Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the active site of DNA polymerase β by molecular dynamics and quantum chemical calculation

It is well established that the fully formed polymerase active site of the DNA repair enzyme, polymerase β (pol β), including two bound Mg2+ cations and the nucleoside triphosphate (dNTP) substrate, exists at only one point in the catalytic cycle just prior to the chemical nucleotidyl transfer step. The structure of the active conformation has been the subject of much interest as it relates to the mechanism of the chemical step and also to the question of fidelity assurance. Although crystal structures of ternary pol β–(primer‐template) DNA–dNTP complexes have provided the main structural features of the active site, they are necessarily incomplete due to intentional alterations (e.g., removal of the 3′OH groups from primer and substrate) needed to obtain a structure from midcycle. Working from the crystal structure closest to the fully formed active site [Protein Data Bank (PDB) code: 1bpy], two molecular dynamics (MD) simulations of the solvated ternary complex were performed: one with the missing 3′OHs restored, via modeling, to the primer and substrate, and the other without restoration of the 3′OHs. The results of the simulations, together with ab initio optimizations on simplified active‐site models, indicate that the missing primer 3′OH in the crystal structure is responsible for a significant perturbation in the coordination sphere of the catalytic cation and allow us to suggest several corrections and additions to the active‐site structure as observed by crystallography. In addition, the calculations help to resolve questions raised regarding the protonation states of coordinating ligands. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
A multi-sensor physically based weather / non-weather radar echo classifier using polarimetric and environmental data in a real-time national system

Polarimetric radar observations provide information regarding the hydrometeor shape, size, and phase as well as an improved skill in differentiating radar echoes of hydrometeors from those of non-hydrometeors. In this work, a multi-sensor physically based algorithm is designed to classify weather/non-weather radar echoes. The algorithm uses reflectivity, correlation coefficient, and temperature sounding data to quality control the reflectivity data by applying a set of explicit meteorological rules. The proposed methodology are tested with a large number of real data cases across different geographical regions and seasons and showed a high accuracy (Heidke Skill Score of 0.83) in segregating weather and nonweather echoes. Comparing to other quality control methodologies using all polarimetric variables, this algorithm’s advantage is in its simplicity, effectiveness and computational efficiency. The current methodology is also demonstrated in a real-time multi-radar and multi-sensor national mosaic system.
A 0.5V VMIN 6T SRAM in 28nm UTBB FDSOI Technology Using Compensated WLUD Scheme with Zero Performance Loss

A low Vmin, 6T-SRAM is realized in 28nm UTBB (Ultra-Thin Body and BOX) FDSOI technology using read and write assist methods. We could reduce the Vmin of SRAM cell to 0.5V for the 0.120um2 high density 6T-SRAM. Read margin of the SRAM cell is recovered using a compensated under driven word line scheme. Write assist is realized using negative bit-line approach. Bit-line is pulled to a required negative value in order to provide sufficient assistance for the write operation. Required word line under drive is 90mV to ensure correct read operation. For write assist, the undershoot requirement is 114mV. We could achieve a performance of 1.2MHz at 0.5V and 40MHz at 0.6V for a 288Kb capacity SRAM with 2K words of 144bits width. The area overhead of the read and write assist scheme is 1.0 percent and 2.5 percent respectively.
A NEW ERA FOR COUPLE THERAPY: THEORY, RESEARCH, AND PRACTICE IN CONCERT

In this plenary address, presented at the Emotionally Focused Therapy “Summit” in 2006, Sue Johnson describes attachment theory as the new way of understanding adult love. It provides the road map for couple therapists to make their way through the complicated territory of adult attachment and attachment injuries. She suggests that couple therapy is more than a set a techniques in search of a theory because attachment theory offers a language for adult love—for effective dependency. The points made in this plenary include: 1) People's most basic need is for a safe emotional connection; 2) Seeking a safe haven is a sign of strength, not enmeshment or weakness; 3) This connection provides a secure base to deal with the world; 4) Fights that matter are about the quality of the emotional connection—mutual emotional accessibility and responsiveness; 5) Separation distress follows the pattern of protest, clinging on, to abandonment rage; 6) Intense emotions are the key organizers of the relationship “dance,” an.
Low-overhead segment based motion compensation for H.26L

