Miracle-dz/UniFAR-FTUs huggingface dataset:
Artificial Intelligence for Safety-Critical Systems in Industrial and Transportation Domains: A Survey

Artificial Intelligence (AI) can enable the development of next-generation autonomous safety-critical systems in which Machine Learning (ML) algorithms learn optimized and safe solutions. AI can also support and assist human safety engineers in developing safety-critical systems. However, reconciling both cutting-edge and state-of-the-art AI technology with safety engineering processes and safety standards is an open challenge that must be addressed before AI can be fully embraced in safety-critical systems. Many works already address this challenge, resulting in a vast and fragmented literature. Focusing on the industrial and transportation domains, this survey structures and analyzes challenges, techniques, and methods for developing AI-based safety-critical systems, from traditional functional safety systems to autonomous systems. AI trustworthiness spans several dimensions, such as engineering, ethics and legal, and this survey focuses on the safety engineering dimension.
Historical and Geographic Context for the Evolution of Climate Niche Breadth in Temperate Plants

OF THE DISSERTATION In order to predict how species will respond to global climate change, scientists must understand the relationships between traits, fitness, environments and distributions. Niche theory provides a useful framework. Niche breadth describes the range of environmental conditions necessary for population growth. Among these conditions, climate is especially important. Climate niche breadth in turn may reflect a confluence of different forces. This dissertation presents a series of projects that assess the relative roles of historical, geographic and population processes that contribute to climate niche breadth in temperate plants. The first project evaluates the predictive power of a classical hypothesis. If gene flow slows divergent adaptation, then range fragmentation should promote niche breadth. By quantifying the relationships between environmental difference, geographic distance and genetic isolation among European plants, I show that the effect of allopatry on niche breadth depends on the role of the geographic distance among populations. The remaining projects focus in increasingly finer detail on the evolution of niche breadth in a taxonomically complex group. Dodecatheon sect. Dodecatheon grow in diverse habitats across North America. They have confounded taxonomists with polyploidy, hybridization and convergent adaptation. Currently recognized species are either widespread or rare microclimate specialists. First, with multilocus phylogenetics, I show that the difference in niche breadth among rare and widespread species is not simply due to differences in environmental tolerance. In eastern North America, geographic heterogeneity and paleoclimate history strongly contribute to taxonomic rarity. The next project focuses on this group. Both rare eastern species are considered
Compressed, Real-Time Voice Activity Detection with Open Source Implementation for Small Devices

This paper proposes a real-time voice activity detection (VAD) system that utilizes a compressed convolutional neural network (CNN) model. On general-purpose computers, the system is capable of accurately classifying the presence of speech in audio with low latency. Whereas, when implemented on small devices, the system is showing higher latency, which is presumably an indication of high-load computations in the preprocessing steps. The results of the evaluation indicate that the proposed VAD system is an improvement over the existing solutions, in terms of reducing the model size and improving the level of accuracy among different evaluation metrics. Furthermore, the proposed VAD system offers an extension of the applicability by training the CNN model on a different and more diverse data set. Moreover, the proposed architecture is capable of being compressed to approximately one-eleventh of the size, facilitating eventual deployment on small devices. In contrast to existing closed VAD solutions, the entire pipeline of the proposed VAD system is developed in Python and made available as open source, ensuring the verifiability and accessibility of the work.
Analysis of clinical characteristics in proximal and distal reflux monitoring among patients with gastroesophageal reflux disease

Abstract The purpose of this study was to examine the characteristics of proximal and distal gastroesophageal reflux in patients with gastroesophageal reflux disorder and analyze their clinical symptoms. A total of 67 patients with typical esophageal symptoms were selected for this study. All participants completed the reflux disease questionnaire and a questionnaire survey of extraesophageal symptoms. Diagnosis was made using a 24-h impedance-pH detection and proton pump inhibitor. The results showed that the proximal reflux group had a higher number of acid reflux episodes compared to the distal reflux group (P < 0.05). Similarly, the proximal reflux group also had a higher number of gas reflux episodes compared to the distal reflux group (P < 0.05). On the other hand, the distal reflux group had a higher number of mixed reflux episodes compared to the proximal reflux group (P < 0.05). These differences were statistically significant. This study revealed that acid reflux and gas reflux were more predominant in the proximal reflux group, while mixed reflux was more predominant in the distal reflux group.
TRECVID 2010 Surveillance Event Detection by MMM-TJU ∗

