Strategies of reducing input sample volume for extracting circulating cell-free nuclear DNA and mitochondrial DNA in plasma

Background: Circulating cell-free (ccf) DNA in blood has been suggested as a potential biomarker in many conditions regarding early diagnosis and prognosis. However, misdiagnosis can result due to the limited DNA resources in Biobank's plasma samples or insufficient DNA targets from a predominant DNA background in genetic tests. This study explored several strategies for an efficient DNA extraction to increase DNA amount from limited plasma input. Methods: Ccf plasma DNA was extracted with three different methods, a phenol-chloroform-isoamylalcohol (PCI) method, a High Pure PCR Template Preparation Kit method and a method used for single cell PCR in this group. Subsequently, the total DNA was measured by Nanodrop and the genome equivalents (GE) of the GAPDH housekeeping gene and MTATP 8 gene were measured using a multiplex real-time quantitative PCR for the quantitative assessment of nDNA and mtDNA. Results: Instead of 400-800 μL (routine input in the laboratory), 50 μLof plasma input enabled the extraction of ccf DNA sufficient for quantitative analysis. Using the PCI method and the kit method, both nDNA and mtDNA could be successfully detected in plasma samples, but nDNA extracted using protocol for single cell PCR was not detectable in 25% of plasma samples. In comparison to the other two methods, the PCI method showed lower DNA purity, but higher concentrations and more GE of nDNA and mtDNA. Conclusions: The PCI method was more efficient than the other two methods in the extraction of ccf DNA in plasma. Limited plasma is available for ccf DNA analysi

Reward Collapse in Aligning Large Language Models

The extraordinary capabilities of large language models (LLMs) such as ChatGPT and GPT-4 are in part unleashed by aligning them with reward models that are trained on human preferences, which are often represented as rankings of responses to prompts. In this paper, we document the phenomenon of \textit{reward collapse}, an empirical observation where the prevailing ranking-based approach results in an \textit{identical} reward distribution \textit{regardless} of the prompts during the terminal phase of training. This outcome is undesirable as open-ended prompts like ``write a short story about your best friend'' should yield a continuous range of rewards for their completions, while specific prompts like ``what is the capital of New Zealand'' should generate either high or low rewards. Our theoretical investigation reveals that reward collapse is primarily due to the insufficiency of the ranking-based objective function to incorporate prompt-related information during optimization. This insight allows us to derive closed-form expressions for the reward distribution associated with a set of utility functions in an asymptotic regime. To overcome reward collapse, we introduce a prompt-aware optimization scheme that provably admits a prompt-dependent reward distribution within the interpolating regime. Our experimental results suggest that our proposed prompt-aware utility functions significantly alleviate reward collapse during the training of reward models

Radar Sensing via OTFS Signaling: A Delay Doppler Signal Processing Perspective

The recently proposed orthogonal time frequency space (OTFS) modulation multiplexes data symbols in the delay-Doppler (DD) domain. Since the range and velocity, which can be derived from the delay and Doppler shifts, are the parameters of interest for radar sensing, it is natural to consider implementing DD signal processing for radar sensing. In this paper, we investigate the potential connections between the OTFS and DD domain radar signal processing. Our analysis shows that the range-Doppler matrix computing process in radar sensing is exactly the demodulation of OTFS with a rectangular pulse shaping filter. Furthermore, we propose a two-dimensional (2D) correlation-based algorithm to estimate the fractional delay and Doppler parameters for radar sensing. Simulation results show that the proposed algorithm can efficiently obtain the delay and Doppler shifts associated with multiple targets.Comment: ICC-2023 Accepte

Seeing What You Miss: Vision-Language Pre-training with Semantic Completion Learning

Cross-modal alignment is essential for vision-language pre-training (VLP) models to learn the correct corresponding information across different modalities. For this purpose, inspired by the success of masked language modeling (MLM) tasks in the NLP pre-training area, numerous masked modeling tasks have been proposed for VLP to further promote cross-modal interactions. The core idea of previous masked modeling tasks is to focus on reconstructing the masked tokens based on visible context for learning local-to-local alignment. However, most of them pay little attention to the global semantic features generated for the masked data, resulting in the limited cross-modal alignment ability of global representations. Therefore, in this paper, we propose a novel Semantic Completion Learning (SCL) task, complementary to existing masked modeling tasks, to facilitate global-to-local alignment. Specifically, the SCL task complements the missing semantics of masked data by capturing the corresponding information from the other modality, promoting learning more representative global features which have a great impact on the performance of downstream tasks. Moreover, we present a flexible vision encoder, which enables our model to perform image-text and video-text multimodal tasks simultaneously. Experimental results show that our proposed method obtains state-of-the-art performance on various vision-language benchmarks, such as visual question answering, image-text retrieval, and video-text retrieval

Low distortion reversible database watermarking based on hybrid intelligent algorithm

In many fields, such as medicine and the computer industry, databases are vital in the process of information sharing. However, databases face the risk of being stolen or misused, leading to security threats such as copyright disputes and privacy breaches. Reversible watermarking techniques ensure the ownership of shared relational databases, protect the rights of data owners and enable the recovery of original data. However, most of the methods modify the original data to a large extent and cannot achieve a good balance between protection against malicious attacks and data recovery. In this paper, we proposed a robust and reversible database watermarking technique using a hash function to group digital relational databases, setting the data distortion and watermarking capacity of the band weight function, adjusting the weight of the function to determine the watermarking capacity and the level of data distortion, using firefly algorithms (FA) and simulated annealing algorithms (SA) to improve the efficiency of the search for the location of the watermark embedded and, finally, using the differential expansion of the way to embed the watermark. The experimental results prove that the method maintains the data quality and has good robustness against malicious attacks

