Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi‐LZerD: Multiple protein docking for asymmetric complexes

The tertiary structures of protein complexes provide a crucial insight about the molecular mechanisms that regulate their functions and assembly. However, solving protein complex structures by experimental methods is often more difficult than single protein structures. Here, we have developed a novel computational multiple protein docking algorithm, Multi‐LZerD, that builds models of multimeric complexes by effectively reusing pairwise docking predictions of component proteins. A genetic algorithm is applied to explore the conformational space followed by a structure refinement procedure. Benchmark on eleven hetero‐multimeric complexes resulted in near‐native conformations for all but one of them (a root mean square deviation smaller than 2.5Å). We also show that our method copes with unbound docking cases well, outperforming the methodology that can be directly compared with our approach. Multi‐LZerD was able to predict near‐native structures for multimeric complexes of various topologies.Proteins 2012; © 2012 Wiley Periodicals, Inc.
Quality Assessment in Spatial Clustering of Data Mining

Because of the use of computers and its advances in scientific data handling and advancement of various geo and space borne sensors, we are now faced with a large amount of data. Therefore, the development of new techniques and tools that support the transforming the data into useful knowledge has been the focus of the relatively new and interdisciplinary research area named “knowledge discovery in spatial databases or spatial data mining”. Spatial data mining is a demanding field since huge amounts of spatial data have been collected in various applications such as real-estate marketing, traffic accident analysis, environmental assessment, disaster management and crime analysis. Thus, new and efficient methods are needed to discover knowledge from large databases such as crime databases. Because of the lack of primary knowledge about the data, clustering is one of the most valuable methods in spatial data mining. As there exist a number of methods for clustering, a comparative study to select the best one according to their usage has been done in this research. In this paper we use Self Organization Map (SOM) artificial neural network and K-means methods to evaluate the patterns and clusters resulted from each one. Furthermore, the lack of pattern quality assessment in spatial clustering can lead to meaningless or unknown information. Using compactness and separation criteria, validity of SOM and K-means methods has been examined. Data used in this paper has been divided in two sections. First part contains simulated data contain 2D x,y coordinate and second part of data is real data corresponding to crime investigation. The result of this paper can be used to classify study area, based on property crimes. In this work our study area classified into several classes representing high to low crime locations. Thus, accuracy of region partitioning directly depends on clustering quality.
A 2-Oxoglutarate-Dependent Dioxygenase Mediates the Biosynthesis of Glucoraphasatin in Radish1[OPEN]

Biosynthesis of glucoraphasatin, a major glucosinolate in radish, is mediated by 2-oxoglutarate-dependent dioxygenase. Glucosinolates (GSLs) are secondary metabolites whose degradation products confer intrinsic flavors and aromas to Brassicaceae vegetables. Several structures of GSLs are known in the Brassicaceae, and the biosynthetic pathway and regulatory networks have been elucidated in Arabidopsis (Arabidopsis thaliana). GSLs are precursors of chemical defense substances against herbivorous pests. Specific GSLs can act as feeding blockers or stimulants, depending on the pest species. Natural selection has led to diversity in the GSL composition even within individual species. However, in radish (Raphanus sativus), glucoraphasatin (4-methylthio-3-butenyl glucosinolate) accounts for more than 90% of the total GSLs, and little compositional variation is observed. Because glucoraphasatin is not contained in other members of the Brassicaceae, like Arabidopsis and cabbage (Brassica oleracea), the biosynthetic pathways for glucoraphasatin remain unclear. In this report, we identified and characterized a gene encoding GLUCORAPHASATIN SYNTHASE 1 (GRS1) by genetic mapping using a mutant that genetically lacks glucoraphasatin. Transgenic Arabidopsis, which overexpressed GRS1 cDNA, accumulated glucoraphasatin in the leaves. GRS1 encodes a 2-oxoglutarate-dependent dioxygenase, and it is abundantly expressed in the leaf. To further investigate the biosynthesis and transportation of GSLs in radish, we grafted a grs1 plant onto a wild-type plant. The grafting experiment revealed a leaf-to-root long-distance glucoraphasatin transport system in radish and showed that the composition of GSLs differed among the organs. Based on these observations, we propose a characteristic biosynthesis pathway for glucoraphasatin in radish. Our results should be useful in metabolite engineering for breeding of high-value vegetables.
Anaesthetic management of a unilateral adrenalectomy of an adrenocortical tumour in a dog

