Miracle-dz/UniFAR-FTUs huggingface dataset:
Topological analysis of metabolic networks based on Petri net theory

Petri net concepts provide additional tools for the modelling of metabolic networks. Here, the similarities between the counterparts in traditional biochemical modelling and Petri net theory are discussed. For example the stoichiometry matrix of a metabolic network corresponds to the incidence matrix of the Petri net. The flux modes and conservation relations have the T-invariants, respectively, P-invariants as counterparts. We reveal the biological meaning of some notions specific to the Petri net framework (traps, siphons, deadlocks, liveness). We focus on the topological analysis rather than on the analysis of the dynamic behaviour. The treatment of external metabolites is discussed. Some simple theoretical examples are presented for illustration. Also the Petri nets corresponding to some biochemical networks are built to support our results. For example, the role of triose phosphate isomerase (TPI) in Trypanosoma brucei metabolism is evaluated by detecting siphons and traps. All Petri net properties treated in this contribution are exemplified on a system extracted from nucleotide metabolism.
Fabrication and Performance of ZnO Doped Tantalum Oxide Multilayer Composite Coatings on Ti6Al4V for Orthopedic Application

Ti6Al4V titanium alloy has been widely used as medical implant material in orthopedic surgery, and one of the obstacles preventing it from wide use is toxic metal ions release and bacterial implant infection. In this paper, in order to improve corrosion resistance and antibacterial performance of Ti6Al4V titanium alloy, ZnO doped tantalum oxide (TaxOy) multilayer composite coating ZnO-TaxOy/TaxOy/TaxOy-TiO2/TiO2/Ti (ZnO-TaxOy) was deposited by magnetron sputtering at room temperature. As a comparison, monolayer TaxOy coating was prepared on the surface of Ti6Al4V alloy. The morphology and phase composition of the coatings were investigated by field emission scanning electron microscopy (FE-SEM) and X-ray diffraction (XRD), the elemental chemical states of coating surfaces were investigated by X-ray photoelectron spectroscope (XPS). The adhesion strength and corrosion resistance of the coatings were examined by micro-scratch tester and electrochemical workstations, respectively. The results show that the adhesion strength of multilayer ZnO-TaxOy coating is 16.37 times higher than that of single-layer TaxOy coating. The ZnO-TaxOy composite coating has higher corrosion potential and lower corrosion current density than that of TaxOy coating, showing better corrosion inhibition. Furthermore, antibacterial test revealed that multilayer ZnO-TaxOy coating has a much better antibacterial performance by contrast.
The Emerging Role of Adiponectin in Female Malignancies

Obesity, characterized by excess body weight, is now accepted as a hazardous health condition and an oncogenic factor. In different epidemiological studies obesity has been described as a risk factor in several malignancies. Some biological mechanisms that orchestrate obesity–cancer interaction have been discovered, although others are still not completely understood. The unbalanced secretion of biomolecules, called “adipokines”, released by adipocytes strongly influences obesity-related cancer development. Among these adipokines, adiponectin exerts a critical role. Physiologically adiponectin governs glucose levels and lipid metabolism and is fundamental in the reproductive system. Low adiponectin circulating levels have been found in obese patients, in which its protective effects were lost. In this review, we summarize the epidemiological, in vivo and in vitro data in order to highlight how adiponectin may affect obesity-associated female cancers.
IIV-6 Inhibits NF-κB Responses in Drosophila

The host immune response and virus-encoded immune evasion proteins pose constant, mutual selective pressure on each other. Virally encoded immune evasion proteins also indicate which host pathways must be inhibited to allow for viral replication. Here, we show that IIV-6 is capable of inhibiting the two Drosophila NF-κB signaling pathways, Imd and Toll. Antimicrobial peptide (AMP) gene induction downstream of either pathway is suppressed when cells infected with IIV-6 are also stimulated with Toll or Imd ligands. We find that cleavage of both Imd and Relish, as well as Relish nuclear translocation, three key points in Imd signal transduction, occur in IIV-6 infected cells, indicating that the mechanism of viral inhibition is farther downstream, at the level of Relish promoter binding or transcriptional activation. Additionally, flies co-infected with both IIV-6 and the Gram-negative bacterium, Erwinia carotovora carotovora, succumb to infection more rapidly than flies singly infected with either the virus or the bacterium. These findings demonstrate how pre-existing infections can have a dramatic and negative effect on secondary infections, and establish a Drosophila model to study confection susceptibility.
The Effect of Time Synchronization Error in LAN-Based Digital Substation

