Miracle-dz/UniFAR-FTUs huggingface dataset:
Classifying anomalous events in BGP datasets

Border Gateway Protocol (BGP), which enables Internet interconnectivity, is susceptible to various anomalous events that may affect the Internet performance. Understanding the nature of anomalous events (unintentional or malicious) and their effects helps classify future events and improve the Internet robustness. Determining the rate and causes of these anomalous events is important for assessing loss of data and connectivity. BGP update messages contain network reachability information stored in a Routing Information Base (RIB). In this paper, we use datasets of known malicious attacks and a power outage event and employ machine learning algorithms to identify traffic anomalies.
Characterization of the p-toluenesulfonate operon tsaMBCD and tsaR in Comamonas testosteroni T-2

Comamonas testosteroni T-2 uses a standard, if seldom examined, attack on an aromatic compound and oxygenates the side chain of p-toluenesulfonate (TS) (or p-toluenecarboxylate) to p-sulfobenzoate (or terephthalate) prior to complete oxidation. The expression of the first three catabolic enzymes in the pathway, the TS methyl-monooxygenase system (comprising reductase B and oxygenase M; TsaMB), p-sulfobenzyl alcohol dehydrogenase (TsaC), and p-sulfobenzaldehyde dehydrogenase (TsaD), is coregulated as regulatory unit R1 (H. R. Schlafli Oppenberg, G. Chen, T. Leisinger, and A. M. Cook, Microbiology [Reading] 141:1891-1899, 1995). The components of the oxygenase system were repurified, and the N-terminal amino acid sequences were confirmed and extended. An internal sequence of TsaM was obtained, and the identity of the [2Fe-2S] Rieske center was confirmed by electron paramagnetic resonance spectroscopy. We purified both dehydrogenases (TsaC and TsaD) and determined their molecular weights and N-terminal amino acid sequences. Oligonucleotides derived from the partial sequences of TsaM were used to identify cloned DNA from strain T-2, and about 6 kb of contiguous cloned DNA was sequenced. Regulatory unit R1 was presumed to represent a four-gene operon (tsaMBCD) which was regulated by the LysR-type regulator, TsaR, encoded by a deduced one-gene transcriptional unit. The genes for the inducible TS transport system were not at this locus. The oxygenase system was confirmed to be a class IA mononuclear iron oxygenase, and class IA can now be seen to have two evolutionary groups, the monooxygenases and the dioxygenases, though the divergence is limited to the oxygenase components. The alcohol dehydrogenase TsaC was confirmed to belong to the short-chain, zinc-independent dehydrogenases, and the aldehyde dehydrogenase TsaD was found to resemble several other aldehyde dehydrogenases. The operon and its putative regulator are compared with units of the TOL plasmid.
Codebook for Writer Characterization: A Vocabulary of Patterns or a Mere Representation Space?

Codebook-based representations have been effectively employed for writer identification. Most of the codebook-based methods generate a codebook by clustering a set of patterns extracted from an independent data set. The probability of occurrence of the codebook patterns in a given writing is then used to characterize its author. This study investigates the hypothesis that the codebook is merely a representation space and the codebook patterns themselves do not affect the writer identification performance. The idea is validated by first using codebooks in different scripts from those of writings in question and then by using a synthetically generated codebook. A number of data sets with handwritten samples in Arabic, French, English, German, Urdu and Greek are considered in our series of evaluations. Experiments conducted with different codebooks report interesting results which validate the ideas put forward in this study.
Identifying differential expression for RNA-seq data with no replication

Transcriptional process is a starting point of biological function. In particular, transcriptomes that display differential expression in different conditions are likely to be key elements in understanding mechanisms causing those differences. A number of statistical approaches have been suggested for discovery of differential expression in microarray platform with replicated samples. However, many of sequencing-based studies tend to have very small or even no replicated sample due to high cost. Because accurate variance estimation is not straightforward with no replicated sample, accurate testing of differential expression is not easy. Here, we propose the permutation-based local pooled error (pLPE) method. By permuting local genes, pLPE method estimates variance more reliably and, thus, facilitates a differential expression analysis with no replicated sample.
Aflatoxin-mediated Sperm and Blood Cell Abnormalities in Mice Fed with Contaminated Corn

