Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystallographic and Biochemical Studies of DivK Reveal Novel Features of an Essential Response Regulator in Caulobacter crescentus*

DivK is an essential response regulator in the Gram-negative bacterium Caulobacter crescentus and functions in a complex phosphorelay system that precisely controls the sequence of developmental events during the cell division cycle. Structure determinations of this single domain response regulator at different pH values demonstrated that the five-stranded α/β fold of the DivK protein is fully defined only at acidic pH. The crystal structures of the apoprotein and of metal-bound DivK complexes at higher pH values revealed a synergistic pH- and cation binding-induced flexibility of the β4-α4 loop and of the α4 helix. This motion increases the solvent accessibility of the single cysteine residue in the protein. Solution state studies demonstrated a 200-fold pH-dependent increase in the affinity of manganese for the protein between pH 6.0 and 8.5 that seems to involve deprotonation of an acido-basic couple. Taken together, these results suggest that flexibility of critical regions of the protein, ionization of the cysteine 99 residue and improved K D values for the catalytic metal ion are coupled events. We propose that the molecular events observed in the isolated protein may be required for DivK activation and that they may be achieved in vivothrough the specific protein-protein interactions between the response regulator and its cognate kinases.
Exploiting Database Similarity Joins for Metric Spaces

Similarity Joins are recognized among the most useful data processing and analysis operations and are extensively used in multiple application domains. They retrieve all data pairs whose distances are smaller than a predefined threshold e. Multiple Similarity Join algorithms and implementation techniques have been proposed. They range from out-of-database approaches for only in-memory and external memory data to techniques that make use of standard database operators to answer similarity joins. Recent work has shown that this operation can be efficiently implemented as a physical database operator. However, the proposed operator only support 1D numeric data. This paper presents DBSimJoin, a physical Similarity Join database operator for datasets that lie in any metric space. DBSimJoin is a non-blocking operator that prioritizes the early generation of results. We implemented the proposed operator in PostgreSQL, an open source database system. We show how this operator can be used in multiple real-world data analysis scenarios with multiple data types and distance functions. Particularly, we show the use of DBSimJoin to identify similar images represented as feature vectors, and similar publications in a bibliographic database. We also show that DBSimJoin scales very well when important parameters, e.g., e, data size, increase.
Algorithms for Generating Referring Expressions: Do They Do What People Do?

The natural language generation literature provides many algorithms for the generation of referring expressions. In this paper, we explore the question of whether these algorithms actually produce the kinds of expressions that people produce. We compare the output of three existing algorithms against a data set consisting of human-generated referring expressions, and identify a number of significant differences between what people do and what these algorithms do. On the basis of these observations, we suggest some ways forward that attempt to address these differences.
English Senseval: Report and Results

There are now many computer programs for automatically determining which sense a word is being used in. One would like to be able to say which were better, which worse, and also which words, or varieties of language, presented particular problems to which programs. In 1998 a first evaluation exercise, SENSEVAL, took place. The English component of the exercise is described, and results presented.
Using success stories to share knowledge and lessons learned in health promotion.

BACKGROUND Compelling success stories, rich with details about real-life events and people, are a tool that health agencies can use to convey how their health promotion programs work, why they are successful, what lessons they have learned, and how others can launch similar programs. Success stories describe project accomplishments that are not easily captured by quantitative evaluation methods, such as surveys. METHODS Although success stories have not been widely used in public health, the North Carolina Department of Health and Human Services developed a series of stories, the Community Change Chronicles, to highlight environmental and policy changes that promote cardiovascular health. In 2003, the Well-Integrated Screening and Evaluation for Women Across the Nation (WISEWOMAN) program used the Community Change Chronicles as a model to develop success stories about WISEWOMAN projects. RESULTS WISEWOMAN Works: A Collection of Success Stories from Program Inception Through 2002 includes 12 stories and offers advice on how to create and use success stories in public health. This paper reviews the rationale for developing the stories, presents one success story as an example, and describes the process used to gather information, write the stories, and produce a resource for others interested in developing success stories. We also discuss how the WISEWOMAN success stories are being used to promote women's health and cardiovascular health. CONCLUSIONS As the WISEWOMAN experience suggests, healthcare providers and organizations can use success stories to gain support for successful activities, inform the public about program benefits, complement other quantitative and qualitative evaluation methods, and publicly acknowledge the contributions of staff and organizational partners.
Oxidative metabolism in cord blood monocytes and monocyte-derived macrophages

