Pathogenic Role of Human Rhinovirus Mono-Infection in Pediatric Lower Respiratory Tract Infection.

Background and objective Human rhinovirus (HRV) is one of the leading causes of pediatric respiratory tract infection with a prevalence rate of 30-50%, mostly affecting children below five years of age and causing a substantial amount of economic loss. In children, it can alone or as a co-infection, cause a wide range of symptoms from mild to life-threatening ones. With the above background, the current study was carried out to emphasize the role of HRV mono-infection in pediatric acute respiratory tract infections by correlating clinical and molecular laboratory findings. Methods This study was carried out in a tertiary care teaching hospital over a duration of four years (March 2019-October 2023). Children up to 14 years of age visiting the outpatient department or admitted to the ward with diagnoses of acute respiratory tract infections (ARTIs) were included. The clinical and laboratory data were retrieved and analyzed. A nasopharyngeal swab (NPS) or throat swab (TS) was collected and sent to the Microbiology laboratory maintaining the cold chain. Nucleic acid was extracted and subjected to multiplex real-time polymerase chain reaction (RT-PCR). Result Of the 245 samples tested for the respiratory viral pathogen, 52 samples tested positive for HRV, of which 27 had HRV mono-infection. The clinico-demographic details of these 27 patients were studied in detail. The majority of the cases (24/27; 88.8%) were less than five years of age. Fever and shortness of breath were the most consistent symptoms in all. Nineteen (19/27; 62.9%) HRV mono-infection cases had underlying co-morbidities, all requiring respiratory support. The HRV mono-infection cases either developed bronchiolitis, lower respiratory tract infection, or pneumonia. All mono-infection cases had cycle threshold value (Ct) < 25, while the Ct value of HRV was > 30 in co-infection with other viruses. Conclusion Mono-infection of HRV in under-five children with underlying comorbidities and a lesser Ct value indicates severe disease manifestation and should be dealt with more cautiously.

Multi-class waste segregation using computer vision and robotic arm.

Waste segregation is an essential aspect of a smoothly functioning waste management system. Usually, various recyclable waste types are disposed of together at the source, and this brings in the necessity to segregate them into their categories. Dry waste needs to be separated into its own categories to ensure that the proper procedures are implemented to treat and process it, which leads to an overall increased recycling rate and reduced landfill impact. Paper, plastics, metals, and glass are just a few examples of the many dry waste materials that can be recycled or recovered to create new goods or energy. Over the past years, much research has been conducted to devise effective and productive ways to achieve proper segregation for the waste that is being produced at an ever-increasing rate. This article introduces a multi-class garbage segregation system employing the YOLOv5 object detection model. Our final prototype demonstrates the capability of classifying dry waste categories and segregating them into their respective bins using a 3D-printed robotic arm. Within our controlled test environment, the system correctly segregated waste classes, mainly paper, plastic, metal, and glass, eight out of 10 times successfully. By integrating the principles of artificial intelligence and robotics, our approach simplifies and optimizes the traditional waste segregation process.

Adult microglial TGFß1 is required for microglia homeostasis via an autocrine mechanism to maintain cognitive function in mice.

While TGF-ß signaling is essential for microglial function, the cellular source of TGF-ß1 ligand and its spatial regulation remains unclear in the adult CNS. Our data supports that microglia but not astrocytes or neurons are the primary producers of TGF-ß1 ligands needed for microglial homeostasis. Microglia-Tgfb1 KO leads to the activation of microglia featuring a dyshomeostatic transcriptome that resembles disease-associated, injury-associated, and aged microglia, suggesting microglial self-produced TGF-ß1 ligands are important in the adult CNS. Astrocytes in MG-Tgfb1 inducible (i)KO mice show a transcriptome profile that is closely aligned with an LPS-associated astrocyte profile. Additionally, using sparse mosaic single-cell microglia KO of TGF-ß1 ligand we established an autocrine mechanism for signaling. Here we show that MG-Tgfb1 iKO mice present cognitive deficits, supporting that precise spatial regulation of TGF-ß1 ligand derived from microglia is required for the maintenance of brain homeostasis and normal cognitive function in the adult brain.

MONET: a database for prediction of neoantigens derived from microsatellite loci.