Adrenalectomies in dogs are being more commonly performed, however anaesthetic management of such cases can be challenging due to the multiple aetiologies of adrenal tumours and the physiological role of adrenal glands. This case report describes the anaesthetic management of a dog with clinical signs of hyperadrenocorticism that underwent unilateral adrenalectomy via laparotomy and discusses anaesthetic preparedness, protocol selection and management of complications for dogs undergoing adrenalectomy.
Identification of a Physiological Phosphorylation Site of the Herpes Simplex Virus 1-Encoded Protein Kinase Us3 Which Regulates Its Optimal Catalytic Activity In Vitro and Influences Its Function in Infected Cells

ABSTRACT Us3 is a serine/threonine protein kinase encoded by herpes simplex virus 1 (HSV-1). Here, we report the identification of a physiological Us3 phosphorylation site on serine at position 147 (Ser-147) which regulates its protein kinase activity in vitro. Moreover, mutation of this site influences Us3 function, including correct localization of the enzyme and induction of the usual morphological changes in HSV-1-infected cells. These conclusions are based on the following observations: (i) in in vitro kinase assays, a domain of Us3 containing Ser-147 was specifically phosphorylated by Us3 and protein kinase A, while a mutant domain in which Ser-147 was replaced with alanine was not; (ii) in vitro, alanine replacement of Ser-147 (S147A) in Us3 resulted in significant impairment of the kinase activity of the purified molecule expressed in a baculovirus system; (iii) phosphorylation of Ser-147 in Us3 tagged with the monomeric fluorescent protein (FP) VenusA206K (VenusA206K-Us3) from Vero cells infected with a recombinant HSV-1 encoding VenusA206K-Us3 was specifically detected using an antibody that recognizes phosphorylated serine or threonine residues with arginine at the −3 and −2 positions; and (iv) the S147A mutation influenced some but not all Us3 functions, including the ability of the protein to localize itself properly and to induce wild-type cytopathic effects in infected cells. Our results suggest that some of the regulatory activities of Us3 in infected cells are controlled by phosphorylation at Ser-147.
THE EFFECT OF PQRST (PREVIEW-QUESTION-READ-STATE-TEST) AND QAR (QUESTION-ANSWER RELATIONSHIP) TECHNIQUES ON STUDENTS WITH LOW INTEREST ON THEIR READING COMPREHENSION ON PROCEDURE TEXTS: STUDY AT GRADE VII OF SMPN 2 PADANG

Abstract: Artikel ini menyajikan hasil penemuan penelitian yang bertujuan untuk mengetahui apakah siswa dengan minat rendah yang diajar dengan teknik PQRST memiliki pemahaman baca teks prosedur yang lebih tinggi dari pada siswa dengan minat rendah yang diajar dengan teknik QAR. Penelitian ini adalah penelitian quasi-eksperimen dengan desain penelitian treatment by block. Populasi penelitian ini adalah siswa kelas VII SMPN 2 Padang yang terdaftar pada tahun ajaran 2011/2012 yang terdiri dari 184 siswa yang tersebar di enam kelas. Sampel penelitian ini diambil melalui teknik intact group sampling. Dengan menggunakan lotre diperolehkelas VII.4 sebagai kelas eksperimen dan kelas VII.1 sebagaikelas kontrol yang masing-masingnya terdiri dari30 siswa.Sebelum diberikan treatment, dilakukan penentuan siswa yang minat membacanya tinggi dan rendah. Setelah ditentukan, peneliti fokus pada siswa yang memiliki minat membacanya rendah. Data penelitian dikumpulkan melalui test (pretest dan posttest), dan angket yang kemudian dianalisis dengan uji Chi-Square, uji F (uji varians) dan uji t. Hasil analisis data menunjukkan bahwa siswa dengan minat rendah yang diajar dengan teknik PQRST memiliki pemahaman baca teks prosedur yang lebih tinggi dari pada siswa dengan minat rendah yang diajar dengan teknik QAR. Pengujian hipotesis menghasilkan harga t hitung secara signifikan lebihbesar dari t tabel. Ini berarti bahwa hipotesis nol (H 0 )ditolak dan hipotesis alternatif (H 1 ) diterima. Key words: PQRST technique, QAR technique, students with low interest, reading comprehension, procedure texts
Targeting Mutant p53 by a SIRT1 Activator YK-3-237 Inhibits the Proliferation of Triple-Negative Breast Cancer Cells

