High Biological Relevance Research Articles

Capillary Electrophoresis-Laser Induced Fluorescence Method Development and Validation for Quantification of Nine Gangliosides-Application to Analysis of Cell Lines of CNS Origin.

Gangliosides are sialic acid-containing glycosphingolipids that play an essential role in many biological and pathophysiological processes. They are present in high amounts in the central nervous system and their abnormal metabolism or expression has been observed in many diseases. We have developed and validated a sensitive capillary electrophoresis laser-induced fluorescence (CE-LIF) method for the separation and quantification of oligosaccharides digested from nine gangliosides of high biological relevance. APTS was used for the labeling of the glycans. Reverse polarity CE was performed for the separation of the labeled glycans bearing negative charges. The optimized background electrolyte is a 15 mM lithium acetate buffer with pH of 5 containing 5% w/v linear polyacrylamide, which allows for the separation of all nine gangliosides. Validation parameters including linearity, precision, and accuracy were evaluated. LOQ and LOD were in the nM range, comparable to those of LC-MS techniques. The method was used to identify and quantify the ganglioside pattern of glioblastoma and neuroblastoma cell lines. The presented method is a valuable tool for further investigations aiming at understanding the role of gangliosides in various neurological diseases or CNS tumors.

A novel density based community detection algorithm and its application in detecting potential biomarkers of ESCC

The development of statistically and biologically competent Community Detection Algorithm (CDA) is essential for extracting hidden information from massive biological datasets. This study introduces a novel community index as well as a CDA based on the newly introduced community index. To validate the effectiveness and robustness of the communities identified by the proposed CDA, we compare with six sets of communities identified by well-known CDAs, namely, FastGreedy, infomap, labelProp, leadingEigen, louvain, and walktrap. It is observed that the proposed algorithm outperforms its competing algorithms in terms of several prominent statistical and biological measures. We implement the hardware coding with Verilog, which surprisingly reduces the computation time by 20% compared to R programming while extracting the communities. Next, the communities identified by the proposed algorithm are used for topological and biological analysis with reference to the elite genes, obtained from Genecards, to identify potential biomarkers of Esophageal Squamous Cell Carcinoma (ESCC). Finally, we discover that the genes F2RL3, CALM1, LPAR1, ARPC2, and CLDN7 carry significantly high topological and biological relevance of previously established ESCC elite genes. Further the established wet lab results also substantiate our claims. Hence, we affirm the aforesaid genes, as ESCC potential biomarkers.

An Exceptional Valorization of CuO Nanoparticles in Ionic Liquids as an Efficient Medium for the Electrophilic Substitution of Indole Towards the Formation of Bis(indolyl)methanes

Aim: Ionic liquids are promising green solvents with simple but unique structure-related physical properties such as negligible vapour pressure, exceptional thermal conductivity, remarkable thermal stability and their suitability and inertness towards a broad range of catalytic applications. CuO NPs have been addressed as a cost-effective and a reagent of a choice that necessitates only mild reaction conditions to offer a high yield of the desired products with exceptional selectivity in a short duration of time. Therefore, in the present work, attempts have been made to explore the catalytic potentials of CuO NPs in an ionic liquid medium to synthesize biologically important bis(indolyl)methanes. Background: Catalytic explorations of metal oxide nanoparticles in ionic liquids offers a cooperative effect that has a significant impact on the kinetics as well as on the outcome of the reaction. Therefore, such catalytic systems in the present times have seized the scientific community's interest from the perspectives of sustainable development in synthetic organic chemistry. The combination of metal oxide nanoparticles with highly tunable ionic liquids is not only used to synthesize simple organic molecules but also explored in the synthesis of complex organic molecules of high commercial and biological relevance. Objectives: The current work offers a rapid and robust protocol for synthesizing bis(indolyl)methanes via electrophilic substitution reaction between indole and various aldehydes in the presence of a CuO nanoparticles-ionic liquid system. The discussion focuses on the high tolerance of different functionalities by the catalytic system leading to the synthesis of bis(indolyl)methanes. Methods: CuO NPs have been synthesized via the co-precipitation method using ionic liquid. The applicability of metal oxide nanoparticles-IL matrix was further investigated in synthesizing bis(indolyl)methanes. Results: The FT-IR absorption below 600 cm-1 and the XRD pattern showing all the peaks in the diffraction diagram revealed the formation of CuO NPs. FESEM images show the flake-shaped morphology of CuO NPs and are found to be separated from the agglomerated clusters Conclusion: Ionic liquid-CuO NPs matrix reveals good to exceptional catalytic properties, and their advancements as a catalytic system at room temperature open new avenues for synthetic organic chemists.

