Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of climate change and anthropogenic ocean acidification on underwater acoustic communications

Global climate change is a widely accepted phenomenon and it is well understood that it is also leading to changes in the oceanic conditions. Increased industrial activities have also led to anthropogenic ocean acidification, the effects of which, on marine ecosystems, is a vigorously investigated topic. However, the impact of these phenomenon on underwater acoustic communication has not been investigated thoroughly. Fluctuations in ambient ocean conditions, such as salinity, acidity and temperature can lead to changes in the underwater acoustic channel performance. Since both marine mammals and man-made underwater wireless networks depend upon acoustic communications it is important to understand the effects in this context as well. An insight into the effects of climate change and anthropogenic ocean acidification could aid in designing better communication systems and also help explain some observed changes in marine mammal communication behavior. In this paper we present the results of a study conducted to better understand the effects of global climate change. Along with a brief presentation of the mathematical model, results of increasing temperature and acidity are discussed and effects on digital and marine mammal communication are both explored.
Hint1 gene deficiency enhances the supraspinal nociceptive sensitivity in mice

Previous studies have indicated a possible role of histidine triad nucleotide‐binding protein 1 (HINT1) on sustaining the regulatory crosstalk of N‐methyl‐D‐aspartate acid glutamate receptors (NMDARs) and G‐protein‐coupled receptors (GPCRs) such as the μ‐opioid receptor (MOR). Both receptors are present in the midbrain periaqueductal gray neurons, an area that plays a central role in the supraspinal antinociceptive process.
Crosstalk between Virulence Loci: Regulation of Salmonella enterica Pathogenicity Island 1 (SPI-1) by Products of the std Fimbrial Operon

Invasion of intestinal epithelial cells is a critical step in Salmonella infection and requires the expression of genes located in Salmonella pathogenicity island 1 (SPI-1). A key factor for SPI-1 expression is DNA adenine (Dam) methylation, which activates synthesis of the SPI-1 transcriptional activator HilD. Dam-dependent regulation of hilD is postranscriptional (and therefore indirect), indicating the involvement of unknown cell functions under Dam methylation control. A genetic screen has identified the std fimbrial operon as the missing link between Dam methylation and SPI-1. We show that all genes in the std operon are part of a single transcriptional unit, and describe three previously uncharacterized ORFs (renamed stdD, stdE, and stdF). We present evidence that two such loci (stdE and stdF) are involved in Dam-dependent control of Salmonella SPI-1: in a Dam− background, deletion of stdE or stdF suppresses SPI-1 repression; in a Dam+ background, constitutive expression of StdE and/or StdF represses SPI-1. Repression of SPI-1 by products of std operon explains the invasion defect of Salmonella Dam− mutants, which constitutively express the std operon. Dam-dependent repression of std in the ileum may be required to permit invasion, as indicated by two observations: constitutive expression of StdE and StdF reduces invasion of epithelial cells in vitro (1,000 fold) and attenuates Salmonella virulence in the mouse model (>60 fold). In turn, crosstalk between std and SPI-1 may play a role in intestinal infections by preventing expression of SPI-1 in the caecum, an intestinal compartment in which the std operon is known to be expressed.
Implications of Assist-As-Needed Robotic Step Training after a Complete Spinal Cord Injury on Intrinsic Strategies of Motor Learning

Robotic training paradigms that enforce a fixed kinematic control might be suboptimal for rehabilitative training because they abolish variability, an intrinsic property of neuromuscular control (Jezernik et al., 2003). In the present study we introduce “assist-as-needed” (AAN) robotic training paradigms for rehabilitation of spinal cord injury subjects. To test the efficacy of these robotic control strategies to teach spinal mice to step, we divided 27 adult female Swiss–Webster mice randomly into three groups. Each group was trained robotically by using one of three control strategies: a fixed training trajectory (Fixed group), an AAN training paradigm without interlimb coordination (Band group), and an AAN training paradigm with bilateral hindlimb coordination (Window group). Beginning at 14 d after a complete midthoracic spinal cord transection, the mice were trained daily (10 min/d, 5 d/week) to step on a treadmill 10 min after the administration of quipazine (0.5 mg/kg), a serotonin agonist, for a period of 6 weeks. During weekly performance evaluations, the mice trained with the AAN window paradigm generally showed the highest level of recovery as measured by the number, consistency, and periodicity of steps during the testing sessions. In all three measurements there were no significant differences between the Band and the Fixed training groups. These results indicate that the window training approach, which includes loose alternating interlimb coordination, is more effective than a fixed trajectory paradigm with rigid alternating interlimb coordination or an AAN paradigm without any interlimb constraints in promoting robust postinjury stepping behavior.
On Potts Model Clustering, Kernel K-Means and Density Estimation

