Miracle-dz/UniFAR-FTUs huggingface dataset:
Norges Teknisk-naturvitenskapelige Universitet Neural Learning by Geometric Integration of Reduced 'rigid-body' Equations Neural Learning by Geometric Integration of Reduced 'rigid-body' Equations

In previous contributions we presented a new class of algorithms for or-thonormal learning of linear neural networks with p inputs and m outputs, based on the equations describing the dynamics of a massive rigid frame in a submanifold of IR p. While exhibiting interesting features, such as good numerical stability, strongly binding to the orthonormal manifolds, and good controllability of the learning dynamics, the proposed algorithms were not completely satisfactory from a computational-complexity point of view. The main drawbacks were the non-efficient representation of the learning matrix-quantities and the non-efficient integration of the resulting learning differential equations. In this Technical Report a new and efficient representation of the learning equations is proposed, and a possible way to integrate them is suggested. Numerical experiments concerning Principal Subspace Analysis and Independent Component Analysis were carried out with both synthetic and real-world data in order to confirm the effectiveness of the proposed theory.
A dichotomy for sampling barrier-crossing events of random walks with regularly varying tails

We study how to sample paths of a random walk up to the first time it crosses a fixed barrier, in the setting where the step sizes are iid with negative mean and have a regularly varying right tail. We introduce a desirable property for a change of measure to be suitable for exact simulation. We study whether the change of measure of Blanchet and Glynn (2008) satisfies this property and show that it does so if and only if the tail index $\alpha$ of the right tail lies in the interval $(1, \, 3/2)$.
Inhibition as an adaptive mechanism in memory-based choices

Abstract This study examines the role of inhibitory processes in memory-based choices. In two experiments, the effects of the competitive nature of memory retrieval as well as the valence of the to-be-retrieved items on a recall and a choice task are examined by using the retrieval practice paradigm. The results show a parallel pattern for both tasks. Specifically, neither forgetting nor choice bias were found in the non-competitive retrieval condition, for both positive and negative information. Nevertheless, a retrieval-induced forgetting and a choice bias effect were found in the competitive retrieval condition, although only for positive information. Interestingly, this negativity effect disappeared when positive information was excluded from to-be-learned material. These findings suggest the way in which the lasting consequences of inhibition affect choice processes.
Detection of retinal changes in Parkinson’s disease with spectral-domain optical coherence tomography

Purpose This pilot study investigated whether high-resolution spectral-domain optical coherence tomography (SD-OCT) could detect differences in inner retinal layer (IRL), peripapillary retinal nerve fiber layer (RNFL), and macular thickness between patients with Parkinson’s disease (PD) and controls. Methods Both eyes of patients with PD and age-matched controls were imaged with the Heidelberg Spectralis® HRA + OCT. RNFL, IRL, and macular thickness were measured for each eye using Heidelberg software. These measurements were compared with validated, published normal values for macular and RNFL thickness, and compared with matched controls for IRL thickness. Results Eighteen eyes from nine subjects with PD and 19 eyes of 16 control subjects were evaluated using SD-OCT. The average age of PD patients was 64 years with a range of 52–75 years. The average age of controls was 67 years with a range of 50–81 years. No significant reduction in IRL thickness was detected between PD patients and age-matched controls at 13 points along a 6 mm horizontal section through the fovea. No significant difference in RNFL thickness was detected between PD patients and published normal values. Overall average RNFL thickness was 97 μm for PD patients, which exactly matched the normative database value. However, significant differences in macular thickness were detected in three of nine subfields between PD subjects and published normal values. In PD subjects, the outer superior subfield was 2.8% thinner (P = 0.026), while the outer nasal and inner inferior subfields were 2.8% (P = 0.016) and 2.7% (P = 0.001) thicker compared to published normal values. Conclusion In this pilot study, significant differences in macular thickness were detected in three of nine subfields by SD-OCT. However, SD-OCT did not detect significant reductions in peripapillary RNFL and IRL thickness between PD patients and controls. This suggests that macular thickness measurements by SD-OCT may potentially be used as an objective, noninvasive, and easily quantifiable in vivo biomarker in PD. Larger, longitudinal studies are needed to explore these relationships further.
Sodium channel β2 subunit promotes filopodia-like processes and expansion of the dendritic tree in developing rat hippocampal neurons

