Miracle-dz/UniFAR-FTUs huggingface dataset:
COMPUTATIONAL TOOLS FOR PREDICTION OF NUCLEAR RECEPTOR MEDIATED EFFECTS

Endocrine disrupting chemicals pose a significant threat to human health, society and the environment. Many of these chemicals elicit their toxicological effects through nuclear hormone receptors, like the estrogen receptor. Computational tools for predicting receptor mediated effects have been envisaged for their potential to be used for prioritization of chemicals for toxicological evaluation to reduce the amount of costly experimental testing and enable early alerts for newly designed compounds. In silico tools like knowledge-based expert systems and (quantitative) structure-activity relationship models have been created or upgraded on the yearly basis and also widely advertized to be used as primary screening technique in studies related to receptor mediated effects. The aim of this study is to provide an overview of the present most popular commercial and non-commercial in silico tools applicable for research studies in the field of receptor mediated effects.
REALIZED LAPLACE TRANSFORMS FOR PURE-JUMP

We consider specification and inference for the stochastic scale of discretely-observed pure-jump semimartingales with locally stable Lévy densities in the setting where both the time span of the data set increases and the mesh of the observation grid decreases. The estimation is based on constructing nonparametric estimate for the empirical Laplace transform of the stochastic scale over a given interval of time by aggregating high-frequency increments of the observed process on that time interval into a statistic we call realized Laplace transform. The realized Laplace transform depends on the activity of the driving pure-jump martingale and we consider both cases when the latter is known or has to be inferred from the data.
Potential biomarkers associated with diabetic glomerulopathy through proteomics

Abstract Diabetic nephropathy (DN) is characterized by the development of progressive glomerulosclerotic lesions gradually leading to an increasing loss of functioning kidney parenchyma. Relatively little proteomic research of isolated glomeruli of experimental animal models has been done so far. Isolated glomerular proteomics is an innovative tool that potentially detects simultaneous expressions of glomeruli in diabetic pathological contexts. We compared the isolated glomerular profiles of rats with and without diabetes. The proteins in the aliquots of glomeruli were subjected to two-dimensional gel electrophoresis. The protein spots were matched and quantified using an imaging analysis system. The peptide mass fingerprints were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and a bioinformation search. We found that diabetes increased collagen type I and collagen type IV levels in diabetic glomeruli when compared to normal control group using Dynabeads. We found that rats with diabetes had significantly higher abundance of the Protein disulfide isomerase associated 3, Aspartoacylase-3,3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase, Lactamase beta 2 and Agmat protein. However, diabetic glomeruli in rats had significantly lower levels of the Regucalcin, rCG52140, Aldo-keto reductase family 1, Peroxiredoxin 1, and l-arginine: glycine amidinotransferase. These proteins of interest were reported to modulate disturbances in the homeostasis of endoplasmic reticulum stress, disturbance of inflammatory and fibrinogenic activities, impairing endothelial function, and dysregulation in the antioxidation capacity/oxidative stress in several tissue types under pathological contexts. Taken together, our high-throughput isolated glomerular proteomic findings indicated that multiple pathological reactions presumably occurred in DN.
The streaming capacity of sparsely-connected P2P systems with distributed control

Peer-to-Peer (P2P) streaming technologies can take advantage of the upload capacity of clients, and hence can scale to large content distribution networks with lower cost. A fundamental question for P2P streaming systems is the maximum streaming rate that all users can sustain. Prior works have studied the optimal streaming rate for a complete network, where every peer is assumed to communicate with all other peers. This is however an impractical assumption in real systems. In this paper, we are interested in the achievable streaming rate when each peer can only connect to a small number of neighbors. We show that even with a random peer selection algorithm and uniform rate allocation, as long as each peer maintains Ω(logN) downstream neighbors, where N is the total number of peers in the system, the system can asymptotically achieve a streaming rate that is close to the optimal streaming rate of a complete network.We then extend our analysis to multi-channel P2P networks, and we study the scenario where “helpers” from channels with excessive upload capacity can help peers in channels with insufficient upload capacity. We show that by letting each peer select Ω(logN) neighbors randomly from either the peers in the same channel or from the helpers, we can achieve a close-to-optimal streaming capacity region. Simulation results are provided to verify our analysis.
Type 1 serrated polyposis represents a predominantly female disease with a high prevalence of dysplastic serrated adenomas, without germline mutation in MUTYH, APC, and PTEN genes

