Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Dynamics of the Glycine-binding Domain of the N-Methyl-d-Aspartate Receptor*

Background: The agonist glycine binds to a cleft in the bilobed extracellular domain of NMDA receptors. Results: The full agonist-bound forms of the agonist-binding domain populate more of the higher efficiency closed-cleft states of the receptor. Conclusion: Cleft closure dynamics differ for the full and partial agonist-bound forms. Significance: Dynamics and the extent of cleft closure control agonist efficacy. N-Methyl-d-aspartate receptors mediate the slow component of excitatory neurotransmission in the central nervous system. These receptors are obligate heteromers containing glycine- and glutamate-binding subunits. The ligands bind to a bilobed agonist-binding domain of the receptor. Previous x-ray structures of the glycine-binding domain of NMDA receptors showed no significant changes between the partial and full agonist-bound structures. Here we have used single molecule fluorescence resonance energy transfer (smFRET) to investigate the cleft closure conformational states that the glycine-binding domain of the receptor adopts in the presence of the antagonist 5,7-dichlorokynurenic acid (DCKA), the partial agonists 1-amino-1-cyclobutanecarboxylic acid (ACBC) and l-alanine, and full agonists glycine and d-serine. For these studies, we have incorporated the unnatural amino acid p-acetyl-l-phenylalanine for specific labeling of the protein with hydrazide derivatives of fluorophores. The single molecule fluorescence resonance energy transfer data show that the agonist-binding domain can adopt a wide range of cleft closure states with significant overlap in the states occupied by ligands of varying efficacy. The difference lies in the fraction of the protein in a more closed-cleft form, with full agonists having a larger fraction in the closed-cleft form, suggesting that the ability of ligands to select for these states could dictate the extent of activation.
Automatic Machine Learning Classification of Alzheimer's Disease Based on Selected Slices from 3D Magnetic Resonance Imagining

The most dominant form of dementia, memory loss, is Alzheimer's disease (AD). Imaging is important for monitoring, diagnosis, and education of Alzheimer's disease prediction. Automated classification of subjects could provide support for clinicians. This study examined two classification methods to separate among elderly persons with normal cognitive (NC), Alzheimer's disease (AD), and mild cognitive impairment (MCI) by using images from the magnetic resonance imaging (MRI). The dataset consists of 120 subjects separated into 40 ADs, 40 MCIs, and 40 NCs. The first technique was K-Nearest Neighbor (KNN) and the second technique was Support Vector Machine (SVM), firstly all the subjects were filtered and normalized, secondly twelve features were extracted. After feature selection, two techniques of classification were examined with Permutations and combinations for all features in order to select the best features which have the highest accuracy for identification the classes. The best average accuracy was 97.92% using SVM polynomial order three, and best all average accuracy was 95.833% using KNN with K=6, and K=7 for random selection of testing data with SVM and KNN. The results show a relatively high classification accuracy between the three clinical categories. In summary, the proposed automatic classification technique can be used as a noninvasive diagnostic tool for Alzheimer's disease, with the capability of defining early stages of the disease.
Models of satisfaction with police service

Purpose – This paper aims to examine the process of citizen satisfaction with police service, so police can emphasize important aspects of service and maintain high satisfaction.Design/methodology/approach – Citizens of Colorado Springs (n=3591) participated in one of four yearly surveys (2002‐2005) to test two structural equations models. One model used data from 2002‐2005 and latent variables of victimization, neighborhood safety, enough officers and police response to predict satisfaction with police service. A second model used data only from 2005 and 12 latent variables.Findings – The five‐variable model fits the data very well (CFI=0.95). It did not vary from 2002 to 2005. The 12‐variable model explained the satisfaction process more completely but fits less well (CFI=0.91). Neither model varied by demographic characteristics of respondents.Practical implications – Police should implement a process‐based model of service that emphasizes citizens' feelings of neighborhood safety and police response a.
Astrocyte-Derived Proinflammatory Cytokines Induce Hypomyelination in the Periventricular White Matter in the Hypoxic Neonatal Brain

