Miracle-dz/UniFAR-FTUs huggingface dataset:
Directed self‐immobilization of alkaline phosphatase on micro‐patterned substrates via genetically fused metal‐binding peptide

Current biotechnological applications such as biosensors, protein arrays, and microchips require oriented immobilization of enzymes. The characteristics of recognition, self‐assembly and ease of genetic manipulation make inorganic binding peptides an ideal molecular tool for site‐specific enzyme immobilization. Herein, we demonstrate the utilization of gold binding peptide (GBP1) as a molecular linker genetically fused to alkaline phosphatase (AP) and immobilized on gold substrate. Multiple tandem repeats (n = 5, 6, 7, 9) of gold binding peptide were fused to N‐terminus of AP (nGBP1‐AP) and the enzymes were expressed in E. coli cells. The binding and enzymatic activities of the bi‐functional fusion constructs were analyzed using quartz crystal microbalance spectroscopy and biochemical assays. Among the multiple‐repeat constructs, 5GBP1‐AP displayed the best bi‐functional activity and, therefore, was chosen for self‐immobilization studies. Adsorption and assembly properties of the fusion enzyme, 5GBP1‐AP, were studied via surface plasmon resonance spectroscopy and atomic force microscopy. We demonstrated self‐immobilization of the bi‐functional enzyme on micro‐patterned substrates where genetically linked 5GBP1‐AP displayed higher enzymatic activity per area compared to that of AP. Our results demonstrate the promising use of inorganic binding peptides as site‐specific molecular linkers for oriented enzyme immobilization with retained activity. Directed assembly of proteins on solids using genetically fused specific inorganic‐binding peptides has a potential utility in a wide range of biosensing and bioconversion processes. Biotechnol. Bioeng. 2009;103: 696–705. © 2009 Wiley Periodicals, Inc.
Flotation Assembly of Large-Area Ultrathin MWCNT Nanofilms for Construction of Bioelectrodes

We report a simple, versatile, and rapid method for the fabrication of optically-transparent large-area carbon nanotube (CNT) films via flotation assembly. After solvent-induced assembly, floating films were transferred to a flat supporting substrate to form conductive and transparent CNT film electrodes. The resulting electrodes, with uniform 40 ± 20 nm multi-walled CNT (MWCNT) layers, were characterized by electrochemical and microscopy methods. The flotation method does not require specialized thin-film instrumentation and avoids the need for surfactants and pre-oxidized CNTs which can hamper electrochemical performance. A proof-of-concept nanostructured bioelectrode demonstrating high sensitivity for glucose was developed with an electropolymerized poly(pyrene-adamantane) layer for host–guest immobilization of active β-cyclodextrin tagged GOx enzymes. The polymer provides pyrene groups for cross-linking to CNTs and pendant adamantane groups for binding the β-cyclodextrin groups of the tagged enzyme. This demonstration offers a new approach for the preparation of stable and transparent CNT film electrodes with attractive electrochemical properties towards future photobio- and bio-electrochemical fuel cells, electrochemical sensors, and electroanalysis.
Expression of the X Gene of Hepatitis B Virus

The hepatitis B virus (HBV) genome carries an open reading frame of 462 bases, the X region, but the corresponding protein has yet to be identified as a natural product. In rodent cells cotransformed with the thymidine kinase gene of herpes simplex virus and HBV DNA, however, Gough [1983] identified a mRNA that hybridises uniquely with the X region of the HBV genome. A large fragment of the X region was inserted into plasmid pCL19LDY‐T in order to produce, in Escherichia coli, the X gene product, HBxAg, as a polypeptide fused to the N‐terminal part of the phage þcro gene product. Antisera raised against this fused polypeptide gave positive immunofluorescence reactions with the transformed rodent cells. This provides direct evidence for the expression of the HBxAg gene in eukaryotic cells transformed with HBV DNA. The approach used here should be generally applicable.
Cost Evaluation of Optical Packet Switches Equipped With Limited-Range and Full-Range Converters for Contention Resolution