Many types of mutations in tumor suppressor p53 are oncogenic through gain-of-function. Therefore, targeting mutant p53 (mtp53) is a promising therapeutic approach to fight against many types of cancers. We report here a small molecule compound YK-3-237 that reduces acetylation of mtp53 and exhibits anti-proliferative effects toward triple-negative breast cancer (TNBC) cells carrying mtp53. YK-3-237 activates SIRT1 enzyme activities in vitro and deacetylation of both mtp53 and wild type p53 (WTp53) in a SIRT1-dependent manner. Deacetylation of mtp53 resulted in depletion of mtp53 protein level and up-regulated the expression of WTp53-target genes, PUMA and NOXA. YK-3-237 also induces PARP-dependent apoptotic cell death and arrests the cell cycle at G2/M phase in mtp53 TNBC cells. Taken together, our data suggest that targeting acetylation of mtp53 is a potential target to treat human cancers.
Cowherd's injury: Traumatic retrospondyloptosis of L1 over L2 in a 7-year-old child

Traumatic retrolisthesis of the first lumbar vertebra is a rare injury and only one case has been documented in the literature. We report a case of traumatic retrolisthesis of the first lumbar vertebra in a 7-year old child. He was injured after being dragged by a cow and presented with Frenkel grade A paraplegia. His plain radiographs revealed complete retrolisthesis of the first lumbar vertebra over the second. The patient was treated surgically with open reduction and sublaminar wire loop rectangle fixation. The patient showed Frankle grade D (Frankle grade) neurological recovery in the postoperative period over a period of 15 months. This case is reported in view of rarity and mechanism of injury is described.
Power line communication using timed transmission

This paper reviews established methods of communication using in-building power conductors with particular attention to the 100 kHz to 450 kHz frequency range. It also reviews line characteristic impedance and it presents new measurements of attenuation and noise on the power conductors. Measurements illustrate interfering noise caused by individual electrical loads and also the combined noise at power outlets in an office environment. Using a simple FSK transmission system, bit errors were measured as a function of time and these were found to coincide with noise bursts that occur at regular times during the 60 Hz cycle. The paper concludes by proposing an interference avoidance scheme where transmission is suspended during periods of high interference and then continues during quiet intervals.
Building Support Vector Machines with Reduced Classifier Complexity

Support vector machines (SVMs), though accurate, are not preferred in applications requiring great classification speed, due to the number of support vectors being large. To overcome this problem we devise a primal method with the following properties: (1) it decouples the idea of basis functions from the concept of support vectors; (2) it greedily finds a set of kernel basis functions of a specified maximum size (dmax) to approximate the SVM primal cost function well; (3) it is efficient and roughly scales as O(ndmax2) where n is the number of training examples; and, (4) the number of basis functions it requires to achieve an accuracy close to the SVM accuracy is usually far less than the number of SVM support vectors.
Triazole-containing monophosphate mRNA cap analogs as effective translation inhibitors

