Miracle-dz/UniFAR-FTUs huggingface dataset:
Replacing the Axial Ligand Tyrosine 75 or Its Hydrogen Bond Partner Histidine 83 Minimally Affects Hemin Acquisition by the Hemophore HasAp from Pseudomonas aeruginosa

Hemophores from Pseudomonas aeruginosa (HasAp), Serratia marcescens (HasAsm), and Yersinia pestis (HasAyp) bind hemin between two loops. One of the loops harbors conserved axial ligand Tyr75 (Y75 loop) in all three structures, whereas the second loop (H32 loop) contains axial ligand His32 in HasAp and HasAsm, but a noncoordinating Gln32 in HasAyp. Binding of hemin to the Y75 loop of HasAp or HasAsm causes a large rearrangement of the H32 loop that allows His32 coordination. The Q32 loop in apo-HasAyp is already in the closed conformation, such that binding of hemin to the conserved Y75 loop occurs with minimal structural rearrangement and without coordinative interaction with the Q32 loop. In this study, structural and spectroscopic investigations of the hemophore HasAp were conducted to probe (i) the role of the conserved Tyr75 loop in hemin binding and (ii) the proposed requirement of the His83–Tyr75 hydrogen bond to allow the coordination of hemin by Tyr75. High-resolution crystal structures of H83A holo-HasAp obtained at pH 6.5 (0.89 Å) and pH 5.4 (1.25 Å) show that Tyr75 remains coordinated to the heme iron, and that a water molecule can substitute for Nδ of His83 to interact with the Oη atom of Tyr75, likely stabilizing the Tyr75–Fe interaction. Nuclear magnetic resonance spectroscopy revealed that in apo-Y75A and apo-H83A HasAp, the Y75 loop is disordered, and that disorder propagates to nearby elements of secondary structure, suggesting that His83 Nδ–Tyr75 Oη interaction is important to the organization of the Y75 loop in apo-HasA. Kinetic analysis of hemin loading conducted via stopped-flow UV–vis and rapid-freeze-quench resonance Raman shows that both mutants load hemin with biphasic kinetic parameters that are not significantly dissimilar from those previously observed for wild-type HasAp. When the structural and kinetic data are taken together, a tentative model emerges, which suggests that HasA hemophores utilize hydrophobic, π–π stacking, and van der Waals interactions to load hemin efficiently, while axial ligation likely functions to slow hemin release, thus allowing the hemophore to meet the challenge of capturing hemin under inhospitable conditions and delivering it selectively to its cognate receptor.
On particle Gibbs sampling

The particle Gibbs sampler is a Markov chain Monte Carlo (MCMC) algorithm to sample from the full posterior distribution of a state-space model. It does so by executing Gibbs sampling steps on an extended target distribution defined on the space of the auxiliary variables generated by an interacting particle system. This paper makes the following contributions to the theoretical study of this algorithm. Firstly, we present a coupling construction between two particle Gibbs updates from different starting points and we show that the coupling probability may be made arbitrarily close to one by increasing the number of particles. We obtain as a direct corollary that the particle Gibbs kernel is uniformly ergodic. Secondly, we show how the inclusion of an additional Gibbs sampling step that reselects the ancestors of the particle Gibbs' extended target distribution, which is a popular approach in practice to improve mixing, does indeed yield a theoretically more efficient algorithm as measured by the asymptotic variance. Thirdly, we extend particle Gibbs to work with lower variance resampling schemes. A detailed numerical study is provided to demonstrate the efficiency of particle Gibbs and the proposed variants.
A collaborative names recommendation in the Twitter environment based on location