Two architectures are proposed for a wavelength-division multiplexed optical packet switch equipped with both limited-range wavelength converters (LRWCs) and shared full-range wavelength converters (FRWCs). The FRWCs are used to overcome the performance degradation in terms of packet loss probability due to the use of LRWCs only. Two different sharing strategies of the FRWCs are considered. In the first architecture, a pool of FRWCs is shared among the arriving packets. In the second one, the sharing is only partial and the packets directed to the same output share a same pool of FRWCs. A probabilistic model is proposed to dimension the number of shared FRWCs so that the same packet loss probability of a switch equipped with only shared FRWCs is guaranteed. After introducing a cost model of the converters depending on the conversion range, we show that the architectures may allow a conversion cost savings on the order of 90%.
A compact low power ASK demodulator for passive UHF RFID tags

A Low power Amplitude Shift Keying (ASK) demodulator circuit for passive UHF Radio Frequency Identification (RFID) tag is designed in this paper with several area-saving techniques. Current source is employed to realize the envelop detector instead of resistor to reduce the area. Differential circuit is inserted into the demodulator to enhance the performance of demodulation. Diode-connected PMOS pair is used to clamp or average the input signal while the area is saved dramatically. The ASK demodulator is powered by on-chip power of 1.8V with current consumption of less than 0. 5μA from the rectifier block. The power supply voltage can be reduced further to save more power.
Relaxation of replication control in chaperone‐independent initiator mutants of plasmid P1.

Escherichia coli chaperones DnaJ, DnaK and GrpE increase P1 plasmid initiator binding to the origin by promoting initiator folding. The binding allows initiation and also promotes pairing of origins which is believed to control initiation frequency. Chaperone‐independent DNA binding mutants are often defective in replication control. We show here that these mutants have increased rates of association for DNA binding and defects in origin pairing. The increases in association rates were found to be due either to increased protein folding into active forms or to increases in the association rate constant, kon. Since the dissociation rate constants for DNA release with these mutants are not changed, it is unlikely that the DNA binding domain is affected. The pairing domain may thus control replication and modulate DNA binding. The role of the pairing domain in DNA binding can be significant in vivo as the selection for chaperone‐independent binding favors pairing‐defective mutants.
Chronic stress and antidepressant treatment have opposite effects on P-glycoprotein at the blood—brain barrier: an experimental PET study in rats

The multi-drug efflux transporter P-glycoprotein is expressed in high concentrations at the blood—brain barrier and has a major function in the transport of drugs. In a recent PET-study evidence was found for an increased function of P-glycoprotein at the blood—brain barrier in medicated patients suffering from major depressive disorder. We used small-animal PET and [11C]-verapamil to study P-glycoprotein function at the blood—brain barrier of rats, either being administered as venlafaxine, an antidepressant, or subjected to chronic stress, a factor contributing to the development of depression. In a first experiment, male Wistar rats underwent a three-week foot shock procedure as a model of human depression. In a second experiment, rats were chronically treated with the antidepressant venlafaxine (25 mg/kg/d via an implanted osmotic minipump). In both experiments, a [11C]-verapamil PET scan was performed. In the chronically stressed rats, the distribution volume (VT) of [11C]-verapamil was significantly increased, whereas treatment with venlafaxine had the opposite effect and caused a significant reduction in VT. The changes in VT could not be attributed to the influx rate constant (K1). Our data suggest that P-glycoprotein function at the blood—brain barrier is inhibited by chronic stress and increased by chronic administration of venlafaxine.
Overexpression of the HER-2/ neu Oncogene in Pancreatic Adenocarcinoma

