A 3D cell death assay to quantitatively determine ferroptosis in spheroids

The failure of drug efficacy in clinical trials remains a big issue in cancer research. This is largely due to the limitations of two-dimensional (2D) cell cultures, the most used tool in drug screening. Nowadays, three-dimensional (3D) cultures, including spheroids, are acknowledged to be a better model of the in vivo environment, but detailed cell death assays for 3D cultures (including those for ferroptosis) are scarce. In this work, we show that a new cell death analysis method, named 3D Cell Death Assay (3DELTA), can efficiently determine different cell death types including ferroptosis and quantitatively assess cell death in tumour spheroids. Our method uses Sytox dyes as a cell death marker and Triton X-100, which efficiently permeabilizes all cells in spheroids, was used to establish 100% cell death. After optimization of Sytox concentration, Triton X-100 concentration and timing, we showed that the 3DELTA method was able to detect signals from all cells without the need to disaggregate spheroids. Moreover, in this work we demonstrated that 2D experiments cannot be extrapolated to 3D cultures as 3D cultures are less sensitive to cell death induction. In conclusion, 3DELTA is a more cost-effective way to identify and measure cell death type in 3D cultures, including spheroids.</jats:p

Exploiting Domain-Specific Structures For End-User Programming Support Tools

In previous work we have tried to transfer ideas that have been successful in general-purpose programming languages and mainstream software engineering into the realm of spreadsheets, which is one important example of an end-user programming environment. More specifically, we have addressed the questions of how to employ the concepts of type checking, program generation and maintenance, and testing in spreadsheets. While the primary objective of our work has been to offer improvements for end-user productivity, we have tried to follow two particular principles to guide our research. (1) Keep the number of new concepts to be learned by end users at a minimum. (2) Exploit as much as possible information offered by the internal structure of spreadsheets. In this short paper we will illustrate our research approach with several examples

ENHANCED CHAOTIC IMAGE ENCRYPTION ALGORITHM BASED ON TRIGONOMETRIC FUNCTIONS

The advent of wireless communications, both inside and outside the home-office environment has led to an Increased demand for effective encryption systems. The encryption of images is quite different from that of the texts due to the bulk data capacity and high redundancy of images. Traditional methods are difficult to handle the image encryption because of their small space of pseudo random sequence. At present, the chaotic maps have been widely used in image encryption for their extreme sensitivity to tiny changes of initial conditions. The chaos based algorithms have suggested a new and efficient way to deal with the problem of fast and highly secure image encryption. In this paper, we propose an algorithm in which two one-dimensional chaotic maps are used instead of a one-dimensional chaotic map. We also use an external secret key of 96-bits. Thereby it significantly increases the resistance to statistical and differential attacks. The results of experiment, statistical analysis, correlation coefficient analysis and key sensitivity tests show that the algorithm is of great security and practicability

A Noval Saliency Based Iris Segmentation Framework

Iris recognition is regarded as the most reliable and accurate biometric identification system available. In Iris recognition system, iris segmentation is the most time consuming and critical step, in concern to the accuracy of the process. This is a new method of iris segmentation based on the saliency map of an image. In this paper, first the saliency map which provides the visually important region has been designed to specifically locate the iris region. Then a color based masking is done to get the iris boundary. Since this method is computationally simple, a fast and reliable method which segment iris has been proposed. The reliability of the method has been checked with different eye images. The result also show that the proposed model is faster compared to the existing methods and gives a comparable accuracy

Whole-blood sorting, enrichment and in situ immunolabeling of cellular subsets using acoustic microstreaming

Analyzing undiluted whole human blood is a challenge due to its complex composition of hematopoietic cellular populations, nucleic acids, metabolites, and proteins. We present a novel multi-functional microfluidic acoustic streaming platform that enables sorting, enrichment and in situ identification of cellular subsets from whole blood. This single device platform, based on lateral cavity acoustic transducers (LCAT), enables (1) the sorting of undiluted donor whole blood into its cellular subsets (platelets, RBCs, and WBCs), (2) the enrichment and retrieval of breast cancer cells (MCF-7) spiked in donor whole blood at rare cell relevant concentrations (10 mL− 1), and (3) on-chip immunofluorescent labeling for the detection of specific target cellular populations by their known marker expression patterns. Our approach thus demonstrates a compact system that integrates upstream sample processing with downstream separation/enrichment, to carry out multi-parametric cell analysis for blood-based diagnosis and liquid biopsy blood sampling