Friendster, Facebook, Twitter and many other microblogs have been introduced since 2004. These web 2.0 applications have become a powerful tool for communication. Each social web site has millions of users whose interact with each other regardless of their location and distance. Therefore, the mechanism of recommendation system for these sites is important for users to find suitable friends. Name recommendation should be made based on the concept of homophily which stated that relationships between individuals who have in common is higher than individuals who have nothing in common. Twitter is one of the popular social web sites that were developed in 2006. Many of the Twitter users are passive users. They just follow other users but on the other side they do not have many followers. This problem arises because reciprocal relationship is not required in Twitter. To overcome this problem, a recommendation system can help users in searching friends by taking into account reciprocal relationships. The main goal of this study is to use collaborative filtering techniques to recommend names based on geographical location. User's location is taken from the user's profile by using coordinates of latitude and longitude. Celebrities profile data sets provided by the Korea Advanced Institute of Science and Technology (KAIST) are taken for testing purposes. The result of the testing indicates the potential of exploiting geographical locations in collaboratively recommending names within Twitter environment.
Report of the Consensus Conference on the Diagnosis of Auditory Processing Disorders in School-Aged Children.

A group of 14 senior scientists and clinicians met at the Callier Center in Dallas over the 2–day period, April 27–28, 2000, in an attempt to reach a consensus on the problem of diagnosing auditory processing disorders in school-aged children. The conference was organized by James Jerger and Frank Musiek. The following individuals participated:Sharon Abel, PhD, University of Toronto, Toronto, ONJane Baran, PhD, University of Massachusetts, Amherst, MAAnthony Cacace, PhD, Albany Medical College, Albany, NYGail Chermak, PhD ‡, Washington State University, Pullman, WASusan Dalebout, PhD, University of Virginia, Charlottesville,VAJay Hall III, PhD, University of Florida, Gainesville, FLLinda Hood, PhD, Louisiana State University Medical Center, New Orleans, LALisa Hunter, PhD, University of Minnesota, Minneapolis, MNJames Jerger, PhD, University of Texas at Dallas, Dallas, TXSusan Jerger, PhD, University of Texas at Dallas, Dallas, TXRobert Keith, PhD, University of Cincinnati, Cincinnati, OHFrank Musiek, PhD, Dartmouth-Hitchcock Medical Center, Hanover, NHRoss Roeser, PhD, University of Texas at Dallas, Dallas, TXChristine Sloan, PhD, Annapolis Valley Regional School Board Berwick, NSMeeting both as separate groups and in plenary session, the conferees reached the consensus summarized below.
An Approach for Calculating Semantic Similarity between Words Using WordNet

This paper presents a new edge-counting based method using Word Net to compute the similarity. The method achieves a similarity that perfectly fits with human rating and effectively simulate the human tHought process that is people prefer to consider more differences when the semantic distance between two word is closer, and vice versa. At last, we weigh up our model against a benchmark set by human similarity judgment, and obtain a much improved result compared with other methods.
Cross‐Cultural Telecommuting Evaluation in Mexico and the United States

This paper tests the impact of differences in culture on telecommuting in the United States and Mexico. The purpose of this study is to determine the impact of each country's culture on the perceptions of telecommuting satisfaction and organizational support for telecommuting. The research questions assess the telecommuting satisfaction, and extent of support by organizational policies for telecommuting in the two countries. These results are compared with the expected outcomes due to the differences in culture in both countries. The tests are done, based on a questionnaire sample of 204 employees in the U.S. and Mexico. The statistical method is crosstabulation analysis. The results show no difference between the two samples regarding job satisfaction. Respondents in the two samples indicate differences on the extent of organizational support for telecommuting. The Mexican sample shows more support for telecommuting arrangements than the U.S. one. This result is unexpected, given the cultural differences in both countries. The findings have implications for telecommuting policies and telecommuting cross‐cultural research.
T H E N I N J a J U K E B O X

We present the design and implementation of the \Ninja Jukebox", an infrastructural service that allows a community of users to build a distributed, collaborative music repository that delivers digital music to Internet clients, and that performs simple collaborative ltering based on users' song preferences inferred by the service. The Jukebox, implemented in Java, was designed to allow rapid service evolution and recon guration, simplicity in participation, and extensibility. We demonstrate that our careful use of a distributed component architecture enabled rapid prototyping of the service, and that our use of carefully designed, strongly typed interfaces enabled the smooth evolution of the service from a simple prototype to a more complex, mature system.
A Novel Location Management Scheme and Routing Protocol for Group Communications in Cellular IP Networks