Novel systemic treatments are needed in pancreatic cancer. The authors sought to establish the frequency of overexpression of the HER-2/ neu oncogene in patients with pancreatic adenocarcinoma to determine the potential role of trastuzumab (Herceptin) as a therapeutic agent in this disease. Tumor specimens from patients with pancreatic adenocarcinoma were analyzed by staining for p185HER2 protein using the DAKO immunohistochemical assay. Patients with and without HER-2/ neu overexpression by immunohistochemistry were compared with respect to clinical and pathologic characteristics. HER-2/neu gene amplification was also evaluated by fluorescence in situ hybridization (FISH). Thirty-two of 154 patients (21%) had pancreatic adenocarcinoma that demonstrated HER-2/ neu overexpression by immunohistochemistry. At initial diagnosis, 16% of resectable cancers, 17% of locally advanced cancers, and 26% of metastatic cancers were determined to have HER-2/ neu overexpression. Three of 11 (27%) patients with HER-2/ neu overexpression by immunohistochemistry had gene amplification by FISH. HER-2/ neu overexpression occurs in a subset of pancreatic cancer. Evaluation of the efficacy of trastuzumab for patients with pancreatic cancer who overexpress HER-2/ neu appears indicated.
Interpretation of the dynamic Allan variance of nonstationary clock data

Atomic clocks are ultra-stable time references, and they have found fundamental applications in several fields, navigation being certainly one of the most successful. Unfortunately, atomic clocks may experience nonstationary behaviors which make their stability a function of time. Even when the change in stability is thought to be small, it can still force the system that uses the clock to fail the design requirements. In navigation systems this might turn into an unwanted degradation of the user localization error. It is therefore essential to monitor the stability of the clock, and to understand and interpret the possible nonstationary behaviors. To this aim, we have recently Introduced the dynamic Allan variance, or DAVAR, a quantity that allows to represent the evolution with time of the clock stability. In this paper we show several cases of nonstationary time series, made by the combination of random processes and deterministic signals, and we discuss their dynamic Allan variance. The ultimate goal is to be able to do the inverse operation, that is to understand and classify the possible nonstationarities directly from the DAVAR representation. Examples with experimental data are presented.
Demographic determinants for Campylobacter infection in England and Wales: implications for future epidemiological studies

SUMMARY Despite a significant public health burden the epidemiology of human Campylobacter infection remains blurred. The identification of demographic determinants for Campylobacter infection is therefore essential for identifying potential areas for intervention. Demographic data from an active, population-based sentinel surveillance system for Campylobacter infection (from 2000 until 2003, n=15 907) were compared with appropriate denominator data from the 2001 United Kingdom Census. Incidence was higher in males from birth until the late teens and in females from 20 to 36 years. Age- and gender-specific differences in Campylobacter incidence were observed in different ethnic and socioeconomic groups and hence are all major drivers for Campylobacter infection. Epidemiological studies on Campylobacter infection need to take these factors into consideration during design and analysis. The collation of detailed epidemiological data and its comparison with appropriate denominator data provides a valuable epidemiological tool for studying infection.
Behavior of the ButterflyTN Parallel Processor in the Presence of Memory Hot Spots

This paper describes a set of experiments designed to measure the behavior of the Butterfly Parallel Processor in the presence of memory "hot spots". The experiments were motivated by a paper by Pfister and Norton [3] that reported results from simulation studies on multistage switching networks for shared memory parallel processors. Their results indicated that, for machines with a large number of processors, very slight non—uniformities in memory reference patterns can lead to severely degraded performance for the entire machine, including processors that avoid referencing the hot memories. The results were explained in terms of a phenomenon called "tree saturation" where traffic to the hot memories backs up into the switch and interferes with other switch traffic. The experiments reported here show that those results do not generalize to the Butterfly Parallel Processor. The access time for a memory that contains a hot spot is degraded, but the presence of the hot spot has little effect on the performance of programs that avoid the hot memory. Furthermore, tree saturation does not occur in the Butterfly Switch.
A Psychometric Evaluation of the Expectations, Perceptions, and Difference-Scores Generated by the IS-Adapted SERVQUAL Instrument

