Multiscale footprints reveal the organization of cis-regulatory elements.

Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.

Forty-eight-hour cold-stored whole blood in paediatric cardiac surgery: Implications for haemostasis and blood donor exposures.

Background And Objectives: Cold-stored whole blood (CS-WB) in paediatric cardiac surgery is making a resurgence, given its identified benefits compared to conventional blood component therapy (CT).

Study Design And Methods: A single-centre retrospective study was conducted from January 2018 to October 2018 by including children <18 years of age undergoing cardiac surgery requiring cardiopulmonary bypass. ABO-compatible CS-WB from non-directed random donors was leukoreduced with platelet-sparing filters and compared with CT.

Advanced chemometric methodologies on single shot hyphenated LIBS data for rapid and reliable characterization of plastic classes.

Background: Plastic Solid Waste (PSW) sorting is a procedure of paramount importance in the mechanical recycling process of plastics waste. The major limitation of the techniques relying on physical properties of plastics is the time taken for analysis and poor accuracy. Spectroscopy has been shown to be a suitable method in plastic sorting due to its atomic and molecular characterization capabilities, and ability to give results in very short time scales.

Cell of origin epigenetic priming determines susceptibility to Tet2 mutation.

Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation.

HPLC-LED-Induced Fluorescence Analysis of Tear Fluids: An Objective Method for Primary Open Angle Glaucoma Diagnosis.

Purpose: The study showcased the application of the lab-assembled HPLC-LED-IF system to analyze proteins in tear fluid samples collected from individuals diagnosed with primary open-angle glaucoma (POAG).

Methods: Clinical application of the said technique was evaluated by recording chromatograms of tear fluid samples from control and POAG subjects and by analyzing the protein profile using multivariate analysis. The data analysis methods involved are principal component analysis (PCA), Match/No-Match, and artificial neural network (ANN) based binary classification for disease diagnosis.

Protein profile pattern analysis: A multifarious, in vitro diagnosis technique for universal screening.

Universal health care is attracting increased attention nowadays, because of the large increase in population all over the world, and a similar increase in life expectancy, leading to an increase in the incidence of non-communicable (various cancers, coronary diseases, neurological and old-age-related diseases) and communicable diseases/pandemics like SARS-COVID 19. This has led to an immediate need for a healthcare technology that should be cost-effective and accessible to all. A technology being considered as a possible one at present is liquid biopsy, which looks for markers in readily available samples like body fluids which can be accessed non- or minimally- invasive manner.

Dosing, Monitoring, Blood Product Utilization, and Thromboembolic Complications of Four-Factor Prothrombin Complex Concentrate as Part of an Institutional Protocol in Pediatric Cardiac Surgery: A Retrospective Cohort Study.

Pediatric cardiac surgery patients are predisposed to blood loss. Blood product administration can lead to complications. Prothrombin complex concentrates (PCCs) offer potential advantages of factor composition, small volume, decreased immunogenicity/infectious risks, and accessibility.

Multiwavelength Photoacoustic Breath Analysis Sensor for the Diagnosis of Lung Diseases: COPD and Asthma.

Breath analysis is emerging as a universal diagnostic method for clinical applications. The possibility of breath analysis is being explored vigorously using different analytical techniques. We have designed and assembled a multiwavelength UV photoacoustic spectroscopy (PAS) sensor for the said application.

Correction: Protein profile analysis of tear fluid with hyphenated HPLC-UV LED-induced fluorescence detection for the diagnosis of dry eye syndrome.

[This corrects the article DOI: 10.1039/D3RA04389D.].

Epigenetic memory of coronavirus infection in innate immune cells and their progenitors.

Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19).

Laser induced fluorescence spectroscopy analysis of kidney tissues: A pilot study for the identification of renal cell carcinoma.

The 325 nm-excited autofluorescence spectra from cancerous and normal renal tissues were collected ex vivo biopsy tissue samples, through an optical fiber probe-based system. Noticeable changes in intensity/wavelength were observed in the fluorescence emissions from endogenous fluorophores such as collagen, Nicotinamide adenine dinucleotide (NADH), Vitamin A (retinol), and flavin adenine dinucleotide, in pathological conditions with respect to the normal state. The energy metabolism involved in clear cell renal cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) are reflected in the fluorescence emission band at 445 nm due to bound NADH attributed to enhanced oxidative phosphorylation in chRCC and emission at 465 nm contributed by free NADH showing higher glycolytic action in ccRCC.

Protein profile analysis of tear fluid with hyphenated HPLC-UV LED-induced fluorescence detection for the diagnosis of dry eye syndrome.

Tear fluid contains organic and inorganic constituents, variations in their relative concentrations could provide valuable information and can be useful for the detection of several ophthalmological diseases. This report describes the application of the lab-assembled light-emitting diode (LED)-based high-performance liquid chromatography system for protein profiling of tear fluids to diagnose dry eye disease. Principal Component Analysis (PCA), match/no-match, and Artificial Neural Network (ANN) based binary classification of protein profile data were performed for disease diagnosis.

Integrated LIBS-Raman spectroscopy: A comprehensive approach to monitor microplastics and heavy metal contamination in water resources.