In this paper, a novel location management scheme called Distributed Group Tracking (DOT) for group communications in Cellular IP networks is proposed. In DGT, Base stations track each member of a group and build a share multicast routing tree called DGT-Tree for the group in a distributed manner. Transmission of multicast packets among group members is along the group's DGT-Tree. Simulation study has demonstrated that a better performance can be achieved by DGT over the gateway-based counterpart in terms of transmission cost as well as link load balance. Moreover, the average number of DGT operations decreases as the group size increases, showing the good scalability of the DGT scheme, and the average number of control packets as well as the cache requirement for performing DGT operations demonstrate the moderate overhead introduced by DGT.
Medical Image De-speckling Based on Improved Polar Coordinate

In recent years, medical image processing has been a hot issue for researchers at home and abroad. Considering the characteristics of medical image collection and speckle noise distribution, a de-speckling algorithm based on an improved polar coordinate is present in this paper. Firstly, a logarithmic transformation is applied to the noisy medical image in polar coordinates system and then full-domain sampling is adopted in any radial direction related to the point estimation. According to the distribution model of speckle noise and the space correlation between sample point and estimate point, the correlation between sample points and estimation points, weighting factors are constructed. Finally, experimental results show that the algorithm proposed in this paper not only can effectively remove the noise, but also can properly preserve the edge details of the medical image
An OLAP data model driven approach to process statistical tables

Statistical tables belong to an important subset of tables published in the Web, because they represent up-to-date, vital information sources for decision makers. These tables are often carefully designed for easy reading by analysts, and then mechanically produced by an OLAP database system. The general practice of extracting attribute-value pairs from statistical tables does not ensure high accuracy when they are used as a database for an information retrieval system. In this paper, we show how a human may visualize a statistical table as an multidimensional object, defined by a suitably modified OLAP model. In this way, the keywords are classified into semantically distinct groups, i.e., dimension hierarchies, without any ontological knowledge or resorting to machine learning. A prototype system which mimics the human reasoning for table processing has been implemented. Experiments on 150 randomly chosen tables from statistics Canada have confirmed the validity of this approach.
Efficient 350 nm LEDs on low edge threading dislocation density AlGaN buffer layers

Improving the crystal quality of AlGaN epitaxial layers is essential for the realization of efficient III-nitride-based light emitting diodes (LEDs) with emission wavelengths below 365 nm. Here, we report on two different approaches to improve the material quality of AlGaN buffer layers for such UV-LEDs, which are known to be effective for the MOVPE growth of GaN layers. Firstly, we grew AlGaN on thin GaN nucleation islands which exhibit a threedimensional facetted structure (3D GaN nucleation). Lateral overgrowth of these islands results in a lateral bending of dislocation lines at the growing facets. Secondly, in-situ deposited SiNx interlayers have been used as nano-masks reducing the dislocation density above the SiNx layers. Both approaches result in reduced asymmetric HRXRD ω-scan peak widths, indicating a reduced edge-type dislocation density. They can be applied to the growth of AlGaN layers with an Al concentration of at least 20%, thus suitable for LEDs emitting around 350 nm. On-wafer electroluminescence measurements at 20 mA show an increase in output power by a factor of 7 and 25 for LED structures grown on 3D GaN nucleation and SiNx interlayer, respectively, compared to structures grown on a purely 2D grown low Al-content AlGaN nucleation layer. Mesa-LEDs fabricated from the LED layer sequences grown on buffers with SiNx interlayer exhibit a low forward voltage of 3.8 V at 20 mA and a maximum continuous wave (cw) output power of 12.2 mW at 300 mA.
Congenital stromal dystrophy of the cornea caused by a mutation in the decorin gene.

