Miracle-dz/UniFAR-FTUs huggingface dataset:
Odor identification as a biomarker of preclinical AD in older adults at risk

Objective: To assess odor identification (OI) as an indicator of presymptomatic Alzheimer disease (AD) pathogenesis in cognitively normal aging individuals at increased risk of AD dementia. Methods: In 274 members of the PREVENT-AD cohort of healthy aging persons with a parental or multiple-sibling history of AD dementia, we assessed the cross-sectional association of OI with potential indicators of presymptomatic AD. Some 101 participants donated CSF, thus enabling assessment of AD pathology with the biomarkers total tau (t-tau), phospho-tau (P181-tau), and their ratios with β-amyloid (Aβ1-42). Adjusted analyses considered age, cognition, APOE ε4 status, education, and sex as covariates. We measured OI using the University of Pennsylvania Smell Identification Test and cognitive performance using the Repeatable Battery for Assessment of Neuropsychological Status. Standard kits provided assays of the AD biomarkers. Analyses used robust-fit linear regression models. Results: Reduced OI was associated with lower cognitive score and older age, as well as increased ratios of CSF t-tau and P181-tau to Aβ1-42 (all p < 0.02). However, the observed associations of OI with age and cognition were unapparent in adjusted models that restricted observations to CSF donors and included AD biomarkers. OI showed little association with CSF Aβ1-42 alone except in APOE ε4 carriers having lowest-quartile Aβ1-42 levels. Conclusions: These findings from healthy high-risk older individuals suggest that OI reflects degree of preclinical AD pathology, while its relationships with age and cognition result from the association of these latter variables with such pathology. Diminished OI may be a practical and affordable biomarker of AD pathology.
Impact of infection rate on scaling law of epidemic routing

Performance modeling of epidemic routing is challenging because of the unguaranteed end-to-end connectivity and lack of global information in delay-tolerant scenarios. Existing works analyze the scaling law of epidemic protocol based on the assumption that each node has the same infectivity. Whereas, the most recent work indicates that the distribution of infected nodes has spatial-temporal correlation rather than homogeneity, i.e., nodes in different locations have different infectivities, which leads to defectiveness of the existing solutions. In this paper, by exploring the reason behind this difference, we try to relax the assumption and rebuild the model for epidemic routing. We first introduce the concept of infection rate to reflect the infectivity of infected nodes. Second, we propose an effective method to compute the average infection rate and use it to derive a generic scaling law. Third, we give an explicit expression for the generic scaling law, which provides us with upper bound. We finally compare our model with the existing works through theoretical analysis and simulations. The results show that our model has a closer match than those of the existing works and gets some insights into the spatial distribution of infection process.
A Single-Channel EOG-Based Speller

Electrooculography (EOG) signals, which can be used to infer the intentions of a user based on eye movements, are widely used in human–computer interface (HCI) systems. Most existing EOG-based HCI systems incorporate a limited number of commands because they generally associate different commands with a few different types of eye movements, such as looking up, down, left, or right. This paper presents a novel single-channel EOG-based HCI that allows users to spell asynchronously by only blinking. Forty buttons corresponding to 40 characters displayed to the user via a graphical user interface are intensified in a random order. To select a button, the user must blink his/her eyes in synchrony as the target button is flashed. Two data processing procedures, specifically support vector machine (SVM) classification and waveform detection, are combined to detect eye blinks. During detection, we simultaneously feed the feature vectors extracted from the ongoing EOG signal into the SVM classification and waveform detection modules. Decisions are made based on the results of the SVM classification and waveform detection. Three online experiments were conducted with eight healthy subjects. We achieved an average accuracy of 94.4% and a response time of 4.14 s for selecting a character in synchronous mode, as well as an average accuracy of 93.43% and a false positive rate of 0.03/min in the idle state in asynchronous mode. The experimental results, therefore, demonstrated the effectiveness of this single-channel EOG-based speller.
Cutaneous Lymphangioma circumscriptum - dermoscopic features**