Hypoxic exposure in the perinatal period causes periventricular white matter damage (PWMD), a condition associated with myelination abnormalities. Under hypoxic conditions, glial cells were activated and released a large number of inflammatory mediators in the PWM in neonatal brain, which may result in oligodendrocyte (OL) loss and axonal injury. This study aims to determine if astrocytes are activated and generate proinflammatory cytokines that may be coupled with the oligodendroglial loss and hypomyelination observed in hypoxic PWMD. Twenty-four 1-day-old Wistar rats were exposed to hypoxia for 2 h. The rats were then allowed to recover under normoxic conditions for 7 or 28 days before being killed. Another group of 24 rats kept outside the chamber was used as age-matched controls. Upregulated expression of TNF-α and IL-1β was observed in astrocytes in the PWM of P7 hypoxic rats by double immunofluorescence, western blotting and real time RT-PCR. This was linked to apoptosis and enhanced expression of TNF-R1 and IL-1R1 in APC+ OLs. PLP expression was decreased significantly in the PWM of P28d hypoxic rats. The proportion of myelinated axons was markedly reduced by electron microscopy (EM) and the average g-ratios were higher in P28d hypoxic rats. Upregulated expression of TNF-α and IL-1β in primary cultured astrocytes as well as their corresponding receptors in primary culture APC+ oligodendrocytes were detected under hypoxic conditions. Our results suggest that following a hypoxic insult, astrocytes in the PWM of neonatal rats produce inflammatory cytokines such as TNF-α and IL-1β, which induce apoptosis of OLs via their corresponding receptors associated with them. This results in hypomyelination in the PWM of hypoxic rats.
PIBASE: a comprehensive database of structurally defined protein interfaces

MOTIVATION In recent years, the Protein Data Bank (PDB) has experienced rapid growth. To maximize the utility of the high resolution protein-protein interaction data stored in the PDB, we have developed PIBASE, a comprehensive relational database of structurally defined interfaces between pairs of protein domains. It is composed of binary interfaces extracted from structures in the PDB and the Probable Quaternary Structure server using domain assignments from the Structural Classification of Proteins and CATH fold classification systems. RESULTS PIBASE currently contains 158,915 interacting domain pairs between 105,061 domains from 2125 SCOP families. A diverse set of geometric, physiochemical and topologic properties are calculated for each complex, its domains, interfaces and binding sites. A subset of the interface properties are used to remove interface redundancy within PDB entries, resulting in 20,912 distinct domain-domain interfaces. The complexes are grouped into 989 topological classes based on their patterns of domain-domain contacts. The binary interfaces and their corresponding binding sites are categorized into 18,755 and 30,975 topological classes, respectively, based on the topology of secondary structure elements. The utility of the database is illustrated by outlining several current applications. AVAILABILITY The database is accessible via the world wide web at http://salilab.org/pibase SUPPLEMENTARY INFORMATION http://salilab.org/pibase/suppinfo.html.
Optimal error exponents in hidden Markov models order estimation

We consider the estimation of the number of hidden states (the order) of a discrete-time finite-alphabet hidden Markov model (HMM). The estimators we investigate are related to code-based order estimators: penalized maximum-likelihood (ML) estimators and penalized versions of the mixture estimator introduced by Liu and Narayan (1994). We prove strong consistency of those estimators without assuming any a priori upper bound on the order and smaller penalties than previous works. We prove a version of Stein's lemma for HMM order estimation and derive an upper bound on underestimation exponents. Then we prove that this upper bound can be achieved by the penalized ML estimator and by the penalized mixture estimator. The proof of the latter result gets around the elusive nature of the ML in HMM by resorting to large-deviation techniques for empirical processes. Finally, we prove that for any consistent HMM order estimator, for most HMM, the overestimation exponent is null.
The Effectiveness of Product Placement in Music Videos: A Study on the Promotion Strategies for Brands and Products to Target the Y Generation in Johannesburg