The effect of aflatoxin-contaminated corn on albino mice was investigated using the sperm morphology assay. Blood parameter levels including; total white blood cells (WBC), total red blood cells (RBC), packed cell volume (PCV), serum bilirubin (SB) and fasting blood sugar (FBS) were also determined in the tested mice. Test mice were exposed to aflatoxin-contaminated corn (contamination level of 100 ppb) for 1~4 weeks while aflatoxin-free corn and cyclophosphamide were used as negative and positive controls, respectively. Sperm cells showed varieties of morphological abnormality when assessed after 5 weeks. The percentage frequencies of the negative and positive controls were 18.8% and 48.87%, respectively, while the percentage abnormalities for the 1, 2, 3 and 4 weeks exposures were 41.38%, 48.17%, 57.13% and 61.67%, respectively. PCV, WBC, total bilirubin and glucose level values of mice in all concentrations were higher and statistically significant as compared to the negative control values using Dunnett’s test. Therefore, abnormal sperm cell induction is concentrationdependent such that continuous consumption of aflatoxin-contaminated corn is capable of negatively affecting spermatogenesis by inducing or increasing the frequency of morphologically abnormal sperm cells produced.
Expression of survivin and correlation with PCNA in osteosarcoma

Survivin is a new anti‐apoptosis gene with reported expression during fetal development and in cancer tissues. Proliferating cell nuclear antigen (PCNA) is essential for the replication of deoxyribonucleic acid (DNA). In this experiment, we examined the expression of survivin and PCNA in human osteosarcoma tissues and investigating whether survivin and PCNA expressions were correlated with histological grades, histological types, and patients' clinical characteristics.
Dehydroepiandrosterone (DHEA) prevents and reverses chronic hypoxic pulmonary hypertension

Pulmonary artery (PA) hypertension was studied in a chronic hypoxic-pulmonary hypertension model (7–21 days) in the rat. Increase in PA pressure (measured by catheterism), cardiac right ventricle hypertrophy (determined by echocardiography), and PA remodeling (evaluated by histology) were almost entirely prevented after oral dehydroepiandrosterone (DHEA) administration (30 mg/kg every alternate day). Furthermore, in hypertensive rats, oral administration, or intravascular injection (into the jugular vein) of DHEA rapidly decreased PA hypertension. In PA smooth muscle cells, DHEA reduced the level of intracellular calcium (measured by microspectrofluorimetry). The effect of DHEA appears to involve a large conductance Ca2+-activated potassium channel (BKCa)-dependent stimulatory mechanism, at both function and expression levels (isometric contraction and Western blot), via a redox-dependent pathway. Voltage-gated potassium (Kv) channels also may be involved because the antagonist 4-amino-pyridine blocked part of the DHEA effect. The possible pathophysiological and therapeutic significance of the results is discussed.
Sound-by-sound thalamic stimulation modulates midbrain auditory excitability and relative binaural sensitivity in frogs