Inducers and Inhibitors of Cytochrome P450 3A4 Substrates and the Management of their Drug Interactions

INTRODUCTION: DRUG INTERACTION:Drug interactions have been recognized for over 100 years. Today, with the increasing availability of complex therapeutic agents and widespread polypharmacy, the potential for drug interactions is enormous and they have become an increasingly important cause of adverse drug reactions (ADR). An interaction is said to occur when the effects of one drug are altered by the co- administration of another drug, herbal medicine, food, drink or other environmental chemical agents. The net effect of the combination may manifest as an additive or enhanced effect of one or more drugs, antagonism of the effect of one or more drugs, or any other alteration in the effect of one or more drugs. Clinically significant interactions refer to a combination of therapeutic agents which have direct consequences on the patient's condition. Therapeutic benefit can be obtained from certain drug interactions, for example, a combination of different antihypertensive drugs may be used to improve blood pressure control or an opioid antagonist may be use to reverse the effect of an overdose of morphine. Most clinically important interactions involve the effect of one drug on the metabolism of another. Metabolism refers to the process by which drugs and other compounds are biochemically modified to facilitate their degradation and subsequent removal from the body. The liver is the principal site of drug metabolism, although other organs such as the gut, kidneys, lung, skin and placenta are involved. Drug metabolism consists of phase I reactions such as oxidation, hydrolysis and reduction, and phase II reactions, which primarily involve conjugation of the drug with substances such as glucuronic acid and sulphuric acid. Phase I metabolism generally involves the cytochrome P450 (CYP450) mixed function oxidase system. The liver is the major site of cytochrome 450-mediated metabolism, but the enterocytes in the small intestinal epithelium are also potentially important. OBJECTIVE OF THE STUDY: To study various inducers and inhibitors of CYP3A4 substrates in clinical practice and to follow a mechanism based approach in their management of drugdrug interactions. DISCUSSION: Hundred drug-drug interaction based on CYP3A4 metabolism of drugs were obtained from the current study. Of these 66 were between CYP3A4 substrates and inhibitors while 34 were between CYP3A4 substrates and inducers. Most prevalent interacting combination of CYP3A4 substrate and inhibitor was clopidogrel + atorvastatin (39.39%) followed by clopidogrel + amlodipine (16.66%). Most frequently observed interacting combination of CYP3A4 substrate with an inducer was atorvastatin + phenytoin (35.29%) followed by esomeprazole + rifampicin (26.47%). The clinical significane of each interacting drug combination along with pharmacist’s recommendation for a suitable therapeutic alternative are discussed below. CLOPIDOGREL + ATORVASTATIN:CYP3A4 based interaction between clopidogrel and atorvastsatin leads to decreased formation of clopidogrel active metabolite in plasma resulting in high platelet activity leading to thrombosis. This is due to the competition with CYP3A4 mediated metabolism of clopidogrel by atorvastatin and inhibition of Pglycoprotien efflux transport of clopidogrel. In presence of pravastatin and rosuvastatin the clearance of clopidogrel reduces to 24% and 46% respectively. Hence instead of atorvastatin either pravastatin or rosuvastatin may be prescribed in combination with clopidogrel. ESOMEPRAZOLE + FLUCANAZOLE: Due the inhibition of CYP2C19 and CYP3A4 mediated esomeprazole metabolism, esomeprazole exposure may increase by more than two fold when administered concurrently with flucanazole. However, flucanazole is a moderately sensitive substrate of CYP3A4 based metabolism of esomeprazole. Patients should be monitored for potentially increased adverse effects of PPIs during coadministration. CONCLUSION: Evaluation of 100 prescriptions in the current study resulted 66 drug-drug interactions between CYP3A4 substrates with inhibitors and 34 between CYP3A4 substrates and inducers. The most commonly identified combination was clopidogrel+atorvastatin (39.39%) and clopidogrel+amlodipine (16.66%). Both atorvastatin and amlodipine act as an inhibitor of CYP3A4 based metabolism of clopidogrel, possibly resulting in decreased formation of copidogrel active metabolite in plasma. Rosuvastatin which is minimally metabolized by CYP enzyme system may be substituted instead of atorvastatin. The study also identified phenytoin (35.92%) and rifampicin (26.47%) as the inducers of CYP3A4 based metabolism of atorvastatin and esomeprazole leading to a decreased plasma concentration of atorvastatin and esomeprazole

