Miracle-dz/UniFAR-FTUs huggingface dataset:
Lung Microbiome Participation in Local Immune Response Regulation in Respiratory Diseases

The lung microbiome composition has critical implications in the regulation of innate and adaptive immune responses. Next-generation sequencing techniques have revolutionized the understanding of pulmonary physiology and pathology. Currently, it is clear that the lung is not a sterile place; therefore, the investigation of the participation of the pulmonary microbiome in the presentation, severity, and prognosis of multiple pathologies, such as asthma, chronic obstructive pulmonary disease, and interstitial lung diseases, contributes to a better understanding of the pathophysiology. Dysregulation of microbiota components in the microbiome–host interaction is associated with multiple lung pathologies, severity, and prognosis, making microbiome study a useful tool for the identification of potential therapeutic strategies. This review integrates the findings regarding the activation and regulation of the innate and adaptive immune response pathways according to the microbiome, including microbial patterns that could be characteristic of certain diseases. Further studies are required to verify whether the microbial profile and its metabolites can be used as biomarkers of disease progression or poor prognosis and to identify new therapeutic targets that restore lung dysbiosis safely and effectively.
Spatiotopic and saccade-specific transsaccadic memory for object detail

The content and nature of transsaccadic memory are still a matter of debate. Brief postsaccadic target blanking was demonstrated to recover transsaccadic memory and defeat saccadic suppression of displacement. We examined whether blanking would also support transsaccadic transfer of detailed form information. Observers saccaded to a peripheral, checkerboard-like stimulus and reported whether an intrasaccadic change had occurred in its upper or lower half. On half of the trials, the stimulus was blanked for 200 ms with saccade onset. In a fixation condition, observers kept fixation but the stimulus was displaced from periphery to fixation, mimicking the retinal events of the saccade condition. Results show that stimulus blanking improves transsaccadic change detection, with performance being far superior to the retinally equivalent fixation condition. Our findings argue in favor of a remapped memory trace that can be accessed only in the blanking condition, when not being overwritten by the salient postsaccadic stimulus.
Estimation with Applications to Tracking and Navigation

From the Publisher: "Estimation with Applications to Tracking and Navigation treats the estimation of various quantities from inherently inaccurate remote observations. It explains state estimator design using a balanced combination of linear systems, probability, and statistics. " "The authors provide a review of the necessary background mathematical techniques and offer an overview of the basic concepts in estimation. They then provide detailed treatments of all the major issues in estimation with a focus on applying these techniques to real systems. " "Suitable for graduate engineering students and engineers working in remote sensors and tracking, Estimation with Applications to Tracking and Navigation provides expert coverage of this important area. "--BOOK JACKET.
Fertility developments in Norway and Sweden since the early 1960s

The purpose of this paper is to give an overview of recent trends in child-bearing in neighboring Norway and Sweden. We use indexes produced by applying indirect standardization to register data of the two countries in order to describe and contrast the fertility developments over the last four decades. Our indexes enable us to decompose overall fertility trends into birth-order specific components and by combining the same kind of data from two countries, we get a very accurate picture of various cross-country differences in fertility levels. We demonstrate how Swedish fertility has fluctuated relatively strongly during the whole study period while Norwegian fertility has evolved more gradually, at least during the last two decades. A turnaround from decreasing to increasing levels of childbearing is evident in 1977 in both countries while a sudden shift to shorter birth intervals is specific to Sweden in the 1980s and contributed to its more spectacular increase in fertility during that decade. (AUTHOR)
CODIT: Code Editing With Tree-Based Neural Models

The way developers edit day-to-day code tends to be repetitive, often using existing code elements. Many researchers have tried to automate repetitive code changes by learning from specific change templates which are applied to limited scope. The advancement of deep neural networks and the availability of vast open-source evolutionary data opens up the possibility of automatically learning those templates from the wild. However, deep neural network based modeling for code changes and code in general introduces some specific problems that needs specific attention from research community. For instance, compared to natural language, source code vocabulary can be significantly larger. Further, good changes in code do not break its syntactic structure. Thus, deploying state-of-the-art neural network models without adapting the methods to the source code domain yields sub-optimal results. To this end, we propose a novel tree-based neural network system to model source code changes and learn code change patterns from the wild. Specifically, we propose a tree-based neural machine translation model to learn the probability distribution of changes in code. We realize our model with a change suggestion engine, Codit, and train the model with more than 24k real-world changes and evaluate it on 5k patches. Our evaluation shows the effectiveness of Codit in learning and suggesting patches. Codit can also learn specific bug fix pattern from bug fixing patches and can fix 25 bugs out of 80 bugs in Defects4J.
Making Method of Moments Great Again? -- How can GANs learn the target distribution

