Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins

Amino acid residues, which play important roles in protein function, are often conserved. Here, we analyze thermodynamic and structural data of protein–DNA interactions to explore a relationship between free energy, sequence conservation and structural cooperativity. We observe that the most stabilizing residues or putative hotspots are those which occur as clusters of conserved residues. The higher packing density of the clusters and available experimental thermodynamic data of mutations suggest cooperativity between conserved residues in the clusters. Conserved singlets contribute to the stability of protein–DNA complexes to a lesser extent. We also analyze structural features of conserved residues and their clusters and examine their role in identifying DNA-binding sites. We show that about half of the observed conserved residue clusters are in the interface with the DNA, which could be identified from their amino acid composition; whereas the remaining clusters are at the protein–protein or protein–ligand interface, or embedded in the structural scaffolds. In protein–protein interfaces, conserved residues are highly correlated with experimental residue hotspots, contributing dominantly and often cooperatively to the stability of protein–protein complexes. Overall, the conservation patterns of the stabilizing residues in DNA-binding proteins also highlight the significance of clustering as compared to single residue conservation.
Rapid high‐resolution T1 mapping by variable flip angles: Accurate and precise measurements in the presence of radiofrequency field inhomogeneity

Rapid 3D mapping of T1 relaxation times is valuable in diverse clinical applications. Recently, the variable flip angle (VFA) spoiled gradient recalled echo approach was shown to be a practical alternative to conventional methods, providing better precision and speed. However, the method is known to be sensitive to transmit field (B1+) inhomogeneity and can result in significant systematic errors in T1 estimates, especially at high field strengths. The main challenge is to improve the accuracy of the VFA approach without sacrificing speed. In this article, the VFA method was optimized for both accuracy and precision by considering the influence of imperfect transmit fields, noise bias, and selection of flip angles. An analytic solution was developed for systematic B1+‐induced T1 errors and allows simple correction of T1 measurements acquired with any imaging parameters. A noise threshold was also identified and provided a guideline for avoiding T1 biases. Finally, it was shown that three flip angles were the most efficient for maintaining accuracy and high precision over large ranges of T1. A rapid B1+ mapping sequence was employed in all phantom experiments and high‐field in vivo brain scans. Experimental results confirmed the theory and validated the accuracy of the proposed method. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Orthogonal Electrode Catheter Array for Mapping of Endocardial Focal Site of Ventricular Activation

Precise location of the endocardial site of origin of ventricular tachycardia may facilitate surgical and catheter ablation of this arrhythmia. The endocardial catheter mapping technique can locate the site of ventricular tachycardia within 4–8 cm2 of the earliest site recorded by the catheter. This report describes an orthogonal electrode catheter array (OECA) for mapping and radiofrequency ablation (RFA) of endocardial focal site of origin of a plunge electrode paced model of ventricular activation in dogs. The OECA is an 8 F five pole catheter with four peripheral electrodes and one central electrode (total surface area 0.8 cm2). In eight mongrel dogs, mapping was performed by arbitrarily dividing the left ventricle (LV) into four segments. Each segment was mapped with OECA to find the earliest segment. Bipolar and unipolar electrograms were obtained. The plunge electrode (not visible on fluoroscopy) site was identified by the earliest wave front arrival times of ‐30 msec or earlier at two or more electrodes (unipolar electrograms) with reference to the earliest recorded surface ECG (I, AVF, and V1). Validation of the proximity of the five electrodes of the OECA to the plunge electrode was performed by digital radiography and RFA. Pathological examination was performed to document the proximity of the OECA to the plunge electrode and also for the width, depth, and microscopic changes of the ablation. To find the segment with the earliest LV activation a total of 10 ± 3 (mean ± SD) positions were mapped. Mean arrival times at the two earlier electrodes were ‐ 39 ± 4 msec and ‐35 ± 3 msec. Digital radiography showed the plunge electrode to be within the area covered by all five electrodes in all eight dogs. The plunge electrode was within 1 cm2 area of the region of RFA in all eight dogs. The width and depth of ablation were 5 ± 3.5 and 7 ± 3.5 mm, respectively. Microscopic changes revealed coagulative necrosis, hemorrhage, and inflammatory changes in all RFAs. In conclusion, the OECA can map the endocardial focal site of origin of paced ventricular activation within 1 cm2 area in a canine model. RFA from the OECA can cause discrete ablations representing all five electrodes or cross‐shaped ablation connecting central electrode to all four peripheral electrodes. This catheter holds promise for extending surgical and clinical catheter ablation procedures.
Precision measurement of dielectric properties for thick ceramic film on a ceramic substrate using the TE011 split-circular cavity resonator at 10GHz band by applying mode-matching method

