carbohydrate quality has long been associated with a low glycemic index. More recently, novel metrics of carbohydrate quality featuring variations of total carbohydrates-fibers-free sugars ratios have been applied to carbohydrate-rich foods, including grains, beans, vegetables, and fruit. High scoring products had higher levels of health-promoting nutrients (protein, dietary fiber, iron, magnesium, zinc, potassium, selenium, and various B-vitamins) and lower levels of nutrients of public health concern (total sugar, added/free sugars, and fat profile). Cross-sectional studies also found variants of carbohydrate quality metrics to be associated with better markers of cardiometabolic disease, including lower levels of blood triglycerides:high-density lipoprotein cholesterol ratio, homeostatic model assessment of insulin resistance, and SBP. SUMMARY: New ratio-based carbohydrate quality metrics are built around high fiber and whole grain content, combined with a low free sugar content. Such metrics allow the identification of food products of higher overall nutritional quality, and are associated with improved diet quality and certain health outcomes.

Single-Administration Long-Acting Microarray Patch with Ultrahigh Loading Capacity and Multiple Releases of Thermally Stable Antibodies.

Current antibody (Ab) therapies require development of stable formulations and an optimal delivery system. Here, we present a new strategy to create a single-administration long-lasting Ab-delivery microarray (MA) patch, which can carry high doses of thermally stabilized Abs. The MA fabricated by an additive three-dimensional manufacturing technology can be fully embedded into the skin via a single application to deliver doses of Abs at multiple programmable time points, thus sustaining Ab concentrations in systemic circulation. We developed an MA formulation that stabilized and delivered human immunoglobulins (hIg) in a time-controlled manner while maintaining their structure and functionality. As an example, the b12 Ab─a broadly neutralizing Ab against HIV-1─maintained antiviral activity in vitro after MA manufacturing and heat exposure. Pharmacokinetic studies of MA patch-delivered hIg in rats successfully provided a proof of concept for concurrent and time-delayed Ab delivery. These MA patches codeliver different Abs, providing a tool for expanded protection against viral infections or combination HIV therapy and prevention.

Deep learning for robust and flexible tracking in behavioral studies for C. elegans.

Robust and accurate behavioral tracking is essential for ethological studies. Common methods for tracking and extracting behavior rely on user adjusted heuristics that can significantly vary across different individuals, environments, and experimental conditions. As a result, they are difficult to implement in large-scale behavioral studies with complex, heterogenous environmental conditions. Recently developed deep-learning methods for object recognition such as Faster R-CNN have advantages in their speed, accuracy, and robustness. Here, we show that Faster R-CNN can be employed for identification and detection of Caenorhabditis elegans in a variety of life stages in complex environments. We applied the algorithm to track animal speeds during development, fecundity rates and spatial distribution in reproductive adults, and behavioral decline in aging populations. By doing so, we demonstrate the flexibility, speed, and scalability of Faster R-CNN across a variety of experimental conditions, illustrating its generalized use for future large-scale behavioral studies.

Measures of carbohydrate quality and their association with diet quality and cardiometabolic health outcomes in Singapore middle-aged and older adults.

BACKGROUND AND AIMS: Carbohydrate quality may play a key role in cardiometabolic health and disease risk. This study aimed to assess the dietary carbohydrate quality of the free-living middle-aged and older adults in Singapore, and its association with overall diet quality and cardiometabolic health. METHODS AND RESULTS: This cross-sectional study examined the diet and cardiometabolic disease risk indicators of middle-aged and older adults in Singapore (n = 104). Dietary carbohydrate quality was assessed as the pass and fail rate of the population to four measures of carbohydrate quality: (i) dietary fiber recommended daily allowance (RDA), (ii) whole-grain recommendation, (iii) free sugar recommendation, and (iv) carbohydrate metrics. The association between each carbohydrate quality measure and diet quality, as well as cardiometabolic health, was assessed. Except for free sugar recommendation, the carbohydrate quality of the population was found to be poor with a low adherence (20-36%) to three measures. Subjects meeting these measures had generally higher intakes of fiber, protein, and most micronutrients compared with subjects who failed. Meeting different variants of the carbohydrate metrics was associated with 60% lower odds of pre-hypertensive blood pressure (p = 0.037; p = 0.047), and meeting the dietary fiber RDA was associated with lower waist circumference (p = 0.021). CONCLUSION: An improvement in carbohydrate quality is warranted among free-living middle-aged and older adults in Singapore. Not all measures of carbohydrate quality were equally effective in preserving overall diet quality; the carbohydrate metrics and dietary fiber RDA can be identified as effective measures in relation to cardiometabolic disease risk. CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/ CLINICAL TRIAL REGISTRATION: NCT03554954, 13 Sept. 2018.

Outcomes of Squamous Cell Carcinoma of the Lip Treated With Mohs Micrographic Surgery: A Retrospective Cohort Study.