The β2 auxiliary subunit of voltage-gated sodium channels (VGSCs) appears at early stages of brain development. It is abundantly expressed in the mammalian central nervous system where it forms complexes with different channel isoforms, including Nav1.2. From the structural point of view, β2 is a transmembrane protein: at its extracellular N-terminus an Ig-like type C2 domain mediates the binding to the pore-forming alpha subunit with disulfide bonds and the interactions with the extracellular matrix. Given this structural versatility, β2 has been suggested to play multiple functions ranging from channel targeting to the plasma membrane and gating modulation to control of cell adhesion. We report that, when expressed in Chinese Hamster Ovary cells CHO-K1, the subunit accumulates at the perimetral region of adhesion and particularly in large lamellipodia-like membrane processes where it induces formation of filopodia-like structures. When overexpressed in developing embryonic rat hippocampal neurons in vitro, β2 specifically promotes formation of filopodia-like processes in dendrites leading to expansion of the arborization tree, while axonal branching remains unaltered. In contrast to this striking and highly specific effect on dendritic morphology, the targeting of functional sodium channels to the plasma membrane, including the preferential localization of Nav1.2 at the axon, and their gating properties are only minimally affected. From these and previously reported observations it is suggested that β2, among its multiple functions, may contribute to promote dendritic outgrowth and to regulate neuronal wiring at specific stages of neuronal development.
Can carotenoids mediate the potentially harmful effects of ultraviolet light in Silurana (Xenopus) tropicalis larvae?

Amphibians have recently experienced unprecedented declines in the wild, the causes of which are often difficult to mitigate. This has increased the importance of ex situ conservation; however, long-term maintenance and breeding of amphibians in captivity often has limited success. In vertebrates, vitamin D is required for calcium homeostasis and is produced endogenously in skin exposed to ultraviolet (UV) light; however, UV light can be harmful to amphibians in some instances. Carotenoids are dietary pigments that may provide protection from UV light. The aim of this study was to assess the protective capability of carotenoids against the potentially harmful effects of UV light in Silurana (=Xenopus) tropicalis larvae raised in an enhanced or limited UV environment. Tadpole survival and the size and developmental stage reached by the end of the study period were measured. Carotenoids had a significantly positive effect on developmental rate in both UV-limited and UV-enhanced environments. Larvae in an enhanced UV environment were significantly larger than those raised under a limited UV environment, irrespective of diet. Carotenoid-fed larvae tended to have increased survival in relation to those raised without carotenoids, but only in a limited UV environment. Carotenoids appear to provide little protection against UV light in this case. The role of carotenoids in amphibian health has not previously been studied. We show that carotenoid availability significantly influences development and may increase survival in S. (X.) tropicalis larvae. This finding may have important implications for recommendations made on the nutrition of amphibians in captivity.
Mixture Distributions for Modeling Lead Time Demand in Coordinated Supply Chains

Abstract : This paper introduces a mixture distribution approach to modeling the probability density function for lead time demand (LTD) in problems where a continuous review inventory system is implemented. The method differs from the typical moment-matching approach by focusing on building up an accurate, closed-form approximation to the LTD distribution from its components by using mixtures of polynomial functions. First, construction of the lead time distribution is illustrated and the approach is compared to two other possible lead time distributions. This distribution is then utilized to determine optimal order policies in a situation where members of a two-level supply chain coordinate their actions.
Fault detection and isolation for PEMFC systems under closed-loop control