Product placements are strategic brand placements within media that are meant to be noticed by the consumer, to further influence purchase intentions. Placements in music videos have grown in recent years however, there is little research on placements in this medium and available research has not measured the influence of product placement on purchase intention. The study addressed the gap where product placement in music videos was under researched. This paper investigated the effectiveness of brands and products placements in music videos in influencing the purchase intentions of the Y generation population living in Johannesburg. A self-administered research questionnaire was used to collect data through a quantitative research method by convenience sampling of 420 randomly chosen respondents, aged between 18-27, obtained from the University of the Witwatersrand and Johannesburg. A six minute music video stimulus was used for respondents to base their opinions about placements. The results indicate reliability of the constructs in the model developed as Cronbach Alphas were greater than 0.6 for the variables. The main findings show the variables individual factors and execution stimulus are significantly related to brand recall, brand recognition and brand choice. In turn, brand recall, brand recognition and brand choice influence the consumer’s purchase intentions. The strongest linear relationship existed between brand choice and purchase intention. Placement strategies are equally effective for consumers in the Y generation of differing genders, income brackers and age groups. The research reveals that music videos are an effective platform to reach the targeted Y generation population and the model adapted for placements in music videos shows the stages of the processing in the consumer’s mind from exposure to placements to the final purchase intention. The findings contribute to the knowledge of strategies marketers should use to promote brands and products to effectively target the South African Y generation. DOI: 10.5901/mjss.2014. v5n20p2095
3D hand tracking by rapid stochastic gradient descent using a skinning model

The main challenge of tracking articulated structures like hands is their large number of degrees of freedom (DOFs). A realistic 3D model of the human hand has at least 26 DOFs. The arsenal of tracking approaches that can track such structures fast and reliably is still very small. This paper proposes a tracker based on ‘Stochastic Meta-Descent’ (SMD) for optimizations in such highdimensional state spaces. This new algorithm is based on a gradient descent approach with adaptive and parameter-specific step sizes. The SMD tracker facilitates the integration of constraints, and combined with a stochastic sampling technique, can get out of spurious local minima. Furthermore, the integration of a deformable hand model based on linear blend skinning and anthropometrical measurements reinforce the robustness of our tracker. Experiments show the efficiency of the SMD algorithm in comparison with common optimization methods.
Facial expressions allow inference of both emotions and their components

Following Yik and Russell (1999) a judgement paradigm was used to examine to what extent differential accuracy of recognition of facial expressions allows evaluation of the well-foundedness of different theoretical views on emotional expression. Observers judged photos showing facial expressions of seven emotions on the basis of: (1) discrete emotion categories; (2) social message types; (3) appraisal results; or (4) action tendencies, and rated their confidence in making choices. Emotion categories and appraisals were judged significantly more accurately and confidently than messages or action tendencies. These results do not support claims of primacy for message or action tendency views of facial expression. Based on a componential model of emotion it is suggested that judges can infer components from categories and vice versa.
Diversity and Activity of Methanotrophic Bacteria in Different Upland Soils

ABSTRACT Samples from diverse upland soils that oxidize atmospheric methane were characterized with regard to methane oxidation activity and the community composition of methanotrophic bacteria (MB). MB were identified on the basis of the detection and comparative sequence analysis of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. MB commonly detected in soils were closely related to Methylocaldum spp. , Methylosinus spp. , Methylocystis spp. , or the “forest sequence cluster” (USC α), which has previously been detected in upland soils and is related to pmoA sequences of type II MB (Alphaproteobacteria). As well, a novel group of sequences distantly related (<75% derived amino acid identity) to those of known type I MB (Gammaproteobacteria) was often detected. This novel “upland soil cluster γ” (USC γ) was significantly more likely to be detected in soils with pH values of greater than 6.0 than in more acidic soils. To identify active MB, four selected soils were incubated with 13CH4 at low mixing ratios (<50 ppm of volume), and extracted methylated phospholipid fatty acids (PLFAs) were analyzed by gas chromatography-online combustion isotope ratio mass spectrometry. Incorporation of 13C into PLFAs characteristic for methanotrophic Gammaproteobacteria was observed in all soils in which USC γ sequences were detected, suggesting that the bacteria possessing these sequences were active methanotrophs. A pattern of labeled PLFAs typical for methanotrophic Alphaproteobacteria was obtained for a sample in which only USC α sequences were detected. The data indicate that different MB are present and active in different soils that oxidize atmospheric methane.
Full-Wave Analysis and Optimization of a TARA-Like Shield-Assisted Paraboloidal Reflector Antenna Using a Nystrom-Type Method