Lymphangiomas are congenital lymphatic malformations and cutaneous lymphangioma circumscriptum is the most common type. It is clinically characterized by clusters of translucent vesicles and the presence of dermoscopically yellow lacunae surrounded by pale septa, as well as reddish to bluish lacunae. In our case, the recently described hypopyon-like feature manifested, aiding in the sometimes difficult differential diagnosis of cutaneous lymphangioma circumscriptum with vascular lesions, further highlighting the importance of dermoscopy in what can be a diagnostic challenge.
Centroid estimation in discrete high-dimensional spaces with applications in biology

Maximum likelihood estimators and other direct optimization-based estimators dominated statistical estimation and prediction for decades. Yet, the principled foundations supporting their dominance do not apply to the discrete high-dimensional inference problems of the 21st century. As it is well known, statistical decision theory shows that maximum likelihood and related estimators use data only to identify the single most probable solution. Accordingly, unless this one solution so dominates the immense ensemble of all solutions that its probability is near one, there is no principled reason to expect such an estimator to be representative of the posterior-weighted ensemble of solutions, and thus represent inferences drawn from the data. We employ statistical decision theory to find more representative estimators, centroid estimators, in a general high-dimensional discrete setting by using a family of loss functions with penalties that increase with the number of differences in components. We show that centroid estimates are obtained by maximizing the marginal probabilities of the solution components for unconstrained ensembles and for an important class of problems, including sequence alignment and the prediction of RNA secondary structure, whose ensembles contain exclusivity constraints. Three genomics examples are described that show that these estimators substantially improve predictions of ground-truth reference sets.
Characterization of inhibition of the spinal nociceptive tail-flick reflex in the rat from the medullary lateral reticular nucleus

Inhibition of the spinal nociceptive tail-flick (TF) reflex by focal electrical stimulation in the caudal medulla was examined and characterized in lightly pentobarbital-anesthetized rats. Systematic mapping studies revealed that inhibition of the TF reflex was produced at low intensities of stimulation (12.5–25 microA) only from the lateral reticular nucleus (LRN). Areas dorsal and medial to the LRN required higher intensities of stimulation to produce descending inhibition of the TF reflex, likely reflecting spread of current to the LRN at these higher intensities of stimulation (50–100 microA). At threshold inhibitory intensities of stimulation in the LRN, changes in blood pressure were not produced. Strength-duration characterization of stimulation and the microinjection of glutamate into the LRN at the same site where focal electrical stimulation was effective suggest that the descending inhibition produced arises from activation of cell bodies in the LRN. The intrathecal administration of a variety of pharmacological antagonists revealed the descending inhibition produced by stimulation in the LRN to be mediated at least in part by spinal alpha 2-adrenoceptors. These findings, together with previous observations, suggest a role for the LRN in the centrifugal modulation of spinal nociceptive transmission.
Highly Luminescent MgZnO/ZnO Multiple Quantum Wells for Photonics Devices

Multiple quantum wells (MQWs) have enabled a myriad of technological applications; however, their optical emission is currently severely constrained by the presence of undesirable defects, which limit their performance in advanced photonic devices. Here, we present a new route to achieve highly luminescent oxide-based MQWs by rapid remote plasma annealing (RRPA) in hydrogen. We demonstrate that the optical emission from the MgZnO/ZnO MQWs can be enhanced substantially by this plasma method, with its emission intensity increased by more than 10 times after being treated for 40 s. Concurrently, the emissions associated with both basal stacking faults and point defects are completely quenched. Based on temperature- and excitation-density-dependent luminescence results, the enhancement of the MQW emission is attributed to the passivation of competitive recombination channels. Additionally, the exciton–optical phonon coupling strength, deduced from the temperature-dependent MQW spectral line width, shows clear.
SW and HW co-design of Connect6 accelerator with scalable streaming cores