In this work, a model-based fault detection and isolation (FDI) is developed for proton exchange membrane (PEM) fuel cell (FC) stack that is under feed-forward plus feedback control. The fault detection is achieved using an independent radial basis function (RBF) network model, whilst the fault isolation is based on the RBF classification. The novelty is that the RBF model of independent mode is used to predict the future outputs of the FC stack and a RBF classifier is used to classify five types of fault introduced to the PEMFC systems. To validate the method, a benchmark model developed by Michigan University is used in the simulation to analyze the effectiveness of the method for actuator, component and three sensor faults. The FDI results corresponding to those scenarios show that the simulated different types of fault are successfully detected and isolated.
Wireless amplified nuclear MR detector (WAND) for high-spatial-resolution MR imaging of internal organs: preclinical demonstration in a rodent model.

PURPOSE To assess the feasibility of imaging deep-lying internal organs at high spatial resolution by imaging kidney glomeruli in a rodent model with use of a newly developed, wireless amplified nuclear magnetic resonance (MR) detector. MATERIALS AND METHODS This study was approved by the Animal Care and Use Committee at the National Institutes of Health/National Institute of Neurologic Disorder and Stroke. As a preclinical demonstration of this new detection technology, five different millimeter-scale wireless amplified nuclear MR detectors configured as double frequency resonators were chronically implanted on the medial surface of the kidney in five Sprague-Dawley rats for MR imaging at 11.7 T. Among these rats, two were administered gadopentetate dimeglumine to visualize renal tubules on T1-weighted gradient-refocused echo (GRE) images, two were administered cationized ferritin to visualize glomeruli on T2*-weighted GRE images, and the remaining rat was administered both gadopentetate dimeglumine and cationized ferritin to visualize the interleaved pattern of renal tubules and glomeruli. The image intensity in each pixel was compared with the local tissue signal intensity average to identify regions of hyper- or hypointensity. RESULTS T1-weighted images with 70-μm in-plane resolution and 200-μm section thickness were obtained within 3.2 minutes to image renal tubules, and T2*-weighted images of the same resolution were obtained within 5.8 minutes to image the glomeruli. Hyperintensity from gadopentetate dimeglumine enabled visualization of renal tubules, and hypointensity from cationic ferritin enabled visualization of the glomeruli. CONCLUSION High-spatial-resolution images have been obtained to observe kidney microstructures in vivo with a wireless amplified nuclear MR detector.
The radiation dose in interventional radiology study: knowledge brings responsibility.

Abbreviations: CD cumulative dose, FDA Food and Drug Administration, HOCM high osmolar contrast material, ICRP International Commission on Radiological Protection, IVC inferior vena cava, LOCM low osmolar contrast material, NCRP National Council of Radiation Protection and Measurements, PSD peak skin dose, RAD-IR Radiation Dose in Interventional Radiology (study), TIPS transjugular intrahepatic portosystemic shunt
Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity

Historically, influenza pandemics have been triggered when an avian influenza virus or a human/avian reassorted virus acquires the ability to replicate efficiently and become transmissible in the human population. Most critically, the major surface glycoprotein hemagglutinin (HA) must adapt to the usage of human‐like (α‐2,6‐linked) sialylated glycan receptors. Therefore, identification of mutations that can switch the currently circulating H5N1 HA receptor binding specificity from avian to human might provide leads to the emergence of pandemic H5N1 viruses. To define such mutations in the H5 subtype, here we provide a computational framework that combines molecular modeling with extensive free energy simulations. Our results show that the simulated binding affinities are in good agreement with currently available experimental data. Moreover, we predict that one double mutation (V135S and A138S) in HA significantly enhances α‐2,6‐linked receptor recognition by the H5 subtype. Our simulations indicate that this double mutation in H5N1 HA increases the binding affinity to α‐2,6‐linked sialic acid receptors by 2.6 ± 0.7 kcal/mol per HA monomer that primarily arises from the electrostatic interactions. Further analyses reveal that introduction of this double mutation results in a conformational change in the receptor binding pocket of H5N1 HA. As a result, a major rearrangement occurs in the hydrogen‐bonding network of HA with the human receptor, making the human receptor binding pattern of double mutant H5N1 HA surprisingly similar to that observed in human H1N1 HA. These large scale molecular simulations on single and double mutants thus provide new insights into our understanding toward human adaptation of the avian H5N1 virus. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
Combining Qualitative Coding and Sentiment Analysis: Deconstructing Perceptions of Usable Security in Organisations