Many clustering methods, such as K -means, kernel K -means, and MNcut clustering, follow the same recipe: (i) choose a measure of similarity between observations; (ii) define a figure of merit assigning a large value to partitions of the data that put similar observations in the same cluster; and (iii) optimize this figure of merit over partitions. Potts model clustering represents an interesting variation on this recipe. Blatt, Wiseman, and Domany defined a new figure of merit for partitions that is formally similar to the Hamiltonian of the Potts model for ferromagnetism, extensively studied in statistical physics. For each temperature T, the Hamiltonian defines a distribution assigning a probability to each possible configuration of the physical system or, in the language of clustering, to each partition. Instead of searching for a single partition optimizing the Hamiltonian, they sampled a large number of partitions from this distribution for a range of temperatures. They proposed a heuristic for choosing an appropriate temperature and from the sample of partitions associated with this chosen temperature, they then derived what we call a consensus clustering: two observations are put in the same consensus cluster if they belong to the same cluster in the majority of the random partitions. In a sense, the consensus clustering is an “average” of plausible configurations, and we would expect it to be more stable (over different samples)than the configuration optimizing the Hamiltonian. The goal of this article is to contribute to the understanding of Potts model clustering and to propose extensions and improvements: (1) We show that the Hamiltonian used in Potts model clustering is closely related to the kernel K -means and MNCutcriteria. (2) We propose a modification of the Hamiltonian penalizing unequal clustersizes and show that it can be interpreted as a weighted version of the kernel K -meanscriterion. (3) We introduce a new version of the Wolff algorithm to simulate configurations from the distribution defined by the penalized Hamiltonian, leading to penalized Potts model clustering. (4) We note a link between kernel based clustering methods and nonparametric density estimation and exploit it to automatically determine locally adaptive kernel bandwidths. (5) We propose a new simple rule for selecting a good temperature T. As an illustration we apply Potts model clustering to gene expression data and compare our results to those obtained by model based clustering and a nonparametric dendrogram sharpening method.
Megsc1 Force Analysis Using a Tapered Ball-end Milling Tool While Machining Titanium Dynamic Response of Peizoelectro-magnetic Smart Structures Using Spectral Finite Element Method Enhancement of Neutron Scatterometer for Void Fraction Measurement in Rod-bundle Channels Determination of Flaws in Ext

Preface MEGSC1 is the first mechanical engineering graduate students conference. The objective of this conference is to provide a forum for discussion and dissemination of knowledge among graduate student in the general area of mechanical engineering. The goal here is to enable two streams of graduate students, those senior graduate students who have built their knowledge and expertise in their field of study and new graduate students, to get together and interact. The hope is that this forum will full fill this objective and help maintaining our high research ranking in the university. The proceedings of abstracts is a joint effort of 22 graduate students working in different areas of mechanical engineering. I strongly believe that the quality and diversity of these abstracts reflect the interest of our students to make it a successful event and open the door for more to come. Let us make the 22 nd of September a remarkable day in the history of mechanical engineering department for starting this successful yearly event. I would like to express my sincere thanks and gratitude to our secretaries Susan Shea and Debbie Basque for their help and effort. Special thanks go to Mr. John Bowles President of the MEGSS for his help in coordinating this event as well as sharing the cost of this event. I would like also to take the opportunity to thank all professors in the mechanical engineering department for participating in this event and encouraging their student to participate. Finally, I hope to see you all at the conference and wish you an enjoyable day.
Motion Recognition of Self & Others on Realistic 3 D Avatars