Using the recently developed method based on the rigorous theory of singular and hypersingular integral equations (IEs) and Nystrom-type discretization, a paraboloidal reflector assisted with a conical shield is investigated. To decrease the computation time we propose a new method of calculation of the Modal Green's Functions in the quasi-optical range. The far and near fields of the studied reflector are analyzed in the transmission and reception cases, and reveal fine features that escape asymptotic analysis. Elementary numerical optimization of the shield-assisted paraboloidal antenna is performed.
Flying Blind : The Case for a Spatial Framework for Semantic Information

Urban environments require cognitive abilities focused on both spatial overview and detailed understanding of uses and places. These abilities are distinct but overlap and reinforce each other. Experimental recall of spatial and semantic information indicates that using a road map enables subjects to demonstrate a significantly better spatial understanding, identify semantic elements more often using common terms, place semantic elements in spatial locations with greater accuracy and recall semantic elements in tighter clusters than when using a GPS. We conclude that a spatial understanding is a necessary framework for organizing semantic information that is useful for inferred tasks.
MIRAGE: Randomizing large chunk allocation via dynamic binary instrumentation

Heap security relies heavily on the randomness of chunk allocations in memory allocators to mitigate heap fengshui and heap spraying attacks, which are the most widely used techniques in modern exploits. However, randomness in large chunk allocation has been overlooked. Memory allocators directly call mmap (sometimes brk) syscall to allocate large chunks, while the Linux kernel does not provide a fine-grained randomization for mmap/brk syscall — only the base address is randomized, but the offset between every two syscalls is predictable. The less randomized large chunk will be vulnerable to heap fengshui and heap spraying attacks. In this paper, we assess the security of three most representative general-purpose memory allocators, Glibc ptmalloc, OpenBSD PHK malloc, and DieHarder, in scenario of large-chunk-based attacks, with successful heap fengshui and heap spraying attacks under Nginx. We then present MIRAGE, a transparent, portable, and memory allocator agnostic, runtime large chunk randomizer to fortify the existing memory allocators against large-chunk-based attacks. Large chunk fengshui and spraying attacks can be successfully mitigated by MIRAGE with a fine-grained randomization in mmap/brk syscall. And, MIRAGE imposes an acceptable overhead in performance.
An angular transform of gait sequences for gait assisted recognition

A new system is proposed for gait analysis and recognition applications. The new system is based on a denoising process and a new angular transform that are applied on binary silhouettes. Each human silhouette in a gait sequence is transformed into a low dimensional feature vector consisting of average pixel distances from the center of the silhouette. The sequence of feature vectors corresponding to a gait sequence is used for identification based on a minimum-distance criterion between test and reference sequences. By using the new system on the gait challenge database, improvements in recognition performance are seen in comparison to other methods of similar or higher complexity.
the impact of outplacement programs on reemployment criteria: a longitudinal study of displaced managers and executives

