Miracle-dz/UniFAR-FTUs huggingface dataset:
Androgen receptor genomic regulation

The transcriptional activity of the androgen receptor (AR) is not only critical for the normal development and function of the prostate but also pivotal to the onset and progression of prostate cancer (PCa). The studies of AR transcriptional regulation were previously limited to a handful of AR-target genes. Owing to the development of various high-throughput genomic technologies, significant advances have been made in recent years. Here we discuss the discoveries of genome-wide androgen-regulated genes in PCa cell lines, animal models and tissues using expression microarray and sequencing, the mapping of genomic landscapes of AR using Combining Chromatin Immunoprecipitation (ChIP)-on-chip and ChIP-seq assays, the interplay of transcriptional cofactors in defining AR binding profiles, and the genomic regulation and AR reprogramming in advanced PCa.
Thrombin Cleavage of Osteopontin Modulates Its Activities in Human Cells In Vitro and Mouse Experimental Autoimmune Encephalomyelitis In Vivo

Osteopontin is a proinflammatory cytokine and plays a pathogenetic role in multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE), by recruiting autoreactive T cells into the central nervous system. Osteopontin functions are modulated by thrombin cleavage generating N- and C-terminal fragment, whose individual roles are only partly known. Published data are difficult to compare since they have been obtained with heterogeneous approaches. Interestingly, thrombin cleavage of osteopontin unmasks a cryptic domain of interaction with α 4 β 1 integrin that is the main adhesion molecule involved in lymphocyte transmigration to the brain and is the target for natalizumab, the most potent drug preventing relapses. We produced recombinant osteopontin and its N- and C-terminal fragments in an eukaryotic system in order to allow their posttranslational modifications. We investigated, in vitro, their effect on human cells and in vivo in EAE. We found that the osteopontin cleavage plays a key role in the function of this cytokine and that the two fragments exert distinct effects both in vitro and in vivo. These findings suggest that drugs targeting each fragment may be used to fine-tune the pathological effects of osteopontin in several diseases.
High Mean Water Vapour Pressure Promotes the Transmission of Bacillary Dysentery

Bacillary dysentery is an infectious disease caused by Shigella dysenteriae, which has a seasonal distribution. External environmental factors, including climate, play a significant role in its transmission. This paper identifies climate-related risk factors and their role in bacillary dysentery transmission. Harbin, in northeast China, with a temperate climate, and Quzhou, in southern China, with a subtropical climate, are chosen as the study locations. The least absolute shrinkage and selectionator operator is applied to select relevant climate factors involved in the transmission of bacillary dysentery. Based on the selected relevant climate factors and incidence rates, an AutoRegressive Integrated Moving Average (ARIMA) model is established successfully as a time series prediction model. The numerical results demonstrate that the mean water vapour pressure over the previous month results in a high relative risk for bacillary dysentery transmission in both cities, and the ARIMA model can successfully perform such a prediction. These results provide better explanations for the relationship between climate factors and bacillary dysentery transmission than those put forth in other studies that use only correlation coefficients or fitting models. The findings in this paper demonstrate that the mean water vapour pressure over the previous month is an important predictor for the transmission of bacillary dysentery.
A study of speed mismatches between communicating Virtual Machines

This work addresses an apparently simple but elusive problem that arises when doing high speed networking on Virtual Machines. When a VM and its peer (usually the hypervisor) process packets at different rates, the work required for synchronization (interrupts and “kicks”) may reduce throughput well below the slowest of the two parties.
Lightweight source model extraction

Reverse engineers depend on the automatic extract ion of information from source code. Some useful kinds of information+ource models—are wellknown: call graphs, file dependence, etc. Predicting every kind of source model that a reverse engineer may need is impossible. We have developed a lightweight approach for generating flexible and tolerant source model extractors from lexical specificat ions. The approach is lightweight in that the specifications are relatively small and easy to write. It is flexible in that there are few constraints on the information in the source that can be extracted (e.g., we can extract from macros, comments, etc.). It is tolerant in that information can be extracted from source that cannot necessarily be compiled or linked. In essence, we scan for source constructs that contribute to the specified source model while ignoring constructs that do not contribute to that source model. We have developed tools to support this approach and applied the tools to the extraction of a number of different source models (file dependence, event interactions, call graphs) from systems implemented in a variety of programming languages (C, C++, CLOS, Eiffel). We discuss our approach and describe its application to extract source models not available using existing systems; for example, we compute the invoked-by relation over Field tools. We compare and contrast our approach to the conventional approach of generating source models from a program database. * This research was funded in part by the NSF grant CCR-8858804 and a Canadian NSERC post-graduate scholarship. Permission to make cfigital~ard copies of all or part of this material without fee is granted provided that the copies are not made or distributed for profit or commercial advantage, the ACM copyrighffsewer notioe, the title of the pubiioation and its date appear, and notice is given that copyright is by permission of the Association for Computing Machinery, Inc. (ACM). To copy otherwise: to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. SIGSOFT ’95 Washington, D.C., USA 01995 ACM 0-89791-71 8-2/95/0010. $3.50
GOES WMSI—progress and developments

