Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Approach to the Statistical Modeling of Wireline Channels

We report here that channel power gain and Root-Mean-Square Delay Spread (RMS-DS) in Low/Medium Voltage power line channels are negatively correlated lognormal random variables. Further analysis of other wireline channels allows us to report a strong similarity between some properties observed in power line channels and the ones observed in other wireline channels, e.g. coaxial cables and phone lines. For example, it is here reported that channel power gain and logarithm of the RMS-DS in DSL links are linearly correlated random variables. Exploiting these results, we here propose a statistical wireline channel model where tap amplitudes and delays are generated in order to reflect these physical properties. Although wireline channels are considered deterministic as their impulse response can be readily calculated once the link topology is known, a statistical wireline channel model is useful because the variability of link topologies and wiring practices give rise to a stochastic aspect of wireline communications that has not been well characterized in the literature. Finally, we also point out that alternative channel models that normalize impulse responses to a common (often unitary) power gain may be misleading when assessing the performance of equalization schemes since this normalization artificially removes the correlation between channel power gain and RMS-DS and, thus, Inter-Symbol Interference (ISI).
Identifiability in Causal Bayesian Networks: A Sound and Complete Algorithm

This paper addresses the problem of identifying causal effects from nonexperimental data in a causal Bayesian network, i.e., a directed acyclic graph that represents causal relationships. The identifiability question asks whether it is possible to compute the probability of some set of (effect) variables given intervention on another set of (intervention) variables, in the presence of non-observable (i.e., hidden or latent) variables. It is well known that the answer to the question depends on the structure of the causal Bayesian network, the set of observable variables, the set of effect variables, and the set of intervention variables. Our work is based on the work of Tian, Pearl, Huang, and Valtorta (Tian & Pearl 2002a; 2002b; 2003; Huang & Valtorta 2006a) and extends it. We show that the identify algorithm that Tian and Pearl define and prove sound for semi-Markovian models can be transfered to general causal graphs and is not only sound, but also complete. This result effectively solves the identifiability question for causal Bayesian networks that Pearl posed in 1995 (Pearl 1995), by providing a sound and complete algorithm for identifiability.
Parallel organization of functionally segregated circuits linking basal ganglia and cortex.

Information about the basal ganglia has accumulated at a prodigious pace over the past decade, necessitating major revisions in our concepts of the structural and functional organization of these nuclei. From earlier data it had appeared that the basal ganglia served primarily to integrate diverse inputs from the entire cerebral cortex and to "funnel" these influences, via the ventrolateral thalamus, to the motor cortex (Allen & Tsukahara 1974, Evarts & Thach 1969, Kemp & Powell 1971). In particular, the basal
Multiple-cloud platform monitoring

A research and a pilot implementation of a monitoring architecture for multiple-cloud infrastructures of VMware, HyperV and OpenStack are presented. A standardized set of monitoring attributes is selected and an efficient architecture to support monitoring itself is implemented. Two different monitoring architectures and their interfaces are described. The pilot is implemented by using the less flexible architecture due to the lack of time. The advantages and disadvantages of both architectures are analyzed. Furthermore two monitoring systems were implemented. One of them serves only as a proof of concept and the other is aa complete monitoring infrastructure for multiple different clouds. On the top of the monitoring system, a fully operational support for SLAs was implemented.
Different Effects of NSF and PCE Superplasticizer on Adsorption, Dynamic Yield Stress and Thixotropy of Cement Pastes

This study compares the differences and similarities of two types of superplasticizers—NSF (Naphthalene Sulfonate Formaldehyde) and PCE (PolyCarboxylate Ester)—in fresh cement paste systems, in terms of adsorption, dynamic yield stress, and thixotropic index. Results show that with either NSF or PCE addition, the more superplasticizer is added, the more it is adsorbed and the more it remains in the interstitial pore solution. The dynamic yield stress and thixotropic index also decrease with increasing addition the amount of either superplasticizer. However, NSF is less efficient in decreasing the dynamic yield stress than PCE. More importantly, the decreasing patterns of dynamic yield stress and thixotropic index are different with NSF and PCE additions; this is tied to the adsorption and dispersing mechanisms of these two types of superplasticizers.
Pharmacokinetic-Pharmacodynamic Modeling of the Electroencephalogram Effect of Imipenem in Healthy Rats

