Miracle-dz/UniFAR-FTUs huggingface dataset:
Depressive Symptoms and Associated Psychopathology in Urban Adolescents: A Cross-Cultural Study of Three Countries

The study aimed to compare cross-cultural trends of comorbid internalizing and externalizing psychopathology, prosocial beliefs, and perceptions of risk in adolescents with and without clinical levels of self-reported depressive symptoms. The Social and Health Assessment, a self-report survey, was conducted in a representative sample of 3309 adolescents 14 to 17 years old from urban communities in the United States (N = 1343), Belgium (N = 946), and Russia (N = 1009). In all three countries, girls reported higher levels of depressive symptoms than boys. The findings also demonstrate that in both genders, depressive symptoms were associated with increased levels of internalizing and externalizing problems, as well as lower levels of prosocial beliefs and low perceptions of harm from risk-taking behavior. Depressed boys had relatively higher levels of externalizing problems than depressed girls. Greater levels of internalizing problems observed in depressed youth, as compared with their nondepressed counterparts, were not gender-specific. Current findings suggest that the relationships between depression and comorbid psychopathology are not culture-specific and have similar patterns in different populations.
Innate Immune Signaling and Porphyromonas gingivalis-accelerated Atherosclerosis

Periodontal diseases are a group of diseases that lead to erosion of the hard and soft tissues of the periodontium, which, in severe cases, can result in tooth loss. Anecdotal clinical observations have suggested that poor oral health may be associated with poor systemic health; however, only recently have appropriate epidemiological studies been initiated, with defined clinical endpoints of periodontal disease, to address the association of periodontal disease with increased risk for cardiovascular and cerebrovascular disease. Although conflicting reports exist, these epidemiological studies support this connection. Paralleling these epidemiological studies, emerging basic scientific studies also support that infection may represent a risk factor for atherosclerosis. With P. gingivalis as a model pathogen, in vitro studies support that this organism can activate host innate immune responses associated with atherosclerosis, and in vivo studies demonstrate that this organism can accelerate atheroma deposition in animal models. In this review, we focus primarily on the basic scientific studies performed to date which support that infection with bacteria, most notably P. gingivalis, accelerates atherosclerosis. Furthermore, we attempt to bring together these studies to provide an up-to-date framework of emerging theories into the mechanisms underlying periodontal disease and increased risk for atherosclerosis, as well as identify intervention strategies to reduce the incidence of periodontal disease in humans, in an attempt to decrease risk for systemic complications of periodontal disease such as atherosclerotic cardiovascular disease.
Changes in cell surface and cortical cytoplasmic organization during early embryogenesis in the preimplantation mouse embryo

Membrane topography and organization of cortical cytoskeletal elements and organelles during early embryogenesis of the mouse have been studied by transmission and scanning electron microscopy with improved cellular preservation. At the four- and early eight-cell stages, blastomeres are round, and scanning electron microscopy shows a uniform distribution of microvilli over the cell surface. At the onset of morphogenesis, a reorganization of the blastomere surface is observed in which microvilli becomes restricted to an apical region and the basal zone of intercellular contact. As the blastomeres spread on each other during compaction, many microvilli remain in the basal region of imminent cell-cell contacts, but few are present where the cells have completed spreading on each other. Microvilli on the surface of these embryos contain linear arrays of microfilaments with lateral cross bridges. Microtubules and mitochondria become localized beneath the apposed cell membranes during compaction. Arrays of cortical microtubules are aligned parallel to regions of apposed membranes. During cytokinesis, microtubules become redistributed in the region of the mitotic spindle, and fewer microvilli are present on most of the cell surface. The cell surface and cortical changes initiated during compaction are the first manifestations of cell polarity in embryogenesis. These and previous findings are interpreted as evidence that cell surface changes associated with trophoblast development appear as early as the eight-cell stage. Our observations suggest that morphogenesis involves the activation of a developmental program which coordinately controls cortical cytoplasmic and cell surface organization.
Adaptive Motion Smoothening for Video Stabilization

Persons using low coast hand held cameras are untrained, thus captured videos suffers from severe handshakes and jitters. Hence digital video stabilization algorithm is required to acquire video sequences by removing these unwanted handshakes and jitters. This paper proposed an adaptive motion smoothening method that removes high frequency jitters, by filtering the accumulated global motion vectors. A modified method for motion vector validation implemented on global motion vectors using adaptive threshold. Proposed method not only removes the jitters but also preserves the scene information. The proposed method reduces the missing image areas significantly. This allows using a simplified edge completion method to generate the full frame stabilized video, which performs better in the presence of large moving object in the scene.
Collaborative Discovery: A study of Guru-follower dynamics