The increased use of plastic products and global industrial conditions have contaminated natural resources, especially water, with pollutants such as microplastics and trace elements, including heavy metals. Hence, continuous monitoring of water samples is an urgent requirement. However, the existing microplastic-heavy metal monitoring methodologies require discrete and sophisticated sampling approaches.

Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements.

-regulatory elements control gene expression and are dynamic in their structure, reflecting changes to the composition of diverse effector proteins over time. Here we sought to connect the structural changes at regulatory elements to alterations in cellular fate and function. To do this we developed PRINT, a computational method that uses deep learning to correct sequence bias in chromatin accessibility data and identifies multi-scale footprints of DNA-protein interactions.

Serum protein profile study of myocardial infarction using a LED induced fluorescence based HPLC system.

Cardiovascular diseases (CVDs) are the major health conditions for high mortality and morbidity in humans. Delay in the diagnosis of CVDs effect patients long and short-term health condition. In -house assembled UV-light emitting diode (LED) based fluorescence detector for high -performance liquid chromatography (HPLC) (HPLC-LED-IF) system is used to record serum chromatograms of three categories of samples namely, before medicated- myocardial infarction (B-MI), after medicated- MI (A-MI), and normal.

Functional inference of gene regulation using single-cell multi-omics.

Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time.

spectroscopy: optical fiber probes for clinical applications.

Introduction: Fiber optic probe-based spectroscopy techniques are fast and highly objective methods for intraoperative diagnoses and minimally invasive surgical interventions for all procedures where endoscopic observations are carried out for cancers of different types. The Raman spectral features provide molecular fingerprint-type information and can reveal the subjects' pathological state in label-free manner, making endoscopy multiplexed fiber optic probe-based devices with the potential for translation from bench to bedside for routine applications.

Areas Covered: This review provides a general overview of different fiber-optic probes for measurements with emphasis on Raman spectroscopy for biomedical application.

Cardiovascular biomarkers in body fluids: progress and prospects in optical sensors.

Cardiovascular diseases (CVD) are the major causative factors for high mortality and morbidity in developing and developed nations. The biomarker detection plays a crucial role in the early diagnosis of several non-infectious and life-threatening diseases like CVD and many cancers, which in turn will help in more successful therapy, reducing the mortality rate. Biomarkers have diagnostic, prognostic and therapeutic significances.

Development of an inter-confirmatory plastic characterization system using spectroscopic techniques for waste management.

Ever-accumulating amounts of plastic waste raises alarming concern over environmental and public health. A practical solution for addressing this threat is recycling, and the success of an industry-oriented plastic recycling system relies greatly on the accuracy of the waste sorting technique adapted. We propose a multi-modal spectroscopic sensor which combines laser-induced breakdown spectroscopy (LIBS) and Raman spectroscopy in a single optical platform for characterizing plastics based on elemental and molecular information to assist the plastic identification-sorting process in recycling industries.

Post-COVID syndrome screening through breath analysis using electronic nose technology.

There is an urgent need to have reliable technologies to diagnose post-coronavirus disease syndrome (PCS), as the number of people affected by COVID-19 and related complications is increasing worldwide. Considering the amount of risks associated with the two chronic lung diseases, asthma and chronic obstructive pulmonary disease (COPD), there is an immediate requirement for a screening method for PCS, which also produce symptoms similar to these conditions, especially since very often, many COVID-19 cases remain undetected because a good share of such patients is asymptomatic. Breath analysis techniques are getting attention since they are highly non-invasive methods for disease diagnosis, can be implemented easily for point-of-care applications even in primary health care centres.

Development of a spectroscopic technique that enables the saliva based detection of COVID-19 at safe distances.

Research activities are in full swing globally to translate the use of saliva as a non-invasive and highly potential specimen for clinical diagnostics, particularly for COVID-19 detection. Being comprised of a pool of biomarkers also enriched with ACE-2 receptors, saliva can provide vital information regarding the state of the human body. Advancements in biophotonics tools for saliva investigation may offer promise for developing rapid, highly objective, optical modalities for COVID- 19 detection.

Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung.

/ encodes for one of two mutually exclusive ATPases present in mammalian SWI/SNF chromatin remodeling complexes and is frequently mutated in human lung adenocarcinoma. However, the functional consequences of mutation on tumor initiation, progression, and chromatin regulation in lung cancer remain poorly understood. Here, we demonstrate that loss of sensitizes club cell secretory protein-positive cells within the lung in a cell type-dependent fashion to malignant transformation and tumor progression, resulting in highly advanced dedifferentiated tumors and increased metastatic incidence.

Human tear fluid analysis for clinical applications: progress and prospects.

: Human blood and saliva are increasingly under investigation for the detection of biomarkers for early diagnosis of non-communicable (e.g.cancers) and communicable diseases like COVID-19.

Photonics of human saliva: potential optical methods for the screening of abnormal health conditions and infections.

Human saliva can be treated as a pool of biological markers able to reflect on the state of personal health. Recent years have witnessed an increase in the use of optical devices for the analysis of body fluids. Several groups have carried out studies investigating the potential of saliva as a non-invasive and reliable clinical specimen for use in medical diagnostics.