Miracle-dz/UniFAR-FTUs huggingface dataset:
The Fur Homologue in Borrelia burgdorferi

ABSTRACT Borrelia burgdorferi contains a gene that codes for a Fur homologue. The function of this Fur protein is unknown; however, spirochetes grown at 23 or 35°C expressed fur as determined by reverse transcriptase PCR. The fur gene (BB0647) was cloned and overexpressed as a His-Fur fusion protein in Escherichia coli. The fusion protein was purified by zinc-chelate chromatography, and the N-terminal His tag was removed to generate recombinant Fur for use in mobility shift studies. Fur bound DNA containing the E. coli Fur box sequence (GATAATGATAATCATTATC) or Bacillus subtilis Per box sequence (TTATAAT-ATTATAA) with an apparent Kd of ∼20 nM. Fur also bound the upstream sequences of three Borrelia genes: BB0646 (gene encoding a hydrolase of the α/β-fold family), BB0647 (fur), and BB0690 (napA). Addition of metal ions was not required. Binding activity was greatly decreased by either exposure to oxidizing agents (H2O2, t-butyl hydroperoxide, cumene hydroperoxide, or diamide) or by addition of Zn2+. B. burgdorferi NapA is a homologue of Dps. Dps functions in E. coli to protect DNA against damage during periods of redox stress. Fur may function in B. burgdorferi as a repressor and regulate oxidative stress genes. Additional genes (10 chromosomal and 15 plasmid) that may be Fur regulated were identified by in silico analysis.
The DNA invertase Gin of phage Mu: formation of a covalent complex with DNA via a phosphoserine at amino acid position 9.

The DNA invertase Gin encoded by bacteriophage Mu catalyses efficient site‐specific recombination between inverted repeat sequences (IR) in vivo and in vitro in the presence of the host factor FIS and the recombinational enhancer. We demonstrate that Gin alone is able to introduce single strand breaks into duplex DNA fragments which contain the IR sequence. Strand cleavage is site‐specific and can occur on either strand within the IR. Cleaved molecules contain Gin covalently attached to DNA. The covalent complex is formed through linkage of Gin to the 5′ DNA phosphate at the site of the break via a phosphoserine. Extensive site‐directed mutational analysis showed that all mutants altered at serine position 9 were completely recombination deficient in vivo and in vitro. The mutant proteins bind to DNA but lack topoisomerase activity and are unable to introduce nicks. This holds true even for a conservative amino acid substitution at position 9. We conclude that serine at position 9 is part of the catalytic domain of Gin. The intriguing finding that the DNA invertase Gin has the same catalytic center as the DNA resolvases that promote deletions without recombinational enhancer and host factor FIS is discussed.
Rational Screening Set Design and Compound Selection: Cascaded Clustering

The use of cascaded clustering is reported. This technique was developed to permit the application of Jarvis-Patrick clustering based on structural fingerprints to large chemical databases, while keeping the maximum cluster size and the number of singletons produced at reasonable levels. The basis for the algorithm, its implementation, and validation are described. In the first part of the paper, the approach is used to create a representative subset of compounds for biological testing from the corporate compound repository. A variation of the method is then used for the comparison of relatively large databases. Finally, compound selection using cascaded clustering is shown to be complementary to the Diverse Property-Derived approach, which is based on partitioning by six molecular descriptors.
Detection of Helicobacter pylori DNA in inflamed dental pulp specimens from Japanese children and adolescents.