Background: Microsatellite instability (MSI) secondary to mismatch repair (MMR) deficiency is characterized by insertions and deletions (indels) in short DNA sequences across the genome. These indels can generate neoantigens, which are ideal targets for precision immune interception. However, current neoantigen databases lack information on neoantigens arising from coding microsatellites. To address this gap, we introduce The MicrOsatellite Neoantigen Discovery Tool (MONET). Method: MONET identifies potential mutated tumor-specific neoantigens (neoAgs) by predicting frameshift mutations in coding microsatellite sequences of the human genome. Then MONET annotates these neoAgs with key features such as binding affinity, stability, expression, frequency, and potential pathogenicity using established algorithms, tools, and public databases. A user-friendly web interface (https://monet.mdanderson.org/) facilitates access to these predictions. Results: MONET predicts over 4 million and 15 million Class I and Class II potential frameshift neoAgs, respectively. Compared to existing databases, MONET demonstrates superior coverage (>85% vs. <25%) using a set of experimentally validated neoAgs. Conclusion: MONET is a freely available, user-friendly web tool that leverages publicly available resources to identify neoAgs derived from microsatellite loci. This systems biology approach empowers researchers in the field of precision immune interception.

Association of large core middle cerebral artery stroke and hemorrhagic transformation with hospitalization outcomes.

Historically, investigators have not differentiated between patients with and without hemorrhagic transformation (HT) in large core ischemic stroke at risk for life-threatening mass effect (LTME) from cerebral edema. Our objective was to determine whether LTME occurs faster in those with HT compared to those without. We conducted a two-center retrospective study of patients with ≥ 1/2 MCA territory infarct between 2006 and 2021. We tested the association of time-to-LTME and HT subtype (parenchymal, petechial) using Cox regression, controlling for age, mean arterial pressure, glucose, tissue plasminogen activator, mechanical thrombectomy, National Institute of Health Stroke Scale, antiplatelets, anticoagulation, temperature, and stroke side. Secondary and exploratory outcomes included mass effect-related death, all-cause death, disposition, and decompressive hemicraniectomy. Of 840 patients, 358 (42.6%) had no HT, 403 (48.0%) patients had petechial HT, and 79 (9.4%) patients had parenchymal HT. LTME occurred in 317 (37.7%) and 100 (11.9%) had mass effect-related deaths. Parenchymal (HR 8.24, 95% CI 5.46-12.42, p < 0.01) and petechial HT (HR 2.47, 95% CI 1.92-3.17, p < 0.01) were significantly associated with time-to-LTME and mass effect-related death. Understanding different risk factors and sequelae of mass effect with and without HT is critical for informed clinical decisions.

The Role of Obstructive Sleep Apnea in Hypercapnic Respiratory Failure Identified in Critical Care, Inpatient, and Outpatient Settings.

An emerging body of literature describes the prevalence and consequences of hypercapnic respiratory failure. While device qualifications, documentation practices, and previously performed clinical studies often encourage conceptualizing patients as having a single "cause" of hypercapnia, many patients encountered in practice have several contributing conditions. Physiologic and epidemiologic data suggest that sleep-disordered breathing-particularly obstructive sleep apnea (OSA)-often contributes to the development of hypercapnia. In this review, the authors summarize the frequency of contributing conditions to hypercapnic respiratory failure among patients identified in critical care, emergency, and inpatient settings with an aim toward understanding the contribution of OSA to the development of hypercapnia.

Chronic Cough and Obstructive Sleep Apnea.

Chronic cough, defined as a cough lasting more than 8 weeks, is a common medical condition occurring in 5% to 10% of the population. Its overlap with another highly prevalent disorder, obstructive sleep apnea (OSA), is therefore not surprising. The relationship between chronic cough and OSA extends beyond this overlap with higher prevalence of OSA in patients with chronic cough than in the general population. The use of continuous positive airway pressure can result in improvement in chronic cough although further studies are needed to understand which patients will experience benefit in their cough from the treatment of comorbid OSA.

Using Repeated Measurements to Predict Cardiovascular Risk in Patients With Type 2 Diabetes Mellitus.