Surveillance Event Detection Semantic event detection in the huge amount of surveillance video in both retrospective and real-time styles is essential to a variety of higher-level applications in the public security. In TRECVID 2010, to overcome the limitations of the traditional human action analysis method with human detection/tracking and domain knowledge, we evaluate the general framework for multiple human behaviors modeling with the philosophy of bag of spatiotemporal feature (BoSTF). The brief introduction to each run is shown in Table 1. Table 1 SED RUNs ActDCR Description SED_Runs ActDCR Descriptions TJUMM_1 6.6931 MoSIFT, SVM with 2 χ kernel, 0.50 (threshold) TJUMM_2 5.2067 MoSIFT, SVM with 2 χ kernel, 0.60 (threshold) TJUMM_3 4.4773 MoSIFT, SVM with 2 χ kernel, 0.65 (threshold) TJUMM_4 3.7913 MoSIFT, SVM with 2 χ kernel, 0.70 (threshold) TJUMM_5 3.1070 MoSIFT, SVM with 2 χ kernel, 0.75 (threshold) TJUMM_6 2.4753 MoSIFT, SVM with 2 χ kernel, 0.80 (threshold) TJUMM_7 1.9196 MoSIFT, SVM with 2 χ kernel, 0.85 (threshold) TJUMM_8 1.4527 MoSIFT, SVM with 2 χ kernel, 0.90 (threshold) Semantic Indexing Semantics indexing is extremely helpful for automatic semantic discovery and annotation. In TRECVID 2010, we mainly evaluate three kinds of features, two global features (grid-based color moments and texture feature) , and one local feature (Scale-Invariant Feature Transform, SIFT) for semantic modeling. The cascade Support Vector Machine (SVM) is implemented for each concept model leaning in two ways. First, for each concept three kinds of classifiers are learned with individuals. Second, the decision of three experts above are fused with average fusion algorithm to take advantage of the superiority of individuals. Therefore, we obtained four runs for evaluation of the High Level Feature Extraction test in TRECVID 2010. The brief introduction to each run is shown in Table 2. Table 2 SIN RUNs infMAP Description SIN_Runs InfMAP Descriptions L_A_MMM-TJU1_1 0.0156 GCM Feature and Cascade SVM L_A_MMM-TJU2_2 0.0052 Texture Feature and Cascade SVM L_A_MMM-TJU3_3 0.0238 SIFT Feature and Cascade SVM L_A_MMM-TJU4_4 0.0267 Fusing All Results TRECVID 2010 Surveillance Event Detection by MMM-TJU An-An Liu 1 , Zan Gao 1,2 1 School of Electronic Information Engineering, Tianjin University, Tianjin 300072 P.R. China 2 School of Information and Telecommunication Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, P.R. China
Informedia@TRECVID 2014

: We report on our system used in the TRECVID 2014 Semantic Indexing (SIN) task. We highlight the following new components: 1) self-paced learning pipeline for concept training, 2)dense trajectory with fisher vector encoding, 3) multi-modal pseudo relevance feedback for final results reranking and 4) deep convolutional neural networks directly trained on SIN keyframes. With the help of the above components, we were ranked top 3 among all type A runs (using only TRECVID IACC training data).
Global Distribution of Barrier Islands in Terms of Tectonic Setting