Generative Adversarial Networks (GANs) are widely used models to learn complex real-world distributions. In GANs, the training of the generator usually stops when the discriminator can no longer distinguish the generator's output from the set of training examples. A central question of GANs is that when the training stops, whether the generated distribution is actually close to the target distribution, and how can the training process reach to such configurations efficiently? In this paper, we established a theoretical results towards understanding this generator-discriminator training process. We observe that during the earlier stage of the GANs training, the discriminator is trying to force the generator to match the low degree moments between the generator's output and the target distribution. Moreover, by simply matching these empirical moments over polynomially many training examples, we prove that the generator can already learn notable class of distributions, including those that can be generated by two-layer neural networks.
Parameter-Transferred Wasserstein Generative Adversarial Network (PT-WGAN) for Low-Dose PET Image Denoising

Due to the widespread of positron emission tomography (PET) in clinical practice, the potential risk of PET-associated radiation dose to patients needs to be minimized. However, with the reduction in the radiation dose, the resultant images may suffer from noise and artifacts that compromise diagnostic performance. In this article, we propose a parameter-transferred Wasserstein generative adversarial network (PT-WGAN) for low-dose PET image denoising. The contributions of this article are twofold: 1) a PT-WGAN framework is designed to denoise low-dose PET images without compromising structural details and 2) a task-specific initialization based on transfer learning is developed to train PT-WGAN using trainable parameters transferred from a pretrained model, which significantly improves the training efficiency of PT-WGAN. The experimental results on clinical data show that the proposed network can suppress image noise more effectively while preserving better image fidelity than recently published state-of-the-art methods. We make our code available at https://github.com/90n9-yu/PT-WGAN.
An analytical investigation of the indirect measurement method of estimating the acoustic impedance of a time-varying source

This paper presents an analytical investigation of the direct method of measurement of the source impedance of a linear time-variant source. The direct method yields a frequency-dependent effective source impedance which is routinely used in a time-invariant analysis to determine the insertion loss of two different acoustic loads applied to the same source. In such an analysis the strength of the source is assumed to be invariant with load. It is shown here that there is generally no precise correspondence between the effective source impedance as given by the direct method and the characteristics of the actual source. Furthermore, it is shown that the effective source impedance values given by the direct method are functions of the acoustic load and the location of the injected signal as used in the measurement. However, the effective source resistance is always found to be positive, in accordance with experimental measurements. In this regard the direct method is an improvement on the indirect method, where physically implausible negative resistance values are often found. Finally, it is shown that the effective impedance values as given by the direct method when used with a time-invariant analysis give rise to very accurate predictions of insertion loss, even when the strength of the actual time-variant source is allowed to vary with the acoustic load.
Chiral symmetry and taste symmetry from the eigenvalue spectrum of staggered Dirac operators

We investigate general properties of the eigenvalue spectrum for improved staggered quarks. We introduce a new chirality operator $[\gamma_5 \otimes 1]$ and a new shift operator $[1 \otimes \xi_5]$, which respect the same recursion relation as the $\gamma_5$ operator in the continuum. Then we show that matrix elements of the chirality operator sandwiched between two eigenstates of the staggered Dirac operator are related to those of the shift operator by the Ward identity of the conserved $U(1)_A$ symmetry of staggered fermion actions. We perform a numerical study in quenched QCD using HYP staggered quarks to demonstrate the Ward identity. We introduce a new concept of leakage patterns which collectively represent the matrix elements of the chirality operator and the shift operator sandwiched between two eigenstates of the staggered Dirac operator. The leakage pattern provides a new method to identify zero modes and non-zero modes in the Dirac eigenvalue spectrum. This method is as robust as the spectral flow method but requires much less computing power. Analysis using a machine learning technique confirms that the leakage pattern is universal, since the staggered Dirac eigenmodes on normal gauge configurations respect it. In addition, the leakage pattern can be used to determine a ratio of renormalization factors as a by-product. We conclude that it might be possible and realistic to measure the topological charge $Q$ using the Atiya-Singer index theorem and the leakage pattern of the chirality operator in the staggered fermion formalism.
Block-Approximated Exponential Random Graphs