Background: A person’s security behavior is driven by underlying mental constructs, perceptions and beliefs. Examination of security behavior is often based on dialogue with users of security, which is analysed in textual form by qualitative research methods such as Qualitative Coding (QC). Yet QC has drawbacks: security issues are often time-sensitive but QC is extremely timeconsuming. QC is often carried out by a single researcher raising questions about the validity and repeatability of the results. Previous research has identified frequent tensions between security and other tasks, which can evoke emotional responses. Sentiment Analysis (SA) is simpler to execute and has been shown to deliver accurate and repeatable results. / Aim: By combining QC with SA we aim to focus the analysis to areas of strongly represented sentiment. Additionally we can analyse the variations in sentiment across populations for each of the QC codes, allowing us to identify beneficial and harmful security practises. Method: We code QC-annotated transcripts independently for sentiment. The distribution of sentiment for each QC code is statistically tested against the distribution of sentiment of all other QC codes. Similarly we also test the sentiment of each QC code across population subsets. We compare our findings with the results from the original QC analysis. Here we analyse 21 QCtreated interviews with 9 security specialists, 9 developers and 3 usability experts, at 3 large organisations claiming to develop ‘usable security products’. This combines 4983 manually annotated instances of sentiment with 3737 quotations over 76 QC codes. / Results: The methodology identified 83 statistically significant variations (with p < 0.05). The original qualitative analysis implied that organisations considered usability only when not doing so impacted revenue; our approach finds that developers appreciate usability tools to aid the development process, but that conflicts arise due to the disconnect of customers and developers. We find organisational cultures which put security first, creating an artificial trade-off for developers between security and usability. / Conclusions: Our methodology confirmed many of the QC findings, but gave more nuanced insights. The analysis across different organisations and employees con- firmed the repeatability of our approach, and provided evidence of variations that were lost in the QC findings alone. The methodology adds objectivity to QC in the form of reliable SA, but does not remove the need for interpretation. Instead it shifts it from large QC data to condensed statistical tables which make it more accessible to a wider audience not necessarily versed in QC and SA.
The Relationship between Professional Identity and Collective Self- esteem in School Counselors

This Dissertation is protected by copyright and/or related rights. It has been brought to you by ScholarWorks@UNO with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself.
Rfam: annotating non-coding RNAs in complete genomes

Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 complete genome sequences. The data provide the first glimpses of conservation of multiple ncRNA families across a wide taxonomic range. A small number of large families are essential in all three kingdoms of life, with large numbers of smaller families specific to certain taxa. Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger. ac.uk/Software/Rfam/ and http://rfam.wustl. edu/.
Recognizing Underlying Sparsity in Optimization B-428 Recognizing Underlying Sparsity in Optimization