Measurements of the global abundance of barrier islands indicate that 49% occur along coastlines of trailing continent margins; 24%, along collision plate margins; and, 27%, along coasts of marginal seas. Based on 2619 shelf width measurements, evidence is presented to show that for only trailing margins is shelf gradient related to barrier island abundance. Of those barrier islands situated along trailing margin coasts, 75% occur along Amero-trailing margins (average gradient 0.57 m/km); 19%, along Afro-trailing margins (average gradient 2.4 m/km); and, 6% along Neo-trailing margins (average gradient 5.9 m/km). Because sediments supplying barrier islands today are generated mainly on the inner shelf and shoreface in response to both nearshore processes and to rising sea level, barrier islands occur in greatest abundance where broad, low-relief coastal plains lie adjacent to the inner shelf and where both are comprised of abundant uncon-solidated detritus. Elsewhere, barrier island occurrence is sparse to absent along very low gradient shelves where the coastal plain-continental shelf sedimentary prism is absent. The tectonic setting of the continental margin is fundamental in controlling factors governing barrier island abundance.
Land use change and effects on water quality and ecosystem health in the Lake Tahoe basin, Nevada and California

Human activity in the Lake Tahoe Basin has increased substantially in the past four decades, causing significant impacts on the quality and clarity of the lake's famous deep, clear water. Protection of Lake Tahoe and the surrounding environment has become an important activity in recent years. A variety of agencies, including the Tahoe Regional Planning Agency, Tahoe Research Group of the University of California at Davis, Desert Research Institute of the University and Community College System of Nevada, U.S. Geological Survey (USGS), and a host of State (both Nevada and California) and local agencies have been monitoring and conducting research in the Basin in order to understand how the lake functions and to what extent humans have affected its landscape and ecosystem processes. In spite of all of these activities, there remains a lack of comprehensive land use change data and analysis for the Basin. A project is underway that unites the land cover mapping expertise of the USGS National Mapping Discipline with the hydrologic expertise of the Water Resources Discipline to assess the impacts of urban growth and land use change in the Lake Tahoe Basin. Three activities are planned over the next 3 years: (1) mapping the current and historic state of the land surface, (2) conducting analysis to document patterns, rates, and trends in urbanization, land use change, and ecosystem health, and (3) assessing the causes and consequences of land use change with regard to water quality and ecosystem health. We hypothesize that changes in the extent of urban growth and the corresponding increases in impervious surfaces and decreases in natural vegetation have resulted in severe impacts on ecosystem health and integrity, riparian zones and water quality over time. We are acting on multiple fronts to test this hypothesis through the quantification of landscape disturbances and impacts.
Cult and Architecture in the Chalcolithic Period of the Southern Levant: The Case of En-Gedi and Teleilat Ghassul

Abstract We studied the architectural remains of two Chalcolithic (Ghassulian) cultic complexes at En-Gedi and Teleilat Ghassul Area E in order to trace aspects of the architectural planning principles and methods involved in their design and construction. Architectural Formal Analysis has brought to light hitherto unnoticed spatial relations between architectural elements that seem to have structured the ritual activity at the two sites. The discerned geometric regularities imply that specific mathematical knowledge and the same set of design principles and methods were used in the planning of both complexes. The emerging pictures of highly structured ritual and of the use of geometry in Ghassulian cultic production may be used to support suggestions regarding some sort of cultic establishment (priesthood) during the Chalcolithic Ghassulian.
Use of ergodic reasoning to reconstruct the historical range of variability and evolutionary trajectory of rivers

Applications of ergodic reasoning (or location for time substitution) aid efforts at environmental reconstruction and prediction, providing a useful tool to analyse and communicate stages of landscape evolution. Analysis of the historical range of behaviour and change that a river system has experienced can be used to interpret thresholds that have been breached, and underlying controls and/or triggers for adjustment and change. This information can be used to forecast future trajectories of adjustment and provide target conditions for management activities. This paper uses a case study from upper Wollombi Brook, New South Wales, Australia to demonstrate how ergodic reasoning can be used to assess river behaviour, change and responses to natural and human‐disturbances. The ‘river evolution diagram’ developed by Brierley and Fryirs (Geomorphology and River Management: Applications of the River Styles Framework. Blackwell Publishing: Oxford, 2005) is presented as a means for depicting the range of behaviour and evolutionary variability of this river. These approaches can be readily applied in other systems. Implications for approaches to analysis of river evolution and management are outlined. Copyright © 2012 John Wiley & Sons, Ltd.
Proximal protein landscapes of the type I interferon signaling cascade reveal negative regulation by the E3 ubiquitin ligase PJA2