PURPOSE To describe the clinical and pathologic characteristics of a family with a congenital stromal dystrophy of the cornea and to identify the genetic basis for this disorder. METHODS All family members in three generations underwent ophthalmic examination. Stored corneal buttons were examined by transmission electron microscopy. Molecular genetic studies, including a genome-wide scan with microsatellite markers, linkage analysis, and DNA sequencing, were performed. RESULTS The dystrophy was inherited in an autosomal dominant pattern and was seen as clouded corneas shortly after birth. No associated systemic abnormalities or congenital diseases were present. After penetrating keratoplasty (PK), the grafts remained completely clear in 56% of the eyes with a mean (range) observation period of 19.5 years (3-36). Transmission electron microscopy of corneal buttons revealed lamellae with normal arrangement of collagen fibrils separated by abnormal fibrillar layers. Genome-wide screening revealed linkage to chromosome 12q22, with a maximum LOD score of 4.68 at D12S351. Subsequent sequencing of candidate genes revealed a frameshift mutation in the DCN gene (c.967delT) that encodes for decorin, predicting a C-terminal truncation of the decorin protein (p.S323fsX5). CONCLUSIONS The authors hypothesize that truncated decorin binds to collagen in a suboptimal way, disturbing the regularity of corneal collagen fibril formation and thereby causing corneal opacities. To the best of the authors' knowledge, this is the first description of a disorder associated with an inherited alteration in the decorin gene in humans.
Towards a learning design authoring tool that generates personalized units of learning for CSCL

The generation of personalized Unit of Learning (UoLs), such as a course, module, or lesson, is one of the most studied topics within the field of adaptive learning environments. Nevertheless, the authoring of these UoLs in the context of Computer Supported Collaborative Learning (CSCL) using current learning design authoring tools is a complex task that requires practice and experience. Usually, practitioners (i.e. non-expert teachers) have difficulties to use these tools because they must manually define all UoL components (such as group composition, students' roles, learning activities/goals, types of interactions, and so on) taking into account the needs and preferences of each learner. This paper introduces a learning design authoring tool, referred to as Adaptive Learning Design (ALD), that helps instructional designers to semi-automatically generate personalized UoLs for CSCL. ALD uses a courseware web service that employs the representation of Instructional Design (ID) using CSCL Script Design Patterns as Hierarchical Task Network (HTN) Planning. We present the architecture of this courseware and others web services used by ALD, our goal is to show the facility of our approach and some of the functionalities it offers for non-expert.
Evolution, Expression Differentiation and Interaction Specificity of Heterotrimeric G-Protein Subunit Gene Family in the Mesohexaploid Brassica rapa

Heterotrimeric G-proteins, comprising of Gα, Gβ, and Gγ subunits, are important signal transducers which regulate many aspects of fundamental growth and developmental processes in all eukaryotes. Initial studies in model plants Arabidopsis and rice suggest that the repertoire of plant G-protein is much simpler than that observed in metazoans. In order to assess the consequence of whole genome triplication events within Brassicaceae family, we investigated the multiplicity of G-protein subunit genes in mesohexaploid Brassica rapa, a globally important vegetable and oilseed crop. We identified one Gα (BraA.Gα1), three Gβ (BraA.Gβ1, BraA.Gβ2, and BraA.Gβ3), and five Gγ (BraA.Gγ1, BraA.Gγ2, BraA.Gγ3, BraA.Gγ4, and BraA.Gγ5) genes from B. rapa, with a possibility of 15 Gαβγ heterotrimer combinations. Our analysis suggested that the process of genome triplication coupled with gene-loss (gene-fractionation) phenomenon have shaped the quantitative and sequence diversity of G-protein subunit genes in the extant B. rapa genome. Detailed expression analysis using qRT-PCR assays revealed that the G-protein genes have retained ubiquitous but distinct expression profiles across plant development. The expression of multiple G-protein genes was differentially regulated during seed-maturation and germination stages, and in response to various phytohormone treatments and stress conditions. Yeast-based interaction analysis showed that G-protein subunits interacted in most of the possible combinations, with some degree of subunit-specific interaction specificity, to control the functional selectivity of G-protein heterotrimer in different cell and tissue-types or in response to different environmental conditions. Taken together, this research identifies a highly diverse G-protein signaling network known to date from B. rapa, and provides a clue about the possible complexity of G-protein signaling networks present across globally important Brassica species.
Coding theorem for general stationary memoryless channel based on hash property