BACKGROUND: Cutaneous squamous cell carcinomas (cSCCs) of the lip have been reported to be at higher risk for poorer post-treatment outcomes. OBJECTIVE: To examine outcomes of patients with SCC of the lip treated with Mohs micrographic surgery (MMS) and identify factors for recurrence. MATERIALS AND METHODS: This retrospective review of a single tertiary referral center's Mohs case logs from 2010 to 2019 identified cases of lip SCC. Clinicopathologic characteristics and outcomes (local recurrence [LR], metastasis, and disease-specific death) were reviewed. RESULTS: One hundred ninety cases of SCC of the lip were identified and demonstrated that MMS offered a disease-free survival of 96.8% over an average follow-up period of 42 months. Younger age (61 vs 74 years p = .006), increased MMS stages ( p = .009), and higher American Joint Committee on Cancer and Brigham and Women's Hospital T stages were risk factors for LR. Immunosuppression, large tumor size, mucosal lip involvement, aggressive histology, and perineural invasion were not associated with LR. CONCLUSION: The results of this study show that SCC of the lip behaved similarly to cSCC outside the lip area, and that both primary and recurrent lesions can be treated effectively with MMS.

Cardio- and reno-protective effects of dipeptidyl peptidase III in diabetic mice.

Diabetes mellitus (DM) causes injury to tissues and organs, including to the heart and kidney, resulting in increased morbidity and mortality. Thus, novel potential therapeutics are continuously required to minimize DM-related organ damage. We have previously shown that dipeptidyl peptidase III (DPPIII) has beneficial roles in a hypertensive mouse model, but it is unknown whether DPPIII has any effects on DM. In this study, we found that intravenous administration of recombinant DPPIII in diabetic db/db mice for 8 weeks suppressed the DM-induced cardiac diastolic dysfunctions and renal injury without alteration of the blood glucose level. This treatment inhibited inflammatory cell infiltration and fibrosis in the heart and blocked the increase in albuminuria by attenuating the disruption of the glomerular microvasculature and inhibiting the effacement of podocyte foot processes in the kidney. The beneficial role of DPPIII was, at least in part, mediated by the cleavage of a cytotoxic peptide, named Peptide 2, which was increased in db/db mice compared with normal mice. This peptide consisted of nine amino acids, was a digested fragment of complement component 3 (C3), and had an anaphylatoxin-like effect determined by the Miles assay and chemoattractant analysis. The effect was dependent on its interaction with the C3a receptor and protein kinase C-mediated RhoA activation downstream of the receptor in endothelial cells. In conclusion, DPPIII plays a protective role in the heart and kidney in a DM animal model through cleavage of a peptide that is a part of C3.

Importance of Carbohydrate Quality: What Does It Mean and How to Measure It?

Dietary carbohydrates are our main source of energy. Traditionally, they are classified based on the polymer length between simple and complex carbohydrates, which does not necessarily reflect their impact on health. Simple sugars, such as fructose, glucose, and lactose, despite having a similar energy efficiency and caloric content, have very distinct metabolic effects, leading to increased risk for various chronic diseases when consumed in excess. In addition, beyond the absolute amount of carbohydrate consumed, recent data point out that the food form or processing level can modulate both the energy efficiency and the cardiometabolic risk associated with specific carbohydrates. To account for both of these aspects-the quality of carbohydrates as well as its food form-several metrics can be proposed to help identifying carbohydrate-rich food sources and distinguish between those that would favor the development of chronic diseases and those that may contribute to prevent these. This review summarizes the findings presented during the American Society of Nutrition Satellite symposium on carbohydrate quality, in which these different aspects were presented.

Realguard: A Lightweight Network Intrusion Detection System for IoT Gateways.

Cyber security has become increasingly challenging due to the proliferation of the Internet of things (IoT), where a massive number of tiny, smart devices push trillion bytes of data to the Internet. However, these devices possess various security flaws resulting from the lack of defense mechanisms and hardware security support, therefore making them vulnerable to cyber attacks. In addition, IoT gateways provide very limited security features to detect such threats, especially the absence of intrusion detection methods powered by deep learning. Indeed, deep learning models require high computational power that exceeds the capacity of these gateways. In this paper, we introduce Realguard, an DNN-based network intrusion detection system (NIDS) directly operated on local gateways to protect IoT devices within the network. The superiority of our proposal is that it can accurately detect multiple cyber attacks in real time with a small computational footprint. This is achieved by a lightweight feature extraction mechanism and an efficient attack detection model powered by deep neural networks. Our evaluations on practical datasets indicate that Realguard could detect ten types of attacks (e.g., port scan, Botnet, and FTP-Patator) in real time with an average accuracy of 99.57%, whereas the best of our competitors is 98.85%. Furthermore, our proposal effectively operates on resource-constraint gateways (Raspberry PI) at a high packet processing rate reported about 10.600 packets per second.

Triplex Direct Quantitative Polymerase Chain Reaction for the Identification of Streptococcus pneumoniae Serotypes.

The quantitative polymerase chain reaction (qPCR) method presented in this study allows the identification of pneumococcal capsular serotypes in cerebrospinal fluid without first performing DNA extraction. This testing approach, which saves time and resources, demonstrated similar sensitivity and a high level of agreement between cycle threshold values when it was compared side-by-side with the standard qPCR method with extracted DNA.

Dynamic Impairment of Olfactory Behavior and Signaling Mediated by an Olfactory Corticofugal System.