In this study, the mode-matching method was applied to formulate an analytical model for a split cylindrical cavity resonator with a thick ceramic film layer sandwiched between two-layer alumina substrates. Next, resonant frequencies with the TE011 mode were computed with an eigenvalue problem approach using the model formula. The Q value of the resonator was also calculated by applying the perturbation method to the analytical model. The validity of the proposed analytical technique was confirmed using the procedure described below by applying this method to the estimation of complex permittivity for thick film with an inverse problem approach. The complex permittivity of 2-μm-thick ceramic thick films was estimated in the TE011 mode using a split cylindrical cavity resonator synthesized by the chemical solution method onto a 200-μm thick, 50-mm-diameter alumina substrate. It was confirmed that the estimated results for relative permittivity and the tan d values of these ceramic thick films were affected by the estimated relative permittivity value of the alumina substrate.
Chronic nicotine exposure alters blood–brain barrier permeability and diminishes brain uptake of methyllycaconitine

Methyllycaconitine (MLA) is reported to be a selective antagonist for the nicotinic acetylcholine receptor α7 subtype and has been found in animal behavioral studies to reduce nicotine self‐administration and attenuate nicotine withdrawal symptoms. While MLA crosses the blood–brain barrier (BBB), no studies have assessed brain uptake in animals subjected to chronic nicotine exposure. Given that chronic nicotine administration has been reported to alter BBB parameters that may affect the kinetic BBB passage of MLA, we evaluated MLA brain uptake in naive and S‐(–)nicotine‐exposed rats (4.5 mg/kg/day for 28 days; osmotic minipumps) using in situ rat brain perfusions. Our results demonstrate that in situ3H‐MLA brain uptake rates in naive animals approximate to intravenous kinetic data (Kin, 3.24 ± 0.71 × 10−4 mL/s/g). However, 28‐day nicotine exposure diminished 3H‐MLA brain uptake by ∼60% (Kin, 1.29 ± 0.4 × 10−4 mL/s/g). This reduction was not related to nicotine‐induced 3H‐MLA brain efflux or BBB transport alterations. Similar experiments also demonstrated that the passive permeation of 14C‐thiourea was diminished ∼24% after chronic nicotine exposure. Therefore, it appears that chronic nicotine exposure diminishes the blood–brain passive diffusion of compounds with very low extraction rates (i.e. permeability‐limited compounds). These findings imply that the pharmacokinetics of neuropharmaceutical agents that are permeability limited may need to be re‐evaluated in individuals exposed to nicotine.
Locating seed points for automatic multi-organ segmentation using non-rigid registration and organ annotations

Organ segmentation is helpful for decision-support in diagnostic medicine. Region-growing segmentation algorithms are popular but usually require that clinicians place seed points in structures manually. A method to automatically calculate the seed points for segmenting organs in three-dimensional (3D), non-annotated Computed Tomography (CT) and Magnetic Resonance (MR) volumes from the VISCERAL dataset is presented in this paper. It precludes the need for manual placement of seeds, thereby saving time. It also has the advantage of being a simple yet effective means of finding reliable seed points for segmentation. Affine registration followed by B-spline registration are used to align expert annotations of each organ of interest in order to build a probability map for their respective location in a chosen reference frame. The centroid of each is determined. The same registration framework as above is used to warp the calculated centroids onto the volumes to be segmented. Existing segmentation algorithms may then be applied with the mapped centroids as seed points and the warped probability maps as an aid to the stopping criteria for segmentation. The above method was tested on contrast{enhanced, thorax-abdomen CT images to see if calculated centroids lay within target organs, which would equate to successful segmentation if an effective segmentation algorithm were used. Promising results were obtained and are presented in this paper. The causes for observed failures were identified and countermeasures were proposed in order to achieve even better results in the next stage of development that will involve a wider variety of MR and CT images.
Modulation of microglial superoxide production by α‐tocopherol in vitro: attenuation of p67phox translocation by a protein phosphatase‐dependent pathway