The oral cavity has been implicated as a source of Helicobacter pylori infection in childhood. Various PCR methods have been used to detect H. pylori DNA in oral specimens with various detection rates reported. Such disparity in detection rates complicates the estimation of the true infection rate of H. pylori in the oral cavity. In the present study, we constructed a novel PCR system for H. pylori detection and used it to analyse oral specimens. Firstly, the nucleotide alignments of genes commonly used for H. pylori detection were compared using the complete genome information for 48 strains registered in the GenBank database. Candidate primer sets with an estimated amplification size of approximately 300-400 bp were selected, and the specificity and sensitivity of the detection system using each primer set were evaluated. Five sets of primers targeting ureA were considered appropriate, of which a single primer set was chosen for inclusion in the PCR system. The sensitivity of the system was considered appropriate and its detection limit established as one to ten cells per reaction. The novel PCR system was used to examine H. pylori distribution in oral specimens (40 inflamed pulp tissues, 40 saliva samples) collected from Japanese children, adolescents and young adults. PCR analysis revealed that the detection rate of H. pylori in inflamed pulp was 15 %, whereas no positive reaction was found in any of the saliva specimens. Taken together, our novel PCR system was found to be reliable for detecting H. pylori. The results obtained showed that H. pylori was detected in inflamed pulp but not saliva specimens, indicating that an infected root canal may be a reservoir for H. pylori.
Gas Cell Input radiation from the atmosphere Radiation after filtering by the gas cell Electronics Lock-in amplifier Detector Output Signal Modulation Control

The Measurement of Pollution in the Troposphere (MOPITT) instrument is an eight-channel gas correlation adiometer to be launched on the Earth Observing System (EOS) Terra spacecraft in 1999. Its main measurement objectives are tropospheric carbon monoxide (CO) profiles and total column. This paper gives a detailed description of MOPITT CO retrieval algorithm, which derives total CO column and tropospheric CO mixing ratios at a number of atmospheric pressure levels from MOPITT radiance observations. Retrieval performance evaluation using simulated MOPITT data are discussed.
Nitrate reduction as a marker for hypoxic shiftdown of Mycobacterium tuberculosis.

SETTING In vitro cultures. OBJECTIVE To characterize nitrate reduction during aerobic growth and hypoxic shiftdown to non-replicating persistence of Mycobacterium tuberculosis cultures. DESIGN The rates of reduction of nitrate to nitrite were measured in cultures of M. tuberculosis growing aerobically or undergoing hypoxic shiftdown. RESULTS Tubercle bacilli growing aerobically in the presence of nitrate reduce nitrate at a rate proportional to the substrate concentration, continuing until the substrate is exhausted. When the bacilli in an oxygen restricted model enter microaerophilic non-replicating persistence (NRP) stage 1, they exhibit a marked increase in rate of nitrate reduction that is independent of substrate concentration, and terminates by feedback inhibition when the concentration of nitrite produced approaches 2.5 mM. When bacilli in the oxygen restricted model are not supplemented with nitrate until they enter microaerophilic NRP stage 1, they exhibit an induction period before the rapid nitrate reduction starts. When the nitrate is not added until the bacilli have entered the anaerobic NRP stage 2, reduction of the substrate starts immediately. Nitrite is not reduced by M. tuberculosis in any stage of its growth or NRP. CONCLUSION The hypoxically induced nitrate reduction probably serves a respiratory function in supporting hypoxic shiftdown of M. tuberculosis from aerobic growth to non-replication persistence and represents a useful new marker for monitoring that shiftdown. This response may help the bacilli survive in oxygen depleted regions of inflammatory or necrotic tissue, where nitrate can occur as a degradation product of nitric oxide.
The modified Beer–Lambert law revisited

The modified Beer–Lambert law (MBLL) is the basis of continuous-wave near-infrared tissue spectroscopy (cwNIRS). The differential form of MBLL (dMBLL) states that the change in light attenuation is proportional to the changes in the concentrations of tissue chromophores, mainly oxy- and deoxyhaemoglobin. If attenuation changes are measured at two or more wavelengths, concentration changes can be calculated. The dMBLL is based on two assumptions: (1) the absorption of the tissue changes homogeneously, and (2) the scattering loss is constant. It is known that absorption changes are usually inhomogeneous, and therefore dMBLL underestimates the changes in concentrations (partial volume effect) and every calculated value is influenced by the change in the concentration of other chromophores (cross-talk between chromophores). However, the error introduced by the second assumption (cross-talk of scattering changes) has not been assessed previously. An analytically treatable special case (semi-infinite, homogeneous medium, with optical properties of the cerebral cortex) is utilized here to estimate its order of magnitude. We show that the per cent change of the transport scattering coefficient and that of the absorption coefficient have an approximately equal effect on the changes of attenuation, and a 1% increase in scattering increases the estimated concentration changes by about 0.5 µM.
Ultrasonic scanner for in vivo measurement of cancellous bone properties from backscattered data