Bats (Mammalia: Chiroptera) from two priority areas for biodiversity conservation in the Brazilian Amazon and range extension for Carollia benkeithi (Phyllostomidae)

Abstract Amazonian tropical forests host the highest bat diversity in South America. The central area Brazilian Amazon encompasses one of the largest pristine areas within this biome, where Amanã and Mamirauá Sustainable Development Reserves (SDRs) are located. These two reserves hold the status of Priority Areas for Biodiversity Conservation due to their high biological relevance. The aim of this study was to identify the bat species richness within these SDRs to minimize the Wallacean shortfall of the chiropterofauna in the Amazon. A total of 274 specimens, collected 20 years ago and housed in the mammal collection at the Museu Paraense Emílio Goeldi, were sorted and identified. They are distributed across four families, 18 genera, and 26 species: Artibeus planirostris and Carollia perspicillata were the most abundant vouchers. We identified a range extension for Carollia benkeithi and a possible new taxon for the genus Micronycteris.

Abstract 83: NK cell ADCC assays: Leveraging flow cytometry and reporter cell lines for enhanced biological relevance and throughput

Abstract Amid the growing arsenal of cancer treatments, antibody-dependent cellular cytotoxicity (ADCC) assays have emerged as a significant contributor to the quest for more effective therapies. The ADCC-based antibody therapy often exploits Natural Killer (NK) cells as effectors. This immunotherapeutic approach harnesses the innate cytotoxic potential of NK cells, offering a promising solution for the precision targeting of malignant cells. In this study, we employed two methods that can be used to measure ADCC potency and specificity during preclinical drug discovery. The first was a flow cytometry-based approach that focused on enhancing biological relevance by utilizing primary human peripheral blood mononuclear cells (PBMCs) as a source for NK effector cells. To this end, target cells were fluorescently labeled with CFSE and cultured with freshly isolated PBMCs at 3 effector to target (E:T) ratios, in the presence of ADCC antibody. After 16h incubation, a viability dye was added, and percent cytotoxicity was measured in CFSE+ targets cells by flow cytometry. The second method offered a high-throughput plate reader-based approach (ADCC Reporter Bioassay; Promega), that utilized an ADCC reporter effector cell line harboring a luciferase cassette driven by an NFAT promoter, which is activated when effector and targets cells are bridged by a therapeutic antibody. Cytotoxicity was read out by measuring light output on a Cytation 3 plate imaging reader (Agilent Technologies) after a 6h cell culture incubation using the recommended 6:1 E:T ratio. Preclinical application for both assays was demonstrated using an anti-HER2 therapeutic antibody (trastuzumab) against BT-474, which is a HER2 positive cell line. To demonstrate specificity, an anti-VEGF antibody (bevacizumab) and Hs 578T cells (HER2 low) were used as controls. Our results revealed trastuzumab induced a strong dose-dependent increase in cytotoxicity in the BT-474 cells but not the Hs 578T cell line (range: 40-70%) while bevacizumab failed to induce any cytotoxicity above background levels at any concentration. Furthermore, the flow cytometry and plate reader methodologies produced similar trends. In summary, both applications can be used to produce reliable ADCC drug screening assessments. Additional considerations include investigational needs surrounding high throughput capability versus biological relevance. Unlike traditional models using immortalized cell lines, primary human PBMCs more faithfully recapitulate the physiological interactions between effector cells and target cells. On the other hand, the more streamlined reporter cell line approach not only accelerates assay throughput but also ensures consistent and reliable results in an attractive option for large-scale screening and drug development efforts. Citation Format: David William Draper, Yewei Xing, Scott Wise. NK cell ADCC assays: Leveraging flow cytometry and reporter cell lines for enhanced biological relevance and throughput [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 83.