This article describes the results of a study assessing the psychometric properties of the expectations and perceptions-of-performance instruments and the difference-score data contained within the information systems (IS)-Adapted SERVQUAL measurement paradigm. The central claim of this study is: In order for rational inferences to be made about service expectations, service performance perceptions, or the gap between them, each of the two instruments must exhibit reasonable psychometric properties in isolation before difference-scores are taken. Analysis of data from a field study (N= 401) through structural equation modeling (SEM) techniques produces empirical evidence indicating that both of the instruments exhibit low psychometric quality and yet the difference-scores exhibit “psychometric inflation. ” That is, the quality of the difference-score data is in many ways apparently superior to the raw data from both instruments. Negative conclusions are reached as to the efficacy of either individual instrument and, thus, the full IS-Adapted SERVQUAL paradigm. Questions and prospects for further research in this important area of service quality measurement/management are presented, and a potentially rich future for IS service quality is outlined. It is strongly suggested that future IS service quality research be based on development of a new instrument, grounded in attributes endemic to IS services and developed using the best available development techniques.
A 1.65W fully integrated 90nm Bulk CMOS Intrinsic Charge Recycling capacitive DC-DC converter: Design & techniques for high power density

A fully integrated high power density capacitive 2∶1 step-down DC-DC converter is designed in a standard Bulk CMOS technology. The implemented converter can deliver a maximum output power of 1.65W on a chip area of 2.14mm2, resulting in a power conversion density of 0.77W/mm2. Besides the primary goal of high power density a peak power conversion efficiency of 69% is achieved. This for a voltage step-down conversion from twice the nominal supply voltage of a 90nm technology (2Vdd = 2.4V) to 1V. Both the design as the implementation techniques to achieve the resulting power density, are discussed.
Simplifying composite placement in the interproximal zone

shades and opacities were stratified, clinicians observed a ‘polychromatic effect’ (Dietschi, 1995). However, by utilising an anatomic stratification with successive layers of dentine, enamel and incisal composite, a more realistic depth of colour could be achieved, as well as surface and optical characteristics that mimic nature (Jefferies, 1998; Donly, Browning, 1992). The improvements in the restorative quality and aesthetic result that have developed from the inequities of these different composite resin systems (hybrid and microfill), in conjunction with the use of innovative placement techniques to optimise the materials’ properties, have stimulated scientists, researchers, clinicians and manufacturers to explore and develop new nanoparticle formulations of restorative biomaterials. Materials that are not only applied in relationship to the natural tissue anatomy, but that have physical, mechanical, and optical properties similar to that of tooth structure.
Quantification of microvascular cerebral blood flux and late‐stage tumor compartmentalization in 9L gliosarcoma using flow enhanced MRI

Measurements of tumor microvasculature are important to obtain an understanding of tumor angiogenesis and for the evaluation of therapies. In this work, we characterize the evolution of the microvascular flux at different stages of tumor growth in the 9L rat brain tumor model. The absolute quantification of cerebral blood flux is achieved with MRI at 7 T using the flow enhanced signal intensity (FENSI) method. FENSI flux maps were obtained between 5 and 14 days after glioma cell inoculation. Based on cerebral blood flux maps, we highlighted two main stages of tumor growth, below and above 3 mm, presenting distinct flux patterns and vascular properties. No significant difference emerged from the group analysis performed on the data collected at an early developmental stage (tumor size < 3 mm) when compared with healthy tissue. At a late developmental stage (tumor size > 3 mm), we observed a significant decrease in the cerebral blood flux inside the gliosarcoma (−33%, p < 0.01) and compartmentalization of the tumor (p < 0.05). FENSI flux maps delineated a low‐flux tumor core (58 ± 17 μL/min/cm2) and higher vascularized regions around the tumor periphery (85 ± 21 μL/min/cm2). Histology was performed on 11 animals to finely probe the intratumor heterogeneity and microvessel density, and the results were compared with the information derived from FENSI flux maps. The hyper‐ and hypoperfused tumor regions revealed with FENSI at the late tumor developmental stage correlated well with the ratios of high and low blood vessel density (R2 = 0.41) and fractional vascular surface (R2 = 0.67) observed with fluorescence microscopy [cluster of differentiation 31 (CD31) staining]. Copyright © 2013 John Wiley & Sons, Ltd.
DNA Methylase Activity as a Marker for the Presence of a Family of Phage-Like Elements Conferring Efflux-Mediated Macrolide Resistance in Streptococci