An important challenge in the field of exponential random graphs (ERGs) is the fitting of non-trivial ERGs on large graphs. By utilizing fast matrix block-approximation techniques, we propose an approximative framework to such non-trivial ERGs that result in dyadic independence (i.e., edge independent) distributions, while being able to meaningfully model local information of the graph (e.g., degrees) as well as global information (e.g., clustering coefficient, assortativity, etc.) if desired. This allows one to efficiently generate random networks with similar properties as an observed network, and the models can be used for several downstream tasks such as link prediction. Our methods are scalable to sparse graphs consisting of millions of nodes.Empirical evaluation demonstrates competitiveness in terms of both speed and accuracy with state-of-the-art methods—which are typically based on embedding the graph into some low-dimensional space— for link prediction, showcasing the potential of a more direct and interpretable probablistic model for this task.
The Effects of Exogenous ABA on Osmotic Adjustment in Maize Roots under Osmotic Stress

The maize roots were treated with ABA under osmotic stress. The water potential, osmotic potential, osmotic adjustment of maize roots and 4 kinds of soluble materials were measured. It is indicated that, ABA decreased the osmotic potential, increased the osmotic adjustment and water potential in maize roots under osmotic stress, and the effect of ABA on Luyu No.14(a drought resistant variety) is greater than Yedan No. 13(a drought sensitive one). Under normal condition, ABA can increase the water potential of the maize roots in a way, but it has no effects on the osmotic potential. The exogenous ABA can observably increase the concentration of proline in roots not only under osmotic stress but also under normal water condition. ABA can also increase the concentration of soluble sugar under osmotic stress in a way, but have no observably effect on free amino acid and K +. The effect of ABA on accumulating proline can restrain by cycloheximide(CHI) which is a protein synthesis inhibitor. This result suggests that the effect of ABA on proline is related with the gene expression
The Response of the Glycerophosphocholine Metabolite Lipidome to Experimental Autoimmune Encephalomyelitis and Cycling Female Sex Hormones in the Hippocampus and Temporal-Parietal-Entorhinal Cortex of Female Mice