The QRISK cardiovascular disease (CVD) risk assessment model is not currently optimized for patients with type 2 diabetes mellitus (T2DM). We aim to identify if the abundantly available repeatedly measured data for patients with T2D improves the predictive capability of QRISK to support the decision-making process regarding CVD prevention in patients with T2DM. We identified patients with T2DM aged 25 to 85, not on statin treatment and without pre-existing CVD from the IQVIA Medical Research Data United Kingdom primary care database and then followed them up until the first diagnosis of CVD, ischemic heart disease, or stroke/transient ischemic attack. We included traditional, nontraditional risk factors and relevant treatments for our analysis. We then undertook a Cox's hazards model accounting for time-dependent covariates to estimate the hazard rates for each risk factor and calculated a 10-year risk score. Models were developed for males and females separately. We tested the performance of our models using validation data and calculated discrimination and calibration statistics. The study included 198,835 (180,143 male with 11,976 outcomes and 90,466 female with 8,258 outcomes) patients. The 10-year predicted survival probabilities for females was 0.87 (0.87 to 0.87), whereas the observed survival estimates from the Kaplan-Meier curve for all female models was 0.87 (0.86 to 0.87). The predicted and observed survival estimates for males were 0.84 (0.84 to 0.84) and 0.84 (0.83 to 0.84) respectively. The Harrell's C-index of all female models and all male models were 0.71 and 0.69 respectively. We found that including time-varying repeated measures, only mildly improved CVD risk prediction for T2DM patients in comparison to the current practice standard. We advocate for further research using time-varying data to identify if the involvement of further covariates may improve the accuracy of currently accepted prediction models.

Major sources of sinking particulate organic matter in the western Bay of Bengal.

Impacts of river discharge on coastal ocean processes are multi-dimensional. Studies on sinking particle fluxes, composition and their seasonal variability in coastal oceans are very limited. In this study, we investigated the impact of river discharge on seasonal variability in sinking fluxes of total mass, biogenic and lithogenic material in a river-dominated continental margin, western coastal Bay of Bengal. Higher POC, lithogenic and total mass fluxes were found during early southwest monsoon, and are decoupled with peak river discharge and elevated primary production. It is attributed to cross-shelf transport of re-suspended surface sediments from shelf region. Peak river discharge followed by elevated chlorophyll-a suggest nutrients supply though river discharge support primary production. Elemental C:N ratios, δ13C and δ15N results likely suggest that both marine and terrestrial sources contributed to sinking POM, . Overall, higher sinking fluxes during southwest monsoon than rest of the year suggest that seasonal river discharge exerts considerable impact on sinking fluxes in the western coastal Bay of Bengal.

Deep Few-view High-resolution Photon-counting Extremity CT at Halved Dose for a Clinical Trial.

The latest X-ray photon-counting computed tomography (PCCT) for extremity allows multi-energy high-resolution (HR) imaging for tissue characterization and material decomposition. However, both radiation dose and imaging speed need improvement for contrast-enhanced and other studies. Despite the success of deep learning methods for 2D few-view reconstruction, applying them to HR volumetric reconstruction of extremity scans for clinical diagnosis has been limited due to GPU memory constraints, training data scarcity, and domain gap issues. In this paper, we propose a deep learning-based approach for PCCT image reconstruction at halved dose and doubled speed in a New Zealand clinical trial. Particularly, we present a patch-based volumetric refinement network to alleviate the GPU memory limitation, train network with synthetic data, and use model-based iterative refinement to bridge the gap between synthetic and real-world data. The simulation and phantom experiments demonstrate consistently improved results under different acquisition conditions on both in- and off-domain structures using a fixed network. The image quality of 8 patients from the clinical trial are evaluated by three radiologists in comparison with the standard image reconstruction with a full-view dataset. It is shown that our proposed approach is essentially identical to or better than the clinical benchmark in terms of diagnostic image quality scores. Our approach has a great potential to improve the safety and efficiency of PCCT without compromising image quality.

Current Trends in Vaccine Development for Hereditary Colorectal Cancer Syndromes.