A dedicated ultrasonic scanner for acquiring RF echoes backscattered from the trabecular bone was developed. The design of device is based on the goal of minimizing of custom electronics and computations executed solely on the main computer processor and the graphics card. The electronic encoder-digitizer module executing all of the transmission and reception functions is based on a single low-cost field programmable gate array (FPGA). The scanner is equipped with a mechanical sector-scan probe with a concave transducer with 50 mm focal length, center frequency of 1.5 MHz and 60% bandwidth at -6 dB. The example of femoral neck bone examination shows that the scanner can provide ultrasonic data from deeply located bones with the ultrasound penetrating the trabecular bone up to a depth of 20 mm. It is also shown that the RF echo data acquired with the scanner allow for the estimation of attenuation coefficient and frequency dependence of backscattering coefficient of trabecular bone. The values of the calculated parameters are in the range of corresponding in vitro data from the literature but their variation is relatively high.
Characterization and modeling of waffle MOSFETs for high frequency applications

The high frequency characteristics of waffle MOSFETs are studied. In addition to area saving and reduction of junction capacitance, enhancement on RF characteristics and extra flexibility in the design window are also provided by waffle MOSFETs. The waffle layout has been applied to MOSFETs fabricated using a 0.35-/spl mu/m CMOS bulk technology and compared with those designed with conventional multi-finger layouts. The waffle MOSFET offers about 50% reduction in the gate resistance, 30%-50% enhancement in f/sub max/ and 15% improvement on linearity (IIP3). With the validity of small-signal model demonstrated by the good matching between the model prediction and the measured S-parameter data, it indicates that the waffle MOSFET is capable of offering RF performance improvement with careful design.
Basic Dye Adsorption onto Clay/MnFe2O4 Composite: A Mechanistic Study

Native, HCl pretreated clay and MnFe2O4/clay composite were investigated as an adsorbent for crystal violet (CV) removal. The adsorption behavior of dye was studied in batch experiments as a function of contact time, adsorbent dose, pH, dye initial concentration and temperature. The medium pH 8, contact time 30 min, MnFe2O4/clay composite dose 0.05 mg/L, temperature 35 °C and 100 mg/L dye initial concentration furnished maximum CV adsorption. Adsorption data fitted well to the Langmuir isotherm model and maximum CV dye adsorption capacity of composite was 49.74 mg/g. The thermodynamic parameters revealed that the adsorption process of CV was exothermic and spontaneous in nature. CV adsorption followed the pseudo second order kinetic model. MnFe2O4/clay composite exhibited good CV adsorption capacity and can be used as an alternative adsorbent for the removal of basic dyes from effluents.
Negative Energy Balance Blocks Neural and Behavioral Responses to Acute Stress by “Silencing” Central Glucagon-Like Peptide 1 Signaling in Rats

Previous reports indicate that caloric restriction attenuates anxiety and other behavioral responses to acute stress, and blunts the ability of stress to increase anterior pituitary release of adrenocorticotropic hormone. Since hindbrain glucagon-like peptide-1 (GLP-1) neurons and noradrenergic prolactin-releasing peptide (PrRP) neurons participate in behavioral and endocrine stress responses, and are sensitive to the metabolic state, we examined whether overnight food deprivation blunts stress-induced recruitment of these neurons and their downstream hypothalamic and limbic forebrain targets. A single overnight fast reduced anxiety-like behavior assessed in the elevated-plus maze and acoustic startle test, including marked attenuation of light-enhanced startle. Acute stress [i.e., 30 min restraint (RES) or 5 min elevated platform exposure] robustly activated c-Fos in GLP-1 and PrRP neurons in fed rats, but not in fasted rats. Fasting also significantly blunted the ability of acute stress to activate c-Fos expression within the anterior ventrolateral bed nucleus of the stria terminalis (vlBST). Acute RES stress suppressed dark-onset food intake in rats that were fed ad libitum, whereas central infusion of a GLP-1 receptor antagonist blocked RES-induced hypophagia, and reduced the ability of RES to activate PrRP and anterior vlBST neurons in ad libitum-fed rats. Thus, an overnight fast “silences” GLP-1 and PrRP neurons, and reduces both anxiety-like and hypophagic responses to acute stress. The partial mimicking of these fasting-induced effects in ad libitum-fed rats after GLP-1 receptor antagonism suggests a potential mechanism by which short-term negative energy balance attenuates neuroendocrine and behavioral responses to acute stress. SIGNIFICANCE STATEMENT The results from this study reveal a potential central mechanism for the “metabolic tuning” of stress responsiveness. A single overnight fast, which markedly reduces anxiety-like behavior in rats, reduces or blocks the ability of acute stress to activate hindbrain neurons that are immunoreactive for either prolactin-releasing peptide or glucagon-like peptide 1, and attenuates the activation of their stress-sensitive projection targets in the limbic forebrain. In nonfasted rats, central antagonism of glucagon-like peptide 1 receptors partially mimics the effect of an overnight fast by blocking the ability of acute stress to inhibit food intake, and by attenuating stress-induced activation of hindbrain and limbic forebrain neurons. We propose that caloric restriction attenuates behavioral and physiological responses to acute stress by “silencing” central glucagon-like peptide 1 signaling pathways.
Posterior approach vertebrectomy in the thoracolumbar spine with expandable cage reconstruction: indications and techniques based on eight cases