Processing of olfactory information is modulated by centrifugal projections from cortical areas, yet their behavioral relevance and underlying neural mechanisms remain unclear in most cases. The anterior olfactory nucleus (AON) is part of the olfactory cortex, and its extensive connections to multiple upstream and downstream brain centers place it in a prime position to modulate early sensory information in the olfactory system. Here, we show that optogenetic activation of AON neurons in awake male and female mice was not perceived as an odorant equivalent cue. However, AON activation during odorant presentation reliably suppressed behavioral odor responses. This AON-mediated effect was fast and constant across odors and concentrations. Likewise, activation of glutamatergic AON projections to the olfactory bulb (OB) transiently inhibited the excitability of mitral/tufted cells (MTCs) that relay olfactory input to the cortex. Single-unit MTC recordings revealed that optogenetic activation of glutamatergic AON terminals in the OB transiently decreased sensory-evoked MTC spiking, regardless of the strength or polarity of the sensory response. The reduction in MTC firing during optogenetic stimulation was confirmed in recordings in awake mice. These findings suggest that glutamatergic AON projections to the OB impede early olfactory signaling by inhibiting OB output neurons, thereby dynamically gating sensory throughput to the cortex.SIGNIFICANCE STATEMENT The anterior olfactory nucleus (AON) as an olfactory information processing area sends extensive projections to multiple brain centers, but the behavioral consequences of its activation have been scarcely investigated. Using behavioral tests in combination with optogenetic manipulation, we show that, in contrast to what has been suggested previously, the AON does not seem to form odor percepts but instead suppresses behavioral odor responses across odorants and concentrations. Furthermore, this study shows that AON activation inhibits olfactory bulb output neurons in both anesthetized as well as awake mice, pointing to a potential mechanism by which the olfactory cortex can actively and dynamically gate sensory throughput to higher brain centers.

New Acetophenones and Chromenes from the Leaves of Melicope barbigera A. Gray.

The dichloromethane extract from leaves of Melicope barbigera (Rutaceae), endemic to the Hawaiian island of Kaua'i, yielded four new and three previously known acetophenones and 2H-chromenes, all found for the first time in M. barbigera. The structures of the new compounds obtained from the dichloromethane extract after purification by chromatographic methods were unambiguously elucidated by spectroscopic analyses including 1D/2D NMR spectroscopy and HRESIMS. The absolute configuration was determined by modified Mosher's method. Compounds 2, 4 and the mixture of 6 and 7 exhibited moderate cytotoxic activities against the human ovarian cancer cell line A2780 with IC50 values of 30.0 and 75.7 µM for 2 and 4, respectively, in a nuclear shrinkage cytotoxicity assay.

mPartition: A Model-Based Method for Partitioning Alignments.

Maximum likelihood (ML) analysis of nucleotide or amino-acid alignments is widely used to infer evolutionary relationships among species. Computing the likelihood of a phylogenetic tree from such alignments is a complicated task because the evolutionary processes typically vary across sites. A number of studies have shown that partitioning alignments into sub-alignments of sites, where each sub-alignment is analyzed using a different model of evolution (e.g., GTR + I + G), is a sensible strategy. Current partitioning methods group sites into subsets based on the inferred rates of evolution at the sites. However, these do not provide sufficient information to adequately reflect the substitution processes of characters at the sites. Moreover, the site rate-based methods group all invariant sites into one subset, potentially resulting in wrong phylogenetic trees. In this study, we propose a partitioning method, called mPartition, that combines not only the evolutionary rates but also substitution models at sites to partition alignments. Analyses of different partitioning methods on both real and simulated datasets showed that mPartition was better than the other partitioning methods tested. Notably, mPartition overcame the pitfall of grouping all invariant sites into one subset. Using mPartition may lead to increased accuracy of ML-based phylogenetic inference, especially for multiple loci or whole genome datasets.

Identification of Polymethylene-Interrupted Polyunsaturated Fatty Acids (PMI-PUFA) by Solvent-Mediated Covalent Adduct Chemical Ionization Triple Quadrupole Tandem Mass Spectrometry.

Pine nuts and other edible gymnosperm seeds contain unusual, bioactive polymethylene-interrupted polyunsaturated fatty acids (PMI-PUFAs), a subset of nonmethylene-interrupted PUFA with (-CH2-)n≥2 intervening between double bonds. Conventional methods for structure elucidation of PMI-PUFAs require special derivatization risking rearrangement artifacts. Here we introduce a facile solvent-mediated (SM) covalent adduct chemical ionization (CACI) system modified with a triple quadrupole MS, which distinguishes PMI-PUFAs from their analogues in direct methyl ester form. The prominent Δ5 desaturated PMI-PUFAs exhibit characteristic fragmentation at C6-7 to yield ω diagnostic ions and share their fragmentation pattern with normal methylene interrupted PUFAs for the α diagnostic ion. H• transfer upon CID dissociation of PMI-PUFAs was found to be dependent on the relative position of isolated lone double bonds and cleavage points. Ginkgo and five species of pine nuts were characterized for their unique Δ5 fatty acid profile, without the need for chemical standards.