Diversity in genetic risk of recurrent stroke: a genome-wide association study meta-analysis

IntroductionStroke is a leading cause of death and disability worldwide. Recurrent strokes are seven times more lethal than initial ones, with 54% leading to long-term disability. Substantial recurrent stroke risk disparities exist among ancestral groups. Notably, Africans face double the risk and higher fatality rates compared to Europeans. Although genetic studies, particularly GWAS, hold promise for uncovering biological insights into recurrent stroke, they remain underexplored. Our study addresses this gap through meta-analyses of recurrent stroke GWAS, considering specific ancestral groups and a combined approach.MethodsWe utilized four independent study cohorts for African, European, and Combined ancestry recurrent stroke GWAS with genotyping, imputation, and strict quality control. We harmonized recurrent stroke phenotype and effect allele estimates across cohorts. The logistic regression GWAS model was adjusted for age, sex, and principal components. We assessed how well genetic risk of stroke informs recurrent stroke risk using Receiver Operating Characteristic (ROC) curve analysis with the GIGASTROKE Consortium's polygenic risk scores (PRS).ResultsHarmonization included 4,420 participants (818 African ancestry and 3,602 European ancestry) with a recurrent stroke rate of 16.8% [median age 66.9 (59.1, 73.6) years; 56.2% male]. We failed to find genome-wide significant variants (p < 5e−8). However, we found 18 distinct suggestive (p < 5e−6) genetic loci with high biological relevance consistent across African and European ancestries, including PPARGC1B, CCDC3, OPRL1, and MYH11 genes. These genes affect vascular stenosis through constriction and dilation. We also observed an association with SDK1 gene, which has been previous linked with hypertension in Nigerian and Japanese populations). ROC analysis showed poor performance of the ischemic stroke PRS in discriminating recurrent stroke status (area under the curve = 0.48).DiscussionOur study revealed genetic associations with recurrent stroke not previously associated with incident ischemic stroke. We found suggestive associations in genes previously linked with hypertension. We also determined that knowing the genetic risk of incident stroke does currently not inform recurrent stroke risk. We urgently need more studies to understand better the overlap or lack thereof between incident and recurrent stroke biology.

Patient-Derived Microphysiological Systems for Precision Medicine.

Patient-derived microphysiological systems (P-MPS) have emerged as powerful tools in precision medicine that provide valuable insight into individual patient characteristics. This review discusses the development of P-MPS as an integration of patient-derived samples, including patient-derived cells, organoids, and induced pluripotent stem cells, into well-defined MPSs. Emphasizing the necessity of P-MPS development, its significance as a nonclinical assessment approach that bridges the gap between traditional in vitro models and clinical outcomes is highlighted. Additionally, guidance is provided for engineering approaches to develop microfluidic devices and high-content analysis for P-MPSs, enabling high biological relevance and high-throughput experimentation. The practical implications of the P-MPS are further examined by exploring the clinically relevant outcomes obtained from various types of patient-derived samples. The construction and analysis of these diverse samples within the P-MPS have resulted in physiologically relevant data, paving the way for the development of personalized treatment strategies. This study describes the significance of the P-MPS in precision medicine, as well as its unique capacity to offer valuable insights into individual patient characteristics.

Whole exome sequencing of patients with varicella-zoster virus and herpes simplex virus induced acute retinal necrosis reveals rare disease-associated genetic variants.

Herpes simplex virus (HSV) and varicella-zoster virus (VZV) are neurotropic human alphaherpesviruses endemic worldwide. Upon primary infection, both viruses establish lifelong latency in neurons and reactivate intermittently to cause a variety of mild to severe diseases. Acute retinal necrosis (ARN) is a rare, sight-threatening eye disease induced by ocular VZV or HSV infection. The virus and host factors involved in ARN pathogenesis remain incompletely described. We hypothesize an underlying genetic defect in at least part of ARN cases. We collected blood from 17 patients with HSV-or VZV-induced ARN, isolated DNA and performed Whole Exome Sequencing by Illumina followed by analysis in Varseq with criteria of CADD score > 15 and frequency in GnomAD < 0.1% combined with biological filters. Gene modifications relative to healthy control genomes were filtered according to high quality and read-depth, low frequency, high deleteriousness predictions and biological relevance. We identified a total of 50 potentially disease-causing genetic variants, including missense, frameshift and splice site variants and on in-frame deletion in 16 of the 17 patients. The vast majority of these genes are involved in innate immunity, followed by adaptive immunity, autophagy, and apoptosis; in several instances variants within a given gene or pathway was identified in several patients. We propose that the identified variants may contribute to insufficient viral control and increased necrosis ocular disease presentation in the patients and serve as a knowledge base and starting point for the development of improved diagnostic, prophylactic, and therapeutic applications.