Warm Season Event: 7 June 2004 East Texas Downbursts A multi-cellular cluster of deep convective storms developed over east-central Texas, near College Station, during the afternoon of 7 June 2004. The air mass in which the convective activity was developing was statically unstable, due to intense solar heating of the surface, as displayed by the 1800 UTC GOES WMSI image. High WMSI values, as well as the presence of widespread towering cumulus convection, were an indicator of the strong instability in the region into which the convective cluster was propagating. Also apparent was the presence of a mid-tropospheric layer of dry (low θe) air that could be entrained into the downdraft of a mature convective storm and result in subsequent downdraft acceleration and downburst development. The first observed downburst wind gust of 40 kt (21 m s-1) occurred at Palestine at 1925 UTC, where a well-defined bow echo was indicated in radar reflectivity imagery. The bow echo continued to track to the northeast during the next hour into a progressively more unstable air mass with increasing WMSI values. At 2011, a stronger downburst wind gust of 55 kt (28 m s-1) was observed at Tyler, where a considerably higher WMSI value of 172 was indicated. Data from the GOES WMSI was collected during the 2003 convective season from 29 July to 11 September and during the 2004 convective season from 2 June to 24 September for a total of 135 downburst events (89 daytime, 36 nighttime) and validated against conventional surface data. Data was also collected for the period from 24 November 2004 to 6 April 2005 to assess the performance of the WMSI product during the cold season. Validation was conducted in the manner described by Pryor and Ellrod (2004). Validation, as presented in the table below, determined that there exists a statistically significant correlation, and thus a strong positive linear relationship, between GOES WMSI and observed surface wind gusts for both daytime and nighttime events during the warm season. Also shown in the table, a strong relationship between surface and mid-tropospheric dry layer winds, during the cold season, was found to be associated with downburst events. Based on hypothesis testing, this relationship was determined to be statistically significant. However, the correlation between WMSI values and surface wind gust magnitude was much weaker and determined to be statistically insignificant. Based on previous research and the case studies presented, the strong correlation between mid-tropospheric and surface winds suggested that downward transport of momentum from the midlevels of a convective storm environment to the surface played a major role in the downburst magnitude during this observation period.
Direct computation of generator internal dynamic states from terminal measurements

Estimating the dynamic state variables of a synchronous generator has been a long standing research problem in power system control designs. In this paper, we present a technique to compute approximately the state variables of a synchronous generator, purely from terminal measurements. The approximation follows from an analysis of the fundamental equations describing synchronous machine models. The method assumes the availablity of the measurements: real and reactive power, terminal voltage, and the field current. By exploiting the structure of the flux linkage equations, approximate formulas for the machine rotor angle (with respect to the phase of the terminal voltage) as well as for the internal flux linkages are derived, and they are shown to be excellent approximations in simulations of detailed machine models.
Rule Learning by Rats

Using rules extracted from experience to solve problems in novel situations involves cognitions such as analogical reasoning and language learning and is considered a keystone of humans' unique abilities. Nonprimates, it has been argued, lack such rule transfer. We report that Rattus norvegicus can learn simple rules and apply them to new situations. Rats learned that sequences of stimuli consistent with a rule (such as XYX) were different from other sequences (such as XXY or YXX). When novel stimuli were used to construct sequences that did or did not obey the previously learned rule, rats transferred their learning. Therefore, rats, like humans, can transfer structural knowledge from sequential experiences.
The Open University ’ s repository of research publications and other research outputs Relevance in technicolor Conference Item

In this article we propose the concept of relevance criteria profiles, which provide a global view of user behaviour in judging the relevance of retrieved information. We further propose a plotting technique which provides a session based overview of the relevance judgement processes interlaced with interactions that allow the researcher to visualise and quickly detect emerging patterns in both interactions and relevance criteria usage. We discuss by example, using data from a user study conducted between the months of January and August of 2008, how these tools support the better understanding of task based user valuation of documents that is likely to lead to recommendations for improving enduser services in digital libraries.
Membrane Protein Solubilization: Recent Advances and Challenges in Solubilization of Serotonin1A Receptors