The coming of age for cancer treatment has experienced exponential growth in the last decade with the addition of immunotherapy as the fourth pillar to the fundamentals of cancer treatment-chemotherapy, surgery, and radiation-taking oncology to an astounding new frontier. In this time, rapid developments in computational biology coupled with immunology have led to the exploration of priming the host immune system through vaccination to prevent and treat certain subsets of cancer such as melanoma and hereditary colorectal cancer. By targeting the immune system through tumor-specific antigens-namely, neoantigens (neoAgs)-the future of cancer prevention may lie within arm's reach by employing neoAg vaccines as an immune-preventive modality for hereditary cancer syndromes like Lynch syndrome. In this review, we discuss the history, current trends, utilization, and future direction of neoAg-based vaccines in the setting of hereditary colorectal cancer.

Laryngeal Dysfunction Manifesting as Chronic Refractory Cough and Dyspnea: Laryngeal Physiology in Respiratory Health and Disease.

TOPIC IMPORTANCE: Laryngeal dysfunction as a cause of chronic refractory cough (CRC) and episodic dyspnea is often missed, which results in unnecessary testing and delays in diagnosis. Understanding laryngeal roles in breathing and airway protection can help to appreciate the propensity to laryngeal dysfunction with aging, chronic lung disease, and sleep apnea. REVIEW FINDINGS: The human larynx is a complex muscular structure that is responsible for multiple roles of breathing, vocalization, coughing, and swallowing. To undertake these activities, the larynx has a high density of sensory and motor innervation. In addition to common embryological origins with the pharynx and esophagus, with which many laryngeal activities are shared, somatomotor and autonomic pathways regulate emotional, cognitive, and complex motor sequence-planning activities within the larynx. Due to its unique location, the larynx is susceptible to infectious and gastroesophageal reflux-related insults. Couple this with key roles in regulation of airflow and mediation of airway protective reflexes, it is not surprising that neuropathic abnormalities and muscle dysfunction frequently develop. The expression of laryngeal dysfunction as hypersensitivity to mechanical, thermal, chemical, and other stimuli leads to exaggerated airway protective reflexes (laryngeal adductor reflex and cough reflex) manifesting as dyspnea and cough. SUMMARY: Pulmonologists should incorporate assessment of laryngeal dysfunction during evaluation of CRC and dyspnea. Recognition of laryngeal hypersensitivity in patient with CRC can identify patients who may benefit from cough suppression therapies. Similarly, timely identification of inducible laryngeal obstruction may not only resolve episodic dyspnea but lessen the need for unnecessary testing and treatments.

Genome Sequence Analysis of Calcifying Bacteria Bacillus paranthracis CT5 and Its Biomineralization Efficacy to Improve the Strength and Durability Properties of Civil Structures.

Bacteria producing urea amidohydrolases (UA) and carbonic anhydrases (CA) are of great importance in civil engineering as these enzymes are responsible for microbially induced calcium carbonate precipitation (MICCP). In this investigation, genomic insights of Bacillus paranthracis CT5 and the expression of genes underlying in MICCP were studied. B. paranthracis produced a maximum level of UA (669.3 U/ml) and CA (125 U/ml) on 5th day of incubation and precipitated 197 mg/100 ml CaCO3 after 7 days of incubation. After 28 days of curing, compressive strength of bacterial admixed and bacterial cured (B-B) specimens was 13.7% higher compared to water-mixed and water-cured (W-W) specimens. A significant decrease in water absorption was observed in bacterial-cured specimens compared to water-cured specimens after 28 days of curing. For genome analysis, reads were assembled de novo producing 5,402,771 bp assembly with N50 of 273,050 bp. RAST annotation detected six amidohydrolase and three carbonic anhydrase genes. Among 5700 coding sequences found in genome, COG gene annotation grouped 4360 genes into COG categories with highest number of genes to transcription (435 genes), amino acid transport and metabolism (362 genes) along with cell wall/membrane/envelope biogenesis and ion transport and metabolism. KEGG functional classification predicted 223 pathways consisting of 1,960 genes and the highest number of genes belongs to two-component system (101 genes) and ABC transporter pathways (98 genes) enabling bacteria to sense and respond to environmental signals and actively transport various minerals and organic molecules, which facilitate the active transport of molecules required for MICCP.

Defining the T cell transcriptional landscape in pediatric liver transplant rejection at single cell resolution.