In this paper, we describe a low-overhead MB based motion model proposed to a coding candidate architecture of emerging ITU-T video coding standard H.26L and show that it outperforms the current H.26L motion model at a lower range (e.g., 16Kbps–64Kbps) of bitrate. The current H.26L's motion compensation employs a granularity scaling strategy, which scales accuracy of motion compensation depending on an available bitrate. This results in the degradation of the prediction performance in case of lower bitrate coding, where the bit budget for motion representation has to be reduced. We propose a better harmony of overhead and gain in prediction, by introducing a motion boundary model in place of H.26L's motion compensation, that provides a better prediction performance at the lower bitrates. Our experimental results show that the proposed model achieves bit-rate saving up to 5% compared with H.26L. A Rate-Distortion analysis verifies the advantage of the proposed motion model.
Casein Kinase 2α Regulates Multidrug Resistance-Associated Protein 1 Function via Phosphorylation of Thr249

We have shown previously that the function of Ycf1p, yeast ortholog of multidrug resistance-associated protein 1 (MRP1), is regulated by yeast casein kinase 2α (Cka1p) via phosphorylation at Ser251. In this study, we explored whether casein kinase 2α (CK2α), the human homolog of Cka1p, regulates MRP1 by phosphorylation at the semiconserved site Thr249. Knockdown of CK2α in MCF7-derived cells expressing MRP1 [MRP1 CK2α(−)] resulted in increased doxorubicin sensitivity. MRP1-dependent transport of leukotriene C4 and estradiol-17β-d-glucuronide into vesicles derived from MRP1 CK2α(−) cells was decreased compared with MRP1 vesicles. Moreover, mutation of Thr249 to alanine (MRP1-T249A) also resulted in decreased MRP1-dependent transport, whereas a phosphomimicking mutation (MRP1-T249E) led to dramatic increase in MRP1-dependent transport. Studies in tissue culture confirmed these findings, showing increased intracellular doxorubicin accumulation in MRP1 CK2α(−) and MRP1-T249A cells compared with MRP1 cells. Inhibition of CK2 kinase by 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole resulted in increased doxorubicin accumulation in MRP1 cells, but not in MRP1 CK2α(−), MRP1-T249A, or MRP1-T249E cells, suggesting that CK2α regulates MRP1 function via phosphorylation of Thr249. Indeed, CK2α and MRP1 interact physically, and recombinant CK2 phosphorylates MRP1-derived peptide in vitro in a Thr249-dependent manner, whereas knockdown of CK2α results in decreased phosphorylation at MRP1-Thr249. The role of CK2 in regulating MRP1 was confirmed in other cancer cell lines where CK2 inhibition decreased MRP1-mediated efflux of doxorubicin and increased doxorubicin cytotoxicity. This study supports a model in which CK2α potentiates MRP1 function via direct phosphorylation of Thr249.
Attachment Representations in School-Age Children: The Early Development of the Child Attachment Interview (CAI)

(2002). Attachment Representations in School-Age Children: The Early Development of the Child Attachment Interview (CAI) Journal of Infant, Child, and Adolescent Psychotherapy: Vol. 2, Attachment. Current Research, Theory, and Clinical Practice. Proceedings of a Conference Held in New York, December 1–2, 2000, pp. 91-105.
Capture models for generalized fading channels

In classic analysis of capture effect, well-known expressions exist for the capture probabilities in the uplink of multiple-access wireless networks in Rayleigh fading channels. In this paper, we derive new analytical expressions for the average capture probabilities and PDFs of SIR in generalized (Nakagami-m) fading channels (capture model 1). The capture model 2 relates the capture effect with the receiver's BER performance and produces more realistic results for the capture probability in Nakagami-m channels.
Iterated Pythagorean Fractal Tree Multiband Antenna