Rapid On-Resin N-Formylation of Peptides as One-Pot Reaction.

N-formylation is a common pre- and post-translational modification of the N-terminus or the lysine side chain of peptides and proteins that plays a role in the initiation of immune responses, gene expression, or epigenetics. Despite its high biological relevance, protocols for the chemical N-formylation of synthetic peptides are scarce. The few available methods are elaborate in their execution and the yields are highly sequence-dependent. We present a rapid, easy-to-use one-pot procedure that runs at room temperature and can be used to formylate protected peptides at both the N-terminus and the lysine side chain on the resin in near-quantitative yields. Only insensitive, storage-stable standard chemicals - formic acid, acetic anhydride, pyridine and DMF - are used. Formylation works for both short and long peptides of up to 34 amino acids and over the spectrum of canonical amino acids.

Newly synthesized glycoprotein profiling to identify molecular signatures of warm ischemic injury in donor lungs.

Despite recent technological advances such as ex vivo lung perfusion (EVLP), the outcome of lung transplantation remains unsatisfactory with ischemic injury being a common cause for primary graft dysfunction. New therapeutic developments are hampered by limited understanding of pathogenic mediators of ischemic injury to donor lung grafts. Here, to identify novel proteomic effectors underlying the development of lung graft dysfunction, using bioorthogonal protein engineering, we selectively captured and identified newly synthesized glycoproteins (NewS-glycoproteins) produced during EVLP with unprecedented temporal resolution of 4 h. Comparing the NewS-glycoproteomes in lungs with and without warm ischemic injury, we discovered highly specific proteomic signatures with altered synthesis in ischemic lungs, which exhibited close association to hypoxia response pathways. Inspired by the discovered protein signatures, pharmacological modulation of the calcineurin pathway during EVLP of ischemic lungs offered graft protection and improved posttransplantation outcome. In summary, the described EVLP-NewS-glycoproteomics strategy delivers an effective new means to reveal molecular mediators of donor lung pathophysiology and offers the potential to guide future therapeutic development.NEW & NOTEWORTHY This study developed and implemented a bioorthogonal strategy to chemoselectively label, enrich, and characterize newly synthesized (NewS-)glycoproteins during 4-h ex vivo lung perfusion (EVLP). Through this approach, the investigators uncovered specific proteomic signatures associated with warm ischemic injury in donor lung grafts. These signatures exhibit high biological relevance to ischemia-reperfusion injury, validating the robustness of the presented approach.

Dipsacus and Scabiosa Species-The Source of Specialized Metabolites with High Biological Relevance: A Review.

The genera Dipsacus L. and Scabiosa L. of the Caprifoliaceae family are widely distributed in Europe, Asia, and Africa. This work reviews the available literature on the phytochemical profiles, ethnomedicinal uses, and biological activities of the most popular species. These plants are rich sources of many valuable specialized metabolites with beneficial medicinal properties, such as triterpenoid derivatives, iridoids, phenolic acids, and flavonoids. They are also sources of essential oils. The genus Dipsacus has been used for centuries in Chinese and Korean folk medicines to treat bone (osteoporosis) and joint problems (rheumatic arthritis). The Korean Herbal Pharmacopoeia and Chinese Pharmacopoeia include Dipsaci radix, the dried roots of D. asperoides C.Y.Cheng & T.M.Ai. In addition, S. comosa Fisch. ex Roem & Schult. and S. tschiliiensis Grunning are used in traditional Mongolian medicine to treat liver diseases. The current scientific literature data indicate that these plants and their constituents have various biological properties, including inter alia antiarthritic, anti-neurodegenerative, anti-inflammatory, antioxidant, anticancer, and antimicrobial activities; they have also been found to strengthen tendon and bone tissue and protect the liver, heart, and kidney. The essential oils possess antibacterial, antifungal, and insecticidal properties. This paper reviews the key biological values of Dipsacus and Scabiosa species, as identified by in vitro and in vivo studies, and presents their potential pharmacological applications.