Acute cellular rejection (ACR) affects >80% of pediatric liver transplant recipients within 5 years, and late ACR is associated with graft failure. Traditional anti-rejection therapy for late ACR is ineffective and has remained unchanged for six decades. Although CD8+ T cells promote late ACR, little has been done to define their specificity and gene expression. Here, we used single-cell sequencing and immune repertoire profiling (10X Genomics) on 30 cryopreserved 16G liver biopsies from 14 patients (5 pre-transplant or with no ACR, 9 with ACR). We identified expanded intragraft CD8+ T cell clonotypes (CD8EXP) and their gene expression profiles in response to anti-rejection treatment. Notably, we found that expanded CD8+ clonotypes (CD8EXP) bore markers of effector and CD56hiCD161- 'NK-like' T cells, retaining their clonotype identity and phenotype in subsequent biopsies from the same patients despite histologic ACR resolution. CD8EXP clonotypes localized to portal infiltrates during active ACR, and persisted in the lobule after histologic ACR resolution. CellPhoneDB analysis revealed differential crosstalk between KC and CD8EXP during late ACR, with activation of the LTB-LTBR pathway and downregulation of TGFß signaling. Therefore, persistently-detected intragraft CD8EXP clones remain active despite ACR treatment and may contribute to long-term allograft fibrosis and failure of operational tolerance.

Isothermal titration calorimetry and surface plasmon resonance methods to probe protein-protein interactions.

Isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are two commonly used methods to probe biomolecular interactions. ITC can provide information about the binding affinity, stoichiometry, changes in Gibbs free energy, enthalpy, entropy, and heat capacity upon binding. SPR can provide information about the association and dissociation kinetics, binding affinity, and stoichiometry. Both methods can determine the nature of protein-protein interactions and help understand the physicochemical principles underlying complex biochemical pathways and communication networks. This methods article discusses the practical knowledge of how to set up and troubleshoot these two experiments with some examples.

Gait Analysis and Functional Knee Scores in Primary Knee Osteoarthritis and Their Correlation with Progression of the Disease in the Indian Population.

Introduction: Osteoarthritis of the knee is a leading cause of disability and is a multi-factorial disease. Moreover, it is partly considered a mechanically driven disease in which higher abnormally disbursed forces play a prime role. With the progression of the disease, the gait function declines, so a comprehensive and objective evaluation of gait function would help in prognostic evaluation and management. Materials and Methods: This study included two groups: patients with primary knee osteoarthritis and a control group of healthy volunteers. Gait analysis and functional knee scores were evaluated for all the subjects. The KOOS score, temporal parameters excluding the step length, and spatial parameters excluding the stance phase percentage were evaluated for an individual as a whole. The KSS score, kinetic parameters, kinematic parameters, step length, and stance phase percentage were calculated for each knee separately. Each knee of the patient and controls was taken as 1 sample and categorized as per Kellgren-Lawrence score. An asymptomatic control group of subjects were included in group A. Symptomatic patients with KL grades 1, 2 were included in group M, and those with KL grades 3, 4 were included in group S. The kinetic and kinematic parameters and KSS score were compared among the three groups. Results: A total of 60 subjects were included of which 40 were patients and 20 were controls. In the control group, the age ranged from 22 to 48 years with a mean age of 28.6 years. In the patient group, the mean age was 60.3 years. Patients with knee osteoarthritis were significantly obese with slower walking speed, short stride length, longer stride time, and decreased cadence compared to the asymptomatic group. There was a significant difference in spatiotemporal parameters, functional scores, and kinetic and kinematic parameters among the groups. Conclusion: Various spatiotemporal, kinetic, and kinematic parameters like peak knee flexion angle, abduction/adduction angle, peak knee adduction moment, range of knee flexion, peak knee flexion, and gait deviation index along with functional scores varied significantly with the progression of the disease. Supplementary Information: The online version contains supplementary material available at 10.1007/s43465-024-01103-9.

Characterization of Lysophospholipase D Activity in Mammalian Cell Membranes.