Descending circuitry can modulate auditory processing, biasing sensitivity to particular stimulus parameters and locations. Using awake in vivo single unit recordings, this study tested whether electrical stimulation of the thalamus modulates auditory excitability and relative binaural sensitivity in neurons of the amphibian midbrain. In addition, by using electrical stimuli that were either longer than the acoustic stimuli (i.e., seconds) or presented on a sound-by-sound basis (ms), experiments addressed whether the form of modulation depended on the temporal structure of the electrical stimulus. Following long duration electrical stimulation (3–10 s of 20 Hz square pulses), excitability (spikes/acoustic stimulus) to free-field noise stimuli decreased by 32%, but returned over 600 s. In contrast, sound-by-sound electrical stimulation using a single 2 ms duration electrical pulse 25 ms before each noise stimulus caused faster and varied forms of modulation: modulation lasted <2 s and, in different cells, excitability either decreased, increased or shifted in latency. Within cells, the modulatory effect of sound-by-sound electrical stimulation varied between different acoustic stimuli, including for different male calls, suggesting modulation is specific to certain stimulus attributes. For binaural units, modulation depended on the ear of input, as sound-by-sound electrical stimulation preceding dichotic acoustic stimulation caused asymmetric modulatory effects: sensitivity shifted for sounds at only one ear, or by different relative amounts for both ears. This caused a change in the relative difference in binaural sensitivity. Thus, sound-by-sound electrical stimulation revealed fast and ear-specific (i.e., lateralized) auditory modulation that is potentially suited to shifts in auditory attention during sound segregation in the auditory scene.
The ribosome assembly factor Nep1 responsible for Bowen–Conradi syndrome is a pseudouridine-N1-specific methyltransferase

Nep1 (Emg1) is a highly conserved nucleolar protein with an essential function in ribosome biogenesis. A mutation in the human Nep1 homolog causes Bowen–Conradi syndrome—a severe developmental disorder. Structures of Nep1 revealed a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases suggesting that Nep1 acts as a methyltransferase in ribosome biogenesis. The target for this putative methyltransferase activity has not been identified yet. We characterized the RNA-binding specificity of Methanocaldococcus jannaschii Nep1 by fluorescence- and NMR-spectroscopy as well as by yeast three-hybrid screening. Nep1 binds with high affinity to short RNA oligonucleotides corresponding to nt 910–921 of M. jannaschii 16S rRNA through a highly conserved basic surface cleft along the dimer interface. Nep1 only methylates RNAs containing a pseudouridine at a position corresponding to a previously identified hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Ψ) in eukaryotic 18S rRNAs. Analysis of the methylated nucleoside by MALDI-mass spectrometry, HPLC and NMR shows that the methyl group is transferred to the N1 of the pseudouridine. Thus, Nep1 is the first identified example of an N1-specific pseudouridine methyltransferase. This enzymatic activity is also conserved in human Nep1 suggesting that Nep1 is the methyltransferase in the biosynthesis of m1acp3-Ψ in eukaryotic 18S rRNAs.
Under Consideration for Publication in Theory and Practice of Logic Programming Products of Weighted Logic Programs *

Weighted logic programming, a generalization of bottom-up logic programming, is a well-suited framework for specifying dynamic programming algorithms. In this setting, proofs correspond to the algorithm's output space, such as a path through a graph or a grammatical derivation, and are given a real-valued score (often interpreted as a probability) that depends on the real weights of the base axioms used in the proof. The desired output is a function over all possible proofs, such as a sum of scores or an optimal score. We describe the PRODUCT transformation, which can merge two weighted logic programs into a new one. The resulting program optimizes a product of proof scores from the original programs, constituting a scoring function known in machine learning as a " product of experts. " Through the addition of intuitive constraining side conditions, we show that several important dynamic programming algorithms can be derived by applying PRODUCT to weighted logic programs corresponding to simpler weighted logic programs. In addition, we show how the computation of Kullback-Leibler divergence, an information-theoretic measure, can be interpreted using PRODUCT.
Monotone circuits for matching require linear depth

We prove that monotone circuits computing the perfect matching function on n-vertex graphs require Ω(n) depth. This implies an exponential gap between the depth of monotone and nonmonotone circuits. CR categories: F.1. 1, Models of Computation, Unbounded Action Devices. ∗This research was partially supported by the American-Israeli Binational Science Foundation grant number 87-00082
Plasma Lipids and Vascular Dysfunction in Preeclampsia