As in other phagocytic cells, the NADPH‐oxidase system in microglia is thought to be primarily responsible for the production of superoxide anion radicals (O2−·), a potentially cytotoxic reactive oxygen species. The assembly of a functional NADPH‐oxidase complex at the plasma membrane depends on the phosphorylation and subsequent translocation of several cytosolic subunits. Immunocytochemical and subcellular fractionation experiments performed during the present study revealed that the NADPH‐oxidase subunit p67phox translocates from the cytosol to the plasma membrane upon stimulation. Pre‐incubation of microglia in α‐tocopherol (αTocH) containing medium decreased O2−· production in a time‐ and concentration‐dependent manner, findings attributed to attenuated p67phox translocation to the plasma membrane. Moreover, αTocH‐supplementation of the culture medium resulted in decreased microglial protein kinase C (PKC) activities, an effect that could be partially or completely reversed by the addition of protein phosphatase inhibitors (okadaic acid and calyculin A). The addition of the PKC‐inhibitor staurosporine inhibited the microglial respiratory burst in a manner comparable to αTocH. The addition of okadaic acid or calyculin A completely restored O2−· production in αTocH‐supplemented cells. The present findings suggest that αTocH inactivates PKC via a PP1 or PP2A‐mediated pathway and, as a consequence, blocks the phosphorylation‐dependent translocation of p67phox to the plasma membrane. As a result, O2−· production by the microglial NADPH‐oxidase system is substantially inhibited.
Corporate Political Transparency

Corporations are facing a growing demand for the transparency of political contributions. In the United States, this demand has largely focused on the implementation of a mandatory disclosure law. It rests on the assumption that legal enforcement can make it easier to observe the ties between corporations and political parties. In this study, I challenge this assumption. I build my case by first developing a conceptual foundation of corporate political transparency (CPT). I argue that in the absence of economic benefits, legal enforcement has a limited effect on CPT. Instead of encouraging transparency, mandatory disclosure can lead to the concealment of corporate political contributions. To develop a model of concealment, I borrow the characterizations of disguise from theatrical drama. Using the context of Indian firms, I show the limitation of mandatory disclosure and the efficacy of regulatory incentive. My study highlights the need for a broader debate on CPT to understand the relative implications of regulatory policies.
Distributed Intrusion Detection System for Wireless Sensor Networks

Wireless Sensor Networks is extensively used in many of applications related to different fields. Some of those applications deal with confidential and critical data that must be protected from unauthorized access. Some other systems use WSNs that are deployed in very harsh environments with limited energy resources. Those systems cannot tolerate network failures that can be caused by network intruders. In this paper, an efficient intrusion detection model is introduced. The model uses intelligent techniques to detect intrusions. Two different architectures are introduced. The first architecture represents the level of sensor node, sink node, and base station. The second architecture represents the levels of sensor and sink nodes. This work proposes two intrusion detection algorithms, one uses a supervised learning mechanism to be used on the level of the sensor node and the other uses an unsupervised learning mechanism to be used on the levels of both the sink node and base station. The output of the algorithms is a set of detection rules which are structured in the form of binary tree. The introduced algorithms provided a high detection accuracy using less number of selected features, compared to previous work for intrusion detection, which decreases the complexity and the processing time. The proposed learning algorithms used only 10% of the data for training. An enhancement for J48 classification algorithm is also introduced which decreases the size of the algorithm's decision tree and makes it suitable to be used for intrusion detection in WSNs.
Mutual Enhancement for Detection of Multiple Logos in Sports Videos