Deciphering the intricate dynamic events governing type I interferon (IFN) signaling is critical to unravel key regulatory mechanisms in host antiviral defense. Here, we leveraged TurboID-based proximity labeling coupled with affinity purification-mass spectrometry to comprehensively map the proximal proteomes of all seven canonical human type I IFN signaling cascade members under basal and IFN-stimulated conditions. This established a network of 103 proteins in close proximity to the core members IFNAR1, IFNAR2, JAK1, TYK2, STAT1, STAT2, and IRF9. We validated several known constitutive protein assemblies, while also revealing novel stimulus-dependent and -independent associations between key signaling molecules. Functional screening further identified PJA2 as a negative regulator of IFN signaling via its E3 ubiquitin ligase activity. Mechanistically, PJA2 interacts with the Janus kinases, TYK2 and JAK1, and promotes their non-lysine and non-degradative ubiquitination, resulting in restrained downstream STAT signaling. Our high-resolution proximal protein landscapes provide global insights into the type I IFN signaling network, and serve as a valuable resource for future exploration of its functional complexities.
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors

Regulation of gene expression during cell development and differentiation is chiefly orchestrated by distal noncoding regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors rely on the cellular and context specificity of regulatory DNA elements to express therapeutic transgenes in the correct location and time. Here, we develop a straight-forward, one-shot approach to screen putative regulatory sequences identified in large-scale epigenomics profiling experiments for precise and programmable control of transgenes encoded within gene therapy viral vectors. We designed a library of 15,000 short sequences (∼200bp) derived from a set of developmentally active DHS elements during human ex vivo erythropoiesis and cloned them into a GFP reporter lentiviral vector. In an erythroid progenitor cell line, these elements display a gradient of transcriptional enhancer activity, with some demonstrating equivalent activity to the canonical β-globin μLCR despite a 9-fold smaller size. We show that these elements are both highly cell type restricted and developmental stage specific both in vitro and in vivo. Finally, we replace the μLCR element with one of the novel short enhancers in a β-thalassemia lentiviral therapeutic vector and efficiently correct the thalassemic phenotype in patient-derived HSPCs. More broadly, our approach provides further insights into enhancer biology with wider implications into the development of highly cell type specific and efficacious viral vectors for human gene therapy.
Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Over the last decades, extensive genome-wide resequencing studies have highlighted the extent of hybridization and introgression between closely related species. Animal and plant species went through cycles of contractions and expansions as a result of glacial cycles. These repeated sequences of reproductive isolation and admixture at continental scales have led to the accumulation over time of an ancient, deep-seated and complex genetic structure. This structure was blurred by extensive gene flow, or reinforced by strong local adaptation. This already multi-layered structure has often been further enhanced by hybridization. We investigated this complexity in Norway spruce (Picea abies) and Siberian spruce (P. obovata), two closely related species dominating Eurasian boreal forests and forming a vast hybrid zone. Here, we genotyped 542 individuals of both species and their hybrids at 480K SNPs. Individuals came from 55 populations, extending from western Europe to Siberia with a focus on the main hybrid zone. Despite extensive gene flow and a clear Isolation-by-Distance pattern at the continental scale, distinct genetic clusters emerged, indicating barriers and corridors to migration. Coalescent-based demographic inferences revealed that Norway and Siberian spruce repeatedly hybridized during the Pleistocene with introgression pattern varying depending on the latitude. In northern ranges, P. obovata expanded into P. abies while P. abies expanded into P. obovata in the southern parts. Two cryptic refugia located in the large hybrid zone played a critical role in shaping the current distribution of the two species. Our study highlights the importance of considering the whole species complex instead of separate entities to shed light on their complex demographic histories.
Comparative Proteomic Study of Retinal Ganglion Cells Undergoing Various Types of Cellular Stressors