In this paper, the effect of time synchronization error on protection algorithms are studied for the usage of the LAN-based collaborative protection. In order to derive the effect of time synchronization, this paper proposes a substation model which is constructed with IEEE 1588 Precision Time Protocol (PTP) supported intelligent electronic devices. The proposed model is used as an example of a target platform to study the effect of time synchronization error with two typical substation protection algorithms, i.e., current differential-based substation protection and distance protection algorithms. From the analyzed and the simulated results, it was well observed that time synchronization error is a significant error-causing factor for both protection algorithms, resulting in erroneous detection of faults and erroneous estimation of fault distances, respectively. The results of research performed in this paper are expected to provide a good guide for constructing the future LAN-based digital power substation with precise time synchronization.
A novel rules optimizer with feature selection using rough-entropy-coverage partitioning based reduci

This paper presents a novel approach for optimizing the number of decision rules and select important features based on reduct. We compute the reduct using entropy value of conditional attribute then eradicates the redundant dataset, noisy features and uncertainty of dataset using coverage factor and generate optimized number of rules. Experimental results show that this approach achieves high data reduction with important feature selection as well as optimize the number of rules compared to earlier works.
A Neurodynamical Model of Brightness Induction in V1

Brightness induction is the modulation of the perceived intensity of an area by the luminance of surrounding areas. Recent neurophysiological evidence suggests that brightness information might be explicitly represented in V1, in contrast to the more common assumption that the striate cortex is an area mostly responsive to sensory information. Here we investigate possible neural mechanisms that offer a plausible explanation for such phenomenon. To this end, a neurodynamical model which is based on neurophysiological evidence and focuses on the part of V1 responsible for contextual influences is presented. The proposed computational model successfully accounts for well known psychophysical effects for static contexts and also for brightness induction in dynamic contexts defined by modulating the luminance of surrounding areas. This work suggests that intra-cortical interactions in V1 could, at least partially, explain brightness induction effects and reveals how a common general architecture may account for several different fundamental processes, such as visual saliency and brightness induction, which emerge early in the visual processing pathway.
Noninvasive cuffless blood pressure estimation using pulse transit time, Womersley number, and photoplethysmogram intensity ratio

Objective: Continuous cuffless blood pressure (BP) monitoring research has emerged as blood pressure is one of the dynamic parameters which reflects cardiac arrhythmias and rheological disorders without the drawbacks of current techniques. All the existing measurement techniques are cuff-based with drawbacks such as being discontinuous in nature, being uncomfortable for the patient, etc. Therefore, the goal is to develop an algorithm to estimate BP accurately using the pulse transit time (PTT), photoplethysmogram intensity ratio (PIR) and Womersley number (α) in a noninvasive way. Approach: The PTT technique holds the promise of real-time, cuffless, continuous BP monitoring in clinical settings. However, the non-Newtonian fluid nature of blood is considered insignificant in the conventional PTT model-based BP modeling. In the proposed work, α, representing viscous effects, along with PTT and PIR, is included in the algorithm since it is also one of the parameters that affects the BP. Main results: The proposed algorithm is evaluated with 42 healthy and 39 diseased subjects and compared with the other conventional techniques to evaluate the importance of viscous effects in BP, using performance metrics like mean ± standard deviation, and 95% confidence interval for bias and limits of agreement; a better estimate is achieved with the proposed algorithm. Significance: The proposed algorithm reflects the influences of vasomotor tone and baroflex as well, which makes it suitable for the assessment of BP in both healthy and diseased subjects, with improved accuracy than the current measurement techniques.
Toolchain for Programming, Simulating and Studying the XMT Many-Core Architecture