Aim The aim of this article is to clarify the epidemiologic, clinical, endoscopic, biological and genetic characteristics of type 1 serrated polyposis patients. Patients and methods Consecutive patients responding to the WHO definition of type 1 serrated polyposis in one reference center for polyposis patients accepted genetic counseling. Detailed data on previous endoscopies, histology, and life habits were recorded, after informed consent, germline analysis of MUTYH, APC, and PTEN germline mutations. Molecular biology was tested on available fixed tissue from different lesion types. Results We included 29 patients (mean age 53.5 years, 21 women (72.4%)), four with a personal history of colorectal cancer (CRC), with a mean of 11.6 SSAs, with associated hyperplastic polyps in 93.1% and adenomas in 82.8%. SSAs showed no dysplasia in 46.9% of lesions (three of 29 patients), LGD in 51.9% (22/29 patients), and HGD in 1.2% (four of 29 patients). Dysplasia was more frequent in proximal SSAs and in women. Colectomy 15 patients (51.7%), upper digestive neoplasms: eight patients (27.5%); smokers: 24 patients (82.8%); family history of CRC: 16 patients (55.2%). Biology: MSI-H phenotype in one SSA, V600E BRAF mutation in 95% of SSAs; MGMT hypermethylation in three of 17 SSAs. No germline mutation was detected in MYH, APC or PTEN genes. Conclusion Type 1 serrated polyposis corresponds to a majority of women, with a high prevalence of smokers, a high prevalence of dysplastic serrated adenomas, particularly in females, without identified germline mutation in targeted predisposing genes.
A Novel, Nonsurgical Method for the Treatment of Tibiotarsal Rotation in Houbara Bustard (Chlamydotis macqueenii) Chicks

ABSTRACT Rotational limb deformity due to tibiotarsal rotation can affect captive-bred houbara bustard chicks (Chlamydotis macqueenii) from an early age. If not completely corrected, the affected birds can neither be released into the wild nor used in captive-breeding projects. A nonsurgical orthopedic method was developed to correct this deformity before growth is completed. The method consists of hobbling digits III and the distal part of the tarsometatarsus of each leg with a self-adhesive conforming bandage that keeps digits III parallel with enough freedom of movement to allow walking. The tibiotarsal bones are left free. This treatment was successful when it was implemented for 20 days on 10-day-old houbara bustard chicks presenting with 60° to 90° unilateral tibiotarsal rotation. Implementing the same corrective method at an older age was not successful. This cheap, accessible, and noninvasive technique may be applicable to other avian species.
Realization of L2 Cache Defect Tolerance Using Multi-bit ECC

This paper presents a design solution that enables the use of powerful multi-bit error-correcting code (ECC) to realize L2 cache defect tolerance at minimal latency and silicon area cost. This work is motivated by the observation that the continuous CMOS Technology scaling may result in an increasing level defect density and make conventional cache memory defect tolerance strategies inadequate. The basic idea is to complement conventional L2 cache core with two separate fully associative caches, one stores multi-bit ECC check bits for realizing area-efficient selective multi-bit ECC protection and another one stores the most recently decoded multi-bit ECC code word to minimize the impact of explicit multi-bit ECC decoding on L2 cache access latency. Its effectiveness has been demonstrated using SimpleScalar and Cacti tools. At the defect density of 0.5%, this design approach can maintain almost the same instruction per cycle (IPC) performance over a wide spectrum of benchmarks compared with ideal L2 cache without defects, while only incurring less than 2.5% of silicon area overhead.
Secure e-Health System on Passive RFID: Outpatient Clinic and Emergency Care

In recent years, many researches have demonstrated several RFID-based solutions to enhance patient medication safety and avoid human errors. Although RFID-based procedure is more efficient than traditional process, patient's information may be attacked (or stolen) during the data transmission period. This will cause inappropriate medication use and medical errors. In this paper, we introduce a robust RFID-based e-Health system which strengthens the system security and protects the patient's privacy as well. In addition, our e-Health system can provide better efficiency of outpatient clinic procedure and emergency care procedure in hospital environment.
Synthesis of customised hardware from ADA

Tools which permit the synthesis of hardware from high-level specifications are vital for reliable design on an acceptable timescale, and are opening up exciting possibilities in the use of custom coprocessors, rapid prototyping and the design of flexible mixed hardware-software systems. We are exploring a method for the translation of standard ADA code into hardware, by compiling ADA into a standard HDL format which can be synthesised by existing commercial packages. This paper sets out our approach of using an Intermediate Table Format (ITF) for high-level transformations and compilation into synthesisable HDL code. <<ETX>>
5 GHz Monolithic VCO with prescaler using BiCMOS SiGe technology