This paper presents the design & analysis of a planar multiband antenna (Iterated Pythagorean fractal tree antenna) with impedance steps in base path. Impedance steps are adopted with finite ground plane for better impedance matching, multiband & bandwidth characteristics as compare to non-iterated form. As tree iteration increases new resonance frequency will obtained, Iterated Pythagorean fractal multiband tree antenna (IPTFA) has compact size of 41.08*41.08*1.57 mm 3 and operates over the frequency band of 2.4 GHz. The improvement in multiband behavior id investigated & discussed with VSWR<2.
Workplace Employee Representatives , 1980-2004

This paper focuses on the changing prevalence and activities of workplace employee representatives over the period 1980-2004. The broad changes that affected industrial relations in Britain over this period had profound effects for trade unions. How did these changes affect employee representation in the workplace? The paper assesses whether the numbers of shop stewards fell in line with union membership. It also investigates changes in the characteristics of shop stewards changed over time, and changes in their role. The paper also considers whether a declining preference for unionism combined with legislative support for employee consultation to breed more extensive systems of nonunion employee representation.
Unified theory of resistive and inertial ballooning modes in three-dimensional configurations

Analytic results for the stability of resistive ballooning modes (RBMs) and electron inertial ballooning modes are obtained using a two-scale analysis. This work generalizes previous calculations used for axisymmetric s−α geometry [R. H. Hastie, J. J. Ramos, and F. Porcelli, Phys. Plasmas 10, 4405 (2003)] to general three-dimensional geometry. A unified theory is developed for RBMs and inertial ballooning modes, in which the effects of both ideal magnetohydrodynamic free energy (as measured by the asymptotic matching parameter Δ′) and geodesic curvature drives in the nonideal layer are included in the dispersion relation. This unified theory can be applied to determine the stability of drift-resistive-inertial ballooning modes in the low temperature edge regions of tokamak and stellarator plasmas where steep density gradients exist.
Triphase Interface Synthesis of Plasmonic Gold Bellflowers as Near-Infrared Light Mediated Acoustic and Thermal Theranostics

We present a novel gold bellflower (GBF) platform with multiple-branched petals, prepared by a liquid–liquid–gas triphase interface system, for photoacoustic imaging (PAI)-guided photothermal therapy (PTT). Upon near-infrared (NIR) laser irradiation, the GBFs, with strong NIR absorption, showed very strong PA response and an ultrahigh photothermal conversion efficiency (η, ∼74%) among the reported photothermal conversion agents. The excellent performance in PAI and PTT is mainly attributed to the unique features of the GBFs: (i) multiple-branched petals with an enhanced local electromagnetic field, (ii) long narrow gaps between adjacent petals that induce a strong plasmonic coupling effect, and (iii) a bell-shaped nanostructure that can effectively amplify the acoustic signals during the acoustic propagation. Besides the notable PTT and an excellent PAI effect, the NIR-absorbing GBFs may also find applications in NIR light-triggered drug delivery, catalysis, surface enhanced Raman scattering, stealth, antireflection, IR sensors, telecommunications, and the like.
Protecting Sensitive Association Rules in Privacy Preserving Data Mining using Genetic Algorithms

and security risks taken place from the application of different data mining techniques to great organizational data storehouses have been exclusively inspected by a new research domain, the so-called privacy preserving data mining. Association rule hiding is one of the privacy preserving techniques which study the problem of hiding sensitive association rules. There are many algorithms and techniques were developed to solve this problem. In this research work, we have used genetic algorithm optimization technique for protecting sensitive association rules.
The impact of impermanent Web-located citations: A study of 123 scholarly conference publications