Little is known about phagocytosis-associated oxidative metabolism in mononuclear phagocytes from the human neonate. We investigated this phenomenon in monocytes from the cord blood of term newborn infants by measuring generation of superoxide anion (O2-) and hydroxyl radical (X OH) after stimulation with opsonized zymosan or phorbol myristate acetate. Production of these microbicidal oxygen metabolites by monocytes from neonates and healthy adult volunteers was equivalent. When cultured in the presence of the macrophage activator lipopolysaccharide or muramyl dipeptide, monocytes from neonates and adults differentiated into cells with the appearance of macrophages and with an enhanced capacity to release O2- compared with cells cultured in the absence of an activator. Monocyte-derived macrophages from neonates produced only slightly less O2- than did adult cells. Thus, unlike the cord blood neutrophil, which exhibits abnormalities in oxidative metabolism, the cord blood mononuclear phagocyte has a respiratory burst that is quantitatively comparable to that of the adult cell.
Extracting users pattern from web log data using decision tree and association rule

Web usage mining is the task of applying data mining technique to discover usage patterns from web log file in order to understand and better serve the users navigating the web. Extracting users behaviour pattern is an important and challenging research topic of web usage mining. Analysing such patterns helps to determine the lifetime value of customers, cross marketing strategies across products and provides valuable information to improve the design of a website. This paper proposes an idea to find frequent patterns in two phases. In the first phase the pre-processed data is categorised into focused subsets using decision tree. In the second phase association rule is applied to find frequent pattern.
Let's Talk Topically with Artificial Agents! - Providing Agents with Humanlike Topic Awareness in Everyday Dialog Situations

Spoken interactions between humans are characterized by coherent sequences of utterances assigning a thematical structure to the whole conversation. Such coherence and the success of a meaningful and flexible dialog are based on the cognitive ability to be aware of the ongoing conversational topic. This paper presents how to enable such topically coherent conversations between humans and interactive systems by emulating humanlike topic awareness in artificial agents. Therefore, we firstly automated human topic awareness on the basis of preprocessed Wikipedia knowledge and secondly transferred such computer-based awareness to a virtual agent. As a result, we contribute to improve human-agent dialogs by enabling topical talk between human and artificial conversation partners.
In Silico Prediction of Human Sulfotransferase 1E1 Activity Guided by Pharmacophores from Molecular Dynamics Simulations*

Acting during phase II metabolism, sulfotransferases (SULTs) serve detoxification by transforming a broad spectrum of compounds from pharmaceutical, nutritional, or environmental sources into more easily excretable metabolites. However, SULT activity has also been shown to promote formation of reactive metabolites that may have genotoxic effects. SULT subtype 1E1 (SULT1E1) was identified as a key player in estrogen homeostasis, which is involved in many physiological processes and the pathogenesis of breast and endometrial cancer. The development of an in silico prediction model for SULT1E1 ligands would therefore support the development of metabolically inert drugs and help to assess health risks related to hormonal imbalances. Here, we report on a novel approach to develop a model that enables prediction of substrates and inhibitors of SULT1E1. Molecular dynamics simulations were performed to investigate enzyme flexibility and sample protein conformations. Pharmacophores were developed that served as a cornerstone of the model, and machine learning techniques were applied for prediction refinement. The prediction model was used to screen the DrugBank (a database of experimental and approved drugs): 28% of the predicted hits were reported in literature as ligands of SULT1E1. From the remaining hits, a selection of nine molecules was subjected to biochemical assay validation and experimental results were in accordance with the in silico prediction of SULT1E1 inhibitors and substrates, thus affirming our prediction hypotheses.
H2O2-dependent Activation of GCLC-ARE4 Reporter Occurs by Mitogen-activated Protein Kinase Pathways without Oxidation of Cellular Glutathione or Thioredoxin-1*

The gp91phox homologue Nox1 produces H2O2, which induces cell growth, transformation, and tumorigenicity. However, it has not been clear whether H2O2 effects are mediated indirectly via a generally oxidizing cellular environment or whether H2O2 more directly targets specific signaling pathways. Here, we investigated signaling by H2O2 induced by Nox1 overexpression using a luciferase reporter regulated by the antioxidant response element ARE4. Surprisingly, Nox1-derived H2O2 activated the reporter gene 15-fold with no effect on the redox state of the major thiol antioxidant substances, glutathione and thioredoxin. H2O2 signaling to ARE4 was mediated by activation of both the c-Jun N-terminal kinase and ERK1/2 pathways modulated by Ras. Thus, “redox signaling” resulting in kinase signaling pathways is distinct from “oxidative stress,” and is mediated by discrete, localized redox circuitry.
Intestinal barrier analysis by assessment of mucins, tight junctions, and α-defensins in healthy C57BL/6J and BALB/cJ mice