ABSTRACT Recently, two related chimeric genetic elements (Tn1207.3 and Φ10394.4) were shown to carry the macrolide efflux gene mef in Streptococcus pyogenes (group A streptococci [GAS]). The dissemination of elements belonging to the Tn1207.3/Φ10394. 4 family in recent isolates of GAS, Streptococcus dysgalactiae subsp. equisimilis, Streptococcus pneumoniae, and Streptococcus agalactiae recovered in Portugal was surveyed. In total, 149 GAS, 18 S. pneumoniae, 4 S. dysgalactiae subsp. equisimilis, and 5 S. agalactiae isolates from infections, presenting the M phenotype of macrolide resistance and containing the mef gene, were screened for the presence of Tn1207.3/Φ10394. 4 by PCR targeting open reading frames (ORFs) specific for these related elements. All the GAS isolates tested and one of the S. dysgalactiae subsp. equisimilis isolates carried Tn1207.3. However, neither of these elements was found in the isolates of the other streptococcal species. It was also noted that the DNAs of the isolates carrying Tn1207.3 were resistant to cleavage by the endonuclease SmaI. Cloning and expression of ORF12 of Tn1207.3 in Escherichia coli showed that it encoded a methyltransferase that rendered DNA refractory to cleavage by SmaI (M.Spy10394I). Using this characteristic as a marker for the presence of the Tn1207.3/Φ10394. 4 family, we reviewed the literature and concluded that these genetic elements are widely distributed among tetracycline-susceptible GAS isolates presenting the M phenotype from diverse geographic origins and may have played an important role in the dissemination of macrolide resistance in this species.
Dysadherin Expression is Associated with Advanced Tumorstage while Complexity Index is Related to Poorly Differentiated Tumors in Colon Carcinoma

Dysadherin expressions are associated with the aggressive tumors that show poor prognosis in different types of cancers. Aggressive tumors often presented with infiltrative type of growth pattern in colon cancer and that has been associated with poor prognosis as well. The aim of this was to evaluate Dysadherin expression in paired normal and tumor samples, and tumor growth pattern in the form of complexity index in the same patient colon cancer samples, and finally to correlate with each other and different clinical and pathological parameters. To evaluate Dysadherin expression, we selected 45 patients and performed RT-qPCR on normal and paired tumor samples. To determine growth pattern, we captured pictures from the immunohistochemically stained tumor invasive fronts and then evaluated by using Photoshop CS, Fovea Pro, and Image J computer programs. Paired t test was applied for the Dysadherin expression between normal and paired normal samples while Pearson chi square and Fischer exact test between dichotomized Dysadherin expression, complexity index and different clinicopathological parameters. Mean Dysadherin expression in normal samples was 0.155+0.0167 and in tumor 0.869+0.083 and was significantly different between two groups of samples (P value<0.0001). In dichotomized groups, increased Dysadherin expression was significantly correlated with the lymph node metastasis and advanced Dukes stages. Higher complexity index was significantly associated with low differentiated tumors while non-significantly with other clinicopathological parameters. In conclusion, Dysadherin expression and tumor growth pattern are independent features, where Dysadherin expression is associated with advanced Dukes staged tumors and complexity index with the poorly differentiated tumors.