The Explicit Multi-Threading (XMT) is a general-purpose many-core computing platform, with the vision of a 1000-core chip that is easy to program but does not compromise on performance. This paper presents a publicly available tool chain for XMT, complete with a highly configurable cycle-accurate simulator and an optimizing compiler. The XMT tool chain has matured and has been validated to a point where its description merits publication. In particular, research and experimentation enabled by the tool chain played a central role in supporting the ease-of-programming and performance aspects of the XMT architecture. The compiler and the simulator are also important milestones for an efficient programmer's workflow from PRAM algorithms to programs that run on the shared memory XMT hardware. This workflow is a key component in accomplishing the dual goal of ease-of-programming and performance. The applicability of our tool chain extends beyond specific XMT choices. It can be used to explore the much greater design space of shared memory many-cores by system researchers or by programmers. As the tool chain can practically run on any computer, it provides a supportive environment for teaching parallel algorithmic thinking with a programming component. Unobstructed by techniques such as decomposition-first and programming for locality, this environment may be useful in deferring the teaching of these techniques, when desired, to more advanced or platform-specific courses.
Metabolites Associated with Vigor to Frailty Among Community-Dwelling Older Black Men

Black versus white older Americans are more likely to experience frailty, a condition associated with adverse health outcomes. To reduce racial disparities in health, a complete understanding of the pathophysiology of frailty is needed. Metabolomics may further our understanding by characterizing differences in the body during a vigorous versus frail state. We sought to identify metabolites and biological pathways associated with vigor to frailty among 287 black men ages 70–81 from the Health, Aging, and Body Composition study. Using liquid chromatography-mass spectrometry, 350 metabolites were measured in overnight-fasting plasma. The Scale of Aging Vigor in Epidemiology (SAVE) measured vigor to frailty based on weight change, strength, energy, gait speed, and physical activity. Thirty-seven metabolites correlated with SAVE scores (p < 0.05), while adjusting for age and site. Fourteen metabolites remained significant after multiple comparisons adjustment (false discovery rate < 0.30). Lower values of tryptophan, methionine, tyrosine, asparagine, C14:0 sphingomyelin, and 1-methylnicotinamide, and higher values of glucoronate, N-carbamoyl-beta-alanine, isocitrate, creatinine, C4-OH carnitine, cystathionine, hydroxyphenylacetate, and putrescine were associated with frailer SAVE scores. Pathway analyses identified nitrogen metabolism, aminoacyl-tRNA biosynthesis, and the citric acid cycle. Future studies need to confirm these SAVE-associated metabolites and pathways that may indicate novel mechanisms involved in the frailty syndrome.
Design of a microphone array for near-field conferencing applications

Microphone arrays are becoming increasingly popular for conferencing applications and near-field speech recording. In this work, a 16-element cylindrical microphone array is designed for beamforming toward a nearby speaker, while reducing the influence of competing talkers. A two-stage approach is used to obtain the desired array directivity pattern, optimizing both microphone locations and filter weights. The positions of the microphones are optimized by using a hybrid optimization technique, taking into account the influence of the nearby acoustic environment (array shape and conferencing desk). FIR filter coefficients for each microphone are derived from a regularized least-squares (LSQR) solution, combined with null-steering. An implementation of the array is made with digital MEMS microphones and the performance of the design is evaluated experimentally and compared with a classically used goose-neck microphone.
Data-Driven UPLC-Orbitrap MS Analysis in Astrochemistry