A model is suggested for abstracting the interaction between a guru and her followers. A guru has mental powers of insight that surpass those of her followers, but they (i) might not believe in her powers and (ii) have limited attention span, so may terminate interaction with her before reaching full “enlightenment”. The main question that interests us is to understand when are gurus likely to retain their flock. This question affects not only spiritual leaders, but also automated processes competing to retain users in a congested information world. Our model assumes followers interact with the guru while keeping in mind a single “retention parameter” that measures the strength of their belief in her predictive power, and the guru’s objective is to reinforce and maximize this parameter through “informative” and “correct” predictions. We make three contributions. First, we define a natural class of retentive scoring rules to model the way followers update their retention parameter and thus evaluate gurus they interact with. These rules are shown to be tightly connected to truth-eliciting “proper scoring rules” studied in Decision Theory since the 1950’s [McCarthy, PNAS 1956]. Second, we focus on the intrinsic properties of phenomena that are amenable to collaborative discovery with a guru. Assuming follower types (or “identities”) are sampled from a distribution D, the retention complexity of D is the minimal initial retention value (or “strength of faith”) that a follower must have before approaching the guru, in order for the guru to retain that follower throughout the collaborative discovery, during which the follower “discovers” his true “identity”. Third and last, we take a modest first step towards relating retention complexity to other established computational complexity measures, namely, dual distance and query complexity, when D is a uniform distribution over a linear space. We show that (i) the retention complexity of Walsh-Hadamard codes is constant and (ii) that of random Low Density Parity Check (LDPC) codes is, with high probability, linear in the code’s blocklength; intriguingly, for these two interesting families of linear codes, retention complexity is roughly equal to query complexity as locally testable codes.
Cancer vaccines

Cancer vaccines – a dream or a reality? There is no doubt that a time will come when this new approach to cancer treatment will provide opportunities that will be both complementary and synergistic with existing treatments. Novelty is often linked to risk, and if there is a given medical field that desperately needs therapeutic improvement, cancer is it. Recent advances on the understanding of the functioning and manipulation of the immune system and on the host–tumour relationship, and on tumour escape, will soon pay off. However, the development of cancer vaccines is not an easy undertaking and the multitude of obstacles are presented and reviewed in this article. The cancer vaccine ‘detractors’ that are arguing negatively on the chances of success are, to this date, correct. Nevertheless, a parallel could be drawn from the monoclonal antibodies, which have suffered from a long and difficult history, to hold promise in man. Recent technological progress has once again demonstrated that one can eventually bypass the commonly accepted barriers, as there are now monoclonal-based products currently helping patients. The entire oncology community is eagerly awaiting the next chapter in the cancer vaccine story.
Extracting Latent Economic Signal from Online Activity Streams

Online activity generates a myriad of weak economically relevant signals, ranging from content-rich interactions such as blog posts, venue reviews and status updates, to more transient or even autonomic signal such as search queries, purchases or realtime ad auctions. In this work we develop an approach to distilling latent economic indicators from large collections of realtime activity streams. In particular we investigate the relative contribution of several online activity streams on forecasting a large cross-section of economic indicators. In order to effectively overcome noise inherent in the extracted weak signals and prevent overﬁtting, we develop a low-rank vector autoregression (VAR) formulation based on sparse matrix factorization. Large-scale mining of online activity data can potentially augment traditional economic analyses in several ways: (1) improving forecasting : E.g., we ﬁnd social network factors are more predictive of unemployment and consumer discretionary spending than a basket of econometric factors, (2) capturing network effects via cross-domain social transfer : E.g., increases in unemployment indicators lead to technology and computing-related searches; wedding planning on Yelp is a leading indicator of positive sentiment on Facebook, and (3) the development of macroeconomic and sentiment indicators with signiﬁcantly lower latency than is traditionally available.
How do software engineers understand code changes?: an exploratory study in industry

Software evolves with continuous source-code changes. These code changes usually need to be understood by software engineers when performing their daily development and maintenance tasks. However, despite its high importance, such change-understanding practice has not been systematically studied. Such lack of empirical knowledge hinders attempts to evaluate this fundamental practice and improve the corresponding tool support. To address this issue, in this paper, we present a large-scale quantitative and qualitative study at Microsoft. The study investigates the role of understanding code changes during software-development process, explores engineers' information needs for understanding changes and their requirements for the corresponding tool support. The study results reinforce our beliefs that understanding code changes is an indispensable task performed by engineers in software-development process. A number of insufficiencies in the current practice also emerge from the study results. For example, it is difficult to acquire important information needs such as a change's completeness, consistency, and especially the risk imposed by it on other software components. In addition, for understanding a composite change, it is valuable to decompose it into sub-changes that are aligned with individual development issues; however, currently such decomposition lacks tool support.
Are Distributional Representations Ready for the Real World? Evaluating Word Vectors for Grounded Perceptual Meaning