The aim of this paper is to prove the achievability of the general (asymmetric) channel coding problem based on the hash property introduced in [14][15]. Since an ensemble of q-ary sparse matrices (the maximum column weight grows logarithmically in the block length) satisfies the hash property, it is proved that the rate of codes using sparse matrices can achieve the channel capacity.
Rethinking The Demand For Institutional Innovation Land Rights And Land Markets In The West African Sahel

In contrast to literature which focuses on the how collective action problems inhibit the supply of efficient institutions, this paper uses dynamic stochastic general equilibrium methods to study the demand for institutional innovation. Focusing on the innovation of alienabile land rights in the West African Sahel, this microeconomic approach offers several contributions to the theory of institutional innovation. First, in contrast to the representative agent or aggregate benefit-cost approaches used to derive the demand for institutional innovation in much of the literature, this paper explores the heterogeneity of demand across agents. Second, in contrast to prior studies of the evolution of land rights, this analysis shows that, in West Africa at least, the demand for private property rights in land is likely to rest on more than generalized land scarcity. Indeed, in terms of this paper's dynamic option value metric, the strongest demand for a land market emanates from the collapse of traditional risk management institutions and the desire of low wealth agents to use the market to buffer unmediated production risk. The demand for marketable rights, and indeed the appearance of some land transactions, may ultimately reflect a displaced demand for the innovation of contingency and other financial markets. In this second best environment, a policy of land privatization may be dominated by a policy that addresses those elements in the economic and institutional environment which create the sharp (displaced) demand for marketability rights.
Learning Mappings between Models of Data

Information Integration systems today deal with data originating at multiple autonomous and heterogeneous data sources. This heterogeneity means that applications simultaneously manipulate data available in multiple models or schemas. Such interactions are enabled by the presence of semantic mappings between the different models. Mappings make it possible to reason about data and answer queries across different data models. However, determining these semantic mappings is a difficult task because of a variety of reasons models use different vocabularies, different design methodologies and might have different design goals. Further the large sizes of models, the need to incorporate multiple and varied evidences and the ubiquitous nature of applications that require mappings, necessitate the building of tools for automatic or semi-automatic (involving some user interaction) generation of mappings. In this proposal I look at issues in learning mappings between models specifically, building tools that learn mappings by incorporating multiple types of evidences. I discuss the various types of mappings that are needed for applications and the requirements they place on the representation of the mappings that we are trying to learn. I present a proposal for research investigating particular aspects of mappings.
Effects of a PPAR -gamma receptor agonist and an angiotensin receptor antagonist on aortic contractile responses to alpha receptor agonists in diabetic and/or hypertensive rats

Summary Aim The aim of this study was to investigate the effects of pioglitazone and losartan pre-treatment on the aortic contractile response to the alpha-1 agonist, phenylephrine, and the alpha-2 agonist, clonidine, in L-NAME-induced hypertensive, STZ-induced diabetic, and hypertensive diabetic rats. Methods Male Wistar rats were randomly allocated to four groups: control, diabetic (DM), hypertensive (HT) and hypertensive diabetic (HT + DM) groups. Three weeks after drug application, in vitro dose–response curves to phenylephrine (Phe) (10-9–10-5 M) and clonidine (Clo) (10-9–10-5 M) were recorded in aortic rings in the absence (control) and presence of pioglitazone (10 μM) and/or losartan (10 μM). Results Pioglitazone and losartan caused a shift to the right in contractile response to phenylephrine in all groups. The sensitivity of the aortic rings to phenylephrine was decreased in the presence of pioglitazone and/or losartan in all groups. The contractile response of clonidine decreased in the presence of pioglitazone and/or losartan in the control, HT and DM groups. Conclusion The sensitivity of aortic rings to alpha-1 and alpha-2 adrenoceptors was decreased in the presence of pioglitazone and/or losartan in diabetic and hypertensive rats. Concomitant use of PPAR-gamma agonists, thiazolidinediones, and angiotensin receptor blockers may be effective treatment for diabetes and hypertension.