Abstract 5776: Advancing a screening platform with panels of patient-derived organoid models for drug discovery and development

Abstract High-throughput screening (HTS) offers the potential to rapidly evaluate the activities of anticancer single agents and combinations in many types of cell-based tumor models; however, successful translation of the findings to patients requires tumor models with high biological relevance. The National Cancer Institute’s Patient-Derived Models Repository (PDMR, https://pdmr.cancer.gov) continues to develop a collection of highly characterized patient-derived organoid models representing a variety of cancer types including rare and recalcitrant malignancies and tumors from patients of diverse ancestry. More than 230 publicly available organoid models are undergoing characterization of their suitability for incorporation into HTS panels based on their recovery from cryopreservation, reproducible growth and expansion capacity, and assay performance metrics in a 384-well format with a CellTiter-Glo 3D viability endpoint. Organoid models with suitable characteristics are being screened with a library of 166 FDA-approved oncology drugs (https://dtp.cancer.gov/organization/dscb/obtaining/default.htm). Over a 7-day period, the organoids are exposed to five concentrations of each drug with a 1-log dilution series ranging from 0.01 µM to 100 µM. The concentration-response profiles of patient-derived organoids will provide reference data for the organoid screen and will eventually include data from all approved and most investigational oncology agents (approximately 1,000 small molecules). NCI-60 cell lines were screened as monolayers in a 384-well format with a CellTiter-Glo viability endpoint after a 3-day exposure to the same oncology drug concentrations. Both monolayer and 3D tumor models were tested using a custom designed fully automated screening system and data analysis software platform. A comparison of the FDA-approved drug responses of a panel of 3D colon cancer organoids and a corresponding panel of 9 colon carcinoma NCI-60 cell lines elucidated similarities and differences attributable to the assay methodologies as well as the tumor model characteristics, such as the presence of a BRAF V600E variant or other clinically relevant genetic alterations (APC, ARID1A, BRCA2, etc.). As the characterization of PDMR organoid models for HTS continues, these pharmacological datasets will be made available as a resource for the cancer research community. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261201500003I. Citation Format: Annamaria Rapisarda, Eric Jones, Curtis Hose, Erik Harris, Petreena S. Campbell, Mariaestela Ortiz, John Connelly, Nanda Mahashetty, Thomas Silvers, Zahra Davoudi, Penny Sellers Brady, Tiffany Nikirk Rohrer, Julie Grams, Karen Martin, Patricia Ramsey, Lori Bowles, John R. Britt, Ralph E. Parchment, Thomas S. Dexheimer, Beverly A. Teicher, James H. Doroshow, Nathan P. Coussens. Advancing a screening platform with panels of patient-derived organoid models for drug discovery and development. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5776.

Abstract 56: Unlocking primary cell culture for more relevant in vitro models

Abstract Tumor cell lines are commonly used to investigate biological and translational questions. However, many cell lines have been cultured in serum-containing medium for decades, continuously accumulating genetic and epigenetic aberrations. Without a doubt, these cell lines have very little in common with the tumor they originate from, resulting in low biological and clinical relevance. Despite these drawbacks, cell lines are still the most frequent research tool when it comes to the use of ex vivo models. Yet, in light of higher consistency, reproducibility, and biological relevance, more and more researchers are paying attention to which cells and culture medium to use. Although primary cell cultures certainly reflect cellular and genetic heterogeneity of the original tumor, finding a suitable medium that supports their growth and maintains genetic heterogeneity remains challenging. To this end, we developed serum-free cell culture media to cultivate primary epithelial tumor cells of pancreatic, renal, and ovarian origin. Notably, generating in vitro models with high biological relevance was successful when using our media during the derivation and expansion of tumor cell lines from primary and xenotransplanted tumors. Here, we present another serum-free cell culture media supporting the in vitro growth of primary colon adenocarcinoma. Using this optimized medium, we had a 42% success rate in establishing a primary cell culture for a given tumor sample, higher than for any other media tested in our hands. Next to 2D cell culture, our formulation supports 3D tumoroid formation when cells are embedded in a basement membrane matrix. Furthermore, targeted sequencing of 486 tumor-associated genes revealed that more than 99% of the detected genetic variants in an early passage (p11) were also present after extended time in culture (p53). In summary, our new serum-free medium enables the efficient derivation and expansion of primary tumor and xenograft-derived colon adenocarcinoma cell cultures in 2D and 3D, yet retaining their genetic identity. Citation Format: Benjamin Theek, Anne Franke, David Agorku, Katharina Lamfried, Nojan Jelveh, Michael Linnebacher, Lilian Martinez Carrera, Olaf Hardt. Unlocking primary cell culture for more relevant in vitro models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 56.