This paper presents software and hardware co-design of an FPGA-based Connect6 solver with scalable streaming cores. The solver searches a game tree by using the miniMax algorithm with alpha-beta pruning. Since evaluation of board situations is the most time-consuming part, we adopted an approach to accelerate it with dedicated hardware while other parts are executed by software. We design a custom accelerator composed of multiple streaming-cores, each of which independently evaluates possible connectabilities with six stones. We use the ALTERA's SOPC (system on programmable chip) development tool to implement the system, which contains an NIOS II processor and the custom accelerator. The implemented system operates at 100 MHz on ALTERA Cyclone IV EP4CE115 FPGA of DE2–115 board. We could implement up to 32 streaming-cores on the FPGA. In a preliminary experiment where only a single core is used to search a game tree with a depth of 1, the FPGA-based solver wins against the given software opponent at a rate of 100 % with 33.2 stones on average.
Clonal Diversity and Turnover of Streptococcus mitis bv. 1 on Shedding and Nonshedding Oral Surfaces of Human Infants during the First Year of Life

ABSTRACT Streptococcus mitis bv. 1 is a pioneer colonizer of the human oral cavity. Studies of its population dynamics within parents and their infants and within neonates have shown extensive diversity within and between subjects. We examined the genetic diversity and clonal turnover of S. mitis bv. 1 isolated from the cheeks, tongue, and primary incisors of four infants from birth to 1 year of age. In addition, we compared the clonotypes of S. mitis bv. 1 isolated from their mothers' saliva collected in parallel to determine whether the mother was the origin of the clones colonizing her infant. Of 859 isolates obtained from the infants, 568 were unique clones. Each of the surfaces examined, whether shedding or nonshedding, displayed the same degree of diversity. Among the four infants it was rare to detect the same clone colonizing more than one surface at a given visit. There was little evidence for persistence of clones, but when clones were isolated on multiple visits they were not always found on the same surface. A similar degree of clonal diversity of S. mitis bv. 1 was observed in the mothers' saliva as in their infants' mouths. Clones common to both infant and mothers' saliva were found infrequently suggesting that this is not the origin of the infants' clones. It is unclear whether mucosal immunity exerts the environmental pressure driving the genetic diversity and clonal turnover of S. mitis bv. 1, which may be mechanisms employed by this bacterium to evade immune elimination.
Military Technology and the Duration of Civil Conflict

Why do some civil conflicts end quickly, while others last for years? This paper argues that an incumbent government’s military forces play a crucial role in conflict duration. Specifically, “combined arms” militaries – which bring to bear a mixture of mechanized infantry, armor, and aircraft – make short conflicts more likely. The use of mechanized ground forces in combination with airpower increases the likelihood of decisive engagements early in a conflict, helping to mitigate information asymmetries that can drive violence. By contrast, less-mechanized forces have greater difficulty bringing the fight to the enemy. Combined-arms militaries therefore tend to bring conflicts to more rapid conclusions. However, like maneuver warfare in conventional interstate conflict, these outcomes are not always favorable for the incumbent governments. To test this argument, we employ new, detailed data on military mechanization and airpower from civil conflicts between 1967 and 2003. The results indicate that national militaries with high combined arms capabilities are associated with significantly shorter conflicts. Perhaps surprisingly, this relationship remains robust even when the analysis is limited to insurgencies. For helpful comments on previous drafts, we thank Nikolaos Biziouras, Alexander Downes, Scott Gartner, Benjamin Graham, Mark Paradis, Brian Rathbun, and Brian Urlacher. Thanks to Callum Ingram and Abigail Post for expert research assistance.
Note onset detection in musical signals via neural–network–based multi–ODF fusion

Abstract The problem of note onset detection in musical signals is considered. The proposed solution is based on known approaches in which an onset detection function is defined on the basis of spectral characteristics of audio data. In our approach, several onset detection functions are used simultaneously to form an input vector for a multi-layer non-linear perceptron, which learns to detect onsets in the training data. This is in contrast to standard methods based on thresholding the onset detection functions with a moving average or a moving median. Our approach is also different from most of the current machine-learning-based solutions in that we explicitly use the onset detection functions as an intermediate representation, which may therefore be easily replaced with a different one, e.g., to match the characteristics of a particular audio data source. The results obtained for a database containing annotated onsets for 17 different instruments and ensembles are compared with state-of-the-art solutions.
Loading-related Regulation of Transcription Factor EGR2/Krox-20 in Bone Cells Is ERK1/2 Protein-mediated and Prostaglandin, Wnt Signaling Pathway-, and Insulin-like Growth Factor-I Axis-dependent*

