Miracle-dz/UniFAR-FTUs huggingface dataset:
The degradation of glial scar and enhancement of chronic intracortical recording electrode performance through the local delivery of dexamethasone and chondroitinase

The ability of conducting polymers such as poly(3,4-ethylenedioxythiophene) (PEDOT) to store a drug as a dopant and release it following electrical stimulus make them an intriguing coating possibility for intracortical electrodes, along with their ability to reduce electrode impedance. The mechanism allows for the release of an assortment of useful agents, including anti-inflammatory drugs and neuromodulatory chemicals. We evaluated the release capabilities of a multi-walled carbon nanotube (MWCNT)-doped PEDOT coating incorporating the anti-inflammatory steroid dexamethasone in vitro using sputtered-gold macroelectrodes, and then applied the coating to half of the electrodes within 16-shank platinum/iridium floating microelectrode arrays for chronic in vivo evaluation in rat visual cortex. Impedance measurement, neurophysiological recording, and cyclic voltammetric release stimulus (-0.9 V to 0.6 V, 1 V/s, 20 cycles) was performed daily to all channels. On the 11th day, histology was performed to quantitatively characterize inflammatory tissue response using OX42 (microglia) and GFAP (astroglia). Equivalent circuit analysis was performed to assist the interpretation of impedance data. Our results indicated that the MWCNT/PEDOT-coated gold macroelectrodes released double the amount of dexamethasone using passive release followed by CV stimulation (10 sets of 20 cycles) compared to passive release alone. Coatings applied to Pt/Ir microelectrodes reduced 1 kHz impedance in PBS by approximately 38%. Coated probes in vivo exhibited a significant decrease in 1 kHz impedance for the initial three days of implantation followed by an increase, between days 4 and 7, to values equivalent to those exhibited by uncoated probes. Neurophysiological recording performance of coated and uncoated probes remained equivalent for the duration of the experiment, in terms of signal-to-noise ratio and noise amplitude. Histology revealed no significant difference in tissue inflammatory response to coated and uncoated electrodes. Explant imaging revealed the presence of a membranous film enveloping coated electrodes, and equivalent circuit analysis suggested that the day 4-7 increase in 1 kHz impedance of coated electrodes was due to a decrease in effective surface area of the coatings as well as the core electrodes. Additional work was also performed developing a model for the in vivo microinjection of the enzyme Chondroitinase ABC into tissue surrounding implanted microelectrodes.
A Macroecological Approach to Understanding Drivers of Riverine Fish Community Composition

iii Acknowledgements . iv Background . 1 Chapter 1. A Macroecological Approach to Understanding Drivers of Riverine Fish Community Composition . 3 Introduction . 4 Methods . 6 Results . 11 Discussion . 13 References . 18 Figures and Tables . 22 Appendix 1 . 27
Resource allocation between initialization and optimization under computational expensive environment

Initialization techniques are normally considered as “resource-free” and their computational complexities are seldom addressed. Since many techniques require objective function evaluations to generate initial solutions, this “resource-free” assumption is invalid under computational expensive environment. In this paper, we propose an Computational Resource Optimization Problem (CROP) between initialization and optimization under such environment. We provide a comparison metric among different initialization techniques. Four popular initialization techniques, namely, Pseudo Random Number Generator (PRNG), Opposition-based Learning (OBL), Quasi-Opposition-based Learning (QOBL) and Quadratic Interpolation (QI) are studied. Differential Evolution (DE) is used as the underlying optimization technique, while Chemical Reaction Optimization (CRO) is used to solve CROP. The CEC2014 computational expensive problem set is used as test cases. Our results show the importance of considering resource allocation between initialization and optimization in computational expensive environment.
Low counts of Faecalibacterium prausnitzii in colitis microbiota