Meteorites have been found to be rich and highly diverse in organic compounds. Next to previous direct infusion high resolution mass spectrometry experiments (DI-HR-MS), we present here data-driven strategies to evaluate UPLC-Orbitrap MS analyses. This allows a comprehensive mining of structural isomers extending the level of information on the molecular diversity in astrochemical materials. As a proof-of-concept study, Murchison and Allende meteorites were analyzed. Both, global organic fingerprint and specific isomer analyses are discussed. Up to 31 different isomers per molecular composition are present in Murchison suggesting the presence of ≈440,000 different compounds detected therein. By means of this time-resolving high resolution mass spectrometric method, we go one step further toward the characterization of chemical structures within complex extraterrestrial mixtures, enabling a better understanding of organic chemical evolution, from interstellar ices toward small bodies in the Solar System.
On Metrics for Error Correction in Network Coding

The problem of error correction in both coherent and noncoherent network coding is considered under an adversarial model. For coherent network coding, where knowledge of the network topology and network code is assumed at the source and destination nodes, the error correction capability of an (outer) code is succinctly described by the rank metric; as a consequence, it is shown that universal network error correcting codes achieving the Singleton bound can be easily constructed and efficiently decoded. For noncoherent network coding, where knowledge of the network topology and network code is not assumed, the error correction capability of a (subspace) code is given exactly by a new metric, called the injection metric, which is closely related to, but different than, the subspace metric of KOumltter and Kschischang. In particular, in the case of a non-constant-dimension code, the decoder associated with the injection metric is shown to correct more errors then a minimum-subspace-distance decoder. All of these results are based on a general approach to adversarial error correction, which could be useful for other adversarial channels beyond network coding.
The role of Raf-1 in the regulation of extracellular signal-regulated kinase 2 by the T cell antigen receptor

Triggering of the T cell antigen receptor (TCR) complex activates the serine/threonine kinase Raf-1 whose function is necessary for TCR induction of the interleukin 2 gene. Raf-1 has been identified as a candidate mitogen-activated protein (MAP) kinase kinase kinase (MKKK) and thus has the potential to couple the TCR to the activation of the MAP kinases such as ERK2. In the present study, the role of Raf-1 in ERK2 regulation of ERK2 in T cells has been explored. A constitutively active Raf-1 kinase, v-raf, or a dominant inhibitory Raf-1 mutant were expressed transiently from the pEF BOS vector in Jurkat cells and the effects of these Raf-1 mutants on a coexpressed ERK2 reporter was assessed. The action of the constitutively active Raf-1 was to stimulate the ERK2 kinase, whereas the dominant negative version of Raf- 1 inhibited the ERK2 activation induced by triggering of the TCR. These data indicate a role for Raf-1 in the regulation of ERK2 in T cells.
A Multi-Cast Communication Scheme Using Weak Electrical Current for Intra-Body Networks

Implantable medical devices have paved the way for realizing intra-body networks (IBNs) that are capable of communicating information from within the body. Traditional forms of RF-based based communication face drawbacks in terms of high absorption within tissues and can potentially result in security and privacy issues, owing to the omnidirectional radiation. Instead, we propose the use of weak electrical current as a means of intra-body communication for implants within the human body and to a relay and gateway node located on the surface of the skin that facilitates remote patient monitoring. The main contributions of this paper are: (i) signal reflection and refraction analysis of electromagnetic waves through human tissue boundaries, and (ii) the design of a combined multi-hop and multi-cast communication scheme for communication between implants. Our results reveal that a multi-cast communication scheme can be achieved for IBNs with the appropriate selection of transmission parameters.
Non-Surgical Management of Teeth with Wide Open Apices and Large Periapical Lesions: A Conservative Reality.

CASE-1 A 26-year-old male visited the Department of Conservative Dentistry and Endodontics after referral from Oral Surgery for opinion regarding maxillary right lateral incisor. Diagnosis established in Oral Surgery was of an infected cyst in relation to tooth #12 and the treatment suggested was enucleation and curettage. Patient’s dental history revealed anterior trauma at 10 years of age and his chief complaint was found to be recurrent swelling and pus discharge in relation to maxillary right anteriors for the past 1-2 years. Clinical examination revealed a discolored tooth #12 [Table/ Fig-1a] and sinus opening within an erythematous area measuring 0.5cm on the palate [Table/Fig-1b]. On palpation, the palatal region had a paper like soft consistency. Thermal and electrical pulp testing elicited no response in tooth #12 but positive responses in both tooth #11 and tooth #13. Pre-operative radiograph revealed a large radiolucency approximately 15mmX15mm, involving tooth #12, and extending up till teeth #11 and #13 [Table/Fig-1c]. Tooth #12 showed large canal space, open root apex, and ragged irregular margins at the apex suggesting inflammatory external resorption. We decided to treat tooth #12 conservatively and include surgical intervention, only if deemed necessary.
DPYD and Fluorouracil-Based Chemotherapy: Mini Review and Case Report