ABSTRACT A pharmacokinetic-pharmacodynamic (PK-PD) modeling approach was developed to investigate the epileptogenic activity of imipenem in rats. Initially, animals received an intravenous infusion of imipenem at a rate of 2.65 mg min−1 for 30 min. Blood samples were collected for drug assay, and an electroencephalogram (EEG) was recorded during infusion and postinfusion. A dramatic delay was observed between concentrations of imipenem in serum and the EEG effect; this effect was accompanied by tremors and partial seizures. Indirect-effect models failed to describe these data, which were successfully fitted using an effect compartment model. The relationship between effect and concentration at the effect site was best described by a spline function. The elimination rate constant from the effect compartment was severalfold lower than that from the central compartment. The robustness of the model was then confirmed after administering the imipenem dose over 60 and 90 min. In conclusion, the successful PK-PD modeling of the imipenem EEG effect in rats constitutes a major improvement for better prediction of the epileptogenic risk associated with this antibiotic.
Endogenous peptides of a soluble major histocompatibility complex class I molecule, H-2Lds: sequence motif, quantitative binding, and molecular modeling of the complex

To gain insight into the rules that govern the binding of endogenous and viral peptides to a given major histocompatibility complex (MHC) class I molecule, we characterized the amino acid sequences of a set of self peptides bound by a soluble analogue of murine H-2Ld, H-2Lds. We tested corresponding synthetic peptides quantitatively for binding in several different assays, and built three-dimensional computer models of eight peptide/H-2Lds complexes, based on the crystallographic structure of the human HLA-B27/peptide complex. Comparison of primary and tertiary structures of bound self and antigenic peptides revealed that residues 2 and 9 were not only restricted in sequence and tolerant of conservative substitutions, but were spatially constrained in the three-dimensional models. The degree of sequence variability of specific residues in MHC-restricted peptides reflected the lack of structural constraint on those amino acids. Thus, amino acid residues that define a peptide motif represent side chains required or preferred for a close fit with the MHC class I heavy chain.
Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics.

Likelihood ratio tests (LRTs) for comparing models of sequence evolution have become popular over the last few years (Goldman 1993; Yang, Goldman and Friday 1994, 1995; Huelsenbeck and Crandall 1997; Huelsenbeck and Rannala 1997). In their simplest form, such tests compare a simpler null hypothesis (H 0) with a more complex alternative hypotheses (H 1) which is a generalization of H0. H0 can be derived from H 1 by fixing one or more of its free parameters at particular values, and the hypotheses are described as nested. Although it is also possible to test non-nested models (Goldman 1993), nested models are often preferred, as statistical tests are simpler to perform and their results can be easier to interpret. The test statistic for an LRT can be written as 2 2 where and ˆ ˆ ˆ ˆ ˆ ln(L /L ) 2(ln(L ) ln(L )), L H H H H H 1 0 1 0 0 are the maximum-likelihood (ML) scores under hyL̂H1 potheses H0 and H1, respectively. This statistic measures how much improvement H 1 gives over H0, and when the hypotheses are nested, 2 will always be nonnegative. For these nested hypotheses, and under certain regularity conditions, the asymptotic distribution of 2 (i.e., for large amounts of data) will be . Here, k is the 2 k number of degrees of freedom by which H 0 and H1 differ, that is, the number of free parameters of H 1 whose values must be fixed to derive H 0 (Wald 1949; Silvey 1975; Felsenstein 1981; Goldman 1993; Yang, Goldman, and Friday 1994, 1995). (In effect, each free parameter contributes a variate to the distribution of 2 , 2 1 with the sum ofk independent variates being distrib2 1 uted as ) Statistical tests assessed using such 2 dis2 . k tributions have now become a widespread and useful tool in phylogenetics (Huelsenbeck and Crandall 1997; Huelsenbeck and Rannala 1997). Recently, there has been renewed interest in testing whether the predicted 2 distribution gives a reliable estimate of the true distribution of 2 under realistic conditions (e.g., with finite sequence lengths). Whelan and Goldman (1999) investigated cases in which the competing hypotheses were different models of nucleotide substitution. Under three specimen experimental designs (representing realistic phylogenies and nucleotide substitution processes), we found that the 2 distribution was acceptable for performing tests of the significance of parameters describing the relative rate of transition
Expression of CD64 on Circulating Neutrophils Favoring Systemic Inflammatory Status in Erythema Nodosum Leprosum