We present a series of eight patients undergoing circumferential neural decompression and stabilization of the thoracolumbar spine via a single midline posterior approach, with complete vertebrectomy for a variety of indications. Four had primary tumours, two secondary tumours, one patient had tuberculosis and one had delayed deformity due to trauma. This single posterior approach is made possible via the use of an expandable cage that may be expanded in situ to offer anterior and middle column reconstruction. There were no major neurological complications and all patients with deficits improved postoperatively. Extensive posterior fixation was avoided with five patients undergoing a one above/one below fixation and three undergoing a two above/two below fixation. When combined with pedicle screw and rod fixation this anterior reconstruction makes a sound construct. The flexibility of this approach in the thoracolumbar spine, some of the biomechanical advantages and pitfalls are considered.
Study on the Measurement System for Current Velocity and Direction at Closure Gap

Based on GPS PPK technique, attitude determination technique, INS orientation technique and information acquisition and processing technique, a drifting system for the determination of velocity and direction of surface current at closure water area is presented in this paper. The methods on PPK data processing, quality control, attitude correction and the determination of gravity center of buoy as well as the determination of current velocity and direction on water surface are studied. By means of the system and these methods studied in this paper, the current velocity and direction are determined at the river closure. The system was used for an actual project and achieved ideal results.
IBM's S/390 G5 microprocessor design

The IBM S/390 G5 microprocessor in IBM's newest CMOS mainframe system provides more than twice the performance of the previous generation, the G4. The G5 system offers improved reliability and availability, along with new architectural features such as support for IEEE floating-point arithmetic and a redesigned L2 cache and processor interconnect. The G5 system implements the ESA/390 instruction-set architecture, which is based on and compatible with the original S/360 architecture. Therefore, it has no RISC (reduced-instruction-set computing) concepts and is one of the most complex of all CISC (complex-instruction-set computing) architectures. Designers had to meet a unique set of challenges to achieve the G5's level of performance-for example, achieving a very high frequency given the complexity of the architecture.
Delayed Quick Spins after Vestibular Nerve Section Respond to Anticonvulsant Therapy

Objective: To describe the clinical features of patients with failed vestibular nerve section that have a response to anticonvulsant medication. Study Design: Retrospective case review. Setting: Ambulatory tertiary referral center. Patients: We report three patients who were afflicted with frequent brief spinning spells, or "quick spins," after vestibular neurectomy for Ménière's disease. Intervention: Treatment with anticonvulsants. Main Outcome Measure: Relief of vertigo. Results: All cases had an excellent therapeutic response to carbamazepine or oxcarbazepine, agents conventionally used for neuralgia, suggesting that these symptoms are caused by a hyperexcitable vestibular nerve. Conclusion: Treatment of neuralgia should be considered when the symptom of quick spins arises after vestibular neurectomy.
Synthesis of GF(3) Based Reversible/Quantum Logic Circuits without Garbage Output