II LIST OF ABBREVIATIONS VII ACKOWLEDGMENTS IX CHAPTER ONE 1 1.1 MULTIPLE SCLEROSIS 1 1.1.1 MULTIPLE SCLEROSIS IS AN AUTOIMMUNE NEURODEGENERATIVE DISEASE OF THE CENTRAL NERVOUS SYSTEM CHARACTERIZED BY DEMYELINATION AND AXONAL LOSS. 1 1.1.2 NEUROINFLAMMATION, MEDIATED BY AUTOREACTIVE T-CELLS THAT CROSS THE BLOOD-BRAIN BARRIER, IS A CONTRIBUTING FACTOR TO DEMYELINATION AND AXONAL LOSS IN MS. 3 1.1.3 IN ADDITION TO INFLAMMATION, NEURODEGENERATION ALSO CONTRIBUTES TO MS PATHOGENESIS THROUGH DYSFUNCTIONAL MITOCHONDRIA AND TOXIC CALCIUM ACCUMULATION. 9 1.1.4 MS CAN BE DIVIDED INTO DISTINCT SUBCLASSES: REMITTING MS AND PROGRESSIVE MS. 13 1.1.5 CURRENTLY AVAILABLE TREATMENTS ARE ONLY EFFECTIVE FOR RRMS PATIENTS, AND THEY TARGET ONLY THE IMMUNOLOGICAL COMPONENT OF THE DISEASE. 13 1.1. 6 ALTHOUGH MS HAS TRADITIONALLY BEEN CONSIDERED AUTOIMMUNE IN NATURE, SOME ARE QUESTIONING WHETHER MS MAY TRULY BE A NEURODEGENERATIVE DISEASE WITH AN INFLAMMATORY COMPONENT. 16 1.1. 7 COGNITIVE IMPAIRMENTS ARE COMMON AND APPEAR EARLY IN MS PATIENTS. 19 1.2 EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS 22 1.2. 1 THE BEST MODEL AVAILABLE FOR STUDYING THE IMMUNOLOGICAL COMPONENT OF MS IS EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS. 22 1.2. 2 MICE SUBJECTED TO EAE DEMONSTRATE COGNITIVE IMPAIRMENTS, PARTICULARLY IN MEMORY FUNCTION. 25 1.3 HORMONAL REGULATION OF DISEASE SEVERITY IN EAE AND MS 26 1.3. 1 ESTROGENS MAY BE PROTECTIVE FOR EAE MICE AND MS PATIENTS. 26 1.3. 2 FEMALE SEX HORMONE LEVELS IN CYCLING INDIVIDUALS FOLLOW A TYPICAL PATTERN KNOWN AS THE MENSTRUAL CYCLE IN HUMANS AND THE ESTROUS CYCLE IN MICE. 27 1.4 GLYCEROPHOSPHOLIPIDS 29 1.4. 1 LIPIDS ARE DIVERSE, DYNAMIC MOLECULES THAT ARE ESPECIALLY IMPORTANT IN CELL MEMBRANES. 29 1.4. 2 STRUCTURAL GLYCEROPHOSPHOCHOLINES IN THE MEMBRANE CAN BE REMODELED TO PRODUCE BIOACTIVE METABOLITES THAT PARTICIPATE IN CELL SIGNALING. 31 1.4. 3 THE LAND’S CYCLE IS RESPONSIBLE FOR CONTROLLING PRODUCTION OF GPC METABOLITES. 38 1.4. 4 GPC METABOLISM MAY PLAY A ROLE IN MS AND EAE PATHOLOGY. 47 1.5 OBJECTIVE AND HYPOTHESIS 50
Philopatry and Dispersal within a Black Guillemot Colony

-We studied patterns of dispersal and philopatry within a Black Guillemot (Cepphus grylle) colony, based on a 22-year capture-recapture study of individually-marked birds. The study colony in western Iceland was divided into 15 subcolonies. Out of 356 local recruits, 122 settled in their natal subcolony, a far higher proportion than expected from a random distribution. The western part of the colony attracted significantly more recruits than did the eastern part. Breeding dispersal among subcolonies only occurred in one percent of all cases in which a bird was captured in two successive years. We suggest that potential recruits select their breeding site based on an assessment of quality as expressed by conspecific breeding success, and also that philopatry occurs because this information acquisition is less than perfect and birds bias their search towards their natal site. Received 18 May 1998, initially accepted 24 November 1998, final acceptance 15 May 1999.
Characterization of Motor Unit Discharge Rate in Patients with Amyotrophic Lateral Sclerosis