ABSTRACT The intestinal barrier is gaining increasing attention because it is related to intestinal homeostasis and disease. Different parameters have been used in the past to assess intestinal barrier functions in experimental studies; however most of them are poorly defined in healthy mice. Here, we compared a number of barrier markers in healthy mice, established normal values and correlations. In 48 mice (24 C57BL/6J, 24 BALB/cJ background), we measured mucus thickness, and expression of mucin-2, α-defensin-1 and -4, zonula occludens-1, occludin, junctional adhesion molecule-A, claudin-1, 2 and -5. We also analyzed claudin-3 and fatty acid binding protein-2 in urine and plasma, respectively. A higher expression of mucin-2 protein was found in the colon compared to the ileum. In contrast, the α-defensins-1 and -4 were expressed almost exclusively in the ileum. The protein expression of the tight junction molecules claudin-1, occludin and zonula occludens-1 did not differ between colon and ileum, although some differences occurred at the mRNA level. No age- or gender-related differences were found. Differences between C57BL/6J and BALB/cJ mice were found for α-defensin-1 and -4 mRNA expression, and for urine and plasma marker concentrations. The α-defensin-1 mRNA correlated with claudin-5 mRNA, whereas α-defensin-4 mRNA correlated with claudin-3 concentrations in urine. In conclusion, we identified a number of murine intestinal barrier markers requiring tissue analyses or measurable in urine or plasma. We provide normal values for these markers in mice of different genetic background. Such data might be helpful for future animal studies in which the intestinal barrier is of interest.
Automatic control in TCP over wireless

Over the last decade, both the Internet and mobile telephony has become parts of daily life, changing the ways we communicate and search for information. These two distinct tools are now slowly merging. The topic of this thesis is TCP over wireless, and the automatic control that is used both within the system, from the link-layer power control to the end-to-end congestion control. It consists of three main contributions. The first contribution is a proposed split-connection scheme for downloads to a mobile terminal. A wireless mobile terminal requests a file or a web page from a proxy, which in turn requests the data from a server on the Internet. During the file transfer, the radio network controller (RNC) sends radio network feedback (RNF) messages to the proxy. These messages include information about bandwidth changes over the radio channel, and the current RNC queue length. A novel control mechanism in the proxy uses this information to adjust the sending rate. The stability and convergence speed of the proxy controller is analyzed theoretically. The performance of the proposed controller is compared to end-to-end TCP Reno, using ns-2 simulations of realistic use cases. It is shown that the proxy control is able to reduce the response time experienced by users, and increase the utilization of the radio channel. The changes are loalized to the RNC and the proxy; no changes are required to the TCP implementation in terminal or server. The second contribution is the analysis of an uplink channel using power control and link-layer retransmissions. To be able to design the link-layer mechanisms in a systematic way, good models for the link-layer processes, and their interaction with TCP, are essential.The use of link-layer retransmissions transforms a link with constant delay and random losses into a link with random delay and almost no losses. As seen from the TCP end points, the difference between such a link and a wired one is no longer the loss rate, but the packet delay distribution. Models for the power control and link-layer retransmissions on the link are used to derive packet delay distribution, and its impact on TCP performance is investigated. The final contribution considers ways to optimize the link-layer processes. The main result is that TCP performance, over a wireless link with random retransmission delays, can be improved by adding carefully chosen artificial delays to certain packets. The artificial delays are optimized off-line and applied on-line. The additional delay that is applied to a packet depends only on the retransmission delay experienced by that same packet, and this information is available locally at the link.
0.5-V input digital LDO with 98.7% current efficiency and 2.7-µA quiescent current in 65nm CMOS

Digital LDO is proposed to provide the low noise and tunable power supply voltage to the 0.5-V near-threshold logic circuits. Because the conventional LDO feedback-controlled by the operational amplifier fail to operate at 0.5V, the digital LDO eliminates all analog circuits and is controlled by digital circuits, which enables the 0.5-V operation. The developed digital LDO in 65nm CMOS achieved the 0.5-V input voltage and 0.45-V output voltage with 98.7% current efficiency and 2.7-µA quiescent current at 200-µA load current. Both the input voltage and the quiescent current are the lowest values in the published LDO's, which indicates the good energy efficiency of the digital LDO at 0.5-V operation.
Decisional autonomy of planetary rovers