Current 3D capture and modeling technology can rapidly generate highly photo-realistic 3D avatars of human subjects. However, while the avatars look like their human counterparts, their movements often do not mimic their own due to existing challenges in accurate motion capture and re-targeting. A better understanding of factors that influence the perception of biological motion would be valuable for creating virtual avatars that capture the essence of their human subjects. To investigate these issues, we captured 22 subjects walking in an open space. We then performed a study where participants were asked to identify their own motion in varying visual representations and scenarios. Similarly, participants were asked to identify the motion of familiar individuals. Unlike prior studies that used captured footage with simple “point-light” displays, we rendered the motion on photo-realistic 3D virtual avatars of the subject. We found that self-recognition was significantly higher for virtual avatars than with point-light representations. Users were more confident of their responses when identifying their motion presented on their virtual avatar. Recognition rates varied considerably between motion types for recognition of others, but not for self-recognition. Overall, our results are consistent with previous studies that used recorded footage, and offer key insights into the perception of motion rendered on virtual avatars.
Multiple Spike Time Patterns Occur at Bifurcation Points of Membrane Potential Dynamics

The response of a neuron to repeated somatic fluctuating current injections in vitro can elicit a reliable and precisely timed sequence of action potentials. The set of responses obtained across trials can also be interpreted as the response of an ensemble of similar neurons receiving the same input, with the precise spike times representing synchronous volleys that would be effective in driving postsynaptic neurons. To study the reproducibility of the output spike times for different conditions that might occur in vivo, we somatically injected aperiodic current waveforms into cortical neurons in vitro and systematically varied the amplitude and DC offset of the fluctuations. As the amplitude of the fluctuations was increased, reliability increased and the spike times remained stable over a wide range of values. However, at specific values called bifurcation points, large shifts in the spike times were obtained in response to small changes in the stimulus, resulting in multiple spike patterns that were revealed using an unsupervised classification method. Increasing the DC offset, which mimicked an overall increase in network background activity, also revealed bifurcation points and increased the reliability. Furthermore, the spike times shifted earlier with increasing offset. Although the reliability was reduced at bifurcation points, a theoretical analysis showed that the information about the stimulus time course was increased because each of the spike time patterns contained different information about the input.
A Theory of the Budgetary Process

There are striking regularities in the budgetary process. The evidence from over half of the non-defense agencies indicates that the behavior of the budgetary process of the United States government results in aggregate decisions similar to those produced by a set of simple decision rules that are linear and temporally stable. For the agencies considered, certain equations are specified and compared with data composed of agency requests (through the Bureau of the Budget) and Congressional appropriations from 1947 through 1963. The comparison indicates that these equations summarize accurately aggregate outcomes of the budgetary process for each agency. In the first section of the paper we present an analytic summary of the federal budgetary process, and we explain why basic features of the process lead us to believe that it can be represented by simple models which are stable over periods of time, linear, and stochastic. In the second section we propose and discuss the alternative specifications for the agency-Budget Bureau and Congressional decision equations. The empirical results are presented in section three. In section four we provide evidence on deviant cases, discuss predictions, and future work to explore some of the problems indicated by this kind of analysis. An appendix contains informal definitions and a discussion of the statistical terminology used in the paper.
FUNDUS AUTOFLUORESCENCE PATTERNS IN EYES WITH PRIMARY INTRAOCULAR LYMPHOMA

Purpose: To evaluate the fundus autofluorescence (FAF) patterns in the eyes with primary intraocular lymphomas (PIOLs). Methods: A review of the medical charts of four consecutive patients (five eyes) with PIOL who had been studied by FAF. A fundus camera was used to obtain the FAF images. Optical coherence tomography was also performed. Results: The ophthalmoscopically observed brown clumps on the surface of greasy yellowish masses beneath the retinal pigmented epithelium had a bright hyperfluorescence appearance by FAF. This FAF hyperfluorescence was completely reversed to hypofluorescence in the fluorescein angiograms. The diffuse infiltration of the cells making up the PIOL above the retinal pigmented epithelium was ophthalmoscopically observed as a retinal whitening and was hypofluorescent by FAF. These areas of hypofluorescence were also reversed to areas of hyperfluorescence in the fluorescein angiogram. Fundus autofluorescence clearly delineated the retinal pigmented epithelium atrophy, which developed after the spontaneous resolution of the PIOL as a hypoautofluorescent area. Conclusion: Because FAF can reveal various findings of PIOLs, it can be used to differentiate the patients with PIOL from those with ocular inflammatory diseases. Although further studies are required to determine whether these findings are characteristic to PIOL, this noninvasive method can then lead to earlier diagnosis and treatment.
Meso-Scale Modeling of Polycrystal Deformation