Retinal ganglion cell (RGC) damage serves as a key indicator of various retinal degenerative diseases, including diabetic retinopathy (DR), glaucoma, retinal arterial and retinal vein occlusions, as well as inflammatory and traumatic optic neuropathies. Despite the growing body of data on the RGC proteomics associated with these conditions, there has been no dedicated study conducted to compare the molecular signaling pathways involved in the mechanism of neuronal cell death. Therefore, we launched the study using two different insults leading to RGC death: glutamate excitotoxicity and optic nerve crush (ONC). C57BL/6 mice were used for the study and underwent NMDA- and ONC-induced damages. Twenty-four hours after ONC and 1 hour after NMDA injection, we collected RGCs using CD90.2 coupled magnetic beads, prepared protein extracts, and employed LC-MS for the global proteomic analysis of RGCs. Statistically significant changes in proteins were analyzed using the Shiny Go program to identify GO biological processes and molecular functions resulting from the treatment. We identified unique and common alterations in protein profiles in RGCs undergoing different types of cellular stressors. Additionally, we observed the absence of certain proteins in treated RGCs compared to the control group. Our study not only identified both unique and shared proteomic changes but also laid the groundwork for the future development of a therapeutic platform for testing gene candidates for DR and glaucoma.
Fine-tuning FAM161A gene augmentation therapy to restore retinal function

In 15 years, inherited retinal diseases have seen gene therapy as a springboard to hope. Many preclinical investigations focused on vectors with maximal gene expression capabilities. But despite an efficient gene transfer, little physiological improvement was noted for certain ciliopathies. FAM161A is an essential protein for the structure of photoreceptor connecting cilium (CC). In the absence of FAM161A, cilia disorganize resulting in outersegment collapses and vision impairment. Within the human retina, FAM161A produces two isoforms: the long with exon 4, and the short, lacking it. To restore CC in Fam161a-deficient mice, we compared AAV vectors with different promoter activities, doses, and human isoforms injected subretinally in 14-days Fam161atm1b/tm1b mice, shortly after the onset of cilium disorganization. All vectors improved cell survival, but only combining both isoforms using the weak FCBR1-F0.4 promoter allowed precise FAM161A expression in the CC and enhanced retinal function. Our study on FAM161A gene replacement for RP28, a rod-cone-related disease, underscores the critical need for precise therapeutic gene regulation, appropriate vector dosing and delivery of both isoforms. Fine tuning of therapeutic gene expression, tailored to disease traits, is crucial for restoring retinal function. This precision is pivotal for secure gene therapy involving structural proteins like FAM161A.
Liver-specific glucocorticoid action in alcoholic liver disease: study of glucocorticoid receptor knockout and knockin mice

Background Glucocorticoids are the only first-line drugs for severe alcoholic hepatitis (AH), with limited efficacy and various side effects on extrahepatic tissues. Liver-targeting glucocorticoid therapy may have multiple advantages over systemic glucocorticoid for AH. The purpose of this study was to determine the role of hepatocellular glucocorticoid receptor (GR) in alcoholic steatosis (AS) and AH. Methods AS was induced by a high-fat diet plus binge alcohol in adult male and female mice with liver-specific knockout (LKO) and heterozygote of GR. AH was induced by chronic-plus-binge in middle-aged male mice with liver-specific knockin of GR. Changes in hepatic mRNA and protein expression were determined by qPCR and Western blot. Results GR LKO aggravated steatosis and decreased hepatic expression and circulating levels of albumin in both genders of AS mice but only increased markers of liver injury in male AS mice. Marked steatosis in GR LKO mice was associated with induction of lipogenic genes and down-regulation of bile acid synthetic genes. Hepatic protein levels of GR, hepatocyte nuclear factor 4α, and phosphorylated STAT3 were gene-dosage-dependently decreased, whereas that of lipogenic ATP citrate lyase was increased in male GR heterozygote and LKO mice. Interestingly, hepatic expression of estrogen receptor α (ERα) was induced, and the essential estrogen-inactivating enzyme sulfotransferase 1E1 was gene-dosage-dependently down-regulated in GR heterozygote and knockout AS mice, which was associated with induction of ERα-target genes. Liver-specific knockin of GR protected against liver injury and steatohepatitis in middle-aged AH mice. Conclusions Hepatocellular GR is important for protection against AS and AH.