To achieve the ever increasing demand for science return, planetary exploration rovers require more autonomy to successfully perform their missions. Indeed, the communication delays are such that teleoperation is unrealistic. Although the current rovers (such as MER) demonstrate a limited navigation autonomy, and mostly rely on ground mission planning, the next generation (e.g., NASA Mars Science Laboratory and ESA Exomars) will have to regularly achieve long range autonomous navigation tasks. However, fully autonomous long range navigation in partially known planetary‐like terrains is still an open challenge for robotics. Navigating hundreds of meters without any human intervention requires the robot to be able to build adequate representations of its environment, to plan and execute trajectories according to the kind of terrain traversed, to control its motions, and to localize itself as it moves. All these activities have to be planned, scheduled, and performed according to the rover context, and controlled so that the mission is correctly fulfilled. To achieve these objectives, we have developed a temporal planner and an execution controller, which exhibit plan repair and replanning capabilities. The planner is in charge of producing plans composed of actions for navigation, science activities (moving and operating instruments), communication with Earth and with an orbiter or a lander, while managing resources (power, memory, etc.) and respecting temporal constraints (communication visibility windows, rendezvous, etc.). High level actions also need to be refined and their execution temporally and logically controlled. Finally, in such critical applications, we believe it is important to deploy a component that protects the system against dangerous or even fatal situations resulting from unexpected interactions between subsystems (e.g., move the robot while the robot arm is unstowed) and/or software components (e.g., take and store a picture in a buffer while the previous one is still being processed). In this article we review the aforementioned capabilities, which have been developed, tested, and evaluated on board our rovers (Lama and Dala). After an overview of the architecture design principle adopted, we summarize the perception, localization, and motion generation functions required by autonomous navigation, and their integration and concurrent operation in a global architecture. We then detail the decisional components: a high level temporal planner that produces the robot activity plan on board, and temporal and procedural execution controllers. We show how some failures or execution delays are being taken care of with online local repair, or replanning. © 2007 Wiley Periodicals, Inc.
Cox11p Is Required for Stable Formation of the CuBand Magnesium Centers of Cytochrome c Oxidase*

Assembly of the core subunits of theaa 3-type cytochrome c oxidase in mitochondria and aerobic bacteria such as Rhodobacter sphaeroides requires the association of three subunits and the formation of five to seven metal centers. Several assembly proteins are required for the late stages of oxidase assembly in eukaryotes; some of these are also present in Rb. sphaeroides. To investigate the role of one of these proteins, Cox11p, the mitochondrial-like oxidase of Rb. sphaeroides was overexpressed and purified from cells that lacked cox11, the gene for Cox11p. The oxidase that assembled in the absence of Cox11p lacked CuBat the active site and contained greatly reduced amounts of metal at the magnesium/manganese-binding site between subunits I and II. This inactive oxidase, however, did contain hemes a anda 3, CuA, and all three subunits. These results indicate that Cox11p is required at a late, perhaps final, step in the assembly of cytochrome oxidase, most likely the insertion of CuB. Oxidase which assembled in a strain with a low copy number of cox11 appeared nearly wild type, suggesting that Cox11p is required in substoichiometric amounts for its role in oxidase assembly.
Protecting data privacy in private information retrieval schemes

Private information retrieval (PIR) schemes allow a user to retrieve the ith bit of an n-bit data string x, replicated in k? 2 databases (in the information-theoretic setting) or in k? 1 databases (in the computational setting), while keeping the value of i private. The main cost measure for such a scheme is its communication complexity. In this paper we introduce a model of symmetrically-private information retrieval (SPIR), where the privacy of the data, as well as the privacy of the user, is guaranteed. That is, in every invocation of a SPIR protocol, the user learns only a single physical bit of x and no other information about the data. Previously known PIR schemes severely fail to meet this goal. We show how to transform PIR schemes into SPIR schemes (with information-theoretic privacy), paying a constant factor in communication complexity. To this end, we introduce and utilize a new cryptographic primitive, called conditional disclosure of secrets, which we believe may be a useful building block for the design of other cryptographic protocols. In particular, we get a k-database SPIR scheme of complexity O(n1/(2k? 1)) for every constant k? 2 and an O(logn)-database SPIR scheme of complexity O(log2n·loglogn). All our schemes require only a single round of interaction, and are resilient to any dishonest behavior of the user. These results also yield the first implementation of a distributed version of (n1)-OT (1-out-of-n oblivious transfer) with information-theoretic security and sublinear communication complexity.
Virtualization and Programmability in Mobile Wireless Networks: Architecture and Resource Management

We present a high-level end-to-end architecture for virtualization and programmability in next-generation mobile wireless networks. Our architecture envisions three major players: Service Providers, who wish to orchestrate wireless networks with particular characteristics to support particular applications; Resource Providers, who contribute resources such as spectrum, access points, backhaul infrastructure, and computing; and Virtual Network Builders, who marshal resources into networks for Service Providers. We take into account resource sharing and investigate how virtualization and programmability affect resource management. We show that: (i) virtualization reduces cost significantly, (ii) this cost reduction does not degrade the user satisfaction, and (iii) non-virtualized networks need to keep a large amount of idle capacity to satisfy coverage.
An Evaluation of Symbolic Feature Sets and Their Combination for Music Genre Classification

The automatic music genre classification task is an active area of research in the field of Music Information Retrieval. In this paper we use two different symbolic feature sets for genre classification and combine them using an early fusion approach. Our results show that early fusion achieves better classification accuracy than using any of the individual feature sets. Furthermore, when compared with some of the state of the art approaches using the same experimental conditions, early fusion of symbolic features is ranked the second best method.