ii DEDICATION. iv ACKNOWLEDGEMENTS. v VITA. vi PUBLICATIONS. vi FIELDS OF STUDY. vii TABLE OF CONTENTS.viii LIST OF TABLES. xi LIST OF FIGURES . xiii 1. INTRODUCTORY NOTE. 1 2. BACKGROUND. 3 2.1 Polycrystal Plasticity Models . 4 2.2 Theories on Evolution of Dislocation Densities in Plasticity Models . 7 2.3 HallPetch Law. 11 3. SINGLE CRYSTAL CONSTITUTIVE EQUATIONS. 22 3.1 Abstract . 22 ix 3.2 Introduction . 23 3.3 Crystal Plasticity based on Single Crystal Constitutive Equations . 29 3.3.1 Common Elements of SCCE-T and SCCE-D. 30 3.3.2 Single-Crystal Constitutive Equations developed for Texture models (SCCE-T). 31 3.3.3 Single-Crystal Constitutive Equations based on the Dislocation density model (SCCE-D) . 32 3.4 CP-FEM Implementation . 36 3.5 Prediction of Single Crystal Stress-strain Response . 37 3.6 Prediction of stress-strain response and texture evolution in polycrystals. 53 3.7 Role of qlat/qself in SCCE-T . 59 3.8 Conclusions . 60 4. TWO-SCALE MODEL. 62 4.1 Abstract . 62 4.2 Introduction . 63 4.3 Simulation Procedures. 66 4.3.1 Grain-Scale Simulation (GSS). 69 4.3.2 Meso-Scale Simulation (MSS) . 72 4.3.3 1D stressed pileup. 80
Effects of Vasopeptidase Inhibition on Renal Function and Tubuloglomerular Feedback in Spontaneously Hypertensive Rats

Vasopeptidase inhibitors are a novel class of antihypertensive agents that concomitantly inhibit angiotensin converting enzyme and neutral endopeptidase. Our purpose was to investigate the effects of omapatrilat, a vasopeptidase inhibitor, on renal function and tubuloglomerular feedback (TGF) response in anesthetized 9–10-week-old spontaneously hypertensive rats (SHR). Intravenous injection of omapatrilat at 10 μmol/kg decreased systemic blood pressure and renal vascular resistance. Renal plasma flow was unchanged, whereas glomerular filtration rate (GFR) and filtration fraction (FF) were reduced. Increased urinary sodium excretion of tubular origin was observed. These parameters remained unaltered with vehicle treatment. Micropuncture study revealed that the maximal reduction of early proximal flow rate (EPFR) induced by orthograde perfusion of Henle's loop with artificial tubular fluid (ATF) was significantly reduced by omapatrilat treatment (28.5 ±3.1% vs. 72.0±2.8% of control) and was not significantly changed in the vehicle-treated group (vehicle 70.8±1.7% vs. control 71.0 ±2.1%). EPFR at zero perfusion was comparable between omapatrilat and vehicle treatment (29.7±2.2 vs. 31.3 ±2.1 nl/min, respectively). Luminal perfusion of 10-4 mol/l 7-nitroindazole in ATF abrogated the blunting of TGF response by omapatrilat but elicited no change in the vehicle-treated group. The suppression of the TGF mechanism and the reduction in FF suggest that omapatrilat respectively dilates the afferent and efferent arterioles. Under such conditions, reduction of GFR may indicate a fall in intraglomerular pressure. The restoration of nitric oxide signaling in the juxtaglomerular apparatus of SHR seems to participate in the inhibition of TGF by omapatrilat. These findings suggest that omapatrilat may provide a novel approach to the treatment of systemic and glomerular hypertension.
Attenuation of ischemia and/or reperfusion injury during myocardial infarction using mild hypothermia in rats: An immunohistochemical study of Bcl‐2, Bax, Bak and TUNEL