Detecting logo frequency and duration in sports videos provides sponsors an effective way to evaluate their advertising efforts. However, general-purposed object detection methods cannot address all the challenges in sports videos. In this paper, we propose a mutual-enhanced approach that can improve the detection of a logo through the information obtained from other simultaneously occurred logos. In a Fast-RCNN-based framework, we first introduce a homogeneity-enhanced re-ranking method by analyzing the characteristics of homogeneous logos in each frame, including type repetition, color consistency, and mutual exclusion. Different from conventional enhance mechanism that improves the weak proposals with the dominant proposals, our mutual method can also enhance the relatively significant proposals with weak proposals. Mutual enhancement is also included in our frame propagation mechanism that improves logo detection by utilizing the continuity of logos across frames. We use a tennis video dataset and an associated logo collection for detection evaluation. Experiments show that the proposed method outperforms existing methods with a higher accuracy.
Enhancement of Patch Antenna Gain Using Cylindrical Shell-Shaped Superstrate

A novel structure to enhance patch antenna gain based on phase compensation concept is presented. Putting a superstrate as flat artificial lens over normal patch antenna, phases of distributed electric field arrows will be same, leading to patch antenna gain enhancement. By introducing a novel criterion named phase pattern consideration for phase compensation method, a new shaped superstrate for this method is designed. Since design strategy for the superstrate is extracting from phase pattern of distributed electric field, antenna gain is increased 48% compared to the previous structure for patch antenna gain enhancement using phase compensation method. While resonance frequency and impedance bandwidth of normal patch antenna and patch antenna presented in the previous work are almost the same with proposed antenna, antenna gain is intensified from 6.9 to 10.2 dB. Moreover, a method for compacting antenna size based on 3 dB angular beamwidth is suggested. Finally, the proposed antenna is fabricated, and its measurement results verify gain enhancement.
Teaching College Writing in a High School Setting: The Impact of Concurrent Enrollment on Teacher Learning and Practice

Teaching College Writing in a High School Setting: The Impact of Concurrent Enrollment Teacher Learning and Practice Cornelia Anne Kirking Chair of the Supervisory Committee: Heather Hebard, Ph.D. College of Education Curriculum and Instruction In today’s educational climate, in which preparing all K-12 students to succeed in college and career is paramount, a prominent concern is to ensure that students leave high school with “college level” writing skills (Acker & Halasek, 2008; Crank, 2012; Moss & Bordelon, 2010). Notably, these discussions revolve around ensuring students are ready to cross the threshold between high school and college writing, and around giving them the tools they need to bridge the gap. With few avenues for conversation or collaboration with university faculty, high school teachers aiming to prepare students for college writing sometimes feel as though they are “in the dark” (Davies, 2006). This perennial separation means that secondary teachers, who are charged with preparing their students for college with little current knowledge about expectations in college courses, end up reifying “divides” and “gaps” separating high school and college. My study considered Concurrent Enrollment (CE) composition programs as one model for attempting to facilitate communication and collaboration between high school and college stakeholders. To investigate the potential CE programs have to serve as learning opportunities
TolB protein of Escherichia coli K‐12 interacts with the outer membrane peptidoglycan‐associated proteins Pal, Lpp and OmpA

The Tol–Pal proteins of Escherichia coli are involved in maintaining outer membrane integrity. Transmembrane domains of TolQ, TolR and TolA interact in the cytoplasmic membrane, while TolB and Pal form a complex near the outer membrane. TolB and the central domain of TolA interact in vitro with the outer membrane porins. In this study, both genetic and biochemical analyses were carried out to analyse the links between TolB, Pal and other components of the cell envelope. It was shown that TolB could be cross‐linked in vivo with Pal, OmpA and Lpp, while Pal was associated with TolB and OmpA. The isolation of pal and tolB mutants disrupting some interactions between these proteins represents a first approach to characterizing the residues contributing to the interactions. We propose that TolB and Pal are part of a multiprotein complex that links the peptidoglycan to the outer membrane. The Tol–Pal proteins might form transenvelope complexes that bring the two membranes into close proximity and help some outer membrane components to reach their final destination.
Cortisol Infusion Decreases Renin, But Not PGHS-2, EP2, or EP4 mRNA Expression in the Kidney of the Fetal Sheep at Days 109–116