Erythema Nodosum Leprosum (ENL) is an immune reaction in leprosy that aggravates the patient´s clinical condition. ENL presents systemic symptoms of an acute infectious syndrome with high leukocytosis and intense malaise clinically similar to sepsis. The treatment of ENL patients requires immunosuppression and thus needs to be early and efficient to prevent both disabilities and permanent nerve damage. Some patients experience multiple episodes of ENL and prolonged use of immunosuppressive drugs may lead to serious adverse effects. Thalidomide treatment is extremely effective at ameliorating ENL symptoms. Several mechanisms have been proposed to explain the efficacy of thalidomide in ENL, including the inhibition of TNF production. Given its teratogenicity, thalidomide is prohibitive for women of childbearing age. A rational search for molecular targets during ENL episodes is essential to better understand the disease mechanisms involved, which may also lead to the discovery of new drugs and diagnostic tests. Previous studies have demonstrated that IFN-γ and GM-CSF, involved in the induction of CD64 expression, increase during ENL. The aim of the present study was to investigate CD64 expression during ENL and whether thalidomide treatment modulated its expression. Leprosy patients were allocated to one of five groups: (1) Lepromatous leprosy, (2) Borderline leprosy, (3) Reversal reaction, (4) ENL, and (5) ENL 7 days after thalidomide treatment. The present study demonstrated that CD64 mRNA and protein were expressed in ENL lesions and that thalidomide treatment reduced CD64 expression and neutrophil infiltrates—a hallmark of ENL. We also showed that ENL blood neutrophils exclusively expressed CD64 on the cell surface and that thalidomide diminished overall expression. Patient classification based on clinical symptoms found that severe ENL presented high levels of neutrophil CD64. Collectively, these data revealed that ENL neutrophils express CD64, presumably contributing to the immunopathogenesis of the disease.
Investigation of on-chip coil in 130 nm standard CMOS for WPT and bio-applications

The wireless power transfer (WPT) systems, in conjunction with active implantable medical devices (AIMDs), belong to the most discussed topics in last years. Recently, the low frequency (inductive) or near-field electromagnetic energy transfer make the integration of AIMDs easier and simplified that supports their miniaturization. This paper deals with the possibilities of realization of the secondary coil directly on integrated circuit (IC) chip in standard UMC 130 nm CMOS process. We also bring a comparison of the proposed solution to the most related work. At this stage, the verification was done by simulation. Designed symmetrical multilayer stacked inductor achieves the maximum quality factor of 6.24 at 224.1 MHz, 51.33 nH inductance at the maximum quality factor, the maximum inductance of 224.73 nH, and self-resonance frequency (SFR) of 462 MHz. The paper also brings discussion about how the presence of biocompatible or biostable dielectric isolators (with low and high relative permittivity) influences the inductor parameters and performance.
Mitochondrial fission determines cisplatin sensitivity in tongue squamous cell carcinoma through the BRCA1–miR-593-5p–MFF axis

Cisplatin has been widely employed as a cornerstone chemotherapy treatment for a wide spectrum of solid neoplasms; increasing tumor responsiveness to cisplatin has been a topic of interest for the past 30 years. Strong evidence has indicated that mitochondrial fission participates in the regulation of apoptosis in many diseases; however, whether mitochondrial fission regulates cisplatin sensitivity remains poorly understood. Here, we show that MFF mediated mitochondrial fission and apoptosis in tongue squamous cell carcinoma (TSCC) cells after cisplatin treatment and that miR-593-5p was downregulated in this process. miR-593-5p attenuated mitochondrial fission and cisplatin sensitivity by targeting the 3′ untranslated region sequence of MFF and inhibiting its translation. In exploring the underlying mechanism of miR-593-5p downregulation, we observed that BRCA1 transactivated miR-593-5p expression and attenuated cisplatin sensitivity in vitro. The BRCA1-miR-593-5p-MFF axis also affected cisplatin sensitivity in vivo. Importantly, in a retrospective analysis of multiple centers, we further found that the BRCA1-miR-593-5p-MFF axis was significantly associated with cisplatin sensitivity and the survival of patients with TSCC. Together, our data reveal a model for mitochondrial fission regulation at the transcriptional and post-transcriptional levels; we also reveal a new pathway for BRCA1 in determining cisplatin sensitivity through the mitochondrial fission program.
The role of Artificial Intelligence in Software Engineering