Synthetic analogs of the 5′ end of mRNA (cap structure) are widely used in molecular studies on mechanisms of cellular processes such as translation, intracellular transport, splicing, and turnover. The best-characterized cap binding protein is translation initiation factor 4E (eIF4E). Recognition of the mRNA cap by eIF4E is a critical, rate-limiting step for efficient translation initiation and is considered a major target for anticancer therapy. Here, we report a facile methodology for the preparation of N2-triazole-containing monophosphate cap analogs and present their biological evaluation as inhibitors of protein synthesis. Five analogs possessing this unique hetero-cyclic ring spaced from the m7-guanine of the cap structure at a distance of one or three carbon atoms and/or additionally substituted by various groups containing the benzene ring were synthesized. All obtained compounds turned out to be effective translation inhibitors with IC50 similar to dinucleotide triphosphate m7GpppG. As these compounds possess a reduced number of phosphate groups and, thereby, a negative charge, which may support their cell penetration, this type of cap analog might be promising in terms of designing new potential therapeutic molecules. In addition, an exemplary dinucleotide from a corresponding mononucleotide containing benzyl substituted 1,2,3-triazole was prepared and examined. The superior inhibitory properties of this analog (10-fold vs. m7GpppG) suggest the usefulness of such compounds for the preparation of mRNA transcripts with high translational activity.
Lossless Representation of Graphs using Distributions

We consider complete graphs with edge weights and/or node weights taking values in some set. In the first part of this paper, we show that a large number of graphs are completely determined, up to isomorphism, by the distribution of their sub-triangles. In the second part, we propose graph representations in terms of one-dimensional distributions (e.g., distribution of the node weights, sum of adjacent weights, etc.). For the case when the weights of the graph are real-valued vectors, we show that all graphs, except for a set of measure zero, are uniquely determined, up to isomorphism, from these distributions. The motivating application for this paper is the problem of browsing through large sets of graphs.
An Opportunity for Prevention: Prevalence, Incidence, and Sexual Risk for HIV Among Young Asian and Pacific Islander Men Who Have Sex With Men, San Francisco

Objectives: We investigated HIV prevalence and incidence and related risk factors among young Asian and Pacific Islander (API) men who have sex with men (MSM). Design: We conducted a cross-sectional survey. Methods: A venue-based sample of 496 young API MSM in San Francisco completed face-to-face questionnaires and received HIV counseling and testing. Results: HIV prevalence was 2.6% and annualized HIV incidence was 1.8% per year. In multivariate analysis, being American-born, having 51+ lifetime sex partners, and having attended a “‘circuit party” (multiday large MSM gatherings) were associated with HIV infection. Forty-seven percent of the sample reported unprotected anal intercourse in the past 6 months. Conclusions: The current levels of HIV prevalence, HIV incidence, and sexual risk behavior suggest an emerging HIV epidemic among young API MSM in San Francisco.
Solar Active Region Flux Fragmentation, Subphotospheric Flows, and Flaring

We explore the properties of the fragmentation of magnetic flux in solar active regions. We apply gradient-based tessellation to magnetograms of 59 active regions to identify flux fragments. First, we find that the distribution function of flux fragments in these regions is highly consistent with lognormal form, which is the most direct evidence yet obtained that repeated random bifurcation dominates fragmentation and coalescence in all active regions. Second, we apply nonparametric statistical methods to the variance of the lognormal distribution of fragment flux, the flare X-ray energy output of the active regions, and kinetic helicity measurements in the upper convection zone to show that there is no significant statistical relationship between the amount of fragmentation of an active region's flux at photospheric levels and the amplitude of either its average kinetic helicity density in the upper convection zone or its X-ray flare energy output.
Unifying on-chip and inter-node switching within the Anton 2 network

The design of network architectures has become increasingly complex as the chips connected by inter-node networks have emerged as distributed systems in their own right, complete with their own on-chip networks. In Anton 2, a massively parallel special-purpose supercomputer for molecular dynamics simulations, we managed this complexity by reusing the on-chip network as a switch for inter-node traffic. This unified network approach introduces several design challenges. Maintaining fairness within the inter-node network is difficult, as each hop becomes a sequence of many on-chip routing decisions. We addressed this problem with an inverse-weighted arbiter that ensures fairness with low implementation costs. Balancing the load of inter-node traffic across the on-chip network is also critical, and we adopted an optimization approach to design an appropriate routing algorithm. Finally, the on-chip routers carry inter-node traffic, so they must implement inter-node virtual channels to avoid deadlock. In order to keep the routers small and fast, we developed a deadlock-free routing algorithm that reduces the number of virtual channels by one-third relative to previous approaches. The resulting Anton 2 network implementation efficiently utilizes its inter-node channels and provides low messaging latency, while occupying a modest amount of silicon area.
Metabolic Serum Uric Acid Is a Determinant of Metabolic Syndrome in a Population-Based Study