We present a method of synthesizing Ternary GaloisField (GF(3)) based reversible/quantum logic circuits without any ancillary trits/qutrits and hence without any garbage outputs. We realize multi input ternary Toffoli gate and square functions of GF(3) variables using linear ion trap realizable Muthukrishnan-Stroud (M-S) gates and shift gates in the absence of ancillary qutrits. Then based on the Galois Field Sum of Products (GFSOP)expression of a multi-variable GF(3) function, we synthesize the corresponding circuit.
Preliminary results on the assessment of WirelessHART networks in transient fault scenarios

WirelessHART currently appears as a leading solution for interconnection of wireless devices in industrial process control applications. However, the lack of knowledge about the influence of transient faults in WirelessHART networks can lead to the choice of less reliable topologies. In this work, we propose a simulation model to evaluate WirelessHART networks in the presence of transient faults. We assume that these faults result from noisy environments that disturb communications between devices. The model was developed using the Stochastic Petri Net (SPN) formalism, supported by the Mbbius tool. For further developments, we target the development of an application that automates the assessment of a WirelessHART network in transient fault scenarios.
High-Resolution Mobile Monitoring of Carbon Monoxide and Ultrafine Particle Concentrations in a Near-Road Environment

Abstract Assessment of near-road air quality is challenging in urban environments that have roadside structures, elevated road sections, or depressed roads that may impact the dispersion of traffic emissions. Vehicles traveling on arterial roadways may also contribute to air pollution spatial variability in urban areas. To characterize the nature of near-road air quality in a complex urban environment, an instrumented all-electric vehicle was deployed to perform high spatial- and temporal-resolution mapping of ultra-fine particles (UFPs, particle diameter <100 nm) and carbon monoxide (CO). Sampling was conducted in areas surrounding a highway in Durham, NC, with multiple repeats of the driving route accomplished within a morning or evening commute time frame. Six different near-road transects were driven, which included features such as noise barriers, vegetation, frontage roads, and densely built houses. Under downwind conditions, median UFP and CO levels in near-road areas located 20–150 m from the highway were a factor of 1.8 and 1.2 higher, respectively, than in areas characterized as urban background. Sampling in multiple near-road neighborhoods during downwind conditions revealed significant variability in absolute UFP and CO concentrations as well as in the rate of concentration attenuation with increasing distance from the highway. During low-speed meandering winds, regional UFP and CO concentrations nearly doubled relative to crosswind conditions; however, near-road UFP levels were still higher than urban background levels by a factor of 1.2, whereas near-road CO concentrations were not significantly different than the urban background.
Study of an effective way of detecting unexpected permission authorization to mobile apps

The recent boom in Android mobile device usage has caused a shift in the information technology and has affected the way how information and data are stored, shared among the mobile users. The advent of social networking applications also demands the availability of resources that can be shared among the authentic users. This paper reviews and compares the available techniques and solutions for detecting Unexpected Permission Authorization to Mobile Apps. It is observed that malware for the android system is also growing significantly, current solutions for detecting malware on smartphones are still ineffective.
Akt and Hypoxia-Inducible Factor-1 Independently Enhance Tumor Growth and Angiogenesis

Recent reports have suggested that phosphatidylinositol 3-kinase/Akt signaling can induce angiogenesis and tumor growth by activating the hypoxia-inducible factor-1 (HIF-1). However, the absence of specific biochemical inhibitors of HIF-1 signaling has prevented a direct test of the requirement for HIF-1 activity in Akt-dependent tumorigenesis. To genetically test the relationship between HIF-1 and Akt, activated Akt was expressed in a hepatoma cell line lacking HIF-1. Akt expression was associated with a dramatic increase in tumor size, despite the absence of HIF-1. Tumor size was not further increased in cells with reconstituted HIF-1 activity, indicating that the effects of Akt on tumorigenesis were not limited by the absence of HIF-1. Increased tumor size in Akt-expressing, HIF-deficient cells was associated with vascular endothelial growth factor secretion and tumor vascularization. In addition to vascular endothelial growth factor production, Akt also conferred a cell-autonomous competitive advantage to tumor cells in an in vivo competition experiment. Thus, Akt has potent, HIF-1-independent oncogenic and angiogenic activities.