The aim of the present study was to determine the beneficial effect of mild hypothermia during ischemia and/or reperfusion injury in myocardial infarction. Sprague–Dawley rats (400 ± 20 g) were subjected to 30 min occlusion of the left coronary artery followed by 24 h reperfusion. Rats were divided into normothermic (NT; 37°C) and hypothermic (HT; 34°C) groups. In the HT group hypothermia was maintained during coronary occlusion and continued for 30 min following reperfusion. Histological analysis revealed dead cardiomyocytes and polymorphonuclear neutrophil infiltration after 24 h. Myocardial infarction, measured using an image analyzer, showed that the percentage area of infarction was significantly decreased in the HT group. Immunohistochemical analysis was carried out using antibodies against Bcl‐2, Bax and Bak. DNA fragments were labeled in situ using the 3′‐OH end‐labeling method (TUNEL). In the HT group Bcl‐2 was induced in many myocytes, whereas Bax and Bak were induced in only a few myocytes. A higher number of TUNEL‐positive cells were recorded in the NT group than in the HT group, but these were more thinly scattered in the HT group. The expression pattern revealed that many myocytes could survive at the border zone in the HT group; in contrast, few myocytes in the NT group were able to survive. Our results suggest that mild hypothermia selectively interferes with, and mitigates, reperfusion injury.
The Relative Odds of Progressing by Structural and Functional Tests in Glaucoma

Purpose The purpose of this study was to evaluate the effect of disease severity and number of tests acquired during follow-up on the relative odds of identifying progression by structural or functional tests in glaucoma. Methods This was an observational cohort study involving 462 eyes of 305 patients with glaucoma and 62 eyes of 49 healthy subjects. Glaucoma patients and healthy subjects were followed for an average of 3.6 ± 0.9 and 3.8 ± 0.9 years, with a median (interquantile range) of 8 (6–9) and 7 (6–8) visits, respectively. At each visit, subjects underwent visual field assessment with standard automated perimetry (SAP) and retinal nerve fiber layer (RNFL) evaluation by spectral-domain optical coherence tomography (SD-OCT). Slopes of change in SAP mean sensitivity and OCT RNFL thickness over time were estimated by linear regression using progressively cumulative visits over time. Cutoff values for age-related expected rates of change for each test were obtained from the healthy group. Progression by SD-OCT and/or SAP was determined if the slope of change was statistically significant and also lower (faster) than the fifth percentile cutoff calculated from the healthy group. A generalized estimating equation logistic regression model was used to evaluate the relative odds of progressing by OCT versus SAP in glaucoma eyes. Results Eyes with less severe disease at baseline had a higher chance of being detected as progressing by SD-OCT but not by SAP, whereas an increase in disease severity at baseline increased the chance that the eye would be detected as progressing by SAP but not SD-OCT. Each 1 dB higher MD was associated with a 5% increase in the odds of detecting progression by SD-OCT versus SAP (odds ratio = 1.05 per 1 dB; 95% confidence interval: 1.01–1.09; P = 0.005). Conclusions The ability to detect glaucoma progression by SAP versus SD-OCT is significantly influenced by the stage of disease. Our results may provide useful information for guiding clinicians on the relative utility of these tests for detecting change throughout the disease continuum.
Antibacterial Action of Jineol Isolated from Scolopendra subspinipes mutilans against Selected Foodborne Pathogens

This study was undertaken to assess the antibacterial potential of 3,8-dihydroxyquinoline (jineol) isolated from Scolopendra subspinipes mutilans against selected foodborne pathogens Escherichia coli O157:H7 and Staphylococcus aureus KCTC-1621. Jineol at the tested concentration (50 μL; corresponding to 250 μg/disk) exhibited significant antibacterial effects as a diameter of inhibition zones (11.6–13.6 mm), along with minimum inhibitory concentration (MIC) and minimum bactericidal concentration values found in the range of (62.5–125 μg/mL) and (125–250 μg/mL), respectively. Jineol also exhibited significant antibacterial effects as confirmed by the reduction in bacterial cell viabilities, increasing release of potassium (K+) ions (650 and 700 mmole/L) and 260 nm materials (optical density: 2.98–3.12) against both the tested pathogens, E. coli O157:H7 and S. aureus KCTC-1621, respectively. Moreover, changes in the cell wall morphology of E. coli O157:H7 and S. aureus KCTC-1621 cells treated with jineol at MIC further confirmed its inhibitory potential against the tested pathogens, suggesting its role as an effective antimicrobial to control foodborne pathogens.