Lessons from the Total Synthesis of Highly Substituted Benzophenone Natural Products

AbstractIn this account, we summarize the results and experience gained during 20 years of research in the field of polyketidic natural products displaying a tetra-ortho-substituted benzophenone substructure. As demonstrated by the various approaches towards mumbaistatin and pestalone as targets of high biological relevance, the synthesis of such systems is surprisingly difficult due to the intense interactions of the functional groups adjacent to the ketone bridge. We report successes and failures, as well as the discovery of surprising reactivities that are important for understanding the non-enzymatic formation of related compounds in Nature.1 Introduction2 Mumbaistatin3 Pestalone4 Conclusion

Quantification of Muscle Satellite Stem Cell Divisions by High-Content Analysis.

High-content screening is commonly performed on 2D cultured cells, which is high throughput but has low biological relevance. In contrast, single myofiber culture assay preserves the satellite cell niche between the basal lamina and sarcolemma and consequently has high biological relevance but is low throughput. We describe here a high-content screening method that utilizes single myofiber culture that addresses the caveats of both techniques. Our method utilizes the transgenic reporter allele Myf5-Cre:R26R-eYFP to differentiate stem and committed cells within a dividing couplet that can be quantified by high-content throughput immunodetection and bioinformatic analysis.

Quantitative Prediction of Steatosis in Patients with Non-Alcoholic Fatty Liver by Means of Hepatic MicroRNAs Present in Serum and Correlating with Hepatic Fat.

Non-alcoholic fatty liver disease (NAFLD) is the most prevalent form of chronic liver disease worldwide, but a reliable non-invasive method to quantify liver steatosis in primary healthcare is not available. Circulating microRNAs have been proposed as biomarkers of severe/advanced NAFLD (steatohepatitis and fibrosis). However, the use of circulating miRNAs to quantitatively assess the % of liver fat in suspected NAFLD patients has not been investigated. We performed global miRNA sequencing in two sets of samples: human livers from organ donors (n = 20), and human sera from biopsy-proven NAFLD patients (n = 23), both with a wide range of steatosis quantified in their liver biopsies. Partial least squares (PLS) regression combined with recursive feature elimination (RFE) was used to select miRNAs associated with steatosis. Moreover, regression models with only 2 or 3 miRNAs, with high biological relevance, were built. Comprehensive microRNA sequencing of liver and serum samples resulted in two sets of abundantly expressed miRNAs (418 in liver and 351 in serum). Pearson correlation analyses indicated that 18% of miRNAs in liver and 14.5% in serum were significantly associated with the amount of liver fat. PLS-RFE models demonstrated that 50 was the number of miRNAs providing the lowest error in both liver and serum models predicting steatosis. Comparison of the two miRNA subsets showed 19 coincident miRNAs that were ranked according to biological significance (guide/passenger strand, relative abundance in liver and serum, number of predicted lipid metabolism target genes, correlation significance, etc.). Among them, miR-10a-5p, miR-98-5p, miR-19a-3p, miR-30e-5p, miR-32-5p and miR-145-5p showed the highest biological relevance. PLS regression models with serum levels of 2–3 of these miRNAs predicted the % of liver fat with errors <5%.

Development and Validation of the AIIMS Facial Toolbox for Emotion Recognition.

Emotional facial expression database, used in emotion regulation studies, is a special set of pictures with high social and biological relevance. We present the AIIMS Facial Toolbox for Emotion Recognition (AFTER) database. It consists of pictures of 15 adult professional artists displaying seven facial expressions-neutral, happiness, anger, sadness, disgust, fear, and surprise. This cross-sectional study enrolled 15 volunteer students from a professional drama college in India (six males and nine females; mean age = 26.2 ± 1.93 years). They were instructed to pose with different emotional expressions in high and low intensity. A total of 240 pictures were captured in a brightly lit room against a common, light background. Each picture was validated independently by 19 mental health professionals and two professional teachers of dramatic art. Apart from recognition of emotional quality, ratings were done for each emotion on a 5-point Likert scale with respect to three dimensions-intensity, clarity, and genuineness. Results are discussed in terms of mean scores on all four parameters. The percentage hit rate for all the emotions, after exclusion of contempt, was 84.3%, with the mean kappa for emotional expression being 0.68. Mean scores on intensity, clarity, and genuineness of the emotions depicted in the pictures were high. The database would be useful in the Indian context for researching facial emotion recognition. It has been validated among a group of experts and was found to have high inter-rater reliability.