Background: The intestinal microbiota is suspected to play a role in colitis and particularly in inflammatory bowel disease (IBD) pathogenesis. The aim was to compare the fecal microbiota composition of patients with colitis to that of healthy subjects (HS). Methods: fecal samples from 22 active Crohn's disease (A‐CD) patients, 10 CD patients in remission (R‐CD), 13 active ulcerative colitis (A‐UC) patients, 4 UC patients in remission (R‐UC), 8 infectious colitis (IC) patients, and 27 HS were analyzed by quantitative real‐time polymerase chain reaction (PCR) targeting the 16S rRNA gene. Bacterial counts were transformed to logarithms (Log10 CFU) for statistical analysis. Results: Bacteria of the phylum Firmicutes (Clostridium leptum and Clostridium coccoides groups) were less represented in A‐IBD patients (9.7; P = 0.004) and IC (9.4; P = 0.02), compared to HS (10.8). Faecalibacterium prausnitzii species (a major representative of the C. leptum group) had lower counts in A‐IBD and IC patients compared to HS (8.8 and 8.3 versus 10.4; P = 0.0004 and P = 0.003). The Firmicutes/Bacteroidetes ratio was lower in A‐IBD (1.3; P = 0.0001) and IC patients (0.4; P = 0.002). Compared to HS, Bifidobacteria were less represented in A‐IBD and IC (7.9 and 7.7 versus 9.2; P = 0.001 and P = 0.01). Conclusions: The fecal microbiota of patients with IBD differs from that of HS. The phylum Firmicutes and particularly the species F. prausnitzii, are underrepresented in A‐IBD patients as well as in IC patients. These bacteria could be crucial to gut homeostasis since lower counts of F. prausnitzii are consistently associated with a reduced protection of the gut mucosa. (Inflamm Bowel Dis 2009)
Adaptive processing of structural data: from sequences to trees and beyond

There are several challenging real-world problems, for instance in the fields of medical and technical diagnosis, molecular biology, or document and image processing, where the objects of interest are significantly structured, and their component parts have a continuous nature and are subjected to different types of noise. For a number of practical tasks, the solution can be described by example data, but there is no or only partial and uncertain prior expert knowledge about the relevant structural concepts. Thus, it would be advantageous to have methods and tools to (automatically) infer the solutions, i.e. the desired input-output mapping, from the given example data. In computer science, structural (for example causal, topological, or hierarchical) relationships between parts of a object are commonly represented by symbolic formalisms such as graphs, terms or diagrams. Symbolic machine learning approaches can deal with these representations, but fail if the range of the intended mapping is of continuous nature. On the other hand, existing analog models of computation and learning are tailored to the processing of continuous information. However, these models assume that data are organized according relatively poor structures, by and large, arrays and sequences. This work contributes in bridging this gap. We propose tree-recursive dynamical systems (TRDS), a new class of deterministic state machines that operate in a continuous state space. These machines enable the representation and the inductive inference of structure mappings. The most general admissible domain is characterized by rooted labeled ordered trees (and a certain class of rooted labeled directed ordered acyclic graphs) whose vertices can be labeled by continuous feature vectors. The range of these mappings may either be (a subspace of) the Euclidean vector space or a finite set of categorical values. Adaptivity is incorporated into TRDS by choosing parameterized functions for the state transition map and the output map. Inductive learning tasks, such as the classification or the regression of tree structures, can be re-formulated as the optimization (minimization) of an error criterion. If the given error criterion is stated by a continuously differentiable function, then gradient-based optimization methods are usually taken into account to solve the learning task. We develop and analyze two different algorithms for the calculation of gradient information, backpropagation through structure (BPTS) and tree-recursive gradient computation (TRGC). Both algorithms can be used to calculate the first-order gradient for arbitrary continuous and differentiable criteria where tree structures are embedded via TRDS mappings. This enables attacking inductive learning tasks on structural data by means of TRDS and a variety of
Xenopus laevis U2 snRNA genes: tandemly repeated transcription units sharing 5′ and 3′ flanking homology with other RNA polymerase II transcribed genes.