The dominating hypothesis of the preeclampsia syndrome (PES) is that placentally derived factors are released to the maternal circulation. These factors are believed to alter endothelial properties resulting in disturbed vasomotor function, increased endothelial permeability, and activation of thrombogenic factors. However, the impact of placentally derived factors on the endothelial cells is influenced by another major variable: the "sensitivity" of the maternal endothelium to the placental factors. Several maternal factors may play a role in determining this sensitivity. They include chronic hypertension, diabetes, and hyperlipidemia. In this article we discuss the possible role of hyperlipidemia (especially high free fatty acids and hypertriglyceridemia) in the pathogenesis of preeclampsia, viewed from this perspective. Pregnancy in general, preeclamptic pregnancy in particular, is associated with a marked hyperlipidemia. We suggest a parallel to atherosclerotic diseases, wherein hyperlipidemia induces endothelial dysfunction, probably by promoting oxidative stress in the arterial wall. The hyperlipidemia of pregnancy may have a similar effect on the endothelial cells. When placentally derived endothelial disturbing factors, like lipid peroxides and trophoblastic components, are released into the maternal circulation, their effects on the endothelium may be enhanced because of hyperlipidemia-mediated activation or "sensitization" of the endothelial cells. Alternatively, placentally derived factors like peroxides may combine with lipoproteins, forming complexes that are more disturbing to cells than the placental factors or lipoproteins are individually. We also discuss the possible role of maternal hyperlipidemia in aggravating placental insufficiency caused by poorly transformed spiral arteries. The hemodynamic flow pattern may be markedly different in completely and incompletely transformed spiral arteries. By analogy to the fundamental role of hemodynamic factors in development of atherosclerosis, we pose the hypothesis that abnormally transformed spiral arteries have an "atherogenic" blood flow pattern that promotes lipid deposition and "acute atherosis".
Self-Monitoring of Blood Glucose: The Use of the First or the Second Drop of Blood

OBJECTIVE There is no general agreement regarding the use of the first or second drop of blood for glucose monitoring. This study investigated whether capillary glucose concentrations, as measured in the first and second drops of blood, differed ≥10% compared with a control glucose concentration in different situations. RESEARCH DESIGN AND METHODS Capillary glucose concentrations were measured in two consecutive drops of blood in the following circumstances in 123 patients with diabetes: without washing hands, after exposing the hands to fruit, after washing the fruit-exposed hands, and during application of different amounts of external pressure around the finger. The results were compared with control measurements. RESULTS Not washing hands led to a difference in glucose concentration of ≥10% in the first and in the second drops of blood in 11% and 4% of the participants, respectively. In fruit-exposed fingers, these differences were found in 88% and 11% of the participants, respectively. Different external pressures led to ≥10% differences in glucose concentrations in 5–13% of the participants. CONCLUSIONS We recommend washing the hands with soap and water, drying them, and using the first drop of blood for self-monitoring of blood glucose. If washing hands is not possible, and they are not visibly soiled or exposed to a sugar-containing product, it is acceptable to use the second drop of blood after wiping away the first drop. External pressure may lead to unreliable readings.
Recessive Loci Pps-1 and OM Differentially Regulate PISTILLATA-1 and APETALA3-1 Expression for Sepal and Petal Development in Papaver somniferum

The involvement of PISTILLATA (PI) and APETALA (AP) transcription factors in the development of floral organs has previously been elucidated but little is known about their upstream regulation. In this investigation, two novel mutants generated in Papaver somniferum were analyzed - one with partially petaloid sepals and another having sepaloid petals. Progeny from reciprocal crosses of respective mutant parent genotypes showed a good fit to the monogenic Mendelian inheritance model, indicating that the mutant traits are likely controlled by the single, recessive nuclear genes named “Pps-1” and “OM” in the partially petaloid sepal and sepaloid petal phenotypes, respectively. Both paralogs of PISTILLATA (PapsPI-1 and PapsPI-3) were obtained from the sepals and petals of P. somniferum. Ectopic expression of PapsPI-1 in tobacco resulted in a partially petaloid sepal phenotype at a low frequency. Upregulation of PapsPI-1 and PapsAP3-1 in the petal and the petal part of partially petaloid sepal mutant and down-regulation of the same in sepaloid petal mutant indicates a differential pattern of regulation for flowering-related genes in various whorls. Similarly, it was found that the recessive mutation OM in sepaloid petal mutant downregulates PapsPI-1 and PapsAP3-1 transcripts. The recessive nature of the mutations was confirmed by the segregation ratios obtained in this analysis.
Batch derivation of piezoresistive coefficient tensor by matrix algebra