Bipolar VCO and prescaler for 5GHz low cost wireless applications are presented. These circuits are implemented in a 0.35¿m BiCMOS SiGe process (FT=45GHz). Phase noise value for a 4.82GHz bipolar VCO is ¿12ldBc/Hz at 1MHz frequency offset. Based on CML architecture, a 5GHz 7/8 prescaler is designed and tested. These circuits are the two HF critical buildings blocks in designing wireless communication systems, and in particular, PLL frequency synthesisers.
Effects of food restriction across stages of juvenile and early adult development on body weight, survival and adult life history

Organisms have to allocate limited resources among multiple life‐history traits, which can result in physiological trade‐offs, and variation in environmental conditions experienced during ontogeny can influence reproduction later in life. Food restriction may lead to an adaptive reallocation of the limited resources among traits as a phenotypically plastic adjustment, or it can act as an overall constraint with detrimental effects throughout reproductive life. In this study, we investigated experimentally the effects of food restriction during different stages of the juvenile and early adult development on body weight, survival and reproductive success in females and males of the European earwig Forficula auricularia. Individuals either received limited or unlimited access to food across three different stages of development (fully crossed) allowing us to identify sensitive periods during development and to test both additive and interactive effects of food limitation across stages on development and reproduction. Food restriction during the early and late juvenile stage had additive negative effects on juvenile survival and adult body weight. With regard to reproductive success of females which produce up to two clutches in their lifetime, restriction specifically in the late juvenile stage led to smaller first and second clutch size, lower probability of second clutch production and reduced hatching success in the second clutch. Reproductive success of females was not significantly affected when their male mates experienced food restriction during their development. Our findings in general support the ‘silver‐spoon’ hypothesis in that food restriction during juvenile development poses constraints on development and reproduction throughout life.
Dynamic Persistence of Antibiotic-Stressed Mycobacteria

All About Noise How individual cells behave within a larger “average” population can be surprising. Wakamoto et al. (p. 91) developed a method for investigating the consequences of phenotypic variability in single mycobacterial cells exposed to the pro-drug, isoniazid. Isoniazid needs to be activated by bacterial catalase. In the isoniazid–mycobacterium system, random fluctuations in catalase activity were important for cell survival. Because catalase is essential, it cannot be ablated; however, catalase activity pulsed randomly in the mycobacteria. Thus, a subpopulation of individual cells manage to avoid being killed by the activated antibiotic. Bacterial cells that divide before a pulse of catalase expression survive the application of the antibiotic isoniazid. Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing “persisters. ” Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure.
Sun's big splash [Niagara microprocessor chip]

A new microprocessor chip was developed by Sun Microsystems Inc. that is intended for volume servers that are at the heart of data centers running the information and Web processing for businesses, universities, hospitals, factories, and the like. The new chip, called Niagara for the torrent of data and instructions that flow between the chip and its memory, was designed from the ground up to do away with the impact of latency - the idle time a microprocessor spends for data or instructions to arrive from memory. The goal of the design is to build a microprocessor that works 10 times as efficiently as existing devices for processing applications at half the power consumption of comparable devices. This paper discusses the development of the Niagara chip and its advantages from other microprocessors.
Cytoplasmic expression of survivin is an independent predictor of poor prognosis in patients with salivary gland cancer

Stenner M, Weinell A, Ponert T, Hardt A, Hahn M, Preuss S F, Guntinas‐Lichius O & Klussmann J P (2010) Histopathology 57, 699–706 Cytoplasmic expression of survivin is an independent predictor of poor prognosis in patients with salivary gland cancer
Multiple regulatory inputs converge on cortactin to control invadopodia biogenesis and extracellular matrix degradation

Invadopodia are proteolytically active protrusions formed by invasive tumoral cells when grown on an extracellular matrix (ECM) substratum. Although many molecular components have been defined, less is known of the formation and regulation of invadopodia. The multidomain protein cortactin, which is involved in the regulation of actin polymerisation, is one such component, but how cortactin is modulated to control the formation of invadopodia has not been elucidated. Here, a new invadopodia synchronization protocol is used to show that the cortactin N-terminal acidic and SH3 domains, involved in Arp2/3 complex and N-WASP binding and activation, respectively, are both required for invadopodia biogenesis. In addition, through a combination of RNA interference and a wide array of cortactin phosphorylation mutants, we were able to show that three convergent regulatory inputs based on the regulation of cortactin phosphorylation by Src-family kinases, Erk1/Erk2 and PAK are necessary for invadopodia formation and extracellular matrix degradation. These findings suggest that cortactin is a scaffold protein bringing together the different components necessary for the formation of the invadopodia, and that a fine balance between different phosphorylation events induces subtle changes in structure to calibrate cortactin function.
Gramene: a resource for comparative grass genomics