There has been a recent surge in interest in the application of Artificial Intelligence (AI) techniques to Software Engineering (SE) problems. The work is typified by recent advances in Search Based Software Engineering, but also by long established work in Probabilistic reasoning and machine learning for Software Engineering. This paper explores some of the relationships between these strands of closely related work, arguing that they have much in common and sets out some future challenges in the area of AI for SE.
Coding In-depth Semistructured Interviews

Many social science studies are based on coded in-depth semistructured interview transcripts. But researchers rarely report or discuss coding reliability in this work. Nor is there much literature on the subject for this type of data. This article presents a procedure for developing coding schemes for such data. It involves standardizing the units of text on which coders work and then improving the coding scheme’s discriminant capability (i.e., reducing coding errors) to an acceptable point as indicated by measures of either intercoder reliability or intercoder agreement. This approach is especially useful for situations where a single knowledgeable coder will code all the transcripts once the coding scheme has been established. This approach can also be used with other types of qualitative data and in other circumstances.
TMS-EEG Signatures of GABAergic Neurotransmission in the Human Cortex

Combining transcranial magnetic stimulation (TMS) and electroencephalography (EEG) constitutes a powerful tool to directly assess human cortical excitability and connectivity. TMS of the primary motor cortex elicits a sequence of TMS-evoked EEG potentials (TEPs). It is thought that inhibitory neurotransmission through GABA-A receptors (GABAAR) modulates early TEPs (<50 ms after TMS), whereas GABA-B receptors (GABABR) play a role for later TEPs (at ∼100 ms after TMS). However, the physiological underpinnings of TEPs have not been clearly elucidated yet. Here, we studied the role of GABAA/B-ergic neurotransmission for TEPs in healthy subjects using a pharmaco-TMS-EEG approach. In Experiment 1, we tested the effects of a single oral dose of alprazolam (a classical benzodiazepine acting as allosteric-positive modulator at α1, α2, α3, and α5 subunit-containing GABAARs) and zolpidem (a positive modulator mainly at the α1 GABAAR) in a double-blind, placebo-controlled, crossover study. In Experiment 2, we tested the influence of baclofen (a GABABR agonist) and diazepam (a classical benzodiazepine) versus placebo on TEPs. Alprazolam and diazepam increased the amplitude of the negative potential at 45 ms after stimulation (N45) and decreased the negative component at 100 ms (N100), whereas zolpidem increased the N45 only. In contrast, baclofen specifically increased the N100 amplitude. These results provide strong evidence that the N45 represents activity of α1-subunit-containing GABAARs, whereas the N100 represents activity of GABABRs. Findings open a novel window of opportunity to study alteration of GABAA-/GABAB-related inhibition in disorders, such as epilepsy or schizophrenia.
Stochastic ADMM for Nonsmooth Optimization

We present a stochastic setting for optimization problems with nonsmooth convex separable objective functions over linear equality constraints. To solve such problems, we propose a stochastic Alternating Direction Method of Multipliers (ADMM) algorithm. Our algorithm applies to a more general class of nonsmooth convex functions that does not necessarily have a closed-form solution by minimizing the augmented function directly. We also demonstrate the rates of convergence for our algorithm under various structural assumptions of the stochastic functions: $O(1/\sqrt{t})$ for convex functions and $O(\log t/t)$ for strongly convex functions. Compared to previous literature, we establish the convergence rate of ADMM algorithm, for the first time, in terms of both the objective value and the feasibility violation.
Modeling Cooperative Gene Regulation Using Fast Orthogonal Search