The purpose of this study was to examine longitudinally the impact of outplacement support (e.g., counseling and psychological assessment) on several reemployment criteria. A sample of 1,880 managers and executives using the services of a large outplacement organization was examined. Controlling for past salary, severance, and demographics, results demonstrated that displaced managers and executives participating in programs that demonstrated higher levels of outplacement support took more time to find reemployment, had greater likelihood of reemployment, and had higher salaries in new jobs than individuals participating in programs with lower levels of outplacement support. Implications for organizations reducing their workforces are discussed.
Clonal Polymorphism of Borrelia burgdorferi Strain B31 MI: Implications for Mutagenesis in an Infectious Strain Background

ABSTRACT A major obstacle to studying the functions of particular gene products in the mouse-tick infectious cycle of Borrelia burgdorferi has been an inability to knock out genes in pathogenic strains. Here, we investigated conditions for site-directed mutagenesis in B31 MI, the low-passage-number, infectious B. burgdorferi strain whose genome was sequenced. We inactivated several plasmid and chromosomal genes in B31 MI and determined that clones carrying these mutations were not infectious for mice. However, we found extensive heterogeneity among clones and mutants derived from B31 MI based on colony phenotype, growth rate, plasmid content, protein profile, and transformability. Significantly, several B31 MI clones that were not subjected to mutagenesis but that lacked particular plasmids also exhibited defects at various stages in the infectious cycle. Therefore, the high degree of clonal polymorphism within B31 MI complicates the assessment of the contributions of individual genes to the observed phenotypes of the mutants. Our results indicate that B31 MI is not an appropriate strain background for genetic studies in infectious B. burgdorferi, and a well-defined isogenic clone is a prerequisite for targeted mutagenesis. To this end, we derived several wild-type clones from B31 MI that were infectious for mice, and gene inactivation was successful in one of these clones. Due to the instability of the genome with in vitro propagation, careful monitoring of plasmid content of derived mutants and complementation of inactivated genes will be crucial components of genetic studies with this pathogen.
The “Finger Puppets”

The resource review we examine here is provided by the Unemployed Philosophers Guild http://www.philosophersguild. com/Finger-Puppets/). On the company’s website they comment: “. we have discovered that people seem to really like the giants of our culture reduced to little finger puppets . ” In particular, we consider the use of the “finger puppets” to generate a liminal moment (Hawkins & Edwards, 2013) in management education. Liminal moments have been described as “moments in and out of time” (Delanty, 2010, p. 31). A sense of “neither here nor there; they are betwixt and between the positions assigned and arrayed by law, custom, convention, and ceremony” . that allow for the “realm of pure possibility” (Turner, 1967, p. 95). We explore the use of this resource as a liminal tool and its value to management education.
ThingML: a language and code generation framework for heterogeneous targets

One of the selling points of Model-Driven Software Engineering (MDSE) is the increase in productivity offered by automatically generating code from models. However, the practical adoption of code generation remains relatively slow and limited to niche applications. Tooling issues are often pointed out but more fundamentally, experience shows that: (i) models and modeling languages used for other purposes are not necessarily well suited for code generation and (ii) code generators are often seen as black-boxes which are not easy to trust and produce sub-optimal code. This paper presents and discusses our experiences applying the ThingML approach to different domains. ThingML includes a modeling language and tool designed for supporting code generation and a highly customizable multi-platform code generation framework. The approach is implemented in an open-source tool providing a family of code generators targeting heterogeneous platforms. It has been evaluated through several case studies and is being used for in the development of a commercial ambient assisted living system.
WiFiRe: rural area broadband access using the WiFi PHY and a multisector TDD MAC

The needs of Indian rural telecom, and the economics of currently available broadband access technologies, motivate a new system for rural broadband access, which we call WiFiRe (WiFi rural extension). The system leverages the widely available, and highly cost-reduced, WiFi chipsets. We, however, retain only the PHY from these chipsets and propose a single-channel, multisector, TDD MAC using directional antennas. The proposed WiFiRe MAC is similar to the WiMAX MAC in several respects. In this article we motivate our approach, describe the system architecture and the MAC, analyse the spatial reuse, and then, using a simple scheduler, provide an assessment of the voice and data capacity of a WiFiRe system