5-Fluorouracil remains a foundational component of chemotherapy for solid tumour malignancies. While considered a generally safe and effective chemotherapeutic, 5-fluorouracil has demonstrated severe adverse event rates of up to 30%. Understanding the pharmacokinetics of 5-fluorouracil can improve the precision medicine approaches to this therapy. A single enzyme, dihydropyrimidine dehydrogenase (DPD), mediates 80% of 5-fluorouracil elimination, through hepatic metabolism. Importantly, it has been known for over 30-years that adverse events during 5-fluorouracil therapy are linked to high systemic exposure, and to those patients who exhibit DPD deficiency. To date, pre-treatment screening for DPD deficiency in patients with planned 5-fluorouracil-based therapy is not a standard of care. Here we provide a focused review of 5-fluorouracil metabolism, and the efforts to improve predictive dosing through screening for DPD deficiency. We also outline the history of key discoveries relating to DPD deficiency and include relevant information on the potential benefit of therapeutic drug monitoring of 5-fluorouracil. Finally, we present a brief case report that highlights a limitation of pharmacogenetics, where we carried out therapeutic drug monitoring of 5-fluorouracil in an orthotopic liver transplant recipient. This case supports the development of robust multimodality precision medicine services, capable of accommodating complex clinical dilemmas.
Analysis of order statistic filters applied to ultrasonic flaw detection using split-spectrum processing

Split-spectrum processing of broadband ultrasonic signals coupled with order statistic filtering has proven to be effective in improving the flaw-to-clutter ratio of backscattered signals. It is shown that an optimal rank can be obtained with a prior knowledge of flaw-to-clutter ratio and the underlying distributions. The order statistic filter performs well where the flaw and clutter echoes have good statistical separation in a given quantile region representing a particular rank (e.g. minimum, median, maximum). Order statistic filters are analyzed for the situation in which the observations do not contain equivalent statistical information. Experimental and simulated results are presented to show how effectively the order statistic filter can utilize information contained in different frequency bands to improve flaw detection. <<ETX>>
Small Ribosomal Protein Subunit S7 Suppresses Ovarian Tumorigenesis through Regulation of the PI3K/AKT and MAPK Pathways

Small ribosomal protein subunit S7 (RPS7) has been reported to be associated with various malignancies, but the role of RPS7 in ovarian cancer remains unclear. In this study, we found that silencing of RPS7 by a specific shRNA promoted ovarian cancer cell proliferation, accelerated cell cycle progression, and slightly reduced cell apoptosis and response to cisplatin treatment. Knockdown of RPS7 resulted in increased expression of P85α, P110α, and AKT2. Although the basal levels of ERK1/2, MEK1/2, and P38 were inconsistently altered in ovarian cancer cells, the phosphorylated forms of MEK1/2 (Ser217/221), ERK1/2 (Thr202/Tyr204), JNK1/2 (Thr183/Tyr185), and P38 (Thr180/Tyr182) were consistently reduced after RPS7 was silenced. Both the in vitro anchorage-independent colony formation and in vivo animal tumor formation capability of cells were enhanced after RPS7 was depleted. We also showed that silencing of RPS7 enhanced ovarian cancer cell migration and invasion. In sum, our results suggest that RPS7 suppresses ovarian tumorigenesis and metastasis through PI3K/AKT and MAPK signal pathways. Thus, RPS7 may be used as a potential marker for diagnosis and treatment of ovarian cancer.