Xenopus laevis U2 small nuclear RNA (snRNA) genes were isolated and expressed by microinjection into frog oocytes. The genes are organised in short tandemly repeated units of approximately 830 bp. Some of the cloned tandem repeats are closely linked to genes coding for U5 snRNA, tRNA and an uncharacterised 7S RNA. No evidence was found for U2 snRNA pseudogenes. Single repeat units are transcriptionally active, showing that all the signals necessary for U2 snRNA transcription are included in an 831‐bp segment of DNA. Sequence analysis of a cloned repeat unit showed that Xenopus and rat U2 snRNAs are 94% homologous. Flanking regions 5′ and 3′ to the coding sequence were found which shared extensive homology with similarly positioned sequences in human U1 snRNA genes. Part of the 3′ non‐coding region homology (consensus TTTNAAAGAAT) was found in many other genes transcribed by RNA polymerase II.
A Longitudinal Bilingual Frisian-Dutch Radio Broadcast Database Designed for Code-Switching Research

We present a new speech database containing 18.5 hours of annotated radio broadcasts in the Frisian language. Frisian is mostly spoken in the province Fryslan and it is the second official language of the Netherlands. The recordings are collected from the archives of Omrop Fryslan, the regional public broadcaster of the province Fryslan. The database covers almost a 50-year time span. The native speakers of Frisian are mostly bilingual and often code-switch in daily conversations due to the extensive influence of the Dutch language. Considering the longitudinal and code-switching nature of the data, an appropriate annotation protocol has been designed and the data is manually annotated with the orthographic transcription, speaker identities, dialect information, code-switching details and background noise/music information.
Understanding the pathology and mechanisms of type I diabetic bone loss

Type I (T1) diabetes, also called insulin dependent diabetes mellitus (IDDM), is characterized by little or no insulin production and hyperglycemia. One of the less well known complications of T1‐diabetes is bone loss which occurs in humans and animal models. This complication is receiving increased attention because T1‐diabetics are living longer due to better therapeutics, and are faced with their existing health concerns being compounded by complications associated with aging, such as osteoporosis. Both male and female, endochondrial and intra‐membranous, and axial and appendicular bones are susceptible to T1‐diabetic bone loss. Exact mechanisms accounting for T1‐diabetic bone loss are not known. Existing data indicate that the bone defect in T1‐diabetes is anabolic rather than catabolic, suggesting that anabolic therapeutics may be more effective in preventing bone loss. Potential contributors to T1‐diabetic suppression of bone formation are discussed in this review and include: increased marrow adiposity, hyperlipidemia, reduced insulin signaling, hyperglycemia, inflammation, altered adipokine and endocrine factors, increased cell death, and altered metabolism. Differences between T1‐diabetic‐ and age‐associated bone loss underlie the importance of condition specific, individualized treatments for osteoporosis. Optimizing therapies that prevent bone loss or restore bone density will allow T1‐diabetic patients to live longer with strong healthy bones. J. Cell. Biochem. 102: 1343–1357, 2007. © 2007 Wiley‐Liss, Inc.
Functionally expanded streaming data as input to classification processes using ensembles of constructive neural networks

Machine learning (ML) based applications that require data stream processing have become quite common over the past few years. To deal with continuous and massive streams of data, low computational and memory costs are required from the ML techniques employed; these requirements can be partially fulfilled by using constructive neural networks (CoNN) algorithms. The automatic definition of the Neural Network (NN) architecture, as well as its fast training, promote the high adaptability of such NNs, which allows to skip the conventional model selection phase during the learning process. However, such advantages usually come with the drawback of promoting lower accuracy rates, when compared to other learning approaches. The work described in this paper proposes an ensemble of CoNNs combined with functional expansion techniques to cope with data stream classification. The experiment results, followed by a comparative analysis, showed that CoNN accuracy performance along streaming data does improve with the use of functional expansion. Considering that to functionally expand the input data has a low computational cost, the obtained results turn CoNN algorithms an interesting approach to be considered in data stream classification.
Soft errors induced by natural radiation at ground level in floating gate flash memories

This work reports the combined characterization at mountain altitude (on the ASTEP Platform at 2552 m) and at sea-level of more than ~50 Gbit of 90 nm NOR flash memories subjected to natural radiation (atmospheric neutrons). This wafer-level experiment evidences a limited impact of the terrestrial radiation at ground level on the memory SER evaluated without ECC. Experimental values are compared to estimations obtained from Monte Carlo simulation using the TIARA-G4 code combined with a physical model for charge loss in such floating-gate devices.
Does Confidence Reporting from the Crowd Benefit Crowdsourcing Performance?