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. Rice, in addition to being an economically important crop, is also a model monocot for understanding other agronomically important grass genomes. Gramene replaces the existing AceDB database 'RiceGenes' with a relational database based on Oracle. Gramene provides curated and integrative information about maps, sequence, genes, genetic markers, mutants, QTLs, controlled vocabularies and publications. Its aims are to use the rice genetic, physical and sequence maps as fundamental organizing units, to provide a common denominator for moving from one crop grass to another and is to serve as a portal for interconnecting with other web-based crop grass resources. This paper describes the initial steps we have taken towards realizing these goals.
Neuro fuzzy modeling and prediction of wear rate in composite manufacturing

Composites play a major role in manufacturing firms due to its less weight and good strength. Development of metal matrix composite draws the application of the fabrication of aircraft and aerospace structures. Hence manufacturing of composites needs attention. This paper discusses an investigation of developing Adaptive Neuro Fuzzy Inference System (ANFIS) neuro fuzzy model to predict wear rate for the developed composite under given set of parameters such as applied load, sliding velocity and distance travelled. Taguchi method is employed to conduct experiments. Obtained results were employed to train and test the proposed ANFIS model. Finally trained ANFIS model is validated and presented.
Dispersion engineered right/left-handed transmission lines enabling near-octave bandwidths for wideband CP patch arrays

Composite right/left-handed (CRLH) transmission lines have recently attracted a significant interest due to their abilities to generate phase characteristics which go beyond the typical right-handed lines. In this work, we demonstrate their use in generating a wideband quadrature phase excitation for creating circular polarization (CP) with antenna systems capable of generating two orthogonal polarizations. In particular, we investigate their application towards a patch antenna array of sequentially rotated elements. By engineering the dispersion of the CRLH lines, we have been able to measure roughly 60% AR-S11 bandwidth with a prototyped 2 × 2 array of sequentially rotated wideband, single layer patch antennas.
Use of Behavior and Influence Functions for Relay Selection in Cooperative Communications

This paper uses a novel set of functions to model the relay selection process in a scenario of cooperative wireless communications. We define a utility function that reflects the behavior and influence that a selected relay may have on the quality of the link to be established for the forwarding of data. The utility function takes into account also the strategies of other players. To this end, we define a relay selection game and a supporting Nash Equilibrium (NE) algorithm for the choice of a relay during communication. The successful selection of a relay is evaluated by simulations in terms of Influence and Behavior to assess the effect on the system performance.
Glutamate release from activated microglia requires the oxidative burst and lipid peroxidation

When activated by proinflammatory stimuli, microglia release substantial levels of glutamate, and mounting evidence suggests this contributes to neuronal damage during neuroinflammation. Prior studies indicated a role for the Xc exchange system, an amino acid transporter that antiports glutamate for cystine. Because cystine is used for synthesis of glutathione (GSH) synthesis, we hypothesized that glutamate release is an indirect consequence of GSH depletion by the respiratory burst, which produces superoxide from NADPH oxidase. Microglial glutamate release triggered by lipopolysaccharide was blocked by diphenylene iodonium chloride and apocynin, inhibitors of NADPH oxidase. This glutamate release was also blocked by vitamin E and elicited by lipid peroxidation products 4‐hydroxynonenal and acrolein, suggesting that lipid peroxidation makes crucial demands on GSH. Although NADPH oxidase inhibitors also suppressed nitrite accumulation, vitamin E did not; moreover, glutamate release was largely unaffected by nitric oxide donors, inhibitors of nitric oxide synthase, or changes in gene expression. These findings indicate that a considerable degree of the neurodegenerative consequences of neuroinflammation may result from conversion of oxidative stress to excitotoxic stress. This phenomenon entails a biochemical chain of events initiated by a programmed oxidative stress and resultant mass‐action amino acid transport. Indeed, some of the neuroprotective effects of antioxidants may be due to interference with these events rather than direct protection against neuronal oxidation.
Quantitative bioanalytical validation of fosfomycin in human whole blood with volumetric absorptive microsampling.

BACKGROUND Fosfomycin is an antibiotic of considerable interest for the treatment of infection by multidrug-resistant bacteria. Translating microsampling techniques into clinical PK studies may provide effective dosing information to improve patient outcomes and minimize the potential development of resistance. RESULTS Accuracy and precision results were within ±15%; the method was validated across the range of 5-2000 µg/ml of fosfomycin using volumetric absorptive microsampling (VAMS) devices. CONCLUSION The VAMS techniques provide acceptable validation data as assessed for lower limit of quantification, linearity, intra- and interday precision and accuracy, selectivity and matrix effects. Results from the recovery and stability studies suggest challenges remain for the analysis of fosfomycin in whole blood using VAMS.