Of the 1,328 genes revealed by microarray to be differentially regulated by disuse, or at 8 h following a single short period of osteogenic loading of the mouse tibia, analysis by predicting associated transcription factors from annotated affinities revealed the transcription factor EGR2/Krox-20 as being more closely associated with more pathways and functions than any other. Real time quantitative PCR confirmed up-regulation of Egr2 mRNA expression by loading of the tibia in vivo. In vitro studies where strain was applied to primary cultures of mouse tibia-derived osteoblastic cells and the osteoblast UMR106 cell line also showed up-regulation of Egr2 mRNA expression. In UMR106 cells, inhibition of β1/β3 integrin function had no effect on strain-related Egr2 expression, but it was inhibited by a COX2-selective antagonist and imitated by exogenous prostaglandin E2 (PGE2). This response to PGE2 was mediated chiefly through the EP1 receptor and involved stimulation of PKC and attenuation by cAMP/PKA. Neither activators nor inhibitors of nitric oxide, estrogen signaling, or LiCl had any effect on Egr2 mRNA expression, but it was increased by both insulin-like growth factor-1 and high, but not low, dose parathyroid hormone and exogenous Wnt-3a. The increases by strain, PGE2, Wnt-3a, and phorbol 12-myristate 13-acetate were attenuated by inhibition of MEK-1. EGR2 appears to be involved in many of the signaling pathways that constitute early responses of bone cells to strain. These pathways all have multiple functions. Converting their strain-related responses into coherent “instructions” for adaptive (re)modeling is likely to depend upon their contextual activation, suppression, and interaction probably on more than one occasion.
Expression of the bacteriophage T4 denV structural gene in Escherichia coli

The expression of the T4 denV gene, which previously had been cloned in plasmid constructs downstream of the bacteriophage lambda hybrid promoter-operator oLpR, was analyzed under a variety of growth parameters. Expression of the denV gene product, endonuclease V, was confirmed in DNA repair-deficient Escherichia coli (uvrA recA) by Western blot analyses and by enhancements of resistance to UV irradiation.
Arabidopsis Histone Deacetylase HDA6 Is Required for Maintenance of Transcriptional Gene Silencing and Determines Nuclear Organization of rDNA Repeats

Histone acetylation and deacetylation are connected with transcriptional activation and silencing in many eukaryotic organisms. Gene families for enzymes that accomplish these modifications show a surprising multiplicity in sequence and expression levels, suggesting a high specificity for different targets. We show that mutations in Arabidopsis (Arabidopsis thaliana) HDA6, a putative class I histone deacetylase gene, result in loss of transcriptional silencing from several repetitive transgenic and endogenous templates. Surprisingly, total levels of histone H4 acetylation are only slightly affected, whereas significant hyperacetylation is restricted to the nucleolus organizer regions that contain the rDNA repeats. This switch coincides with an increase of histone 3 methylation at Lys residue 4, a modified DNA methylation pattern, and a concomitant decondensation of the chromatin. These results indicate that HDA6 might play a role in regulating activity of rRNA genes, and this control might be functionally linked to silencing of other repetitive templates and to its previously assigned role in RNA-directed DNA methylation.
At-speed self-testing of high-performance pipe-lined processing architectures