Solubilization of integral membrane proteins is a process in which the proteins and lipids that are held together in native membranes are suitably dissociated in a buffered detergent solution. The controlled dissociation of the membrane results in formation of small protein and lipid clusters that remain dissolved in the aqueous solution. Effective solubilization and purification of membrane proteins, especially heterologously‐expressed proteins in mammalian cells in culture, in functionally active forms represent important steps in understanding structure‐function relationship of membrane proteins. In this review, critical factors determining functional solubilization of membrane proteins are highlighted with the solubilization of the serotonin1A receptor taken as a specific example. IUBMB Life, 57: 505‐512, 2005
ITAM Signaling by Vav Family Rho Guanine Nucleotide Exchange Factors Regulates Interstitial Transit Rates of Neutrophils In Vivo

Background In response to infection, neutrophils are quickly recruited from the blood into inflamed tissues. The interstitial migration of neutrophils is crucial for the efficient capture and control of rapidly proliferating microbes before microbial growth can overwhelm the host's defenses. However, the molecular mechanisms that regulate interstitial migration are incompletely understood. Methodology/Principal Findings Here, we use two-photon microscopy (2PM) to study discrete steps of neutrophil responses during subcutaneous infection with bacteria. Our study demonstrates that signals emanating from ITAM-containing receptors mediated by Vav family Rho GEFs control the velocity, but not the directionality, of neutrophil migration towards sites of bacterial infection. Conclusions/Significance Here we show that during neutrophil migration towards sites of bacterial infection, signals emanating from ITAM-containing receptors specifically control interstitial neutrophil velocity.
Interaction of Daptomycin with Lipid Bilayers: A Lipid Extracting Effect

Daptomycin is the first approved member of a new structural class of antibiotics, the cyclic lipopeptides. The peptide interacts with the lipid matrix of cell membranes, inducing permeability of the membrane to ions, but its molecular mechanism has been a puzzle. Unlike the ubiquitous membrane-acting host-defense antimicrobial peptides, daptomycin does not induce pores in the cell membranes. Thus, how it affects the permeability of a membrane to ions is not clear. We studied its interaction with giant unilamellar vesicles (GUVs) and discovered a lipid-extracting phenomenon that correlates with the direct action of daptomycin on bacterial membranes observed in a recent fluorescence microscopy study. Lipid extraction occurred only when the GUV lipid composition included phosphatidylglycerol and in the presence of Ca2+ ions, the same condition found to be necessary for daptomycin to be effective against bacteria. Furthermore, it occurred only when the peptide/lipid ratio exceeded a threshold value, which could be the basis of the minimal inhibitory concentration of daptomycin. In this first publication on the lipid extracting effect, we characterize its dependence on ions and lipid compositions. We also discuss possibilities for connecting the lipid extracting effect to the antibacterial activity of daptomycin.
The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent

The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N-1-methyladenosine (m1A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m1A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol was tailored to the simultaneous analysis of RT-arrest and misincorporation patterns. By application to a variety of native and synthetic RNA preparations, we found a characteristic signature of m1A, which, in addition to an arrest rate, features misincorporation as a significant component. Detailed analysis suggests that the signature depends on RNA structure and on the nature of the nucleotide 3′ of m1A in the template RNA, meaning it is sequence dependent. The RT-signature of m1A was used for inspection and confirmation of suspected modification sites and resulted in the identification of hitherto unknown m1A residues in trypanosomal tRNA.
A Novel Classification Approach through Integration of Rough Sets and Back-Propagation Neural Network

Classification is an important theme in data mining. Rough sets and neural networks are the most common techniques applied in data mining problems. In order to extract useful knowledge and classify ambiguous patterns effectively, this paper presented a hybrid algorithm based on the integration of rough sets and BP neural network to construct a novel classification system. The attribution values were discretized through PSO algorithm firstly to establish a decision table. The attribution reduction algorithm and rules extraction method based on rough sets were proposed, and the flowchart of proposed approach was designed. Finally, a prototype system was developed and some simulation examples were carried out. Simulation results indicated that the proposed approach was feasible and accurate and was outperforming others.
The maize (Zea mays) desynaptic (dy) mutation defines a pathway for meiotic chromosome segregation, linking nuclear morphology, telomere distribution and synapsis