This paper reports on research that examined the viable nature of 1068 Web-located citations in 123 academic conference papers published between 1995 and 2003. The study appears to be one of the few but increasing number of investigations that examines the growing practice of authors citing URLs in their publications to support and argue their scholarly research. The research found that some 46% of all citations to Web-located sources could not be accessed- with the HTTP 404 message (61.5%) being the greatest cause of missing citations. Collectively, the missing citations accounted for 22.0% of all citations, which represents a significant reduction in the theoretical knowledge base underpinning many scholarly articles. Furthermore, this paper argues that the consequences of disappearing Web-located citations has led to diminished opportunities for future researchers to examination the underlaying foundations of discourse and argument in scholarly articles.
Nature versus Nurture in Longevity

This paper estimates the contribution of nature and nurture to the variance of longevity in a cross section of individuals. Our approach di¤ers from that used in the genetics and biological literature in that we develop a simple model of longevity determination and use it to bound the contribution of nature to longevity. Using estimates of the key model parameters available in the demographic and genetics literature as well as our own estimate of the genetic transmission parameter (based on a new longevity dataset), we nd that genetic factors (nature) cannot explain more than 32 percent of the cross-sectional variance in longevity. Our estimates also imply a weak intergenerational transmission of environmental factors. As a consequence, most of the variance in longevity is due to the variance of non-inherited environmental factors.
BASIC SCIENCE REVIEW

Background. In the normal host, there are a variety of cellular systems that ensure the accurate replication and repair of DNA. Recent evidence suggests that there are individual variations in the ability to preserve the genome. Certain individuals have defects in these checkpoints and have an inherent genomic instability. They are susceptible to the accumulation of DNA damage and are prone to carcinogenesis. This article examines the role of genomic instability in the development of head and neck
Declarative Systems for Large-Scale Machine Learning

In this article, we make the case for a declarative foundation for data-intensive machine learning systems. Instead of creating a new system for each specific flavor of machine learning task, or hardcoding new optimizations, we argue for the use of recursive queries to program a variety of machine learning algorithms. By taking this approach, database query optimization techniques can be utilized to identify effective execution plans, and the resulting runtime plans can be executed on a single unified data-parallel query processing engine.
Vandetanib in Children and Adolescents with Multiple Endocrine Neoplasia Type 2B Associated Medullary Thyroid Carcinoma

Purpose: Medullary thyroid carcinoma (MTC) is a manifestation of multiple endocrine neoplasia type 2 (MEN2) syndromes caused by germline, activating mutations in the RET (REarranged during Transfection) proto-oncogene. Vandetanib, a VEGF and EGF receptor inhibitor, blocks RET tyrosine kinase activity and is active in adults with hereditary MTC. Experimental Design: We conducted a phase I/II trial of vandetanib for children (5–12 years) and adolescents (13–18 years) with MTC to define a recommended dose and assess antitumor activity. The starting dose was 100 mg/m2 administered orally, once daily, continuously for 28-day treatment cycles. The dose could be escalated to 150 mg/m2/d after two cycles. Radiographic response to vandetanib was quantified using RECIST (v1.0), biomarker response was measured by comparing posttreatment serum calcitonin and carcinoembryonic antigen (CEA) levels to baseline, and a patient-reported outcome was used to assess clinical benefit. Results: Sixteen patients with locally advanced or metastatic MTC received vandetanib for a median (range) 27 (2–52) cycles. Eleven patients remain on protocol therapy. Diarrhea was the primary dose-limiting toxicity. In subjects with M918T RET germline mutations (n = 15) the confirmed objective partial response rate was 47% (exact 95% confidence intervals, 21%–75%). Biomarker partial response was confirmed for calcitonin in 12 subjects and for CEA in 8 subjects. Conclusion: Using an innovative trial design and selecting patients based on target gene expression, we conclude that vandetanib 100 mg/m2/d is a well-tolerated and highly active new treatment for children and adolescents with MEN2B and locally advanced or metastatic MTC. Clin Cancer Res; 19(15); 4239–48. ©2013 AACR.
Neorickettsia sennetsu as a Neglected Cause of Fever in South-East Asia