Results: Metabolic syndrome was present in 39.1% of the cohort. Linear regression analysis of uric acid levels in a model comprising 13 variables identified gender, waist girth, total cholesterol (TC), alcohol usage, triglycerides, log C-reactive protein (CRP), and log -glutamyl transferase (GGT), and in women diuretic use and elevated blood pressure (BP), as significant independent covariates whereby the largest contribution (1.6 mg/dL) was generated by waist girth. Logistic regression analysis of serum uric acid for MS disclosed for the top versus the bottom tertile an odds ratio (OR) of 1.89 (95% confidence interval [CI]: 1.45–2.46) in men and women combined, after ajustment for sex, age, TC, log CRP, log GGT, alcohol, and
Phenotypic Detection of Carbapenemase-Producing Enterobacteriaceae by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and the Carba NP Test

ABSTRACT We compared the diagnostic accuracy of the Carba NP test with that of a straightforward matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) method for detecting carbapenemase-producing Enterobacteriaceae (CPE). Using PCR as the reference method, both tests demonstrated a sensitivity of 87% and a specificity of 100%. MALDI-TOF MS offers a potential alternative for the rapid detection of CPE in the clinical laboratory setting.
Researching young people’s orientations to the future: the methodological challenges of using arts practice

Visual and arts-based methods are now widely used in the social sciences. In youth research they are considered to promote engagement and empowerment. This article contributes to debates on the challenges of using arts-based methods in research with young people. We discuss the experience of a multidisciplinary project investigating how young people imagine their futures – Imagine Sheppey – to critically consider the use of arts-based methods and the kinds of data produced through these practices. We make two sets of arguments. First, that the challenges of participation and collaboration are not overcome by using apparently ‘youth-friendly’ research tools. Second, that the nature of data produced through arts-based methods can leave researchers with significant problems of interpretation. We highlight these issues in relation to the focus of this project on researching the future.
Real-time ego-motion estimation using Lidar and a vehicle model based Extended Kalman Filter

Automated driving maneuvers enable a highly reproducible validation of preventive vehicle safety systems. However, the automation of vehicle guidance requires an exact and reliable knowledge of current vehicle position and motion. This paper presents a new method for the real-time estimation of the vehicle position and of further longitudinal and lateral dynamic state variables. Fundamental idea is the fusion of the Lidar-based range and bearing measurements of landmarks with the information of various vehicle sensors by means of an advanced vehicle model based Extended Kalman Filter. It takes into account the nonlinear tire characteristics at the limits of driving physics when estimating the variables. Moreover, the proposed ego-localization and ego-motion estimation scheme incorporates an approach for the automated association of Lidar-detected objects to predefined landmarks. Using the experimental results of a highly dynamic driving maneuver the accuracy and robustness of the proposed method is demonstrated.
Estimation of the Number of Endmembers Using Robust Outlier Detection Method

This paper introduces a novel approach for estimating the numbers of endmembers in hyperspectral imagery. It exploits the geometrical properties of the noise hypersphere and considers the signal as outlier of the noise hypersphere. The proposed method, called outlier detection method (ODM), is automatic and non-parametric. In a principal component space, noise is spherically symmetric in all directions and lies on the surface of a hypersphere with a constant radius. Reversely, signal radiuses are much larger that noise radius and vary in all directions, thus signal lies in a hyperellipsoid. The proposed method involves three steps: 1) noise estimation; 2) minimum noise fraction transformation; and 3) outlier detection using inter quartile range. Estimation of the number of endmembers is accomplished by the estimation of the number of noise hypersphere outliers using a robust outlier detection method. The ODM was evaluated using simulated and real hyperspectral data, and it was also compared with well-known methods for estimating the number of endmembers. Evaluation of the method showed that the method produces robust and satisfactory results, and outperforms in relation to its competitors.