Distributional word representation methods exploit word co-occurrences to build compact vector encodings of words. While these representations enjoy widespread use in modern natural language processing, it is unclear whether they accurately encode all necessary facets of conceptual meaning. In this paper, we evaluate how well these representations can predict perceptual and conceptual features of concrete concepts, drawing on two semantic norm datasets sourced from human participants. We find that several standard word representations fail to encode many salient perceptual features of concepts, and show that these deficits correlate with word-word similarity prediction errors. Our analyses provide motivation for grounded and embodied language learning approaches, which may help to remedy these deficits.
Lecture Concepts and Strategies in Retinal Gene Therapy

Genetic defects of the retina or retinal pigment epithelium (RPE) cause a substantial number of sightimpairing or blinding disorders, many of which eventually cause the degeneration and death of the visual cells. Previously considered incurable, some of these retinal diseases can now be treated, at least experimentally, by gene therapy. Disciplines Medicine and Health Sciences | Veterinary Medicine This journal article is available at ScholarlyCommons: https://repository.upenn. edu/vet_papers/159
A Novel Pathogenicity Island Integrated Adjacent to the thrW tRNA Gene of Avian Pathogenic Escherichia coli Encodes a Vacuolating Autotransporter Toxin

ABSTRACT We report the complete nucleotide sequence and genetic organization of the Vat-encoding pathogenicity island (PAI) of avian pathogenic Escherichia coli strain Ec222. The 22,139-bp PAI is situated adjacent to the 3′ terminus of the thrW tRNA gene, has a G+C content of 41.2%, and includes a bacteriophage SfII integrase gene, mobile genetic elements, two open reading frames with products exhibiting sequence similarity to known proteins, and several other open reading frames of unknown function. The PAI encodes an autotransporter protein, Vat (vacuolating autotransporter toxin), which induces the formation of intracellular vacuoles resulting in cytotoxic effects similar to those caused by the VacA toxin from Helicobacter pylori. The predicted 148.3-kDa protein product possesses the three domains that are typical of serine protease autotransporters of Enterobacteriaceae: an N-terminal signal sequence of 55 amino acids, a 111.8-kDa passenger domain containing a modified serine protease site (ATSGSG), and a C-terminal outer membrane translocator of 30.5 kDa. Vat has 75% protein homology with the hemagglutinin Tsh, an autotransporter of avian pathogenic E. coli. A vat deletion mutant of Ec222 showed no virulence in respiratory and cellulitis infection models of disease in broiler chickens. We conclude that the newly described PAI and Vat may be involved in the pathogenicity of avian septicemic E. coli strain Ec222 and other avian pathogenic E. coli strains.
The staying power of adhesion-associated antioxidant activity in Mytilus californianus

The California mussel, Mytilus californianus, adheres in the highly oxidizing intertidal zone with a fibrous holdfast called the byssus using 3, 4-dihydroxyphenyl-l-alanine (DOPA)-containing adhesive proteins. DOPA is susceptible to oxidation in seawater and, upon oxidation, loses adhesion. Successful mussel adhesion thus depends critically on controlling oxidation and reduction. To explore how mussels regulate redox during their functional adhesive lifetime, we tracked extractable protein concentration, DOPA content and antioxidant activity in byssal plaques over time. In seawater, DOPA content and antioxidant activity in the byssus persisted much longer than expected—50% of extractable DOPA and 30% of extractable antioxidant activity remained after 20 days. Antioxidant activity was located at the plaque–substrate interface, demonstrating that antioxidant activity keeps DOPA reduced for durable and dynamic adhesion. We also correlated antioxidant activity to cysteine and DOPA side chains of mussel foot proteins (mfps), suggesting that mussels use both cysteine and DOPA redox reservoirs for controlling interfacial chemistry. These data are discussed in the context of the biomaterial structure and properties of the marine mussel byssus.
Performance comparison of multiple and single surrogate models for pumping optimization of coastal aquifers