Exploiting sparsity is essential to improve the efficiency of solving large optimization problems. We present a method for recognizing the underlying sparsity structure of a nonlinear partially separable problem, and show how the sparsity of the Hessian matrices of the problem’s functions can be improved by performing a nonsingular linear transformation in the space corresponding to the vector of variables. A combinatorial optimization problem is then formulated to increase the number of zeros of the Hessian matrices in the resulting transformed space, and a heuristic greedy algorithm is applied to this formulation. The resulting method can thus be viewed as a preprocessor for converting a problem with hidden sparsity into one in which sparsity is explicit. When it is combined with the sparse semidefinite programming (SDP) relaxation by Waki et al. for polynomial optimization problems (POPs), the proposed method is shown to extend the performance and applicability of this relaxation technique. Preliminary numerical results are presented to illustrate this claim. ] This manuscript was also issued as Report 06/02, Department of Mathematics, University of Namur, 61, rue de Bruxelles, B-5000 Namur, Belgium, EU. Department of Mathematics, Ewha Women’s University, 11-1 Dahyun-dong, Sudaemoon-gu, Seoul 120-750 Korea. The research was supported by Kosef R012005-000-10271-0. skim@ewha.ac. kr † Department of Mathematical and Computing Sciences, Tokyo Institute of Technology, 2-12-1 Oh-Okayama, Meguro-ku, Tokyo 152-8552 Japan. This research was supported by Grant-in-Aid for Scientific Research on Priority Areas 16016234. kojima@is.titech. ac.jp ‡ Department of Mathematics, The University of Namur, 61, rue de Bruxelles, B5000 Namur, Belgium, EU. philippe.toint@fundp.ac. be
Neurobehavioral testing in subarachnoid hemorrhage: A review of methods and current findings in rodents

The most important aspect of a preclinical study seeking to develop a novel therapy for neurological diseases is whether the therapy produces any clinically relevant functional recovery. For this purpose, neurobehavioral tests are commonly used to evaluate the neuroprotective efficacy of treatments in a wide array of cerebrovascular diseases and neurotrauma. Their use, however, has been limited in experimental subarachnoid hemorrhage studies. After several randomized, double-blinded, controlled clinical trials repeatedly failed to produce a benefit in functional outcome despite some improvement in angiographic vasospasm, more rigorous methods of neurobehavioral testing became critical to provide a more comprehensive evaluation of the functional efficacy of proposed treatments. While several subarachnoid hemorrhage studies have incorporated an array of neurobehavioral assays, a standardized methodology has not been agreed upon. Here, we review neurobehavioral tests for rodents and their potential application to subarachnoid hemorrhage studies. Developing a standardized neurobehavioral testing regimen in rodent studies of subarachnoid hemorrhage would allow for better comparison of results between laboratories and a better prediction of what interventions would produce functional benefits in humans.
Assessment the Effect of Pomegranate Molasses against Diazinon Toxicity in Male Rats

Diazinon (DZN) is one of the organophosphorus (OP) insecticides, can affect both animals and man even after exposure to a single dose. Pomegranate molasses (PM), a concentrated pomegranate juice, may be rich in more efficient antioxidants than that found in the juice, but no research has been done on this product. Therefore, the aim of this study was to evaluate the possible protective effect of PM against single half lethal dose of DZN (300mg/Kg b wt) induced adverse effects on contents of Malondialdehyde (MAD) and reduced glutathione (GSH) in rat liver and brain tissues, haematological and some biochemical parameters. Thirty six male albino rats were divided into four groups for ten days as follows: Group1, rats from that group were fed orally with 0.5ml from a corn oil (6 rats). Group (2) rats were injected orally with a single dose of LD50 of DZN (300mg/kg) (12 rats), group (3) rats were given 0.5ml PM plus 0.5ml distilled water / day for 10 days (6 rats), Group (4) animals were given the same single dose of DZN as group plus PM / day for 10 days (12 rats). The results demonstrated that treatment with DZN induced significant increase in MDA and significant decrease in GSH levels in liver and brain tissues. These changes were almost returned to normalcy in rats supplemented with PM +DZN except brain MAD still higher than control group. Red blood corpuscles (RBC) count, hemoglobin (Hb) concentrations and hematocrit (Hct) showed significant reduction, while the value of white blood corpuscles (WBC) count was statistically increased in rats exposed to DZN. Significant increases in the values of serum total protein (TP), globulin (Glob), total cholesterol (TC), triglyceride (TG), urea, uric acid and calcium (Ca) were observed in DZN administrated rats compared to control group. However, PM supplementation together with DZN improved all these alterations except albumin (Alb) and TG significant increased than control group.