We propose a new methodology for Built-In Self-Test (BIST) where contrary to the traditional scan-path based logic BIST, the proposed solution for test generation does not need any additional hardware, and will not have any impact on the working performance of the system. A class of digital systems organized as pipe-lined signal processing architectures is targeted. The data used for processing in the system are used as test pattern sources. Testing at normal working conditions, and with typically processed data, allows exercise the system on-line and at-speed, facilitating the detection of dynamic faults like delays and cross-talks to achieve high test quality. The proposed new self-test method is free from the negative aspect of over-testing, compared to the traditional logic BIST approaches, and uses a minimal amount of additional hardware. Experimental research was based on the case study of a specialized bio-signal processor architecture, and the results showed promising results in reducing the cost of testing and achieving high fault coverage.
Survival of Adult Generated Hippocampal Neurons Is Altered in Circadian Arrhythmic Mice

The subgranular zone of the hippocampal formation gives rise to new neurons that populate the dentate gyrus throughout life. Cells in the hippocampus exhibit rhythmic clock gene expression and the circadian clock is known to regulate the cycle of cell division in other areas of the body. These facts suggest that the circadian clock may regulate adult neurogenesis in the hippocampus as well. In the present study, neurogenesis in the hippocampal subgranular zone was examined in arrhythmic Bmal1 knockout (-KO) mice and their rhythmic heterozygous and wildtype littermates. Proliferation and survival of newly generated subgranular zone cells were examined using bromodeoxyuridine labelling, while pyknosis (a measure of cell death) and hippocampal volume were examined in cresyl violet stained sections. There was no significant difference in cellular proliferation between any of the groups, yet survival of proliferating cells, 6 weeks after the bromodeoxyuridine injection, was significantly greater in the BMAL1-KO animals. The number of pyknotic cells was significantly decreased in Bmal1-KO animals, yet hippocampal volume remained the same across genotypes. These findings suggest that while a functional circadian clock is not necessary for normal proliferation of neuronal precursor cells, the normal pruning of newly generated neurons in the hippocampus may require a functional circadian clock.
A simple closed-form solution for overdetermined blind separation of locally sparse quasi-stationary sources

We consider the scenario of an unknown overdetermined instantaneous mixture of quasi-stationary sources. Blind source separation (BSS) under this scenario has drawn much attention, motivated by applications such as speech and audio separation. The ideas in the existing BSS works often focus on exploiting the time-varying statistics characteristics of quasi-stationary sources, through various kinds of formulations and optimization methods. In this paper, we are interested in further assuming that the sources exhibit some form of local sparsity, which is generally satisfied in speech. By exploiting this additional assumption, we show that there is a simple closed-form solution for the BSS problem. Simulation results based on real speech show that the proposed closed-form algorithm is computationally much lower than some existing BSS algorithms, while delivering a promising mean-square-error performance.
Cd4+ T Cells from Lupus-Prone Mice Are Hyperresponsive to T Cell Receptor Engagement with Low and High Affinity Peptide Antigens

Polyclonal CD4+ T cell activation is characteristic of spontaneous lupus. As a potential explanation for this phenotype, we hypothesized that T cells from lupus-prone mice are intrinsically hyperresponsive to stimulation with antigen, particularly to those peptide ligands having a low affinity for the T cell receptor (TCR). To test this hypothesis, we backcrossed the α and β chain genes of the AND TCR specific for amino acids 88–104 of pigeon cytochrome C (PCC) to the Fas-intact MRL/Mp+ Fas-lpr and to the H-2k–matched control backgrounds B10.BR and CBA/CaJ (MRL.AND, B10.AND, and CBA.AND, respectively), and assessed naive CD4+ TCR transgenic T cell activation in vitro after its encounter with cognate antigen and lower affinity altered peptide ligands (APLs). MRL.AND T cells, compared with control B10.AND and CBA.AND cells, proliferated more when stimulated with agonist antigen. More strikingly, MRL.AND T cells proliferated significantly more and produced more interleukin 2 when stimulated with the APLs of PCC 88–104, having lower affinity for the transgenic TCR. These results imply that one of the forces driving polyclonal activation of α/β T cells in lupus is an intrinsically heightened response to peptide antigen, particularly those with low affinity for the TCR, independent of the nature of the antigen-presenting cell and degree of costimulation.