ABSTRACT Single and multiple surrogate models were compared for single-objective pumping optimization problems of a hypothetical and a real-world coastal aquifer. Different instances of radial basis functions and kriging surrogates were utilized to reduce the computational cost of direct optimization with variable density and salt transport models. An adaptive surrogate update scheme was embedded in the operations of an evolutionary algorithm to efficiently control the feasibility of optimal solutions in pumping optimization problems with multiple constraints. For a set of independent optimization runs, results showed that multiple surrogates, either by selecting the best or by using ensembles, did not necessarily outperform the single surrogate approach. Nevertheless, the ensemble with optimal weights produced slightly better results than selecting only the best surrogates or applying a simple averaging approach. For all cases, the computational cost, by using single or multiple surrogate models, was reduced by up to 90% of the direct optimization.
Increased survival of antibiotic resistant Escherichia coli inside the 1 macrophages 2

7 Mutations causing antibiotic resistance usually incur a fitness cost in the absence of 8 antibiotics. The magnitude of such cost is known to vary with the environment. Little is 9 known about the fitness effects of antibiotic resistance mutations when bacteria confront 10 the host’s immune system. Here we study the fitness effects of mutations in the rpoB, 11 rpsL and gyrA genes, which confer resistance to rifampicin, streptomycin and nalidixic 12 acid, respectively. These antibiotics are frequently used in the treatment of bacterial 13 infections. We measured two important fitness traits – growth rate and survival ability – 14 of twelve Escherichia coli K-12 strains, each carrying a single resistance mutation, in 15 the presence of macrophages. Strikingly, we found that 67% of the mutants survived 16 better than the susceptible bacteria in the intracellular niche of the phagocytic cells. In 17 particular, all E. coli streptomycin resistant mutants exhibit an intracellular advantage. 18 On the other hand, 42% of the mutants were costly when bacteria were allowed to 19 divide outside macrophages. This study shows that single non-synonymous changes 20 affecting fundamental processes in the cell can contribute to prolonged survival of E. 21 coli in the context of an infection. 22 Copyright © 2012, American Society for Microbiology. All Rights Reserved. Antimicrob. Agents Chemother. doi:10.1128/AAC.01632-12 AAC Accepts, published online ahead of print on 22 October 2012 on A ril 8, 2021 by gest httpaac.asm . rg/ D ow nladed fom
Boxelization

We present a method for transforming a 3D object into a cube or a box using a continuous folding sequence. Our method produces a single, connected object that can be physically fabricated and folded from one shape to the other. We segment the object into voxels and search for a voxel-tree that can fold from the input shape to the target shape. This involves three major steps: finding a good voxelization, finding the tree structure that can form the input and target shapes' configurations, and finding a non-intersecting folding sequence. We demonstrate our results on several input 3D objects and also physically fabricate some using a 3D printer.
Robust lossless image data hiding

Recently, among various data hiding techniques, a new subset, lossless data hiding, has drawn tremendous interest. Most existing lossless data hiding algorithms are, however, fragile in the sense that they can be defeated when compression or other small alteration is applied to the marked image. The method of C. De Vleeschouwer et al. (see IEEE Trans. Multimedia, vol.5, p.97-105, 2003) is the only existing semi-fragile lossless data hiding technique (also referred to as robust lossless data hiding), which is robust against high quality JPEG compression. We first point out that this technique has a fatal problem: salt-and-pepper noise caused by using modulo 256 addition. We then propose a novel robust lossless data hiding technique, which does not generate salt-and-pepper noise. This technique has been successfully applied to many commonly used images (including medical images, more than 1000 images in the CorelDRAW database, and JPEG2000 test images), thus demonstrating its generality. The experimental results show that the visual quality, payload and robustness are acceptable. In addition to medical and law enforcement fields, it has been applied to authenticate losslessly compressed JPEG2000 images.
Effects of Stimulus Type and of Error-Correcting Code Design on BCI Speller Performance

From an information-theoretic perspective, a noisy transmission system such as a visual Brain-Computer Interface (BCI) speller could benefit from the use of error-correcting codes. However, optimizing the code solely according to the maximal minimum-Hamming-distance criterion tends to lead to an overall increase in target frequency of target stimuli, and hence a significantly reduced average target-to-target interval (TTI), leading to difficulties in classifying the individual event-related potentials (ERPs) due to overlap and refractory effects. Clearly any change to the stimulus setup must also respect the possible psychophysiological consequences. Here we report new EEG data from experiments in which we explore stimulus types and codebooks in a within-subject design, finding an interaction between the two factors. Our data demonstrate that the traditional, row-column code has particular spatial properties that lead to better performance than one would expect from its TTIs and Hamming-distances alone, but nonetheless error-correcting codes can improve performance provided the right stimulus type is used.