We explore the design of an effective crowdsourcing system for an M-ary classification task. Crowd workers complete simple binary microtasks whose results are aggregated to give the final classification decision. We consider the scenario where the workers have a reject option so that they are allowed to skip microtasks when they are unable to or choose not to respond to binary microtasks. Additionally, the workers report quantized confidence levels when they are able to submit definitive answers. We present an aggregation approach using a weighted majority voting rule, where each worker's response is assigned an optimized weight to maximize crowd's classification performance. We obtain a couterintuitive result that the classification performance does not benefit from workers reporting quantized confidence. Therefore, the crowdsourcing system designer should employ the reject option without requiring confidence reporting.
[The early predictors of ventricular remodeling after myocardial infarction: the role of tumor necrosis factor-alpha].

OBJECTIVE Ventricular remodeling (VR) is a pathologic process characterized by progressive ventricular dilatation occurring after acute myocardial infarction (MI) leading to left ventricular systolic dysfunction. The purpose of the study was to evaluate the efficacy of plasma tumor necrosis factor alpha (TNF-alpha) levels to predict the left VR. METHODS This prospective observational cohort study included 72 consecutive patients with newly diagnosed MI with age ranging between 38-87 years (mean 59 +/- 12 years). Control group was consisted of 30 patients with no additional systemic disease and normal coronary arteriograms. Transthoracic echocardiography was performed to all patients and controls both in the beginning of the study and in the 6th follow-up. A coronary arteriography was also performed to all patients. Patients with an increment in the diastolic volume index more than 20% in the follow-up compared with basal values included in the VR subgroup. The patient subgroup with VR consisted of 19 patients. Statistical analyses were performed using ANOVA and Kruskal Wallis tests for comparison of variables between groups. Logistic regression and ROC analyses were used for evaluation of accuracy of TNF-alpha in prediction of VR. RESULTS There were no significant differences between groups according to demographic characters. The basal plasma levels of TNF-alpha were higher in the patient subgroup with VR as compared with patients without VR and controls (14.59 +/- 4.28 pg/ml vs 7.30 +/- 4.48 pg/ml, and 1.64 +/- 1.49 pg/ml, p< 0.001). In logistic regression analysis only TNF-alpha predicted the VR (OR-1.356, 95% CI 1.117-1.647). Plasma TNF-alpha levels with a cut-off > or = 10.33 pg/ml were found to have 89.5% sensitivity and 79.3% specificity to predict the development of VR. CONCLUSION These results demonstrate the increment of plasma TNF-alpha levels in the acute phase of MI and the close relationship between the TNF-alpha levels and VR in the patients with first MI.
Meander-line antenna with arc structure for UHF- RFID Tag

The new configuration of the RFID tag antenna is presented in this paper. It consists of meander-line with arc structure and T-matching technique to accomplish the very small tag antenna for an operation of the frequency band 920–925 MHz, corresponding to the standard of UHF RFID in Thailand. The electrical size of the proposed tag antenna is approximately 0. 025λ0× 0. 24λ0 or 0.8 mm×79 mm, and it is designed by using NXP G2XL IC chip with the impedance of 21.29–j191.7 Ω at the frequency of 922.5 MHz. The proposed tag antenna obtains the omnidirectional pattern with 0.91 dBi gain. It is fabricated on FR 4 with the thickness of 0.25 mm. The maximum read range is 8 m, which was measured by 4 W EIRP reader.
Dysregulated coherence of subjective and cardiac emotional activation in adolescents with internalizing and externalizing problems.