Summary Meiosis involves a dramatic reorganization of the genetic material, along with changes in the architecture of the nucleoplasm and cytoplasm. In the opisthokonts, nuclear envelope and meiotic chromosome behavior are coordinated by forces generated in the cytoplasm and transferred to the nucleus by the nuclear-envelope protein linkers SUN and KASH. During meiotic prophase I, the telomere bouquet arrangement has roles in interhomolog recognition, pairing, synapsis, interlock resolution and homologous chromosome recombination. The maize desynaptic (dy) mutant is defective in homologous chromosome synapsis, recombination, telomere–nuclear envelope interactions and chromosome segregation. A detailed three-dimensional cytological analysis of dy revealed telomere misplacement during the bouquet stage, synaptic irregularities, nuclear envelope distortion and chromosome bridges at anaphase I. Using linkage and B-A translocation mapping, we placed dy on the long arm of chromosome 3, genetic bin 3.06. SSR marker analysis narrowed the mapping interval to 9 cM. Candidate genes in this region include a PM3-type SUN domain protein, ZmSUN3. No obvious genetic lesions were found in the ZmSUN3 allele of dy, but a conspicuous splice variant, ZmSUN3-sv1, was observed in mRNA from dy. The variant message is predicted to result in the synthesis of a truncated ZmSUN3 protein lacking two C-terminal transmembrane domains. Other potential candidate genes relevant to the documented phenotypes were also considered. In summary, this study reveals that dy causes disruption of a central meiotic pathway connecting nuclear envelope integrity to telomere localization and synapsis during meiotic prophase.
Real-Time Space-Efficient Synchronized Tree-Based Web Visualization and Design

Although the World Wide Web is popularly referred to as “cyberspace”, the extent to which it constitutes a space in the everyday sense of the word is questionable. While looking for information on the Web, regular users are quickly lost in the cyberspace. Hence, it is important that one be able to categorize, understand and present Web data efficiently to the users. The structure of the World Wide Web can be modeled as a graph: the nodes are HTML pages, and a hyperlink from one page to another is represented as a directed edge. However, trees have much simpler structures than graphs, which make it easier to display trees in an aesthetically pleasing manner. In this paper we present a novel Web browsing and visualization method with an innovative combination of features: (i) Web data is retrieved and displayed in real-time (i.e. Web data is not pre-recorded), (ii) browsing and visualization are synchronized together in the same interface, (iii) tree-based visualization engine, (iv) space-efficient display of visualization, and (v) the amount of resources needed from the host computer is limited. In addition, the tree-based rings engine used to create the visualization displays the information in a smaller area than previous systems, thus either taking smaller screen space or displaying more information to the user. Even though in this paper we apply it on visualizing Web data, our method can be applied to portray any information hierarchy.
Hardware design experiences in ZebraNet

The enormous potential for wireless sensor networks to make a positive impact on our society has spawned a great deal of research on the topic, and this research is now producing environment-ready systems. Current technology limits coupled with widely-varying application requirements lead to a diversity of hardware platforms for different portions of the design space. In addition, the unique energy and reliability constraints of a system that must function for months at a time without human intervention mean that demands on sensor network hardware are different from the demands on standard integrated circuits. This paper describes our experiences designing sensor nodes and low level software to control them. In the ZebraNet system we use GPS technology to record fine-grained position data in order to track long term animal migrations [14]. The ZebraNet hardware is composed of a 16-bit TI microcontroller, 4 Mbits of off-chip flash memory, a 900 MHz radio, and a low-power GPS chip. In this paper, we discuss our techniques for devising efficient power supplies for sensor networks, methods of managing the energy consumption of the nodes, and methods of managing the peripheral devices including the radio, flash, and sensors. We conclude by evaluating the design of the ZebraNet nodes and discussing how it can be improved. Our lessons learned in developing this hardware can be useful both in designing future sensor nodes and in using them in real systems.
Quantitative Blood Flow Measurements in Gliomas Using Arterial Spin-Labeling at 3T: Intermodality Agreement and Inter- and Intraobserver Reproducibility Study

BACKGROUND AND PURPOSE: QUASAR is a particular application of the ASL method and facilitates the user-independent quantification of brain perfusion. The purpose of this study was to assess the intermodality agreement of TBF measurements obtained with ASL and DSC MR imaging and the inter- and intraobserver reproducibility of glioma TBF measurements acquired by ASL at 3T. MATERIALS AND METHODS: Two observers independently measured TBF in 24 patients with histologically proved glioma. ASL MR imaging with QUASAR and DSC MR imaging were performed on 3T scanners. The observers placed 5 regions of interest in the solid tumor on rCBF maps derived from ASL and DSC MR images and 1 region of interest in the contralateral brain and recorded the measured values. Maximum and average sTBF values were calculated. Intermodality and intra- and interobsever agreement were determined by using 95% Bland-Altman limits of agreement and ICCs. RESULTS: The intermodality agreement for maximum sTBF was good to excellent on DSC and ASL images; ICCs ranged from 0.718 to 0.884. The 95% limits of agreement ranged from 59.2% to 65.4% of the mean. ICCs for intra- and interobserver agreement for maximum sTBF ranged from 0.843 to 0.850 and from 0.626 to 0.665, respectively. The reproducibility of maximum sTBF measurements obtained by methods was similar. CONCLUSIONS: In the evaluation of sTBF in gliomas, ASL with QUASAR at 3T yielded measurements and reproducibility similar to those of DSC perfusion MR imaging.