In this study, we used a custom made quadrifilar needle electrode and multichannel electromyography (EMG) software tool to decompose EMG signals and investigate the behavior of motor unit discharge rate (MUDR) of concurrently active motor units in patients with amyotrophic lateral sclerosis (ALS). Decomposition is a technique used to break down the complex EMG signal into its constituent motor units. A motor unit is a single alpha motor neuron and all the muscle fibers it innervates. ALS is a progressive degenerative disorder of both the upper and lower motor neurons. We recorded four differentially amplified EMG signals from the first dorsal interosseous (FDI) muscle of six ALS patients (four with predominant lower motor neuron pathology and two with predominant upper motor neuron pathology) and seven control subjects. Recordings were made from force contractions of 20 and 50 % of maximum voluntary contraction (MVC). All control subjects were between the ages of 40 and 70 years and were examined by a practicing physiatrist for exclusion criteria including neuromuscular disorders or any medications that might affect muscle activity. We observed differences in initial firing rates and variability of active motor units between control subjects and ALS patients. Furthermore we observed differences in firing rates and variability of active motor units between ALS patients with predominant upper motor neuron pathology and ALS patients with predominant lower motor neuron pathol1 2 ogy. Initial motor unit firing rates for control subjects were 16.22 ± 2.06 Hz at 20% MVC and 19.79 ± 1.66 Hz at 50% MVC. As expected, initial motor unit firing rates from patients with predominant lower motor neuron pathology were higher than those of control subjects; 18.87 ± 4.73 Hz at 20% MVC and 24.28 ± 5.01 Hz at 50% MVC. ALS patients with predominant upper motor neuron pathology, as expected, had initial motor unit firing rates that were lower than those observed in control subjects; 9.22 ± 1.68 Hz at 20% MVC and 12.83 ± 2.26 Hz at 50% MVC. Motor unit firing rate time series in ALS patients with predominant upper motor neuron pathology showed decreased variability, 0.99 ± 0.17 Hz at 20% MVC and 1.70 ± 0.52 Hz at 50% MVC, when compared to control subjects, 2.37±0.67 at 20% MVC and 4.20± 1.00 at 50% MVC. Variability of motor unit firing rate time series in ALS patients with predominant lower motor neuron were high, 3.38 ± 1.2 Hz at 20% MVC and 4.07 ± 1.56 Hz at 50% MVC, compared to control subjects. At 50% MVC, motor unit substitution was observed in ALS patients with predominant upper motor neuron pathology despite the contractions lasting just a few seconds. Motor unit action potentials (MUAPs) recorded from patients were polyphasic when compared to those from control subjects, as is characteristically found in practice.
Molecular biology of flower development in Viola pubescens , a species with the chasmogamous-cleistogamous mixed breeding system

WANG, YUNJING, Ph.D., March 2008. Molecular and Cellular Biology MOLECULAR BIOLOGY OF FLOWER DEVELOPMENT IN VIOLA PUBESCENS, A SPECIES WITH THE CHASMOGAMOUS-CLEISTOGAMOUS MIXED BREEDING SYSTEM (109 pp.) Directors of Dissertation: Sarah E. Wyatt and Harvey E. Ballard, Jr. Plants with both open, out-crossing chasmogamous and closed, self-pollinating cleistogamous flowers are distributed over 50 angiosperm families. The chasmogamouscleistogamous mixed breeding system is a successful reproductive strategy because it can ensure seed output over a range of environmental and pollinator conditions and maintain sexually produced progeny even in the absence of pollination agents. Many ecologists and biologists have conducted research on the mixed breeding system, but the underlying molecular mechanisms remain largely unknown. The research presented here examined the molecular biology of flower development in a widespread North American violet, Viola pubescens. The plant growth regulator gibberellic acid (GA) was reported to induce chasmogamous flowers from cleistogamous ones in some species. Two genes, VGA20ox and VGA3ox, which encode key enzymes (GA20 oxidase and GA3 oxidase) in the biosynthesis of GA, were identified by reverse transcriptase polymerase chain reactions (RT-PCR) from V. pubescens. Semi-quantitative RT-PCR indicated that both genes exhibited increased expression in chasmogamous flowers compared to cleistogamous flowers. Exogenous application of GA3, however, did not induce cleistogamous flowers to open. Thus, GA is involved in the mixed breeding system, but 4 it is not sufficient to convert the closed status of cleistogamous flowers in V. pubescens. GA was demonstrated to target the floral meristem identity gene LEAFY (LFY) in Arabidopsis. Two LFY orthologs (VLFY1 and VLFY2) were obtained by screening a genomic library of V. pubescens. Semi-quantitative RT-PCR suggested the two LFY orthologs function together in the early stages of development of both flower types. Analysis of their promoters indicated they might be differentially regulated. The ABCE floral organ identity genes come into play once the floral meristems are determined. Two A class genes (VAP1 and VAP2), two B class genes (VAP3 and VPI), one C class gene (VAG) and one E class gene (VSEP3) were identified by RT-PCR. The differential expression patterns of the ABCE floral genes between the chasmogamous and cleistogamous flowers were consistent with their morphological differences. Taken together, most of the floral genes examined here in V. pubescens were expressed differently between the two flower types, which might be a response to the different environmental conditions under which the two flower types were produced, contributing to the production of both chasmogamous and cleistogamous flowers. Approved: _____________________________________________________________