Gene regulation is a complex and relatively poorly understood process. While a number of methods have sug- gested means by which gene transcription is activated, there are factors at work that no model has been able to fully ex- plain. In eukaryotes, gene regulation is quite complex, so models have primarily focused on a relatively simple species, Saccharomyces cerevisiae. Because of the inherent complexity in higher species, and even in yeast, a method of identify- ing transcription factor (TF) binding motifs must be efficient and thorough in its analysis. Here we propose a method us- ing the very efficient Fast Orthogonal Search (FOS) algorithm in order to uncover motifs as well as cooperatively binding groups of motifs that can explain variations in gene expression. The algorithm is very fast, exploring a motif list and con- structing a final model within seconds or a few minutes, produces model terms that are consistent with known motifs while also revealing new motifs and interactions, and causes impressive reduction in variance with relatively few model terms over the cell cycle.
FIVE NEW HIGH-REDSHIFT QUASAR LENSES FROM THE SLOAN DIGITAL SKY SURVEY

We report the discovery of five gravitationally lensed quasars from the Sloan Digital Sky Survey (SDSS). All five systems are selected as two-image lensed quasar candidates from a sample of high-redshift (z > 2.2) SDSS quasars. We confirmed their lensing nature with additional imaging and spectroscopic observations. The new systems are SDSS J0819+5356 (source redshift zs = 2.237, lens redshift zl = 0.294, and image separation θ = 4.″04), SDSS J1254+2235 (zs = 3.626, θ = 1.″56), SDSS J1258+1657 (zs = 2.702, θ = 1.″28), SDSS J1339+1310 (zs = 2.243, θ = 1.″69), and SDSS J1400+3134 (zs = 3.317, θ = 1.″74). We estimate the lens redshifts of the latter four systems to be zl = 0.2–0.8 from the colors and magnitudes of the lensing galaxies. We find that the image configurations of all systems are well reproduced by standard mass models. Although these lenses will not be included in our statistical sample of zs < 2.2 lenses, they expand the number of lensed quasars which can be used for high-redshift galaxy and quasar studies.
Initial Observations on the Inclusion of High Protein Distillers Dried Grain into Rainbow Trout Diets

An initial investigation into the inclusion of high protein distillers dried grain with solubles (HPDDG) in juvenile rainbow trout Oncorhynchus mykiss diets was conducted during a 36-day feeding trial. Four experimental diets containing either 10% or 20% HPDDG with supplemental amino acids, and either with or without phytase, were compared to a fish-meal-based, non-HPDDG, diet. There was no significant difference among any of the diets in total weight gain, percent weight gain, feed conversion ratio, or percent mortality. There was also no significant difference in length, weight, condition factor, hepatosomatic index, viscerosomatic index, or any fish health parameter in fishes fed any of the diets. Fillet composition, as determined by crude protein, crude lipid, water, and ash were also not significantly different from fish reared on any of the diets. Estimated protein digestibility coefficients were significantly less in the fish receiving the diet void of HPDDG compared to any of the other diets. The addition of phytase had no effect on any rearing parameters. The results suggest that HPDDG, if supplemented with essential amino acids, may be included at concentrations of at least 20% (dry weight) in rainbow trout diets and that more detailed investigation into the use of HPDDG is warranted.
Maximum likelihood estimation of cloud height from multi-angle satellite imagery

We develop a new estimation technique for recovering depth-of-field from multiple stereo images. Depth-of-field is estimated by determining the shift in image location resulting from different camera viewpoints. When this shift is not divisible by pixel width, the multiple stereo images can be combined to form a super-resolution image. By modeling this super-resolution image as a realization of a random field, one can view the recovery of depth as a likelihood estimation problem. We apply these modeling techniques to the recovery of cloud height from multiple viewing angles provided by the MISR instrument on the Terra Satellite. Our efforts are focused on a two layer cloud ensemble where both layers are relatively planar, the bottom layer is optically thick and textured, and the top layer is optically thin. Our results demonstrate that with relative ease, we get comparable estimates to the M2 stereo matcher which is the same algorithm used in the current MISR standard product (details can be found in [IEEE Transactions on Geoscience and Remote Sensing 40 (2002) 1547--1559]). Moreover, our techniques provide the possibility of modeling all of the MISR data in a unified way for cloud height estimation. Research is underway to extend this framework for fast, quality global estimates of cloud height.