Symplectic integrators for classical spin systems

We suggest a numerical integration procedure for solving the equations of motion of certain classical spin systems which preserves the underlying symplectic structure of the phase space. Such symplectic integrators have been successfully utilized for other Hamiltonian systems, e. g. for molecular dynamics or non-linear wave equations. Our procedure rests on a decomposition of the spin Hamiltonian into a sum of two completely integrable Hamiltonians and on the corresponding Lie-Trotter decomposition of the time evolution operator. In order to make this method widely applicable we provide a large class of integrable spin systems whose time evolution consists of a sequence of rotations about fixed axes. We test the proposed symplectic integrator for small spin systems, including the model of a recently synthesized magnetic molecule, and compare the results for variants of different order

BatchPrompt: Accomplish more with less

As the ever-increasing token limits of large language models (LLMs) have enabled long context as input, prompting with single data samples might no longer an efficient way. A straightforward strategy improving efficiency is to batch data within the token limit (e.g., 8k for gpt-3.5-turbo; 32k for GPT-4), which we call BatchPrompt. We have two initial observations for prompting with batched data. First, we find that prompting with batched data in longer contexts will inevitably lead to worse performance, compared to single-data prompting. Second, the performance of the language model is significantly correlated with the positions and order of the batched data, due to the corresponding change in decoder context. To retain efficiency and overcome performance loss, we propose Batch Permutation and Ensembling (BPE), and a novel Self-reflection-guided EArly Stopping (SEAS) technique. Our comprehensive experimental evaluation demonstrates that BPE can boost the performance of BatchPrompt with a striking margin on a range of popular NLP tasks, including question answering (Boolq), textual entailment (RTE), and duplicate questions identification (QQP). These performances are even competitive with/higher than single-data prompting(SinglePrompt), while BatchPrompt requires much fewer LLM calls and input tokens (For SinglePrompt v.s. BatchPrompt with batch size 32, using just 9%-16% the number of LLM calls, Boolq accuracy 90.6% to 90.9% with 27.4% tokens, QQP accuracy 87.2% to 88.4% with 18.6% tokens, RTE accuracy 91.5% to 91.1% with 30.8% tokens). To the best of our knowledge, this is the first work to technically improve prompting efficiency of large language models. We hope our simple yet effective approach will shed light on the future research of large language models. The code will be released.Comment: 20 pages, 5 figure

Convergent patterns suggest parallel processes of insular anuran diversification between oceanic archipelagos of the Southwest Pacific and the sky islands of the continental Western Ghats

The unprecedented surge in frog species descriptions over the last two decades has been attributed to increasing access to remote regions, more advanced technology and techniques, and greater interest in these groups. The advent of genetic methods had been welcomed by practitioners as a boon in identifying species and their relationships. Suggestions were made that significant diversity was yet unrecognized and that the genetic tools would help uncover “cryptic” species that are not obvious. This notion, however, is contentious, and has been debated. As part of my dissertation thesis, I re-evaluate groups of frogs from two highly biodiverse tropical regions in the Western Ghats of India and the Philippines Archipelago of the Western Pacific. In my first chapter, I revisit a clade of Nyctibatrachus Nightfrogs in the Southern Western Ghats with an integrative approach utilizing morphologic, molecular, bioacoustic, developmental and life history data and reveal that species diversity may likely be inflated in that group (the Nyctibatrachus aliciae group). In my second chapter, I similarly reevaluate a clade of Philippine Limnonectes Fanged Frogs and find evidence to reconfigure species boundaries in the Limnonectes magnus clade. The third chapter addressed the same Limnonectes clade, but with genomic data using the newly developed FrogCap protocol, and finds geneflow between some groups identified in the previous chapter, but not so in other groups, reinforcing some species boundaries while questioning others. My fourth chapter evaluates a species complex of Philippine endemic Pulchrana Spotted Frogs in the eastern islands of the archipelago with genomic data. The results show that Pulchrana grandocula and P. similis cluster together as a group with the remaining Philippine species of Pulchrana forming another. I also find that two formerly recognized rare species represented by singleton specimens have highly admixed genotypes calling into question whether these are indeed unique taxa. My final chapter explores a higher level genomic dataset of frogs of the superfamily Ranoidea with the inclusion of the three paleoendemic Indian ranoid families of Nyctibatrachidae, Micrixalidae and Ranixalidae. My results show for the first time that these three families form a single clade representing an Indian subcontinent-wide ancient in-situ radiation. Additionally, preliminary biogeography results based on this dataset support of a “ferry India” model that suggests that several non-African crown groups of ranoids may have evolved on an insular India during its transit from Gondwana to become Eurasia