Membrane Cholesterol Prediction from Human Receptor using Rough Set based Mean-Shift Approach

In human physiology, cholesterol plays an imperative part in membrane cells which regulates the function of G-protein-coupled receptors (GPCR) family. Cholesterol is an individual type of lipid structure and about 90 percent of cellular cholesterol is present at plasma membrane region. Cholesterol Recognition/interaction Amino acid Consensus (CRAC) sequence, generally referred as the CRAC (L/V)-X1−5-(Y)-X1−5-(K/R) and the new cholesterol-binding domain is similar to the CRAC sequence, but exhibits the inverse orientation along the polypeptide chain i.e. CARC (K/R)-X1−5-(Y/F)-X1−5-(L/V). GPCR is treated as a biggest super family in human physiology and probably more than 900 protein genes included in this family. Among all membrane proteins GPCR is responsible for novel drug discovery in all pharmaceuticals industry. In earlier researches the researchers did not find the required number of valid motifs in terms of helices and motif types so they were lacking clinical relevance. The research gap here is that they were not able to predict the motifs effectively which are belonging to multiple motif types. To find out better motif sequences from human GPCR, we explored a hybrid computational model consisting of hybridization of Rough Set with Mean-Shift algorithm. In this paper we made comparison among our resulted output with other techniques such as fuzzy C-means (FCM), FCM with spectral clustering and we concluded that our proposed method targeted well on CRAC region in comparison to CARC region which have higher biological relevance in medicine industry and drug discovery.

Combining high intensity ultrasound and experimental design to improve carotenoid extraction efficiency from Buriti (Mauritia flexuosa)

Buriti (Mauritia flexuosa L.) is a significant source of carotenoids, but these compounds have been extracted using laborious and low-effective methods. The present work evaluated the high-intensity ultrasound combined with a chemometric approach to developing an optimal extraction method of carotenoids from buriti pulp. The multivariate optimization was carried out through two steps. First, a simplex-lattice mixture design was used to optimize the extractor solution finding higher extraction yield (903 ± 21 µg g−1) with the acetone:ethanol (75/25) mixture. After, sample mass (80 mg) and sonication time (30 min) were optimized applying central composite design (CCD) which provided a 14% improvement in the extraction method yield. So, the total carotenoid content (TCC) with optimal extraction conditions was 1026 ± 13 µg g−1which is almost twice the yield of methods known in the literature for buriti. The RP-HPLC-DAD analysis revealed that the carotenoids are gently extracted and β-carotene is the major compound in the extracts. To confirm the accuracy, buriti samples spiked with β-carotene standard and the developed method showed recovery >84% and precision <6.5%. Furthermore, the optimized ultrasound-assisted extraction (UAE) method was applied to other samples (tomato, guava, carrot, mango, acerola, papaya, and pumpkin) and presented a yield to 5.5-fold higher when compared to the reported methods indicating high robustness. Based on results, the UAE method developed has demonstrated feasibility and reliability for the study of carotenoids in buriti pulp as well as in other plant matrices with high biological relevance.

Formation of Temporary Negative Ions and Their Subsequent Fragmentation upon Electron Attachment to CoQ0 and CoQ0 H2.

Ubiquinone molecules have a high biological relevance due to their action as electron carriers in the mitochondrial electron transport chain. Here, we studied the dissociative interaction of free electrons with CoQ0, the smallest ubiquinone derivative with no isoprenyl units, and its fully reduced form, 2,3‐dimethoxy‐5‐methylhydroquinone (CoQ0H2), an ubiquinol derivative. The anionic products produced upon dissociative electron attachment (DEA) were detected by quadrupole mass spectrometry and studied theoretically through quantum chemical and electron scattering calculations. Despite the structural similarity of the two studied molecules, remarkably only a few DEA reactions are present for both compounds, such as abstraction of a neutral hydrogen atom or the release of a negatively charged methyl group. While the loss of a neutral methyl group represents the most abundant reaction observed in DEA to CoQ0, this pathway is not observed for CoQ0H2. Instead, the loss of a neutral OH radical from the CoQ0H2 temporary negative ion is observed as the most abundant reaction channel. Overall, this study gives insights into electron attachment properties of simple derivatives of more complex molecules found in biochemical pathways.