To commemorate the important discovery of the piezoresistance effect of germanium and silicon by C S Smith half a century ago, we present a new method of deriving the piezoresistive (PR) coefficient tensor for diamond structure material using matrix algebra. Using this method, all the components of the PR coefficient tensor (of the fourth rank) in an arbitrary Cartesian coordinate system can be obtained in a batch and the relation between the components is clearly shown.
Speech signal analysis for the estimation of heart rates under different emotional states

A non-invasive method for the monitoring of heart activity can help to reduce the deaths caused by heart disorders such as stroke, arrhythmia and heart attack. Human voice can be considered as a biometric data that can be used for estimation of heart rate. In this paper, we propose a method for estimating the heart rate from human speech dynamically using voice signal analysis and by development of a empirical linear predictor model. The correlation between voice signal and heart rate are established by classifiers and prediction of the heart rates with or without emotions are done using linear models. The prediction accuracy was tested using the data collected from 15 subjects, it is about 4050 samples of speech signals and corresponding electrocardiogram samples. The proposed approach can use for early non-invasive detection of heart rate changes that can be correlated to emotional state of the individual and also can be used as tool for diagnosis of heart conditions in real-time situations.
Effect of the integrator settling behavior on SC ΣΔ modulator characteristics: A theoretical study

The effect of the integrator settling behavior on the performances of switched-capacitor (SC) sigma-delta modulator (SigmaDeltaM) is investigated in this paper. The analysis is performed by means of behavioral simulations exploiting a new generic integrator settling model introduced to describe common high-order time responses characterizing real integrator implementations. The results of the performed investigation show that high-order poles and zeros in the integrator frequency response tend to affect even significantly the overall modulator characteristics. As a consequence when high-order integrator dynamics occur, early-design guidelines obtained from behavioral simulations based on classical first-order integrator settling descriptions can turn out to be quite rough in order to carry out a careful transistor-level modulator design. A more careful behavioral analysis based on the proposed strategy proves to be very useful to identify well-defined design specifications for the integrator in order to achieve the desired SigmaDeltaM performances avoiding costly transistor-level parameters tuning.
Data Providing Services Clustering and Management for Facilitating Service Discovery and Replacement

In service-oriented computing, a user usually needs to locate a desired service for: (i) fulfilling her requirements or (ii) replacing a service, which disappears or is unavailable for some reasons, to perform an interaction. With the increasing number of services available within an enterprise and over the Internet, locating a service online may not be appropriate from the performance perspective, especially in large Internet-based service repositories. Instead, services usually need to be clustered according to their similarity. Thereafter, services in one or several clusters are necessary to be examined online during dynamic service discovery. In this paper, we propose to cluster data providing (DP) services using a refined fuzzy C-means algorithm. We consider the composite relation between DP service elements (i.e., input, output, and semantic relation between them) when representing DP services in terms of vectors. A DP service vector is assigned to one or multiple clusters with certain degrees. In addition, we introduce some operations for managing service clusters, when new services emerge or existing services disappear or become unavailable. When grouping similar services into one cluster, while partitioning different services into different clusters, the capability of service search engine is improved significantly. We have prototyped our approach and the source code is freely available on the web. We have evaluated our clustering approach in different settings and the results are very promising.