BACKGROUND Effective emotion regulation should be reflected in greater coherence between physiological and subjective aspects of emotional responses. METHOD Youths with normative to clinical levels of internalizing problems (IP) and externalizing problems (EP) watched emotionally evocative film-clips while having heart rate (HR) recorded, and reported subjective feelings. RESULTS Hierarchical linear modeling revealed weaker coherence between HR and negative feelings in youths, especially boys, with more EP. Youths with IP showed coherence between HR and negative feelings that did not match the affect portrayed in the eliciting stimuli, but atypical positive emotions: they felt happier when they had slower HR. Youths without problems predominantly showed normative emotional coherence. CONCLUSIONS Youths with EP and IP experience atypical patterns of activation across physiological and experiential emotion systems which could undermine emotion regulation in evocative situations.
A novel variation-aware low-power keeper architecture for wide fan-in dynamic gates

Substantial increase in leakage current and threshold voltage fluctuations are making design of robust wide fan-in dynamic gates a challenging task. Traditionally, a PMOS keeper transistor has been employed to compensate for leakage current of pull down (NMOS) network. However, to maintain acceptable noise margin level in sub-100 nm technologies, large PMOS is necessary, which results in substantial contention (during pull down) and severe loss of performance. In this paper, a novel keeper architecture is proposed which is capable of significantly reducing the contention and improving the performance and power consumption. Using circuit simulations, superior characteristics of the proposed keeper is demonstrated in comparison to those of the traditional as well as state-of-the-art keepers. It is shown that for an 8-input OR gate, in presence of 15% Vth fluctuations, the proposed architecture can lead to 20%, 15%, and more than 40% reduction in power consumption, mean delay, and standard deviation of delay, respectively, when compared to traditional keeper circuit
The impact of the phase of an epidemic of sexually transmitted infection on the evolution of the organism

The evolution of any sexually transmitted organism will be influenced by prevailing epidemiological interactions. The optimum strategy for an organism to overcome treatment, either through drug resistance or cryptic infections, depends upon whether the method for identifying patients is passive (treating symptoms alone favours asymptomatic organisms) or active (screening favours resistant organisms). The use of mathematical models of competing strains of infection allows theoretical predictions for the outcome of evolution under a range of assumptions about potential phenotypes. The course of pathogen evolution has implications for the success of interventions, but the predictions presented need to be tested at the level of the community in carefully monitored interventions.
Plasmodium falciparum Genotypes, Low Complexity of Infection, and Resistance to Subsequent Malaria in Participants in the Asembo Bay Cohort Project

ABSTRACT To assess the relationship between the within-host diversity of malaria infections and the susceptibility of the host to subsequent infection, we genotyped 60 children's successive infections from birth through 3 years of life. MSP-1 Block2 genotypes were used to estimate the complexity of infection (COI). Malaria transmission and age were positively associated with the number of K1 and Mad20 alleles detected (COIKM) (P < 0.003). Controlling for previous parasitemia, transmission, drug treatment, parasite density, sickle cell, and age, COIKM was negatively correlated with resistance to parasitemia of >500/μl (P < 0.0001). Parasitemias with the RO-genotype were more resistant than those without this genotype (P < 0.0000). The resistance in low COIKM infections was not genotype specific. We discuss the impact of genotype-transcending immunity to conserved antigenic determinants. We also propose a diversity-driven immunomodulation hypothesis that may explain the delayed development of natural immunity in the first few years of life and suggest that interventions that decrease the COIKM could facilitate the development of protective immunity.
Adaptive and repetitive controller for robotic manipulators with slowly updating scheme using B-spline shape function

This paper studies the real-time adaptive and repetitive control problem using the Desired Compensation Learning Law (DCLL) that has the advantage of robustness under the presence of unknown parameters with low memory requirement. The control structure of DCLL consists of a feedforward compensator that is designed by a linear combination of shape functions that is adaptable to parameter variations; hence the selection of appropriate shape functions plays an important role in the adaptive ability and accuracy of DCLL. In this study, the B-spline shape function is proposed to be used under the slowly updating scheme and the obtained results show that the robustness and accuracy of the tracking can be greatly improved even under payload variation and torque limits.