Lysophosphatidic acid (LPA) is a lipid mediator that binds to G-protein-coupled receptors, eliciting a wide variety of responses in mammalian cells. Lyso-phospholipids generated via phospholipase A2 (PLA2) can be converted to LPA by a lysophospholipase D (lyso-PLD). Secreted lyso-PLDs have been studied in more detail than membrane-localized lyso-PLDs. This study utilized in vitro enzyme assays with fluorescent substrates to examine LPA generation in membranes from multiple mammalian cell lines (PC12, rat pheochromocytoma; A7r5, rat vascular smooth muscle; Rat-1, rat fibroblast; PC-3, human prostate carcinoma; and SKOV-3 and OVCAR-3, human ovarian carcinoma). The results show that membranes contain a lyso-PLD activity that generates LPA from a fluorescent alkyl-lyso-phosphatidylcholine, as well as from naturally occurring acyl-linked lysophospholipids. Membrane lyso-PLD and PLD activities were distinguished by multiple criteria, including lack of effect of PLD2 over-expression on lyso-PLD activity and differential sensitivities to vanadate (PLD inhibitor) and iodate (lyso-PLD inhibitor). Based on several lines of evidence, including siRNA knockdown, membrane lyso-PLD is distinct from autotaxin, a secreted lyso-PLD. PC-3 cells express GDE4 and GDE7, recently described lyso-PLDs that localize to membranes. These findings demonstrate that membrane-associated lyso-D activity, expressed by multiple mammalian cell lines, can contribute to LPA production.

Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels.

Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-ß (MENß) are two long noncoding RNAs upregulated in multiple cancers, marking these RNAs as therapeutic targets. While traditional small-molecule and antisense-based approaches are effective, we report a locked nucleic acid (LNA)-based approach that targets the MALAT1 and MENß triple helices, structures comprised of a U-rich internal stem-loop and an A-rich tract. Two LNA oligonucleotides resembling the A-rich tract (i.e., A9GCA4) were examined: an LNA (L15) and a phosphorothioate LNA (PS-L15). L15 binds tighter than PS-L15 to the MALAT1 and MENß stem loops, although both L15 and PS-L15 enable RNA•LNA-RNA triple-helix formation. Based on UV thermal denaturation assays, both LNAs selectively stabilize the Hoogsteen interface by 5-13 °C more than the Watson-Crick interface. Furthermore, we show that L15 and PS-L15 displace the A-rich tract from the MALAT1 and MENß stem loop and methyltransferase-like protein 16 (METTL16) from the METTL16-MALAT1 triple-helix complex. Human colorectal carcinoma (HCT116) cells transfected with LNAs have 2-fold less MALAT1 and MENß. This LNA-based approach represents a potential therapeutic strategy for the dual targeting of MALAT1 and MENß.

Genomic Landscape of Lynch Syndrome Colorectal Neoplasia Identifies Shared Mutated Neoantigens for Immunoprevention.

BACKGROUND & AIMS: Lynch syndrome (LS) carriers develop mismatch repair-deficient neoplasia with high neoantigen (neoAg) rates. No detailed information on targetable neoAgs from LS precancers exists, which is crucial for vaccine development and immune-interception strategies. We report a focused somatic mutation and frameshift-neoAg landscape of microsatellite loci from colorectal polyps without malignant potential (PWOMP), precancers, and early-stage cancers in LS carriers. METHODS: We generated paired whole-exome and transcriptomic sequencing data from 8 colorectal PWOMP, 41 precancers, 8 advanced precancers, and 12 early-stage cancers of 43 LS carriers. A computational pipeline was developed to predict, rank, and prioritize the top 100 detected mutated neoAgs that were validated in vitro using ELISpot and tetramer assays. RESULTS: Mutation calling revealed >10 mut/Mb in 83% of cancers, 63% of advanced precancers, and 20% of precancers. Cancers displayed an average of 616 MHC-I neoAgs/sample, 294 in advanced precancers, and 107 in precancers. No neoAgs were detected in PWOMP. A total of 65% of our top 100 predicted neoAgs were immunogenic in vitro, and were present in 92% of cancers, 50% of advanced precancers, and 29% of precancers. We observed increased levels of naïve CD8+ and memory CD4+ T cells in mismatch repair-deficient cancers and precancers via transcriptomics analysis. CONCLUSIONS: Shared frameshift-neoAgs are generated within unstable microsatellite loci at initial stages of LS carcinogenesis and can induce T-cell responses, generating opportunities for vaccine development, targeting LS precancers and early-stage cancers.