Renal prostaglandins (PG), renin, and cortisol are necessary for normal kidney development and function during fetal life. We examined the effects of cortisol infusion before completion of nephrogenesis (d 109–116 gestation; 2.0–3.0 mg hydrocortisone succinate/24 h) on the renal mRNA expression of PGHS-2, the PGE2 receptors, EP2 and EP4, and renin in fetal sheep. Cortisol infusion raised plasma cortisol levels to 42.8 ± 6.0 nmol/L compared with saline infusion levels of 1.5 ± 0.5 nmol/L (p < 0.001), but had no effect on fetal body weight, proportional kidney mass, or blood gases. Cortisol decreased significantly the relative expression of renin mRNA (saline: 0.93 ± 0.06 units; cortisol: 0.32 ± 0.03 units, p < 0.05), however it had no effect upon the expression of PGHS-2, EP2, or EP4 mRNA in fetal sheep kidney. Although there is substantial evidence that PGE2 acting through either the EP2 or EP4 receptor stimulates renin synthesis in the adult kidney, our results have demonstrated that before the completion of nephrogenesis, cortisol down-regulation of renin mRNA expression is independent of any change in the expression of PGHS-2, EP2, or EP4 mRNA expression. During nephrogenesis, the insensitivity of PGHS-2, EP2, and EP4 expression to down-regulation by cortisol may permit continued PG regulation of renal development and urine formation.
The Drosophila Cyclin D–Cdk4 complex promotes cellular growth

Mammalian cyclin D–Cdk4 complexes have been characterized as growth factor‐responsive cell cycle regulators. Their levels rise upon growth factor stimulation, and they can phosphorylate and thus neutralize Retinoblastoma (Rb) family proteins to promote an E2F‐dependent transcriptional program and S‐phase entry. Here we characterize the in vivo function of Drosophila Cyclin D (CycD). We find that Drosophila CycD–Cdk4 does not act as a direct G1/S‐phase regulator, but instead promotes cellular growth (accumulation of mass). The cellular response to CycD–Cdk4‐driven growth varied according to cell type. In undifferentiated proliferating wing imaginal cells, CycD–Cdk4 caused accelerated cell division (hyperplasia) without affecting cell cycle phasing or cell size. In endoreplicating salivary gland cells, CycD–Cdk4 caused excessive DNA replication and cell enlargement (hypertrophy). In differentiating eyes, CycD–Cdk4 caused cell enlargement (hypertrophy) in post‐mitotic cells. Interaction tests with a Drosophila Rb homolog, RBF, indicate that CycD–Cdk4 can counteract the cell cycle suppressive effects of RBF, but that its growth promoting activity is mediated at least in part via other targets.
Diosgenin, a Novel Aldose Reductase Inhibitor, Attenuates the Galactosemic Cataract in Rats

Objective To seek efficient aldose reductase inhibitors (ARIs) with excellent in vitro and in vivo biological activities against rat galactosemic cataract. Methods The method was firstly optimized to screen strong ARIs from nonoriented synthetic compounds and natural extracts. Then, diosgenin was assessed on osmotic expansion of primarily cultured lens epithelial cells (LECs) induced by galactose (50 mM). Diosgenin was administered to galactosemic rats by oral (100 and 200 mg/kg) or direct drinking (0.1%) to evaluate its anticataract effects. Results Diosgenin was found as the strongest ARI with IC50 of 4.59 × 10−6 mol/L. Diosgenin (10 μM) evidently inhibited the formation of tiny vacuoles and upregulation of AR mRNA in LECs. In vivo, diosgenin delayed lens opacification, inhibited the increase of ratio of lens weight to body weight, and decreased AR activity, galactitol level, and AR mRNA expression, especially in the diosgenin drinking (0.1%) group. Conclusions Diosgenin was an efficient ARI, which not only significantly decreased the LECs' osmotic expansion in vitro but also markedly delayed progression of rat galactosemic cataract in vivo. Thus, diosgenin rich food can be recommended to diabetic subjects as dietary management to postpone the occurrence of sugar cataract, and diosgenin deserves further investigation for chronic diabetic complications.