A Tamarisk Habitat Suitability Map for the Continental US

This paper presents a national-scale map of habitat suitability for a high-priority invasive species, Tamarisk (Tamarisk spp., salt cedar). We successfully integrate satellite data and tens of thousands of field sampling points through logistic regression modeling to create a habitat suitability map that is 90% accurate. This interagency effort uses field data collected and coordinated through the US Geological Survey and nation-wide environmental data layers derived from NASA s MODerate Resolution Imaging Spectroradiometer (MODIS). We demonstrate the utilization of the map by ranking the lower 48 US states (and the District of Columbia) based upon their absolute, as well as proportional, areas of highly likely and moderately likely habitat for Tamarisk. The interagency effort and modeling approach presented here could be applied to map other harmful species in the US and globally

Golgi-associated LC3 lipidation requires V-ATPase in noncanonical autophagy

Autophagy is an evolutionarily conserved catabolic process by which cells degrade intracellular proteins and organelles in the lysosomes. Canonical autophagy requires all autophagy proteins (ATGs), whereas noncanonical autophagy is activated by diverse agents in which some of the essential autophagy proteins are dispensable. How noncanonical autophagy is induced and/or inhibited is still largely unclear. In this study, we demonstrated that AMDE-1, a recently identified chemical that can induce canonical autophagy, was able to elicit noncanonical autophagy that is independent of the ULK1 (unc-51-like kinase 1) complex and the Beclin1 complex. AMDE-1-induced noncanonical autophagy could be specifically suppressed by various V-ATPase (vacuolar-type H(+)-ATPase) inhibitors, but not by disturbance of the lysosome function or the intracellular ion redistribution. Similar findings were applicable to a diverse group of stimuli that can induce noncanonical autophagy in a FIP200-independent manner. AMDE-1-induced LC3 lipidation was colocalized with the Golgi complex, and was inhibited by the disturbance of Golgi complex. The integrity of the Golgi complex was also required for multiple other agents to stimulate noncanonical LC3 lipidation. These results suggest that the Golgi complex may serve as a membrane platform for noncanonical autophagy where V-ATPase is a key player. V-ATPase inhibitors could be useful tools for studying noncanonical autophagy

An exploration on the art of photography & the practices of its craft through the relationship between object & subject

The art of photography and the practices of its craft investigate the relationship between the Object and Subject. Through alternative photographic processes, photographers explore various experimental methods and mediums in the making of images. This project aims to enrich the senses through a versatile photographic system which allows the user to switch between historical and contemporary practices. As such, expanding the photographic experiences which are fading from today’s societal practices with digital technology as tools change the way we engage with the subject matter.Bachelor of Fine Art

Production d'hydrogène par reformage de l'éthanol sur catalyseurs à base d'iridium et rhodium supportés sur cérine

Thèse soutenue en co-tutelle avec l'Institut de Chimie Physique de Dalian, Académie Chinoise de SciencesThe main objective of the thesis was to investigate the catalytic performance of stable, active and selective catalytic systems for ethanol steam reforming, ethanol partial oxidation and the combined auto-thermal reforming of ethanol. Two main formulations Ir/CeO2 and Rh/CeO2 were selected to i) investigate surface reaction of adsorbed ethanol via FT-IR and TPD techniques to investigate reaction mechanism; ii) check the ethanol reforming reaction in fixed-bed and micro-structured reactor. Ceria support was found to prevent the highly dispersed active metal particles from sintering and to inhibit coke formation through strong metal-support interactions and redox property. In addition, ceria dispersion was shown to monitor the extent of ethanol conversion and therefore the aging properties of the catalytic systems. It was also possible to identify key elementary steps in reaction mechanism, revealing intermediate products, characteristic of transient, low temperature and short contact time regimes. For the three reactions, excellent performances were obtained with the micro-structured reactor, essentially due to a better heat management, offering real perspectives for an industrial developmentL'objectif principal de ce travail était l'étude de systèmes catalytiques stables, actifs et sélectifs pour les réactions de vapo-reformage, oxyvaporeformage et oxydation partielle de l'éthanol en vu de produire de l'hydrogène. avec une concentration réduite de monoxyde de carbone. Deux formulations principales, Ir/CeO2 et Rh/CeO2, ont été sélectionnées pour étudier le mécanisme des réactions de surface de l'éthanol adsorbé par FT-IR et TPD et pour être testées en micro-réacteur structuré. Il a été montré que la cérine joue un rôle déterminant quant à la dispersion de la phase active en évitant son frittage lors de la réaction et quant à l'inhibition du cokage du fait de ses propriétés rédox. Par ailleurs, la dispersion de ce support qui peut décroître lors de tests de longue durée détermine le niveau de conversion de l'éthanol et le vieillissement du catalyseur. Les principales étapes élémentaires du mécanisme réactionnel ont été identifiées, liées à la formation de produits intermédiaires dans les régimes transitoires et/ou lorsque la conversion de l'éthanol reste partielle (à basse température, faibles temps de contact). Pour les trois réactions étudiées, les excellentes performances obtenues en réacteur microstructuré proviennent essentiellement d'une meilleure gestion des effets thermiques, ce qui ouvre de réelles perspectives d'application industriell