Neorickettsia sennetsu infection is rarely recognized, with less than 100 globally reported patients over the last 50 years. The disease is thought to be contracted by eating raw fish, a staple of many South-East Asian cuisines. In 2009, the first patient with sennetsu was identified in the Lao PDR (Laos), raising the question as to how common this organism and related species are in patients presenting with fever. We investigated the frequency of N. sennetsu infection at hospitals in diverse areas of Laos. Consenting febrile hospital inpatients from central (Vientiane: n = 1,013), northern (Luang Namtha: n = 453) and southern (Salavan: n = 171) Laos were screened by PCR for N. sennetsu, if no previous positive direct diagnostic test was available. A PCR-restriction fragment length polymorphism assay was developed to differentiate between N. sennetsu, Ehrlichia chaffeensis and Anaplasma phagocytophilum. To allow more detailed studies of N. sennetsu, culture was successfully established using a reference strain (ATCC VR-367), identifying a canine-macrophage cell line (DH82) to be most suitable to visually identify infection. After screening, N. sennetsu was identified and sequence confirmed in four (4/1,637; 0.2%) Lao patients. Despite the previously identified high seroprevalence of N. sennetsu antibodies in the Lao population (~17%), acute N. sennetsu infection with sufficient clinical signs to prompt hospitalization appears to be rare. The reservoir, zoonotic cycle and pathogenicity of N. sennetsu remain unclear and require further investigations.
The bilingual advantage in the Stroop task: simultaneous vs. early bilinguals*

The Stroop task has become a popular paradigm in investigations of bilingual cognitive control. While several studies show a cognitive control advantage for bilinguals, recent studies have countered these findings. The present study investigates two factors that may account for conflicting results: participant grouping and task difficulty. While we find no differences between simultaneous and early bilinguals (age groups traditionally both classified as “early” bilinguals) when the task uses only one language, we find a significant difference between the two when languages are mixed. We suggest treating the two groups as distinct, and note the importance of the bilingual context.
DEM: A discrete electromagnetism-like mechanism for solving discrete problems

In this paper a novel model based on Electromagnetism-Like Mechanism (EM) is proposed which is highly compatible with discrete space problems. The proposed method utilizes the EM operators to move particles towards an optimal or near optimal solutions. In fact, the proposed algorithm exploits the crossover operator to calculate forces on particles and move them according to these forces. To keep the algorithm from getting sock on local maxima a mutation approach is used. To show the performance of the proposed method it is applied on a discrete space problem called Multidimensional Knapsack Problem (MKP). To compare our results, some standard test benches of the MKP are used and the results are compared with other methods. Experimental results showed that the proposed method outperforms some new methods in terms of the number of needed iterations to find best known solutions (about 73% in average) and CPU time (about 77%). Furthermore, the DEM is applied on some bigger MKPs and the experiments showed that the algorithm works very well and had very small error from best known optimums (0.17% error in average).
A novel interaction method based on a mobile device in intelligent space

In this video, we propose a new interaction method using mobile devices in Intelligent Space (iSpace). This interaction, called R-Fii (Real-world Flexible Interaction Interface), uses mobile devices, mainly cellular phones, as stable interface channels to iSpace. The users are able to control any objects and get information of the objects in iSpace with R-Fii.
Semantic segmentation using Three-Dimensional Cellular Evolutionary Networks

Image segmentation and image recognition are challenging processes, and the methods of merging those two processes like semantic segmentation have been studied. However, it is a lot of labor to construct the processes of segmentation and recognition manually, so automatic construction of those approaches using machine learning or evolutionary computation have been proposed. In this paper, we propose a model of pixel-wise image segmentation and recognition using Cellular Evolutionary Networks (CEN). Our proposed model is composed of a regular array of the identical feed forward networks, represented in Cartesian Genetic Programming (CGP), and each CGP connects with neighbor CGPs. Besides, we also propose a new model of CEN called Three-Dimensional Cellular Evolutionary Networks (3D-CEN), which is composed of multiple CENs. We applied CEN and 3D-CEN to road scene images and verified the effectiveness of our method, and experimental results showed that our new model acquired better performance compared with other methods if efficient evolution for CEN is done.